diff --git a/LICENSE.md b/LICENSE.md index ed5bc6e8..da8a376d 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ The MIT License -Copyright (c) 2015-2025 [EPAM Systems, Inc.](https://www.epam.com/) +Copyright (c) 2015-2026 [EPAM Systems, Inc.](https://www.epam.com/) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 57842b69..82683fa8 100644 --- a/README.md +++ b/README.md @@ -39,10 +39,10 @@ is to reference a CDN version: - + - - + +
@@ -70,4 +70,4 @@ for submitting pull requests. [MIT](LICENSE.md) -Copyright (c) 2015–2025 [EPAM Systems, Inc.](https://www.epam.com/) +Copyright (c) 2015–2026 [EPAM Systems, Inc.](https://www.epam.com/) diff --git a/package.json b/package.json index ed37a164..fe25bb56 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "miew-monorepo", - "version": "0.11.0", + "version": "0.12.0", "license": "MIT", "private": true, "workspaces": [ diff --git a/packages/miew-app/CHANGELOG.md b/packages/miew-app/CHANGELOG.md index 71000ce9..1c8f1330 100644 --- a/packages/miew-app/CHANGELOG.md +++ b/packages/miew-app/CHANGELOG.md @@ -7,6 +7,25 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] +## [0.12.0] - 2026-06-09 + +### Changed + +- Replaced the custom Miew viewer implementation with the `miew-react` wrapper component. +- Migrated Redux state management from plain Redux to Redux Toolkit. +- Removed the non-serializable Miew instance from the Redux store; components now access it + through React context instead. +- Upgraded to React 19. + +### Fixed + +- Restored the "Fork me on GitHub" ribbon in the application header. + +### Internal + +- Moved test files next to the source files they cover. +- Updated third-party dependencies. + ## [0.11.0] - 2024-08-26 ### Added @@ -16,5 +35,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. [`miew-app`]: https://github.com/epam/miew/tree/main/packages/miew-app -[Unreleased]: https://github.com/epam/miew/compare/v0.11.0...HEAD +[Unreleased]: https://github.com/epam/miew/compare/v0.12.0...HEAD +[0.12.0]: https://github.com/epam/miew/compare/v0.11.0...v0.12.0 [0.11.0]: https://github.com/epam/miew/compare/v0.9.0...v0.11.0 diff --git a/packages/miew-app/README.md b/packages/miew-app/README.md index c3c97a3f..272f7186 100644 --- a/packages/miew-app/README.md +++ b/packages/miew-app/README.md @@ -18,4 +18,4 @@ Please read [CONTRIBUTING.md](../../CONTRIBUTING.md) for details on our code of [MIT](../../LICENSE.md) -Copyright (c) 2015–2025 [EPAM Systems, Inc.](https://www.epam.com/) +Copyright (c) 2015–2026 [EPAM Systems, Inc.](https://www.epam.com/) diff --git a/packages/miew-app/package.json b/packages/miew-app/package.json index 6e1f9a1b..3dd58245 100644 --- a/packages/miew-app/package.json +++ b/packages/miew-app/package.json @@ -1,6 +1,6 @@ { "name": "miew-app", - "version": "0.11.0", + "version": "0.12.0", "description": "React application demonstrating capabilities of Miew library", "author": "EPAM Systems, Inc.", "private": true, diff --git a/packages/miew-app/src/components/menu/panelslist/panels/AboutPanel/AboutPanel.jsx b/packages/miew-app/src/components/menu/panelslist/panels/AboutPanel/AboutPanel.jsx index d8063c23..14ae4b09 100644 --- a/packages/miew-app/src/components/menu/panelslist/panels/AboutPanel/AboutPanel.jsx +++ b/packages/miew-app/src/components/menu/panelslist/panels/AboutPanel/AboutPanel.jsx @@ -19,7 +19,7 @@ const AboutPanel = () => {

Miew – 3D Molecular Viewer

{version}

-

Copyright © 2015–2025 EPAM Systems, Inc.

+

Copyright © 2015–2026 EPAM Systems, Inc.

https://epa.ms/miew

diff --git a/packages/miew-app/src/components/menu/terminal/Terminal.jsx b/packages/miew-app/src/components/menu/terminal/Terminal.jsx index b43b50cc..1b721041 100644 --- a/packages/miew-app/src/components/menu/terminal/Terminal.jsx +++ b/packages/miew-app/src/components/menu/terminal/Terminal.jsx @@ -32,7 +32,7 @@ function Terminal({ isTerminalVisible }) { } const terminalConfig = { - greetings: 'Miew - 3D Molecular Viewer\nCopyright © 2015-2025 EPAM Systems, Inc.\n', + greetings: 'Miew - 3D Molecular Viewer\nCopyright © 2015-2026 EPAM Systems, Inc.\n', prompt: 'miew> ', name: 'miew', scrollOnEcho: true, diff --git a/packages/miew-react/CHANGELOG.md b/packages/miew-react/CHANGELOG.md index 5da1f0d8..29618ec7 100644 --- a/packages/miew-react/CHANGELOG.md +++ b/packages/miew-react/CHANGELOG.md @@ -7,6 +7,23 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] +## [0.12.0] - 2026-06-09 + +### Added + +- The `Viewer` component now accepts `className`, `style`, `id`, `title`, event handlers, + `data-*` and `aria-*` attributes, and other standard HTML `
` props, making it easy + to style and integrate the viewer into any layout. +- Added comprehensive prop validation and error handling to the `Viewer` component. + +### Changed + +- Upgraded the React peer dependency to version 19. + +### Internal + +- Updated third-party dependencies. + ## [0.11.0] - 2024-08-26 ### Added @@ -15,5 +32,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. as a separate [miew-react](https://www.npmjs.com/package/miew-react) package on npm. [`miew-react`]: https://github.com/epam/miew/tree/main/packages/miew-react -[Unreleased]: https://github.com/epam/miew/compare/v0.11.0...HEAD +[Unreleased]: https://github.com/epam/miew/compare/v0.12.0...HEAD +[0.12.0]: https://github.com/epam/miew/compare/v0.11.0...v0.12.0 [0.11.0]: https://github.com/epam/miew/compare/v0.9.0...v0.11.0 diff --git a/packages/miew-react/LICENSE.md b/packages/miew-react/LICENSE.md index ed5bc6e8..da8a376d 100644 --- a/packages/miew-react/LICENSE.md +++ b/packages/miew-react/LICENSE.md @@ -1,6 +1,6 @@ The MIT License -Copyright (c) 2015-2025 [EPAM Systems, Inc.](https://www.epam.com/) +Copyright (c) 2015-2026 [EPAM Systems, Inc.](https://www.epam.com/) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/packages/miew-react/README.md b/packages/miew-react/README.md index ec758164..f3fa90f9 100644 --- a/packages/miew-react/README.md +++ b/packages/miew-react/README.md @@ -71,4 +71,4 @@ Please read [CONTRIBUTING.md](../../CONTRIBUTING.md) for details on our code of [MIT](LICENSE.md) -Copyright (c) 2015–2025 [EPAM Systems, Inc.](https://www.epam.com/) +Copyright (c) 2015–2026 [EPAM Systems, Inc.](https://www.epam.com/) diff --git a/packages/miew-react/package.json b/packages/miew-react/package.json index 245d6cab..f347893f 100644 --- a/packages/miew-react/package.json +++ b/packages/miew-react/package.json @@ -1,13 +1,13 @@ { "name": "miew-react", - "version": "0.11.0", + "version": "0.12.0", "description": "Miew - 3D Molecular Viewer (React component)", "author": "EPAM Systems, Inc.", "homepage": "https://github.com/epam/miew#readme", "license": "MIT", "repository": { "type": "git", - "url": "https://github.com/epam/miew.git", + "url": "git+https://github.com/epam/miew.git", "directory": "packages/miew-react" }, "bugs": { diff --git a/packages/miew/CHANGELOG.md b/packages/miew/CHANGELOG.md index c63c30f1..a2db9e96 100644 --- a/packages/miew/CHANGELOG.md +++ b/packages/miew/CHANGELOG.md @@ -7,6 +7,25 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] +## [0.12.0] - 2026-06-09 + +### Changed + +- Upgraded the WebGL renderer to WebGL 2.0, replacing deprecated extension APIs with built-in + WebGL 2.0 equivalents. This may affect applications that rely on the specific WebGL 1.0 + extension behavior. +- Updated shaders to GLSL 3.0, restoring ambient occlusion, shadows, electron density, + sprite-based rendering modes, and other visual effects that had regressed with the + newer Three.js renderer. + +### Fixed + +- Fixed an always-false condition check in the component edit mode. + +### Internal + +- Updated third-party dependencies. + ## [0.11.1] - 2025-10-14 ### Fixed @@ -648,7 +667,8 @@ in [0.7.7+hotfix] and later releases. - Update dependencies to the latest supported versions. - Move the project to GitHub. -[Unreleased]: https://github.com/epam/miew/compare/v0.11.1...HEAD +[Unreleased]: https://github.com/epam/miew/compare/v0.12.0...HEAD +[0.12.0]: https://github.com/epam/miew/compare/v0.11.1...v0.12.0 [0.11.1]: https://github.com/epam/miew/compare/v0.11.0...v0.11.1 [0.11.0]: https://github.com/epam/miew/compare/v0.9.0...v0.11.0 [0.10.0]: https://github.com/epam/miew/compare/v0.9.0...v0.10.0 diff --git a/packages/miew/LICENSE.md b/packages/miew/LICENSE.md index ed5bc6e8..da8a376d 100644 --- a/packages/miew/LICENSE.md +++ b/packages/miew/LICENSE.md @@ -1,6 +1,6 @@ The MIT License -Copyright (c) 2015-2025 [EPAM Systems, Inc.](https://www.epam.com/) +Copyright (c) 2015-2026 [EPAM Systems, Inc.](https://www.epam.com/) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/packages/miew/README.md b/packages/miew/README.md index a5fcfc49..4f73a736 100644 --- a/packages/miew/README.md +++ b/packages/miew/README.md @@ -30,10 +30,10 @@ or built with a bundler of your choice. For more details refer to: - + - - + +
@@ -116,4 +116,4 @@ Please read [CONTRIBUTING.md](../../CONTRIBUTING.md) for details on our code of [MIT](LICENSE.md) -Copyright (c) 2015–2025 [EPAM Systems, Inc.](https://www.epam.com/) +Copyright (c) 2015–2026 [EPAM Systems, Inc.](https://www.epam.com/) diff --git a/packages/miew/demo/menu.html b/packages/miew/demo/menu.html index f27fe17c..eb17de69 100644 --- a/packages/miew/demo/menu.html +++ b/packages/miew/demo/menu.html @@ -396,7 +396,7 @@

-

Copyright © 2015–2025 EPAM Systems, Inc.

+

Copyright © 2015–2026 EPAM Systems, Inc.

https://epa.ms/miew

diff --git a/packages/miew/demo/scripts/ui/Menu.js b/packages/miew/demo/scripts/ui/Menu.js index 1c050e95..4f2c18d0 100644 --- a/packages/miew/demo/scripts/ui/Menu.js +++ b/packages/miew/demo/scripts/ui/Menu.js @@ -137,7 +137,7 @@ Menu.prototype._initializeTerminal = function () { } }, { - greetings: 'Miew - 3D Molecular Viewer\nCopyright © 2015-2025 EPAM Systems, Inc.\n', + greetings: 'Miew - 3D Molecular Viewer\nCopyright © 2015-2026 EPAM Systems, Inc.\n', prompt: 'miew> ', name: 'miew', scrollOnEcho: true, diff --git a/packages/miew/dist/Miew.css b/packages/miew/dist/Miew.css index 84f89740..1748e745 100644 --- a/packages/miew/dist/Miew.css +++ b/packages/miew/dist/Miew.css @@ -72,7 +72,7 @@ right: 10px; border-radius: 4px; color: silver; - background-color: rgba(64, 64, 64, 0.75); + background-color: rgb(64, 64, 64, 0.75); display: flex; align-items: left; justify-content: left; diff --git a/packages/miew/dist/Miew.js b/packages/miew/dist/Miew.js index 8f3b416d..8f4c4b1b 100644 --- a/packages/miew/dist/Miew.js +++ b/packages/miew/dist/Miew.js @@ -1,4 +1,4 @@ -/*! Miew - 3D Molecular Viewer v0.11.1 Copyright (c) 2015-2025 EPAM Systems, Inc. */ +/*! Miew - 3D Molecular Viewer v0.12.0 Copyright (c) 2015-2026 EPAM Systems, Inc. */ (function webpackUniversalModuleDefinition(root, factory) { if(typeof exports === 'object' && typeof module === 'object') module.exports = factory(require("lodash"), require("three")); @@ -12,8 +12,8 @@ return /******/ (() => { // webpackBootstrap /******/ var __webpack_modules__ = ({ -/***/ 89: -/***/ ((module) => { +/***/ 89 +(module) { /* eslint-disable */ // DO NOT EDIT! Automatically generated from .jison @@ -360,7 +360,8 @@ var parser = function () { switch (yystate) { case 1: return $$[$0 - 1]; - break; + // removed by dead control flow + case 3: this.$ = yy.miew.reset(false); yy.ClearContext(); @@ -2590,248 +2591,329 @@ var parser = function () { break; case 1: return ''; - break; + // removed by dead control flow + case 2: return ''; - break; + // removed by dead control flow + case 3: return 42; - break; + // removed by dead control flow + case 4: return 35; - break; + // removed by dead control flow + case 5: return 77; - break; + // removed by dead control flow + case 6: return 78; - break; + // removed by dead control flow + case 7: return 78; - break; + // removed by dead control flow + case 8: return 8; - break; + // removed by dead control flow + case 9: return 6; - break; + // removed by dead control flow + case 10: return 82; - break; + // removed by dead control flow + case 11: return 7; - break; + // removed by dead control flow + case 12: return 9; - break; + // removed by dead control flow + case 13: return 59; - break; + // removed by dead control flow + case 14: return 13; - break; + // removed by dead control flow + case 15: return 15; - break; + // removed by dead control flow + case 16: return 17; - break; + // removed by dead control flow + case 17: return 18; - break; + // removed by dead control flow + case 18: return 19; - break; + // removed by dead control flow + case 19: return 20; - break; + // removed by dead control flow + case 20: return 11; - break; + // removed by dead control flow + case 21: return 62; - break; + // removed by dead control flow + case 22: return 64; - break; + // removed by dead control flow + case 23: return 23; - break; + // removed by dead control flow + case 24: return 25; - break; + // removed by dead control flow + case 25: return 26; - break; + // removed by dead control flow + case 26: return 27; - break; + // removed by dead control flow + case 27: return 30; - break; + // removed by dead control flow + case 28: return 34; - break; + // removed by dead control flow + case 29: return 33; - break; + // removed by dead control flow + case 30: return 65; - break; + // removed by dead control flow + case 31: return 66; - break; + // removed by dead control flow + case 32: return 37; - break; + // removed by dead control flow + case 33: return 41; - break; + // removed by dead control flow + case 34: return 43; - break; + // removed by dead control flow + case 35: return 52; - break; + // removed by dead control flow + case 36: return 54; - break; + // removed by dead control flow + case 37: return 55; - break; + // removed by dead control flow + case 38: return 46; - break; + // removed by dead control flow + case 39: return 48; - break; + // removed by dead control flow + case 40: return 45; - break; + // removed by dead control flow + case 41: return 49; - break; + // removed by dead control flow + case 42: return 56; - break; + // removed by dead control flow + case 43: return 58; - break; + // removed by dead control flow + case 44: return 44; - break; + // removed by dead control flow + case 45: return 83; - break; + // removed by dead control flow + case 46: return 84; - break; + // removed by dead control flow + case 47: return 85; - break; + // removed by dead control flow + case 48: return 86; - break; + // removed by dead control flow + case 49: return 87; - break; + // removed by dead control flow + case 50: return 88; - break; + // removed by dead control flow + case 51: return 89; - break; + // removed by dead control flow + case 52: return 90; - break; + // removed by dead control flow + case 53: return 91; - break; + // removed by dead control flow + case 54: return 92; - break; + // removed by dead control flow + case 55: return 93; - break; + // removed by dead control flow + case 56: return 94; - break; + // removed by dead control flow + case 57: return 95; - break; + // removed by dead control flow + case 58: return 70; - break; + // removed by dead control flow + case 59: return 70; - break; + // removed by dead control flow + case 60: return 72; - break; + // removed by dead control flow + case 61: return 72; - break; + // removed by dead control flow + case 62: return 74; - break; + // removed by dead control flow + case 63: return 74; - break; + // removed by dead control flow + case 64: return 74; - break; + // removed by dead control flow + case 65: return 31; - break; + // removed by dead control flow + case 66: return 36; - break; + // removed by dead control flow + case 67: return 96; - break; + // removed by dead control flow + case 68: return 97; - break; + // removed by dead control flow + case 69: return 98; - break; + // removed by dead control flow + case 70: return 99; - break; + // removed by dead control flow + case 71: yy_.yytext = yy.utils.unquoteString(yy_.yytext); return 14; - break; + // removed by dead control flow + case 72: return 38; - break; + // removed by dead control flow + case 73: return 5; - break; + // removed by dead control flow + case 74: return 101; - break; + // removed by dead control flow + case 75: return 103; - break; + // removed by dead control flow + case 76: return '\\'; - break; + // removed by dead control flow + case 77: return 28; - break; + // removed by dead control flow + case 78: return 61; - break; + // removed by dead control flow + case 79: return 29; - break; + // removed by dead control flow + case 80: return 57; - break; + // removed by dead control flow + case 81: return 71; - break; + // removed by dead control flow + } }, rules: [/^(?:\s+)/i, /^(?:[#].*)/i, /^(?:\/\/.*)/i, /^(?:([_A-Z0-9\/\+]+==))/i, /^(?:-?[0-9]+(\.[0-9]+)?\b)/i, /^(?:0[xX][0-9A-F]+\b)/i, /^(?:false\b)/i, /^(?:true\b)/i, /^(?:all\b)/i, /^(?:reset\b)/i, /^(?:clear\b)/i, /^(?:build\b)/i, /^(?:help\b)/i, /^(?:load\b)/i, /^(?:get\b)/i, /^(?:set\b)/i, /^(?:set_save\b)/i, /^(?:set_restore\b)/i, /^(?:set_reset\b)/i, /^(?:preset\b)/i, /^(?:motm\b)/i, /^(?:add\b)/i, /^(?:rep\b)/i, /^(?:remove\b)/i, /^(?:hide\b)/i, /^(?:show\b)/i, /^(?:list\b)/i, /^(?:select\b)/i, /^(?:within\b)/i, /^(?:selector\b)/i, /^(?:mode\b)/i, /^(?:color\b)/i, /^(?:material\b)/i, /^(?:view\b)/i, /^(?:unit\b)/i, /^(?:line\b)/i, /^(?:listobj\b)/i, /^(?:removeobj\b)/i, /^(?:rotate\b)/i, /^(?:translate\b)/i, /^(?:scale\b)/i, /^(?:center\b)/i, /^(?:url\b)/i, /^(?:screenshot\b)/i, /^(?:dssp\b)/i, /^(?:file_list\b)/i, /^(?:file_register\b)/i, /^(?:file_delete\b)/i, /^(?:preset_add\b)/i, /^(?:preset_delete\b)/i, /^(?:preset_update\b)/i, /^(?:preset_rename\b)/i, /^(?:preset_open\b)/i, /^(?:create_scenario\b)/i, /^(?:reset_scenario\b)/i, /^(?:delete_scenario\b)/i, /^(?:add_scenario_item\b)/i, /^(?:list_scenario\b)/i, /^(?:s\b)/i, /^(?:mt\b)/i, /^(?:m\b)/i, /^(?:c\b)/i, /^(?:x\b)/i, /^(?:y\b)/i, /^(?:z\b)/i, /^(?:as\b)/i, /^(?:of\b)/i, /^(?:pdb\b)/i, /^(?:delay\b)/i, /^(?:prst\b)/i, /^(?:desc\b)/i, /^(?:((?:"(?:\\.|[^\\"])*"|'(?:\\.|[^\\'])*')))/i, /^(?:([_A-Z0-9]+))/i, /^(?:$)/i, /^(?:\.)/i, /^(?:\/)/i, /^(?:\\)/i, /^(?:-e\b)/i, /^(?:-f\b)/i, /^(?:-s\b)/i, /^(?:-v\b)/i, /^(?:=)/i], @@ -2856,10 +2938,10 @@ module.exports = { parser: parser }; -/***/ }), +/***/ }, -/***/ 99: -/***/ ((module) => { +/***/ 99 +(module) { /* eslint-disable */ // DO NOT EDIT! Automatically generated from .jison @@ -3011,7 +3093,8 @@ var parser = function () { switch (yystate) { case 1: return $$[$0 - 1]; - break; + // removed by dead control flow + case 3: this.$ = yy.keyword('or')($$[$0 - 2], $$[$0]); break; @@ -3601,65 +3684,85 @@ var parser = function () { break; case 1: return 20; - break; + // removed by dead control flow + case 2: return 7; - break; + // removed by dead control flow + case 3: return 8; - break; + // removed by dead control flow + case 4: return 9; - break; + // removed by dead control flow + case 5: return 12; - break; + // removed by dead control flow + case 6: return 16; - break; + // removed by dead control flow + case 7: return 14; - break; + // removed by dead control flow + case 8: return 10; - break; + // removed by dead control flow + case 9: return 11; - break; + // removed by dead control flow + case 10: return 19; - break; + // removed by dead control flow + case 11: return 21; - break; + // removed by dead control flow + case 12: return '<='; - break; + // removed by dead control flow + case 13: return '>='; - break; + // removed by dead control flow + case 14: return '<'; - break; + // removed by dead control flow + case 15: return '>'; - break; + // removed by dead control flow + case 16: yy_.yytext = yy_.yytext.substr(1, yy_.yyleng - 2); return 24; - break; + // removed by dead control flow + case 17: return 13; - break; + // removed by dead control flow + case 18: return 23; - break; + // removed by dead control flow + case 19: return 5; - break; + // removed by dead control flow + case 20: return 'INVALID'; - break; + // removed by dead control flow + } }, rules: [/^(?:\s+)/i, /^(?:(-?(?:[1-9][0-9]+|[0-9]))\b)/i, /^(?:OR\b)/i, /^(?:AND\b)/i, /^(?:NOT\b)/i, /^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\b)/i, /^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\b)/i, /^(?:((SERIAL|SEQUENCE|RESIDX))\b)/i, /^(?:\()/i, /^(?:\))/i, /^(?:,)/i, /^(?::)/i, /^(?:<=)/i, /^(?:>=)/i, /^(?:<)/i, /^(?:>)/i, /^(?:((?:"(?:\\.|[^\\"])*"|'(?:\\.|[^\\'])*')))/i, /^(?:(@[_A-Z0-9]+))/i, /^(?:([_A-Z0-9]+))/i, /^(?:$)/i, /^(?:.)/i], @@ -3684,10 +3787,10 @@ module.exports = { parser: parser }; -/***/ }), +/***/ }, -/***/ 690: -/***/ (function(__unused_webpack_module, exports) { +/***/ 690 +(__unused_webpack_module, exports) { /* Smooth.js version 0.1.7 @@ -4081,16 +4184,17 @@ Licensed under MIT license (see "Smooth.js MIT license.txt") ( true && exports !== null ? exports : window).Smooth = Smooth; }).call(this); -/***/ }), +/***/ }, -/***/ 660: -/***/ (function(module, exports) { +/***/ 660 +(module, exports) { var __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!function (r, t) { if (true) !(__WEBPACK_AMD_DEFINE_ARRAY__ = [exports], __WEBPACK_AMD_DEFINE_FACTORY__ = (t), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), - __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));else {} + __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));else // removed by dead control flow +{} }(this, function (r) { "use strict"; @@ -4731,23 +4835,23 @@ var __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_ r.encode = Q, r.decode = Y, r.traverse = K, r.fetch = $, r.fetchReduced = _, r.version = er, r.fetchUrl = or, r.fetchReducedUrl = ar, r.encodeMsgpack = o, r.encodeMmtf = R, r.decodeMsgpack = H, r.decodeMmtf = X; }); -/***/ }), +/***/ }, -/***/ 535: -/***/ ((module) => { +/***/ 535 +(module) { "use strict"; module.exports = __WEBPACK_EXTERNAL_MODULE__535__; -/***/ }), +/***/ }, -/***/ 698: -/***/ ((module) => { +/***/ 698 +(module) { "use strict"; module.exports = __WEBPACK_EXTERNAL_MODULE__698__; -/***/ }) +/***/ } /******/ }); /************************************************************************/ @@ -4807,7 +4911,7 @@ module.exports = __WEBPACK_EXTERNAL_MODULE__698__; /******/ /************************************************************************/ var __webpack_exports__ = {}; -// This entry need to be wrapped in an IIFE because it need to be in strict mode. +// This entry needs to be wrapped in an IIFE because it needs to be in strict mode. (() => { "use strict"; @@ -4821,7 +4925,7 @@ var external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_ = _ var external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_default = /*#__PURE__*/__webpack_require__.n(external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_); // EXTERNAL MODULE: external {"module":"three","commonjs":"three","commonjs2":"three","amd":"three","root":"THREE"} var external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_ = __webpack_require__(698); -;// CONCATENATED MODULE: ../../node_modules/spin.js/spin.js +;// ../../node_modules/spin.js/spin.js var __assign = undefined && undefined.__assign || function () { __assign = Object.assign || function (t) { for (var s, i = 1, n = arguments.length; i < n; i++) { @@ -4992,7 +5096,7 @@ function convertOffset(x, y, degrees) { var cos = Math.cos(radians); return [Math.round((x * cos + y * sin) * 1000) / 1000, Math.round((-x * sin + y * cos) * 1000) / 1000]; } -;// CONCATENATED MODULE: ./src/Timer.js +;// ./src/Timer.js //---------------------------------------------------------------------------- // Timer @@ -5031,7 +5135,7 @@ Timer.now = function () { const p = typeof window !== 'undefined' && window.performance; return p && p.now ? p.now.bind(p) : Date.now; }(); -;// CONCATENATED MODULE: ./src/gfx/Stats.js +;// ./src/gfx/Stats.js const { now @@ -5084,7 +5188,7 @@ class Stats { } } /* harmony default export */ const gfx_Stats = (Stats); -;// CONCATENATED MODULE: ./src/utils/EventDispatcher.js +;// ./src/utils/EventDispatcher.js /** * This class introduces the simplest event system. */ @@ -5157,7 +5261,7 @@ EventDispatcher.prototype.dispatchEvent = function (event) { }); }; /* harmony default export */ const utils_EventDispatcher = (EventDispatcher); -;// CONCATENATED MODULE: ./src/utils/logger.js +;// ./src/utils/logger.js /** * This module contains class for logging. * Returns an instance of a logger that have already been created. @@ -5307,7 +5411,7 @@ Logger.prototype._message = function (priority, message) { }); }; /* harmony default export */ const logger = (new Logger()); -;// CONCATENATED MODULE: ./src/utils.js +;// ./src/utils.js const browserType = { @@ -5388,7 +5492,7 @@ function resolveURL(str) { return new URL(str, window.location).href; } return new URL(str).href; - } catch (error) { + } catch { // IE 11 has a URL object with no constructor available so just try a different approach instead } } @@ -5515,16 +5619,13 @@ function DebugTracer(namespace) { let indent = 0; const methods = Object.keys(namespace); function wrap(method_, name_) { - return function () { + return function (...args) { const spaces = DebugTracer.spaces.substr(0, indent * 2); if (enabled) { logger.debug(`${spaces + name_} {`); } indent++; - for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) { - args[_key] = arguments[_key]; - } - const result = method_.apply(this, args); // eslint-disable-line no-invalid-this + const result = method_.apply(this, args); indent--; if (enabled) { logger.debug(`${spaces}} // ${name_}`); @@ -5565,7 +5666,7 @@ function allocateTyped(TypedArrayName, size) { //---------------------------------------------------------------------------- // Float array conversion -function bytesToBase64( /** ArrayBuffer */buffer) { +function bytesToBase64(/** ArrayBuffer */buffer) { const bytes = new Uint8Array(buffer); let binary = ''; for (let i = 0; i < bytes.byteLength; i++) { @@ -5573,7 +5674,7 @@ function bytesToBase64( /** ArrayBuffer */buffer) { } return window.btoa(binary); } -function bytesFromBase64( /** string */str) { +function bytesFromBase64(/** string */str) { const binary = window.atob(str); const bytes = new Uint8Array(binary.length); for (let i = 0; i < bytes.length; ++i) { @@ -5581,10 +5682,10 @@ function bytesFromBase64( /** string */str) { } return bytes.buffer; } -function arrayToBase64( /** number[] */array, /** function */TypedArrayClass) { +function arrayToBase64(/** number[] */array, /** function */TypedArrayClass) { return bytesToBase64(new TypedArrayClass(array).buffer); } -function arrayFromBase64( /** string */str, /** function */TypedArrayClass) { +function arrayFromBase64(/** string */str, /** function */TypedArrayClass) { return Array.prototype.slice.call(new TypedArrayClass(bytesFromBase64(str))); } @@ -5839,7 +5940,7 @@ function mergeTypedArraysUnsafe(array) { concatTypedArraysUnsafe, mergeTypedArraysUnsafe }); -;// CONCATENATED MODULE: ./src/utils/JobHandle.js +;// ./src/utils/JobHandle.js class JobHandle extends utils_EventDispatcher { constructor() { @@ -5865,7 +5966,7 @@ class JobHandle extends utils_EventDispatcher { }); } } -;// CONCATENATED MODULE: ./src/settings.js +;// ./src/settings.js @@ -6800,7 +6901,7 @@ utils.deriveClass(Settings, utils_EventDispatcher, { } }); /* harmony default export */ const settings = (new Settings()); -;// CONCATENATED MODULE: ./src/options.js +;// ./src/options.js @@ -7228,7 +7329,7 @@ function toScript(opts) { toURL, toScript }); -;// CONCATENATED MODULE: ./src/chem/Atom.js +;// ./src/chem/Atom.js /** * Atom measurements. * @@ -7328,7 +7429,7 @@ class Atom { }; } /* harmony default export */ const chem_Atom = (Atom); -;// CONCATENATED MODULE: ./src/chem/Element.js +;// ./src/chem/Element.js class Element { constructor(number, name, fullName, weight, radius, radiusBonding, hValency) { this.number = number; @@ -7340,39 +7441,32 @@ class Element { this.hydrogenValency = hValency; } static Constants = { - /* eslint-disable no-magic-numbers */ U1: 1, Lead: 2, U2: 3, Wing: 4, U18: 18 - /* eslint-enable no-magic-numbers */ }; - static Role = (() => ({ - /* eslint-disable no-magic-numbers */ + static Role = { N: Element.Constants.U1, CA: Element.Constants.Lead, C: Element.Constants.U2, O: Element.Constants.Wing, SG: Element.Constants.U18 - /* eslint-enable no-magic-numbers */ - }))(); + }; // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. - static ByAtomicNumber = (() => [/* eslint-disable no-magic-numbers */ - null, new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]), new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]), new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]), new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]), new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]), new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]), new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]), new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]), new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]), new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]), new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]), new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]), new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]), new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]), new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]), new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]), new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]), new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]), new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]), new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]), new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]), new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]), new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]), new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]), new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]), new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]), new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]), new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]), new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]), new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]), new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]), new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]), new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]), new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]), new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]), new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]), new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]), new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]), new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]), new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]), new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]), new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]), new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]), new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]), new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]), new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]), new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]), new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]), new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]), new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]), new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]), new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]), new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]), new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]), new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]), new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]), new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]), new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]), new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]), new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]), new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]), new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]), new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]), new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]), new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]), new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]), new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]), new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]), new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]), new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]), new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]), new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]), new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]), new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]), new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]), new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]), new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]), new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]), new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]), new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]), new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]), new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]), new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]), new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]), new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]), new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]), new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]), new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]), new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]), new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]), new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]), new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]), new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]), new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]), new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]), new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]), new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]), new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]), new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]), new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]), new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]), new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]), new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]), new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]), new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]), new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]), new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]), new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]), new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0]) - /* eslint-enable no-magic-numbers */])(); + static ByAtomicNumber = [null, new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]), new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]), new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]), new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]), new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]), new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]), new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]), new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]), new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]), new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]), new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]), new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]), new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]), new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]), new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]), new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]), new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]), new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]), new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]), new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]), new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]), new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]), new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]), new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]), new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]), new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]), new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]), new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]), new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]), new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]), new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]), new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]), new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]), new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]), new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]), new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]), new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]), new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]), new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]), new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]), new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]), new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]), new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]), new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]), new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]), new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]), new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]), new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]), new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]), new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]), new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]), new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]), new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]), new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]), new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]), new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]), new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]), new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]), new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]), new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]), new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]), new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]), new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]), new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]), new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]), new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]), new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]), new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]), new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]), new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]), new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]), new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]), new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]), new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]), new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]), new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]), new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]), new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]), new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]), new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]), new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]), new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]), new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]), new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]), new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]), new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]), new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]), new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]), new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]), new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]), new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]), new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]), new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]), new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]), new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]), new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]), new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]), new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]), new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]), new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]), new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]), new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]), new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]), new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]), new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]), new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]), new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]), new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]), new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0])]; // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. - static ByName = (() => ({ + static ByName = { // Duplicate atomic numbers (isotopes) - /* eslint-disable no-magic-numbers */ + D: new Element(1, 'D', 'Deuterium', 2.014, 1.2, 0.23, [1]), T: new Element(1, 'T', 'Tritium', 3.016, 1.2, 0.23, [1]) - /* eslint-enable no-magic-numbers */ // All regular elements will be added later, automatically - }))(); + }; } (function () { const byAtomicNumber = Element.ByAtomicNumber; @@ -7394,7 +7488,7 @@ Element.getByName = function (element) { return type; }; /* harmony default export */ const chem_Element = (Element); -;// CONCATENATED MODULE: ./src/chem/Bond.js +;// ./src/chem/Bond.js const cBondTypes = { /** Was generated manually */ UNKNOWN: 0, @@ -7569,11 +7663,11 @@ class Bond { firstV.normalize(); return this._fixDir(secondPos, firstV, posGetter); } - static BondType = (() => cBondTypes)(); + static BondType = cBondTypes; } Bond.prototype.BondType = cBondTypes; /* harmony default export */ const chem_Bond = (Bond); -;// CONCATENATED MODULE: ./src/chem/Residue.js +;// ./src/chem/Residue.js @@ -7844,7 +7938,7 @@ class Residue { } } /* harmony default export */ const chem_Residue = (Residue); -;// CONCATENATED MODULE: ./src/chem/ResidueType.js +;// ./src/chem/ResidueType.js /** * Residue type. * @@ -7869,8 +7963,7 @@ class ResidueType { } // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py. - static StandardTypes = (() => ({ - /* eslint-disable no-magic-numbers */ + static StandardTypes = { ALA: new ResidueType('ALA', 'Alanine', 'A'), ARG: new ResidueType('ARG', 'Arginine', 'R'), ASN: new ResidueType('ASN', 'Asparagine', 'N'), @@ -7917,8 +8010,7 @@ class ResidueType { DOD: new ResidueType('DOD', 'Water', ''), UNK: new ResidueType('UNK', 'Unknown', ''), UNL: new ResidueType('UNL', 'Unknown Ligand', '') - /* eslint-enable no-magic-numbers */ - }))(); + }; /** * Enumeration of residue flag values. @@ -8014,7 +8106,7 @@ function _addParam(param, list) { } _addParam('hydrophobicity', hydro); /* harmony default export */ const chem_ResidueType = (ResidueType); -;// CONCATENATED MODULE: ./src/chem/Chain.js +;// ./src/chem/Chain.js @@ -8183,7 +8275,7 @@ class Chain { } } /* harmony default export */ const chem_Chain = (Chain); -;// CONCATENATED MODULE: ./src/chem/StructuralElement.js +;// ./src/chem/StructuralElement.js /** An element of protein secondary structure. */ @@ -8315,7 +8407,7 @@ StructuralElement.genericByType = { [StructuralElementType.HELIX]: StructuralElementGeneric.HELIX }; /* harmony default export */ const chem_StructuralElement = (StructuralElement); -;// CONCATENATED MODULE: ./src/chem/Helix.js +;// ./src/chem/Helix.js const Helix_StructuralElementType = chem_StructuralElement.Type; const typeByPDBHelixClass = { @@ -8367,7 +8459,7 @@ class Helix extends chem_StructuralElement { } } /* harmony default export */ const chem_Helix = (Helix); -;// CONCATENATED MODULE: ./src/chem/Strand.js +;// ./src/chem/Strand.js /** @@ -8441,7 +8533,7 @@ class Strand extends chem_StructuralElement { } } /* harmony default export */ const chem_Strand = (Strand); -;// CONCATENATED MODULE: ./src/chem/Sheet.js +;// ./src/chem/Sheet.js /** @@ -8488,7 +8580,7 @@ class Sheet { } } /* harmony default export */ const chem_Sheet = (Sheet); -;// CONCATENATED MODULE: ./src/chem/SGroup.js +;// ./src/chem/SGroup.js /** @@ -8547,7 +8639,7 @@ class SGroup { /* harmony default export */ const chem_SGroup = (SGroup); // EXTERNAL MODULE: ./src/utils/SelectionParser.js var SelectionParser = __webpack_require__(99); -;// CONCATENATED MODULE: ./src/chem/selectors/selectArgs.js +;// ./src/chem/selectors/selectArgs.js //---------------------------------------------------------------------------- @@ -8678,7 +8770,7 @@ class ValueList extends List { } } -;// CONCATENATED MODULE: ./src/chem/selectors/selectorsBase.js +;// ./src/chem/selectors/selectorsBase.js /** Base class for atom selectors. */ @@ -8731,7 +8823,7 @@ class AllSelector extends Selector { AllSelector.prototype.name = 'All'; AllSelector.prototype.keyword = 'all'; -;// CONCATENATED MODULE: ./src/chem/selectors/selectOps.js +;// ./src/chem/selectors/selectOps.js //---------------------------------------------------------------------------- @@ -8769,7 +8861,7 @@ class InfixOperator extends Selector { } InfixOperator.prototype.priority = 1000; -;// CONCATENATED MODULE: ./src/chem/selectors.js +;// ./src/chem/selectors.js @@ -8786,12 +8878,7 @@ function defineSelector(name, SelectorClass) { const keyword = name.toLowerCase(); SelectorClass.prototype.keyword = keyword; SelectorClass.prototype.name = name; - const factory = function () { - for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) { - args[_key] = arguments[_key]; - } - return new SelectorClass(...args); - }; + const factory = (...args) => new SelectorClass(...args); factory.SelectorClass = SelectorClass; keywords[keyword] = factory; return SelectorClass; @@ -8955,7 +9042,7 @@ SelectionParser.parser.yy = selectors; SelectionParser.parser.yy.parseError = SelectionParser.parser.parseError; // workaround for incorrect JISON parser generator for AMD module /* harmony default export */ const chem_selectors = (selectors); -;// CONCATENATED MODULE: ./src/chem/BiologicalUnit.js +;// ./src/chem/BiologicalUnit.js @@ -9028,7 +9115,7 @@ class BiologicalUnit { finalize() {} } /* harmony default export */ const chem_BiologicalUnit = (BiologicalUnit); -;// CONCATENATED MODULE: ./src/chem/Assembly.js +;// ./src/chem/Assembly.js @@ -9094,7 +9181,7 @@ class Assembly extends chem_BiologicalUnit { } } /* harmony default export */ const chem_Assembly = (Assembly); -;// CONCATENATED MODULE: ./src/chem/Component.js +;// ./src/chem/Component.js /** * This class represents connected component as a part of a complex. * WARNING! The whole component entity is build under the assumption that residues @@ -9244,7 +9331,7 @@ class Component { } } /* harmony default export */ const chem_Component = (Component); -;// CONCATENATED MODULE: ./src/chem/AtomPairs.js +;// ./src/chem/AtomPairs.js const cMaxPairsForHashCode = 32; const cHashTableSize = 1024 * 1024; @@ -9315,7 +9402,7 @@ class AtomPairs { } } /* harmony default export */ const chem_AtomPairs = (AtomPairs); -;// CONCATENATED MODULE: ./src/chem/AutoBond.js +;// ./src/chem/AutoBond.js const cProfileBondBuilder = false; @@ -9497,7 +9584,7 @@ class AutoBond { } } /* harmony default export */ const chem_AutoBond = (AutoBond); -;// CONCATENATED MODULE: ./src/chem/AromaticLoopsMarker.js +;// ./src/chem/AromaticLoopsMarker.js @@ -9729,7 +9816,7 @@ class AromaticLoopsMarker { } } /* harmony default export */ const chem_AromaticLoopsMarker = (AromaticLoopsMarker); -;// CONCATENATED MODULE: ./src/chem/VoxelWorld.js +;// ./src/chem/VoxelWorld.js @@ -9843,8 +9930,8 @@ class VoxelWorld { * @param {Vector3} point - a point in 3D * @returns {number} - index of voxel */ - static _zero = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(0, 0, 0))(); - static _voxel = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3())(); + static _zero = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(0, 0, 0); + static _voxel = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); _findVoxel(point) { const zero = VoxelWorld._zero; const voxel = VoxelWorld._voxel; @@ -9873,9 +9960,9 @@ class VoxelWorld { * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside */ - static _xRange = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector2())(); - static _yRange = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector2())(); - static _zRange = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector2())(); + static _xRange = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector2(); + static _yRange = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector2(); + static _zRange = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector2(); _forEachVoxelWithinRadius(center, radius, process) { const xRange = VoxelWorld._xRange; const yRange = VoxelWorld._yRange; @@ -9931,7 +10018,7 @@ class VoxelWorld { * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside */ - static _vCenter = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3())(); + static _vCenter = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); _forEachVoxelWithinRadiusSimple(center, radius, process) { const xRange = VoxelWorld._xRange; const yRange = VoxelWorld._yRange; @@ -10100,7 +10187,7 @@ class VoxelWorld { } } /* harmony default export */ const chem_VoxelWorld = (VoxelWorld); -;// CONCATENATED MODULE: ./src/chem/HBondInfo.js +;// ./src/chem/HBondInfo.js const MINIMAL_DISTANCE = 0.5; @@ -10334,7 +10421,7 @@ class HBondInfo { return result; } } -;// CONCATENATED MODULE: ./src/chem/SecondaryStructureMap.js +;// ./src/chem/SecondaryStructureMap.js const BridgeType = Object.freeze({ @@ -10761,7 +10848,7 @@ class SecondaryStructureMap { } } SecondaryStructureMap.StructureType = StructureType; -;// CONCATENATED MODULE: ./src/chem/Complex.js +;// ./src/chem/Complex.js @@ -11004,17 +11091,13 @@ class Complex { return this._residueTypes[name] || null; } getUnifiedSerial(chain, serial, iCode) { - /* eslint-disable no-magic-numbers */ const maxSerial = 65536; const chainShift = maxSerial * 256; - /* eslint-enable no-magic-numbers */ return serial + iCode * maxSerial + chain * chainShift; } splitUnifiedSerial(uniSerial) { - /* eslint-disable no-magic-numbers */ const maxSerial = 65536; const chainShift = maxSerial * 256; - /* eslint-enable no-magic-numbers */ const chainId = Math.floor(uniSerial / chainShift); const remnant = uniSerial - chainId * chainShift; const insCode = Math.floor(remnant / maxSerial); @@ -11414,7 +11497,7 @@ class Complex { try { this._voxelWorld = new chem_VoxelWorld(this.getDefaultBoundaries().boundingBox, new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(VOXEL_SIZE, VOXEL_SIZE, VOXEL_SIZE)); this._voxelWorld.addAtoms(this); - } catch (e) { + } catch { logger.warn('Unable to create voxel world'); this._voxelWorld = null; } @@ -11578,7 +11661,7 @@ class Complex { Complex.prototype.id = 'Complex'; Complex.prototype.name = ''; /* harmony default export */ const chem_Complex = (Complex); -;// CONCATENATED MODULE: ./src/chem/Volume.js +;// ./src/chem/Volume.js function pow2ceil(v) { @@ -11829,7 +11912,7 @@ class Volume { } } } - const texture = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.DataTexture(data, width, height, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LuminanceFormat, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.UnsignedByteType, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.UVMapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.ClampToEdgeWrapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.ClampToEdgeWrapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter); + const texture = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.DataTexture(data, width, height, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.RedFormat, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.UnsignedByteType, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.UVMapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.ClampToEdgeWrapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.ClampToEdgeWrapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter); texture.needsUpdate = true; return texture; } @@ -11858,7 +11941,7 @@ class Volume { } Volume.prototype.id = 'Volume'; /* harmony default export */ const chem_Volume = (Volume); -;// CONCATENATED MODULE: ./src/chem/Molecule.js +;// ./src/chem/Molecule.js /** * Residue Molecule. * @@ -11897,7 +11980,7 @@ class Molecule { } } /* harmony default export */ const chem_Molecule = (Molecule); -;// CONCATENATED MODULE: ./src/chem.js +;// ./src/chem.js @@ -11932,7 +12015,7 @@ class Molecule { selectors: chem_selectors, Molecule: chem_Molecule }); -;// CONCATENATED MODULE: ./src/gfx/CSS2DObject.js +;// ./src/gfx/CSS2DObject.js /** * @author mrdoob / http://mrdoob.com/ */ @@ -11982,7 +12065,7 @@ class CSS2DObject extends external_module_three_commonjs_three_commonjs2_three_a } } /* harmony default export */ const gfx_CSS2DObject = (CSS2DObject); -;// CONCATENATED MODULE: ./src/gfx/RCGroup.js +;// ./src/gfx/RCGroup.js class RCGroup extends external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Group { raycast(raycaster, intersects) { @@ -12043,14 +12126,13 @@ class RCGroup extends external_module_three_commonjs_three_commonjs2_three_amd_t } } /* harmony default export */ const gfx_RCGroup = (RCGroup); -;// CONCATENATED MODULE: ./src/gfx/shaders/ScreenQuad.vert -const ScreenQuad_namespaceObject = "uniform mat4 projectionMatrix;\r\nuniform mat4 modelViewMatrix;\r\n\r\nattribute vec2 uv;\r\nattribute vec3 position;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vUv = uv;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4( position, 1.0 );\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/ScreenQuadFromTex.frag -const ScreenQuadFromTex_namespaceObject = "precision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform float opacity;\r\n\r\nvoid main() {\r\n vec4 color = texture2D(srcTex, vUv);\r\n gl_FragColor = vec4(color.xyz, color.a * opacity);\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/ScreenQuadFromTexWithDistortion.frag -const ScreenQuadFromTexWithDistortion_namespaceObject = "precision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform float coef;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n float r2 = dot(uv, uv);\r\n vec2 tc = uv * (1.0 + coef * r2);\r\n if (!all(lessThan(abs(tc), vec2(1.0))))\r\n discard;\r\n tc = 0.5 * (tc + 1.0);\r\n gl_FragColor = texture2D(srcTex, tc);\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/gfxutils.js -/* eslint-disable no-magic-numbers */ +;// ./src/gfx/shaders/ScreenQuad.vert +const ScreenQuad_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nuniform mat4 projectionMatrix;\r\nuniform mat4 modelViewMatrix;\r\n\r\nattribute vec2 uv;\r\nattribute vec3 position;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vUv = uv;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4( position, 1.0 );\r\n}\r\n"; +;// ./src/gfx/shaders/ScreenQuadFromTex.frag +const ScreenQuadFromTex_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform float opacity;\r\n\r\nvoid main() {\r\n vec4 color = texture2D(srcTex, vUv);\r\n gl_FragColor = vec4(color.xyz, color.a * opacity);\r\n}\r\n"; +;// ./src/gfx/shaders/ScreenQuadFromTexWithDistortion.frag +const ScreenQuadFromTexWithDistortion_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform float coef;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n float r2 = dot(uv, uv);\r\n vec2 tc = uv * (1.0 + coef * r2);\r\n if (!all(lessThan(abs(tc), vec2(1.0))))\r\n discard;\r\n tc = 0.5 * (tc + 1.0);\r\n gl_FragColor = texture2D(srcTex, tc);\r\n}\r\n"; +;// ./src/gfx/gfxutils.js @@ -12470,7 +12552,7 @@ external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Insta getMiddlePoint, LAYERS }); -;// CONCATENATED MODULE: ./src/Visual.js +;// ./src/Visual.js const _defaultBoundaries = { @@ -12496,7 +12578,7 @@ class Visual extends gfxutils.RCGroup { } } /* harmony default export */ const src_Visual = (Visual); -;// CONCATENATED MODULE: ./src/utils/EntityList.js +;// ./src/utils/EntityList.js function _ensureArray(x) { if (x === null || x === undefined || Array.isArray(x)) { return x; @@ -12515,9 +12597,7 @@ class EntityList { * By default, a single `.id` property is used. * @see EntityList#register */ - constructor() { - let entities = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : []; - let indices = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : ['id']; + constructor(entities = [], indices = ['id']) { this._list = []; this._dict = {}; this._indices = [...indices]; @@ -12684,7 +12764,7 @@ class EntityList { } } /* harmony default export */ const utils_EntityList = (EntityList); -;// CONCATENATED MODULE: ./src/utils/makeContextDependent.js +;// ./src/utils/makeContextDependent.js function makeContextDependent(prototype) { @@ -12702,14 +12782,14 @@ function makeContextDependent(prototype) { }); } /* harmony default export */ const utils_makeContextDependent = (makeContextDependent); -;// CONCATENATED MODULE: ./src/gfx/geometries/SphereCollisionGeo.js +;// ./src/gfx/geometries/SphereCollisionGeo.js class CollisionSphere { constructor(position, radius) { this._position = position; this._radius = radius; } - static _sphere = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Sphere())(); + static _sphere = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Sphere(); raycast(raycaster) { const sphere = CollisionSphere._sphere; sphere.set(this._position, this._radius); @@ -12724,10 +12804,7 @@ class CollisionSphere { } } const SphereCollisionGeo = base => class extends base { - constructor(count) { - for (var _len = arguments.length, args = new Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) { - args[_key - 1] = arguments[_key]; - } + constructor(count, ...args) { super(...args); this._objects = new Array(count); this.boundingSphere = null; @@ -12783,7 +12860,7 @@ const SphereCollisionGeo = base => class extends base { } }; /* harmony default export */ const geometries_SphereCollisionGeo = (SphereCollisionGeo); -;// CONCATENATED MODULE: ./src/gfx/geometries/InstancedSpheresGeometry.js +;// ./src/gfx/geometries/InstancedSpheresGeometry.js @@ -12808,7 +12885,7 @@ function setArrayXYZW(arr, idx, x, y, z, w) { class InstancedSpheresGeometry extends geometries_SphereCollisionGeo(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.InstancedBufferGeometry) { constructor(spheresCount, sphereComplexity, useZSprites) { super(spheresCount); - this._sphGeometry = useZSprites ? new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.PlaneGeometry(2, 2, 1, 1) : new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.SphereBufferGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI); + this._sphGeometry = useZSprites ? new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.PlaneGeometry(2, 2, 1, 1) : new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.SphereGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI); this._init(spheresCount, this._sphGeometry); } setItem(itemIdx, itemPos, itemRad) { @@ -12859,7 +12936,7 @@ class InstancedSpheresGeometry extends geometries_SphereCollisionGeo(external_mo } } /* harmony default export */ const geometries_InstancedSpheresGeometry = (InstancedSpheresGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/ChunkedObjectsGeometry.js +;// ./src/gfx/geometries/ChunkedObjectsGeometry.js @@ -12983,7 +13060,7 @@ class ChunkedObjectsGeometry extends external_module_three_commonjs_three_common } } /* harmony default export */ const geometries_ChunkedObjectsGeometry = (ChunkedObjectsGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/SimpleSpheresGeometry.js +;// ./src/gfx/geometries/SimpleSpheresGeometry.js @@ -12991,7 +13068,7 @@ class ChunkedObjectsGeometry extends external_module_three_commonjs_three_common const SimpleSpheresGeometry_VEC_SIZE = 3; class SimpleSpheresGeometry extends geometries_SphereCollisionGeo(geometries_ChunkedObjectsGeometry) { constructor(spheresCount, sphereComplexity) { - const sphGeometry = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.SphereBufferGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI); + const sphGeometry = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.SphereGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI); super(spheresCount, sphGeometry, spheresCount); const normals = this._normals; const geoNormals = sphGeometry.attributes.normal.array; @@ -13017,7 +13094,7 @@ class SimpleSpheresGeometry extends geometries_SphereCollisionGeo(geometries_Chu } } /* harmony default export */ const geometries_SimpleSpheresGeometry = (SimpleSpheresGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/Simple2CCylindersGeometry.js +;// ./src/gfx/geometries/Simple2CCylindersGeometry.js @@ -13080,7 +13157,7 @@ class Simple2CCylindersGeometry extends geometries_ChunkedObjectsGeometry { } } /* harmony default export */ const geometries_Simple2CCylindersGeometry = (Simple2CCylindersGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/CylinderBufferGeometry.js +;// ./src/gfx/geometries/CylinderBufferGeometry.js const MAX_POINTS_COUNT_16BIT = 65536; @@ -13104,13 +13181,9 @@ class CylinderBufferGeometry extends external_module_three_commonjs_three_common const vertexCount = (heightSegments + 1) * radialSegments + hasTop * (radialSegments + 1) + hasBottom * (radialSegments + 1); const facesCount = (2 * heightSegments + hasTop + hasBottom) * radialSegments; const heightHalf = height / 2; - - /* eslint-disable no-magic-numbers */ const positions = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3); const normals = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3); const indices = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Uint16BufferAttribute(utils.allocateTyped(Uint16Array, facesCount * PTS_PER_TRIANGLE), 1); - /* eslint-enable no-magic-numbers */ - const uvs = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 2), 2); console.assert(vertexCount < MAX_POINTS_COUNT_16BIT, 'DEBUG: Cylinder Geometry has too many vertices (65536 max).'); let currVtxIdx = 0; @@ -13200,7 +13273,7 @@ class CylinderBufferGeometry extends external_module_three_commonjs_three_common } } /* harmony default export */ const geometries_CylinderBufferGeometry = (CylinderBufferGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/Instanced2CCylindersGeometry.js +;// ./src/gfx/geometries/Instanced2CCylindersGeometry.js @@ -13387,7 +13460,7 @@ class Instanced2CCylindersGeometry extends external_module_three_commonjs_three_ } } /* harmony default export */ const geometries_Instanced2CCylindersGeometry = (Instanced2CCylindersGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/ExtrudedObjectsGeometry.js +;// ./src/gfx/geometries/ExtrudedObjectsGeometry.js @@ -13440,9 +13513,7 @@ class ExtrudedObjectsGeometry extends geometries_ChunkedObjectsGeometry { tmpShape[i] = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); } } - setItem(itemIdx, matrices) { - let hasSlope = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : false; - let hasCut = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : false; + setItem(itemIdx, matrices, hasSlope = false, hasCut = false) { const ptsCount = this._chunkGeo._positions.length; const ringsCount = this._ringsCount; const chunkStartIdx = ptsCount * this._ringsCount * itemIdx * ExtrudedObjectsGeometry_VEC_SIZE; @@ -13560,7 +13631,7 @@ class ExtrudedObjectsGeometry extends geometries_ChunkedObjectsGeometry { } } /* harmony default export */ const geometries_ExtrudedObjectsGeometry = (ExtrudedObjectsGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/ThickLinesGeometry.js +;// ./src/gfx/geometries/ThickLinesGeometry.js @@ -13708,7 +13779,7 @@ class ThickLinesGeometry extends external_module_three_commonjs_three_commonjs2_ } } /* harmony default export */ const geometries_ThickLinesGeometry = (ThickLinesGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/LinesGeometry.js +;// ./src/gfx/geometries/LinesGeometry.js @@ -13765,7 +13836,7 @@ class LinesGeometry extends geometries_ThickLinesGeometry { } } /* harmony default export */ const geometries_LinesGeometry = (LinesGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/CylinderCollisionGeo.js +;// ./src/gfx/geometries/CylinderCollisionGeo.js @@ -13808,7 +13879,7 @@ class CylinderCollisionGeo extends geometries_ChunkedObjectsGeometry { } } /* harmony default export */ const geometries_CylinderCollisionGeo = (CylinderCollisionGeo); -;// CONCATENATED MODULE: ./src/gfx/geometries/ChunkedLinesGeometry.js +;// ./src/gfx/geometries/ChunkedLinesGeometry.js const COLLISION_RAD = 0.1; @@ -13914,7 +13985,7 @@ class ChunkedLinesGeometry extends geometries_LinesGeometry { } } /* harmony default export */ const geometries_ChunkedLinesGeometry = (ChunkedLinesGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/TwoColorLinesGeometry.js +;// ./src/gfx/geometries/TwoColorLinesGeometry.js @@ -13962,7 +14033,7 @@ class TwoColorLinesGeometry extends geometries_LinesGeometry { // (???)parent = LinesGeometry.prototype; /* harmony default export */ const geometries_TwoColorLinesGeometry = (TwoColorLinesGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/CrossGeometry.js +;// ./src/gfx/geometries/CrossGeometry.js @@ -13990,7 +14061,7 @@ class CrossGeometry extends geometries_SphereCollisionGeo(geometries_ChunkedLine } } /* harmony default export */ const geometries_CrossGeometry = (CrossGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurfaceGeometry.js +;// ./src/gfx/geometries/IsoSurfaceGeometry.js const POS_RAD_SIZE = 4; @@ -14043,7 +14114,7 @@ class IsoSurfaceGeometry extends external_module_three_commonjs_three_commonjs2_ } } /* harmony default export */ const geometries_IsoSurfaceGeometry = (IsoSurfaceGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurfaceMarchCube.js +;// ./src/gfx/geometries/IsoSurfaceMarchCube.js /** @@ -14076,13 +14147,9 @@ class IsoSurfaceMarchCube { this.pointsValuesLinear = null; } } - -/* eslint-disable no-magic-numbers */ IsoSurfaceMarchCube.prototype.striIndicesMarchCube = [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 9, 2, 10, 0, 2, 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8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1, 0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1, 3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1, 3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1, 0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1, 9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1, 1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1]; -/* eslint-enable no-magic-numbers */ - /* harmony default export */ const geometries_IsoSurfaceMarchCube = (IsoSurfaceMarchCube); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurface.js +;// ./src/gfx/geometries/IsoSurface.js @@ -14200,12 +14267,12 @@ class IsoSurface { vertex.lerpVectors(p1, p2, mu); normal.lerpVectors(n1, n2, mu); } - static _triTable = (() => geometries_IsoSurfaceMarchCube.prototype.striIndicesMarchCube)(); + static _triTable = geometries_IsoSurfaceMarchCube.prototype.striIndicesMarchCube; static _arrSize = 12; static _firstIndices = [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3]; static _secondIndices = [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7]; - static _vertexList = (() => createArray(IsoSurface._arrSize))(); - static _normalList = (() => createArray(IsoSurface._arrSize))(); + static _vertexList = createArray(IsoSurface._arrSize); + static _normalList = createArray(IsoSurface._arrSize); _polygonize(grid, isoLevel, triangles) { const { cubeIndex @@ -14302,8 +14369,6 @@ class IsoSurface { for (let y = 0; y < ySize - step; y += step) { let idx = vol.getDirectIdx(0, y, z); for (let x = 0; x < xSize - step; x += step, idx += stepX) { - /* eslint-disable no-multi-spaces */ - /* eslint-disable computed-property-spacing */ gcVal[0] = volData[idx]; gcVal[1] = volData[idx + stepX]; gcVal[3] = volData[idx + stepY]; @@ -14312,8 +14377,6 @@ class IsoSurface { gcVal[5] = volData[idx + stepX + stepZ]; gcVal[7] = volData[idx + stepY + stepZ]; gcVal[6] = volData[idx + stepX + stepY + stepZ]; - /* eslint-enable no-multi-spaces */ - /* eslint-enable computed-property-spacing */ // Determine the index into the edge table which // tells us which vertices are inside of the surface @@ -14594,7 +14657,7 @@ class IsoSurface { } } /* harmony default export */ const geometries_IsoSurface = (IsoSurface); -;// CONCATENATED MODULE: ./src/gfx/geometries/VolumeSurfaceGeometry.js +;// ./src/gfx/geometries/VolumeSurfaceGeometry.js @@ -14701,7 +14764,7 @@ class VolumeSurfaceGeometry extends geometries_IsoSurfaceGeometry { } } /* harmony default export */ const geometries_VolumeSurfaceGeometry = (VolumeSurfaceGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/QuickSurfGeometry.js +;// ./src/gfx/geometries/QuickSurfGeometry.js const { @@ -14834,7 +14897,7 @@ class QuickSurfGeometry extends geometries_VolumeSurfaceGeometry { } } /* harmony default export */ const geometries_QuickSurfGeometry = (QuickSurfGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/ContactSurface.js +;// ./src/gfx/geometries/ContactSurface.js @@ -15377,7 +15440,7 @@ function ContactSurface(packedArrays, boundaries, params, _indexList) { }; } /* harmony default export */ const geometries_ContactSurface = (ContactSurface); -;// CONCATENATED MODULE: ./src/gfx/geometries/ContactSurfaceGeometry.js +;// ./src/gfx/geometries/ContactSurfaceGeometry.js @@ -15406,7 +15469,7 @@ class ContactSurfaceGeometry extends geometries_VolumeSurfaceGeometry { } } /* harmony default export */ const geometries_ContactSurfaceGeometry = (ContactSurfaceGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurfaceAtomColored.js +;// ./src/gfx/geometries/IsoSurfaceAtomColored.js /** @@ -15428,7 +15491,7 @@ class IsoSurfaceAtomColored { } } /* harmony default export */ const geometries_IsoSurfaceAtomColored = (IsoSurfaceAtomColored); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsosurfaceBuildNormals.js +;// ./src/gfx/geometries/IsosurfaceBuildNormals.js @@ -15765,7 +15828,7 @@ class IsosurfaceBuildNormals { } } /* harmony default export */ const geometries_IsosurfaceBuildNormals = (IsosurfaceBuildNormals); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurfaceGeo.js +;// ./src/gfx/geometries/IsoSurfaceGeo.js /** @@ -15810,7 +15873,7 @@ class IsoSurfaceGeo { } } /* harmony default export */ const geometries_IsoSurfaceGeo = (IsoSurfaceGeo); -;// CONCATENATED MODULE: ./src/gfx/geometries/SSIsosurfaceGeometry.js +;// ./src/gfx/geometries/SSIsosurfaceGeometry.js @@ -16201,10 +16264,7 @@ class SSIsosurfaceGeometry extends geometries_IsoSurfaceGeometry { return numIntersectedCells; } getType(letter) { - /* eslint-disable no-magic-numbers */ const atomT = [0, 0, 1, 1, 2, 6, 3, 6, 4, 6, 5, 6, 6, 0, 7, 3, 8, 2, 9, 6, 10, 6, 11, 6, 12, 6, 13, 6, 14, 6, 15, 4, 16, 5, 17, 6, 18, 6, 19, 6, 20, 6, 21, 6, 22, 6, 23, 6, 24, 6, 25, 6, 26, 6, 27, 6, 28, 6, 29, 6, 30, 6, 31, 6, 32, 6, 33, 6, 34, 6, 35, 6, 36, 6, 37, 6, 38, 6, 39, 6, 40, 6, 41, 6, 42, 6, 43, 6, 44, 6, 45, 6, 46, 6, 47, 6, 48, 6, 49, 6, 50, 6, 51, 6, 52, 6, 53, 6, 54, 6, 55, 6, 56, 6, 57, 6, 58, 6, 59, 6, 60, 6, 61, 6, 62, 6, 63, 6, 64, 6, 65, 6, 66, 6, 67, 6, 68, 6, 69, 6, 70, 6, 71, 6, 72, 6, 73, 6, 74, 6, 75, 6, 76, 6, 77, 6, 78, 6, 79, 6, 80, 6, 81, 6, 82, 6, 83, 6, 84, 6, 85, 6, 86, 6, 87, 6, 88, 6, 89, 6, 90, 6, 91, 6, 92, 6, 93, 6, 94, 6, 95, 6, 96, 6, 97, 6, 98, 6, 99, 6, 100, 6, 101, 6, 102, 6, 103, 6, 104, 6, 105, 6, 106, 6, 107, 6, 108, 6, 109, 6]; - /* eslint-enable no-magic-numbers */ - if (letter < 1 || letter > atomT.length / 2 || Object.keys(SSIsosurfaceGeometry_Element.ByAtomicNumber).length * 2 !== atomT.length) { throw new Error('atomT.length should be equal Element.ByAtomicNumber.length * 2'); } @@ -16227,10 +16287,7 @@ class SSIsosurfaceGeometry extends geometries_IsoSurfaceGeometry { const side3 = side2 * side; const vCorner = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); const vDif = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); - /* eslint-disable no-magic-numbers */ const aLot = +1.0e12; - /* eslint-enable no-magic-numbers */ - for (let i = 0; i < side3; i++) { corners[i] = aLot; // to large value } @@ -16589,7 +16646,7 @@ class SSIsosurfaceGeometry extends geometries_IsoSurfaceGeometry { // All code below must be erased from every device and each developer's memory /* harmony default export */ const geometries_SSIsosurfaceGeometry = (SSIsosurfaceGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/LabelsGeometry.js +;// ./src/gfx/geometries/LabelsGeometry.js function createLabel(fieldTxt, className) { @@ -16685,7 +16742,7 @@ class LabelsGeometry extends utils_EventDispatcher { } } /* harmony default export */ const geometries_LabelsGeometry = (LabelsGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/geometries.js +;// ./src/gfx/geometries/geometries.js @@ -16712,11 +16769,11 @@ class LabelsGeometry extends utils_EventDispatcher { SSIsosurfaceGeometry: geometries_SSIsosurfaceGeometry, LabelsGeometry: geometries_LabelsGeometry }); -;// CONCATENATED MODULE: ./src/gfx/shaders/Uber.vert -const Uber_namespaceObject = "float INSTANCED_SPRITE_OVERSCALE = 1.3;\r\n\r\nattribute vec3 normal;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n varying vec3 viewNormal;\r\n#endif\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n varying vec3 vNormal;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n attribute vec4 position; // W contains vert pos or neg offset\r\n#else\r\n attribute vec3 position;\r\n#endif\r\n\r\nvarying vec3 vWorldPosition;\r\nvarying vec3 vViewPosition;\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n attribute float alphaColor;\r\n varying float alphaCol;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n attribute vec3 color;\r\n varying vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n attribute vec3 color2;\r\n varying vec3 vColor2;\r\n attribute vec2 uv;\r\n #ifndef CYLINDER_SPRITE\r\n varying vec2 vUv;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_POS\r\n attribute vec4 offset;\r\n #ifdef SPHERE_SPRITE\r\n varying vec4 instOffset;\r\n varying vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n attribute vec4 matVector1;\r\n attribute vec4 matVector2;\r\n attribute vec4 matVector3;\r\n attribute vec4 invmatVector1;\r\n attribute vec4 invmatVector2;\r\n attribute vec4 invmatVector3;\r\n\r\n #ifdef CYLINDER_SPRITE\r\n varying vec4 matVec1;\r\n varying vec4 matVec2;\r\n varying vec4 matVec3;\r\n varying vec4 invmatVec1;\r\n varying vec4 invmatVec2;\r\n varying vec4 invmatVec3;\r\n varying vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\nuniform mat4 modelViewMatrix; // optional\r\nuniform mat4 projectionMatrix; // optional\r\nuniform mat3 normalMatrix; // optional\r\nuniform mat4 modelMatrix; // optional\r\n\r\n#ifdef DASHED_LINE\r\n attribute float lineDistance;\r\n varying float vLineDistance;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n attribute vec3 direction;\r\n uniform mat4 projMatrixInv;\r\n uniform vec2 viewport;\r\n uniform float lineWidth;\r\n\r\n vec4 transform(vec4 coord){\r\n return projectionMatrix * modelViewMatrix * coord;\r\n }\r\n\r\n vec2 project(vec4 device){\r\n vec3 device_normal = device.xyz/device.w;\r\n vec2 clip_pos = (device_normal*0.5+0.5).xy;\r\n return clip_pos * viewport;\r\n }\r\n\r\n vec4 unproject(vec2 screen, float z, float w){\r\n vec2 clip_pos = screen/viewport;\r\n vec2 device_normal = clip_pos*2.0-1.0;\r\n return vec4(device_normal*w, z, w);\r\n }\r\n#endif\r\n\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n alphaCol = alphaColor;\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n vec3 objectNormal = vec3(\r\n dot(normal, matVector1.xyz),\r\n dot(normal, matVector2.xyz),\r\n dot(normal, matVector3.xyz));\r\n#else\r\n vec3 objectNormal = vec3( normal );\r\n#endif\r\n\r\nvec3 transformedNormal = normalMatrix * objectNormal;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n vNormal = normalize(transformedNormal);\r\n#endif\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n viewNormal = normalize(mat3(modelViewMatrix)*objectNormal);\r\n#endif\r\n\r\n vec4 localPos = vec4(position.xyz, 1.0);\r\n vec4 worldPos = modelMatrix * localPos;\r\n vec4 mvPosition = modelViewMatrix * localPos;\r\n\r\n// make thick line offset\r\n#ifdef THICK_LINE\r\n // get screen pos\r\n vec4 dPos = transform(vec4(position.xyz, 1.0));\r\n vec2 sPos = project(dPos);\r\n // move pos forward\r\n vec3 position2 = position.xyz + direction.xyz * 0.5;\r\n // get screen offset pos\r\n vec4 dPos2 = transform(vec4(position2.xyz, 1.0));\r\n vec2 sPos2 = project(dPos2);\r\n // screen line direction\r\n vec2 sDir = normalize(sPos2 - sPos);\r\n // vertex offset (orthogonal to line direction)\r\n vec2 offset1 = vec2(-sDir.y, sDir.x);\r\n // move screen vertex\r\n vec2 newPos = sPos + offset1 * position.w * lineWidth;\r\n // get moved pos in view space\r\n vec4 dNewPos = unproject(newPos, dPos.z, dPos.w);\r\n mvPosition.xyz = (projMatrixInv * dNewPos).xyz;\r\n#endif // THICK_LINE\r\n\r\n#ifdef INSTANCED_POS\r\n #ifdef SPHERE_SPRITE\r\n instOffset = offset;\r\n\r\n vec4 posEye = modelViewMatrix * vec4( offset.xyz, 1.0 );\r\n float scale = length(modelViewMatrix[0]);\r\n mvPosition = posEye + vec4( position.xyz * offset.w * scale * INSTANCED_SPRITE_OVERSCALE, 0.0 );\r\n posEye.w = offset.w * scale;\r\n\r\n spritePosEye = posEye;\r\n #else\r\n localPos = vec4( offset.xyz + position.xyz * offset.w, 1.0 );\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n #ifdef CYLINDER_SPRITE\r\n matVec1 = matVector1;\r\n matVec2 = matVector2;\r\n matVec3 = matVector3;\r\n invmatVec1 = invmatVector1;\r\n invmatVec2 = invmatVector2;\r\n invmatVec3 = invmatVector3;\r\n\r\n // calculate eye coords of cylinder endpoints\r\n vec4 v = vec4(0, -0.5, 0, 1);\r\n vec4 p1 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n v.y = 0.5;\r\n vec4 p2 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n\r\n // sprite is placed at the center of cylinder\r\n vec4 posEye;\r\n posEye.xyz = mix(p1.xyz, p2.xyz, 0.5);\r\n posEye.w = 1.0;\r\n spritePosEye = posEye;\r\n\r\n // cylinder radius in eye space\r\n float rad = length(modelViewMatrix[0]) * length(vec3(matVector1.x, matVector2.x, matVector3.x));\r\n vec2 spriteSize;\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // In ortho projection we skip z coordinate\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy - p1.xy);\r\n\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * (spriteSizeScreen + 2.0 * rad);\r\n #else\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy / p2.z - p1.xy / p1.z);\r\n\r\n // full sprite size in eye coords\r\n float minZ = min(abs(p1.z), abs(p2.z));\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * abs(posEye.z) * (spriteSizeScreen + 2.0 * rad / minZ);\r\n #endif\r\n\r\n mvPosition = posEye + vec4( position.xy * 0.5 * spriteSize, 0, 0 );\r\n #else\r\n localPos = vec4(dot(localPos, matVector1), dot(localPos, matVector2), dot(localPos, matVector3), 1.0);\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n gl_Position = projectionMatrix * mvPosition;\r\n\r\n vWorldPosition = worldPos.xyz;\r\n vViewPosition = - mvPosition.xyz;\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t vec4 worldPosition;\r\n\t // see THREE.WebGLProgram.unrollLoops\r\n\t #pragma unroll_loop_start\r\n\t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirectionalShadowCoord[ i ] = directionalShadowMatrix[ i ] * vec4(vWorldPosition, 1.0);\r\n vDirectionalShadowNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(objectNormal, 0.0))).xyz;\r\n\t }\r\n\t #pragma unroll_loop_end\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n vColor = color.xyz;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n vColor2 = color2;\r\n #ifndef CYLINDER_SPRITE\r\n vUv = uv;\r\n #endif\r\n#endif\r\n\r\n#ifdef DASHED_LINE\r\n vLineDistance = lineDistance;\r\n#endif\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/Uber.frag -const gfx_shaders_Uber_namespaceObject = "#if defined (NORMALS_TO_G_BUFFER)\r\n #define fragColor gl_FragData[0]\r\n#else\r\n #define fragColor gl_FragColor\r\n#endif\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n varying float alphaCol;\r\n#endif\r\n\r\n#ifdef COLOR_FROM_POS\r\n uniform mat4 world2colorMatrix;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform sampler2D directionalShadowMap[ NUM_DIR_LIGHTS ];\r\n uniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ]; //only for sprites\r\n\t\tvarying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n vec4 vDirLightWorldCoord[ NUM_DIR_LIGHTS ];\r\n vec3 vDirLightWorldNormal[ NUM_DIR_LIGHTS ];\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n // We use 4 instead uniform variable or define because this value is used in for(... i < value; ...) with\r\n // unroll_loop and unroll_loop has pattern:\r\n // /#pragma unroll_loop[\\s]+?for \\( int i \\= (\\d+)\\; i < (\\d+)\\; i \\+\\+ \\) \\{([\\s\\S]+?)(?=\\})\\}/g\r\n uniform vec2 samplesKernel[4]; // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n uniform sampler2D noiseTex;\r\n uniform vec2 noiseTexelSize;\r\n uniform vec2 srcTexelSize;\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n varying vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n varying vec3 vColor2;\r\n #ifndef CYLINDER_SPRITE\r\n varying vec2 vUv;\r\n #endif\r\n#endif\r\n\r\nuniform vec3 diffuse;\r\nuniform vec3 emissive;\r\nuniform vec3 specular;\r\nuniform float shininess;\r\nuniform vec3 fixedColor;\r\nuniform float opacity;\r\nuniform float zClipValue;\r\nuniform float clipPlaneValue;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n varying vec3 viewNormal;\r\n#endif\r\n\r\n#define RECIPROCAL_PI 0.31830988618\r\n#define saturate(a) clamp( a, 0.0, 1.0 )\r\n\r\n#ifdef USE_FOG\r\n uniform vec3 fogColor;\r\n uniform float fogAlpha;\r\n uniform float fogNear;\r\n uniform float fogFar;\r\n#endif\r\n\r\nvarying vec3 vWorldPosition; // world position of the pixel (invalid when INSTANCED_SPRITE is defined)\r\nvarying vec3 vViewPosition;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n varying vec3 vNormal;\r\n#endif\r\n\r\n/////////////////////////////////////////// ZSprites ////////////////////////////////////////////////\r\n#if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n uniform float nearPlaneValue;\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n varying vec4 spritePosEye;\r\n#endif\r\n\r\n#if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n uniform float zOffset;\r\n\r\n #if !defined(USE_LIGHTS) || !defined(SHADOWMAP) || !defined(SHADOWMAP_PCF_RAND) || !(NUM_DIR_LIGHTS > 0)\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\r\n float calcDepthForSprites(vec4 pixelPosEye, float zOffset, mat4 projMatrix) {\r\n vec4 pixelPosScreen = projMatrix * pixelPosEye;\r\n return 0.5 * (pixelPosScreen.z / pixelPosScreen.w + 1.0) + zOffset;\r\n }\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n varying vec4 instOffset;\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n\r\n bool intersect_ray_sphere(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray, ray);\r\n float b = dot(ray, origin);\r\n float c = dot(origin, origin) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n // choose nearest point inside frustum\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all spheres the point with smaller 't' is visible\r\n // t1 is always smaller than t2 (from calculations)\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_sphere_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into sphere local coords\r\n origin = pixelPosEye.xyz - spritePosEye.xyz;\r\n origin = (invModelViewMatrix * vec4(origin, 0.0)).xyz / instOffset.w;\r\n\r\n // transform camera orientation vector into sphere local coords\r\n ray = (invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0)).xyz;\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n vec4 v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into sphere local coords\r\n v = invModelViewMatrix * v;\r\n origin = (v.xyz - instOffset.xyz) / instOffset.w;\r\n\r\n // transform vector from camera pos to curPixel into sphere local coords\r\n ray = (invModelViewMatrix * vec4(pixelPosEye, 0.0)).xyz;\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_sphere(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n varying vec4 matVec1;\r\n varying vec4 matVec2;\r\n varying vec4 matVec3;\r\n varying vec4 invmatVec1;\r\n varying vec4 invmatVec2;\r\n varying vec4 invmatVec3;\r\n\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n varying vec4 spritePosEye;\r\n\r\n bool intersect_ray_cylinder(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray.xz, ray.xz);\r\n float b = dot(ray.xz, origin.xz);\r\n float c = dot(origin.xz, origin.xz) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n float halfHeight = 0.5;\r\n\r\n // choose nearest point\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all cylinders the point with smaller 't' is visible\r\n // if it is not outside of cylinnder (t1 is always smaller than t2).\r\n if (p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0 && p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0 && p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_cylinder_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n vec4 v;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye.xyz - spritePosEye.xyz, 0.0);\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform camera orientation vector into cylinder local coords\r\n v = invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into cylinder local coords\r\n v = invModelViewMatrix * v;\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform vector from camera pos to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_cylinder(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n///////////////////////////////////// Pack and unpack ///////////////////////////////////////////////\r\nconst float PackUpscale = 256. / 255.; // fraction -> 0..1 (including 1)\r\nconst float UnpackDownscale = 255. / 256.; // 0..1 -> fraction (excluding 1)\r\n\r\nconst vec3 PackFactors = vec3( 256. * 256. * 256., 256. * 256., 256. );\r\nconst vec4 UnpackFactors = UnpackDownscale / vec4( PackFactors, 1. );\r\n\r\n\r\nconst float ShiftRight8 = 1. / 256.;\r\n\r\nvec4 packDepthToRGBA( const in float v ) {\r\n vec4 r = vec4( fract( v * PackFactors ), v );\r\n r.yzw -= r.xyz * ShiftRight8; // tidy overflow\r\n return r * PackUpscale;\r\n}\r\n\r\nfloat unpackRGBAToDepth( const in vec4 v ) {\r\n return dot( v, UnpackFactors );\r\n}\r\n\r\n////////////////////////////////////////// All Lighting /////////////////////////////////////////////////\r\n#ifdef TOON_SHADING\r\n #define LOW_TOON_BORDER 0.0\r\n #define MEDIUM_TOON_BORDER 0.7\r\n #define HIGH_TOON_BORDER 1.0\r\n\r\n #define MEDIUM_TOON_RANGE 0.5\r\n #define HIGH_TOON_RANGE 0.95\r\n#endif\r\n#if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n struct ReflectedLight {\r\n vec3 directDiffuse;\r\n vec3 directSpecular;\r\n vec3 indirectDiffuse;\r\n };\r\n\r\n struct BlinnPhongMaterial {\r\n vec3 diffuseColor;\r\n vec3 specularColor;\r\n float specularShininess;\r\n };\r\n\r\n struct GeometricContext {\r\n vec3 normal;\r\n vec3 viewDir;\r\n };\r\n\r\n struct DirectionalLight {\r\n vec3 direction;\r\n vec3 color;\r\n };\r\n uniform DirectionalLight directionalLights[ NUM_DIR_LIGHTS ];\r\n\r\n struct DirectionalLightShadow {\r\n vec2 shadowMapSize;\r\n float shadowBias;\r\n float shadowRadius;\r\n };\r\n uniform DirectionalLightShadow directionalLightShadows[ NUM_DIR_LIGHTS ];\r\n\r\n uniform vec3 ambientLightColor;\r\n\r\n /////////////////////////////////////////// Shadowmap ////////////////////////////////////////////////\r\n\r\n #if defined(SHADOWMAP)\r\n \tfloat texture2DCompare( sampler2D depths, vec2 uv, float compare ) {\r\n \t\treturn step( compare, unpackRGBAToDepth( texture2D( depths, uv ) ) );\r\n \t}\r\n\r\n float getShadow( sampler2D shadowMap, DirectionalLightShadow dirLight, vec4 shadowCoord, vec3 vViewPosition, vec3 vNormal ) {\r\n \t float shadow = 0.0;\r\n\r\n // When shadows for sprites will appear use here for them normals as it done for G-buffer\r\n shadowCoord.xyz += dirLight.shadowBias * vNormal;\r\n shadowCoord.xyz /= shadowCoord.w;\r\n\r\n bvec4 inFrustumVec = bvec4 ( shadowCoord.x >= 0.0, shadowCoord.x <= 1.0, shadowCoord.y >= 0.0, shadowCoord.y <= 1.0 );\r\n bool inFrustum = all( inFrustumVec );\r\n bvec2 frustumTestVec = bvec2( inFrustum, shadowCoord.z <= 1.0 );\r\n bool frustumTest = all( frustumTestVec );\r\n\r\n if ( frustumTest ) {\r\n #ifdef SHADOWMAP_BASIC\r\n \t shadow = texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z );\r\n \t#endif\r\n\r\n \t#ifdef SHADOWMAP_PCF_SHARP\r\n \t vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n float dx0 = - texelSize.x * dirLight.shadowRadius;\r\n float dy0 = - texelSize.y * dirLight.shadowRadius;\r\n float dx1 = + texelSize.x * dirLight.shadowRadius;\r\n float dy1 = + texelSize.y * dirLight.shadowRadius;\r\n\r\n shadow = (\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z )\r\n ) * ( 1.0 / 9.0 );\r\n #endif\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n vec4 vUv = ((projectionMatrix * vec4(vViewPosition, 1.0)) + 1.0) / 2.0;\r\n vec2 vUvNoise = vUv.xy / srcTexelSize * noiseTexelSize;\r\n\r\n vec2 noiseVec = normalize(texture2D(noiseTex, vUvNoise).rg);\r\n mat2 mNoise = mat2(noiseVec.x, noiseVec.y, -noiseVec.y, noiseVec.x);\r\n\r\n vec2 offset;\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < 4; i ++ ) { // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n offset = mNoise * ( normalize( samplesKernel[ i ]) * texelSize * dirLight.shadowRadius );\r\n shadow += texture2DCompare( shadowMap, shadowCoord.xy + offset, shadowCoord.z );\r\n }\r\n #pragma unroll_loop_end\r\n shadow /= float( 4 ); // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n #endif\r\n }\r\n return shadow;//(shadow != 1.0) ? 0.5 : 1.0;//vec4(shadow, shadow, shadow, 1.0);\r\n }\r\n #endif\r\n\r\n /////////////////////////////////////////// Lighting /////////////////////////////////////////////////\r\n\r\n vec3 BRDF_Diffuse_Lambert( const in vec3 diffuseColor ) {\r\n return RECIPROCAL_PI * diffuseColor;\r\n } // validated\r\n\r\n vec3 F_Schlick( const in vec3 specularColor, const in float dotLH ) {\r\n // Original approximation by Christophe Schlick '94\r\n //;float fresnel = pow( 1.0 - dotLH, 5.0 );\r\n // Optimized variant (presented by Epic at SIGGRAPH '13)\r\n float fresnel = exp2( ( -5.55473 * dotLH - 6.98316 ) * dotLH );\r\n return ( 1.0 - specularColor ) * fresnel + specularColor;\r\n } // validated\r\n\r\n float G_BlinnPhong_Implicit( /* const in float dotNL, const in float dotNV */ ) {\r\n // geometry term is (n dot l)(n dot v) / 4(n dot l)(n dot v)\r\n return 0.25;\r\n }\r\n\r\n float D_BlinnPhong( const in float shininess, const in float dotNH ) {\r\n return RECIPROCAL_PI * ( shininess * 0.5 + 1.0 ) * pow( dotNH, shininess );\r\n }\r\n\r\n vec3 BRDF_Specular_BlinnPhong( const in DirectionalLight incidentLight, const in GeometricContext geometry, const in vec3 specularColor, const in float shininess ) {\r\n vec3 halfDir = normalize( incidentLight.direction + geometry.viewDir );\r\n float dotNH = saturate(dot( geometry.normal, halfDir ));\r\n float dotLH = saturate(dot( incidentLight.direction, halfDir ));\r\n\r\n vec3 F = F_Schlick( specularColor, dotLH );\r\n float G = G_BlinnPhong_Implicit( /* dotNL, dotNV */ );\r\n float D = D_BlinnPhong( shininess, dotNH );\r\n\r\n return F * ( G * D );\r\n } // validated\r\n\r\n void RE_Direct_BlinnPhong( const in DirectionalLight directLight, const in GeometricContext geometry, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight, float penumbra ) {\r\n\r\n float dotNL = saturate( dot( geometry.normal, directLight.direction ));\r\n #ifdef TOON_SHADING\r\n if(dotNL < MEDIUM_TOON_RANGE){\r\n dotNL = LOW_TOON_BORDER;\r\n }\r\n else if(dotNL < HIGH_TOON_RANGE){\r\n dotNL = MEDIUM_TOON_BORDER;\r\n }\r\n else{\r\n dotNL = HIGH_TOON_BORDER;\r\n }\r\n #endif\r\n\r\n vec3 irradiance = dotNL * directLight.color;\r\n reflectedLight.directDiffuse += penumbra * irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n reflectedLight.directSpecular += penumbra * irradiance * BRDF_Specular_BlinnPhong( directLight, geometry, material.specularColor, material.specularShininess );\r\n }\r\n\r\n void RE_IndirectDiffuse_BlinnPhong( const in vec3 irradiance, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) {\r\n reflectedLight.indirectDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n }\r\n\r\n vec3 calcLighting(const in GeometricContext geometry, const in BlinnPhongMaterial material, vec3 vViewPosition) {\r\n ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ));\r\n vec3 irradiance = ambientLightColor;\r\n\r\n float shadowMask = 1.0;\r\n // see THREE.WebGLProgram.unrollLoops\r\n \t#pragma unroll_loop_start\r\n \t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n \t #ifdef SHADOWMAP\r\n \t shadowMask = getShadow( directionalShadowMap[ i ], directionalLightShadows[ i ], vDirLightWorldCoord[ i ], vViewPosition, vDirLightWorldNormal[ i ] );\r\n #endif\r\n\r\n \t\t if ( shadowMask > 0.0 ) RE_Direct_BlinnPhong( directionalLights[ i ], geometry, material, reflectedLight, shadowMask );\r\n \t\t}\r\n \t\t#pragma unroll_loop_end\r\n\r\n RE_IndirectDiffuse_BlinnPhong(irradiance, material, reflectedLight);\r\n\r\n return saturate(reflectedLight.indirectDiffuse + reflectedLight.directDiffuse + reflectedLight.directSpecular);\r\n }\r\n#endif\r\n\r\n/////////////////////////////////////////// Dashed Line ///////////////////////////////////////////////\r\n#ifdef DASHED_LINE\r\n uniform float dashedLineSize;\r\n uniform float dashedLinePeriod;\r\n varying float vLineDistance;\r\n#endif\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef CLIP_PLANE\r\n if (vViewPosition.z < clipPlaneValue) discard;\r\n#endif\r\n\r\n#ifdef ZCLIP\r\n if (vViewPosition.z < zClipValue) discard;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = vDirectionalShadowCoord[ i ];\r\n vDirLightWorldNormal[ i ] = vDirectionalShadowNormal[ i ];\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n#endif\r\n\r\n vec4 pixelPosWorld = vec4(vWorldPosition, 1.0);\r\n vec4 pixelPosEye;\r\n\r\n#ifdef SPHERE_SPRITE\r\n\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n vec3 normal;\r\n\r\n/* quick-and-dirty method\r\n normal.xy = ' + INSTANCED_SPRITE_OVERSCALE + ' * (2.0 * vUv - 1.0);\r\n float r2 = dot(normal.xy, normal.xy);\r\n if (r2 > 1.0) discard;\r\n float normalZ = sqrt(1.0 - r2);\r\n normal.z = normalZ;\r\n normal = normal * ( -1.0 + 2.0 * float( gl_FrontFacing ) );\r\n pixelPosEye = vec4(spritePosEye.xyz, 1.0);\r\n pixelPosEye.z += spritePosEye.w * normalZ;\r\n*/\r\n\r\n // ray-trace sphere surface\r\n {\r\n vec3 p;\r\n if (!get_sphere_point(-vViewPosition, p, frontFaced)) discard;\r\n vec4 v = vec4(instOffset.xyz + p * instOffset.w, 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n normal = normalize(normalMatrix * p);\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*p);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(p, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n vec3 normal;\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n float cylinderY = 0.0;\r\n\r\n // ray-trace cylinder surface\r\n {\r\n vec3 p;\r\n if (!get_cylinder_point(-vViewPosition, p, frontFaced)) discard;\r\n\r\n cylinderY = 0.5 * (p.y + 1.0);\r\n\r\n vec4 v = vec4(p, 1.0);\r\n v = vec4(dot(v, matVec1), dot(v, matVec2), dot(v, matVec3), 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n\r\n vec3 localNormal = normalize(vec3(p.x, 0.0, p.z));\r\n normal = vec3(\r\n dot(localNormal, matVec1.xyz),\r\n dot(localNormal, matVec2.xyz),\r\n dot(localNormal, matVec3.xyz));\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*normal);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(normal, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n\r\n normal = normalize(normalMatrix * normal);\r\n }\r\n#endif\r\n\r\n #ifdef ATTR_COLOR\r\n vec3 vertexColor = vColor;\r\n #else\r\n vec3 vertexColor = vec3(1.0, 1.0, 1.0);\r\n #endif\r\n\r\n #ifdef ATTR_COLOR2\r\n #ifdef CYLINDER_SPRITE\r\n float colorCoef = cylinderY; // cylinder parameter is calculated from ray-tracing\r\n #else\r\n float colorCoef = vUv.y; // cylinder parameter is interpolated as tex coord\r\n #endif\r\n // choose either color or color2\r\n vertexColor = mix(vColor2, vColor, step(0.5, colorCoef));\r\n #endif\r\n\r\n // negative red component is a special condition\r\n if (vertexColor.x < 0.0) discard;\r\n\r\n #ifdef DASHED_LINE\r\n if ( mod( vLineDistance, dashedLinePeriod ) > dashedLineSize ) discard;\r\n #endif\r\n\r\n // transparency prepass writes only z, so we don't need to calc the color\r\n #ifdef PREPASS_TRANSP\r\n fragColor = vec4(1.0, 1.0, 1.0, 1.0);\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n return;\r\n #endif\r\n\r\n float totalOpacity = opacity;\r\n\r\n #ifdef ATTR_ALPHA_COLOR\r\n totalOpacity *= alphaCol;\r\n #endif\r\n\r\n // discard fully transparent pixels\r\n if (totalOpacity == 0.0) discard;\r\n\r\n #ifdef FAKE_OPACITY\r\n // discard pixels in checker pattern\r\n vec2 dm_coord = floor(gl_FragCoord.xy);\r\n dm_coord = fract(dm_coord * 0.5);\r\n if (totalOpacity < 1.0 && (dm_coord.x < 0.5 ^^ dm_coord.y < 0.5)) discard;\r\n vec4 diffuseColor = vec4(diffuse, 1.0);\r\n #else\r\n vec4 diffuseColor = vec4(diffuse, totalOpacity);\r\n #endif\r\n\r\n float flipNormal;\r\n #if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n flipNormal = 1.0;\r\n #ifdef DOUBLE_SIDED\r\n flipNormal = float( gl_FrontFacing );\r\n #endif\r\n vec3 normal = normalize( vNormal ) * flipNormal;\r\n #endif\r\n\r\n diffuseColor.rgb *= vertexColor;\r\n\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n\r\n #ifdef NORMALS_TO_G_BUFFER\r\n #if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n vec3 viewNormaInColor = viewNormalSprites;\r\n #else\r\n vec3 viewNormaInColor = viewNormal;\r\n float frontFaced = float( gl_FrontFacing );\r\n #endif\r\n // [-1, 1] -> [0, 1]\r\n viewNormaInColor = 0.5 * viewNormaInColor + 0.5;\r\n gl_FragData[1] = vec4(viewNormaInColor, frontFaced);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n vec3 viewDir;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDir = -pixelPosEye.xyz;\r\n #else\r\n viewDir = vViewPosition;\r\n #endif\r\n GeometricContext geometry = GeometricContext(normal, normalize( viewDir ));\r\n BlinnPhongMaterial material = BlinnPhongMaterial(diffuseColor.rgb, specular, shininess);\r\n vec3 outgoingLight = calcLighting(geometry, material, viewDir);\r\n #else\r\n vec3 outgoingLight = diffuseColor.rgb;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_DEPTH\r\n float depth = 0.0;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n depth = gl_FragDepthEXT;\r\n #else\r\n depth = gl_FragCoord.z;\r\n #endif\r\n fragColor = packDepthToRGBA(depth);\r\n return;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_POS\r\n fragColor = world2colorMatrix * pixelPosWorld;\r\n #else\r\n #ifdef OVERRIDE_COLOR\r\n fragColor = vec4(fixedColor, diffuseColor.a);\r\n #else\r\n fragColor = vec4(outgoingLight, diffuseColor.a);//vec4(vNormal, 1.0);\r\n #endif\r\n\r\n #ifdef USE_FOG\r\n float viewDistance;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDistance = abs(pixelPosEye.z);\r\n #else\r\n viewDistance = vViewPosition.z;\r\n #endif\r\n float fogFactor = smoothstep( fogNear, fogFar, viewDistance) * fogAlpha;\r\n #ifdef FOG_TRANSPARENT\r\n fragColor.a = fragColor.a * (1.0 - fogFactor);\r\n #else\r\n fragColor.rgb = mix( fragColor.rgb, fogColor, fogFactor );\r\n #endif\r\n #endif\r\n\r\n #endif\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/capabilities.js +;// ./src/gfx/shaders/Uber.vert +const Uber_namespaceObject = "/*\r\n * GLSL Version: ES 3.00 (WebGL 2.0 compatible)\r\n * No #version directive in this file (injected by Three.js).\r\n * Use GLSL3 semantics (`in`/`out`).\r\n * Set `glslVersion: THREE.GLSL3` in ShaderMaterial/RawShaderMaterial.\r\n */\r\n\r\nfloat INSTANCED_SPRITE_OVERSCALE = 1.3;\r\n\r\nin vec3 normal;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n out vec3 viewNormal;\r\n#endif\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n out vec3 vNormal;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n in vec4 position; // W contains vert pos or neg offset\r\n#else\r\n in vec3 position;\r\n#endif\r\n\r\nout vec3 vWorldPosition;\r\nout vec3 vViewPosition;\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n in float alphaColor;\r\n out float alphaCol;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ];\r\n\t\tout vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tout vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n in vec3 color;\r\n out vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n in vec3 color2;\r\n out vec3 vColor2;\r\n in vec2 uv;\r\n #ifndef CYLINDER_SPRITE\r\n out vec2 vUv;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_POS\r\n in vec4 offset;\r\n #ifdef SPHERE_SPRITE\r\n out vec4 instOffset;\r\n out vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n in vec4 matVector1;\r\n in vec4 matVector2;\r\n in vec4 matVector3;\r\n in vec4 invmatVector1;\r\n in vec4 invmatVector2;\r\n in vec4 invmatVector3;\r\n\r\n #ifdef CYLINDER_SPRITE\r\n out vec4 matVec1;\r\n out vec4 matVec2;\r\n out vec4 matVec3;\r\n out vec4 invmatVec1;\r\n out vec4 invmatVec2;\r\n out vec4 invmatVec3;\r\n out vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\nuniform mat4 modelViewMatrix; // optional\r\nuniform mat4 projectionMatrix; // optional\r\nuniform mat3 normalMatrix; // optional\r\nuniform mat4 modelMatrix; // optional\r\n\r\n#ifdef DASHED_LINE\r\n in float lineDistance;\r\n out float vLineDistance;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n in vec3 direction;\r\n uniform mat4 projMatrixInv;\r\n uniform vec2 viewport;\r\n uniform float lineWidth;\r\n\r\n vec4 transform(vec4 coord){\r\n return projectionMatrix * modelViewMatrix * coord;\r\n }\r\n\r\n vec2 project(vec4 device){\r\n vec3 device_normal = device.xyz/device.w;\r\n vec2 clip_pos = (device_normal*0.5+0.5).xy;\r\n return clip_pos * viewport;\r\n }\r\n\r\n vec4 unproject(vec2 screen, float z, float w){\r\n vec2 clip_pos = screen/viewport;\r\n vec2 device_normal = clip_pos*2.0-1.0;\r\n return vec4(device_normal*w, z, w);\r\n }\r\n#endif\r\n\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n alphaCol = alphaColor;\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n vec3 objectNormal = vec3(\r\n dot(normal, matVector1.xyz),\r\n dot(normal, matVector2.xyz),\r\n dot(normal, matVector3.xyz));\r\n#else\r\n vec3 objectNormal = vec3( normal );\r\n#endif\r\n\r\nvec3 transformedNormal = normalMatrix * objectNormal;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n vNormal = normalize(transformedNormal);\r\n#endif\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n viewNormal = normalize(mat3(modelViewMatrix)*objectNormal);\r\n#endif\r\n\r\n vec4 localPos = vec4(position.xyz, 1.0);\r\n vec4 worldPos = modelMatrix * localPos;\r\n vec4 mvPosition = modelViewMatrix * localPos;\r\n\r\n// make thick line offset\r\n#ifdef THICK_LINE\r\n // get screen pos\r\n vec4 dPos = transform(vec4(position.xyz, 1.0));\r\n vec2 sPos = project(dPos);\r\n // move pos forward\r\n vec3 position2 = position.xyz + direction.xyz * 0.5;\r\n // get screen offset pos\r\n vec4 dPos2 = transform(vec4(position2.xyz, 1.0));\r\n vec2 sPos2 = project(dPos2);\r\n // screen line direction\r\n vec2 sDir = normalize(sPos2 - sPos);\r\n // vertex offset (orthogonal to line direction)\r\n vec2 offset1 = vec2(-sDir.y, sDir.x);\r\n // move screen vertex\r\n vec2 newPos = sPos + offset1 * position.w * lineWidth;\r\n // get moved pos in view space\r\n vec4 dNewPos = unproject(newPos, dPos.z, dPos.w);\r\n mvPosition.xyz = (projMatrixInv * dNewPos).xyz;\r\n#endif // THICK_LINE\r\n\r\n#ifdef INSTANCED_POS\r\n #ifdef SPHERE_SPRITE\r\n instOffset = offset;\r\n\r\n vec4 posEye = modelViewMatrix * vec4( offset.xyz, 1.0 );\r\n float scale = length(modelViewMatrix[0]);\r\n mvPosition = posEye + vec4( position.xyz * offset.w * scale * INSTANCED_SPRITE_OVERSCALE, 0.0 );\r\n posEye.w = offset.w * scale;\r\n\r\n spritePosEye = posEye;\r\n #else\r\n localPos = vec4( offset.xyz + position.xyz * offset.w, 1.0 );\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n #ifdef CYLINDER_SPRITE\r\n matVec1 = matVector1;\r\n matVec2 = matVector2;\r\n matVec3 = matVector3;\r\n invmatVec1 = invmatVector1;\r\n invmatVec2 = invmatVector2;\r\n invmatVec3 = invmatVector3;\r\n\r\n // calculate eye coords of cylinder endpoints\r\n vec4 v = vec4(0, -0.5, 0, 1);\r\n vec4 p1 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n v.y = 0.5;\r\n vec4 p2 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n\r\n // sprite is placed at the center of cylinder\r\n vec4 posEye;\r\n posEye.xyz = mix(p1.xyz, p2.xyz, 0.5);\r\n posEye.w = 1.0;\r\n spritePosEye = posEye;\r\n\r\n // cylinder radius in eye space\r\n float rad = length(modelViewMatrix[0]) * length(vec3(matVector1.x, matVector2.x, matVector3.x));\r\n vec2 spriteSize;\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // In ortho projection we skip z coordinate\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy - p1.xy);\r\n\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * (spriteSizeScreen + 2.0 * rad);\r\n #else\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy / p2.z - p1.xy / p1.z);\r\n\r\n // full sprite size in eye coords\r\n float minZ = min(abs(p1.z), abs(p2.z));\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * abs(posEye.z) * (spriteSizeScreen + 2.0 * rad / minZ);\r\n #endif\r\n\r\n mvPosition = posEye + vec4( position.xy * 0.5 * spriteSize, 0, 0 );\r\n #else\r\n localPos = vec4(dot(localPos, matVector1), dot(localPos, matVector2), dot(localPos, matVector3), 1.0);\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n gl_Position = projectionMatrix * mvPosition;\r\n\r\n vWorldPosition = worldPos.xyz;\r\n vViewPosition = - mvPosition.xyz;\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t vec4 worldPosition;\r\n\t // see THREE.WebGLProgram.unrollLoops\r\n\t #pragma unroll_loop_start\r\n\t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirectionalShadowCoord[ i ] = directionalShadowMatrix[ i ] * vec4(vWorldPosition, 1.0);\r\n vDirectionalShadowNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(objectNormal, 0.0))).xyz;\r\n\t }\r\n\t #pragma unroll_loop_end\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n vColor = color.xyz;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n vColor2 = color2;\r\n #ifndef CYLINDER_SPRITE\r\n vUv = uv;\r\n #endif\r\n#endif\r\n\r\n#ifdef DASHED_LINE\r\n vLineDistance = lineDistance;\r\n#endif\r\n}\r\n"; +;// ./src/gfx/shaders/Uber.frag +const gfx_shaders_Uber_namespaceObject = "/*\r\n * GLSL Version: ES 3.00 (WebGL 2.0 compatible)\r\n * No #version directive in this file (injected by Three.js).\r\n * Use GLSL3 semantics (`in`/`out`, `layout(location=...)`, `texture`).\r\n * Set `glslVersion: THREE.GLSL3` in ShaderMaterial/RawShaderMaterial.\r\n */\r\n\r\n#if defined (NORMALS_TO_G_BUFFER)\r\n layout(location = 0) out vec4 fragColor;\r\n layout(location = 1) out vec4 fragNormal;\r\n#else\r\n out vec4 fragColor;\r\n#endif\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n in float alphaCol;\r\n#endif\r\n\r\n#ifdef COLOR_FROM_POS\r\n uniform mat4 world2colorMatrix;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform sampler2D directionalShadowMap[ NUM_DIR_LIGHTS ];\r\n uniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ]; //only for sprites\r\n\t\tin vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tin vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n vec4 vDirLightWorldCoord[ NUM_DIR_LIGHTS ];\r\n vec3 vDirLightWorldNormal[ NUM_DIR_LIGHTS ];\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n // We use 4 instead uniform variable or define because this value is used in for(... i < value; ...) with\r\n // unroll_loop and unroll_loop has pattern:\r\n // /#pragma unroll_loop[\\s]+?for \\( int i \\= (\\d+)\\; i < (\\d+)\\; i \\+\\+ \\) \\{([\\s\\S]+?)(?=\\})\\}/g\r\n uniform vec2 samplesKernel[4]; // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n uniform sampler2D noiseTex;\r\n uniform vec2 noiseTexelSize;\r\n uniform vec2 srcTexelSize;\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n in vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n in vec3 vColor2;\r\n #ifndef CYLINDER_SPRITE\r\n in vec2 vUv;\r\n #endif\r\n#endif\r\n\r\nuniform vec3 diffuse;\r\nuniform vec3 emissive;\r\nuniform vec3 specular;\r\nuniform float shininess;\r\nuniform vec3 fixedColor;\r\nuniform float opacity;\r\nuniform float zClipValue;\r\nuniform float clipPlaneValue;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n in vec3 viewNormal;\r\n#endif\r\n\r\n#define RECIPROCAL_PI 0.31830988618\r\n#define saturate(a) clamp( a, 0.0, 1.0 )\r\n\r\n#ifdef USE_FOG\r\n uniform vec3 fogColor;\r\n uniform float fogAlpha;\r\n uniform float fogNear;\r\n uniform float fogFar;\r\n#endif\r\n\r\nin vec3 vWorldPosition; // world position of the pixel (invalid when INSTANCED_SPRITE is defined)\r\nin vec3 vViewPosition;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n in vec3 vNormal;\r\n#endif\r\n\r\n/////////////////////////////////////////// ZSprites ////////////////////////////////////////////////\r\n#if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n uniform float nearPlaneValue;\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n in vec4 spritePosEye;\r\n#endif\r\n\r\n#if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n uniform float zOffset;\r\n\r\n #if !defined(USE_LIGHTS) || !defined(SHADOWMAP) || !defined(SHADOWMAP_PCF_RAND) || !(NUM_DIR_LIGHTS > 0)\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\r\n float calcDepthForSprites(vec4 pixelPosEye, float zOffset, mat4 projMatrix) {\r\n vec4 pixelPosScreen = projMatrix * pixelPosEye;\r\n return 0.5 * (pixelPosScreen.z / pixelPosScreen.w + 1.0) + zOffset;\r\n }\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n in vec4 instOffset;\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n\r\n bool intersect_ray_sphere(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray, ray);\r\n float b = dot(ray, origin);\r\n float c = dot(origin, origin) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n // choose nearest point inside frustum\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all spheres the point with smaller 't' is visible\r\n // t1 is always smaller than t2 (from calculations)\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_sphere_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into sphere local coords\r\n origin = pixelPosEye.xyz - spritePosEye.xyz;\r\n origin = (invModelViewMatrix * vec4(origin, 0.0)).xyz / instOffset.w;\r\n\r\n // transform camera orientation vector into sphere local coords\r\n ray = (invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0)).xyz;\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n vec4 v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into sphere local coords\r\n v = invModelViewMatrix * v;\r\n origin = (v.xyz - instOffset.xyz) / instOffset.w;\r\n\r\n // transform vector from camera pos to curPixel into sphere local coords\r\n ray = (invModelViewMatrix * vec4(pixelPosEye, 0.0)).xyz;\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_sphere(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n in vec4 matVec1;\r\n in vec4 matVec2;\r\n in vec4 matVec3;\r\n in vec4 invmatVec1;\r\n in vec4 invmatVec2;\r\n in vec4 invmatVec3;\r\n\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n in vec4 spritePosEye;\r\n\r\n bool intersect_ray_cylinder(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray.xz, ray.xz);\r\n float b = dot(ray.xz, origin.xz);\r\n float c = dot(origin.xz, origin.xz) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n float halfHeight = 0.5;\r\n\r\n // choose nearest point\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all cylinders the point with smaller 't' is visible\r\n // if it is not outside of cylinnder (t1 is always smaller than t2).\r\n if (p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0 && p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0 && p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_cylinder_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n vec4 v;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye.xyz - spritePosEye.xyz, 0.0);\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform camera orientation vector into cylinder local coords\r\n v = invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into cylinder local coords\r\n v = invModelViewMatrix * v;\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform vector from camera pos to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_cylinder(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n///////////////////////////////////// Pack and unpack ///////////////////////////////////////////////\r\nconst float PackUpscale = 256. / 255.; // fraction -> 0..1 (including 1)\r\nconst float UnpackDownscale = 255. / 256.; // 0..1 -> fraction (excluding 1)\r\n\r\nconst vec3 PackFactors = vec3( 256. * 256. * 256., 256. * 256., 256. );\r\nconst vec4 UnpackFactors = UnpackDownscale / vec4( PackFactors, 1. );\r\n\r\n\r\nconst float ShiftRight8 = 1. / 256.;\r\n\r\nvec4 packDepthToRGBA( const in float v ) {\r\n vec4 r = vec4( fract( v * PackFactors ), v );\r\n r.yzw -= r.xyz * ShiftRight8; // tidy overflow\r\n return r * PackUpscale;\r\n}\r\n\r\nfloat unpackRGBAToDepth( const in vec4 v ) {\r\n return dot( v, UnpackFactors );\r\n}\r\n\r\n////////////////////////////////////////// All Lighting /////////////////////////////////////////////////\r\n#ifdef TOON_SHADING\r\n #define LOW_TOON_BORDER 0.0\r\n #define MEDIUM_TOON_BORDER 0.7\r\n #define HIGH_TOON_BORDER 1.0\r\n\r\n #define MEDIUM_TOON_RANGE 0.5\r\n #define HIGH_TOON_RANGE 0.95\r\n#endif\r\n#if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n struct ReflectedLight {\r\n vec3 directDiffuse;\r\n vec3 directSpecular;\r\n vec3 indirectDiffuse;\r\n };\r\n\r\n struct BlinnPhongMaterial {\r\n vec3 diffuseColor;\r\n vec3 specularColor;\r\n float specularShininess;\r\n };\r\n\r\n struct GeometricContext {\r\n vec3 normal;\r\n vec3 viewDir;\r\n };\r\n\r\n struct DirectionalLight {\r\n vec3 direction;\r\n vec3 color;\r\n };\r\n uniform DirectionalLight directionalLights[ NUM_DIR_LIGHTS ];\r\n\r\n struct DirectionalLightShadow {\r\n vec2 shadowMapSize;\r\n float shadowBias;\r\n float shadowRadius;\r\n };\r\n uniform DirectionalLightShadow directionalLightShadows[ NUM_DIR_LIGHTS ];\r\n\r\n uniform vec3 ambientLightColor;\r\n\r\n /////////////////////////////////////////// Shadowmap ////////////////////////////////////////////////\r\n\r\n #if defined(SHADOWMAP)\r\n \tfloat texture2DCompare( sampler2D depths, vec2 uv, float compare ) {\r\n \t\treturn step( compare, unpackRGBAToDepth( texture( depths, uv ) ) );\r\n \t}\r\n\r\n float getShadow( sampler2D shadowMap, DirectionalLightShadow dirLight, vec4 shadowCoord, vec3 vViewPosition, vec3 vNormal ) {\r\n \t float shadow = 0.0;\r\n\r\n // When shadows for sprites will appear use here for them normals as it done for G-buffer\r\n shadowCoord.xyz += dirLight.shadowBias * vNormal;\r\n shadowCoord.xyz /= shadowCoord.w;\r\n\r\n bvec4 inFrustumVec = bvec4 ( shadowCoord.x >= 0.0, shadowCoord.x <= 1.0, shadowCoord.y >= 0.0, shadowCoord.y <= 1.0 );\r\n bool inFrustum = all( inFrustumVec );\r\n bvec2 frustumTestVec = bvec2( inFrustum, shadowCoord.z <= 1.0 );\r\n bool frustumTest = all( frustumTestVec );\r\n\r\n if ( frustumTest ) {\r\n #ifdef SHADOWMAP_BASIC\r\n \t shadow = texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z );\r\n \t#endif\r\n\r\n \t#ifdef SHADOWMAP_PCF_SHARP\r\n \t vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n float dx0 = - texelSize.x * dirLight.shadowRadius;\r\n float dy0 = - texelSize.y * dirLight.shadowRadius;\r\n float dx1 = + texelSize.x * dirLight.shadowRadius;\r\n float dy1 = + texelSize.y * dirLight.shadowRadius;\r\n\r\n shadow = (\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z )\r\n ) * ( 1.0 / 9.0 );\r\n #endif\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n vec4 vUv = ((projectionMatrix * vec4(vViewPosition, 1.0)) + 1.0) / 2.0;\r\n vec2 vUvNoise = vUv.xy / srcTexelSize * noiseTexelSize;\r\n\r\n vec2 noiseVec = normalize(texture(noiseTex, vUvNoise).rg);\r\n mat2 mNoise = mat2(noiseVec.x, noiseVec.y, -noiseVec.y, noiseVec.x);\r\n\r\n vec2 offset;\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < 4; i ++ ) { // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n offset = mNoise * ( normalize( samplesKernel[ i ]) * texelSize * dirLight.shadowRadius );\r\n shadow += texture2DCompare( shadowMap, shadowCoord.xy + offset, shadowCoord.z );\r\n }\r\n #pragma unroll_loop_end\r\n shadow /= float( 4 ); // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n #endif\r\n }\r\n return shadow;//(shadow != 1.0) ? 0.5 : 1.0;//vec4(shadow, shadow, shadow, 1.0);\r\n }\r\n #endif\r\n\r\n /////////////////////////////////////////// Lighting /////////////////////////////////////////////////\r\n\r\n vec3 BRDF_Diffuse_Lambert( const in vec3 diffuseColor ) {\r\n return RECIPROCAL_PI * diffuseColor;\r\n } // validated\r\n\r\n vec3 F_Schlick( const in vec3 specularColor, const in float dotLH ) {\r\n // Original approximation by Christophe Schlick '94\r\n //;float fresnel = pow( 1.0 - dotLH, 5.0 );\r\n // Optimized variant (presented by Epic at SIGGRAPH '13)\r\n float fresnel = exp2( ( -5.55473 * dotLH - 6.98316 ) * dotLH );\r\n return ( 1.0 - specularColor ) * fresnel + specularColor;\r\n } // validated\r\n\r\n float G_BlinnPhong_Implicit( /* const in float dotNL, const in float dotNV */ ) {\r\n // geometry term is (n dot l)(n dot v) / 4(n dot l)(n dot v)\r\n return 0.25;\r\n }\r\n\r\n float D_BlinnPhong( const in float shininess, const in float dotNH ) {\r\n return RECIPROCAL_PI * ( shininess * 0.5 + 1.0 ) * pow( dotNH, shininess );\r\n }\r\n\r\n vec3 BRDF_Specular_BlinnPhong( const in DirectionalLight incidentLight, const in GeometricContext geometry, const in vec3 specularColor, const in float shininess ) {\r\n vec3 halfDir = normalize( incidentLight.direction + geometry.viewDir );\r\n float dotNH = saturate(dot( geometry.normal, halfDir ));\r\n float dotLH = saturate(dot( incidentLight.direction, halfDir ));\r\n\r\n vec3 F = F_Schlick( specularColor, dotLH );\r\n float G = G_BlinnPhong_Implicit( /* dotNL, dotNV */ );\r\n float D = D_BlinnPhong( shininess, dotNH );\r\n\r\n return F * ( G * D );\r\n } // validated\r\n\r\n void RE_Direct_BlinnPhong( const in DirectionalLight directLight, const in GeometricContext geometry, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight, float penumbra ) {\r\n\r\n float dotNL = saturate( dot( geometry.normal, directLight.direction ));\r\n #ifdef TOON_SHADING\r\n if(dotNL < MEDIUM_TOON_RANGE){\r\n dotNL = LOW_TOON_BORDER;\r\n }\r\n else if(dotNL < HIGH_TOON_RANGE){\r\n dotNL = MEDIUM_TOON_BORDER;\r\n }\r\n else{\r\n dotNL = HIGH_TOON_BORDER;\r\n }\r\n #endif\r\n\r\n vec3 irradiance = dotNL * directLight.color;\r\n reflectedLight.directDiffuse += penumbra * irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n reflectedLight.directSpecular += penumbra * irradiance * BRDF_Specular_BlinnPhong( directLight, geometry, material.specularColor, material.specularShininess );\r\n }\r\n\r\n void RE_IndirectDiffuse_BlinnPhong( const in vec3 irradiance, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) {\r\n reflectedLight.indirectDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n }\r\n\r\n vec3 calcLighting(const in GeometricContext geometry, const in BlinnPhongMaterial material, vec3 vViewPosition) {\r\n ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ));\r\n vec3 irradiance = ambientLightColor;\r\n\r\n float shadowMask = 1.0;\r\n // see THREE.WebGLProgram.unrollLoops\r\n \t#pragma unroll_loop_start\r\n \t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n \t #ifdef SHADOWMAP\r\n \t shadowMask = getShadow( directionalShadowMap[ i ], directionalLightShadows[ i ], vDirLightWorldCoord[ i ], vViewPosition, vDirLightWorldNormal[ i ] );\r\n #endif\r\n\r\n \t\t if ( shadowMask > 0.0 ) RE_Direct_BlinnPhong( directionalLights[ i ], geometry, material, reflectedLight, shadowMask );\r\n \t\t}\r\n \t\t#pragma unroll_loop_end\r\n\r\n RE_IndirectDiffuse_BlinnPhong(irradiance, material, reflectedLight);\r\n\r\n return saturate(reflectedLight.indirectDiffuse + reflectedLight.directDiffuse + reflectedLight.directSpecular);\r\n }\r\n#endif\r\n\r\n/////////////////////////////////////////// Dashed Line ///////////////////////////////////////////////\r\n#ifdef DASHED_LINE\r\n uniform float dashedLineSize;\r\n uniform float dashedLinePeriod;\r\n in float vLineDistance;\r\n#endif\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef CLIP_PLANE\r\n if (vViewPosition.z < clipPlaneValue) discard;\r\n#endif\r\n\r\n#ifdef ZCLIP\r\n if (vViewPosition.z < zClipValue) discard;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = vDirectionalShadowCoord[ i ];\r\n vDirLightWorldNormal[ i ] = vDirectionalShadowNormal[ i ];\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n#endif\r\n\r\n vec4 pixelPosWorld = vec4(vWorldPosition, 1.0);\r\n vec4 pixelPosEye;\r\n\r\n#ifdef SPHERE_SPRITE\r\n\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n vec3 normal;\r\n\r\n/* quick-and-dirty method\r\n normal.xy = ' + INSTANCED_SPRITE_OVERSCALE + ' * (2.0 * vUv - 1.0);\r\n float r2 = dot(normal.xy, normal.xy);\r\n if (r2 > 1.0) discard;\r\n float normalZ = sqrt(1.0 - r2);\r\n normal.z = normalZ;\r\n normal = normal * ( -1.0 + 2.0 * float( gl_FrontFacing ) );\r\n pixelPosEye = vec4(spritePosEye.xyz, 1.0);\r\n pixelPosEye.z += spritePosEye.w * normalZ;\r\n*/\r\n\r\n // ray-trace sphere surface\r\n {\r\n vec3 p;\r\n if (!get_sphere_point(-vViewPosition, p, frontFaced)) discard;\r\n vec4 v = vec4(instOffset.xyz + p * instOffset.w, 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n normal = normalize(normalMatrix * p);\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*p);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(p, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n vec3 normal;\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n float cylinderY = 0.0;\r\n\r\n // ray-trace cylinder surface\r\n {\r\n vec3 p;\r\n if (!get_cylinder_point(-vViewPosition, p, frontFaced)) discard;\r\n\r\n cylinderY = 0.5 * (p.y + 1.0);\r\n\r\n vec4 v = vec4(p, 1.0);\r\n v = vec4(dot(v, matVec1), dot(v, matVec2), dot(v, matVec3), 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n\r\n vec3 localNormal = normalize(vec3(p.x, 0.0, p.z));\r\n normal = vec3(\r\n dot(localNormal, matVec1.xyz),\r\n dot(localNormal, matVec2.xyz),\r\n dot(localNormal, matVec3.xyz));\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*normal);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(normal, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n\r\n normal = normalize(normalMatrix * normal);\r\n }\r\n#endif\r\n\r\n #ifdef ATTR_COLOR\r\n vec3 vertexColor = vColor;\r\n #else\r\n vec3 vertexColor = vec3(1.0, 1.0, 1.0);\r\n #endif\r\n\r\n #ifdef ATTR_COLOR2\r\n #ifdef CYLINDER_SPRITE\r\n float colorCoef = cylinderY; // cylinder parameter is calculated from ray-tracing\r\n #else\r\n float colorCoef = vUv.y; // cylinder parameter is interpolated as tex coord\r\n #endif\r\n // choose either color or color2\r\n vertexColor = mix(vColor2, vColor, step(0.5, colorCoef));\r\n #endif\r\n\r\n // negative red component is a special condition\r\n if (vertexColor.x < 0.0) discard;\r\n\r\n #ifdef DASHED_LINE\r\n if ( mod( vLineDistance, dashedLinePeriod ) > dashedLineSize ) discard;\r\n #endif\r\n\r\n // transparency prepass writes only z, so we don't need to calc the color\r\n #ifdef PREPASS_TRANSP\r\n fragColor = vec4(1.0, 1.0, 1.0, 1.0);\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n return;\r\n #endif\r\n\r\n float totalOpacity = opacity;\r\n\r\n #ifdef ATTR_ALPHA_COLOR\r\n totalOpacity *= alphaCol;\r\n #endif\r\n\r\n // discard fully transparent pixels\r\n if (totalOpacity == 0.0) discard;\r\n\r\n #ifdef FAKE_OPACITY\r\n // discard pixels in checker pattern\r\n vec2 dm_coord = floor(gl_FragCoord.xy);\r\n dm_coord = fract(dm_coord * 0.5);\r\n if (totalOpacity < 1.0 && (dm_coord.x < 0.5 ^^ dm_coord.y < 0.5)) discard;\r\n vec4 diffuseColor = vec4(diffuse, 1.0);\r\n #else\r\n vec4 diffuseColor = vec4(diffuse, totalOpacity);\r\n #endif\r\n\r\n float flipNormal;\r\n #if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n flipNormal = 1.0;\r\n #ifdef DOUBLE_SIDED\r\n flipNormal = float( gl_FrontFacing );\r\n #endif\r\n vec3 normal = normalize( vNormal ) * flipNormal;\r\n #endif\r\n\r\n diffuseColor.rgb *= vertexColor;\r\n\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n\r\n #ifdef NORMALS_TO_G_BUFFER\r\n #if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n vec3 viewNormaInColor = viewNormalSprites;\r\n #else\r\n vec3 viewNormaInColor = viewNormal;\r\n float frontFaced = float( gl_FrontFacing );\r\n #endif\r\n // [-1, 1] -> [0, 1]\r\n viewNormaInColor = 0.5 * viewNormaInColor + 0.5;\r\n fragNormal = vec4(viewNormaInColor, frontFaced);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n vec3 viewDir;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDir = -pixelPosEye.xyz;\r\n #else\r\n viewDir = vViewPosition;\r\n #endif\r\n GeometricContext geometry = GeometricContext(normal, normalize( viewDir ));\r\n BlinnPhongMaterial material = BlinnPhongMaterial(diffuseColor.rgb, specular, shininess);\r\n vec3 outgoingLight = calcLighting(geometry, material, viewDir);\r\n #else\r\n vec3 outgoingLight = diffuseColor.rgb;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_DEPTH\r\n float depth = 0.0;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n depth = gl_FragDepth;\r\n #else\r\n depth = gl_FragCoord.z;\r\n #endif\r\n fragColor = packDepthToRGBA(depth);\r\n return;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_POS\r\n fragColor = world2colorMatrix * pixelPosWorld;\r\n #else\r\n #ifdef OVERRIDE_COLOR\r\n fragColor = vec4(fixedColor, diffuseColor.a);\r\n #else\r\n fragColor = vec4(outgoingLight, diffuseColor.a);//vec4(vNormal, 1.0);\r\n #endif\r\n\r\n #ifdef USE_FOG\r\n float viewDistance;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDistance = abs(pixelPosEye.z);\r\n #else\r\n viewDistance = vViewPosition.z;\r\n #endif\r\n float fogFactor = smoothstep( fogNear, fogFar, viewDistance) * fogAlpha;\r\n #ifdef FOG_TRANSPARENT\r\n fragColor.a = fragColor.a * (1.0 - fogFactor);\r\n #else\r\n fragColor.rgb = mix( fragColor.rgb, fogColor, fogFactor );\r\n #endif\r\n #endif\r\n\r\n #endif\r\n}\r\n"; +;// ./src/gfx/capabilities.js /* harmony default export */ const capabilities = ({ precision: 'mediump', /** @@ -16727,7 +16784,7 @@ const gfx_shaders_Uber_namespaceObject = "#if defined (NORMALS_TO_G_BUFFER)\r\n this.precision = renderer.capabilities.getMaxPrecision('highp'); } }); -;// CONCATENATED MODULE: ./src/gfx/noiseTexture.js +;// ./src/gfx/noiseTexture.js const noiseWidth = 4; const noiseHeight = 4; @@ -16744,9 +16801,7 @@ noiseTexture.needsUpdate = true; noiseHeight, noiseTexture }); -;// CONCATENATED MODULE: ./src/gfx/shaders/UberMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/UberMaterial.js @@ -16956,9 +17011,10 @@ class UberMaterial extends external_module_three_commonjs_three_commonjs2_three_ // set default values super.setValues({ - uniforms: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.UniformsUtils.clone(defaultUniforms), + glslVersion: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.GLSL3, vertexShader: this.precisionString() + Uber_namespaceObject, fragmentShader: this.precisionString() + gfx_shaders_Uber_namespaceObject, + uniforms: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.UniformsUtils.clone(defaultUniforms), lights: true, fog: true, side: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.DoubleSide @@ -17144,12 +17200,12 @@ class UberMaterial extends external_module_three_commonjs_three_commonjs2_three_ } UberMaterial.prototype.uberOptions = uberOptions; /* harmony default export */ const shaders_UberMaterial = (UberMaterial); -;// CONCATENATED MODULE: ./src/gfx/meshes/UberObject.js +;// ./src/gfx/meshes/UberObject.js /* harmony default export */ function UberObject(SuperClass) { class NewObjectType extends SuperClass { - constructor() { - super(...arguments); + constructor(...rest) { + super(...rest); this.onBeforeRender = NewObjectType.prototype.onBeforeRender; } onBeforeRender(renderer, scene, camera, geometry, material, group) { @@ -17171,13 +17227,13 @@ UberMaterial.prototype.uberOptions = uberOptions; } return NewObjectType; } -;// CONCATENATED MODULE: ./src/gfx/meshes/ZSpriteMesh.js +;// ./src/gfx/meshes/ZSpriteMesh.js const Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Mesh); class ZSpriteMesh extends Mesh { - constructor() { - super(...arguments); + constructor(...rest) { + super(...rest); this.castShadow = true; this.receiveShadow = true; } @@ -17201,7 +17257,7 @@ class ZSpriteMesh extends Mesh { } } /* harmony default export */ const meshes_ZSpriteMesh = (ZSpriteMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/ZClippedMesh.js +;// ./src/gfx/meshes/ZClippedMesh.js const ZClippedMesh_Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Mesh); @@ -17211,9 +17267,9 @@ class ZClippedMesh extends ZClippedMesh_Mesh { this.castShadow = true; this.receiveShadow = true; } - static _mvLength = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3())(); - static _center = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3())(); - static _modelView = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Matrix4())(); + static _mvLength = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); + static _center = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); + static _modelView = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Matrix4(); _onBeforeRender(renderer, scene, camera) { ZClippedMesh_Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera); const geo = this.geometry; @@ -17235,7 +17291,7 @@ class ZClippedMesh extends ZClippedMesh_Mesh { } } /* harmony default export */ const meshes_ZClippedMesh = (ZClippedMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/TextMesh.js +;// ./src/gfx/meshes/TextMesh.js @@ -17297,7 +17353,7 @@ class TextMesh extends external_module_three_commonjs_three_commonjs2_three_amd_ } } /* harmony default export */ const meshes_TextMesh = (TextMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/SimpleMesh.js +;// ./src/gfx/meshes/SimpleMesh.js const SimpleMesh_Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Mesh); @@ -17309,7 +17365,7 @@ class SimpleMesh extends SimpleMesh_Mesh { } } /* harmony default export */ const meshes_SimpleMesh = (SimpleMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/ThickLineMesh.js +;// ./src/gfx/meshes/ThickLineMesh.js const ThickLineMesh_Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Mesh); @@ -17328,19 +17384,19 @@ class ThickLineMesh extends ThickLineMesh_Mesh { } } /* harmony default export */ const meshes_ThickLineMesh = (ThickLineMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/InstancedMesh.js +;// ./src/gfx/meshes/InstancedMesh.js const InstancedMesh_Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Mesh); class InstancedMesh extends InstancedMesh_Mesh { - constructor() { - super(...arguments); + constructor(...rest) { + super(...rest); this.castShadow = true; this.receiveShadow = true; } } /* harmony default export */ const meshes_InstancedMesh = (InstancedMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/meshes.js +;// ./src/gfx/meshes/meshes.js @@ -17359,7 +17415,7 @@ class InstancedMesh extends InstancedMesh_Mesh { ThickLineMesh: meshes_ThickLineMesh, Instanced: meshes_InstancedMesh }); -;// CONCATENATED MODULE: ./src/gfx/meshes/MeshCreator.js +;// ./src/gfx/meshes/MeshCreator.js @@ -17482,12 +17538,12 @@ class MeshCreator { } } /* harmony default export */ const meshes_MeshCreator = (MeshCreator); -;// CONCATENATED MODULE: ./src/gfx/meshes/TransformGroup.js +;// ./src/gfx/meshes/TransformGroup.js class TransformGroup extends external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Object3D { - static _inverseMatrix = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Matrix4())(); - static _ray = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Ray())(); + static _inverseMatrix = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Matrix4(); + static _ray = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Ray(); constructor(geometry, geoParams, material, transforms) { super(); this._geometry = geometry; @@ -17557,7 +17613,7 @@ class TransformGroup extends external_module_three_commonjs_three_commonjs2_thre } } /* harmony default export */ const meshes_TransformGroup = (TransformGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/ChemGroup.js +;// ./src/gfx/modes/groups/ChemGroup.js function wrapper(Name, args) { @@ -17616,7 +17672,7 @@ class ChemGroup extends gfx_RCGroup { } } /* harmony default export */ const groups_ChemGroup = (ChemGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsGroup.js +;// ./src/gfx/modes/groups/AtomsGroup.js class AtomsGroup extends groups_ChemGroup { raycast(raycaster, intersects) { @@ -17654,7 +17710,7 @@ class AtomsGroup extends groups_ChemGroup { } } /* harmony default export */ const groups_AtomsGroup = (AtomsGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsSphereGroup.js +;// ./src/gfx/modes/groups/AtomsSphereGroup.js class AtomsSphereGroup extends groups_AtomsGroup { _makeGeoArgs() { @@ -17698,7 +17754,7 @@ class AtomsSphereGroup extends groups_AtomsGroup { } } /* harmony default export */ const groups_AtomsSphereGroup = (AtomsSphereGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsSurfaceGroup.js +;// ./src/gfx/modes/groups/AtomsSurfaceGroup.js class AtomsSurfaceGroup extends groups_AtomsSphereGroup { _makeGeoArgs() { @@ -17717,7 +17773,7 @@ class AtomsSurfaceGroup extends groups_AtomsSphereGroup { } } /* harmony default export */ const groups_AtomsSurfaceGroup = (AtomsSurfaceGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsSASSESGroupStub.js +;// ./src/gfx/modes/groups/AtomsSASSESGroupStub.js /* This is a stub class keep it until SAS/SES is refactored */ @@ -17740,7 +17796,7 @@ class AtomsSASSESGroupStub extends groups_AtomsSphereGroup { } } /* harmony default export */ const groups_AtomsSASSESGroupStub = (AtomsSASSESGroupStub); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsTextGroup.js +;// ./src/gfx/modes/groups/AtomsTextGroup.js function adjustColor(color) { @@ -17884,7 +17940,7 @@ class AtomsTextGroup extends groups_AtomsGroup { } } /* harmony default export */ const groups_AtomsTextGroup = (AtomsTextGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AromaticGroup.js +;// ./src/gfx/modes/groups/AromaticGroup.js function _slerp(omega, v1, v2, t) { @@ -17946,7 +18002,7 @@ class AromaticGroup extends groups_AtomsGroup { } } /* harmony default export */ const groups_AromaticGroup = (AromaticGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AromaticTorusGroup.js +;// ./src/gfx/modes/groups/AromaticTorusGroup.js @@ -17988,7 +18044,7 @@ class AromaticTorusGroup extends groups_AromaticGroup { } } /* harmony default export */ const groups_AromaticTorusGroup = (AromaticTorusGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AromaticLinesGroup.js +;// ./src/gfx/modes/groups/AromaticLinesGroup.js class AromaticLinesGroup extends groups_AromaticGroup { _build() { @@ -18011,7 +18067,7 @@ class AromaticLinesGroup extends groups_AromaticGroup { } } /* harmony default export */ const groups_AromaticLinesGroup = (AromaticLinesGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/ResiduesGroup.js +;// ./src/gfx/modes/groups/ResiduesGroup.js class ResiduesGroup extends groups_ChemGroup { raycast(raycaster, intersects) { @@ -18049,7 +18105,7 @@ class ResiduesGroup extends groups_ChemGroup { } } /* harmony default export */ const groups_ResiduesGroup = (ResiduesGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/NucleicItemGroup.js +;// ./src/gfx/modes/groups/NucleicItemGroup.js class NucleicItemGroup extends groups_ResiduesGroup { raycast(raycaster, intersects) { @@ -18125,7 +18181,7 @@ class NucleicItemGroup extends groups_ResiduesGroup { } } /* harmony default export */ const groups_NucleicItemGroup = (NucleicItemGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/NucleicCylindersGroup.js +;// ./src/gfx/modes/groups/NucleicCylindersGroup.js class NucleicCylindersGroup extends groups_NucleicItemGroup { _makeGeoArgs() { @@ -18138,7 +18194,7 @@ class NucleicCylindersGroup extends groups_NucleicItemGroup { } } /* harmony default export */ const groups_NucleicCylindersGroup = (NucleicCylindersGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/NucleicSpheresGroup.js +;// ./src/gfx/modes/groups/NucleicSpheresGroup.js class NucleicSpheresGroup extends groups_NucleicItemGroup { _makeGeoArgs() { @@ -18157,7 +18213,7 @@ class NucleicSpheresGroup extends groups_NucleicItemGroup { /* harmony default export */ const groups_NucleicSpheresGroup = (NucleicSpheresGroup); // EXTERNAL MODULE: ./vendor/js/Smooth.js var Smooth = __webpack_require__(690); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/CartoonHelper.js +;// ./src/gfx/modes/groups/CartoonHelper.js @@ -18333,7 +18389,7 @@ class CartoonHelper { } } /* harmony default export */ const groups_CartoonHelper = (CartoonHelper); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/ResiduesSubseqGroup.js +;// ./src/gfx/modes/groups/ResiduesSubseqGroup.js @@ -18395,9 +18451,7 @@ class ResiduesSubseqGroup extends groups_ResiduesGroup { const geo = this._geo; let chunkIdx = 0; const chunkIdc = []; - _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, function (currRes, mtc) { - let hasSlope = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : false; - let hasCut = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : false; + _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, (currRes, mtc, hasSlope = false, hasCut = false) => { const color = colorer.getResidueColor(currRes, parent); chunkIdc[chunkIdx] = currRes._index; geo.setItem(chunkIdx, mtc, hasSlope, hasCut); @@ -18430,7 +18484,7 @@ class ResiduesSubseqGroup extends groups_ResiduesGroup { } } /* harmony default export */ const groups_ResiduesSubseqGroup = (ResiduesSubseqGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/ResiduesTraceGroup.js +;// ./src/gfx/modes/groups/ResiduesTraceGroup.js class ResiduesTraceGroup extends groups_ChemGroup { _makeGeoArgs() { @@ -18554,7 +18608,7 @@ class ResiduesTraceGroup extends groups_ChemGroup { } } /* harmony default export */ const groups_ResiduesTraceGroup = (ResiduesTraceGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/BondsGroup.js +;// ./src/gfx/modes/groups/BondsGroup.js function getCylinderCount(bondOrder) { @@ -18623,7 +18677,7 @@ class BondsGroup extends groups_ChemGroup { } } /* harmony default export */ const groups_BondsGroup = (BondsGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/BondsCylinderGroup.js +;// ./src/gfx/modes/groups/BondsCylinderGroup.js class BondsCylinderGroup extends groups_BondsGroup { @@ -18715,7 +18769,7 @@ class BondsCylinderGroup extends groups_BondsGroup { } } /* harmony default export */ const groups_BondsCylinderGroup = (BondsCylinderGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/BondsLinesGroup.js +;// ./src/gfx/modes/groups/BondsLinesGroup.js const STEP_SIZE = 0.15; @@ -18826,7 +18880,7 @@ class BondsLinesGroup extends groups_BondsGroup { } } /* harmony default export */ const groups_BondsLinesGroup = (BondsLinesGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/groups.js +;// ./src/gfx/modes/groups/groups.js @@ -18853,7 +18907,7 @@ class BondsLinesGroup extends groups_BondsGroup { BondsCylinderGroup: groups_BondsCylinderGroup, BondsLinesGroup: groups_BondsLinesGroup }); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/AtomsProcessor.js +;// ./src/gfx/modes/processors/AtomsProcessor.js class AtomsProcessor extends gfx_RCGroup { constructor(AtomsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -18907,7 +18961,7 @@ class AtomsProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_AtomsProcessor = (AtomsProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/OrphanAtomsProcessor.js +;// ./src/gfx/modes/processors/OrphanAtomsProcessor.js class OrphanAtomsProcessor extends processors_AtomsProcessor { _checkAtom(atom, mask) { @@ -18926,7 +18980,7 @@ class OrphanAtomsProcessor extends processors_AtomsProcessor { } } /* harmony default export */ const processors_OrphanAtomsProcessor = (OrphanAtomsProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/ResiduesProcessor.js +;// ./src/gfx/modes/processors/ResiduesProcessor.js class ResiduesProcessor extends gfx_RCGroup { constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -18978,7 +19032,7 @@ class ResiduesProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_ResiduesProcessor = (ResiduesProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/NucleicProcessor.js +;// ./src/gfx/modes/processors/NucleicProcessor.js class NucleicProcessor extends processors_ResiduesProcessor { _checkResidue(residue, mask) { @@ -18986,7 +19040,7 @@ class NucleicProcessor extends processors_ResiduesProcessor { } } /* harmony default export */ const processors_NucleicProcessor = (NucleicProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/SubseqsProcessor.js +;// ./src/gfx/modes/processors/SubseqsProcessor.js class SubseqsProcessor extends gfx_RCGroup { constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -19040,7 +19094,7 @@ class SubseqsProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_SubseqsProcessor = (SubseqsProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/BondsProcessor.js +;// ./src/gfx/modes/processors/BondsProcessor.js class BondsProcessor extends gfx_RCGroup { constructor(BondsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -19092,7 +19146,7 @@ class BondsProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_BondsProcessor = (BondsProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/AromaticProcessor.js +;// ./src/gfx/modes/processors/AromaticProcessor.js class AromaticProcessor extends gfx_RCGroup { constructor(AromaticGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -19152,7 +19206,7 @@ class AromaticProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_AromaticProcessor = (AromaticProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/processors.js +;// ./src/gfx/modes/processors/processors.js @@ -19169,7 +19223,7 @@ class AromaticProcessor extends gfx_RCGroup { Bonds: processors_BondsProcessor, Aromatic: processors_AromaticProcessor }); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/GroupsFactory.js +;// ./src/gfx/modes/groups/GroupsFactory.js @@ -19237,7 +19291,7 @@ class GroupsFactory { } } /* harmony default export */ const groups_GroupsFactory = (GroupsFactory); -;// CONCATENATED MODULE: ./src/gfx/modes/Mode.js +;// ./src/gfx/modes/Mode.js @@ -19319,7 +19373,7 @@ Mode.prototype.id = '__'; */ Mode.prototype.depGroups = []; /* harmony default export */ const modes_Mode = (Mode); -;// CONCATENATED MODULE: ./src/gfx/modes/LinesMode.js +;// ./src/gfx/modes/LinesMode.js function getRenderParams() { return { @@ -19357,8 +19411,7 @@ LinesMode.prototype.name = 'Lines'; LinesMode.prototype.shortName = 'Lines'; LinesMode.prototype.depGroups = ['ALoopsLines', 'BondsLines', 'OrphanedAtomsCrosses']; /* harmony default export */ const modes_LinesMode = (LinesMode); -;// CONCATENATED MODULE: ./src/gfx/modes/LicoriceMode.js -/* eslint-disable no-magic-numbers */ +;// ./src/gfx/modes/LicoriceMode.js class LicoriceMode extends modes_Mode { static id = 'LC'; @@ -19386,8 +19439,7 @@ LicoriceMode.prototype.name = 'Licorice'; LicoriceMode.prototype.shortName = 'Licorice'; LicoriceMode.prototype.depGroups = ['AtomsSpheres', 'BondsCylinders', 'ALoopsTorus']; /* harmony default export */ const modes_LicoriceMode = (LicoriceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/BallsAndSticksMode.js -/* eslint-disable no-magic-numbers */ +;// ./src/gfx/modes/BallsAndSticksMode.js class BallsAndSticksMode extends modes_Mode { static id = 'BS'; @@ -19415,7 +19467,7 @@ BallsAndSticksMode.prototype.name = 'Balls and Sticks'; BallsAndSticksMode.prototype.shortName = 'Balls'; BallsAndSticksMode.prototype.depGroups = ['AtomsSpheres', 'BondsCylinders', 'ALoopsTorus']; /* harmony default export */ const modes_BallsAndSticksMode = (BallsAndSticksMode); -;// CONCATENATED MODULE: ./src/gfx/modes/VanDerWaalsMode.js +;// ./src/gfx/modes/VanDerWaalsMode.js class VanDerWaalsMode extends modes_Mode { static id = 'VW'; @@ -19428,7 +19480,7 @@ VanDerWaalsMode.prototype.name = 'Van der Waals'; VanDerWaalsMode.prototype.shortName = 'VDW'; VanDerWaalsMode.prototype.depGroups = ['AtomsSpheres']; /* harmony default export */ const modes_VanDerWaalsMode = (VanDerWaalsMode); -;// CONCATENATED MODULE: ./src/gfx/modes/TraceMode.js +;// ./src/gfx/modes/TraceMode.js class TraceMode extends modes_Mode { static id = 'TR'; @@ -19441,7 +19493,7 @@ TraceMode.prototype.name = 'Trace'; TraceMode.prototype.shortName = 'Trace'; TraceMode.prototype.depGroups = ['TraceChains']; /* harmony default export */ const modes_TraceMode = (TraceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/TubeMode.js +;// ./src/gfx/modes/TubeMode.js class TubeMode extends modes_Mode { @@ -19466,7 +19518,7 @@ TubeMode.prototype.name = 'Tube'; TubeMode.prototype.shortName = 'Tube'; TubeMode.prototype.depGroups = ['CartoonChains']; /* harmony default export */ const modes_TubeMode = (TubeMode); -;// CONCATENATED MODULE: ./src/gfx/modes/CartoonMode.js +;// ./src/gfx/modes/CartoonMode.js class CartoonMode extends modes_Mode { @@ -19549,7 +19601,7 @@ CartoonMode.prototype.name = 'Cartoon'; CartoonMode.prototype.shortName = 'Cartoon'; CartoonMode.prototype.depGroups = ['CartoonChains', 'NucleicSpheres', 'NucleicCylinders']; /* harmony default export */ const modes_CartoonMode = (CartoonMode); -;// CONCATENATED MODULE: ./src/gfx/modes/SurfaceMode.js +;// ./src/gfx/modes/SurfaceMode.js const { @@ -19588,7 +19640,7 @@ class SurfaceMode extends modes_Mode { SurfaceMode.prototype.isSurface = true; SurfaceMode.prototype.surfaceNames = []; /* harmony default export */ const modes_SurfaceMode = (SurfaceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/QuickSurfaceMode.js +;// ./src/gfx/modes/QuickSurfaceMode.js class QuickSurfaceMode extends modes_SurfaceMode { static id = 'QS'; @@ -19609,7 +19661,7 @@ QuickSurfaceMode.prototype.name = 'Quick Surface'; QuickSurfaceMode.prototype.shortName = 'Quick Surf'; QuickSurfaceMode.prototype.surfaceNames = ['QuickSurfGeo']; /* harmony default export */ const modes_QuickSurfaceMode = (QuickSurfaceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/IsoSurfaceMode.js +;// ./src/gfx/modes/IsoSurfaceMode.js class IsoSurfaceMode extends modes_SurfaceMode { constructor(excludeProbe, opts) { @@ -19637,7 +19689,7 @@ IsoSurfaceMode.prototype.surfaceNames = ['SASSESSurfaceGeo']; IsoSurfaceMode.prototype._radScale = 1; IsoSurfaceMode.prototype._excludeProbe = false; /* harmony default export */ const modes_IsoSurfaceMode = (IsoSurfaceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/IsoSurfaceSASMode.js +;// ./src/gfx/modes/IsoSurfaceSASMode.js class IsoSurfaceSASMode extends modes_IsoSurfaceMode { static id = 'SA'; @@ -19649,7 +19701,7 @@ IsoSurfaceSASMode.prototype.id = 'SA'; IsoSurfaceSASMode.prototype.name = 'Solvent Accessible Surface'; IsoSurfaceSASMode.prototype.shortName = 'SAS'; /* harmony default export */ const modes_IsoSurfaceSASMode = (IsoSurfaceSASMode); -;// CONCATENATED MODULE: ./src/gfx/modes/IsoSurfaceSESMode.js +;// ./src/gfx/modes/IsoSurfaceSESMode.js class IsoSurfaceSESMode extends modes_IsoSurfaceMode { static id = 'SE'; @@ -19661,7 +19713,7 @@ IsoSurfaceSESMode.prototype.id = 'SE'; IsoSurfaceSESMode.prototype.name = 'Solvent Excluded Surface'; IsoSurfaceSESMode.prototype.shortName = 'SES'; /* harmony default export */ const modes_IsoSurfaceSESMode = (IsoSurfaceSESMode); -;// CONCATENATED MODULE: ./src/gfx/modes/ContactSurfaceMode.js +;// ./src/gfx/modes/ContactSurfaceMode.js class ContactSurfaceMode extends modes_SurfaceMode { static id = 'CS'; @@ -19684,7 +19736,7 @@ ContactSurfaceMode.prototype.shortName = 'Contact Surf'; ContactSurfaceMode.prototype.isSurface = true; ContactSurfaceMode.prototype.surfaceNames = ['ContactSurfaceGeo']; /* harmony default export */ const modes_ContactSurfaceMode = (ContactSurfaceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/TextMode.js +;// ./src/gfx/modes/TextMode.js class TextMode extends modes_Mode { @@ -19705,7 +19757,7 @@ TextMode.prototype.name = 'Text mode'; TextMode.prototype.shortName = 'Text'; TextMode.prototype.depGroups = ['TextLabelsGeo']; /* harmony default export */ const modes_TextMode = (TextMode); -;// CONCATENATED MODULE: ./src/gfx/modes.js +;// ./src/gfx/modes.js @@ -19721,7 +19773,7 @@ TextMode.prototype.depGroups = ['TextLabelsGeo']; const modes = new utils_EntityList([modes_LinesMode, modes_LicoriceMode, modes_BallsAndSticksMode, modes_VanDerWaalsMode, modes_TraceMode, modes_TubeMode, modes_CartoonMode, modes_QuickSurfaceMode, modes_IsoSurfaceSASMode, modes_IsoSurfaceSESMode, modes_ContactSurfaceMode, modes_TextMode]); /* harmony default export */ const gfx_modes = (modes); -;// CONCATENATED MODULE: ./src/gfx/palettes/Palette.js +;// ./src/gfx/palettes/Palette.js function clamp(x, a, b) { return x <= b ? x < 0 ? 0 : x : b; @@ -19744,13 +19796,11 @@ class Palette { this.name = name || 'Custom'; this.id = id || 'CP'; } - getElementColor(name) { - let asIs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; + getElementColor(name, asIs = false) { const color = this.elementColors[name]; return color === undefined && !asIs ? this.defaultElementColor : color; } - getResidueColor(name) { - let asIs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; + getResidueColor(name, asIs = false) { const color = this.residueColors[name]; return color === undefined && !asIs ? this.defaultResidueColor : color; } @@ -19759,8 +19809,7 @@ class Palette { chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F) % this.chainColors.length; return this.chainColors[chain]; } - getSecondaryColor(type) { - let asIs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; + getSecondaryColor(type, asIs = false) { const color = this.secondaryColors[type]; return color === undefined && !asIs ? this.defaultSecondaryColor : color; } @@ -19783,8 +19832,7 @@ class Palette { left = clamp(left, 0, count - 1); return lerpColor(gradient[left], gradient[right], index - left); } - getNamedColor(name) { - let asIs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; + getNamedColor(name, asIs = false) { const color = this.namedColors[name]; return color === undefined && !asIs ? this.defaultNamedColor : color; } @@ -19807,8 +19855,6 @@ external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_default( ['indianred', 0xcd5c5c], ['lightcoral', 0xf08080], ['salmon', 0xfa8072], ['darksalmon', 0xe9967a], ['lightsalmon', 0xffa07a], ['crimson', 0xdc143c], ['red', 0xff0000], ['firebrick', 0xb22222], ['darkred', 0x8b0000], ['pink', 0xffc0cb], ['lightpink', 0xffb6c1], ['hotpink', 0xff69b4], ['deeppink', 0xff1493], ['mediumvioletred', 0xc71585], ['palevioletred', 0xdb7093], ['coral', 0xff7f50], ['tomato', 0xff6347], ['orangered', 0xff4500], ['darkorange', 0xff8c00], ['orange', 0xffa500], ['gold', 0xffd700], ['yellow', 0xffff00], ['lightyellow', 0xffffe0], ['lemonchiffon', 0xfffacd], ['lightgoldenrodyellow', 0xfafad2], ['papayawhip', 0xffefd5], ['moccasin', 0xffe4b5], ['peachpuff', 0xffdab9], ['palegoldenrod', 0xeee8aa], ['khaki', 0xf0e68c], ['darkkhaki', 0xbdb76b], ['lavender', 0xe6e6fa], ['thistle', 0xd8bfd8], ['plum', 0xdda0dd], ['violet', 0xee82ee], ['orchid', 0xda70d6], ['fuchsia', 0xff00ff], ['magenta', 0xff00ff], ['mediumorchid', 0xba55d3], ['mediumpurple', 0x9370db], ['rebeccapurple', 0x663399], ['blueviolet', 0x8a2be2], ['darkviolet', 0x9400d3], ['darkorchid', 0x9932cc], ['darkmagenta', 0x8b008b], ['purple', 0x800080], ['indigo', 0x4b0082], ['slateblue', 0x6a5acd], ['mediumslateblue', 0x7b68ee], ['darkslateblue', 0x483d8b], ['greenyellow', 0xadff2f], ['chartreuse', 0x7fff00], ['lawngreen', 0x7cfc00], ['lime', 0x00ff00], ['limegreen', 0x32cd32], ['palegreen', 0x98fb98], ['lightgreen', 0x90ee90], ['mediumspringgreen', 0x00fa9a], ['springgreen', 0x00ff7f], ['mediumseagreen', 0x3cb371], ['seagreen', 0x2e8b57], ['forestgreen', 0x228b22], ['green', 0x008000], ['darkgreen', 0x006400], ['yellowgreen', 0x9acd32], ['olivedrab', 0x6b8e23], ['olive', 0x808000], ['darkolivegreen', 0x556b2f], ['mediumaquamarine', 0x66cdaa], ['darkseagreen', 0x8fbc8f], ['lightseagreen', 0x20b2aa], ['darkcyan', 0x008b8b], ['teal', 0x008080], ['aqua', 0x00ffff], ['cyan', 0x00ffff], ['lightcyan', 0xe0ffff], ['paleturquoise', 0xafeeee], ['aquamarine', 0x7fffd4], ['turquoise', 0x40e0d0], ['mediumturquoise', 0x48d1cc], ['darkturquoise', 0x00ced1], ['cadetblue', 0x5f9ea0], ['steelblue', 0x4682b4], ['lightsteelblue', 0xb0c4de], ['powderblue', 0xb0e0e6], ['lightblue', 0xadd8e6], ['skyblue', 0x87ceeb], ['lightskyblue', 0x87cefa], ['deepskyblue', 0x00bfff], ['dodgerblue', 0x1e90ff], ['cornflowerblue', 0x6495ed], ['royalblue', 0x4169e1], ['blue', 0x0000ff], ['mediumblue', 0x0000cd], ['darkblue', 0x00008b], ['navy', 0x000080], ['midnightblue', 0x191970], ['cornsilk', 0xfff8dc], ['blanchedalmond', 0xffebcd], ['bisque', 0xffe4c4], ['navajowhite', 0xffdead], ['wheat', 0xf5deb3], ['burlywood', 0xdeb887], ['tan', 0xd2b48c], ['rosybrown', 0xbc8f8f], ['sandybrown', 0xf4a460], ['goldenrod', 0xdaa520], ['darkgoldenrod', 0xb8860b], ['peru', 0xcd853f], ['chocolate', 0xd2691e], ['saddlebrown', 0x8b4513], ['sienna', 0xa0522d], ['brown', 0xa52a2a], ['maroon', 0x800000], ['white', 0xffffff], ['snow', 0xfffafa], ['honeydew', 0xf0fff0], ['mintcream', 0xf5fffa], ['azure', 0xf0ffff], ['aliceblue', 0xf0f8ff], ['ghostwhite', 0xf8f8ff], ['whitesmoke', 0xf5f5f5], ['seashell', 0xfff5ee], ['beige', 0xf5f5dc], ['oldlace', 0xfdf5e6], ['floralwhite', 0xfffaf0], ['ivory', 0xfffff0], ['antiquewhite', 0xfaebd7], ['linen', 0xfaf0e6], ['lavenderblush', 0xfff0f5], ['mistyrose', 0xffe4e1], ['gainsboro', 0xdcdcdc], ['lightgray', 0xd3d3d3], ['silver', 0xc0c0c0], ['darkgray', 0xa9a9a9], ['gray', 0x808080], ['dimgray', 0x696969], ['lightslategray', 0x778899], ['slategray', 0x708090], ['darkslategray', 0x2f4f4f], ['black', 0x000000] /* eslint-enable no-multi-spaces */], namedColors: {}, - /* eslint-enable no-magic-numbers */ - gradients: { rainbow: [0x0000ff, // blue @@ -19869,13 +19915,12 @@ for (let i = 0, { namedColors[name] = value; } /* harmony default export */ const palettes_Palette = (Palette); -;// CONCATENATED MODULE: ./src/gfx/palettes/cpkPalette.js +;// ./src/gfx/palettes/cpkPalette.js const palette = new palettes_Palette('CPK', 'CP'); // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. palette.elementColors = { - /* eslint-disable no-magic-numbers */ H: 0xFFFFFF, C: 0x202020, N: 0x2060FF, @@ -19890,15 +19935,13 @@ palette.elementColors = { CU: 0xD0D0D0, BR: 0x008800, I: 0x005500 - /* eslint-enable no-magic-numbers */ }; /* harmony default export */ const cpkPalette = (palette); -;// CONCATENATED MODULE: ./src/gfx/palettes/jmolPalette.js +;// ./src/gfx/palettes/jmolPalette.js const jmolPalette_palette = new palettes_Palette('Jmol', 'JM'); -jmolPalette_palette.colors = [/* eslint-disable no-magic-numbers */ -0x0000FF, +jmolPalette_palette.colors = [0x0000FF, // blue 0x0055FF, // @@ -19933,11 +19976,10 @@ jmolPalette_palette.colors = [/* eslint-disable no-magic-numbers */ 0xAB00FF, // 0x5500FF // -/* eslint-enable no-magic-numbers */]; +]; // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. jmolPalette_palette.elementColors = { - /* eslint-disable no-magic-numbers */ H: 0xFFFFFF, D: 0xFFFFC0, T: 0xFFFFA0, @@ -20049,13 +20091,11 @@ jmolPalette_palette.elementColors = { BH: 0xE00038, HS: 0xE6002E, MT: 0xEB0026 - /* eslint-enable no-magic-numbers */ }; jmolPalette_palette.defaultResidueColor = 0xBEA06E; // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py. jmolPalette_palette.residueColors = { - /* eslint-disable no-magic-numbers */ ALA: 0xC8C8C8, ARG: 0x145AFF, ASN: 0x00DCDC, @@ -20094,7 +20134,6 @@ jmolPalette_palette.residueColors = { '+I': 0x80FFFF, '+T': 0xA0FFA0, '+U': 0xFF8080 - /* eslint-enable no-magic-numbers */ }; jmolPalette_palette.chainColors = [ // ' '->0 'A'->1, 'B'->2 @@ -20166,12 +20205,11 @@ jmolPalette_palette.secondaryColors = { rna: 0xFD0162 }; /* harmony default export */ const jmolPalette = (jmolPalette_palette); -;// CONCATENATED MODULE: ./src/gfx/palettes/vmdPalette.js +;// ./src/gfx/palettes/vmdPalette.js const vmdPalette_palette = new palettes_Palette('VMD', 'VM'); -vmdPalette_palette.colors = [/* eslint-disable no-magic-numbers */ -0x0000FF, +vmdPalette_palette.colors = [0x0000FF, // blue 0xFF0000, // red @@ -20202,25 +20240,22 @@ vmdPalette_palette.colors = [/* eslint-disable no-magic-numbers */ 0x804D00, // ochre 0x8080C0 // ice blue -/* eslint-enable no-magic-numbers */]; +]; vmdPalette_palette.defaultElementColor = 0x804D00; // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. vmdPalette_palette.elementColors = { - /* eslint-disable no-magic-numbers */ H: 0xFFFFFF, C: 0x40BFBF, N: 0x0000FF, O: 0xFF0000, P: 0x808033, S: 0xFFFF00 - /* eslint-enable no-magic-numbers */ }; vmdPalette_palette.defaultResidueColor = 0x40C0C0; // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py. vmdPalette_palette.residueColors = { - /* eslint-disable no-magic-numbers */ ALA: 0x0000FF, ARG: 0xFFFFFF, ASN: 0x808033, @@ -20259,7 +20294,6 @@ vmdPalette_palette.residueColors = { WAT: 0x40C0C0, H2O: 0x40C0C0, HOH: 0x40C0C0 - /* eslint-enable no-magic-numbers */ }; vmdPalette_palette.chainColors = [0xFFFFFF].concat(vmdPalette_palette.colors); const vmdPalette_StructuralElementType = chem_StructuralElement.Type; @@ -20272,14 +20306,14 @@ vmdPalette_palette.secondaryColors = { [vmdPalette_StructuralElementType.TURN]: 0x40C0C0 }; /* harmony default export */ const vmdPalette = (vmdPalette_palette); -;// CONCATENATED MODULE: ./src/gfx/palettes.js +;// ./src/gfx/palettes.js const palettes = new utils_EntityList([cpkPalette, jmolPalette, vmdPalette]); /* harmony default export */ const gfx_palettes = (palettes); -;// CONCATENATED MODULE: ./src/gfx/colorers/Colorer.js +;// ./src/gfx/colorers/Colorer.js @@ -20338,7 +20372,7 @@ class Colorer { Colorer.prototype.id = '__'; /* harmony default export */ const colorers_Colorer = (Colorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ElementColorer.js +;// ./src/gfx/colorers/ElementColorer.js /** @@ -20370,7 +20404,7 @@ ElementColorer.prototype.id = 'EL'; ElementColorer.prototype.name = 'Element'; ElementColorer.prototype.shortName = 'Element'; /* harmony default export */ const colorers_ElementColorer = (ElementColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ResidueTypeColorer.js +;// ./src/gfx/colorers/ResidueTypeColorer.js /** @@ -20394,7 +20428,7 @@ ResidueTypeColorer.prototype.id = 'RT'; ResidueTypeColorer.prototype.name = 'Residue Type'; ResidueTypeColorer.prototype.shortName = 'Residue'; /* harmony default export */ const colorers_ResidueTypeColorer = (ResidueTypeColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/SequenceColorer.js +;// ./src/gfx/colorers/SequenceColorer.js class SequenceColorer extends colorers_Colorer { static id = 'SQ'; @@ -20415,7 +20449,7 @@ SequenceColorer.prototype.id = 'SQ'; SequenceColorer.prototype.name = 'Sequence'; SequenceColorer.prototype.shortName = 'Sequence'; /* harmony default export */ const colorers_SequenceColorer = (SequenceColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ChainColorer.js +;// ./src/gfx/colorers/ChainColorer.js class ChainColorer extends colorers_Colorer { static id = 'CH'; @@ -20430,7 +20464,7 @@ ChainColorer.prototype.id = 'CH'; ChainColorer.prototype.name = 'Chain'; ChainColorer.prototype.shortName = 'Chain'; /* harmony default export */ const colorers_ChainColorer = (ChainColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/SecondaryStructureColorer.js +;// ./src/gfx/colorers/SecondaryStructureColorer.js class SecondaryStructureColorer extends colorers_Colorer { @@ -20460,7 +20494,7 @@ SecondaryStructureColorer.prototype.id = 'SS'; SecondaryStructureColorer.prototype.name = 'Secondary Structure'; SecondaryStructureColorer.prototype.shortName = 'Structure'; /* harmony default export */ const colorers_SecondaryStructureColorer = (SecondaryStructureColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/UniformColorer.js +;// ./src/gfx/colorers/UniformColorer.js class UniformColorer extends colorers_Colorer { static id = 'UN'; @@ -20475,7 +20509,7 @@ UniformColorer.prototype.id = 'UN'; UniformColorer.prototype.name = 'Uniform'; UniformColorer.prototype.shortName = 'Uniform'; /* harmony default export */ const colorers_UniformColorer = (UniformColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ConditionalColorer.js +;// ./src/gfx/colorers/ConditionalColorer.js @@ -20514,7 +20548,7 @@ ConditionalColorer.prototype.id = 'CO'; ConditionalColorer.prototype.name = 'Conditional'; ConditionalColorer.prototype.shortName = 'Conditional'; /* harmony default export */ const colorers_ConditionalColorer = (ConditionalColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ConformationColorer.js +;// ./src/gfx/colorers/ConformationColorer.js class ConformationColorer extends colorers_Colorer { static id = 'CF'; @@ -20529,7 +20563,7 @@ ConformationColorer.prototype.id = 'CF'; ConformationColorer.prototype.name = 'Conformation'; ConformationColorer.prototype.shortName = 'Conformation'; /* harmony default export */ const colorers_ConformationColorer = (ConformationColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/TemperatureColorer.js +;// ./src/gfx/colorers/TemperatureColorer.js /** @@ -20584,7 +20618,7 @@ TemperatureColorer.prototype.id = 'TM'; // [T]e[M]perature TemperatureColorer.prototype.name = 'Temperature'; TemperatureColorer.prototype.shortName = 'Temperature'; /* harmony default export */ const colorers_TemperatureColorer = (TemperatureColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/OccupancyColorer.js +;// ./src/gfx/colorers/OccupancyColorer.js /** @@ -20625,7 +20659,7 @@ OccupancyColorer.prototype.id = 'OC'; // [OC]cupancy OccupancyColorer.prototype.name = 'Occupancy'; OccupancyColorer.prototype.shortName = 'Occupancy'; /* harmony default export */ const colorers_OccupancyColorer = (OccupancyColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/HydrophobicityColorer.js +;// ./src/gfx/colorers/HydrophobicityColorer.js class HydrophobicityColorer extends colorers_Colorer { static id = 'HY'; @@ -20647,7 +20681,7 @@ HydrophobicityColorer.prototype.id = 'HY'; HydrophobicityColorer.prototype.name = 'Hydrophobicity'; HydrophobicityColorer.prototype.shortName = 'Hydrophobicity'; /* harmony default export */ const colorers_HydrophobicityColorer = (HydrophobicityColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/MoleculeColorer.js +;// ./src/gfx/colorers/MoleculeColorer.js class MoleculeColorer extends colorers_Colorer { static id = 'MO'; @@ -20667,7 +20701,7 @@ MoleculeColorer.prototype.id = 'MO'; MoleculeColorer.prototype.name = 'Molecule'; MoleculeColorer.prototype.shortName = 'Molecule'; /* harmony default export */ const colorers_MoleculeColorer = (MoleculeColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/CarbonColorer.js +;// ./src/gfx/colorers/CarbonColorer.js function scaleColor(c, factor) { @@ -20705,7 +20739,7 @@ CarbonColorer.prototype.id = 'CB'; CarbonColorer.prototype.name = 'Carbon'; CarbonColorer.prototype.shortName = 'Carbon'; /* harmony default export */ const colorers_CarbonColorer = (CarbonColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers.js +;// ./src/gfx/colorers.js @@ -20722,7 +20756,7 @@ CarbonColorer.prototype.shortName = 'Carbon'; const colorers = new utils_EntityList([colorers_ElementColorer, colorers_ResidueTypeColorer, colorers_SequenceColorer, colorers_ChainColorer, colorers_SecondaryStructureColorer, colorers_UniformColorer, colorers_ConditionalColorer, colorers_ConformationColorer, colorers_TemperatureColorer, colorers_OccupancyColorer, colorers_HydrophobicityColorer, colorers_MoleculeColorer, colorers_CarbonColorer]); /* harmony default export */ const gfx_colorers = (colorers); -;// CONCATENATED MODULE: ./src/gfx/materials.js +;// ./src/gfx/materials.js function neutralColor(intensity) { @@ -20883,7 +20917,7 @@ const materialList = [{ }]; const materials = new utils_EntityList(materialList); /* harmony default export */ const gfx_materials = (materials); -;// CONCATENATED MODULE: ./src/gfx/meshutils.js +;// ./src/gfx/meshutils.js /** * Utils functions which is worked with meshes * @@ -21085,7 +21119,7 @@ function countTriangles(group) { forEachMeshInGroup, countTriangles }); -;// CONCATENATED MODULE: ./src/gfx/Representation.js +;// ./src/gfx/Representation.js @@ -21266,7 +21300,7 @@ class Representation { } } /* harmony default export */ const gfx_Representation = (Representation); -;// CONCATENATED MODULE: ./src/ComplexVisualEdit.js +;// ./src/ComplexVisualEdit.js @@ -21586,7 +21620,7 @@ class ComplexFragmentEditor extends ComplexEditor { ComponentEditor: ComplexComponentEditor, FragmentEditor: ComplexFragmentEditor }); -;// CONCATENATED MODULE: ./src/ComplexVisual.js +;// ./src/ComplexVisual.js @@ -22184,7 +22218,8 @@ class ComplexVisual extends src_Visual { throw e; } } - if (false) {} + if (false) // removed by dead control flow +{} } hasGeometry = errorOccured || hasGeometry || gfxutils.groupHasGeometryToRender(repr.geo); if (repr.geo) { @@ -22342,9 +22377,7 @@ class ComplexVisual extends src_Visual { finalizeEdit() { this._editor = null; } - setMaterialValues(values) { - let needTraverse = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; - let process = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : undefined; + setMaterialValues(values, needTraverse = false, process = undefined) { for (let i = 0, n = this._reprList.length; i < n; ++i) { const rep = this._reprList[i]; rep.material.setValues(values); @@ -22402,21 +22435,19 @@ class ComplexVisual extends src_Visual { // 32 bits = 30 bits for reps + 1 for selection + 1 for selection expansion ComplexVisual.NUM_REPRESENTATION_BITS = 30; /* harmony default export */ const src_ComplexVisual = (ComplexVisual); -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeFaces.vert -const VolumeFaces_namespaceObject = "varying vec3 pos;\r\n\r\nvoid main() {\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n pos = position.xyz + 0.5;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n}"; -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeFaces.frag -const gfx_shaders_VolumeFaces_namespaceObject = "varying vec3 pos;\r\n\r\nvoid main() {\r\n gl_FragColor = vec4(pos, 0.5);\r\n}"; -;// CONCATENATED MODULE: ./src/gfx/shaders/Volume.vert -const shaders_Volume_namespaceObject = "varying vec4 screenSpacePos;\r\n\r\nvoid main() {\r\n screenSpacePos = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n gl_Position = screenSpacePos;\r\n}"; -;// CONCATENATED MODULE: ./src/gfx/shaders/Volume.frag -const src_gfx_shaders_Volume_namespaceObject = "uniform mat4 projectionMatrix;\r\n\r\n// 3D volume texture\r\nuniform vec3 volumeDim; // volume dimensions, pixels\r\nuniform sampler2D tileTex; // tiled texture containing all Z-slices of a 3D data\r\nuniform vec2 tileTexSize; // size of tiled texture, pixels\r\nuniform vec2 tileStride; // UV stride between slices in tile tex, pixels\r\n\r\nuniform vec3 boxAngles;//value of angles({x: alpha, y:beta, z:gamma}) types 1 - if angle is obtuse, 0 - if acute\r\nuniform vec3 delta; //Projection box delta's from non-orthogonal origin axes; {x: XY, y : XZ, z: YZ}\r\n\r\nuniform vec3 _isoLevel0;\r\nuniform float _flipV;\r\nuniform sampler2D _BFLeft;\r\nuniform sampler2D _BFRight;\r\nuniform sampler2D _FFLeft;\r\nuniform sampler2D _FFRight;\r\nuniform sampler2D _WFFLeft;\r\nuniform sampler2D _WFFRight;\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\n#define NO_COLOR vec4(0., 0., 0., 0.)\r\n\r\nvec4 sample3DTexture(vec3 texCoord) {\r\n // a pair of Z slices is determined by nearest slice border\r\n float zSliceBorder = floor(texCoord.z * volumeDim.z + 0.5);\r\n float zSliceNumber1 = max(zSliceBorder - 1.0, 0.0);\r\n float zSliceNumber2 = min(zSliceBorder, volumeDim.z - 1.0);\r\n\r\n float rowTiles = floor(tileTexSize.x / tileStride.x);\r\n\r\n // calculate coords in tile texture for both slices\r\n vec2 tileOffset = vec2(mod(zSliceNumber1, rowTiles), floor(zSliceNumber1 / rowTiles));\r\n vec2 texCoordSlice1 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n tileOffset = vec2(mod(zSliceNumber2, rowTiles), floor(zSliceNumber2 / rowTiles));\r\n vec2 texCoordSlice2 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n\r\n // bilinear filtering\r\n vec4 colorSlice1 = texture2D(tileTex, texCoordSlice1);\r\n vec4 colorSlice2 = texture2D(tileTex, texCoordSlice2);\r\n float weightSlice2 = texCoord.z * volumeDim.z - (zSliceNumber1 + 0.5);\r\n return mix(colorSlice1, colorSlice2, weightSlice2);\r\n}\r\n\r\nvec4 sample3DTextureInclined(vec3 boxCoord) { // delta:{ x: XY, y : XZ, z: YZ }\r\n vec3 textCoord = boxCoord;\r\n vec2 currDelta = mix(boxCoord.zz, vec2(1., 1.) - boxCoord.zz, boxAngles.yx) * delta.yz;\r\n\r\n textCoord.y = (boxCoord.y - currDelta.y) / (1. - delta.z);\r\n if (textCoord.y < 0.0 || textCoord.y > 1.0)\r\n return NO_COLOR;\r\n\r\n currDelta.x += mix(textCoord.y, 1.0 - textCoord.y, boxAngles.z) * delta.x;\r\n\r\n textCoord.x = (boxCoord.x - currDelta.x) / (1. - delta.x - delta.y);\r\n if (textCoord.x < 0.0 || textCoord.x > 1.0)\r\n return NO_COLOR;\r\n\r\n return sample3DTexture(textCoord);\r\n}\r\n\r\nfloat CalcColor(vec3 iter, vec3 dir) {\r\n float d = 1. / 128.;\r\n vec3 dx = vec3(d, 0.0, 0.0);\r\n vec3 dy = vec3(0.0, d, 0.0);\r\n vec3 dz = vec3(0.0, 0.0, d);\r\n\r\n // #Opt: coordInc.x:(iter + dx).x > 1. ? 0.: sample3DTextureInclined(iter + dx).x,\r\n vec3 coordInc = mix(\r\n vec3(\r\n sample3DTextureInclined(iter + dx).x,\r\n sample3DTextureInclined(iter + dy).x,\r\n sample3DTextureInclined(iter + dz).x\r\n ),\r\n vec3(0. ,0. , 0.),\r\n vec3(floor((iter + dx).x), floor((iter + dy).y), floor((iter + dz).z))\r\n );\r\n\r\n // #Opt: coordDec.x:(iter - dx).x < 0. ? 0.: sample3DTextureInclined(iter - dx).x,\r\n vec3 coordDec = mix(\r\n vec3(0. ,0. , 0.),\r\n vec3(\r\n sample3DTextureInclined(iter - dx).x,\r\n sample3DTextureInclined(iter - dy).x,\r\n sample3DTextureInclined(iter - dz).x\r\n ),\r\n vec3(ceil((iter - dx).x), ceil((iter - dy).y), ceil((iter - dz).z))\r\n );\r\n\r\n vec3 N = normalize(coordInc - coordDec);\r\n float dif = max(0.0, dot(N, dir));\r\n return dif;\r\n}\r\n\r\nvec3 AccuracyIso(vec3 left, vec3 right, float volLeft, float threshold) {\r\n for (int i = 0; i < 5; i++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if ((volLeft - threshold) * (vol - threshold) < 0.)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec3 CorrectIso(vec3 left, vec3 right, float tr) {\r\n for (int j = 0; j < 5; j++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if (vol < tr)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec4 GetIso1(vec3 start, vec3 back, float molDist, vec3 dir, float tr, int count) {\r\n float vol, stepSize = (float(count) + 2.) / float(STEPS_COUNT);\r\n vec3 step = stepSize * dir, iterator = start, left, right;\r\n vec4 acc = NO_COLOR;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n vol = sample3DTextureInclined(iterator).r;\r\n if (length(iterator - back) <= stepSize || (vol > tr))\r\n break;\r\n }\r\n\r\n if (vol > tr)\r\n acc = vec4(CorrectIso(iterator, iterator - step, tr).xyz, 1.);\r\n\r\n return acc;\r\n}\r\n\r\nfloat easeOut(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return 1.0 - (1.0 - t) * (1.0 - t);\r\n}\r\n\r\nfloat easeIn(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return t * t;\r\n}\r\n\r\nvec3 GetColSimple(float vol) {\r\n float t = easeOut(_isoLevel0.x, _isoLevel0.y, vol);\r\n float s = easeIn(_isoLevel0.y, _isoLevel0.z, vol);\r\n return vec3(0.5, 0.6, 0.7) * (1.0 - t) + 2.0 * vec3(s, 0, 0);\r\n}\r\n\r\nvec4 VolRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 acc = NO_COLOR, iso;\r\n vec3 iterator = start, sumColor = vec3(0., 0., 0.);\r\n float stepSize, alpha, sumAlpha = 0.0, vol, curStepSize, molD;\r\n vec3 step, col, colOld, right;\r\n float tr0 = _isoLevel0.x;\r\n float dif, r, kd, finish;\r\n int count = 0, stopMol = 0;\r\n\r\n for (int k = 0; k < 3; k++) {\r\n stepSize = (float(k) + 2.) / float(STEPS_COUNT);\r\n kd = 140. * tr0 * stepSize;\r\n r = 1. - kd;\r\n step = stepSize * dir;\r\n iso = GetIso1(iterator, back, molDist, dir, tr0, k);\r\n if (iso.a < 0.1 || length(iso.xyz - start) > molDist)\r\n break;\r\n iterator = iso.xyz;\r\n dif = 1.;// CalcColor(iterator, dir);\r\n colOld = GetColSimple(tr0);\r\n curStepSize = stepSize;\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n molD = length(iterator - start);\r\n vol = sample3DTextureInclined(iterator).r;\r\n finish = distance(iterator, back) - stepSize;\r\n if (finish < 0.0 || vol < tr0 || (sumAlpha > 0.97) || molD > molDist)\r\n break;\r\n alpha = (1. - r);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4.* colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n colOld = col;\r\n } // for i\r\n\r\n if (finish < 0.0 || sumAlpha > 0.97)\r\n break;\r\n\r\n if (molD > molDist) {\r\n curStepSize = stepSize - (molD - molDist);\r\n right = iterator - (molD - molDist) * dir;\r\n vol = sample3DTextureInclined(right).r;\r\n } else {\r\n vec3 left = iterator - step;\r\n right = CorrectIso(left, iterator, tr0);\r\n curStepSize = distance(left, right);\r\n vol = tr0;\r\n }\r\n\r\n alpha = (1. - r) * curStepSize / stepSize;\r\n dif = 1.;// CalcColor(right, dir);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * curStepSize / stepSize * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4. * colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n\r\n if (molD > molDist)\r\n break;\r\n } // for k\r\n acc.rgb = 1. * sumColor / sumAlpha;\r\n acc.a = sumAlpha;\r\n return acc;\r\n}\r\n\r\nvec4 VolRender1(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n float stepSize = 1.0 / float(STEPS_COUNT);\r\n float len = length(back - start);\r\n vec3 step = stepSize * dir;\r\n vec3 iterator = start;\r\n float acc = 0.0;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n if (float(i) * stepSize > len)\r\n break;\r\n iterator = iterator + step;\r\n if (sample3DTextureInclined(iterator).r > _isoLevel0.x)\r\n acc += 10. * sample3DTextureInclined(iterator).r / float(STEPS_COUNT);\r\n }\r\n\r\n return vec4(1.,1.,1., acc);\r\n}\r\n\r\nvec4 IsoRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 tst = GetIso1(start, back, 2., dir, _isoLevel0.x, 0);\r\n vec4 col = NO_COLOR;\r\n\r\n if (length(tst.xyz - start) < molDist && tst.a > 0.1) {\r\n float dif = CalcColor(tst.xyz, dir);\r\n dif = 0.9 * dif * dif;\r\n col = vec4(dif, dif, dif, 1);\r\n }\r\n return col;\r\n}\r\n\r\nvec4 VolRender2(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n return sample3DTexture(start);\r\n}\r\n\r\nvoid main() {\r\n vec3 tc = screenSpacePos.xyz / screenSpacePos.w * 0.5 + 0.5;\r\n\r\n if (_flipV > 0.0) {\r\n tc.y = 1.0 - tc.y;\r\n }\r\n\r\n vec3 start;\r\n vec3 back;\r\n vec3 molBack;\r\n if (projectionMatrix[0][2] < 0.0) {\r\n start = texture2D(_FFLeft, tc.xy).xyz;\r\n back = texture2D(_BFLeft, tc.xy).xyz;\r\n molBack = texture2D(_WFFLeft, tc.xy).xyz;\r\n } else {\r\n start = texture2D(_FFRight, tc.xy).xyz;\r\n back = texture2D(_BFRight, tc.xy).xyz;\r\n molBack = texture2D(_WFFRight, tc.xy).xyz;\r\n }\r\n\r\n vec3 dir = normalize(back - start);\r\n\r\n float molDist = 2.0;\r\n if (length(molBack) > 0.001) {\r\n molDist = distance(start, molBack);\r\n }\r\n\r\n #ifdef ISO_MODE\r\n gl_FragColor = IsoRender(start, back, molDist, dir);\r\n #else\r\n gl_FragColor = VolRender(start, back, molDist, dir);\r\n #endif\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeFarPlane.vert -const VolumeFarPlane_namespaceObject = "varying vec4 volPos;\r\nuniform float aspectRatio;\r\nuniform float farZ;\r\nuniform float tanHalfFOV;\r\nuniform mat4 matWorld2Volume;\r\n\r\nvoid main() {\r\n // rescale plane to fill in the whole far plane area seen from camera\r\n vec3 pos = position.xyz;\r\n pos.x = pos.x * tanHalfFOV * farZ * aspectRatio;\r\n pos.y = pos.y * tanHalfFOV * farZ;\r\n // common transformation\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(pos, 1.0);\r\n // calc pos in volume CS\r\n volPos = matWorld2Volume * modelMatrix * vec4(pos, 1.0);\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n volPos = volPos + 0.5;\r\n volPos.w = 0.5;\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeFarPlane.frag -const gfx_shaders_VolumeFarPlane_namespaceObject = "varying vec4 volPos;\r\n\r\nvoid main() {\r\n gl_FragColor = volPos;\r\n}"; -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/VolumeFaces.vert +const VolumeFaces_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec3 pos;\r\n\r\nvoid main() {\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n pos = position.xyz + 0.5;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n}"; +;// ./src/gfx/shaders/VolumeFaces.frag +const gfx_shaders_VolumeFaces_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec3 pos;\r\n\r\nvoid main() {\r\n gl_FragColor = vec4(pos, 0.5);\r\n}"; +;// ./src/gfx/shaders/Volume.vert +const shaders_Volume_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\nvoid main() {\r\n screenSpacePos = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n gl_Position = screenSpacePos;\r\n}"; +;// ./src/gfx/shaders/Volume.frag +const src_gfx_shaders_Volume_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nuniform mat4 projectionMatrix;\r\n\r\n// 3D volume texture\r\nuniform vec3 volumeDim; // volume dimensions, pixels\r\nuniform sampler2D tileTex; // tiled texture containing all Z-slices of a 3D data\r\nuniform vec2 tileTexSize; // size of tiled texture, pixels\r\nuniform vec2 tileStride; // UV stride between slices in tile tex, pixels\r\n\r\nuniform vec3 boxAngles;//value of angles({x: alpha, y:beta, z:gamma}) types 1 - if angle is obtuse, 0 - if acute\r\nuniform vec3 delta; //Projection box delta's from non-orthogonal origin axes; {x: XY, y : XZ, z: YZ}\r\n\r\nuniform vec3 _isoLevel0;\r\nuniform float _flipV;\r\nuniform sampler2D _BFLeft;\r\nuniform sampler2D _BFRight;\r\nuniform sampler2D _FFLeft;\r\nuniform sampler2D _FFRight;\r\nuniform sampler2D _WFFLeft;\r\nuniform sampler2D _WFFRight;\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\n#define NO_COLOR vec4(0., 0., 0., 0.)\r\n\r\nvec4 sample3DTexture(vec3 texCoord) {\r\n // a pair of Z slices is determined by nearest slice border\r\n float zSliceBorder = floor(texCoord.z * volumeDim.z + 0.5);\r\n float zSliceNumber1 = max(zSliceBorder - 1.0, 0.0);\r\n float zSliceNumber2 = min(zSliceBorder, volumeDim.z - 1.0);\r\n\r\n float rowTiles = floor(tileTexSize.x / tileStride.x);\r\n\r\n // calculate coords in tile texture for both slices\r\n vec2 tileOffset = vec2(mod(zSliceNumber1, rowTiles), floor(zSliceNumber1 / rowTiles));\r\n vec2 texCoordSlice1 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n tileOffset = vec2(mod(zSliceNumber2, rowTiles), floor(zSliceNumber2 / rowTiles));\r\n vec2 texCoordSlice2 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n\r\n // bilinear filtering\r\n vec4 colorSlice1 = texture2D(tileTex, texCoordSlice1);\r\n vec4 colorSlice2 = texture2D(tileTex, texCoordSlice2);\r\n float weightSlice2 = texCoord.z * volumeDim.z - (zSliceNumber1 + 0.5);\r\n return mix(colorSlice1, colorSlice2, weightSlice2);\r\n}\r\n\r\nvec4 sample3DTextureInclined(vec3 boxCoord) { // delta:{ x: XY, y : XZ, z: YZ }\r\n vec3 textCoord = boxCoord;\r\n vec2 currDelta = mix(boxCoord.zz, vec2(1., 1.) - boxCoord.zz, boxAngles.yx) * delta.yz;\r\n\r\n textCoord.y = (boxCoord.y - currDelta.y) / (1. - delta.z);\r\n if (textCoord.y < 0.0 || textCoord.y > 1.0)\r\n return NO_COLOR;\r\n\r\n currDelta.x += mix(textCoord.y, 1.0 - textCoord.y, boxAngles.z) * delta.x;\r\n\r\n textCoord.x = (boxCoord.x - currDelta.x) / (1. - delta.x - delta.y);\r\n if (textCoord.x < 0.0 || textCoord.x > 1.0)\r\n return NO_COLOR;\r\n\r\n return sample3DTexture(textCoord);\r\n}\r\n\r\nfloat CalcColor(vec3 iter, vec3 dir) {\r\n float d = 1. / 128.;\r\n vec3 dx = vec3(d, 0.0, 0.0);\r\n vec3 dy = vec3(0.0, d, 0.0);\r\n vec3 dz = vec3(0.0, 0.0, d);\r\n\r\n // #Opt: coordInc.x:(iter + dx).x > 1. ? 0.: sample3DTextureInclined(iter + dx).x,\r\n vec3 coordInc = mix(\r\n vec3(\r\n sample3DTextureInclined(iter + dx).x,\r\n sample3DTextureInclined(iter + dy).x,\r\n sample3DTextureInclined(iter + dz).x\r\n ),\r\n vec3(0. ,0. , 0.),\r\n vec3(floor((iter + dx).x), floor((iter + dy).y), floor((iter + dz).z))\r\n );\r\n\r\n // #Opt: coordDec.x:(iter - dx).x < 0. ? 0.: sample3DTextureInclined(iter - dx).x,\r\n vec3 coordDec = mix(\r\n vec3(0. ,0. , 0.),\r\n vec3(\r\n sample3DTextureInclined(iter - dx).x,\r\n sample3DTextureInclined(iter - dy).x,\r\n sample3DTextureInclined(iter - dz).x\r\n ),\r\n vec3(ceil((iter - dx).x), ceil((iter - dy).y), ceil((iter - dz).z))\r\n );\r\n\r\n vec3 N = normalize(coordInc - coordDec);\r\n float dif = max(0.0, dot(N, dir));\r\n return dif;\r\n}\r\n\r\nvec3 AccuracyIso(vec3 left, vec3 right, float volLeft, float threshold) {\r\n for (int i = 0; i < 5; i++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if ((volLeft - threshold) * (vol - threshold) < 0.)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec3 CorrectIso(vec3 left, vec3 right, float tr) {\r\n for (int j = 0; j < 5; j++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if (vol < tr)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec4 GetIso1(vec3 start, vec3 back, float molDist, vec3 dir, float tr, int count) {\r\n float vol, stepSize = (float(count) + 2.) / float(STEPS_COUNT);\r\n vec3 step = stepSize * dir, iterator = start, left, right;\r\n vec4 acc = NO_COLOR;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n vol = sample3DTextureInclined(iterator).r;\r\n if (length(iterator - back) <= stepSize || (vol > tr))\r\n break;\r\n }\r\n\r\n if (vol > tr)\r\n acc = vec4(CorrectIso(iterator, iterator - step, tr).xyz, 1.);\r\n\r\n return acc;\r\n}\r\n\r\nfloat easeOut(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return 1.0 - (1.0 - t) * (1.0 - t);\r\n}\r\n\r\nfloat easeIn(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return t * t;\r\n}\r\n\r\nvec3 GetColSimple(float vol) {\r\n float t = easeOut(_isoLevel0.x, _isoLevel0.y, vol);\r\n float s = easeIn(_isoLevel0.y, _isoLevel0.z, vol);\r\n return vec3(0.5, 0.6, 0.7) * (1.0 - t) + 2.0 * vec3(s, 0, 0);\r\n}\r\n\r\nvec4 VolRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 acc = NO_COLOR, iso;\r\n vec3 iterator = start, sumColor = vec3(0., 0., 0.);\r\n float stepSize, alpha, sumAlpha = 0.0, vol, curStepSize, molD;\r\n vec3 step, col, colOld, right;\r\n float tr0 = _isoLevel0.x;\r\n float dif, r, kd, finish;\r\n int count = 0, stopMol = 0;\r\n\r\n for (int k = 0; k < 3; k++) {\r\n stepSize = (float(k) + 2.) / float(STEPS_COUNT);\r\n kd = 140. * tr0 * stepSize;\r\n r = 1. - kd;\r\n step = stepSize * dir;\r\n iso = GetIso1(iterator, back, molDist, dir, tr0, k);\r\n if (iso.a < 0.1 || length(iso.xyz - start) > molDist)\r\n break;\r\n iterator = iso.xyz;\r\n dif = 1.;// CalcColor(iterator, dir);\r\n colOld = GetColSimple(tr0);\r\n curStepSize = stepSize;\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n molD = length(iterator - start);\r\n vol = sample3DTextureInclined(iterator).r;\r\n finish = distance(iterator, back) - stepSize;\r\n if (finish < 0.0 || vol < tr0 || (sumAlpha > 0.97) || molD > molDist)\r\n break;\r\n alpha = (1. - r);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4.* colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n colOld = col;\r\n } // for i\r\n\r\n if (finish < 0.0 || sumAlpha > 0.97)\r\n break;\r\n\r\n if (molD > molDist) {\r\n curStepSize = stepSize - (molD - molDist);\r\n right = iterator - (molD - molDist) * dir;\r\n vol = sample3DTextureInclined(right).r;\r\n } else {\r\n vec3 left = iterator - step;\r\n right = CorrectIso(left, iterator, tr0);\r\n curStepSize = distance(left, right);\r\n vol = tr0;\r\n }\r\n\r\n alpha = (1. - r) * curStepSize / stepSize;\r\n dif = 1.;// CalcColor(right, dir);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * curStepSize / stepSize * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4. * colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n\r\n if (molD > molDist)\r\n break;\r\n } // for k\r\n acc.rgb = 1. * sumColor / sumAlpha;\r\n acc.a = sumAlpha;\r\n return acc;\r\n}\r\n\r\nvec4 VolRender1(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n float stepSize = 1.0 / float(STEPS_COUNT);\r\n float len = length(back - start);\r\n vec3 step = stepSize * dir;\r\n vec3 iterator = start;\r\n float acc = 0.0;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n if (float(i) * stepSize > len)\r\n break;\r\n iterator = iterator + step;\r\n if (sample3DTextureInclined(iterator).r > _isoLevel0.x)\r\n acc += 10. * sample3DTextureInclined(iterator).r / float(STEPS_COUNT);\r\n }\r\n\r\n return vec4(1.,1.,1., acc);\r\n}\r\n\r\nvec4 IsoRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 tst = GetIso1(start, back, 2., dir, _isoLevel0.x, 0);\r\n vec4 col = NO_COLOR;\r\n\r\n if (length(tst.xyz - start) < molDist && tst.a > 0.1) {\r\n float dif = CalcColor(tst.xyz, dir);\r\n dif = 0.9 * dif * dif;\r\n col = vec4(dif, dif, dif, 1);\r\n }\r\n return col;\r\n}\r\n\r\nvec4 VolRender2(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n return sample3DTexture(start);\r\n}\r\n\r\nvoid main() {\r\n vec3 tc = screenSpacePos.xyz / screenSpacePos.w * 0.5 + 0.5;\r\n\r\n if (_flipV > 0.0) {\r\n tc.y = 1.0 - tc.y;\r\n }\r\n\r\n vec3 start;\r\n vec3 back;\r\n vec3 molBack;\r\n if (projectionMatrix[0][2] < 0.0) {\r\n start = texture2D(_FFLeft, tc.xy).xyz;\r\n back = texture2D(_BFLeft, tc.xy).xyz;\r\n molBack = texture2D(_WFFLeft, tc.xy).xyz;\r\n } else {\r\n start = texture2D(_FFRight, tc.xy).xyz;\r\n back = texture2D(_BFRight, tc.xy).xyz;\r\n molBack = texture2D(_WFFRight, tc.xy).xyz;\r\n }\r\n\r\n vec3 dir = normalize(back - start);\r\n\r\n float molDist = 2.0;\r\n if (length(molBack) > 0.001) {\r\n molDist = distance(start, molBack);\r\n }\r\n\r\n #ifdef ISO_MODE\r\n gl_FragColor = IsoRender(start, back, molDist, dir);\r\n #else\r\n gl_FragColor = VolRender(start, back, molDist, dir);\r\n #endif\r\n}\r\n"; +;// ./src/gfx/shaders/VolumeFarPlane.vert +const VolumeFarPlane_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 volPos;\r\nuniform float aspectRatio;\r\nuniform float farZ;\r\nuniform float tanHalfFOV;\r\nuniform mat4 matWorld2Volume;\r\n\r\nvoid main() {\r\n // rescale plane to fill in the whole far plane area seen from camera\r\n vec3 pos = position.xyz;\r\n pos.x = pos.x * tanHalfFOV * farZ * aspectRatio;\r\n pos.y = pos.y * tanHalfFOV * farZ;\r\n // common transformation\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(pos, 1.0);\r\n // calc pos in volume CS\r\n volPos = matWorld2Volume * modelMatrix * vec4(pos, 1.0);\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n volPos = volPos + 0.5;\r\n volPos.w = 0.5;\r\n}\r\n"; +;// ./src/gfx/shaders/VolumeFarPlane.frag +const gfx_shaders_VolumeFarPlane_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 volPos;\r\n\r\nvoid main() {\r\n gl_FragColor = volPos;\r\n}"; +;// ./src/gfx/shaders/VolumeMaterial.js @@ -22572,7 +22603,7 @@ class VolumeMaterial extends external_module_three_commonjs_three_commonjs2_thre FrontFacePosMaterial, VolumeMaterial }); -;// CONCATENATED MODULE: ./src/gfx/VolumeMesh.js +;// ./src/gfx/VolumeMesh.js @@ -22614,12 +22645,12 @@ class VolumeMesh extends external_module_three_commonjs_three_commonjs2_three_am geo.setAttribute('position', new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.BufferAttribute(new Float32Array(this.vertices.length * 3), 3)); this.name = 'VolumeMesh'; } - static _corners = (() => [ + static _corners = [ // x, y, z, edge1, edge2, edge3 - [-1, -1, -1, 0, 4, 8], [1, -1, -1, 0, 5, 9], [1, 1, -1, 1, 5, 10], [-1, 1, -1, 1, 4, 11], [-1, -1, 1, 2, 6, 8], [1, -1, 1, 2, 7, 9], [1, 1, 1, 3, 7, 10], [-1, 1, 1, 3, 6, 11]])(); - static _edges = (() => [ + [-1, -1, -1, 0, 4, 8], [1, -1, -1, 0, 5, 9], [1, 1, -1, 1, 5, 10], [-1, 1, -1, 1, 4, 11], [-1, -1, 1, 2, 6, 8], [1, -1, 1, 2, 7, 9], [1, 1, 1, 3, 7, 10], [-1, 1, 1, 3, 6, 11]]; + static _edges = [ // corner1, corner2, center_x, center_y, center_z - [0, 1, 0, -1, -1], [2, 3, 0, 1, -1], [4, 5, 0, -1, 1], [6, 7, 0, 1, 1], [0, 3, -1, 0, -1], [1, 2, 1, 0, -1], [4, 7, -1, 0, 1], [5, 6, 1, 0, 1], [0, 4, -1, -1, 0], [1, 5, 1, -1, 0], [2, 6, -1, 1, 0], [3, 7, 1, 1, 0]])(); + [0, 1, 0, -1, -1], [2, 3, 0, 1, -1], [4, 5, 0, -1, 1], [6, 7, 0, 1, 1], [0, 3, -1, 0, -1], [1, 2, 1, 0, -1], [4, 7, -1, 0, 1], [5, 6, 1, 0, 1], [0, 4, -1, -1, 0], [1, 5, 1, -1, 0], [2, 6, -1, 1, 0], [3, 7, 1, 1, 0]]; static _edgeIntersections = function () { const edgeIntersections = []; for (let j = 0; j < 12; ++j) { @@ -22897,11 +22928,11 @@ class VolumeMesh extends external_module_three_commonjs_three_commonjs2_three_am this.material.uniforms._isoLevel0.value.set(level(kSigma), level(kSigmaMed), level(kSigmaMax)); } static _nearClipPlaneOffset = 0.2; - static _pos = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3())(); - static _norm = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3())(); - static _norm4D = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector4())(); - static _matrixWorldToLocal = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Matrix4())(); - static _clipPlane = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Plane())(); + static _pos = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); + static _norm = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); + static _norm4D = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector4(); + static _matrixWorldToLocal = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Matrix4(); + static _clipPlane = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Plane(); rebuild(camera) { const nearClipPlaneOffset = VolumeMesh._nearClipPlaneOffset; const pos = VolumeMesh._pos; @@ -22934,7 +22965,7 @@ class VolumeMesh extends external_module_three_commonjs_three_commonjs2_three_am } } /* harmony default export */ const gfx_VolumeMesh = (VolumeMesh); -;// CONCATENATED MODULE: ./src/gfx/VolumeBounds.js +;// ./src/gfx/VolumeBounds.js function _flattenArray(input) { @@ -23011,7 +23042,7 @@ class VolumeBounds { } } /* harmony default export */ const gfx_VolumeBounds = (VolumeBounds); -;// CONCATENATED MODULE: ./src/gfx/VolumeFarPlane.js +;// ./src/gfx/VolumeFarPlane.js @@ -23077,7 +23108,7 @@ class VolumeFarPlane { } } /* harmony default export */ const gfx_VolumeFarPlane = (VolumeFarPlane); -;// CONCATENATED MODULE: ./src/VolumeVisual.js +;// ./src/VolumeVisual.js @@ -23113,7 +23144,7 @@ class VolumeVisual extends src_Visual { } } /* harmony default export */ const src_VolumeVisual = (VolumeVisual); -;// CONCATENATED MODULE: ./src/io/loaders/LoaderList.js +;// ./src/io/loaders/LoaderList.js /** @@ -23131,8 +23162,7 @@ class LoaderList extends utils_EntityList { * automatically register at creation time. * @see LoaderList#register */ - constructor() { - let someLoaders = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : []; + constructor(someLoaders = []) { super(someLoaders, ['types']); } @@ -23154,7 +23184,7 @@ class LoaderList extends utils_EntityList { } } /* harmony default export */ const loaders_LoaderList = (LoaderList); -;// CONCATENATED MODULE: ./src/io/loaders/Loader.js +;// ./src/io/loaders/Loader.js class Loader extends utils_EventDispatcher { @@ -23179,7 +23209,7 @@ class Loader extends utils_EventDispatcher { } } utils_makeContextDependent(Loader.prototype); -;// CONCATENATED MODULE: ./src/io/loaders/FileLoader.js +;// ./src/io/loaders/FileLoader.js class FileLoader extends Loader { constructor(source, options) { @@ -23221,7 +23251,7 @@ class FileLoader extends Loader { } } FileLoader.types = ['file', 'blob']; -;// CONCATENATED MODULE: ./src/io/loaders/XHRLoader.js +;// ./src/io/loaders/XHRLoader.js @@ -23277,7 +23307,7 @@ class XHRLoader extends Loader { } } XHRLoader.types = ['url']; -;// CONCATENATED MODULE: ./src/io/loaders/ImmediateLoader.js +;// ./src/io/loaders/ImmediateLoader.js class ImmediateLoader extends Loader { load() { @@ -23293,7 +23323,7 @@ class ImmediateLoader extends Loader { } } ImmediateLoader.types = ['immediate']; -;// CONCATENATED MODULE: ./src/io/loaders.js +;// ./src/io/loaders.js @@ -23301,7 +23331,7 @@ ImmediateLoader.types = ['immediate']; /* harmony default export */ const loaders = (new loaders_LoaderList([ // note: order might be important FileLoader, XHRLoader, ImmediateLoader])); -;// CONCATENATED MODULE: ./src/io/parsers/ParserList.js +;// ./src/io/parsers/ParserList.js /** @@ -23319,8 +23349,7 @@ class ParserList extends utils_EntityList { * automatically register at creation time. * @see ParserList#register */ - constructor() { - let someParsers = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : []; + constructor(someParsers = []) { super(someParsers, ['formats', 'extensions']); } @@ -23347,7 +23376,7 @@ class ParserList extends utils_EntityList { } } /* harmony default export */ const parsers_ParserList = (ParserList); -;// CONCATENATED MODULE: ./src/io/parsers/Parser.js +;// ./src/io/parsers/Parser.js class Parser { constructor(data, options) { @@ -23383,7 +23412,7 @@ class Parser { } } utils_makeContextDependent(Parser.prototype); -;// CONCATENATED MODULE: ./src/io/parsers/pdb/Remark290.js +;// ./src/io/parsers/pdb/Remark290.js /** @@ -23433,7 +23462,7 @@ class Remark290 { } Remark290.prototype.id = 290; /* harmony default export */ const pdb_Remark290 = (Remark290); -;// CONCATENATED MODULE: ./src/io/parsers/pdb/Remark350.js +;// ./src/io/parsers/pdb/Remark350.js const { @@ -23507,7 +23536,7 @@ class Remark350 { } Remark350.prototype.id = 350; /* harmony default export */ const pdb_Remark350 = (Remark350); -;// CONCATENATED MODULE: ./src/io/parsers/PDBStream.js +;// ./src/io/parsers/PDBStream.js /** Helper class for stream-like reading input files. */ class PDBStream { /** @@ -23620,7 +23649,7 @@ class PDBStream { } } /* harmony default export */ const parsers_PDBStream = (PDBStream); -;// CONCATENATED MODULE: ./src/io/parsers/PDBParser.js +;// ./src/io/parsers/PDBParser.js @@ -23769,8 +23798,6 @@ class PDBParser extends Parser { if (this._modelId !== 1) { return; } - - /* eslint-disable no-magic-numbers */ const het = stream.readCharCode(1) === 0x48; // field names according to wwPDB Format @@ -23789,7 +23816,7 @@ class PDBParser extends Parser { const tempFactor = stream.readFloat(61, 66); const element = stream.readString(77, 78).trim() || nameToElement(name); const charge = stream.readInt(79, 80) || 0; - /* eslint-enable no-magic-numbers */ + // skip waters (there may be lots of them) if (this.settings.now.nowater) { if (resName === 'HOH' || resName === 'WAT') { @@ -23821,14 +23848,11 @@ class PDBParser extends Parser { this._modelId += 1; } _parseCONECT(stream) { - /* eslint-disable no-magic-numbers */ const serial0 = stream.readInt(7, 11); const serial1 = stream.readInt(12, 16); const serial2 = stream.readInt(17, 21); const serial3 = stream.readInt(22, 26); const serial4 = stream.readInt(27, 31); - /* eslint-enable no-magic-numbers */ - const complex = this._complex; // Keep bonds ordered by atom serial @@ -23846,11 +23870,9 @@ class PDBParser extends Parser { } } _parseCOMPND(stream) { - /* eslint-disable no-magic-numbers */ const str = stream.readString(11, 80); const tokenIdx = str.indexOf(':'); this._compndCurrToken = tokenIdx > 0 ? str.substring(0, tokenIdx).trim() : this._compndCurrToken; - /* eslint-enable no-magic-numbers */ // start reading new molecule if (this._compndCurrToken === 'MOL_ID') { @@ -23876,9 +23898,7 @@ class PDBParser extends Parser { } } _parseREMARK(stream) { - /* eslint-disable no-magic-numbers */ const remarkNum = stream.readInt(8, 10); - /* eslint-enable no-magic-numbers */ // create remark parser if needed let remark = this._remarks[remarkNum]; @@ -23895,18 +23915,14 @@ class PDBParser extends Parser { } } _parseHELIX(stream) { - /* eslint-disable no-magic-numbers */ const fields = [20, 22, 32, 34]; - /* eslint-enable no-magic-numbers */ this._parseSTRUCTURE(stream, fields, obj => { this._complex.addHelix(obj); this._complex.structures.push(obj); }); } _parseSHEET(stream) { - /* eslint-disable no-magic-numbers */ const fields = [22, 23, 33, 34]; - /* eslint-enable no-magic-numbers */ this._parseSTRUCTURE(stream, fields, obj => { this._complex.addSheet(obj); }); @@ -23918,7 +23934,7 @@ class PDBParser extends Parser { const endIndex = 3; // identify fields: debugging and stuff - /* eslint-disable no-magic-numbers */ + const codeOfS = 0x53; const serialNumber = stream.readInt(8, 10); const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim() @@ -23928,7 +23944,7 @@ class PDBParser extends Parser { const shWidth = stream.readInt(15, 16); const shCur = stream.readInt(42, 45); const shPrev = stream.readInt(57, 60); - /* eslint-enable no-magic-numbers */ + // file fields const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0); const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0); @@ -23986,7 +24002,7 @@ class PDBParser extends Parser { const line = stream.readInt(9, 10) || 1; metadata.title[line - 1] = stream.readString(11, 80).trim(); } - static tagParsers = (() => ({ + static tagParsers = { HEADER: PDBParser.prototype._parseHEADER, 'TITLE ': PDBParser.prototype._parseTITLE, 'ATOM ': PDBParser.prototype._parseATOM, @@ -24008,7 +24024,7 @@ class PDBParser extends Parser { 'ATOM 7': PDBParser.prototype._parseATOM, 'ATOM 8': PDBParser.prototype._parseATOM, 'ATOM 9': PDBParser.prototype._parseATOM - }))(); + }; parseSync() { const stream = new parsers_PDBStream(this._data); const result = this._complex = new PDBParser_Complex(); @@ -24041,7 +24057,7 @@ class PDBParser extends Parser { PDBParser.formats = ['pdb']; PDBParser.extensions = ['.pdb', '.ent']; /* harmony default export */ const parsers_PDBParser = (PDBParser); -;// CONCATENATED MODULE: ./src/io/parsers/CMLParser.js +;// ./src/io/parsers/CMLParser.js @@ -24633,7 +24649,7 @@ CMLParser.extensions = ['.cml']; // EXTERNAL MODULE: ./vendor/js/mmtf.js var mmtf = __webpack_require__(660); var mmtf_default = /*#__PURE__*/__webpack_require__.n(mmtf); -;// CONCATENATED MODULE: ./src/io/parsers/MMTFParser.js +;// ./src/io/parsers/MMTFParser.js @@ -25061,7 +25077,7 @@ MMTFParser.formats = ['mmtf']; MMTFParser.extensions = ['.mmtf']; MMTFParser.binary = true; /* harmony default export */ const parsers_MMTFParser = (MMTFParser); -;// CONCATENATED MODULE: ./src/io/parsers/ParsingError.js +;// ./src/io/parsers/ParsingError.js class ParsingError extends Error { constructor(message, line, column) { super(`data:${line}:${column}: ${message}`); @@ -25074,7 +25090,7 @@ class ParsingError extends Error { } } /* harmony default export */ const parsers_ParsingError = (ParsingError); -;// CONCATENATED MODULE: ./src/io/parsers/readCIF.js +;// ./src/io/parsers/readCIF.js @@ -25349,7 +25365,7 @@ function readCIF(source) { } return result; } -;// CONCATENATED MODULE: ./src/io/parsers/CIFParser.js +;// ./src/io/parsers/CIFParser.js @@ -25843,7 +25859,7 @@ class CIFParser extends Parser { CIFParser.formats = ['cif', 'mmcif']; CIFParser.extensions = ['.cif', '.mmcif']; /* harmony default export */ const parsers_CIFParser = (CIFParser); -;// CONCATENATED MODULE: ./src/io/parsers/VolumeModel.js +;// ./src/io/parsers/VolumeModel.js @@ -25855,7 +25871,7 @@ const valueType = { }; class VolumeModel { _xyz2crs = []; - _origin = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(0, 0, 0))(); + _origin = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(0, 0, 0); constructor() { this._header = {}; this._boxSize = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); @@ -25966,7 +25982,7 @@ class VolumeModel { } } /* harmony default export */ const parsers_VolumeModel = (VolumeModel); -;// CONCATENATED MODULE: ./src/io/parsers/CCP4Parser.js +;// ./src/io/parsers/CCP4Parser.js const CCP4Header = { @@ -26102,7 +26118,7 @@ CCP4Parser.formats = ['ccp4']; CCP4Parser.extensions = ['.ccp4', '.map', '.mrc']; CCP4Parser.binary = true; /* harmony default export */ const parsers_CCP4Parser = (CCP4Parser); -;// CONCATENATED MODULE: ./src/io/parsers/XYZParser.js +;// ./src/io/parsers/XYZParser.js @@ -26190,7 +26206,7 @@ class XYZParser extends Parser { static extensions = ['.xyz']; } /* harmony default export */ const parsers_XYZParser = (XYZParser); -;// CONCATENATED MODULE: ./src/io/parsers/PubChemParser.js +;// ./src/io/parsers/PubChemParser.js @@ -26263,7 +26279,7 @@ class PubChemParser extends Parser { PubChemParser.formats = ['pubchem', 'pubchem+json', 'pc']; PubChemParser.extensions = ['.json']; /* harmony default export */ const parsers_PubChemParser = (PubChemParser); -;// CONCATENATED MODULE: ./src/io/parsers/SDFStream.js +;// ./src/io/parsers/SDFStream.js class SDFStream { constructor(data) { @@ -26314,7 +26330,7 @@ class SDFStream { return this._currentStringIndx < this._strings.length - 2; } } -;// CONCATENATED MODULE: ./src/io/parsers/SDFParser.js +;// ./src/io/parsers/SDFParser.js @@ -26630,7 +26646,7 @@ class SDFParser extends Parser { } SDFParser.formats = ['mol', 'sdf']; SDFParser.extensions = ['.mol', '.sdf']; -;// CONCATENATED MODULE: ./src/io/parsers/DSN6Parser.js +;// ./src/io/parsers/DSN6Parser.js @@ -26774,7 +26790,7 @@ DSN6Parser.formats = ['dsn6']; DSN6Parser.extensions = ['.dsn6', '.omap']; DSN6Parser.binary = true; /* harmony default export */ const parsers_DSN6Parser = (DSN6Parser); -;// CONCATENATED MODULE: ./src/io/parsers/GROReader.js +;// ./src/io/parsers/GROReader.js /** @@ -26798,7 +26814,7 @@ class GROReader extends parsers_PDBStream { } } /* harmony default export */ const parsers_GROReader = (GROReader); -;// CONCATENATED MODULE: ./src/io/parsers/GROParser.js +;// ./src/io/parsers/GROParser.js @@ -27003,7 +27019,7 @@ class GROParser extends Parser { GROParser.formats = ['gro']; GROParser.extensions = ['.gro']; /* harmony default export */ const parsers_GROParser = (GROParser); -;// CONCATENATED MODULE: ./src/io/parsers/MOL2Parser.js +;// ./src/io/parsers/MOL2Parser.js @@ -27280,7 +27296,7 @@ class MOL2Parser extends Parser { MOL2Parser.formats = ['mol2']; MOL2Parser.extensions = ['.mol2', '.ml2', '.sy2']; /* harmony default export */ const parsers_MOL2Parser = (MOL2Parser); -;// CONCATENATED MODULE: ./src/io/parsers.js +;// ./src/io/parsers.js @@ -27296,7 +27312,7 @@ MOL2Parser.extensions = ['.mol2', '.ml2', '.sy2']; /* harmony default export */ const parsers = (new parsers_ParserList([ // note: order might be important parsers_PDBParser, parsers_CIFParser, parsers_MMTFParser, parsers_XYZParser, parsers_CMLParser, parsers_PubChemParser, SDFParser, parsers_CCP4Parser, parsers_DSN6Parser, parsers_GROParser, parsers_MOL2Parser])); -;// CONCATENATED MODULE: ./src/io/exporters/ExporterList.js +;// ./src/io/exporters/ExporterList.js /** @@ -27314,8 +27330,7 @@ class ExporterList extends utils_EntityList { * automatically register at creation time. * @see ExporterList#register */ - constructor() { - let someExporters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : []; + constructor(someExporters = []) { super(someExporters, ['formats']); } @@ -27335,7 +27350,7 @@ class ExporterList extends utils_EntityList { } } /* harmony default export */ const exporters_ExporterList = (ExporterList); -;// CONCATENATED MODULE: ./src/io/exporters/Exporter.js +;// ./src/io/exporters/Exporter.js class Exporter { constructor(source, options) { @@ -27365,7 +27380,7 @@ class Exporter { } } utils_makeContextDependent(Exporter.prototype); -;// CONCATENATED MODULE: ./src/io/exporters/PDBResult.js +;// ./src/io/exporters/PDBResult.js class PDBResult { @@ -27546,7 +27561,7 @@ class PDBResult { } } } -;// CONCATENATED MODULE: ./src/io/exporters/PDBExporter.js +;// ./src/io/exporters/PDBExporter.js @@ -27793,7 +27808,7 @@ class PDBExporter extends Exporter { } PDBExporter.formats = ['pdb']; PDBExporter.SourceClass = chem_Complex; -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBXModel.js +;// ./src/io/exporters/fbx/FBXModel.js const FBX_POS_SIZE = 3; const FBX_NORM_SIZE = 3; @@ -27937,7 +27952,7 @@ class FBXModel { this.setColors(geo.colors, 0, geo.vertsCount, size.color); } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBXGeometry.js +;// ./src/io/exporters/fbx/FBXGeometry.js /** Base class for fbx geometry contains simply organized attributes: positions+normals+colors, indices. */ class FBXGeometry { /** @@ -27968,7 +27983,7 @@ class FBXGeometry { }; } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBX1CGeometry.js +;// ./src/io/exporters/fbx/FBX1CGeometry.js /** @@ -28012,7 +28027,7 @@ class FBX1CGeometry extends FBXGeometry { } } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBX2CCylinder.js +;// ./src/io/exporters/fbx/FBX2CCylinder.js /** @@ -28133,7 +28148,7 @@ class FBX2CCylinder extends FBXGeometry { } } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBXInfoExtractor.js +;// ./src/io/exporters/fbx/FBXInfoExtractor.js @@ -28491,7 +28506,7 @@ class FBXInfoExtractor { matrix.set(scale, 0, 0, x, 0, scale, 0, y, 0, 0, scale, z, 0, 0, 0, 1); } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBXResult.js +;// ./src/io/exporters/fbx/FBXResult.js // Forming default definitions block const defaultDefinitions = ` Definitions: { @@ -28660,7 +28675,7 @@ class FBXResult { const creator = `Miew FBX Exporter v${this._info.version}`; // Supposed to be an engine return `; FBX 6.1.0 project file -; Created by ${creator} Copyright (c) 2015-2024 EPAM Systems, Inc. +; Created by ${creator} Copyright (c) 2015-2026 EPAM Systems, Inc. ; For support please contact miew@epam.com ; ---------------------------------------------------- @@ -28949,7 +28964,7 @@ Connections: { }`; } } -;// CONCATENATED MODULE: ./src/io/exporters/FBXExporter.js +;// ./src/io/exporters/FBXExporter.js @@ -28980,12 +28995,12 @@ class FBXExporter extends Exporter { } FBXExporter.formats = ['fbx']; FBXExporter.SourceClass = src_ComplexVisual; -;// CONCATENATED MODULE: ./src/io/exporters.js +;// ./src/io/exporters.js /* harmony default export */ const exporters = (new exporters_ExporterList([PDBExporter, FBXExporter])); -;// CONCATENATED MODULE: ./src/io/io.js +;// ./src/io/io.js @@ -28994,7 +29009,7 @@ FBXExporter.SourceClass = src_ComplexVisual; parsers: parsers, exporters: exporters }); -;// CONCATENATED MODULE: ./src/gfx/CSS2DRenderer.js +;// ./src/gfx/CSS2DRenderer.js /** * @author mrdoob / http://mrdoob.com/ */ @@ -29095,19 +29110,19 @@ class CSS2DRenderer { } } /* harmony default export */ const gfx_CSS2DRenderer = (CSS2DRenderer); -;// CONCATENATED MODULE: ./src/utils/getTopWindow.js +;// ./src/utils/getTopWindow.js function getTopWindow() { // intercept the exception if we have cross-origin iframe try { if (window.top.location.href !== undefined) { return window.top; } - } catch (e) { + } catch { // provide fallback } return window; } -;// CONCATENATED MODULE: ./src/ui/ObjectControls.js +;// ./src/ui/ObjectControls.js @@ -29862,7 +29877,7 @@ ObjectControls.prototype.setPivot = function (newPivot) { }); }; /* harmony default export */ const ui_ObjectControls = (ObjectControls); -;// CONCATENATED MODULE: ./src/ui/Picker.js +;// ./src/ui/Picker.js @@ -30083,7 +30098,7 @@ Picker.prototype.dispose = function () { } }; /* harmony default export */ const ui_Picker = (Picker); -;// CONCATENATED MODULE: ./src/gfx/Axes.js +;// ./src/gfx/Axes.js class Axes { constructor(target, targetCamera) { @@ -30124,7 +30139,7 @@ class Axes { } } /* harmony default export */ const gfx_Axes = (Axes); -;// CONCATENATED MODULE: ./src/gfx/FrameInfo.js +;// ./src/gfx/FrameInfo.js const cDataOffset = 12; @@ -30411,7 +30426,7 @@ class FrameInfo { * Returns link to atom pos vector, clone it if needed */ - static _vec = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3())(); + static _vec = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.Vector3(); getAtomPos(atomIdx) { const vec = FrameInfo._vec; const self = this; @@ -30429,7 +30444,7 @@ class FrameInfo { } } /* harmony default export */ const gfx_FrameInfo = (FrameInfo); -;// CONCATENATED MODULE: ./src/gfx/objects/SceneObject.js +;// ./src/gfx/objects/SceneObject.js @@ -30504,7 +30519,7 @@ class SceneObject { */ SceneObject.prototype.type = '__'; /* harmony default export */ const objects_SceneObject = (SceneObject); -;// CONCATENATED MODULE: ./src/gfx/objects/LinesObj.js +;// ./src/gfx/objects/LinesObj.js @@ -30573,11 +30588,9 @@ class LinesObj extends objects_SceneObject { LinesObj.prototype.constructor = LinesObj; LinesObj.prototype.type = 'line'; /* harmony default export */ const objects_LinesObj = (LinesObj); -;// CONCATENATED MODULE: ./src/gfx/shaders/Outline.frag -const Outline_namespaceObject = "precision highp float;\r\n\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexSize;\r\nuniform vec2 thickness;\r\nvarying vec2 vUv;\r\n\r\n#ifdef DEPTH_OUTLINE\r\n uniform sampler2D srcDepthTex; //depthTexture\r\n uniform vec3 color;\r\n uniform float threshold;\r\n#endif\r\n\r\nvoid main() {\r\n\r\n vec2 pixelSize = thickness / srcTexSize;\r\n\r\n #ifdef DEPTH_OUTLINE\r\n float c00 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,-pixelSize.y)).x;\r\n float c01 = texture2D(srcDepthTex, vUv + vec2(0,-pixelSize.y)).x;\r\n float c02 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,-pixelSize.y)).x;\r\n float c10 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,0)).x;\r\n float c12 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,0)).x;\r\n float c20 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,pixelSize.y)).x;\r\n float c21 = texture2D(srcDepthTex, vUv + vec2(0,pixelSize.y)).x;\r\n float c22 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,pixelSize.y)).x;\r\n\r\n float horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n float vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n float grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n\r\n gl_FragColor = ( grad > threshold ) ? vec4(color.rgb, 1.0) : gl_FragColor = texture2D(srcTex, vUv);\r\n\r\n #else\r\n vec4 c00 = texture2D(srcTex, vUv + vec2(-pixelSize.x,-pixelSize.y));\r\n vec4 c01 = texture2D(srcTex, vUv + vec2(0,-pixelSize.y));\r\n vec4 c02 = texture2D(srcTex, vUv + vec2(pixelSize.x,-pixelSize.y));\r\n vec4 c10 = texture2D(srcTex, vUv + vec2(-pixelSize.x,0));\r\n vec4 c12 = texture2D(srcTex, vUv + vec2(pixelSize.x,0));\r\n vec4 c20 = texture2D(srcTex, vUv + vec2(-pixelSize.x,pixelSize.y));\r\n vec4 c21 = texture2D(srcTex, vUv + vec2(0,pixelSize.y));\r\n vec4 c22 = texture2D(srcTex, vUv + vec2(pixelSize.x,pixelSize.y));\r\n\r\n vec4 horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n vec4 vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n vec4 grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n gl_FragColor = grad;\r\n #endif\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/OutlineMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/Outline.frag +const Outline_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexSize;\r\nuniform vec2 thickness;\r\nvarying vec2 vUv;\r\n\r\n#ifdef DEPTH_OUTLINE\r\n uniform sampler2D srcDepthTex; //depthTexture\r\n uniform vec3 color;\r\n uniform float threshold;\r\n#endif\r\n\r\nvoid main() {\r\n\r\n vec2 pixelSize = thickness / srcTexSize;\r\n\r\n #ifdef DEPTH_OUTLINE\r\n float c00 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,-pixelSize.y)).x;\r\n float c01 = texture2D(srcDepthTex, vUv + vec2(0,-pixelSize.y)).x;\r\n float c02 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,-pixelSize.y)).x;\r\n float c10 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,0)).x;\r\n float c12 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,0)).x;\r\n float c20 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,pixelSize.y)).x;\r\n float c21 = texture2D(srcDepthTex, vUv + vec2(0,pixelSize.y)).x;\r\n float c22 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,pixelSize.y)).x;\r\n\r\n float horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n float vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n float grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n\r\n gl_FragColor = ( grad > threshold ) ? vec4(color.rgb, 1.0) : gl_FragColor = texture2D(srcTex, vUv);\r\n\r\n #else\r\n vec4 c00 = texture2D(srcTex, vUv + vec2(-pixelSize.x,-pixelSize.y));\r\n vec4 c01 = texture2D(srcTex, vUv + vec2(0,-pixelSize.y));\r\n vec4 c02 = texture2D(srcTex, vUv + vec2(pixelSize.x,-pixelSize.y));\r\n vec4 c10 = texture2D(srcTex, vUv + vec2(-pixelSize.x,0));\r\n vec4 c12 = texture2D(srcTex, vUv + vec2(pixelSize.x,0));\r\n vec4 c20 = texture2D(srcTex, vUv + vec2(-pixelSize.x,pixelSize.y));\r\n vec4 c21 = texture2D(srcTex, vUv + vec2(0,pixelSize.y));\r\n vec4 c22 = texture2D(srcTex, vUv + vec2(pixelSize.x,pixelSize.y));\r\n\r\n vec4 horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n vec4 vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n vec4 grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n gl_FragColor = grad;\r\n #endif\r\n}\r\n"; +;// ./src/gfx/shaders/OutlineMaterial.js @@ -30646,11 +30659,9 @@ class OutlineMaterial extends external_module_three_commonjs_three_commonjs2_thr } OutlineMaterial.prototype.depth = false; /* harmony default export */ const shaders_OutlineMaterial = (OutlineMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/FXAA.frag -const FXAA_namespaceObject = "precision highp float;\r\n\r\n// edge end finding algorithm parameters\r\n#define FXAA_QUALITY_PS 8\r\n#define FXAA_QUALITY_P0 1.0\r\n#define FXAA_QUALITY_P1 1.5\r\n#define FXAA_QUALITY_P2 2.0\r\n#define FXAA_QUALITY_P3 2.0\r\n#define FXAA_QUALITY_P4 2.0\r\n#define FXAA_QUALITY_P5 2.0\r\n#define FXAA_QUALITY_P6 4.0\r\n#define FXAA_QUALITY_P7 12.0\r\n// constants\r\nfloat fxaaQualityEdgeThreshold = 0.125;\r\nfloat fxaaQualityEdgeThresholdMin = 0.0625;\r\nfloat fxaaQualitySubpix = 0.7; //0.65;\r\n// global params\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexelSize;\r\nuniform vec3 bgColor;\r\n// from vs\r\nvarying vec2 vUv;\r\n//=====================================================================//\r\n// calc luminance from rgb\r\n//'float FxaaLuma(vec3 rgb) {return rgb.y * (0.587/0.299) + rgb.x; } // Lotte's idea about game luminance\r\nfloat FxaaLuma(vec3 rgb) {return dot(rgb, vec3(0.299, 0.587, 0.114)); } // real luminance calculation\r\n // for non-real scene rendering\r\n// texture sampling by pixel position(coords) and offset(in pixels)\r\n vec3 FxaaTex(sampler2D tex, vec2 pos, vec2 off, vec2 res ) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos + off * res );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos + off * res ).xyz;\r\n #endif\r\n}\r\nvec3 FxaaTexTop(sampler2D tex, vec2 pos) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos).xyz;\r\n #endif\r\n}\r\nvec4 FxaaTexTopAlpha(sampler2D tex, vec2 pos) {\r\n return texture2D( tex, pos);\r\n}\r\n\r\n//=====================================================================//\r\nvoid main() {\r\n // renaming\r\n vec2 posM = vUv;\r\n // get luminance for neighbours\r\n float lumaS = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, 1.0 ), srcTexelSize));\r\n float lumaE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 0.0 ), srcTexelSize));\r\n float lumaN = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, -1.0 ), srcTexelSize));\r\n float lumaW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 0.0 ), srcTexelSize));\r\n float lumaM = FxaaLuma(FxaaTexTop(srcTex, posM));\r\n // find max and min luminance\r\n float rangeMax = max(max(lumaN, lumaW), max(lumaE, max(lumaS, lumaM)));\r\n float rangeMin = min(min(lumaN, lumaW), min(lumaE, min(lumaS, lumaM)));\r\n // calc maximum non-edge range\r\n float rangeMaxScaled = rangeMax * fxaaQualityEdgeThreshold;\r\n float range = rangeMax - rangeMin;\r\n float rangeMaxClamped = max(fxaaQualityEdgeThresholdMin, rangeMaxScaled);\r\n // exit when luma contrast is small (is not edge)\r\n if(range < rangeMaxClamped){\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n return;\r\n }\r\n float subpixRcpRange = 1.0/range;\r\n // note: the sampling coordinates can be calculated in vertex shader but the approach doesn't affect performance\r\n // visibly, thus we decided to leave calculation here for better readability.\r\n // calc other neighbours luminance\r\n float lumaNE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, -1.0 ), srcTexelSize));\r\n float lumaSW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 1.0 ), srcTexelSize));\r\n float lumaSE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 1.0 ), srcTexelSize));\r\n float lumaNW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, -1.0 ), srcTexelSize));\r\n/*--------------span calculation and subpix amount calulation-----------------*/\r\n float lumaNS = lumaN + lumaS;\r\n float lumaWE = lumaW + lumaE;\r\n float subpixNSWE = lumaNS + lumaWE;\r\n float edgeHorz1 = (-2.0 * lumaM) + lumaNS;\r\n float edgeVert1 = (-2.0 * lumaM) + lumaWE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNESE = lumaNE + lumaSE;\r\n float lumaNWNE = lumaNW + lumaNE;\r\n float edgeHorz2 = (-2.0 * lumaE) + lumaNESE;\r\n float edgeVert2 = (-2.0 * lumaN) + lumaNWNE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNWSW = lumaNW + lumaSW;\r\n float lumaSWSE = lumaSW + lumaSE;\r\n float edgeHorz4 = (abs(edgeHorz1) * 2.0) + abs(edgeHorz2);\r\n float edgeVert4 = (abs(edgeVert1) * 2.0) + abs(edgeVert2);\r\n float edgeHorz3 = (-2.0 * lumaW) + lumaNWSW;\r\n float edgeVert3 = (-2.0 * lumaS) + lumaSWSE;\r\n float edgeHorz = abs(edgeHorz3) + edgeHorz4;\r\n float edgeVert = abs(edgeVert3) + edgeVert4;\r\n/*--------------------subpix amount calulation------------------------------*/\r\n float subpixNWSWNESE = lumaNWSW + lumaNESE;\r\n float lengthSign = srcTexelSize.x;\r\n bool horzSpan = edgeHorz >= edgeVert;\r\n // debug code edge span visualization\r\n/*' if (horzSpan)\r\n gl_FragColor = vec4(0.0, 0.0, 1.0, 1.0);\r\n else\r\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\r\n return;*/\r\n float subpixA = subpixNSWE * 2.0 + subpixNWSWNESE;\r\n/*--------------------------------------------------------------------------*/\r\n if(!horzSpan) lumaN = lumaW;\r\n if(!horzSpan) lumaS = lumaE;\r\n if(horzSpan) lengthSign = srcTexelSize.y;\r\n float subpixB = (subpixA * (1.0/12.0)) - lumaM;\r\n/*--------------------------------------------------------------------------*/\r\n float gradientN = lumaN - lumaM;\r\n float gradientS = lumaS - lumaM;\r\n float lumaNN = lumaN + lumaM;\r\n float lumaSS = lumaS + lumaM;\r\n bool pairN = abs(gradientN) >= abs(gradientS);\r\n float gradient = max(abs(gradientN), abs(gradientS));\r\n if(pairN) lengthSign = -lengthSign;\r\n float subpixC = clamp(abs(subpixB) * subpixRcpRange, 0.0, 1.0);\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posB;\r\n posB = posM;\r\n vec2 offNP;\r\n offNP.x = (!horzSpan) ? 0.0 : srcTexelSize.x;\r\n offNP.y = ( horzSpan) ? 0.0 : srcTexelSize.y;\r\n if(!horzSpan) posB.x += lengthSign * 0.5;\r\n if( horzSpan) posB.y += lengthSign * 0.5;\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posN;\r\n posN = posB - offNP * FXAA_QUALITY_P0;\r\n vec2 posP;\r\n posP = posB + offNP * FXAA_QUALITY_P0;\r\n float subpixD = ((-2.0)*subpixC) + 3.0;\r\n float lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN));\r\n float subpixE = subpixC * subpixC;\r\n float lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP));\r\n/*--------------------------------------------------------------------------*/\r\n if(!pairN) lumaNN = lumaSS;\r\n float gradientScaled = gradient * 1.0/4.0;\r\n float lumaMM = lumaM - lumaNN * 0.5;\r\n float subpixF = subpixD * subpixE;\r\n bool lumaMLTZero = lumaMM < 0.0;\r\n/*---------------------looped edge-end search-------------------------------*/\r\n lumaEndN -= lumaNN * 0.5;\r\n lumaEndP -= lumaNN * 0.5;\r\n bool doneN = abs(lumaEndN) >= gradientScaled;\r\n bool doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P1;\r\n bool doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P1;\r\n/*--------------------------------------------------------------------------*/\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P2;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P2;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 3)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P3;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P3;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 4)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P4;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P4;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 5)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P5;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P5;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 6)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P6;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P6;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 7)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P7;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P7;\r\n/*--------------------------------------------------------------------------*/\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n/*----------------calculate subpix offset due to edge ends-------------------*/\r\n float dstN = posM.x - posN.x;\r\n float dstP = posP.x - posM.x;\r\n if(!horzSpan) dstN = posM.y - posN.y;\r\n if(!horzSpan) dstP = posP.y - posM.y;\r\n/*--------------------------------------------------------------------------*/\r\n bool goodSpanN = (lumaEndN < 0.0) != lumaMLTZero;\r\n float spanLength = (dstP + dstN);\r\n bool goodSpanP = (lumaEndP < 0.0) != lumaMLTZero;\r\n float spanLengthRcp = 1.0 / spanLength;\r\n/*--------------------------------------------------------------------------*/\r\n bool directionN = dstN < dstP;\r\n float dst = min(dstN, dstP);\r\n bool goodSpan = directionN ? goodSpanN : goodSpanP;\r\n float subpixG = subpixF * subpixF;\r\n float pixelOffset = (dst * (-spanLengthRcp)) + 0.5;\r\n float subpixH = subpixG * fxaaQualitySubpix;\r\n/*-----------------calc texture offest using subpix-------------------------*/\r\n float pixelOffsetGood = goodSpan ? pixelOffset : 0.0;\r\n float pixelOffsetSubpix = max(pixelOffsetGood, subpixH);\r\n\r\n float offset = pixelOffsetSubpix * lengthSign;\r\n #ifdef BG_TRANSPARENT\r\n // get original texel\r\n vec4 rgbaA = FxaaTexTopAlpha(srcTex, posM);\r\n // calc step to blended texel\r\n vec2 step = sign((!horzSpan) ? vec2 (offset, 0.0) : vec2 (0.0, offset));\r\n // get neighboring texel\r\n vec4 rgbaB = FxaaTexTopAlpha(srcTex, posM + step * srcTexelSize);\r\n // calc blend factor from offset\r\n float f = (!horzSpan) ? offset / srcTexelSize.x : offset / srcTexelSize.y;\r\n f = abs(f);\r\n // calc alpha (special formula to emulate blending with bg)\r\n gl_FragColor.a = 1.0 - mix(1.0 - rgbaA.a, 1.0 - rgbaB.a, f);\r\n // calc color (special formula to emulate blending with bg)\r\n gl_FragColor.rgb = mix(rgbaA.rgb * rgbaA.a, rgbaB.rgb * rgbaB.a, f) / gl_FragColor.a;\r\n #else\r\n if(!horzSpan) {\r\n posM.x += offset;\r\n } else {\r\n posM.y += offset;\r\n }\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n #endif\r\n return;\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/FXAAMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/FXAA.frag +const FXAA_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\n// edge end finding algorithm parameters\r\n#define FXAA_QUALITY_PS 8\r\n#define FXAA_QUALITY_P0 1.0\r\n#define FXAA_QUALITY_P1 1.5\r\n#define FXAA_QUALITY_P2 2.0\r\n#define FXAA_QUALITY_P3 2.0\r\n#define FXAA_QUALITY_P4 2.0\r\n#define FXAA_QUALITY_P5 2.0\r\n#define FXAA_QUALITY_P6 4.0\r\n#define FXAA_QUALITY_P7 12.0\r\n// constants\r\nfloat fxaaQualityEdgeThreshold = 0.125;\r\nfloat fxaaQualityEdgeThresholdMin = 0.0625;\r\nfloat fxaaQualitySubpix = 0.7; //0.65;\r\n// global params\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexelSize;\r\nuniform vec3 bgColor;\r\n// from vs\r\nvarying vec2 vUv;\r\n//=====================================================================//\r\n// calc luminance from rgb\r\n//'float FxaaLuma(vec3 rgb) {return rgb.y * (0.587/0.299) + rgb.x; } // Lotte's idea about game luminance\r\nfloat FxaaLuma(vec3 rgb) {return dot(rgb, vec3(0.299, 0.587, 0.114)); } // real luminance calculation\r\n // for non-real scene rendering\r\n// texture sampling by pixel position(coords) and offset(in pixels)\r\n vec3 FxaaTex(sampler2D tex, vec2 pos, vec2 off, vec2 res ) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos + off * res );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos + off * res ).xyz;\r\n #endif\r\n}\r\nvec3 FxaaTexTop(sampler2D tex, vec2 pos) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos).xyz;\r\n #endif\r\n}\r\nvec4 FxaaTexTopAlpha(sampler2D tex, vec2 pos) {\r\n return texture2D( tex, pos);\r\n}\r\n\r\n//=====================================================================//\r\nvoid main() {\r\n // renaming\r\n vec2 posM = vUv;\r\n // get luminance for neighbours\r\n float lumaS = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, 1.0 ), srcTexelSize));\r\n float lumaE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 0.0 ), srcTexelSize));\r\n float lumaN = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, -1.0 ), srcTexelSize));\r\n float lumaW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 0.0 ), srcTexelSize));\r\n float lumaM = FxaaLuma(FxaaTexTop(srcTex, posM));\r\n // find max and min luminance\r\n float rangeMax = max(max(lumaN, lumaW), max(lumaE, max(lumaS, lumaM)));\r\n float rangeMin = min(min(lumaN, lumaW), min(lumaE, min(lumaS, lumaM)));\r\n // calc maximum non-edge range\r\n float rangeMaxScaled = rangeMax * fxaaQualityEdgeThreshold;\r\n float range = rangeMax - rangeMin;\r\n float rangeMaxClamped = max(fxaaQualityEdgeThresholdMin, rangeMaxScaled);\r\n // exit when luma contrast is small (is not edge)\r\n if(range < rangeMaxClamped){\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n return;\r\n }\r\n float subpixRcpRange = 1.0/range;\r\n // note: the sampling coordinates can be calculated in vertex shader but the approach doesn't affect performance\r\n // visibly, thus we decided to leave calculation here for better readability.\r\n // calc other neighbours luminance\r\n float lumaNE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, -1.0 ), srcTexelSize));\r\n float lumaSW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 1.0 ), srcTexelSize));\r\n float lumaSE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 1.0 ), srcTexelSize));\r\n float lumaNW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, -1.0 ), srcTexelSize));\r\n/*--------------span calculation and subpix amount calulation-----------------*/\r\n float lumaNS = lumaN + lumaS;\r\n float lumaWE = lumaW + lumaE;\r\n float subpixNSWE = lumaNS + lumaWE;\r\n float edgeHorz1 = (-2.0 * lumaM) + lumaNS;\r\n float edgeVert1 = (-2.0 * lumaM) + lumaWE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNESE = lumaNE + lumaSE;\r\n float lumaNWNE = lumaNW + lumaNE;\r\n float edgeHorz2 = (-2.0 * lumaE) + lumaNESE;\r\n float edgeVert2 = (-2.0 * lumaN) + lumaNWNE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNWSW = lumaNW + lumaSW;\r\n float lumaSWSE = lumaSW + lumaSE;\r\n float edgeHorz4 = (abs(edgeHorz1) * 2.0) + abs(edgeHorz2);\r\n float edgeVert4 = (abs(edgeVert1) * 2.0) + abs(edgeVert2);\r\n float edgeHorz3 = (-2.0 * lumaW) + lumaNWSW;\r\n float edgeVert3 = (-2.0 * lumaS) + lumaSWSE;\r\n float edgeHorz = abs(edgeHorz3) + edgeHorz4;\r\n float edgeVert = abs(edgeVert3) + edgeVert4;\r\n/*--------------------subpix amount calulation------------------------------*/\r\n float subpixNWSWNESE = lumaNWSW + lumaNESE;\r\n float lengthSign = srcTexelSize.x;\r\n bool horzSpan = edgeHorz >= edgeVert;\r\n // debug code edge span visualization\r\n/*' if (horzSpan)\r\n gl_FragColor = vec4(0.0, 0.0, 1.0, 1.0);\r\n else\r\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\r\n return;*/\r\n float subpixA = subpixNSWE * 2.0 + subpixNWSWNESE;\r\n/*--------------------------------------------------------------------------*/\r\n if(!horzSpan) lumaN = lumaW;\r\n if(!horzSpan) lumaS = lumaE;\r\n if(horzSpan) lengthSign = srcTexelSize.y;\r\n float subpixB = (subpixA * (1.0/12.0)) - lumaM;\r\n/*--------------------------------------------------------------------------*/\r\n float gradientN = lumaN - lumaM;\r\n float gradientS = lumaS - lumaM;\r\n float lumaNN = lumaN + lumaM;\r\n float lumaSS = lumaS + lumaM;\r\n bool pairN = abs(gradientN) >= abs(gradientS);\r\n float gradient = max(abs(gradientN), abs(gradientS));\r\n if(pairN) lengthSign = -lengthSign;\r\n float subpixC = clamp(abs(subpixB) * subpixRcpRange, 0.0, 1.0);\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posB;\r\n posB = posM;\r\n vec2 offNP;\r\n offNP.x = (!horzSpan) ? 0.0 : srcTexelSize.x;\r\n offNP.y = ( horzSpan) ? 0.0 : srcTexelSize.y;\r\n if(!horzSpan) posB.x += lengthSign * 0.5;\r\n if( horzSpan) posB.y += lengthSign * 0.5;\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posN;\r\n posN = posB - offNP * FXAA_QUALITY_P0;\r\n vec2 posP;\r\n posP = posB + offNP * FXAA_QUALITY_P0;\r\n float subpixD = ((-2.0)*subpixC) + 3.0;\r\n float lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN));\r\n float subpixE = subpixC * subpixC;\r\n float lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP));\r\n/*--------------------------------------------------------------------------*/\r\n if(!pairN) lumaNN = lumaSS;\r\n float gradientScaled = gradient * 1.0/4.0;\r\n float lumaMM = lumaM - lumaNN * 0.5;\r\n float subpixF = subpixD * subpixE;\r\n bool lumaMLTZero = lumaMM < 0.0;\r\n/*---------------------looped edge-end search-------------------------------*/\r\n lumaEndN -= lumaNN * 0.5;\r\n lumaEndP -= lumaNN * 0.5;\r\n bool doneN = abs(lumaEndN) >= gradientScaled;\r\n bool doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P1;\r\n bool doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P1;\r\n/*--------------------------------------------------------------------------*/\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P2;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P2;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 3)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P3;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P3;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 4)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P4;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P4;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 5)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P5;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P5;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 6)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P6;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P6;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 7)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P7;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P7;\r\n/*--------------------------------------------------------------------------*/\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n/*----------------calculate subpix offset due to edge ends-------------------*/\r\n float dstN = posM.x - posN.x;\r\n float dstP = posP.x - posM.x;\r\n if(!horzSpan) dstN = posM.y - posN.y;\r\n if(!horzSpan) dstP = posP.y - posM.y;\r\n/*--------------------------------------------------------------------------*/\r\n bool goodSpanN = (lumaEndN < 0.0) != lumaMLTZero;\r\n float spanLength = (dstP + dstN);\r\n bool goodSpanP = (lumaEndP < 0.0) != lumaMLTZero;\r\n float spanLengthRcp = 1.0 / spanLength;\r\n/*--------------------------------------------------------------------------*/\r\n bool directionN = dstN < dstP;\r\n float dst = min(dstN, dstP);\r\n bool goodSpan = directionN ? goodSpanN : goodSpanP;\r\n float subpixG = subpixF * subpixF;\r\n float pixelOffset = (dst * (-spanLengthRcp)) + 0.5;\r\n float subpixH = subpixG * fxaaQualitySubpix;\r\n/*-----------------calc texture offest using subpix-------------------------*/\r\n float pixelOffsetGood = goodSpan ? pixelOffset : 0.0;\r\n float pixelOffsetSubpix = max(pixelOffsetGood, subpixH);\r\n\r\n float offset = pixelOffsetSubpix * lengthSign;\r\n #ifdef BG_TRANSPARENT\r\n // get original texel\r\n vec4 rgbaA = FxaaTexTopAlpha(srcTex, posM);\r\n // calc step to blended texel\r\n vec2 step = sign((!horzSpan) ? vec2 (offset, 0.0) : vec2 (0.0, offset));\r\n // get neighboring texel\r\n vec4 rgbaB = FxaaTexTopAlpha(srcTex, posM + step * srcTexelSize);\r\n // calc blend factor from offset\r\n float f = (!horzSpan) ? offset / srcTexelSize.x : offset / srcTexelSize.y;\r\n f = abs(f);\r\n // calc alpha (special formula to emulate blending with bg)\r\n gl_FragColor.a = 1.0 - mix(1.0 - rgbaA.a, 1.0 - rgbaB.a, f);\r\n // calc color (special formula to emulate blending with bg)\r\n gl_FragColor.rgb = mix(rgbaA.rgb * rgbaA.a, rgbaB.rgb * rgbaB.a, f) / gl_FragColor.a;\r\n #else\r\n if(!horzSpan) {\r\n posM.x += offset;\r\n } else {\r\n posM.y += offset;\r\n }\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n #endif\r\n return;\r\n}\r\n"; +;// ./src/gfx/shaders/FXAAMaterial.js @@ -30703,11 +30714,9 @@ class FXAAMaterial extends external_module_three_commonjs_three_commonjs2_three_ } FXAAMaterial.prototype.bgTransparent = false; /* harmony default export */ const shaders_FXAAMaterial = (FXAAMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/AO.frag -const AO_namespaceObject = "precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 32\r\nuniform vec3 samplesKernel[MAX_SAMPLES_COUNT];\r\nuniform sampler2D noiseTexture;\r\nuniform vec2 noiseTexelSize;\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D depthTexture;\r\nuniform sampler2D normalTexture;\r\nuniform vec2 srcTexelSize;\r\nuniform vec2 camNearFar;\r\nuniform mat4 projMatrix;\r\n\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\nuniform float kernelRadius;\r\nuniform float depthThreshold;\r\nuniform float factor;\r\n\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n // remap coordinates to prevent noise exture rescale\r\n vec2 vUvNoise = vUv / srcTexelSize * noiseTexelSize;\r\n vec4 normalData = texture2D(normalTexture, vUv);\r\n // return for background fragments (their normals are zero vectors)\r\n if (length(normalData.rgb) < EPSILON) {\r\n // 0.0 in alpha component means that it is background fragment\r\n gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);\r\n return;\r\n }\r\n //[0, 1] -> [-1, 1]\r\n vec3 normal = (normalData.rgb * 2.0 - 1.0);\r\n // normalData.a store 1.0 if normal was build for frontfaced surface\r\n // and 0.0 in other case\r\n if (normalData.a < EPSILON) {\r\n normal *= -1.0;\r\n }\r\n // get random vector for sampling sphere rotation\r\n vec3 randN = texture2D(noiseTexture, vUvNoise).rgb * 2.0 - 1.0;\r\n randN = normalize(randN);\r\n // build TBN (randomly rotated around normal)\r\n vec3 tangent = normalize(randN - normal * dot(randN, normal));\r\n vec3 bitangent = cross(tangent, normal);\r\n mat3 TBN = mat3(tangent, bitangent, normal);\r\n // calc AO value\r\n float AO = 0.0;\r\n for (int i = 0 ; i < MAX_SAMPLES_COUNT ; i++) {\r\n // rotate sampling kernel around normal\r\n vec3 reflectedSample = TBN * samplesKernel[i];\r\n // get sample\r\n vec3 samplePos = viewPos + reflectedSample * kernelRadius;\r\n\r\n // project sample to screen to get sample's screen pos\r\n vec4 SampleScrPos = vec4(samplePos, 1.0);\r\n // eye -> clip\r\n SampleScrPos = projMatrix * SampleScrPos;\r\n // normalize\r\n SampleScrPos.xy /= SampleScrPos.w;\r\n //[-1, 1] -> [0, 1]\r\n SampleScrPos.xy = (SampleScrPos.xy + vec2(1.0)) * 0.5;\r\n\r\n // get view z for sample projected to the objct surface\r\n float sampleDepth = CalcViewZ(SampleScrPos.xy);\r\n // calc occlusion made by object surface at the sample\r\n AO += step(samplePos.z, sampleDepth);\r\n }\r\n // calc result AO-map color\r\n AO = 1.0 - max(0.0, AO / float(MAX_SAMPLES_COUNT) * factor);\r\n // write value to AO-map\r\n gl_FragColor = vec4(AO, AO, AO, 1.0);\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/AOMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/AO.frag +const AO_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 32\r\nuniform vec3 samplesKernel[MAX_SAMPLES_COUNT];\r\nuniform sampler2D noiseTexture;\r\nuniform vec2 noiseTexelSize;\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D depthTexture;\r\nuniform sampler2D normalTexture;\r\nuniform vec2 srcTexelSize;\r\nuniform vec2 camNearFar;\r\nuniform mat4 projMatrix;\r\n\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\nuniform float kernelRadius;\r\nuniform float depthThreshold;\r\nuniform float factor;\r\n\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n // remap coordinates to prevent noise exture rescale\r\n vec2 vUvNoise = vUv / srcTexelSize * noiseTexelSize;\r\n vec4 normalData = texture2D(normalTexture, vUv);\r\n // return for background fragments (their normals are zero vectors)\r\n if (length(normalData.rgb) < EPSILON) {\r\n // 0.0 in alpha component means that it is background fragment\r\n gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);\r\n return;\r\n }\r\n //[0, 1] -> [-1, 1]\r\n vec3 normal = (normalData.rgb * 2.0 - 1.0);\r\n // normalData.a store 1.0 if normal was build for frontfaced surface\r\n // and 0.0 in other case\r\n if (normalData.a < EPSILON) {\r\n normal *= -1.0;\r\n }\r\n // get random vector for sampling sphere rotation\r\n vec3 randN = texture2D(noiseTexture, vUvNoise).rgb * 2.0 - 1.0;\r\n randN = normalize(randN);\r\n // build TBN (randomly rotated around normal)\r\n vec3 tangent = normalize(randN - normal * dot(randN, normal));\r\n vec3 bitangent = cross(tangent, normal);\r\n mat3 TBN = mat3(tangent, bitangent, normal);\r\n // calc AO value\r\n float AO = 0.0;\r\n for (int i = 0 ; i < MAX_SAMPLES_COUNT ; i++) {\r\n // rotate sampling kernel around normal\r\n vec3 reflectedSample = TBN * samplesKernel[i];\r\n // get sample\r\n vec3 samplePos = viewPos + reflectedSample * kernelRadius;\r\n\r\n // project sample to screen to get sample's screen pos\r\n vec4 SampleScrPos = vec4(samplePos, 1.0);\r\n // eye -> clip\r\n SampleScrPos = projMatrix * SampleScrPos;\r\n // normalize\r\n SampleScrPos.xy /= SampleScrPos.w;\r\n //[-1, 1] -> [0, 1]\r\n SampleScrPos.xy = (SampleScrPos.xy + vec2(1.0)) * 0.5;\r\n\r\n // get view z for sample projected to the objct surface\r\n float sampleDepth = CalcViewZ(SampleScrPos.xy);\r\n // calc occlusion made by object surface at the sample\r\n AO += step(samplePos.z, sampleDepth);\r\n }\r\n // calc result AO-map color\r\n AO = 1.0 - max(0.0, AO / float(MAX_SAMPLES_COUNT) * factor);\r\n // write value to AO-map\r\n gl_FragColor = vec4(AO, AO, AO, 1.0);\r\n}\r\n"; +;// ./src/gfx/shaders/AOMaterial.js @@ -30788,11 +30797,9 @@ class AOMaterial extends external_module_three_commonjs_three_commonjs2_three_am } } /* harmony default export */ const shaders_AOMaterial = (AOMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/AOHorBlur.frag -const AOHorBlur_namespaceObject = "precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = res;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x + samplesOffsets[i] * srcTexelSize.x, y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb = res.rgb / weightSum;\r\n gl_FragColor = res;\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/AOHorBlurMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/AOHorBlur.frag +const AOHorBlur_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = res;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x + samplesOffsets[i] * srcTexelSize.x, y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb = res.rgb / weightSum;\r\n gl_FragColor = res;\r\n}\r\n"; +;// ./src/gfx/shaders/AOHorBlurMaterial.js @@ -30830,11 +30837,9 @@ class AOHorBlurMaterial extends external_module_three_commonjs_three_commonjs2_t } } /* harmony default export */ const shaders_AOHorBlurMaterial = (AOHorBlurMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/AOVertBlurWithBlend.frag -const AOVertBlurWithBlend_namespaceObject = "precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nuniform mat4 projMatrix;\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\n#ifdef USE_FOG\r\n uniform vec2 fogNearFar;\r\n uniform vec4 fogColor;\r\n#endif\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 color = texture2D(diffuseTexture, vec2(x, y));\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = color;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x, y + samplesOffsets[i] * srcTexelSize.y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb /= weightSum;\r\n\r\n #if defined(USE_FOG) && !defined(FOG_TRANSPARENT)\r\n // Add fog to the result value\r\n // Proper way to get an image with fog and ao requires formula:\r\n // gl_FragColor = fragColor*AO*(1-fogFactor) + fogColor*fogFactor\r\n // But we have already fogged molecule to add AO too. Let's split the straight formula into our real steps!\r\n // We have: AO, fogFactor, fogColor,\r\n // color = fragColor*(1-fogFactor) + fogColor*fogFactor (it comes from diffuseTexture,\r\n // where molecule has been already drawn with fog)\r\n // Transform:\r\n // fragColor*AO*(1-fogFactor) + fogColor*fogFactor =\r\n // = [fragColor*(1-fogFactor) = color - fogColor*fogFactor] =\r\n // = (color - fogColor*fogFactor)*AO + fogColor*fogFactor =\r\n // = color*AO + fogColor*fogFactor*(1 - AO)\r\n // Result: gl_FragColor = color*AO + fogColor*fogFactor*(1 - AO)\r\n float fogFactor = smoothstep(fogNearFar.x, fogNearFar.y, - viewPos.z) * fogColor.a;\r\n gl_FragColor.rgb = color.rgb * res.rgb + fogColor.rgb * fogFactor *(vec3(1.0, 1.0, 1.0) - res.rgb);\r\n #else\r\n gl_FragColor.rgb = color.rgb * res.rgb;\r\n #endif\r\n gl_FragColor.a = color.a;\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/AOVertBlurWithBlendMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/AOVertBlurWithBlend.frag +const AOVertBlurWithBlend_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nuniform mat4 projMatrix;\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\n#ifdef USE_FOG\r\n uniform vec2 fogNearFar;\r\n uniform vec4 fogColor;\r\n#endif\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 color = texture2D(diffuseTexture, vec2(x, y));\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = color;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x, y + samplesOffsets[i] * srcTexelSize.y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb /= weightSum;\r\n\r\n #if defined(USE_FOG) && !defined(FOG_TRANSPARENT)\r\n // Add fog to the result value\r\n // Proper way to get an image with fog and ao requires formula:\r\n // gl_FragColor = fragColor*AO*(1-fogFactor) + fogColor*fogFactor\r\n // But we have already fogged molecule to add AO too. Let's split the straight formula into our real steps!\r\n // We have: AO, fogFactor, fogColor,\r\n // color = fragColor*(1-fogFactor) + fogColor*fogFactor (it comes from diffuseTexture,\r\n // where molecule has been already drawn with fog)\r\n // Transform:\r\n // fragColor*AO*(1-fogFactor) + fogColor*fogFactor =\r\n // = [fragColor*(1-fogFactor) = color - fogColor*fogFactor] =\r\n // = (color - fogColor*fogFactor)*AO + fogColor*fogFactor =\r\n // = color*AO + fogColor*fogFactor*(1 - AO)\r\n // Result: gl_FragColor = color*AO + fogColor*fogFactor*(1 - AO)\r\n float fogFactor = smoothstep(fogNearFar.x, fogNearFar.y, - viewPos.z) * fogColor.a;\r\n gl_FragColor.rgb = color.rgb * res.rgb + fogColor.rgb * fogFactor *(vec3(1.0, 1.0, 1.0) - res.rgb);\r\n #else\r\n gl_FragColor.rgb = color.rgb * res.rgb;\r\n #endif\r\n gl_FragColor.a = color.a;\r\n}\r\n"; +;// ./src/gfx/shaders/AOVertBlurWithBlendMaterial.js @@ -30916,11 +30921,9 @@ class AOVertBlurWithBlendMaterial extends external_module_three_commonjs_three_c AOVertBlurWithBlendMaterial.prototype.useFog = true; AOVertBlurWithBlendMaterial.prototype.fogTransparent = false; /* harmony default export */ const shaders_AOVertBlurWithBlendMaterial = (AOVertBlurWithBlendMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/Anaglyph.frag -const Anaglyph_namespaceObject = "precision highp float;\r\n\r\nuniform sampler2D srcL;\r\nuniform sampler2D srcR;\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vec4 l = texture2D(srcL, vUv);\r\n vec4 r = texture2D(srcR, vUv);\r\n gl_FragColor = vec4(l.r, r.g, r.b, 1.0);\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/AnaglyphMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/Anaglyph.frag +const Anaglyph_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nuniform sampler2D srcL;\r\nuniform sampler2D srcR;\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vec4 l = texture2D(srcL, vUv);\r\n vec4 r = texture2D(srcR, vUv);\r\n gl_FragColor = vec4(l.r, r.g, r.b, 1.0);\r\n}\r\n"; +;// ./src/gfx/shaders/AnaglyphMaterial.js @@ -30948,7 +30951,7 @@ class AnaglyphMaterial extends external_module_three_commonjs_three_commonjs2_th } } /* harmony default export */ const shaders_AnaglyphMaterial = (AnaglyphMaterial); -;// CONCATENATED MODULE: ./src/gfx/ViewInterpolator.js +;// ./src/gfx/ViewInterpolator.js class View { @@ -31030,7 +31033,7 @@ class ViewInterpolator { return new View(); } } -;// CONCATENATED MODULE: ./src/utils/Cookies.js +;// ./src/utils/Cookies.js const MAX_COOKIE_LEN = 4000; @@ -31139,7 +31142,7 @@ Cookies.prototype._exists = function (key) { return document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`)); }; /* harmony default export */ const utils_Cookies = (Cookies); -;// CONCATENATED MODULE: ./src/gfx/vr/createWebVRButton.js +;// ./src/gfx/vr/createWebVRButton.js /* * Toggling WebVR is done through button.click because of limitations on calling requestPresent in webVR: * VRDisplay::requestPresent should be called from user gesture: @@ -31153,7 +31156,7 @@ Cookies.prototype._exists = function (key) { button.style.width = '100px'; button.textContent = 'ENTER VR'; let currentSession = null; - function onSessionEnded( /* event */ + function onSessionEnded(/* event */ ) { currentSession.removeEventListener('end', onSessionEnded); button.textContent = 'ENTER VR'; @@ -31231,7 +31234,7 @@ Cookies.prototype._exists = function (key) { stylizeElement(message); return message; } -;// CONCATENATED MODULE: ./src/gfx/vr/WebVRPoC.js +;// ./src/gfx/vr/WebVRPoC.js @@ -31482,9 +31485,9 @@ class WebVRPoC { return gfx && gfx.renderer ? gfx.renderer.domElement : null; } } -;// CONCATENATED MODULE: ./src/gfx/shaders/ScreenQuadFromDistortionTex.frag -const ScreenQuadFromDistortionTex_namespaceObject = "precision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform vec3 aberration;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n \r\n gl_FragColor.r = texture2D(srcTex, 0.5 * (uv * aberration[0] + 1.0)).r;\r\n gl_FragColor.g = texture2D(srcTex, 0.5 * (uv * aberration[1] + 1.0)).g;\r\n gl_FragColor.b = texture2D(srcTex, 0.5 * (uv * aberration[2] + 1.0)).b;\r\n gl_FragColor.a = 1.0;\r\n}"; -;// CONCATENATED MODULE: ./src/Miew.js +;// ./src/gfx/shaders/ScreenQuadFromDistortionTex.frag +const ScreenQuadFromDistortionTex_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform vec3 aberration;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n \r\n gl_FragColor.r = texture2D(srcTex, 0.5 * (uv * aberration[0] + 1.0)).r;\r\n gl_FragColor.g = texture2D(srcTex, 0.5 * (uv * aberration[1] + 1.0)).g;\r\n gl_FragColor.b = texture2D(srcTex, 0.5 * (uv * aberration[2] + 1.0)).b;\r\n gl_FragColor.a = 1.0;\r\n}"; +;// ./src/Miew.js /* global PACKAGE_VERSION:false */ @@ -31877,12 +31880,6 @@ Miew.prototype._requestAnimationFrame = function (callback) { } requestAnimationFrame(callback); }; -function arezSpritesSupported(context) { - return context.getExtension('EXT_frag_depth'); -} -function isAOSupported(context) { - return context.getExtension('WEBGL_depth_texture') && context.getExtension('WEBGL_draw_buffers'); -} /** * Initialize WebGL and set 3D scene up. @@ -31902,19 +31899,11 @@ Miew.prototype._initGfx = function () { webGLOptions.antialias = true; } gfx.renderer2d = new gfx_CSS2DRenderer(); - gfx.renderer = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGL1Renderer(webGLOptions); + gfx.renderer = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderer(webGLOptions); gfx.renderer.shadowMap.enabled = settings.now.shadow.on; gfx.renderer.shadowMap.autoUpdate = false; gfx.renderer.shadowMap.type = external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.PCFShadowMap; capabilities.init(gfx.renderer); - - // z-sprites and ambient occlusion possibility - if (!arezSpritesSupported(gfx.renderer.getContext())) { - settings.set('zSprites', false); - } - if (!isAOSupported(gfx.renderer.getContext())) { - settings.set('ao', false); - } gfx.renderer.autoClear = false; gfx.renderer.setPixelRatio(window.devicePixelRatio); gfx.renderer.setSize(gfx.width, gfx.height); @@ -31971,10 +31960,8 @@ Miew.prototype._initGfx = function () { format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.RGBAFormat, depthBuffer: true }); - if (gfx.renderer.getContext().getExtension('WEBGL_depth_texture')) { - gfx.offscreenBuf.depthTexture = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.DepthTexture(); - gfx.offscreenBuf.depthTexture.type = external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.UnsignedShortType; - } + gfx.offscreenBuf.depthTexture = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.DepthTexture(); + gfx.offscreenBuf.depthTexture.type = external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.UnsignedShortType; gfx.offscreenBuf2 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderTarget(deviceWidth, deviceHeight, { minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, @@ -31997,35 +31984,31 @@ Miew.prototype._initGfx = function () { gfx.volFFTex = gfx.offscreenBuf4; gfx.volWFFTex = gfx.offscreenBuf; - // use float textures for volume rendering if possible - if (gfx.renderer.getContext().getExtension('OES_texture_float')) { - gfx.offscreenBuf5 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderTarget(deviceWidth, deviceHeight, { - minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, - magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, - format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.RGBAFormat, - type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.FloatType, - depthBuffer: false - }); - gfx.offscreenBuf6 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderTarget(deviceWidth, deviceHeight, { - minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, - magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, - format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.RGBAFormat, - type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.FloatType, - depthBuffer: false - }); - gfx.offscreenBuf7 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderTarget(deviceWidth, deviceHeight, { - minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, - magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, - format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.RGBAFormat, - type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.FloatType, - depthBuffer: true - }); - gfx.volBFTex = gfx.offscreenBuf5; - gfx.volFFTex = gfx.offscreenBuf6; - gfx.volWFFTex = gfx.offscreenBuf7; - } else { - this.logger.warn('Device doesn\'t support OES_texture_float extension'); - } + // use float textures for volume rendering (WebGL2 core feature) + gfx.offscreenBuf5 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderTarget(deviceWidth, deviceHeight, { + minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, + magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, + format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.RGBAFormat, + type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.FloatType, + depthBuffer: false + }); + gfx.offscreenBuf6 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderTarget(deviceWidth, deviceHeight, { + minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, + magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, + format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.RGBAFormat, + type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.FloatType, + depthBuffer: false + }); + gfx.offscreenBuf7 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderTarget(deviceWidth, deviceHeight, { + minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, + magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, + format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.RGBAFormat, + type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.FloatType, + depthBuffer: true + }); + gfx.volBFTex = gfx.offscreenBuf5; + gfx.volFFTex = gfx.offscreenBuf6; + gfx.volWFFTex = gfx.offscreenBuf7; gfx.stereoBufL = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.WebGLRenderTarget(deviceWidth, deviceHeight, { minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_.LinearFilter, @@ -32547,12 +32530,11 @@ Miew.prototype._setUberMaterialValues = function (values) { Miew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) { const gfx = this._gfx; const gl = gfx.renderer.getContext(); - const ext = gl.getExtension('WEBGL_draw_buffers'); const { properties } = gfx.renderer; if (!on) { - ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, null]); + gl.drawBuffers([gl.COLOR_ATTACHMENT0, null]); return; } @@ -32571,10 +32553,10 @@ Miew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) { fb.width = renderBuffer.width; fb.height = renderBuffer.height; gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT0, gl.TEXTURE_2D, tx, 0); - gl.framebufferTexture2D(gl.FRAMEBUFFER, ext.COLOR_ATTACHMENT1_WEBGL, gl.TEXTURE_2D, tx8, 0); + gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT1, gl.TEXTURE_2D, tx8, 0); - // mapping textures - ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, ext.COLOR_ATTACHMENT1_WEBGL]); + // mapping textures (MRT is core feature in WebGL2) + gl.drawBuffers([gl.COLOR_ATTACHMENT0, gl.COLOR_ATTACHMENT1]); }; Miew.prototype._renderScene = function () { return function (camera, distortion, target) { @@ -33407,7 +33389,7 @@ Miew.prototype._startAnimation = function (fileData) { self.logger.error(message); } }); - } catch (e) { + } catch { this.logger.error('Animation file does not fit to current complex!'); return; } @@ -33470,7 +33452,7 @@ Miew.prototype._continueAnimation = function () { self._refreshTitle(` Frame ${self._frameInfo._currFrame} of ${self._frameInfo._framesCount} time interval - ${self._frameInfo._timeStep}`); try { self._frameInfo.nextFrame(); - } catch (e) { + } catch { self.logger.error('Error during animation'); self._stopAnimation(); return; @@ -33974,7 +33956,7 @@ Miew.prototype._enterComponentEditMode = function () { editors.push(editor); } }); - if (editors === []) { + if (editors.length === 0) { return; } this._editors = editors; @@ -34831,9 +34813,7 @@ Miew.prototype._updateShadowmapMeshes = function (process) { } }); }; -Miew.prototype._updateMaterials = function (values) { - let needTraverse = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; - let process = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : undefined; +Miew.prototype._updateMaterials = function (values, needTraverse = false, process = undefined) { this._forEachComplexVisual(visual => visual.setMaterialValues(values, needTraverse, process)); for (let i = 0, n = this._objects.length; i < n; ++i) { const obj = this._objects[i]; @@ -34892,21 +34872,12 @@ Miew.prototype._initOnSettingsChanged = function () { this._onBgColorChanged(); }); on('ao', () => { - if (settings.now.ao && !isAOSupported(this._gfx.renderer.getContext())) { - this.logger.warn('Your device or browser does not support ao'); - settings.set('ao', false); - } else { - const values = { - normalsToGBuffer: settings.now.ao - }; - this._setUberMaterialValues(values); - } + const values = { + normalsToGBuffer: settings.now.ao + }; + this._setUberMaterialValues(values); }); on('zSprites', () => { - if (settings.now.zSprites && !arezSpritesSupported(this._gfx.renderer.getContext())) { - this.logger.warn('Your device or browser does not support zSprites'); - settings.set('zSprites', false); - } this.rebuildAll(); }); on('fogColor', () => { @@ -35404,7 +35375,7 @@ Miew.prototype.motm = function () { visual.resetReps(rep); }); }; -Miew.prototype.VERSION = true && "0.11.1" || 0; +Miew.prototype.VERSION = true && "0.12.0" || 0; // Uncomment this to get debug trace: // Miew.prototype.debugTracer = new utils.DebugTracer(Miew.prototype); @@ -35445,7 +35416,7 @@ external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_default( /* harmony default export */ const src_Miew = (Miew); // EXTERNAL MODULE: ./src/utils/MiewCLIParser.js var MiewCLIParser = __webpack_require__(89); -;// CONCATENATED MODULE: ./src/utils/MiewCLIHelp.js +;// ./src/utils/MiewCLIHelp.js const modeIdDesc = { @@ -35656,7 +35627,7 @@ const help = { } }; /* harmony default export */ const MiewCLIHelp = (help); -;// CONCATENATED MODULE: ./src/Miew-cli.js +;// ./src/Miew-cli.js @@ -35997,7 +35968,7 @@ src_Miew.prototype.callNextCmd = function () { MiewCLIParser.parser.yy = cliutils; // workaround for incorrect JISON parser generator for AMD module MiewCLIParser.parser.yy.parseError = MiewCLIParser.parser.parseError; -;// CONCATENATED MODULE: ./src/index.js +;// ./src/index.js /* harmony default export */ const src = (src_Miew); diff --git a/packages/miew/dist/Miew.js.map b/packages/miew/dist/Miew.js.map index e5715c83..c9a607be 100644 --- a/packages/miew/dist/Miew.js.map +++ b/packages/miew/dist/Miew.js.map @@ -1 +1 @@ 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function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.miew.reset(false); yy.ClearContext(); yy.miew.resetReps(\"empty\");\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.miew.rebuild();\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.miew.rebuildAll(); yy.miew.rebuild();\r\nbreak;\r\ncase 6:\r\nthis.$ = yy.echo(yy.utils.help().toString());\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.echo(yy.utils.help($$[$0]).toString());\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.miew.motm();\r\nbreak;\r\ncase 10: case 11:\r\nthis.$ = yy.utils.propagateProp($$[$0]); yy.echo(yy.miew.get($$[$0]).toString());\r\nbreak;\r\ncase 12: case 13:\r\nthis.$ = yy.miew.set($$[$0-1], yy.utils.propagateProp($$[$0-1], $$[$0]));;\r\nbreak;\r\ncase 14:\r\nthis.$ = yy.miew.saveSettings();;\r\nbreak;\r\ncase 15:\r\nthis.$ = yy.miew.restoreSettings();;\r\nbreak;\r\ncase 16:\r\nthis.$ = yy.miew.resetSettings();;\r\nbreak;\r\ncase 17:\r\nthis.$ = yy.miew.resetReps();\r\nbreak;\r\ncase 18:\r\nthis.$ = yy.miew.applyPreset($$[$0]);\r\nbreak;\r\ncase 21:\r\nthis.$ = yy.miew.repRemove($$[$0]); yy.representations.remove($$[$0]);\r\nbreak;\r\ncase 22:\r\nthis.$ = yy.miew.repHide($$[$0]);\r\nbreak;\r\ncase 23:\r\nthis.$ = yy.miew.repHide($$[$0], false);\r\nbreak;\r\ncase 24:\r\nthis.$ = yy.echo(yy.utils.listRep(yy.miew, yy.representations, $$[$0], '-e'));\r\nbreak;\r\ncase 25:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations));\r\nbreak;\r\ncase 26:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations, $$[$0]));\r\nbreak;\r\ncase 27:\r\nthis.$ = yy.echo(yy.utils.listSelector(yy.miew, yy.Context));\r\nbreak;\r\ncase 28:\r\nthis.$ = yy.miew.select(yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0], true));\r\nbreak;\r\ncase 29:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.utils.checkArg($$[$0-3].toLowerCase(), $$[$0-2], true); yy.miew.select(yy.Context[$$[$0].toLowerCase()]);\r\nbreak;\r\ncase 30:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {selector : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0])});\r\nbreak;\r\ncase 31:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.miew.within(yy.utils.checkArg(\"select\", $$[$0-2], true), Number($$[$0-4]));\r\nbreak;\r\ncase 32:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {material : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 35:\r\nthis.$ = yy.echo(yy.miew.view());\r\nbreak;\r\ncase 36: case 37:\r\nthis.$ = yy.miew.view($$[$0]);\r\nbreak;\r\ncase 38:\r\nthis.$ = yy.echo(yy.miew.changeUnit());\r\nbreak;\r\ncase 39:\r\nthis.$ = yy.echo(yy.miew.changeUnit($$[$0]));\r\nbreak;\r\ncase 40:\r\nthis.$ = yy.miew.dssp();\r\nbreak;\r\ncase 41:\r\nthis.$ = yy.miew.scale($$[$0]);\r\nbreak;\r\ncase 42:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.rotate($$[$0][i]['x'] * Math.PI / 180.0, $$[$0][i]['y'] * Math.PI / 180.0, $$[$0][i]['z'] * Math.PI / 180.0)} \r\nbreak;\r\ncase 43:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.translate($$[$0][i]['x'] || 0, $$[$0][i]['y'] || 0, $$[$0][i]['z'] || 0)} \r\nbreak;\r\ncase 44:\r\nthis.$ = yy.miew.center();\r\nbreak;\r\ncase 45:\r\nthis.$ = yy.miew.center($$[$0]);\r\nbreak;\r\ncase 48: case 49:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-1], $$[$0]]}, true);\r\nbreak;\r\ncase 50: case 51:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-2], $$[$0-1]], opts:$$[$0].toJSO(yy.utils, 'objects', 'line')}, true);\r\nbreak;\r\ncase 52:\r\nthis.$ = yy.echo(yy.utils.listObjs(yy.miew));\r\nbreak;\r\ncase 53:\r\nthis.$ = yy.miew.removeObject($$[$0]);\r\nbreak;\r\ncase 54:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: false}));\r\nbreak;\r\ncase 55:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: true}));\r\nbreak;\r\ncase 56:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: false}));\r\nbreak;\r\ncase 57: case 58:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: true}));\r\nbreak;\r\ncase 59:\r\nthis.$ = yy.miew.screenshotSave();\r\nbreak;\r\ncase 60:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0]));\r\nbreak;\r\ncase 61:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0-1]), Number($$[$0]));\r\nbreak;\r\ncase 62: case 63: case 64:\r\nthis.$ = yy.utils.load(yy.miew, $$[$0]); yy.representations.clear();\r\nbreak;\r\ncase 65:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd()));\r\nbreak;\r\ncase 66:\r\nthis.$ = yy.echo(yy.representations.add($$[$0], yy.miew.repAdd()));\r\nbreak;\r\ncase 67:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 68:\r\nthis.$ = yy.echo(yy.representations.add($$[$0-1], yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 69:\r\nthis.$ = yy.miew.rep($$[$0]); yy.miew.repCurrent($$[$0]);\r\nbreak;\r\ncase 70:\r\nthis.$ = yy.miew.rep($$[$0-1], $$[$0]); yy.miew.repCurrent($$[$0-1]);\r\nbreak;\r\ncase 71:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 72:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 73:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 74:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 75:\r\nthis.$ = Number(yy.representations.get($$[$0]));\r\nbreak;\r\ncase 76: case 92:\r\nthis.$ = Number($$[$0]);\r\nbreak;\r\ncase 77:\r\nthis.$ = $$[$0];\r\nbreak;\r\ncase 78:\r\nthis.$ = yy._.assign($$[$0-1], $$[$0]);\r\nbreak;\r\ncase 79:\r\nthis.$ = yy._.assign($$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 80:\r\nthis.$ = yy._.assign($$[$0-3], $$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 81: case 82:\r\nthis.$ = yy.CreateObjectPair($$[$0].key, $$[$0].val);\r\nbreak;\r\ncase 83:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].key, new Array($$[$0-1].val, $$[$0].toJSO(yy.utils, $$[$0-1].key, $$[$0-1].val)));\r\nbreak;\r\ncase 84: case 85:\r\nthis.$ = Object.create({'key': yy.keyRemap($$[$0-2]), 'val': yy.utils.checkArg($$[$0-2], $$[$0])});\r\nbreak;\r\ncase 86:\r\nthis.$ = [$$[$0]];\r\nbreak;\r\ncase 87:\r\nthis.$ = $$[$0-1].concat($$[$0]);\r\nbreak;\r\ncase 88:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].toLowerCase(), Number($$[$0]));\r\nbreak;\r\ncase 89:\r\nthis.$ = new yy.ArgList($$[$0]);\r\nbreak;\r\ncase 90:\r\nthis.$ = $$[$0-1].append($$[$0]);\r\nbreak;\r\ncase 91:\r\nthis.$ = new yy.Arg($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 93:\r\nthis.$ = parseInt($$[$0]);\r\nbreak;\r\ncase 94:\r\nthis.$ = JSON.parse($$[$0]);\r\nbreak;\r\ncase 95: case 96:\r\nthis.$ = String($$[$0]);\r\nbreak;\r\ncase 157: case 158: case 161: case 162: case 163:\r\nthis.$ = $$[$0-2] + $$[$0-1] + $$[$0] //cause of could be color word in path;\r\nbreak;\r\ncase 166:\r\nthis.$ = $$[$0-2] = $$[$0-2] + $$[$0-1] + $$[$0];\r\nbreak;\r\n}\r\n},\r\ntable: 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,[2,90]),{14:$VS,16:197,35:$VT,38:$VU,77:$VV,78:$VW},{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,33:$Ve,34:$Vf,35:[1,199],37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,79:198,80:52,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN},o($V41,[2,84]),o($V31,[2,85]),{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,32:200,33:$Ve,34:$Vf,37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,70:$Vx,72:$Vy,74:$Vz,79:184,80:52,81:185,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN,96:$VO,97:$VP,98:$VQ,99:$VR},{5:[2,80]},o($V31,[2,91]),o($V61,[2,157]),o($V61,[2,158]),{5:[2,31]}],\r\ndefaultActions: {3:[2,2],4:[2,3],7:[2,8],8:[2,9],11:[2,14],12:[2,15],13:[2,16],15:[2,19],16:[2,20],25:[2,33],26:[2,34],29:[2,40],34:[2,46],35:[2,47],37:[2,52],46:[2,1],47:[2,5],107:[2,11],110:[2,18],116:[2,21],119:[2,22],120:[2,23],121:[2,24],122:[2,26],123:[2,27],125:[2,30],127:[2,32],128:[2,36],129:[2,37],130:[2,39],131:[2,41],136:[2,45],139:[2,53],140:[2,62],141:[2,63],142:[2,64],143:[2,164],145:[2,67],158:[2,12],159:[2,13],166:[2,68],174:[2,70],177:[2,57],178:[2,58],179:[2,61],183:[2,29],184:[2,99],185:[2,100],196:[2,80],200:[2,31]},\r\nparseError: function parseError (str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function(match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex () {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin (condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState () {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules () {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState (n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState (condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* ignore whitespace */\r\nbreak;\r\ncase 1:return '';\r\nbreak;\r\ncase 2:return '';\r\nbreak;\r\ncase 3:return 42;\r\nbreak;\r\ncase 4:return 35;\r\nbreak;\r\ncase 5:return 77;\r\nbreak;\r\ncase 6:return 78;\r\nbreak;\r\ncase 7:return 78;\r\nbreak;\r\ncase 8:return 8;\r\nbreak;\r\ncase 9:return 6;\r\nbreak;\r\ncase 10:return 82;\r\nbreak;\r\ncase 11:return 7;\r\nbreak;\r\ncase 12:return 9;\r\nbreak;\r\ncase 13:return 59;\r\nbreak;\r\ncase 14:return 13\r\nbreak;\r\ncase 15:return 15\r\nbreak;\r\ncase 16:return 17\r\nbreak;\r\ncase 17:return 18\r\nbreak;\r\ncase 18:return 19\r\nbreak;\r\ncase 19:return 20\r\nbreak;\r\ncase 20:return 11\r\nbreak;\r\ncase 21:return 62\r\nbreak;\r\ncase 22:return 64\r\nbreak;\r\ncase 23:return 23\r\nbreak;\r\ncase 24:return 25\r\nbreak;\r\ncase 25:return 26\r\nbreak;\r\ncase 26:return 27\r\nbreak;\r\ncase 27:return 30\r\nbreak;\r\ncase 28:return 34\r\nbreak;\r\ncase 29:return 33\r\nbreak;\r\ncase 30:return 65\r\nbreak;\r\ncase 31:return 66\r\nbreak;\r\ncase 32:return 37\r\nbreak;\r\ncase 33:return 41\r\nbreak;\r\ncase 34:return 43\r\nbreak;\r\ncase 35:return 52\r\nbreak;\r\ncase 36:return 54\r\nbreak;\r\ncase 37:return 55\r\nbreak;\r\ncase 38:return 46\r\nbreak;\r\ncase 39:return 48\r\nbreak;\r\ncase 40:return 45\r\nbreak;\r\ncase 41:return 49\r\nbreak;\r\ncase 42:return 56\r\nbreak;\r\ncase 43:return 58;\r\nbreak;\r\ncase 44:return 44\r\nbreak;\r\ncase 45:return 83\r\nbreak;\r\ncase 46:return 84\r\nbreak;\r\ncase 47:return 85\r\nbreak;\r\ncase 48:return 86\r\nbreak;\r\ncase 49:return 87\r\nbreak;\r\ncase 50:return 88\r\nbreak;\r\ncase 51:return 89\r\nbreak;\r\ncase 52:return 90\r\nbreak;\r\ncase 53:return 91\r\nbreak;\r\ncase 54:return 92\r\nbreak;\r\ncase 55:return 93\r\nbreak;\r\ncase 56:return 94\r\nbreak;\r\ncase 57:return 95\r\nbreak;\r\ncase 58:return 70\r\nbreak;\r\ncase 59:return 70\r\nbreak;\r\ncase 60:return 72\r\nbreak;\r\ncase 61:return 72\r\nbreak;\r\ncase 62:return 74\r\nbreak;\r\ncase 63:return 74\r\nbreak;\r\ncase 64:return 74\r\nbreak;\r\ncase 65:return 31\r\nbreak;\r\ncase 66:return 36\r\nbreak;\r\ncase 67:return 96\r\nbreak;\r\ncase 68:return 97\r\nbreak;\r\ncase 69:return 98\r\nbreak;\r\ncase 70:return 99\r\nbreak;\r\ncase 71:yy_.yytext = yy.utils.unquoteString(yy_.yytext); return 14;\r\nbreak;\r\ncase 72:return 38;\r\nbreak;\r\ncase 73:return 5;\r\nbreak;\r\ncase 74:return 101;\r\nbreak;\r\ncase 75:return 103;\r\nbreak;\r\ncase 76:return '\\\\';\r\nbreak;\r\ncase 77:return 28\r\nbreak;\r\ncase 78:return 61\r\nbreak;\r\ncase 79:return 29\r\nbreak;\r\ncase 80:return 57\r\nbreak;\r\ncase 81:return 71\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:[#].*)/i,/^(?:\\/\\/.*)/i,/^(?:([_A-Z0-9\\/\\+]+==))/i,/^(?:-?[0-9]+(\\.[0-9]+)?\\b)/i,/^(?:0[xX][0-9A-F]+\\b)/i,/^(?:false\\b)/i,/^(?:true\\b)/i,/^(?:all\\b)/i,/^(?:reset\\b)/i,/^(?:clear\\b)/i,/^(?:build\\b)/i,/^(?:help\\b)/i,/^(?:load\\b)/i,/^(?:get\\b)/i,/^(?:set\\b)/i,/^(?:set_save\\b)/i,/^(?:set_restore\\b)/i,/^(?:set_reset\\b)/i,/^(?:preset\\b)/i,/^(?:motm\\b)/i,/^(?:add\\b)/i,/^(?:rep\\b)/i,/^(?:remove\\b)/i,/^(?:hide\\b)/i,/^(?:show\\b)/i,/^(?:list\\b)/i,/^(?:select\\b)/i,/^(?:within\\b)/i,/^(?:selector\\b)/i,/^(?:mode\\b)/i,/^(?:color\\b)/i,/^(?:material\\b)/i,/^(?:view\\b)/i,/^(?:unit\\b)/i,/^(?:line\\b)/i,/^(?:listobj\\b)/i,/^(?:removeobj\\b)/i,/^(?:rotate\\b)/i,/^(?:translate\\b)/i,/^(?:scale\\b)/i,/^(?:center\\b)/i,/^(?:url\\b)/i,/^(?:screenshot\\b)/i,/^(?:dssp\\b)/i,/^(?:file_list\\b)/i,/^(?:file_register\\b)/i,/^(?:file_delete\\b)/i,/^(?:preset_add\\b)/i,/^(?:preset_delete\\b)/i,/^(?:preset_update\\b)/i,/^(?:preset_rename\\b)/i,/^(?:preset_open\\b)/i,/^(?:create_scenario\\b)/i,/^(?:reset_scenario\\b)/i,/^(?:delete_scenario\\b)/i,/^(?:add_scenario_item\\b)/i,/^(?:list_scenario\\b)/i,/^(?:s\\b)/i,/^(?:mt\\b)/i,/^(?:m\\b)/i,/^(?:c\\b)/i,/^(?:x\\b)/i,/^(?:y\\b)/i,/^(?:z\\b)/i,/^(?:as\\b)/i,/^(?:of\\b)/i,/^(?:pdb\\b)/i,/^(?:delay\\b)/i,/^(?:prst\\b)/i,/^(?:desc\\b)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:\\.)/i,/^(?:\\/)/i,/^(?:\\\\)/i,/^(?:-e\\b)/i,/^(?:-f\\b)/i,/^(?:-s\\b)/i,/^(?:-v\\b)/i,/^(?:=)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","/* eslint-disable */\r\n// DO NOT EDIT! Automatically generated from .jison\r\n/* parser generated by jison 0.4.18 */\r\n/*\r\n Returns a Parser object of the following structure:\r\n\r\n Parser: {\r\n yy: {}\r\n }\r\n\r\n Parser.prototype: {\r\n yy: {},\r\n trace: function(),\r\n symbols_: {associative list: name ==> number},\r\n terminals_: {associative list: number ==> name},\r\n productions_: [...],\r\n performAction: function anonymous(yytext, yyleng, yylineno, yy, yystate, $$, _$),\r\n table: [...],\r\n defaultActions: {...},\r\n parseError: function(str, hash),\r\n parse: function(input),\r\n\r\n lexer: {\r\n EOF: 1,\r\n parseError: function(str, hash),\r\n setInput: function(input),\r\n input: function(),\r\n unput: function(str),\r\n more: function(),\r\n less: function(n),\r\n pastInput: function(),\r\n upcomingInput: function(),\r\n showPosition: function(),\r\n test_match: function(regex_match_array, rule_index),\r\n next: function(),\r\n lex: function(),\r\n begin: function(condition),\r\n popState: function(),\r\n _currentRules: function(),\r\n topState: function(),\r\n pushState: function(condition),\r\n\r\n options: {\r\n ranges: boolean (optional: true ==> token location info will include a .range[] member)\r\n flex: boolean (optional: true ==> flex-like lexing behaviour where the rules are tested exhaustively to find the longest match)\r\n backtrack_lexer: boolean (optional: true ==> lexer regexes are tested in order and for each matching regex the action code is invoked; the lexer terminates the scan when a token is returned by the action code)\r\n },\r\n\r\n performAction: function(yy, yy_, $avoiding_name_collisions, YY_START),\r\n rules: [...],\r\n conditions: {associative list: name ==> set},\r\n }\r\n }\r\n\r\n\r\n token location info (@$, _$, etc.): {\r\n first_line: n,\r\n last_line: n,\r\n first_column: n,\r\n last_column: n,\r\n range: [start_number, end_number] (where the numbers are indexes into the input string, regular zero-based)\r\n }\r\n\r\n\r\n the parseError function receives a 'hash' object with these members for lexer and parser errors: {\r\n text: (matched text)\r\n token: (the produced terminal token, if any)\r\n line: (yylineno)\r\n }\r\n while parser (grammar) errors will also provide these members, i.e. parser errors deliver a superset of attributes: {\r\n loc: (yylloc)\r\n expected: (string describing the set of expected tokens)\r\n recoverable: (boolean: TRUE when the parser has a error recovery rule available for this particular error)\r\n }\r\n*/\r\nvar parser = (function(){\r\nvar o=function(k,v,o,l){for(o=o||{},l=k.length;l--;o[k[l]]=v);return o},$V0=[1,4],$V1=[1,5],$V2=[1,6],$V3=[1,7],$V4=[1,8],$V5=[1,9],$V6=[1,11],$V7=[1,12],$V8=[5,7,8,11],$V9=[1,17],$Va=[1,22],$Vb=[1,20],$Vc=[1,21],$Vd=[5,7,8,11,19];\r\nvar parser = {trace: function trace() { },\r\nyy: {},\r\nsymbols_: {\"error\":2,\"Program\":3,\"Expression\":4,\"EOF\":5,\"Selector\":6,\"OR\":7,\"AND\":8,\"NOT\":9,\"(\":10,\")\":11,\"SELECTOR\":12,\"NAMED_SELECTOR\":13,\"SELECTOR_RANGED\":14,\"RangeList\":15,\"SELECTOR_NAMED\":16,\"NameList\":17,\"Range\":18,\",\":19,\"NUMBER\":20,\":\":21,\"Name\":22,\"IDENTIFIER\":23,\"STRING\":24,\"$accept\":0,\"$end\":1},\r\nterminals_: {2:\"error\",5:\"EOF\",7:\"OR\",8:\"AND\",9:\"NOT\",10:\"(\",11:\")\",12:\"SELECTOR\",13:\"NAMED_SELECTOR\",14:\"SELECTOR_RANGED\",16:\"SELECTOR_NAMED\",19:\",\",20:\"NUMBER\",21:\":\",23:\"IDENTIFIER\",24:\"STRING\"},\r\nproductions_: [0,[3,2],[4,1],[4,3],[4,3],[4,2],[4,3],[6,1],[6,1],[6,2],[6,2],[15,1],[15,3],[18,1],[18,3],[17,1],[17,3],[22,1],[22,1],[22,1]],\r\nperformAction: function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.keyword('or')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.keyword('and')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.keyword('not')($$[$0]);\r\nbreak;\r\ncase 6:\r\nthis.$ = $$[$0-1];\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.keyword($$[$0])();\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.GetSelector($$[$0].toLowerCase().slice(1, $$[$0].length));\r\nbreak;\r\ncase 9: case 10:\r\nthis.$ = yy.keyword($$[$0-1])($$[$0]);\r\nbreak;\r\ncase 11:\r\nthis.$ = new yy.RangeList($$[$0]);\r\nbreak;\r\ncase 12: case 16:\r\nthis.$ = $$[$0-2].append($$[$0]);\r\nbreak;\r\ncase 13:\r\nthis.$ = new yy.Range(Number($$[$0]));\r\nbreak;\r\ncase 14:\r\nthis.$ = new yy.Range(Number($$[$0-2]), Number($$[$0]));\r\nbreak;\r\ncase 15:\r\nthis.$ = new yy.ValueList($$[$0]);\r\nbreak;\r\n}\r\n},\r\ntable: [{3:1,4:2,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{1:[3]},{5:[1,10],7:$V6,8:$V7},o($V8,[2,2]),{4:13,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:14,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,7]),o($V8,[2,8]),{15:15,18:16,20:$V9},{17:18,20:$Va,22:19,23:$Vb,24:$Vc},{1:[2,1]},{4:23,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:24,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,5]),{7:$V6,8:$V7,11:[1,25]},o($V8,[2,9],{19:[1,26]}),o($Vd,[2,11]),o($Vd,[2,13],{21:[1,27]}),o($V8,[2,10],{19:[1,28]}),o($Vd,[2,15]),o($Vd,[2,17]),o($Vd,[2,18]),o($Vd,[2,19]),o([5,7,11],[2,3],{8:$V7}),o($V8,[2,4]),o($V8,[2,6]),{18:29,20:$V9},{20:[1,30]},{20:$Va,22:31,23:$Vb,24:$Vc},o($Vd,[2,12]),o($Vd,[2,14]),o($Vd,[2,16])],\r\ndefaultActions: {10:[2,1]},\r\nparseError: function parseError(str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function (match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex() {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin(condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState() {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules() {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState(n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState(condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* skip whitespace */\r\nbreak;\r\ncase 1:return 20;\r\nbreak;\r\ncase 2:return 7;\r\nbreak;\r\ncase 3:return 8;\r\nbreak;\r\ncase 4:return 9;\r\nbreak;\r\ncase 5:return 12;\r\nbreak;\r\ncase 6:return 16;\r\nbreak;\r\ncase 7:return 14;\r\nbreak;\r\ncase 8:return 10;\r\nbreak;\r\ncase 9:return 11;\r\nbreak;\r\ncase 10:return 19;\r\nbreak;\r\ncase 11:return 21;\r\nbreak;\r\ncase 12:return '<=';\r\nbreak;\r\ncase 13:return '>=';\r\nbreak;\r\ncase 14:return '<';\r\nbreak;\r\ncase 15:return '>';\r\nbreak;\r\ncase 16:yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2); return 24;\r\nbreak;\r\ncase 17:return 13;\r\nbreak;\r\ncase 18:return 23;\r\nbreak;\r\ncase 19:return 5;\r\nbreak;\r\ncase 20:return 'INVALID';\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:(-?(?:[1-9][0-9]+|[0-9]))\\b)/i,/^(?:OR\\b)/i,/^(?:AND\\b)/i,/^(?:NOT\\b)/i,/^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\\b)/i,/^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\\b)/i,/^(?:((SERIAL|SEQUENCE|RESIDX))\\b)/i,/^(?:\\()/i,/^(?:\\))/i,/^(?:,)/i,/^(?::)/i,/^(?:<=)/i,/^(?:>=)/i,/^(?:<)/i,/^(?:>)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:(@[_A-Z0-9]+))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:.)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","\r\n/*\r\nSmooth.js version 0.1.7\r\n\r\nTurn arrays into smooth functions.\r\n\r\nCopyright 2012 Spencer Cohen\r\nLicensed under MIT license (see \"Smooth.js MIT license.txt\")\r\n*/\r\n\r\n/*Constants (these are accessible by Smooth.WHATEVER in user space)\r\n*/\r\n\r\n(function() {\r\n var AbstractInterpolator, CubicInterpolator, Enum, LinearInterpolator, NearestInterpolator, PI, SincFilterInterpolator, Smooth, clipClamp, clipMirror, clipPeriodic, defaultConfig, getColumn, getType, isValidNumber, k, makeLanczosWindow, makeScaledFunction, makeSincKernel, normalizeScaleTo, shallowCopy, sin, sinc, v, validateNumber, validateVector,\r\n __hasProp = Object.prototype.hasOwnProperty,\r\n __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor; child.__super__ = parent.prototype; return child; };\r\n\r\n Enum = {\r\n /*Interpolation methods\r\n */\r\n METHOD_NEAREST: 'nearest',\r\n METHOD_LINEAR: 'linear',\r\n METHOD_CUBIC: 'cubic',\r\n METHOD_LANCZOS: 'lanczos',\r\n METHOD_SINC: 'sinc',\r\n /*Input clipping modes\r\n */\r\n CLIP_CLAMP: 'clamp',\r\n CLIP_ZERO: 'zero',\r\n CLIP_PERIODIC: 'periodic',\r\n CLIP_MIRROR: 'mirror',\r\n /* Constants for control over the cubic interpolation tension\r\n */\r\n CUBIC_TENSION_DEFAULT: 0,\r\n CUBIC_TENSION_CATMULL_ROM: 0\r\n };\r\n\r\n defaultConfig = {\r\n method: Enum.METHOD_CUBIC,\r\n cubicTension: Enum.CUBIC_TENSION_DEFAULT,\r\n clip: Enum.CLIP_CLAMP,\r\n scaleTo: 0,\r\n sincFilterSize: 2,\r\n sincWindow: void 0\r\n };\r\n\r\n /*Index clipping functions\r\n */\r\n\r\n clipClamp = function(i, n) {\r\n return Math.max(0, Math.min(i, n - 1));\r\n };\r\n\r\n clipPeriodic = function(i, n) {\r\n i = i % n;\r\n if (i < 0) i += n;\r\n return i;\r\n };\r\n\r\n clipMirror = function(i, n) {\r\n var period;\r\n period = 2 * (n - 1);\r\n i = clipPeriodic(i, period);\r\n if (i > n - 1) i = period - i;\r\n return i;\r\n };\r\n\r\n /*\r\n Abstract scalar interpolation class which provides common functionality for all interpolators\r\n \r\n Subclasses must override interpolate().\r\n */\r\n\r\n AbstractInterpolator = (function() {\r\n\r\n function AbstractInterpolator(array, config) {\r\n this.array = array.slice(0);\r\n this.length = this.array.length;\r\n if (!(this.clipHelper = {\r\n clamp: this.clipHelperClamp,\r\n zero: this.clipHelperZero,\r\n periodic: this.clipHelperPeriodic,\r\n mirror: this.clipHelperMirror\r\n }[config.clip])) {\r\n throw \"Invalid clip: \" + config.clip;\r\n }\r\n }\r\n\r\n AbstractInterpolator.prototype.getClippedInput = function(i) {\r\n if ((0 <= i && i < this.length)) {\r\n return this.array[i];\r\n } else {\r\n return this.clipHelper(i);\r\n }\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperClamp = function(i) {\r\n return this.array[clipClamp(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperZero = function(i) {\r\n return 0;\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperPeriodic = function(i) {\r\n return this.array[clipPeriodic(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperMirror = function(i) {\r\n return this.array[clipMirror(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.interpolate = function(t) {\r\n throw 'Subclasses of AbstractInterpolator must override the interpolate() method.';\r\n };\r\n\r\n return AbstractInterpolator;\r\n\r\n })();\r\n\r\n NearestInterpolator = (function(_super) {\r\n\r\n __extends(NearestInterpolator, _super);\r\n\r\n function NearestInterpolator() {\r\n NearestInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n NearestInterpolator.prototype.interpolate = function(t) {\r\n return this.getClippedInput(Math.round(t));\r\n };\r\n\r\n return NearestInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n LinearInterpolator = (function(_super) {\r\n\r\n __extends(LinearInterpolator, _super);\r\n\r\n function LinearInterpolator() {\r\n LinearInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n LinearInterpolator.prototype.interpolate = function(t) {\r\n var k;\r\n k = Math.floor(t);\r\n t -= k;\r\n return (1 - t) * this.getClippedInput(k) + t * this.getClippedInput(k + 1);\r\n };\r\n\r\n return LinearInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n CubicInterpolator = (function(_super) {\r\n\r\n __extends(CubicInterpolator, _super);\r\n\r\n function CubicInterpolator(array, config) {\r\n this.tangentFactor = 1 - Math.max(-1, Math.min(1, config.cubicTension));\r\n CubicInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n CubicInterpolator.prototype.getTangent = function(k) {\r\n return this.tangentFactor * (this.getClippedInput(k + 1) - this.getClippedInput(k - 1)) / 2;\r\n };\r\n\r\n CubicInterpolator.prototype.interpolate = function(t) {\r\n var k, m, p, t2, t3;\r\n k = Math.floor(t);\r\n m = [this.getTangent(k), this.getTangent(k + 1)];\r\n p = [this.getClippedInput(k), this.getClippedInput(k + 1)];\r\n t -= k;\r\n t2 = t * t;\r\n t3 = t * t2;\r\n return (2 * t3 - 3 * t2 + 1) * p[0] + (t3 - 2 * t2 + t) * m[0] + (-2 * t3 + 3 * t2) * p[1] + (t3 - t2) * m[1];\r\n };\r\n\r\n return CubicInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n sin = Math.sin, PI = Math.PI;\r\n\r\n sinc = function(x) {\r\n if (x === 0) {\r\n return 1;\r\n } else {\r\n return sin(PI * x) / (PI * x);\r\n }\r\n };\r\n\r\n makeLanczosWindow = function(a) {\r\n return function(x) {\r\n return sinc(x / a);\r\n };\r\n };\r\n\r\n makeSincKernel = function(window) {\r\n return function(x) {\r\n return sinc(x) * window(x);\r\n };\r\n };\r\n\r\n SincFilterInterpolator = (function(_super) {\r\n\r\n __extends(SincFilterInterpolator, _super);\r\n\r\n function SincFilterInterpolator(array, config) {\r\n SincFilterInterpolator.__super__.constructor.apply(this, arguments);\r\n this.a = config.sincFilterSize;\r\n if (!config.sincWindow) throw 'No sincWindow provided';\r\n this.kernel = makeSincKernel(config.sincWindow);\r\n }\r\n\r\n SincFilterInterpolator.prototype.interpolate = function(t) {\r\n var k, n, sum, _ref, _ref2;\r\n k = Math.floor(t);\r\n sum = 0;\r\n for (n = _ref = k - this.a + 1, _ref2 = k + this.a; _ref <= _ref2 ? n <= _ref2 : n >= _ref2; _ref <= _ref2 ? n++ : n--) {\r\n sum += this.kernel(t - n) * this.getClippedInput(n);\r\n }\r\n return sum;\r\n };\r\n\r\n return SincFilterInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n getColumn = function(arr, i) {\r\n var row, _i, _len, _results;\r\n _results = [];\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n row = arr[_i];\r\n _results.push(row[i]);\r\n }\r\n return _results;\r\n };\r\n\r\n makeScaledFunction = function(f, baseScale, scaleRange) {\r\n var scaleFactor, translation;\r\n if (scaleRange.join === '0,1') {\r\n return f;\r\n } else {\r\n scaleFactor = baseScale / (scaleRange[1] - scaleRange[0]);\r\n translation = scaleRange[0];\r\n return function(t) {\r\n return f(scaleFactor * (t - translation));\r\n };\r\n }\r\n };\r\n\r\n getType = function(x) {\r\n return Object.prototype.toString.call(x).slice('[object '.length, -1);\r\n };\r\n\r\n validateNumber = function(n) {\r\n if (isNaN(n)) throw 'NaN in Smooth() input';\r\n if (getType(n) !== 'Number') throw 'Non-number in Smooth() input';\r\n if (!isFinite(n)) throw 'Infinity in Smooth() input';\r\n };\r\n\r\n validateVector = function(v, dimension) {\r\n var n, _i, _len;\r\n if (getType(v) !== 'Array') throw 'Non-vector in Smooth() input';\r\n if (v.length !== dimension) throw 'Inconsistent dimension in Smooth() input';\r\n for (_i = 0, _len = v.length; _i < _len; _i++) {\r\n n = v[_i];\r\n validateNumber(n);\r\n }\r\n };\r\n\r\n isValidNumber = function(n) {\r\n return (getType(n) === 'Number') && isFinite(n) && !isNaN(n);\r\n };\r\n\r\n normalizeScaleTo = function(s) {\r\n var invalidErr;\r\n invalidErr = \"scaleTo param must be number or array of two numbers\";\r\n switch (getType(s)) {\r\n case 'Number':\r\n if (!isValidNumber(s)) throw invalidErr;\r\n s = [0, s];\r\n break;\r\n case 'Array':\r\n if (s.length !== 2) throw invalidErr;\r\n if (!(isValidNumber(s[0]) && isValidNumber(s[1]))) throw invalidErr;\r\n break;\r\n default:\r\n throw invalidErr;\r\n }\r\n return s;\r\n };\r\n\r\n shallowCopy = function(obj) {\r\n var copy, k, v;\r\n copy = {};\r\n for (k in obj) {\r\n if (!__hasProp.call(obj, k)) continue;\r\n v = obj[k];\r\n copy[k] = v;\r\n }\r\n return copy;\r\n };\r\n\r\n Smooth = function(arr, config) {\r\n var baseDomainEnd, dimension, i, interpolator, interpolatorClass, interpolators, k, n, properties, smoothFunc, v;\r\n if (config == null) config = {};\r\n properties = {};\r\n config = shallowCopy(config);\r\n properties.config = shallowCopy(config);\r\n if (config.scaleTo == null) config.scaleTo = config.period;\r\n if (config.sincFilterSize == null) {\r\n config.sincFilterSize = config.lanczosFilterSize;\r\n }\r\n for (k in defaultConfig) {\r\n if (!__hasProp.call(defaultConfig, k)) continue;\r\n v = defaultConfig[k];\r\n if (config[k] == null) config[k] = v;\r\n }\r\n if (!(interpolatorClass = {\r\n nearest: NearestInterpolator,\r\n linear: LinearInterpolator,\r\n cubic: CubicInterpolator,\r\n lanczos: SincFilterInterpolator,\r\n sinc: SincFilterInterpolator\r\n }[config.method])) {\r\n throw \"Invalid method: \" + config.method;\r\n }\r\n if (config.method === 'lanczos') {\r\n config.sincWindow = makeLanczosWindow(config.sincFilterSize);\r\n }\r\n if (arr.length < 2) throw 'Array must have at least two elements';\r\n properties.count = arr.length;\r\n smoothFunc = (function() {\r\n var _i, _j, _len, _len2;\r\n switch (getType(arr[0])) {\r\n case 'Number':\r\n properties.dimension = 'scalar';\r\n if (Smooth.deepValidation) {\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n n = arr[_i];\r\n validateNumber(n);\r\n }\r\n }\r\n interpolator = new interpolatorClass(arr, config);\r\n return function(t) {\r\n return interpolator.interpolate(t);\r\n };\r\n case 'Array':\r\n properties.dimension = dimension = arr[0].length;\r\n if (!dimension) throw 'Vectors must be non-empty';\r\n if (Smooth.deepValidation) {\r\n for (_j = 0, _len2 = arr.length; _j < _len2; _j++) {\r\n v = arr[_j];\r\n validateVector(v, dimension);\r\n }\r\n }\r\n interpolators = (function() {\r\n var _results;\r\n _results = [];\r\n for (i = 0; 0 <= dimension ? i < dimension : i > dimension; 0 <= dimension ? i++ : i--) {\r\n _results.push(new interpolatorClass(getColumn(arr, i), config));\r\n }\r\n return _results;\r\n })();\r\n return function(t) {\r\n var interpolator, _k, _len3, _results;\r\n _results = [];\r\n for (_k = 0, _len3 = interpolators.length; _k < _len3; _k++) {\r\n interpolator = interpolators[_k];\r\n _results.push(interpolator.interpolate(t));\r\n }\r\n return _results;\r\n };\r\n default:\r\n throw \"Invalid element type: \" + (getType(arr[0]));\r\n }\r\n })();\r\n if (config.clip === 'periodic') {\r\n baseDomainEnd = arr.length;\r\n } else {\r\n baseDomainEnd = arr.length - 1;\r\n }\r\n config.scaleTo || (config.scaleTo = baseDomainEnd);\r\n properties.domain = normalizeScaleTo(config.scaleTo);\r\n smoothFunc = makeScaledFunction(smoothFunc, baseDomainEnd, properties.domain);\r\n properties.domain.sort();\r\n /*copy properties\r\n */\r\n for (k in properties) {\r\n if (!__hasProp.call(properties, k)) continue;\r\n v = properties[k];\r\n smoothFunc[k] = v;\r\n }\r\n return smoothFunc;\r\n };\r\n\r\n for (k in Enum) {\r\n if (!__hasProp.call(Enum, k)) continue;\r\n v = Enum[k];\r\n Smooth[k] = v;\r\n }\r\n\r\n Smooth.deepValidation = true;\r\n\r\n (typeof exports !== \"undefined\" && exports !== null ? exports : window).Smooth = Smooth;\r\n\r\n}).call(this);\r\n","!function(r,t){if(\"function\"==typeof define&&define.amd)define([\"exports\"],t);else if(\"object\"==typeof exports&&\"undefined\"!=typeof module)t(exports);else t(r.MMTF=r.MMTF||{})}(this,function(r){\"use strict\";function t(r,t,n){for(var e=(r.byteLength,0),i=n.length;i>e;e++){var o=n.charCodeAt(e);if(128>o)r.setUint8(t++,o>>>0&127|0);else if(2048>o)r.setUint8(t++,o>>>6&31|192),r.setUint8(t++,o>>>0&63|128);else if(65536>o)r.setUint8(t++,o>>>12&15|224),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128);else{if(!(1114112>o))throw new Error(\"bad codepoint \"+o);r.setUint8(t++,o>>>18&7|240),r.setUint8(t++,o>>>12&63|128),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128)}}}function n(r){for(var t=0,n=0,e=r.length;e>n;n++){var i=r.charCodeAt(n);if(128>i)t+=1;else if(2048>i)t+=2;else if(65536>i)t+=3;else{if(!(1114112>i))throw new Error(\"bad codepoint \"+i);t+=4}}return t}function e(r,i,o){var a=typeof r;if(\"string\"===a){var u=n(r);if(32>u)return i.setUint8(o,160|u),t(i,o+1,r),1+u;if(256>u)return i.setUint8(o,217),i.setUint8(o+1,u),t(i,o+2,r),2+u;if(65536>u)return 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zIndex: 2e9,\n className: 'spinner',\n top: '50%',\n left: '50%',\n shadow: '0 0 1px transparent', // prevent aliased lines\n position: 'absolute',\n};\nvar Spinner = /** @class */ (function () {\n function Spinner(opts) {\n if (opts === void 0) { opts = {}; }\n this.opts = __assign(__assign({}, defaults), opts);\n }\n /**\n * Adds the spinner to the given target element. If this instance is already\n * spinning, it is automatically removed from its previous target by calling\n * stop() internally.\n */\n Spinner.prototype.spin = function (target) {\n this.stop();\n this.el = document.createElement('div');\n this.el.className = this.opts.className;\n this.el.setAttribute('role', 'progressbar');\n this.el.style.position = this.opts.position;\n this.el.style.width = \"0\";\n this.el.style.zIndex = this.opts.zIndex.toString();\n this.el.style.left = this.opts.left;\n this.el.style.top = this.opts.top;\n this.el.style.transform = \"scale(\".concat(this.opts.scale, \")\");\n if (target) {\n target.insertBefore(this.el, target.firstChild || null);\n }\n drawLines(this.el, this.opts);\n return this;\n };\n /**\n * Stops and removes the Spinner.\n * Stopped spinners may be reused by calling spin() again.\n */\n Spinner.prototype.stop = function () {\n if (this.el) {\n if (this.el.parentNode) {\n this.el.parentNode.removeChild(this.el);\n }\n this.el = undefined;\n }\n return this;\n };\n return Spinner;\n}());\nexport { Spinner };\n/**\n * Returns the line color from the given string or array.\n */\nfunction getColor(color, idx) {\n return typeof color == 'string' ? color : color[idx % color.length];\n}\n/**\n * Internal method that draws the individual lines.\n */\nfunction drawLines(el, opts) {\n var borderRadius = (Math.round(opts.corners * opts.width * 500) / 1000) + 'px';\n var shadow = 'none';\n if (opts.shadow === true) {\n shadow = '0 2px 4px #000'; // default shadow\n }\n else if (typeof opts.shadow === 'string') {\n shadow = opts.shadow;\n }\n var shadows = parseBoxShadow(shadow);\n for (var i = 0; i < opts.lines; i++) {\n var degrees = ~~(360 / opts.lines * i + opts.rotate);\n var backgroundLine = document.createElement('div');\n backgroundLine.style.position = 'absolute';\n backgroundLine.style.top = \"\".concat(-opts.width / 2, \"px\");\n backgroundLine.style.width = (opts.length + opts.width) + 'px';\n backgroundLine.style.height = opts.width + 'px';\n backgroundLine.style.background = getColor(opts.fadeColor, i);\n backgroundLine.style.borderRadius = borderRadius;\n backgroundLine.style.transformOrigin = 'left';\n backgroundLine.style.transform = \"rotate(\".concat(degrees, \"deg) translateX(\").concat(opts.radius, \"px)\");\n var delay = i * opts.direction / opts.lines / opts.speed;\n delay -= 1 / opts.speed; // so initial animation state will include trail\n var line = document.createElement('div');\n line.style.width = '100%';\n line.style.height = '100%';\n line.style.background = getColor(opts.color, i);\n line.style.borderRadius = borderRadius;\n line.style.boxShadow = normalizeShadow(shadows, degrees);\n line.style.animation = \"\".concat(1 / opts.speed, \"s linear \").concat(delay, \"s infinite \").concat(opts.animation);\n backgroundLine.appendChild(line);\n el.appendChild(backgroundLine);\n }\n}\nfunction parseBoxShadow(boxShadow) {\n var regex = /^\\s*([a-zA-Z]+\\s+)?(-?\\d+(\\.\\d+)?)([a-zA-Z]*)\\s+(-?\\d+(\\.\\d+)?)([a-zA-Z]*)(.*)$/;\n var shadows = [];\n for (var _i = 0, _a = boxShadow.split(','); _i < _a.length; _i++) {\n var shadow = _a[_i];\n var matches = shadow.match(regex);\n if (matches === null) {\n continue; // invalid syntax\n }\n var x = +matches[2];\n var y = +matches[5];\n var xUnits = matches[4];\n var yUnits = matches[7];\n if (x === 0 && !xUnits) {\n xUnits = yUnits;\n }\n if (y === 0 && !yUnits) {\n yUnits = xUnits;\n }\n if (xUnits !== yUnits) {\n continue; // units must match to use as coordinates\n }\n shadows.push({\n prefix: matches[1] || '', // could have value of 'inset' or undefined\n x: x,\n y: y,\n xUnits: xUnits,\n yUnits: yUnits,\n end: matches[8],\n });\n }\n return shadows;\n}\n/**\n * Modify box-shadow x/y offsets to counteract rotation\n */\nfunction normalizeShadow(shadows, degrees) {\n var normalized = [];\n for (var _i = 0, shadows_1 = shadows; _i < shadows_1.length; _i++) {\n var shadow = shadows_1[_i];\n var xy = convertOffset(shadow.x, shadow.y, degrees);\n normalized.push(shadow.prefix + xy[0] + shadow.xUnits + ' ' + xy[1] + shadow.yUnits + shadow.end);\n }\n return normalized.join(', ');\n}\nfunction convertOffset(x, y, degrees) {\n var radians = degrees * Math.PI / 180;\n var sin = Math.sin(radians);\n var cos = Math.cos(radians);\n return [\n Math.round((x * cos + y * sin) * 1000) / 1000,\n Math.round((-x * sin + y * cos) * 1000) / 1000,\n ];\n}\n","//----------------------------------------------------------------------------\r\n// Timer\r\n\r\nexport default class Timer {\r\n constructor() {\r\n this.startTime = 0;\r\n this.oldTime = 0;\r\n this.elapsedTime = 0;\r\n this.running = false;\r\n }\r\n\r\n start() {\r\n this.startTime = Timer.now();\r\n this.oldTime = this.startTime;\r\n this.running = true;\r\n }\r\n\r\n stop() {\r\n this.getElapsedTime();\r\n this.running = false;\r\n }\r\n\r\n getElapsedTime() {\r\n this.update();\r\n return this.elapsedTime;\r\n }\r\n\r\n update() {\r\n let delta = 0;\r\n if (this.running) {\r\n const newTime = Timer.now();\r\n delta = 0.001 * (newTime - this.oldTime);\r\n this.oldTime = newTime;\r\n this.elapsedTime += delta;\r\n }\r\n\r\n return delta;\r\n }\r\n}\r\n\r\nTimer.now = (function () {\r\n const p = typeof window !== 'undefined' && window.performance;\r\n return (p && p.now) ? p.now.bind(p) : Date.now;\r\n}());\r\n","import Timer from '../Timer';\r\n\r\nconst { now } = Timer;\r\n\r\nfunction createElement(tag, id, css) {\r\n const element = document.createElement(tag);\r\n element.id = id;\r\n element.style.cssText = css;\r\n return element;\r\n}\r\n\r\nclass Stats {\r\n constructor() {\r\n this.domElement = createElement('div', 'stats', 'padding:8px');\r\n this._text = createElement('p', 'fps', 'margin:0;color:silver;font-size:large');\r\n this.domElement.appendChild(this._text);\r\n\r\n this._startTime = now();\r\n this._prevTime = this._startTime;\r\n\r\n this._deltas = new Array(20);\r\n this._index = 0;\r\n this._total = 0.0;\r\n this._count = 0;\r\n }\r\n\r\n end() {\r\n const time = now();\r\n const delta = time - this._startTime;\r\n\r\n if (this._count < this._deltas.length) {\r\n this._count++;\r\n } else {\r\n this._total -= this._deltas[this._index];\r\n }\r\n this._total += delta;\r\n this._deltas[this._index] = delta;\r\n this._index = (this._index + 1) % this._deltas.length;\r\n\r\n this.ms = this._total / this._count;\r\n this.fps = 1000 / this.ms;\r\n\r\n if (time > this._prevTime + 1000) {\r\n this._text.textContent = this.fps.toPrecision(2);\r\n this._prevTime = time;\r\n }\r\n\r\n return time;\r\n }\r\n\r\n update() {\r\n this._startTime = this.end();\r\n }\r\n\r\n show(on) {\r\n if (on === undefined) {\r\n on = true;\r\n }\r\n this.domElement.style.display = on ? 'block' : 'none';\r\n }\r\n}\r\n\r\nexport default Stats;\r\n","/**\r\n * This class introduces the simplest event system.\r\n */\r\n\r\nimport _ from 'lodash';\r\n\r\nfunction isUndefOrEqual(param, value) {\r\n return !param || param === value;\r\n}\r\n\r\n/**\r\n * Creates empty dispatcher.\r\n *\r\n * @exports EventDispatcher\r\n * @constructor\r\n */\r\nfunction EventDispatcher() {\r\n this._handlers = {};\r\n}\r\n\r\n/**\r\n * Binds callback on specific event type. Optional `context` parameter\r\n * could be used as 'this' for the `callback`.\r\n * @param {string} type Event name.\r\n * @param {function} callback Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.addEventListener = function (type, callback, context) {\r\n let handlers = this._handlers[type];\r\n\r\n if (!handlers) {\r\n this._handlers[type] = [];\r\n handlers = this._handlers[type];\r\n }\r\n\r\n const params = [callback, context];\r\n function _checkPar(par) {\r\n return par[0] === params[0] && par[1] === params[1];\r\n }\r\n\r\n if (_.find(handlers, _checkPar) === undefined) {\r\n handlers.push(params);\r\n }\r\n};\r\n\r\n/**\r\n * Removes a previously-bound callback function from an object.\r\n * If no `context` is specified, all versions of the `callback` with different\r\n * contexts will be removed.\r\n * If no `callback` is specified, all callbacks of the `type` will be removed.\r\n * If no `type` is specified, callbacks for all events will be removed.\r\n * @param {?string} [type] Event type.\r\n * @param {function} [callback] Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.removeEventListener = function (type, callback, context) {\r\n const self = this;\r\n _.forEach(self._handlers, (handler, ev) => {\r\n _.remove(handler, (values) => isUndefOrEqual(type, ev)\r\n && isUndefOrEqual(callback, values[0])\r\n && isUndefOrEqual(context, values[1] || self));\r\n });\r\n\r\n this._handlers = _.omitBy(self._handlers, (handler) => handler.length === 0);\r\n};\r\n\r\n/**\r\n * Makes all the callbacks for the specific `event` to trigger.\r\n * @param {Object} event Event.\r\n * @param {string} event.type Type of the event.\r\n */\r\nEventDispatcher.prototype.dispatchEvent = function (event) {\r\n const self = this;\r\n\r\n _.forEach(this._handlers[event.type], (callback) => {\r\n const context = callback[1] || self;\r\n callback[0].apply(context, [event]);\r\n });\r\n};\r\n\r\nexport default EventDispatcher;\r\n","/**\r\n * This module contains class for logging.\r\n * Returns an instance of a logger that have already been created.\r\n * Allows users to log messages for five different levels,\r\n * enable console output and catch signal on each message.\r\n */\r\nimport _ from 'lodash';\r\nimport EventDispatcher from './EventDispatcher';\r\n\r\nconst priorities = {\r\n debug: 0,\r\n info: 1,\r\n report: 2,\r\n warn: 3,\r\n error: 4,\r\n};\r\n\r\n/**\r\n * Create new Logger.\r\n *\r\n * @exports Logger\r\n * @extends EventDispatcher\r\n * @constructor\r\n */\r\nfunction Logger() {\r\n EventDispatcher.call(this);\r\n /** Boolean flag that toggles output to browser console.\r\n * @type {boolean}\r\n */\r\n this.console = false;\r\n this._priority = priorities.warn;\r\n}\r\n\r\nLogger.prototype = Object.create(EventDispatcher.prototype);\r\nLogger.prototype.constructor = Logger;\r\n\r\n/**\r\n * Create new clean instance of the logger.\r\n * @returns {Logger}\r\n */\r\nLogger.prototype.instantiate = function () {\r\n return new Logger();\r\n};\r\n\r\nfunction verify(number) {\r\n if (!_.isNumber(number)) {\r\n throw new Error('Wrong log level specified!');\r\n }\r\n return number;\r\n}\r\n\r\n/**\r\n * @property {string} current threshold for signals and console output.\r\n * @name Logger#level\r\n */\r\nObject.defineProperty(Logger.prototype, 'level', {\r\n get() {\r\n return _.findKey(priorities, (value) => value === this._priority);\r\n },\r\n set(level) {\r\n this._priority = verify(priorities[level]);\r\n },\r\n});\r\n\r\n/**\r\n * Returns the list of all possible level values.\r\n * @returns {Array}\r\n */\r\nLogger.prototype.levels = function () {\r\n return Object.keys(priorities);\r\n};\r\n\r\n/**\r\n * Add new message with specified level.\r\n * @param {string} level - level of the message, must be one of the\r\n * {'debug' | 'info' | 'report' | 'warn' | 'error'}\r\n * @param {string} message\r\n */\r\nLogger.prototype.message = function (level, message) {\r\n const priority = verify(priorities[level]);\r\n this._message(priority, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('debug', ...);\r\n * @param message\r\n */\r\nLogger.prototype.debug = function (message) {\r\n this._message(priorities.debug, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('info', ...);\r\n * @param message\r\n */\r\nLogger.prototype.info = function (message) {\r\n this._message(priorities.info, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('report', ...);\r\n * @param message\r\n */\r\nLogger.prototype.report = function (message) {\r\n this._message(priorities.report, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('warn', ...);\r\n * @param message\r\n */\r\nLogger.prototype.warn = function (message) {\r\n this._message(priorities.warn, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('error', ...);\r\n * @param message\r\n */\r\nLogger.prototype.error = function (message) {\r\n this._message(priorities.error, message);\r\n};\r\n\r\n/**\r\n * Add new message with specified priority.\r\n * @param {number} priority - priority of the message\r\n * @param {string} message\r\n * @private\r\n */\r\nLogger.prototype._message = function (priority, message) {\r\n if (priority < this._priority) {\r\n return;\r\n }\r\n const level = _.findKey(priorities, (value) => value === priority);\r\n message = String(message);\r\n if (this.console) {\r\n const output = `miew:${level}: ${message}`;\r\n if (level === 'error') {\r\n console.error(output); // NOSONAR\r\n } else if (level === 'warn') {\r\n console.warn(output); // NOSONAR\r\n } else {\r\n console.log(output); // NOSONAR\r\n }\r\n }\r\n this.dispatchEvent({ type: 'message', level, message });\r\n};\r\n\r\nexport default new Logger();\r\n","import _ from 'lodash';\r\nimport logger from './utils/logger';\r\n\r\nconst browserType = {\r\n DEFAULT: 0,\r\n SAFARI: 1,\r\n};\r\n//----------------------------------------------------------------------------\r\n// Query string\r\n\r\n/**\r\n * Escape only dangerous chars in a query string component, use a plus instead of a space.\r\n *\r\n * [RFC 3986](https://tools.ietf.org/html/rfc3986) allows the following chars in the query (see 3.4):\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! $ & ' ( ) * + , ; = : @ / ?\r\n *\r\n * For query string elements we need to escape ampersand, equal sign, and plus,\r\n * but encodeURIComponent() function encodes anything except for the following:\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! ' ( ) *\r\n *\r\n * @param {string} text - key or value to encode\r\n * @param {string} excludeExp - regexp for symbols to exclude from encoding\r\n * @returns {string} encoded string\r\n */\r\nfunction encodeQueryComponent(text, excludeExp) {\r\n const encode = (code) => String.fromCharCode(parseInt(code.substr(1), 16));\r\n return encodeURIComponent(text).replace(excludeExp, encode).replace(/%20/g, '+');\r\n}\r\n\r\n/**\r\n * Unescape dangerous chars in a query string component.\r\n *\r\n * @param {string} text - encoded key or value\r\n * @returns {string} decoded string\r\n * @see {@link encodeQueryComponent}\r\n */\r\nfunction decodeQueryComponent(text) {\r\n return decodeURIComponent(text.replace(/\\+/g, ' '));\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Array} array of (key, value) pairs.\r\n */\r\nfunction getUrlParameters(url) {\r\n url = url || window.location.search;\r\n\r\n const query = url.substring(url.indexOf('?') + 1);\r\n const search = /([^&=]+)=?([^&]*)/g;\r\n const result = [];\r\n let match;\r\n\r\n while ((match = search.exec(query)) !== null) { // eslint-disable-line no-cond-assign\r\n result.push([decodeQueryComponent(match[1]), decodeQueryComponent(match[2])]);\r\n }\r\n\r\n return result;\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters as a hash.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Object}\r\n */\r\nfunction getUrlParametersAsDict(url) {\r\n const result = {};\r\n const a = getUrlParameters(url);\r\n for (let i = 0; i < a.length; ++i) {\r\n const [key, value] = a[i];\r\n result[key] = value;\r\n }\r\n return result;\r\n}\r\n\r\nfunction resolveURL(str) {\r\n if (typeof URL !== 'undefined') {\r\n try {\r\n if (typeof window !== 'undefined') {\r\n return new URL(str, window.location).href;\r\n }\r\n return new URL(str).href;\r\n } catch (error) {\r\n // IE 11 has a URL object with no constructor available so just try a different approach instead\r\n }\r\n }\r\n if (typeof document !== 'undefined') {\r\n const anchor = document.createElement('a');\r\n anchor.href = str;\r\n return anchor.href;\r\n }\r\n return str;\r\n}\r\n\r\n/**\r\n * Generates regular expression object that includes all symbols\r\n * listed in the argument\r\n * @param symbolStr {string} - String containing characters list.\r\n * @returns {RegExp} - Regular expression.\r\n */\r\nfunction generateRegExp(symbolStr) {\r\n const symbolList = [];\r\n\r\n for (let i = 0, n = symbolStr.length; i < n; ++i) {\r\n symbolList[symbolList.length] = symbolStr[i].charCodeAt(0).toString(16);\r\n }\r\n\r\n const listStr = symbolList.join('|');\r\n\r\n return new RegExp(`%(?:${listStr})`, 'gi');\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Create HTML element\r\n\r\nfunction createElement(tag, attrs, content) {\r\n const element = document.createElement(tag);\r\n let i;\r\n let n;\r\n if (attrs) {\r\n const keys = Object.keys(attrs);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n element.setAttribute(key, attrs[key]);\r\n }\r\n }\r\n if (content) {\r\n if (!(content instanceof Array)) {\r\n content = [content];\r\n }\r\n for (i = 0, n = content.length; i < n; ++i) {\r\n const child = content[i];\r\n if (typeof child === 'string') {\r\n element.appendChild(document.createTextNode(child));\r\n } else if (child instanceof HTMLElement) {\r\n element.appendChild(child);\r\n }\r\n }\r\n }\r\n return element;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Easy inheritance\r\n\r\n/**\r\n * Derive the class from the base.\r\n * @param cls {function} - Class (constructor) to derive.\r\n * @param base {function} - Class (constructor) to derive from.\r\n * @param members {object=} - Optional instance members to add.\r\n * @param statics {object=} - Optional static class members to add.\r\n * @returns {function} Original class.\r\n */\r\nfunction deriveClass(cls, base, members, statics) {\r\n cls.prototype = _.assign(Object.create(base.prototype), { constructor: cls }, members);\r\n if (statics) {\r\n _.assign(cls, statics);\r\n }\r\n return cls;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Deep prototyping\r\n\r\nfunction deriveDeep(obj, needZeroOwnProperties) {\r\n let res = obj;\r\n let i;\r\n let n;\r\n if (obj instanceof Array) {\r\n res = new Array(obj.length);\r\n for (i = 0, n = obj.length; i < n; ++i) {\r\n res[i] = deriveDeep(obj[i]);\r\n }\r\n } else if (obj instanceof Object) {\r\n res = Object.create(obj);\r\n const keys = Object.keys(obj);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = obj[key];\r\n const copy = deriveDeep(value);\r\n if (copy !== value) {\r\n res[key] = copy;\r\n }\r\n }\r\n if (needZeroOwnProperties && Object.keys(res).length > 0) {\r\n res = Object.create(res);\r\n }\r\n }\r\n return res;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Colors\r\n\r\nfunction hexColor(color) {\r\n const hex = (`0000000${color.toString(16)}`).substr(-6);\r\n return `#${hex}`;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Debug tracing\r\n\r\nfunction DebugTracer(namespace) {\r\n let enabled = false;\r\n\r\n this.enable = function (on) {\r\n enabled = on;\r\n };\r\n\r\n let indent = 0;\r\n const methods = Object.keys(namespace);\r\n\r\n function wrap(method_, name_) {\r\n return function (...args) {\r\n const spaces = DebugTracer.spaces.substr(0, indent * 2);\r\n if (enabled) {\r\n logger.debug(`${spaces + name_} {`);\r\n }\r\n indent++;\r\n const result = method_.apply(this, args); // eslint-disable-line no-invalid-this\r\n indent--;\r\n if (enabled) {\r\n logger.debug(`${spaces}} // ${name_}`);\r\n }\r\n return result;\r\n };\r\n }\r\n\r\n for (let i = 0, n = methods.length; i < n; ++i) {\r\n const name = methods[i];\r\n const method = namespace[name];\r\n if (method instanceof Function && name !== 'constructor') {\r\n namespace[name] = wrap(method, name);\r\n }\r\n }\r\n}\r\n\r\nDebugTracer.spaces = ' ';\r\n\r\nclass OutOfMemoryError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'OutOfMemoryError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction allocateTyped(TypedArrayName, size) {\r\n let result = null;\r\n try {\r\n result = new TypedArrayName(size);\r\n } catch (e) {\r\n if (e instanceof RangeError) {\r\n throw new OutOfMemoryError(e.message);\r\n } else {\r\n throw e;\r\n }\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Float array conversion\r\n\r\nfunction bytesToBase64(/** ArrayBuffer */ buffer) {\r\n const bytes = new Uint8Array(buffer);\r\n let binary = '';\r\n for (let i = 0; i < bytes.byteLength; i++) {\r\n binary += String.fromCharCode(bytes[i]);\r\n }\r\n return window.btoa(binary);\r\n}\r\n\r\nfunction bytesFromBase64(/** string */ str) {\r\n const binary = window.atob(str);\r\n const bytes = new Uint8Array(binary.length);\r\n for (let i = 0; i < bytes.length; ++i) {\r\n bytes[i] = binary[i].charCodeAt(0);\r\n }\r\n return bytes.buffer;\r\n}\r\n\r\nfunction arrayToBase64(/** number[] */ array, /** function */ TypedArrayClass) {\r\n return bytesToBase64(new TypedArrayClass(array).buffer);\r\n}\r\n\r\nfunction arrayFromBase64(/** string */ str, /** function */ TypedArrayClass) {\r\n return Array.prototype.slice.call(new TypedArrayClass(bytesFromBase64(str)));\r\n}\r\n\r\n// NOTE: this is 1-level comparison\r\nfunction compareOptionsWithDefaults(opts, defOpts) {\r\n const optsStr = [];\r\n if (defOpts && opts) {\r\n const keys = Object.keys(opts);\r\n for (let p = 0; p < keys.length; ++p) {\r\n const key = keys[p];\r\n const value = opts[key];\r\n // TODO add processing for tree structure\r\n if (!(value instanceof Object) && typeof defOpts[key] !== 'undefined' && defOpts[key] !== value) {\r\n optsStr.push(`${key}:${value}`);\r\n }\r\n }\r\n if (optsStr.length > 0) {\r\n return `!${optsStr.join()}`;\r\n }\r\n }\r\n return '';\r\n}\r\n\r\nfunction isAlmostPlainObject(o) {\r\n if (_.isPlainObject(o)) {\r\n return true;\r\n }\r\n const proto = o && Object.getPrototypeOf(o);\r\n return !!proto && !proto.hasOwnProperty('constructor') && isAlmostPlainObject(proto);\r\n}\r\n\r\n/**\r\n * Build an object that contains properties (and subproperties) of `src` different from those\r\n * in `dst`. Objects are parsed recursively, other values (including arrays) are compared for\r\n * equality using `_.isEqual()`.\r\n * @param {!object} src - a new object to compare, may contain changed or new properties\r\n * @param {!object} dst - an old reference object\r\n */\r\nfunction objectsDiff(src, dst) {\r\n const diff = {};\r\n _.forIn(src, (srcValue, key) => {\r\n const dstValue = dst[key];\r\n if (isAlmostPlainObject(srcValue) && isAlmostPlainObject(dstValue)) {\r\n const deepDiff = objectsDiff(srcValue, dstValue);\r\n if (!_.isEmpty(deepDiff)) {\r\n diff[key] = deepDiff;\r\n }\r\n } else if (!_.isEqual(srcValue, dstValue)) {\r\n diff[key] = srcValue;\r\n }\r\n });\r\n return diff;\r\n}\r\n\r\nfunction forInRecursive(object, callback) {\r\n function iterateThrough(obj, prefix) {\r\n _.forIn(obj, (value, key) => {\r\n const newPref = prefix + (prefix.length > 0 ? '.' : '');\r\n if (value instanceof Object) {\r\n iterateThrough(value, newPref + key);\r\n } else if (value !== undefined) {\r\n callback(value, newPref + key);\r\n }\r\n });\r\n }\r\n iterateThrough(object, '');\r\n}\r\n\r\nfunction enquoteString(value) {\r\n if (_.isString(value)) {\r\n return `\"${value.replace(/\"/g, '\\\\\"')}\"`;\r\n }\r\n return value;\r\n}\r\n\r\nfunction unquoteString(value) {\r\n if (!_.isString(value)) {\r\n return value;\r\n }\r\n if (value[0] === '\"' && value[value.length - 1] === '\"') {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\\"/g, '\"');\r\n }\r\n if (value[0] === \"'\" && value[value.length - 1] === \"'\") {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\'/g, \"'\");\r\n }\r\n throw new SyntaxError('Incorrect string format, can\\'t unqute it');\r\n}\r\n\r\nfunction getFileExtension(fileName) {\r\n return fileName.slice((Math.max(0, fileName.lastIndexOf('.')) || Infinity));\r\n}\r\n\r\nfunction splitFileName(fileName) {\r\n const ext = getFileExtension(fileName);\r\n const name = fileName.slice(0, fileName.length - ext.length);\r\n return [name, ext];\r\n}\r\n\r\nfunction dataUrlToBlob(url) {\r\n const parts = url.split(/[:;,]/);\r\n const partsCount = parts.length;\r\n if (partsCount >= 3 && parts[partsCount - 2] === 'base64') {\r\n return new Blob([bytesFromBase64(parts[partsCount - 1])]);\r\n }\r\n return null;\r\n}\r\n\r\nfunction getBrowser() {\r\n if (navigator.vendor && navigator.vendor.indexOf('Apple') > -1\r\n && navigator.userAgent\r\n && navigator.userAgent.indexOf('CriOS') === -1\r\n && navigator.userAgent.indexOf('FxiOS') === -1) {\r\n return browserType.SAFARI;\r\n }\r\n return browserType.DEFAULT;\r\n}\r\n\r\nfunction shotOpen(url) {\r\n if (typeof window !== 'undefined') {\r\n window.open().document.write(``);\r\n }\r\n}\r\n\r\nfunction shotDownload(dataUrl, filename) {\r\n if (!dataUrl || dataUrl.substr(0, 5) !== 'data:') {\r\n return;\r\n }\r\n if (!filename) {\r\n filename = ['screenshot-', +new Date(), '.png'].join('');\r\n }\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(dataUrlToBlob(dataUrl), filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(dataUrlToBlob(dataUrl));\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction download(data, filename, type) {\r\n const blobData = new Blob([data]);\r\n\r\n if (!filename) {\r\n filename = ['data', +new Date()].join('');\r\n }\r\n\r\n if (!type) {\r\n filename += blobData.type || '.bin';\r\n } else {\r\n filename += `.${type}`;\r\n }\r\n\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(blobData, filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(blobData);\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction copySubArrays(src, dst, indices, itemSize) {\r\n for (let i = 0, n = indices.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n dst[i * itemSize + j] = src[indices[i] * itemSize + j];\r\n }\r\n }\r\n}\r\n\r\nfunction shallowCloneNode(node) {\r\n const newNode = node.cloneNode(true);\r\n newNode.worldPos = node.worldPos;\r\n // .style property is readonly, so \"newNode.style = node.style;\" won't work (and we don't need it, right?)\r\n return newNode;\r\n}\r\n\r\nconst unquotedStringRE = /^[a-zA-Z0-9_]*$/;\r\nconst enquoteHelper = ['\"', '', '\"'];\r\n\r\n// verify and correct if needed selctor identifier\r\nfunction correctSelectorIdentifier(value) {\r\n if (unquotedStringRE.test(value)) {\r\n return value;\r\n }\r\n // quote incorrect identifier\r\n enquoteHelper[1] = value;\r\n return enquoteHelper.join('');\r\n}\r\n\r\n/**\r\n * Concatenates two TypedArray. Doesn't check null refs o type equality\r\n * Attention! It must be use very rarely because requires memory reallocation every time. Use MergeTypedArraysUnsafe to\r\n * unite array of subarrays.\r\n * @param{TypedArray} first - destination array\r\n * @param{TypedArray} second - source array\r\n * @returns{TypedArray} resulting concatenated array\r\n */\r\nfunction concatTypedArraysUnsafe(first, second) {\r\n const result = new first.constructor(first.length + second.length);\r\n result.set(first);\r\n result.set(second, first.length);\r\n return result;\r\n}\r\n\r\n/**\r\n * Merges array of TypedArray into TypedArray. Doesn't check null refs o type equality\r\n * @param{array} array - source array of subarrays\r\n * @returns{TypedArray} resulting merged array\r\n */\r\nfunction mergeTypedArraysUnsafe(array) {\r\n if (array.length <= 0) {\r\n return null;\r\n }\r\n // count the size\r\n const size = array.reduce((acc, cur) => acc + cur.length, 0);\r\n // create combined array\r\n const result = new array[0].constructor(size);\r\n for (let i = 0, start = 0; i < array.length; i++) {\r\n const count = array[i].length;\r\n result.set(array[i], start);\r\n start += count;\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Exports\r\n\r\nexport default {\r\n browserType,\r\n encodeQueryComponent,\r\n decodeQueryComponent,\r\n getUrlParameters,\r\n getUrlParametersAsDict,\r\n resolveURL,\r\n generateRegExp,\r\n createElement,\r\n deriveClass,\r\n deriveDeep,\r\n hexColor,\r\n DebugTracer,\r\n OutOfMemoryError,\r\n allocateTyped,\r\n bytesFromBase64,\r\n bytesToBase64,\r\n arrayFromBase64,\r\n arrayToBase64,\r\n compareOptionsWithDefaults,\r\n objectsDiff,\r\n forInRecursive,\r\n enquoteString,\r\n unquoteString,\r\n getBrowser,\r\n shotOpen,\r\n shotDownload,\r\n copySubArrays,\r\n shallowCloneNode,\r\n correctSelectorIdentifier,\r\n getFileExtension,\r\n splitFileName,\r\n download,\r\n concatTypedArraysUnsafe,\r\n mergeTypedArraysUnsafe,\r\n};\r\n","import EventDispatcher from './EventDispatcher';\r\n\r\nexport default class JobHandle extends EventDispatcher {\r\n constructor() {\r\n super();\r\n this._shouldCancel = false;\r\n }\r\n\r\n cancel() {\r\n this._shouldCancel = true;\r\n this.dispatchEvent({ type: 'cancel' });\r\n }\r\n\r\n shouldCancel() {\r\n return this._shouldCancel;\r\n }\r\n\r\n // slaves use this to notify master about their events\r\n // master routes these notifications to a single event slot\r\n notify(event) {\r\n this.dispatchEvent({ type: 'notification', slaveEvent: event });\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport utils from './utils';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\n\r\nconst VERSION = 0;\r\n\r\n//----------------------------------------------------------------------------\r\n// DEFAULT SETTINGS\r\n//----------------------------------------------------------------------------\r\n\r\n/**\r\n * Polygonal complexity settings.\r\n *\r\n * @typedef PolyComplexity\r\n * @property {number} poor\r\n * @property {number} low\r\n * @property {number} medium\r\n * @property {number} high\r\n * @property {number} ultra\r\n */\r\n\r\n/**\r\n * @alias SettingsObject\r\n * @namespace\r\n */\r\nconst defaults = {\r\n /**\r\n * Default options for all available modes.\r\n * Use {@link Mode.id} as a dictionary key to access mode options.\r\n *\r\n * Usually you don't need to override these settings. You may specify mode options as a parameter during\r\n * {@link Mode} construction.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {LinesModeOptions} LN - Lines mode options.\r\n * @property {LicoriceModeOptions} LC - Licorice mode options.\r\n * @property {BallsAndSticksModeOptions} BS - Balls and Sticks mode options.\r\n * @property {VanDerWaalsModeOptions} VW - Van der Waals mode options.\r\n * @property {TraceModeOptions} TR - Trace mode options.\r\n * @property {TubeModeOptions} TU - Tube mode options.\r\n * @property {CartoonModeOptions} CA - Cartoon mode options.\r\n * @property {QuickSurfaceModeOptions} QS - Contact Surface mode options.\r\n * @property {IsoSurfaceSASModeOptions} SA - Solvent Accessible Surface mode options.\r\n * @property {IsoSurfaceSESModeOptions} SE - Solvent Excluded Surface mode options.\r\n * @property {ContactSurfaceModeOptions} CS - Contact Surface mode options.\r\n * @property {TextModeOptions} TX - Text mode options.\r\n * @property {VolumeDensityModeOptions} VD - Volume Density mode options.\r\n */\r\n modes: {\r\n //----------------------------------------------------------------------------\r\n // BALLS AND STICKS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Balls and Sticks mode options.\r\n *\r\n * @typedef BallsAndSticksModeOptions\r\n *\r\n * @property {number} atom - Sphere radius as a fraction of Van der Waals atom radius.\r\n * @property {number} bond - Cylinder radius in angstroms.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n BS: {\r\n atom: 0.23,\r\n bond: 0.15,\r\n space: 0.5,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VAN DER WAALS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Van der Waals mode options.\r\n *\r\n * @typedef VanDerWaalsModeOptions\r\n *\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VW: {\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 8,\r\n high: 16,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LINES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Lines mode options.\r\n *\r\n * @typedef LinesModeOptions\r\n *\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {number} offsarom - Offset between bonds and aromatic cycle.\r\n * @property {number} chunkarom - Number of pieces in a-loop arc, corresponding to atom.\r\n * @property {number} atom - Collision radius for atoms picking.\r\n * @property {number} lineWidth - Line width in pixels (not used in thin lines).\r\n */\r\n LN: {\r\n multibond: true,\r\n showarom: true,\r\n offsarom: 0.2,\r\n chunkarom: 10,\r\n atom: 0.23,\r\n lineWidth: 2,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LICORICE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Licorice mode options.\r\n *\r\n * @typedef LicoriceModeOptions\r\n *\r\n * @property {number} bond - Bond cylinder radius.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Poly complexity values for render modes.\r\n */\r\n LC: {\r\n bond: 0.20,\r\n space: 0.0,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SAS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Accessible Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSASModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SA: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Excluded Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSESModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SE: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // QUICK SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Quick Surface mode options.\r\n *\r\n * @typedef QuickSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} scale - Radius scale for the surface being built.\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} gaussLim - Gauss lim for coloring the bigger the value, the smoother our colors are.\r\n * @property {PolyComplexity} gridSpacing - Poly complexity values for render modes. In this case the value\r\n * corresponds to the grid density.\r\n */\r\n QS: {\r\n isoValue: 0.5,\r\n gaussLim: {\r\n poor: 1.5,\r\n low: 2.0,\r\n medium: 2.5,\r\n high: 3.0,\r\n ultra: 4.0,\r\n },\r\n scale: 1.0,\r\n wireframe: false,\r\n gridSpacing: {\r\n poor: 2,\r\n low: 1.5,\r\n medium: 1,\r\n high: 0.5,\r\n ultra: 0.25,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CONTACT SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Contact Surface mode options.\r\n *\r\n * @typedef ContactSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} probeRadius - Probe radius.\r\n * @property {number} probePositions\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Radius scale for the surface being built.\r\n * Poly complexity values for render modes. In this case the value corresponds to the grid density.\r\n */\r\n CS: {\r\n probeRadius: 1.4,\r\n isoValue: 1.5,\r\n wireframe: false,\r\n probePositions: 30,\r\n polyComplexity: {\r\n poor: 0.5,\r\n low: 1.0,\r\n medium: 1.5,\r\n high: 1.75,\r\n ultra: 2.0,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TRACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Trace mode options.\r\n *\r\n * @typedef TraceModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n TR: {\r\n radius: 0.30,\r\n polyComplexity: {\r\n poor: 12,\r\n low: 16,\r\n medium: 32,\r\n high: 64,\r\n ultra: 64,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TUBE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Tube mode options.\r\n *\r\n * @typedef TubeModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {number} tension - Tension for interpolation.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n TU: {\r\n radius: 0.30,\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CARTOON\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Cartoon mode options.\r\n *\r\n * @typedef CartoonModeOptions\r\n *\r\n * @property {number} radius - Standard tube radius.\r\n * @property {number} depth - Height of the secondary structure ribbon.\r\n * @property {number} tension - Tension for interpolation.\r\n * @proprety {object} ss - Secondary structure parameters.\r\n * @proprety {object} ss.helix - Options for helices render.\r\n * @proprety {number} ss.helix.width - Width of the secondary structure ribbon.\r\n * @proprety {number} ss.helix.arrow - Secondary structure's arrow width.\r\n * @proprety {object} ss.strand - Options for strands render.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * polyComplexity must be even for producing symmetric arrows.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n CA: {\r\n radius: 0.30,\r\n depth: 0.25,\r\n ss: {\r\n helix: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n strand: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n },\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TEXT\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Text mode options.\r\n *\r\n * @typedef TextModeOptions\r\n *\r\n * @property {string} template - Format string for building output text.\r\n * @property {string} horizontalAlign - Text alignment ('left', 'right', 'center').\r\n * @property {string} verticalAlign - Vertical text box alignment ('top', 'bottom', 'middle').\r\n * @property {number} dx - Text offset x in angstroms.\r\n * @property {number} dy - Text offset y in angstroms.\r\n * @property {number} dz - Text offset z in angstroms.\r\n * @property {string} fg - Color rule for foreground.\r\n * @property {string} bg - Color rule for background.\r\n * @property {boolean} showBg - Flag, that toggles background rendering.\r\n *\r\n */\r\n TX: {\r\n template: '{{Chain}}.{{Residue}}{{Sequence}}.{{Name}}',\r\n horizontalAlign: 'center',\r\n verticalAlign: 'middle',\r\n dx: 0,\r\n dy: 0,\r\n dz: 1,\r\n fg: 'none',\r\n bg: '0x202020',\r\n showBg: true,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VOLUME DENSITY\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Volume density mode options.\r\n *\r\n * @typedef VolumeDensityModeOptions\r\n *\r\n * @property {number} kSigma - Noise threshold coefficient.\r\n * @property {boolean} frame - flag, that turns on box frame painting.\r\n * @property {boolean} isoMode - flag, that turns on IsoSurface mode instead of Volume Rendering.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VD: {\r\n kSigma: 1.0,\r\n kSigmaMed: 2.0,\r\n kSigmaMax: 4.0,\r\n frame: true,\r\n isoMode: false,\r\n polyComplexity: {\r\n poor: 2,\r\n low: 3,\r\n medium: 4,\r\n high: 8,\r\n ultra: 10,\r\n },\r\n },\r\n },\r\n\r\n /**\r\n * Default options for all available colorers.\r\n * Use {@link Colorer.id} as a dictionary key to access colorer options.\r\n *\r\n * Usually you don't need to override these settings. You may specify colorer options as a parameter during\r\n * {@link Colorer} construction.\r\n *\r\n * Not all colorers have options.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {ElementColorerOptions} EL - Element colorer options.\r\n * @property {SequenceColorerOptions} SQ - Sequence colorer options.\r\n * @property {MoleculeColorerOptions} MO - Molecule colorer options.\r\n * @property {UniformColorerOptions} UN - Uniform colorer options.\r\n * @property {ConditionalColorerOptions} CO - Conditional colorer options.\r\n * @property {TemperatureColorerOptions} TM - Temperature colorer options.\r\n * @property {OccupancyColorerOptions} OC - Occupancy colorer options.\r\n * @property {HydrophobicityColorerOptions} HY - Hydrophobicity colorer options.\r\n */\r\n colorers: {\r\n /**\r\n * Element colorer options.\r\n *\r\n * @typedef ElementColorerOptions\r\n *\r\n * @property {number} carbon - Carbon color or -1 to use default.\r\n */\r\n EL: {\r\n carbon: -1,\r\n },\r\n\r\n /**\r\n * Uniform colorer options.\r\n *\r\n * @typedef UniformColorerOptions\r\n *\r\n * @property {number} color - Single color to paint with.\r\n */\r\n UN: {\r\n color: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Conditional colorer options.\r\n *\r\n * @typedef ConditionalColorerOptions\r\n *\r\n * @property {string} subset - Selector string.\r\n * @property {number} color - Color of selected atoms.\r\n * @property {number} baseColor - Color of other atoms.\r\n */\r\n CO: {\r\n subset: 'charged',\r\n color: 0xFF0000,\r\n baseColor: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Carbon colorer options.\r\n *\r\n * @typedef CarbonColorerOptions\r\n *\r\n * @property {number} color - Single color to paint carbons\r\n * @property {number} factor - Color factor for not carbon atoms.\r\n */\r\n CB: {\r\n color: 0x909090,\r\n factor: 0.6,\r\n },\r\n\r\n /**\r\n * Sequence colorer options.\r\n *\r\n * @typedef SequenceColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n SQ: {\r\n gradient: 'rainbow',\r\n },\r\n\r\n /**\r\n * Temperature colorer options.\r\n *\r\n * @typedef TemperatureColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n * @property {number} min - Minimal temperature.\r\n * @property {number} max - Maximal temperature.\r\n */\r\n TM: {\r\n gradient: 'temp',\r\n min: 5,\r\n max: 40,\r\n },\r\n\r\n /**\r\n * Occupancy colorer options.\r\n *\r\n * @typedef OccupancyColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n OC: {\r\n gradient: 'reds',\r\n },\r\n\r\n /**\r\n * Hydrophobicity colorer options.\r\n *\r\n * @typedef HydrophobicityColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n HY: {\r\n gradient: 'blue-red',\r\n },\r\n\r\n /**\r\n * Molecule colorer options.\r\n *\r\n * @typedef MoleculeColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n MO: {\r\n gradient: 'rainbow',\r\n },\r\n },\r\n\r\n /*\r\n * Use antialiasing in WebGL.\r\n * @type {boolean}\r\n */\r\n antialias: true,\r\n\r\n /*\r\n * Camera field of view in degrees.\r\n * @type {number}\r\n */\r\n camFov: 45.0,\r\n\r\n /*\r\n * Camera near plane distance.\r\n * @type {number}\r\n */\r\n camNear: 0.5,\r\n\r\n /*\r\n * Camera far plane distance.\r\n * @type {number}\r\n */\r\n camFar: 100.0,\r\n\r\n camDistance: 2.5,\r\n\r\n radiusToFit: 1.0,\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogNearFactor: 0.5, // [0, 1]\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogFarFactor: 1, // [0, 1]\r\n fogAlpha: 1.0,\r\n fogColor: 0x000000,\r\n fogColorEnable: false,\r\n\r\n /**\r\n * Palette used for molecule coloring.\r\n * @type {string}\r\n */\r\n palette: 'JM',\r\n\r\n /*\r\n * Geometry resolution.\r\n * @type {string}\r\n */\r\n resolution: 'medium',\r\n\r\n autoResolution: false/* true */,\r\n\r\n autoPreset: true,\r\n\r\n preset: 'default', // TODO: remove 'preset' from settings, implement autodetection\r\n\r\n presets: {\r\n // Default\r\n default: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n empty: [],\r\n\r\n // Wireframe\r\n wire: [{\r\n mode: 'LN',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Small molecules\r\n small: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Proteins, nucleic acids etc.\r\n macro: [{\r\n mode: 'CA',\r\n colorer: 'SS',\r\n selector: 'not hetatm',\r\n material: 'SF',\r\n }, {\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'hetatm and not water',\r\n material: 'SF',\r\n }],\r\n },\r\n\r\n objects: {\r\n line: {\r\n color: 0xFFFFFFFF,\r\n dashSize: 0.3,\r\n gapSize: 0.05,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n\r\n bg: {\r\n color: 0x202020,\r\n transparent: false,\r\n },\r\n\r\n draft: {\r\n clipPlane: false,\r\n clipPlaneFactor: 0.5,\r\n clipPlaneSpeed: 0.00003,\r\n },\r\n\r\n /*\r\n * Separate group for plugins.\r\n * Each plugin handles its field by itself.\r\n */\r\n plugins: {\r\n\r\n },\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n axes: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fog: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fps: true,\r\n\r\n /**\r\n * Switch using of z-sprites for sphere and cylinder geometry\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zSprites: true,\r\n\r\n isoSurfaceFakeOpacity: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n suspendRender: true,\r\n\r\n nowater: false,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autobuild: true,\r\n\r\n /**\r\n * Anti-aliasing.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fxaa: true,\r\n /**\r\n * Outline depths\r\n * @type {boolean}\r\n * @instance\r\n */\r\n outline: {\r\n on: false,\r\n color: 0x000000,\r\n threshold: 0.1,\r\n thickness: 1,\r\n },\r\n\r\n /**\r\n * Ambient Occlusion special effect.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n ao: false,\r\n\r\n /**\r\n * Shadows options.\r\n *\r\n * @property {boolean} shadowMap - enable/disable.\r\n * @property {string} basic/percentage-closer filtering/non-uniform randomizing pcf.\r\n * @property {number} radius for percentage-closer filtering.\r\n */\r\n shadow: {\r\n on: false,\r\n type: 'random'/* basic, pcf, random */,\r\n radius: 1.0,\r\n },\r\n\r\n /**\r\n * Auto-rotation with constant speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n autoRotation: 0.0,\r\n\r\n /**\r\n * Set maximum fps for animation.\r\n * @type {number}\r\n * @instance\r\n */\r\n maxfps: 30,\r\n\r\n /**\r\n * Set fbx output precision.\r\n * @type {number}\r\n * @instance\r\n */\r\n fbxprec: 4,\r\n\r\n /**\r\n * Auto-rotation axis.\r\n *\r\n * - true: complex auto-rotation is about vertical axis\r\n * - false: rotation axis is defined by last user rotation\r\n *\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autoRotationAxisFixed: true,\r\n\r\n /**\r\n * Enable zooming with mouse wheel or pinch gesture.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zooming: true,\r\n\r\n /**\r\n * Enable picking atoms & residues with left mouse button or touch.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n picking: true,\r\n\r\n /**\r\n * Set picking mode ('atom', 'residue', 'chain', 'molecule').\r\n * @type {string}\r\n * @instance\r\n */\r\n pick: 'atom',\r\n\r\n /**\r\n * Make \"component\" and \"fragment\" editing modes available.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n editing: false,\r\n\r\n /**\r\n * Detect aromatic loops.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n aromatic: false,\r\n\r\n /**\r\n * Load only one biological unit from all those described in PDB file.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n singleUnit: true,\r\n\r\n /**\r\n * Set stereo mode ('NONE', 'SIMPLE', 'DISTORTED', 'ANAGLYPH', 'WEBVR').\r\n * @type {string}\r\n * @instance\r\n */\r\n stereo: 'NONE',\r\n\r\n /**\r\n * Enable smooth transition between views\r\n * @type {boolean}\r\n * @instance\r\n */\r\n interpolateViews: true,\r\n\r\n /**\r\n * Set transparency mode ('standard', 'prepass').\r\n * @type {string}\r\n * @instance\r\n */\r\n transparency: 'prepass',\r\n\r\n /**\r\n * Mouse translation speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n translationSpeed: 2,\r\n\r\n debug: {\r\n example: 3.5,\r\n text: 'hello!',\r\n good: true,\r\n ssaoKernelRadius: 0.7,\r\n ssaoFactor: 0.7,\r\n stereoBarrel: 0.25,\r\n },\r\n use: {\r\n multiFile: false,\r\n },\r\n};\r\n\r\n//----------------------------------------------------------------------------\r\n// SETTINGS CLASS\r\n//----------------------------------------------------------------------------\r\n\r\nfunction Settings() {\r\n EventDispatcher.call(this);\r\n\r\n this.old = null;\r\n this.now = {};\r\n this._changed = {};\r\n\r\n this.reset();\r\n}\r\n\r\nutils.deriveClass(Settings, EventDispatcher, {\r\n defaults,\r\n\r\n set(path, value) {\r\n if (_.isString(path)) {\r\n const oldValue = _.get(this.now, path);\r\n if (oldValue !== value) {\r\n _.set(this.now, path, value);\r\n this._notifyChange(path, value);\r\n }\r\n } else {\r\n const diff = utils.objectsDiff(path, this.now);\r\n if (!_.isEmpty(diff)) {\r\n _.merge(this.now, diff);\r\n this._notifyChanges(diff);\r\n }\r\n }\r\n },\r\n\r\n get(path, defaultValue) {\r\n return _.get(this.now, path, defaultValue);\r\n },\r\n\r\n reset() {\r\n const diff = utils.objectsDiff(defaults, this.now);\r\n this.now = _.cloneDeep(defaults);\r\n this.old = null;\r\n this._notifyChanges(diff);\r\n this._changed = {};\r\n },\r\n\r\n checkpoint() {\r\n this.old = _.cloneDeep(this.now);\r\n this._changed = {};\r\n },\r\n\r\n _notifyChange(path, value) {\r\n this._changed[path] = true;\r\n this.dispatchEvent({ type: `change:${path}`, value });\r\n },\r\n\r\n _notifyChanges(diff) {\r\n utils.forInRecursive(diff, (deepValue, deepPath) => {\r\n this._notifyChange(deepPath, deepValue);\r\n });\r\n },\r\n\r\n changed() {\r\n if (!this.old) {\r\n return [];\r\n }\r\n const { old, now } = this;\r\n const keys = _.filter(Object.keys(this._changed), (key) => _.get(old, key) !== _.get(now, key));\r\n return keys;\r\n },\r\n\r\n applyDiffs(diffs) {\r\n if (diffs.hasOwnProperty('VERSION') && diffs.VERSION !== VERSION) {\r\n throw new Error('Settings version does not match!');\r\n }\r\n // VERSION shouldn't be presented inside settings structure\r\n delete diffs.VERSION;\r\n this.reset();\r\n this.set(diffs);\r\n },\r\n\r\n getDiffs(versioned) {\r\n const diffs = utils.objectsDiff(this.now, defaults);\r\n if (versioned) {\r\n diffs.VERSION = VERSION;\r\n }\r\n return diffs;\r\n },\r\n\r\n setPluginOpts(plugin, opts) {\r\n defaults.plugins[plugin] = _.cloneDeep(opts);\r\n this.now.plugins[plugin] = _.cloneDeep(opts);\r\n },\r\n});\r\n\r\nexport default new Settings();\r\n","import _ from 'lodash';\r\nimport settings from './settings';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\n\r\nlet repIndex = 0;\r\n\r\nfunction asBoolean(value) {\r\n return !(!value || value === '0' || (_.isString(value) && value.toLowerCase() === 'false'));\r\n}\r\n\r\nconst adapters = {\r\n string: String,\r\n number: Number,\r\n boolean: asBoolean,\r\n};\r\n\r\n// Level 1 assignment symbol\r\nconst cL1Ass = '=';\r\n\r\nconst cOptsSep = '!';\r\n// Level 2 (options) assignment symbol\r\nconst cL2Ass = ':';\r\n// Level 2 (options) separator symbol\r\nconst cLSep = ',';\r\n\r\nconst cCommonIgnoreSymbols = '$;@/?';\r\n/**\r\n * We may (and should) leave as is for better readability:\r\n *\r\n * $ , ; : @ / ?\r\n */\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n */\r\nfunction getLevel1ExcludedExpr() {\r\n const cLevel1Ignores = ':,';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel1Ignores);\r\n}\r\n\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n * (options, etc, ..)\r\n */\r\nfunction getLevel2ExcludedExpr() {\r\n const cLevel2Ignores = ' ';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel2Ignores);\r\n}\r\n\r\nconst cL1ExclExpr = getLevel1ExcludedExpr();\r\nfunction encodeQueryComponentL1(value) {\r\n return utils.encodeQueryComponent(value, cL1ExclExpr);\r\n}\r\n\r\nconst cL2ExclExpr = getLevel2ExcludedExpr();\r\nfunction encodeQueryComponentL2(value) {\r\n return utils.encodeQueryComponent(value, cL2ExclExpr);\r\n}\r\n\r\nfunction ensureRepList(opts) {\r\n let { reps } = opts;\r\n if (!reps) {\r\n const { presets } = settings.now;\r\n let preset = opts.preset || settings.now.preset;\r\n reps = presets[preset];\r\n if (!reps) {\r\n logger.warn(`Unknown preset \"${preset}\"`);\r\n [preset] = Object.keys(presets);\r\n reps = presets[preset]; // fall back to any preset\r\n }\r\n opts.preset = preset;\r\n opts.reps = utils.deriveDeep(reps, true);\r\n }\r\n}\r\n\r\nfunction ensureRepAssign(opts, prop, value) {\r\n ensureRepList(opts);\r\n const rep = opts.reps[repIndex];\r\n // prop specified twice therefore start new rep by cloning the current\r\n if (rep.hasOwnProperty(prop)) {\r\n repIndex = opts.reps.length;\r\n opts.reps[repIndex] = utils.deriveDeep(rep, true);\r\n }\r\n if (value !== undefined) {\r\n opts.reps[repIndex][prop] = value;\r\n }\r\n}\r\n\r\nfunction addObject(opts, params, options) {\r\n if (opts._objects === undefined) {\r\n opts._objects = [];\r\n }\r\n\r\n const [type, newOpts] = options;\r\n const newObj = {\r\n type,\r\n params,\r\n };\r\n\r\n if (newOpts !== undefined) {\r\n newObj.opts = newOpts;\r\n }\r\n\r\n opts._objects[opts._objects.length] = newObj;\r\n}\r\n\r\nfunction parseParams(str, params) {\r\n const sep = str.indexOf(',');\r\n if (sep >= 0) {\r\n params.push(str.substr(sep + 1).split(','));\r\n return str.substr(0, sep);\r\n }\r\n // keep this untouched if no params were extracted\r\n return str;\r\n}\r\n\r\nfunction extractArgs(input, defaultsDict, params) {\r\n if (input) {\r\n const bang = input.indexOf(cOptsSep);\r\n const inputVal = parseParams(input.substr(0, bang >= 0 ? bang : undefined), params);\r\n if (bang >= 0) {\r\n const args = input.substr(bang + 1).split(cLSep);\r\n input = inputVal;\r\n if (defaultsDict) {\r\n const defaults = defaultsDict[input];\r\n const opts = utils.deriveDeep(defaults, true);\r\n args.forEach((arg) => {\r\n const pair = arg.split(cL2Ass, 2);\r\n const key = decodeURIComponent(pair[0]);\r\n const value = decodeURIComponent(pair[1]);\r\n const adapter = adapters[typeof _.get(defaults, key)];\r\n if (adapter) {\r\n _.set(opts, key, adapter(value));\r\n } else {\r\n logger.warn(`Unknown argument \"${key}\" for option \"${input}\"`);\r\n }\r\n });\r\n if (Object.keys(opts).length > 0) {\r\n input = [input, opts];\r\n }\r\n }\r\n } else {\r\n input = inputVal;\r\n }\r\n }\r\n return input;\r\n}\r\n\r\nconst actions = {\r\n\r\n l: 'load',\r\n load: String,\r\n t: 'type',\r\n type: String,\r\n v: 'view',\r\n view: String,\r\n u: 'unit',\r\n unit: Number,\r\n menu: asBoolean,\r\n\r\n // Commands\r\n\r\n o: 'object',\r\n object(value, opts) {\r\n const params = [];\r\n let options = extractArgs(value, settings.defaults.objects, params);\r\n if (!Array.isArray(options)) {\r\n options = [options];\r\n }\r\n addObject(opts, params[0], options);\r\n },\r\n\r\n p: 'preset',\r\n preset(value, opts) {\r\n opts.preset = value;\r\n opts.reps = null;\r\n ensureRepList(opts);\r\n },\r\n\r\n r: 'rep',\r\n rep(value, opts) {\r\n ensureRepList(opts);\r\n repIndex = Number(value);\r\n // clamp the index to one greater than the last\r\n repIndex = repIndex <= opts.reps.length ? (repIndex < 0 ? 0 : repIndex) : opts.reps.length;\r\n // create a new rep if it is adjacent to the existing ones\r\n if (repIndex === opts.reps.length) {\r\n // if there is no rep to derive from, derive from the first rep of the default\r\n opts.reps[repIndex] = repIndex > 0 ? utils.deriveDeep(opts.reps[repIndex - 1], true)\r\n : utils.deriveDeep(settings.defaults.presets.default[0], true);\r\n }\r\n },\r\n\r\n s: 'select',\r\n select(value, opts) {\r\n ensureRepAssign(opts, 'selector', value);\r\n },\r\n\r\n m: 'mode',\r\n mode(value, opts) {\r\n ensureRepAssign(opts, 'mode', extractArgs(value, settings.defaults.modes));\r\n },\r\n\r\n c: 'color',\r\n color(value, opts) {\r\n ensureRepAssign(opts, 'colorer', extractArgs(value, settings.defaults.colorers));\r\n },\r\n\r\n mt: 'material',\r\n material(value, opts) {\r\n ensureRepAssign(opts, 'material', extractArgs(value, settings.defaults.materials));\r\n },\r\n\r\n dup(value, opts) {\r\n ensureRepList(opts);\r\n const { reps } = opts;\r\n const rep = reps[repIndex];\r\n repIndex = reps.length;\r\n reps[repIndex] = utils.deriveDeep(rep, true);\r\n },\r\n\r\n // Settings shortcuts\r\n\r\n ar: 'autoResolution',\r\n};\r\n\r\nfunction _fromArray(entries) {\r\n repIndex = 0;\r\n\r\n const opts = {};\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const /** string[] */ entry = entries[i];\r\n let /** string? */ key = entry[0];\r\n const /** string? */ value = entry[1];\r\n let /** function|string? */ action = actions[key];\r\n\r\n // unwind shortcuts and aliases\r\n while (_.isString(action)) {\r\n key = action;\r\n action = actions[key];\r\n }\r\n\r\n // either set a property or use specialized parser\r\n if (!action) {\r\n const adapter = adapters[typeof _.get(settings.defaults, key)];\r\n if (adapter) {\r\n _.set(opts, `settings.${key}`, adapter(value));\r\n } else {\r\n logger.warn(`Unknown option \"${key}\"`);\r\n }\r\n } else if (_.isFunction(action)) {\r\n const result = action(value, opts);\r\n if (result !== undefined) {\r\n opts[key] = result;\r\n }\r\n }\r\n }\r\n\r\n return opts;\r\n}\r\n\r\nfunction fromAttr(attr) {\r\n return _fromArray(utils.getUrlParameters(`?${attr || ''}`));\r\n}\r\n\r\nfunction fromURL(url) {\r\n return _fromArray(utils.getUrlParameters(url));\r\n}\r\n\r\nfunction _processOptsForURL(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = encodeQueryComponentL2(key) + cL2Ass + encodeQueryComponentL2(value);\r\n });\r\n return str.join(cLSep);\r\n}\r\n\r\nfunction _processArgsForURL(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]}${cOptsSep}${_processOptsForURL(args[1])}`;\r\n}\r\n\r\nfunction _processObjForURL(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += `,${objOpts.params.join(',')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += cOptsSep + _processOptsForURL(objOpts.opts);\r\n }\r\n return res;\r\n}\r\n\r\nfunction toURL(opts) {\r\n const stringList = [];\r\n let idx = 0;\r\n\r\n function checkAndAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n stringList[idx++] = encodeQueryComponentL1(prefix)\r\n + cL1Ass + encodeQueryComponentL1(value);\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n if (_.isEmpty(repList[i])) {\r\n continue;\r\n }\r\n checkAndAdd('r', i);\r\n checkAndAdd('s', repList[i].selector);\r\n checkAndAdd('m', _processArgsForURL(repList[i].mode));\r\n checkAndAdd('c', _processArgsForURL(repList[i].colorer));\r\n checkAndAdd('mt', _processArgsForURL(repList[i].material));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('o', _processObjForURL(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('l', opts.load);\r\n checkAndAdd('u', opts.unit);\r\n checkAndAdd('p', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n checkAndAdd('v', opts.view);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(key, value);\r\n });\r\n\r\n let url = '';\r\n if (typeof window !== 'undefined') {\r\n const { location } = window;\r\n url = `${location.protocol}//${location.host}${location.pathname}`;\r\n }\r\n if (stringList.length > 0) {\r\n url += `?${stringList.join('&')}`;\r\n }\r\n\r\n return url;\r\n}\r\n\r\nfunction _processOptsForScript(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = `${key}=${utils.enquoteString(value)}`;\r\n });\r\n return str.join(' ');\r\n}\r\n\r\nfunction _processArgsForScript(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]} ${_processOptsForScript(args[1])}`;\r\n}\r\n\r\nfunction _processObjForScript(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += ` ${objOpts.params.map(utils.enquoteString).join(' ')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += ` ${_processOptsForScript(objOpts.opts)}`;\r\n }\r\n return res;\r\n}\r\n\r\nfunction _processRepsForScript(rep, index) {\r\n const repString = [];\r\n let strIdx = 0;\r\n function localAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n repString[strIdx++] = prefix + value;\r\n }\r\n }\r\n if (_.isEmpty(rep)) {\r\n return null;\r\n }\r\n localAdd('', index);\r\n localAdd('s=', utils.enquoteString(rep.selector));\r\n localAdd('m=', _processArgsForScript(rep.mode));\r\n localAdd('c=', _processArgsForScript(rep.colorer));\r\n localAdd('mt=', _processArgsForScript(rep.material));\r\n return repString.join(' ');\r\n}\r\n\r\nfunction toScript(opts) {\r\n const commandsList = [];\r\n let idx = 0;\r\n function checkAndAdd(command, value, saveQuotes) {\r\n if (value !== null && value !== undefined) {\r\n const quote = (typeof value === 'string' && saveQuotes) ? '\"' : '';\r\n commandsList[idx++] = `${command} ${quote}${value}${quote}`.trim();\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n checkAndAdd('rep', _processRepsForScript(repList[i], i));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('', _processObjForScript(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('set', 'autobuild false');\r\n checkAndAdd('load', opts.load, true);\r\n checkAndAdd('unit', opts.unit);\r\n checkAndAdd('preset', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(`set ${key}`, value, true);\r\n });\r\n checkAndAdd('view', opts.view);\r\n checkAndAdd('set', 'autobuild true');\r\n return commandsList.join('\\n');\r\n}\r\n\r\nexport default {\r\n fromURL,\r\n fromAttr,\r\n adapters,\r\n toURL,\r\n toScript,\r\n};\r\n","/**\r\n * Atom measurements.\r\n *\r\n * @param {Residue} residue - (required) Residue containing the atom\r\n * @param {string} name - (required) Name, unique in the residue\r\n * @param {Element} type - (required) Chemical element reference\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n *\r\n * @param {number} role - Role of atom inside monomer: Lead and wing are particularity interesting\r\n * @param {boolean} het - Non-standard residue indicator\r\n *\r\n * @param {number} serial - Serial number, unique in the model\r\n * @param {string} location - Alternative location indicator (usually space or A-Z)\r\n * @param {number} occupancy - Occupancy percentage, from 0 to 1\r\n * @param {number} temperature - Temperature\r\n * @param {number} charge - Charge\r\n *\r\n * @exports Atom\r\n * @constructor\r\n */\r\n\r\nclass Atom {\r\n constructor(residue, name, type, position, role, het, serial, location, occupancy, temperature, charge) {\r\n this.index = -1;\r\n this.residue = residue;\r\n this.name = name;\r\n this.element = type;\r\n this.position = position;\r\n this.role = role;\r\n this.mask = 1 | 0;\r\n\r\n this.het = het;\r\n\r\n this.serial = serial;\r\n this.location = (location || ' ').charCodeAt(0);\r\n this.occupancy = occupancy || 1;\r\n this.temperature = temperature;\r\n this.charge = charge;\r\n this.hydrogenCount = -1; // explicitly invalid\r\n this.radicalCount = 0;\r\n this.valence = -1; // explicitly invalid\r\n\r\n this.bonds = [];\r\n\r\n this.flags = 0x0000;\r\n if (type.name === 'H') {\r\n this.flags |= Atom.Flags.HYDROGEN;\r\n } else if (type.name === 'C') {\r\n this.flags |= Atom.Flags.CARBON;\r\n }\r\n }\r\n\r\n isHet() {\r\n return this.het;\r\n }\r\n\r\n isHydrogen() {\r\n return this.element.number === 1;\r\n }\r\n\r\n getVisualName() {\r\n const { name } = this;\r\n if (name.length > 0) {\r\n return name;\r\n }\r\n return this.element.name.trim();\r\n }\r\n\r\n forEachBond(process) {\r\n const { bonds } = this;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n getFullName() {\r\n let name = '';\r\n if (this.residue !== null) {\r\n if (this.residue._chain !== null) {\r\n name += `${this.residue._chain.getName()}.`;\r\n }\r\n name += `${this.residue._sequence}.`;\r\n }\r\n name += this.name;\r\n return name;\r\n }\r\n\r\n /**\r\n * Enumeration of atom flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n CARBON: 0x0001,\r\n // OXYGEN: 0x0002,\r\n // NITROGEN: 0x0004,\r\n HYDROGEN: 0x0008,\r\n /** Non-polar hydrogen (it is also a HYDROGEN) */\r\n NONPOLARH: 0x1008,\r\n };\r\n}\r\n\r\nexport default Atom;\r\n","class Element {\r\n constructor(number, name, fullName, weight, radius, radiusBonding, hValency) {\r\n this.number = number;\r\n this.name = name;\r\n this.fullName = fullName;\r\n this.weight = weight;\r\n this.radius = radius;\r\n this.radiusBonding = radiusBonding;\r\n this.hydrogenValency = hValency;\r\n }\r\n\r\n static Constants = {\r\n /* eslint-disable no-magic-numbers */\r\n U1: 1,\r\n Lead: 2,\r\n U2: 3,\r\n Wing: 4,\r\n U18: 18,\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n static Role = {\r\n /* eslint-disable no-magic-numbers */\r\n N: Element.Constants.U1,\r\n CA: Element.Constants.Lead,\r\n C: Element.Constants.U2,\r\n O: Element.Constants.Wing,\r\n SG: Element.Constants.U18,\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByAtomicNumber = [\r\n /* eslint-disable no-magic-numbers */\r\n null,\r\n new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]),\r\n new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]),\r\n new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]),\r\n new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]),\r\n new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]),\r\n new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]),\r\n new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]),\r\n new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]),\r\n new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]),\r\n new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]),\r\n new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]),\r\n new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]),\r\n new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]),\r\n new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]),\r\n new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]),\r\n new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]),\r\n new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]),\r\n new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]),\r\n new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]),\r\n new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]),\r\n new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]),\r\n new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]),\r\n new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]),\r\n new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]),\r\n new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]),\r\n new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]),\r\n new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]),\r\n new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]),\r\n new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]),\r\n new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]),\r\n new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]),\r\n new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]),\r\n new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]),\r\n new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]),\r\n new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]),\r\n new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]),\r\n new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]),\r\n new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]),\r\n new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]),\r\n new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]),\r\n new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]),\r\n new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]),\r\n new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]),\r\n new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]),\r\n new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]),\r\n new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]),\r\n new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]),\r\n new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]),\r\n new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]),\r\n new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]),\r\n new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]),\r\n new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]),\r\n new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]),\r\n new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]),\r\n new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]),\r\n new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]),\r\n new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]),\r\n new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]),\r\n new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]),\r\n new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]),\r\n new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]),\r\n new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]),\r\n new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]),\r\n new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]),\r\n new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]),\r\n new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]),\r\n new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]),\r\n new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]),\r\n new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]),\r\n new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]),\r\n new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]),\r\n new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]),\r\n new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]),\r\n new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]),\r\n new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]),\r\n new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]),\r\n new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]),\r\n new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]),\r\n new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]),\r\n new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]),\r\n new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]),\r\n new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]),\r\n new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]),\r\n new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]),\r\n new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]),\r\n new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]),\r\n new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]),\r\n new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]),\r\n new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]),\r\n new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]),\r\n new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]),\r\n new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]),\r\n new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]),\r\n new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]),\r\n new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]),\r\n new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]),\r\n new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]),\r\n new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]),\r\n new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]),\r\n new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]),\r\n new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]),\r\n new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]),\r\n new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]),\r\n new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]),\r\n new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]),\r\n new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]),\r\n new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]),\r\n new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]),\r\n new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0]),\r\n /* eslint-enable no-magic-numbers */\r\n ];\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByName = {\r\n // Duplicate atomic numbers (isotopes)\r\n /* eslint-disable no-magic-numbers */\r\n D: new Element(1, 'D', 'Deuterium', 2.014, 1.2, 0.23, [1]),\r\n T: new Element(1, 'T', 'Tritium', 3.016, 1.2, 0.23, [1]),\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // All regular elements will be added later, automatically\r\n };\r\n}\r\n\r\n(function () {\r\n const byAtomicNumber = Element.ByAtomicNumber;\r\n const byName = Element.ByName;\r\n for (let i = 0, n = byAtomicNumber.length; i < n; ++i) {\r\n const element = byAtomicNumber[i];\r\n if (element) {\r\n byName[element.name] = element;\r\n }\r\n }\r\n}());\r\n\r\n// find atom type by chemical element (or create if missing)\r\nElement.getByName = function (element) {\r\n let type = Element.ByName[element];\r\n if (!type) {\r\n type = Element.ByName[element] = new Element(0, element, 'Unknown', 0, 1.0, 0.01, [0]);\r\n }\r\n return type;\r\n};\r\n\r\nexport default Element;\r\n","const cBondTypes = {\r\n /** Was generated manually */\r\n UNKNOWN: 0,\r\n /** Simple covalent bond */\r\n COVALENT: 1,\r\n /** Aromatic bond */\r\n AROMATIC: 2,\r\n};\r\n\r\nfunction getAtomPos(atom) {\r\n return atom.position;\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Atom} left - The first atom.\r\n * @param {Atom} right - The second atom.\r\n * @param {number} order - Order of current bond.\r\n * @param {number} type - Bond type.\r\n * @param {boolean} fixed - Indicator of a pre-specified connection (in contrast with guessed one).\r\n *\r\n * @exports Bond\r\n * @constructor\r\n */\r\nclass Bond {\r\n constructor(left, right, order, type, fixed) {\r\n this._left = left;\r\n this._right = right;\r\n this._fixed = fixed;\r\n this._index = -1;\r\n if (left > right) {\r\n throw new Error('In a bond atom indices must be in increasing order');\r\n }\r\n this._order = order;\r\n this._type = type;\r\n }\r\n\r\n getLeft() {\r\n return this._left;\r\n }\r\n\r\n getRight() {\r\n return this._right;\r\n }\r\n\r\n getOrder() {\r\n return this._order;\r\n }\r\n\r\n calcLength() {\r\n return this._left.position.distanceTo(this._right.position);\r\n }\r\n\r\n _forEachNeighbour(currAtom, process) {\r\n const { bonds } = currAtom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]._left !== currAtom ? bonds[i]._left : bonds[i]._right);\r\n }\r\n }\r\n\r\n forEachLevelOne(process) {\r\n const left = this._left;\r\n const right = this._right;\r\n this._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n this._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n }\r\n\r\n forEachLevelTwo(process) {\r\n // TODO refactor this piece of an art?\r\n const left = this._left;\r\n const right = this._right;\r\n const self = this;\r\n self._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === left) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n self._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === right) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n }\r\n\r\n _fixDir(refPoint, currDir, posGetter) {\r\n // count atoms to the right and to the left of the current plane\r\n let rightCount = 0;\r\n let leftCount = 0;\r\n const tmpVec = refPoint.clone();\r\n function checkDir(atom) {\r\n tmpVec.copy(posGetter(atom));\r\n tmpVec.sub(refPoint);\r\n const dotProd = currDir.dot(tmpVec);\r\n if (dotProd > 0) {\r\n ++rightCount;\r\n } else {\r\n ++leftCount;\r\n }\r\n }\r\n function checkCarbon(atom) {\r\n if (atom.element.name === 'C') {\r\n checkDir(atom);\r\n }\r\n }\r\n // count all atoms to the left and right of our plane, start from level 1 and carbons\r\n const stages = [\r\n [this.forEachLevelOne, checkCarbon],\r\n [this.forEachLevelOne, checkDir],\r\n [this.forEachLevelTwo, checkCarbon],\r\n [this.forEachLevelTwo, checkDir],\r\n ];\r\n\r\n for (let stageId = 0; stageId < stages.length; ++stageId) {\r\n stages[stageId][0].call(this, stages[stageId][1]);\r\n if (leftCount > rightCount) {\r\n return currDir.multiplyScalar(-1);\r\n }\r\n if (leftCount < rightCount) {\r\n return currDir;\r\n }\r\n }\r\n return currDir;\r\n }\r\n\r\n calcNormalDir(posGetter) {\r\n const left = this._left;\r\n const right = this._right;\r\n let first = left;\r\n let second = right;\r\n posGetter = posGetter === undefined ? getAtomPos : posGetter;\r\n if (left.bonds.length > right.bonds.length) {\r\n first = right;\r\n second = left;\r\n }\r\n let third = first;\r\n let maxNeibs = 0;\r\n const { bonds } = second;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n let another = bonds[i]._left;\r\n if (bonds[i]._left === second) {\r\n another = bonds[i]._right;\r\n }\r\n if (another.bonds.length > maxNeibs && another !== first) {\r\n third = another;\r\n maxNeibs = another.bonds.length;\r\n }\r\n }\r\n const secondPos = posGetter(second);\r\n const firstV = posGetter(first).clone().sub(secondPos);\r\n const secondV = posGetter(third).clone().sub(secondPos);\r\n secondV.crossVectors(firstV, secondV);\r\n if (secondV.lengthSq() < 0.0001) {\r\n secondV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n secondV.normalize();\r\n firstV.crossVectors(secondV, firstV);\r\n if (firstV.lengthSq() < 0.0001) {\r\n firstV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n return this._fixDir(secondPos, firstV, posGetter);\r\n }\r\n\r\n static BondType = cBondTypes;\r\n}\r\n\r\nBond.prototype.BondType = cBondTypes;\r\n\r\nexport default Bond;\r\n","import * as THREE from 'three';\r\nimport Atom from './Atom';\r\nimport Element from './Element';\r\n\r\nconst cNucleicControlNames = ['C3\\'', 'C3*', 'P', 'H5T', 'H3T'];\r\nconst cNucleicWing1Names = ['OP1', 'O1P'];\r\nconst cNucleicWing2Names = ['OP2', 'O2P'];\r\n\r\nconst cCylinderSource = ['C3\\'', 'C3*', 'C1', 'C1\\'', 'C1*', 'P'];\r\nconst cCylinderTarget = [{\r\n types: ['A', 'DA', 'G', 'DG'],\r\n atoms: ['N1'],\r\n}, {\r\n types: ['C', 'DC'],\r\n atoms: ['N3'],\r\n}, {\r\n types: ['T', 'DT', 'U', 'DU'],\r\n atoms: ['O4'],\r\n}];\r\n\r\n/**\r\n * Residue instance.\r\n *\r\n * @param {Chain} chain - Chain this residue belongs to.\r\n * @param {ResidueType} type - Generic residue instance type.\r\n * @param {number} sequence - Sequence ID.\r\n * @param {string} icode - One character insertion code (usually space or A-Z).\r\n *\r\n * @exports Residue\r\n * @constructor\r\n */\r\nclass Residue {\r\n constructor(chain, type, sequence, icode) {\r\n this._chain = chain;\r\n this._component = null;\r\n this._type = type;\r\n this._sequence = sequence;\r\n this._icode = icode;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n\r\n this._atoms = [];\r\n this._secondary = null;\r\n this._firstAtom = null;\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n this._lastAtom = null;\r\n this._controlPoint = null;\r\n this._midPoint = null;\r\n this._wingVector = null;\r\n this._cylinders = null;\r\n this._isValid = true;\r\n this._het = false;\r\n this._molecule = null;\r\n this.temperature = null;\r\n this.occupancy = null;\r\n }\r\n\r\n // Getters and setters\r\n getChain() {\r\n return this._chain;\r\n }\r\n\r\n getMolecule() {\r\n return this._molecule;\r\n }\r\n\r\n getType() {\r\n return this._type;\r\n }\r\n\r\n getSequence() {\r\n return this._sequence;\r\n }\r\n\r\n getSecondary() {\r\n return this._secondary;\r\n }\r\n\r\n getICode() {\r\n return this._icode;\r\n }\r\n\r\n // Other methods\r\n\r\n addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge) {\r\n const atom = new Atom(this, name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n const complex = this._chain.getComplex();\r\n complex.addAtom(atom);\r\n this._atoms.push(atom);\r\n this._het = this._het || het;\r\n return atom;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (process(atoms[i])) {\r\n break;\r\n }\r\n }\r\n }\r\n\r\n _findAtomByName(name) {\r\n let res = null;\r\n this.forEachAtom((atom) => {\r\n if (atom.name === name) {\r\n res = atom;\r\n return true;\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _findFirstAtomInList(names) {\r\n let res = null;\r\n for (let i = 0; i < names.length; ++i) {\r\n res = this._findAtomByName(names[i]);\r\n if (res !== null) {\r\n return res;\r\n }\r\n }\r\n return res;\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n mask &= atoms[i].mask;\r\n }\r\n this._mask = mask;\r\n }\r\n\r\n getCylinderTargetList() {\r\n const type = this._type._name;\r\n for (let i = 0, n = cCylinderTarget.length; i < n; ++i) {\r\n for (let j = 0, m = cCylinderTarget[i].types.length; j < m; ++j) {\r\n if (type === cCylinderTarget[i].types[j]) {\r\n return cCylinderTarget[i].atoms;\r\n }\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n _detectLeadWing(dst, next, getAtomPosition) {\r\n const leadAtom = this._findFirstAtomInList(cNucleicControlNames);\r\n let wingStart = this._findFirstAtomInList(cNucleicWing1Names);\r\n let wingEnd = this._findFirstAtomInList(cNucleicWing2Names);\r\n\r\n if (wingStart === null && next !== null) {\r\n wingStart = next._findFirstAtomInList(cNucleicWing1Names);\r\n }\r\n\r\n if (wingEnd === null && next !== null) {\r\n wingEnd = next._findFirstAtomInList(cNucleicWing2Names);\r\n }\r\n\r\n if (leadAtom === null || wingStart === null || wingEnd === null) {\r\n return;\r\n }\r\n\r\n dst._leadAtom = leadAtom;\r\n dst._controlPoint = getAtomPosition(leadAtom);\r\n dst._wingVector = getAtomPosition(wingEnd).clone().sub(getAtomPosition(wingStart));\r\n dst._isValid = true;\r\n\r\n const cylSource = this._findFirstAtomInList(cCylinderSource);\r\n const targetList = this.getCylinderTargetList();\r\n const cylTarget = targetList !== null ? this._findFirstAtomInList(targetList) : null;\r\n if (cylSource === null || cylTarget === null) {\r\n return;\r\n }\r\n dst._cylinders = [getAtomPosition(cylSource), getAtomPosition(cylTarget)];\r\n }\r\n\r\n calcWing(prevLeadPos, currLeadPos, prevWingPos, prevWing) {\r\n const vectorA = currLeadPos.clone().sub(prevLeadPos);\r\n const vectorB = prevLeadPos.clone().sub(prevWingPos);\r\n vectorB.crossVectors(vectorA, vectorB);\r\n vectorB.crossVectors(vectorA, vectorB).normalize();\r\n if (prevWing !== null && prevWing.length() > 0.0001) {\r\n const needToNegate = vectorB.length() > 0.0001 && Math.abs(prevWing.angleTo(vectorB)) > Math.PI / 2;\r\n if (needToNegate) {\r\n vectorB.negate();\r\n }\r\n }\r\n return vectorB;\r\n }\r\n\r\n _innerFinalize(prevRes, prev, nextRes, dst, chainAsNucleic, getAtomPosition) {\r\n const bFirstInChain = prev === null;\r\n\r\n const lp = getAtomPosition(this._leadAtom);\r\n const currLeadPos = new THREE.Vector3(lp.x, lp.y, lp.z);\r\n if (chainAsNucleic) {\r\n this._detectLeadWing(dst, nextRes, getAtomPosition);\r\n return;\r\n }\r\n\r\n if (bFirstInChain) { // for first one in chain\r\n dst._midPoint = getAtomPosition(this._firstAtom).clone();\r\n } else {\r\n const prevLeadPos = prev._controlPoint; // lead point of previous monomer\r\n dst._midPoint = prevLeadPos.clone().lerp(currLeadPos, 0.5);\r\n dst._wingVector = this.calcWing(prevLeadPos, currLeadPos, getAtomPosition(prevRes._wingAtom), prev._wingVector);\r\n }\r\n dst._controlPoint = currLeadPos;\r\n }\r\n\r\n _finalize2(prev, next, asNucleic) {\r\n // Should be called AFTER first finalize\r\n this._innerFinalize(prev, prev, next, this, asNucleic, (atom) => atom.position);\r\n }\r\n\r\n isConnected(anotherResidue) {\r\n if (this._chain !== anotherResidue._chain) {\r\n return false;\r\n }\r\n if (this === anotherResidue) {\r\n return true;\r\n }\r\n let res = false;\r\n this.forEachAtom((atom) => {\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue === anotherResidue || bond._right.residue === anotherResidue) {\r\n res = true;\r\n return true;\r\n }\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _finalize() {\r\n const self = this;\r\n [this._firstAtom] = this._atoms;\r\n this._lastAtom = this._atoms[this._atoms.length - 1];\r\n\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n\r\n let tempCount = 0;\r\n let temperature = 0; // average temperature\r\n let occupCount = 0;\r\n let occupancy = 0; // average occupancy\r\n this.forEachAtom((a) => {\r\n if (self._leadAtom === null) {\r\n if (a.role === Element.Constants.Lead) {\r\n self._leadAtom = a;\r\n }\r\n }\r\n if (self._wingAtom === null) {\r\n if (a.role === Element.Constants.Wing) {\r\n self._wingAtom = a;\r\n }\r\n }\r\n if (a.temperature) {\r\n temperature += a.temperature;\r\n tempCount++;\r\n }\r\n if (a.occupancy) {\r\n occupancy += a.occupancy;\r\n occupCount++;\r\n }\r\n return (self._leadAtom !== null && self._wingAtom !== null);\r\n });\r\n\r\n if (tempCount > 0) {\r\n this.temperature = temperature / tempCount;\r\n }\r\n if (occupCount > 0) {\r\n this.occupancy = occupancy / occupCount;\r\n }\r\n\r\n // Still try to make monomer look valid\r\n if (this._leadAtom === null || this._wingAtom === null) {\r\n this._isValid = false;\r\n }\r\n if (this._leadAtom === null) {\r\n this._leadAtom = this._firstAtom;\r\n }\r\n if (this._wingAtom === null) {\r\n this._wingAtom = this._lastAtom;\r\n }\r\n }\r\n}\r\n\r\nexport default Residue;\r\n","/**\r\n * Residue type.\r\n *\r\n * Predefined acid or created with HET, HETNAM, etc.\r\n *\r\n * @param {string} name - Short name, either standard (ALA, MET, etc.) or non-standard one.\r\n * @param {string} fullName - Full residue name.\r\n * @param {string} letterCode - 1-letter symbol.\r\n *\r\n * @exports ResidueType\r\n * @constructor\r\n */\r\nclass ResidueType {\r\n constructor(name, fullName, letterCode) {\r\n this._name = name;\r\n this._fullName = fullName;\r\n this.letterCode = letterCode;\r\n this.flags = 0x0000;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\n static StandardTypes = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: new ResidueType('ALA', 'Alanine', 'A'),\r\n ARG: new ResidueType('ARG', 'Arginine', 'R'),\r\n ASN: new ResidueType('ASN', 'Asparagine', 'N'),\r\n ASP: new ResidueType('ASP', 'Aspartic Acid', 'D'),\r\n CYS: new ResidueType('CYS', 'Cysteine', 'C'),\r\n GLN: new ResidueType('GLN', 'Glutamine', 'Q'),\r\n GLU: new ResidueType('GLU', 'Glutamic Acid', 'E'),\r\n GLY: new ResidueType('GLY', 'Glycine', 'G'),\r\n HIS: new ResidueType('HIS', 'Histidine', 'H'),\r\n ILE: new ResidueType('ILE', 'Isoleucine', 'I'),\r\n LEU: new ResidueType('LEU', 'Leucine', 'L'),\r\n LYS: new ResidueType('LYS', 'Lysine', 'K'),\r\n MET: new ResidueType('MET', 'Methionine', 'M'),\r\n PHE: new ResidueType('PHE', 'Phenylalanine', 'F'),\r\n PRO: new ResidueType('PRO', 'Proline', 'P'),\r\n PYL: new ResidueType('PYL', 'Pyrrolysine', 'O'),\r\n SEC: new ResidueType('SEC', 'Selenocysteine', 'U'),\r\n SER: new ResidueType('SER', 'Serine', 'S'),\r\n THR: new ResidueType('THR', 'Threonine', 'T'),\r\n TRP: new ResidueType('TRP', 'Tryptophan', 'W'),\r\n TYR: new ResidueType('TYR', 'Tyrosine', 'Y'),\r\n VAL: new ResidueType('VAL', 'Valine', 'V'),\r\n A: new ResidueType('A', 'Adenine', 'A'),\r\n C: new ResidueType('C', 'Cytosine', 'C'),\r\n G: new ResidueType('G', 'Guanine', 'G'),\r\n I: new ResidueType('I', 'Inosine', 'I'),\r\n T: new ResidueType('T', 'Thymine', 'T'),\r\n U: new ResidueType('U', 'Uracil', 'U'),\r\n DA: new ResidueType('DA', 'Adenine', 'A'),\r\n DC: new ResidueType('DC', 'Cytosine', 'C'),\r\n DG: new ResidueType('DG', 'Guanine', 'G'),\r\n DI: new ResidueType('DI', 'Inosine', 'I'),\r\n DT: new ResidueType('DT', 'Thymine', 'T'),\r\n DU: new ResidueType('DU', 'Uracil', 'U'),\r\n '+A': new ResidueType('+A', 'Adenine', 'A'),\r\n '+C': new ResidueType('+C', 'Cytosine', 'C'),\r\n '+G': new ResidueType('+G', 'Guanine', 'G'),\r\n '+I': new ResidueType('+I', 'Inosine', 'I'),\r\n '+T': new ResidueType('+T', 'Thymine', 'T'),\r\n '+U': new ResidueType('+U', 'Uracil', 'U'),\r\n WAT: new ResidueType('WAT', 'Water', ''),\r\n H2O: new ResidueType('H2O', 'Water', ''),\r\n HOH: new ResidueType('HOH', 'Water', ''),\r\n DOD: new ResidueType('DOD', 'Water', ''),\r\n UNK: new ResidueType('UNK', 'Unknown', ''),\r\n UNL: new ResidueType('UNL', 'Unknown Ligand', ''),\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n /**\r\n * Enumeration of residue flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n // Amino acids\r\n /** Amino acid residue */\r\n PROTEIN: 0x0001,\r\n /** Basic amino acid residue */\r\n BASIC: 0x0002,\r\n /** Acidic amino acid residue */\r\n ACIDIC: 0x0004,\r\n /** Polar uncharged side chain amino acid residue */\r\n POLAR: 0x0008,\r\n /** Non-polar hydrophobic side chain amino acid residue */\r\n NONPOLAR: 0x0010,\r\n /** Aromatic amino acid residue */\r\n AROMATIC: 0x0020,\r\n\r\n // Nucleic acids\r\n\r\n /** Nucleic residue */\r\n NUCLEIC: 0x0100,\r\n /** Purine nucleic residue */\r\n PURINE: 0x0200,\r\n /** Pyrimidine nucleic residue */\r\n PYRIMIDINE: 0x0400,\r\n /** DNA */\r\n DNA: 0x0800,\r\n /** RNA */\r\n RNA: 0x1000,\r\n\r\n /** Water */\r\n WATER: 0x10000,\r\n };\r\n}\r\n\r\n// Flag combinations\r\nfunction _addFlag(flag, list) {\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const res = ResidueType.StandardTypes[list[i]];\r\n if (res) {\r\n res.flags |= flag;\r\n }\r\n }\r\n}\r\n\r\nconst { Flags } = ResidueType;\r\n_addFlag(Flags.WATER, ['WAT', 'H2O', 'HOH', 'DOD']);\r\n\r\n_addFlag(Flags.PROTEIN, [\r\n 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLY', 'GLU', 'GLN', 'HIS', 'ILE',\r\n 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'PYL', 'SEC', 'SER', 'THR', 'TRP',\r\n 'TYR', 'VAL',\r\n]);\r\n_addFlag(Flags.BASIC, ['ARG', 'HIS', 'LYS']);\r\n_addFlag(Flags.ACIDIC, ['ASP', 'GLU']);\r\n_addFlag(Flags.POLAR, ['ASN', 'CYS', 'GLN', 'SER', 'THR', 'TYR']);\r\n_addFlag(Flags.NONPOLAR, ['ALA', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'VAL', 'GLY']);\r\n_addFlag(Flags.AROMATIC, ['PHE', 'TRP', 'TYR']);\r\n\r\n_addFlag(Flags.NUCLEIC, [\r\n 'A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I',\r\n 'C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U',\r\n]);\r\n_addFlag(Flags.PURINE, ['A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I']);\r\n_addFlag(Flags.PYRIMIDINE, ['C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U']);\r\n_addFlag(Flags.DNA, ['DA', 'DG', 'DI', 'DC', 'DT', 'DU']);\r\n_addFlag(Flags.RNA, ['A', 'G', 'I', 'C', 'T', 'U']);\r\n// Table of kdHydrophobicity\r\nconst hydro = {\r\n ILE: 4.5,\r\n VAL: 4.2,\r\n LEU: 3.8,\r\n PHE: 2.8,\r\n CYS: 2.5,\r\n MET: 1.9,\r\n ALA: 1.8,\r\n GLY: -0.4,\r\n THR: -0.7,\r\n SER: -0.8,\r\n TRP: -0.9,\r\n TYR: -1.3,\r\n PRO: -1.6,\r\n HIS: -3.2,\r\n GLU: -3.5,\r\n GLN: -3.5,\r\n ASP: -3.5,\r\n ASN: -3.5,\r\n LYS: -3.9,\r\n ARG: -4.5,\r\n};\r\n\r\nfunction _addParam(param, list) {\r\n const keys = Object.keys(list);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = list[key];\r\n ResidueType.StandardTypes[key][param] = value;\r\n }\r\n}\r\n\r\n_addParam('hydrophobicity', hydro);\r\n\r\nexport default ResidueType;\r\n","import * as THREE from 'three';\r\nimport Residue from './Residue';\r\nimport ResidueType from './ResidueType';\r\n\r\n/**\r\n * Residues in chain are either amino acid either nucleic acid (and water)\r\n * There might be some modified/mutated residues, which type could not be determined by their name (nucleic or amino); In this\r\n * case firstly program definites the chain type (by well-known residues) and then definites modified/mutated residues\r\n */\r\nconst ChainType = {\r\n UNKNOWN: 0,\r\n PROTEIN: 1,\r\n NUCLEIC: 2,\r\n};\r\n\r\n/**\r\n * Residue chain.\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n * @param {string} name - One character identifier (usually space, A-Z, 0-9, or a-z).\r\n *\r\n * @exports Chain\r\n * @constructor\r\n */\r\nclass Chain {\r\n constructor(complex, name) {\r\n this._complex = complex;\r\n this._name = name;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n this._residues = [];\r\n\r\n this.minSequence = Number.POSITIVE_INFINITY;\r\n this.maxSequence = Number.NEGATIVE_INFINITY;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n _determineType() {\r\n const residues = this._residues;\r\n\r\n const { PROTEIN, NUCLEIC } = ResidueType.Flags;\r\n\r\n this.type = ChainType.UNKNOWN;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const { flags } = residues[i]._type;\r\n\r\n if ((flags & NUCLEIC) !== 0) {\r\n this.type = ChainType.NUCLEIC;\r\n break;\r\n } else if ((flags & PROTEIN) !== 0) {\r\n this.type = ChainType.PROTEIN;\r\n break;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Finds thre residue with specified sequence number and inserion code\r\n * @param {Number} seqNum sequence number\r\n * @param {string} iCode insertion code\r\n * @returns {*} Residue or null if not found\r\n */\r\n findResidue(seqNum, iCode) {\r\n const residues = this._residues;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n if (res._sequence === seqNum && res._icode === iCode) {\r\n return [res, i];\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _finalize() {\r\n this._determineType();\r\n\r\n const residues = this._residues;\r\n\r\n let prev = null;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const next = (i + 1 < n) ? residues[i + 1] : null;\r\n const curr = residues[i];\r\n // TODO: skip invalid residues\r\n if (1 /* curr._isValid */) { // eslint-disable-line no-constant-condition\r\n curr._finalize2(prev, next, this.type === ChainType.NUCLEIC);\r\n prev = curr;\r\n }\r\n }\r\n\r\n // fix very first wing\r\n if (residues.length > 1 && residues[1]._wingVector) {\r\n const p = residues[1]._wingVector;\r\n residues[0]._wingVector = new THREE.Vector3(p.x, p.y, p.z);\r\n } else if (residues.length > 0) {\r\n residues[0]._wingVector = new THREE.Vector3(1, 0, 0);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const residues = this._residues;\r\n let prev = null;\r\n let prevData = null;\r\n const frameRes = frameData._residues;\r\n const n = residues.length;\r\n function getAtomPos(atom) {\r\n return frameData.getAtomPos(atom.index);\r\n }\r\n\r\n for (let i = 0; i < n; ++i) {\r\n const curr = residues[i];\r\n const currData = frameRes[curr._index];\r\n const nextRes = (i + 1 < n) ? residues[i + 1] : null;\r\n curr._innerFinalize(prev, prevData, nextRes, currData, this.type === ChainType.NUCLEIC, getAtomPos);\r\n prev = curr;\r\n prevData = currData;\r\n }\r\n\r\n frameRes[residues[0]._index]._wingVector = n > 1\r\n ? frameRes[residues[1]._index]._wingVector\r\n : new THREE.Vector3(1, 0, 0);\r\n }\r\n\r\n /**\r\n * Create a new residue.\r\n *\r\n * @param {string} name - Residue name.\r\n * @param {number} sequence - Residue sequence number.\r\n * @param {string} iCode - Insertion code.\r\n * @returns {Residue} - Newly created residue instance.\r\n */\r\n addResidue(name, sequence, iCode) {\r\n let type = this._complex.getResidueType(name);\r\n if (type === null) {\r\n type = this._complex.addResidueType(name);\r\n }\r\n const residue = new Residue(this, type, sequence, iCode);\r\n this._complex.addResidue(residue);\r\n this._residues.push(residue);\r\n\r\n if (type.flags & (ResidueType.Flags.NUCLEIC | ResidueType.Flags.PROTEIN)) {\r\n if (this.maxSequence < sequence) {\r\n this.maxSequence = sequence;\r\n }\r\n if (this.minSequence > sequence) {\r\n this.minSequence = sequence;\r\n }\r\n }\r\n\r\n return residue;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this._mask = mask;\r\n }\r\n}\r\n\r\nexport default Chain;\r\n","import Residue from './Residue';\r\n\r\n/** An element of protein secondary structure. */\r\nclass StructuralElement {\r\n /**\r\n * Create a secondary structural element of the specified type.\r\n *\r\n * @param {StructuralElement.Type} type Secondary structure type.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n */\r\n constructor(type, init, term) {\r\n /**\r\n * Secondary structure type.\r\n * @type {StructuralElement.Type}\r\n */\r\n this.type = type;\r\n /**\r\n * Generic secondary structure type.\r\n * @type {StructuralElement.Generic}\r\n */\r\n this.generic = StructuralElement.genericByType[this.type] || 'loop';\r\n /**\r\n * Initial residue.\r\n * @type Residue\r\n */\r\n this.init = init;\r\n /**\r\n * Terminal residue.\r\n * @type Residue\r\n */\r\n this.term = term;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n if (this.init instanceof Residue && this.term instanceof Residue) {\r\n return;\r\n }\r\n\r\n // Link all intermediate residues to this structural element\r\n const start = complex.splitUnifiedSerial(this.init);\r\n const end = complex.splitUnifiedSerial(this.term);\r\n for (let chainId = start.chain; chainId <= end.chain; chainId++) {\r\n for (let serialId = start.serial; serialId <= end.serial; serialId++) {\r\n for (let { iCode } = start; iCode <= end.iCode; iCode++) {\r\n const hashCode = complex.getUnifiedSerial(chainId, serialId, iCode);\r\n if (residueHash[hashCode]) {\r\n residueHash[hashCode]._secondary = this;\r\n }\r\n }\r\n }\r\n }\r\n\r\n // Replace unfined serials by objects\r\n this.init = residueHash[this.init];\r\n this.term = residueHash[this.term];\r\n }\r\n}\r\n\r\n/**\r\n * Specific type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Generic\r\n */\r\nStructuralElement.Type = {\r\n /** A strand of a [beta-sheet](https://en.wikipedia.org/wiki/Beta_sheet). */\r\n STRAND: 'E',\r\n /** An isolated beta-bridge (too small for a beta-sheet). */\r\n BRIDGE: 'B',\r\n\r\n /** A [3/10 helix](https://en.wikipedia.org/wiki/310_helix) (hydrogen bonding is 3 residues apart). */\r\n HELIX_310: 'G',\r\n /** An [alpha-helix](https://en.wikipedia.org/wiki/Alpha_helix) (hydrogen bonding is 4 residues apart). */\r\n HELIX_ALPHA: 'H',\r\n /** A [pi-helix](https://en.wikipedia.org/wiki/Pi_helix) (hydrogen bonding is 5 residues apart). */\r\n HELIX_PI: 'I',\r\n /** A generic helix of unspecified bonding distance. */\r\n HELIX: 'X',\r\n\r\n /** An isolated 3/10-like helical turn. */\r\n TURN_310: '3',\r\n /** An isolated alpha-like helical turn. */\r\n TURN_ALPHA: '4',\r\n /** An isolated pi-like helical turn. */\r\n TURN_PI: '5',\r\n /** An isolated helical [turn](https://en.wikipedia.org/wiki/Turn_(biochemistry)) of unspecified bonding distance. */\r\n TURN: 'T',\r\n\r\n /** A bend (a region of high curvature). */\r\n BEND: 'S',\r\n /** Just a protein section with no particular conformation. */\r\n COIL: 'C',\r\n};\r\n\r\n/**\r\n * Generic type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Type\r\n */\r\nStructuralElement.Generic = {\r\n /** A strand of a sheet. */\r\n STRAND: 'strand',\r\n /** A helix. */\r\n HELIX: 'helix',\r\n /** Just a protein section with no particular conformation. */\r\n LOOP: 'loop',\r\n};\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\nconst StructuralElementGeneric = StructuralElement.Generic;\r\n\r\n/**\r\n * A mapping from specific types to generic ones.\r\n * @type {Object}\r\n */\r\nStructuralElement.genericByType = {\r\n [StructuralElementType.STRAND]: StructuralElementGeneric.STRAND,\r\n [StructuralElementType.HELIX_310]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_ALPHA]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_PI]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX]: StructuralElementGeneric.HELIX,\r\n};\r\n\r\nexport default StructuralElement;\r\n","import StructuralElement from './StructuralElement';\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\nexport const typeByPDBHelixClass = {\r\n 1: StructuralElementType.HELIX_ALPHA,\r\n 3: StructuralElementType.HELIX_PI,\r\n 5: StructuralElementType.HELIX_310,\r\n};\r\n\r\n/**\r\n * Helical secondary structure of a protein.\r\n * @extends StructuralElement\r\n */\r\nclass Helix extends StructuralElement {\r\n /**\r\n * Create a helix.\r\n *\r\n * @param {number} helixClass A helix class according to the\r\n * [PDB Format](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX).\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} serial Serial number of the helix (see PDB Format).\r\n * @param {string} name Helix identifier (see PDB Format).\r\n * @param {string} comment Comment about this helix (see PDB Format).\r\n * @param {number} length Length of this helix, in residues (see PDB Format).\r\n */\r\n constructor(helixClass, init, term, serial, name, comment, length) {\r\n super(typeByPDBHelixClass[helixClass] || StructuralElement.Type.HELIX, init, term);\r\n\r\n /**\r\n * Serial number of the helix (see PDB Format).\r\n * @type {number}\r\n */\r\n this.serial = serial;\r\n /**\r\n * Helix identifier (see PDB Format).\r\n * @type {string}\r\n */\r\n this.name = name;\r\n /**\r\n * Comment about this helix (see PDB Format).\r\n * @type {string}\r\n */\r\n this.comment = comment;\r\n /**\r\n * Length of this helix, in residues (see PDB Format).\r\n * @type {number}\r\n */\r\n this.length = length;\r\n }\r\n}\r\n\r\nexport default Helix;\r\n","import StructuralElement from './StructuralElement';\r\n\r\n/**\r\n * A single strand of a sheet in a protein secondary structure.\r\n * @extends StructuralElement\r\n */\r\nclass Strand extends StructuralElement {\r\n /**\r\n * Create a strand.\r\n *\r\n * @param {Sheet} sheet Parent sheet this strand belongs to.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} sense Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @param {Atom} atomCur Atom in current strand (see PDB Format).\r\n * @param {Atom} atomPrev Atom in previous strand (see PDB Format).\r\n */\r\n constructor(sheet, init, term, sense, atomCur, atomPrev) {\r\n super(StructuralElement.Type.STRAND, init, term);\r\n\r\n /**\r\n * Parent sheet this strand belongs to.\r\n * @type {Sheet}\r\n */\r\n this.sheet = sheet;\r\n /**\r\n * Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @type {number}\r\n */\r\n this.sense = sense;\r\n /**\r\n * Atom in current strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomCur = atomCur;\r\n /**\r\n * Atom in previous strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomPrev = atomPrev;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n *\r\n * @override\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n super._finalize(serialAtomMap, residueHash, complex);\r\n\r\n let as = this.atomCur;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomCur = serialAtomMap[as];\r\n }\r\n as = this.atomPrev;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomPrev = serialAtomMap[as];\r\n }\r\n }\r\n}\r\n\r\nexport default Strand;\r\n","import Strand from './Strand';\r\n\r\n/**\r\n * Sheet secondary structure of a protein.\r\n *\r\n * @param {string} name -\r\n * @param {number} width -\r\n *\r\n * @exports Sheet\r\n * @constructor\r\n */\r\nclass Sheet {\r\n constructor(name, width) {\r\n this._name = name;\r\n this._width = width;\r\n\r\n this._strands = [];\r\n }\r\n\r\n // Getters and setters\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getWidth() {\r\n return this._width;\r\n }\r\n\r\n addStrand(strand) {\r\n this._strands.push(strand);\r\n this._width = this._strands.length;\r\n }\r\n\r\n addEmptyStrand() {\r\n this._strands.push(new Strand(null, null, null, null, null, null));\r\n }\r\n\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n const s = this._strands;\r\n for (let i = 0, n = s.length; i < n; ++i) {\r\n s[i]._finalize(serialAtomMap, residueHash, complex);\r\n }\r\n if (!this._width) {\r\n this._width = s.length;\r\n }\r\n if (s.length !== this._width) {\r\n throw new Error(`Sheet ${this._name} is inconsistent.`);\r\n }\r\n }\r\n}\r\n\r\nexport default Sheet;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Atom measurements.\r\n *\r\n * @param {string} id - SGroup id\r\n * @param {string} name - Name of the group\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n * @param {array} atoms - Atoms group consists of\r\n * @param {object} saveNode - XML node from file for saving\r\n *\r\n * @exports SGroup\r\n * @constructor\r\n */\r\nclass SGroup {\r\n constructor(id, name, position, atoms, saveNode) {\r\n this._id = id;\r\n this._name = name;\r\n this._position = position || new THREE.Vector3();\r\n this._atoms = atoms || [];\r\n this._charge = 0; // default group charge\r\n this._repeat = 1; // how many times group repeated: always > 0\r\n this._center = null;\r\n this.xmlNodeRef = saveNode || null;\r\n }\r\n\r\n /**\r\n * Get atom full name.\r\n * @returns {string} Atom full name.\r\n */\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getPosition() {\r\n return this._position;\r\n }\r\n\r\n getCentralPoint() {\r\n return this._center;\r\n }\r\n\r\n _rebuildSGroupOnAtomChange() {\r\n const nLimon = 100000000;\r\n if (this._center === null) {\r\n return; // nothing to do if we are not relative\r\n }\r\n\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n for (let j = 0, n = this._atoms.length; j < n; j++) {\r\n const aPos = this._atoms[j].position;\r\n bLow.set(Math.min(bLow.x, aPos.x), Math.min(bLow.y, aPos.y), Math.min(bLow.z, aPos.z));\r\n bHight.set(Math.max(bHight.x, aPos.x), Math.max(bHight.y, aPos.y), Math.max(bHight.z, aPos.z));\r\n }\r\n this._center.addVectors(bLow, bHight);\r\n this._center.multiplyScalar(0.5);\r\n }\r\n}\r\n\r\nexport default SGroup;\r\n","import utils from '../../utils';\r\n\r\n//----------------------------------------------------------------------------\r\nclass Range {\r\n constructor(min, max) {\r\n this.min = min;\r\n this.max = typeof max === 'undefined' ? min : max;\r\n }\r\n\r\n includes(value) {\r\n return this.min <= value && value <= this.max;\r\n }\r\n\r\n toString() {\r\n const { min, max } = this;\r\n return min === max ? String(min) : [min, max].join(':');\r\n }\r\n\r\n toJSON() {\r\n return [this.min, this.max];\r\n }\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\nclass List {\r\n constructor(arg) {\r\n if (arg instanceof this.constructor) {\r\n // delegate construction to a different class\r\n // eslint-disable-next-line no-constructor-return\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n }\r\n\r\n append(value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n }\r\n\r\n toString() {\r\n return this._values.join(',');\r\n }\r\n\r\n toJSON() {\r\n const values = this._values;\r\n const result = [];\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n result[i] = value.toJSON ? value.toJSON() : value;\r\n }\r\n return result;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nclass RangeList extends List {\r\n includes(value) {\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n if (list[i].includes(value)) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nconst valuesArray = [];\r\n\r\nclass ValueList extends List {\r\n constructor(arg, upperOnly) {\r\n const list = super(arg);\r\n if (upperOnly) {\r\n this.upperOnly = true;\r\n const values = list._values;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n if (typeof value === 'string') {\r\n values[i] = value.toUpperCase();\r\n }\r\n }\r\n } else {\r\n this.upperOnly = false;\r\n }\r\n // return constructed object\r\n // eslint-disable-next-line no-constructor-return\r\n return list;\r\n }\r\n\r\n includes(value) {\r\n // we do not convert to upper case here for perfomance reasons\r\n // if list is upper case only, value must be converted before it is sent up to here\r\n return this._values.indexOf(value) !== -1;\r\n }\r\n\r\n toString() {\r\n // Quote values that are not correct identifiers\r\n const values = this._values;\r\n valuesArray.length = 0;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n valuesArray[i] = utils.correctSelectorIdentifier(String(values[i]));\r\n }\r\n return valuesArray.join(',');\r\n }\r\n\r\n _validate(value) {\r\n return (this.upperOnly && typeof value === 'string') ? value.toUpperCase() : value;\r\n }\r\n\r\n append(value) {\r\n super.append(this._validate(value));\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n super.remove(this._validate(value));\r\n return this;\r\n }\r\n}\r\n\r\nexport {\r\n Range,\r\n List,\r\n RangeList,\r\n ValueList,\r\n};\r\n","import { RangeList, ValueList } from './selectArgs';\r\n\r\n/** Base class for atom selectors. */\r\nclass Selector {\r\n toString() {\r\n return this.keyword;\r\n }\r\n\r\n toJSON() {\r\n return [this.name];\r\n }\r\n}\r\n\r\nSelector.prototype.name = 'Error';\r\nSelector.prototype.keyword = 'error';\r\n\r\n/** Base class for list-based atom selectors. */\r\nclass ListSelector extends Selector {\r\n constructor(list) {\r\n super();\r\n this.list = list;\r\n }\r\n\r\n toString() {\r\n return `${this.keyword} ${this.list}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.list.toJSON()];\r\n }\r\n}\r\n\r\nclass RangeListSelector extends ListSelector {\r\n constructor(arg) {\r\n super(new RangeList(arg));\r\n }\r\n}\r\n\r\nclass ValueListSelector extends ListSelector {\r\n constructor(arg, caseSensitive) {\r\n super(new ValueList(arg, !caseSensitive));\r\n }\r\n}\r\n\r\nclass NoneSelector extends Selector {\r\n includesAtom(_atom) {\r\n return false;\r\n }\r\n}\r\n\r\nNoneSelector.prototype.name = 'None';\r\nNoneSelector.prototype.keyword = 'none';\r\n\r\nclass AllSelector extends Selector {\r\n includesAtom(_atom) {\r\n return true;\r\n }\r\n}\r\n\r\nAllSelector.prototype.name = 'All';\r\nAllSelector.prototype.keyword = 'all';\r\n\r\nexport {\r\n Selector,\r\n ListSelector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n};\r\n","import { Selector, NoneSelector } from './selectorsBase';\r\n\r\n//----------------------------------------------------------------------------\r\n// Operators\r\n//----------------------------------------------------------------------------\r\nconst none = new NoneSelector();\r\n\r\nclass PrefixOperator extends Selector {\r\n constructor(rhs) {\r\n super();\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nPrefixOperator.prototype.priority = 1;\r\n\r\nclass InfixOperator extends Selector {\r\n constructor(lhs, rhs) {\r\n super();\r\n this.lhs = lhs || none;\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const lhs = this.lhs.priority && this.lhs.priority > this.priority ? `(${this.lhs})` : this.lhs;\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${lhs} ${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.lhs.toJSON(), this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nInfixOperator.prototype.priority = 1000;\r\n\r\nexport { PrefixOperator, InfixOperator };\r\n","import Atom from './Atom';\r\nimport ResidueType from './ResidueType';\r\nimport { parser } from '../utils/SelectionParser';\r\nimport { Range, RangeList, ValueList } from './selectors/selectArgs';\r\nimport { PrefixOperator, InfixOperator } from './selectors/selectOps';\r\nimport {\r\n Selector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n} from './selectors/selectorsBase';\r\n\r\nconst keywords = {};\r\n\r\n//----------------------------------------------------------------------------\r\n// Named selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineSelector(name, SelectorClass) {\r\n const keyword = name.toLowerCase();\r\n SelectorClass.prototype.keyword = keyword;\r\n SelectorClass.prototype.name = name;\r\n\r\n const factory = ((...args) => new SelectorClass(...args));\r\n factory.SelectorClass = SelectorClass;\r\n keywords[keyword] = factory;\r\n\r\n return SelectorClass;\r\n}\r\n\r\ndefineSelector('Serial', class SerialSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.serial);\r\n }\r\n});\r\n\r\ndefineSelector('Name', class NameSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.name);\r\n }\r\n});\r\n\r\ndefineSelector('AltLoc', class AltLocSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(String.fromCharCode(atom.location));\r\n }\r\n});\r\n\r\ndefineSelector('Elem', class ElemSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.element.name);\r\n }\r\n});\r\n\r\ndefineSelector('Residue', class ResidueSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._type._name);\r\n }\r\n});\r\n\r\ndefineSelector('Sequence', class SequenceSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._sequence);\r\n }\r\n});\r\n\r\ndefineSelector('ICode', class ICodeSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._icode);\r\n }\r\n});\r\n\r\ndefineSelector('ResIdx', class ResIdxSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._index);\r\n }\r\n});\r\n\r\ndefineSelector('Chain', class ChainSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._chain._name);\r\n }\r\n});\r\n\r\ndefineSelector('Hetatm', class HetatmSelector extends Selector {\r\n includesAtom(atom) {\r\n return atom.het;\r\n }\r\n});\r\n\r\ndefineSelector('PolarH', class PolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.HYDROGEN;\r\n }\r\n});\r\n\r\ndefineSelector('NonPolarH', class NonPolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.NONPOLARH;\r\n }\r\n});\r\n\r\ndefineSelector('All', AllSelector);\r\n\r\ndefineSelector('None', NoneSelector);\r\n\r\nconst NULL_SELECTOR = keywords.none();\r\n\r\n//----------------------------------------------------------------------------\r\n// Named operators\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineOperator(name, priority, OperatorClass) {\r\n OperatorClass.prototype.priority = priority;\r\n return defineSelector(name, OperatorClass);\r\n}\r\ndefineOperator('Not', 1, class NotOperator extends PrefixOperator {\r\n includesAtom(atom) {\r\n return !this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('And', 2, class AndOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) && this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('Or', 3, class OrOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) || this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\n//----------------------------------------------------------------------------\r\n// Flag selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction byResidueTypeFlag(flag, name) {\r\n return defineSelector(name, class extends Selector {\r\n includesAtom(atom) {\r\n return (atom.residue._type.flags & flag) !== 0;\r\n }\r\n });\r\n}\r\n\r\nbyResidueTypeFlag(ResidueType.Flags.PROTEIN, 'Protein');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC, 'Basic');\r\nbyResidueTypeFlag(ResidueType.Flags.ACIDIC, 'Acidic');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC | ResidueType.Flags.ACIDIC, 'Charged');\r\nbyResidueTypeFlag(ResidueType.Flags.POLAR, 'Polar');\r\nbyResidueTypeFlag(ResidueType.Flags.NONPOLAR, 'NonPolar');\r\nbyResidueTypeFlag(ResidueType.Flags.AROMATIC, 'Aromatic');\r\nbyResidueTypeFlag(ResidueType.Flags.NUCLEIC, 'Nucleic');\r\nbyResidueTypeFlag(ResidueType.Flags.PURINE, 'Purine');\r\nbyResidueTypeFlag(ResidueType.Flags.PYRIMIDINE, 'Pyrimidine');\r\nbyResidueTypeFlag(ResidueType.Flags.WATER, 'Water');\r\n\r\n//----------------------------------------------------------------------------\r\nconst selectors = Object.create(keywords);\r\n\r\nselectors.Selector = Selector;\r\nselectors.RangeListSelector = RangeListSelector;\r\nselectors.ValueListSelector = ValueListSelector;\r\nselectors.Range = Range;\r\nselectors.RangeList = RangeList;\r\nselectors.ValueList = ValueList;\r\nselectors.PrefixOperator = PrefixOperator;\r\nselectors.InfixOperator = InfixOperator;\r\nselectors.Context = Object.create({});\r\n\r\nselectors.GetSelector = function (key) {\r\n if (!selectors.Context.hasOwnProperty(key)) {\r\n const exc = { message: `selector ${key} is not registered` };\r\n throw exc;\r\n }\r\n return selectors.Context[key] || NULL_SELECTOR;\r\n};\r\n\r\nselectors.ClearContext = function () {\r\n Object.keys(selectors.Context).forEach((k) => { delete selectors.Context[k]; });\r\n};\r\n\r\nselectors.keyword = function (key) {\r\n return keywords[key.toLowerCase()] || keywords.none;\r\n};\r\n\r\nselectors.parse = function (str) {\r\n const res = {};\r\n try {\r\n res.selector = parser.parse(str);\r\n } catch (e) {\r\n res.selector = NULL_SELECTOR;\r\n res.error = e.message;\r\n }\r\n return res;\r\n};\r\n\r\nparser.yy = selectors;\r\nparser.yy.parseError = parser.parseError; // workaround for incorrect JISON parser generator for AMD module\r\n\r\nexport default selectors;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\n\r\n/**\r\n * Basic biological unit class.\r\n *\r\n * @exports BiologicalUnit\r\n * @constructor\r\n */\r\nclass BiologicalUnit {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._selector = selectors.keyword('All')();\r\n this._boundaries = {\r\n boundingBox: new THREE.Box3(),\r\n boundingSphere: new THREE.Sphere(),\r\n };\r\n }\r\n\r\n computeBoundaries() {\r\n const atoms = this._complex._atoms;\r\n const n = atoms.length;\r\n const selector = this._selector;\r\n\r\n const { boundingBox } = this._boundaries;\r\n boundingBox.makeEmpty();\r\n if (n === 1) {\r\n boundingBox.expandByPoint(atoms[0].position);\r\n const bbc = new THREE.Vector3();\r\n boundingBox.getCenter(bbc);\r\n const s = 2 * atoms[0].element.radius;\r\n boundingBox.setFromCenterAndSize(bbc, new THREE.Vector3(s, s, s));\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (selector.includesAtom(atoms[i])) {\r\n boundingBox.expandByPoint(atoms[i].position);\r\n }\r\n }\r\n }\r\n\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n if (n === 1) {\r\n this._boundaries.boundingSphere.set(center, atoms[0].element.radius);\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (!selector.includesAtom(atoms[i])) {\r\n continue;\r\n }\r\n const pos = atoms[i].position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n this._boundaries.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n }\r\n\r\n getTransforms() {\r\n return [];\r\n }\r\n\r\n getSelector() {\r\n return this._selector;\r\n }\r\n\r\n getBoundaries() {\r\n return this._boundaries;\r\n }\r\n\r\n finalize() {\r\n }\r\n}\r\n\r\nexport default BiologicalUnit;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\nimport BiologicalUnit from './BiologicalUnit';\r\n\r\n/**\r\n * Biological assembly.\r\n *\r\n * @exports Assembly\r\n * @constructor\r\n */\r\n\r\nclass Assembly extends BiologicalUnit {\r\n constructor(complex) {\r\n super(complex);\r\n this.chains = [];\r\n this.matrices = [];\r\n }\r\n\r\n computeBoundaries() {\r\n super.computeBoundaries();\r\n // fix up the boundaries\r\n const { matrices } = this;\r\n const oldCenter = this._boundaries.boundingSphere.center;\r\n const oldRad = this._boundaries.boundingSphere.radius;\r\n const boundingBox = this._boundaries.boundingBox = new THREE.Box3();\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = matrices.length; i < n; ++i) {\r\n boundingBox.expandByPoint(oldCenter.clone().applyMatrix4(matrices[i]));\r\n }\r\n\r\n const newRad = boundingBox.max.distanceTo(boundingBox.min) / 2 + oldRad;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n this._boundaries.boundingSphere = new THREE.Sphere().set(center, newRad);\r\n boundingBox.max.addScalar(oldRad);\r\n boundingBox.min.subScalar(oldRad);\r\n }\r\n\r\n /**\r\n * Mark a chain as belonging to this biological assembly.\r\n * @param {string} chain - chain identifier, usually a single letter\r\n */\r\n addChain(chain) {\r\n this.chains[this.chains.length] = chain;\r\n }\r\n\r\n /**\r\n * Add a transformation matrix.\r\n * @param {THREE.Matrix4} matrix - transformation matrix\r\n */\r\n addMatrix(matrix) {\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n getTransforms() {\r\n return this.matrices;\r\n }\r\n\r\n finalize() {\r\n if (this.chains.length > 0) {\r\n this._selector = selectors.keyword('Chain')(this.chains);\r\n } else {\r\n this._selector = selectors.keyword('None')();\r\n }\r\n }\r\n}\r\n\r\nexport default Assembly;\r\n","/**\r\n * This class represents connected component as a part of a complex.\r\n * WARNING! The whole component entity is build under the assumption that residues\r\n * are placed in the chains and complex in ascending order of indices\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n *\r\n * @exports Component\r\n * @constructor\r\n */\r\nclass Component {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._index = -1;\r\n this._residueIndices = [];\r\n this._cycles = [];\r\n this._subDivs = [];\r\n this._residueCount = 0;\r\n }\r\n\r\n getResidues() {\r\n return this._complex._residues;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residueCount;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._complex._residues;\r\n const resIdc = this._residueIndices;\r\n for (let idIdc = 0, idCount = resIdc.length; idIdc < idCount; ++idIdc) {\r\n for (let idx = resIdc[idIdc].start, last = resIdc[idIdc].end; idx <= last; ++idx) {\r\n process(residues[idx]);\r\n }\r\n }\r\n }\r\n\r\n setSubDivs(subDivs) {\r\n this._subDivs = subDivs;\r\n let curr = 0;\r\n const resIdc = [];\r\n let resCnt = 0;\r\n for (let i = 0, n = subDivs.length; i < n; ++i) {\r\n if (i === n - 1 || subDivs[i].end + 1 !== subDivs[i + 1].start) {\r\n const { start } = subDivs[curr];\r\n const { end } = subDivs[i];\r\n resIdc[resIdc.length] = {\r\n start,\r\n end,\r\n };\r\n resCnt += end - start + 1;\r\n curr = i + 1;\r\n }\r\n }\r\n\r\n this._residueIndices = resIdc;\r\n this._residueCount = resCnt;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._complex._bonds;\r\n\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue._component === this) {\r\n process(bond);\r\n }\r\n }\r\n }\r\n\r\n update() {\r\n this.forEachCycle((cycle) => {\r\n cycle.update();\r\n });\r\n }\r\n\r\n forEachAtom(process) {\r\n this.forEachResidue((residue) => {\r\n residue.forEachAtom(process);\r\n });\r\n }\r\n\r\n addCycle(cycle) {\r\n this._cycles.push(cycle);\r\n }\r\n\r\n forEachCycle(process) {\r\n const cycles = this._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n process(cycles[i]);\r\n }\r\n }\r\n\r\n markResidues() {\r\n const self = this;\r\n self.forEachResidue((residue) => {\r\n residue._component = self;\r\n });\r\n }\r\n\r\n _forEachSubChain(mask, process) {\r\n const residues = this._complex._residues;\r\n const subs = this._subDivs;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let idx = subs[i].start, last = subs[i].end; idx <= last; ++idx) {\r\n const currRes = residues[idx];\r\n if (mask & currRes._mask && currRes._isValid) {\r\n let end = idx + 1;\r\n for (; end <= last; ++end) {\r\n const endRes = residues[end];\r\n if (!(mask & endRes._mask && endRes._isValid)) {\r\n break;\r\n }\r\n }\r\n process(i, idx, end - 1);\r\n idx = end;\r\n }\r\n }\r\n }\r\n }\r\n\r\n getMaskedSequences(mask) {\r\n const subs = [];\r\n let idx = 0;\r\n this._forEachSubChain(mask, (_subIdx, start, end) => {\r\n subs[idx++] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n\r\n getMaskedSubdivSequences(mask) {\r\n const subs = [];\r\n let currIdx = -1;\r\n let lastSubIdx = -1;\r\n const subDivs = this._subDivs;\r\n\r\n this._forEachSubChain(mask, (subIdx, start, end) => {\r\n if (lastSubIdx !== subIdx) {\r\n ++currIdx;\r\n subs[currIdx] = {\r\n arr: [],\r\n boundaries: subDivs[subIdx],\r\n };\r\n lastSubIdx = subIdx;\r\n }\r\n subs[currIdx].arr[subs[currIdx].arr.length] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n}\r\n\r\nexport default Component;\r\n","import utils from '../utils';\r\n\r\nconst cMaxPairsForHashCode = 32;\r\nconst cHashTableSize = 1024 * 1024;\r\nconst cNumbersPerPair = 4;\r\nconst cMaxNeighbours = 14;\r\nconst cInvalidVal = -1;\r\n// 89237 is a large simple number, can be used for pseudo random hash code create\r\nconst cBigPrime = 89237;\r\n\r\nclass AtomPairs {\r\n constructor(maxPairsEstimate) {\r\n this.numPairs = 0;\r\n this.numMaxPairs = maxPairsEstimate;\r\n this.intBuffer = utils.allocateTyped(Int32Array, maxPairsEstimate * cNumbersPerPair);\r\n for (let i = 0; i < maxPairsEstimate * cNumbersPerPair; i++) {\r\n this.intBuffer[i] = cInvalidVal;\r\n }\r\n this.hashBuffer = utils.allocateTyped(Int32Array, cHashTableSize * cMaxPairsForHashCode);\r\n for (let i = 0; i < cHashTableSize * cMaxPairsForHashCode; i++) {\r\n this.hashBuffer[i] = cInvalidVal;\r\n }\r\n }\r\n\r\n /**\r\n * Destroy all pairs memory\r\n */\r\n destroy() {\r\n this.intBuffer = null;\r\n this.hashBuffer = null;\r\n }\r\n\r\n /**\r\n * Add pair of atoms to collection\r\n * @param {number} indexA - Index of the 1st vertex.\r\n * @param {number} indexB - Index of the 2nd vertex.\r\n */\r\n addPair(indexA, indexB) {\r\n const ia = (indexA < indexB) ? indexA : indexB;\r\n const ib = (indexA > indexB) ? indexA : indexB;\r\n const codeToAdd = ia + (ib << cMaxNeighbours);\r\n\r\n const hashCode = (ia + (ib * cBigPrime)) & (cHashTableSize - 1);\r\n let j = hashCode * cMaxPairsForHashCode;\r\n let apI = 0;\r\n for (; apI < cMaxPairsForHashCode; apI++) {\r\n const code = this.hashBuffer[j + apI];\r\n if (code === cInvalidVal) {\r\n break;\r\n }\r\n if (code === codeToAdd) {\r\n return false;\r\n }\r\n }\r\n // add this new hash code\r\n if (apI >= cMaxPairsForHashCode) {\r\n throw new Error('addPair: increase cMaxPairsForHashCode');\r\n }\r\n this.hashBuffer[j + apI] = codeToAdd;\r\n\r\n // actually add\r\n if (this.numPairs >= this.numMaxPairs) {\r\n throw new Error('addPair: increase num pairs');\r\n }\r\n j = this.numPairs * cNumbersPerPair;\r\n this.intBuffer[j] = ia;\r\n this.intBuffer[j + 1] = ib;\r\n this.intBuffer[j + 2] = codeToAdd;\r\n this.numPairs++;\r\n return true;\r\n }\r\n}\r\n\r\nexport default AtomPairs;\r\n","import AtomPairs from './AtomPairs';\r\nimport Bond from './Bond';\r\n\r\nconst cProfileBondBuilder = false;\r\nconst cEstBondsMultiplier = 4;\r\nconst cSpaceCode = 32;\r\nconst cBondTolerance = 0.45;\r\nconst cVMDTolerance = 0.6;\r\nconst cBondRadInJMOL = true;\r\nconst cEpsilon = 0.001;\r\n\r\n/**\r\n * Get radius used for building bonds.\r\n *\r\n * @param {Atom} atom - Atom object.\r\n * @returns {number} special value for bonding radius for this atom\r\n */\r\nfunction _getBondingRadius(atom) {\r\n const { element } = atom;\r\n if (element) {\r\n return element.radiusBonding;\r\n }\r\n throw new Error('_getBondingRadius: Logic error.');\r\n}\r\n\r\nfunction _isAtomEligible(atom) {\r\n // build for all non-hetatm and for hetatm without bonds\r\n return !atom.isHet() || (atom.bonds && atom.bonds.length === 0);\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Complex} complex molecular complex\r\n\r\n * @exports AutoBond\r\n * @constructor\r\n */\r\nclass AutoBond {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._maxRad = 1.8;\r\n const bBox = this._complex.getDefaultBoundaries().boundingBox;\r\n this._vBoxMin = bBox.min.clone();\r\n this._vBoxMax = bBox.max.clone();\r\n\r\n this._pairCollection = null;\r\n }\r\n\r\n /**\r\n * Add existing pairs of connectors (from pdb file after its reading)\r\n * @returns {number} 0\r\n */\r\n _addExistingPairs() {\r\n const atoms = this._complex.getAtoms();\r\n const numAtoms = atoms.length;\r\n let aInd = 0;\r\n const collection = this._pairCollection;\r\n\r\n for (; aInd < numAtoms; aInd++) {\r\n const { bonds } = atoms[aInd];\r\n const numBondsForAtom = bonds.length;\r\n for (let bInd = 0; bInd < numBondsForAtom; bInd++) {\r\n const bond = bonds[bInd];\r\n const indTo = bond._left.index;\r\n if (indTo === aInd) {\r\n collection.addPair(aInd, bond._right.index);\r\n }\r\n } // for (b) all bonds in atom\r\n } // for (a)\r\n return 0;\r\n }\r\n\r\n _findPairs() {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const atoms = this._complex._atoms;\r\n const atomsNum = atoms.length;\r\n const self = this;\r\n\r\n let rA;\r\n let isHydrogenA;\r\n let posA;\r\n let locationA;\r\n let atomA;\r\n\r\n const processAtom = function (atomB) {\r\n if (isHydrogenA && atomB.isHydrogen()) {\r\n return;\r\n }\r\n\r\n const locationB = atomB.location;\r\n if ((locationA !== cSpaceCode)\r\n && (locationB !== cSpaceCode)\r\n && (locationA !== locationB)) {\r\n return;\r\n }\r\n\r\n const dist2 = posA.distanceToSquared(atomB.position);\r\n const rB = atomB.element.radiusBonding;\r\n const maxAcceptable = cBondRadInJMOL ? rA + rB + cBondTolerance : cVMDTolerance * (rA + rB);\r\n\r\n if (dist2 > (maxAcceptable * maxAcceptable)) {\r\n return;\r\n }\r\n\r\n if (dist2 < cEpsilon) {\r\n return;\r\n }\r\n\r\n self._pairCollection.addPair(atomA.index, atomB.index);\r\n };\r\n\r\n for (let i = 0; i < atomsNum; ++i) {\r\n atomA = atoms[i];\r\n if (!_isAtomEligible(atomA)) {\r\n continue;\r\n }\r\n\r\n rA = atomA.element.radiusBonding;\r\n isHydrogenA = atomA.isHydrogen();\r\n posA = atomA.position;\r\n locationA = atomA.location;\r\n\r\n vw.forEachAtomWithinRadius(posA, 2 * this._maxRad + cBondTolerance, processAtom);\r\n }\r\n }\r\n\r\n _addPairs() {\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0, k = 0; i < this._pairCollection.numPairs; i++, k += 4) {\r\n const iA = this._pairCollection.intBuffer[k];\r\n const iB = this._pairCollection.intBuffer[k + 1];\r\n this._addPair(atoms[iA], atoms[iB]);\r\n }\r\n }\r\n\r\n _addPair(atomA, atomB) {\r\n const bondsA = atomA.bonds;\r\n const indexA = atomA.index;\r\n const indexB = atomB.index;\r\n for (let j = 0, numBonds = bondsA.length; j < numBonds; ++j) {\r\n const bond = bondsA[j];\r\n if (bond._left.index === indexB || bond._right.index === indexB) {\r\n return;\r\n }\r\n }\r\n const left = indexA < indexB ? atomA : atomB;\r\n const right = indexA < indexB ? atomB : atomA;\r\n const newBond = this._complex.addBond(left, right, 0, Bond.BondType.UNKNOWN, false);\r\n bondsA.push(newBond);\r\n atomB.bonds.push(newBond);\r\n }\r\n\r\n build() {\r\n if (cProfileBondBuilder) {\r\n console.time('Bonds Builder');\r\n }\r\n this._buildInner();\r\n\r\n if (cProfileBondBuilder) {\r\n console.timeEnd('Bonds Builder');\r\n }\r\n }\r\n\r\n _buildInner() {\r\n const atoms = this._complex._atoms;\r\n if (atoms.length < 2) {\r\n return;\r\n }\r\n if (atoms[0].index < 0) {\r\n throw new Error('AutoBond: Atoms in complex were not indexed.');\r\n }\r\n\r\n this._calcBoundingBox();\r\n this._pairCollection = new AtomPairs(atoms.length * cEstBondsMultiplier);\r\n this._addExistingPairs();\r\n this._findPairs();\r\n this._addPairs();\r\n }\r\n\r\n _calcBoundingBox() {\r\n const atoms = this._complex._atoms;\r\n const nAtoms = atoms.length;\r\n let maxRad = _getBondingRadius(atoms[0]);\r\n for (let i = 1; i < nAtoms; ++i) {\r\n maxRad = Math.max(maxRad, _getBondingRadius(atoms[i]));\r\n }\r\n this._vBoxMax.addScalar(maxRad);\r\n this._vBoxMin.addScalar(-maxRad);\r\n this._maxRad = maxRad * 1.2;\r\n }\r\n\r\n destroy() {\r\n if (this._pairCollection) {\r\n this._pairCollection.destroy();\r\n }\r\n }\r\n}\r\n\r\nexport default AutoBond;\r\n","import * as THREE from 'three';\r\nimport Bond from './Bond';\r\nimport Element from './Element';\r\n\r\nconst cCrossThresh = 0.1;\r\nconst cAromaticType = Bond.BondType.AROMATIC;\r\nconst cAromaticAtoms = [\r\n Element.ByName.C.number,\r\n Element.ByName.N.number,\r\n // Element.ByName.O.number,\r\n // Element.ByName.S.number,\r\n];\r\n\r\n/** Conditions for bonds:\r\n * - Cross product with each subsequent bond to add is collinear and point to the same direction\r\n * - Each pair of a adjacent bonds belong to not more than one cycle\r\n * - If there is more than one candidates we try them in ascending order of angle values\r\n */\r\n\r\nconst _coDirVectors = (function () {\r\n const v1Tmp = new THREE.Vector3();\r\n const v2Tmp = new THREE.Vector3();\r\n const cp = new THREE.Vector3();\r\n return function (v1, v2) {\r\n v1Tmp.copy(v1).normalize();\r\n v2Tmp.copy(v2).normalize();\r\n cp.crossVectors(v1Tmp, v2Tmp);\r\n if (cp.length() > cCrossThresh) {\r\n return false;\r\n }\r\n // zero vector in out terms must be collinear to any\r\n return v1Tmp.dot(v2Tmp) >= 0;\r\n };\r\n}());\r\n\r\nfunction _insertAscending(arr, val) {\r\n let idx = 0;\r\n while (idx < arr.length && arr[idx] < val) {\r\n ++idx;\r\n }\r\n arr.splice(idx, 0, val);\r\n}\r\n\r\nfunction _anotherAtom(bond, currAtom) {\r\n return bond._left === currAtom ? bond._right : bond._left;\r\n}\r\n\r\nfunction _cosBetween(v1, v2) {\r\n const theta = v1.dot(v2) / (Math.sqrt(v1.lengthSq() * v2.lengthSq()));\r\n return THREE.MathUtils.clamp(theta, -1, 1);\r\n}\r\n\r\nfunction _markAromatic(bond) {\r\n bond._type = cAromaticType;\r\n}\r\n\r\nclass Cycle {\r\n constructor(atomsList) {\r\n this.atoms = atomsList;\r\n this.update();\r\n }\r\n\r\n update() {\r\n const { atoms } = this;\r\n const center = new THREE.Vector3();\r\n const nA = atoms.length;\r\n for (let j = 0; j < nA; ++j) {\r\n center.add(atoms[j].position);\r\n }\r\n center.multiplyScalar(1.0 / nA);\r\n this.center = center;\r\n this.radius = center.distanceTo(atoms[0].position.clone().lerp(atoms[1].position, 0.5));\r\n }\r\n\r\n forEachBond(process) {\r\n const { atoms } = this;\r\n const nA = atoms.length;\r\n let currAtom = atoms[0];\r\n let nextAtom;\r\n\r\n function checkBond(bond) {\r\n if (bond._left === nextAtom || bond._right === nextAtom) {\r\n process(bond);\r\n }\r\n }\r\n\r\n for (let i = 0; i < nA; ++i) {\r\n nextAtom = atoms[(i + 1) % nA];\r\n currAtom.forEachBond(checkBond);\r\n currAtom = nextAtom;\r\n }\r\n }\r\n}\r\n\r\nfunction _isAromatic(bond) {\r\n return bond._type === cAromaticType;\r\n}\r\n\r\nfunction _isPossibleAromatic(bond) {\r\n if (bond.type === cAromaticType) {\r\n return true;\r\n }\r\n const rightIdx = cAromaticAtoms.indexOf(bond._right.element.number);\r\n const leftIdx = cAromaticAtoms.indexOf(bond._left.element.number);\r\n return rightIdx !== -1 && leftIdx !== -1;\r\n}\r\n\r\nfunction _checkCycleSimple(cycle) {\r\n return cycle.length > 3;\r\n}\r\n\r\nfunction _checkCycleComplex(cycle) {\r\n console.assert(cycle.length > 2);\r\n return true;\r\n}\r\n\r\nclass AromaticLoopsMarker {\r\n constructor(complex) {\r\n this._complex = complex;\r\n const bondsData = new Array(complex._bonds.length);\r\n const bondMarks = new Array(complex._bonds.length);\r\n for (let i = 0, n = bondsData.length; i < n; ++i) {\r\n bondsData[i] = [];\r\n bondMarks[i] = false;\r\n }\r\n this._bondsData = bondsData;\r\n this._bondMarks = bondMarks;\r\n this._resetCycles();\r\n }\r\n\r\n _resetCycles() {\r\n this._cycles = [];\r\n this._currIdx = -1;\r\n }\r\n\r\n _haveSameCycle(bondsData, bond1, bond2) {\r\n const arr1 = bondsData[bond1._index];\r\n const arr2 = bondsData[bond2._index];\r\n const n1 = arr1.length;\r\n const n2 = arr2.length;\r\n let i1 = 0;\r\n let i2 = 0;\r\n while (i1 < n1 && i2 < n2) {\r\n if (arr1[i1] === arr2[i2]) {\r\n return true;\r\n }\r\n if (arr1[i1] > arr2[i2]) {\r\n ++i2;\r\n } else {\r\n ++i1;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _tryBond(prevBond, currRight, currDir) {\r\n const bondsOrder = [];\r\n const bondsData = this._bondsData;\r\n const currLeft = _anotherAtom(prevBond, currRight);\r\n const currVec = currRight.position.clone().sub(currLeft.position);\r\n const startAtomRef = this._currStart;\r\n const self = this;\r\n const bondMarks = this._bondMarks;\r\n let checkAromatic = this._checkBond;\r\n bondMarks[prevBond._index] = true;\r\n checkAromatic = checkAromatic === undefined ? _isAromatic : checkAromatic;\r\n currRight.forEachBond((newBond) => {\r\n if (!checkAromatic(newBond)\r\n || newBond === prevBond\r\n || bondMarks[newBond._index]\r\n || self._haveSameCycle(bondsData, prevBond, newBond)) {\r\n return;\r\n }\r\n const anotherAtom = _anotherAtom(newBond, currRight);\r\n const anotherVec = anotherAtom.position.clone().sub(currRight.position);\r\n const val = anotherAtom === startAtomRef ? -2.0 : 1 - _cosBetween(currVec, anotherVec);\r\n const newDir = anotherVec.cross(currVec);\r\n if (!_coDirVectors(newDir, currDir)) {\r\n return;\r\n }\r\n let idx = 0;\r\n while (idx < bondsOrder.length && bondsOrder[idx].val < val) {\r\n ++idx;\r\n }\r\n bondsOrder.splice(idx, 0, { bond: newBond, val, dir: newDir });\r\n });\r\n\r\n for (let i = 0, n = bondsOrder.length; i < n; ++i) {\r\n const { bond } = bondsOrder[i];\r\n const newRight = bond._left === currRight ? bond._right : bond._left;\r\n if (newRight === startAtomRef) {\r\n ++this._currIdx;\r\n this._cycles.push([currRight]);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n if (this._tryBond(bond, newRight, bondsOrder[i].dir)) {\r\n _insertAscending(bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(currRight);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n }\r\n bondMarks[prevBond._index] = false;\r\n return false;\r\n }\r\n\r\n _startCycle(bond) {\r\n // start from left to right\r\n this._currStart = bond._left;\r\n if (this._tryBond(bond, bond._right, new THREE.Vector3())) {\r\n _insertAscending(this._bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(bond._left);\r\n }\r\n }\r\n\r\n _findLoops(checkBond, checkCycle) {\r\n this._checkBond = checkBond;\r\n const complex = this._complex;\r\n const self = this;\r\n\r\n complex.forEachComponent((component) => {\r\n self._resetCycles();\r\n component.forEachBond((bond) => {\r\n if (checkBond(bond)) {\r\n self._startCycle(bond);\r\n }\r\n });\r\n const cycles = self._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n const cycle = cycles[i];\r\n if (!checkCycle(cycle)) {\r\n continue;\r\n }\r\n const newCycle = new Cycle(cycle);\r\n newCycle.forEachBond(_markAromatic);\r\n component.addCycle(newCycle);\r\n }\r\n });\r\n }\r\n\r\n markCycles() {\r\n this._findLoops(_isAromatic, _checkCycleSimple);\r\n }\r\n\r\n detectCycles() {\r\n this._findLoops(_isPossibleAromatic, _checkCycleComplex);\r\n }\r\n}\r\n\r\nexport default AromaticLoopsMarker;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\n/**\r\n * Calculate min & max radius of a sphere slice between zMin & zMax\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {number} zMin - lower bound of the slice\r\n * @param {number} zMax - upper bound of the slice\r\n */\r\nfunction _getSphereSliceRadiusRange(center, radius, zMin, zMax) {\r\n const dzMin = zMin - center.z;\r\n const dzMax = zMax - center.z;\r\n const rzMin = Math.sqrt(Math.max(radius * radius - dzMin * dzMin, 0.0));\r\n const rzMax = Math.sqrt(Math.max(radius * radius - dzMax * dzMax, 0.0));\r\n\r\n const rMin = Math.min(rzMin, rzMax);\r\n let rMax;\r\n\r\n if (zMin <= center.z && zMax >= center.z) {\r\n // sphere's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(rzMin, rzMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * Calculate min & max radius of a circle slice between yMin & yMax.\r\n *\r\n * To maintain analogy with _getSphereSliceRadiusRange we call radius what in fact is\r\n * half-width (along X axis) of the slice, i.e. 1D-sphere radius.\r\n *\r\n * @param {Vector3} center - center of the circle (z can be ignored)\r\n * @param {number} radius - circle radius\r\n * @param {number} yMin - lower bound of the slice\r\n * @param {number} yMax - upper bound of the slice\r\n * @returns {Array} - array of two numbers (min & max radius, or half-width)\r\n */\r\nfunction _getCircleSliceRadiusRange(center, radius, yMin, yMax) {\r\n const dyMin = yMin - center.y;\r\n const dyMax = yMax - center.y;\r\n const ryMin = Math.sqrt(Math.max(radius * radius - dyMin * dyMin, 0.0));\r\n const ryMax = Math.sqrt(Math.max(radius * radius - dyMax * dyMax, 0.0));\r\n\r\n const rMin = Math.min(ryMin, ryMax);\r\n let rMax;\r\n\r\n if (yMin <= center.y && yMax >= center.y) {\r\n // slice's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(ryMin, ryMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * VoxelWorld constructor\r\n *\r\n * @param {Box3} box - bounding box of the volume to be partitioned\r\n * @param {Vector3} vCellSizeHint - target voxel size (actual voxel size may differ from this)\r\n */\r\nclass VoxelWorld {\r\n constructor(box, vCellSizeHint) {\r\n this._box = box.clone();\r\n const size = new THREE.Vector3();\r\n box.getSize(size);\r\n this._count = size.clone().divide(vCellSizeHint).floor().max(new THREE.Vector3(1, 1, 1));\r\n this._last = this._count.clone().subScalar(1);\r\n this._cellSize = size.clone().divide(this._count);\r\n this._cellInnerR = 0.5 * Math.min(Math.min(this._cellSize.x, this._cellSize.y), this._cellSize.z);\r\n this._cellOuterR = 0.5 * Math.sqrt(this._cellSize.dot(this._cellSize));\r\n\r\n // array of voxels, each element contains index of first atom in voxel\r\n const numVoxels = this._count.x * this._count.y * this._count.z;\r\n this._voxels = utils.allocateTyped(Int32Array, numVoxels);\r\n for (let i = 0; i < numVoxels; ++i) {\r\n this._voxels[i] = -1;\r\n }\r\n\r\n // array of atoms that stores multiple single-linked lists\r\n // two elements for each atom: Atom ref, index of next atom (in this array\r\n this._atoms = [];\r\n }\r\n\r\n /**\r\n * Add all atoms from a complex to voxel world\r\n *\r\n * @param {Complex} complex - complex\r\n */\r\n addAtoms(complex) {\r\n const self = this;\r\n\r\n let idx = this._atoms.length;\r\n\r\n // resize array of atoms\r\n this._atoms.length += 2 * complex.getAtomCount();\r\n\r\n complex.forEachAtom((atom) => {\r\n // find which voxel contains this atom\r\n const voxelIdx = self._findVoxel(atom.position);\r\n\r\n // push current atom to the head of voxel's atom list\r\n self._atoms[idx] = atom;\r\n self._atoms[idx + 1] = self._voxels[voxelIdx];\r\n self._voxels[voxelIdx] = idx;\r\n\r\n idx += 2;\r\n });\r\n }\r\n\r\n /**\r\n * Get voxel that contains specified 3D point (we use clamp at the edges)\r\n *\r\n * @param {Vector3} point - a point in 3D\r\n * @returns {number} - index of voxel\r\n */\r\n static _zero = new THREE.Vector3(0, 0, 0);\r\n\r\n static _voxel = new THREE.Vector3();\r\n\r\n _findVoxel(point) {\r\n const zero = VoxelWorld._zero;\r\n const voxel = VoxelWorld._voxel;\r\n voxel.copy(point)\r\n .sub(this._box.min)\r\n .divide(this._cellSize)\r\n .floor()\r\n .clamp(zero, this._last);\r\n return voxel.x + this._count.x * (voxel.y + this._count.y * voxel.z);\r\n }\r\n\r\n /**\r\n * Call a function for each atom in voxel\r\n *\r\n * @param {number} voxel - index of voxel\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomInVoxel(voxel, process) {\r\n for (let i = this._voxels[voxel]; i >= 0; i = this._atoms[i + 1]) {\r\n process(this._atoms[i]);\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _xRange = new THREE.Vector2();\r\n\r\n static _yRange = new THREE.Vector2();\r\n\r\n static _zRange = new THREE.Vector2();\r\n\r\n _forEachVoxelWithinRadius(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n\r\n // switch to a faster method unless cell size is much smaller than sphere radius\r\n if (radius / this._cellInnerR < 10) {\r\n this._forEachVoxelWithinRadiusSimple(center, radius, process);\r\n return;\r\n }\r\n\r\n let rRangeXY;\r\n let rRangeX;\r\n let xVal;\r\n let yVal;\r\n let zVal;\r\n let isInsideX;\r\n let isInsideY;\r\n let isInsideZ;\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor()\r\n .clampScalar(0, this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n\r\n isInsideZ = (center.z - radius <= zVal[0]) && (zVal[1] <= center.z + radius);\r\n\r\n rRangeXY = _getSphereSliceRadiusRange(center, radius, zVal[0], zVal[1]);\r\n\r\n yRange.set(center.y - rRangeXY[1], center.y + rRangeXY[1]);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor()\r\n .clampScalar(0, this._count.y - 1);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n\r\n isInsideY = (center.y - rRangeXY[0] <= yVal[0]) && (yVal[1] <= center.y + rRangeXY[0]);\r\n\r\n rRangeX = _getCircleSliceRadiusRange(center, rRangeXY[1], yVal[0], yVal[1]);\r\n\r\n xRange.set(center.x - rRangeX[1], center.x + rRangeX[1]);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor()\r\n .clampScalar(0, this._count.x - 1);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n isInsideX = (center.x - rRangeX[0] <= xVal[0]) && (xVal[1] <= center.x + rRangeX[0]);\r\n\r\n process(x + this._count.x * (y + this._count.y * z), isInsideX && isInsideY && isInsideZ);\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n * This is a version of method that doesn't try to \"calculate\" what voxels fall inside radius\r\n * but instead just checks all voxels inside sphere's bounding box. This should be faster\r\n * unless cell size is much smaller than sphere radius.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _vCenter = new THREE.Vector3();\r\n\r\n _forEachVoxelWithinRadiusSimple(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n const vCenter = VoxelWorld._vCenter;\r\n\r\n const distTouch2 = (radius + this._cellOuterR) * (radius + this._cellOuterR);\r\n let distInside2 = -1.0;\r\n if (radius > this._cellOuterR) {\r\n distInside2 = (radius - this._cellOuterR) * (radius - this._cellOuterR);\r\n }\r\n\r\n // calculate bounding box for the sphere\r\n xRange.set(center.x - radius, center.x + radius);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor();\r\n xRange.x = Math.min(Math.max(xRange.x, 0), this._count.x - 1);\r\n xRange.y = Math.min(Math.max(xRange.y, 0), this._count.x - 1);\r\n\r\n yRange.set(center.y - radius, center.y + radius);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor();\r\n yRange.x = Math.min(Math.max(yRange.x, 0), this._count.y - 1);\r\n yRange.y = Math.min(Math.max(yRange.y, 0), this._count.y - 1);\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor();\r\n zRange.x = Math.min(Math.max(zRange.x, 0), this._count.z - 1);\r\n zRange.y = Math.min(Math.max(zRange.y, 0), this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n const zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n vCenter.z = 0.5 * (zVal[0] + zVal[1]);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n const yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n vCenter.y = 0.5 * (yVal[0] + yVal[1]);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n const xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n vCenter.x = 0.5 * (xVal[0] + xVal[1]);\r\n\r\n const d2 = center.distanceToSquared(vCenter);\r\n if (d2 <= distTouch2) {\r\n process(x + this._count.x * (y + this._count.y * z), d2 <= distInside2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each atom within given sphere\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinRadius(center, radius, process) {\r\n const self = this;\r\n const r2 = radius * radius;\r\n\r\n self._forEachVoxelWithinRadius(center, radius, (voxel, isInside) => {\r\n if (isInside) {\r\n self._forEachAtomInVoxel(voxel, process);\r\n } else {\r\n self._forEachAtomInVoxel(voxel, (atom) => {\r\n if (center.distanceToSquared(atom.position) <= r2) {\r\n process(atom);\r\n }\r\n });\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by mask\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} mask - bit mask\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromMasked(complex, mask, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by selector\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} selector - selector\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromSelected(complex, selector, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms\r\n *\r\n * @param {function} forEachAtom - enumerator of atoms in the group\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomWithinDistFromGroup(forEachAtom, dist, process) {\r\n const self = this;\r\n const r2 = dist * dist;\r\n\r\n const voxels = [];\r\n const atoms = [];\r\n let idx = 0;\r\n\r\n // build \"within radius\" atom list for each voxel\r\n forEachAtom((atom) => {\r\n self._forEachVoxelWithinRadius(atom.position, dist, (voxel, isInside) => {\r\n if (isInside) {\r\n // this voxel is inside circle -- no check will be required\r\n voxels[voxel] = -1;\r\n } else if (typeof voxels[voxel] === 'undefined') {\r\n // this voxel isn't covered yet -- start building list of atoms\r\n atoms.push(atom);\r\n atoms.push(-1);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n } else if (voxels[voxel] !== -1) {\r\n // this voxel has a list of atoms required for distance check -- add atom to the list\r\n atoms.push(atom);\r\n atoms.push(voxels[voxel]);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n }\r\n });\r\n });\r\n\r\n let voxel;\r\n\r\n const processIfWithin = function (atom) {\r\n if (typeof voxels[voxel] === 'undefined') {\r\n return;\r\n }\r\n\r\n idx = voxels[voxel];\r\n if (idx === -1) {\r\n // this voxel is fully covered\r\n process(atom);\r\n return;\r\n }\r\n\r\n // check distance to each atom within radius from this voxel\r\n for (; idx >= 0; idx = atoms[idx + 1]) {\r\n if (atom.position.distanceToSquared(atoms[idx].position) < r2) {\r\n process(atom);\r\n break;\r\n }\r\n }\r\n };\r\n\r\n // for each marked voxel\r\n for (voxel in voxels) {\r\n if (voxels.hasOwnProperty(voxel)) {\r\n self._forEachAtomInVoxel(voxel, processIfWithin);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default VoxelWorld;\r\n","import ResidueType from './ResidueType';\r\nimport PairCollection from './AtomPairs';\r\n\r\nconst MINIMAL_DISTANCE = 0.5;\r\nconst MIN_HBOND_ENERGY = -9.9;\r\nconst MAX_HBOND_ENERGY = -0.5;\r\nconst COUPLING_CONSTANT = -27.888; // = -332 * 0.42 * 0.2\r\nconst MAX_COUPLING_DISTANCE = 5.0; // how far is the closest atom of a potential partner residue from CA atom\r\nconst MAX_RESIDUES_THRESHOLD = 1000;\r\n\r\nexport default class HBondInfo {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._hbonds = []; // array of bond info for each residue\r\n if (this._complex._residues.length > MAX_RESIDUES_THRESHOLD) {\r\n this._buildVW(); // optimized version using voxel grid\r\n } else {\r\n this._build(); // test all pairs of residues\r\n }\r\n }\r\n\r\n isBond(from, to) {\r\n if (this._hbonds[from]) {\r\n const [acc0, acc1] = this._hbonds[from].acceptor;\r\n if (acc0 && acc0.residue === to && acc0.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n if (acc1 && acc1.residue === to && acc1.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n\r\n for (let i = 0; i < this._complex._residues.length - 1; ++i) {\r\n const ri = this._complex._residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let preri = null;\r\n if (i > 0 && (this._complex._residues[i - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && ri._sequence === this._complex._residues[i - 1]._sequence + 1) {\r\n preri = this._complex._residues[i - 1];\r\n }\r\n\r\n for (let j = i + 1; j < this._complex._residues.length; ++j) {\r\n const rj = this._complex._residues[j];\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = null;\r\n if ((this._complex._residues[j - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && rj._sequence === this._complex._residues[j - 1]._sequence + 1) {\r\n prerj = this._complex._residues[j - 1];\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (j !== i + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _buildVW() {\r\n const self = this;\r\n const residues = this._complex._residues;\r\n let ri;\r\n let preri;\r\n\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const pairs = new PairCollection(this._complex._residues.length * this._complex._residues.length / 2);\r\n\r\n function processAtom(atom) {\r\n const rj = atom.residue;\r\n\r\n if (rj._index === ri._index) {\r\n return;\r\n }\r\n\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n return;\r\n }\r\n\r\n if (!pairs.addPair(ri._index, rj._index)) {\r\n // we've seen this pair\r\n return;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = rj._index > 0 ? residues[rj._index - 1] : null;\r\n if (prerj\r\n && ((prerj.getType().flags & ResidueType.Flags.PROTEIN) === 0 || rj._sequence !== prerj._sequence + 1)) {\r\n prerj = null;\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (rj._index !== ri._index + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n\r\n for (let i = 0; i < residues.length - 1; ++i) {\r\n ri = residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n preri = i > 0 ? residues[i - 1] : null;\r\n if (preri\r\n && ((preri.getType().flags & ResidueType.Flags.PROTEIN) === 0 || ri._sequence !== preri._sequence + 1)) {\r\n preri = null;\r\n }\r\n\r\n vw.forEachAtomWithinRadius(this._residueGetCAlpha(ri), MAX_COUPLING_DISTANCE, processAtom);\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _residueGetCO(res) {\r\n let c = null;\r\n let o = null;\r\n\r\n res.forEachAtom((a) => {\r\n if (a.name === 'C') {\r\n c = a.position;\r\n } else if (a.name === 'O') {\r\n o = a.position;\r\n }\r\n });\r\n\r\n return [c, o];\r\n }\r\n\r\n // TODO Support hydrogen defined in complex\r\n _residueGetNH(prev, res) {\r\n const [c, o] = this._residueGetCO(prev);\r\n\r\n let n;\r\n res.forEachAtom((a) => {\r\n if (a.name === 'N') {\r\n n = a.position;\r\n }\r\n });\r\n\r\n if (c && o && n) {\r\n // calculate hydrogen position\r\n const h = c.clone();\r\n h.sub(o);\r\n h.multiplyScalar(1.0 / h.length());\r\n h.add(n);\r\n\r\n return [n, h];\r\n }\r\n\r\n return [null, null];\r\n }\r\n\r\n _calcHBondEnergy(predonor, donor, acceptor) {\r\n let result = 0;\r\n\r\n if (predonor === null) {\r\n return result;\r\n }\r\n\r\n if (donor.getType().getName() !== 'PRO') {\r\n const [n, h] = this._residueGetNH(predonor, donor);\r\n const [c, o] = this._residueGetCO(acceptor);\r\n\r\n if (n === null || h === null || c === null || o === null) {\r\n return result;\r\n }\r\n\r\n const distanceHO = h.distanceTo(o);\r\n const distanceHC = h.distanceTo(c);\r\n const distanceNC = n.distanceTo(c);\r\n const distanceNO = n.distanceTo(o);\r\n\r\n if (distanceHO < MINIMAL_DISTANCE || distanceHC < MINIMAL_DISTANCE\r\n || distanceNC < MINIMAL_DISTANCE || distanceNO < MINIMAL_DISTANCE) {\r\n result = MIN_HBOND_ENERGY;\r\n } else {\r\n result = COUPLING_CONSTANT / distanceHO - COUPLING_CONSTANT / distanceHC\r\n + COUPLING_CONSTANT / distanceNC - COUPLING_CONSTANT / distanceNO;\r\n }\r\n\r\n // DSSP compatibility mode:\r\n result = Math.round(result * 1000) / 1000;\r\n\r\n if (result < MIN_HBOND_ENERGY) {\r\n result = MIN_HBOND_ENERGY;\r\n }\r\n }\r\n\r\n // update donor\r\n if (typeof this._hbonds[donor._index] === 'undefined') {\r\n this._hbonds[donor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const donorInfo = this._hbonds[donor._index];\r\n\r\n if (donorInfo.acceptor.length < 2) {\r\n donorInfo.acceptor.push({\r\n residue: acceptor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (donorInfo.acceptor.length > 1) {\r\n if (result < donorInfo.acceptor[0].energy) {\r\n donorInfo.acceptor[1].residue = donorInfo.acceptor[0].residue;\r\n donorInfo.acceptor[1].energy = donorInfo.acceptor[0].energy;\r\n donorInfo.acceptor[0].residue = acceptor._index;\r\n donorInfo.acceptor[0].energy = result;\r\n } else if (result < donorInfo.acceptor[1].energy) {\r\n donorInfo.acceptor[1].residue = acceptor._index;\r\n donorInfo.acceptor[1].energy = result;\r\n }\r\n }\r\n\r\n // update acceptor\r\n if (typeof this._hbonds[acceptor._index] === 'undefined') {\r\n this._hbonds[acceptor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const accInfo = this._hbonds[acceptor._index];\r\n\r\n if (accInfo.donor.length < 2) {\r\n accInfo.donor.push({\r\n residue: donor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (accInfo.donor.length > 1) {\r\n if (result < accInfo.donor[0].energy) {\r\n accInfo.donor[1].residue = accInfo.donor[0].residue;\r\n accInfo.donor[1].energy = accInfo.donor[0].energy;\r\n accInfo.donor[0].residue = donor._index;\r\n accInfo.donor[0].energy = result;\r\n } else if (result < accInfo.donor[1].energy) {\r\n accInfo.donor[1].residue = donor._index;\r\n accInfo.donor[1].energy = result;\r\n }\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n","import HBondInfo from './HBondInfo';\r\nimport ResidueType from './ResidueType';\r\n\r\nconst BridgeType = Object.freeze({\r\n NO_BRIDGE: 0,\r\n PARALLEL: 1,\r\n ANTI_PARALLEL: 2,\r\n});\r\n\r\nconst HelixFlag = Object.freeze({\r\n START: 1,\r\n MIDDLE: 2,\r\n END: 3,\r\n START_AND_END: 4,\r\n});\r\n\r\nconst StructureType = Object.freeze({\r\n STRAND: 'E',\r\n BRIDGE: 'B',\r\n HELIX_310: 'G',\r\n HELIX_ALPHA: 'H',\r\n HELIX_PI: 'I',\r\n TURN: 'T',\r\n BEND: 'S',\r\n LOOP: ' ',\r\n});\r\n\r\nexport default class SecondaryStructureMap {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._build();\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n this._hbonds = new HBondInfo(this._complex);\r\n this._ss = []; // DSSP map by residue\r\n\r\n // auxilliary data\r\n this._sheet = [];\r\n this._betaPartners = [];\r\n this._bend = [];\r\n for (let i = 0; i < this._complex.getResidues().length; ++i) {\r\n this._betaPartners[i] = [];\r\n }\r\n this._helixFlags = [];\r\n this._helixFlags[3] = [];\r\n this._helixFlags[4] = [];\r\n this._helixFlags[5] = [];\r\n\r\n // calculate peptide chain lengths\r\n this._chainLengths = [];\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i].getResidues();\r\n let len = 0;\r\n for (; len < chain.length; ++len) {\r\n if ((chain[len].getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n break;\r\n }\r\n }\r\n this._chainLengths[i] = len;\r\n }\r\n\r\n this._buildBetaSheets();\r\n\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n self._buildAlphaHelices(this._complex._chains[i].getResidues(), this._chainLengths[i], false);\r\n }\r\n }\r\n\r\n _buildAlphaHelices(inResidues, chainLength, inPreferPiHelices) {\r\n // Helix and Turn\r\n for (let stride = 3; stride <= 5; ++stride) {\r\n if (inResidues.length < stride) {\r\n break;\r\n }\r\n\r\n for (let i = 0; i + stride < chainLength; ++i) {\r\n if (this._hbonds.isBond(inResidues[i + stride]._index, inResidues[i]._index)\r\n /* && NoChainBreak(res[i], res[i + stride]) */) {\r\n this._helixFlags[stride][inResidues[i + stride]._index] = HelixFlag.END;\r\n for (let j = i + 1; j < i + stride; ++j) {\r\n if (typeof this._helixFlags[stride][inResidues[j]._index] === 'undefined') {\r\n this._helixFlags[stride][inResidues[j]._index] = HelixFlag.MIDDLE;\r\n }\r\n }\r\n\r\n if (this._helixFlags[stride][inResidues[i]._index] === HelixFlag.END) {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START_AND_END;\r\n } else {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 2; i < chainLength - 2; ++i) {\r\n const kappa = this._kappa(inResidues[i - 2], inResidues[i], inResidues[i + 2]);\r\n this._bend[inResidues[i]._index] = (kappa !== 360 && kappa > 70);\r\n }\r\n\r\n for (let i = 1; i + 4 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 4) && this._isHelixStart(inResidues[i - 1]._index, 4)) {\r\n for (let j = i; j <= i + 3; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_ALPHA;\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 3 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 3) && this._isHelixStart(inResidues[i - 1]._index, 3)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 2; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_310;\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 2; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_310;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 5 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 5) && this._isHelixStart(inResidues[i - 1]._index, 5)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 4; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_PI\r\n || (inPreferPiHelices && this._ss[inResidues[j]._index] === StructureType.HELIX_ALPHA);\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 4; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_PI;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 1 < chainLength; ++i) {\r\n if (typeof this._ss[inResidues[i]._index] === 'undefined') {\r\n let isTurn = false;\r\n for (let stride = 3; stride <= 5 && !isTurn; ++stride) {\r\n for (let k = 1; k < stride && !isTurn; ++k) {\r\n isTurn = (i >= k) && this._isHelixStart(inResidues[i - k]._index, stride);\r\n }\r\n }\r\n\r\n if (isTurn) {\r\n this._ss[inResidues[i]._index] = StructureType.TURN;\r\n } else if (this._bend[inResidues[i]._index]) {\r\n this._ss[inResidues[i]._index] = StructureType.BEND;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _cosinusAngle(p1, p2, p3, p4) {\r\n const v12 = p1.clone().sub(p2);\r\n const v34 = p3.clone().sub(p4);\r\n\r\n let result = 0;\r\n\r\n const x = v12.dot(v12) * v34.dot(v34);\r\n if (x > 0) {\r\n result = v12.dot(v34) / Math.sqrt(x);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _kappa(prevPrev, res, nextNext) {\r\n const curCA = this._residueGetCAlpha(res);\r\n const ppCA = this._residueGetCAlpha(prevPrev);\r\n const nnCA = this._residueGetCAlpha(nextNext);\r\n if (curCA === null || ppCA === null || nnCA === null) {\r\n return 180;\r\n }\r\n\r\n const ckap = this._cosinusAngle(curCA, ppCA, nnCA, curCA);\r\n const skap = Math.sqrt(1 - ckap * ckap);\r\n return Math.atan2(skap, ckap) * 180 / Math.PI;\r\n }\r\n\r\n _isHelixStart(res, stride) {\r\n return (this._helixFlags[stride][res] === HelixFlag.START\r\n || this._helixFlags[stride][res] === HelixFlag.START_AND_END);\r\n }\r\n\r\n _buildBetaSheets() {\r\n // find bridges\r\n // check each chain against each other chain, and against itself\r\n const bridges = [];\r\n for (let a = 0; a < this._complex._chains.length; ++a) {\r\n const lenA = this._chainLengths[a];\r\n if (lenA <= 4) {\r\n continue;\r\n }\r\n\r\n const chainA = this._complex._chains[a].getResidues();\r\n\r\n for (let b = a; b < this._complex._chains.length; ++b) {\r\n const lenB = this._chainLengths[b];\r\n if (lenB <= 4) {\r\n continue;\r\n }\r\n\r\n const chainB = this._complex._chains[b].getResidues();\r\n\r\n for (let i = 1; i + 1 < lenA; ++i) {\r\n const ri = chainA[i];\r\n\r\n let j = 1;\r\n if (b === a) {\r\n j = i + 3; // check for self-bridges forward down the chain\r\n }\r\n\r\n for (; j + 1 < lenB; ++j) {\r\n const rj = chainB[j];\r\n\r\n const type = this._testBridge(chainA, i, chainB, j);\r\n if (type === BridgeType.NO_BRIDGE) {\r\n continue;\r\n }\r\n\r\n // there is a bridge, try to attach it to previously found sequence\r\n let found = false;\r\n for (const bridge of bridges) {\r\n if (type !== bridge.type || ri._index !== bridge.i[bridge.i.length - 1] + 1) {\r\n continue;\r\n }\r\n\r\n if (type === BridgeType.PARALLEL && bridge.j[bridge.j.length - 1] + 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.push(rj._index);\r\n found = true;\r\n break;\r\n }\r\n\r\n if (type === BridgeType.ANTI_PARALLEL && bridge.j[0] - 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.unshift(rj._index);\r\n found = true;\r\n break;\r\n }\r\n }\r\n\r\n // this bridge cannot be attached anywhere, start a new sequence\r\n if (!found) {\r\n bridges.push({\r\n type,\r\n i: [ri._index],\r\n chainI: ri.getChain()._index,\r\n j: [rj._index],\r\n chainJ: rj.getChain()._index,\r\n });\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // extend ladders\r\n bridges.sort((a, b) => {\r\n if (a.chainI < b.chainI || (a.chainI === b.chainI && a.i[0] < b.i[0])) {\r\n return -1;\r\n }\r\n return 1;\r\n });\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n for (let j = i + 1; j < bridges.length; ++j) {\r\n const ibi = bridges[i].i[0];\r\n const iei = bridges[i].i[bridges[i].i.length - 1];\r\n const jbi = bridges[i].j[0];\r\n const jei = bridges[i].j[bridges[i].j.length - 1];\r\n const ibj = bridges[j].i[0];\r\n const iej = bridges[j].i[bridges[j].i.length - 1];\r\n const jbj = bridges[j].j[0];\r\n const jej = bridges[j].j[bridges[j].j.length - 1];\r\n\r\n if (bridges[i].type !== bridges[j].type\r\n || this._hasChainBreak(Math.min(ibi, ibj), Math.max(iei, iej))\r\n || this._hasChainBreak(Math.min(jbi, jbj), Math.max(jei, jej))\r\n || ibj - iei >= 6 || (iei >= ibj && ibi <= iej)) {\r\n continue;\r\n }\r\n\r\n let bulge = false;\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bulge = ((jbj - jei < 6 && ibj - iei < 3) || (jbj - jei < 3));\r\n } else {\r\n bulge = ((jbi - jej < 6 && ibj - iei < 3) || (jbi - jej < 3));\r\n }\r\n\r\n if (bulge) {\r\n bridges[i].i = bridges[i].i.concat(bridges[j].i);\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bridges[i].j = bridges[i].j.concat(bridges[j].j);\r\n } else {\r\n bridges[i].j = bridges[j].j.concat(bridges[i].j);\r\n }\r\n bridges.splice(j--, 1);\r\n }\r\n }\r\n }\r\n\r\n // Sheet\r\n const ladderset = new Set();\r\n for (let i = 0; i < bridges.length; ++i) {\r\n ladderset.add(bridges[i]);\r\n }\r\n\r\n let sheet = 1;\r\n let ladder = 0;\r\n while (ladderset.size > 0) {\r\n let bridge = ladderset.values().next().value;\r\n ladderset.delete(bridge);\r\n\r\n const sheetset = new Set();\r\n sheetset.add(bridge);\r\n\r\n let toMove;\r\n do {\r\n toMove = new Set();\r\n for (const a of sheetset.values()) {\r\n for (const b of ladderset.values()) {\r\n if (this._areBridgesLinked(a, b)) {\r\n toMove.add(b);\r\n }\r\n }\r\n }\r\n for (bridge of toMove.values()) {\r\n sheetset.add(bridge);\r\n ladderset.delete(bridge);\r\n }\r\n } while (toMove.size > 0);\r\n\r\n for (bridge of sheetset.values()) {\r\n bridge.ladder = ladder;\r\n bridge.sheet = sheet;\r\n bridge.link = sheetset;\r\n ++ladder;\r\n }\r\n\r\n ++sheet;\r\n }\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n const bridge = bridges[i];\r\n\r\n // find out if any of the i and j set members already have\r\n // a bridge assigned, if so, we're assigning bridge 2\r\n\r\n let betai = 0;\r\n let betaj = 0;\r\n\r\n for (let l = 0; l < bridge.i.length; ++l) {\r\n if (this._betaPartners[bridge.i[l]][0]) {\r\n betai = 1;\r\n break;\r\n }\r\n }\r\n\r\n for (let l = 0; l < bridge.j.length; ++l) {\r\n if (this._betaPartners[bridge.j[l]][0]) {\r\n betaj = 1;\r\n break;\r\n }\r\n }\r\n\r\n let ss = StructureType.BRIDGE;\r\n if (bridge.i.length > 1) {\r\n ss = StructureType.STRAND;\r\n }\r\n\r\n if (bridge.type === BridgeType.PARALLEL) {\r\n let j = 0;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n\r\n j = 0;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n } else {\r\n let j = bridge.j.length - 1;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n\r\n j = bridge.i.length - 1;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n }\r\n\r\n for (let k = bridge.i[0]; k <= bridge.i[bridge.i.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n\r\n for (let k = bridge.j[0]; k <= bridge.j[bridge.j.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _testBridge(chainA, from, chainB, to) {\r\n let result = BridgeType.NO_BRIDGE;\r\n\r\n const a = chainA[from - 1]._index;\r\n const b = chainA[from]._index;\r\n const c = chainA[from + 1]._index;\r\n const d = chainB[to - 1]._index;\r\n const e = chainB[to]._index;\r\n const f = chainB[to + 1]._index;\r\n\r\n const isBond = this._hbonds.isBond.bind(this._hbonds);\r\n if ((isBond(c, e) && isBond(e, a)) || (isBond(f, b) && isBond(b, d))) {\r\n result = BridgeType.PARALLEL;\r\n } else if ((isBond(c, d) && isBond(f, a)) || (isBond(e, b) && isBond(b, e))) {\r\n result = BridgeType.ANTI_PARALLEL;\r\n }\r\n return result;\r\n }\r\n\r\n // return true if any of the residues in bridge a is identical to any of the residues in bridge b\r\n _areBridgesLinked(a, b) {\r\n const ai = new Set(a.i);\r\n const aj = new Set(a.j);\r\n\r\n for (const i of b.i) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n for (const i of b.j) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n }\r\n\r\n _hasChainBreak(from, to) {\r\n for (let i = from + 1; i <= to; ++i) {\r\n if (this._complex._residues[i]._sequence !== this._complex._residues[i - 1]._sequence + 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\nSecondaryStructureMap.StructureType = StructureType;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport Atom from './Atom';\r\nimport Chain from './Chain';\r\nimport Helix from './Helix';\r\nimport Strand from './Strand';\r\nimport Sheet from './Sheet';\r\nimport Component from './Component';\r\nimport ResidueType from './ResidueType';\r\nimport Bond from './Bond';\r\nimport AutoBond from './AutoBond';\r\nimport AromaticLoopsMarker from './AromaticLoopsMarker';\r\nimport BiologicalUnit from './BiologicalUnit';\r\nimport selectors from './selectors';\r\nimport VoxelWorld from './VoxelWorld';\r\nimport SecondaryStructureMap from './SecondaryStructureMap';\r\nimport StructuralElement from './StructuralElement';\r\n\r\nconst VOXEL_SIZE = 5.0;\r\n\r\nconst { StructureType } = SecondaryStructureMap;\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX\r\nconst helixClassMap = {\r\n [StructureType.HELIX_ALPHA]: 1,\r\n [StructureType.HELIX_PI]: 3,\r\n [StructureType.HELIX_310]: 5,\r\n};\r\n\r\nconst loopMap = {\r\n [StructureType.BRIDGE]: StructuralElementType.BRIDGE,\r\n [StructureType.TURN]: StructuralElementType.TURN,\r\n [StructureType.BEND]: StructuralElementType.BEND,\r\n [StructureType.LOOP]: StructuralElementType.COIL,\r\n};\r\n\r\n/**\r\n * The entire complex of the molecules under study.\r\n *\r\n * @exports Complex\r\n * @constructor\r\n */\r\nclass Complex {\r\n constructor() {\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n\r\n this._residueTypes = Object.create(ResidueType.StandardTypes);\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n this._molecules = [];\r\n this._maskNeedsUpdate = false;\r\n\r\n this.metadata = {};\r\n\r\n this.symmetry = [];\r\n this.units = [new BiologicalUnit(this)];\r\n this._currentUnit = 0; // default biological unit is the asymmetric unit\r\n }\r\n\r\n addAtom(atom) {\r\n const index = this._atoms.length;\r\n this._atoms.push(atom);\r\n return index;\r\n }\r\n\r\n addSheet(sheet) {\r\n const index = this._sheets.length;\r\n this._sheets.push(sheet);\r\n return index;\r\n }\r\n\r\n addHelix(helix) {\r\n const index = this._helices.length;\r\n this._helices.push(helix);\r\n return index;\r\n }\r\n\r\n getAtoms() {\r\n return this._atoms;\r\n }\r\n\r\n getBonds() {\r\n return this._bonds;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n addResidue(residue) {\r\n const index = this._residues.length;\r\n this._residues.push(residue);\r\n return index;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n this.forEachChain((chain) => {\r\n chain.updateToFrame(frameData);\r\n });\r\n }\r\n\r\n addResidueType(resName) {\r\n const rt = this._residueTypes[resName] = new ResidueType(resName, 'Unknown', '');\r\n return rt;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n getSGroupCount() {\r\n return this._sgroups.length;\r\n }\r\n\r\n getSGroups() {\r\n return this._sgroups;\r\n }\r\n\r\n /*\r\n Extract atom by its fullname: #chainName#.#residueId#.#atomName#\r\n */\r\n getAtomByFullname(fullName) {\r\n const parts = fullName.split('.');\r\n if (parts.length !== 3) {\r\n return null;\r\n }\r\n\r\n const chainName = parts[0];\r\n const resId = parseInt(parts[1], 10);\r\n if (Number.isNaN(resId)) {\r\n return null;\r\n }\r\n const atomName = parts[2].toUpperCase();\r\n\r\n let currAtom = null;\r\n this.forEachChain((chain) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (chain._name.localeCompare(chainName) === 0) {\r\n chain.forEachResidue((residue) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (residue._sequence === resId) {\r\n residue.forEachAtom((atom) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (atomName.localeCompare(atom.name) === 0) {\r\n currAtom = atom;\r\n }\r\n });\r\n }\r\n });\r\n }\r\n });\r\n\r\n return currAtom;\r\n }\r\n\r\n /**\r\n * Create a new chain.\r\n *\r\n * @param {string} name - Chain name.\r\n * @returns {Chain} - Newly created chain.\r\n */\r\n addChain(name) {\r\n const result = new Chain(this, name);\r\n this._chains.push(result);\r\n return result;\r\n }\r\n\r\n getChain(name) {\r\n for (let i = 0, n = this._chains.length; i < n; ++i) {\r\n const chain = this._chains[i];\r\n if (chain.getName() === name) {\r\n return chain;\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n getChainCount() {\r\n return this._chains.length;\r\n }\r\n\r\n getMolecules() {\r\n return this._molecules;\r\n }\r\n\r\n getMoleculeCount() {\r\n return this._molecules.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n process(atoms[i]);\r\n }\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._bonds;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n forEachChain(process) {\r\n const chains = this._chains;\r\n for (let i = 0, n = chains.length; i < n; ++i) {\r\n process(chains[i]);\r\n }\r\n }\r\n\r\n forEachMolecule(process) {\r\n const molecules = this._molecules;\r\n const n = molecules.length;\r\n for (let i = 0; i < n; ++i) {\r\n process(molecules[i]);\r\n }\r\n }\r\n\r\n forEachSGroup(process) {\r\n const groups = this._sgroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n process(groups[i]);\r\n }\r\n }\r\n\r\n forEachComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n forEachVisibleComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n addBond(left, right, order, type, fixed) {\r\n const bond = new Bond(left, right, order, type, fixed);\r\n this._bonds.push(bond);\r\n return bond;\r\n }\r\n\r\n getBondCount() {\r\n return this._bonds.length;\r\n }\r\n\r\n getResidueType(name) {\r\n return this._residueTypes[name] || null;\r\n }\r\n\r\n getUnifiedSerial(chain, serial, iCode) {\r\n /* eslint-disable no-magic-numbers */\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n /* eslint-enable no-magic-numbers */\r\n return serial + iCode * maxSerial + chain * chainShift;\r\n }\r\n\r\n splitUnifiedSerial(uniSerial) {\r\n /* eslint-disable no-magic-numbers */\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n /* eslint-enable no-magic-numbers */\r\n const chainId = Math.floor(uniSerial / chainShift);\r\n const remnant = uniSerial - chainId * chainShift;\r\n const insCode = Math.floor(remnant / maxSerial);\r\n const ser = remnant - insCode * maxSerial;\r\n return { chain: chainId, serial: ser, iCode: insCode };\r\n }\r\n\r\n _fillCmpEdit() {\r\n const self = this;\r\n const components = this._components;\r\n\r\n function addComp() {\r\n const comp = new Component(self);\r\n comp._index = components.length;\r\n components[comp._index] = comp;\r\n return comp;\r\n }\r\n\r\n this.forEachChain((chain) => {\r\n const residues = chain._residues;\r\n const resCount = residues.length;\r\n if (resCount < 1) {\r\n return;\r\n }\r\n let comp = addComp();\r\n let currStart = residues[0]._index;\r\n\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)\r\n || currRes._index !== nextRes._index - 1) {\r\n // the last condition is broken and incorrect\r\n // the refactoring of the Component is required in order to fix this issue\r\n comp.setSubDivs([{\r\n start: currStart,\r\n end: currRes._index,\r\n }]);\r\n if (nextRes) {\r\n currStart = nextRes._index;\r\n comp = addComp();\r\n }\r\n }\r\n }\r\n });\r\n }\r\n\r\n // This function was added in the moment of despair\r\n // It was the dark times for miew\r\n _fillCmpNoedit() {\r\n const comp = new Component(this);\r\n comp._index = 0;\r\n\r\n const residues = this._residues;\r\n const resCount = residues.length;\r\n if (resCount === 0) {\r\n return;\r\n }\r\n\r\n const currSubDivs = [];\r\n let currStart = 0;\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)) {\r\n // wrap up this interval\r\n currSubDivs[currSubDivs.length] = {\r\n start: currStart,\r\n end: i,\r\n };\r\n if (nextRes) {\r\n currStart = i + 1;\r\n }\r\n }\r\n }\r\n\r\n comp.setSubDivs(currSubDivs);\r\n this._components[comp._index] = comp;\r\n }\r\n\r\n /**\r\n * Fill components information.\r\n * @param {boolean} enableEditing - Restructure Complex to enable per-component editing.\r\n */\r\n _fillComponents(enableEditing) {\r\n if (enableEditing) {\r\n this._fillCmpEdit();\r\n } else {\r\n this._fillCmpNoedit();\r\n }\r\n }\r\n\r\n getCurrentUnit() {\r\n return this._currentUnit;\r\n }\r\n\r\n getDefaultBoundaries() {\r\n return this.units[0].getBoundaries();\r\n }\r\n\r\n getBoundaries() {\r\n return this.units[this._currentUnit].getBoundaries();\r\n }\r\n\r\n getTransforms() {\r\n return this.units[this._currentUnit].getTransforms();\r\n }\r\n\r\n getSelector() {\r\n return this.units[this._currentUnit].getSelector();\r\n }\r\n\r\n resetCurrentUnit() {\r\n this._currentUnit = 0;\r\n this.setCurrentUnit(1);\r\n }\r\n\r\n setCurrentUnit(newUnit) {\r\n if (newUnit !== null && newUnit !== undefined\r\n && newUnit !== this._currentUnit\r\n && newUnit >= 0\r\n && newUnit < this.units.length) {\r\n this._currentUnit = newUnit;\r\n return true;\r\n }\r\n return false;\r\n }\r\n\r\n _computeBounds() {\r\n const { units } = this;\r\n for (let i = 0, n = units.length; i < n; ++i) {\r\n units[i].computeBoundaries();\r\n }\r\n }\r\n\r\n onAtomPositionChanged() {\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n this.forEachComponent((c) => {\r\n c.update();\r\n });\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n this._finalizeBonds();\r\n this.forEachSGroup((s) => {\r\n s._rebuildSGroupOnAtomChange();\r\n });\r\n }\r\n\r\n update() {\r\n if (this._maskNeedsUpdate) {\r\n this.updateStructuresMask();\r\n this._maskNeedsUpdate = false;\r\n }\r\n }\r\n\r\n _finalizeBonds() {\r\n const bonds = this.getBonds();\r\n const n = bonds.length;\r\n for (let i = 0; i < n; ++i) {\r\n bonds[i]._index = i;\r\n }\r\n }\r\n\r\n /**\r\n * Finalizes complex's inner data(i.e. after parsing).\r\n * @param {objects} opts - Build bonds automatically.\r\n * @param {boolean} opts.needAutoBonding - Build bonds automatically.\r\n * @param {boolean} opts.detectAromaticLoops - Find/mark aromatic loops.\r\n * @param {boolean} opts.enableEditing - Restructure Complex to enable per-component editing.\r\n * @param {Array} [opts.serialAtomMap] - Array of atoms ordered by their serials.\r\n */\r\n finalize(opts) {\r\n opts = opts || {};\r\n // Put bonds into atoms\r\n const bonds = this._bonds;\r\n let i;\r\n let n;\r\n // remove invalid bonds\r\n for (i = bonds.length - 1; i >= 0; i--) {\r\n const bond = bonds[i];\r\n if (bond._left === null || bond._right === null) {\r\n bonds.splice(i, 1);\r\n } else {\r\n bond._left.bonds.push(bond);\r\n bond._right.bonds.push(bond);\r\n }\r\n }\r\n\r\n const residues = this._residues;\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._finalize();\r\n }\r\n\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n\r\n // WARNING! this MUST be done BEFORE computeBounds is called\r\n const { units } = this;\r\n for (i = 0, n = units.length; i < n; ++i) {\r\n units[i].finalize();\r\n }\r\n // try setting first biomolecule by defaults\r\n this.setCurrentUnit(1);\r\n\r\n const residueHash = {};\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n // This code is extremely dangerous for non-PDB formats\r\n residueHash[this.getUnifiedSerial(\r\n res.getChain().getName().charCodeAt(0),\r\n res.getSequence(),\r\n res.getICode().charCodeAt(0),\r\n )] = res;\r\n }\r\n\r\n const { structures } = this;\r\n for (i = 0, n = structures.length; i < n; ++i) {\r\n structures[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const helices = this._helices;\r\n for (i = 0, n = helices.length; i < n; ++i) {\r\n helices[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const sheets = this._sheets;\r\n for (i = 0, n = sheets.length; i < n; ++i) {\r\n sheets[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n\r\n const atoms = this._atoms;\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const currAtom = atoms[i];\r\n currAtom.index = i;\r\n }\r\n\r\n if (opts.needAutoBonding) {\r\n // Ignore errors during autobonding\r\n try {\r\n const autoConnector = new AutoBond(this);\r\n autoConnector.build();\r\n autoConnector.destroy();\r\n } catch (e) {\r\n console.warn('Autobonding failed:', e);\r\n }\r\n }\r\n\r\n const chains = this._chains;\r\n for (i = 0, n = chains.length; i < n; ++i) {\r\n chains[i]._index = i;\r\n }\r\n\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._index = i;\r\n }\r\n\r\n // mark non-polar hydrogens\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n if (atom.flags & Atom.Flags.HYDROGEN && atom.bonds.length === 1) {\r\n const bond = atom.bonds[0];\r\n const other = (bond._left !== atom && bond._left) || bond._right;\r\n if (other.flags & Atom.Flags.CARBON) {\r\n atom.flags |= Atom.Flags.NONPOLARH;\r\n }\r\n }\r\n }\r\n\r\n this._finalizeBonds();\r\n this._fillComponents(opts.enableEditing);\r\n\r\n const marker = new AromaticLoopsMarker(this);\r\n marker.markCycles();\r\n if (opts.detectAromaticLoops) { // TODO remove this condition clause, it is for debug purposes only!\r\n marker.detectCycles(); // TODO add conditional detection\r\n }\r\n\r\n this._finalizeMolecules();\r\n }\r\n\r\n _finalizeMolecules() {\r\n // add reference to molecule into residue\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const molecule = this._molecules[i];\r\n const count = molecule.residues.length;\r\n for (let j = 0; j < count; j++) {\r\n const residue = molecule.residues[j];\r\n residue._molecule = molecule;\r\n }\r\n }\r\n }\r\n\r\n updateStructuresMask() {\r\n const updater = (structure) => structure.collectMask();\r\n this.forEachResidue(updater);\r\n this.forEachChain(updater);\r\n this.forEachMolecule(updater);\r\n }\r\n\r\n countAtomsByMask(mask) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n getNumAtomsBySelector(selector) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n resetAtomMask(mask) {\r\n this.forEachAtom((atom) => {\r\n atom.mask = mask;\r\n });\r\n }\r\n\r\n markAtoms(selector, mask) {\r\n const setMask = mask;\r\n const clearMask = ~setMask;\r\n let count = 0;\r\n const totalSelector = selectors.keyword('And')(selector, this.getSelector());\r\n\r\n this.forEachAtom((atom) => {\r\n if (totalSelector.includesAtom(atom)) {\r\n atom.mask |= setMask;\r\n count++;\r\n } else {\r\n atom.mask &= clearMask;\r\n }\r\n });\r\n this._maskNeedsUpdate = true;\r\n\r\n return count;\r\n }\r\n\r\n markAtomsAdditionally(selector, mask) {\r\n const setMask = mask;\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom) && (atom.mask & mask) !== mask) {\r\n atom.mask |= setMask;\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n clearAtomBits(mask) {\r\n const clearMask = ~mask;\r\n this.forEachAtom((atom) => {\r\n atom.mask &= clearMask;\r\n });\r\n const reseter = (a) => {\r\n a._mask &= clearMask;\r\n };\r\n this.forEachAtom(reseter);\r\n this.forEachResidue(reseter);\r\n this.forEachChain(reseter);\r\n this.forEachMolecule(reseter);\r\n }\r\n\r\n getAtomNames() {\r\n if (this.hasOwnProperty('_atomNames')) {\r\n return this._atomNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.name] = 1;\r\n });\r\n this._atomNames = Object.keys(dict);\r\n\r\n return this._atomNames;\r\n }\r\n\r\n getElements() {\r\n if (this.hasOwnProperty('_elements')) {\r\n return this._elements;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.element.name] = 1;\r\n });\r\n this._elements = Object.keys(dict);\r\n\r\n return this._elements;\r\n }\r\n\r\n getResidueNames() {\r\n if (this.hasOwnProperty('_residueNames')) {\r\n return this._residueNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachResidue((res) => {\r\n dict[res._type._name] = 1;\r\n });\r\n this._residueNames = Object.keys(dict);\r\n\r\n return this._residueNames;\r\n }\r\n\r\n getChainNames() {\r\n if (this.hasOwnProperty('_chainNames')) {\r\n return this._chainNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachChain((chain) => {\r\n dict[chain._name] = 1;\r\n });\r\n this._chainNames = Object.keys(dict);\r\n\r\n return this._chainNames;\r\n }\r\n\r\n getAltLocNames() {\r\n if (this.hasOwnProperty('_altlocNames')) {\r\n return this._altlocNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[String.fromCharCode(atom.location)] = 1;\r\n });\r\n this._altlocNames = Object.keys(dict);\r\n\r\n return this._altlocNames;\r\n }\r\n\r\n getVoxelWorld() {\r\n if (!this.hasOwnProperty('_voxelWorld')) {\r\n try {\r\n this._voxelWorld = new VoxelWorld(\r\n this.getDefaultBoundaries().boundingBox,\r\n new THREE.Vector3(VOXEL_SIZE, VOXEL_SIZE, VOXEL_SIZE),\r\n );\r\n this._voxelWorld.addAtoms(this);\r\n } catch (e) {\r\n logger.warn('Unable to create voxel world');\r\n this._voxelWorld = null;\r\n }\r\n }\r\n\r\n return this._voxelWorld;\r\n }\r\n\r\n /**\r\n * Simple function to make unified routine procedure without code duplication.\r\n * @param {Array} srcArray - Source chemical structure array (will be part of resulting chemical structure array).\r\n * @param {Array} dstArray - Resulting chemical structure array.\r\n * @param {number} param - Parameter for processor.\r\n * @param {function} functor - Processor for every element in array.\r\n */\r\n addElement(srcArray, dstArray, param, functor) {\r\n const { length } = srcArray;\r\n for (let i = 0; i < length; ++i) {\r\n const elem = srcArray[i];\r\n functor(elem, param);\r\n dstArray.push(elem);\r\n }\r\n }\r\n\r\n // this function joins multiple complexes into one (this)\r\n // atom, bond, ... objects are reused -- so input complexes are no longer valid\r\n joinComplexes(complexes) {\r\n // clear target complex\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n\r\n const self = this;\r\n let atomBias = 0;\r\n let bondBias = 0;\r\n let residueBias = 0;\r\n let chainBias = 0;\r\n let componentBias = 0;\r\n\r\n function processAtom(atom, bias) {\r\n atom.serial += bias;\r\n atom.index += bias;\r\n }\r\n\r\n function processBond(bond, bias) {\r\n bond._index += bias;\r\n }\r\n\r\n function processResidue(residue, bias) {\r\n residue._index += bias;\r\n }\r\n\r\n function processChain(chain, bias) {\r\n chain._complex = self;\r\n chain._index += bias;\r\n }\r\n\r\n function processComponent(component, bias) {\r\n component._complex = self;\r\n component._index += bias;\r\n }\r\n\r\n /**\r\n * Simple function to do nothing.\r\n */\r\n function doNothing() {\r\n }\r\n\r\n for (let i = 0; i < complexes.length; ++i) {\r\n const c = complexes[i];\r\n this.addElement(c._atoms, this._atoms, atomBias, processAtom);\r\n this.addElement(c._bonds, this._bonds, bondBias, processBond);\r\n this.addElement(c._residues, this._residues, residueBias, processResidue);\r\n this.addElement(c._chains, this._chains, chainBias, processChain);\r\n this.addElement(c._sheets, this._sheets, 0, doNothing);\r\n this.addElement(c._helices, this._helices, 0, doNothing);\r\n this.addElement(c._sgroups, this._sgroups, 0, doNothing);\r\n this.addElement(c._components, this._components, componentBias, processComponent);\r\n this.addElement(c.structures, this.structures, 0, doNothing);\r\n // merge residue types\r\n for (const rt in c._residueTypes) {\r\n if (c._residueTypes.hasOwnProperty(rt)) {\r\n this._residueTypes[rt] = c._residueTypes[rt];\r\n }\r\n }\r\n\r\n atomBias += c._atoms.length;\r\n bondBias += c._bonds.length;\r\n residueBias += c._residues.length;\r\n chainBias += c._chains.length;\r\n componentBias += c._components.length;\r\n }\r\n\r\n this._computeBounds();\r\n }\r\n\r\n /**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n */\r\n dssp() {\r\n const ssMap = new SecondaryStructureMap(this);\r\n\r\n const structures = this.structures = [];\r\n const helices = this._helices = [];\r\n const sheets = this._sheets = [];\r\n\r\n const getSheet = (index) => {\r\n let item = sheets[index];\r\n if (!item) {\r\n item = sheets[index] = new Sheet(String(index), 0);\r\n }\r\n return item;\r\n };\r\n\r\n let lastCode;\r\n let lastSheetIndex;\r\n let lastHelixIndex = 0;\r\n let curStructure = null;\r\n for (let i = 0, n = this._residues.length; i < n; ++i) {\r\n const curCode = ssMap._ss[i];\r\n const curResidue = this._residues[i];\r\n const curSheetIndex = ssMap._sheet[i];\r\n\r\n // expand the last structure\r\n if (curCode === lastCode && curSheetIndex === lastSheetIndex) {\r\n curResidue._secondary = curStructure;\r\n if (curStructure) {\r\n curStructure.term = curResidue;\r\n }\r\n if (curStructure instanceof Helix) {\r\n curStructure.length++;\r\n }\r\n continue;\r\n }\r\n\r\n // create a new structure\r\n const helixClass = helixClassMap[curCode];\r\n const loopType = loopMap[curCode];\r\n if (curCode === StructureType.STRAND) {\r\n const curSheet = getSheet(curSheetIndex);\r\n curStructure = new Strand(curSheet, curResidue, curResidue, 0, null, null);\r\n curSheet.addStrand(curStructure);\r\n } else if (helixClass !== undefined) {\r\n lastHelixIndex++;\r\n curStructure = new Helix(helixClass, curResidue, curResidue, lastHelixIndex, String(lastHelixIndex), '', 1);\r\n helices.push(curStructure);\r\n } else if (loopType !== undefined) {\r\n curStructure = new StructuralElement(loopType, curResidue, curResidue);\r\n } else {\r\n curStructure = null;\r\n }\r\n\r\n if (curStructure) {\r\n structures.push(curStructure);\r\n }\r\n\r\n curResidue._secondary = curStructure;\r\n\r\n lastCode = curCode;\r\n lastSheetIndex = curSheetIndex;\r\n }\r\n\r\n this._sheets = sheets.filter((_sheet) => true); // squeeze sheets array\r\n }\r\n}\r\n\r\nComplex.prototype.id = 'Complex';\r\nComplex.prototype.name = '';\r\n\r\nexport default Complex;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\nfunction pow2ceil(v) {\r\n let p = 2;\r\n v = (v - 1) >> 1;\r\n while (v) {\r\n p <<= 1;\r\n v >>= 1;\r\n }\r\n return p;\r\n}\r\n\r\n/**\r\n * Volume constructor\r\n *\r\n * @param {Object} type - Float32Array, Int8Array, etc...\r\n * @param {Object|Array} dimensions - number of data points on each axis (x, y, z)\r\n * @param {Box3} box - bounding box defining data place in metric space,\r\n * it's corners correspond to extreme data points\r\n * @param {Number} vecSize - dimension of the field data point (1 = scalar, 3 = 3D vector)\r\n * @param {Object} data - typed array of the same type as specified by the 1st parameter,\r\n * layout: point by point along X,\r\n * row by row along Y,\r\n * plane by plane along Z\r\n * @param {Number} volumeInfo - volume info values to define threshold to filter the noise\r\n */\r\n\r\nclass Volume {\r\n constructor(type, dimensions, box, vecSize, data, volumeInfo) {\r\n this._box = box.clone();\r\n this._dimVec = Math.max(Math.floor(vecSize || 1), 1);\r\n this._volumeInfo = volumeInfo;\r\n\r\n if (dimensions instanceof Array) {\r\n [this._dimX, this._dimY, this._dimZ] = dimensions;\r\n } else {\r\n this._dimX = dimensions.x;\r\n this._dimY = dimensions.y;\r\n this._dimZ = dimensions.z;\r\n }\r\n this._dimX = Math.max(Math.floor(this._dimX), 1);\r\n this._dimY = Math.max(Math.floor(this._dimY), 1);\r\n this._dimZ = Math.max(Math.floor(this._dimZ), 1);\r\n\r\n this._rowElements = this._dimVec * this._dimX;\r\n this._planeElements = this._rowElements * this._dimY;\r\n this._totalElements = this._planeElements * this._dimZ;\r\n\r\n this._data = data || utils.allocateTyped(type, this._totalElements);\r\n\r\n // override getter/setter for vector fields\r\n switch (this._dimVec) {\r\n case 1:\r\n break;\r\n\r\n case 2:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n };\r\n break;\r\n\r\n case 3:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1], this._data[idx + 2]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n this._data[idx + 2] = c;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n this._data[idx + 2] += c;\r\n };\r\n break;\r\n\r\n default:\r\n throw new Error('Volume: invalid vector dimension');\r\n }\r\n }\r\n\r\n // default getter assumes it's a scalar field\r\n getValue(x, y, z) {\r\n return this._data[x + y * this._rowElements + z * this._planeElements];\r\n }\r\n\r\n // default setter assumes it's a scalar field\r\n setValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] = val;\r\n }\r\n\r\n // default adder assumes it's a scalar field\r\n addValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] += val;\r\n }\r\n\r\n getDimensions() {\r\n return [this._dimX, this._dimY, this._dimZ];\r\n }\r\n\r\n getBox() {\r\n return this._box;\r\n }\r\n\r\n getVolumeInfo() {\r\n return this._volumeInfo;\r\n }\r\n\r\n getCellSize() {\r\n const boxSize = new THREE.Vector3();\r\n this._box.getSize(boxSize);\r\n const res = new THREE.Vector3();\r\n res.x = this._dimX > 1 ? boxSize.x / (this._dimX - 1) : 0;\r\n res.y = this._dimY > 1 ? boxSize.y / (this._dimY - 1) : 0;\r\n res.z = this._dimZ > 1 ? boxSize.z / (this._dimZ - 1) : 0;\r\n return res;\r\n }\r\n\r\n computeGradient() {\r\n if (this._dimVec !== 1) {\r\n // gradient can only be computed for scalar fields\r\n return null;\r\n }\r\n\r\n // create a 3D vector field of gradients\r\n const gradient = new Volume(Float32Array, [this._dimX, this._dimY, this._dimZ], this._box, 3);\r\n\r\n // calculate cell side lengths\r\n const vl = this.getCellSize();\r\n\r\n // gradient axis scaling values and averaging factors, to correctly\r\n // calculate the gradient for volumes with irregular cell spacing\r\n const vs = new THREE.Vector3(-0.5 / vl.x, -0.5 / vl.y, -0.5 / vl.z);\r\n\r\n // TODO Check for intended bug in VMD (min is zero)\r\n function clamp(val, min, max) {\r\n return Math.min(max, Math.max(min, val));\r\n }\r\n\r\n const xSize = this._dimX;\r\n const ySize = this._dimY;\r\n const zSize = this._dimZ;\r\n const volMap = this._data;\r\n\r\n function _voxelValue(x, y, z) {\r\n return volMap[z * xSize * ySize + y * xSize + x];\r\n }\r\n\r\n for (let zi = 0; zi < zSize; ++zi) {\r\n const zm = clamp(zi - 1, 0, zSize - 1);\r\n const zp = clamp(zi + 1, 0, zSize - 1);\r\n\r\n for (let yi = 0; yi < ySize; ++yi) {\r\n const ym = clamp(yi - 1, 0, ySize - 1);\r\n const yp = clamp(yi + 1, 0, ySize - 1);\r\n\r\n for (let xi = 0; xi < xSize; ++xi) {\r\n const xm = clamp(xi - 1, 0, xSize - 1);\r\n const xp = clamp(xi + 1, 0, xSize - 1);\r\n\r\n // Calculate the volume gradient at each grid cell.\r\n // Gradients are now stored unnormalized, since we need them in pure\r\n // form in order to draw field lines etc. Shading code will now have\r\n // to do renormalization for itself on-the-fly.\r\n\r\n // XXX this gradient is only correct for orthogonal grids, since\r\n // we're using the array index offsets rather to calculate the gradient\r\n // rather than voxel coordinate offsets. This will have to be\r\n // re-worked for non-orthogonal datasets.\r\n\r\n gradient.setValue(\r\n xi,\r\n yi,\r\n zi,\r\n (_voxelValue(xp, yi, zi) - _voxelValue(xm, yi, zi)) * vs.x,\r\n (_voxelValue(xi, yp, zi) - _voxelValue(xi, ym, zi)) * vs.y,\r\n (_voxelValue(xi, yi, zp) - _voxelValue(xi, yi, zm)) * vs.z,\r\n );\r\n }\r\n }\r\n }\r\n\r\n return gradient;\r\n }\r\n\r\n normalize() {\r\n const data = this._data;\r\n\r\n // get min/max\r\n let min = data[0];\r\n let max = data[0];\r\n for (let i = 1; i < data.length; ++i) {\r\n min = Math.min(min, data[i]);\r\n max = Math.max(max, data[i]);\r\n }\r\n\r\n const d = 1.0 / (max - min);\r\n if (d === 0) {\r\n return;\r\n }\r\n\r\n // normalize\r\n for (let i = 0; i < data.length; ++i) {\r\n data[i] = d * (data[i] - min);\r\n }\r\n }\r\n\r\n getTiledTextureStride() {\r\n return [this._dimX + 2, this._dimY + 2];\r\n }\r\n\r\n buildTiledTexture() {\r\n let tilesX = Math.ceil(Math.sqrt(this._dimZ * this._dimY / this._dimX));\r\n\r\n let width = tilesX * (this._dimX + 2) - 1;\r\n width = pow2ceil(width);\r\n tilesX = Math.floor(width / (this._dimX + 2));\r\n\r\n const tilesY = Math.ceil(this._dimZ / tilesX);\r\n let height = tilesY * (this._dimY + 2) - 1;\r\n height = pow2ceil(height);\r\n\r\n const data = new Uint8Array(width * height);\r\n\r\n let src;\r\n let dst;\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // process each pixel row of this tile row\r\n for (let row = 0; row < this._dimY; ++row) {\r\n src = tileRow * tilesX * this._planeElements + row * this._rowElements;\r\n dst = width * (tileRow * (this._dimY + 2) + row);\r\n // copy a series of rows through several XY planes\r\n for (let t = 0; t < tilesX; ++t) {\r\n // copy one row of one XY plane\r\n for (let x = 0; x < this._dimX; ++x) {\r\n data[dst++] = 255.0 * this._data[src++];\r\n }\r\n\r\n // repeat last pixel of previous tile\r\n data[dst++] = 255.0 * this._data[src - 1];\r\n\r\n if (t < tilesX - 1) {\r\n // skip to the same row of next XY plane\r\n src += this._planeElements - this._rowElements;\r\n // repeat first pixel of next tile\r\n data[dst++] = 255.0 * this._data[src];\r\n }\r\n }\r\n }\r\n }\r\n\r\n // fill pixels between tile rows with copy of edge pixels\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // copy last pixel row of this tile row to the following pixel row of the texture\r\n src = width * (tileRow * (this._dimY + 2) + this._dimY - 1);\r\n dst = src + width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n if (tileRow < tilesY - 1) {\r\n // copy first pixel row of next tile row to the preceding pixel row of the texture\r\n src = width * (tileRow + 1) * (this._dimY + 2);\r\n dst = src - width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n }\r\n }\r\n\r\n const texture = new THREE.DataTexture(\r\n data,\r\n width,\r\n height,\r\n THREE.LuminanceFormat,\r\n THREE.UnsignedByteType,\r\n THREE.UVMapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.LinearFilter,\r\n THREE.LinearFilter,\r\n );\r\n texture.needsUpdate = true;\r\n return texture;\r\n }\r\n\r\n /* ********************************************************************************\r\n *\r\n * Methods that provide direct access to internal array (for better performance)\r\n *\r\n ******************************************************************************** */\r\n\r\n getData() {\r\n return this._data;\r\n }\r\n\r\n getDirectIdx(x, y, z) {\r\n return x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n }\r\n\r\n getStrideX() {\r\n return this._dimVec;\r\n }\r\n\r\n getStrideY() {\r\n return this._rowElements;\r\n }\r\n\r\n getStrideZ() {\r\n return this._planeElements;\r\n }\r\n}\r\n\r\nVolume.prototype.id = 'Volume';\r\n\r\nexport default Volume;\r\n","/**\r\n * Residue Molecule.\r\n *\r\n * @param {Complex} complex - Molecular complex this Molecule belongs to.\r\n * @param {String} name - Molecule's name.\r\n * @param {Integer} index - Molecule's index in file.\r\n *\r\n * @exports Molecule\r\n * @constructor\r\n */\r\nclass Molecule {\r\n constructor(complex, name, index) {\r\n this.complex = complex;\r\n this.name = name || '';\r\n this.residues = [];\r\n this.mask = 1 | 0;\r\n this.index = index || -1; // start with 1\r\n }\r\n\r\n forEachResidue(process) {\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this.mask = mask;\r\n }\r\n}\r\n\r\nexport default Molecule;\r\n","import Atom from './chem/Atom';\r\nimport Element from './chem/Element';\r\nimport Bond from './chem/Bond';\r\nimport Residue from './chem/Residue';\r\nimport ResidueType from './chem/ResidueType';\r\nimport Chain from './chem/Chain';\r\nimport Helix from './chem/Helix';\r\nimport Strand from './chem/Strand';\r\nimport Sheet from './chem/Sheet';\r\nimport SGroup from './chem/SGroup';\r\nimport Assembly from './chem/Assembly';\r\nimport Complex from './chem/Complex';\r\nimport Volume from './chem/Volume';\r\nimport VoxelWorld from './chem/VoxelWorld';\r\nimport selectors from './chem/selectors';\r\nimport Molecule from './chem/Molecule';\r\n\r\nexport default {\r\n Atom,\r\n Element,\r\n Bond,\r\n Residue,\r\n ResidueType,\r\n Chain,\r\n Helix,\r\n Strand,\r\n Sheet,\r\n SGroup,\r\n Assembly,\r\n Complex,\r\n Volume,\r\n VoxelWorld,\r\n selectors,\r\n Molecule,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\n\r\nclass CSS2DObject extends THREE.Object3D {\r\n constructor(element) {\r\n super();\r\n const self = this;\r\n this._element = element;\r\n this._element.style.position = 'absolute';\r\n this.addEventListener('removed', () => {\r\n if (self._element.parentNode !== null) {\r\n self._element.parentNode.removeChild(self._element);\r\n }\r\n });\r\n }\r\n\r\n getElement() {\r\n return this._element;\r\n }\r\n\r\n /**\r\n * Sets label transparency.\r\n *\r\n * @param {number} transp - in [0; 1] 1 means fully transparent\r\n */\r\n setTransparency(transp) {\r\n const el = this.getElement();\r\n if (el === null) {\r\n return;\r\n }\r\n if (transp === 1.0) {\r\n el.style.display = 'none';\r\n return;\r\n }\r\n el.style.display = 'inline';\r\n const op = 1.0 - transp;\r\n const top = op.toString();\r\n const op100 = op * 100;\r\n el.style.opacity = top;\r\n el.style.filter = `alpha(opacity=${op100})`; // IE fallback\r\n }\r\n\r\n clone() {\r\n const obj = new CSS2DObject(this._element);\r\n obj.copy(this);\r\n return obj;\r\n }\r\n}\r\n\r\nexport default CSS2DObject;\r\n","import * as THREE from 'three';\r\n\r\nclass RCGroup extends THREE.Group {\r\n raycast(raycaster, intersects) {\r\n if (!this.visible) {\r\n return;\r\n }\r\n\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n children[i].raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].enableSubset) {\r\n children[i].enableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].disableSubset) {\r\n children[i].disableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n isEmpty() {\r\n return this.children.length === 0;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].updateToFrame) {\r\n children[i].updateToFrame(frameData);\r\n }\r\n }\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n Array.prototype.push.apply(totalSubset, children[i].getSubset(mask, innerOnly));\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default RCGroup;\r\n","/* eslint-disable no-magic-numbers */\r\nimport * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport CSS2DObject from './CSS2DObject';\r\nimport RCGroup from './RCGroup';\r\nimport vertexScreenQuadShader from './shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromTex from './shaders/ScreenQuadFromTex.frag';\r\nimport fragmentScreenQuadFromTexWithDistortion from './shaders/ScreenQuadFromTexWithDistortion.frag';\r\n\r\nconst LAYERS = {\r\n DEFAULT: 0, VOLUME: 1, TRANSPARENT: 2, PREPASS_TRANSPARENT: 3, VOLUME_BFPLANE: 4, COLOR_FROM_POSITION: 5, SHADOWMAP: 6,\r\n};\r\n\r\nconst SELECTION_LAYERS = [ // These layers, that are used in the selection by ray casting\r\n LAYERS.DEFAULT, LAYERS.TRANSPARENT,\r\n];\r\n\r\nTHREE.Object3D.prototype.resetTransform = function () {\r\n this.position.set(0, 0, 0);\r\n this.quaternion.set(0, 0, 0, 1);\r\n this.scale.set(1, 1, 1);\r\n};\r\n\r\n// update world matrix of this object and all its ancestors\r\nTHREE.Object3D.prototype.updateMatrixWorldRecursive = function () {\r\n if (this.parent != null) {\r\n this.parent.updateMatrixWorldRecursive();\r\n }\r\n this.updateMatrixWorld();\r\n};\r\n// add object to parent, saving objects' world transform\r\nTHREE.Object3D.prototype.addSavingWorldTransform = (function () {\r\n const _worldMatrixInverse = new THREE.Matrix4();\r\n\r\n return function (object) {\r\n if (object instanceof THREE.Object3D) {\r\n _worldMatrixInverse.copy(this.matrixWorld).invert();\r\n _worldMatrixInverse.multiply(object.matrixWorld);\r\n object.matrix.copy(_worldMatrixInverse);\r\n object.matrix.decompose(object.position, object.quaternion, object.scale);\r\n this.add(object);\r\n }\r\n };\r\n}());\r\n\r\n// render a tiny transparent quad in the center of the screen\r\nTHREE.WebGLRenderer.prototype.renderDummyQuad = (function () {\r\n const _material = new THREE.MeshBasicMaterial({ transparent: true, opacity: 0.0, depthWrite: false });\r\n\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(0.01, 0.01), _material);\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function () {\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuad = (function () {\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(1.0, 1.0));\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function (material) {\r\n _quad.material = material;\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.isIdentity = (function () {\r\n const identity = new THREE.Matrix4();\r\n return function () {\r\n return identity.equals(this);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.applyToPointsArray = function (array, stride, w) {\r\n if (!array || !stride || stride < 3) {\r\n return array;\r\n }\r\n w = w || 0; // use point as normal by default\r\n const e = this.elements;\r\n for (let i = 0; i < array.length; i += stride) {\r\n const x = array[i];\r\n const y = array[i + 1];\r\n const z = array[i + 2];\r\n\r\n const persp = 1 / (e[3] * x + e[7] * y + e[11] * z + e[15]);\r\n\r\n array[i] = (e[0] * x + e[4] * y + e[8] * z + e[12] * w) * persp;\r\n array[i + 1] = (e[1] * x + e[5] * y + e[9] * z + e[13] * w) * persp;\r\n array[i + 2] = (e[2] * x + e[6] * y + e[10] * z + e[14] * w) * persp;\r\n }\r\n return array;\r\n};\r\n\r\nclass ScreenQuadMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n if (params.uniforms === undefined) {\r\n params.uniforms = {};\r\n }\r\n params.uniforms.srcTex = { type: 't', value: null };\r\n params.vertexShader = vertexScreenQuadShader;\r\n params.transparent = false;\r\n params.depthTest = false;\r\n params.depthWrite = false;\r\n super(params);\r\n }\r\n}\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTex = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { opacity: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTex,\r\n transparent: true,\r\n });\r\n\r\n return function (srcTex, opacity) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.transparent = (opacity < 1.0);\r\n _material.uniforms.opacity.value = opacity;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTexWithDistortion = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { coef: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTexWithDistortion,\r\n });\r\n\r\n return function (srcTex, coef) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.uniforms.coef.value = coef;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\n/**\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setMinimalFov = function (angle) {\r\n if (this.aspect >= 1.0) {\r\n this.fov = angle;\r\n } else {\r\n this.fov = THREE.MathUtils.radToDeg(2 * Math.atan(Math.tan(THREE.MathUtils.degToRad(angle) * 0.5) / this.aspect));\r\n }\r\n};\r\n\r\n/**\r\n * @param {THREE.PerspectiveCamera} camera - Base camera for this stereo camera.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.StereoCamera.prototype.updateHalfSized = function (camera, angle) {\r\n const originalAspect = camera.aspect;\r\n const originalFov = camera.fov;\r\n\r\n camera.aspect = originalAspect / 2.0;\r\n camera.setMinimalFov(angle);\r\n camera.updateProjectionMatrix();\r\n\r\n this.update(camera);\r\n\r\n camera.aspect = originalAspect;\r\n camera.fov = originalFov;\r\n camera.updateProjectionMatrix();\r\n};\r\n\r\n/**\r\n * @param {number} radius - Radius of bounding sphere in angstroms to fit on screen.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setDistanceToFit = function (radius, angle) {\r\n this.position.z = radius / Math.sin(0.5 * THREE.MathUtils.degToRad(angle));\r\n};\r\n\r\n/**\r\n * @param {RCGroup} gfxObj - All objects on scene.\r\n * @param {THREE.PerspectiveCamera} camera - Camera used for rendering.\r\n * @param {number} clipPlane - Distance to clip plane.\r\n * @param {number} fogFarPlane - Distance to fog far plane.\r\n */\r\nTHREE.Raycaster.prototype.intersectVisibleObject = function (gfxObj, camera, clipPlane, fogFarPlane) {\r\n const intersects = this.intersectObject(gfxObj, false);\r\n if (intersects.length === 0) {\r\n return null;\r\n }\r\n\r\n // find point closest to camera that doesn't get clipped by camera near plane or clipPlane (if it exists)\r\n const nearPlane = Math.min(camera.near, clipPlane);\r\n let i;\r\n let p = intersects[0];\r\n const v = new THREE.Vector3();\r\n for (i = 0; i < intersects.length; ++i) {\r\n p = intersects[i];\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -nearPlane) {\r\n break;\r\n }\r\n }\r\n if (i === intersects.length) {\r\n return null;\r\n }\r\n\r\n // check that selected intersection point is not clipped by camera far plane or occluded by fog (if it exists)\r\n const farPlane = Math.min(camera.far, fogFarPlane);\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -farPlane) {\r\n return null;\r\n }\r\n return p;\r\n};\r\n\r\nTHREE.Matrix4.prototype.extractScale = (function () {\r\n const _v = new THREE.Vector3();\r\n\r\n return function (scale) {\r\n if (scale === undefined) {\r\n logger.debug('extractScale(): new is too expensive operation to do it on-the-fly');\r\n scale = _v.clone();\r\n }\r\n\r\n const te = this.elements;\r\n scale.x = _v.set(te[0], te[1], te[2]).length();\r\n scale.y = _v.set(te[4], te[5], te[6]).length();\r\n scale.z = _v.set(te[8], te[9], te[10]).length();\r\n\r\n // if determine is negative, we need to invert one scale\r\n const det = this.determinant();\r\n if (det < 0) {\r\n scale.x = -scale.x;\r\n }\r\n return scale;\r\n };\r\n}());\r\n\r\nfunction _calcCylinderMatrix(posBegin, posEnd, radius) {\r\n const posCenter = posBegin.clone().lerp(posEnd, 0.5);\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(radius, posBegin.distanceTo(posEnd), radius);\r\n\r\n const matRotHalf = new THREE.Matrix4();\r\n matRotHalf.makeRotationX(Math.PI / 2);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n const vUp = new THREE.Vector3(0, 1, 0);\r\n matRotLook.lookAt(posCenter, posEnd, vUp);\r\n\r\n matRotLook.multiply(matRotHalf);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(posCenter);\r\n return matRotLook;\r\n}\r\n\r\nfunction _calcChunkMatrix(eye, target, up, rad) {\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(rad.x, rad.y, 0);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n matRotLook.lookAt(eye, target, up);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(eye);\r\n\r\n return matRotLook;\r\n}\r\n\r\nfunction _groupHasGeometryToRender(group) {\r\n let hasGeoms = false;\r\n group.traverse((node) => {\r\n if (node.hasOwnProperty('geometry') || node instanceof CSS2DObject) {\r\n hasGeoms = true;\r\n }\r\n });\r\n return hasGeoms;\r\n}\r\n\r\nfunction _buildDistorionMesh(widthSegments, heightSegements, coef) {\r\n // solve equation r_u = r_d * (1 + k * r_d^2)\r\n // for r_d using iterations\r\n // takes: r_u^2\r\n // returns: r_d / r_u factor that can be used to distort point coords\r\n function calcInverseBarrel(r2) {\r\n const epsilon = 1e-5;\r\n let prevR2 = 0.0;\r\n let curR2 = r2;\r\n let dr = 1.0;\r\n while (Math.abs(curR2 - prevR2) > epsilon) {\r\n dr = 1.0 + coef * curR2;\r\n prevR2 = curR2;\r\n curR2 = r2 / (dr * dr);\r\n }\r\n\r\n return 1.0 / dr;\r\n }\r\n\r\n const geo = new THREE.PlaneGeometry(2.0, 2.0, widthSegments, heightSegements);\r\n\r\n const pos = geo.getAttribute('position');\r\n for (let i = 0; i < pos.count; ++i) {\r\n const x = pos.array[3 * i];\r\n const y = pos.array[3 * i + 1];\r\n const c = calcInverseBarrel(x * x + y * y);\r\n pos.setXY(i, c * x, c * y);\r\n }\r\n\r\n return geo;\r\n}\r\n\r\nTHREE.BufferAttribute.prototype.copyAtList = function (attribute, indexList) {\r\n console.assert(\r\n this.itemSize === attribute.itemSize,\r\n 'DEBUG: BufferAttribute.copyAtList buffers have different item size.',\r\n );\r\n const { itemSize } = this;\r\n for (let i = 0, n = indexList.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n this.array[i * itemSize + j] = attribute.array[indexList[i] * itemSize + j];\r\n }\r\n }\r\n return this;\r\n};\r\n\r\nfunction fillArray(array, value, startIndex, endIndex) {\r\n startIndex = (typeof startIndex !== 'undefined') ? startIndex : 0;\r\n endIndex = (typeof endIndex !== 'undefined') ? endIndex : array.length;\r\n for (let i = startIndex; i < endIndex; ++i) {\r\n array[i] = value;\r\n }\r\n}\r\n\r\n/** @param {THREE.Object3D} object - Parent object. */\r\nfunction removeChildren(object) {\r\n const { children } = object;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n child.parent = null;\r\n child.dispatchEvent({ type: 'removed' });\r\n }\r\n object.children = [];\r\n}\r\n\r\nfunction clearTree(object) {\r\n object.traverse((obj) => {\r\n if (obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line) {\r\n obj.geometry.dispose();\r\n }\r\n });\r\n removeChildren(object);\r\n}\r\n\r\nfunction destroyObject(object) {\r\n clearTree(object);\r\n if (object.parent) {\r\n object.parent.remove(object);\r\n } else {\r\n object.dispatchEvent({ type: 'removed' });\r\n }\r\n}\r\n\r\nfunction belongToSelectLayers(object) {\r\n for (let i = 0; i < SELECTION_LAYERS.length; i++) {\r\n if (((object.layers.mask >> SELECTION_LAYERS[i]) & 1) === 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n}\r\n\r\nfunction processObjRenderOrder(root, idMaterial) {\r\n // set renderOrder to 0 for Backdrop and to 1 in other cases to render Backdrop earlier all other materials\r\n const renderOrder = +(idMaterial !== 'BA');\r\n root.traverse((object) => {\r\n if (object.isGroup) {\r\n object.renderOrder = renderOrder;\r\n }\r\n });\r\n}\r\n\r\nfunction applySelectionMaterial(geo) {\r\n geo.traverse((node) => {\r\n if ('material' in node) {\r\n node.material = node.material.clone(true);\r\n // using z-offset to magically fix selection rendering artifact (on z-sprites)\r\n node.material.setValues({\r\n depthFunc: THREE.LessEqualDepth,\r\n overrideColor: true,\r\n fog: false,\r\n lights: false,\r\n shadowmap: false,\r\n });\r\n node.material.setUberOptions({ fixedColor: new THREE.Color(0xFFFF00), zOffset: -1e-6 });\r\n }\r\n });\r\n}\r\n\r\nfunction getMiddlePoint(point1, point2, optionalTarget) {\r\n const result = optionalTarget || new THREE.Vector3();\r\n\r\n result.set(0, 0, 0);\r\n result.addScaledVector(point1, 0.5);\r\n result.addScaledVector(point2, 0.5);\r\n\r\n return result;\r\n}\r\n\r\n// Monkey-patch for \"InstancedBufferGeometry.instanceCount becomes undefined after copy()\"\r\n// https://github.com/mrdoob/three.js/issues/22151\r\nconst _oldInstancedBufferGeometryCopy = THREE.InstancedBufferGeometry.prototype.copy;\r\n\r\nTHREE.InstancedBufferGeometry.prototype.copy = function (source) {\r\n _oldInstancedBufferGeometryCopy.call(this, source);\r\n if (this.instanceCount === undefined) {\r\n this.instanceCount = Infinity;\r\n }\r\n};\r\n\r\nexport default {\r\n calcCylinderMatrix: _calcCylinderMatrix,\r\n calcChunkMatrix: _calcChunkMatrix,\r\n groupHasGeometryToRender: _groupHasGeometryToRender,\r\n buildDistorionMesh: _buildDistorionMesh,\r\n RCGroup,\r\n fillArray,\r\n clearTree,\r\n destroyObject,\r\n belongToSelectLayers,\r\n processObjRenderOrder,\r\n applySelectionMaterial,\r\n getMiddlePoint,\r\n LAYERS,\r\n};\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfx/gfxutils';\r\n\r\nconst _defaultBoundaries = {\r\n boundingBox: new THREE.Box3(new THREE.Vector3(-1, -1, -1), new THREE.Vector3(1, 1, 1)),\r\n boundingSphere: new THREE.Sphere(new THREE.Vector3(0, 0, 0), 1),\r\n};\r\n\r\nclass Visual extends gfxutils.RCGroup {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this.name = name;\r\n this._dataSource = dataSource;\r\n }\r\n\r\n release() {\r\n if (this.parent) {\r\n this.parent.remove(this);\r\n }\r\n }\r\n\r\n getDataSource() {\r\n return this._dataSource;\r\n }\r\n\r\n getBoundaries() {\r\n return _defaultBoundaries;\r\n }\r\n}\r\n\r\nexport default Visual;\r\n","function _ensureArray(x) {\r\n if (x === null || x === undefined || Array.isArray(x)) {\r\n return x;\r\n }\r\n return [x];\r\n}\r\n\r\n/** An indexed list of objects or classes. */\r\nclass EntityList {\r\n /**\r\n * Create a list of objects.\r\n * The objects can be indexed by one or more properties for the later retrieval.\r\n *\r\n * @param {!Array=} entities A list of objects to automatically register at creation time.\r\n * @param {!Array=} indices A list of property names to use for case-insensitive indexing.\r\n * By default, a single `.id` property is used.\r\n * @see EntityList#register\r\n */\r\n constructor(entities = [], indices = ['id']) {\r\n this._list = [];\r\n this._dict = {};\r\n this._indices = [...indices];\r\n this._indices.forEach((index) => {\r\n this._dict[index] = {};\r\n });\r\n\r\n entities.forEach((entity) => this.register(entity));\r\n }\r\n\r\n /**\r\n * Add a value to the end of a list.\r\n * The list will contain only one copy of the value.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromList\r\n * @see EntityList.registerInDict\r\n */\r\n static registerInList(list, value) {\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n }\r\n\r\n /**\r\n * Remove a value from a list if it is there.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to remove.\r\n * @see EntityList.registerInList\r\n */\r\n static unregisterFromList(list, value) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n }\r\n\r\n /**\r\n * Add a value to a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromDict\r\n * @see EntityList.registerInList\r\n */\r\n static registerInDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key] = dict[key] || [];\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Remove a value from a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.registerInDict\r\n */\r\n static unregisterFromDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key];\r\n if (list) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n if (list.length === 0) {\r\n delete dict[key];\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Add an entity to this list.\r\n *\r\n * @param {!Object} entity An object or a class to register. The object must include all\r\n * properties specified as indices on construction.\r\n * @see EntityList#unregister\r\n */\r\n register(entity) {\r\n EntityList.registerInList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.registerInDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * Remove an entity from this list.\r\n *\r\n * @param {!Object} entity An object or a class to unregister. The object may be\r\n * missing from the list but it must include all properties specified as indices\r\n * on construction.\r\n * @see EntityList#register\r\n */\r\n unregister(entity) {\r\n EntityList.unregisterFromList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.unregisterFromDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * An ordered list of all registered entities.\r\n * It is a read-only copy, use {@link EntityList#register} and {@link EntityList#unregister}\r\n * to modify it.\r\n *\r\n * @type {!Array}\r\n */\r\n get all() {\r\n return [...this._list];\r\n }\r\n\r\n /**\r\n * The first registered entity.\r\n * Use it if you do not care which entity you are referring to.\r\n *\r\n * @type {Object=}\r\n */\r\n get first() {\r\n return this._list[0];\r\n }\r\n\r\n /**\r\n * Retrieve a list of keys for the index.\r\n *\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {!Array} An unordered list of keys in the index, i.e. particular property\r\n * values for all registered entities.\r\n */\r\n keys(index) {\r\n return Object.keys(this._dict[index || this._indices[0]]);\r\n }\r\n\r\n /**\r\n * Retrieve an entity by its key.\r\n *\r\n * @param {string} key A case-insensitive property value to look-up.\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {Object=} An object registered in the index under the key. If there are multiple\r\n * objects under the same key, the first one is returned.\r\n */\r\n get(key, index) {\r\n const dict = this._dict[index || this._indices[0]];\r\n if (dict) {\r\n const values = dict[key && key.toLowerCase()];\r\n return values && values.length > 0 ? values[0] : undefined;\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nexport default EntityList;\r\n","import settings from '../settings';\r\nimport logger from './logger';\r\n\r\nfunction makeContextDependent(prototype) {\r\n Object.defineProperties(prototype, {\r\n logger: {\r\n get() {\r\n return this.context && this.context.logger ? this.context.logger : logger;\r\n },\r\n },\r\n settings: {\r\n get() {\r\n return this.context && this.context.settings ? this.context.settings : settings;\r\n },\r\n },\r\n });\r\n}\r\n\r\nexport default makeContextDependent;\r\n","import * as THREE from 'three';\r\n\r\nclass CollisionSphere {\r\n constructor(position, radius) {\r\n this._position = position;\r\n this._radius = radius;\r\n }\r\n\r\n static _sphere = new THREE.Sphere();\r\n\r\n raycast(raycaster) {\r\n const sphere = CollisionSphere._sphere;\r\n sphere.set(this._position, this._radius);\r\n\r\n const p = new THREE.Vector3();\r\n if (raycaster.ray.intersectSphere(sphere, p)) {\r\n return {\r\n distance: raycaster.ray.origin.distanceTo(p),\r\n point: p,\r\n };\r\n }\r\n return null;\r\n }\r\n}\r\n\r\nconst SphereCollisionGeo = (base) => class extends base {\r\n constructor(count, ...args) {\r\n super(...args);\r\n this._objects = new Array(count);\r\n this.boundingSphere = null;\r\n this.boundingBox = null;\r\n }\r\n\r\n setSphere(idx, position, radius) {\r\n this._objects[idx] = new CollisionSphere(position, radius);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n // TODO raycast with bounding sphere? How to deal with updates?\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const inters = this._objects[i].raycast(raycaster);\r\n if (inters) {\r\n inters.chunkIdx = i;\r\n intersects.push(inters);\r\n }\r\n }\r\n }\r\n\r\n computeBoundingBox() {\r\n const objects = this._objects;\r\n let { boundingBox } = this;\r\n if (boundingBox === null) {\r\n this.boundingBox = boundingBox = new THREE.Box3();\r\n }\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n boundingBox.expandByPoint(objects[i]._position);\r\n }\r\n }\r\n\r\n computeBoundingSphere() {\r\n this.computeBoundingBox();\r\n const objects = this._objects;\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n const pos = objects[i]._position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n if (this.boundingSphere === null) {\r\n this.boundingSphere = new THREE.Sphere();\r\n }\r\n this.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n};\r\nexport default SphereCollisionGeo;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst tmpColor = new THREE.Color();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\nclass InstancedSpheresGeometry extends SphereCollisionGeo(THREE.InstancedBufferGeometry) {\r\n constructor(spheresCount, sphereComplexity, useZSprites) {\r\n super(spheresCount);\r\n this._sphGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new THREE.SphereBufferGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI);\r\n this._init(spheresCount, this._sphGeometry);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n setArrayXYZW(this._offsets, itemIdx * OFFSET_SIZE, itemPos.x, itemPos.y, itemPos.z, itemRad);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n\r\n setColor(itemIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n setArrayXYZ(this._colors, itemIdx * COLOR_SIZE, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('offset').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[chunkIndices[i]] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._sphGeometry);\r\n\r\n copySubArrays(this._offsets, geom._offsets, chunkIndices, OFFSET_SIZE);\r\n copySubArrays(this._colors, geom._colors, chunkIndices, COLOR_SIZE);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(spheresCount, sphereGeo) {\r\n this.copy(sphereGeo);\r\n\r\n this._offsets = utils.allocateTyped(Float32Array, spheresCount * OFFSET_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, spheresCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('offset', new THREE.InstancedBufferAttribute(this._offsets, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._colors, COLOR_SIZE, false, 1));\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(alpha, 1, false, 1));\r\n }\r\n}\r\nexport default InstancedSpheresGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VEC_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n */\r\n\r\nclass ChunkedObjectsGeometry extends THREE.BufferGeometry {\r\n constructor(chunkGeo, chunksCount) {\r\n super();\r\n\r\n if (this.constructor === ChunkedObjectsGeometry) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n\r\n this._chunkGeo = chunkGeo;\r\n\r\n this._init(chunkGeo, chunksCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('normal').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n const idx = i * VEC_SIZE;\r\n colors[idx] = tmpColor.r;\r\n colors[idx + 1] = tmpColor.g;\r\n colors[idx + 2] = tmpColor.b;\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n _.fill(alphaArr, value, left, left + chunkSize);\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n // use THREE.Mesh raycasting interface for the Geometry. The Mesh is\r\n // created with existed geometry and default material, so it doesn't slowdown.\r\n const mesh = new THREE.Mesh();\r\n mesh.geometry = this;\r\n mesh.raycast(raycaster, inters);\r\n\r\n const facesPerChunk = this._chunkGeo.index.count / 3;\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('faceIndex')) {\r\n continue;\r\n }\r\n inters[i].chunkIdx = Math.floor(inters[i].faceIndex / facesPerChunk);\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.BufferGeometry();\r\n this._init.call(geom, this._chunkGeo, instanceCount);\r\n\r\n const srcPos = this._positions;\r\n const srcNorm = this._normals;\r\n const srcColor = this._colors;\r\n\r\n const dstPos = geom._positions;\r\n const dstNorm = geom._normals;\r\n const dstColor = geom._colors;\r\n\r\n const chunkSize = this._chunkSize * VEC_SIZE;\r\n\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const ptIdxBegin = chunkIndices[i] * chunkSize;\r\n const ptIdxEnd = ptIdxBegin + chunkSize;\r\n dstPos.set(srcPos.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstNorm.set(srcNorm.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstColor.set(srcColor.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n }\r\n\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(chunkGeo, chunksCount) {\r\n const chunkSize = this._chunkSize = chunkGeo.attributes.position.count;\r\n const chunkIndex = chunkGeo.index.array;\r\n const chunkIndexSize = chunkIndex.length;\r\n const pointsCount = this._chunkSize * chunksCount;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n const indexSize = chunkIndexSize * chunksCount;\r\n const index = this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, indexSize);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._normals = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n for (let i = 0; i < chunksCount; ++i) {\r\n const offset = i * chunkIndexSize;\r\n const posOffset = i * chunkSize;\r\n index.set(chunkIndex, offset);\r\n for (let j = 0; j < chunkIndexSize; ++j) {\r\n index[offset + j] += posOffset;\r\n }\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, VEC_SIZE));\r\n this.setAttribute('normal', new THREE.BufferAttribute(this._normals, VEC_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, VEC_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n }\r\n}\r\nexport default ChunkedObjectsGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst VEC_SIZE = 3;\r\n\r\nclass SimpleSpheresGeometry extends SphereCollisionGeo(ChunkedObjectsGeometry) {\r\n constructor(spheresCount, sphereComplexity) {\r\n const sphGeometry = new THREE.SphereBufferGeometry(\r\n 1,\r\n sphereComplexity * 2,\r\n sphereComplexity,\r\n 0,\r\n Math.PI * 2,\r\n 0,\r\n Math.PI,\r\n );\r\n super(spheresCount, sphGeometry, spheresCount);\r\n\r\n const normals = this._normals;\r\n const geoNormals = sphGeometry.attributes.normal.array;\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._tmpPositions = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n for (let i = 0; i < spheresCount; ++i) {\r\n normals.set(geoNormals, chunkSize * VEC_SIZE * i);\r\n }\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n const tmpPos = this._tmpPositions;\r\n const chunkSize = this._chunkSize;\r\n const geoPos = this._chunkPos;\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n const idx = i * 3;\r\n tmpPos[idx] = itemPos.x + geoPos[idx] * itemRad;\r\n tmpPos[idx + 1] = itemPos.y + geoPos[idx + 1] * itemRad;\r\n tmpPos[idx + 2] = itemPos.z + geoPos[idx + 2] * itemRad;\r\n }\r\n\r\n this._positions.set(tmpPos, chunkSize * itemIdx * VEC_SIZE);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n}\r\nexport default SimpleSpheresGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst centerPos = new THREE.Vector3();\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass Simple2CCylindersGeometry extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, 2 * instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const firstOffset = chunkSize * 2 * itemIdx * VEC_SIZE;\r\n const secondOffset = firstOffset + chunkSize * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n centerPos.lerpVectors(botPos, topPos, 0.5);\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, centerPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, firstOffset);\r\n\r\n // now shift center to get another part of the cylinder\r\n centerPos.sub(botPos);\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpArray[idx] += centerPos.x;\r\n tmpArray[idx + 1] += centerPos.y;\r\n tmpArray[idx + 2] += centerPos.z;\r\n }\r\n this._positions.set(tmpArray, secondOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, firstOffset);\r\n this._normals.set(tmpArray, secondOffset);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const first = 2 * itemIdx;\r\n super.setColor(first, colorVal1);\r\n\r\n const second = first + 1;\r\n super.setColor(second, colorVal2);\r\n }\r\n}\r\n\r\nexport default Simple2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_POINTS_COUNT_16BIT = 65536;\r\nconst PTS_PER_TRIANGLE = 3;\r\n\r\nclass CylinderBufferGeometry extends THREE.BufferGeometry {\r\n constructor(\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n ) {\r\n super();\r\n\r\n const thetaStart = 0;\r\n const thetaLength = 2 * Math.PI;\r\n\r\n this.type = 'CylinderBufferGeometry';\r\n\r\n this.parameters = {\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n };\r\n\r\n const hasTop = openEnded === false && radiusTop > 0;\r\n const hasBottom = openEnded === false && radiusBottom > 0;\r\n const vertexCount = (heightSegments + 1) * radialSegments\r\n + hasTop * (radialSegments + 1)\r\n + hasBottom * (radialSegments + 1);\r\n const facesCount = (2 * heightSegments + hasTop + hasBottom) * radialSegments;\r\n\r\n const heightHalf = height / 2;\r\n\r\n /* eslint-disable no-magic-numbers */\r\n const positions = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const normals = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const indices = new THREE.Uint16BufferAttribute(utils.allocateTyped(Uint16Array, facesCount * PTS_PER_TRIANGLE), 1);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n const uvs = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 2), 2);\r\n console.assert(vertexCount < MAX_POINTS_COUNT_16BIT, 'DEBUG: Cylinder Geometry has too many vertices (65536 max).');\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n const tanTheta = -(radiusBottom - radiusTop) / height;\r\n\r\n // setup cylinder data\r\n for (let y = 0; y <= heightSegments; y++) {\r\n // faces\r\n if (y !== heightSegments) {\r\n for (let i = 0; i < radialSegments; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + radialSegments + i;\r\n const v3 = currVtxIdx + radialSegments + ((i + 1) % radialSegments);\r\n const v4 = currVtxIdx + ((i + 1) % radialSegments);\r\n\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n // vertices\r\n const v = y / heightSegments;\r\n const radius = v * (radiusBottom - radiusTop) + radiusTop;\r\n\r\n for (let x = 0; x < radialSegments; x++) {\r\n const u = x / radialSegments;\r\n\r\n const vx = radius * Math.sin(u * thetaLength + thetaStart);\r\n const vy = v * height - heightHalf;\r\n const vz = radius * Math.cos(u * thetaLength + thetaStart);\r\n\r\n const normal = new THREE.Vector3(\r\n vx,\r\n Math.sqrt(vx * vx + vz * vz) * tanTheta,\r\n vz,\r\n ).normalize();\r\n\r\n positions.setXYZ(currVtxIdx, vx, vy, vz);\r\n normals.setXYZ(currVtxIdx, normal.x, normal.y, normal.z);\r\n uvs.setXY(currVtxIdx, u, v);\r\n ++currVtxIdx;\r\n }\r\n }\r\n\r\n // top cap\r\n if (hasTop) {\r\n const startTIdx = currVtxIdx;\r\n const lastIdx = currVtxIdx + radialSegments;\r\n for (let fTIdx = 0; fTIdx < radialSegments; ++fTIdx) {\r\n const currSrcIdx = currVtxIdx - radialSegments;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcIdx),\r\n positions.getY(currSrcIdx),\r\n positions.getZ(currSrcIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n\r\n const nextTVtx = startTIdx + ((fTIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, currVtxIdx, nextTVtx, lastIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n ++currVtxIdx;\r\n }\r\n\r\n // bottom cap\r\n if (hasBottom) {\r\n const startBIdx = currVtxIdx;\r\n const lastBIdx = currVtxIdx + radialSegments;\r\n for (let fBIdx = 0; fBIdx < radialSegments; ++fBIdx) {\r\n const currSrcBIdx = fBIdx;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcBIdx),\r\n positions.getY(currSrcBIdx),\r\n positions.getZ(currSrcBIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n\r\n const nextBVtx = startBIdx + ((fBIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, nextBVtx, currVtxIdx, lastBIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, -heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n }\r\n\r\n this.setIndex(indices);\r\n this.setAttribute('position', positions);\r\n this.setAttribute('normal', normals);\r\n this.setAttribute('uv', uvs);\r\n }\r\n\r\n clone() {\r\n const { parameters } = this;\r\n\r\n return new CylinderBufferGeometry(\r\n parameters.radiusTop,\r\n parameters.radiusBottom,\r\n parameters.height,\r\n parameters.radialSegments,\r\n parameters.heightSegments,\r\n parameters.openEnded,\r\n );\r\n }\r\n}\r\n\r\nexport default CylinderBufferGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport CylinderBufferGeometry from './CylinderBufferGeometry';\r\n\r\nconst tmpColor = new THREE.Color();\r\nconst invMatrix = new THREE.Matrix4();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction sortNumber(a, b) {\r\n return a - b;\r\n}\r\n\r\nfunction _prepareCylinderInfo(chunkIndices) {\r\n chunkIndices.sort(sortNumber);\r\n const chunksIdx = [];\r\n const cylinderInfo = [];\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const val = chunkIndices[i];\r\n const even = (val | 0) % 2 === 0;\r\n const newPar = {\r\n first: false,\r\n second: false,\r\n };\r\n if (even) {\r\n newPar.first = true;\r\n newPar.second = i + 1 < n && chunkIndices[i + 1] === chunkIndices[i] + 1;\r\n if (newPar.second) {\r\n ++i;\r\n }\r\n } else {\r\n newPar.second = true;\r\n }\r\n chunksIdx.push(Math.floor(val / 2));\r\n cylinderInfo.push(newPar);\r\n }\r\n return { indices: chunksIdx, cylinderInfo };\r\n}\r\n\r\nfunction _assignOpacity(cylinderInfo, color1, color2) {\r\n for (let i = 0, n = cylinderInfo.length; i < n; ++i) {\r\n const info = cylinderInfo[i];\r\n if (!info.first) {\r\n color1[COLOR_SIZE * i] = -0.5;\r\n }\r\n if (!info.second) {\r\n color2[COLOR_SIZE * i] = -0.5;\r\n }\r\n }\r\n}\r\nclass Instanced2CCylindersGeometry extends THREE.InstancedBufferGeometry {\r\n constructor(instanceCount, polyComplexity, useZSprites, openEnded) {\r\n super();\r\n this._useZSprites = useZSprites;\r\n this._cylGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new CylinderBufferGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, openEnded);\r\n this._init(instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n this._collisionGeo = new Simple2CCylindersGeometry(instanceCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const matrix = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n let me = matrix.elements;\r\n const mtxOffset = itemIdx * OFFSET_SIZE;\r\n\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, itemRad);\r\n setArrayXYZW(this._matVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._matVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._matVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n\r\n if (this._useZSprites) {\r\n invMatrix.copy(matrix).invert();\r\n me = invMatrix.elements;\r\n setArrayXYZW(this._invmatVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._invmatVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._invmatVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n }\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const colorIdx = itemIdx * COLOR_SIZE;\r\n tmpColor.set(colorVal1);\r\n setArrayXYZ(this._color1, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n tmpColor.set(colorVal2);\r\n setArrayXYZ(this._color2, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n computeBoundingSphere() {\r\n this._collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = this._collisionGeo.boundingSphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n this._collisionGeo.computeBoundingBox();\r\n this.boundingBox = this._collisionGeo.boundingBox;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('matVector1').needsUpdate = true;\r\n this.getAttribute('matVector2').needsUpdate = true;\r\n this.getAttribute('matVector3').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('color2').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n if (this._useZSprites) {\r\n this.getAttribute('invmatVector1').needsUpdate = true;\r\n this.getAttribute('invmatVector2').needsUpdate = true;\r\n this.getAttribute('invmatVector3').needsUpdate = true;\r\n }\r\n\r\n this._collisionGeo.finishUpdate();\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[Math.floor(chunkIndices[i] / 2)] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const info = _prepareCylinderInfo(chunkIndices);\r\n const cylinderIndices = info.indices;\r\n const instanceCount = cylinderIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n copySubArrays(this._matVector1, geom._matVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector2, geom._matVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector3, geom._matVector3, cylinderIndices, OFFSET_SIZE);\r\n\r\n if (this._useZSprites) {\r\n copySubArrays(this._invmatVector1, geom._invmatVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector2, geom._invmatVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector3, geom._invmatVector3, cylinderIndices, OFFSET_SIZE);\r\n }\r\n\r\n copySubArrays(this._color1, geom._color1, cylinderIndices, COLOR_SIZE);\r\n copySubArrays(this._color2, geom._color2, cylinderIndices, COLOR_SIZE);\r\n _assignOpacity(info.cylinderInfo, geom._color1, geom._color2);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n getGeoParams() {\r\n return this._cylGeometry.parameters;\r\n }\r\n\r\n _init(instanceCount, cylinderGeo, useZSprites) {\r\n this.copy(cylinderGeo);\r\n this._matVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._color1 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n this._color2 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, instanceCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('matVector1', new THREE.InstancedBufferAttribute(this._matVector1, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector2', new THREE.InstancedBufferAttribute(this._matVector2, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector3', new THREE.InstancedBufferAttribute(this._matVector3, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._color1, COLOR_SIZE, false, 1));\r\n this.setAttribute('color2', new THREE.InstancedBufferAttribute(this._color2, COLOR_SIZE, false, 1));\r\n\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(this._alpha, 1, false, 1));\r\n\r\n if (useZSprites) {\r\n this._invmatVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n\r\n this.setAttribute(\r\n 'invmatVector1',\r\n new THREE.InstancedBufferAttribute(this._invmatVector1, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector2',\r\n new THREE.InstancedBufferAttribute(this._invmatVector2, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector3',\r\n new THREE.InstancedBufferAttribute(this._invmatVector3, OFFSET_SIZE, false, 1),\r\n );\r\n }\r\n }\r\n}\r\n\r\nexport default Instanced2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst TRI_SIZE = 3;\r\nconst tmpPrev = new THREE.Vector3();\r\nconst tmpNext = new THREE.Vector3();\r\nconst tmpRes = new THREE.Vector3();\r\nconst simpleNormal = new THREE.Vector3(1.0, 0.0, 0.0);\r\nconst normalOnCut = new THREE.Vector3();\r\nconst nearRingPt = new THREE.Vector3();\r\n\r\nfunction _createExtrudedChunkGeometry(shape, ringsCount) {\r\n const geo = new THREE.BufferGeometry();\r\n const ptsCount = shape.length;\r\n const totalPts = ptsCount * ringsCount;\r\n const type = totalPts <= 65536 ? Uint16Array : Uint32Array;\r\n const facesPerChunk = (ringsCount - 1) * ptsCount * 2;\r\n const indices = new THREE.BufferAttribute(utils.allocateTyped(type, facesPerChunk * TRI_SIZE), 1);\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n for (let y = 0; y < ringsCount; y++) {\r\n // faces\r\n if (y !== ringsCount - 1) {\r\n for (let i = 0; i < ptsCount; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + ptsCount + i;\r\n const v3 = currVtxIdx + ptsCount + ((i + 1) % ptsCount);\r\n const v4 = currVtxIdx + ((i + 1) % ptsCount);\r\n\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n currVtxIdx += ptsCount;\r\n }\r\n\r\n geo.setIndex(indices);\r\n const pos = utils.allocateTyped(Float32Array, totalPts * VEC_SIZE);\r\n geo.setAttribute('position', new THREE.BufferAttribute(pos, VEC_SIZE));\r\n\r\n geo._positions = shape;\r\n\r\n return geo;\r\n}\r\n\r\nclass ExtrudedObjectsGeometry extends ChunkedObjectsGeometry {\r\n constructor(shape, ringsCount, chunksCount) {\r\n const chunkGeo = _createExtrudedChunkGeometry(shape, ringsCount);\r\n super(chunkGeo, chunksCount);\r\n this._ringsCount = ringsCount;\r\n\r\n const tmpShape = this._tmpShape = [];\r\n for (let i = 0; i < shape.length; ++i) {\r\n tmpShape[i] = new THREE.Vector3();\r\n }\r\n }\r\n\r\n setItem(itemIdx, matrices, hasSlope = false, hasCut = false) {\r\n const ptsCount = this._chunkGeo._positions.length;\r\n const ringsCount = this._ringsCount;\r\n const chunkStartIdx = ptsCount * this._ringsCount * itemIdx * VEC_SIZE;\r\n\r\n this._setPoints(matrices, ptsCount, ringsCount, chunkStartIdx);\r\n\r\n if (hasSlope) {\r\n this._setSlopeNormals(ptsCount, ringsCount, chunkStartIdx);\r\n } else {\r\n this._setBaseNormals(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n\r\n if (hasCut) {\r\n this._addCut(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n }\r\n\r\n _setPoints(matrices, ptsCount, ringsCount, chunkStartIdx) {\r\n const tmpShape = this._tmpShape;\r\n const positions = this._positions;\r\n const shape = this._chunkGeo._positions;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i) {\r\n const mtx = matrices[i];\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpShape[j].copy(shape[j]).applyMatrix4(mtx).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _setBaseNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, false);\r\n }\r\n }\r\n\r\n _setSlopeNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const normals = this._normals;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First ring\r\n // In all cases, besides cut, second ring is coincident to first. So values of first ring's normals doesn't\r\n // matter (In the cut case special handler will be applied later and will set them to correct values)\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n simpleNormal.toArray(normals, vtxIdx);\r\n }\r\n // second ring\r\n // If it isn't first Item we take normals' values from the last ring of the previous item (these rings are coincident)\r\n // else we count normals' values based on next ring information\r\n if (vtxIdx - 2 * nPtsInRing > 0) {\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(normals, vtxIdx - 2 * nPtsInRing).toArray(normals, vtxIdx);\r\n }\r\n } else {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, +nPtsInRing);\r\n vtxIdx += nPtsInRing;\r\n }\r\n // other rings\r\n // we count normals' values based on previous ring information\r\n for (let i = 2; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, -nPtsInRing);\r\n }\r\n }\r\n\r\n // Counting normals:\r\n // - Slope\r\n // Radius changes throught part => normals aren't parallel with the plane contains section points\r\n // normal = vTangentInSectionPlane x vToSuchPointInPrevSection (all vectors are scaled for being 1 in length)\r\n // - No slope\r\n // Radius doesn't change throught part => normals are parallel with the plane contains section points\r\n // normal = vToPrevPointInSection + vToNextPointInSection (all vectors are scaled for being 1 in length)\r\n _countNormalsInRing(ptsCount, vtxIdx, isSlope, shiftToExtraPt) {\r\n const tmpShape = this._tmpShape;\r\n const normals = this._normals;\r\n\r\n tmpShape[0].fromArray(this._positions, vtxIdx);\r\n tmpShape[ptsCount - 1].fromArray(this._positions, vtxIdx + (ptsCount - 1) * VEC_SIZE);\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n if (j < ptsCount - 1) {\r\n tmpShape[j + 1].fromArray(this._positions, vtxIdx + VEC_SIZE);\r\n }\r\n\r\n if (isSlope) {\r\n nearRingPt.fromArray(this._positions, vtxIdx + shiftToExtraPt);\r\n\r\n tmpPrev.subVectors(tmpShape[(j + ptsCount - 1) % ptsCount], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], nearRingPt).normalize();\r\n tmpRes.crossVectors(tmpNext, tmpPrev).normalize().toArray(normals, vtxIdx);\r\n } else {\r\n tmpPrev.subVectors(tmpShape[j], tmpShape[(j + ptsCount - 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpRes.addVectors(tmpPrev, tmpNext).normalize().toArray(normals, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _addCut(ptsCount, ringsCount, chunkStartIdx) {\r\n // Nothing to do if item is flat or only line\r\n if (ptsCount < 3 || ringsCount < 2) {\r\n return;\r\n }\r\n const positions = this._positions;\r\n const normals = this._normals;\r\n const tmpShape = this._tmpShape;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n // Normal to the cut plane is equal to cross product of two vectors which are lying in it\r\n tmpShape[0].fromArray(positions, chunkStartIdx);\r\n tmpShape[1].fromArray(positions, chunkStartIdx + VEC_SIZE);\r\n tmpShape[2].fromArray(positions, chunkStartIdx + 2 * VEC_SIZE);\r\n\r\n tmpPrev.subVectors(tmpShape[1], tmpShape[0]).normalize();\r\n tmpNext.subVectors(tmpShape[1], tmpShape[2]).normalize();\r\n normalOnCut.crossVectors(tmpPrev, tmpNext).normalize();\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First and second rings normals' values are equal to value of normal to the cutting plane\r\n for (let j = 0; j < ptsCount * 2; ++j, vtxIdx += VEC_SIZE) {\r\n normalOnCut.toArray(normals, vtxIdx);\r\n }\r\n if (ringsCount > 2) {\r\n // Third ring points are coincident to first ring points, but have different normals. It makes sharp angle near cut\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(positions, vtxIdx - nPtsInRing).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default ExtrudedObjectsGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VERTEX_PER_SEGMENT = 4;\r\nconst POS_SIZE = 4;\r\nconst DIR_SIZE = 3;\r\nconst COL_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\nconst direction = new THREE.Vector3();\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction getSubset(arr, startSegmentIdx, segmentsCount, elemSize) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT;\r\n const end = start + segmentsCount * VERTEX_PER_SEGMENT;\r\n return arr.subarray(start * elemSize, end * elemSize);\r\n}\r\n\r\n/**\r\n * This class represents lines geometry which consists of screen-aligned narrow quad of variable width.\r\n *\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * collision geometry.\r\n */\r\n\r\nclass ThickLinesGeometry extends THREE.BufferGeometry {\r\n constructor(segmentsCount) {\r\n super();\r\n this._initVertices(segmentsCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n this.getAttribute('direction').needsUpdate = true;\r\n }\r\n\r\n setColor(segmentIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n setSegment(segmentIdx, pos1, pos2) {\r\n direction.subVectors(pos1, pos2);\r\n direction.normalize();\r\n const positions = this._positions;\r\n const directions = this._directions;\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n let dirIdx = segmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n }\r\n\r\n setOpacity(startSegIdx, endSegIdx, value) {\r\n const start = startSegIdx * VERTEX_PER_SEGMENT;\r\n const end = endSegIdx * VERTEX_PER_SEGMENT;\r\n _.fill(this.alpha, value, end, start);\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubsetSegments(startSegmentIdx, segmentsCount) {\r\n return [\r\n getSubset(this._positions, startSegmentIdx, segmentsCount, POS_SIZE),\r\n getSubset(this._directions, startSegmentIdx, segmentsCount, DIR_SIZE),\r\n ];\r\n }\r\n\r\n getSubsetColors(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._colors, startSegmentIdx, segmentsCount, COL_SIZE);\r\n }\r\n\r\n getSubsetOpacities(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._alpha, startSegmentIdx, segmentsCount, 1);\r\n }\r\n\r\n getNumVertexPerSegment() {\r\n return VERTEX_PER_SEGMENT;\r\n }\r\n\r\n getPositionSize() {\r\n return POS_SIZE;\r\n }\r\n\r\n setSegments(startSegmentIdx, positions) {\r\n const startPos = startSegmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n if (positions instanceof Array && positions.length === 2) {\r\n this._positions.set(positions[0], startPos);\r\n const startDir = startSegmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n this._directions.set(positions[1], startDir); // dirs are geo part of vertex\r\n } else {\r\n this._positions.set(positions, startPos);\r\n }\r\n }\r\n\r\n setColors(startSegmentIdx, colors) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n this._colors.set(colors, start);\r\n }\r\n\r\n _initVertices(segmentsCount) {\r\n this._buffersSize = segmentsCount * VERTEX_PER_SEGMENT;\r\n const pointsCount = this._buffersSize;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, segmentsCount * 6);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * POS_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * COL_SIZE);\r\n this._directions = utils.allocateTyped(Float32Array, pointsCount * DIR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n const index = this._index;\r\n let indexOffset = 0;\r\n let pointOffset = 0;\r\n for (let j = 0; j < segmentsCount; j++, indexOffset += 6, pointOffset += VERTEX_PER_SEGMENT) {\r\n index[indexOffset] = pointOffset;\r\n index[indexOffset + 1] = pointOffset + 1;\r\n index[indexOffset + 2] = pointOffset + 3;\r\n index[indexOffset + 3] = pointOffset;\r\n index[indexOffset + 4] = pointOffset + 2;\r\n index[indexOffset + 5] = pointOffset + 3;\r\n }\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, POS_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, COL_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n this.setAttribute('direction', new THREE.BufferAttribute(this._directions, DIR_SIZE));\r\n }\r\n}\r\n\r\nexport default ThickLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport BaseLinesGeometry from './ThickLinesGeometry';\r\n\r\n/**\r\n * This class represents geometry which consists lines. This can build bounding volumes\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n */\r\nclass LinesGeometry extends BaseLinesGeometry {\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n if (boundingBox) {\r\n boundingBox.getCenter(center);\r\n }\r\n const positions = this._positions;\r\n const sphere = this.boundingSphere || new THREE.Sphere();\r\n const size = this._positions.length;\r\n const pos = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n pos.set(positions[i], positions[i + 1], positions[i + 2]);\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n sphere.set(center, Math.sqrt(radiusSquared));\r\n this.boundingSphere = sphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n const positions = this._positions;\r\n const box = new THREE.Box3();\r\n const size = this._positions.length;\r\n const tmpVec = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n tmpVec.set(positions[i], positions[i + 1], positions[i + 2]);\r\n box.expandByPoint(tmpVec);\r\n }\r\n this.boundingBox = box;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n}\r\n\r\nexport default LinesGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass CylinderCollisionGeo extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const itemOffset = chunkSize * itemIdx * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, itemOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, itemOffset);\r\n }\r\n}\r\nexport default CylinderCollisionGeo;\r\n","import LinesGeometry from './LinesGeometry';\r\nimport CylinderCollisionGeo from './CylinderCollisionGeo';\r\n\r\nconst COLLISION_RAD = 0.1;\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n *\r\n * @param {number} chunksCount Total chunks count.\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * @param {boolean} enableCollision Enable or disable collision where each segment is\r\n * a collidable cylinder.\r\n * collision geometry.\r\n */\r\nclass ChunkedLinesGeometry extends LinesGeometry {\r\n constructor(chunksCount, segmentsCount, enableCollision) {\r\n super(chunksCount * segmentsCount);\r\n this._init(segmentsCount);\r\n this._collisionGeo = enableCollision ? new CylinderCollisionGeo(chunksCount * segmentsCount, 3) : null;\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = collisionGeo.boundingSphere;\r\n return;\r\n }\r\n super.computeBoundingSphere();\r\n }\r\n\r\n computeBoundingBox() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingBox();\r\n this.boundingBox = collisionGeo.boundingBox;\r\n return;\r\n }\r\n super.computeBoundingBox();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const collisionGeo = this._collisionGeo;\r\n if (!collisionGeo) {\r\n return;\r\n }\r\n const segCount = this._chunkSize;\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n for (let i = 0, n = intersects.length; i < n; ++i) {\r\n let { chunkIdx } = intersects[i];\r\n if (chunkIdx === undefined) {\r\n continue;\r\n }\r\n chunkIdx = (chunkIdx / segCount) | 0;\r\n intersects[i].chunkIdx = chunkIdx;\r\n }\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n super.setColor(i, colorVal);\r\n }\r\n }\r\n\r\n setSegment(chunkIdx, segIdx, pos1, pos2) {\r\n const chunkSize = this._chunkSize;\r\n const idx = chunkIdx * chunkSize + segIdx;\r\n super.setSegment(idx, pos1, pos2);\r\n if (this._collisionGeo) {\r\n this._collisionGeo.setItem(chunkIdx * chunkSize + segIdx, pos1, pos2, COLLISION_RAD);\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n super.setOpacity(left, left + chunkSize - 1, value);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const chunkSize = this._chunkSize;\r\n const subset = new ChunkedLinesGeometry(instanceCount, chunkSize, false);\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const startSegIdx = chunkIndices[i] * chunkSize;\r\n subset.setSegments(dstPtOffset, this.getSubsetSegments(startSegIdx, chunkSize));\r\n subset.setColors(dstPtOffset, this.getSubsetColors(startSegIdx, chunkSize));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(chunkSize) {\r\n this._chunkSize = chunkSize;\r\n }\r\n}\r\n\r\nexport default ChunkedLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport LinesGeometry from './LinesGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\n\r\nconst COLLISION_RAD = 0.3;\r\nconst tmpVector = new THREE.Vector3();\r\n\r\nclass TwoColorLinesGeometry extends LinesGeometry {\r\n constructor(segmentsCount) {\r\n super(segmentsCount * 2);\r\n this._init(segmentsCount);\r\n this._collisionGeo = new Simple2CCylindersGeometry(segmentsCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos) {\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, COLLISION_RAD);\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n tmpVector.lerpVectors(botPos, topPos, 0.5);\r\n super.setSegment(offset, botPos, tmpVector);\r\n super.setSegment(offset + 1, tmpVector, topPos);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n super.setColor(offset, colorVal1);\r\n super.setColor(offset + 1, colorVal2);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n if (this._collisionGeo) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n getSubset(segmentIndices) {\r\n const instanceCount = segmentIndices.length;\r\n const subset = new TwoColorLinesGeometry(instanceCount, false);\r\n for (let i = 0, n = instanceCount; i < n; ++i) {\r\n const startSegIdx = segmentIndices[i];\r\n subset.setSegments(i, this.getSubsetSegments(startSegIdx, 1));\r\n subset.setColors(i, this.getSubsetColors(startSegIdx, 1));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(segmentsCount) {\r\n this._segCounts = segmentsCount * 2;\r\n }\r\n}\r\n// (???)parent = LinesGeometry.prototype;\r\n\r\nexport default TwoColorLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst vectors = [\r\n new THREE.Vector3(1, 0, 0),\r\n new THREE.Vector3(-1, 0, 0),\r\n new THREE.Vector3(0, 1, 0),\r\n new THREE.Vector3(0, -1, 0),\r\n new THREE.Vector3(0, 0, 1),\r\n new THREE.Vector3(0, 0, -1),\r\n];\r\nconst vecCount = vectors.length;\r\nconst tempPos1 = new THREE.Vector3();\r\nconst tempPos2 = new THREE.Vector3();\r\n\r\nclass CrossGeometry extends SphereCollisionGeo(ChunkedLinesGeometry) {\r\n constructor(chunksCount) {\r\n super(chunksCount, chunksCount, (vecCount / 2) | 0, false);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n\r\n for (let i = 0; i < vecCount / 2; ++i) {\r\n const first = i * 2;\r\n tempPos1.x = itemPos.x + vectors[first].x * itemRad;\r\n tempPos1.y = itemPos.y + vectors[first].y * itemRad;\r\n tempPos1.z = itemPos.z + vectors[first].z * itemRad;\r\n const second = first + 1;\r\n tempPos2.x = itemPos.x + vectors[second].x * itemRad;\r\n tempPos2.y = itemPos.y + vectors[second].y * itemRad;\r\n tempPos2.z = itemPos.z + vectors[second].z * itemRad;\r\n this.setSegment(itemIdx, i, tempPos1, tempPos2);\r\n }\r\n }\r\n}\r\nexport default CrossGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst POS_RAD_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This is a base class for isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\nclass IsoSurfaceGeometry extends THREE.BufferGeometry {\r\n constructor(spheresCount, opts) {\r\n super();\r\n\r\n this._opts = opts;\r\n this.zClip = this._opts.zClip;\r\n this._posRad = utils.allocateTyped(Float32Array, spheresCount * POS_RAD_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n }\r\n\r\n setItem(chunkIdx, pos, radius) {\r\n const posRad = this._posRad;\r\n let idx = POS_RAD_SIZE * chunkIdx;\r\n posRad[idx++] = pos.x;\r\n posRad[idx++] = pos.y;\r\n posRad[idx++] = pos.z;\r\n posRad[idx] = radius;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n let idx = COLOR_SIZE * chunkIdx;\r\n colors[idx++] = tmpColor.r;\r\n colors[idx++] = tmpColor.g;\r\n colors[idx] = tmpColor.b;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n finishUpdate() {\r\n this._build();\r\n }\r\n\r\n setOpacity() {\r\n // not implemented\r\n }\r\n\r\n raycast() {\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\nexport default IsoSurfaceGeometry;\r\n","import utils from '../../utils';\r\n\r\n/**\r\n * Class for marching cube\r\n * Stores 8 points and 8 float values are stored together in linear array\r\n * Int values for has intersection or not - in integer32 linear array\r\n * Int values for bits flags - in integer32 linear array\r\n *\r\n */\r\nclass IsoSurfaceMarchCube {\r\n constructor() {\r\n this.pointsValuesLinear = null;\r\n this.hasIntersection = null;\r\n this.bitsInside = null;\r\n }\r\n\r\n create(numCellsPerSide) {\r\n const vx7000000 = 0x7000000;\r\n const n3 = numCellsPerSide * numCellsPerSide * numCellsPerSide;\r\n if (n3 > vx7000000) {\r\n throw new Error('Too large cube dimension: lead to memory huge uasge');\r\n }\r\n this.pointsValuesLinear = utils.allocateTyped(Float32Array, (2 << (2 + 2)) * n3);\r\n this.hasIntersection = utils.allocateTyped(Int32Array, n3);\r\n this.bitsInside = utils.allocateTyped(Int32Array, n3);\r\n return 0;\r\n }\r\n\r\n destroy() {\r\n this.bitsInside = null;\r\n this.hasIntersection = null;\r\n this.pointsValuesLinear = null;\r\n }\r\n}\r\n\r\n/* eslint-disable no-magic-numbers */\r\nIsoSurfaceMarchCube.prototype.striIndicesMarchCube = [\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 0, 2, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 8, 3, 2, 10, 8, 10, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 8, 11, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 2, 1, 9, 11, 9, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 1, 11, 10, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 10, 1, 0, 8, 10, 8, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 9, 0, 3, 11, 9, 11, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 7, 3, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 1, 9, 4, 7, 1, 7, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 4, 7, 3, 0, 4, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 9, 0, 2, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 8, 4, 7, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 4, 7, 11, 2, 4, 2, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 8, 4, 7, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1, -1, -1, -1, -1,\r\n 3, 10, 1, 3, 11, 10, 7, 8, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4, -1, -1, -1, -1,\r\n 4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 4, 7, 11, 4, 11, 9, 9, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 1, 5, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 5, 4, 8, 3, 5, 3, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 10, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 2, 10, 5, 4, 2, 4, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8, -1, -1, -1, -1,\r\n 9, 5, 4, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 0, 8, 11, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 0, 1, 5, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5, -1, -1, -1, -1,\r\n 10, 3, 11, 10, 1, 3, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10, -1, -1, -1, -1,\r\n 5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 5, 4, 8, 5, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 5, 7, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 3, 0, 9, 5, 3, 5, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 8, 0, 1, 7, 1, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 9, 5, 7, 10, 1, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3, -1, -1, -1, -1,\r\n 8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2, -1, -1, -1, -1,\r\n 2, 10, 5, 2, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 9, 5, 7, 8, 9, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7, -1, -1, -1, -1,\r\n 11, 2, 1, 11, 1, 7, 7, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11, -1, -1, -1, -1,\r\n 5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0, -1,\r\n 11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0, -1,\r\n 11, 10, 5, 7, 11, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 1, 9, 8, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 2, 6, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 1, 2, 6, 3, 0, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 6, 5, 9, 0, 6, 0, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 0, 8, 11, 2, 0, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11, -1, -1, -1, -1,\r\n 6, 3, 11, 6, 5, 3, 5, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9, -1, -1, -1, -1,\r\n 6, 5, 9, 6, 9, 11, 11, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 4, 7, 3, 6, 5, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 5, 10, 6, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 6, 1, 2, 6, 5, 1, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7, -1, -1, -1, -1,\r\n 8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6, -1, -1, -1, -1,\r\n 7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9, -1,\r\n 3, 11, 2, 7, 8, 4, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1,\r\n 9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6, -1,\r\n 8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11, -1,\r\n 0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7, -1,\r\n 6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9, -1, -1, -1, -1,\r\n 10, 4, 9, 6, 4, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 10, 6, 4, 9, 10, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 0, 1, 10, 6, 0, 6, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 1, 4, 9, 1, 2, 4, 2, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4, -1, -1, -1, -1,\r\n 0, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 2, 8, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 4, 9, 10, 6, 4, 11, 2, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6, -1, -1, -1, -1,\r\n 3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1, -1,\r\n 9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3, -1, -1, -1, -1,\r\n 8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1, -1,\r\n 3, 11, 6, 3, 6, 0, 0, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 4, 8, 11, 6, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 10, 6, 7, 8, 10, 8, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10, -1, -1, -1, -1,\r\n 10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0, -1, -1, -1, -1,\r\n 10, 6, 7, 10, 7, 1, 1, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9, -1,\r\n 7, 8, 0, 7, 0, 6, 6, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 3, 2, 6, 7, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7, -1,\r\n 1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11, -1,\r\n 11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1, -1, -1, -1, -1,\r\n 8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6, -1,\r\n 0, 9, 1, 11, 6, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0, -1, -1, -1, -1,\r\n 7, 11, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 9, 8, 3, 1, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 8, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 9, 0, 2, 10, 9, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8, -1, -1, -1, -1,\r\n 7, 2, 3, 6, 2, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 0, 8, 7, 6, 0, 6, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 7, 6, 2, 3, 7, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6, -1, -1, -1, -1,\r\n 10, 7, 6, 10, 1, 7, 1, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8, -1, -1, -1, -1,\r\n 0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7, -1, -1, -1, -1,\r\n 7, 6, 10, 7, 10, 8, 8, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 8, 4, 11, 8, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 3, 0, 6, 0, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 6, 11, 8, 4, 6, 9, 0, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6, -1, -1, -1, -1,\r\n 6, 8, 4, 6, 11, 8, 2, 10, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6, -1, -1, -1, -1,\r\n 4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9, -1, -1, -1, -1,\r\n 10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3, -1,\r\n 8, 2, 3, 8, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8, -1, -1, -1, -1,\r\n 1, 9, 4, 1, 4, 2, 2, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1, -1, -1, -1, -1,\r\n 10, 1, 0, 10, 0, 6, 6, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3, -1,\r\n 10, 9, 4, 6, 10, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 5, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 1, 5, 4, 0, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5, -1, -1, -1, -1,\r\n 9, 5, 4, 10, 1, 2, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5, -1, -1, -1, -1,\r\n 7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2, -1, -1, -1, -1,\r\n 3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6, -1,\r\n 7, 2, 3, 7, 6, 2, 5, 4, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7, -1, -1, -1, -1,\r\n 3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0, -1, -1, -1, -1,\r\n 6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8, -1,\r\n 9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7, -1, -1, -1, -1,\r\n 1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4, -1,\r\n 4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10, -1,\r\n 7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10, -1, -1, -1, -1,\r\n 6, 9, 5, 6, 11, 9, 11, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5, -1, -1, -1, -1,\r\n 0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11, -1, -1, -1, -1,\r\n 6, 11, 3, 6, 3, 5, 5, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6, -1, -1, -1, -1,\r\n 0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10, -1,\r\n 11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5, -1,\r\n 6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3, -1, -1, -1, -1,\r\n 5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2, -1, -1, -1, -1,\r\n 9, 5, 6, 9, 6, 0, 0, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8, -1,\r\n 1, 5, 6, 2, 1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6, -1,\r\n 10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0, -1, -1, -1, -1,\r\n 0, 3, 8, 5, 6, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 5, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 7, 5, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 11, 7, 5, 8, 3, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 11, 7, 5, 10, 11, 1, 9, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1, -1, -1, -1, -1,\r\n 11, 1, 2, 11, 7, 1, 7, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11, -1, -1, -1, -1,\r\n 9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7, -1, -1, -1, -1,\r\n 7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2, -1,\r\n 2, 5, 10, 2, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2, -1, -1, -1, -1,\r\n 9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2, -1,\r\n 1, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 7, 0, 7, 1, 1, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 3, 9, 3, 5, 5, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 7, 5, 9, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 8, 4, 5, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5, -1, -1, -1, -1,\r\n 10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4, -1,\r\n 2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8, -1, -1, -1, -1,\r\n 0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11, -1,\r\n 0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5, -1,\r\n 9, 4, 5, 2, 11, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4, -1, -1, -1, -1,\r\n 5, 10, 2, 5, 2, 4, 4, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9, -1,\r\n 5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 3, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 5, 1, 0, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5, -1, -1, -1, -1,\r\n 9, 4, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 11, 7, 4, 9, 11, 9, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11, -1, -1, -1, -1,\r\n 1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11, -1, -1, -1, -1,\r\n 3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4, -1,\r\n 4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2, -1, -1, -1, -1,\r\n 9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3, -1,\r\n 11, 7, 4, 11, 4, 2, 2, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4, -1, -1, -1, -1,\r\n 2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9, -1, -1, -1, -1,\r\n 9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7, -1,\r\n 3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10, -1,\r\n 1, 10, 2, 8, 7, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 7, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1, -1, -1, -1, -1,\r\n 4, 0, 3, 7, 4, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 8, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1,\r\n 0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1,\r\n 1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n];\r\n/* eslint-enable no-magic-numbers */\r\n\r\nexport default IsoSurfaceMarchCube;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport utils from '../../utils';\r\n\r\nconst edgeTable = [\r\n 0x0, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c,\r\n 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00,\r\n 0x190, 0x99, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c,\r\n 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90,\r\n 0x230, 0x339, 0x33, 0x13a, 0x636, 0x73f, 0x435, 0x53c,\r\n 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30,\r\n 0x3a0, 0x2a9, 0x1a3, 0xaa, 0x7a6, 0x6af, 0x5a5, 0x4ac,\r\n 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0,\r\n 0x460, 0x569, 0x663, 0x76a, 0x66, 0x16f, 0x265, 0x36c,\r\n 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60,\r\n 0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0xff, 0x3f5, 0x2fc,\r\n 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0,\r\n 0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x55, 0x15c,\r\n 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950,\r\n 0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0xcc,\r\n 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0,\r\n 0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc,\r\n 0xcc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0,\r\n 0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c,\r\n 0x15c, 0x55, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650,\r\n 0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc,\r\n 0x2fc, 0x3f5, 0xff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0,\r\n 0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c,\r\n 0x36c, 0x265, 0x16f, 0x66, 0x76a, 0x663, 0x569, 0x460,\r\n 0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac,\r\n 0x4ac, 0x5a5, 0x6af, 0x7a6, 0xaa, 0x1a3, 0x2a9, 0x3a0,\r\n 0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c,\r\n 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x33, 0x339, 0x230,\r\n 0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c,\r\n 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x99, 0x190,\r\n 0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c,\r\n 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x0];\r\n\r\nfunction _voxelGradientFast(v, point, grad) {\r\n const g = v.getValue(point.x, point.y, point.z);\r\n grad.set(g[0], g[1], g[2]);\r\n}\r\n\r\n// Helper class GridCell\r\nclass GridCell {\r\n constructor() {\r\n this._arrSize = 8;\r\n this.p = new Array(this._arrSize);\r\n this.g = new Array(this._arrSize);\r\n this.val = new Array(this._arrSize);\r\n for (let i = 0; i < this._arrSize; ++i) {\r\n this.p[i] = new THREE.Vector3();\r\n this.g[i] = new THREE.Vector3();\r\n }\r\n this.cubeIndex = 0;\r\n }\r\n}\r\n\r\n// Helper class Triangle\r\nclass Triangle {\r\n constructor() {\r\n this.a = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.b = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.c = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n }\r\n}\r\n\r\nfunction createArray(arrSize) {\r\n const arr = new Array(arrSize);\r\n for (let i = 0; i < arrSize; ++i) {\r\n arr[i] = new THREE.Vector3();\r\n }\r\n\r\n return arr;\r\n}\r\n\r\nclass IsoSurface {\r\n constructor() {\r\n this._numTriangles = 0;\r\n this._numVertices = 0;\r\n this._position = [];\r\n this._normals = [];\r\n this._colors = null;\r\n this._indices = [];\r\n this._volumetricData = null;\r\n this._xAxis = new THREE.Vector3();\r\n this._yAxis = new THREE.Vector3();\r\n this._zAxis = new THREE.Vector3();\r\n this._xDir = new THREE.Vector3();\r\n this._yDir = new THREE.Vector3();\r\n this._zDir = new THREE.Vector3();\r\n }\r\n\r\n _prepareAxesAndDirs() {\r\n const volData = this._volumetricData;\r\n\r\n const cellSize = volData.getCellSize();\r\n\r\n // calculate cell axes\r\n const xAxis = this._xAxis;\r\n const yAxis = this._yAxis;\r\n const zAxis = this._zAxis;\r\n const xDir = this._xDir;\r\n const yDir = this._yDir;\r\n const zDir = this._zDir;\r\n\r\n xAxis.set(cellSize.x, 0, 0);\r\n yAxis.set(0, cellSize.y, 0);\r\n zAxis.set(0, 0, cellSize.z);\r\n\r\n xDir.set(1, 0, 0);\r\n yDir.set(0, 1, 0);\r\n zDir.set(0, 0, 1);\r\n\r\n // flip normals if coordinate system is in the wrong handedness\r\n const tmp = new THREE.Vector3();\r\n tmp.crossVectors(xDir, yDir);\r\n if (tmp.dot(zDir) < 0) {\r\n xDir.negate();\r\n yDir.negate();\r\n zDir.negate();\r\n }\r\n\r\n // check that the grid is in the all-positive octant of the coordinate system\r\n if (xDir.x < 0 || xDir.y < 0 || xDir.z < 0\r\n || yDir.x < 0 || yDir.y < 0 || yDir.z < 0\r\n || zDir.x < 0 || zDir.y < 0 || zDir.z < 0) {\r\n return false;\r\n }\r\n\r\n // check that the grid is axis-aligned\r\n const notZero = (axe) => Math.abs(axe) > Number.EPSILON;\r\n return !(notZero(xAxis.y) || notZero(xAxis.z)\r\n || notZero(yAxis.x) || notZero(yAxis.z)\r\n || notZero(zAxis.x) || notZero(zAxis.y));\r\n }\r\n\r\n _vertexInterp(isoLevel, grid, ind1, ind2, vertex, normal) {\r\n const p1 = grid.p[ind1];\r\n const p2 = grid.p[ind2];\r\n const n1 = grid.g[ind1];\r\n const n2 = grid.g[ind2];\r\n const valP1 = grid.val[ind1];\r\n const valP2 = grid.val[ind2];\r\n const isoDiffP1 = isoLevel - valP1;\r\n const diffValP2P1 = valP2 - valP1;\r\n\r\n let mu = 0.0;\r\n\r\n if (Math.abs(diffValP2P1) > 0.0) {\r\n mu = isoDiffP1 / diffValP2P1;\r\n }\r\n mu = mu > 1.0 ? 1.0 : mu;\r\n vertex.lerpVectors(p1, p2, mu);\r\n normal.lerpVectors(n1, n2, mu);\r\n }\r\n\r\n static _triTable = IsoSurfaceMarchCube.prototype.striIndicesMarchCube;\r\n\r\n static _arrSize = 12;\r\n\r\n static _firstIndices = [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3];\r\n\r\n static _secondIndices = [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7];\r\n\r\n static _vertexList = createArray(IsoSurface._arrSize);\r\n\r\n static _normalList = createArray(IsoSurface._arrSize);\r\n\r\n _polygonize(grid, isoLevel, triangles) {\r\n const { cubeIndex } = grid;\r\n let i = 0;\r\n const arrSize = IsoSurface._arrSize;\r\n const firstIndices = IsoSurface._firstIndices;\r\n const secondIndices = IsoSurface._secondIndices;\r\n const vertexList = IsoSurface._vertexList;\r\n const normalList = IsoSurface._normalList;\r\n\r\n for (; i < arrSize; ++i) {\r\n if (edgeTable[cubeIndex] & (1 << i)) {\r\n this._vertexInterp(\r\n isoLevel,\r\n grid,\r\n firstIndices[i],\r\n secondIndices[i],\r\n vertexList[i],\r\n normalList[i],\r\n );\r\n }\r\n }\r\n\r\n let triCount = 0;\r\n const triTblIdx = cubeIndex * 16;\r\n const triTable = IsoSurface._triTable;\r\n\r\n for (i = 0; triTable[triTblIdx + i] !== -1; i += 3) {\r\n triangles[triCount].a.p.copy(vertexList[triTable[triTblIdx + i]]);\r\n triangles[triCount].a.n.copy(normalList[triTable[triTblIdx + i]]);\r\n\r\n triangles[triCount].b.p.copy(vertexList[triTable[triTblIdx + i + 1]]);\r\n triangles[triCount].b.n.copy(normalList[triTable[triTblIdx + i + 1]]);\r\n\r\n triangles[triCount].c.p.copy(vertexList[triTable[triTblIdx + i + 2]]);\r\n triangles[triCount].c.n.copy(normalList[triTable[triTblIdx + i + 2]]);\r\n ++triCount;\r\n }\r\n\r\n return triCount;\r\n }\r\n\r\n _doGridPosNorms(isoValue, step, appendSimple) {\r\n const vol = this._volumetricData;\r\n const volData = this._volumetricData.getData();\r\n const dim = vol.getDimensions();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n const zSize = dim[2];\r\n const stepX = step * vol.getStrideX();\r\n const stepY = step * vol.getStrideY();\r\n const stepZ = step * vol.getStrideZ();\r\n\r\n const gc = new GridCell();\r\n const gcVal = gc.val;\r\n const gcValSize = gc.val.length;\r\n const additions = [\r\n new THREE.Vector3(0, 0, 0), // 0\r\n new THREE.Vector3(step, 0, 0), // 1\r\n new THREE.Vector3(step, step, 0), // 2\r\n new THREE.Vector3(0, step, 0), // 3\r\n new THREE.Vector3(0, 0, step), // 4\r\n new THREE.Vector3(step, 0, step), // 5\r\n new THREE.Vector3(step, step, step), // 6\r\n new THREE.Vector3(0, step, step), // 7\r\n ];\r\n\r\n const tmpTriCount = 5;\r\n const triangles = new Array(tmpTriCount);\r\n for (let j = 0; j < tmpTriCount; ++j) {\r\n triangles[j] = new Triangle();\r\n }\r\n\r\n let appendVertex;\r\n const self = this;\r\n const positions = this._position;\r\n const normals = this._normals;\r\n if (appendSimple) {\r\n // Special case for axis-aligned grid with positive unit vector normals\r\n appendVertex = (function () {\r\n const axis = new THREE.Vector3(self._xAxis.x, self._yAxis.y, self._zAxis.z);\r\n return function (triVertex) {\r\n const vertex = triVertex.p.clone();\r\n vertex.multiply(axis);\r\n positions.push(vertex.add(self._origin));\r\n normals.push(triVertex.n.clone());\r\n };\r\n }());\r\n } else {\r\n appendVertex = (function () {\r\n const posMtx = new THREE.Matrix3();\r\n posMtx.set(\r\n self._xAxis.x,\r\n self._yAxis.x,\r\n self._zAxis.x,\r\n self._xAxis.y,\r\n self._yAxis.y,\r\n self._zAxis.y,\r\n self._xAxis.z,\r\n self._yAxis.z,\r\n self._zAxis.z,\r\n );\r\n const normMtx = new THREE.Matrix3();\r\n normMtx.set(\r\n self._xDir.x,\r\n self._yDir.x,\r\n self._zDir.x,\r\n self._xDir.y,\r\n self._yDir.y,\r\n self._zDir.y,\r\n self._xDir.z,\r\n self._yDir.z,\r\n self._zDir.z,\r\n );\r\n\r\n return function (triVertex) {\r\n positions.push(triVertex.p.clone().applyMatrix3(posMtx).add(self._origin));\r\n normals.push(triVertex.n.clone().applyMatrix3(normMtx));\r\n };\r\n }());\r\n }\r\n const indices = this._indices;\r\n\r\n let globTriCount = 0;\r\n\r\n for (let z = 0; z < (zSize - step); z += step) {\r\n for (let y = 0; y < (ySize - step); y += step) {\r\n let idx = vol.getDirectIdx(0, y, z);\r\n for (let x = 0; x < (xSize - step); x += step, idx += stepX) {\r\n /* eslint-disable no-multi-spaces */\r\n /* eslint-disable computed-property-spacing */\r\n gcVal[0] = volData[idx];\r\n gcVal[1] = volData[idx + stepX];\r\n gcVal[3] = volData[idx + stepY];\r\n gcVal[2] = volData[idx + stepX + stepY];\r\n gcVal[4] = volData[idx + stepZ];\r\n gcVal[5] = volData[idx + stepX + stepZ];\r\n gcVal[7] = volData[idx + stepY + stepZ];\r\n gcVal[6] = volData[idx + stepX + stepY + stepZ];\r\n /* eslint-enable no-multi-spaces */\r\n /* eslint-enable computed-property-spacing */\r\n\r\n // Determine the index into the edge table which\r\n // tells us which vertices are inside of the surface\r\n let cubeIndex = 0;\r\n let i = 0;\r\n for (; i < gcValSize; ++i) {\r\n if (gcVal[i] < isoValue) {\r\n cubeIndex |= (1 << i);\r\n }\r\n }\r\n\r\n if (edgeTable[cubeIndex] === 0) {\r\n continue;\r\n }\r\n\r\n gc.cubeIndex = cubeIndex;\r\n for (i = 0; i < gcValSize; ++i) {\r\n gc.p[i].set(x + additions[i].x, y + additions[i].y, z + additions[i].z);\r\n _voxelGradientFast(this._gradient, gc.p[i], gc.g[i]);\r\n }\r\n\r\n // calculate vertices and facets for this cube,\r\n // calculate normals by interpolating between the negated\r\n // normalized volume gradients for the 8 reference voxels\r\n const triCount = this._polygonize(gc, isoValue, triangles);\r\n globTriCount += triCount;\r\n\r\n // append triangles using different techniques\r\n for (i = 0; i < triCount; ++i) {\r\n indices.push(this._numTriangles * 3);\r\n indices.push(this._numTriangles * 3 + 1);\r\n indices.push(this._numTriangles * 3 + 2);\r\n ++this._numTriangles;\r\n\r\n appendVertex(triangles[i].a);\r\n appendVertex(triangles[i].b);\r\n appendVertex(triangles[i].c);\r\n }\r\n }\r\n }\r\n }\r\n\r\n return globTriCount;\r\n }\r\n\r\n compute(volData, origin, isoValue, step) {\r\n this._volumetricData = volData;\r\n this._origin = origin;\r\n\r\n this._gradient = volData.computeGradient();\r\n\r\n this._doGridPosNorms(isoValue, step, this._prepareAxesAndDirs());\r\n }\r\n\r\n _remapIndices(vertexMap, idcCount) {\r\n const indices = this._indices;\r\n const newIndices = utils.allocateTyped(Uint32Array, idcCount);\r\n for (let i = 0; i < idcCount; ++i) {\r\n indices[i] = vertexMap[indices[i]];\r\n newIndices[i] = indices[i];\r\n }\r\n this._indices = newIndices;\r\n }\r\n\r\n _remapVertices(vertices, normals, count) {\r\n const newPositions = utils.allocateTyped(Float32Array, count * 3);\r\n const newNormals = utils.allocateTyped(Float32Array, count * 3);\r\n for (let i = 0; i < count; ++i) {\r\n const pos = vertices[i];\r\n newPositions[i * 3] = pos.x;\r\n newPositions[i * 3 + 1] = pos.y;\r\n newPositions[i * 3 + 2] = pos.z;\r\n const norm = normals[i].normalize();\r\n newNormals[i * 3] = norm.x;\r\n newNormals[i * 3 + 1] = norm.y;\r\n newNormals[i * 3 + 2] = norm.z;\r\n }\r\n this._position = newPositions;\r\n this._normals = newNormals;\r\n }\r\n\r\n vertexFusion(offset, len) {\r\n const faceVer = this._indices.length;\r\n const vertices = this._position;\r\n const normals = this._normals;\r\n const oldVerCount = vertices.length | 0;\r\n if (faceVer === 0 || oldVerCount === 0) {\r\n return;\r\n }\r\n const vMap = utils.allocateTyped(Uint32Array, oldVerCount);\r\n vMap[0] = 0;\r\n let newVer = 1;\r\n\r\n let i = 1;\r\n for (; i < oldVerCount; ++i) {\r\n const start = newVer - offset < 0 ? 0 : newVer - offset;\r\n const end = start + len > newVer ? newVer : start + len;\r\n let matchedIndex = -1;\r\n\r\n for (let j = start; j < end; ++j) {\r\n if (Math.abs(vertices[i] - vertices[j]) < Number.EPSILON) {\r\n matchedIndex = j;\r\n break;\r\n }\r\n }\r\n\r\n if (matchedIndex !== -1) {\r\n vMap[i] = matchedIndex;\r\n } else {\r\n vertices[newVer].copy(vertices[i]);\r\n normals[newVer].copy(normals[i]);\r\n vMap[i] = newVer;\r\n ++newVer;\r\n }\r\n }\r\n\r\n this._remapIndices(vMap, faceVer);\r\n this._remapVertices(vertices, normals, newVer);\r\n }\r\n\r\n // Assign per-vertex colors from a volumetric texture map (same dimensions as the original volumetric data).\r\n // Along with color dominating atom is determined for each vertex\r\n // and vertices with atom out of \"visible\" subset get filtered out.\r\n // XXX only handles orthogonal volumes currently\r\n setColorVolTex(colorMap, atomMap, atomWeightMap, visibilitySelector) {\r\n let i;\r\n let idx;\r\n const numVerts = this._position.length / 3;\r\n const vertices = this._position;\r\n const origin = this._origin;\r\n const dim = this._volumetricData.getDimensions();\r\n const xs = dim[0] - 1;\r\n const ys = dim[1] - 1;\r\n const zs = dim[2] - 1;\r\n\r\n const colorData = colorMap.getData();\r\n const strideX = colorMap.getStrideX();\r\n const strideY = colorMap.getStrideY();\r\n const strideZ = colorMap.getStrideZ();\r\n\r\n let atomWeightData;\r\n let atomStrideX;\r\n let atomStrideY;\r\n let atomStrideZ;\r\n\r\n if (visibilitySelector !== null) {\r\n atomWeightData = atomWeightMap.getData();\r\n atomStrideX = atomWeightMap.getStrideX();\r\n atomStrideY = atomWeightMap.getStrideY();\r\n atomStrideZ = atomWeightMap.getStrideZ();\r\n }\r\n\r\n const xInv = 1.0 / this._xAxis.x;\r\n const yInv = 1.0 / this._yAxis.y;\r\n const zInv = 1.0 / this._zAxis.z;\r\n\r\n let atomLookup = [];\r\n let atomWeights = [];\r\n const colors = utils.allocateTyped(Float32Array, numVerts * 3);\r\n\r\n function interp(mu, idx1, idx2, c) {\r\n c[0] = (1 - mu) * colorData[idx1] + mu * colorData[idx2];\r\n c[1] = (1 - mu) * colorData[idx1 + 1] + mu * colorData[idx2 + 1];\r\n c[2] = (1 - mu) * colorData[idx1 + 2] + mu * colorData[idx2 + 2];\r\n }\r\n\r\n function collectWeight(ai, coefX, coefY, coefZ) {\r\n const a = atomMap[ai]; // atomWeightMap is a scalar field, so index into atom map should be the same\r\n if (a != null) {\r\n atomLookup[a.index] = a;\r\n const w = coefX * coefY * coefZ * atomWeightData[ai];\r\n if (typeof atomWeights[a.index] === 'undefined') {\r\n atomWeights[a.index] = w;\r\n } else {\r\n atomWeights[a.index] += w;\r\n }\r\n }\r\n }\r\n\r\n const vMap = utils.allocateTyped(Int32Array, numVerts);\r\n let newVerCount = 0;\r\n\r\n for (i = 0; i < numVerts; i++) {\r\n const ind = i * 3;\r\n const vx = (vertices[ind] - origin.x) * xInv;\r\n const vy = (vertices[ind + 1] - origin.y) * yInv;\r\n const vz = (vertices[ind + 2] - origin.z) * zInv;\r\n const x = Math.min(Math.max(vx, 0), xs) | 0;\r\n const y = Math.min(Math.max(vy, 0), ys) | 0;\r\n const z = Math.min(Math.max(vz, 0), zs) | 0;\r\n\r\n const mux = (vx - x);\r\n const muy = (vy - y);\r\n const muz = (vz - z);\r\n\r\n if (visibilitySelector != null) {\r\n // collect atom weights\r\n atomLookup = [];\r\n atomWeights = [];\r\n idx = atomWeightMap.getDirectIdx(x, y, z);\r\n collectWeight(idx, 1 - mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideX, mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideY, 1 - mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideX + atomStrideY, mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideZ, 1 - mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideZ, mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideY + atomStrideZ, 1 - mux, muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideY + atomStrideZ, mux, muy, muz);\r\n\r\n // find dominant atom\r\n let maxWeight = 0.0;\r\n let dominantIdx = -1;\r\n for (const atomIdx in atomWeights) {\r\n if (atomWeights[atomIdx] > maxWeight) {\r\n dominantIdx = atomIdx;\r\n maxWeight = atomWeights[atomIdx];\r\n }\r\n }\r\n\r\n if (dominantIdx < 0 || !visibilitySelector.includesAtom(atomLookup[dominantIdx])) {\r\n // this vertex doesn't belong to visible subset and will be skipped\r\n vMap[i] = -1;\r\n continue;\r\n }\r\n }\r\n\r\n vMap[i] = newVerCount++;\r\n\r\n // color tri-linear interpolation\r\n const dx = (x < xs) ? strideX : 0;\r\n const dy = (y < ys) ? strideY : 0;\r\n const dz = (z < zs) ? strideZ : 0;\r\n\r\n const c0 = [0, 0, 0];\r\n const c1 = [0, 0, 0];\r\n const c2 = [0, 0, 0];\r\n const c3 = [0, 0, 0];\r\n\r\n idx = colorMap.getDirectIdx(x, y, z);\r\n interp(mux, idx, idx + dx, c0);\r\n interp(mux, idx + dy, idx + dx + dy, c1);\r\n interp(mux, idx + dz, idx + dx + dz, c2);\r\n interp(mux, idx + dy + dz, idx + dx + dy + dz, c3);\r\n\r\n const cz0 = [0, 0, 0];\r\n cz0[0] = (1 - muy) * c0[0] + muy * c1[0];\r\n cz0[1] = (1 - muy) * c0[1] + muy * c1[1];\r\n cz0[2] = (1 - muy) * c0[2] + muy * c1[2];\r\n\r\n const cz1 = [0, 0, 0];\r\n cz1[0] = (1 - muy) * c2[0] + muy * c3[0];\r\n cz1[1] = (1 - muy) * c2[1] + muy * c3[1];\r\n cz1[2] = (1 - muy) * c2[2] + muy * c3[2];\r\n\r\n colors[ind] = (1 - muz) * cz0[0] + muz * cz1[0];\r\n colors[ind + 1] = (1 - muz) * cz0[1] + muz * cz1[1];\r\n colors[ind + 2] = (1 - muz) * cz0[2] + muz * cz1[2];\r\n }\r\n this._colors = colors;\r\n\r\n if (visibilitySelector != null) {\r\n // shift visible vertices towards beginning of array\r\n for (i = 0; i < numVerts; ++i) {\r\n const j = vMap[i];\r\n if (j < 0) {\r\n continue;\r\n }\r\n\r\n // assert: j <= i\r\n this._position[j * 3] = this._position[i * 3];\r\n this._position[j * 3 + 1] = this._position[i * 3 + 1];\r\n this._position[j * 3 + 2] = this._position[i * 3 + 2];\r\n this._normals[j * 3] = this._normals[i * 3];\r\n this._normals[j * 3 + 1] = this._normals[i * 3 + 1];\r\n this._normals[j * 3 + 2] = this._normals[i * 3 + 2];\r\n this._colors[j * 3] = this._colors[i * 3];\r\n this._colors[j * 3 + 1] = this._colors[i * 3 + 1];\r\n this._colors[j * 3 + 2] = this._colors[i * 3 + 2];\r\n }\r\n\r\n // rebuild index list\r\n const numTriangles = this._indices.length / 3;\r\n let newTriCount = 0;\r\n for (i = 0; i < numTriangles; ++i) {\r\n const i0 = vMap[this._indices[3 * i]];\r\n const i1 = vMap[this._indices[3 * i + 1]];\r\n const i2 = vMap[this._indices[3 * i + 2]];\r\n if (i0 >= 0 && i1 >= 0 && i2 >= 0) {\r\n this._indices[3 * newTriCount] = i0;\r\n this._indices[3 * newTriCount + 1] = i1;\r\n this._indices[3 * newTriCount + 2] = i2;\r\n ++newTriCount;\r\n }\r\n }\r\n\r\n // shrink arrays to data size\r\n this._position = new Float32Array(this._position.buffer.slice(0, newVerCount * 3 * 4));\r\n this._normals = new Float32Array(this._normals.buffer.slice(0, newVerCount * 3 * 4));\r\n this._colors = new Float32Array(this._colors.buffer.slice(0, newVerCount * 3 * 4));\r\n this._indices = new Uint32Array(this._indices.buffer.slice(0, newTriCount * 3 * 4));\r\n }\r\n }\r\n\r\n toMesh() {\r\n const geo = new THREE.BufferGeometry();\r\n geo.setIndex(new THREE.BufferAttribute(this._indices, 1));\r\n geo.setAttribute('position', new THREE.BufferAttribute(this._position, 3));\r\n geo.setAttribute('normal', new THREE.BufferAttribute(this._normals, 3));\r\n geo.setAttribute('color', new THREE.BufferAttribute(this._colors, 3));\r\n geo.computeBoundingSphere();\r\n return geo;\r\n }\r\n}\r\nexport default IsoSurface;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurface from './IsoSurface';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * This is a base class for volumetric maps based isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass VolumeSurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n const params = this._opts;\r\n this.numVoxels = [128, 128, 128];\r\n this.xAxis = new THREE.Vector3(1.0, 0.0, 0.0);\r\n this.yAxis = new THREE.Vector3(0.0, 1.0, 0.0);\r\n this.zAxis = new THREE.Vector3(0.0, 0.0, 1.0);\r\n\r\n this.origin = new THREE.Vector3(0.0, 0.0, 0.0);\r\n this._visibilitySelector = params.visibilitySelector;\r\n\r\n this._calcSurface(params);\r\n }\r\n\r\n _findMinMax(posRadArray) {\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n const maxPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n const minPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n for (let i = 1; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n for (let itemIdx = 0; itemIdx < itemSize; ++itemIdx) {\r\n const tmpVal = posRadArray[ind + itemIdx];\r\n maxPosRad[itemIdx] = Math.max(tmpVal, maxPosRad[itemIdx]);\r\n minPosRad[itemIdx] = Math.min(tmpVal, minPosRad[itemIdx]);\r\n }\r\n }\r\n return { maxPosRad, minPosRad };\r\n }\r\n\r\n _findNumVoxels(posRadArray, params) {\r\n const { numVoxels } = this;\r\n const minMaxValues = this._findMinMax(posRadArray);\r\n const minCoordRad = minMaxValues.minPosRad;\r\n const maxCoordRad = minMaxValues.maxPosRad;\r\n\r\n // minrad\r\n if (minCoordRad[3] > 4.0) {\r\n params.gridSpacing *= minCoordRad[3];\r\n }\r\n\r\n let gridPadding = params.radScale * maxCoordRad[3] * 1.7;\r\n let padRad = gridPadding;\r\n padRad = 0.65 * Math.sqrt(4.0 / 3.0 * Math.PI * padRad * padRad * padRad);\r\n gridPadding = Math.max(gridPadding, padRad);\r\n\r\n let i = 0;\r\n for (; i < 3; ++i) {\r\n minCoordRad[i] -= gridPadding;\r\n maxCoordRad[i] += gridPadding;\r\n }\r\n\r\n for (i = 0; i < 3; ++i) {\r\n numVoxels[i] = Math.ceil((maxCoordRad[i] - minCoordRad[i]) / params.gridSpacing);\r\n }\r\n this.xAxis.x = (numVoxels[0] - 1) * params.gridSpacing;\r\n this.yAxis.y = (numVoxels[1] - 1) * params.gridSpacing;\r\n this.zAxis.z = (numVoxels[2] - 1) * params.gridSpacing;\r\n\r\n [this.origin.x, this.origin.y, this.origin.z] = minCoordRad;\r\n\r\n return { bbox: minMaxValues, dim: numVoxels };\r\n }\r\n\r\n _makeSurface(surface, params) {\r\n const isoSurf = new IsoSurface();\r\n isoSurf.compute(surface.volMap, this.origin, params.isoValue, 1);\r\n isoSurf.vertexFusion(9, 9);// normalization is included\r\n\r\n if (isoSurf._numTriangles > 0) {\r\n isoSurf.setColorVolTex(surface.volTexMap, surface.atomMap, surface.atomWeightMap, this._visibilitySelector);\r\n this.setIndex(new THREE.BufferAttribute(isoSurf._indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(isoSurf._position, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(isoSurf._normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(isoSurf._colors, 3));\r\n } else { // geometry should have at least empty position attributes to be processed in wireframe mode by three.js\r\n this.setAttribute('position', new THREE.BufferAttribute(utils.allocateTyped(Float32Array, 0), 3));\r\n }\r\n }\r\n\r\n _calcSurface(params) {\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n\r\n if (packedArrays.posRad.length === 0) {\r\n return;\r\n }\r\n const boundaries = this._findNumVoxels(packedArrays.posRad, params);\r\n\r\n const box = new THREE.Box3(\r\n this.origin,\r\n new THREE.Vector3(this.xAxis.x, this.yAxis.y, this.zAxis.z).add(this.origin),\r\n );\r\n const surface = this._computeSurface(packedArrays, box, boundaries, params);\r\n\r\n this._makeSurface(surface, params);\r\n }\r\n}\r\n\r\nexport default VolumeSurfaceGeometry;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass QuickSurfGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n // beware of shifting this multiple times!\r\n this._shiftByOrigin(packedArrays.posRad);\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3),\r\n };\r\n\r\n if (this._visibilitySelector != null) {\r\n surface.atomMap = [];\r\n surface.atomWeightMap = new Volume(Float32Array, this.numVoxels, box);\r\n }\r\n\r\n this.gaussdensity(surface, packedArrays, null, params);\r\n return surface;\r\n }\r\n\r\n gaussdensity(surface, packedArrays, atomicNum, params) {\r\n const numAtoms = packedArrays.posRad.length / 4;\r\n const { posRad, colors } = packedArrays;\r\n const { numVoxels } = this;\r\n const { radScale, gaussLim, gridSpacing } = params;\r\n const invIsoValue = 1.0 / params.isoValue;\r\n const invGridSpacing = 1.0 / gridSpacing;\r\n const maxVoxelX = numVoxels[0] - 1;\r\n const maxVoxelY = numVoxels[1] - 1;\r\n const maxVoxelZ = numVoxels[2] - 1;\r\n // TODO is densityMap and volTexMap initialized?\r\n\r\n const { volMap, volTexMap } = surface;\r\n const volData = volMap.getData();\r\n const strideX = volMap.getStrideX();\r\n\r\n const volTexData = volTexMap.getData();\r\n const texStrideX = volTexMap.getStrideX();\r\n\r\n let atomWeightData;\r\n if (this._visibilitySelector != null) {\r\n atomWeightData = surface.atomWeightMap.getData();\r\n }\r\n\r\n const { atomMap } = surface;\r\n\r\n for (let i = 0; i < numAtoms; ++i) {\r\n const ind = i * 4;\r\n const scaledRad = posRad[ind + 3] * radScale;\r\n const atomicNumFactor = atomicNum === null ? 1.0 : atomicNum[i];\r\n const radInv = 1 / (2 * scaledRad * scaledRad);\r\n let radLim = gaussLim * scaledRad;\r\n const radLim2 = radLim * radLim;\r\n radLim *= invGridSpacing;\r\n\r\n let tmp = posRad[ind] * invGridSpacing;\r\n const xMin = Math.max((tmp - radLim) | 0, 0);\r\n const xMax = Math.min((tmp + radLim) | 0, maxVoxelX);\r\n tmp = posRad[ind + 1] * invGridSpacing;\r\n const yMin = Math.max((tmp - radLim) | 0, 0);\r\n const yMax = Math.min((tmp + radLim) | 0, maxVoxelY);\r\n tmp = posRad[ind + 2] * invGridSpacing;\r\n const zMin = Math.max((tmp - radLim) | 0, 0);\r\n const zMax = Math.min((tmp + radLim) | 0, maxVoxelZ);\r\n\r\n let dz = zMin * gridSpacing - posRad[ind + 2];\r\n for (let z = zMin; z <= zMax; ++z, dz += gridSpacing) {\r\n let dy = yMin * gridSpacing - posRad[ind + 1];\r\n for (let y = yMin; y <= yMax; ++y, dy += gridSpacing) {\r\n const dy2dz2 = dy * dy + dz * dz;\r\n\r\n if (dy2dz2 >= radLim2) {\r\n continue;\r\n }\r\n\r\n let addr = volMap.getDirectIdx(xMin, y, z);\r\n let texAddr = volTexMap.getDirectIdx(xMin, y, z);\r\n let dx = xMin * gridSpacing - posRad[ind];\r\n for (let x = xMin; x <= xMax; ++x, dx += gridSpacing, addr += strideX, texAddr += texStrideX) {\r\n const r2 = dx * dx + dy2dz2;\r\n const expVal = -r2 * radInv;\r\n\r\n let density = Math.exp(expVal) * atomicNumFactor;\r\n\r\n // store most relevant atom (with highest density)\r\n if (this._visibilitySelector != null\r\n && density > atomWeightData[addr]) { // NOSONAR\r\n atomWeightData[addr] = density;\r\n // we use same index into atom map and atomWeightMap\r\n atomMap[addr] = packedArrays.atoms[i];\r\n }\r\n\r\n volData[addr] += density;\r\n\r\n // TODO check for volTexMap routine?\r\n density *= invIsoValue;\r\n const colInd = i * 3;\r\n volTexData[texAddr] += density * colors[colInd];\r\n volTexData[texAddr + 1] += density * colors[colInd + 1];\r\n volTexData[texAddr + 2] += density * colors[colInd + 2];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n _shiftByOrigin(posRadArray) {\r\n const originX = this.origin.x;\r\n const originY = this.origin.y;\r\n const originZ = this.origin.z;\r\n\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n for (let i = 0; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n posRadArray[ind] -= originX;\r\n posRadArray[ind + 1] -= originY;\r\n posRadArray[ind + 2] -= originZ;\r\n }\r\n }\r\n}\r\n\r\nexport default QuickSurfGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * Modifed from SpatialHash\r\n *\r\n * Main differences are:\r\n * - Optimized grid size to ensure we only ever need to look +/-1 cell\r\n * - Aware of atomic radii and will only output atoms within rAtom + rExtra\r\n * (see withinRadii method)\r\n *\r\n * (Uses rounding rather than bitshifting as consequence of arbitrary grid size)\r\n * @class\r\n * @param {Float32Array} posRad - x, y, z coordinates and radiuses\r\n * @param {Float32Array} min - xyz min coordinates\r\n * @param {Float32Array} max - xyz max coordinates\r\n * @param {number} maxDistance - max distance\r\n */\r\nfunction AVHash(posRad, min, max, maxDistance) {\r\n const itemSize = 4;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const minX = min[0];\r\n const minY = min[1];\r\n const minZ = min[2];\r\n\r\n const maxX = max[0];\r\n const maxY = max[1];\r\n const maxZ = max[2];\r\n\r\n function hashFunc(w, minW) {\r\n return Math.floor((w - minW) / maxDistance);\r\n }\r\n\r\n const iDim = hashFunc(maxX, minX) + 1;\r\n const jDim = hashFunc(maxY, minY) + 1;\r\n const kDim = hashFunc(maxZ, minZ) + 1;\r\n\r\n const nCells = iDim * jDim * kDim;\r\n\r\n const jkDim = jDim * kDim;\r\n\r\n /* Get cellID for cartesian x,y,z */\r\n const cellID = function (x, y, z) {\r\n return (((hashFunc(x, minX) * jDim) + hashFunc(y, minY)) * kDim) + hashFunc(z, minZ);\r\n };\r\n\r\n /* Initial building, could probably be optimized further */\r\n const preHash = [];\r\n let i;\r\n let cid;\r\n for (i = 0; i < nAtoms; i++) {\r\n const iIdx = itemSize * i;\r\n cid = cellID(posRad[iIdx], posRad[iIdx + 1], posRad[iIdx + 2]);\r\n\r\n if (preHash[cid] === undefined) {\r\n preHash[cid] = [i];\r\n } else {\r\n preHash[cid].push(i);\r\n }\r\n }\r\n\r\n const cellOffsets = utils.allocateTyped(Uint32Array, nCells);\r\n const cellLengths = utils.allocateTyped(Uint16Array, nCells);\r\n const data = utils.allocateTyped(Uint32Array, nAtoms);\r\n\r\n let offset = 0;\r\n let maxCellLength = 0;\r\n let j;\r\n for (i = 0; i < nCells; i++) {\r\n const start = cellOffsets[i] = offset;\r\n\r\n const subArray = preHash[i];\r\n\r\n if (subArray !== undefined) {\r\n for (j = 0; j < subArray.length; j++) {\r\n data[offset] = subArray[j];\r\n offset++;\r\n }\r\n }\r\n\r\n const cellLength = offset - start;\r\n cellLengths[i] = cellLength;\r\n\r\n if (cellLength > maxCellLength) {\r\n maxCellLength = cellLength;\r\n }\r\n }\r\n\r\n // Maximum number of neighbours we could ever produce (27 adjacent cells of equal population)\r\n this.neighbourListLength = (27 * maxCellLength) + 1;\r\n\r\n /**\r\n * Populate the supplied out array with atom indices that are within rAtom + rExtra\r\n * of x,y,z\r\n *\r\n * -1 in out array indicates the end of the list\r\n *\r\n * @param {number} x - x coordinate\r\n * @param {number} y - y coordinate\r\n * @param {number} z - z coordinate\r\n * @param {number} rExtra - additional radius\r\n * @param {Float32Array} out - pre-allocated output array\r\n * @return {undefined}\r\n */\r\n this.withinRadii = function (x, y, z, rExtra, out) {\r\n let outIdx = 0;\r\n\r\n const nearI = hashFunc(x, minX);\r\n const nearJ = hashFunc(y, minY);\r\n const nearK = hashFunc(z, minZ);\r\n\r\n const loI = Math.max(0, nearI - 1);\r\n const loJ = Math.max(0, nearJ - 1);\r\n const loK = Math.max(0, nearK - 1);\r\n\r\n const hiI = Math.min(iDim - 1, nearI + 1);\r\n const hiJ = Math.min(jDim - 1, nearJ + 1);\r\n const hiK = Math.min(kDim - 1, nearK + 1);\r\n\r\n for (i = loI; i <= hiI; ++i) {\r\n const iOffset = i * jkDim;\r\n\r\n for (j = loJ; j <= hiJ; ++j) {\r\n const jOffset = j * kDim;\r\n\r\n for (let k = loK; k <= hiK; ++k) {\r\n cid = iOffset + jOffset + k;\r\n\r\n const cellStart = cellOffsets[cid];\r\n const cellEnd = cellStart + cellLengths[cid];\r\n\r\n for (let dataIndex = cellStart; dataIndex < cellEnd; dataIndex++) {\r\n const atomIndex = data[dataIndex];\r\n const baseIndex = itemSize * atomIndex;\r\n const dx = posRad[baseIndex] - x;\r\n const dy = posRad[baseIndex + 1] - y;\r\n const dz = posRad[baseIndex + 2] - z;\r\n const rSum = posRad[baseIndex + 3] + rExtra;\r\n\r\n if ((dx * dx + dy * dy + dz * dz) <= (rSum * rSum)) {\r\n out[outIdx++] = data[dataIndex];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n // Add terminator\r\n out[outIdx] = -1;\r\n };\r\n}\r\nfunction ContactSurface(packedArrays, boundaries, params, _indexList) {\r\n // Field generation method adapted from AstexViewer (Mike Hartshorn)\r\n // by Fred Ludlow.\r\n // Other parts based heavily on NGL (Alexander Rose) EDT Surface class\r\n //\r\n // Should work as a drop-in alternative to EDTSurface (though some of\r\n // the EDT paramters are not relevant in this method).\r\n\r\n const itemSize = 4;\r\n const { posRad, colors, atoms } = packedArrays;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const { bbox } = boundaries;\r\n\r\n const min = bbox.minPosRad;\r\n const max = bbox.maxPosRad;\r\n\r\n let r2; // Atom positions, expanded radii (squared)\r\n let maxRadius;\r\n\r\n // Parameters\r\n let probeRadius;\r\n let scaleFactor;\r\n let probePositions;\r\n\r\n // Cache last value for obscured test\r\n let lastClip = -1;\r\n\r\n // Grid params\r\n let dim;\r\n let grid;\r\n let volTex;\r\n let weights;\r\n let weightsMap = null;\r\n let atomMap = null;\r\n let visibilitySelector = null;\r\n\r\n // grid indices -> xyz coords\r\n let gridx;\r\n let gridy;\r\n let gridz;\r\n\r\n // Lookup tables:\r\n let sinTable;\r\n let cosTable;\r\n\r\n // Spatial Hash\r\n let hash;\r\n\r\n // Neighbour array to be filled by hash\r\n let neighbours;\r\n\r\n // Vectors for Torus Projection\r\n const mid = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n1 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n2 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n let ngTorus;\r\n\r\n function uniformArray(TypeName, n, a) {\r\n const array = utils.allocateTyped(TypeName, n);\r\n for (let innI = 0; innI < n; ++innI) {\r\n array[innI] = a;\r\n }\r\n\r\n return array;\r\n }\r\n\r\n function fillGridDim(a, start, step) {\r\n for (let innI = 0; innI < a.length; innI++) {\r\n a[innI] = start + (step * innI);\r\n }\r\n }\r\n\r\n function initializeGrid() {\r\n ({ scaleFactor } = params);\r\n ({ dim } = boundaries);\r\n\r\n ngTorus = Math.min(5, 2 + Math.floor(probeRadius * scaleFactor));\r\n\r\n const gridSize = dim[0] * dim[1] * dim[2];\r\n grid = uniformArray(Float32Array, gridSize, -1001.0);\r\n volTex = utils.allocateTyped(Float32Array, gridSize * 3);\r\n weights = utils.allocateTyped(Float32Array, gridSize);\r\n if (visibilitySelector) {\r\n weightsMap = utils.allocateTyped(Float32Array, gridSize);\r\n atomMap = [];\r\n }\r\n\r\n gridx = utils.allocateTyped(Float32Array, dim[0]);\r\n gridy = utils.allocateTyped(Float32Array, dim[1]);\r\n gridz = utils.allocateTyped(Float32Array, dim[2]);\r\n\r\n fillGridDim(gridx, min[0], 1 / scaleFactor);\r\n fillGridDim(gridy, min[1], 1 / scaleFactor);\r\n fillGridDim(gridz, min[2], 1 / scaleFactor);\r\n }\r\n\r\n function initializeAngleTables() {\r\n let theta = 0.0;\r\n const step = 2 * Math.PI / probePositions;\r\n\r\n cosTable = utils.allocateTyped(Float32Array, probePositions);\r\n sinTable = utils.allocateTyped(Float32Array, probePositions);\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n cosTable[innI] = Math.cos(theta);\r\n sinTable[innI] = Math.sin(theta);\r\n theta += step;\r\n }\r\n }\r\n\r\n function initializeHash() {\r\n hash = new AVHash(posRad, min, max, 2.01 * maxRadius);\r\n neighbours = new Int32Array(hash.neighbourListLength);\r\n }\r\n\r\n function init() {\r\n ({\r\n probeRadius,\r\n scaleFactor,\r\n probePositions,\r\n visibilitySelector,\r\n } = params);\r\n r2 = utils.allocateTyped(Float32Array, nAtoms);\r\n maxRadius = 0;\r\n for (let innI = 0; innI < nAtoms; ++innI) {\r\n const rExt = posRad[innI * itemSize + 3] += probeRadius;\r\n if (rExt > maxRadius) {\r\n maxRadius = rExt;\r\n }\r\n r2[innI] = rExt * rExt;\r\n }\r\n\r\n initializeGrid();\r\n initializeAngleTables();\r\n initializeHash();\r\n\r\n lastClip = -1;\r\n }\r\n\r\n function singleAtomObscures(ai, innX, innY, innZ) {\r\n const innCI = itemSize * ai;\r\n const ra2 = r2[ai];\r\n const dx = posRad[innCI] - innX;\r\n const dy = posRad[innCI + 1] - innY;\r\n const dz = posRad[innCI + 2] - innZ;\r\n const d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n return d2 < ra2;\r\n }\r\n\r\n function obscured(innX, innY, innZ, a, b) {\r\n // Is the point at x,y,z obscured by any of the atoms\r\n // specifeid by indices in neighbours. Ignore indices\r\n // a and b (these are the relevant atoms in projectPoints/Torii)\r\n\r\n // Cache the last clipped atom (as very often the same one in\r\n // subsequent calls)\r\n let ai;\r\n\r\n if (lastClip !== -1) {\r\n ai = lastClip;\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n return ai;\r\n }\r\n lastClip = -1;\r\n }\r\n\r\n let ni = 0;\r\n ai = neighbours[ni];\r\n while (ai >= 0) {\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n lastClip = ai;\r\n return ai;\r\n }\r\n ai = neighbours[++ni];\r\n }\r\n\r\n lastClip = -1;\r\n\r\n return -1;\r\n }\r\n\r\n function projectPoints() {\r\n // For each atom:\r\n // Iterate over a subsection of the grid, for each point:\r\n // If current value < 0.0, unvisited, set positive\r\n //\r\n // In any case: Project this point onto surface of the atomic sphere\r\n // If this projected point is not obscured by any other atom\r\n // Calcualte delta distance and set grid value to minimum of\r\n // itself and delta\r\n\r\n // Should we alias frequently accessed closure constiables??\r\n // Assume JS engine capable of optimizing this\r\n // anyway...\r\n const maxRad = 4.0;\r\n const sigma = (maxRad) / 3;\r\n const sigma2Inv = 1 / (2 * sigma * sigma);\r\n\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innCI = itemSize * innI;\r\n const ax = posRad[innCI];\r\n const ay = posRad[innCI + 1];\r\n const az = posRad[innCI + 2];\r\n const ar = posRad[innCI + 3];\r\n const ar2 = r2[innI];\r\n\r\n hash.withinRadii(ax, ay, az, ar, neighbours);\r\n\r\n // Number of grid points, round this up...\r\n const ng = Math.ceil(ar * scaleFactor);\r\n\r\n // Center of the atom, mapped to grid points (take floor)\r\n const iax = Math.floor(scaleFactor * (ax - min[0]));\r\n const iay = Math.floor(scaleFactor * (ay - min[1]));\r\n const iaz = Math.floor(scaleFactor * (az - min[2]));\r\n\r\n // Extents of grid to consider for this atom\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n // Add two to these points:\r\n // - iax are floor'd values so this ensures coverage\r\n // - these are loop limits (exclusive)\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n const colIdx = innI * 3;\r\n const cr = colors[colIdx];\r\n const cg = colors[colIdx + 1];\r\n const cb = colors[colIdx + 2];\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n const dz = gridz[iz] - az;\r\n const zOffset = dim[1] * dim[0] * iz;\r\n\r\n for (let iy = miny; iy < maxy; iy++) {\r\n const dy = gridy[iy] - ay;\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n\r\n for (let ix = minx; ix < maxx; ix++) {\r\n const idx = ix + zyOffset;\r\n const dx = gridx[ix] - ax;\r\n const d2 = dzy2 + dx * dx;\r\n\r\n if (d2 < ar2) {\r\n const w = Math.exp(-d2 * sigma2Inv);\r\n const cIdx = idx * 3;\r\n volTex[cIdx] += cr * w;\r\n volTex[cIdx + 1] += cg * w;\r\n volTex[cIdx + 2] += cb * w;\r\n weights[idx] += w;\r\n if (visibilitySelector !== null && w > weightsMap[idx]) {\r\n weightsMap[idx] = w;\r\n atomMap[idx] = atoms[innI];\r\n }\r\n\r\n if (grid[idx] < 0.0) {\r\n // Unvisited, make positive\r\n grid[idx] = -grid[idx];\r\n }\r\n // Project on to the surface of the sphere\r\n // sp is the projected point ( dx, dy, dz ) * ( ra / d )\r\n const d = Math.sqrt(d2);\r\n const ap = ar / d;\r\n let spx = dx * ap;\r\n let spy = dy * ap;\r\n let spz = dz * ap;\r\n\r\n spx += ax;\r\n spy += ay;\r\n spz += az;\r\n\r\n if (obscured(spx, spy, spz, innI, -1) === -1) {\r\n const dd = ar - d;\r\n if (dd < grid[idx]) {\r\n grid[idx] = dd;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function normalToLine(out, p) {\r\n out.x = out.y = out.z = 1.0;\r\n if (p.x !== 0) {\r\n out.x = (p.y + p.z) / -p.x;\r\n } else if (p.y !== 0) {\r\n out.y = (p.x + p.z) / -p.y;\r\n } else if (p.z !== 0) {\r\n out.z = (p.x + p.y) / -p.z;\r\n }\r\n return out;\r\n }\r\n\r\n function projectTorus(a, b) {\r\n const aIdx = itemSize * a;\r\n const bIdx = itemSize * b;\r\n const xa = posRad[aIdx];\r\n const ya = posRad[aIdx + 1];\r\n const za = posRad[aIdx + 2];\r\n const r1 = posRad[aIdx + 3];\r\n let dx = mid.x = posRad[bIdx] - xa;\r\n let dy = mid.y = posRad[bIdx + 1] - ya;\r\n let dz = mid.z = posRad[bIdx + 2] - za;\r\n const innR2 = posRad[bIdx + 3];\r\n let d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n // This check now redundant as already done in AVHash.withinRadii\r\n // if( d2 > (( r1 + r2 ) * ( r1 + r2 )) ){ return; }\r\n\r\n const d = Math.sqrt(d2);\r\n\r\n // Find angle between a->b vector and the circle\r\n // of their intersection by cosine rule\r\n const cosA = (r1 * r1 + d * d - innR2 * innR2) / (2.0 * r1 * d);\r\n\r\n // distance along a->b at intersection\r\n const dmp = r1 * cosA;\r\n\r\n mid.normalize();\r\n\r\n // Create normal to line\r\n normalToLine(n1, mid);\r\n n1.normalize();\r\n\r\n // Cross together for second normal vector\r\n n2.crossVectors(mid, n1);\r\n n2.normalize();\r\n\r\n // r is radius of circle of intersection\r\n const rInt = Math.sqrt(r1 * r1 - dmp * dmp);\r\n\r\n n1.multiplyScalar(rInt);\r\n n2.multiplyScalar(rInt);\r\n mid.multiplyScalar(dmp);\r\n\r\n mid.x += xa;\r\n mid.y += ya;\r\n mid.z += za;\r\n\r\n lastClip = -1;\r\n\r\n const ng = ngTorus;\r\n\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n const cost = cosTable[innI];\r\n const sint = sinTable[innI];\r\n\r\n const px = mid.x + cost * n1.x + sint * n2.x;\r\n const py = mid.y + cost * n1.y + sint * n2.y;\r\n const pz = mid.z + cost * n1.z + sint * n2.z;\r\n\r\n if (obscured(px, py, pz, a, b) === -1) {\r\n // As above, iterate over our grid...\r\n // px, py, pz in grid coords\r\n const iax = Math.floor(scaleFactor * (px - min[0]));\r\n const iay = Math.floor(scaleFactor * (py - min[1]));\r\n const iaz = Math.floor(scaleFactor * (pz - min[2]));\r\n\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n dz = pz - gridz[iz];\r\n const zOffset = dim[1] * dim[0] * iz;\r\n for (let iy = miny; iy < maxy; iy++) {\r\n dy = py - gridy[iy];\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n for (let ix = minx; ix < maxx; ix++) {\r\n dx = px - gridx[ix];\r\n d2 = dzy2 + dx * dx;\r\n const idx = ix + zyOffset;\r\n const current = grid[idx];\r\n\r\n if (current > 0.0 && d2 < (current * current)) {\r\n grid[idx] = Math.sqrt(d2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function projectTorii() {\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innIdx = itemSize * innI;\r\n hash.withinRadii(\r\n posRad[innIdx],\r\n posRad[innIdx + 1],\r\n posRad[innIdx + 2],\r\n posRad[innIdx + 3],\r\n neighbours,\r\n );\r\n let ia = 0;\r\n let ni = neighbours[ia];\r\n while (ni >= 0) {\r\n if (innI < ni) {\r\n projectTorus(innI, ni);\r\n }\r\n ni = neighbours[++ia];\r\n }\r\n }\r\n }\r\n\r\n function fixNegatives() {\r\n for (let innI = 0, n = grid.length; innI < n; innI++) {\r\n if (grid[innI] < 0) grid[innI] = 0;\r\n let w = weights[innI];\r\n if (w > 0) {\r\n w = 1 / w;\r\n const innInnI = innI * 3;\r\n volTex[innInnI] *= w;\r\n volTex[innInnI + 1] *= w;\r\n volTex[innInnI + 2] *= w;\r\n }\r\n }\r\n }\r\n\r\n function getVolume() {\r\n // Basic steps are:\r\n // 1) Initialize\r\n // 2) Project points\r\n // 3) Project torii\r\n console.time('ContactSurface.getVolume');\r\n\r\n console.time('ContactSurface.init');\r\n init();\r\n console.timeEnd('ContactSurface.init');\r\n\r\n console.time('ContactSurface.projectPoints');\r\n projectPoints();\r\n console.timeEnd('ContactSurface.projectPoints');\r\n\r\n console.time('ContactSurface.projectTorii');\r\n projectTorii();\r\n console.timeEnd('ContactSurface.projectTorii');\r\n fixNegatives();\r\n console.timeEnd('ContactSurface.getVolume');\r\n }\r\n\r\n this.build = function () {\r\n // type and cutoff left in for compatibility with EDTSurface.getSurface\r\n // function signature\r\n getVolume();\r\n this.volTexMap = volTex;\r\n this.weightsMap = weightsMap;\r\n this.atomMap = atomMap;\r\n this.volMap = grid;\r\n };\r\n}\r\nexport default ContactSurface;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport ContactSurface from './ContactSurface';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'contact' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass ContactSurfaceGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n const contactSurface = new ContactSurface(packedArrays, boundaries, params);\r\n contactSurface.build();\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.volMap),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3, contactSurface.volTexMap),\r\n atomMap: contactSurface.atomMap,\r\n atomWeightMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.weightsMap),\r\n };\r\n return surface;\r\n }\r\n}\r\n\r\nexport default ContactSurfaceGeometry;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for colored atom. Need for atom structure clusterization\r\n *\r\n * @param {Vector3} vCenter Center of atom\r\n * @param {number} radiusAt Radius of atom\r\n */\r\nclass IsoSurfaceAtomColored {\r\n constructor(vCenter, radiusAt) {\r\n this.coord = new THREE.Vector3();\r\n this.coord.copy(vCenter);\r\n this.radius = radiusAt;\r\n this.colorX = 0.99999;\r\n this.colorY = 0.0;\r\n this.colorZ = 0.0;\r\n this.atomType = 0;\r\n this.srcAtom = null;\r\n }\r\n}\r\nexport default IsoSurfaceAtomColored;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n// suppress some JSHint warnings\r\n/* jshint bitwise: false */\r\n\r\n/**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numAtoms - Number of atoms in molecule\r\n * @param {Element} atoms - Array of atoms\r\n * @param {Vector3} vBoxMin - Bounding box min\r\n * @param {Vector3} vBoxMax - Bounding box max\r\n * @param {number} probeRadius - Normals for output\r\n *\r\n */\r\nclass IsosurfaceBuildNormals {\r\n constructor(numAtoms, atoms, vBoxMin, vBoxMax, probeRadius) {\r\n this._numAtoms = numAtoms;\r\n this._atoms = atoms;\r\n this._vBoxMin = new THREE.Vector3();\r\n this._vBoxMax = new THREE.Vector3();\r\n this._vBoxMin.copy(vBoxMin);\r\n this._vBoxMax.copy(vBoxMax);\r\n this._probeRadius = probeRadius;\r\n\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n }\r\n\r\n createVoxels() {\r\n let numAtomsRefs;\r\n let rad;\r\n const ATOM_VOXEL_REF_SCALE = 4.5;\r\n\r\n const numAtoms = this._numAtoms | 0;\r\n const atoms = this._atoms;\r\n const dx = this._vBoxMax.x - this._vBoxMin.x;\r\n const dy = this._vBoxMax.y - this._vBoxMin.y;\r\n const dz = this._vBoxMax.z - this._vBoxMin.z;\r\n let w = (dx < dy) ? dx : dy;\r\n w = (dz < w) ? dz : w;\r\n let maxRad = 0.0;\r\n let aveRad = 0.0;\r\n\r\n let i;\r\n for (i = 0; i < numAtoms; i++) {\r\n rad = (atoms[i].radius + this._probeRadius) * 2.0;\r\n maxRad = (rad > maxRad) ? rad : maxRad;\r\n aveRad += rad;\r\n }\r\n let numCells = Math.floor(w / maxRad);\r\n if (numCells < 2) {\r\n numCells = 2;\r\n }\r\n aveRad /= numAtoms;\r\n\r\n this._numCells = numCells;\r\n this._aveRad = aveRad;\r\n this._maxRad = maxRad;\r\n\r\n const side = numCells;\r\n const side2 = numCells * numCells;\r\n const side3 = numCells * numCells * numCells;\r\n\r\n const xScale = this._xScale = 1.0 / (this._vBoxMax.x - this._vBoxMin.x);\r\n const yScale = this._yScale = 1.0 / (this._vBoxMax.y - this._vBoxMin.y);\r\n const zScale = this._zScale = 1.0 / (this._vBoxMax.z - this._vBoxMin.z);\r\n\r\n // estimate number of individual atom refs in each voxel list\r\n let maxAtomsRefs = 0;\r\n\r\n const xNumVoxMult = xScale * numCells;\r\n const yNumVoxMult = yScale * numCells;\r\n const zNumVoxMult = zScale * numCells;\r\n\r\n for (i = 0; i < numAtoms; i++) {\r\n const radAffect = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n const diaAffect = radAffect * 2.0;\r\n let numVoxX = Math.floor(xNumVoxMult * diaAffect + 0.8);\r\n let numVoxY = Math.floor(yNumVoxMult * diaAffect + 0.8);\r\n let numVoxZ = Math.floor(zNumVoxMult * diaAffect + 0.8);\r\n // avoid case numVox? == 0\r\n // also use loop i <=\r\n numVoxX++;\r\n numVoxY++;\r\n numVoxZ++;\r\n maxAtomsRefs += numVoxX * numVoxY * numVoxZ;\r\n } // for (i)\r\n // maxAtomsRefs = numAtoms * MAX_ATOMS_IN_SINGLE_VOXEL;\r\n\r\n this._voxelList = utils.allocateTyped(Int32Array, side3);\r\n const atomsList = [];\r\n atomsList.length = maxAtomsRefs;\r\n if ((this._voxelList === null) || (atomsList === null)) {\r\n return 0 - 1;\r\n }\r\n // init voxel list\r\n for (i = 0; i < side3; i++) {\r\n this._voxelList[i] = -1;\r\n }\r\n numAtomsRefs = 0;\r\n\r\n // create voxel lists\r\n for (i = 0; i < numAtoms; i++) {\r\n // use multiplier 4 to locate this atom in different voxels\r\n rad = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n let xIndMin = Math.floor((atoms[i].coord.x - this._vBoxMin.x - rad) * numCells * xScale);\r\n let yIndMin = Math.floor((atoms[i].coord.y - this._vBoxMin.y - rad) * numCells * yScale);\r\n let zIndMin = Math.floor((atoms[i].coord.z - this._vBoxMin.z - rad) * numCells * zScale);\r\n let xIndMax = Math.floor((atoms[i].coord.x - this._vBoxMin.x + rad) * numCells * xScale);\r\n let yIndMax = Math.floor((atoms[i].coord.y - this._vBoxMin.y + rad) * numCells * yScale);\r\n let zIndMax = Math.floor((atoms[i].coord.z - this._vBoxMin.z + rad) * numCells * zScale);\r\n\r\n xIndMin = (xIndMin >= 0) ? xIndMin : 0;\r\n yIndMin = (yIndMin >= 0) ? yIndMin : 0;\r\n zIndMin = (zIndMin >= 0) ? zIndMin : 0;\r\n\r\n xIndMax = (xIndMax < numCells) ? xIndMax : (numCells - 1);\r\n yIndMax = (yIndMax < numCells) ? yIndMax : (numCells - 1);\r\n zIndMax = (zIndMax < numCells) ? zIndMax : (numCells - 1);\r\n\r\n for (let z = zIndMin; z <= zIndMax; z++) {\r\n for (let y = yIndMin; y <= yIndMax; y++) {\r\n for (let x = xIndMin; x <= xIndMax; x++) {\r\n // add atom with index \"i\" to this voxel list\r\n const indVoxel = x + y * side + z * side2;\r\n // assert indVoxel >= 0\r\n // assert indVoxel < side3\r\n\r\n // add first\r\n if (this._voxelList[indVoxel] < 0) {\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = 0 - 1;\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n numAtomsRefs++;\r\n // assert numAtomsRefs < maxAtomsRefs - 1\r\n continue;\r\n }\r\n // insert into head of list\r\n const indexNext = this._voxelList[indVoxel];\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = indexNext;\r\n numAtomsRefs++;\r\n } // for (x)\r\n } // for (y)\r\n } // for (z)\r\n } // for (i)\r\n\r\n // convert Array to Int32Array\r\n this._atomsList = Int32Array.from(atomsList);\r\n\r\n return 0;\r\n }\r\n\r\n destroyVoxels() {\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n\r\n this._atoms = null;\r\n this._vertices = null;\r\n this._vBoxMin = null;\r\n this._vBoxMax = null;\r\n }\r\n\r\n /**\r\n * Enumerate all atoms affecting specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n * @param {func(atom)} process - function to call for each atom\r\n */\r\n forEachRelatedAtom(point, process) {\r\n // find corresponding voxel\r\n const xInd = Math.floor((point.x - this._vBoxMin.x) * this._numCells * this._xScale);\r\n const yInd = Math.floor((point.y - this._vBoxMin.y) * this._numCells * this._yScale);\r\n const zInd = Math.floor((point.z - this._vBoxMin.z) * this._numCells * this._zScale);\r\n const indVoxel = xInd + yInd * this._numCells + zInd * this._numCells * this._numCells;\r\n\r\n // run through atoms affecting this voxel\r\n const atoms = this._atoms;\r\n for (let ref = this._voxelList[indVoxel]; ref >= 0; ref = this._atomsList[ref * 2 + 1]) {\r\n const indexAtom = this._atomsList[ref * 2];\r\n process(atoms[indexAtom]);\r\n }\r\n }\r\n\r\n /**\r\n * Get atom closest to specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n *\r\n * @returns {IsoSurfaceAtomColored} atom, or null if not found\r\n */\r\n getClosestAtom(point) {\r\n let closest = null;\r\n let minDist2 = Number.MAX_VALUE;\r\n\r\n this.forEachRelatedAtom(point, (atom) => {\r\n const dist2 = point.distanceToSquared(atom.coord);\r\n if (dist2 < minDist2) {\r\n minDist2 = dist2;\r\n closest = atom;\r\n }\r\n });\r\n\r\n return closest;\r\n }\r\n\r\n /**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} normals - Normals for output\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildNormals(numVertices, vertices, normals) {\r\n const self = this;\r\n let numCloseAtoms = 0;\r\n let vx = 0;\r\n let vy = 0;\r\n let vz = 0;\r\n let dist2;\r\n let vNormalX = 0;\r\n let vNormalY = 0;\r\n let vNormalZ = 0;\r\n let koef = 0;\r\n let w = 0;\r\n const r25 = 2.5;\r\n const r01 = 0.1;\r\n\r\n const maxRadAffect = this._aveRad * r25;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n const expScale = -this._aveRad * r01;\r\n\r\n // some stats\r\n // numSlowAtoms = 0;\r\n\r\n const gatherNormals = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = Math.exp(expScale * koef);\r\n\r\n vNormalX += dx * w;\r\n vNormalY += dy * w;\r\n vNormalZ += dz * w;\r\n numCloseAtoms++;\r\n };\r\n\r\n let maxClosedAtoms = 0;\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n numCloseAtoms = 0;\r\n vNormalX = vNormalY = vNormalZ = 0.0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherNormals);\r\n\r\n maxClosedAtoms = (numCloseAtoms > maxClosedAtoms) ? numCloseAtoms : maxClosedAtoms;\r\n\r\n // normalize vNormal\r\n dist2 = vNormalX * vNormalX + vNormalY * vNormalY + vNormalZ * vNormalZ;\r\n if (numCloseAtoms > 0) {\r\n koef = 1.0 / Math.sqrt(dist2);\r\n vNormalX *= koef;\r\n vNormalY *= koef;\r\n vNormalZ *= koef;\r\n }\r\n normals[i].x = vNormalX;\r\n normals[i].y = vNormalY;\r\n normals[i].z = vNormalZ;\r\n } // for (i) all vertices\r\n\r\n return 0;\r\n }\r\n\r\n /**\r\n * Build vertex colors for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} colors - Colors for output\r\n * @param {number} radiusColorSmoothness - Radius of smoothness sphere\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildColors(numVertices, vertices, colors, radiusColorSmoothness) {\r\n const self = this;\r\n let vx = 0.0;\r\n let vy = 0.0;\r\n let vz = 0.0;\r\n let koef = 0.0;\r\n let w = 0.0;\r\n const KOEF_ADD = 0.8;\r\n\r\n const maxRadAffect = radiusColorSmoothness;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n\r\n let colorsClose = [];\r\n let weights = [];\r\n let weightsSum = 0;\r\n\r\n const gatherColors = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = 1.0 / (KOEF_ADD + koef);\r\n\r\n colorsClose.push([atom.colorX, atom.colorY, atom.colorZ]);\r\n weights.push(w); // save weights for use\r\n weightsSum += w; // calc sum of weights fo further normalization\r\n };\r\n\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n colorsClose = [];\r\n weights = [];\r\n weightsSum = 0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherColors);\r\n\r\n // normalized weighted sum of colors\r\n for (let j = 0; j < colorsClose.length; ++j) {\r\n const weightNormalized = weights[j] / weightsSum;\r\n colors[i].x += colorsClose[j][0] * weightNormalized;\r\n colors[i].y += colorsClose[j][1] * weightNormalized;\r\n colors[i].z += colorsClose[j][2] * weightNormalized;\r\n }\r\n } // for (i) all vertices\r\n return 0;\r\n }\r\n}\r\nexport default IsosurfaceBuildNormals;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for geometry (triangle mesh) representation\r\n *\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices in mesh\r\n * @param {number} maxNumTriangles Maximum possible number of triangles in mesh\r\n * @param {boolean} needVertexColors Obvious\r\n */\r\nclass IsoSurfaceGeo {\r\n constructor(maxNumVertices, maxNumTriangles, needVertexColors) {\r\n this._maxNumVertices = maxNumVertices;\r\n this._maxNumTriangles = maxNumTriangles;\r\n this._vertices = new Array(maxNumVertices);\r\n this._normals = new Array(maxNumVertices);\r\n this._colors = null;\r\n if (needVertexColors) {\r\n this._colors = new Array(maxNumVertices);\r\n }\r\n this._indices = new Array(maxNumTriangles * (1 + 2));\r\n this._numVertices = 0;\r\n this._numTriangles = 0;\r\n\r\n let i;\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._vertices[i] = new THREE.Vector3();\r\n this._normals[i] = new THREE.Vector3();\r\n }\r\n for (i = 0; i < maxNumTriangles * (1 + 2); i++) {\r\n this._indices[i] = -1;\r\n }\r\n if (needVertexColors) {\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._colors[i] = new THREE.Vector3();\r\n }\r\n }\r\n }\r\n\r\n destroy() {\r\n this._vertices = null;\r\n this._normals = null;\r\n this._indices = null;\r\n }\r\n}\r\nexport default IsoSurfaceGeo;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurfaceAtomColored from './IsoSurfaceAtomColored';\r\nimport IsosurfaceBuildNormals from './IsosurfaceBuildNormals';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport IsoSurfaceGeo from './IsoSurfaceGeo';\r\nimport chem from '../../chem';\r\nimport utils from '../../utils';\r\n\r\nconst COLOR_SIZE = 3;\r\nconst HASH_SIZE = 32768;\r\nconst { Element } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass SSIsosurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n // convert geoOut into arrays of positions, indices, normals\r\n this._innerBuild();\r\n const geoOut = this.getGeo();\r\n this.destroy();\r\n this._fromGeo(geoOut);\r\n }\r\n\r\n _fromGeo(geoOut) {\r\n let colors = null;\r\n const positions = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n const normals = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n if (geoOut._colors !== null) {\r\n colors = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n }\r\n const indices = utils.allocateTyped(Uint32Array, (1 + 2) * geoOut._numTriangles);\r\n\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++) {\r\n positions[j + 0] = (geoOut._vertices[i].x);\r\n positions[j + 1] = (geoOut._vertices[i].y);\r\n positions[j + 2] = (geoOut._vertices[i].z);\r\n normals[j + 0] = geoOut._normals[i].x;\r\n normals[j + 1] = geoOut._normals[i].y;\r\n normals[j + 2] = geoOut._normals[i].z;\r\n j += 3;\r\n }\r\n if (colors !== null) {\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++, j += 3) {\r\n colors[j + 0] = geoOut._colors[i].x;\r\n colors[j + 1] = geoOut._colors[i].y;\r\n colors[j + 2] = geoOut._colors[i].z;\r\n }\r\n }\r\n\r\n const numTri3 = geoOut._numTriangles * (1 + 2);\r\n for (let i = 0; i < numTri3; i++) {\r\n indices[i] = geoOut._indices[i];\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(positions, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(colors, 3));\r\n this.computeBoundingBox();\r\n this.computeBoundingSphere();\r\n\r\n geoOut.destroy();\r\n }\r\n\r\n convertToAtomsColored(packedArrays, atomsColored) {\r\n const { atoms, colors } = packedArrays;\r\n for (let i = 0, numAtoms = atoms.length; i < numAtoms; i++) {\r\n const vCenter = atoms[i].position;\r\n const { radius } = atoms[i].element;\r\n atomsColored[i] = new IsoSurfaceAtomColored(vCenter, radius);\r\n const nm = atoms[i].element.number;\r\n atomsColored[i].atomType = this.getType(nm);\r\n let cIdx = COLOR_SIZE * i;\r\n atomsColored[i].colorX = colors[cIdx++];\r\n atomsColored[i].colorY = colors[cIdx++];\r\n atomsColored[i].colorZ = colors[cIdx];\r\n atomsColored[i].srcAtom = atoms[i];\r\n }\r\n }\r\n\r\n getGeo() {\r\n return this.geoOut;\r\n }\r\n\r\n destroy() {\r\n this.atoms = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n }\r\n\r\n /**\r\n * Calculates bounding box for array with spheres (atoms)\r\n *\r\n * @param {Object} atoms Atoms array\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n */\r\n getBoundingBox(atoms, vBoxMin, vBoxMax) {\r\n const bigNum = 10000000.0;\r\n\r\n vBoxMin.x = vBoxMin.y = vBoxMin.z = bigNum;\r\n vBoxMax.x = vBoxMax.y = vBoxMax.z = 0 - bigNum;\r\n\r\n const probeRadius2 = this.probeRadius * this.atomRadiusScale;\r\n let radMax = 0.0;\r\n for (let i = 0, num = atoms.length; i < num; i++) {\r\n const vCenter = atoms[i].coord;\r\n const rad = atoms[i].radius + probeRadius2;\r\n radMax = (rad > radMax) ? rad : radMax;\r\n if (vCenter.x - rad < vBoxMin.x) {\r\n vBoxMin.x = vCenter.x - rad;\r\n }\r\n if (vCenter.y - rad < vBoxMin.y) {\r\n vBoxMin.y = vCenter.y - rad;\r\n }\r\n if (vCenter.z - rad < vBoxMin.z) {\r\n vBoxMin.z = vCenter.z - rad;\r\n }\r\n if (vCenter.x + rad > vBoxMax.x) {\r\n vBoxMax.x = vCenter.x + rad;\r\n }\r\n if (vCenter.y + rad > vBoxMax.y) {\r\n vBoxMax.y = vCenter.y + rad;\r\n }\r\n if (vCenter.z + rad > vBoxMax.z) {\r\n vBoxMax.z = vCenter.z + rad;\r\n }\r\n }\r\n vBoxMin.x -= radMax;\r\n vBoxMin.y -= radMax;\r\n vBoxMin.z -= radMax;\r\n vBoxMax.x += radMax;\r\n vBoxMax.y += radMax;\r\n vBoxMax.z += radMax;\r\n }\r\n\r\n /**\r\n * Calculate (x,y,z) cordinate of the cell corner point\r\n *\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {number} x Cell integer x coordinate\r\n * @param {number} y Cell integer y coordinate\r\n * @param {number} z Cell integer z coordinate\r\n * @param {number} numPoints NUm points in cell on side\r\n * @param {Vector3} vOut Output vector\r\n */\r\n getCornerCoord(vBoxMin, vBoxMax, x, y, z, numPoints, vOut) {\r\n const invNP = 1.0 / (numPoints - 1.0);\r\n const tx = x * invNP;\r\n const ty = y * invNP;\r\n const tz = z * invNP;\r\n\r\n vOut.x = vBoxMin.x * (1.0 - tx) + vBoxMax.x * tx;\r\n vOut.y = vBoxMin.y * (1.0 - ty) + vBoxMax.y * ty;\r\n vOut.z = vBoxMin.z * (1.0 - tz) + vBoxMax.z * tz;\r\n }\r\n\r\n /**\r\n * Calculate point of intersection of sphere surface\r\n * and cell edge, given by [indexA, indexB] line\r\n *\r\n * @param {number} indexA Cell vertex index in [0..11]\r\n * @param {number} indexB Cell vertex index in [0..11]\r\n * @param {array} sign Sign array for all 8 vertices\r\n * @param {object} cube Cube\r\n * @param {number} indexPointValue for value placement\r\n * @param {Vector3} vOut Point of intersection\r\n */\r\n buildEdgePoint(indexA, indexB, sign, cube, indexPointValue, vOut) {\r\n if (sign[indexA] ^ sign[indexB]) {\r\n const cTwentyFour = 24;\r\n const t = (0 - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA])\r\n / (cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexB]\r\n - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA]);\r\n const xa = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 0];\r\n const ya = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 1];\r\n const za = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 2];\r\n const xb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 0];\r\n const yb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 1];\r\n const zb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 2];\r\n\r\n vOut.x = xa * (1.0 - t) + xb * t;\r\n vOut.y = ya * (1.0 - t) + yb * t;\r\n vOut.z = za * (1.0 - t) + zb * t;\r\n }\r\n }\r\n\r\n /**\r\n * Check if triangle is visible (vertices are close to atoms included in visibility set)\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} true if triangle is visible\r\n */\r\n isTriangleVisible(v0, v1, v2) {\r\n const a0 = this.voxelWorld.getClosestAtom(v0);\r\n const a1 = this.voxelWorld.getClosestAtom(v1);\r\n const a2 = this.voxelWorld.getClosestAtom(v2);\r\n if (a0 === null || a1 === null || a2 === null\r\n || a0.srcAtom === null || a1.srcAtom === null || a2.srcAtom === null) {\r\n return false;\r\n }\r\n\r\n return this.visibilitySelector.includesAtom(a0.srcAtom)\r\n && this.visibilitySelector.includesAtom(a1.srcAtom)\r\n && this.visibilitySelector.includesAtom(a2.srcAtom);\r\n }\r\n\r\n /**\r\n * Add triangle to result geometry\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} false if no more triangles can be added\r\n */\r\n addTriangle(v0, v1, v2) {\r\n if (this.visibilitySelector && !this.isTriangleVisible(v0, v1, v2)) {\r\n return true;\r\n }\r\n\r\n const geo = this.geoOut;\r\n\r\n if (geo._numTriangles >= this.maxNumTriangles) {\r\n return false;\r\n }\r\n\r\n // Add vertex with optimize\r\n const indInGeo0 = this.addVertexToGeo(geo, v0);\r\n const indInGeo1 = this.addVertexToGeo(geo, v1);\r\n const indInGeo2 = this.addVertexToGeo(geo, v2);\r\n if ((indInGeo0 | indInGeo1 | indInGeo2) < 0) {\r\n return false;\r\n }\r\n\r\n const itr = 3 * geo._numTriangles;\r\n geo._indices[itr + 0] = indInGeo0;\r\n geo._indices[itr + 1] = indInGeo1;\r\n geo._indices[itr + 2] = indInGeo2;\r\n geo._numTriangles++;\r\n return true;\r\n }\r\n\r\n /**\r\n * Build result geometry (triangle mesh) from marching cube cells\r\n *\r\n * @param {number} meshRes Marchnig cube vertex count on each side\r\n * @param {Vector3} vBoxMin Bounding box point min\r\n * @param {Vector3} vBoxMax Bounding box point max\r\n * @param {number} corners float values array for each cube point\r\n * @param {Vector3} vCellStep vector to next cube cell diagonal point\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} 0, if success (<0) is error\r\n */\r\n buildGeoFromCorners(meshRes, vBoxMin, vBoxMax, corners, vCellStep, cube) {\r\n const arrSize = 12;\r\n const cNumVerts = 8;\r\n const numCells = meshRes - 1;\r\n const side = meshRes;\r\n const side2 = meshRes * meshRes;\r\n\r\n const vaEdges = new Array(arrSize);\r\n for (let i = 0; i < arrSize; i++) {\r\n vaEdges[i] = new THREE.Vector3();\r\n }\r\n const sign = [];\r\n for (let i = 0; i < cNumVerts; i++) {\r\n sign[i] = 1.0;\r\n }\r\n const vCorner = new THREE.Vector3();\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n if (!cube.hasIntersection[indCell]) {\r\n // next cell\r\n indCell++;\r\n continue;\r\n }\r\n const bitsInside = cube.bitsInside[indCell];\r\n\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, meshRes, vCorner);\r\n\r\n const indPointValues = indCell * (2 << (2 + 2));\r\n for (let i = 0, j = 0; i < cNumVerts; i++) {\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.x;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.y;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.z;\r\n }\r\n\r\n cube.pointsValuesLinear[indPointValues + 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 2 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3] += vCellStep.x;\r\n\r\n cube.pointsValuesLinear[indPointValues + 2 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 3 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 2] += vCellStep.z;\r\n\r\n cube.pointsValuesLinear[indPointValues + 4 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 1] += vCellStep.y;\r\n\r\n // now current cell has intersections (from -x to +x) on some cube edges\r\n const indValues = indPointValues + 24;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n sign[i] = (cube.pointsValuesLinear[indValues + i] < 0.0) ? 1 : 0;\r\n }\r\n\r\n this.buildEdgePoint(0, 1, sign, cube, indPointValues, vaEdges[0]);\r\n this.buildEdgePoint(1, 2, sign, cube, indPointValues, vaEdges[1]);\r\n this.buildEdgePoint(2, 3, sign, cube, indPointValues, vaEdges[2]);\r\n this.buildEdgePoint(3, 0, sign, cube, indPointValues, vaEdges[3]);\r\n\r\n this.buildEdgePoint(4, 5, sign, cube, indPointValues, vaEdges[4]);\r\n this.buildEdgePoint(5, 6, sign, cube, indPointValues, vaEdges[5]);\r\n this.buildEdgePoint(6, 7, sign, cube, indPointValues, vaEdges[6]);\r\n this.buildEdgePoint(7, 4, sign, cube, indPointValues, vaEdges[7]);\r\n\r\n this.buildEdgePoint(0, 4, sign, cube, indPointValues, vaEdges[8]);\r\n this.buildEdgePoint(1, 5, sign, cube, indPointValues, vaEdges[9]);\r\n this.buildEdgePoint(2, 6, sign, cube, indPointValues, vaEdges[10]);\r\n this.buildEdgePoint(3, 7, sign, cube, indPointValues, vaEdges[11]);\r\n\r\n const offs = bitsInside * (2 << (1 + 2));\r\n for (let numTri = 0, indTri = 0; numTri < (2 + 2 + 2); numTri++, indTri += 3) {\r\n // s_triIndicesMarchCube is external array, defined in mold_ind.js\r\n const i0 = cube.striIndicesMarchCube[offs + indTri];\r\n if (i0 < 0) {\r\n break;\r\n }\r\n const i1 = cube.striIndicesMarchCube[offs + indTri + 1];\r\n const i2 = cube.striIndicesMarchCube[offs + indTri + 2];\r\n\r\n if (!this.addTriangle(vaEdges[i0], vaEdges[i1], vaEdges[i2])) {\r\n return 0 - 2;\r\n }\r\n } // for numTri\r\n\r\n // next cell (cube)\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return 0;\r\n }\r\n\r\n /**\r\n * Returns number of cell with intersection with at least one sphere.\r\n * Using this number, we can estimate required number of vertices\r\n * and triangles to build result mesh.\r\n *\r\n * @param {number} side Number of points in cube voxels\r\n * @param {number} numCells Number of cells in cube voxels (per direction)\r\n * @param {array} corners Array of float values for cube corner points\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} numIntersectedCells\r\n */\r\n getNumIntersectedCells(side, numCells, corners, cube) {\r\n const side2 = side * side;\r\n const cNumVerts = 8;\r\n let numIntersectedCells = 0;\r\n\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n const cubeValuesIndex = indCell * (2 << (2 + 2)) + 24;\r\n const indCorner = x + indZ + indY;\r\n\r\n cube.pointsValuesLinear[cubeValuesIndex] = corners[indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 1] = corners[indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 2] = corners[indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 3] = corners[indCorner + side];\r\n cube.pointsValuesLinear[cubeValuesIndex + 4] = corners[side2 + indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 5] = corners[side2 + indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 6] = corners[side2 + indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 7] = corners[side2 + indCorner + side];\r\n\r\n // check read exception\r\n // assert(side2 + indCorner + side + 1 < side3);\r\n\r\n // get bit flags inside\r\n let bitsInside = 0;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n if (cube.pointsValuesLinear[cubeValuesIndex + i] < 0.0) {\r\n bitsInside |= (1 << i);\r\n }\r\n }\r\n\r\n if ((bitsInside === 0) || (bitsInside === ((1 << cNumVerts) - 1))) {\r\n cube.hasIntersection[indCell] = false;\r\n } else {\r\n cube.hasIntersection[indCell] = true;\r\n numIntersectedCells++;\r\n }\r\n cube.bitsInside[indCell] = bitsInside;\r\n // next cell\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return numIntersectedCells;\r\n }\r\n\r\n getType(letter) {\r\n /* eslint-disable no-magic-numbers */\r\n const atomT = [0, 0, 1, 1, 2, 6, 3, 6, 4, 6, 5, 6, 6, 0, 7, 3, 8, 2, 9, 6, 10, 6, 11, 6, 12, 6, 13, 6, 14, 6, 15, 4,\r\n 16, 5, 17, 6, 18, 6, 19, 6, 20, 6, 21, 6, 22, 6, 23, 6, 24, 6, 25, 6, 26, 6, 27, 6, 28, 6, 29, 6, 30, 6, 31, 6,\r\n 32, 6, 33, 6, 34, 6, 35, 6, 36, 6, 37, 6, 38, 6, 39, 6, 40, 6, 41, 6, 42, 6, 43, 6, 44, 6, 45, 6, 46, 6, 47, 6,\r\n 48, 6, 49, 6, 50, 6, 51, 6, 52, 6, 53, 6, 54, 6, 55, 6, 56, 6, 57, 6, 58, 6, 59, 6, 60, 6, 61, 6, 62, 6, 63, 6,\r\n 64, 6, 65, 6, 66, 6, 67, 6, 68, 6, 69, 6, 70, 6, 71, 6, 72, 6, 73, 6, 74, 6, 75, 6, 76, 6, 77, 6, 78, 6, 79, 6,\r\n 80, 6, 81, 6, 82, 6, 83, 6, 84, 6, 85, 6, 86, 6, 87, 6, 88, 6, 89, 6, 90, 6, 91, 6, 92, 6, 93, 6, 94, 6, 95, 6,\r\n 96, 6, 97, 6, 98, 6, 99, 6, 100, 6, 101, 6, 102, 6, 103, 6, 104, 6, 105, 6, 106, 6, 107, 6, 108, 6, 109, 6];\r\n /* eslint-enable no-magic-numbers */\r\n\r\n if (letter < 1 || letter > atomT.length / 2\r\n || (Object.keys(Element.ByAtomicNumber).length * 2) !== atomT.length) {\r\n throw new Error('atomT.length should be equal Element.ByAtomicNumber.length * 2');\r\n }\r\n return atomT[letter * 2];\r\n }\r\n\r\n /**\r\n * Calculate values for marching cube grid points\r\n * positive values are outside sphere, negative - is inside\r\n *\r\n * @param {array} corners array of float values\r\n * @param {number} side Number of point in cube in 1 dimennsion\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {array} atoms Array of input atoms\r\n * @param {number} probeRad radius for atom probing\r\n */\r\n calculateGridCorners(corners, side, vBoxMin, vBoxMax, atoms, probeRad) {\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const vCorner = new THREE.Vector3();\r\n const vDif = new THREE.Vector3();\r\n /* eslint-disable no-magic-numbers */\r\n const aLot = +1.0e12;\r\n /* eslint-enable no-magic-numbers */\r\n\r\n for (let i = 0; i < side3; i++) {\r\n corners[i] = aLot; // to large value\r\n }\r\n\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n for (let s = 0, numAtoms = atoms.length; s < numAtoms; s++) {\r\n const atom = atoms[s];\r\n const radius = atom.radius + probeRad;\r\n\r\n const fx = ((atom.coord.x - radius) - vBoxMin.x) * xScale;\r\n const fy = ((atom.coord.y - radius) - vBoxMin.y) * yScale;\r\n const fz = ((atom.coord.z - radius) - vBoxMin.z) * zScale;\r\n\r\n const indXMin = Math.floor(fx);\r\n const indYMin = Math.floor(fy);\r\n const indZMin = Math.floor(fz);\r\n\r\n let indXMax = Math.floor(((atom.coord.x + radius) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((atom.coord.y + radius) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((atom.coord.z + radius) - vBoxMin.z) * zScale);\r\n\r\n indXMax++;\r\n indYMax++;\r\n indZMax++;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let y = indYMin; y <= indYMax; y++) {\r\n const indY = y * side2;\r\n for (let z = indZMin; z <= indZMax; z++) {\r\n const indZ = z * side;\r\n for (let x = indXMin; x <= indXMax; x++) {\r\n const ind = indY + indZ + x;\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, side, vCorner);\r\n vDif.x = vCorner.x - atom.coord.x;\r\n vDif.y = vCorner.y - atom.coord.y;\r\n vDif.z = vCorner.z - atom.coord.z;\r\n const distToSphere = Math.sqrt(vDif.x * vDif.x + vDif.y * vDif.y + vDif.z * vDif.z);\r\n // val: < 0, if inside sphere\r\n // val: > 0, if outside sphere\r\n const val = distToSphere - radius;\r\n if (val < corners[ind]) {\r\n corners[ind] = val;\r\n }\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n } // for (s)\r\n }\r\n\r\n /**\r\n * Create memory pool for vertex hash management\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices (that will be build)\r\n * @param {number} maxNumTriangles Maximum possible number of triangles (that will be build)\r\n * @returns {number} 0, if success. (<0) is non memory\r\n */\r\n createVertexHash(maxNumVertices, maxNumTriangles) {\r\n this.hashLines = utils.allocateTyped(Int32Array, HASH_SIZE * 2);\r\n if (this.hashLines === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < HASH_SIZE; i++) {\r\n this.hashLines[j++] = 0; // num vertices in this hash line\r\n this.hashLines[j++] = 0 - 1; // index of the first entry\r\n }\r\n\r\n this.maxNumVertices = maxNumVertices;\r\n this.maxNumTriangles = maxNumTriangles;\r\n\r\n this.numHashEtriesAllocated = maxNumVertices;\r\n this.hashEntries = utils.allocateTyped(Int32Array, 2 * this.numHashEtriesAllocated);\r\n if (this.hashEntries === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < this.numHashEtriesAllocated; i++) {\r\n this.hashEntries[j++] = 0 - 1; // index of vertex\r\n this.hashEntries[j++] = 0 - 1; // next hash entry index\r\n }\r\n this.numHashEntryIndex = 0;\r\n return 0;\r\n }\r\n\r\n /**\r\n * Allocate and return new hash entry. Just check possible amount.\r\n *\r\n * @returns {number} index of hash entry, that can be used for geometry add vertex functionality\r\n */\r\n getNewHashEntry() {\r\n if (this.numHashEntryIndex < this.numHashEtriesAllocated) {\r\n const i = this.numHashEntryIndex;\r\n this.numHashEntryIndex++;\r\n return i;\r\n }\r\n return 0 - 1;\r\n }\r\n\r\n /**\r\n * Add vertex to geometry structure\r\n * using vertex hash table to quickly check, is this vertex already exist in geometry\r\n *\r\n * @param {object} geoOut Geometry to build\r\n * @param {Vector3} vAdd Vertex to add\r\n * @returns {number} index of added (or existing) vertex in geometry.\r\n */\r\n addVertexToGeo(geoOut, vAdd) {\r\n let entry;\r\n const oneHynberes = 0.01;\r\n const n815851 = 815851;\r\n const n37633 = 37633;\r\n const n2453543 = 2453543;\r\n const r106 = 1.0e-6;\r\n\r\n const hashResolution = this.marCubeResoultion << 2;\r\n const v = new THREE.Vector3();\r\n const ix = Math.floor(hashResolution * (vAdd.x - this.vBoxMin.x) / (this.vBoxMax.x + oneHynberes - this.vBoxMin.x));\r\n const iy = Math.floor(hashResolution * (vAdd.y - this.vBoxMin.y) / (this.vBoxMax.y + oneHynberes - this.vBoxMin.y));\r\n const iz = Math.floor(hashResolution * (vAdd.z - this.vBoxMin.z) / (this.vBoxMax.z + oneHynberes - this.vBoxMin.z));\r\n let iHash = ix * n815851 + iz * n37633 + iy * n2453543;\r\n iHash &= (HASH_SIZE - 1);\r\n const hLineIndex = iHash + iHash;\r\n\r\n // search vertex via hash\r\n // search in hash list\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n for (entry = this.hashLines[hLineIndex + 1]; entry >= 0; entry = this.hashEntries[entry * 2 + 1]) {\r\n const ind = this.hashEntries[entry * 2 + 0]; // vertex index\r\n v.copy(geoOut._vertices[ind]);\r\n v.x -= vAdd.x;\r\n v.y -= vAdd.y;\r\n v.z -= vAdd.z;\r\n const dot2 = v.x * v.x + v.y * v.y + v.z * v.z;\r\n if (dot2 < r106) {\r\n return ind;\r\n } // if (found)\r\n } // for (entry)\r\n } // search\r\n\r\n // add new vertex to geometry\r\n if (geoOut._numVertices >= this.maxNumVertices) {\r\n return 0 - 1;\r\n }\r\n\r\n const iVertAdd = geoOut._numVertices;\r\n geoOut._vertices[iVertAdd].copy(vAdd);\r\n\r\n // add to hash\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n entry = this.getNewHashEntry();\r\n if (entry < 0) {\r\n return 0 - 1;\r\n }\r\n const entryFirst = this.hashLines[hLineIndex + 1];\r\n this.hashLines[hLineIndex + 1] = entry;\r\n this.hashEntries[entry * 2 + 0] = iVertAdd;\r\n this.hashEntries[entry * 2 + 1] = entryFirst;\r\n\r\n this.hashLines[hLineIndex + 0]++; // num vertices in line ++\r\n }\r\n geoOut._numVertices++;\r\n return iVertAdd;\r\n }\r\n\r\n /**\r\n *\r\n * @param {number} side some placeholder description\r\n * @param {number} probeSphereRadius some placeholder description\r\n * @param {object} vBoxMin some placeholder description\r\n * @param {object} vBoxMax some placeholder description\r\n * @param {object} geoOut some placeholder description\r\n * @param {object} corners some placeholder description\r\n * @returns {number} always 0\r\n */\r\n modifyExcludedFromGeo(\r\n side,\r\n probeSphereRadius,\r\n vBoxMin,\r\n vBoxMax,\r\n geoOut,\r\n corners,\r\n ) {\r\n let ind;\r\n let distToSphere;\r\n let distToBorder;\r\n const r11 = 1.1;\r\n\r\n function innerBlockWorkAround() {\r\n if (distToBorder > 0.0) {\r\n // point is inside probe sphere\r\n if (corners[ind] < 0.0) {\r\n corners[ind] = distToBorder; // was inside surface, now is oustide ( > 0)\r\n }\r\n if (distToBorder > corners[ind]) {\r\n corners[ind] = distToBorder; // find positive maximum\r\n }\r\n } else if (distToBorder > corners[ind]) { // point is outside sphere\r\n corners[ind] = distToBorder; // find negative maximum\r\n }\r\n }\r\n\r\n const side2 = side * side;\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n const probeSpRad2 = (probeSphereRadius * 2) * (probeSphereRadius * 2);\r\n const sideInv = 1.0 / (side - 1);\r\n\r\n for (let i = 0; i < geoOut._numVertices; i++) {\r\n const vCenter = geoOut._vertices[i];\r\n\r\n const radEst = probeSphereRadius * r11;\r\n\r\n let indXMin = Math.floor(((vCenter.x - radEst) - vBoxMin.x) * xScale);\r\n let indYMin = Math.floor(((vCenter.y - radEst) - vBoxMin.y) * yScale);\r\n let indZMin = Math.floor(((vCenter.z - radEst) - vBoxMin.z) * zScale);\r\n\r\n let indXMax = Math.floor(((vCenter.x + radEst) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((vCenter.y + radEst) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((vCenter.z + radEst) - vBoxMin.z) * zScale);\r\n\r\n indXMin = (indXMin >= 0) ? indXMin : 0;\r\n indYMin = (indYMin >= 0) ? indYMin : 0;\r\n indZMin = (indZMin >= 0) ? indZMin : 0;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let iy = indYMin; iy <= indYMax; iy++) {\r\n const indY = iy * side2;\r\n for (let iz = indZMin; iz <= indZMax; iz++) {\r\n const indZ = iz * side;\r\n for (let ix = indXMin; ix <= indXMax; ix++) {\r\n ind = indY + indZ + ix;\r\n // getCornerCoord(vBoxMin, vBoxMax, ix, iy, iz, side, &vCorner);\r\n let t = ix * sideInv;\r\n const xCorner = vBoxMin.x * (1.0 - t) + vBoxMax.x * t;\r\n t = iy * sideInv;\r\n const yCorner = vBoxMin.y * (1.0 - t) + vBoxMax.y * t;\r\n t = iz * sideInv;\r\n const zCorner = vBoxMin.z * (1.0 - t) + vBoxMax.z * t;\r\n\r\n const dx = xCorner - vCenter.x;\r\n const dy = yCorner - vCenter.y;\r\n const dz = zCorner - vCenter.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 < probeSpRad2) {\r\n distToSphere = Math.sqrt(dist2);\r\n distToBorder = -(distToSphere - probeSphereRadius);\r\n innerBlockWorkAround();\r\n } // if (dist from corner point to sphere center more 2 radiuses)\r\n } // for (ix)\r\n } // for (iz)\r\n } // for (iy)\r\n } // for (i) all geo vertices\r\n return 0;\r\n }\r\n\r\n _innerBuild() {\r\n let ok;\r\n const expandFactor = 1.2;\r\n\r\n // performance test\r\n // this.performanceTest();\r\n\r\n // Create temporary atoms (but colored)\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n this.complex = this._opts.parent;\r\n this.atoms = packedArrays.atoms;\r\n this.meshResolution = this._opts.gridSpacing;\r\n this.atomRadiusScale = this._opts.radScale;\r\n this.colorMode = this._opts.colorMode;\r\n this.probeRadius = this._opts.probeRadius;\r\n this.useVertexColors = true;\r\n this.excludeProbe = this._opts.excludeProbe;\r\n this.visibilitySelector = this._opts.visibilitySelector;\r\n\r\n this.geoOut = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n this.numHashEtriesAllocated = 0;\r\n this.numHashEntryIndex = 0;\r\n this.maxNumVertices = 0;\r\n this.maxNumTriangles = 0;\r\n\r\n const atomsColored = new Array(this.atoms.length);\r\n this.convertToAtomsColored(packedArrays, atomsColored);\r\n\r\n // find bbox for spheres scene\r\n const vBoxMin = this.vBoxMin = new THREE.Vector3();\r\n const vBoxMax = this.vBoxMax = new THREE.Vector3();\r\n this.getBoundingBox(atomsColored, vBoxMin, vBoxMax);\r\n\r\n const marCubeResoultion = this.marCubeResoultion = this.meshResolution * (2 + 2);\r\n\r\n // build grid corners for Marching cube algorithm\r\n const side = marCubeResoultion;\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const corners = utils.allocateTyped(Float32Array, side3);\r\n const rProbeRadius = this.probeRadius * this.atomRadiusScale;\r\n\r\n this.calculateGridCorners(corners, side, vBoxMin, vBoxMax, atomsColored, rProbeRadius);\r\n\r\n const numCells = marCubeResoultion - 1;\r\n const cube = new IsoSurfaceMarchCube();\r\n ok = cube.create(numCells);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // copy corners to cells\r\n const vCellStep = new THREE.Vector3();\r\n vCellStep.x = (vBoxMax.x - vBoxMin.x) / numCells;\r\n vCellStep.y = (vBoxMax.y - vBoxMin.y) / numCells;\r\n vCellStep.z = (vBoxMax.z - vBoxMin.z) / numCells;\r\n\r\n let numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n let maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n let maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n\r\n // build voxel world (used to check triangle-to-atom tie and to calculate normals and colors)\r\n let probeRadForNormalsColors = rProbeRadius;\r\n if (this.excludeProbe) {\r\n probeRadForNormalsColors = 0.01;\r\n }\r\n this.voxelWorld = new IsosurfaceBuildNormals(\r\n atomsColored.length,\r\n atomsColored,\r\n vBoxMin,\r\n vBoxMax,\r\n probeRadForNormalsColors,\r\n );\r\n this.voxelWorld.createVoxels();\r\n\r\n ok = this.buildGeoFromCorners(marCubeResoultion, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n if (this.excludeProbe) {\r\n // using 3d mesh (geoOut) as a surface points\r\n // move probe sphere and try to minimuze corners values\r\n this.modifyExcludedFromGeo(side, rProbeRadius, vBoxMin, vBoxMax, this.geoOut, corners);\r\n\r\n // delete old builded geo\r\n this.geoOut._vertices = null;\r\n this.geoOut._colors = null;\r\n this.geoOut._indices = null;\r\n this.geoOut._normals = null;\r\n this.geoOut._numVertices = 0;\r\n this.geoOut._numTriangles = 0;\r\n this.geoOut = null;\r\n\r\n // estimage geo vertices budget again\r\n numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n // creates empty new geometry\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // build vertices and triangles from corners values\r\n ok = this.buildGeoFromCorners(side, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n }\r\n\r\n // build vertex normals\r\n this.voxelWorld.buildNormals(this.geoOut._vertices.length, this.geoOut._vertices, this.geoOut._normals);\r\n // More value : more smooth color mixing\r\n // value about 0.7: very rough colors borders\r\n let radiusColorSmoothness = 6.5;\r\n if (this.excludeProbe) {\r\n radiusColorSmoothness -= 1.5;\r\n }\r\n if (this.useVertexColors) {\r\n this.voxelWorld.buildColors(\r\n this.geoOut._vertices.length,\r\n this.geoOut._vertices,\r\n this.geoOut._colors,\r\n radiusColorSmoothness,\r\n );\r\n }\r\n this.voxelWorld.destroyVoxels();\r\n this.voxelWorld = null;\r\n\r\n // remove objects\r\n cube.destroy();\r\n\r\n return ok;\r\n }\r\n}\r\n\r\n// All code below must be erased from every device and each developer's memory\r\n\r\nexport default SSIsosurfaceGeometry;\r\n","import * as THREE from 'three';\r\nimport EventDispatcher from '../../utils/EventDispatcher';\r\n\r\nfunction createLabel(fieldTxt, className) {\r\n const text = document.createElement('div');\r\n text.className = className;\r\n\r\n if (typeof fieldTxt === 'string') {\r\n const spanText = document.createElement('span');\r\n spanText.style.fontSize = '150%';\r\n const strings = fieldTxt.split('\\n');\r\n\r\n for (let i = 0, n = strings.length; i < n; ++i) {\r\n const spanNodeP = document.createElement('span');\r\n const spanNodeText = document.createTextNode(strings[i]);\r\n spanNodeP.appendChild(spanNodeText);\r\n spanText.appendChild(spanNodeP);\r\n if (i < n - 1) {\r\n spanText.appendChild(document.createElement('br'));\r\n }\r\n }\r\n\r\n text.appendChild(spanText);\r\n } else {\r\n text.appendChild(fieldTxt);\r\n }\r\n text.worldPos = new THREE.Vector3();\r\n return text;\r\n}\r\nclass LabelsGeometry extends EventDispatcher {\r\n constructor(instanceCount, opts) {\r\n super();\r\n this._opts = opts;\r\n this.items = [];\r\n this.needsUpdate = false;\r\n\r\n let xTranslation = -50;\r\n let yTranslation = -50;\r\n switch (opts.horizontalAlign) {\r\n case 'left':\r\n xTranslation = 0;\r\n break;\r\n case 'right':\r\n xTranslation = -100;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n switch (opts.verticalAlign) {\r\n case 'top':\r\n yTranslation = -100;\r\n break;\r\n case 'bottom':\r\n yTranslation = 0;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n const deltaPos = new THREE.Vector3(opts.dx || 0, opts.dy || 0, opts.dz || 0);\r\n this.userData = {\r\n translation: `translate(${xTranslation}%, ${yTranslation}%)`,\r\n offset: deltaPos,\r\n };\r\n }\r\n\r\n setItem(itemIdx, itemPos, fieldTxt) {\r\n const opts = this._opts;\r\n const text = this.items[itemIdx] || createLabel(fieldTxt, 'label');\r\n\r\n text.worldPos.copy(itemPos);\r\n text.style.textAlign = opts.horizontalAlign;\r\n text.style.verticalAlign = opts.verticalAlign;\r\n this.items[itemIdx] = text;\r\n }\r\n\r\n setColor(itemIdx, fColor, bColor) {\r\n const text = this.items[itemIdx];\r\n text.opts = {\r\n color: fColor,\r\n background: bColor,\r\n };\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.needsUpdate = true;\r\n this.dispatchEvent({ type: 'update' });\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n }\r\n\r\n // unimplemented functions\r\n raycast() {\r\n }\r\n\r\n setOpacity() {\r\n\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\n\r\nexport default LabelsGeometry;\r\n","import InstancedSpheresGeometry from './InstancedSpheresGeometry';\r\nimport SimpleSpheresGeometry from './SimpleSpheresGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport Instanced2CCylindersGeometry from './Instanced2CCylindersGeometry';\r\nimport ExtrudedObjectsGeometry from './ExtrudedObjectsGeometry';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport TwoColorLinesGeometry from './TwoColorLinesGeometry';\r\nimport CrossGeometry from './CrossGeometry';\r\nimport QuickSurfGeometry from './QuickSurfGeometry';\r\nimport ContactSurfaceGeometry from './ContactSurfaceGeometry';\r\nimport SSIsosurfaceGeometry from './SSIsosurfaceGeometry';\r\nimport LabelsGeometry from './LabelsGeometry';\r\n\r\nexport default {\r\n InstancedSpheresGeometry,\r\n SimpleSpheresGeometry,\r\n Simple2CCylindersGeometry,\r\n Instanced2CCylindersGeometry,\r\n ExtrudedObjectsGeometry,\r\n ChunkedLinesGeometry,\r\n TwoColorLinesGeometry,\r\n CrossGeometry,\r\n QuickSurfGeometry,\r\n ContactSurfaceGeometry,\r\n SSIsosurfaceGeometry,\r\n LabelsGeometry,\r\n};\r\n","export default {\r\n\r\n precision: 'mediump',\r\n\r\n /**\r\n *\r\n * @param {THREE.WebGLRenderer} renderer\r\n */\r\n init(renderer) {\r\n this.precision = renderer.capabilities.getMaxPrecision('highp');\r\n },\r\n};\r\n","import * as THREE from 'three';\r\n\r\nconst noiseWidth = 4;\r\nconst noiseHeight = 4;\r\nconst _noiseData = new Uint8Array([\r\n 24, 52, 0, 255, 254, 145, 0, 255, 122, 0, 0, 255, 7, 170, 0, 255,\r\n 34, 214, 0, 255, 173, 8, 0, 255, 86, 249, 0, 255, 160, 4, 0, 255,\r\n 226, 46, 0, 255, 224, 211, 0, 255, 3, 157, 0, 255, 174, 247, 0, 255,\r\n 12, 182, 0, 255, 220, 216, 0, 255, 1, 109, 0, 255, 253, 154, 0, 255,\r\n]);\r\nconst _noiseWrapS = THREE.RepeatWrapping;\r\nconst _noiseWrapT = THREE.RepeatWrapping;\r\nconst _noiseMinFilter = THREE.NearestFilter;\r\nconst _noiseMagFilter = THREE.NearestFilter;\r\nconst _noiseMapping = THREE.UVMapping;\r\nconst noiseTexture = new THREE.DataTexture(\r\n _noiseData,\r\n noiseWidth,\r\n noiseHeight,\r\n THREE.RGBAFormat,\r\n THREE.UnsignedByteType,\r\n _noiseMapping,\r\n _noiseWrapS,\r\n _noiseWrapT,\r\n _noiseMagFilter,\r\n _noiseMinFilter,\r\n 1,\r\n);\r\nnoiseTexture.needsUpdate = true;\r\n\r\nexport default {\r\n noiseWidth,\r\n noiseHeight,\r\n noiseTexture,\r\n};\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './Uber.vert';\r\nimport fragmentShader from './Uber.frag';\r\nimport capabilities from '../capabilities';\r\nimport noise from '../noiseTexture';\r\n\r\n// Length of _samplesKernel is used in Uber.frag\r\n// If you want to change length of _samplesKernel, please, remember change it in Uber.frag too.\r\n// You can easy find places for replace using word:_samplesKernel\r\nconst _samplesKernel = [\r\n new THREE.Vector2(-0.541978, 0.840393),\r\n new THREE.Vector2(0.125533, -0.992089),\r\n new THREE.Vector2(0.374329, 0.927296),\r\n new THREE.Vector2(-0.105475, 0.994422),\r\n];\r\n\r\nconst defaultUniforms = THREE.UniformsUtils.merge([\r\n\r\n THREE.UniformsLib.fog,\r\n THREE.UniformsLib.lights,\r\n\r\n {\r\n // are updated automatically by three.js (see THREE.ShaderLib.common)\r\n diffuse: { value: new THREE.Color(0xeeeeee) },\r\n opacity: { value: 1.0 },\r\n\r\n specular: { type: 'c', value: new THREE.Color(0x111111) },\r\n shininess: { type: 'f', value: 30 },\r\n fixedColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n zOffset: { type: 'f', value: 0.0 },\r\n zClipValue: { type: 'f', value: 0.0 },\r\n clipPlaneValue: { type: 'f', value: 0.0 },\r\n nearPlaneValue: { type: 'f', value: -0.5 },\r\n invModelViewMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n world2colorMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n dashedLineSize: { type: 'f', value: 0.1 },\r\n dashedLinePeriod: { type: 'f', value: 0.2 },\r\n projMatrixInv: { type: '4fv', value: new THREE.Matrix4() },\r\n viewport: { type: 'v2', value: new THREE.Vector2() },\r\n lineWidth: { type: 'f', value: 2.0 },\r\n // default value must be the same as settings\r\n fogAlpha: { type: 'f', value: 1.0 },\r\n samplesKernel: { type: 'v2v', value: null },\r\n noiseTex: { type: 't', value: null },\r\n noiseTexelSize: { type: 'v2', value: null },\r\n srcTexelSize: { type: 'v2', value: null },\r\n },\r\n\r\n]);\r\n\r\nconst uberOptionNames = [\r\n 'shininess',\r\n 'opacity',\r\n 'zOffset',\r\n 'diffuse',\r\n 'specular',\r\n 'fixedColor',\r\n 'zClipCoef',\r\n 'zClipValue',\r\n 'clipPlaneValue',\r\n 'world2colorMatrix',\r\n 'dashedLineSize',\r\n 'dashedLinePeriod',\r\n 'projMatrixInv',\r\n 'viewport',\r\n 'lineWidth',\r\n 'fogAlpha',\r\n 'samplesKernel',\r\n 'noiseTex',\r\n 'noiseTexelSize',\r\n 'srcTexelSize',\r\n];\r\n\r\n// properties that convert to uniforms\r\nconst uberOptions = {\r\n diffuse: new THREE.Color(0xffffff), // used in phong lighting\r\n specular: new THREE.Color(0x111111), // used in phong lighting\r\n shininess: 30, // used in phong lighting\r\n opacity: 1, // set mesh opacity\r\n fixedColor: new THREE.Color(0xffffff), // color to override (see OVERRIDE_COLOR)\r\n zOffset: 0.0, // used fo zsprites (see SPHERE_SPRITE CYLINDER_SPRITE)\r\n zClipCoef: 2.0, // use for Surfs clipping (mesh param, isn't used in shader) FIXME move to representation param\r\n zClipValue: 0.0, // value to clip Surfs in shader (see ZCLIP)\r\n clipPlaneValue: 0.0, // value to clip scene globally (see CLIPPLANE)\r\n world2colorMatrix: new THREE.Matrix4(),\r\n dashedLineSize: 0.1,\r\n dashedLinePeriod: 0.3,\r\n projMatrixInv: new THREE.Matrix4(),\r\n viewport: new THREE.Vector2(800, 600),\r\n lineWidth: 2.0,\r\n fogAlpha: 1.0,\r\n samplesKernel: _samplesKernel,\r\n noiseTex: noise.noiseTexture,\r\n noiseTexelSize: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight),\r\n srcTexelSize: new THREE.Vector2(1.0 / 800.0, 1.0 / 600.0),\r\n copy(source) {\r\n this.diffuse.copy(source.diffuse);\r\n this.specular.copy(source.specular);\r\n this.shininess = source.shininess;\r\n this.opacity = source.opacity;\r\n this.fixedColor.copy(source.fixedColor);\r\n this.zOffset = source.zOffset;\r\n this.zClipCoef = source.zClipCoef;\r\n this.zClipValue = source.zClipValue;\r\n this.clipPlaneValue = source.clipPlaneValue;\r\n this.world2colorMatrix.copy(source.world2colorMatrix);\r\n this.dashedLineSize = source.dashedLineSize;\r\n this.dashedLinePeriod = source.dashedLinePeriod;\r\n this.projMatrixInv = source.projMatrixInv;\r\n this.viewport = source.viewport;\r\n this.lineWidth = source.lineWidth; // used for thick lines only\r\n this.toonShading = source.toonShading;\r\n this.fogAlpha = source.fogAlpha;\r\n this.samplesKernel = source.samplesKernel;\r\n this.noiseTex = source.noiseTex;\r\n this.noiseTexelSize = source.noiseTexelSize;\r\n this.srcTexelSize = source.srcTexelSize;\r\n },\r\n};\r\n\r\nclass UberMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // add fog\r\n this.fog = true;\r\n // used for instanced geometry\r\n this.instancedPos = false;\r\n this.instancedMatrix = false;\r\n // atoms and links color\r\n this.attrColor = false;\r\n // second link color for cylinders\r\n this.attrColor2 = false;\r\n //\r\n this.attrAlphaColor = false;\r\n // overrides color for all vertices (used in selection)\r\n this.overrideColor = false;\r\n // zsrpites\r\n this.sphereSprite = false;\r\n this.cylinderSprite = false;\r\n // clip Surfs individually\r\n this.zClip = false;\r\n // clip scene with global clip plane\r\n this.clipPlane = false;\r\n // enable fake (chess-like) opacity\r\n this.fakeOpacity = false;\r\n // render only depth, don't take care about the pixel color (used for transparency depth prepass)\r\n this.prepassTransparancy = false;\r\n // used to render pixel positions\r\n this.colorFromPos = false;\r\n // used to render shadowmap\r\n this.shadowmap = false;\r\n // used to describe shadowmap type\r\n this.shadowmapType = 'random';\r\n // used to render pixel view deph\r\n this.colorFromDepth = false;\r\n // mark that rendering is for orthographic camera\r\n this.orthoCam = false;\r\n // used to render dashed line\r\n this.dashedLine = false;\r\n // mark as transparent\r\n this.transparent = true;\r\n // mark as thick lines\r\n this.thickLine = false;\r\n // makes fog begin transparency (required for transparent background)\r\n this.fogTransparent = false;\r\n // used to render surface normals to G buffer for ssao effect\r\n this.normalsToGBuffer = false;\r\n // used for toon material\r\n this.toonShading = false;\r\n\r\n // uber options of \"root\" materials are inherited from single uber-options object that resides in prototype\r\n this.uberOptions = Object.create(UberMaterial.prototype.uberOptions);\r\n\r\n // set default values\r\n super.setValues({\r\n uniforms: THREE.UniformsUtils.clone(defaultUniforms),\r\n vertexShader: this.precisionString() + vertexShader,\r\n fragmentShader: this.precisionString() + fragmentShader,\r\n lights: true,\r\n fog: true,\r\n side: THREE.DoubleSide,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n precisionString() {\r\n const { precision } = capabilities;\r\n const str = `precision ${precision} float;\\n`\r\n + `precision ${precision} int;\\n\\n`;\r\n return str;\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n\r\n this.fragmentShader = source.fragmentShader;\r\n this.vertexShader = source.vertexShader;\r\n\r\n this.uniforms = THREE.UniformsUtils.clone(source.uniforms);\r\n this.defines = { ...source.defines };\r\n this.extensions = source.extensions;\r\n\r\n this.fog = source.fog;\r\n this.instancedPos = source.instancedPos;\r\n this.instancedMatrix = source.instancedMatrix;\r\n this.attrColor = source.attrColor;\r\n this.attrColor2 = source.attrColor2;\r\n this.attrAlphaColor = source.attrAlphaColor;\r\n this.overrideColor = source.overrideColor;\r\n this.sphereSprite = source.sphereSprite;\r\n this.cylinderSprite = source.cylinderSprite;\r\n this.zClip = source.zClip;\r\n this.clipPlane = source.clipPlane;\r\n this.fakeOpacity = source.fakeOpacity;\r\n this.colorFromPos = source.colorFromPos;\r\n this.shadowmap = source.shadowmap;\r\n this.shadowmapType = source.shadowmapType;\r\n this.colorFromDepth = source.colorFromDepth;\r\n this.orthoCam = source.orthoCam;\r\n this.prepassTransparancy = source.prepassTransparancy;\r\n this.dashedLine = source.dashedLine;\r\n this.thickLine = source.thickLine;\r\n this.fogTransparent = source.fogTransparent;\r\n this.normalsToGBuffer = source.normalsToGBuffer;\r\n this.toonShading = source.toonShading;\r\n\r\n this.uberOptions.copy(source.uberOptions);\r\n\r\n return this;\r\n }\r\n\r\n // create copy of this material\r\n // its options are prototyped after this material's options\r\n createInstance() {\r\n const inst = new UberMaterial();\r\n inst.copy(this);\r\n inst.uberOptions = Object.create(this.uberOptions);\r\n return inst;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n const extensions = {};\r\n\r\n if (this.fog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.instancedPos) {\r\n defines.INSTANCED_POS = 1;\r\n }\r\n if (this.instancedMatrix) {\r\n defines.INSTANCED_MATRIX = 1;\r\n }\r\n if (this.attrColor) {\r\n defines.ATTR_COLOR = 1;\r\n }\r\n if (this.attrColor2) {\r\n defines.ATTR_COLOR2 = 1;\r\n }\r\n if (this.attrAlphaColor) {\r\n defines.ATTR_ALPHA_COLOR = 1;\r\n }\r\n if (this.overrideColor) {\r\n defines.OVERRIDE_COLOR = 1;\r\n }\r\n if (this.sphereSprite) {\r\n defines.SPHERE_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.cylinderSprite) {\r\n defines.CYLINDER_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.zClip) {\r\n defines.ZCLIP = 1;\r\n }\r\n if (this.clipPlane) {\r\n defines.CLIP_PLANE = 1;\r\n }\r\n if (this.fakeOpacity) {\r\n defines.FAKE_OPACITY = 1;\r\n }\r\n if (this.lights) {\r\n defines.USE_LIGHTS = 1;\r\n }\r\n if (this.colorFromPos) {\r\n defines.COLOR_FROM_POS = 1;\r\n }\r\n if (this.shadowmap) {\r\n defines.SHADOWMAP = 1;\r\n if (this.shadowmapType === 'pcf') {\r\n defines.SHADOWMAP_PCF_SHARP = 1;\r\n } else if (this.shadowmapType === 'random') {\r\n defines.SHADOWMAP_PCF_RAND = 1;\r\n } else {\r\n defines.SHADOWMAP_BASIC = 1;\r\n }\r\n }\r\n if (this.colorFromDepth) {\r\n defines.COLOR_FROM_DEPTH = 1;\r\n }\r\n if (this.orthoCam) {\r\n defines.ORTHOGRAPHIC_CAMERA = 1;\r\n }\r\n if (this.prepassTransparancy) {\r\n defines.PREPASS_TRANSP = 1;\r\n }\r\n if (this.dashedLine) {\r\n defines.DASHED_LINE = 1;\r\n }\r\n if (this.thickLine) {\r\n defines.THICK_LINE = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n if (this.normalsToGBuffer) {\r\n extensions.drawBuffers = true;\r\n defines.NORMALS_TO_G_BUFFER = 1;\r\n }\r\n if (this.toonShading) {\r\n defines.TOON_SHADING = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n this.extensions = extensions;\r\n }\r\n\r\n setUberOptions(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n for (const key in values) {\r\n if (!values.hasOwnProperty(key)) {\r\n continue;\r\n }\r\n\r\n if (this.uberOptions[key] instanceof THREE.Color) {\r\n this.uberOptions[key] = values[key].clone();\r\n } else {\r\n this.uberOptions[key] = values[key];\r\n }\r\n }\r\n }\r\n\r\n clone(shallow) {\r\n if (!shallow) {\r\n return super.clone();\r\n }\r\n return this.createInstance();\r\n }\r\n\r\n updateUniforms() {\r\n const self = this;\r\n\r\n uberOptionNames.forEach((p) => {\r\n if (self.uniforms.hasOwnProperty(p)) {\r\n if (self.uberOptions[p] instanceof THREE.Color\r\n || self.uberOptions[p] instanceof THREE.Matrix4) {\r\n self.uniforms[p].value = self.uberOptions[p].clone();\r\n } else {\r\n self.uniforms[p].value = self.uberOptions[p];\r\n }\r\n }\r\n });\r\n }\r\n}\r\n\r\nUberMaterial.prototype.uberOptions = uberOptions;\r\n\r\nexport default UberMaterial;\r\n","import UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default function (SuperClass) {\r\n class NewObjectType extends SuperClass {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.onBeforeRender = NewObjectType.prototype.onBeforeRender;\r\n }\r\n\r\n onBeforeRender(renderer, scene, camera, geometry, material, group) {\r\n this._onBeforeRender(renderer, scene, camera, geometry, material, group);\r\n this._update();\r\n }\r\n\r\n _onBeforeRender() {\r\n }\r\n\r\n _update() {\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material instanceof UberMaterial) {\r\n material.updateUniforms();\r\n }\r\n }\r\n }\r\n\r\n return NewObjectType;\r\n}\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZSpriteMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material.uniforms.invModelViewMatrix) {\r\n // NOTE: update of modelViewMatrix inside threejs is done after onBeforeRender call,\r\n // so we have to do it manually in that place\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n // get inverse matrix\r\n material.uniforms.invModelViewMatrix.value.copy(this.modelViewMatrix).invert();\r\n material.uniforms.nearPlaneValue.value = camera.near;\r\n material.uniformsNeedUpdate = true;\r\n }\r\n }\r\n}\r\n\r\nexport default ZSpriteMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZClippedMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n static _mvLength = new THREE.Vector3();\r\n\r\n static _center = new THREE.Vector3();\r\n\r\n static _modelView = new THREE.Matrix4();\r\n\r\n _onBeforeRender(renderer, scene, camera) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n\r\n const geo = this.geometry;\r\n const { material } = this;\r\n if (!geo.zClip || !material.uberOptions) {\r\n return;\r\n }\r\n\r\n const zClipCoef = 0.5;\r\n\r\n const modelView = ZClippedMesh._modelView;\r\n const mvLength = ZClippedMesh._mvLength;\r\n const center = ZClippedMesh._center;\r\n\r\n modelView.multiplyMatrices(this.matrixWorld, camera.matrixWorldInverse);\r\n const s = mvLength.setFromMatrixColumn(modelView, 0).length();\r\n center.copy(geo.boundingSphere.center);\r\n\r\n this.localToWorld(center);\r\n material.uberOptions.zClipValue = camera.position.z - center.z\r\n - s * (zClipCoef * geo.boundingSphere.radius);\r\n }\r\n}\r\n\r\nexport default ZClippedMesh;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from '../CSS2DObject';\r\nimport utils from '../../utils';\r\n\r\nclass TextMesh extends THREE.Group {\r\n constructor(geometry, _material) {\r\n super();\r\n this.geometry = geometry;\r\n\r\n const self = this;\r\n self.initialized = false;\r\n this.geometry.addEventListener('update', () => {\r\n self.update();\r\n });\r\n }\r\n\r\n init() {\r\n const { children } = this;\r\n for (let i = children.length - 1; i >= 0; --i) {\r\n this.remove(children[i]);\r\n }\r\n\r\n const { items, userData } = this.geometry;\r\n for (let i = 0, n = items.length; i < n; ++i) {\r\n const srcItem = items[i];\r\n if (!srcItem) {\r\n continue;\r\n }\r\n const item = utils.shallowCloneNode(srcItem);\r\n const label = new CSS2DObject(item);\r\n label.userData = _.clone(userData);\r\n const el = label.getElement();\r\n el.style.visibility = 'visible';\r\n label.source = srcItem;\r\n this.add(label);\r\n }\r\n this.initialized = true;\r\n }\r\n\r\n update() {\r\n const geo = this.geometry;\r\n if (!geo.needsUpdate) {\r\n return;\r\n }\r\n const { children } = this;\r\n if (!this.initialized) {\r\n this.init();\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n const item = child.source;\r\n child.position.copy(item.worldPos);\r\n child.userData.color = item.opts.color;\r\n child.userData.background = item.opts.background;\r\n }\r\n }\r\n}\r\n\r\nexport default TextMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass SimpleMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default SimpleMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\nconst _viewport = new THREE.Vector2();\r\n\r\nclass ThickLineMesh extends Mesh {\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!material.uberOptions) {\r\n return;\r\n }\r\n\r\n material.uberOptions.projMatrixInv.copy(camera.projectionMatrix).invert();\r\n renderer.getSize(_viewport);\r\n material.uberOptions.viewport.set(_viewport.width, _viewport.height);\r\n }\r\n}\r\n\r\nexport default ThickLineMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass InstancedMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default InstancedMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\nimport ZSpriteMesh from './ZSpriteMesh';\r\nimport ZClippedMesh from './ZClippedMesh';\r\nimport TextMesh from './TextMesh';\r\nimport SimpleMesh from './SimpleMesh';\r\nimport ThickLineMesh from './ThickLineMesh';\r\nimport InstancedMesh from './InstancedMesh';\r\n\r\nexport default {\r\n ZClipped: ZClippedMesh,\r\n ZSprite: ZSpriteMesh,\r\n Text: TextMesh,\r\n Line: UberObject(THREE.Line),\r\n LineSegments: UberObject(THREE.LineSegments),\r\n Mesh: SimpleMesh,\r\n ThickLineMesh,\r\n Instanced: InstancedMesh,\r\n};\r\n","import geometries from '../geometries/geometries';\r\nimport meshes from './meshes';\r\nimport ThickLinesGeometry from '../geometries/ThickLinesGeometry';\r\n\r\nfunction setMatParams(params, uniforms) {\r\n return function (material) {\r\n material.setValues(params);\r\n material.setUberOptions(uniforms);\r\n };\r\n}\r\n\r\nfunction _createInstancedCylinders(useZSprites, openEnded) {\r\n function Geometry(a, b) {\r\n return new geometries.Instanced2CCylindersGeometry(a, b, useZSprites, openEnded);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedMatrix: true,\r\n attrColor: true,\r\n attrColor2: true,\r\n attrAlphaColor: true,\r\n cylinderSprite: useZSprites,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createLineSegmentsGeoTriplet(geo, renderParams) {\r\n const thickLines = geo.prototype instanceof ThickLinesGeometry;\r\n const lineWidth = renderParams.lineWidth || 0;\r\n return {\r\n Geometry: geo,\r\n Object: thickLines ? meshes.ThickLineMesh : meshes.LineSegments,\r\n initMaterial: setMatParams({\r\n lights: false,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n thickLine: thickLines,\r\n }, {\r\n lineWidth,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createSimpleGeoTriplet(geoClass) {\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.Mesh,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createIsoSurfaceGeoTriplet(geoClass, caps, settings, renderParams) {\r\n const surfaceOpts = {\r\n wireframe: !!renderParams.wireframe,\r\n fakeOpacity: settings.now.isoSurfaceFakeOpacity,\r\n zClip: renderParams.zClip,\r\n };\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.ZClipped,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: false,\r\n wireframe: surfaceOpts.wireframe,\r\n fakeOpacity: surfaceOpts.fakeOpacity,\r\n zClip: surfaceOpts.zClip,\r\n }),\r\n };\r\n}\r\n\r\nclass MeshCreator {\r\n static createSpheres(caps, settings) {\r\n const useZSprites = settings.now.zSprites;\r\n function Geometry(a, b) {\r\n return new geometries.InstancedSpheresGeometry(a, b, useZSprites);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedPos: true,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n sphereSprite: useZSprites,\r\n }),\r\n };\r\n }\r\n\r\n static create2CClosedCylinders(_caps, _settings) {\r\n return _createInstancedCylinders(false, false);\r\n }\r\n\r\n static create2CCylinders(caps, settings) {\r\n return _createInstancedCylinders(settings.now.zSprites, true);\r\n }\r\n\r\n static create2CLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.TwoColorLinesGeometry, renderParams);\r\n }\r\n\r\n static createCrosses(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.CrossGeometry, renderParams);\r\n }\r\n\r\n static createExtrudedChains(_caps, _settings) {\r\n return _createSimpleGeoTriplet(geometries.ExtrudedObjectsGeometry);\r\n }\r\n\r\n static createChunkedLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.ChunkedLinesGeometry, renderParams);\r\n }\r\n\r\n static createQuickSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.QuickSurfGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createContactSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.ContactSurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createSASSES(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.SSIsosurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createLabels(_caps, _settings) {\r\n return {\r\n Geometry: geometries.LabelsGeometry,\r\n Object: meshes.Text,\r\n initMaterial() {\r\n },\r\n };\r\n }\r\n}\r\n\r\nexport default MeshCreator;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../gfxutils';\r\n\r\nclass TransformGroup extends THREE.Object3D {\r\n static _inverseMatrix = new THREE.Matrix4();\r\n\r\n static _ray = new THREE.Ray();\r\n\r\n constructor(geometry, geoParams, material, transforms) {\r\n super();\r\n this._geometry = geometry;\r\n this._geoParams = geoParams;\r\n const mat = material.createInstance();\r\n geoParams.initMaterial(mat);\r\n this._material = mat;\r\n this._transforms = transforms.length > 0 ? transforms : [new THREE.Matrix4()];\r\n const meshes = this._createMeshes(geometry);\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n this.add(meshes[i]);\r\n }\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const ray = TransformGroup._ray;\r\n const inverseMatrix = TransformGroup._inverseMatrix;\r\n const { children } = this;\r\n ray.copy(raycaster.ray);\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n\r\n if (!gfxutils.belongToSelectLayers(child)) {\r\n continue;\r\n }\r\n\r\n child.updateMatrixWorld();\r\n const mtx = child.matrixWorld;\r\n inverseMatrix.copy(mtx).invert();\r\n raycaster.ray.copy(ray).applyMatrix4(inverseMatrix);\r\n const childIntersects = [];\r\n this._geometry.raycast(raycaster, childIntersects);\r\n\r\n for (let j = 0, ciCount = childIntersects.length; j < ciCount; ++j) {\r\n const inters = childIntersects[j];\r\n if (inters.point) {\r\n inters.point.applyMatrix4(mtx);\r\n inters.distance = ray.origin.distanceTo(inters.point);\r\n }\r\n inters.object = child;\r\n intersects[intersects.length] = inters;\r\n }\r\n }\r\n raycaster.ray.copy(ray);\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const geos = this._geometry.getSubset(chunkIndices);\r\n const subset = [];\r\n let subIdx = 0;\r\n\r\n for (let i = 0, n = geos.length; i < n; ++i) {\r\n const meshes = this._createMeshes(geos[i]);\r\n for (let j = 0, meshCnt = meshes.length; j < meshCnt; ++j) {\r\n subset[subIdx++] = meshes[j];\r\n }\r\n }\r\n\r\n return subset;\r\n }\r\n\r\n _createMeshes(geometry) {\r\n const transforms = this._transforms;\r\n const Mesh = this._geoParams.Object;\r\n const material = this._material;\r\n const meshes = [];\r\n for (let i = 0, n = transforms.length; i < n; ++i) {\r\n const mesh = new Mesh(geometry, material);\r\n mesh.applyMatrix4(transforms[i]);\r\n meshes[i] = mesh;\r\n }\r\n\r\n return meshes;\r\n }\r\n}\r\n\r\nexport default TransformGroup;\r\n","import RCGroup from '../../RCGroup';\r\nimport TransformGroup from '../../meshes/TransformGroup';\r\n\r\nfunction wrapper(Name, args) {\r\n const params = [Name].concat(args);\r\n return Name.bind(...params);\r\n}\r\n\r\nclass ChemGroup extends RCGroup {\r\n constructor(geoParams, selection, colorer, mode, transforms, polyComplexity, material) {\r\n super();\r\n if (this.constructor === ChemGroup) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n this._selection = selection;\r\n this._mode = mode;\r\n this._colorer = colorer;\r\n this._chunksIdc = selection.chunks;\r\n this._polyComplexity = polyComplexity;\r\n this._geo = new (wrapper(geoParams.Geometry, this._makeGeoArgs()))();\r\n this._mesh = new TransformGroup(this._geo, geoParams, material, transforms);\r\n this.add(this._mesh);\r\n this._build();\r\n }\r\n\r\n _makeGeoArgs() {\r\n throw new Error('ChemGroup subclass must override _makeGeoArgs() method');\r\n }\r\n\r\n /**\r\n * Builds subset geometry by ATOMS index list\r\n *\r\n * @param {Number} mask - Representation mask\r\n * @param {Boolean} innerOnly - if true returns inner bonds only - without halves\r\n * @returns {Array} Subset geometry\r\n */\r\n getSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : false;\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return [];\r\n }\r\n return this._mesh.getSubset(chunksList);\r\n }\r\n\r\n _changeSubsetOpacity(mask, value, innerOnly) {\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return;\r\n }\r\n this._geo.setOpacity(chunksList, value);\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 1.0, innerOnly);\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 0.0, innerOnly);\r\n }\r\n}\r\n\r\nexport default ChemGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass AtomsGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { atoms } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const atomsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const atomIdx = atomsIdc[inters[i].chunkIdx];\r\n if (atomIdx < atoms.length) {\r\n inters[i].atom = atoms[atomIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { atoms } = this._selection;\r\n const atomsIdc = this._chunksIdc;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n if ((atom.mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default AtomsGroup;\r\n","import AtomsGroup from './AtomsGroup';\r\n\r\nclass AtomsSphereGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, atom.position, mode.calcAtomRadius(atom));\r\n geo.setColor(i, colorer.getAtomColor(atom, parent));\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), mode.calcAtomRadius(atom));\r\n if (updateColor) {\r\n geo.setColor(i, frameData.getAtomColor(colorer, atom));\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsSphereGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSurfaceGroup extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n return [n, opts];\r\n }\r\n}\r\nexport default AtomsSurfaceGroup;\r\n","/* This is a stub class keep it until SAS/SES is refactored */\r\n\r\nimport AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSASSESGroupStub extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n opts.selection = this._selection;\r\n opts.colorMode = this._colorer;\r\n return [n, opts];\r\n }\r\n}\r\n\r\nexport default AtomsSASSESGroupStub;\r\n","import AtomsGroup from './AtomsGroup';\r\nimport utils from '../../../utils';\r\n\r\nfunction adjustColor(color) {\r\n let r = (color >> 16) & 255;\r\n let g = (color >> 8) & 255;\r\n let b = color & 255;\r\n\r\n if (0.2126 * r + 0.7152 * g + 0.0722 * b > 127) {\r\n r = r * 3 / 10;\r\n g = g * 3 / 10;\r\n b = b * 3 / 10;\r\n } else {\r\n r = 255 - ((255 - r) * 3 / 10);\r\n g = 255 - ((255 - g) * 3 / 10);\r\n b = 255 - ((255 - b) * 3 / 10);\r\n }\r\n\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nfunction inverseColor(color) {\r\n const r = (color >> 16) & 255;\r\n const g = (color >> 8) & 255;\r\n const b = color & 255;\r\n\r\n return ((255 - r) << 16) | ((255 - g) << 8) | (255 - b);\r\n}\r\n\r\nfunction getAtomText(atom) {\r\n if (atom.name.getNode() !== null) {\r\n return atom.name.getNode();\r\n }\r\n\r\n return atom.getVisualName();\r\n}\r\n\r\nconst colorMappings = {\r\n none(c) {\r\n return c;\r\n },\r\n adjust: adjustColor,\r\n inverse: inverseColor,\r\n};\r\n\r\nfunction propagateColor(color, rule) {\r\n let result;\r\n if (colorMappings.hasOwnProperty(rule)) {\r\n result = utils.hexColor(colorMappings[rule](color));\r\n } else {\r\n const val = parseInt(rule, 16);\r\n if (!Number.isNaN(val) && rule.toLowerCase().startsWith('0x')) {\r\n result = utils.hexColor(val);\r\n } else {\r\n result = '#000000';\r\n }\r\n }\r\n return result;\r\n}\r\n\r\nconst templateMappings = {\r\n serial(a) {\r\n return a.serial;\r\n },\r\n name(a) {\r\n return a.getVisualName();\r\n },\r\n elem(a) {\r\n return a.element.name;\r\n },\r\n residue(a) {\r\n return a.residue.getType().getName();\r\n },\r\n sequence(a) {\r\n return a.residue.getSequence();\r\n },\r\n chain(a) {\r\n return a.residue.getChain().getName();\r\n },\r\n hetatm(a) {\r\n return a.isHet();\r\n },\r\n water(a) {\r\n return a.residue.getType().getName() === 'HOH' || a.residue.getType().getName() === 'WAT';\r\n },\r\n};\r\n\r\nconst parseTemplate = function (atom, str) {\r\n return str.replace(/\\{\\{(\\s*\\w+\\s*)\\}\\}/g, (m) => {\r\n let key = m.replace(/\\s+/g, '');\r\n key = key.substring(2, key.length - 2).toLowerCase();\r\n\r\n if (templateMappings.hasOwnProperty(key)) {\r\n return templateMappings[key](atom);\r\n }\r\n return 'null';\r\n });\r\n};\r\n\r\nclass AtomsTextGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n const opts = this._mode.getLabelOpts();\r\n return [this._selection.chunks.length, opts];\r\n }\r\n\r\n _build() {\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = colorer.getAtomColor(atom, parent);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, atom.position, text);\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = frameData.getAtomColor(colorer, atom);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), text);\r\n if (updateColor) {\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsTextGroup;\r\n","import * as THREE from 'three';\r\nimport AtomsGroup from './AtomsGroup';\r\n\r\nfunction _slerp(omega, v1, v2, t) {\r\n const oSin = Math.sin(omega);\r\n return v1.clone().multiplyScalar(Math.sin((1 - t) * omega) / oSin).addScaledVector(v2, Math.sin(t * omega) / oSin);\r\n}\r\n\r\nclass AromaticGroup extends AtomsGroup {\r\n _buildInner(radOffset, addChunk) {\r\n const chunksToIdx = this._selection.chunks;\r\n\r\n const prevVector = new THREE.Vector3();\r\n const currVector = new THREE.Vector3();\r\n const segmentsHeight = this._segmentsHeight;\r\n const leprStep = 1.0 / segmentsHeight;\r\n const colorer = this._colorer;\r\n\r\n const { cycles, parent } = this._selection;\r\n let chunkIdx = 0;\r\n let currAtomIdx = chunksToIdx[chunkIdx];\r\n\r\n for (let cIdx = 0, cCount = cycles.length; cIdx < cCount; ++cIdx) {\r\n const cycle = cycles[cIdx];\r\n const cycAtoms = cycle.atoms;\r\n const chunkPoints = [];\r\n const tmpDir = [];\r\n const { center } = cycle;\r\n const cycleRad = cycle.radius - radOffset;\r\n const n = cycAtoms.length;\r\n let i = 0;\r\n const prevPos = cycAtoms[n - 1].position;\r\n let currPos = cycAtoms[i].position;\r\n prevVector.subVectors(prevPos, center);\r\n currVector.subVectors(currPos, center);\r\n const upDir = currVector.clone().cross(prevVector).normalize();\r\n\r\n for (; i < n; ++i) {\r\n const omega = prevVector.angleTo(currVector);\r\n tmpDir[i] = _slerp(omega, prevVector, currVector, 0.5).normalize();\r\n currPos = cycAtoms[(i + 1) % n].position;\r\n prevVector.copy(currVector);\r\n currVector.subVectors(currPos, center);\r\n }\r\n\r\n for (i = 0; i < n; ++i) {\r\n if (cycAtoms[i].index !== currAtomIdx) {\r\n continue;\r\n }\r\n const start = tmpDir[i];\r\n const end = tmpDir[(i + 1) % n];\r\n const color = colorer.getAtomColor(cycAtoms[i], parent);\r\n const currAngle = start.angleTo(end);\r\n\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n chunkPoints[j] = _slerp(currAngle, start, end, j * leprStep).multiplyScalar(cycleRad).add(center);\r\n }\r\n\r\n addChunk(chunkIdx++, color, chunkPoints, center, upDir);\r\n currAtomIdx = chunksToIdx[chunkIdx];\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default AromaticGroup;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../../gfxutils';\r\nimport AromaticGroup from './AromaticGroup';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n for (let i = 0; i < parts; ++i) {\r\n const a = -2 * i / parts * Math.PI;\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\nconst { calcChunkMatrix } = gfxutils;\r\n\r\nclass AromaticTorusGroup extends AromaticGroup {\r\n _build() {\r\n const segmentsHeight = this._segmentsHeight;\r\n const torusRad = this._mode.getAromRadius();\r\n const radiusV = new THREE.Vector2(torusRad, torusRad);\r\n const radOffset = this._mode.calcStickRadius() + 2 * torusRad;\r\n const lookAtVector = new THREE.Vector3();\r\n const mtc = [];\r\n const geo = this._geo;\r\n this._buildInner(radOffset, (chunkIdx, color, points, center, upDir) => {\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n const currDir = currPoint.clone().sub(center).cross(upDir);\r\n lookAtVector.addVectors(currPoint, currDir);\r\n mtc[j] = calcChunkMatrix(currPoint, lookAtVector, upDir, radiusV);\r\n }\r\n geo.setItem(chunkIdx, mtc);\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._polyComplexity;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length];\r\n }\r\n}\r\n\r\nexport default AromaticTorusGroup;\r\n","import AromaticGroup from './AromaticGroup';\r\n\r\nclass AromaticLinesGroup extends AromaticGroup {\r\n _build() {\r\n const geo = this._geo;\r\n const radOffset = this._mode.getAromaticOffset();\r\n this._buildInner(radOffset, (chunkIdx, color, points) => {\r\n let prevPt = points[0];// do not replace with start\r\n for (let j = 1; j <= this._segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n geo.setSegment(chunkIdx, j - 1, prevPt, currPoint);\r\n prevPt = currPoint;\r\n }\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._mode.getAromaticArcChunks();\r\n return [this._selection.chunks.length, this._segmentsHeight, true];\r\n }\r\n}\r\n\r\nexport default AromaticLinesGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[inters[i].chunkIdx];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesGroup;\r\n","import ResiduesGroup from './ResiduesGroup';\r\n\r\nclass NucleicItemGroup extends ResiduesGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[Math.floor(inters[i].chunkIdx / 2)];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n let chunkIdx = 0;\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList[chunkIdx++] = 2 * i;\r\n chunksList[chunkIdx++] = 2 * i + 1;\r\n }\r\n }\r\n return chunksList;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finishUpdate();\r\n }\r\n}\r\n\r\nexport default NucleicItemGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicCylindersGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n geo.setItem(chunkIdx, cyl1, cyl2, stickRad);\r\n geo.setColor(chunkIdx, color, color);\r\n }\r\n}\r\n\r\nexport default NucleicCylindersGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicSpheresGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length * 2, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n let idx = chunkIdx * 2;\r\n geo.setItem(idx, cyl1, stickRad);\r\n geo.setColor(idx, color);\r\n idx++;\r\n geo.setItem(idx, cyl2, stickRad);\r\n geo.setColor(idx, color);\r\n }\r\n}\r\n\r\nexport default NucleicSpheresGroup;\r\n","import * as THREE from 'three';\r\nimport { Smooth } from '../../../../vendor/js/Smooth';\r\nimport gfxutils from '../../gfxutils';\r\nimport chem from '../../../chem';\r\n\r\nconst { ResidueType } = chem;\r\n\r\nconst calcMatrix = gfxutils.calcChunkMatrix;\r\n\r\nfunction _buildStructureInterpolator(points, tension) {\r\n const path = Smooth(points, {\r\n method: Smooth.METHOD_CUBIC,\r\n clip: Smooth.CLIP_CLAMP,\r\n cubicTension: tension,\r\n scaleTo: 1,\r\n });\r\n\r\n return function (t, argTrans) {\r\n let transformT = argTrans;\r\n if (transformT === null) {\r\n // map our range to the [second .. last but one]\r\n transformT = function (tt) {\r\n return (tt * ((points.length - 1) - 2) + 1) / (points.length - 1);\r\n };\r\n }\r\n const newt = transformT(t);\r\n const ans = path(newt);\r\n return new THREE.Vector3(ans[0], ans[1], ans[2]);\r\n };\r\n}\r\n\r\nfunction _addPoints(centerPoints, topPoints, idx, residue) {\r\n if (!residue._isValid) {\r\n centerPoints[idx] = centerPoints[idx - 1];\r\n topPoints[idx] = topPoints[idx - 1];\r\n return;\r\n }\r\n const cp = residue._controlPoint;\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n const tp = cp.clone().add(residue._wingVector);\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n}\r\n\r\nfunction _addPointsForLoneResidue(centerPoints, topPoints, idx, residue) {\r\n const nucleic = (residue._type.flags & ResidueType.Flags.NUCLEIC) !== 0;\r\n const nameFrom = nucleic ? 'C5\\'' : 'N';\r\n const nameTo = nucleic ? 'C3\\'' : 'C';\r\n\r\n let posFrom;\r\n let posTo;\r\n residue.forEachAtom((atom) => {\r\n const name = atom.getVisualName();\r\n if (!posFrom && name === nameFrom) {\r\n posFrom = atom.position;\r\n } else if (!posTo && name === nameTo) {\r\n posTo = atom.position;\r\n }\r\n });\r\n\r\n // provide a fallback for unknown residues\r\n if (!(posFrom && posTo)) {\r\n posFrom = residue._firstAtom.position;\r\n posTo = residue._lastAtom.position;\r\n }\r\n\r\n if (posFrom && posTo) {\r\n const shift = posTo.clone().sub(posFrom);\r\n\r\n const wing = residue._wingVector;\r\n const cp = residue._controlPoint;\r\n const tp = cp.clone().add(wing);\r\n\r\n const cpPrev = cp.clone().sub(shift);\r\n const tpPrev = cpPrev.clone().add(wing);\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n ++idx;\r\n\r\n const cpNext = cp.clone().add(shift);\r\n const tpNext = cpNext.clone().add(wing);\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n ++idx;\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n }\r\n}\r\n\r\nfunction _calcPoints(residues, firstIdx, lastIdx, boundaries) {\r\n const left = boundaries.start;\r\n const right = boundaries.end;\r\n function _prevIdx(idx) {\r\n return idx > left && residues[idx - 1]._isValid ? idx - 1 : idx;\r\n }\r\n function _nextIdx(idx) {\r\n return idx < right && residues[idx + 1]._isValid ? idx + 1 : idx;\r\n }\r\n\r\n const topPoints = [];\r\n const centerPoints = [];\r\n let arrIdx = 0;\r\n function _extrapolate2(currIdx, otherIdx) {\r\n const cp = residues[currIdx]._controlPoint.clone().lerp(residues[otherIdx]._controlPoint, -0.25);\r\n const tp = cp.clone().add(residues[currIdx]._wingVector);\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n }\r\n\r\n // a single disconnected residue\r\n const prevIdx = _prevIdx(firstIdx);\r\n const nextIdx = _nextIdx(lastIdx);\r\n if (prevIdx === nextIdx) {\r\n _addPointsForLoneResidue(centerPoints, topPoints, arrIdx, residues[firstIdx]);\r\n return { centerPoints, topPoints };\r\n }\r\n\r\n // Two points (prev-prev and next-next) are added to support edge conditions for cubic splines, they are ignored\r\n // Another two (prev and next) were added to support the outside of the sub chain\r\n\r\n // prev and prev-prev\r\n if (firstIdx === prevIdx) {\r\n // do the extrapolation\r\n _extrapolate2(firstIdx, _nextIdx(firstIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[_prevIdx(prevIdx)]);\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[prevIdx]);\r\n }\r\n\r\n // main loop\r\n for (let idx = firstIdx; idx <= lastIdx; ++idx) {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[idx]);\r\n }\r\n\r\n // next and next-next\r\n if (nextIdx === _nextIdx(nextIdx)) {\r\n // do the extrapolation\r\n _extrapolate2(lastIdx, _prevIdx(lastIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[nextIdx]);\r\n _addPoints(centerPoints, topPoints, arrIdx, residues[_nextIdx(nextIdx)]);\r\n }\r\n return { centerPoints, topPoints };\r\n}\r\n\r\nclass CartoonHelper {\r\n constructor(residues, startIdx, endIdx, segmentsCount, tension, boundaries) {\r\n const pointsArrays = _calcPoints(residues, startIdx, endIdx, boundaries);\r\n this._topInterp = _buildStructureInterpolator(pointsArrays.topPoints, tension);\r\n this._centerInterp = _buildStructureInterpolator(pointsArrays.centerPoints, tension);\r\n\r\n this._shift = 0.5 / (endIdx - startIdx + 2);\r\n this._valueStep = (1.0 - 2 * this._shift) / (2 * (endIdx - startIdx + 1) * (segmentsCount - 1));\r\n this._segmentsCount = segmentsCount;\r\n }\r\n\r\n prepareMatrices(idx, firstRad, secondRad) {\r\n const mtcCount = this._segmentsCount;\r\n const outMtc = new Array(mtcCount);\r\n const currRad = new THREE.Vector2(0, 0);\r\n\r\n const topInterp = this._topInterp;\r\n const cenInterp = this._centerInterp;\r\n\r\n let currentValue = this._shift + this._valueStep * (mtcCount - 1) * idx;\r\n\r\n for (let mtxIdx = 0; mtxIdx < mtcCount; ++mtxIdx) {\r\n const lerpVal = Math.min(1.0, mtxIdx / (mtcCount - 1));\r\n currRad.lerpVectors(firstRad, secondRad, lerpVal);\r\n\r\n const currTop = topInterp(currentValue, null);\r\n const currCenter = cenInterp(currentValue, null);\r\n currentValue += this._valueStep;\r\n const nextCenter = cenInterp(currentValue, null);\r\n\r\n outMtc[mtxIdx] = calcMatrix(currCenter.clone(), nextCenter.clone(), currTop.clone().sub(currCenter), currRad);\r\n }\r\n\r\n return outMtc;\r\n }\r\n}\r\n\r\nexport default CartoonHelper;\r\n","import * as THREE from 'three';\r\nimport ResiduesGroup from './ResiduesGroup';\r\nimport CartoonHelper from './CartoonHelper';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n\r\n for (let i = 0; i < parts; ++i) {\r\n // starts from pi/2 because it's important that points are lied on the angles of arrows (visual issues if not)\r\n const a = Math.PI / 2.0 - 2 * Math.PI * i / parts;\r\n\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\n\r\nfunction _loopThrough(subDiv, residues, segmentsHeight, tension, mode, callback) {\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n const { boundaries } = subDiv[subDivI];\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const idc = [subs[i].start, subs[i].end];\r\n const matrixHelper = new CartoonHelper(residues, idc[0], idc[1], segmentsHeight, tension, boundaries);\r\n let prevLast = null;\r\n const startIdx = subs[i].start * 2;\r\n const endIdx = subs[i].end * 2 + 1;\r\n let prevSecondRad = mode.getResidueRadius(residues[0], 0);\r\n for (let idx = startIdx; idx <= endIdx; ++idx) {\r\n const resIdx = (idx / 2 | 0);\r\n const currRes = residues[resIdx];\r\n const firstRad = mode.getResidueRadius(currRes, idx % 2);\r\n const secondRad = mode.getResidueRadius(currRes, 1 + (idx % 2));\r\n\r\n const mtc = matrixHelper.prepareMatrices(idx - idc[0] * 2, firstRad, secondRad);\r\n mtc.unshift(prevLast === null ? mtc[0] : prevLast);\r\n\r\n // Slope - radius is changed along this residue part\r\n const hasSlope = (firstRad.x !== secondRad.x) || (firstRad.y !== secondRad.y);\r\n // Cut - end radius of previous part not equal to start radius of this part. First section of this part lies in the orthogonal plane\r\n const hasCut = (firstRad.x !== prevSecondRad.x) || (firstRad.y !== prevSecondRad.y);\r\n\r\n callback(currRes, mtc, hasSlope, hasCut);\r\n\r\n prevLast = mtc[segmentsHeight];\r\n prevSecondRad = secondRad;\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ResiduesSubseqGroup extends ResiduesGroup {\r\n _makeGeoArgs() {\r\n const cmpMultiplier = this._mode.getHeightSegmentsRatio();\r\n this._segmentsHeight = this._polyComplexity * cmpMultiplier | 0;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length * 2];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, (currRes, mtc, hasSlope = false, hasCut = false) => {\r\n const color = colorer.getResidueColor(currRes, parent);\r\n chunkIdc[chunkIdx] = currRes._index;\r\n geo.setItem(chunkIdx, mtc, hasSlope, hasCut);\r\n geo.setColor(chunkIdx++, color);\r\n });\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n const frameRes = frameData.getResidues();\r\n let chunkIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n _loopThrough(this._selection.subdivs, frameRes, this._segmentsHeight, tension, mode, (currRes, mtc) => {\r\n geo.setItem(chunkIdx, mtc);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n });\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default ResiduesSubseqGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesTraceGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const subDiv = this._selection.subdivs;\r\n let chunksCount = 0;\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n chunksCount += subs[i].end - subs[i].start;\r\n }\r\n }\r\n return [chunksCount, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n chunkIdc[chunkIdx] = { first: prevRes._index, second: currRes._index };\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n geo.finalize();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n const { residues } = this._selection;\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksToIdx = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const chunk = chunksToIdx[Math.floor(chunkIdx / 2)];\r\n const resIdx = chunkIdx % 2 === 0 ? chunk.first : chunk.second;\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const chunksToIdx = this._chunksIdc;\r\n const { residues } = this._selection;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const chunk = chunksToIdx[i];\r\n if (residues[chunk.first]._mask & mask) {\r\n chunksList.push(i * 2);\r\n }\r\n if (residues[chunk.second]._mask & mask) {\r\n chunksList.push(i * 2 + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesTraceGroup;\r\n","import ChemGroup from './ChemGroup';\r\nimport Bond from '../../../chem/Bond';\r\n\r\nfunction getCylinderCount(bondOrder) {\r\n return bondOrder < 2 ? 1 : bondOrder;\r\n}\r\n\r\nclass BondsGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const drawMultiple = this._mode.drawMultiorderBonds();\r\n const showAromatic = this._mode.showAromaticLoops();\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n let bondsCount = 0;\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n bondsCount += this.getBondOrder(bonds[bondsIdc[i]], drawMultiple, showAromatic);\r\n }\r\n return [bondsCount, this._polyComplexity];\r\n }\r\n\r\n getBondOrder(bond, drawMultiple, showAromatic) {\r\n let bondOrder = 1;\r\n if (drawMultiple && (!showAromatic || bond._type !== Bond.BondType.AROMATIC)) {\r\n bondOrder = getCylinderCount(bond._order);\r\n }\r\n return bondOrder;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const { bonds } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const bondsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const bondIdx = bondsIdc[Math.floor(chunkIdx / 2)];\r\n if (bondIdx < bonds.length) {\r\n const bond = bonds[bondIdx];\r\n inters[i].atom = chunkIdx % 2 === 0 ? bond._left : bond._right;\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask, innerOnly) {\r\n const chunksList = [];\r\n const { bonds } = this._selection;\r\n const chunksToIdx = this._chunksIdc;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const bond = bonds[chunksToIdx[i]];\r\n if ((bond._left.mask & mask) && (!innerOnly || (bond._right.mask & mask))) {\r\n chunksList.push(2 * i);\r\n }\r\n if ((bond._right.mask & mask) && (!innerOnly || (bond._left.mask & mask))) {\r\n chunksList.push(2 * i + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default BondsGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nclass BondsCylinderGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsCylinderGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nconst STEP_SIZE = 0.15;\r\n\r\nclass BondsLinesGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsLinesGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\nimport AtomsSurfaceGroup from './AtomsSurfaceGroup';\r\nimport AtomsSASSESGroupStub from './AtomsSASSESGroupStub';\r\nimport AtomsTextGroup from './AtomsTextGroup';\r\nimport AromaticTorusGroup from './AromaticTorusGroup';\r\nimport AromaticLinesGroup from './AromaticLinesGroup';\r\nimport NucleicCylindersGroup from './NucleicCylindersGroup';\r\nimport NucleicSpheresGroup from './NucleicSpheresGroup';\r\nimport ResiduesSubseqGroup from './ResiduesSubseqGroup';\r\nimport ResiduesTraceGroup from './ResiduesTraceGroup';\r\nimport BondsCylinderGroup from './BondsCylinderGroup';\r\nimport BondsLinesGroup from './BondsLinesGroup';\r\n\r\nexport default {\r\n AtomsSphereGroup,\r\n AtomsSurfaceGroup,\r\n AtomsSASSESGroupStub,\r\n AtomsTextGroup,\r\n AromaticTorusGroup,\r\n AromaticLinesGroup,\r\n NucleicCylindersGroup,\r\n NucleicSpheresGroup,\r\n ResiduesSubseqGroup,\r\n ResiduesTraceGroup,\r\n BondsCylinderGroup,\r\n BondsLinesGroup,\r\n};\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AtomsProcessor extends RCGroup {\r\n constructor(AtomsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n this._mode = mode;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let atomCount = 0;\r\n component.forEachAtom((atom) => {\r\n if (!self._checkAtom(atom, mask)) {\r\n return;\r\n }\r\n atomsIdc[atomCount++] = atom.index;\r\n });\r\n if (atomCount === 0) {\r\n return;\r\n }\r\n const atomsGroup = new AtomsGroup(geoParams, {\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n _checkAtom(atom, mask) {\r\n return atom.mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AtomsProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\n\r\nclass OrphanAtomsProcessor extends AtomsProcessor {\r\n _checkAtom(atom, mask) {\r\n if (!(atom.mask & mask)) {\r\n return false;\r\n }\r\n\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n if ((bonds[i]._left.mask & mask) && (bonds[i]._right.mask & mask)) {\r\n return false;\r\n }\r\n }\r\n return true;\r\n }\r\n}\r\n\r\nexport default OrphanAtomsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass ResiduesProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n component.forEachResidue((residue) => {\r\n if (self._checkResidue(residue, mask)) {\r\n resIdc[chunksCount++] = residue._index;\r\n }\r\n });\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n checkResidue(residue, mask) {\r\n return residue._mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default ResiduesProcessor;\r\n","import ResidueProcessor from './ResiduesProcessor';\r\n\r\nclass NucleicProcessor extends ResidueProcessor {\r\n _checkResidue(residue, mask) {\r\n return mask & residue._mask && residue._cylinders !== null;\r\n }\r\n}\r\nexport default NucleicProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass SubseqsProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const subDivs = component.getMaskedSubdivSequences(mask);\r\n\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n for (let subDivI = 0, subDivN = subDivs.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDivs[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let j = subs[i].start, jEnd = subs[i].end; j <= jEnd; ++j) {\r\n resIdc[chunksCount++] = residues[j]._index;\r\n }\r\n }\r\n }\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n subdivs: subDivs,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default SubseqsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass BondsProcessor extends RCGroup {\r\n constructor(BondsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const bonds = complex.getBonds();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const bondsIdc = [];\r\n let bondsCount = 0;\r\n component.forEachBond((bond) => {\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n if (!(atom1.mask & mask) || !(atom2.mask & mask)) {\r\n return;\r\n }\r\n bondsIdc[bondsCount++] = bond._index;\r\n });\r\n if (bondsCount === 0) {\r\n return;\r\n }\r\n const bondsGroup = new BondsGroup(geoParams, {\r\n bonds,\r\n chunks: bondsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n bondsGroup._component = component;\r\n self.add(bondsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default BondsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AromaticProcessor extends RCGroup {\r\n constructor(AromaticGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n if (!mode.showAromaticLoops()) {\r\n return;\r\n }\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let chunksCount = 0;\r\n const cycles = [];\r\n let cycleIdx = 0;\r\n component.forEachCycle((cycle) => {\r\n const cycAtoms = cycle.atoms;\r\n let perCycle = 0;\r\n for (let i = 0, n = cycAtoms.length; i < n; ++i) {\r\n if ((cycAtoms[i].mask & mask) !== 0) {\r\n ++perCycle;\r\n atomsIdc[chunksCount++] = cycAtoms[i].index;\r\n }\r\n }\r\n if (perCycle > 0) {\r\n cycles[cycleIdx++] = cycle;\r\n }\r\n });\r\n\r\n const atomsGroup = new AromaticGroup(geoParams, {\r\n cycles,\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AromaticProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\nimport OrphanAtomsProcessor from './OrphanAtomsProcessor';\r\nimport ResiduesProcessor from './ResiduesProcessor';\r\nimport NucleicProcessor from './NucleicProcessor';\r\nimport SubseqsProcessor from './SubseqsProcessor';\r\nimport BondsProcessor from './BondsProcessor';\r\nimport AromaticProcessor from './AromaticProcessor';\r\n\r\nexport default {\r\n Atoms: AtomsProcessor,\r\n OrphanAtoms: OrphanAtomsProcessor,\r\n Residues: ResiduesProcessor,\r\n Nucleic: NucleicProcessor,\r\n Subseqs: SubseqsProcessor,\r\n Bonds: BondsProcessor,\r\n Aromatic: AromaticProcessor,\r\n};\r\n","import MeshCreator from '../../meshes/MeshCreator';\r\nimport groups from './groups';\r\nimport processors from '../processors/processors';\r\n\r\nfunction _bakeGroup(triplet, Processor, Group) {\r\n return function (complex, colorer, mode, polyComplexity, mask, material) {\r\n return new Processor(Group, triplet, complex, colorer, mode, polyComplexity, mask, material);\r\n };\r\n}\r\n\r\nclass GroupsFactory {\r\n static AtomsSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static OrphanedAtomsCrosses(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createCrosses(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.OrphanAtoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static BondsCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsCylinderGroup);\r\n }\r\n\r\n static BondsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.create2CLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsLinesGroup);\r\n }\r\n\r\n static CartoonChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesSubseqGroup);\r\n }\r\n\r\n static TraceChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CClosedCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesTraceGroup);\r\n }\r\n\r\n static NucleicSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicSpheresGroup);\r\n }\r\n\r\n static NucleicCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicCylindersGroup);\r\n }\r\n\r\n static ALoopsTorus(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticTorusGroup);\r\n }\r\n\r\n static ALoopsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createChunkedLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticLinesGroup);\r\n }\r\n\r\n static QuickSurfGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createQuickSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static ContactSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createContactSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static SASSESSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createSASSES(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSASSESGroupStub);\r\n }\r\n\r\n static TextLabelsGeo(caps, settings) {\r\n const gfxTriplet = MeshCreator.createLabels(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsTextGroup);\r\n }\r\n}\r\n\r\nexport default GroupsFactory;\r\n","import _ from 'lodash';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport factory from './groups/GroupsFactory';\r\n\r\n/**\r\n * Create new mode.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the mode after its creation.\r\n *\r\n * @exports Mode\r\n * @this Mode\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available modes used for building and displaying molecule geometry.\r\n */\r\nclass Mode {\r\n constructor(opts) {\r\n if (this.constructor === Mode) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Mode options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts);\r\n }\r\n\r\n /**\r\n * Get mode identification, probably with options.\r\n * @returns {string|Array} Mode identifier string ({@link Mode#id}) or two-element array containing both mode\r\n * identifier and options ({@link Mode#opts}).\r\n * Options are returned if they were changed during or after the mode creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, this.settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const polyComplexity = this.opts.polyComplexity ? this.opts.polyComplexity[this.settings.now.resolution] : 0;\r\n const groupList = this.depGroups;\r\n const groupCount = groupList.length;\r\n const group = new gfxutils.RCGroup();\r\n const self = this;\r\n for (let i = 0; i < groupCount; ++i) {\r\n let currGroup = groupList[i];\r\n let renderParams = {};\r\n if (_.isArray(currGroup)) {\r\n renderParams = currGroup[1].call(this);\r\n [currGroup] = currGroup;\r\n }\r\n const Group = factory[currGroup](null, this.settings, renderParams);\r\n const newGroup = new Group(complex, colorer, self, polyComplexity, mask, material);\r\n if (newGroup.children.length > 0) {\r\n group.add(newGroup);\r\n }\r\n }\r\n return group;\r\n }\r\n}\r\n\r\nmakeContextDependent(Mode.prototype);\r\n\r\n/**\r\n* Mode identifier.\r\n* @type {string}\r\n*/\r\nMode.prototype.id = '__';\r\n\r\n/**\r\n * Mode geo groups.\r\n * @type {Array}\r\n */\r\nMode.prototype.depGroups = [];\r\n\r\nexport default Mode;\r\n","import Mode from './Mode';\r\n\r\nfunction getRenderParams() {\r\n return {\r\n lineWidth: this.opts.lineWidth,\r\n };\r\n}\r\n\r\nclass LinesMode extends Mode {\r\n static id = 'LN';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const groups = this.depGroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n groups[i] = [groups[i], getRenderParams];\r\n }\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n\r\n calcAtomRadius() {\r\n return this.opts.atom;\r\n }\r\n\r\n getAromaticOffset() {\r\n return this.opts.offsarom;\r\n }\r\n\r\n getAromaticArcChunks() {\r\n return this.opts.chunkarom;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n}\r\n\r\nLinesMode.prototype.id = 'LN';\r\nLinesMode.prototype.name = 'Lines';\r\nLinesMode.prototype.shortName = 'Lines';\r\nLinesMode.prototype.depGroups = [\r\n 'ALoopsLines',\r\n 'BondsLines',\r\n 'OrphanedAtomsCrosses',\r\n];\r\n\r\nexport default LinesMode;\r\n","/* eslint-disable no-magic-numbers */\r\nimport Mode from './Mode';\r\n\r\nclass LicoriceMode extends Mode {\r\n static id = 'LC';\r\n\r\n calcAtomRadius(_atom) {\r\n return this.opts.bond;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nLicoriceMode.prototype.id = 'LC';\r\nLicoriceMode.prototype.name = 'Licorice';\r\nLicoriceMode.prototype.shortName = 'Licorice';\r\nLicoriceMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default LicoriceMode;\r\n","/* eslint-disable no-magic-numbers */\r\nimport Mode from './Mode';\r\n\r\nclass BallsAndSticksMode extends Mode {\r\n static id = 'BS';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius * this.opts.atom;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nBallsAndSticksMode.prototype.id = 'BS';\r\nBallsAndSticksMode.prototype.name = 'Balls and Sticks';\r\nBallsAndSticksMode.prototype.shortName = 'Balls';\r\nBallsAndSticksMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default BallsAndSticksMode;\r\n","import Mode from './Mode';\r\n\r\nclass VanDerWaalsMode extends Mode {\r\n static id = 'VW';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n}\r\n\r\nVanDerWaalsMode.prototype.id = 'VW';\r\nVanDerWaalsMode.prototype.name = 'Van der Waals';\r\nVanDerWaalsMode.prototype.shortName = 'VDW';\r\nVanDerWaalsMode.prototype.depGroups = ['AtomsSpheres'];\r\n\r\nexport default VanDerWaalsMode;\r\n","import Mode from './Mode';\r\n\r\nclass TraceMode extends Mode {\r\n static id = 'TR';\r\n\r\n calcStickRadius() {\r\n return this.opts.radius;\r\n }\r\n}\r\n\r\nTraceMode.prototype.id = 'TR';\r\nTraceMode.prototype.name = 'Trace';\r\nTraceMode.prototype.shortName = 'Trace';\r\nTraceMode.prototype.depGroups = ['TraceChains'];\r\n\r\nexport default TraceMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass TubeMode extends Mode {\r\n static id = 'TU';\r\n\r\n getResidueRadius(_residue) {\r\n return this.TUBE_RADIUS;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const rad = this.opts.radius;\r\n this.TUBE_RADIUS = new THREE.Vector2(rad, rad);\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nTubeMode.prototype.id = 'TU';\r\nTubeMode.prototype.name = 'Tube';\r\nTubeMode.prototype.shortName = 'Tube';\r\nTubeMode.prototype.depGroups = ['CartoonChains'];\r\n\r\nexport default TubeMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass CartoonMode extends Mode {\r\n static id = 'CA';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n // cache for secondary structure options\r\n this.secCache = {};\r\n }\r\n\r\n getResidueStartRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (!second || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return secOpts.start;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueEndRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (second === null || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return this.ARROW_END;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueRadius(residue, val) {\r\n const startRad = this.getResidueStartRadius(residue);\r\n if (val === 0) {\r\n return startRad;\r\n }\r\n\r\n const endRad = this.getResidueEndRadius(residue);\r\n if (val === 2) {\r\n return endRad;\r\n }\r\n\r\n return startRad.clone().lerp(endRad, val / 2.0);\r\n }\r\n\r\n calcStickRadius(_res) {\r\n return this.opts.radius;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const tubeRad = this.opts.radius;\r\n const secHeight = this.opts.depth;\r\n\r\n this.TUBE_RADIUS = new THREE.Vector2(tubeRad, tubeRad);\r\n this.ARROW_END = new THREE.Vector2(secHeight, tubeRad);\r\n const secCache = {};\r\n const secData = this.opts.ss;\r\n /* eslint-disable guard-for-in */\r\n for (const prop in secData) {\r\n secCache[prop] = {\r\n center: new THREE.Vector2(secHeight, secData[prop].width),\r\n start: new THREE.Vector2(secHeight, secData[prop].arrow),\r\n };\r\n }\r\n this.secCache = secCache;\r\n /* eslint-enable guard-for-in */\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nCartoonMode.prototype.id = 'CA';\r\nCartoonMode.prototype.name = 'Cartoon';\r\nCartoonMode.prototype.shortName = 'Cartoon';\r\nCartoonMode.prototype.depGroups = [\r\n 'CartoonChains',\r\n 'NucleicSpheres',\r\n 'NucleicCylinders',\r\n];\r\n\r\nexport default CartoonMode;\r\n","import chem from '../../chem';\r\nimport Mode from './Mode';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction getRenderParams() {\r\n return {\r\n wireframe: this.opts.wireframe,\r\n zClip: this.opts.zClip,\r\n };\r\n}\r\n\r\nclass SurfaceMode extends Mode {\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const surfaces = this.surfaceNames;\r\n const groups = this.depGroups;\r\n for (let i = 0, n = surfaces.length; i < n; ++i) {\r\n groups[groups.length] = [surfaces[i], getRenderParams];\r\n }\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getVisibilitySelector() {\r\n let visibilitySelector = null;\r\n if (this.opts.subset !== '') {\r\n const res = selectors.parse(this.opts.subset);\r\n if (!res.error) {\r\n visibilitySelector = res.selector;\r\n }\r\n }\r\n return visibilitySelector;\r\n }\r\n}\r\n\r\nSurfaceMode.prototype.isSurface = true;\r\nSurfaceMode.prototype.surfaceNames = [];\r\n\r\nexport default SurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass QuickSurfaceMode extends SurfaceMode {\r\n static id = 'QS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n useBeads: false,\r\n isoValue: this.opts.isoValue,\r\n gaussLim: this.opts.gaussLim[this.settings.now.resolution],\r\n radScale: this.opts.scale,\r\n gridSpacing: this.opts.gridSpacing[this.settings.now.resolution],\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nQuickSurfaceMode.prototype.id = 'QS';\r\nQuickSurfaceMode.prototype.name = 'Quick Surface';\r\nQuickSurfaceMode.prototype.shortName = 'Quick Surf';\r\nQuickSurfaceMode.prototype.surfaceNames = ['QuickSurfGeo'];\r\n\r\nexport default QuickSurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass IsoSurfaceMode extends SurfaceMode {\r\n constructor(excludeProbe, opts) {\r\n super(opts);\r\n this._excludeProbe = excludeProbe;\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getSurfaceOpts() {\r\n return {\r\n gridSpacing: this.opts.polyComplexity[this.settings.now.resolution],\r\n radScale: this._radScale,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n probeRadius: this.opts.probeRadius,\r\n excludeProbe: this._excludeProbe,\r\n };\r\n }\r\n}\r\n\r\nIsoSurfaceMode.prototype.id = 'SU';\r\nIsoSurfaceMode.prototype.name = 'Surface';\r\nIsoSurfaceMode.prototype.shortName = 'Surface';\r\nIsoSurfaceMode.prototype.surfaceNames = ['SASSESSurfaceGeo'];\r\n\r\nIsoSurfaceMode.prototype._radScale = 1;\r\nIsoSurfaceMode.prototype._excludeProbe = false;\r\n\r\nexport default IsoSurfaceMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSASMode extends IsoSurfaceMode {\r\n static id = 'SA';\r\n\r\n constructor(opts) {\r\n super(false, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSASMode.prototype.id = 'SA';\r\nIsoSurfaceSASMode.prototype.name = 'Solvent Accessible Surface';\r\nIsoSurfaceSASMode.prototype.shortName = 'SAS';\r\n\r\nexport default IsoSurfaceSASMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSESMode extends IsoSurfaceMode {\r\n static id = 'SE';\r\n\r\n constructor(opts) {\r\n super(true, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSESMode.prototype.id = 'SE';\r\nIsoSurfaceSESMode.prototype.name = 'Solvent Excluded Surface';\r\nIsoSurfaceSESMode.prototype.shortName = 'SES';\r\n\r\nexport default IsoSurfaceSESMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass ContactSurfaceMode extends SurfaceMode {\r\n static id = 'CS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n probeRadius: this.opts.probeRadius,\r\n radScale: this.opts.polyComplexity[this.settings.now.resolution],\r\n scaleFactor: this.opts.polyComplexity[this.settings.now.resolution],\r\n gridSpacing: 1.0 / this.opts.polyComplexity[this.settings.now.resolution],\r\n isoValue: this.opts.isoValue,\r\n probePositions: this.opts.probePositions,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nContactSurfaceMode.prototype.id = 'CS';\r\nContactSurfaceMode.prototype.name = 'Contact Surface';\r\nContactSurfaceMode.prototype.shortName = 'Contact Surf';\r\nContactSurfaceMode.prototype.isSurface = true;\r\nContactSurfaceMode.prototype.surfaceNames = ['ContactSurfaceGeo'];\r\n\r\nexport default ContactSurfaceMode;\r\n","import _ from 'lodash';\r\nimport Mode from './Mode';\r\n\r\nclass TextMode extends Mode {\r\n static id = 'TX';\r\n\r\n getTemplateOptions() {\r\n return this.opts.template;\r\n }\r\n\r\n getLabelOpts() {\r\n return _.merge(this.opts, {\r\n colors: true,\r\n adjustColor: true,\r\n transparent: true,\r\n });\r\n }\r\n}\r\n\r\nTextMode.prototype.id = 'TX';\r\nTextMode.prototype.name = 'Text mode';\r\nTextMode.prototype.shortName = 'Text';\r\nTextMode.prototype.depGroups = ['TextLabelsGeo'];\r\n\r\nexport default TextMode;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport LinesMode from './modes/LinesMode';\r\nimport LicoriceMode from './modes/LicoriceMode';\r\nimport BallsAndSticksMode from './modes/BallsAndSticksMode';\r\nimport VanDerWaalsMode from './modes/VanDerWaalsMode';\r\nimport TraceMode from './modes/TraceMode';\r\nimport TubeMode from './modes/TubeMode';\r\nimport CartoonMode from './modes/CartoonMode';\r\nimport QuickSurfaceMode from './modes/QuickSurfaceMode';\r\nimport IsoSurfaceSASMode from './modes/IsoSurfaceSASMode';\r\nimport IsoSurfaceSESMode from './modes/IsoSurfaceSESMode';\r\nimport ContactSurfaceMode from './modes/ContactSurfaceMode';\r\nimport TextMode from './modes/TextMode';\r\n\r\nconst modes = new EntityList([\r\n LinesMode,\r\n LicoriceMode,\r\n BallsAndSticksMode,\r\n VanDerWaalsMode,\r\n TraceMode,\r\n TubeMode,\r\n CartoonMode,\r\n QuickSurfaceMode,\r\n IsoSurfaceSASMode,\r\n IsoSurfaceSESMode,\r\n ContactSurfaceMode,\r\n TextMode,\r\n]);\r\n\r\nexport default modes;\r\n","import _ from 'lodash';\r\n\r\nfunction clamp(x, a, b) {\r\n return x <= b ? x < 0 ? 0 : x : b;\r\n}\r\n\r\nfunction lerpColor(c1, c2, alpha) {\r\n const beta = 1 - alpha;\r\n const r1 = (c1 >> 16) & 0xff;\r\n const g1 = (c1 >> 8) & 0xff;\r\n const b1 = c1 & 0xff;\r\n const r2 = (c2 >> 16) & 0xff;\r\n const g2 = (c2 >> 8) & 0xff;\r\n const b2 = c2 & 0xff;\r\n const r = beta * r1 + alpha * r2;\r\n const g = beta * g1 + alpha * g2;\r\n const b = beta * b1 + alpha * b2;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nclass Palette {\r\n constructor(name, id) {\r\n this.name = name || 'Custom';\r\n this.id = id || 'CP';\r\n }\r\n\r\n getElementColor(name, asIs = false) {\r\n const color = this.elementColors[name];\r\n return color === undefined && !asIs ? this.defaultElementColor : color;\r\n }\r\n\r\n getResidueColor(name, asIs = false) {\r\n const color = this.residueColors[name];\r\n return color === undefined && !asIs ? this.defaultResidueColor : color;\r\n }\r\n\r\n getChainColor(name) {\r\n let chain = name.charCodeAt(0);\r\n chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F)\r\n % this.chainColors.length;\r\n return this.chainColors[chain];\r\n }\r\n\r\n getSecondaryColor(type, asIs = false) {\r\n const color = this.secondaryColors[type];\r\n return color === undefined && !asIs ? this.defaultSecondaryColor : color;\r\n }\r\n\r\n getSequentialColor(index) {\r\n const { colors } = this;\r\n const len = colors.length;\r\n return index < 0 ? colors[(index % len) + len] : colors[index % len];\r\n }\r\n\r\n getGradientColor(value, gradientName) {\r\n const gradient = this.gradients[gradientName];\r\n if (!gradient) {\r\n return this.defaultNamedColor;\r\n }\r\n const count = gradient.length;\r\n const index = value * (count - 1);\r\n let left = Math.floor(index);\r\n const right = clamp(left + 1, 0, count - 1);\r\n left = clamp(left, 0, count - 1);\r\n return lerpColor(gradient[left], gradient[right], index - left);\r\n }\r\n\r\n getNamedColor(name, asIs = false) {\r\n const color = this.namedColors[name];\r\n return color === undefined && !asIs ? this.defaultNamedColor : color;\r\n }\r\n}\r\n\r\n_.assign(Palette.prototype, {\r\n colors: [0xFFFFFF, 0xFF0000, 0x00FF00, 0x0000FF, 0x808080],\r\n\r\n minRangeColor: 0x000000,\r\n midRangeColor: 0x7F7F7F,\r\n maxRangeColor: 0xFFFFFF,\r\n\r\n defaultElementColor: 0xFFFFFF,\r\n elementColors: {},\r\n\r\n defaultResidueColor: 0xFFFFFF,\r\n residueColors: {},\r\n\r\n chainColors: [0xFFFFFF],\r\n\r\n defaultSecondaryColor: 0xFFFFFF,\r\n secondaryColors: {},\r\n\r\n defaultGradientColor: 0x000000,\r\n\r\n defaultNamedColor: 0xFFFFFF,\r\n namedColorsArray: [\r\n /* eslint-disable no-multi-spaces */\r\n ['indianred', 0xcd5c5c],\r\n ['lightcoral', 0xf08080],\r\n ['salmon', 0xfa8072],\r\n ['darksalmon', 0xe9967a],\r\n ['lightsalmon', 0xffa07a],\r\n ['crimson', 0xdc143c],\r\n ['red', 0xff0000],\r\n ['firebrick', 0xb22222],\r\n ['darkred', 0x8b0000],\r\n ['pink', 0xffc0cb],\r\n ['lightpink', 0xffb6c1],\r\n ['hotpink', 0xff69b4],\r\n ['deeppink', 0xff1493],\r\n ['mediumvioletred', 0xc71585],\r\n ['palevioletred', 0xdb7093],\r\n ['coral', 0xff7f50],\r\n ['tomato', 0xff6347],\r\n ['orangered', 0xff4500],\r\n ['darkorange', 0xff8c00],\r\n ['orange', 0xffa500],\r\n ['gold', 0xffd700],\r\n ['yellow', 0xffff00],\r\n ['lightyellow', 0xffffe0],\r\n ['lemonchiffon', 0xfffacd],\r\n ['lightgoldenrodyellow', 0xfafad2],\r\n ['papayawhip', 0xffefd5],\r\n ['moccasin', 0xffe4b5],\r\n ['peachpuff', 0xffdab9],\r\n ['palegoldenrod', 0xeee8aa],\r\n ['khaki', 0xf0e68c],\r\n ['darkkhaki', 0xbdb76b],\r\n ['lavender', 0xe6e6fa],\r\n ['thistle', 0xd8bfd8],\r\n ['plum', 0xdda0dd],\r\n ['violet', 0xee82ee],\r\n ['orchid', 0xda70d6],\r\n ['fuchsia', 0xff00ff],\r\n ['magenta', 0xff00ff],\r\n ['mediumorchid', 0xba55d3],\r\n ['mediumpurple', 0x9370db],\r\n ['rebeccapurple', 0x663399],\r\n ['blueviolet', 0x8a2be2],\r\n ['darkviolet', 0x9400d3],\r\n ['darkorchid', 0x9932cc],\r\n ['darkmagenta', 0x8b008b],\r\n ['purple', 0x800080],\r\n ['indigo', 0x4b0082],\r\n ['slateblue', 0x6a5acd],\r\n ['mediumslateblue', 0x7b68ee],\r\n ['darkslateblue', 0x483d8b],\r\n ['greenyellow', 0xadff2f],\r\n ['chartreuse', 0x7fff00],\r\n ['lawngreen', 0x7cfc00],\r\n ['lime', 0x00ff00],\r\n ['limegreen', 0x32cd32],\r\n ['palegreen', 0x98fb98],\r\n ['lightgreen', 0x90ee90],\r\n ['mediumspringgreen', 0x00fa9a],\r\n ['springgreen', 0x00ff7f],\r\n ['mediumseagreen', 0x3cb371],\r\n ['seagreen', 0x2e8b57],\r\n ['forestgreen', 0x228b22],\r\n ['green', 0x008000],\r\n ['darkgreen', 0x006400],\r\n ['yellowgreen', 0x9acd32],\r\n ['olivedrab', 0x6b8e23],\r\n ['olive', 0x808000],\r\n ['darkolivegreen', 0x556b2f],\r\n ['mediumaquamarine', 0x66cdaa],\r\n ['darkseagreen', 0x8fbc8f],\r\n ['lightseagreen', 0x20b2aa],\r\n ['darkcyan', 0x008b8b],\r\n ['teal', 0x008080],\r\n ['aqua', 0x00ffff],\r\n ['cyan', 0x00ffff],\r\n ['lightcyan', 0xe0ffff],\r\n ['paleturquoise', 0xafeeee],\r\n ['aquamarine', 0x7fffd4],\r\n ['turquoise', 0x40e0d0],\r\n ['mediumturquoise', 0x48d1cc],\r\n ['darkturquoise', 0x00ced1],\r\n ['cadetblue', 0x5f9ea0],\r\n ['steelblue', 0x4682b4],\r\n ['lightsteelblue', 0xb0c4de],\r\n ['powderblue', 0xb0e0e6],\r\n ['lightblue', 0xadd8e6],\r\n ['skyblue', 0x87ceeb],\r\n ['lightskyblue', 0x87cefa],\r\n ['deepskyblue', 0x00bfff],\r\n ['dodgerblue', 0x1e90ff],\r\n ['cornflowerblue', 0x6495ed],\r\n ['royalblue', 0x4169e1],\r\n ['blue', 0x0000ff],\r\n ['mediumblue', 0x0000cd],\r\n ['darkblue', 0x00008b],\r\n ['navy', 0x000080],\r\n ['midnightblue', 0x191970],\r\n ['cornsilk', 0xfff8dc],\r\n ['blanchedalmond', 0xffebcd],\r\n ['bisque', 0xffe4c4],\r\n ['navajowhite', 0xffdead],\r\n ['wheat', 0xf5deb3],\r\n ['burlywood', 0xdeb887],\r\n ['tan', 0xd2b48c],\r\n ['rosybrown', 0xbc8f8f],\r\n ['sandybrown', 0xf4a460],\r\n ['goldenrod', 0xdaa520],\r\n ['darkgoldenrod', 0xb8860b],\r\n ['peru', 0xcd853f],\r\n ['chocolate', 0xd2691e],\r\n ['saddlebrown', 0x8b4513],\r\n ['sienna', 0xa0522d],\r\n ['brown', 0xa52a2a],\r\n ['maroon', 0x800000],\r\n ['white', 0xffffff],\r\n ['snow', 0xfffafa],\r\n ['honeydew', 0xf0fff0],\r\n ['mintcream', 0xf5fffa],\r\n ['azure', 0xf0ffff],\r\n ['aliceblue', 0xf0f8ff],\r\n ['ghostwhite', 0xf8f8ff],\r\n ['whitesmoke', 0xf5f5f5],\r\n ['seashell', 0xfff5ee],\r\n ['beige', 0xf5f5dc],\r\n ['oldlace', 0xfdf5e6],\r\n ['floralwhite', 0xfffaf0],\r\n ['ivory', 0xfffff0],\r\n ['antiquewhite', 0xfaebd7],\r\n ['linen', 0xfaf0e6],\r\n ['lavenderblush', 0xfff0f5],\r\n ['mistyrose', 0xffe4e1],\r\n ['gainsboro', 0xdcdcdc],\r\n ['lightgray', 0xd3d3d3],\r\n ['silver', 0xc0c0c0],\r\n ['darkgray', 0xa9a9a9],\r\n ['gray', 0x808080],\r\n ['dimgray', 0x696969],\r\n ['lightslategray', 0x778899],\r\n ['slategray', 0x708090],\r\n ['darkslategray', 0x2f4f4f],\r\n ['black', 0x000000],\r\n /* eslint-enable no-multi-spaces */\r\n ],\r\n\r\n namedColors: {},\r\n /* eslint-enable no-magic-numbers */\r\n\r\n gradients: {\r\n rainbow: [\r\n 0x0000ff, // blue\r\n 0x00ffff, // cyan\r\n 0x00ff00, // green\r\n 0xffff00, // yellow\r\n 0xff0000, // red\r\n ],\r\n temp: [\r\n 0x0000ff, // blue\r\n 0x007fff, // light-blue\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n hot: [\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n cold: [\r\n 0xffffff, // white\r\n 0x007fff, // light-blue\r\n 0x0000ff, // blue\r\n ],\r\n 'blue-red': [\r\n 0x0000ff, // blue\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n reds: [\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n blues: [\r\n 0xffffff, // white\r\n 0x0000ff, // blue\r\n ],\r\n },\r\n});\r\n\r\nconst { namedColorsArray, namedColors } = Palette.prototype;\r\n\r\nfor (let i = 0, { length } = namedColorsArray; i < length; ++i) {\r\n const [name, value] = namedColorsArray[i];\r\n namedColors[name] = value;\r\n}\r\n\r\nexport default Palette;\r\n","import Palette from './Palette';\r\n\r\nconst palette = new Palette('CPK', 'CP');\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n C: 0x202020,\r\n N: 0x2060FF,\r\n O: 0xEE2010,\r\n F: 0x00FF00,\r\n P: 0x8020FF,\r\n S: 0xFFFF00,\r\n CL: 0x00BB00,\r\n FE: 0xD0D0D0,\r\n CO: 0xD0D0D0,\r\n NI: 0xD0D0D0,\r\n CU: 0xD0D0D0,\r\n BR: 0x008800,\r\n I: 0x005500,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('Jmol', 'JM');\r\n\r\npalette.colors = [\r\n /* eslint-disable no-magic-numbers */\r\n 0x0000FF, // blue\r\n 0x0055FF, //\r\n 0x00ABFF, //\r\n 0x00FFFF, // cyan\r\n 0x00FFAB, //\r\n 0x00FF55, //\r\n 0x00FF00, // green\r\n 0x55FF00, //\r\n 0xABFF00, //\r\n 0xFFFF00, // yellow\r\n 0xFFAB00, //\r\n 0xFF5500, //\r\n 0xFF0000, // red\r\n 0xFF0055, //\r\n 0xFF00AB, //\r\n 0xFF00FF, // magenta\r\n 0xAB00FF, //\r\n 0x5500FF, //\r\n /* eslint-enable no-magic-numbers */\r\n];\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n D: 0xFFFFC0,\r\n T: 0xFFFFA0,\r\n HE: 0xD9FFFF,\r\n LI: 0xCC80FF,\r\n BE: 0xC2FF00,\r\n B: 0xFFB5B5,\r\n C: 0x909090,\r\n N: 0x3050F8,\r\n O: 0xFF0D0D,\r\n F: 0x90E050,\r\n NE: 0xB3E3F5,\r\n NA: 0xAB5CF2,\r\n MG: 0x8AFF00,\r\n AL: 0xBFA6A6,\r\n SI: 0xF0C8A0,\r\n P: 0xFF8000,\r\n S: 0xFFFF30,\r\n CL: 0x1FF01F,\r\n AR: 0x80D1E3,\r\n K: 0x8F40D4,\r\n CA: 0x3DFF00,\r\n SC: 0xE6E6E6,\r\n TI: 0xBFC2C7,\r\n V: 0xA6A6AB,\r\n CR: 0x8A99C7,\r\n MN: 0x9C7AC7,\r\n FE: 0xE06633,\r\n CO: 0xF090A0,\r\n NI: 0x50D050,\r\n CU: 0xC88033,\r\n ZN: 0x7D80B0,\r\n GA: 0xC28F8F,\r\n GE: 0x668F8F,\r\n AS: 0xBD80E3,\r\n SE: 0xFFA100,\r\n BR: 0xA62929,\r\n KR: 0x5CB8D1,\r\n RB: 0x702EB0,\r\n SR: 0x00FF00,\r\n Y: 0x94FFFF,\r\n ZR: 0x94E0E0,\r\n NB: 0x73C2C9,\r\n MO: 0x54B5B5,\r\n TC: 0x3B9E9E,\r\n RU: 0x248F8F,\r\n RH: 0x0A7D8C,\r\n PD: 0x006985,\r\n AG: 0xC0C0C0,\r\n CD: 0xFFD98F,\r\n IN: 0xA67573,\r\n SN: 0x668080,\r\n SB: 0x9E63B5,\r\n TE: 0xD47A00,\r\n I: 0x940094,\r\n XE: 0x429EB0,\r\n CS: 0x57178F,\r\n BA: 0x00C900,\r\n LA: 0x70D4FF,\r\n CE: 0xFFFFC7,\r\n PR: 0xD9FFC7,\r\n ND: 0xC7FFC7,\r\n PM: 0xA3FFC7,\r\n SM: 0x8FFFC7,\r\n EU: 0x61FFC7,\r\n GD: 0x45FFC7,\r\n TB: 0x30FFC7,\r\n DY: 0x1FFFC7,\r\n HO: 0x00FF9C,\r\n ER: 0x00E675,\r\n TM: 0x00D452,\r\n YB: 0x00BF38,\r\n LU: 0x00AB24,\r\n HF: 0x4DC2FF,\r\n TA: 0x4DA6FF,\r\n W: 0x2194D6,\r\n RE: 0x267DAB,\r\n OS: 0x266696,\r\n IR: 0x175487,\r\n PT: 0xD0D0E0,\r\n AU: 0xFFD123,\r\n HG: 0xB8B8D0,\r\n TL: 0xA6544D,\r\n PB: 0x575961,\r\n BI: 0x9E4FB5,\r\n PO: 0xAB5C00,\r\n AT: 0x754F45,\r\n RN: 0x428296,\r\n FR: 0x420066,\r\n RA: 0x007D00,\r\n AC: 0x70ABFA,\r\n TH: 0x00BAFF,\r\n PA: 0x00A1FF,\r\n U: 0x008FFF,\r\n NP: 0x0080FF,\r\n PU: 0x006BFF,\r\n AM: 0x545CF2,\r\n CM: 0x785CE3,\r\n BK: 0x8A4FE3,\r\n CF: 0xA136D4,\r\n ES: 0xB31FD4,\r\n FM: 0xB31FBA,\r\n MD: 0xB30DA6,\r\n NO: 0xBD0D87,\r\n LR: 0xC70066,\r\n RF: 0xCC0059,\r\n DB: 0xD1004F,\r\n SG: 0xD90045,\r\n BH: 0xE00038,\r\n HS: 0xE6002E,\r\n MT: 0xEB0026,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.defaultResidueColor = 0xBEA06E;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: 0xC8C8C8,\r\n ARG: 0x145AFF,\r\n ASN: 0x00DCDC,\r\n ASP: 0xE60A0A,\r\n CYS: 0xE6E600,\r\n GLN: 0x00DCDC,\r\n GLU: 0xE60A0A,\r\n GLY: 0xEBEBEB,\r\n HIS: 0x8282D2,\r\n ILE: 0x0F820F,\r\n LEU: 0x0F820F,\r\n LYS: 0x145AFF,\r\n MET: 0xE6E600,\r\n PHE: 0x3232AA,\r\n PRO: 0xDC9682,\r\n SER: 0xFA9600,\r\n THR: 0xFA9600,\r\n TRP: 0xB45AB4,\r\n TYR: 0x3232AA,\r\n VAL: 0x0F820F,\r\n A: 0xA0A0FF,\r\n C: 0xFF8C4B,\r\n G: 0xFF7070,\r\n I: 0x80FFFF,\r\n T: 0xA0FFA0,\r\n U: 0xFF8080,\r\n DA: 0xA0A0FF,\r\n DC: 0xFF8C4B,\r\n DG: 0xFF7070,\r\n DI: 0x80FFFF,\r\n DT: 0xA0FFA0,\r\n DU: 0xFF8080,\r\n '+A': 0xA0A0FF,\r\n '+C': 0xFF8C4B,\r\n '+G': 0xFF7070,\r\n '+I': 0x80FFFF,\r\n '+T': 0xA0FFA0,\r\n '+U': 0xFF8080,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.chainColors = [\r\n // ' '->0 'A'->1, 'B'->2\r\n 0xFFffffff, // ' ' & '0' white\r\n //\r\n 0xFFC0D0FF, // skyblue\r\n 0xFFB0FFB0, // pastel green\r\n 0xFFFFC0C8, // pink\r\n 0xFFFFFF80, // pastel yellow\r\n 0xFFFFC0FF, // pastel magenta\r\n 0xFFB0F0F0, // pastel cyan\r\n 0xFFFFD070, // pastel gold\r\n 0xFFF08080, // lightcoral\r\n\r\n 0xFFF5DEB3, // wheat\r\n 0xFF00BFFF, // deepskyblue\r\n 0xFFCD5C5C, // indianred\r\n 0xFF66CDAA, // mediumaquamarine\r\n 0xFF9ACD32, // yellowgreen\r\n 0xFFEE82EE, // violet\r\n 0xFF00CED1, // darkturquoise\r\n 0xFF00FF7F, // springgreen\r\n 0xFF3CB371, // mediumseagreen\r\n\r\n 0xFF00008B, // darkblue\r\n 0xFFBDB76B, // darkkhaki\r\n 0xFF006400, // darkgreen\r\n 0xFF800000, // maroon\r\n 0xFF808000, // olive\r\n 0xFF800080, // purple\r\n 0xFF008080, // teal\r\n 0xFFB8860B, // darkgoldenrod\r\n 0xFFB22222, // firebrick\r\n];\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xFF0080,\r\n [StructuralElementType.HELIX_PI]: 0x600080,\r\n [StructuralElementType.HELIX_310]: 0xA00080,\r\n [StructuralElementType.STRAND]: 0xFFC800,\r\n [StructuralElementType.TURN]: 0x6080FF,\r\n dna: 0xAE00FE,\r\n rna: 0xFD0162,\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('VMD', 'VM');\r\n\r\npalette.colors = [\r\n /* eslint-disable no-magic-numbers */\r\n 0x0000FF, // blue\r\n 0xFF0000, // red\r\n 0x606060, // gray\r\n 0xFF8000, // orange\r\n 0xFFFF00, // yellow\r\n 0x808033, // tan\r\n 0x999999, // silver\r\n 0x00FF00, // green\r\n 0xFFFFFF, // white\r\n 0xFF9999, // pink\r\n 0x40C0C0, // cyan\r\n 0xA600A6, // purple\r\n 0x80E666, // lime\r\n 0xE666B3, // mauve\r\n 0x804D00, // ochre\r\n 0x8080C0, // ice blue\r\n /* eslint-enable no-magic-numbers */\r\n];\r\n\r\npalette.defaultElementColor = 0x804D00;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n C: 0x40BFBF,\r\n N: 0x0000FF,\r\n O: 0xFF0000,\r\n P: 0x808033,\r\n S: 0xFFFF00,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.defaultResidueColor = 0x40C0C0;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: 0x0000FF,\r\n ARG: 0xFFFFFF,\r\n ASN: 0x808033,\r\n ASP: 0xFF0000,\r\n CYS: 0xFFFF00,\r\n GLN: 0xFF8000,\r\n GLU: 0xFF9999,\r\n GLY: 0xFFFFFF,\r\n HIS: 0x40C0C0,\r\n ILE: 0x00FF00,\r\n LEU: 0xFF9999,\r\n LYS: 0x40C0C0,\r\n MET: 0xFFFF00,\r\n PHE: 0xA600A6,\r\n PRO: 0x804C00,\r\n SER: 0xFFFF00,\r\n THR: 0xE666B3,\r\n TRP: 0x999999,\r\n TYR: 0x00FF00,\r\n VAL: 0x808033,\r\n A: 0x0000FF,\r\n C: 0xFF8000,\r\n G: 0xFFFF00,\r\n T: 0xA600A6,\r\n U: 0x00FF00,\r\n DA: 0x0000FF,\r\n DC: 0xFF8000,\r\n DG: 0xFFFF00,\r\n DT: 0xA600A6,\r\n DU: 0x00FF00,\r\n '+A': 0x0000FF,\r\n '+C': 0xFF8000,\r\n '+G': 0xFFFF00,\r\n '+T': 0xA600A6,\r\n '+U': 0x00FF00,\r\n WAT: 0x40C0C0,\r\n H2O: 0x40C0C0,\r\n HOH: 0x40C0C0,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.chainColors = [0xFFFFFF].concat(palette.colors);\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xA600A6,\r\n [StructuralElementType.HELIX_310]: 0x0000FF,\r\n [StructuralElementType.HELIX_PI]: 0xFF0000,\r\n [StructuralElementType.STRAND]: 0xFFFF00,\r\n [StructuralElementType.BRIDGE]: 0x808033,\r\n [StructuralElementType.TURN]: 0x40C0C0,\r\n};\r\n\r\nexport default palette;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport cpkPalette from './palettes/cpkPalette';\r\nimport jmolPalette from './palettes/jmolPalette';\r\nimport vmdPalette from './palettes/vmdPalette';\r\n\r\nconst palettes = new EntityList([\r\n cpkPalette,\r\n jmolPalette,\r\n vmdPalette,\r\n]);\r\n\r\nexport default palettes;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport palettes from '../palettes';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports Colorer\r\n * @this Colorer\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available coloring algorithms used for building and displaying molecule geometry.\r\n */\r\nclass Colorer {\r\n constructor(opts) {\r\n if (this.constructor === Colorer) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Colorer options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(settings.now.colorers[this.id], true), opts);\r\n /**\r\n * Palette in use.\r\n * @type {Palette}\r\n */\r\n this.palette = palettes.first;\r\n }\r\n\r\n /**\r\n * Get Colorer identification, probably with options.\r\n * @returns {string|Array} Colorer identifier string ({@link Colorer#id}) or two-element array containing both colorer\r\n * identifier and options ({@link Colorer#opts}).\r\n * Options are returned if they were changed during or after colorer creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, settings.now.colorers[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n}\r\n\r\n/**\r\n * Colorer identifier.\r\n * @type {string}\r\n */\r\n\r\nColorer.prototype.id = '__';\r\n\r\nexport default Colorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Element\r\n *\r\n * @exports ElementColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on chemical element.\r\n */\r\nclass ElementColorer extends Colorer {\r\n static id = 'EL';\r\n\r\n getAtomColor(atom, _complex) {\r\n const type = atom.element.name;\r\n if (type === 'C' && this.opts.carbon >= 0) {\r\n return this.opts.carbon;\r\n }\r\n return this.palette.getElementColor(type);\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nElementColorer.prototype.id = 'EL';\r\nElementColorer.prototype.name = 'Element';\r\nElementColorer.prototype.shortName = 'Element';\r\n\r\nexport default ElementColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Coloring algorithm based on residue type.\r\n *\r\n * @see ResidueType\r\n *\r\n * @exports ResidueTypeColorer\r\n * @constructor\r\n */\r\nclass ResidueTypeColorer extends Colorer {\r\n static id = 'RT';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getResidueColor(residue._type._name);\r\n }\r\n}\r\n\r\nResidueTypeColorer.prototype.id = 'RT';\r\nResidueTypeColorer.prototype.name = 'Residue Type';\r\nResidueTypeColorer.prototype.shortName = 'Residue';\r\n\r\nexport default ResidueTypeColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass SequenceColorer extends Colorer {\r\n static id = 'SQ';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const chain = residue._chain;\r\n if (chain.minSequence === Number.POSITIVE_INFINITY && chain.maxSequence === Number.NEGATIVE_INFINITY) {\r\n return this.palette.defaultNamedColor;\r\n }\r\n const min = chain.minSequence;\r\n const max = chain.maxSequence > min ? chain.maxSequence : min + 1;\r\n return this.palette.getGradientColor((residue._sequence - min) / (max - min), this.opts.gradient);\r\n }\r\n}\r\n\r\nSequenceColorer.prototype.id = 'SQ';\r\nSequenceColorer.prototype.name = 'Sequence';\r\nSequenceColorer.prototype.shortName = 'Sequence';\r\n\r\nexport default SequenceColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ChainColorer extends Colorer {\r\n static id = 'CH';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getChainColor(residue.getChain()._name);\r\n }\r\n}\r\n\r\nChainColorer.prototype.id = 'CH';\r\nChainColorer.prototype.name = 'Chain';\r\nChainColorer.prototype.shortName = 'Chain';\r\n\r\nexport default ChainColorer;\r\n","import Colorer from './Colorer';\r\nimport ResidueType from '../../chem/ResidueType';\r\n\r\nclass SecondaryStructureColorer extends Colorer {\r\n static id = 'SS';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n if (residue._type.flags & ResidueType.Flags.DNA) {\r\n return this.palette.getSecondaryColor('dna');\r\n }\r\n if (residue._type.flags & ResidueType.Flags.RNA) {\r\n return this.palette.getSecondaryColor('rna');\r\n }\r\n const secondary = residue.getSecondary();\r\n if (secondary) {\r\n let color = this.palette.getSecondaryColor(secondary.type, true);\r\n if (color === undefined) {\r\n color = this.palette.getSecondaryColor(secondary.generic);\r\n }\r\n return color;\r\n }\r\n return this.palette.defaultSecondaryColor;\r\n }\r\n}\r\n\r\nSecondaryStructureColorer.prototype.id = 'SS';\r\nSecondaryStructureColorer.prototype.name = 'Secondary Structure';\r\nSecondaryStructureColorer.prototype.shortName = 'Structure';\r\n\r\nexport default SecondaryStructureColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass UniformColorer extends Colorer {\r\n static id = 'UN';\r\n\r\n getAtomColor(_atom, _complex) {\r\n return this.opts.color;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nUniformColorer.prototype.id = 'UN';\r\nUniformColorer.prototype.name = 'Uniform';\r\nUniformColorer.prototype.shortName = 'Uniform';\r\n\r\nexport default UniformColorer;\r\n","import Colorer from './Colorer';\r\nimport selectors from '../../chem/selectors';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports ConditionalColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on a selector string used as a condition.\r\n */\r\nclass ConditionalColorer extends Colorer {\r\n static id = 'CO';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n const parsed = selectors.parse(this.opts.subset);\r\n this._subsetCached = parsed.error ? selectors.none() : parsed.selector;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n return this._subsetCached.includesAtom(atom) ? this.opts.color : this.opts.baseColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const subset = this._subsetCached;\r\n const atoms = residue._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (!subset.includesAtom(atoms[i])) {\r\n return this.opts.baseColor;\r\n }\r\n }\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nConditionalColorer.prototype.id = 'CO';\r\nConditionalColorer.prototype.name = 'Conditional';\r\nConditionalColorer.prototype.shortName = 'Conditional';\r\n\r\nexport default ConditionalColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ConformationColorer extends Colorer {\r\n static id = 'CF';\r\n\r\n getAtomColor(atom, _complex) {\r\n return this.palette.getChainColor(String.fromCharCode(atom.location));\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nConformationColorer.prototype.id = 'CF';\r\nConformationColorer.prototype.name = 'Conformation';\r\nConformationColorer.prototype.shortName = 'Conformation';\r\n\r\nexport default ConformationColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Temperature\r\n *\r\n * @exports TemperatureColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on temperature of chemical element.\r\n */\r\nclass TemperatureColorer extends Colorer {\r\n static id = 'TM';\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n let factor = 1;\r\n if (atom.temperature && opts) {\r\n if (opts.min === opts.max) {\r\n factor = atom.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (atom.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n if (!opts) {\r\n return this.palette.defaultGradientColor;\r\n }\r\n if (residue.temperature) {\r\n let factor = 0;\r\n if (opts.min === opts.max) {\r\n factor = residue.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (residue.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n}\r\n\r\nTemperatureColorer.prototype.id = 'TM'; // [T]e[M]perature\r\nTemperatureColorer.prototype.name = 'Temperature';\r\nTemperatureColorer.prototype.shortName = 'Temperature';\r\n\r\nexport default TemperatureColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Occupancy\r\n *\r\n * @exports OccupancyColorer\r\n * @augments Occupancy\r\n * @constructor\r\n * @classdesc Coloring algorithm based on occupancy of chemical element.\r\n */\r\nclass OccupancyColorer extends Colorer {\r\n static id = 'OC';\r\n\r\n _getColorByOccupancy(occupancy, opts) {\r\n if (occupancy !== undefined) {\r\n const factor = 1 - occupancy;\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(atom.occupancy, opts);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(residue.occupancy, opts);\r\n }\r\n}\r\n\r\nOccupancyColorer.prototype.id = 'OC'; // [OC]cupancy\r\nOccupancyColorer.prototype.name = 'Occupancy';\r\nOccupancyColorer.prototype.shortName = 'Occupancy';\r\n\r\nexport default OccupancyColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass HydrophobicityColorer extends Colorer {\r\n static id = 'HY';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n let color = this.palette.defaultResidueColor;\r\n if (residue._type.hydrophobicity !== undefined) {\r\n // Kyte Doolitle hydro [-4.5,4.5]->[0.1]\r\n const min = -4.5;\r\n const max = 4.5;\r\n color = this.palette.getGradientColor((residue._type.hydrophobicity - min) / (max - min), this.opts.gradient);\r\n }\r\n return color;\r\n }\r\n}\r\n\r\nHydrophobicityColorer.prototype.id = 'HY';\r\nHydrophobicityColorer.prototype.name = 'Hydrophobicity';\r\nHydrophobicityColorer.prototype.shortName = 'Hydrophobicity';\r\n\r\nexport default HydrophobicityColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass MoleculeColorer extends Colorer {\r\n static id = 'MO';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const molecule = residue._molecule;\r\n const count = _complex.getMoleculeCount();\r\n if (count > 1) {\r\n return this.palette.getGradientColor((molecule.index - 1) / (count - 1), this.opts.gradient);\r\n }\r\n return this.palette.getGradientColor(0, this.opts.gradient);\r\n }\r\n}\r\n\r\nMoleculeColorer.prototype.id = 'MO';\r\nMoleculeColorer.prototype.name = 'Molecule';\r\nMoleculeColorer.prototype.shortName = 'Molecule';\r\n\r\nexport default MoleculeColorer;\r\n","import Colorer from './Colorer';\r\nimport Atom from '../../chem/Atom';\r\n\r\nfunction scaleColor(c, factor) {\r\n const r1 = (c >> 16) & 0xff;\r\n const g1 = (c >> 8) & 0xff;\r\n const b1 = c & 0xff;\r\n const r = factor * r1;\r\n const g = factor * g1;\r\n const b = factor * b1;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports CarbonColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on selection carbon atoms.\r\n */\r\nclass CarbonColorer extends Colorer {\r\n static id = 'CB';\r\n\r\n getAtomColor(atom, _complex) {\r\n const colorCarbon = this.opts.color;\r\n const colorNotCarbon = scaleColor(colorCarbon, this.opts.factor);\r\n return (atom.flags & Atom.Flags.CARBON) ? colorCarbon : colorNotCarbon;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nCarbonColorer.prototype.id = 'CB';\r\nCarbonColorer.prototype.name = 'Carbon';\r\nCarbonColorer.prototype.shortName = 'Carbon';\r\n\r\nexport default CarbonColorer;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport ElementColorer from './colorers/ElementColorer';\r\nimport ResidueTypeColorer from './colorers/ResidueTypeColorer';\r\nimport SequenceColorer from './colorers/SequenceColorer';\r\nimport ChainColorer from './colorers/ChainColorer';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\nimport UniformColorer from './colorers/UniformColorer';\r\nimport ConditionalColorer from './colorers/ConditionalColorer';\r\nimport ConformationColorer from './colorers/ConformationColorer';\r\nimport TemperatureColorer from './colorers/TemperatureColorer';\r\nimport OccupancyColorer from './colorers/OccupancyColorer';\r\nimport HydrophobicityColorer from './colorers/HydrophobicityColorer';\r\nimport MoleculeColorer from './colorers/MoleculeColorer';\r\nimport CarbonColorer from './colorers/CarbonColorer';\r\n\r\nconst colorers = new EntityList([\r\n ElementColorer,\r\n ResidueTypeColorer,\r\n SequenceColorer,\r\n ChainColorer,\r\n SecondaryStructureColorer,\r\n UniformColorer,\r\n ConditionalColorer,\r\n ConformationColorer,\r\n TemperatureColorer,\r\n OccupancyColorer,\r\n HydrophobicityColorer,\r\n MoleculeColorer,\r\n CarbonColorer,\r\n]);\r\n\r\nexport default colorers;\r\n","import * as THREE from 'three';\r\nimport EntityList from '../utils/EntityList';\r\n\r\nfunction neutralColor(intensity) {\r\n return new THREE.Color(intensity, intensity, intensity);\r\n}\r\n\r\nconst materialList = [\r\n {\r\n id: 'DF',\r\n name: 'Diffuse',\r\n shortName: 'Diffuse',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'SF',\r\n name: 'Soft Plastic',\r\n shortName: 'Soft',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.1),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'PL',\r\n name: 'Glossy Plastic',\r\n shortName: 'Glossy',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.28),\r\n shininess: 100,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'ME',\r\n name: 'Metal',\r\n shortName: 'Metal',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.55),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TR',\r\n name: 'Transparent',\r\n shortName: 'Transparent',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'GL',\r\n name: 'Glass',\r\n shortName: 'Glass',\r\n uberOptions: {\r\n diffuse: neutralColor(0.50),\r\n specular: neutralColor(0.65),\r\n shininess: 100,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'BA',\r\n name: 'Backdrop',\r\n shortName: 'Backdrop',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: false,\r\n depthWrite: false,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TN',\r\n name: 'Toon',\r\n shortName: 'Toon',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: true,\r\n },\r\n }, {\r\n id: 'FL',\r\n name: 'Flat',\r\n shortName: 'Flat',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 0,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n },\r\n },\r\n];\r\n\r\nconst materials = new EntityList(materialList);\r\n\r\nexport default materials;\r\n","/**\r\n * Utils functions which is worked with meshes\r\n *\r\n * functions for doing something with all/specified meshes\r\n * functions for traversihg tree and create auxiliary meshes for transparency/shadowmaps...\r\n * functions for calculating data connected with meshes\r\n */\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _gatherObjects(root, meshTypes) {\r\n const meshes = [];\r\n root.traverse((object) => {\r\n for (let i = 0; i < meshTypes.length; i++) {\r\n if (object instanceof meshTypes[i]) {\r\n meshes[meshes.length] = object;\r\n break;\r\n }\r\n }\r\n });\r\n return meshes;\r\n}\r\n\r\n// new mesh with the same geometry and specified material values and layer\r\nfunction createDerivativeMesh(mesh, values, layer) {\r\n const material = mesh.material.createInstance();\r\n material.setValues(values);\r\n\r\n const newMesh = new mesh.constructor(mesh.geometry, material);\r\n newMesh.material.needsUpdate = true;\r\n newMesh.applyMatrix4(mesh.matrix);\r\n newMesh.layers.set(layer);\r\n return newMesh;\r\n}\r\n\r\nfunction traverseMeshes(root, meshTypes, func) {\r\n const meshes = _gatherObjects(root, meshTypes);\r\n\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n const mesh = meshes[i];\r\n if (!mesh.parent) {\r\n continue;\r\n }\r\n func(mesh);\r\n }\r\n}\r\n\r\nfunction applyTransformsToMeshes(root, mtc) {\r\n const mtcCount = mtc.length;\r\n if (mtcCount < 1) {\r\n return;\r\n }\r\n\r\n const meshTypes = [THREE.Mesh, THREE.LineSegments, THREE.Line];\r\n traverseMeshes(root, meshTypes, (mesh) => {\r\n mesh.applyMatrix4(mtc[0]);\r\n for (let j = 1; j < mtcCount; ++j) {\r\n const newMesh = new mesh.constructor(mesh.geometry, mesh.material);\r\n mesh.parent.add(newMesh);\r\n newMesh.applyMatrix4(mtc[j]);\r\n }\r\n });\r\n}\r\n\r\nconst processTransparentMaterial = (function () {\r\n const matValues = {\r\n prepassTransparancy: true,\r\n fakeOpacity: false,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n mesh.material.setValues({ prepassTransparancy: false, fakeOpacity: false });\r\n mesh.material.needsUpdate = true;\r\n mesh.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n\r\n const prepassTranspMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n mesh.parent.add(prepassTranspMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst processColFromPosMaterial = (function () {\r\n const matValues = {\r\n colorFromPos: true,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n overrideColor: false,\r\n fogTransparent: false,\r\n attrColor: false,\r\n attrColor2: false,\r\n attrAlphaColor: false,\r\n fakeOpacity: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n const colFromPosMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n mesh.parent.add(colFromPosMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst createShadowmapMaterial = (function () {\r\n const matValues = {\r\n colorFromDepth: true,\r\n orthoCam: true,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (!mesh.receiveShadow && mesh.material.shadowmap) { // remove shadow from non-receivers\r\n mesh.material.setValues({ shadowmap: false });\r\n }\r\n if (!mesh.material.lights) { // skip creating shadowmap meshes for materials without lighting\r\n return;\r\n }\r\n if (!mesh.castShadow) { // skip creating shadowmap meshes for non-casters\r\n return;\r\n }\r\n if (!gfxutils.belongToSelectLayers(mesh)) { // skip creating shadowmap meshes for selection layer\r\n return;\r\n }\r\n\r\n const shadowmapMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.SHADOWMAP);\r\n shadowmapMesh.isShadowmapMesh = true;\r\n mesh.parent.add(shadowmapMesh);\r\n });\r\n };\r\n}());\r\n\r\nfunction removeShadowmapMaterial(root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (mesh.isShadowmapMesh) {\r\n mesh.parent.remove(mesh);\r\n }\r\n });\r\n}\r\n\r\nfunction forEachMeshInGroup(group, process) {\r\n function processObj(object) {\r\n if (object instanceof THREE.Mesh) {\r\n process(object);\r\n }\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n processObj(object.children[i]);\r\n }\r\n }\r\n processObj(group);\r\n}\r\n\r\nfunction _countMeshTriangles(mesh) {\r\n const geom = mesh.geometry;\r\n if (geom instanceof THREE.InstancedBufferGeometry) {\r\n const attribs = geom.attributes;\r\n for (const property in attribs) {\r\n if (attribs.hasOwnProperty(property) && attribs[property] instanceof THREE.InstancedBufferAttribute) {\r\n const currAttr = attribs[property];\r\n const indexSize = geom.index ? geom.index.array.length / 3 : 0;\r\n return indexSize * currAttr.array.length / currAttr.itemSize;\r\n }\r\n }\r\n return 0;\r\n }\r\n if (geom instanceof THREE.BufferGeometry) {\r\n return geom.index ? geom.index.array.length / 3 : 0;\r\n }\r\n return geom.faces ? geom.faces.length : 0;\r\n}\r\n\r\nfunction countTriangles(group) {\r\n let totalCount = 0;\r\n forEachMeshInGroup(group, (mesh) => {\r\n totalCount += _countMeshTriangles(mesh);\r\n });\r\n return totalCount;\r\n}\r\n\r\nexport default {\r\n applyTransformsToMeshes,\r\n processTransparentMaterial,\r\n processColFromPosMaterial,\r\n createShadowmapMaterial,\r\n removeShadowmapMaterial,\r\n forEachMeshInGroup,\r\n countTriangles,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\nimport meshutils from './meshutils';\r\nimport settings from '../settings';\r\nimport materials from './materials';\r\nimport chem from '../chem';\r\n\r\nconst { selectors } = chem;\r\n\r\nclass Representation {\r\n constructor(index, mode, colorer, selector) {\r\n const startMaterialValues = {\r\n clipPlane: settings.now.draft.clipPlane,\r\n fogTransparent: settings.now.bg.transparent,\r\n shadowmap: settings.now.shadow.on,\r\n shadowmapType: settings.now.shadow.type,\r\n };\r\n this.index = index;\r\n this.mode = mode;\r\n this.colorer = colorer;\r\n this.selector = selector;\r\n this.selectorString = '';\r\n this.count = 0;\r\n this.material = new UberMaterial();\r\n this.material.setValues(startMaterialValues);\r\n this.material.setUberOptions({ fogAlpha: settings.now.fogAlpha });\r\n this.materialPreset = materials.first;\r\n this.needsRebuild = true;\r\n this.visible = true;\r\n\r\n // apply mode params & preset\r\n this.setMode(mode);\r\n }\r\n\r\n markAtoms(complex) {\r\n this.count = complex.markAtoms(this.selector, 1 << this.index);\r\n this.needsRebuild = true;\r\n return this.count;\r\n }\r\n\r\n unmarkAtoms(complex) {\r\n complex.clearAtomBits(1 << this.index);\r\n this.count = 0;\r\n }\r\n\r\n setMode(mode) {\r\n this.mode = mode;\r\n }\r\n\r\n setMaterialPreset(preset) {\r\n this.materialPreset = preset;\r\n this.material.setUberOptions(preset.uberOptions);\r\n this.material.setValues(preset.values);\r\n }\r\n\r\n reset() {\r\n this.geo = null;\r\n this.selectionGeo = null;\r\n }\r\n\r\n buildGeometry(complex) {\r\n this.reset();\r\n this.needsRebuild = false;\r\n\r\n if (settings.now.ao) {\r\n this.material.setValues({ normalsToGBuffer: settings.now.ao });\r\n }\r\n\r\n this.geo = this.mode.buildGeometry(complex, this.colorer, 1 << this.index, this.material);\r\n\r\n if (this.material.uberOptions.opacity < 0.99 && settings.now.transparency === 'prepass') {\r\n meshutils.processTransparentMaterial(this.geo, this.material);\r\n }\r\n this.geo.visible = this.visible;\r\n\r\n gfxutils.processObjRenderOrder(this.geo, this.materialPreset.id);\r\n meshutils.processColFromPosMaterial(this.geo, this.material);\r\n\r\n if (settings.now.shadow.on) {\r\n meshutils.createShadowmapMaterial(this.geo, this.material);\r\n }\r\n\r\n return this.geo;\r\n }\r\n\r\n buildSelectionGeometry(mask) {\r\n let sg = null;\r\n\r\n if (this.geo && ('getSubset' in this.geo)) {\r\n const meshes = this.geo.getSubset(mask);\r\n if (meshes && meshes.length > 0) {\r\n sg = new THREE.Group();\r\n sg.matrixAutoUpdate = false;\r\n sg.matrix = this.geo.matrix;\r\n\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n sg.add(m);\r\n }\r\n }\r\n }\r\n\r\n if (sg) {\r\n sg.visible = this.visible;\r\n }\r\n\r\n this.selectionGeo = sg;\r\n return this.selectionGeo;\r\n }\r\n\r\n /**\r\n * Create object that represents difference between current and another rep\r\n * anotherRep could be undefined. In this case everything is reported.\r\n */\r\n compare(repSettings) {\r\n const diff = {};\r\n\r\n const selStr = String(this.selector);\r\n if (!repSettings || selStr.valueOf() !== String(repSettings.selector).valueOf()) {\r\n diff.selector = selStr;\r\n }\r\n\r\n const modeDiff = this.mode.identify();\r\n if (!repSettings || Array.isArray(modeDiff) || modeDiff !== repSettings.mode) {\r\n diff.mode = modeDiff;\r\n }\r\n\r\n const colorerDiff = this.colorer.identify();\r\n if (!repSettings || Array.isArray(colorerDiff) || colorerDiff !== repSettings.colorer) {\r\n diff.colorer = colorerDiff;\r\n }\r\n\r\n if (!repSettings || this.materialPreset.id !== repSettings.material) {\r\n diff.material = this.materialPreset.id;\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n /**\r\n * Change representation. Write fields what was changed into new object, return it.\r\n */\r\n change(repSettings, complex, mode, color) {\r\n const diff = {};\r\n\r\n // modify selector\r\n if (repSettings.selector) {\r\n const newSelectorObject = selectors.parse(repSettings.selector).selector;\r\n const newSelector = String(newSelectorObject);\r\n if (this.selectorString !== newSelector) {\r\n diff.selector = newSelector;\r\n this.selectorString = newSelector;\r\n this.selector = newSelectorObject;\r\n this.markAtoms(complex);\r\n }\r\n }\r\n\r\n // modify mode\r\n if (repSettings.mode) {\r\n const newMode = repSettings.mode;\r\n if (!_.isEqual(this.mode.identify(), newMode)) {\r\n diff.mode = newMode;\r\n this.setMode(mode);\r\n }\r\n }\r\n\r\n // modify colorer\r\n if (repSettings.colorer) {\r\n const newColorer = repSettings.colorer;\r\n if (!_.isEqual(this.colorer.identify(), newColorer)) {\r\n diff.colorer = newColorer;\r\n this.colorer = color;\r\n }\r\n }\r\n\r\n // modify material\r\n if (repSettings.material) {\r\n const newMaterial = repSettings.material;\r\n if (!_.isEqual(this.materialPreset.id, newMaterial)) {\r\n diff.material = newMaterial;\r\n this.setMaterialPreset(materials.get(repSettings.material));\r\n }\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n show(visible) {\r\n this.visible = visible;\r\n if (this.geo) {\r\n this.geo.visible = visible;\r\n }\r\n if (this.selectionGeo) {\r\n this.selectionGeo.visible = visible;\r\n }\r\n }\r\n}\r\n\r\nexport default Representation;\r\n","import * as THREE from 'three';\r\nimport logger from './utils/logger';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport './gfx/modes';\r\n\r\nfunction _traverseComponentGroups(root, component, callback) {\r\n const { children } = root;\r\n if (!children) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n if (child._component === component) {\r\n callback(child);\r\n }\r\n if (child instanceof gfxutils.RCGroup) {\r\n _traverseComponentGroups(child, component, callback);\r\n }\r\n }\r\n}\r\n\r\nfunction ComplexEditor() {\r\n}\r\n\r\nclass ComplexComponentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n // init component matrices\r\n this._componentTransforms = [];\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n const component = complex._components[i];\r\n this._componentTransforms[component._index] = new THREE.Object3D();\r\n }\r\n\r\n this._inProgress = true;\r\n\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const complex = this._complexVisual.getComplex();\r\n\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n this._bakeComponentTransform(complex._components[i]);\r\n }\r\n\r\n complex.onAtomPositionChanged();\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n const visual = this._complexVisual;\r\n const component = visual.getSelectedComponent();\r\n\r\n if (component === null) {\r\n return res;\r\n }\r\n\r\n const selection = this._complexVisual.getSelectionGeo();\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n // find all geo nodes for this component\r\n _traverseComponentGroups(visual, component, (child) => {\r\n res.objects.push(child);\r\n });\r\n\r\n // find all selection nodes for this component\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component') && geo._component === component) {\r\n res.objects.push(geo);\r\n }\r\n }\r\n }\r\n\r\n // add dummy object that stores component transformation\r\n res.objects.push(this._componentTransforms[component._index]);\r\n\r\n const bbmin = new THREE.Vector3(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE);\r\n const bbmax = new THREE.Vector3(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE);\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (j = 0; j < atoms.length; ++j) {\r\n if (atoms[j].mask & selectionMask) {\r\n bbmin.min(atoms[j].position);\r\n bbmax.max(atoms[j].position);\r\n }\r\n }\r\n });\r\n\r\n res.pivot.lerpVectors(bbmin, bbmax, 0.5);\r\n return res;\r\n }\r\n\r\n _bakeComponentTransform(component) {\r\n const t = this._componentTransforms[component._index];\r\n if (t && (!(t.position.x === 0 && t.position.y === 0 && t.position.z === 0)\r\n || !(t.quaternion.x === 0 && t.quaternion.y === 0 && t.quaternion.z === 0 && t.quaternion.w === 1))) {\r\n t.updateMatrix();\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (let j = 0; j < atoms.length; ++j) {\r\n atoms[j].position.applyMatrix4(t.matrix);\r\n }\r\n });\r\n }\r\n }\r\n\r\n _resetComponentTransform() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n for (i = 0; i < this._componentTransforms.length; ++i) {\r\n geo = this._componentTransforms[i];\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n\r\n // reset all geo nodes\r\n for (i = 0; i < visual.children.length; ++i) {\r\n reprNode = visual.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n // reset all selection nodes\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ComplexFragmentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n const atoms = this._getSelectionBorderAtoms();\r\n if (atoms.length < 1 || atoms.length > 2) {\r\n logger.error('Can only edit fragments with one or two bound atoms.');\r\n return false;\r\n }\r\n\r\n this._fragmentBoundAtoms = atoms;\r\n\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n\r\n // hide selected fragment in main model\r\n visual.disableSubset(selectionMask, true);\r\n\r\n // hide selection geo in main model\r\n for (let k = 0; k < selection.children.length; ++k) {\r\n selection.children[k].visible = false;\r\n }\r\n\r\n // create visible fragment representation to rotate\r\n const pivotPos = atoms[0].position.clone();\r\n\r\n if (atoms.length === 2) {\r\n pivotPos.lerp(atoms[1].position, 0.5);\r\n }\r\n\r\n this._fragmentGeo = new THREE.Group();\r\n visual.add(this._fragmentGeo);\r\n this._fragmentGeo.position.copy(pivotPos);\r\n\r\n this._fragmentSelectionGeo = new THREE.Group();\r\n selection.add(this._fragmentSelectionGeo);\r\n this._fragmentSelectionGeo.position.copy(pivotPos);\r\n\r\n const offset = pivotPos.clone();\r\n offset.negate();\r\n\r\n for (let i = 0; i < visual.children.length; ++i) {\r\n const g = visual.children[i];\r\n if (!('getSubset' in g)) {\r\n continue;\r\n }\r\n\r\n const vg = new THREE.Group();\r\n this._fragmentGeo.add(vg);\r\n\r\n const sg = new THREE.Group();\r\n this._fragmentSelectionGeo.add(sg);\r\n\r\n const meshes = g.getSubset(selectionMask, true);\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n vg.add(m);\r\n m.position.copy(offset);\r\n }\r\n\r\n const smeshes = g.getSubset(selectionMask, true);\r\n for (let h = 0; h < smeshes.length; h++) {\r\n const sm = smeshes[h];\r\n sg.add(sm);\r\n sm.position.copy(offset);\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(this._fragmentSelectionGeo);\r\n\r\n this._inProgress = true;\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selectionBit = visual.getSelectionBit();\r\n\r\n const p = this._fragmentGeo.position;\r\n const m = this._fragmentGeo.matrix.clone();\r\n m.multiply(new THREE.Matrix4().makeTranslation(-p.x, -p.y, -p.z));\r\n\r\n this._bakeAtomTransform(m, 1 << selectionBit);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << selectionBit, true);\r\n\r\n visual.getComplex().onAtomPositionChanged();\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n this._fragmentGeo.parent.remove(this._fragmentGeo);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << visual.getSelectionBit(), true);\r\n\r\n // show selection geo in main model (+ remove fragment selection geo)\r\n for (let i = 0; i < selection.children.length; ++i) {\r\n const node = selection.children[i];\r\n if (node.visible) {\r\n selection.remove(node);\r\n } else {\r\n node.visible = true;\r\n }\r\n }\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n isFreeRotationAllowed() {\r\n return (this._fragmentBoundAtoms.length < 2);\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n res.objects.push(this._fragmentGeo, this._fragmentSelectionGeo);\r\n\r\n const boundAtoms = this._fragmentBoundAtoms;\r\n if (boundAtoms.length === 1) {\r\n if (boundAtoms[0].bonds.length === 1) {\r\n // single external bond allows rotation about bond axis\r\n const bond = boundAtoms[0].bonds[0];\r\n res.axis = new THREE.Vector3().subVectors(bond._right.position, bond._left.position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n } else if (boundAtoms.length === 2) {\r\n // two bound atoms allow rotation only about axis running through their centers\r\n res.axis = new THREE.Vector3().subVectors(boundAtoms[1].position, boundAtoms[0].position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _getSelectionBorderAtoms() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n const selectionMask = 1 << this._complexVisual.getSelectionBit();\r\n const atomHash = {};\r\n\r\n complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n atomHash[bond._left.index] = 1;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n atomHash[bond._right.index] = 1;\r\n }\r\n });\r\n\r\n const atoms = [];\r\n const keys = Object.keys(atomHash);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const idx = keys[i];\r\n atoms.push(complex._atoms[idx]);\r\n }\r\n\r\n return atoms;\r\n }\r\n\r\n _bakeAtomTransform(matrix, mask) {\r\n this._complexVisual.getComplex().forEachAtom((atom) => {\r\n if (atom.mask & mask) {\r\n atom.position.applyMatrix4(matrix);\r\n }\r\n });\r\n }\r\n}\r\n\r\nexport default {\r\n ComponentEditor: ComplexComponentEditor,\r\n FragmentEditor: ComplexFragmentEditor,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\nimport chem from './chem';\r\nimport settings from './settings';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport Visual from './Visual';\r\nimport ComplexVisualEdit from './ComplexVisualEdit';\r\nimport meshutils from './gfx/meshutils';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction lookupAndCreate(entityList, specs) {\r\n if (!Array.isArray(specs)) {\r\n specs = [specs];\r\n }\r\n const [id, opts] = specs;\r\n const Entity = entityList.get(id) || entityList.first;\r\n return new Entity(opts);\r\n}\r\n\r\nclass ComplexVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._complex = dataSource;\r\n\r\n /** @type {Representation[]} */\r\n this._reprList = [];\r\n /** @type {?Representation} */\r\n this._repr = null;\r\n this._reprListChanged = true;\r\n\r\n this._selectionBit = 0;\r\n this._reprUsedBits = 0;\r\n this._selectionCount = 0;\r\n\r\n this._selectionGeometry = new THREE.Group();\r\n }\r\n\r\n getBoundaries() {\r\n return this._complex.getBoundaries();\r\n }\r\n\r\n release() {\r\n if (this._selectionGeometry.parent) {\r\n this._selectionGeometry.remove(this._selectionGeometry);\r\n }\r\n Visual.prototype.release.call(this);\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getSelectionCount() {\r\n return this._selectionCount;\r\n }\r\n\r\n getSelectionGeo() {\r\n return this._selectionGeometry;\r\n }\r\n\r\n getSelectionBit() {\r\n return this._selectionBit;\r\n }\r\n\r\n getEditor() {\r\n return this._editor;\r\n }\r\n\r\n resetReps(reps) {\r\n // Create all necessary representations\r\n if (this._complex) {\r\n this._complex.clearAtomBits(~0);\r\n }\r\n this._reprListChanged = true;\r\n this._reprUsedBits = 0;\r\n this._reprList.length = reps.length;\r\n for (let i = 0, n = reps.length; i < n; ++i) {\r\n const rep = reps[i];\r\n\r\n let selector;\r\n let selectorString;\r\n if (typeof rep.selector === 'string') {\r\n selectorString = rep.selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else if (typeof rep.selector === 'undefined') {\r\n selectorString = settings.now.presets.default[0].selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else {\r\n ({ selector } = rep);\r\n selectorString = selector.toString();\r\n }\r\n const mode = lookupAndCreate(modes, rep.mode);\r\n const colorer = lookupAndCreate(colorers, rep.colorer);\r\n const material = materials.get(rep.material) || materials.first;\r\n\r\n this._reprList[i] = new Representation(i, mode, colorer, selector);\r\n this._reprList[i].setMaterialPreset(material);\r\n this._reprList[i].selectorString = selectorString;\r\n\r\n if (this._complex) {\r\n this._complex.markAtoms(selector, 1 << i);\r\n }\r\n\r\n this._reprUsedBits |= 1 << i;\r\n }\r\n this._repr = reps.length > 0 ? this._reprList[0] : null;\r\n\r\n this._selectionBit = reps.length;\r\n this._reprUsedBits |= 1 << this._selectionBit; // selection uses one bit\r\n this._selectionCount = 0;\r\n\r\n if (this._complex) {\r\n this._complex.update();\r\n }\r\n }\r\n\r\n /**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\n repCount() {\r\n return this._reprList.length;\r\n }\r\n\r\n /**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\n repCurrent(index) {\r\n if (index >= 0 && index < this._reprList.length) {\r\n this._repr = this._reprList[index];\r\n } else {\r\n index = this._reprList.indexOf(this._repr);\r\n }\r\n return index;\r\n }\r\n\r\n /**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {Object} {desc, index, status} field desc contains rep description, index - index of correspondent rep,\r\n * status - one of three strings: 'created', 'changed', ''. 'created' means new rep was created during this function,\r\n * 'changed' - rep was changed during this function. '' - something else.\r\n */\r\n rep(index, rep) {\r\n // if index is missing then it is the current\r\n if (!rep && (index === undefined || index instanceof Object)) {\r\n rep = index;\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index > this._reprList.length) {\r\n logger.error(`Rep ${index} does not exist!`);\r\n return null;\r\n }\r\n\r\n // a special case of adding just after the end\r\n if (index === this._reprList.length) {\r\n const res = this.repAdd(rep);\r\n logger.warn(`Rep ${index} does not exist! New representation was created.`);\r\n return { desc: res.desc, index, status: 'created' };\r\n }\r\n\r\n // gather description\r\n const target = this._reprList[index];\r\n const desc = {\r\n selector: target.selectorString,\r\n mode: target.mode.identify(),\r\n colorer: target.colorer.identify(),\r\n material: target.materialPreset.id,\r\n };\r\n\r\n // modification is requested\r\n if (rep) {\r\n // modify\r\n const diff = target.change(\r\n rep,\r\n this._complex,\r\n lookupAndCreate(modes, rep.mode),\r\n lookupAndCreate(colorers, rep.colorer),\r\n );\r\n\r\n // something was changed\r\n if (!_.isEmpty(diff)) {\r\n target.needsRebuild = true;\r\n for (const key in diff) {\r\n if (diff.hasOwnProperty(key)) {\r\n desc[key] = diff[key];\r\n logger.debug(`rep[${index}].${key} changed to ${diff[key]}`);\r\n }\r\n }\r\n\r\n // safety trick: lower resolution for surface modes\r\n if (diff.mode && target.mode.isSurface\r\n && (settings.now.resolution === 'ultra' || settings.now.resolution === 'high')) {\r\n logger.report('Surface resolution was changed to \"medium\" to avoid hang-ups.');\r\n settings.set('resolution', 'medium');\r\n }\r\n return { desc, index, status: 'changed' };\r\n }\r\n }\r\n return { desc, index, status: '' };\r\n }\r\n\r\n /**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\n repGet(index) {\r\n // if index is missing then it is the current\r\n if (index === undefined || index instanceof Object) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return null;\r\n }\r\n\r\n return this._reprList[index];\r\n }\r\n\r\n _getFreeReprIdx() {\r\n let bits = this._reprUsedBits;\r\n for (let i = 0; i <= ComplexVisual.NUM_REPRESENTATION_BITS; ++i, bits >>= 1) {\r\n if ((bits & 1) === 0) {\r\n return i;\r\n }\r\n }\r\n return -1;\r\n }\r\n\r\n /**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {Object} {desc, index} field desc contains added rep description, index - index of this rep.\r\n */\r\n repAdd(rep) {\r\n if (this._reprList.length >= ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n return null;\r\n }\r\n\r\n const newSelectionBit = this._getFreeReprIdx();\r\n if (newSelectionBit < 0) {\r\n return null; // no more slots for representations\r\n }\r\n\r\n const originalSelection = this.buildSelectorFromMask(1 << this._selectionBit);\r\n\r\n // Fill in default values\r\n const def = settings.now.presets.default[0];\r\n const desc = _.merge({\r\n selector: def.selector,\r\n mode: def.mode,\r\n colorer: def.colorer,\r\n material: def.material,\r\n }, rep);\r\n\r\n const selector = (typeof desc.selector === 'string') ? selectors.parse(desc.selector).selector : desc.selector;\r\n const target = new Representation(\r\n this._selectionBit,\r\n lookupAndCreate(modes, desc.mode),\r\n lookupAndCreate(colorers, desc.colorer),\r\n selector,\r\n );\r\n target.selectorString = selector.toString();\r\n target.setMaterialPreset(materials.get(desc.material));\r\n target.markAtoms(this._complex);\r\n this._reprList.push(target);\r\n\r\n // change selection bit\r\n this._selectionBit = newSelectionBit;\r\n this._reprUsedBits |= 1 << this._selectionBit;\r\n\r\n // restore selection using new selection bit\r\n this._complex.markAtoms(originalSelection, 1 << this._selectionBit);\r\n\r\n return { desc, index: this._reprList.length - 1 };\r\n }\r\n\r\n /**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\n repRemove(index) {\r\n if (index === undefined) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // catch out of bounds case\r\n let count = this._reprList.length;\r\n if (index < 0 || index >= count || count <= 1) { // do not allow to remove the single rep\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.unmarkAtoms(this._complex);\r\n this._reprUsedBits &= ~(1 << target.index);\r\n\r\n this._reprList.splice(index, 1);\r\n\r\n // update current rep\r\n if (target === this._repr) {\r\n --count;\r\n index = index < count ? index : count - 1;\r\n this._repr = this._reprList[index];\r\n }\r\n this._reprListChanged = true;\r\n }\r\n\r\n /**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\n repHide(index, hide) {\r\n if (hide === undefined) {\r\n hide = true;\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.show(!hide);\r\n }\r\n\r\n /**\r\n * Select atoms with selector\r\n * @param {Selector} selector - selector\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\n select(selector, append) {\r\n if (append) {\r\n this._selectionCount += this._complex.markAtomsAdditionally(selector, 1 << this._selectionBit);\r\n } else {\r\n this._selectionCount = this._complex.markAtoms(selector, 1 << this._selectionBit);\r\n }\r\n this._complex.updateStructuresMask();\r\n this.rebuildSelectionGeometry();\r\n }\r\n\r\n resetSelectionMask() {\r\n if (this._selectionCount !== 0) {\r\n this._selectionCount = 0;\r\n if (this._complex) {\r\n this._complex.clearAtomBits(1 << this._selectionBit);\r\n }\r\n }\r\n }\r\n\r\n updateSelectionMask(pickedObj) {\r\n const self = this;\r\n const { atom } = pickedObj;\r\n let { residue, chain, molecule } = pickedObj;\r\n const setMask = 1 << this._selectionBit;\r\n const clearMask = ~setMask;\r\n\r\n if (atom) {\r\n residue = atom.residue;\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (atom.mask & setMask) {\r\n atom.mask &= clearMask;\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n if (molecule) {\r\n molecule.mask &= clearMask;\r\n }\r\n this._selectionCount--;\r\n } else {\r\n atom.mask |= setMask;\r\n this._selectionCount++;\r\n\r\n // select residue if all atoms in it are selected\r\n residue.collectMask();\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (residue) {\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (residue._mask & setMask) {\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n residue.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n } else {\r\n residue._mask |= setMask;\r\n residue.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (chain || molecule) {\r\n const obj = chain || molecule;\r\n if (obj._mask & setMask) {\r\n obj._mask &= clearMask;\r\n obj.forEachResidue((r) => {\r\n if (r._mask & setMask) {\r\n r._mask &= clearMask;\r\n r.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n r._mask &= clearMask;\r\n }\r\n });\r\n } else {\r\n obj._mask |= setMask;\r\n obj.forEachResidue((r) => {\r\n if (!(r._mask & setMask)) {\r\n r._mask |= setMask;\r\n r.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n const otherObj = chain ? r.getMolecule() : r.getChain();\r\n if (otherObj) {\r\n otherObj.collectMask();\r\n }\r\n }\r\n });\r\n }\r\n } else {\r\n this.resetSelectionMask();\r\n }\r\n }\r\n\r\n expandSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms to add\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // select marked atoms\r\n const deselectionMask = ~tmpMask;\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask = (atom.mask & deselectionMask) | selectionMask;\r\n ++self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n shrinkSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms neighbouring to unselected ones\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // mark hanging atoms\r\n this._complex.forEachAtom((atom) => {\r\n if ((atom.mask & selectionMask) && (atom.bonds.length === 1)) {\r\n atom.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // deselect marked atoms\r\n const deselectionMask = ~(selectionMask | tmpMask);\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask &= deselectionMask;\r\n --self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n getSelectedComponent() {\r\n const selectionMask = 1 << this._selectionBit;\r\n\r\n let component = null;\r\n let multiple = false;\r\n\r\n // find which component is selected (exclusively)\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & selectionMask) {\r\n if (component === null) {\r\n component = atom.residue._component;\r\n } else if (component !== atom.residue._component) {\r\n multiple = true;\r\n }\r\n }\r\n });\r\n\r\n return multiple ? null : component;\r\n }\r\n\r\n getSelectionCenter(center, includesAtom, selRule) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._complex.forEachAtom((atom) => {\r\n if (includesAtom(atom, selRule)) {\r\n center.add(atom.position);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.applyMatrix4(this.matrix);\r\n return true;\r\n }\r\n\r\n needsRebuild() {\r\n if (this._reprListChanged) {\r\n return true;\r\n }\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n if (repr.needsRebuild) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n /**\r\n * Rebuild molecule geometry asynchronously.\r\n */\r\n rebuild() {\r\n const self = this;\r\n\r\n // Destroy current geometry\r\n gfxutils.clearTree(this);\r\n\r\n return new Promise(((resolve) => {\r\n // Nothing to do?\r\n const complex = self._complex;\r\n if (!complex) {\r\n resolve();\r\n return;\r\n }\r\n\r\n let errorOccured = false;\r\n setTimeout(() => {\r\n console.time('build');\r\n const reprList = self._reprList;\r\n const palette = palettes.get(settings.now.palette) || palettes.first;\r\n let hasGeometry = false;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n repr.colorer.palette = palette;\r\n\r\n if (repr.needsRebuild) {\r\n repr.reset();\r\n\r\n try {\r\n repr.buildGeometry(complex);\r\n } catch (e) {\r\n if (e instanceof utils.OutOfMemoryError) {\r\n repr.needsRebuild = false;\r\n repr.reset();\r\n logger.error(`Not enough memory to build geometry for representation ${repr.index + 1}`);\r\n errorOccured = true;\r\n } else {\r\n throw e;\r\n }\r\n }\r\n\r\n if (DEBUG && !errorOccured) {\r\n logger.debug(`Triangles count: ${meshutils.countTriangles(repr.geo)}`);\r\n }\r\n }\r\n\r\n hasGeometry = errorOccured || hasGeometry || gfxutils.groupHasGeometryToRender(repr.geo);\r\n\r\n if (repr.geo) {\r\n self.add(repr.geo);\r\n }\r\n }\r\n\r\n self._reprListChanged = false;\r\n\r\n console.timeEnd('build');\r\n resolve();\r\n }, 10);\r\n }));\r\n }\r\n\r\n setNeedsRebuild() {\r\n // invalidate all representations\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n reprList[i].needsRebuild = true;\r\n }\r\n }\r\n\r\n rebuildSelectionGeometry() {\r\n const mask = 1 << this._selectionBit;\r\n\r\n gfxutils.clearTree(this._selectionGeometry);\r\n\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const repr = this._reprList[i];\r\n const sg = repr.buildSelectionGeometry(mask);\r\n if (!sg) {\r\n continue;\r\n }\r\n\r\n this._selectionGeometry.add(sg);\r\n for (let j = 0; j < sg.children.length; j++) {\r\n const m = sg.children[j];\r\n\r\n // copy component transform (that's not applied yet)\r\n // TODO make this code obsolete, accessing editor is bad\r\n if (this._editor && this._editor._componentTransforms) {\r\n const t = this._editor._componentTransforms[m._component._index];\r\n if (t) {\r\n m.position.copy(t.position);\r\n m.quaternion.copy(t.quaternion);\r\n }\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(sg);\r\n }\r\n }\r\n\r\n _buildSelectorFromSortedLists(atoms, residues, chains) {\r\n const complex = this._complex;\r\n\r\n function optimizeList(list) {\r\n const result = [];\r\n let k = 0;\r\n let first = NaN;\r\n let last = NaN;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const value = list[i];\r\n if (value === last + 1) {\r\n last = value;\r\n } else {\r\n if (!Number.isNaN(first)) {\r\n result[k++] = new selectors.Range(first, last);\r\n }\r\n first = last = value;\r\n }\r\n }\r\n if (!Number.isNaN(first)) {\r\n result[k] = new selectors.Range(first, last);\r\n }\r\n return result;\r\n }\r\n\r\n let expression = null;\r\n if (chains.length === complex._chains.length) {\r\n expression = selectors.all();\r\n } else {\r\n let selector;\r\n if (chains.length > 0) {\r\n selector = selectors.chain(chains);\r\n expression = expression ? selectors.or(expression, selector) : selector;// NOSONAR\r\n }\r\n if (Object.keys(residues).length > 0) {\r\n for (const ch in residues) {\r\n if (residues.hasOwnProperty(ch)) {\r\n selector = selectors.and(\r\n selectors.chain(ch),\r\n selectors.residx(optimizeList(residues[ch])),\r\n );\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n }\r\n }\r\n if (atoms.length > 0) {\r\n selector = selectors.serial(optimizeList(atoms));\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n\r\n if (!expression) {\r\n expression = selectors.none();\r\n }\r\n }\r\n\r\n return expression;\r\n }\r\n\r\n buildSelectorFromMask(mask) {\r\n const complex = this._complex;\r\n const chains = [];\r\n const residues = {};\r\n const atoms = [];\r\n\r\n complex.forEachChain((chain) => {\r\n if (chain._mask & mask) {\r\n chains.push(chain._name);\r\n }\r\n });\r\n\r\n complex.forEachResidue((residue) => {\r\n if (residue._mask & mask && !(residue._chain._mask & mask)) {\r\n const c = residue._chain._name;\r\n if (!(c in residues)) {\r\n residues[c] = [residue._index];\r\n } else {\r\n residues[c].push(residue._index);\r\n }\r\n }\r\n });\r\n\r\n complex.forEachAtom((atom) => {\r\n if (atom.mask & mask && !(atom.residue._mask & mask)) {\r\n atoms.push(atom.serial);\r\n }\r\n });\r\n\r\n return this._buildSelectorFromSortedLists(atoms, residues, chains);\r\n }\r\n\r\n forSelectedResidues(process) {\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.forEachResidue((residue) => {\r\n if (residue._mask & selectionMask) {\r\n process(residue);\r\n }\r\n });\r\n }\r\n\r\n beginComponentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.ComponentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n beginFragmentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.FragmentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n // should only be called by editors\r\n finalizeEdit() {\r\n this._editor = null;\r\n }\r\n\r\n setMaterialValues(values, needTraverse = false, process = undefined) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setValues(values);\r\n if (needTraverse) {\r\n rep.geo.traverse((object) => {\r\n if (object instanceof THREE.Mesh) {\r\n object.material.setValues(values);\r\n\r\n if (process !== undefined) {\r\n process(object);\r\n }\r\n\r\n object.material.needsUpdate = true;\r\n }\r\n });\r\n }\r\n }\r\n }\r\n\r\n setUberOptions(values) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setUberOptions(values);\r\n }\r\n }\r\n\r\n /**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\n within(selector, radius) {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return false;\r\n }\r\n\r\n // mark atoms of the group as selected\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.markAtoms(selector, selectionMask);\r\n\r\n // mark all atoms within distance as selected\r\n if (vw) {\r\n vw.forEachAtomWithinDistFromMasked(this._complex, selectionMask, Number(radius), (atom) => {\r\n atom.mask |= selectionMask;\r\n });\r\n }\r\n\r\n // update selection count\r\n this._selectionCount = this._complex.countAtomsByMask(selectionMask);\r\n\r\n // update secondary structure mask\r\n this._complex.updateStructuresMask();\r\n\r\n return this.buildSelectorFromMask(selectionMask);\r\n }\r\n}\r\n// 32 bits = 30 bits for reps + 1 for selection + 1 for selection expansion\r\nComplexVisual.NUM_REPRESENTATION_BITS = 30;\r\n\r\nexport default ComplexVisual;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexVolumeFaces from './VolumeFaces.vert';\r\nimport fragmentVolumeFaces from './VolumeFaces.frag';\r\nimport vertexVolume from './Volume.vert';\r\nimport fragmentVolume from './Volume.frag';\r\nimport vertexFarPlane from './VolumeFarPlane.vert';\r\nimport fragmentFarPlane from './VolumeFarPlane.frag';\r\nimport settings from '../../settings';\r\n\r\nconst volumeUniforms = THREE.UniformsUtils.merge([\r\n {\r\n volumeDim: { type: 'v3', value: new THREE.Vector3(512, 512, 512) },\r\n tileTex: { type: 't', value: null },\r\n tileTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n tileStride: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n\r\n boxAngles: { type: 'v3', value: new THREE.Vector3(1, 1, 1) },\r\n delta: { type: 'v3', value: new THREE.Vector3(0, 0, 0) },\r\n\r\n _isoLevel0: { type: 'v2', value: new THREE.Vector3(0.5, 0.75, 1.0) },\r\n _flipV: { type: 'f', value: 0.0 },\r\n _BFLeft: { type: 't', value: null },\r\n _BFRight: { type: 't', value: null },\r\n _FFLeft: { type: 't', value: null },\r\n _FFRight: { type: 't', value: null },\r\n _WFFLeft: { type: 't', value: null },\r\n _WFFRight: { type: 't', value: null },\r\n },\r\n]);\r\n\r\nfunction overrideUniforms(params, defUniforms) {\r\n const uniforms = THREE.UniformsUtils.clone(defUniforms);\r\n for (const p in params) {\r\n if (uniforms.hasOwnProperty(p)) {\r\n uniforms[p].value = params[p];\r\n }\r\n }\r\n return uniforms;\r\n}\r\n\r\nfunction facesPosMaterialParams(params, sideType) {\r\n return {\r\n uniforms: overrideUniforms(params, {}),\r\n vertexShader: vertexVolumeFaces,\r\n fragmentShader: fragmentVolumeFaces,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n side: sideType,\r\n };\r\n}\r\n\r\nclass BackFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const backFaceParams = facesPosMaterialParams(params, THREE.BackSide);\r\n super(backFaceParams);\r\n }\r\n}\r\n\r\nclass ShaderParams {\r\n constructor(params, uniforms, vertexShader, fragmentShader) {\r\n this.uniforms = overrideUniforms(params, uniforms);\r\n this.vertexShader = vertexShader;\r\n this.fragmentShader = fragmentShader;\r\n this.transparent = false;\r\n this.depthTest = false;\r\n this.depthWrite = false;\r\n this.side = THREE.FrontSide;\r\n }\r\n}\r\n\r\nclass BackFacePosMaterialFarPlane extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const matUniforms = THREE.UniformsUtils.merge([\r\n {\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n farZ: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n matWorld2Volume: { type: '4fv', value: new THREE.Matrix4() },\r\n },\r\n ]);\r\n\r\n const shaderParams = new ShaderParams(params, matUniforms, vertexFarPlane, fragmentFarPlane);\r\n super(shaderParams);\r\n }\r\n}\r\n\r\nclass FrontFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const frontFaceParams = facesPosMaterialParams(params, THREE.FrontSide);\r\n super(frontFaceParams);\r\n }\r\n}\r\n\r\nclass VolumeMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const shaderParams = new ShaderParams(params, volumeUniforms, vertexVolume, fragmentVolume);\r\n shaderParams.transparent = true;\r\n shaderParams.depthTest = true;\r\n\r\n super(shaderParams);\r\n this.updateDefines();\r\n }\r\n\r\n updateDefines() {\r\n this.defines = {\r\n ISO_MODE: settings.now.modes.VD.isoMode,\r\n STEPS_COUNT: settings.now.modes.VD.polyComplexity[settings.now.resolution] * 100,\r\n };\r\n this.needsUpdate = true;\r\n }\r\n}\r\n\r\nexport default {\r\n BackFacePosMaterial,\r\n BackFacePosMaterialFarPlane,\r\n FrontFacePosMaterial,\r\n VolumeMaterial,\r\n};\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport settings from '../settings';\r\n\r\nclass VolumeMesh extends THREE.Mesh {\r\n volumeInfo = {}; // data for noise filter\r\n\r\n constructor() {\r\n const geo = new THREE.BufferGeometry();\r\n super(geo);\r\n this.clipPlane = new THREE.Plane();\r\n const size = new THREE.Vector3(0.5, 0.5, 0.5);\r\n this.size = size;\r\n\r\n this.cullFlag = [\r\n true, true, true, true,\r\n true, true, true, true,\r\n false, false, false, false, false, false,\r\n ];\r\n\r\n this.faces = [\r\n { indices: [], norm: new THREE.Vector3(0, 0, -1) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 1) },\r\n { indices: [], norm: new THREE.Vector3(0, -1, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 1, 0) },\r\n { indices: [], norm: new THREE.Vector3(-1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 0) },\r\n ];\r\n\r\n this.vertices = [\r\n new THREE.Vector3(-size.x, -size.y, -size.z),\r\n new THREE.Vector3(-size.x, size.y, -size.z),\r\n new THREE.Vector3(size.x, -size.y, -size.z),\r\n new THREE.Vector3(size.x, size.y, -size.z),\r\n new THREE.Vector3(-size.x, -size.y, size.z),\r\n new THREE.Vector3(-size.x, size.y, size.z),\r\n new THREE.Vector3(size.x, -size.y, size.z),\r\n new THREE.Vector3(size.x, size.y, size.z),\r\n new THREE.Vector3(0.0, 0.0, 0.0), // Placeholder for section\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n ];\r\n\r\n geo.setAttribute('position', new THREE.BufferAttribute(new Float32Array(this.vertices.length * 3), 3));\r\n\r\n this.name = 'VolumeMesh';\r\n }\r\n\r\n static _corners = [\r\n // x, y, z, edge1, edge2, edge3\r\n [-1, -1, -1, 0, 4, 8],\r\n [1, -1, -1, 0, 5, 9],\r\n [1, 1, -1, 1, 5, 10],\r\n [-1, 1, -1, 1, 4, 11],\r\n [-1, -1, 1, 2, 6, 8],\r\n [1, -1, 1, 2, 7, 9],\r\n [1, 1, 1, 3, 7, 10],\r\n [-1, 1, 1, 3, 6, 11],\r\n ];\r\n\r\n static _edges = [\r\n // corner1, corner2, center_x, center_y, center_z\r\n [0, 1, 0, -1, -1],\r\n [2, 3, 0, 1, -1],\r\n [4, 5, 0, -1, 1],\r\n [6, 7, 0, 1, 1],\r\n [0, 3, -1, 0, -1],\r\n [1, 2, 1, 0, -1],\r\n [4, 7, -1, 0, 1],\r\n [5, 6, 1, 0, 1],\r\n [0, 4, -1, -1, 0],\r\n [1, 5, 1, -1, 0],\r\n [2, 6, -1, 1, 0],\r\n [3, 7, 1, 1, 0],\r\n ];\r\n\r\n static _edgeIntersections = (function () {\r\n const edgeIntersections = [];\r\n for (let j = 0; j < 12; ++j) {\r\n edgeIntersections.push(new THREE.Vector3());\r\n }\r\n return edgeIntersections;\r\n }());\r\n\r\n _updateVertices() {\r\n // Algorithm:\r\n // 1. Get plane parameters\r\n // 2. Compute culling flags for all vertices\r\n // 3. If intersection occurs => compute from 3 to 6 intersection points\r\n const corners = VolumeMesh._corners;\r\n const edges = VolumeMesh._edges;\r\n const edgeIntersections = VolumeMesh._edgeIntersections;\r\n\r\n let i;\r\n\r\n const norm = this.clipPlane.normal;\r\n const D = this.clipPlane.constant;\r\n\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n const cornerMark = [0, 0, 0, 0, 0, 0, 0, 0];\r\n const edgeMark = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1];\r\n\r\n const curEdge = new THREE.Vector3();\r\n let curEdgeInter = null;\r\n\r\n function CheckX() {\r\n if (norm.x === 0) return 0;\r\n const x = -(norm.dot(curEdge) + D) / norm.x;\r\n if (-size.x <= x && x <= size.x) {\r\n curEdgeInter.set(x, curEdge.y, curEdge.z);\r\n if (x === size.x) return 2;\r\n if (x === -size.x) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckY() {\r\n if (norm.y === 0) return 0;\r\n const y = -(norm.dot(curEdge) + D) / norm.y;\r\n if (-size.y <= y && y <= size.y) {\r\n curEdgeInter.set(curEdge.x, y, curEdge.z);\r\n if (y === size.y) return 2;\r\n if (y === -size.y) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckZ() {\r\n if (norm.z === 0) return 0;\r\n const z = -(norm.dot(curEdge) + D) / norm.z;\r\n if (-size.z <= z && z <= size.z) {\r\n curEdgeInter.set(curEdge.x, curEdge.y, z);\r\n if (z === size.z) return 2;\r\n if (z === -size.z) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n // for each edge\r\n for (let curEdgeIdx = 0; curEdgeIdx < 12; ++curEdgeIdx) {\r\n const curEdgeSource = edges[curEdgeIdx];\r\n curEdgeInter = edgeIntersections[curEdgeIdx];\r\n\r\n curEdge.set(curEdgeSource[2], curEdgeSource[3], curEdgeSource[4]);\r\n curEdge.multiply(size);\r\n\r\n // calculate intersection point\r\n let flag = 0;\r\n if (curEdgeSource[2] === 0) flag = CheckX();\r\n if (curEdgeSource[3] === 0) flag = CheckY();\r\n if (curEdgeSource[4] === 0) flag = CheckZ();\r\n\r\n // mark corresponding corner (if plane cuts through one)\r\n if (flag === -2) {\r\n cornerMark[curEdgeSource[0]] = 1;\r\n } else if (flag === 2) {\r\n cornerMark[curEdgeSource[1]] = 1;\r\n } else if (flag === 0) {\r\n // edge is not intersected by the plane (doesn't produce a vertex)\r\n edgeMark[curEdgeIdx] = 0;\r\n }\r\n }\r\n\r\n const face = {\r\n indices: [],\r\n norm: norm.clone().negate(),\r\n };\r\n\r\n let nextVertex = 8;\r\n\r\n // for each marked corner\r\n for (i = 0; i < 8; ++i) {\r\n if (cornerMark[i] === 1) {\r\n // add corner as vertex to the face\r\n vert[nextVertex].set(corners[i][0], corners[i][1], corners[i][2]).multiply(size);\r\n face.indices.push(nextVertex++);\r\n // skip adjacent edges\r\n edgeMark[corners[i][3]] = 0;\r\n edgeMark[corners[i][4]] = 0;\r\n edgeMark[corners[i][5]] = 0;\r\n }\r\n }\r\n\r\n // for each edge that has internal intersection\r\n for (i = 0; i < 12; ++i) {\r\n if (edgeMark[i] === 1) {\r\n // add intersection point as vertex to the face\r\n vert[nextVertex].copy(edgeIntersections[i]);\r\n face.indices.push(nextVertex++);\r\n }\r\n }\r\n\r\n this.faces[6] = face;\r\n\r\n const diff = new THREE.Vector3();\r\n const coplanarPoint = new THREE.Vector3();\r\n this.clipPlane.coplanarPoint(coplanarPoint);\r\n for (i = 0; i < vert.length; ++i) {\r\n this.cullFlag[i] = false;\r\n if (i < 8) {\r\n // corners should be culled by clipping plane\r\n diff.subVectors(vert[i], coplanarPoint);\r\n this.cullFlag[i] = (norm.dot(diff) >= 0.0);\r\n } else if (i < 8 + face.indices.length) {\r\n // cross section vertices don't get culled\r\n this.cullFlag[i] = true;\r\n }\r\n }\r\n\r\n // write data to vertex buffer\r\n const positions = this.geometry.getAttribute('position');\r\n let idx = 0;\r\n for (i = 0; i < vert.length; ++i) {\r\n positions.array[idx++] = vert[i].x;\r\n positions.array[idx++] = vert[i].y;\r\n positions.array[idx++] = vert[i].z;\r\n }\r\n positions.needsUpdate = true;\r\n }\r\n\r\n _collectVertices(face, filter) {\r\n let i;\r\n const vert = this.vertices;\r\n face.indices = [];\r\n for (i = 0; i < vert.length; ++i) {\r\n if (this.cullFlag[i] && filter(vert[i])) {\r\n face.indices.push(i);\r\n }\r\n }\r\n }\r\n\r\n _sortIndices(face, right) {\r\n let i;\r\n let j;\r\n const vert = this.vertices;\r\n const angle = [];\r\n\r\n const dir = new THREE.Vector3();\r\n for (i = 1; i < face.indices.length; ++i) {\r\n dir.subVectors(vert[face.indices[i]], vert[face.indices[0]]);\r\n dir.normalize();\r\n dir.cross(right);\r\n dir.negate();\r\n angle[i] = face.norm.dot(dir);\r\n }\r\n\r\n // Exchange sort\r\n for (i = 1; i < face.indices.length - 1; ++i) {\r\n for (j = i + 1; j < face.indices.length; ++j) {\r\n if (angle[j] < angle[i]) {\r\n // swap\r\n let t = angle[i];\r\n angle[i] = angle[j];\r\n angle[j] = t;\r\n\r\n t = face.indices[i];\r\n face.indices[i] = face.indices[j];\r\n face.indices[j] = t;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _updateIndices() {\r\n // Algorithm:\r\n // 1. Get plane vertices (from 3 to 6 vertices)\r\n // 2. Get \"right\" vector in plane\r\n // 3. Sort vertices using Graham-like method\r\n // 4. Create indices\r\n\r\n let i;\r\n let faceIdx;\r\n let face;\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n this._collectVertices(this.faces[0], (vertex) => vertex.z === -size.z);\r\n this._collectVertices(this.faces[1], (vertex) => vertex.z === size.z);\r\n this._collectVertices(this.faces[2], (vertex) => vertex.y === -size.y);\r\n this._collectVertices(this.faces[3], (vertex) => vertex.y === size.y);\r\n this._collectVertices(this.faces[4], (vertex) => vertex.x === -size.x);\r\n this._collectVertices(this.faces[5], (vertex) => vertex.x === size.x);\r\n\r\n const vCenter = new THREE.Vector3();\r\n const vRight = new THREE.Vector3();\r\n const vDir = new THREE.Vector3();\r\n\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n\r\n if (face.indices.length === 0) continue;\r\n\r\n vCenter.set(0, 0, 0);\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vCenter.add(vert[face.indices[i]]);\r\n }\r\n vCenter.multiplyScalar(1.0 / face.indices.length);\r\n vRight.subVectors(vert[face.indices[0]], vCenter);\r\n vRight.normalize();\r\n\r\n const rightProj = [];\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vDir.subVectors(vert[face.indices[i]], vCenter);\r\n rightProj[i] = vDir.dot(vRight);\r\n }\r\n for (i = 1; i < face.indices.length; ++i) {\r\n if (rightProj[i] < rightProj[0]) {\r\n // swap\r\n let t = rightProj[0];\r\n rightProj[0] = rightProj[i];\r\n rightProj[i] = t;\r\n\r\n [t] = face.indices;\r\n face.indices[0] = face.indices[i];\r\n face.indices[i] = t;\r\n }\r\n }\r\n\r\n this._sortIndices(face, vRight);\r\n }\r\n\r\n let numIndices = 0;\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n if (face.indices.length >= 3) {\r\n numIndices += 3 * (face.indices.length - 2);\r\n }\r\n }\r\n let offset = 0;\r\n const indices = new Uint16Array(numIndices);\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n for (i = 0; i < face.indices.length - 2; ++i) {\r\n indices[offset] = face.indices[0]; // eslint-disable-line prefer-destructuring\r\n indices[offset + 1] = face.indices[i + 1];\r\n indices[offset + 2] = face.indices[i + 2];\r\n offset += 3;\r\n }\r\n }\r\n\r\n this.geometry.setIndex(new THREE.BufferAttribute(indices, 1));\r\n }\r\n\r\n setDataSource(dataSource) {\r\n const vm = new VolumeMaterial.VolumeMaterial();\r\n const dim = dataSource.getDimensions();\r\n const stride = dataSource.getTiledTextureStride();\r\n const texture = dataSource.buildTiledTexture();\r\n const bbox = dataSource.getBox();\r\n vm.uniforms.volumeDim.value.set(dim[0], dim[1], dim[2]);\r\n vm.uniforms.tileTex.value = texture;\r\n vm.uniforms.tileTexSize.value.set(texture.image.width, texture.image.height);\r\n vm.uniforms.tileStride.value.set(stride[0], stride[1]);\r\n Object.assign(this.volumeInfo, dataSource.getVolumeInfo());\r\n\r\n const volInfo = this.volumeInfo;\r\n vm.uniforms.delta.value.copy(volInfo.delta);\r\n vm.uniforms.boxAngles.value.set(volInfo.obtuseAngle[0], volInfo.obtuseAngle[1], volInfo.obtuseAngle[2]);\r\n\r\n this.material = vm;\r\n\r\n bbox.getSize(this.scale);\r\n bbox.getCenter(this.position);\r\n }\r\n\r\n _updateIsoLevel() {\r\n const { kSigma, kSigmaMed, kSigmaMax } = settings.now.modes.VD;\r\n const volInfo = this.volumeInfo;\r\n const mean = volInfo.dmean - volInfo.dmin;\r\n const span = volInfo.dmax - volInfo.dmin;\r\n const level = (k) => (mean + k * volInfo.sd) / span;\r\n this.material.uniforms._isoLevel0.value.set(level(kSigma), level(kSigmaMed), level(kSigmaMax));\r\n }\r\n\r\n static _nearClipPlaneOffset = 0.2;\r\n\r\n static _pos = new THREE.Vector3();\r\n\r\n static _norm = new THREE.Vector3();\r\n\r\n static _norm4D = new THREE.Vector4();\r\n\r\n static _matrixWorldToLocal = new THREE.Matrix4();\r\n\r\n static _clipPlane = new THREE.Plane();\r\n\r\n rebuild(camera) {\r\n const nearClipPlaneOffset = VolumeMesh._nearClipPlaneOffset;\r\n const pos = VolumeMesh._pos;\r\n const norm = VolumeMesh._norm;\r\n const norm4D = VolumeMesh._norm4D;\r\n const matrixWorldToLocal = VolumeMesh._matrixWorldToLocal;\r\n const clipPlane = VolumeMesh._clipPlane;\r\n\r\n this._updateIsoLevel();\r\n\r\n // get clip plane in local space\r\n camera.getWorldDirection(norm);\r\n camera.getWorldPosition(pos);\r\n pos.addScaledVector(norm, camera.near + nearClipPlaneOffset);\r\n\r\n // transform pos to local CS\r\n matrixWorldToLocal.copy(this.matrixWorld).invert();\r\n pos.applyMatrix4(matrixWorldToLocal);\r\n\r\n // transform norm to local CS\r\n norm4D.set(norm.x, norm.y, norm.z, 0.0); // NOTE: use homogeneous norm for proper transformation\r\n norm4D.applyMatrix4(matrixWorldToLocal);\r\n norm.copy(norm4D);\r\n norm.normalize();\r\n\r\n clipPlane.setFromNormalAndCoplanarPoint(norm, pos);\r\n\r\n if (!this.clipPlane.equals(clipPlane)) {\r\n this.clipPlane = clipPlane.clone();\r\n this._updateVertices();\r\n this._updateIndices();\r\n }\r\n }\r\n}\r\n\r\nexport default VolumeMesh;\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _flattenArray(input) {\r\n const n = input.length;\r\n const output = new Float32Array(n * 3);\r\n for (let i = 0; i < n; ++i) {\r\n const j = 3 * i;\r\n const v = input[i];\r\n output[j] = v.x;\r\n output[j + 1] = v.y;\r\n output[j + 2] = v.z;\r\n }\r\n return output;\r\n}\r\n\r\nclass VolumeBounds {\r\n static _projectionTable = { // corresponds between (origin axes and angles between them) and between saving vector coordinates\r\n XY: ['x', 2],\r\n XZ: ['y', 1],\r\n YZ: ['z', 0],\r\n };\r\n\r\n constructor(bBox, volInfo) {\r\n const { delta } = volInfo; // {x: XY, y : XZ, z: YZ}\r\n const { obtuseAngle } = volInfo; // 1 - obtuse, 0 - acute\r\n\r\n const bSize = new THREE.Vector3();\r\n bBox.getSize(bSize);\r\n bSize.multiplyScalar(0.5);\r\n\r\n const offsetVert = this._getBaseVertices(delta, obtuseAngle);\r\n\r\n const geometry = new THREE.BufferGeometry();\r\n const vertices = [];\r\n\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(offsetVert[i].clone().multiply(bSize));\r\n vertices.push(offsetVert[(i + 1) % 4].clone().multiply(bSize));\r\n }\r\n const translation = new THREE.Vector3(2 * bSize.x * (1 - delta.x - delta.y), 0, 0);\r\n for (let i = 0; i < 8; i++) {\r\n vertices.push(vertices[i].clone().add(translation));\r\n }\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(vertices[i * 2].clone());\r\n vertices.push(vertices[i * 2 + 8].clone());\r\n }\r\n const center = new THREE.Vector3();\r\n bBox.getCenter(center);\r\n vertices.forEach((vertex) => vertex.add(center)); // pivot shift\r\n\r\n const flatVertices = _flattenArray(vertices);\r\n geometry.setAttribute('position', new THREE.BufferAttribute(flatVertices, 3));\r\n\r\n this._lines = new THREE.LineSegments(geometry, new THREE.LineBasicMaterial({ color: 0xFFFFFF }));\r\n this._lines.layers.set(gfxutils.LAYERS.VOLUME);\r\n }\r\n\r\n // Set one edge (4 points) of frame, from which with parallel transfer the rest of the frame points can be obtained\r\n _getBaseVertices(delta, obtuseAngle) {\r\n const projTable = VolumeBounds._projectionTable;\r\n\r\n const proj = ((index, inv) => { // tricky function to take account of projections: their position(related to box) and sign\r\n const currDelta = delta[projTable[index][0]];\r\n const angleValue = -0.5 * (inv - 1) + inv * obtuseAngle[projTable[index][1]];// inv = 1: alpha; inv = -1: 1 - alpha\r\n return angleValue * currDelta;\r\n });\r\n\r\n const offsetVert = [\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', 1)), -1 + 2 * proj('YZ', 1), -1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', 1)), -1 + 2 * proj('YZ', -1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', -1)), 1 - 2 * proj('YZ', 1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', -1)), 1 - 2 * proj('YZ', -1), -1),\r\n ];\r\n\r\n return offsetVert;\r\n }\r\n\r\n getMesh() {\r\n return this._lines;\r\n }\r\n}\r\n\r\nexport default VolumeBounds;\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport meshes from './meshes/meshes';\r\nimport gfxutils from './gfxutils';\r\n\r\n// Thes geometric far plane is required for correct filling in the BFTexture in case, when far plane cuts the volume\r\n// cube. In cut place of cube there is no correct data in BFTexture and volume rendering integral is calculated\r\n// with errors.\r\n// Far plane cuts the cube in case of large volume scale (zoom), because farplane doesn't change\r\nclass VolumeFarPlane {\r\n // create plane with unit corners coords (for future rescale in vshader according to camera properties)\r\n constructor(volume, width, height) {\r\n const planeGeo = this._initPlaneGeo(width, height);\r\n\r\n const mat = new VolumeMaterial.BackFacePosMaterialFarPlane();\r\n this._plane = new meshes.Mesh(planeGeo, mat);\r\n this._plane.frustumCulled = false;\r\n this._plane.doubleSided = true;\r\n const matWorldToVolume = new THREE.Matrix4();\r\n\r\n this._plane._onBeforeRender = function (_renderer, _scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!volume || !material) {\r\n return;\r\n }\r\n\r\n // count point in world at farplane place\r\n const planeCamPos = new THREE.Vector4(0, 0, -(camera.far - 0.1), 1);\r\n planeCamPos.applyMatrix4(camera.matrixWorld);\r\n\r\n // recalc matrices to make plane be placed as farplane in the World relative to camera\r\n this.matrix.identity();\r\n this.matrix.makeTranslation(planeCamPos.x, planeCamPos.y, planeCamPos.z);\r\n this.matrixWorld.copy(this.matrix);\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n this.normalMatrix.getNormalMatrix(this.modelViewMatrix);\r\n\r\n // build worldToVolume matrix to transform plane into volumeCS (volumeCS coords are written to BackFaceTexture)\r\n const volumeMatrix = volume.matrixWorld;\r\n matWorldToVolume.copy(volumeMatrix).invert();\r\n\r\n // update material props\r\n material.uniforms.aspectRatio.value = camera.aspect;\r\n material.uniforms.farZ.value = camera.far;\r\n material.uniforms.tanHalfFOV.value = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * camera.fov);\r\n material.uniforms.matWorld2Volume.value = matWorldToVolume;\r\n };\r\n\r\n // set it to special layer to draw only into BFTexture\r\n this._plane.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n }\r\n\r\n _initPlaneGeo(width, height) {\r\n const planeGeo = new THREE.BufferGeometry();\r\n\r\n width = width || 1;\r\n height = height || 1;\r\n\r\n const vertices = new Float32Array([\r\n -0.5 * width, 0.5 * height, 0,\r\n 0.5 * width, 0.5 * height, 0,\r\n -0.5 * width, -0.5 * height, 0,\r\n 0.5 * width, -0.5 * height, 0,\r\n ]);\r\n\r\n planeGeo.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n planeGeo.setIndex([0, 2, 1, 2, 3, 1]);\r\n\r\n return planeGeo;\r\n }\r\n\r\n getMesh() {\r\n return this._plane;\r\n }\r\n}\r\n\r\nexport default VolumeFarPlane;\r\n","import * as THREE from 'three';\r\nimport VolumeMesh from './gfx/VolumeMesh';\r\nimport VolumeBounds from './gfx/VolumeBounds';\r\nimport VolumeFarPlane from './gfx/VolumeFarPlane';\r\nimport Visual from './Visual';\r\nimport settings from './settings';\r\n\r\nclass VolumeVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._mesh = new VolumeMesh();\r\n this._mesh.setDataSource(dataSource);\r\n this.add(this._mesh);\r\n\r\n this._frame = new VolumeBounds(this.getBoundaries().boundingBox, this._mesh.volumeInfo);\r\n this.add(this._frame.getMesh());\r\n this.showFrame(settings.now.modes.VD.frame);\r\n\r\n this._farPlane = new VolumeFarPlane(this._mesh, 2, 2);\r\n this.add(this._farPlane.getMesh());\r\n }\r\n\r\n getBoundaries() {\r\n const box = this._dataSource.getBox();\r\n const sphere = new THREE.Sphere();\r\n box.getBoundingSphere(sphere);\r\n\r\n return {\r\n boundingBox: box,\r\n boundingSphere: sphere,\r\n };\r\n }\r\n\r\n getMesh() {\r\n return this._mesh;\r\n }\r\n\r\n showFrame(needShow) {\r\n this._frame.getMesh().material.visible = needShow;\r\n }\r\n}\r\n\r\nexport default VolumeVisual;\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available loaders.\r\n * @extends EntityList\r\n */\r\nclass LoaderList extends EntityList {\r\n /**\r\n * Create a list of loaders.\r\n * The loaders are indexed by supported source types (`.types` property of a Loader\r\n * subclass).\r\n * The loaders can be retrieved later by matching against specs (see {@link LoaderList#find}).\r\n *\r\n * @param {!Array=} someLoaders A list of {@link Loader} subclasses to\r\n * automatically register at creation time.\r\n * @see LoaderList#register\r\n */\r\n constructor(someLoaders = []) {\r\n super(someLoaders, ['types']);\r\n }\r\n\r\n /**\r\n * Find a suitable loader for a source type.\r\n *\r\n * @param {Object} specs Loader specifications.\r\n * @param {string=} specs.type Supported source type.\r\n * @param {*=} specs.source Source to load from.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.type) {\r\n list = this._dict.types[specs.type.toLowerCase()] || [];\r\n } else if (specs.source) {\r\n return this._list.filter((SomeLoader) => SomeLoader.canProbablyLoad && SomeLoader.canProbablyLoad(specs.source));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default LoaderList;\r\n","import EventDispatcher from '../../utils/EventDispatcher';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Loader extends EventDispatcher {\r\n constructor(source, options) {\r\n super();\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n this._agent = null;\r\n }\r\n\r\n load() {\r\n return Promise.reject(new Error('Loading from this source is not implemented'));\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n if (this._agent) {\r\n this._agent.abort();\r\n }\r\n }\r\n\r\n static extractName(_source) {\r\n return undefined;\r\n }\r\n}\r\n\r\nmakeContextDependent(Loader.prototype);\r\n","import Loader from './Loader';\r\n\r\nexport default class FileLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = options.binary === true;\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const blob = this._source;\r\n const reader = this._agent = new FileReader();\r\n\r\n reader.addEventListener('load', () => {\r\n resolve(reader.result);\r\n });\r\n reader.addEventListener('error', () => {\r\n reject(reader.error);\r\n });\r\n reader.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n reader.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n if (this._binary) {\r\n reader.readAsArrayBuffer(blob);\r\n } else {\r\n reader.readAsText(blob);\r\n }\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return (File && source instanceof File) || (Blob && source instanceof Blob);\r\n }\r\n\r\n static extractName(source) {\r\n return source && source.name;\r\n }\r\n}\r\n\r\nFileLoader.types = ['file', 'blob'];\r\n","import _ from 'lodash';\r\nimport Loader from './Loader';\r\n\r\n// we don't need to detect all kinds of URLs, just the evident ones\r\nconst urlStartRegexp = /^(https?|ftp):\\/\\//i;\r\n\r\nexport default class XHRLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = (options.binary === true);\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const url = this._source;\r\n const request = this._agent = new XMLHttpRequest();\r\n\r\n request.addEventListener('load', () => {\r\n if (request.status === 200) {\r\n resolve(request.response);\r\n } else {\r\n reject(new Error(`HTTP ${request.status} while fetching ${url}`));\r\n }\r\n });\r\n request.addEventListener('error', () => {\r\n reject(new Error('HTTP request failed'));\r\n });\r\n request.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n request.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n request.open('GET', url);\r\n if (this._binary) {\r\n request.responseType = 'arraybuffer';\r\n } else {\r\n request.responseType = 'text';\r\n }\r\n request.send();\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return _.isString(source) && urlStartRegexp.test(source);\r\n }\r\n\r\n static extractName(source) {\r\n if (source) {\r\n const last = (source.indexOf('?') + 1 || source.lastIndexOf('#') + 1 || source.length + 1) - 1;\r\n return source.slice(source.lastIndexOf('/', last) + 1, last);\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nXHRLoader.types = ['url'];\r\n","import Loader from './Loader';\r\n\r\nexport default class ImmediateLoader extends Loader {\r\n load() {\r\n return new Promise((resolve) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n resolve(this._source);\r\n });\r\n }\r\n\r\n static canProbablyLoad(_source) {\r\n return false;\r\n }\r\n}\r\n\r\nImmediateLoader.types = ['immediate'];\r\n","import LoaderList from './loaders/LoaderList';\r\n\r\nimport FileLoader from './loaders/FileLoader';\r\nimport XHRLoader from './loaders/XHRLoader';\r\nimport ImmediateLoader from './loaders/ImmediateLoader';\r\n\r\nexport default new LoaderList([\r\n // note: order might be important\r\n FileLoader,\r\n XHRLoader,\r\n ImmediateLoader,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available parsers.\r\n * @extends EntityList\r\n */\r\nclass ParserList extends EntityList {\r\n /**\r\n * Create a list of parsers.\r\n * The parsers are indexed by supported data formats and file extensions (`.formats` and\r\n * `.extensions` properties of a Parser subclass).\r\n * The parsers can be retrieved later by matching against specs (see {@link ParsrerList#find}).\r\n *\r\n * @param {!Array=} someParsers A list of {@link Parser} subclasses to\r\n * automatically register at creation time.\r\n * @see ParserList#register\r\n */\r\n constructor(someParsers = []) {\r\n super(someParsers, ['formats', 'extensions']);\r\n }\r\n\r\n /**\r\n * Find a suitable parser for data.\r\n *\r\n * @param {Object} specs Parser specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {string=} specs.ext Supported filename extension.\r\n * @param {*=} specs.data Data to parse.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n } else if (specs.ext) {\r\n list = this._dict.extensions[specs.ext.toLowerCase()] || [];\r\n }\r\n // autodetect only if no format is forced\r\n if (list.length === 0 && !specs.format && specs.data) {\r\n return this._list.filter((SomeParser) => SomeParser.canProbablyParse && SomeParser.canProbablyParse(specs.data));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ParserList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Parser {\r\n constructor(data, options) {\r\n this._data = data;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n parseSync() {\r\n throw new Error('Parsing this type of data is not implemented');\r\n }\r\n\r\n parse() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Parsing aborted'));\r\n }\r\n return resolve(this.parseSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n // only for volume Parsers\r\n getModel() {\r\n this.model._parseHeader(this._data);\r\n return this.model;\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Parser.prototype);\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 290\".\r\n *\r\n * @exports Remark290\r\n * @constructor\r\n */\r\nclass Remark290 {\r\n constructor() {\r\n /** @type {THREE.Matrix4[]} */\r\n this.matrices = [];\r\n\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (stream.readString(12, 18) === ' SMTRY') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === this.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n }\r\n }\r\n}\r\n\r\nRemark290.prototype.id = 290;\r\n\r\nexport default Remark290;\r\n","import * as THREE from 'three';\r\nimport chem from '../../../chem';\r\n\r\nconst { Assembly } = chem;\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 350\".\r\n *\r\n * @exports Remark350\r\n * @constructor\r\n */\r\nclass Remark350 {\r\n constructor(complex) {\r\n /** @type {Complex} */\r\n this._complex = complex;\r\n /** @type {Assembly[]} */\r\n this.assemblies = [];\r\n\r\n /** @type {?Assembly} */\r\n this._assembly = null;\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?Assembly} */\r\n let assembly = this._assembly;\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (assembly && stream.readString(12, 18) === ' BIOMT') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === assembly.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n } else if (assembly && stream.readString(35, 41) === 'CHAINS:') {\r\n const entries = stream.readString(42, 80).split(',');\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const chain = entries[i].trim();\r\n if (chain.length > 0) {\r\n assembly.addChain(chain);\r\n }\r\n }\r\n } else if (stream.readString(12, 23) === 'BIOMOLECULE:') {\r\n // assert molIndex === this.assemblies.length + 1\r\n this._matrix = null;\r\n this._matrixIndex = -1;\r\n this._assembly = assembly = new Assembly(this._complex);\r\n this.assemblies.push(assembly);\r\n }\r\n }\r\n}\r\n\r\nRemark350.prototype.id = 350;\r\n\r\nexport default Remark350;\r\n","/** Helper class for stream-like reading input files. */\r\nclass PDBStream {\r\n /**\r\n * Create a stream\r\n * @param {String} data Input data\r\n */\r\n constructor(data) {\r\n /** @type String */\r\n this._data = data; // Input file\r\n /** @type Number */\r\n this._start = 0; // Starting position of line\r\n /** @type Number */\r\n this._nextCR = -1; // Position of next CR (0x0D)\r\n /** @type Number */\r\n this._nextLF = -1; // Position of next LF (0x0A)\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n /** @type Number */\r\n this._end = data.length; // End of data\r\n\r\n this.next();\r\n }\r\n\r\n /**\r\n * Reading next line.\r\n * @returns {String} Next line in data (ending with LF or CR)\r\n */\r\n readLine() {\r\n return this._data.slice(this._start, this._next);\r\n }\r\n\r\n /**\r\n * Reading character from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {String} Character from position\r\n */\r\n readChar(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data[pos] : ' ';\r\n }\r\n\r\n /**\r\n * Reading character code from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {Number} Character code from position\r\n */\r\n readCharCode(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data.charCodeAt(pos) : 32;\r\n }\r\n\r\n /**\r\n * Reading string from begin to end points.\r\n * For a reason unknown, numbering assumed not to start from 0, but from 1.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {String} String from begin to end\r\n */\r\n readString(begin, end) {\r\n const from = this._start + begin - 1;\r\n const to = this._start + end;\r\n return this._data.slice(from, to < this._next ? to : this._next);\r\n }\r\n\r\n /**\r\n * Reading integer from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Integer from begin to end\r\n */\r\n readInt(begin, end) {\r\n return parseInt(this.readString(begin, end), 10);\r\n }\r\n\r\n /**\r\n * Reading float from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Float from begin to end\r\n */\r\n readFloat(begin, end) {\r\n return parseFloat(this.readString(begin, end));\r\n }\r\n\r\n /**\r\n * Checking for end of data.\r\n * @returns {boolean} True if data is ended, false otherwise\r\n */\r\n end() {\r\n return this._start >= this._end;\r\n }\r\n\r\n /**\r\n * Procedure to re-arrange current pointers in data.\r\n */\r\n next() {\r\n const start = this._next + 1;\r\n this._start = start < this._end ? start : this._end;\r\n\r\n // support CR, LF, CR+LF line endings\r\n // do not support LF+CR, CR+CR+LF, and other strange combinations\r\n\r\n if (this._start > this._nextCR) {\r\n this._nextCR = (this._data.indexOf('\\r', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n if (this._start > this._nextLF) {\r\n this._nextLF = (this._data.indexOf('\\n', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n this._next = this._nextCR + 1 < this._nextLF ? this._nextCR : this._nextLF;\r\n }\r\n}\r\n\r\nexport default PDBStream;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport Remark290 from './pdb/Remark290';\r\nimport Remark350 from './pdb/Remark350';\r\nimport PDBStream from './PDBStream';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst TAG_LENGTH = 6;\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\n// the most frequently used beginnings; although HEADER is mandatory, it is often missing in handmade files\r\nconst pdbStartRegexp = /^(HEADER\\s|COMPND\\s|REMARK\\s|ATOM {2}|HETATM|MODEL )/i;\r\n\r\nconst remarkParsers = {\r\n // NOTE: please forget the idea to build the method name in runtime, it can be obfuscated.\r\n 290: Remark290,\r\n 350: Remark350,\r\n};\r\n\r\nclass PDBParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._sheet = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._compaundFound = false;\r\n this._biomoleculeFound = false;\r\n this._allowedChainsIDs = null;\r\n this._lastMolId = -1;\r\n\r\n this._remarks = {};\r\n this._remark = null;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n this._compndCurrToken = '';\r\n\r\n this._options.fileType = 'pdb';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && pdbStartRegexp.test(data);\r\n }\r\n\r\n _finalize() {\r\n this._fixBondsArray();\r\n this._fixChains();\r\n\r\n // keep crystallographic symmetry transformations\r\n const remark290 = this._remarks[290];\r\n this._complex.symmetry = _.isUndefined(remark290) ? [] : remark290.matrices;\r\n\r\n // add loaded biological assemblies\r\n const remark350 = this._remarks[350];\r\n this._complex.units = this._complex.units.concat(_.isUndefined(remark350) ? [] : remark350.assemblies);\r\n\r\n // add loaded macromolecules\r\n this._finalizeMolecules();\r\n\r\n // create secondary structure etc.\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _finalizeMolecules() {\r\n // get chains from complex\r\n const chainDict = {};\r\n let i;\r\n const chains = this._complex._chains;\r\n for (i = 0; i < chains.length; ++i) {\r\n const chainObj = chains[i];\r\n const chainName = chainObj._name;\r\n chainDict[chainName] = chainObj;\r\n }\r\n\r\n // aggregate residues from chains\r\n for (i = 0; i < this._molecules.length; i++) {\r\n const m = this._molecules[i];\r\n let residues = [];\r\n for (let j = 0; j < m._chains.length; j++) {\r\n const name = m._chains[j];\r\n const chain = chainDict[name];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, m._name, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _fixChains() {\r\n const idChainMap = {};\r\n const complex = this._complex;\r\n\r\n // prepare\r\n for (let i = 0; i < complex._chains.length; i++) {\r\n const chain = complex._chains[i];\r\n idChainMap[chain._name.charCodeAt(0)] = chain;\r\n }\r\n }\r\n\r\n // FIXME: This function is redundant, CONECT records always follow ATOM and HETATM. Build the map online.\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseATOM(stream) {\r\n if (this._modelId !== 1) {\r\n return;\r\n }\r\n\r\n /* eslint-disable no-magic-numbers */\r\n const het = stream.readCharCode(1) === 0x48;\r\n\r\n // field names according to wwPDB Format\r\n // NOTE: Chimera allows (nonstandard) use of columns 6-11 for the integer atom serial number in ATOM records.\r\n const serial = het ? stream.readInt(7, 11) : stream.readInt(6, 11);\r\n let name = stream.readString(13, 16);\r\n const altLoc = stream.readChar(17);\r\n const resName = stream.readString(18, 20).trim();\r\n const chainID = stream.readChar(22);\r\n const resSeq = stream.readInt(23, 26);\r\n const iCode = stream.readChar(27);\r\n const x = stream.readFloat(31, 38);\r\n const y = stream.readFloat(39, 46);\r\n const z = stream.readFloat(47, 54);\r\n const occupancy = stream.readFloat(55, 60);\r\n const tempFactor = stream.readFloat(61, 66);\r\n const element = stream.readString(77, 78).trim() || nameToElement(name);\r\n const charge = stream.readInt(79, 80) || 0;\r\n /* eslint-enable no-magic-numbers */\r\n // skip waters (there may be lots of them)\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n // PDB uses positional system for atom names. It helps derive element type from the name\r\n // but names may include extra spaces. From this point on we don't need those spaces anymore.\r\n name = name.trim();\r\n\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name]; // FIXME: Maybe should use type as additional index (\" CA \" vs. \"CA \")\r\n\r\n // NOTE: Residues of a particular chain are not required to be listed next to each other.\r\n // https://github.com/biasmv/pv/commit/7319b898b7473ba380c26699e3b028b2b1a7e1a1\r\n let chain = this._chain;\r\n if (!chain || chain.getName() !== chainID) {\r\n this._chain = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n _parseENDMDL() {\r\n this._modelId += 1;\r\n }\r\n\r\n _parseCONECT(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const serial0 = stream.readInt(7, 11);\r\n const serial1 = stream.readInt(12, 16);\r\n const serial2 = stream.readInt(17, 21);\r\n const serial3 = stream.readInt(22, 26);\r\n const serial4 = stream.readInt(27, 31);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n const complex = this._complex;\r\n\r\n // Keep bonds ordered by atom serial\r\n if (serial1 && serial1 > serial0) {\r\n complex.addBond(serial0, serial1, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial2 && serial2 > serial0) {\r\n complex.addBond(serial0, serial2, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial3 && serial3 > serial0) {\r\n complex.addBond(serial0, serial3, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial4 && serial4 > serial0) {\r\n complex.addBond(serial0, serial4, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n }\r\n\r\n _parseCOMPND(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const str = stream.readString(11, 80);\r\n const tokenIdx = str.indexOf(':');\r\n this._compndCurrToken = tokenIdx > 0 ? str.substring(0, tokenIdx).trim() : this._compndCurrToken;\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // start reading new molecule\r\n if (this._compndCurrToken === 'MOL_ID') {\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = parseInt(str.substring(tokenIdx + 1, str.indexOf(';')), 10);\r\n this._molecules.push(this._molecule);\r\n // parse molecule name\r\n } else if (this._compndCurrToken === 'MOLECULE' && this._molecule != null) {\r\n this._molecule._name = str.substring(tokenIdx + 1, str.indexOf(';')).trim();\r\n // parse molecule chains\r\n } else if (this._compndCurrToken === 'CHAIN' && this._molecule != null) {\r\n let chainStr = str.substring(tokenIdx + 1, 80).trim();\r\n const lastChar = chainStr[chainStr.length - 1];\r\n if (lastChar === ';' || lastChar === ',') {\r\n chainStr = chainStr.slice(0, -1);\r\n }\r\n chainStr = chainStr.replace(/\\s+/g, '');\r\n const chains = chainStr.split(',');\r\n this._molecule._chains = this._molecule._chains.concat(chains);\r\n }\r\n }\r\n\r\n _parseREMARK(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const remarkNum = stream.readInt(8, 10);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // create remark parser if needed\r\n let remark = this._remarks[remarkNum];\r\n if (_.isUndefined(remark)) {\r\n const RemarkParser = remarkParsers[remarkNum];\r\n if (_.isFunction(RemarkParser)) {\r\n this._remarks[remarkNum] = remark = new RemarkParser(this._complex);\r\n }\r\n }\r\n\r\n // delegate parsing\r\n if (!_.isUndefined(remark)) {\r\n remark.parse(stream);\r\n }\r\n }\r\n\r\n _parseHELIX(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const fields = [20, 22, 32, 34];\r\n /* eslint-enable no-magic-numbers */\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addHelix(obj);\r\n this._complex.structures.push(obj);\r\n });\r\n }\r\n\r\n _parseSHEET(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const fields = [22, 23, 33, 34];\r\n /* eslint-enable no-magic-numbers */\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addSheet(obj);\r\n });\r\n }\r\n\r\n _parseSTRUCTURE(stream, pars, adder) {\r\n const startId = 0;\r\n const startIndex = 1;\r\n const endId = 2;\r\n const endIndex = 3;\r\n\r\n // identify fields: debugging and stuff\r\n /* eslint-disable no-magic-numbers */\r\n const codeOfS = 0x53;\r\n const serialNumber = stream.readInt(8, 10);\r\n const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim()\r\n const comment = stream.readString(41, 70).trim();\r\n const helLength = stream.readInt(72, 76);\r\n const helixClass = stream.readInt(39, 40);\r\n const shWidth = stream.readInt(15, 16);\r\n const shCur = stream.readInt(42, 45);\r\n const shPrev = stream.readInt(57, 60);\r\n /* eslint-enable no-magic-numbers */\r\n // file fields\r\n const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0);\r\n const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0);\r\n const startSequenceNumber = stream.readInt(pars[startIndex], pars[startIndex] + 3);\r\n let iCodeStr = stream.readString(pars[startIndex] + 4, pars[startIndex] + 4);\r\n let startICode = 0;\r\n\r\n if (iCodeStr.length > 0) {\r\n startICode = iCodeStr.charCodeAt(0);\r\n }\r\n const endSequenceNumber = stream.readInt(pars[endIndex], pars[endIndex] + 3);\r\n iCodeStr = stream.readString(pars[endIndex] + 4, pars[endIndex] + 4);\r\n let endICode = 0;\r\n if (iCodeStr.length > 0) {\r\n endICode = iCodeStr.charCodeAt(0);\r\n }\r\n\r\n let obj;\r\n let cs = this._sheet;\r\n if (stream.readCharCode(1) === codeOfS) {\r\n if (cs !== null && cs.getName() !== structureName) {\r\n cs = null;\r\n this._sheet = null;\r\n }\r\n if (cs === null) {\r\n this._sheet = obj = new Sheet(structureName, shWidth);\r\n adder(obj);\r\n } else {\r\n obj = cs;\r\n }\r\n const strand = new Strand(\r\n obj,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n helixClass,\r\n shCur,\r\n shPrev,\r\n );\r\n obj.addStrand(strand);\r\n this._complex.structures.push(strand);\r\n } else {\r\n obj = new Helix(\r\n helixClass,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n serialNumber,\r\n structureName,\r\n comment,\r\n helLength,\r\n );\r\n adder(obj);\r\n }\r\n }\r\n\r\n _parseHEADER(stream) {\r\n const { metadata } = this._complex;\r\n metadata.classification = stream.readString(11, 50).trim();\r\n metadata.date = stream.readString(51, 59).trim();\r\n\r\n const id = stream.readString(63, 66).trim();\r\n metadata.id = id;\r\n if (id) {\r\n this._complex.name = id;\r\n }\r\n metadata.format = 'pdb';\r\n }\r\n\r\n _parseTITLE(stream) {\r\n const { metadata } = this._complex;\r\n metadata.title = metadata.title || [];\r\n\r\n const line = stream.readInt(9, 10) || 1;\r\n metadata.title[line - 1] = stream.readString(11, 80).trim();\r\n }\r\n\r\n static tagParsers = {\r\n HEADER: PDBParser.prototype._parseHEADER,\r\n 'TITLE ': PDBParser.prototype._parseTITLE,\r\n 'ATOM ': PDBParser.prototype._parseATOM,\r\n HETATM: PDBParser.prototype._parseATOM,\r\n ENDMDL: PDBParser.prototype._parseENDMDL,\r\n CONECT: PDBParser.prototype._parseCONECT,\r\n COMPND: PDBParser.prototype._parseCOMPND,\r\n REMARK: PDBParser.prototype._parseREMARK,\r\n // 'SOURCE': PDBParser.prototype._parseSOURCE,\r\n 'HELIX ': PDBParser.prototype._parseHELIX,\r\n 'SHEET ': PDBParser.prototype._parseSHEET,\r\n\r\n // nonstandard extension to allow range 100,000 - 999,999\r\n 'ATOM 1': PDBParser.prototype._parseATOM,\r\n 'ATOM 2': PDBParser.prototype._parseATOM,\r\n 'ATOM 3': PDBParser.prototype._parseATOM,\r\n 'ATOM 4': PDBParser.prototype._parseATOM,\r\n 'ATOM 5': PDBParser.prototype._parseATOM,\r\n 'ATOM 6': PDBParser.prototype._parseATOM,\r\n 'ATOM 7': PDBParser.prototype._parseATOM,\r\n 'ATOM 8': PDBParser.prototype._parseATOM,\r\n 'ATOM 9': PDBParser.prototype._parseATOM,\r\n };\r\n\r\n parseSync() {\r\n const stream = new PDBStream(this._data);\r\n const result = this._complex = new Complex();\r\n\r\n // parse PDB line by line\r\n while (!stream.end()) {\r\n const tag = stream.readString(1, TAG_LENGTH);\r\n const func = PDBParser.tagParsers[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, stream);\r\n }\r\n stream.next();\r\n }\r\n\r\n // Resolve indices and serials to objects\r\n this._finalize();\r\n\r\n // cleanup\r\n this._serialAtomMap = null;\r\n this._sheet = null;\r\n this._residue = null;\r\n this._chain = null;\r\n this._complex = null;\r\n\r\n if (result.getAtomCount() === 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n\r\nPDBParser.formats = ['pdb'];\r\nPDBParser.extensions = ['.pdb', '.ent'];\r\n\r\nexport default PDBParser;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n SGroup,\r\n Bond,\r\n} = chem;\r\n\r\nconst cOrderCharCodes = {\r\n A: 0,\r\n S: 1,\r\n D: 2,\r\n T: 3,\r\n};\r\n\r\nconst cmlStartRegexp = /\\s*<\\?xml\\b[^?>]*\\?>\\s*<(?:cml|molecule)\\b/i;\r\n\r\nclass CMLParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._complex = null;\r\n this._residue = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._lastMolId = -1;\r\n this._readOnlyOneMolecule = false;\r\n this._options.fileType = 'cml';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && cmlStartRegexp.test(data);\r\n }\r\n\r\n _rebuidBondIndexes(atoms, bonds) {\r\n const count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n\r\n const countBonds = bonds.length;\r\n for (let j = 0; j < countBonds; j++) {\r\n const idxs = bonds[j].atomRefs2.split(' ');\r\n if (idxs[0] === atomId) {\r\n bonds[j].start = i;\r\n }\r\n\r\n if (idxs[1] === atomId) {\r\n bonds[j].end = i;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _createSGroup(molecule, moleculeArr) {\r\n const newGroup = new SGroup(\r\n molecule.id,\r\n molecule.fieldData,\r\n new THREE.Vector3(parseFloat(molecule.x), parseFloat(molecule.y), 0),\r\n molecule.atomRefs,\r\n molecule,\r\n );\r\n if (molecule.placement === 'Relative') {\r\n newGroup._center = new THREE.Vector3(0, 0, 0);\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_CHARGE') {\r\n newGroup._charge = parseInt(molecule.fieldData, 10) || 0;\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_COEFFICIENT') {\r\n newGroup._repeat = parseInt(molecule.fieldData, 10) || 1;\r\n }\r\n moleculeArr.push(newGroup);\r\n }\r\n\r\n _extractSGroup(molecule, moleculeArr) {\r\n if (!Array.isArray(moleculeArr)) {\r\n moleculeArr = [];\r\n }\r\n\r\n if (molecule) {\r\n if (Array.isArray(molecule)) {\r\n const count = molecule.length;\r\n for (let i = 0; i < count; i++) {\r\n if (molecule[i].molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule[i].molecule));\r\n }\r\n this._createSGroup(molecule[i], moleculeArr);\r\n }\r\n } else {\r\n if (molecule.molecule) {\r\n if (molecule.molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule.molecule));\r\n }\r\n }\r\n this._createSGroup(molecule, moleculeArr);\r\n }\r\n }\r\n\r\n return moleculeArr;\r\n }\r\n\r\n _extractSGroups(molecule, atoms) {\r\n const moleculeArr = this._extractSGroup(molecule);\r\n\r\n const count = atoms.length;\r\n let i;\r\n let j;\r\n\r\n for (i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n const firstAtomRef = moleculeArr[j]._atoms.split(' ')[0];\r\n if (firstAtomRef === atomId) {\r\n if (!atoms[i].sgroupRef) {\r\n atoms[i].sgroupRef = [];\r\n }\r\n atoms[i].sgroupRef.push(moleculeArr[j]);\r\n }\r\n }\r\n }\r\n // build sGroups centers\r\n let atomMap = {}; // sgrpmap cache\r\n let mapEntry = null;\r\n const nLimon = 100000000;\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n\r\n function cycleFuncInner(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n moleculeArr[j]._atoms.push(mapEntry.a);\r\n }\r\n }\r\n\r\n function cycleFunc(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n bLow.set(Math.min(bLow.x, mapEntry.x), Math.min(bLow.y, mapEntry.y), Math.min(bLow.z, mapEntry.z));\r\n bHight.set(Math.max(bHight.x, mapEntry.x), Math.max(bHight.y, mapEntry.y), Math.max(bHight.z, mapEntry.z));\r\n cycleFuncInner(e);\r\n }\r\n }\r\n\r\n for (i = 0; i < atoms.length; i++) {\r\n atomMap[atoms[i].id] = {};\r\n atomMap[atoms[i].id].x = atoms[i].x2;\r\n if (atoms[i].x3) {\r\n atomMap[atoms[i].id].x = atoms[i].x3;\r\n }\r\n atomMap[atoms[i].id].x = parseFloat(atomMap[atoms[i].id].x);\r\n atomMap[atoms[i].id].y = atoms[i].y2;\r\n if (atoms[i].y3) {\r\n atomMap[atoms[i].id].y = atoms[i].y3;\r\n }\r\n atomMap[atoms[i].id].y = parseFloat(atomMap[atoms[i].id].y);\r\n atomMap[atoms[i].id].z = '0.0';\r\n if (atoms[i].z3) {\r\n atomMap[atoms[i].id].z = atoms[i].z3;\r\n }\r\n atomMap[atoms[i].id].z = parseFloat(atomMap[atoms[i].id].z);\r\n atomMap[atoms[i].id].a = atoms[i];\r\n }\r\n\r\n let atomsRef;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n if (moleculeArr[j]._center !== null) {\r\n bLow.set(nLimon, nLimon, nLimon);\r\n bHight.set(-nLimon, -nLimon, -nLimon);\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFunc);\r\n\r\n moleculeArr[j]._center.addVectors(bLow, bHight);\r\n moleculeArr[j]._center.multiplyScalar(0.5);\r\n } else {\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFuncInner);\r\n }\r\n }\r\n atomMap = null;\r\n }\r\n\r\n _traverseData(dom) {\r\n function isArray(o) {\r\n return Object.prototype.toString.apply(o) === '[object Array]';\r\n }\r\n\r\n function parseNode(xmlNode, result) {\r\n if (xmlNode.nodeName === '#text' && xmlNode.nodeValue.trim() === '') {\r\n return;\r\n }\r\n\r\n const jsonNode = {};\r\n jsonNode.xmlNode = xmlNode;\r\n const existing = result[xmlNode.nodeName];\r\n if (existing) {\r\n if (!isArray(existing)) {\r\n result[xmlNode.nodeName] = [existing, jsonNode];\r\n } else {\r\n result[xmlNode.nodeName].push(jsonNode);\r\n }\r\n } else {\r\n result[xmlNode.nodeName] = jsonNode;\r\n }\r\n\r\n let length;\r\n let i;\r\n if (xmlNode.attributes) {\r\n ({ length } = xmlNode.attributes);\r\n for (i = 0; i < length; i++) {\r\n const attribute = xmlNode.attributes[i];\r\n jsonNode[attribute.nodeName] = attribute.nodeValue;\r\n }\r\n }\r\n\r\n ({ length } = xmlNode.childNodes);\r\n for (i = 0; i < length; i++) {\r\n parseNode(xmlNode.childNodes[i], jsonNode);\r\n }\r\n }\r\n\r\n const result = {};\r\n if (dom.childNodes.length) {\r\n parseNode(dom.childNodes[0], result);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _findSuitableMolecule(data, molSet) {\r\n for (const key in data) {\r\n if (key === 'xmlNode') {\r\n continue;\r\n } else if (key === 'molecule') {\r\n if (data.molecule) {\r\n if (data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n molSet.push(data);\r\n }\r\n if (Array.isArray(data.molecule)) {\r\n for (let i = 0; i < data.molecule.length; i++) {\r\n if (data.molecule[i].atomArray && data.molecule[i].atomArray.atom) {\r\n molSet.push({ molecule: data.molecule[i] });\r\n }\r\n }\r\n }\r\n }\r\n } else if (data[key] && data[key] !== null && typeof (data[key]) === 'object') {\r\n this._findSuitableMolecule(data[key], molSet);\r\n }\r\n }\r\n }\r\n\r\n _selectComponents(text) {\r\n const parser = new DOMParser();\r\n const doc = parser.parseFromString(text, 'application/xml');\r\n const traversedData = this._traverseData(doc);\r\n let rawData;\r\n const self = this;\r\n\r\n function prepareComponentCompound(data) {\r\n let atoms = [];\r\n if (data.molecule && data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n if (!Array.isArray(data.molecule.atomArray.atom)) {\r\n atoms.push(data.molecule.atomArray.atom);\r\n } else {\r\n atoms = data.molecule.atomArray.atom;\r\n }\r\n } else if (!data.molecule) {\r\n const ret = {};\r\n ret.atomLabels = null;\r\n ret.labelsCount = 1;\r\n return ret;\r\n }\r\n\r\n if (data.molecule.molecule) {\r\n self._extractSGroups(data.molecule.molecule, atoms);\r\n }\r\n\r\n let atom;\r\n let count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges = [];\r\n }\r\n\r\n let localBond = [];\r\n if (data.molecule.bondArray && data.molecule.bondArray.bond) {\r\n if (!Array.isArray(data.molecule.bondArray.bond)) {\r\n localBond.push(data.molecule.bondArray.bond);\r\n } else {\r\n localBond = data.molecule.bondArray.bond;\r\n }\r\n }\r\n let bond;\r\n count = localBond.length;\r\n self._rebuidBondIndexes(atoms, localBond);\r\n\r\n function addCurrBond(index) {\r\n bond = localBond[index];\r\n atom = atoms[bond.start];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.end);\r\n atom = atoms[bond.end];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.start);\r\n return true;\r\n }\r\n\r\n for (let i = 0; i < count; i++) {\r\n if (!addCurrBond(i)) {\r\n // ignore invalid bond\r\n continue;\r\n }\r\n const orderAttr = bond.xmlNode.getAttribute('order');\r\n const tc = parseInt(orderAttr, 10);\r\n // the default bond order is unknown\r\n localBond[i].order = 0;\r\n localBond[i].type = Bond.BondType.UNKNOWN;\r\n if (tc > 1) {\r\n localBond[i].order = tc;\r\n } else {\r\n // another option - bond order is a string\r\n const order = cOrderCharCodes[orderAttr];\r\n if (order !== undefined) {\r\n localBond[i].order = order;\r\n if (orderAttr === 'A') {\r\n localBond[i].type = Bond.BondType.AROMATIC;\r\n }\r\n }\r\n }\r\n }\r\n\r\n count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges.sort();\r\n }\r\n\r\n const labels = self._breadWidthSearch(atoms, 0); // for now\r\n\r\n const retStruct = {};\r\n retStruct.atoms = atoms;\r\n retStruct.bonds = localBond;\r\n retStruct.labels = labels.atomLabels;\r\n retStruct.count = Math.min(1, labels.labelsCount); // for now\r\n retStruct.curr = -1;\r\n retStruct.originalCML = doc;\r\n\r\n return retStruct;\r\n }\r\n\r\n if (traversedData.cml) {\r\n rawData = traversedData.cml;\r\n } else {\r\n rawData = traversedData;\r\n }\r\n const retData = [];\r\n const filteredData = [];\r\n this._findSuitableMolecule(rawData, filteredData);\r\n if (this._readOnlyOneMolecule && filteredData.length > 1) {\r\n filteredData.splice(1, filteredData.length - 1);\r\n }\r\n filteredData.forEach((d) => {\r\n const rd = prepareComponentCompound(d);\r\n if (rd.atoms.length > 0) {\r\n retData.push(rd);\r\n }\r\n });\r\n return retData;\r\n }\r\n\r\n _packLabel(compId, molId) {\r\n const shift = 16;\r\n return (molId << shift) + compId;\r\n }\r\n\r\n _unpackLabel(l) {\r\n const shift = 16;\r\n const mask = (1 << shift) - 1;\r\n return { molId: l >>> shift, compId: l & mask };\r\n }\r\n\r\n _breadWidthSearch(atoms, molID) {\r\n const atomLabels = new Array(atoms.length);\r\n\r\n let id;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n atomLabels[id] = this._packLabel(0, molID);\r\n }\r\n\r\n const breadthQueue = [];\r\n let componentID = 0;\r\n let labeledAtoms = atoms.length;\r\n\r\n while (labeledAtoms > 0) {\r\n componentID++;\r\n\r\n let startID = -1;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n if (this._unpackLabel(atomLabels[id]).compId === 0) {\r\n startID = id;\r\n break;\r\n }\r\n }\r\n\r\n if (startID < 0) {\r\n break;\r\n }\r\n\r\n // Bread first search\r\n breadthQueue.push(atoms[startID]);\r\n atomLabels[startID] = this._packLabel(componentID, molID);\r\n labeledAtoms--;\r\n\r\n while (breadthQueue.length > 0) {\r\n const curr = breadthQueue.shift();\r\n if (!curr) {\r\n continue;\r\n }\r\n\r\n for (let i = 0; i < curr.edges.length; i++) {\r\n if (atomLabels[curr.edges[i]] !== componentID) {\r\n breadthQueue.push(atoms[curr.edges[i]]);\r\n atomLabels[curr.edges[i]] = componentID;\r\n labeledAtoms--;\r\n }\r\n }\r\n }\r\n }\r\n const ret = {};\r\n ret.atomLabels = atomLabels;\r\n ret.labelsCount = componentID;\r\n return ret;\r\n }\r\n\r\n _parseBond(eAtom, mainAtom, order, type) {\r\n if (eAtom >= 0) {\r\n const h = [Math.min(eAtom, mainAtom), Math.max(eAtom, mainAtom)];\r\n this._complex.addBond(h[0], h[1], order, type, true);\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseSet(varData) {\r\n const complex = this._complex = new Complex();\r\n const data = varData;\r\n const currentLabel = data.curr;\r\n const { atoms, labels } = data;\r\n let atom = null;\r\n let i;\r\n let j;\r\n const count = atoms.length;\r\n\r\n function addFunc(a) {\r\n a.xmlNodeRef = atom;\r\n if (atom.x2) {\r\n atom.x3 = atom.x2;\r\n delete atom.x2;\r\n }\r\n if (atom.y2) {\r\n atom.y3 = atom.y2;\r\n delete atom.y2;\r\n }\r\n if (!(atom.z3)) {\r\n atom.z3 = '0.0';\r\n }\r\n atom.complexAtom = a;\r\n }\r\n\r\n let chains = {};\r\n // parse atoms in label order\r\n const reorder = [];\r\n for (i = 0; i < count; i++) {\r\n reorder.push(i);\r\n }\r\n reorder.sort((a, b) => labels[a] - labels[b]);\r\n for (i = 0; i < count; i++) {\r\n const atomCharge = 0;\r\n const lLabel = labels[reorder[i]];\r\n if (this._unpackLabel(lLabel).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[reorder[i]];\r\n const atomFullNameStruct = atom.elementType;\r\n\r\n if (atom.sgroupRef) {\r\n const countRef = atom.sgroupRef.length;\r\n for (let k = 0; k < countRef; ++k) {\r\n complex._sgroups.push(atom.sgroupRef[k]);\r\n }\r\n }\r\n\r\n if (atom.x3 || atom.x2) {\r\n const currAtomComp = this._unpackLabel(lLabel).compId;\r\n // use ' ' by default instead of synthetic creation of chain names\r\n const chainID = ' '; //= String.fromCharCode('A'.charCodeAt(0) + currAtomComp);\r\n const resSeq = currAtomComp;\r\n const iCode = ' ';\r\n let strLabel = currAtomComp.toString();\r\n if (strLabel.length === 1) {\r\n strLabel = `0${strLabel}`;\r\n }\r\n const resName = `N${strLabel}`;\r\n let chain = chains[chainID];\r\n if (!chain || chain.getName() !== chainID) {\r\n chains[chainID] = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n // _x, _y, _z, mname, mindex, atomNameFull, atomName, chainID, serial, isHet, atlLocInd, atomNameToTypeF\r\n let xyz = null;\r\n if (atom.x3) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x3), parseFloat(atom.y3), parseFloat(atom.z3));\r\n } else if (atom.x2) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x2), parseFloat(atom.y2), 0);\r\n }\r\n let element = Element.ByName[atom.elementType.toUpperCase()];\r\n if (!element) {\r\n element = (JSON.parse(JSON.stringify(Element.ByName[\r\n Object.keys(Element.ByName)[Object.keys(Element.ByName).length - 1]])));\r\n element.number += 1;\r\n element.name = atom.elementType.toUpperCase();\r\n element.fullName = 'Unknown';\r\n Element.ByName[atom.elementType.toUpperCase()] = element;\r\n }\r\n const atomSerial = parseInt(atom.id.replace(/[^0-9]/, ''), 10);\r\n const added = residue.addAtom(\r\n atomFullNameStruct,\r\n element,\r\n xyz,\r\n Element.Role.SG,\r\n true,\r\n atomSerial,\r\n ' ',\r\n 1.0,\r\n 0.0,\r\n atomCharge,\r\n );\r\n if (atom.hydrogenCount) {\r\n added.hydrogenCount = parseInt(atom.hydrogenCount, 10);\r\n }\r\n if (atom.mrvValence) {\r\n added.valence = parseInt(atom.mrvValence, 10);\r\n }\r\n addFunc(added);\r\n }\r\n }\r\n }\r\n chains = null;// NOSONAR\r\n for (i = 0; i < data.bonds.length; i++) {\r\n const cb = data.bonds[i];\r\n if (this._unpackLabel(labels[cb.start]).molId === this._unpackLabel(currentLabel).molId\r\n && this._unpackLabel(labels[cb.end]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[cb.start];\r\n if (!atom || !(atoms[cb.end])) {\r\n continue; // skip invalid\r\n }\r\n this._parseBond(\r\n parseInt(atom.id.replace(/[^0-9]/, ''), 10),\r\n parseInt(atoms[cb.end].id.replace(/[^0-9]/, ''), 10),\r\n cb.order,\r\n cb.type,\r\n );\r\n }\r\n }\r\n\r\n for (i = 0; i < this._complex.getSGroupCount(); i++) {\r\n const sGrp = this._complex.getSGroups()[i];\r\n for (j = 0; j < sGrp._atoms.length; j++) {\r\n sGrp._atoms[j] = sGrp._atoms[j].complexAtom;\r\n }\r\n }\r\n for (i = 0; i < count; i++) {\r\n if (this._unpackLabel(labels[i]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[i];\r\n atom.complexAtom = null;\r\n delete atom.complexAtom;\r\n }\r\n }\r\n this._complex.originalCML = data.originalCML;\r\n this._fixBondsArray();\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n this._serialAtomMap = null;\r\n this._complex = null;\r\n return complex;\r\n }\r\n\r\n parseSync() {\r\n const complexes = [];\r\n const self = this;\r\n const moleculaSet = this._selectComponents(this._data);\r\n moleculaSet.forEach((molSet) => {\r\n molSet.curr = 2;\r\n if (molSet.count === 0) {\r\n molSet.count = 1;\r\n }\r\n for (let i = 0; i < molSet.count; i++) {\r\n molSet.curr = (i + 1);\r\n complexes.push(self._parseSet(molSet, false));\r\n }\r\n });\r\n\r\n let totalAtomsParsed = 0;\r\n complexes.forEach((c) => {\r\n totalAtomsParsed += c.getAtomCount();\r\n });\r\n if (totalAtomsParsed <= 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n if (complexes.length > 1) {\r\n const joinedComplex = new Complex();\r\n joinedComplex.joinComplexes(complexes);\r\n joinedComplex.originalCML = complexes[0].originalCML;\r\n return joinedComplex;\r\n }\r\n if (complexes.length === 1) {\r\n return complexes[0];\r\n }\r\n return new Complex();\r\n }\r\n}\r\n\r\nCMLParser.formats = ['cml'];\r\nCMLParser.extensions = ['.cml'];\r\n\r\nexport default CMLParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport MMTF from '../../../vendor/js/mmtf';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst {\r\n Complex,\r\n Chain,\r\n Atom,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nclass ArrayComparator {\r\n constructor(original) {\r\n this._original = Array.from(original);\r\n this._original.sort();\r\n\r\n this._sum = 0;\r\n for (let i = 0; i < this._original.length; ++i) {\r\n this._sum += this._original[i];\r\n }\r\n }\r\n\r\n compare(candidate) {\r\n const len = candidate.length;\r\n if (len !== this._original.length) {\r\n return false;\r\n }\r\n\r\n let sum = 0;\r\n let i;\r\n for (i = 0; i < len; ++i) {\r\n sum += candidate[i];\r\n }\r\n\r\n if (sum !== this._sum) {\r\n return false;\r\n }\r\n\r\n const sorted = Array.from(candidate);\r\n sorted.sort();\r\n\r\n for (i = 0; i < len; ++i) {\r\n if (sorted[i] !== this._original[i]) {\r\n return false;\r\n }\r\n }\r\n\r\n return true;\r\n }\r\n}\r\n\r\nArrayComparator.prototype.constructor = ArrayComparator;\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see https://github.com/rcsb/mmtf-javascript/blob/master/src/mmtf-traverse.js\r\nconst secStructToType = [\r\n StructuralElementType.HELIX_PI, // 0\r\n StructuralElementType.BEND, // 1\r\n StructuralElementType.HELIX_ALPHA, // 2\r\n StructuralElementType.STRAND, // 3\r\n StructuralElementType.HELIX_310, // 4\r\n StructuralElementType.BRIDGE, // 5\r\n StructuralElementType.TURN, // 6\r\n StructuralElementType.COIL, // 7\r\n];\r\n\r\nfunction getFirstByte(buf) {\r\n const bytes = new Uint8Array(buf, 0, 1);\r\n return bytes[0];\r\n}\r\n\r\nclass MMTFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'mmtf';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n // check if it's binary MessagePack format containing a map (dictionary)\r\n // see https://github.com/msgpack/msgpack/blob/master/spec.md\r\n return _.isArrayBuffer(data) && ((getFirstByte(data) | 1) === 0xDF);\r\n }\r\n\r\n _onModel(_modelData) {\r\n }\r\n\r\n _onChain(chainData) {\r\n if (chainData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const chain = new Chain(this._complex, chainData.chainName);\r\n this._complex._chains[chainData.chainIndex] = chain;\r\n chain._index = chainData.chainIndex;\r\n }\r\n\r\n _onGroup(groupData) {\r\n if (groupData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n if (this.settings.now.nowater) {\r\n // skip water\r\n if (groupData.groupName === 'HOH' || groupData.groupName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n const chain = this._complex._chains[groupData.chainIndex];\r\n const icode = !groupData.insCode.charCodeAt(0) ? '' : groupData.insCode;\r\n const residue = chain.addResidue(groupData.groupName, groupData.groupId, icode);\r\n residue._index = groupData.groupIndex;\r\n\r\n this._updateSecStructure(this._complex, residue, groupData);\r\n }\r\n\r\n _onAtom(atomData) {\r\n if (atomData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const altLoc = !atomData.altLoc.charCodeAt(0) ? '' : atomData.altLoc;\r\n const atom = new Atom(\r\n atomData.groupIndex, // we store residue index here to replace it later with actual reference\r\n atomData.atomName,\r\n Element.getByName(atomData.element.toUpperCase()),\r\n new THREE.Vector3(atomData.xCoord, atomData.yCoord, atomData.zCoord),\r\n Element.Role[atomData.atomName],\r\n false, // hetero atoms will be marked later\r\n atomData.atomId,\r\n altLoc,\r\n atomData.occupancy,\r\n atomData.bFactor,\r\n atomData.formalCharge,\r\n );\r\n\r\n this._complex._atoms[atomData.atomIndex] = atom;\r\n atom.index = atomData.atomIndex;\r\n\r\n this._serialAtomMap[atomData.atomId] = atom;\r\n }\r\n\r\n _onBond(bondData) {\r\n const right = Math.max(bondData.atomIndex1, bondData.atomIndex2);\r\n if (right >= this._complex._atoms.length) {\r\n return;\r\n }\r\n const left = Math.min(bondData.atomIndex1, bondData.atomIndex2);\r\n this._complex.addBond(\r\n this._complex._atoms[left],\r\n this._complex._atoms[right],\r\n bondData.bondOrder,\r\n Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n\r\n _updateSecStructure(complex, residue, groupData) {\r\n const helixClasses = [3, -1, 1, -1, 5];\r\n\r\n if (!_.isUndefined(groupData) && groupData.secStruct === this._ssType) {\r\n residue._secondary = this._ssStruct;\r\n if (this._ssStruct) {\r\n this._ssStruct.term = residue;\r\n }\r\n return;\r\n }\r\n\r\n if (!_.isUndefined(groupData)) {\r\n // start new secondary structure\r\n const type = secStructToType[groupData.secStruct];\r\n this._ssType = groupData.secStruct;\r\n this._ssStart = residue;\r\n\r\n let struct = null;\r\n switch (this._ssType) {\r\n case -1: // undefined\r\n case 7: // coil\r\n break;\r\n case 0: // pi helix\r\n case 2: // alpha helix\r\n case 4: // 3-10 helix\r\n struct = new Helix(helixClasses[this._ssType], residue, residue, 0, '', '', 0);\r\n complex._helices.push(struct);\r\n break;\r\n case 3: { // extended\r\n const sheet = new Sheet('', 0);\r\n complex._sheets.push(sheet);\r\n struct = new Strand(sheet, residue, residue, 0, null, null);\r\n break;\r\n }\r\n default:\r\n if (type !== undefined) {\r\n struct = new StructuralElement(type, residue, residue);\r\n }\r\n break;\r\n }\r\n\r\n this._ssStruct = struct;\r\n residue._secondary = struct;\r\n if (struct) {\r\n complex.structures.push(struct);\r\n }\r\n }\r\n }\r\n\r\n _updateMolecules(mmtfData) {\r\n const entities = mmtfData.entityList;\r\n if (!entities) {\r\n return;\r\n }\r\n\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < entities.length; i++) {\r\n const entity = entities[i];\r\n const chains = entity.chainIndexList;\r\n let residues = [];\r\n for (let j = 0; j < chains.length; j++) {\r\n const chainIndex = chains[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, entity.description, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n // populate complex with chains, residues and atoms\r\n _traverse(mmtfData) {\r\n const self = this;\r\n\r\n // get metadata\r\n const { metadata } = this._complex;\r\n metadata.id = mmtfData.structureId;\r\n metadata.title = [];\r\n metadata.title[0] = mmtfData.title;\r\n metadata.date = mmtfData.releaseDate;\r\n metadata.format = 'mmtf';\r\n\r\n // create event callback functions\r\n const eventCallbacks = {\r\n onModel(modelData) {\r\n self._onModel(modelData);\r\n },\r\n onChain(chainData) {\r\n self._onChain(chainData);\r\n },\r\n onGroup(groupData) {\r\n self._onGroup(groupData);\r\n },\r\n onAtom(atomData) {\r\n self._onAtom(atomData);\r\n },\r\n onBond(bondData) {\r\n self._onBond(bondData);\r\n },\r\n };\r\n\r\n // temporary variables used during traversal to track secondary structures\r\n this._ssType = -1;\r\n this._ssStruct = null;\r\n this._ssStart = null;\r\n\r\n // traverse the structure and listen to the events\r\n MMTF.traverse(mmtfData, eventCallbacks);\r\n\r\n this._updateSecStructure(this._complex);\r\n this._updateMolecules(mmtfData);\r\n }\r\n\r\n // During traversal atoms and residues don't come sequentially\r\n // so a residue for certain atom can be unavailable. Thus we\r\n // store residue index in atom.\r\n // This function being called after traversal replaces the index\r\n // with actual reference, and also populates atom lists in residues.\r\n _linkAtomsToResidues() {\r\n for (let i = 0; i < this._complex._atoms.length; ++i) {\r\n const atom = this._complex._atoms[i];\r\n const residue = this._complex._residues[atom.residue];\r\n atom.residue = residue;\r\n residue._atoms.push(atom);\r\n }\r\n }\r\n\r\n _findSynonymousChains() {\r\n const named = {};\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!named.hasOwnProperty(name)) {\r\n named[name] = [];\r\n }\r\n\r\n named[name].push(chain._index);\r\n }\r\n\r\n return named;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _parseAssemblyInfo(mmtfData) {\r\n let i;\r\n let j;\r\n let k;\r\n const assemblies = [];\r\n const { logger } = this;\r\n\r\n for (i = 0; i < mmtfData.bioAssemblyList.length; ++i) {\r\n const baInfo = mmtfData.bioAssemblyList[i];\r\n if (baInfo.transformList.length === 0) {\r\n continue;\r\n }\r\n\r\n const chains = baInfo.transformList[0].chainIndexList;\r\n const chainListCheck = new ArrayComparator(chains);\r\n\r\n // build list of chain names\r\n const chainNames = {};\r\n for (j = 0; j < chains.length; ++j) {\r\n chainNames[this._complex._chains[chains[j]].getName()] = 1;\r\n }\r\n\r\n // all chains with the same name should belong to assembly if one of them belongs\r\n const allChains = [];\r\n let name;\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n // just concat arrays -- there should be no duplicates\r\n Array.prototype.push.apply(allChains, this._chainsByName[name]);\r\n }\r\n }\r\n if (!chainListCheck.compare(allChains)) {\r\n // assembly is missing some of the chains\r\n logger.debug('MMTF: Assembly is missing some of the synonymous chains. Skipping...');\r\n }\r\n\r\n const a = new Assembly(this._complex);\r\n\r\n // add chains to assembly\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n a.addChain(name);\r\n }\r\n }\r\n\r\n // add unique matrices to assembly\r\n a.addMatrix(new THREE.Matrix4().fromArray(baInfo.transformList[0].matrix).transpose());\r\n for (j = 1; j < baInfo.transformList.length; ++j) {\r\n const transform = baInfo.transformList[j];\r\n\r\n if (!chainListCheck.compare(transform.chainIndexList)) {\r\n // list of chains for this transform doesn't match that for other transforms\r\n // this is illegal in our structure\r\n logger.debug('MMTF: Chain lists differ for different transforms in one assembly. Skipping...');\r\n continue;\r\n }\r\n\r\n const m = new THREE.Matrix4().fromArray(transform.matrix).transpose();\r\n\r\n // check if matrix is already in the list\r\n for (k = 0; k < a.matrices.length; ++k) {\r\n if (a.matrices[k].equals(m)) {\r\n break;\r\n }\r\n }\r\n\r\n if (k === a.matrices.length) {\r\n a.addMatrix(m);\r\n }\r\n }\r\n\r\n a.finalize();\r\n assemblies.push(a);\r\n }\r\n\r\n return assemblies;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _markHeteroAtoms(mmtfData) {\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < mmtfData.entityList.length; ++i) {\r\n const entity = mmtfData.entityList[i];\r\n if (entity.type !== 'polymer') {\r\n for (let j = 0; j < entity.chainIndexList.length; ++j) {\r\n const chainIndex = entity.chainIndexList[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n for (let k = 0; k < chain._residues.length; ++k) {\r\n const res = chain._residues[k];\r\n for (let m = 0; m < res._atoms.length; ++m) {\r\n res._atoms[m].het = true;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // joins chains with the same name into single chain\r\n _joinSynonymousChains() {\r\n let i;\r\n let j;\r\n\r\n const primaryChainsArray = [];\r\n const primaryChainsHash = {};\r\n\r\n // join chains\r\n for (i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!primaryChainsHash.hasOwnProperty(name)) {\r\n // new name -- this is a primary chain\r\n primaryChainsHash[name] = chain;\r\n chain._index = primaryChainsArray.length; // update index as this array will later replace original chain list\r\n primaryChainsArray.push(chain);\r\n continue;\r\n }\r\n\r\n // this chain should be joined with the primary chain of the same name\r\n const primary = primaryChainsHash[name];\r\n for (j = 0; j < chain._residues.length; ++j) {\r\n const residue = chain._residues[j];\r\n primary._residues.push(residue);\r\n residue._chain = primary;\r\n }\r\n }\r\n\r\n // replace chains list with one containing only primary chains\r\n // dropping references to all chains but primary\r\n this._complex._chains = primaryChainsArray;\r\n }\r\n\r\n parseSync() {\r\n const mmtfData = MMTF.decode(this._data);\r\n\r\n this._complex = new Complex();\r\n this._serialAtomMap = {}; // filled during traversal\r\n\r\n this._traverse(mmtfData);\r\n this._linkAtomsToResidues();\r\n this._markHeteroAtoms(mmtfData);\r\n this._chainsByName = this._findSynonymousChains();\r\n Array.prototype.push.apply(this._complex.units, this._parseAssemblyInfo(mmtfData));\r\n this._joinSynonymousChains();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n return this._complex;\r\n }\r\n}\r\n\r\nMMTFParser.formats = ['mmtf'];\r\nMMTFParser.extensions = ['.mmtf'];\r\nMMTFParser.binary = true;\r\n\r\nexport default MMTFParser;\r\n","class ParsingError extends Error {\r\n constructor(message, line, column) {\r\n super(`data:${line}:${column}: ${message}`);\r\n\r\n if (Error.captureStackTrace) {\r\n Error.captureStackTrace(this, ParsingError);\r\n }\r\n\r\n this.name = 'ParsingError';\r\n this.parseLine = line;\r\n this.parseColumn = column;\r\n }\r\n}\r\n\r\nexport default ParsingError;\r\n","import _ from 'lodash';\r\nimport ParsingError from './ParsingError';\r\n\r\n// Implemented and being tested against: https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax\r\n\r\nfunction _isWhitespace(ch) {\r\n return ch === 32 || ch === 10 || ch === 13 || ch === 9;\r\n}\r\n\r\nfunction _inlineIndexOf(ch0, str, idx) {\r\n const len = str.length;\r\n let ch = -1;\r\n while (idx < len) {\r\n ch = str.charCodeAt(idx);\r\n if (ch === ch0 || ch === 10) {\r\n break;\r\n }\r\n ++idx;\r\n }\r\n return ch === ch0 ? idx : -1;\r\n}\r\n\r\nexport default function readCIF(source) {\r\n let i = 0;\r\n let j = 0;\r\n const n = source.length;\r\n let code = NaN;\r\n let newline = true;\r\n let line = 1;\r\n let column = 1;\r\n let begin;\r\n let state = 0; // 0 - start, 1 - block, 2 - item, 3 - loop, 4 - values, 5 - value\r\n const result = {};\r\n let block = {};\r\n let keys = [];\r\n let keysCount = 0;\r\n let key = '';\r\n let values = [];\r\n let valuesCount = 0;\r\n let value;\r\n\r\n function _parseValue() {\r\n let val;\r\n if ((code === 46 || code === 63) && (i + 1 >= n || _isWhitespace(source.charCodeAt(i + 1)))) { // '.' or '?' .....\r\n // it's a missing value\r\n ++column;\r\n ++i;\r\n return undefined;\r\n }\r\n if (newline && code === 59) { // ';' ......................................................................\r\n // parse multi-line string\r\n j = i;\r\n let lines = 0;\r\n do {\r\n j = _inlineIndexOf(10, source, j + 1); // '\\n'\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated text block found', line, column);\r\n }\r\n ++lines;\r\n } while ((j + 1 < n && source.charCodeAt(j + 1) !== code) || j + 1 >= n);\r\n val = source.substring(i + 1, j).replace(/\\r/g, '');\r\n i = j + 2;\r\n line += lines;\r\n column = 1;\r\n newline = false;\r\n return val;\r\n }\r\n if (code === 39 || code === 34) { // ''' or '\"' ...........................................................\r\n // parse quoted string\r\n j = i;\r\n do {\r\n j = _inlineIndexOf(code, source, j + 1);\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated quoted string found', line, column);\r\n }\r\n } while (j + 1 < n && !_isWhitespace(source.charCodeAt(j + 1)));\r\n val = source.substring(i + 1, j);\r\n column += j - i + 1;\r\n i = j + 1;\r\n return val;\r\n } // ......................................................................................................\r\n // parse until the first whitespace\r\n j = i;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n val = source.substring(i, j);\r\n column += j - i;\r\n i = j;\r\n // try to convert to a number\r\n const num = Number(val);\r\n if (!Number.isNaN(num)) {\r\n return num;\r\n }\r\n // or leave as an unquoted string\r\n return val;\r\n }\r\n\r\n function _storeKey(tag) {\r\n keys[keysCount++] = tag;\r\n }\r\n\r\n function _storeValue(val) {\r\n const keyIndex = valuesCount % keysCount;\r\n values[keyIndex].push(val);\r\n ++valuesCount;\r\n return val;\r\n }\r\n\r\n while (i <= n) {\r\n code = source.charCodeAt(i); // 'NaN' in place of ''\r\n if (code === 13) { // '\\r' .......................................................................................\r\n // just ignore\r\n } else if (code === 10) { // '\\n' ................................................................................\r\n // take note of new lines\r\n newline = true;\r\n ++line;\r\n column = 1;\r\n } else {\r\n // process inline characters\r\n if (code === 32 || code === 9) { // ' ' or '\\t' ................................................................\r\n // just ignore\r\n } else if (code === 35) { // '#' ...............................................................................\r\n // skip the comment until before the end of the line\r\n i = _inlineIndexOf(10, source, i + 1); // '\\n'\r\n if (i === -1) {\r\n break;\r\n } else {\r\n continue; // don't forget to process the new line\r\n }\r\n } else if (state === 0) { // start =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n j = i + 5;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new data block\r\n result[source.substring(begin, i)] = block = {};\r\n state = 1; // block\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Data block name missing', line, column);\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 1) { // block =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n continue; // parse again in a different state\r\n } else if (code === 95) { // '_' .............................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // start new item\r\n key = source.substring(begin, i);\r\n state = 2; // item\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n i += 5;\r\n column += 5;\r\n if (i < n && !_isWhitespace(source.charCodeAt(i))) {\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n } else {\r\n // start new loop\r\n keys = [];\r\n keysCount = 0;\r\n values = [];\r\n valuesCount = 0;\r\n state = 3; // loop\r\n continue; // don't forget to process the whitespace\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 2) { // item ==============================================================================\r\n if (Number.isNaN(code)) {\r\n break;\r\n }\r\n value = _parseValue();\r\n _.set(block, key, value);\r\n state = 1; // block\r\n continue;\r\n } else if (state === 3) { // loop ==============================================================================\r\n if (code === 95) { // '_' ....................................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new key\r\n _storeKey(source.substring(begin, i));\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else { // ..................................................................................................\r\n if (keysCount > 0) {\r\n for (let keyIndex = 0; keyIndex < keysCount; ++keyIndex) {\r\n value = [];\r\n values[keyIndex] = value;\r\n _.set(block, keys[keyIndex], value);\r\n }\r\n state = 4;\r\n continue; // parse again in a different state\r\n }\r\n throw new ParsingError('Data tags are missing inside a loop', line, column);\r\n }\r\n } else if (state === 4) { // values ============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n } else if (code === 95) { // '_' .............................................................................\r\n state = 1; // block\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n state = 1; // block\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n state = 0;\r\n } else { // ..................................................................................................\r\n _storeValue(_parseValue());\r\n }\r\n continue; // parse again in a different state\r\n } else { // ====================================================================================================\r\n throw new ParsingError(`Unexpected internal state ${state}`, line, column);\r\n }\r\n\r\n newline = false;\r\n ++column;\r\n }\r\n ++i;\r\n }\r\n\r\n if (state === 2) { // item\r\n throw new ParsingError(`Unexpected end of file in state ${state}`, line, column);\r\n }\r\n\r\n return result;\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\nimport readCIF from './readCIF';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nconst cRequiredAtomFields = [\r\n 'auth_seq_id',\r\n 'Cartn_x',\r\n 'Cartn_y',\r\n 'Cartn_z',\r\n 'label_atom_id',\r\n];\r\n\r\nconst cSecondaryCoding = {\r\n helx: 'helix',\r\n turn: 'turn',\r\n strn: 'strand',\r\n};\r\n\r\nfunction getTypeFromId(string) {\r\n const typeId = /[A-Za-z]+/.exec(string);\r\n if (!typeId) {\r\n return null;\r\n }\r\n\r\n return cSecondaryCoding[typeId[0].toLowerCase()];\r\n}\r\n\r\n/**\r\n * Make valid object an array\r\n * @param arrayLikeObject\r\n * @return {array, object} array or object\r\n */\r\nfunction arrize(arrayLikeObject) {\r\n if (arrayLikeObject === null || arrayLikeObject === undefined || _.isArray(arrayLikeObject)) {\r\n return arrayLikeObject;\r\n }\r\n return [arrayLikeObject];\r\n}\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\nclass AtomDataError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'AtomDataError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction _getOperations(operList) {\r\n if (!operList) {\r\n return null;\r\n }\r\n const idc = arrize(operList.id);\r\n const { matrix, vector } = operList;\r\n if (!idc || !matrix || !vector) {\r\n return null;\r\n }\r\n\r\n const ops = [];\r\n for (let i = 0, n = idc.length; i < n; ++i) {\r\n const mtx = new THREE.Matrix4();\r\n const { elements } = mtx;\r\n\r\n for (let row = 0; row < 3; ++row) {\r\n const matrixData = matrix[row + 1];\r\n elements[row] = arrize(matrixData[1])[i];\r\n elements[row + 4] = arrize(matrixData[2])[i];\r\n elements[row + 8] = arrize(matrixData[3])[i];\r\n elements[row + 12] = arrize(vector[row + 1])[i];\r\n }\r\n ops[idc[i]] = mtx;\r\n }\r\n return ops;\r\n}\r\n\r\nfunction _extractOperations(assemblyGen, opsDict) {\r\n assemblyGen = _.isString(assemblyGen) ? assemblyGen : `${assemblyGen}`;\r\n const l = assemblyGen.replace(/\\)\\s*\\(/g, '!').replace(/[()']/g, '');\r\n const groupStr = l.split('!');\r\n const gps = [];\r\n\r\n for (let grIdx = 0, grCount = groupStr.length; grIdx < grCount; ++grIdx) {\r\n const gr = groupStr[grIdx].split(',');\r\n const gp = [];\r\n let idx = 0;\r\n for (let i = 0, n = gr.length; i < n; ++i) {\r\n const s = gr[i];\r\n if (s.includes('-')) {\r\n const es = s.split('-');\r\n let j = parseInt(es[0], 10);\r\n const m = parseInt(es[1], 10);\r\n for (; j <= m; ++j) {\r\n gp[idx++] = opsDict[j];\r\n }\r\n } else {\r\n gp[idx++] = opsDict[s];\r\n }\r\n }\r\n gps.push(gp);\r\n }\r\n\r\n // traverse all groups from the end of array and make all mults\r\n const matrices = [];\r\n let cnt = 0;\r\n function traverse(level, mtx) {\r\n for (let ii = 0, nn = gps[level].length; ii < nn; ++ii) {\r\n const newMtx = mtx ? mtx.clone() : new THREE.Matrix4();\r\n newMtx.multiplyMatrices(gps[level][ii], newMtx);\r\n if (level === 0) {\r\n matrices[cnt++] = newMtx;\r\n } else {\r\n traverse(level - 1, newMtx);\r\n }\r\n }\r\n }\r\n traverse(gps.length - 1);\r\n return matrices;\r\n}\r\n\r\nclass CIFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this.asymDict = {};\r\n this.molecules = [];\r\n this._options.fileType = 'cif';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*data_/i.test(data);\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing CIF file..');\r\n const data = readCIF(this._data);\r\n return this._toComplex(data);\r\n }\r\n\r\n /**\r\n * Convert intermediate structure into our valid Complex object\r\n * @param cifData intermediate CIF object\r\n * @returns {Complex} complex\r\n * @private\r\n */\r\n _toComplex(cifData) {\r\n const complex = new Complex();\r\n const complexData = cifData[Object.keys(cifData)[0]];\r\n this._extractAtoms(complex, complexData);\r\n this._extractSecondary(complex, complexData);\r\n this._extractAssemblies(complex, complexData);\r\n this._extractMolecules(complex, complexData);\r\n this._extractMetadata(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n\r\n return complex;\r\n }\r\n\r\n /**\r\n * Extract metadata\r\n * @param complex structure to fill\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n\r\n _extractMetadata(complex, complexData) {\r\n const { metadata } = complex;\r\n metadata.id = complexData.entry.id;\r\n metadata.classification = complexData.struct_keywords.pdbx_keywords;\r\n const databaserev = complexData.database_PDB_rev;\r\n metadata.date = (databaserev && databaserev.date_original) ? databaserev.date_original : '';\r\n metadata.format = 'cif';\r\n metadata.title = [];\r\n metadata.title[0] = complexData.struct.title;\r\n }\r\n\r\n /**\r\n * Extract molecules information from CIF structure (should be called strictly after _extractAtoms)\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractMolecules(complex, complexData) {\r\n const molData = complexData.entity;\r\n const names = arrize(molData.pdbx_description);\r\n const count = names.length;\r\n let i;\r\n\r\n // molecules names from cif\r\n for (i = 0; i < count; i++) {\r\n if (this.molecules[i]) { // molecule was created during atoms processing\r\n this.molecules[i].name = names[i];\r\n } else { // molecule wasn't created, because there is no atom which is contained\r\n this.molecules[i] = { name: names[i], residues: [] };\r\n }\r\n }\r\n\r\n // reorganize molecules for complex and check chains\r\n const molecules = complex.getMolecules();\r\n for (i = 0; i < count; i++) {\r\n const molecule = this.molecules[i];\r\n molecules[i] = new Molecule(complex, molecule.name, i + 1);\r\n molecules[i].residues = molecule.residues;\r\n }\r\n }\r\n\r\n /**\r\n * Extract atom information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAtoms(complex, complexData) {\r\n const atomData = complexData.atom_site;\r\n if (!atomData) {\r\n throw new AtomDataError('CIF parsing error: atom_site is not specified!');\r\n }\r\n\r\n for (let f = 0, n = cRequiredAtomFields.length; f < n; ++f) {\r\n if (!atomData[cRequiredAtomFields[f]]) {\r\n throw new AtomDataError(`CIF parsing error: requires field ${cRequiredAtomFields[f]} not found!`);\r\n }\r\n }\r\n\r\n const { asymDict } = this;\r\n // required fields\r\n const resIdc = arrize(atomData.auth_seq_id);\r\n const x = arrize(atomData.Cartn_x);\r\n const y = arrize(atomData.Cartn_y);\r\n const z = arrize(atomData.Cartn_z);\r\n const names = arrize(atomData.label_atom_id);\r\n const count = names.length;\r\n // optional fields\r\n const group = arrize(atomData.group_PDB) || [];\r\n const chainIdc = arrize(atomData.auth_asym_id) || [];\r\n const chainLabelIdc = arrize(atomData.label_asym_id) || [];\r\n const serials = arrize(atomData.id) || [];\r\n const iCodes = arrize(atomData.pdbx_PDB_ins_code) || [];\r\n const resNames = arrize(atomData.label_comp_id) || [];\r\n const elements = arrize(atomData.type_symbol) || [];\r\n const tempFactors = arrize(atomData.B_iso_or_equiv) || [];\r\n const occupancies = arrize(atomData.occupancy) || [];\r\n const charges = arrize(atomData.pdbx_formal_charge) || [];\r\n const altLocs = arrize(atomData.label_alt_id) || [];\r\n const models = arrize(atomData.pdbx_PDB_model_num) || [];\r\n const molecules = arrize(atomData.label_entity_id) || [];\r\n\r\n let chain = null;\r\n let residue = null;\r\n for (let i = 0; i < count; ++i) {\r\n const model = models[i] || 1;\r\n if (model !== 1) {\r\n continue;\r\n }\r\n const chainID = String(chainIdc[i] || ' ');\r\n\r\n if (!chain || chain.getName() !== chainID) {\r\n chain = complex.getChain(chainID) || complex.addChain(chainID);\r\n }\r\n asymDict[String(chainLabelIdc[i] || ' ')] = chainID;\r\n const resSeq = resIdc[i];\r\n const iCode = String(iCodes[i] || ' ');\r\n const resName = String(resNames[i] || '');\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n residue = chain.addResidue(resName, resSeq, iCode);\r\n\r\n // store residue in appropriate molecule\r\n const moleculeIdx = molecules[i] - 1;\r\n let entity = this.molecules[moleculeIdx];\r\n if (!entity) { // create new molecule if it hasn't been created\r\n this.molecules[moleculeIdx] = { name: '', residues: [] };\r\n entity = this.molecules[moleculeIdx];\r\n }\r\n entity.residues.push(residue);\r\n }\r\n\r\n const name = names[i];\r\n const element = elements[i] || nameToElement(name);\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name.trim()];\r\n const xyz = new THREE.Vector3(x[i], y[i], z[i]);\r\n const het = group[i] === 'HETATM' || false;\r\n const serial = serials[i] || i;\r\n const tempFactor = tempFactors[i] || 0.0;\r\n const occupancy = occupancies[i] || 0.0;\r\n const altLoc = String(altLocs[i] || '');\r\n const charge = charges[i] || 0;\r\n\r\n residue.addAtom(\r\n name,\r\n type,\r\n xyz,\r\n role,\r\n het,\r\n serial,\r\n altLoc,\r\n occupancy,\r\n tempFactor,\r\n charge,\r\n );\r\n }\r\n }\r\n\r\n /**\r\n * Extracts secondary structure information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex - complex to fill\r\n * @param complexData - CIF complex data\r\n * @private\r\n */\r\n _extractSecondary(complex, complexData) {\r\n if (complexData.struct_conf) {\r\n this._extractConfs(complex, complexData.struct_conf);\r\n }\r\n if (complexData.struct_sheet_range) {\r\n this._extractSheets(complex, complexData.struct_sheet_range);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts sheets information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param sheetData\r\n * @private\r\n */\r\n _extractSheets(complex, sheetData) {\r\n const { asymDict } = this;\r\n if (!sheetData.sheet_id || !sheetData.id || !sheetData.beg_label_seq_id || !sheetData.end_label_seq_id\r\n || !sheetData.beg_label_asym_id) {\r\n return;\r\n }\r\n // Strand(sheet, start, end, sense, cur, prev)\r\n const sheets = complex._sheets;\r\n\r\n function getSheet(name) {\r\n const n = sheets.length;\r\n for (let i = 0; i < n; ++i) {\r\n if (sheets[i]._name === name) {\r\n return sheets[i];\r\n }\r\n }\r\n sheets[n] = new Sheet(name, 0);\r\n return sheets[n];\r\n }\r\n\r\n const sheetNames = arrize(sheetData.sheet_id);\r\n const strandNames = arrize(sheetData.id);\r\n const starts = arrize(sheetData.beg_auth_seq_id);\r\n const ends = arrize(sheetData.end_auth_seq_id);\r\n const chains = arrize(sheetData.beg_label_asym_id);\r\n const stICodes = arrize(sheetData.pdbx_beg_PDB_ins_code) || [];\r\n const endICodes = arrize(sheetData.pdbx_end_PDB_ins_code) || [];\r\n\r\n for (let i = 0, n = strandNames.length; i < n; ++i) {\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n const sheet = getSheet(sheetNames[i]);\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n\r\n const strand = new Strand(sheet, start[0], end[0], 0, null, null);\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = strand;\r\n }\r\n sheet.addStrand(strand);\r\n complex.structures.push(strand);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts helix/turn/strand(?) information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param helicesData\r\n * @private\r\n */\r\n _extractConfs(complex, helicesData) {\r\n const { asymDict } = this;\r\n if (!helicesData.conf_type_id || !helicesData.beg_label_seq_id || !helicesData.end_label_seq_id\r\n || !helicesData.beg_label_asym_id) {\r\n return;\r\n }\r\n\r\n const types = arrize(helicesData.conf_type_id);\r\n const starts = arrize(helicesData.beg_auth_seq_id);\r\n const stICodes = arrize(helicesData.pdbx_beg_PDB_ins_code) || [];\r\n const ends = arrize(helicesData.end_auth_seq_id);\r\n const endICodes = arrize(helicesData.pdbx_end_PDB_ins_code) || [];\r\n const comments = arrize(helicesData.details) || [];\r\n const lengths = arrize(helicesData.pdbx_PDB_helix_length) || [];\r\n const helixClasses = arrize(helicesData.pdbx_PDB_helix_class) || [];\r\n const names = arrize(helicesData.id) || [];\r\n const chains = arrize(helicesData.beg_label_asym_id);\r\n\r\n for (let i = 0, n = types.length; i < n; ++i) {\r\n const type = getTypeFromId(types[i]);\r\n if (!type) {\r\n continue;\r\n }\r\n const name = names[i] || types[i];\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n const comment = comments[i] || '';\r\n const length = lengths[i] || 0;\r\n const helixClass = helixClasses[i] || ' ';\r\n let struct;\r\n if (type === 'helix') {\r\n const idx = complex._helices.length;\r\n struct = new Helix(helixClass, start[0], end[0], idx, name, comment, length);\r\n complex.addHelix(struct);\r\n complex.structures.push(struct);\r\n } else if (type === 'turn') {\r\n struct = new StructuralElement(StructuralElement.Type.TURN, start[0], end[0]);\r\n complex.structures.push(struct);\r\n } else {\r\n struct = null;\r\n }\r\n if (!struct) {\r\n continue;\r\n }\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = struct;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Extract biological assemblies information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAssemblies(complex, complexData) {\r\n const { asymDict } = this;\r\n const asmGen = complexData.pdbx_struct_assembly_gen;\r\n if (!asmGen) {\r\n return;\r\n }\r\n\r\n const asmIdx = arrize(asmGen.assembly_id);\r\n const asmOper = arrize(asmGen.oper_expression);\r\n const asmList = arrize(asmGen.asym_id_list);\r\n if (!asmIdx || !asmOper || !asmList) {\r\n return;\r\n }\r\n\r\n const operList = _getOperations(complexData.pdbx_struct_oper_list);\r\n if (!operList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = asmIdx.length; i < n; ++i) {\r\n const asm = new Assembly(complex);\r\n const assemblyOps = _extractOperations(asmOper[i], operList);\r\n const entries = asmList[i].split(',');\r\n for (let ii = 0, nn = entries.length; ii < nn; ++ii) {\r\n const chain = entries[ii].trim();\r\n if (chain.length > 0) {\r\n asm.addChain(asymDict[chain]);\r\n }\r\n }\r\n asm.matrices = assemblyOps;\r\n complex.units.push(asm);\r\n }\r\n }\r\n}\r\n\r\nCIFParser.formats = ['cif', 'mmcif'];\r\nCIFParser.extensions = ['.cif', '.mmcif'];\r\n\r\nexport default CIFParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Volume from '../../chem/Volume';\r\n\r\nexport const valueType = {\r\n singular: 0,\r\n vector: 1,\r\n array: 2,\r\n buffer: 3,\r\n};\r\n\r\nclass VolumeModel {\r\n _xyz2crs = [];\r\n\r\n _origin = new THREE.Vector3(0, 0, 0);\r\n\r\n constructor() {\r\n this._header = {};\r\n this._boxSize = new THREE.Vector3();\r\n this._boxStart = new THREE.Vector3();\r\n this._header.delta = {};\r\n this._header.extent = [];\r\n this._header.nstart = [];\r\n this._header.grid = [];\r\n this._header.crs2xyz = [];\r\n this._header.cellDims = new THREE.Vector3();\r\n this._header.angles = [];\r\n this._header.origin = new THREE.Vector3(0, 0, 0);\r\n this._header.dmin = 0;\r\n this._header.dmean = 0;\r\n this._header.dmax = 0;\r\n }\r\n\r\n _typedCheck() {\r\n if (_.isTypedArray(this._buff)) {\r\n this._buff = this._buff.buffer;\r\n } else if (!_.isArrayBuffer(this._buff)) {\r\n throw new TypeError('Expected ArrayBuffer or TypedArray');\r\n }\r\n }\r\n\r\n _fillHeader(headerFormat, arrays) {\r\n for (const key in headerFormat) {\r\n if (headerFormat.hasOwnProperty(key)) {\r\n switch (headerFormat[key][0]) {\r\n case valueType.singular:\r\n this._header[key] = arrays[headerFormat[key][1]][headerFormat[key][2]];\r\n break;\r\n\r\n case valueType.array:\r\n this._parseArray(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.vector:\r\n this._parseVector(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.buffer:\r\n this._header[key] = new Uint8Array(\r\n arrays[headerFormat[key][1]],\r\n [headerFormat[key][2]] * 4,\r\n [headerFormat[key][3]] * 4,\r\n );\r\n break;\r\n\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _parseVector(vector, arr, pos) {\r\n [vector.x, vector.y, vector.z] = [arr[pos], arr[pos + 1], arr[pos + 2]];\r\n }\r\n\r\n _parseArray(vector, arr, pos) {\r\n vector[0] = arr[pos];\r\n vector[1] = arr[pos + 1];\r\n vector[2] = arr[pos + 2];\r\n }\r\n\r\n _parseHeader(_buffer) {}\r\n\r\n _setAxisIndices() {}\r\n\r\n _setOrigins() {}\r\n\r\n _getAxis() {\r\n const header = this._header;\r\n\r\n const xScale = header.cellDims.x / header.grid[0];\r\n const yScale = header.cellDims.y / header.grid[1];\r\n const zScale = header.cellDims.z / header.grid[2];\r\n\r\n const [alpha, beta, gamma] = header.angles;\r\n\r\n const z1 = Math.cos(beta);\r\n const z2 = (Math.cos(alpha) - Math.cos(beta)\r\n * Math.cos(gamma)) / Math.sin(gamma);\r\n const z3 = Math.sqrt(1.0 - z1 * z1 - z2 * z2);\r\n\r\n const xaxis = new THREE.Vector3(xScale, 0, 0);\r\n const yaxis = new THREE.Vector3(Math.cos(gamma) * yScale, Math.sin(gamma) * yScale, 0);\r\n const zaxis = new THREE.Vector3(z1 * zScale, z2 * zScale, z3 * zScale);\r\n\r\n return [xaxis, yaxis, zaxis];\r\n }\r\n\r\n _getXYZdim() {\r\n return [this._header.extent[this._xyz2crs[0]],\r\n this._header.extent[this._xyz2crs[1]],\r\n this._header.extent[this._xyz2crs[2]]];\r\n }\r\n\r\n _getVolumeInfo() {\r\n const volInfo = _.pick(this._header, ['dmean', 'dmin', 'dmax', 'sd', 'delta']);\r\n volInfo.obtuseAngle = this._header.angles.map((angle) => Number(angle >= (Math.PI / 2)));\r\n return volInfo;\r\n }\r\n\r\n _setBoxParams(xaxis, yaxis, zaxis) {\r\n // if axes are not orthogonal, the origins might not match with box coordinates - need to make shift\r\n let shiftX = 0;\r\n let shiftY = 0;\r\n const [alpha, beta, gamma] = this._header.angles;\r\n\r\n if (gamma >= Math.PI / 2) {\r\n shiftX += Math.abs(yaxis.x);\r\n }\r\n if (beta >= Math.PI / 2) {\r\n shiftX += Math.abs(zaxis.x);\r\n }\r\n if (alpha >= Math.PI / 2) {\r\n shiftY += Math.abs(zaxis.y);\r\n }\r\n\r\n this._boxStart = new THREE.Vector3(this._origin.x - shiftX, this._origin.y - shiftY, this._origin.z);\r\n this._boxSize = new THREE.Vector3(\r\n Math.abs(xaxis.x) + Math.abs(yaxis.x) + Math.abs(zaxis.x),\r\n Math.abs(yaxis.y) + Math.abs(zaxis.y),\r\n Math.abs(zaxis.z),\r\n );\r\n\r\n const delta = (axe, proj) => (Math.abs(axe[proj]) / this._boxSize[proj]);\r\n this._header.delta.x = delta(yaxis, 'x');\r\n this._header.delta.y = delta(zaxis, 'x');\r\n this._header.delta.z = delta(zaxis, 'y');\r\n }\r\n\r\n _getXYZbox() {\r\n return new THREE.Box3(this._boxStart.clone(), this._boxStart.clone().add(this._boxSize));\r\n }\r\n\r\n _toXYZData() {}\r\n\r\n parse(data) {\r\n this._parseHeader(data);\r\n this._setOrigins();\r\n return new Volume(Float32Array, this._getXYZdim(), this._getXYZbox(), 1, this._toXYZData(), this._getVolumeInfo());\r\n }\r\n}\r\n\r\nexport default VolumeModel;\r\n","import Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\nconst CCP4Header = {\r\n extent: [valueType.array, 'u32', 0],\r\n type: [valueType.singular, 'u32', 3],\r\n nstart: [valueType.array, 'i32', 4],\r\n grid: [valueType.array, 'u32', 7],\r\n cellDims: [valueType.vector, 'f32', 10],\r\n angles: [valueType.array, 'f32', 13],\r\n crs2xyz: [valueType.array, 'i32', 16],\r\n dmin: [valueType.singular, 'f32', 19],\r\n dmax: [valueType.singular, 'f32', 20],\r\n dmean: [valueType.singular, 'f32', 21],\r\n ispg: [valueType.singular, 'u32', 22],\r\n nsymbt: [valueType.singular, 'u32', 23],\r\n lksflg: [valueType.singular, 'u32', 24],\r\n customData: [valueType.buffer, 'buffer', 25, 9],\r\n origin: [valueType.vector, 'f32', 34],\r\n map: [valueType.buffer, 'buffer', 52, 1],\r\n machine: [valueType.singular, 'u32', 53],\r\n sd: [valueType.singular, 'f32', 54],\r\n nlabel: [valueType.singular, 'f32', 55],\r\n label: [valueType.buffer, 'buffer', 56, 200],\r\n};\r\n\r\nclass Ccp4Model extends VolumeModel {\r\n // read header (http://www.ccp4.ac.uk/html/maplib.html)\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n const arrays = {};\r\n arrays.u32 = new Uint32Array(this._buff, 0, 56);\r\n arrays.i32 = new Int32Array(this._buff, 0, 56);\r\n arrays.f32 = new Float32Array(this._buff, 0, 56);\r\n arrays.buffer = this._buff;\r\n const header = this._header;\r\n\r\n this._fillHeader(CCP4Header, arrays);\r\n\r\n // calculate non-orthogonal unit cell coordinates\r\n header.angles.forEach((angle, i, a) => { a[i] *= Math.PI / 180.0; });\r\n }\r\n\r\n _setAxisIndices() {\r\n const header = this._header;\r\n\r\n if (header.cellDims.x === 0.0 && header.cellDims.y === 0.0 && header.cellDims.z === 0.0) {\r\n header.cellDims.set(1.0, 1.0, 1.0);\r\n }\r\n // Apply header conversion\r\n // Mapping between CCP4 column, row, section and VMD x, y, z.\r\n const { crs2xyz } = this._header;\r\n if (crs2xyz[0] === 0 && crs2xyz[1] === 0 && crs2xyz[2] === 0) {\r\n crs2xyz[0] = 1;\r\n crs2xyz[1] = 2;\r\n crs2xyz[2] = 3;\r\n }\r\n\r\n const xyz2crs = this._xyz2crs;\r\n xyz2crs[crs2xyz[0] - 1] = 0; // column\r\n xyz2crs[crs2xyz[1] - 1] = 1; // row\r\n xyz2crs[crs2xyz[2] - 1] = 2; // section\r\n }\r\n\r\n _setOrigins() {\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n const header = this._header;\r\n const xyz2crs = this._xyz2crs;\r\n // Handle both MRC-2000 and older format maps\r\n if (header.origin.x === 0.0 && header.origin.y === 0.0 && header.origin.z === 0.0) {\r\n this._origin.addScaledVector(xaxis, header.nstart[xyz2crs[0]]);\r\n this._origin.addScaledVector(yaxis, header.nstart[xyz2crs[1]]);\r\n this._origin.addScaledVector(zaxis, header.nstart[xyz2crs[2]]);\r\n } else {\r\n this._origin = header.origin;\r\n // Use ORIGIN records rather than old n[xyz]start records\r\n // http://www2.mrc-lmb.cam.ac.uk/image2000.html\r\n // XXX the ORIGIN field is only used by the EM community, and\r\n // has undefined meaning for non-orthogonal maps and/or non-cubic voxels, etc.\r\n }\r\n xaxis.multiplyScalar(header.extent[xyz2crs[0]] - 1);\r\n yaxis.multiplyScalar(header.extent[xyz2crs[1]] - 1);\r\n zaxis.multiplyScalar(header.extent[xyz2crs[2]] - 1);\r\n\r\n if (header.type === 2) {\r\n this._data = new Float32Array(\r\n this._buff,\r\n 1024 + header.nsymbt,\r\n header.extent[0] * header.extent[1] * header.extent[2],\r\n );\r\n } else {\r\n throw new Error(`CCP4: Unsupported format ${header.type}`);\r\n }\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const data = this._data;\r\n const xyz2crs = this._xyz2crs;\r\n const xyzData = new Float32Array(data.length);\r\n\r\n const dim = this._getXYZdim();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n\r\n let crsIdx = 0;\r\n const coord = [];\r\n let x;\r\n let y;\r\n let z;\r\n for (coord[2] = 0; coord[2] < header.extent[2]; coord[2]++) { // Site\r\n for (coord[1] = 0; coord[1] < header.extent[1]; coord[1]++) { // Row\r\n for (coord[0] = 0; coord[0] < header.extent[0]; coord[0]++, crsIdx++) { // Column\r\n x = coord[xyz2crs[0]];\r\n y = coord[xyz2crs[1]];\r\n z = coord[xyz2crs[2]];\r\n xyzData[x + xSize * (y + ySize * z)] = data[crsIdx];\r\n }\r\n }\r\n }\r\n\r\n return xyzData;\r\n }\r\n}\r\n\r\nclass CCP4Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'ccp4';\r\n this.model = new Ccp4Model();\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false; // Autodetection is not implemented yet\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nCCP4Parser.formats = ['ccp4'];\r\nCCP4Parser.extensions = ['.ccp4', '.map', '.mrc'];\r\nCCP4Parser.binary = true;\r\n\r\nexport default CCP4Parser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element, Molecule } = chem;\r\n\r\nclass XYZParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n this._options.fileType = 'xyz';\r\n this._fileName = options.name;\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*\\d+ *\\n[^\\n]*\\n\\s*\\w{1,3}\\s+-?\\d/.test(data);\r\n }\r\n\r\n _parseToAtomsInf(source) {\r\n const endnAtoms = source.indexOf('\\n');\r\n const nAtoms = parseInt(source.substring(0, endnAtoms), 10);\r\n const endComment = source.indexOf('\\n', endnAtoms + 1);\r\n let comment = source.slice(endnAtoms + 1, endComment).trim();\r\n if (comment.length === 0) {\r\n comment = this._fileName;\r\n }\r\n\r\n const startAtomsInf = endComment + source.substring(endComment).search(/\\S/);\r\n this._atomsInf = source.substring(startAtomsInf).split(/[\\s,]*\\n[\\s,]*/);\r\n if (!Number.isNaN(nAtoms) && (this._atomsInf.length - 1 !== nAtoms)) {\r\n this._complex.error = {\r\n message: 'wrong number of atoms',\r\n };\r\n return;\r\n }\r\n\r\n this._complex.metadata.format = 'xyz';\r\n this._complex.name = comment;\r\n }\r\n\r\n _parseAtomsInf() {\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n\r\n const chain = this._complex.addChain('A');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0; i < this._atomsInf.length - 1; i++) {\r\n const words = this._atomsInf[i].split(/[\\s,]+/);\r\n\r\n if (words.length !== 4) {\r\n this._complex.error = {\r\n message: 'missed parameters',\r\n };\r\n break;\r\n }\r\n\r\n const serial = i + 1;\r\n const name = words[0];\r\n const xyz = new THREE.Vector3(parseFloat(words[1]), parseFloat(words[2]), parseFloat(words[3]));\r\n const type = Element.getByName(name);\r\n const role = undefined;\r\n\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n const molecule = new Molecule(this._complex, this._complex.name, 1);\r\n molecule.residues = residue;\r\n this._complex._molecules[0] = molecule;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n\r\n this._parseToAtomsInf(this._data);\r\n this._parseAtomsInf();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n return result;\r\n }\r\n\r\n static formats = ['xyz'];\r\n\r\n static extensions = ['.xyz'];\r\n}\r\n\r\nexport default XYZParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element } = chem;\r\n\r\nclass PubChemParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'pubchem+json';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && data[0] === '{';\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing PubChem JSON file...');\r\n return this._toComplex(JSON.parse(this._data));\r\n }\r\n\r\n _toComplex(jsonData) {\r\n const complex = new Complex();\r\n const complexData = jsonData.PC_Compounds && jsonData.PC_Compounds[0];\r\n if (complexData) {\r\n this._extractAtoms(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n }\r\n return complex;\r\n }\r\n\r\n _extractAtoms(complex, complexData) {\r\n let aids = complexData.atoms && complexData.atoms.aid;\r\n let elements = aids && complexData.atoms.element;\r\n if (!elements || aids.length !== elements.length) {\r\n throw new Error('Unable to parse atom elements');\r\n }\r\n elements = _.fromPairs(_.zip(aids, elements));\r\n const atoms = {};\r\n\r\n const coords = complexData.coords && complexData.coords[0];\r\n const model = coords && coords.conformers && coords.conformers[0];\r\n const xs = model && model.x;\r\n const ys = model && model.y;\r\n const zs = (model && model.z) || [];\r\n aids = coords && coords.aid;\r\n if (!aids || !xs || !ys) {\r\n throw new Error('Coordinates are not found in the file');\r\n }\r\n\r\n const chain = complex.addChain(' ');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0, n = aids.length; i < n; ++i) {\r\n const aid = aids[i];\r\n const element = Element.ByAtomicNumber[elements[aid]];\r\n const xyz = new THREE.Vector3(xs[i], ys[i], zs[i] || 0.0);\r\n atoms[aid] = residue.addAtom(element.name, element, xyz, undefined, true, aid, ' ', 1.0, 0.0, 0);\r\n }\r\n\r\n const aids1 = complexData.bonds && complexData.bonds.aid1;\r\n const aids2 = complexData.bonds && complexData.bonds.aid2;\r\n const orders = (complexData.bonds && complexData.bonds.order) || [];\r\n if (!aids1 || !aids2 || aids1.length !== aids2.length) {\r\n return;\r\n }\r\n\r\n for (let j = 0, m = aids1.length; j < m; ++j) {\r\n complex.addBond(atoms[aids1[j]], atoms[aids2[j]], orders[j] || 1, 0, true);\r\n }\r\n }\r\n}\r\n\r\nPubChemParser.formats = ['pubchem', 'pubchem+json', 'pc'];\r\nPubChemParser.extensions = ['.json'];\r\n\r\nexport default PubChemParser;\r\n","import _ from 'lodash';\r\n\r\nexport default class SDFStream {\r\n constructor(data) {\r\n this._strings = data.split(/\\r?\\n|\\r/);\r\n this._currentStart = 0;\r\n this._currentStringIndx = 0;\r\n }\r\n\r\n setStart(start) {\r\n if (start >= this._strings.length) {\r\n this._currentStart = this._strings.length - 1;\r\n this._currentStringIndx = this._strings.length - 1;\r\n } else {\r\n this._currentStart = start;\r\n this._currentStringIndx = start;\r\n }\r\n }\r\n\r\n getNextString() {\r\n return this._strings[++this._currentStringIndx];\r\n }\r\n\r\n getCurrentString() {\r\n return this._strings[this._currentStringIndx];\r\n }\r\n\r\n getStringFromStart(numb) {\r\n this._currentStringIndx = this._currentStart + numb;\r\n return this._strings[this._currentStart + numb];\r\n }\r\n\r\n findNextDataItem() {\r\n let curStr = this.getNextString();\r\n let res = false;\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n if (curStr.match(/>\\s+<(.*)>/)) {\r\n res = true;\r\n break;\r\n }\r\n curStr = this.getNextString();\r\n }\r\n\r\n return res;\r\n }\r\n\r\n findNextCompoundStart() {\r\n let curStr = this.getCurrentString();\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n curStr = this.getNextString();\r\n }\r\n this.setStart(++this._currentStringIndx);\r\n return this.probablyHaveDataToParse();\r\n }\r\n\r\n probablyHaveDataToParse() {\r\n return this._currentStringIndx < this._strings.length - 2;\r\n }\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport SDFStream from './SDFStream';\r\nimport Assembly from '../../chem/Assembly';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst chargeMap = [0, 3, 2, 1, 0, -1, -2, -3];\r\nconst orderMap = [0, 1, 2, 3, 1, 1, 1, 2];\r\nconst typeMap = [\r\n Bond.BondType.UNKNOWN, // 0 - error\r\n Bond.BondType.COVALENT, // 1 - single\r\n Bond.BondType.COVALENT, // 2 - double\r\n Bond.BondType.COVALENT, // 3 - triple\r\n Bond.BondType.AROMATIC, // 4 - aromatic\r\n Bond.BondType.UNKNOWN, // 5 - single or double\r\n Bond.BondType.AROMATIC, // 6 - single or aromatic\r\n Bond.BondType.AROMATIC, // 7 - double or aromatic\r\n // 8 - any\r\n // 9 - coordination\r\n // 10 - hydrogen\r\n];\r\n\r\nconst sdfAndMolRegexp = /.*(M\\s\\sEND).*|.*(^$$$$).*|.*>\\s+<(.+)>.*/;\r\nconst sdfRegExp = /.*($$$$).*|.*>\\s+<(.+)>.*/;\r\n\r\nconst fileFormat = { SDF: 'sdf', MOL: 'mol' };\r\n\r\nconst possibleNameTags = ['PUBCHEM_IUPAC_TRADITIONAL_NAME', /PUBCHEM_(.+)_NAME/, /(.+)name/, /(.+)NAME/];\r\nconst possibleIDTags = ['PUBCHEM_COMPOUND_CID', 'id', 'ID', /.*CID/, /.*ID/, /.*id/];\r\nconst possibleTitleTags = ['msg', 'MSG', 'message', 'title', 'description', 'desc'];\r\nconst tagsNames = ['name', 'id', 'title'];\r\nconst tags = { name: possibleNameTags, id: possibleIDTags, title: possibleTitleTags };\r\n\r\nfunction buildChainID(index) {\r\n if (!index) {\r\n return 'A';\r\n }\r\n\r\n const codes = [];\r\n while (index) {\r\n codes.push(65 + (index % 26));\r\n index = Math.trunc(index / 26);\r\n }\r\n if (codes.length > 1) {\r\n codes.reverse();\r\n codes[0] -= 1;\r\n }\r\n\r\n return String.fromCharCode(...codes);\r\n}\r\n\r\nexport default class SDFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._format = 'sdf';\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._molecules = null;\r\n this._metadata = {};\r\n this._metadata.molecules = [];\r\n this._currentMolProps = {};\r\n this._compoundIndx = -1;\r\n this._assemblies = [];\r\n this._atomsParsed = 0;\r\n this._atomsIndexes = [];\r\n }\r\n\r\n canProbablyParse(data) {\r\n return _.isString(data) && sdfAndMolRegexp.test(data);\r\n }\r\n\r\n _parseHeader(stream) {\r\n const molecule = {};\r\n molecule.name = stream.getStringFromStart(0);\r\n const date = parseInt(stream.getStringFromStart(1).substr(10, 6).trim(), 10);\r\n molecule.date = date.toString() || '';\r\n molecule.title = stream.getStringFromStart(2);\r\n this._metadata.molecules.push(molecule);\r\n }\r\n\r\n _parseAtoms(stream, atomsNum) {\r\n let curStr;\r\n let serial = this._atomsParsed;\r\n\r\n // each molecule = chain\\residue\r\n const chainID = buildChainID(this._compoundIndx);\r\n const resName = 'UNK';\r\n const resSeq = 1;\r\n\r\n this._chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = this._chain.addResidue(resName, resSeq, ' ');\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n curStr = stream.getNextString();\r\n serial++;\r\n const x = parseFloat(curStr.substr(0, 10));\r\n const y = parseFloat(curStr.substr(10, 10));\r\n const z = parseFloat(curStr.substr(20, 10));\r\n const charge = chargeMap[parseInt(curStr.substr(36, 3), 10)];\r\n const xyz = new THREE.Vector3(x, y, z);\r\n let name = curStr.substr(31, 3).trim().toUpperCase();\r\n const type = Element.getByName(name);\r\n if (!this._atomsIndexes[name]) {\r\n this._atomsIndexes[name] = 0;\r\n }\r\n this._atomsIndexes[name] += 1;\r\n name += this._atomsIndexes[name]; // every atom need to have unique name.\r\n\r\n this._residue.addAtom(name, type, xyz, undefined, true, serial, ' ', 1.0, 0.0, charge);\r\n }\r\n }\r\n\r\n _parseBonds(stream, bondsNum) {\r\n let curStr;\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n curStr = stream.getNextString();\r\n let atom1 = parseInt(curStr.substr(0, 3), 10) + this._atomsParsed;\r\n let atom2 = parseInt(curStr.substr(3, 3), 10) + this._atomsParsed;\r\n const bondType = parseInt(curStr.substr(6, 3), 10);\r\n\r\n if (atom1 > atom2) {\r\n [atom1, atom2] = [atom2, atom1];\r\n }\r\n this._complex.addBond(\r\n atom1,\r\n atom2,\r\n orderMap[bondType] || 1,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _parseMOL(stream) {\r\n this._compoundIndx++;\r\n\r\n this._parseHeader(stream);\r\n const countsLine = stream.getStringFromStart(3);\r\n const atomsNum = parseInt(countsLine.substr(0, 3), 10);\r\n const bondsNum = parseInt(countsLine.substr(3, 3), 10);\r\n this._parseAtoms(stream, atomsNum);\r\n this._parseBonds(stream, bondsNum);\r\n\r\n this._atomsParsed += atomsNum;\r\n\r\n this._metadata.molecules[this._compoundIndx]._residues = [];\r\n this._metadata.molecules[this._compoundIndx]._residues.push(this._residue);\r\n }\r\n\r\n _parseDataItem(stream) {\r\n const tag = stream.getCurrentString();\r\n\r\n let data = [];\r\n let curStr = stream.getNextString();\r\n\r\n // read data\r\n while (curStr.trim() !== '') {\r\n data.push(curStr);\r\n curStr = stream.getNextString();\r\n }\r\n if (data.length === 1) {\r\n [data] = data;\r\n }\r\n this._currentMolProps[tag.replace(/[<>]/g, '').trim()] = data;\r\n }\r\n\r\n _parseCompound(stream) {\r\n this._parseMOL(stream);\r\n\r\n // parse data items block\r\n if (this._format === fileFormat.SDF) {\r\n this._currentMolProps = {};\r\n while (stream.findNextDataItem()) {\r\n this._parseDataItem(stream);\r\n }\r\n if (Object.keys(this._currentMolProps).length !== 0) {\r\n const molecule = this._metadata.molecules[this._compoundIndx];\r\n molecule.props = this._currentMolProps;\r\n this._tryToUpdateMoleculeData(molecule);\r\n }\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n console.log('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _buildAssemblies() {\r\n const chains = this._complex._chains;\r\n\r\n if (chains.length === 1) {\r\n return this._assemblies;\r\n }\r\n\r\n for (let i = 0; i < chains.length; i++) {\r\n const assembly = new Assembly(this._complex);\r\n const matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n assembly.addChain(chains[i]._name);\r\n this._assemblies.push(assembly);\r\n }\r\n\r\n return this._assemblies;\r\n }\r\n\r\n _buildMolecules() {\r\n this._complex._molecules = [];\r\n const { molecules } = this._metadata;\r\n for (let i = 0; i < molecules.length; i++) {\r\n const molecule = new Molecule(this._complex, molecules[i].name, i + 1);\r\n molecule.residues = molecules[i]._residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n\r\n return this._complex._molecules;\r\n }\r\n\r\n _searchTag(tag, props) {\r\n for (let i = 0; i < props.length; i++) {\r\n if ((tag instanceof RegExp && tag.test(props[i].tag)) || tag === props[i].tag) {\r\n return props[i].data;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToFind(tagsList, props) {\r\n for (let j = 0; j < tagsList.length; j++) {\r\n const res = this._searchTag(tagsList[j], props);\r\n if (res) {\r\n return res;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToUpdateMoleculeData(molecule) {\r\n let res = false;\r\n for (let i = 0; i < tagsNames.length; i++) {\r\n const tagPossibleNames = tags[tagsNames[i]];\r\n const data = this._tryToFind(tagPossibleNames, molecule.props);\r\n if (data) {\r\n molecule[tagsNames[i]] = data;\r\n res = true;\r\n }\r\n }\r\n\r\n molecule.name = molecule.name || molecule.id;\r\n if (molecule.name.match(/^\\d+$/)) {\r\n molecule.name = `CID: ${molecule.name}`;\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _finalizeMetadata() {\r\n const { molecules } = this._metadata;\r\n const { metadata } = this._complex;\r\n const complex = this._complex;\r\n\r\n if (molecules.length === 1) {\r\n complex.name = molecules[0].name;\r\n metadata.title = molecules[0].title;\r\n metadata.date = molecules[0].date;\r\n metadata.properties = molecules[0].props;\r\n } else if (molecules.length > 1) {\r\n metadata.molecules = [];\r\n for (let i = 0; i < molecules.length; i++) {\r\n metadata.molecules.push({\r\n name: molecules[i].name, date: molecules[i].date, title: molecules[i].title, properties: molecules[i].props,\r\n });\r\n }\r\n }\r\n }\r\n\r\n _finalize() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n this._complex._finalizeBonds();\r\n this._fixBondsArray();\r\n this._finalizeMetadata();\r\n this._buildAssemblies();\r\n this._complex.units = this._complex.units.concat(this._assemblies);\r\n this._buildMolecules();\r\n this._complex.finalize({\r\n needAutoBonding: false, detectAromaticLoops: false, enableEditing: false, serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n defineFormat(data) {\r\n let format;\r\n if (sdfRegExp.test(data)) {\r\n format = fileFormat.SDF;\r\n } else {\r\n format = fileFormat.MOL;\r\n }\r\n\r\n return format;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const stream = new SDFStream(this._data);\r\n\r\n this._format = this.defineFormat(this._data);\r\n result.metadata.format = this._format;\r\n\r\n do {\r\n this._parseCompound(stream);\r\n } while (stream.findNextCompoundStart());\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nSDFParser.formats = ['mol', 'sdf'];\r\nSDFParser.extensions = ['.mol', '.sdf'];\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\n// http://www.uoxray.uoregon.edu/tnt/manual/node104.html\r\nconst DSN6Header = {\r\n nstart: [valueType.array, 'i16', 0],\r\n extent: [valueType.array, 'i16', 3],\r\n grid: [valueType.array, 'i16', 6],\r\n cellDims: [valueType.vector, 'i16', 9],\r\n angles: [valueType.array, 'i16', 12],\r\n div: [valueType.singular, 'i16', 15],\r\n adder: [valueType.singular, 'i16', 16],\r\n scaleFactor: [valueType.singular, 'i16', 17],\r\n};\r\n\r\nclass DSN6Model extends VolumeModel {\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n\r\n const arrays = {};\r\n arrays.i16 = new Int16Array(this._buff);\r\n\r\n // check and reverse if big endian\r\n if (arrays.i16[18] !== 100) {\r\n for (let i = 0, n = arrays.i16.length; i < n; ++i) {\r\n const val = arrays.i16[i];\r\n arrays.i16[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff);\r\n }\r\n }\r\n if (arrays.i16[18] !== 100) {\r\n throw new Error('DSN6: Incorrect format ');\r\n }\r\n\r\n const header = this._header;\r\n\r\n this._fillHeader(DSN6Header, arrays);\r\n header.cellDims.multiplyScalar(1.0 / header.scaleFactor);\r\n header.angles.forEach((angle, i, a) => { a[i] *= (Math.PI / 180.0) / header.scaleFactor; });\r\n header.div /= 100;\r\n }\r\n\r\n _setAxisIndices() {\r\n this._xyz2crs[0] = 0;\r\n this._xyz2crs[1] = 1;\r\n this._xyz2crs[2] = 2;\r\n }\r\n\r\n _setOrigins() {\r\n const header = this._header;\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n this._origin.addScaledVector(xaxis, header.nstart[0]);\r\n this._origin.addScaledVector(yaxis, header.nstart[1]);\r\n this._origin.addScaledVector(zaxis, header.nstart[2]);\r\n\r\n xaxis.multiplyScalar(header.extent[0]);\r\n yaxis.multiplyScalar(header.extent[1]);\r\n zaxis.multiplyScalar(header.extent[2]);\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _pointCalculate(xyzData, byteBuffer, z, y, x, pos, i) {\r\n const header = this._header;\r\n\r\n if (x < header.extent[0] && y < header.extent[1] && z < header.extent[2]) {\r\n const idx = x + header.extent[0] * (y + header.extent[1] * z);\r\n xyzData[idx] = (byteBuffer[pos.counter] - header.adder) / header.div;\r\n ++pos.counter;\r\n } else {\r\n pos.counter += 8 - i;\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n _blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos) {\r\n for (let k = 0; k < 8; ++k) {\r\n const z = 8 * zBlock + k;\r\n for (let j = 0; j < 8; ++j) {\r\n const y = 8 * yBlock + j;\r\n let inRange = true;\r\n let i = 0;\r\n while (inRange && i < 8) {\r\n const x = 8 * xBlock + i;\r\n inRange = this._pointCalculate(xyzData, byteBuffer, z, y, x, pos, i);\r\n i++;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const byteBuffer = new Uint8Array(this._buff);\r\n const xyzData = new Float32Array(header.extent[0] * header.extent[1] * header.extent[2]);\r\n\r\n const blocks = new THREE.Vector3(header.extent[0] / 8, header.extent[1] / 8, header.extent[2] / 8);\r\n\r\n const pos = {};\r\n pos.counter = 512;\r\n\r\n for (let zBlock = 0; zBlock < blocks.z; ++zBlock) {\r\n for (let yBlock = 0; yBlock < blocks.y; ++yBlock) {\r\n for (let xBlock = 0; xBlock < blocks.x; ++xBlock) {\r\n this._blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos);\r\n }\r\n }\r\n }\r\n this._calculateInfoParams(xyzData);\r\n return xyzData;\r\n }\r\n\r\n _calculateInfoParams(xyzData) {\r\n this._header.dmean /= xyzData.length;\r\n let dispersion = 0;\r\n let minDensity = xyzData[0];\r\n let maxDensity = xyzData[0];\r\n for (let j = 0; j < xyzData.length; j++) {\r\n dispersion += (this._header.dmean - xyzData[j]) ** 2;\r\n\r\n if (xyzData[j] < minDensity) {\r\n minDensity = xyzData[j];\r\n }\r\n if (xyzData[j] > maxDensity) {\r\n maxDensity = xyzData[j];\r\n }\r\n }\r\n this._header.sd = Math.sqrt(dispersion / xyzData.length);\r\n this._header.dmax = maxDensity;\r\n this._header.dmin = minDensity;\r\n }\r\n}\r\n\r\nclass DSN6Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'dsn6';\r\n this.model = new DSN6Model();\r\n }\r\n\r\n static canParse(data, options) {\r\n if (!data) {\r\n return false;\r\n }\r\n return data instanceof ArrayBuffer && Parser.checkDataTypeOptions(options, 'dsn6');\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false;\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nDSN6Parser.formats = ['dsn6'];\r\nDSN6Parser.extensions = ['.dsn6', '.omap'];\r\nDSN6Parser.binary = true;\r\n\r\nexport default DSN6Parser;\r\n","import PDBStream from './PDBStream';\r\n\r\n/**\r\n * Little helper class for GRO Parser usage.\r\n * @extends PDBStream\r\n */\r\nclass GROReader extends PDBStream {\r\n constructor(data) {\r\n super(data);\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n this.next();\r\n }\r\n\r\n /**\r\n * Getting end of string.\r\n * @returns {Number} Pointer to end of string\r\n */\r\n getNext() {\r\n return this._next;\r\n }\r\n}\r\n\r\nexport default GROReader;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport GROReader from './GROReader';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Molecule,\r\n} = chem;\r\n\r\n/**\r\n * Gromos87 file format parser.\r\n * @extends Parser\r\n */\r\nclass GROParser extends Parser {\r\n /**\r\n * Create parser for .gro file format\r\n *\r\n * @param {String} data Input file\r\n * @param {String} options Input options (optional field)\r\n */\r\n constructor(data, options) {\r\n super(data, options);\r\n /** @type Date */\r\n this._time = null; // Time in ps, optional field for animations\r\n /** @type Number */\r\n this._numAtoms = null; // Number of atoms in complex\r\n /** @type Number */\r\n this._residueNumber = null; // Number of exact residue\r\n /** @type String */\r\n this._residueName = ''; // Scientific name of exact residue\r\n /** @type String */\r\n this._atomName = ''; // Scientific name of exact atom\r\n /** @type Number */\r\n this._atomNumber = null; // Sorted number of exact atom\r\n /** @type Array */\r\n this._atomPosition = []; // Array which contains x, y, z position of exact atom\r\n /** @type Array */\r\n this._atomVelocity = []; // Array which contains x, y, z velocity of exact atom (optional)\r\n /** @type Complex */\r\n this._complex = null; // Complex structure for unified molecule representation\r\n /** @type Vector3 */\r\n this._molecules = []; // Molecules array\r\n /** @type Molecule */\r\n this._molecule = null; // Single molecule\r\n /** @type String */\r\n this._options.filetype = 'gro'; // Extension of data file.\r\n }\r\n\r\n /**\r\n * General check for possibility of parsing.\r\n * @param {String} data - Input file\r\n * @returns {boolean} true if this file is in ascii, false otherwise\r\n */\r\n canProbablyParse(data) {\r\n return _.isString(this._data) && /^\\s*[^\\n]*\\n\\s*\\d+ *\\n\\s*\\d+[^\\n\\d]{3}\\s*\\w+\\s*\\d+\\s*-?\\d/.test(data);\r\n }\r\n\r\n /**\r\n * Parsing title of molecule complex.\r\n * NOTE: that names are ESTIMATES, there is no strict rules in Gromos87 standard for first line in input file.\r\n * @param {GROReader} line - Line containing title and time.\r\n */\r\n _parseTitle(line) {\r\n const { metadata } = this._complex;\r\n metadata.id = line.readLine().trim();\r\n metadata.name = metadata.id.slice(metadata.id.lastIndexOf('\\\\') + 1, metadata.id.lastIndexOf('.'));\r\n metadata.format = 'gro';\r\n }\r\n\r\n /**\r\n * Parsing line containing number of atoms information.\r\n * @param {GROReader} line - Line containing number of atoms.\r\n */\r\n _parseNumberOfAtoms(line) {\r\n this._numAtoms = line.readInt(0, line.getNext());\r\n if (Number.isNaN(this._numAtoms)) {\r\n throw new Error('Line 2 is not representing atom number. Consider checking input file');\r\n }\r\n }\r\n\r\n /**\r\n * Parsing line containing information about residues, atoms etc. Also information about box vectors.\r\n * Format of atoms MUST (by Gromos87 standard) be this: (note that numbering starts not from 0, but from 1!)\r\n * ResidueNumber[1 - 5] ResidueName[6 - 10] AtomName[11 - 15] AtomNumber[16 - 20] Position[21 - 45] Velocity[46 - 69]\r\n * @param {GROReader} line - Line containing information about atom.\r\n */\r\n _parseAtom(line) {\r\n this._residueNumber = line.readInt(1, 5);\r\n this._residueName = line.readString(6, 10).trim();\r\n this._atomName = line.readString(11, 15).trim();\r\n this._atomNumber = line.readInt(16, 20);\r\n const positionX = line.readFloat(21, 28) * 10;\r\n const positionY = line.readFloat(29, 36) * 10;\r\n const positionZ = line.readFloat(37, 45) * 10;\r\n if (Number.isNaN(positionX) || Number.isNaN(positionY) || Number.isNaN(positionZ)) {\r\n this._complex.error = {\r\n message: `Atom position is invalid in \"${line.readLine()}\"`,\r\n };\r\n return;\r\n }\r\n /* const velocityX = line.readFloat(46, 53);\r\n const velocityY = line.readFloat(54, 61);\r\n const velocityZ = line.readFloat(62, 69); */\r\n /* Adding residue and atom to complex structure */\r\n const type = Element.getByName(this._atomName[0]); /* MAGIC 0. REASONS: This name is something like \"CA\", where\r\n C - is an element an A is something else. But what about Calcium? */\r\n if (type.fullName === 'Unknown') {\r\n this._complex.error = {\r\n message: `${this._atomName[0]} hasn't been recognised as an atom name.`,\r\n };\r\n return;\r\n }\r\n const role = Element.Role[this._atomName];\r\n /* Firstly, create a dummy chain */\r\n let chain = this._chain;\r\n if (!chain) {\r\n this._chain = chain = this._complex.addChain('A');\r\n }\r\n /* Secondly, add residue to that chain */\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== this._residueNumber) {\r\n this._residue = residue = chain.addResidue(this._residueName, this._residueNumber, ' ');\r\n }\r\n /* Lastly, add atom to that residue */\r\n this._atomPosition = new THREE.Vector3(positionX, positionY, positionZ);\r\n /* Adding default constants to correct atom addition process */\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n residue.addAtom(this._atomName, type, this._atomPosition, role, het, this._atomNumber, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n /**\r\n * Some finalizing procedures. In '.gro' file format there is only 1 chain and 1 molecule.\r\n */\r\n _finalize() {\r\n const molecule = new Molecule(this._complex, this._complex.metadata.name, 1);\r\n // aggregate residues from chain\r\n molecule.residues = this._chain._residues;\r\n molecule._chains = this._chain;\r\n this._complex._molecules[0] = molecule;\r\n this._molecules.push(molecule);\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n /**\r\n * Main parsing procedure.\r\n * @returns {Complex} Complex structure for visualizing.\r\n */\r\n parseSync() {\r\n /* Create \"Complex\" variable */\r\n const result = this._complex = new Complex();\r\n /* Parse input file line-by-line */\r\n const reader = new GROReader(this._data);\r\n let counter = 0; /* Simple counter regarding to format of .gro file */\r\n /* First two lines - technical information, other lines - Atoms */\r\n this._parseTitle(reader);\r\n reader.next();\r\n this._parseNumberOfAtoms(reader);\r\n reader.next();\r\n for (counter = 0; counter < this._numAtoms; ++counter) {\r\n if (!reader.end()) {\r\n this._parseAtom(reader);\r\n reader.next();\r\n } else break;\r\n }\r\n /* If number of atoms in second line is less then actual atoms in file */\r\n if (counter < this._numAtoms) {\r\n this._complex.error = {\r\n message: 'File ended unexpectedly.',\r\n };\r\n }\r\n /* Catch errors occurred in parsing process */\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n\r\n /* Finalizing data */\r\n this._finalize();\r\n\r\n /* Cleaning up */\r\n this._atomPosition = null;\r\n this._complex = null;\r\n this._molecules = null;\r\n this._molecule = null;\r\n\r\n /* Return resulting Complex variable */\r\n return result;\r\n }\r\n}\r\n\r\nGROParser.formats = ['gro'];\r\nGROParser.extensions = ['.gro'];\r\n\r\nexport default GROParser;\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst orderMap = {\r\n un: 0,\r\n 1: 1,\r\n 2: 2,\r\n 3: 3,\r\n ar: 1,\r\n am: 1,\r\n nc: 0,\r\n du: 1,\r\n};\r\nconst typeMap = {\r\n un: Bond.BondType.UNKNOWN, // unknown (cannot be determined from the parameter tables)\r\n 1: Bond.BondType.COVALENT, // single\r\n 2: Bond.BondType.COVALENT, // double\r\n 3: Bond.BondType.COVALENT, // triple\r\n ar: Bond.BondType.AROMATIC, // aromatic\r\n am: Bond.BondType.COVALENT, // amide\r\n nc: Bond.BondType.UNKNOWN, // not connected\r\n du: Bond.BondType.COVALENT, // dummy\r\n};\r\n\r\nconst resNumberRegex = /\\d+$/;\r\nconst spacesRegex = /\\s+/;\r\n\r\nfunction splitToFields(str) {\r\n return str.trim().split(spacesRegex);\r\n}\r\n/* There is no jsdoc documentation because of eslint corrections:\r\n * not all Parser methods are implemented\r\n */\r\n\r\nclass MOL2Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._compoundIndx = -1;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n\r\n this._currPosIdx = 0;\r\n this._currStartIdx = 0;\r\n\r\n this._serialAtomMap = {};\r\n\r\n this._options.fileType = 'mol2';\r\n }\r\n\r\n _parseRawStrings(data) {\r\n return data.split(/\\r?\\n|\\r/);\r\n }\r\n\r\n _toStringFromStart(numb, MOL2Data) {\r\n const newPosIdx = this._currStartIdx + numb;\r\n this._currPosIdx = (newPosIdx < MOL2Data.length) ? newPosIdx : this._currStartIdx;\r\n }\r\n\r\n _toHeaderString(header, MOL2Data) {\r\n this._toStringFromStart(0, MOL2Data);\r\n while (this._currPosIdx < MOL2Data.length) {\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`)) {\r\n return;\r\n }\r\n this._currPosIdx++;\r\n }\r\n this._toStringFromStart(0, MOL2Data);\r\n }\r\n\r\n _toStringFromHeader(header, numb, MOL2Data) {\r\n this._toHeaderString(header, MOL2Data);\r\n const newPosIdx = this._currPosIdx + numb;\r\n\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`) && newPosIdx < MOL2Data.length) {\r\n this._currPosIdx = newPosIdx;\r\n }\r\n }\r\n\r\n _setStart(startPos, MOL2Data) {\r\n if (startPos >= MOL2Data.length) {\r\n this._currStartIdx = this._currPosIdx = MOL2Data.length - 1;\r\n } else {\r\n this._currStartIdx = this._currPosIdx = startPos;\r\n }\r\n }\r\n\r\n _probablyHaveDataToParse(MOL2Data) {\r\n return this._currPosIdx < MOL2Data.length - 2;\r\n }\r\n\r\n _findNextCompoundStart(MOL2Data) {\r\n while (this._currPosIdx < MOL2Data.length && MOL2Data[this._currPosIdx].trim() !== '@MOLECULE>') {\r\n this._currPosIdx++;\r\n }\r\n this._setStart(++this._currPosIdx, MOL2Data);\r\n return this._probablyHaveDataToParse(MOL2Data);\r\n }\r\n\r\n _parseMolecule(MOL2Data) {\r\n this._toHeaderString('MOLECULE', MOL2Data);\r\n\r\n const { metadata } = this._complex;\r\n metadata.name = MOL2Data[++this._currPosIdx];\r\n metadata.format = 'mol2';\r\n\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = this._compoundIndx + 1;\r\n this._molecules.push(this._molecule);\r\n }\r\n\r\n /* Atom format description:\r\n * atomId atomName x y z element [resSeq [resName [charge [statusBit]]]]\r\n * statusBits is the internal SYBYL status bits associated with the atom.\r\n * These should never be set by the user.\r\n * Source: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf\r\n */\r\n _parseAtoms(atomsNum, MOL2Data) {\r\n this._toHeaderString('ATOM', MOL2Data);\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 6) {\r\n throw new Error('MOL2 parsing error: Not enough information to create atom!');\r\n }\r\n const atomId = parseInt(parsedStr[0], 10);\r\n const atomName = parsedStr[1];\r\n\r\n const x = parseFloat(parsedStr[2]);\r\n const y = parseFloat(parsedStr[3]);\r\n const z = parseFloat(parsedStr[4]);\r\n\r\n const element = parsedStr[5].split('.')[0].toUpperCase();\r\n\r\n let charge = 0;\r\n if (parsedStr.length >= 9) {\r\n charge = parseFloat(parsedStr[8]) || 0.0;\r\n }\r\n\r\n let chain = this._chain;\r\n if (!chain) {\r\n // .mol2 may contain information about multiple molecules, but they can't be visualized\r\n // at the same time now. There is no need to create different chain IDs then.\r\n this._chain = chain = this._complex.getChain('A') || this._complex.addChain('A');\r\n this._residue = null;\r\n }\r\n if (!this._setResidue(parsedStr)) {\r\n continue;\r\n }\r\n\r\n // These fields are not listed in mol2 format. Set them default.\r\n // Atoms and het atoms doesn't differ in .mol2,\r\n // but het atoms have special residues. It can be used in next updates\r\n const het = false;\r\n const altLoc = ' ';\r\n const occupancy = 1.0;\r\n const tempFactor = 0.0;\r\n const type = Element.getByName(element);\r\n const role = Element.Role[atomName];\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n this._residue.addAtom(atomName, type, xyz, role, het, atomId, altLoc, occupancy, tempFactor, charge);\r\n }\r\n }\r\n\r\n _setResidue(parsedStr) {\r\n let resSeq = 1;\r\n let resName = 'UNK'; // The same meaning has '<0>' in some mol2 files\r\n\r\n if (parsedStr.length >= 7) {\r\n resSeq = parseInt(parsedStr[6], 10);\r\n }\r\n if (parsedStr.length >= 8 && parsedStr[7] !== '<0>') {\r\n resName = parsedStr[7].replace(resNumberRegex, '');\r\n }\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return false;\r\n }\r\n }\r\n const residue = this._residue;\r\n const chain = this._chain;\r\n if (!residue || residue.getSequence() !== resSeq) {\r\n this._residue = chain.addResidue(resName, resSeq, 'A');\r\n }\r\n return true;\r\n }\r\n\r\n /* Bond format description\r\n * bondId originAtomId targetAtomId bondType [statusBits]\r\n */\r\n _parseBonds(bondsNum, MOL2Data) {\r\n this._toHeaderString('BOND', MOL2Data);\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 3) {\r\n throw new Error('MOL2 parsing error: Missing information about bonds!');\r\n }\r\n\r\n let originAtomId = parseInt(parsedStr[1], 10);\r\n let targetAtomId = parseInt(parsedStr[2], 10);\r\n const bondType = parsedStr[3];\r\n\r\n if (originAtomId > targetAtomId) {\r\n [originAtomId, targetAtomId] = [targetAtomId, originAtomId];\r\n }\r\n this._complex.addBond(\r\n originAtomId,\r\n targetAtomId,\r\n orderMap[bondType] || 0,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _fixSerialAtoms() {\r\n const atoms = this._complex._atoms;\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n this._serialAtomMap[atom.serial] = atom;\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n if (Object.keys(serialAtomMap).length === 0) {\r\n throw new Error('MOL2 parsing error: Missing atom information!');\r\n }\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _finalizeMolecules() {\r\n // Get chain from complex\r\n const chain = this._complex._chains[0];\r\n this._complex._molecules = [];\r\n\r\n // Aggregate residues from chains\r\n // (to be precise from the chain 'A')\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const currMolecule = this._molecules[i];\r\n const molResidues = chain._residues;\r\n const molecule = new Molecule(this._complex, currMolecule._name, i + 1);\r\n molecule.residues = molResidues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _finalize() {\r\n this._complex._finalizeBonds();\r\n this._fixSerialAtoms();\r\n this._fixBondsArray();\r\n this._finalizeMolecules();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _parseCompound(MOL2Data) {\r\n this._compoundIndx++;\r\n this._parseMolecule(MOL2Data);\r\n\r\n // Ignoring comments and everything before @MOLECULE block\r\n this._toStringFromHeader('MOLECULE', 2, MOL2Data);\r\n\r\n const parsedStr = MOL2Data[this._currPosIdx].trim().split(spacesRegex);\r\n const atomsNum = parsedStr[0];\r\n const bondsNum = parsedStr[1];\r\n\r\n this._parseAtoms(atomsNum, MOL2Data);\r\n this._parseBonds(bondsNum, MOL2Data);\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const MOL2Data = this._parseRawStrings(this._data);\r\n do {\r\n this._parseCompound(MOL2Data);\r\n } while (this._findNextCompoundStart(MOL2Data));\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nMOL2Parser.formats = ['mol2'];\r\nMOL2Parser.extensions = ['.mol2', '.ml2', '.sy2'];\r\n\r\nexport default MOL2Parser;\r\n","import ParserList from './parsers/ParserList';\r\n\r\nimport PDBParser from './parsers/PDBParser';\r\nimport CMLParser from './parsers/CMLParser';\r\nimport MMTFParser from './parsers/MMTFParser';\r\nimport CIFParser from './parsers/CIFParser';\r\nimport CCP4Parser from './parsers/CCP4Parser';\r\nimport XYZParser from './parsers/XYZParser';\r\nimport PubChemParser from './parsers/PubChemParser';\r\nimport SDFParser from './parsers/SDFParser';\r\nimport DSN6Parser from './parsers/DSN6Parser';\r\nimport GROParser from './parsers/GROParser';\r\nimport MOL2Parser from './parsers/MOL2Parser';\r\n\r\nexport default new ParserList([\r\n // note: order might be important\r\n PDBParser,\r\n CIFParser,\r\n MMTFParser,\r\n XYZParser,\r\n CMLParser,\r\n PubChemParser,\r\n SDFParser,\r\n CCP4Parser,\r\n DSN6Parser,\r\n GROParser,\r\n MOL2Parser,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available exporters.\r\n * @extends EntityList\r\n */\r\nclass ExporterList extends EntityList {\r\n /**\r\n * Create a list of exporters.\r\n * The exporters are indexed by supported data formats (`.formats` and\r\n * `.extensions` properties of a Exporter subclass).\r\n * The Exporters can be retrieved later by matching against specs (see {@link ExporterList#find}).\r\n *\r\n * @param {!Array=} someExporters A list of {@link Exporter} subclasses to\r\n * automatically register at creation time.\r\n * @see ExporterList#register\r\n */\r\n constructor(someExporters = []) {\r\n super(someExporters, ['formats']);\r\n }\r\n\r\n /**\r\n * Find a suitable exporter for data.\r\n *\r\n * @param {Object} specs Exporter specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {*=} specs.data Data to export.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ExporterList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Exporter {\r\n constructor(source, options) {\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n exportSync() {\r\n throw new Error('Exporting to this source is not implemented');\r\n }\r\n\r\n export() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Export aborted'));\r\n }\r\n return resolve(this.exportSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Exporter.prototype);\r\n","import _ from 'lodash';\r\nimport { Matrix4 } from 'three';\r\n\r\nexport default class PDBResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._currentStr = -1;\r\n this._tag = null;\r\n this._fixedNumeration = false;\r\n this._numeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n\r\n getResult() {\r\n this.writeString('\\n', 81, 81);\r\n return this._resultArray.join('');\r\n }\r\n\r\n _currentStrLength() {\r\n const curStr = this._resultArray[this._currentStr];\r\n return curStr ? curStr.length : 0;\r\n }\r\n\r\n // numeration can be number or boolean\r\n // if numeration is number then just put this number to 8-10 pos in string\r\n // if numeration is boolean then increase number for all new strings\r\n newTag(tag, numeration) {\r\n if (!tag) {\r\n this._tag = null;\r\n } else {\r\n this._tag = tag;\r\n }\r\n if (!_.isUndefined(numeration)) {\r\n if (_.isNumber(numeration)) {\r\n this._tagStrNum = numeration;\r\n this._numeration = true;\r\n this._fixedNumeration = true;\r\n } else if (_.isBoolean(numeration)) {\r\n this._tagStrNum = 0;\r\n this._numeration = numeration;\r\n this._fixedNumeration = false;\r\n }\r\n } else {\r\n this._numeration = false;\r\n this._fixedNumeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n }\r\n\r\n newString(tag) {\r\n this.writeString('\\n', 81, 81);\r\n this._currentStr++;\r\n this._resultArray.push('');\r\n\r\n if (tag) {\r\n this.writeString(tag, 1, 6);\r\n } else if (this._tag) {\r\n this.writeString(this._tag, 1, 6);\r\n }\r\n\r\n if (this._numeration) {\r\n if (!this._fixedNumeration) {\r\n this._tagStrNum++;\r\n }\r\n if (this._tagStrNum !== 1) {\r\n this.writeString(this._tagStrNum.toString(), 10, 8);\r\n }\r\n }\r\n }\r\n\r\n writeEntireString(string, maxStrPos, concat) {\r\n if (!maxStrPos) {\r\n maxStrPos = 81;\r\n }\r\n for (let j = 0; j < string.length; j++) {\r\n if (this._currentStrLength() === maxStrPos && j !== string.length - 1) {\r\n this.newString();\r\n if (concat) { // pretty hardcoddy\r\n this.writeString(concat.tag, concat.begin, concat.end);\r\n }\r\n }\r\n if (string[j] === '\\n') {\r\n this.newString();\r\n } else {\r\n this.writeString(string[j]);\r\n }\r\n }\r\n }\r\n\r\n writeString(string, begin, end) {\r\n let curStr = this._resultArray[this._currentStr];\r\n let str;\r\n\r\n const curStrLength = curStr ? curStr.length : 0;\r\n\r\n if (_.isUndefined(string)) {\r\n return;\r\n }\r\n\r\n if (!_.isNumber(begin)) {\r\n begin = curStrLength + 1;\r\n }\r\n\r\n if (!_.isNumber(end)) {\r\n end = curStrLength + string.length;\r\n }\r\n\r\n if (!_.isString(string)) {\r\n str = string.toString();\r\n } else {\r\n str = string;\r\n }\r\n\r\n const finish = begin < end ? end : begin;\r\n const start = begin < end ? begin : end;\r\n\r\n if (str.length > Math.abs(begin - end) + 1) {\r\n str = str.substr(0, Math.abs(begin - end + 1));\r\n }\r\n\r\n // spaces before start of new data\r\n if (start > curStrLength + 1) {\r\n this._resultArray[this._currentStr] += ' '.repeat(start - curStrLength - 1);\r\n } else if (start <= curStrLength) {\r\n const cStr = this._resultArray[this._currentStr];\r\n this._resultArray[this._currentStr] = cStr.slice(0, start - 1);\r\n }\r\n\r\n // if reverse order\r\n // reverse order of end and begin means that user wants to align text right\r\n if (end < begin) {\r\n const len = begin - end + 1;\r\n str = ' '.repeat(len - str.length) + str;\r\n }\r\n\r\n // some hardcode fix for space between string numeration and data\r\n // (see pdb file format description)\r\n if (start === 11 && this._numeration && this._tagStrNum !== 1) {\r\n str = ` ${str}`;\r\n }\r\n\r\n // append new data to string\r\n this._resultArray[this._currentStr] += str;\r\n curStr = this._resultArray[this._currentStr];\r\n\r\n if (finish > curStr.length) {\r\n this._resultArray[this._currentStr] += ' '.repeat(finish - curStr.length);\r\n }\r\n }\r\n\r\n writeBondsArray(bonds, atom) {\r\n const bondsArrays = this._getSubArrays(bonds, 4);\r\n\r\n for (let k = 0; k < bondsArrays.length; k++) {\r\n this.newString();\r\n this.writeString(atom.serial, 11, 7);\r\n\r\n for (let j = 0; j < bondsArrays[k].length; j++) {\r\n const serial = (bondsArrays[k][j]._left.serial === atom.serial)\r\n ? bondsArrays[k][j]._right.serial : bondsArrays[k][j]._left.serial;\r\n\r\n this.writeString(serial, 16 + 5 * j, 12 + 5 * j);\r\n }\r\n }\r\n }\r\n\r\n _getSubArrays(arr, subArraySize) {\r\n const subArrays = [];\r\n for (let i = 0; i < arr.length; i += subArraySize) {\r\n subArrays.push(arr.slice(i, i + subArraySize));\r\n }\r\n return subArrays;\r\n }\r\n\r\n // function for writing matrix in Remark290 and Remark350 tags\r\n // (see pdb file description)\r\n writeMatrix(matrix, matrixIndx, tag) {\r\n for (let j = 0; j < 3; j++) {\r\n this.newString();\r\n this.writeString(tag, 14, 18);\r\n this.writeString((j + 1).toString(), 19, 19);\r\n this.writeString(matrixIndx.toString(), 23, 20);\r\n for (let k = 0; k < 3; k++) {\r\n const numb = parseFloat(matrix.elements[j * 4 + k]).toFixed(6);\r\n this.writeString(numb.toString(), 33 + k * 10, 24 + k * 10);\r\n }\r\n\r\n const numb = parseFloat(matrix.elements[j * 4 + 3]).toFixed(5);\r\n this.writeString(numb.toString(), 68, 55);\r\n }\r\n }\r\n\r\n writeMatrices(matrices, string) {\r\n if (!matrices) {\r\n return;\r\n }\r\n const matrix = new Matrix4();\r\n for (let j = 0; j < matrices.length; j++) {\r\n matrix.copy(matrices[j]).transpose();\r\n this.writeMatrix(matrix, j + 1, string);\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport Complex from '../../chem/Complex';\r\nimport Exporter from './Exporter';\r\nimport PDBResult from './PDBResult';\r\nimport Assembly from '../../chem/Assembly';\r\nimport { typeByPDBHelixClass } from '../../chem/Helix';\r\n\r\nexport default class PDBExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n this._tags = ['HEADER', 'TITLE', 'COMPND', 'REMARK', 'HELIX', 'SHEET', 'ATOM and HETATM', 'CONECT'];\r\n this._result = null;\r\n this._tagExtractors = {\r\n HEADER: this._extractHEADER,\r\n TITLE: this._extractTITLE,\r\n 'ATOM and HETATM': this._extractATOM,\r\n CONECT: this._extractCONECT,\r\n COMPND: this._extractCOMPND,\r\n REMARK: this._extractREMARK,\r\n HELIX: this._extractHELIX,\r\n SHEET: this._extractSHEET,\r\n };\r\n this._stringForRemark350 = 'COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN\\n'\r\n + 'BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE\\n'\r\n + 'MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS\\n'\r\n + 'GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND\\n'\r\n + 'CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.';\r\n\r\n this._stringForRemark290 = 'CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS\\n'\r\n + 'THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM\\n'\r\n + 'RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY\\n'\r\n + 'RELATED MOLECULES.';\r\n }\r\n\r\n exportSync() {\r\n const result = new PDBResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n for (let i = 0; i < this._tags.length; i++) {\r\n const tag = this._tags[i];\r\n const func = this._tagExtractors[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, result);\r\n }\r\n }\r\n\r\n this._result = result.getResult();\r\n\r\n return this._result;\r\n }\r\n\r\n _extractHEADER(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n result.newTag('HEADER');\r\n result.newString();\r\n if (metadata.classification) {\r\n result.writeString(metadata.classification, 11, 50);\r\n }\r\n if (metadata.date) {\r\n result.writeString(metadata.date, 51, 59);\r\n }\r\n if (metadata.id) {\r\n result.writeString(metadata.id, 63, 66);\r\n }\r\n }\r\n\r\n _extractTITLE(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n if (!metadata.title) {\r\n return;\r\n }\r\n result.newTag('TITLE', true);\r\n for (let i = 0; i < metadata.title.length; i++) {\r\n result.newString();\r\n result.writeString(metadata.title[i], 11, 80);\r\n }\r\n }\r\n\r\n _extractCONECT(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n\r\n const atoms = this._source._atoms;\r\n result.newTag('CONECT');\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const fixedBonds = atoms[i].bonds.filter((bond) => bond._fixed);\r\n if (fixedBonds.length !== 0) {\r\n result.writeBondsArray(fixedBonds.reverse(), atoms[i]);\r\n }\r\n }\r\n }\r\n\r\n _extractSHEET(result) {\r\n if (!this._source._sheets) {\r\n return;\r\n }\r\n\r\n result.newTag('SHEET');\r\n\r\n const sheets = this._source._sheets;\r\n for (let i = 0; i < sheets.length; i++) {\r\n if (sheets[i]._strands) {\r\n const strands = sheets[i]._strands;\r\n for (let j = 0; j < strands.length; j++) {\r\n result.newString();\r\n result.writeString(j + 1, 10, 8);\r\n result.writeString(sheets[i]._name, 14, 12);\r\n result.writeString(strands.length, 16, 15);\r\n result.writeString(strands[j].init._type._name, 18, 20);\r\n result.writeString(strands[j].init._chain._name, 22, 22);\r\n result.writeString(strands[j].init._sequence, 26, 23);\r\n result.writeString(strands[j].init._icode, 27, 27);\r\n result.writeString(strands[j].term._type._name, 29, 31);\r\n result.writeString(strands[j].init._chain._name, 33, 33);\r\n result.writeString(strands[j].term._sequence, 37, 34);\r\n result.writeString(strands[j].term._icode, 38, 38);\r\n result.writeString(strands[j].sense, 40, 39);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _extractHELIX(result) {\r\n if (!this._source._helices) {\r\n return;\r\n }\r\n\r\n result.newTag('HELIX');\r\n const helices = this._source._helices;\r\n for (let i = 0; i < helices.length; i++) {\r\n const helix = helices[i];\r\n const helixClass = _.invert(typeByPDBHelixClass);\r\n result.newString();\r\n result.writeString(helix.serial, 10, 8);\r\n result.writeString(helix.name, 14, 12);\r\n result.writeString(helix.init._type._name, 16, 18);\r\n result.writeString(helix.init._chain._name, 20, 20);\r\n result.writeString(helix.init._sequence, 25, 22);\r\n result.writeString(helix.init._icode, 26, 26);\r\n result.writeString(helix.term._type._name, 28, 30);\r\n result.writeString(helix.term._chain._name, 32, 32);\r\n result.writeString(helix.term._sequence, 37, 34);\r\n result.writeString(helix.term._icode, 38, 38);\r\n result.writeString(helixClass[helix.type], 40, 39);\r\n result.writeString(helix.comment, 41, 70);\r\n result.writeString(helix.length, 76, 72);\r\n }\r\n }\r\n\r\n _extractATOM(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n const atoms = this._source._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const tag = atoms[i].het ? 'HETATM' : 'ATOM';\r\n result.newString(tag);\r\n const startIndx = (atoms[i].element.name.length > 1 || atoms[i].name.length > 3) ? 13 : 14;\r\n result.writeString(atoms[i].serial, 11, 7);\r\n result.writeString(atoms[i].name, startIndx, 16);\r\n result.writeString(String.fromCharCode(atoms[i].location), 17, 17);\r\n result.writeString(atoms[i].residue._type._name, 20, 18);\r\n result.writeString(atoms[i].residue._chain._name, 22, 22);\r\n result.writeString(atoms[i].residue._sequence, 26, 23);\r\n result.writeString(atoms[i].residue._icode, 27, 27);\r\n result.writeString(atoms[i].position.x.toFixed(3), 38, 31);\r\n result.writeString(atoms[i].position.y.toFixed(3), 46, 39);\r\n result.writeString(atoms[i].position.z.toFixed(3), 54, 47);\r\n result.writeString(atoms[i].occupancy.toFixed(2), 60, 55);\r\n result.writeString(atoms[i].temperature.toFixed(2), 66, 61);\r\n result.writeString(atoms[i].element.name, 78, 77);\r\n if (atoms[i].charge) {\r\n result.writeString(atoms[i].charge, 79, 80);\r\n }\r\n }\r\n }\r\n\r\n _extractCOMPND(result) {\r\n if (!this._source._molecules) {\r\n return;\r\n }\r\n const molecules = this._source._molecules;\r\n result.newTag('COMPND', true);\r\n\r\n for (let i = 0; i < molecules.length; i++) {\r\n const chains = this._getMoleculeChains(molecules[i]);\r\n result.newString();\r\n result.writeString(`MOL_ID: ${molecules[i].index};`, 11, 80);\r\n result.newString();\r\n result.writeString(`MOLECULE: ${molecules[i].name};`, 11, 80);\r\n result.newString();\r\n result.writeString('CHAIN: ', 11, 18);\r\n const chainsString = `${chains.join(', ')};`;\r\n result.writeEntireString(chainsString, 81);\r\n }\r\n }\r\n\r\n _extractREMARK(result) {\r\n this._Remark290(result);\r\n this._Remark350(result);\r\n }\r\n\r\n _Remark290(result) {\r\n if (!this._source.symmetry) {\r\n return;\r\n }\r\n\r\n if (this._source.symmetry.length !== 0) {\r\n const matrices = this._source.symmetry;\r\n result.newTag('REMARK', 290);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark290);\r\n result.writeMatrices(matrices, 'SMTRY');\r\n result.newString();\r\n result.newString();\r\n result.writeString('REMARK: NULL', 11, 80);\r\n }\r\n }\r\n\r\n _Remark350(result) {\r\n if (!this._source.units) {\r\n return;\r\n }\r\n const { units } = this._source;\r\n let biomolIndx = 0;\r\n\r\n result.newTag('REMARK', 350);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark350);\r\n\r\n const assemblies = units.filter((unit) => unit instanceof Assembly);\r\n\r\n for (let i = 0; i < assemblies.length; i++) {\r\n result.newString();\r\n result.newString();\r\n biomolIndx++;\r\n result.writeString(`BIOMOLECULE: ${biomolIndx}`, 11, 80);\r\n const chains = assemblies[i].chains.join(', ');\r\n result.newString();\r\n result.writeString('APPLY THE FOLLOWING TO CHAINS: ');\r\n result.writeEntireString(chains, 69, { tag: 'AND CHAINS: ', begin: 31, end: 42 });\r\n\r\n const { matrices } = assemblies[i];\r\n result.writeMatrices(matrices, 'BIOMT');\r\n }\r\n }\r\n\r\n _getMoleculeChains(molecule) {\r\n function getChainName(residue) {\r\n return residue._chain._name;\r\n }\r\n const chainNames = molecule.residues.map(getChainName);\r\n return chainNames.filter((item, pos) => chainNames.indexOf(item) === pos);\r\n }\r\n}\r\n\r\nPDBExporter.formats = ['pdb'];\r\nPDBExporter.SourceClass = Complex;\r\n","import * as THREE from 'three';\r\n\r\nconst FBX_POS_SIZE = 3;\r\nconst FBX_NORM_SIZE = 3;\r\nconst FBX_COL_SIZE = 4;\r\n\r\nfunction copyFbxPoint3(src, srcIdx, dst, dstIdx) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n}\r\n\r\nfunction copyFbxPoint4(src, srcIdx, dst, dstIdx, value) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n dst[dstIdx + 3] = value;\r\n}\r\n\r\nconst vector4 = new THREE.Vector4();\r\nfunction copyTransformedPoint3(src, srcIdx, dst, dstIdx, opts) {\r\n vector4.set(src[srcIdx], src[srcIdx + 1], src[srcIdx + 2], opts.w);\r\n vector4.applyMatrix4(opts.matrix);\r\n dst[dstIdx] = vector4.x;\r\n dst[dstIdx + 1] = vector4.y;\r\n dst[dstIdx + 2] = vector4.z;\r\n}\r\n\r\nfunction setSubArray(src, dst, count, copyFunctor, functorOpts) {\r\n if ((dst.array.length - dst.start) / dst.stride < count\r\n || (src.array.length - src.start) / src.stride < count) {\r\n return; // we've got no space\r\n }\r\n if (src.stride === dst.stride) { // stride is the same\r\n dst.array.set(src.array, dst.start);\r\n } else {\r\n let idx = dst.start;\r\n let arridx = src.start;\r\n for (let i = 0; i < count; ++i, idx += dst.stride, arridx += src.stride) {\r\n copyFunctor(src.array, arridx, dst.array, idx, functorOpts);\r\n }\r\n }\r\n}\r\n\r\nexport default class FBXModel {\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.lastPos = 0;\r\n this.lastNorm = 0;\r\n this.lastCol = 0;\r\n this.lastIdx = 0;\r\n }\r\n\r\n init(vertsCount, indsCount) {\r\n this.positions = new Float32Array(vertsCount * FBX_POS_SIZE);\r\n this.normals = new Float32Array(vertsCount * FBX_NORM_SIZE);\r\n this.colors = new Float32Array(vertsCount * FBX_COL_SIZE);\r\n this.indices = new Int32Array(indsCount);\r\n }\r\n\r\n setPositions(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.positions,\r\n start: this.lastPos,\r\n stride: FBX_POS_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setTransformedPositions(array, start, count, stride, matrix) {\r\n let idx = this.lastPos;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 1 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_POS_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.positions, idx, opts);\r\n }\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setNormals(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.normals,\r\n start: this.lastNorm,\r\n stride: FBX_NORM_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setTransformedNormals(array, start, count, stride, matrix) {\r\n let idx = this.lastNorm;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 0 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_NORM_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.normals, idx, opts);\r\n }\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setColors(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.colors,\r\n start: this.lastCol,\r\n stride: FBX_COL_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint4, 1);\r\n this.lastCol += count * FBX_COL_SIZE;\r\n }\r\n\r\n setIndices(array, start, count) {\r\n this.indices.set(array, this.lastIdx);\r\n this.lastIdx += count;\r\n }\r\n\r\n setShiftedIndices(array, count, shift) {\r\n const shifted = array.map((x) => x + shift);\r\n this.setIndices(shifted, 0, count);\r\n }\r\n\r\n getVerticesNumber() {\r\n return this.lastPos / FBX_POS_SIZE;\r\n }\r\n\r\n addInstance(matrix, geo) {\r\n // add indices at first to take old number of vertices for shift\r\n const currentCount = this.getVerticesNumber();\r\n this.setShiftedIndices(geo.indices, geo.indices.length, currentCount);\r\n // simply write vertices at empty space\r\n const size = geo.itemSize;\r\n this.setTransformedPositions(geo.positions, 0, geo.vertsCount, size.position, matrix);\r\n this.setTransformedNormals(geo.normals, 0, geo.vertsCount, size.normal, matrix);\r\n this.setColors(geo.colors, 0, geo.vertsCount, size.color);\r\n }\r\n}\r\n","/** Base class for fbx geometry contains simply organized attributes: positions+normals+colors, indices. */\r\nexport default class FBXGeometry {\r\n /**\r\n * Create a base geo with necessary members.\r\n */\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.vertsCount = 0;\r\n this.itemSize = null;\r\n }\r\n\r\n /**\r\n * Initialize base geo storing items info from attributes.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n const { attributes } = geo;\r\n // save item size\r\n this.itemSize = {\r\n position: attributes.position.itemSize,\r\n normal: attributes.normal.itemSize,\r\n color: attributes.color.itemSize,\r\n };\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes and creates colors filled with defined value.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX1CGeometry extends FBXGeometry {\r\n /**\r\n * Initialize geo storing positions, normals, indices and create colors.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n super.init(geo, _info);\r\n const {\r\n attributes: {\r\n position,\r\n normal,\r\n },\r\n index,\r\n } = geo;\r\n // copy vertices attributes\r\n this.vertsCount = position.count;\r\n this.positions = position.array;\r\n this.normals = normal.array;\r\n // create color array\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n // indices\r\n this.indices = index.array;\r\n }\r\n\r\n /**\r\n * Set defined color for all items in color attribute\r\n * @param {Object} color - THREE.Color.\r\n */\r\n setColors(color) {\r\n let offset = 0;\r\n for (let i = 0, l = this.colors.length, cl = this.itemSize.color; i < l; i += cl) {\r\n this.colors[offset++] = color.r;\r\n this.colors[offset++] = color.g;\r\n this.colors[offset++] = color.b;\r\n }\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes from cylinder geometry and creates colors filled with two\r\n * defined values.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX2CCylinder extends FBXGeometry {\r\n constructor() {\r\n super();\r\n this._cutRawStart = 0;\r\n this._cutRawEnd = 0;\r\n this._facesPerSlice = 0;\r\n }\r\n\r\n /**\r\n * Initialize geo by creating new attributes, because we extend number of vertices to make cylinder two-colored.\r\n * Indices remain the same. We process open- end close-ended cylinders and consider cylinders od 2 segments\r\n * in height ONLY.\r\n * NOTE: cylinder consists of 2 height segments and stores parts in the order: tube, topCap, bottomCap\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n * @param {Object} info - information needed for geo extend\r\n */\r\n init(geo, info) {\r\n super.init(geo, info);\r\n const {\r\n attributes: {\r\n position,\r\n },\r\n index,\r\n } = geo;\r\n // extend vertices arrays\r\n this.vertsCount = position.count + info.addPerCylinder;\r\n this._facesPerSlice = info.addPerCylinder;\r\n this.positions = new Float32Array(this.vertsCount * position.itemSize);\r\n this.normals = new Float32Array(this.vertsCount * this.itemSize.normal);\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n this._extendVertices(geo, info);\r\n // number of indices stays the same\r\n this.indices = new Uint32Array(index.count);\r\n this._extendIndices(geo, info);\r\n }\r\n\r\n /** Extend vertex attributes to have one more slice to make sharp middle startColor-endColor line. */\r\n _extendVertices(geo, info) {\r\n const { position } = geo.attributes;\r\n const { normal } = geo.attributes;\r\n const geoParams = geo.getGeoParams();\r\n const cutRaw = 1; // we expect cylinders of 2 segments in height => so half segment = 1\r\n this._cutRawStart = cutRaw * geoParams.radialSegments;\r\n this._cutRawEnd = this._cutRawStart + info.addPerCylinder;\r\n { // write first half of cylinder\r\n let temp = position.array.slice(0, this._cutRawEnd * position.itemSize);\r\n this.positions.set(temp, 0);\r\n temp = normal.array.slice(0, this._cutRawEnd * normal.itemSize);\r\n this.normals.set(temp, 0);\r\n }\r\n { // write second part of cylinder\r\n let temp = position.array.slice(this._cutRawStart * position.itemSize, position.array.length);\r\n this.positions.set(temp, this._cutRawEnd * position.itemSize);\r\n temp = normal.array.slice(this._cutRawStart * normal.itemSize, normal.array.length);\r\n this.normals.set(temp, this._cutRawEnd * normal.itemSize);\r\n }\r\n }\r\n\r\n /** Shift values of second part (+caps) indices by newly added vertices count. Number of faces remains the same. */\r\n _extendIndices(geo, info) {\r\n const { index } = geo;\r\n const indicesPerQuad = 6; // quad = 2 triangles => 6 indices\r\n const startToShift = info.addPerCylinder * indicesPerQuad;\r\n const shift = info.addPerCylinder;\r\n let shifted = index.array.slice(startToShift, index.count);\r\n shifted = shifted.map((x) => x + shift); // shift only the endings\r\n this.indices.set(index.array, 0);\r\n this.indices.set(shifted, startToShift);\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {number} start - start color index\r\n * @param {number} end - start color index\r\n * @param {array} array - array of colors\r\n * @param {array} color - color value components\r\n */\r\n _setColorRange(start, end, array, color) {\r\n const colorSize = color.length;\r\n for (let i = start; i < end; i += colorSize) {\r\n array.set(color, i);\r\n }\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {Object} color1 - THREE.Color.\r\n * @param {Object} color2 - THREE.Color.\r\n */\r\n setColors(color1, color2) {\r\n const colorSize = this.itemSize.color;\r\n const part1End = this._cutRawEnd * colorSize;\r\n const part2End = part1End * 2;\r\n this._setColorRange(0, part1End, this.colors, color1.toArray());\r\n this._setColorRange(part1End, part2End, this.colors, color2.toArray());\r\n if (part2End < this.colors.length) { // cylinder has caps, lets paint them\r\n const capSize = (this._facesPerSlice + 1) * colorSize;\r\n const cap1End = part2End + capSize;\r\n this._setColorRange(part2End, cap1End, this.colors, color2.toArray());\r\n const cap2End = cap1End + capSize; // should be equal to this.colors.length;\r\n this._setColorRange(cap1End, cap2End, this.colors, color1.toArray());\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\n\r\nimport utils from '../../../utils';\r\nimport gfxutils from '../../../gfx/gfxutils';\r\nimport logger from '../../../utils/logger';\r\n\r\nimport FBXModel from './FBXModel';\r\nimport ThickLineMesh from '../../../gfx/meshes/ThickLineMesh';\r\nimport ZSpriteMesh from '../../../gfx/meshes/ZSpriteMesh';\r\nimport InstancedSpheresGeometry from '../../../gfx/geometries/InstancedSpheresGeometry';\r\nimport Instanced2CCylindersGeometry from '../../../gfx/geometries/Instanced2CCylindersGeometry';\r\nimport FBX1CGeometry from './FBX1CGeometry';\r\nimport FBX2CCylinder from './FBX2CCylinder';\r\n\r\nexport default class FBXInfoExtractor {\r\n constructor() {\r\n this._materials = [];\r\n this._models = [];\r\n }\r\n\r\n process(data) {\r\n this._extractModelsAndMaterials(data);\r\n const models = this._flattenModels();\r\n\r\n return {\r\n name: data.name,\r\n models,\r\n materials: this._materials,\r\n };\r\n }\r\n\r\n /**\r\n * Extract fbx object information from ComplexVisual\r\n * @param {object} data - complexVisual to get geometry info from\r\n */\r\n _extractModelsAndMaterials(data) {\r\n const layersOfInterest = new THREE.Layers();\r\n layersOfInterest.set(gfxutils.LAYERS.DEFAULT);\r\n layersOfInterest.enable(gfxutils.LAYERS.TRANSPARENT);\r\n data.traverse((object) => {\r\n if (object instanceof THREE.Mesh && object.layers.test(layersOfInterest) && this.checkExportAbility(object)) {\r\n if (object.geometry.type === 'InstancedBufferGeometry') {\r\n this._collectInstancedGeoInfo(object);\r\n } else {\r\n this._collectGeoInfo(object);\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Reworking indices buffer, see https://banexdevblog.wordpress.com/2014/06/23/a-quick-tutorial-about-the-fbx-ascii-format/\r\n * basically, every triangle in Miew has been represented hat way (e.g.) : 0,1,7, but we must (for FBX) rework that\r\n * into: 0,1,-8.\r\n * @param {array} indices - belongs to [0, maxVertIndex]\r\n */\r\n _reworkIndices(indices) {\r\n const faceSize = 3;\r\n for (let i = faceSize - 1; i < indices.length; i += faceSize) {\r\n indices[i] *= -1;\r\n indices[i]--;\r\n }\r\n }\r\n\r\n /**\r\n * Combine geometry from several models having the same material into one Model and finally prepare indices\r\n * @returns {array} models, combined by material id\r\n */\r\n _flattenModels() {\r\n let overallVertsCount = 0;\r\n function shift(x) {\r\n return x + overallVertsCount;\r\n }\r\n const combined = [];\r\n // flatten models geometry\r\n for (let i = 0, n = this._models.length; i < n; i++) {\r\n const models = this._models[i];\r\n let indices = [];\r\n let positions = [];\r\n let normals = [];\r\n let colors = [];\r\n // reorganize every attributes as array of arrays\r\n overallVertsCount = 0;\r\n for (let j = 0; j < models.length; j++) {\r\n const m = models[j];\r\n indices.push(m.indices.map(shift));\r\n overallVertsCount += m.getVerticesNumber();\r\n positions.push(m.positions);\r\n normals.push(m.normals);\r\n colors.push(m.colors);\r\n }\r\n // join all subarrays into one\r\n indices = utils.mergeTypedArraysUnsafe(indices);\r\n this._reworkIndices(indices);\r\n positions = utils.mergeTypedArraysUnsafe(positions);\r\n normals = utils.mergeTypedArraysUnsafe(normals);\r\n colors = utils.mergeTypedArraysUnsafe(colors);\r\n combined.push({\r\n indices,\r\n positions,\r\n normals,\r\n colors,\r\n verticesCount: overallVertsCount,\r\n });\r\n }\r\n return combined;\r\n }\r\n\r\n /**\r\n * Check ability to export the kind of mesh.\r\n * @param {object} mesh - given mesh to check\r\n * @returns {boolean} result of check\r\n */\r\n checkExportAbility(mesh) {\r\n // check mesh on not being empty\r\n if (mesh.geometry.attributes.position.count === 0) {\r\n return false;\r\n }\r\n // check type of mesh\r\n // if (mesh.geometry.isInstancedBufferGeometry && settings.now.zSprites) {\r\n if (mesh instanceof ZSpriteMesh) {\r\n logger.warn('Currently we cannot export \\'sprites\\' modes, like BS, WV, LC. Please turn of settings \\'zSprites\\' and try again');\r\n return false;\r\n }\r\n if (mesh instanceof ThickLineMesh) {\r\n logger.warn('Currently we cannot export Lines mode');\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n /**\r\n * Save geometry info from common mesh, like Surface or Cartoon\r\n */\r\n _collectGeoInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n normal,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const vertCount = position.count;\r\n model.init(vertCount, index.count);\r\n if (matrix.isIdentity()) {\r\n model.setPositions(position.array, 0, vertCount, position.itemSize);\r\n model.setNormals(normal.array, 0, vertCount, normal.itemSize);\r\n } else {\r\n model.setTransformedPositions(position.array, 0, vertCount, position.itemSize, matrix);\r\n model.setTransformedNormals(normal.array, 0, vertCount, normal.itemSize, matrix);\r\n }\r\n model.setColors(color.array, 0, vertCount, color.itemSize);\r\n model.setIndices(index.array, 0, index.count);\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Collect instanced spheres geometry and materials.\r\n * @param {object} mesh - mesh with instanced spheres info\r\n */\r\n _collectSpheresInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount, instCount * indsCount);\r\n const geo = new FBX1CGeometry();\r\n geo.init(mesh.geometry);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const sphereColor = new THREE.Color();\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n sphereColor.fromArray(color.array, colorIdx);\r\n geo.setColors(sphereColor);\r\n // add instance to the model\r\n this._getSphereInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Getting all instanced cylinders from given mesh.\r\n * Divide cylinder (add additional vertexes) for prettiness therefore algorithm is a bit complicated\r\n * @param {object} mesh - given mesh with instanced cylinders\r\n */\r\n _collectCylindersInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n color2,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const oneCCylinder = new FBX1CGeometry();\r\n oneCCylinder.init(mesh.geometry);\r\n const splittingInfo = this._gatherCylindersColoringInfo(mesh.geometry);\r\n let twoCCylinder = null;\r\n if (splittingInfo.needToSplit > 0) {\r\n twoCCylinder = new FBX2CCylinder();\r\n twoCCylinder.init(mesh.geometry, splittingInfo);\r\n }\r\n const additionalVertsCount = splittingInfo.addPerCylinder * splittingInfo.needToSplit;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount + additionalVertsCount, instCount * indsCount);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const colorStart = new THREE.Color();\r\n const colorEnd = new THREE.Color();\r\n let geo = {};\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n if (splittingInfo.is2Colored[instanceIndex]) {\r\n // .color2 contains starting color, and .color contains starting color (see uber.frag ATTR_COLOR2)\r\n colorStart.fromArray(color2.array, colorIdx);\r\n colorEnd.fromArray(color.array, colorIdx);\r\n if (twoCCylinder) {\r\n twoCCylinder.setColors(colorStart, colorEnd);\r\n geo = twoCCylinder;\r\n }\r\n } else {\r\n // has one color per cylinder\r\n colorStart.fromArray(color.array, colorIdx);\r\n oneCCylinder.setColors(colorStart);\r\n geo = oneCCylinder;\r\n }\r\n // add instance to the model\r\n this._getCylinderInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Adding model to pool of models or extend existing ones\r\n * @param {object} model - model to add\r\n * @param {object} material - material to add\r\n */\r\n _addToPool(model, material) {\r\n const materialIdx = this._checkExistingMaterial(material);\r\n if (materialIdx < 0) { // new model-material pair\r\n this._models.push([model]);\r\n this._materials.push(material);\r\n } else { // add model to existing model-material pair\r\n const models = this._models[materialIdx];\r\n models.push(model);\r\n }\r\n }\r\n\r\n /**\r\n * Checking if given material already was registered in materials pool (no need to create new one)\r\n * @param {object} material - given material\r\n * @returns {number} number of model-material pair\r\n */\r\n _checkExistingMaterial(material) {\r\n return _.findIndex(this._materials, (m) => _.isEqual(m, material));\r\n }\r\n\r\n _gatherCylindersColoringInfo(geo) {\r\n const instCount = geo.instanceCount;\r\n const color1 = geo.attributes.color.array;\r\n const color2 = geo.attributes.color2.array;\r\n const stride = geo.attributes.color.itemSize;\r\n const is2Colored = new Array(instCount);\r\n // analyze color instance attributes\r\n let needToSplit = 0;\r\n let colIdx = 0;\r\n for (let i = 0; i < instCount; i++, colIdx += stride) {\r\n const differs = (Math.abs(color1[colIdx] - color2[colIdx]) > 0.0000001) // compare ending colors\r\n || (Math.abs(color1[colIdx + 1] - color2[colIdx + 1]) > 0.0000001)\r\n || (Math.abs(color1[colIdx + 2] - color2[colIdx + 2]) > 0.0000001);\r\n is2Colored[i] = differs;\r\n needToSplit += differs; // count number of 2-colored cylinders\r\n }\r\n // calc number of vertices to add into 2-colored\r\n const geoParams = geo.getGeoParams();\r\n const addPerCylinder = geoParams.radialSegments;\r\n return { is2Colored, needToSplit, addPerCylinder };\r\n }\r\n\r\n /**\r\n * Collect instanced models and materials.\r\n * @param {object} mesh - given mesh with instanced something (spheres or cylinders)\r\n */\r\n _collectInstancedGeoInfo(mesh) {\r\n if (mesh.geometry instanceof InstancedSpheresGeometry) {\r\n this._collectSpheresInfo(mesh);\r\n } else if (mesh.geometry instanceof Instanced2CCylindersGeometry) {\r\n this._collectCylindersInfo(mesh);\r\n }\r\n }\r\n\r\n /**\r\n * Collect Material info from given mesh.\r\n * @param {object} mesh - given mesh with material info\r\n * @returns {object} material\r\n */\r\n _collectMaterialInfo(mesh) {\r\n const { uberOptions } = mesh.material;\r\n return ({\r\n diffuse: uberOptions.diffuse.toArray(),\r\n opacity: uberOptions.opacity,\r\n shininess: uberOptions.shininess,\r\n specular: uberOptions.specular.toArray(),\r\n });\r\n }\r\n\r\n _getCylinderInstanceMatrix(geo, instIdx, matrix) {\r\n const matVector1 = geo.attributes.matVector1.array;\r\n const matVector2 = geo.attributes.matVector2.array;\r\n const matVector3 = geo.attributes.matVector3.array;\r\n const idxOffset = instIdx * 4; // used 4 because offset arrays are stored in quads\r\n matrix.set(\r\n matVector1[idxOffset],\r\n matVector1[idxOffset + 1],\r\n matVector1[idxOffset + 2],\r\n matVector1[idxOffset + 3],\r\n matVector2[idxOffset],\r\n matVector2[idxOffset + 1],\r\n matVector2[idxOffset + 2],\r\n matVector2[idxOffset + 3],\r\n matVector3[idxOffset],\r\n matVector3[idxOffset + 1],\r\n matVector3[idxOffset + 2],\r\n matVector3[idxOffset + 3],\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n\r\n _getSphereInstanceMatrix(geo, instIdx, matrix) {\r\n const { offset } = geo.attributes;\r\n const idx = instIdx * offset.itemSize;\r\n const x = offset.array[idx];\r\n const y = offset.array[idx + 1];\r\n const z = offset.array[idx + 2];\r\n const scale = offset.array[idx + 3];\r\n matrix.set(\r\n scale,\r\n 0,\r\n 0,\r\n x,\r\n 0,\r\n scale,\r\n 0,\r\n y,\r\n 0,\r\n 0,\r\n scale,\r\n z,\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n}\r\n","// Forming default definitions block\r\nconst defaultDefinitions = `\r\nDefinitions: {\r\n Version: 100\r\n Count: 3\r\n ObjectType: \"Model\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Geometry\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Material\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Pose\" {\r\n Count: 1\r\n }\r\n ObjectType: \"GlobalSettings\" {\r\n Count: 1\r\n }\r\n} `;\r\n\r\n// Default model properties\r\nconst defaultProperties = `Properties60: {\r\n Property: \"QuaternionInterpolate\", \"bool\", \"\",0\r\n Property: \"Visibility\", \"Visibility\", \"A\",1\r\n Property: \"Lcl Translation\", \"Lcl Translation\", \"A\",0.000000000000000,0.000000000000000,-1789.238037109375000\r\n Property: \"Lcl Rotation\", \"Lcl Rotation\", \"A\",0.000009334667643,-0.000000000000000,0.000000000000000\r\n Property: \"Lcl Scaling\", \"Lcl Scaling\", \"A\",1.000000000000000,1.000000000000000,1.000000000000000\r\n Property: \"RotationOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationActive\", \"bool\", \"\",0\r\n Property: \"TranslationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMinX\", \"bool\", \"\",0\r\n Property: \"TranslationMinY\", \"bool\", \"\",0\r\n Property: \"TranslationMinZ\", \"bool\", \"\",0\r\n Property: \"TranslationMaxX\", \"bool\", \"\",0\r\n Property: \"TranslationMaxY\", \"bool\", \"\",0\r\n Property: \"TranslationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationOrder\", \"enum\", \"\",0\r\n Property: \"RotationSpaceForLimitOnly\", \"bool\", \"\",0\r\n Property: \"AxisLen\", \"double\", \"\",10\r\n Property: \"PreRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"PostRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationActive\", \"bool\", \"\",0\r\n Property: \"RotationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMinX\", \"bool\", \"\",0\r\n Property: \"RotationMinY\", \"bool\", \"\",0\r\n Property: \"RotationMinZ\", \"bool\", \"\",0\r\n Property: \"RotationMaxX\", \"bool\", \"\",0\r\n Property: \"RotationMaxY\", \"bool\", \"\",0\r\n Property: \"RotationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationStiffnessX\", \"double\", \"\",0\r\n Property: \"RotationStiffnessY\", \"double\", \"\",0\r\n Property: \"RotationStiffnessZ\", \"double\", \"\",0\r\n Property: \"MinDampRangeX\", \"double\", \"\",0\r\n Property: \"MinDampRangeY\", \"double\", \"\",0\r\n Property: \"MinDampRangeZ\", \"double\", \"\",0\r\n Property: \"MaxDampRangeX\", \"double\", \"\",0\r\n Property: \"MaxDampRangeY\", \"double\", \"\",0\r\n Property: \"MaxDampRangeZ\", \"double\", \"\",0\r\n Property: \"MinDampStrengthX\", \"double\", \"\",0\r\n Property: \"MinDampStrengthY\", \"double\", \"\",0\r\n Property: \"MinDampStrengthZ\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthX\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthY\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthZ\", \"double\", \"\",0\r\n Property: \"PreferedAngleX\", \"double\", \"\",0\r\n Property: \"PreferedAngleY\", \"double\", \"\",0\r\n Property: \"PreferedAngleZ\", \"double\", \"\",0\r\n Property: \"InheritType\", \"enum\", \"\",0\r\n Property: \"ScalingActive\", \"bool\", \"\",0\r\n Property: \"ScalingMin\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMax\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMinX\", \"bool\", \"\",0\r\n Property: \"ScalingMinY\", \"bool\", \"\",0\r\n Property: \"ScalingMinZ\", \"bool\", \"\",0\r\n Property: \"ScalingMaxX\", \"bool\", \"\",0\r\n Property: \"ScalingMaxY\", \"bool\", \"\",0\r\n Property: \"ScalingMaxZ\", \"bool\", \"\",0\r\n Property: \"GeometricTranslation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricScaling\", \"Vector3D\", \"\",1,1,1\r\n Property: \"LookAtProperty\", \"object\", \"\"\r\n Property: \"UpVectorProperty\", \"object\", \"\"\r\n Property: \"Show\", \"bool\", \"\",1\r\n Property: \"NegativePercentShapeSupport\", \"bool\", \"\",1\r\n Property: \"DefaultAttributeIndex\", \"int\", \"\",0\r\n Property: \"Color\", \"Color\", \"A+\",0,0,0\r\n Property: \"Size\", \"double\", \"\",100\r\n Property: \"Look\", \"enum\", \"\",1\r\n }`;\r\n\r\n// Default materials layer\r\nconst defaultMaterialLayer = `\r\n LayerElementMaterial: 0 {\r\n Version: 101\r\n Name: \"\"\r\n MappingInformationType: \"AllSame\"\r\n ReferenceInformationType: \"Direct\"\r\n Materials: 0\r\n }`;\r\n\r\n// Default layers block\r\nconst defaultLayerBlock = `\r\n Layer: 0 {\r\n Version: 100\r\n LayerElement: {\r\n Type: \"LayerElementNormal\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementColor\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementMaterial\"\r\n TypedIndex: 0\r\n }\r\n }`;\r\n\r\n/**\r\n * globalSettings info in output file.\r\n */\r\nconst globalSettings = `GlobalSettings: {\r\n Version: 1000\r\n Properties60: {\r\n Property: \"UpAxis\", \"int\", \"\",1\r\n Property: \"UpAxisSign\", \"int\", \"\",1\r\n Property: \"FrontAxis\", \"int\", \"\",2\r\n Property: \"FrontAxisSign\", \"int\", \"\",1\r\n Property: \"CoordAxis\", \"int\", \"\",0\r\n Property: \"CoordAxisSign\", \"int\", \"\",1\r\n Property: \"UnitScaleFactor\", \"double\", \"\",1\r\n }\r\n }`;\r\n\r\nexport default class FBXResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._info = null;\r\n }\r\n\r\n getResult(info) {\r\n this._info = info;\r\n this._resultArray.push(this._writeHeader());\r\n this._resultArray.push(this._writeDefinitions());\r\n this._resultArray.push(this._writeObjects(info.models, info.materials));\r\n this._resultArray.push(this._writeRelations());\r\n this._resultArray.push(this._writeConnections()); // connections between models and materials)\r\n this._info = null;\r\n return this._resultArray.join('');\r\n }\r\n\r\n /**\r\n * Add FBXHeader info to output file.\r\n * Some fields are really confusing, but it seems that all listed fields are very informative\r\n */\r\n _writeHeader() {\r\n const FBXHeaderVersion = 1003; // 1003 is some number which appears to present in many 6.1 ASCII files\r\n const FBXVersion = 6100; // Mandatory and only supported version\r\n const date = new Date();\r\n const timeStampVersion = 1000;\r\n const creator = `Miew FBX Exporter v${this._info.version}`; // Supposed to be an engine\r\n\r\n return `; FBX 6.1.0 project file\r\n; Created by ${creator} Copyright (c) 2015-2024 EPAM Systems, Inc.\r\n; For support please contact miew@epam.com\r\n; ----------------------------------------------------\r\n\r\nFBXHeaderExtension: {\r\n FBXHeaderVersion: ${FBXHeaderVersion}\r\n FBXVersion: ${FBXVersion}\r\n CreationTimeStamp: {\r\n Version: ${timeStampVersion}\r\n Year: ${date.getFullYear()}\r\n Month: ${date.getMonth() + 1}\r\n Day: ${date.getDate()}\r\n Hour: ${date.getHours()}\r\n Minute: ${date.getMinutes()}\r\n Second: ${date.getSeconds()}\r\n Millisecond: ${date.getMilliseconds()}\r\n }\r\n Creator: \"${creator}\"\r\n OtherFlags: {\r\n FlagPLE: 0\r\n }\r\n}\r\nCreationTime: \"${date}\"\r\nCreator: \"${creator}\"\r\n`;\r\n }\r\n\r\n /**\r\n * Add Definitions info to output file.\r\n * Not exactly sure if this section is template section (as it is in 7.4+) or it should every time be like this\r\n */\r\n _writeDefinitions() {\r\n return `\r\n; Object definitions\r\n;------------------------------------------------------------------\r\n\r\n${defaultDefinitions}\r\n`;\r\n }\r\n\r\n /**\r\n * Adding gathered information about Models to resulting string.\r\n * Reminder - there may be more then 1 model in scene, but we must place materials after ALL models.\r\n * @returns {string} string containing all models (vertices, indices, colors, normals etc)\r\n */\r\n _models() {\r\n const modelVersion = 232;\r\n let allModels = '';\r\n const { models } = this._info;\r\n for (let i = 0; i < models.length; ++i) {\r\n const model = models[i];\r\n const vertCount = model.verticesCount;\r\n allModels += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n Version: ${modelVersion}\r\n ${defaultProperties}\r\n ${this._verticesIndices(model.positions, model.indices)}\r\n ${this._normalLayer(model.normals)}\r\n ${this._colorLayer(model.colors, vertCount)}\r\n ${defaultMaterialLayer}\r\n ${defaultLayerBlock}\r\n }`;\r\n }\r\n return allModels;\r\n }\r\n\r\n /**\r\n * Add Material info to result\r\n */\r\n _materials() {\r\n const materialVersion = 102;\r\n let allMaterials = '';\r\n const { materials } = this._info;\r\n for (let i = 0; i < materials.length; ++i) {\r\n const material = materials[i];\r\n allMaterials += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n Version: ${materialVersion}\r\n ShadingModel: \"lambert\"\r\n MultiLayer: 0\r\n ${this._materialProperties(material)}\r\n }`;\r\n }\r\n return allMaterials;\r\n }\r\n\r\n /**\r\n * Add Objects info to output file.\r\n */\r\n _writeObjects() {\r\n return `\r\n; Object properties\r\n;------------------------------------------------------------------\r\n\r\nObjects: {\r\n ${this._models()}\r\n ${this._materials()}\r\n ${globalSettings}\r\n}\r\n`;\r\n }\r\n\r\n /**\r\n * Add Relations info to output file.\r\n */\r\n _writeRelations() {\r\n let modelsList = '';\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n }`;\r\n }\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n }`;\r\n }\r\n\r\n return `\r\n; Object relations\r\n;------------------------------------------------------------------\r\n\r\nRelations: {\r\n ${modelsList}\r\n Model: \"Model::Producer Perspective\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Top\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Bottom\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Front\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Back\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Right\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Left\", \"Camera\" {\r\n }\r\n Model: \"Model::Camera Switcher\", \"CameraSwitcher\" {\r\n }\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Add Connections info to output file.\r\n */\r\n _writeConnections() {\r\n let modelsList = '';\r\n const { name } = this._info;\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Connect: \"OO\", \"Model::${name}_${i}\", \"Model::Scene\"`;\r\n }\r\n\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Connect: \"OO\", \"Material::${name}_${i}_default\", \"Model::${name}_${i}\"`;\r\n }\r\n\r\n return `\r\n; Object connections\r\n;------------------------------------------------------------------\r\n\r\nConnections: {\r\n ${modelsList}\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Write float array to string with limited precision\r\n * @param {Float32Array} array - array to be fixed\r\n * @returns {String} String with fixed floats\r\n */\r\n _floatArrayToString(array) {\r\n const str = [];\r\n for (let i = 0; i < array.length; ++i) {\r\n str[i] = array[i].toFixed(6);\r\n }\r\n return str.join(',');\r\n }\r\n\r\n /**\r\n * Adding color layer to resulting file\r\n * @param {Float32Array} colorArray attribute\r\n * @param {number} vertCount - number of vertices in the model\r\n * @returns {string} color layer info\r\n */\r\n _colorLayer(colorArray, vertCount) {\r\n const layerElementColorNumber = 0;\r\n const layerElementColorVersion = 101;\r\n const layerElementColorName = '';\r\n const colorsStr = this._floatArrayToString(colorArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n // As said [..Array(...)] - fastest and easiest way to produce [0, 1, .....] array\r\n const colorIndices = [...Array(vertCount).keys()];\r\n return `\r\n LayerElementColor: ${layerElementColorNumber} {\r\n Version: ${layerElementColorVersion}\r\n Name: \"${layerElementColorName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Colors: ${colorsStr}\r\n ColorIndex: ${colorIndices}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding normal layer to resulting file\r\n * @param {Float32Array} normalArray attribute\r\n * @returns {string} normal layer info\r\n */\r\n _normalLayer(normalArray) {\r\n const layerElementNormalNumber = 0;\r\n const layerElementNormalVersion = 101;\r\n const layerElementNormalName = '';\r\n const normalsStr = this._floatArrayToString(normalArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n return `\r\n LayerElementNormal: ${layerElementNormalNumber} {\r\n Version: ${layerElementNormalVersion}\r\n Name: \"${layerElementNormalName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Normals: ${normalsStr}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding vertices and indices to resulting string\r\n * @return {string} resulting string in FBX notation\r\n */\r\n _verticesIndices(positions, indices) {\r\n const multiLayer = 0;\r\n const multiTake = 1;\r\n const shading = 'Y';\r\n const culling = 'CullingOff';\r\n const geometryVersion = 124;\r\n const vertStr = this._floatArrayToString(positions);\r\n /* About _correctArrayNotation: Float32Arrays will contains only Float32 numbers, which implies that it will be floating points with 17 numbers after point.\r\n * We cannot (and it's logically incorrect) save all this information, so we convert this Float32Array into Array-like object with numbers with only 6 numbers after point\r\n * Reminder - this is big memory loss (as we must save at one moment two arrays with similar information) */\r\n return `MultiLayer: ${multiLayer}\r\n MultiTake: ${multiTake}\r\n Shading: ${shading}\r\n Culling: \"${culling}\"\r\n Vertices: ${vertStr}\r\n PolygonVertexIndex: ${indices}\r\n GeometryVersion: ${geometryVersion}`;\r\n }\r\n\r\n /**\r\n * Forming material properties block.\r\n * @param {Object} material - given material of model\r\n * @returns {String} material properties string\r\n */\r\n _materialProperties(material) {\r\n return `Properties60: {\r\n Property: \"ShadingModel\", \"KString\", \"\", \"Lambert\"\r\n Property: \"MultiLayer\", \"bool\", \"\",0\r\n Property: \"EmissiveColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"EmissiveFactor\", \"double\", \"\",0.0000\r\n Property: \"AmbientColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"AmbientFactor\", \"double\", \"\",0.0000\r\n Property: \"DiffuseColor\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"DiffuseFactor\", \"double\", \"\",1.0000\r\n Property: \"Bump\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TransparentColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"TransparencyFactor\", \"double\", \"\",0.0000\r\n Property: \"SpecularColor\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"SpecularFactor\", \"double\", \"\",1.0000\r\n Property: \"ShininessExponent\", \"double\", \"\",${material.shininess}\r\n Property: \"ReflectionColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"ReflectionFactor\", \"double\", \"\",1\r\n Property: \"Ambient\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"Diffuse\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"Specular\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"Shininess\", \"double\", \"\",${material.shininess}\r\n Property: \"Opacity\", \"double\", \"\",${material.opacity}\r\n Property: \"Reflectivity\", \"double\", \"\",0\r\n }`;\r\n }\r\n}\r\n","import Exporter from './Exporter';\r\nimport FBXInfoExtractor from './fbx/FBXInfoExtractor';\r\nimport FBXResult from './fbx/FBXResult';\r\nimport ComplexVisual from '../../ComplexVisual';\r\n\r\nexport default class FBXExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n // Data\r\n this._data = source;\r\n this._version = options.miewVersion || '0.0-UNSPECIFIED';\r\n this._extractor = new FBXInfoExtractor();\r\n }\r\n\r\n /**\r\n * Entry point to exporter.\r\n */\r\n exportSync() {\r\n // Creating mandatory blocks\r\n const result = new FBXResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n const info = this._extractor.process(this._data);\r\n info.version = this._version;\r\n this._result = result.getResult(info);\r\n return this._result;\r\n }\r\n}\r\n\r\nFBXExporter.formats = ['fbx'];\r\nFBXExporter.SourceClass = ComplexVisual;\r\n","import ExporterList from './exporters/ExporterList';\r\n\r\nimport PDBExporter from './exporters/PDBExporter';\r\nimport FBXExporter from './exporters/FBXExporter';\r\n\r\nexport default new ExporterList([\r\n PDBExporter,\r\n FBXExporter,\r\n]);\r\n","import loaders from './loaders';\r\nimport parsers from './parsers';\r\nimport exporters from './exporters';\r\n\r\nexport default {\r\n loaders,\r\n parsers,\r\n exporters,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from './CSS2DObject';\r\n\r\nconst tempColor = new THREE.Color();\r\n\r\nclass CSS2DRenderer {\r\n constructor() {\r\n this._width = 0;\r\n this._height = 0;\r\n this._widthHalf = 0;\r\n this._heightHalf = 0;\r\n\r\n this._vector = new THREE.Vector3();\r\n this._viewMatrix = new THREE.Matrix4();\r\n this._projectionMatrix = new THREE.Matrix4();\r\n\r\n this._domElement = document.createElement('div');\r\n this._domElement.style.overflow = 'hidden';\r\n this._domElement.style.position = 'absolute';\r\n this._domElement.style.top = '0';\r\n this._domElement.style.zIndex = '0'; // start a new Stacking Context to enclose all z-ordered children\r\n this._domElement.style.pointerEvents = 'none';\r\n }\r\n\r\n getElement() {\r\n return this._domElement;\r\n }\r\n\r\n reset() {\r\n const myNode = this.getElement();\r\n while (myNode.firstChild) {\r\n myNode.removeChild(myNode.firstChild);\r\n }\r\n }\r\n\r\n setSize(width, height) {\r\n this._width = width;\r\n this._height = height;\r\n\r\n this._widthHalf = this._width / 2;\r\n this._heightHalf = this._height / 2;\r\n\r\n this._domElement.style.width = `${width}px`;\r\n this._domElement.style.height = `${height}px`;\r\n }\r\n\r\n _renderObject(object, camera, scene) {\r\n function lerpColorAsHex(a, b, t) {\r\n tempColor.setHex(a);\r\n tempColor.lerp(b, t);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n function colorAsHex(a) {\r\n tempColor.setHex(a);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n if (object instanceof CSS2DObject) {\r\n this._vector.setFromMatrixPosition(object.matrixWorld);\r\n\r\n if (object.userData !== undefined && object.userData.offset !== undefined) {\r\n const localOffset = new THREE.Vector3(object.userData.offset.x, object.userData.offset.y, 0);\r\n this._vector.add(localOffset.multiplyScalar(object.matrixWorld.getMaxScaleOnAxis()));\r\n }\r\n\r\n this._vector.applyMatrix4(this._viewMatrix);\r\n\r\n const visibility = this._vector.z > -camera.near ? 'hidden' : 'visible';\r\n const zIndex = 10000 * (camera.far - (-this._vector.z)) / (camera.far - camera.near);\r\n\r\n const element = object.getElement();\r\n if (typeof scene.fog === 'undefined') {\r\n element.style.color = colorAsHex(object.userData.color);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = colorAsHex(object.userData.background);\r\n }\r\n } else {\r\n const fogFactor = THREE.MathUtils.smoothstep(-this._vector.z, scene.fog.near, scene.fog.far);\r\n element.style.color = lerpColorAsHex(object.userData.color, scene.fog.color, fogFactor);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = lerpColorAsHex(object.userData.background, scene.fog.color, fogFactor);\r\n }\r\n }\r\n\r\n this._vector.applyMatrix4(this._projectionMatrix);\r\n\r\n const style = `${object.userData !== {} ? object.userData.translation : 'translate(-50%, -50%) '\r\n }translate(${this._vector.x * this._widthHalf + this._widthHalf}px,${\r\n -this._vector.y * this._heightHalf + this._heightHalf}px)`;\r\n element.style.visibility = visibility;\r\n element.style.WebkitTransform = style;\r\n element.style.MozTransform = style;\r\n element.style.oTransform = style;\r\n element.style.transform = style;\r\n element.style.zIndex = Number(zIndex).toFixed(0);\r\n\r\n if (element.parentNode !== this._domElement) {\r\n this._domElement.appendChild(element);\r\n }\r\n }\r\n\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n this._renderObject(object.children[i], camera, scene);\r\n }\r\n }\r\n\r\n render(scene, camera) {\r\n scene.updateMatrixWorld();\r\n\r\n if (camera.parent === null) {\r\n camera.updateMatrixWorld();\r\n }\r\n\r\n camera.matrixWorldInverse.copy(camera.matrixWorld).invert();\r\n\r\n this._viewMatrix.copy(camera.matrixWorldInverse);\r\n this._projectionMatrix.copy(camera.projectionMatrix);\r\n\r\n this._renderObject(scene, camera, scene);\r\n }\r\n}\r\nexport default CSS2DRenderer;\r\n","export default function getTopWindow() {\r\n // intercept the exception if we have cross-origin iframe\r\n try {\r\n if (window.top.location.href !== undefined) {\r\n return window.top;\r\n }\r\n } catch (e) {\r\n // provide fallback\r\n }\r\n return window;\r\n}\r\n","import * as THREE from 'three';\r\nimport Timer from '../Timer';\r\nimport settings from '../settings';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\nimport getTopWindow from '../utils/getTopWindow';\r\n\r\nconst VK_LEFT = 37;\r\nconst VK_UP = 38;\r\nconst VK_RIGHT = 39;\r\nconst VK_DOWN = 40;\r\n\r\nconst STATE = {\r\n NONE: -1, ROTATE: 0, TRANSLATE: 1, SCALE: 2, TRANSLATE_PIVOT: 3,\r\n};\r\n\r\n// pausing for this amount of time before releasing mouse button prevents inertial rotation (seconds)\r\nconst FULL_STOP_THRESHOLD = 0.1;\r\n\r\nconst quaternion = new THREE.Quaternion();\r\nconst matrix4 = new THREE.Matrix4();\r\n\r\n// pivot -- local offset of the rotation pivot point\r\nfunction ObjectHandler(objects, camera, pivot, options) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n this.camera = camera;\r\n this.pivot = pivot;\r\n this.axis = new THREE.Vector3(0, 0, 1);\r\n this.options = options;\r\n\r\n this.lastRotation = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n}\r\n\r\nObjectHandler.prototype._rotate = (function () {\r\n const p = new THREE.Vector3();\r\n const q = new THREE.Quaternion();\r\n const s = new THREE.Vector3();\r\n\r\n const m = new THREE.Matrix4();\r\n\r\n return function (quat) {\r\n const zeroPivot = (this.pivot.x === 0.0 && this.pivot.y === 0.0 && this.pivot.z === 0.0);\r\n\r\n m.copy(this.object.matrix);\r\n\r\n if (zeroPivot) {\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n } else {\r\n m.multiply(matrix4.makeTranslation(this.pivot.x, this.pivot.y, this.pivot.z));\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n m.multiply(matrix4.makeTranslation(-this.pivot.x, -this.pivot.y, -this.pivot.z));\r\n }\r\n\r\n m.decompose(p, q, s);\r\n\r\n // update objects\r\n if (!zeroPivot) {\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].position.copy(p);\r\n }\r\n }\r\n\r\n for (let j = 0; j < this.objects.length; ++j) {\r\n this.objects[j].quaternion.copy(q);\r\n this.objects[j].updateMatrix();\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.setObjects = function (objects) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n};\r\n\r\nObjectHandler.prototype.rotate = (function () {\r\n const rot = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n\r\n return function (quat, mousePrevPos, mouseCurPos, aboutAxis) {\r\n this.mouse2rotation(rot, mousePrevPos, mouseCurPos, aboutAxis);\r\n quat.setFromAxisAngle(rot.axis, rot.angle);\r\n\r\n if (rot.angle) {\r\n this._rotate(quat);\r\n }\r\n\r\n this.lastRotation = rot;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.translate = (function () {\r\n const dir = new THREE.Vector3();\r\n const pivot = new THREE.Vector3();\r\n\r\n return function (delta) {\r\n // reverse-project viewport movement to view coords (compensate for screen aspect ratio)\r\n dir.set(\r\n delta.x / this.camera.projectionMatrix.elements[0],\r\n delta.y / this.camera.projectionMatrix.elements[5],\r\n 0,\r\n );\r\n let dist = dir.length();\r\n dir.normalize();\r\n\r\n // transform movement direction to object local coords\r\n dir.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // visible translate distance shouldn't depend on camera-to-object distance\r\n pivot.copy(this.pivot);\r\n this.object.localToWorld(pivot);\r\n dist *= Math.abs(pivot.z - this.camera.position.z);\r\n\r\n // visible translate distance shouldn't depend on object scale\r\n dist /= this.object.matrixWorld.getMaxScaleOnAxis();\r\n\r\n // all objects are translated similar to principal object\r\n // (we assume they all have identical pivot and scale)\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].translateOnAxis(dir, dist);\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.update = (function () {\r\n const axis = new THREE.Vector3();\r\n\r\n return function (timeSinceLastUpdate, timeSinceMove) {\r\n if (settings.now.autoRotation !== 0.0) {\r\n // auto-rotation with constant speed\r\n\r\n // if rotation axis is fixed or hasn't been defined yet\r\n if (settings.now.autoRotationAxisFixed || this.lastRotation.axis.length() === 0.0) {\r\n // use Y-axis (transformed to local object coords)\r\n axis.set(0, 1, 0).transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n } else {\r\n // use axis defined by last user rotation\r\n axis.copy(this.lastRotation.axis);\r\n }\r\n\r\n this._rotate(quaternion.setFromAxisAngle(axis, settings.now.autoRotation * timeSinceLastUpdate));\r\n return true;\r\n }\r\n\r\n if (this.options.intertia && this.lastRotation.angle) {\r\n // inertial object rotation\r\n const angle = this.lastRotation.angle * ((1.0 - this.options.dynamicDampingFactor) ** (40.0 * timeSinceMove));\r\n\r\n if (Math.abs(angle) <= this.options.intertiaThreshold) {\r\n this.lastRotation.angle = 0.0;\r\n } else {\r\n this._rotate(quaternion.setFromAxisAngle(this.lastRotation.axis, angle));\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.stop = function () {\r\n this.lastRotation.angle = 0.0;\r\n};\r\n\r\n// calculate (axis, angle) pair from mouse/touch movement\r\nObjectHandler.prototype.mouse2rotation = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n const eye = new THREE.Vector3();\r\n const eyeDirection = new THREE.Vector3();\r\n\r\n const cameraUpDirection = new THREE.Vector3();\r\n const cameraSidewaysDirection = new THREE.Vector3();\r\n\r\n const moveDirection = new THREE.Vector3();\r\n\r\n const mouseDelta = new THREE.Vector2();\r\n\r\n return function (rot, mousePrev, mouseCur, aboutAxis) {\r\n if (aboutAxis) {\r\n rot.axis.copy(this.axis);\r\n rot.angle = this.options.axisRotateFactor * (mouseCur.y - mousePrev.y);\r\n\r\n /* cool method that allows rotation around Z axis to be \"tied\" to mouse cursor\r\n\r\n res.axis.copy(this.axis);\r\n\r\n var pivot = this.pivot.clone();\r\n this.object.localToWorld(pivot);\r\n pivot.project(this.camera);\r\n\r\n var v1 = new THREE.Vector3(mousePrev.x, mousePrev.y, this.camera.position.z);\r\n v1.sub(pivot);\r\n var v2 = new THREE.Vector3(mouseCur.x, mouseCur.y, this.camera.position.z);\r\n v2.sub(pivot);\r\n\r\n v1.sub(res.axis.clone().multiplyScalar(v1.dot(res.axis)));\r\n v2.sub(res.axis.clone().multiplyScalar(v2.dot(res.axis)));\r\n\r\n var abs = v1.length() * v2.length();\r\n if (abs > 0) {\r\n res.angle = res.axis.dot(v1.cross(v2)) / abs;\r\n }\r\n */\r\n } else {\r\n mouseDelta.subVectors(mouseCur, mousePrev);\r\n const angle = mouseDelta.length();\r\n if (angle === 0.0) {\r\n return;\r\n }\r\n\r\n center.copy(this.pivot);\r\n this.object.localToWorld(center);\r\n eye.subVectors(this.camera.position, center);\r\n eyeDirection.copy(eye).normalize();\r\n\r\n cameraUpDirection.copy(this.camera.up).normalize();\r\n cameraSidewaysDirection.crossVectors(cameraUpDirection, eyeDirection).normalize();\r\n\r\n cameraUpDirection.setLength(mouseDelta.y);\r\n cameraSidewaysDirection.setLength(mouseDelta.x);\r\n\r\n moveDirection.copy(cameraUpDirection.add(cameraSidewaysDirection));\r\n\r\n rot.axis.crossVectors(moveDirection, eye);\r\n\r\n rot.angle = -angle * this.options.rotateFactor;\r\n }\r\n\r\n rot.axis.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // make sure angle is always positive (thus 'axis' defines both axis and direction of rotation)\r\n if (rot.angle < 0.0) {\r\n rot.axis.negate();\r\n rot.angle = -rot.angle;\r\n }\r\n };\r\n}());\r\n\r\nfunction ObjectControls(object, objectPivot, camera, domElement, getAltObj) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.object = object;\r\n this.objectPivot = objectPivot;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.getAltObj = getAltObj;\r\n\r\n // API\r\n\r\n this.enabled = true;\r\n this.hotkeysEnabled = true;\r\n\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n\r\n this.options = {\r\n rotateFactor: Math.PI, // full screen slide (along short side) would roughly mean 180 deg. rotation\r\n axisRotateFactor: 4 * Math.PI, // full screen slide (along short side) would roughly mean 720 deg. rotation\r\n intertia: true,\r\n dynamicDampingFactor: 0.1,\r\n intertiaThreshold: 1e-3,\r\n };\r\n\r\n // internals\r\n\r\n this._state = STATE.NONE;\r\n\r\n this._mousePrevPos = new THREE.Vector2();\r\n this._mouseCurPos = new THREE.Vector2();\r\n\r\n this._mainObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._altObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._affectedObj = this._mainObj;\r\n this._isAltObjFreeRotationAllowed = true;\r\n this._isTranslationAllowed = true;\r\n this._isKeysTranslatingObj = false;\r\n\r\n this._pressedKeys = [];\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n this._lastUpdateTime = this._clock.getElapsedTime();\r\n\r\n // events\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousewheel',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'DOMMouseScroll',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseout',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchmove',\r\n handler(e) {\r\n self.touchmove(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keydown',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keyup',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'blur',\r\n handler() {\r\n self.resetKeys();\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'contextmenu',\r\n handler(e) {\r\n self.contextmenu(e);\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n\r\n this.resetKeys();\r\n\r\n // force an update at start\r\n this.update();\r\n}\r\n\r\n// methods\r\n\r\nObjectControls.prototype = Object.create(EventDispatcher.prototype);\r\nObjectControls.prototype.constructor = ObjectControls;\r\n\r\nObjectControls.prototype.resetKeys = function () {\r\n this._pressedKeys[VK_LEFT] = false;\r\n this._pressedKeys[VK_UP] = false;\r\n this._pressedKeys[VK_RIGHT] = false;\r\n this._pressedKeys[VK_DOWN] = false;\r\n};\r\n\r\nObjectControls.prototype.contextmenu = function (e) {\r\n e.stopPropagation();\r\n e.preventDefault();\r\n};\r\n\r\nObjectControls.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nObjectControls.prototype.enable = function (enable) {\r\n this.enabled = enable;\r\n};\r\n\r\nObjectControls.prototype.enableHotkeys = function (enable) {\r\n this.hotkeysEnabled = enable;\r\n};\r\n\r\nObjectControls.prototype.allowTranslation = function (allow) {\r\n this._isTranslationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.allowAltObjFreeRotation = function (allow) {\r\n this._isAltObjFreeRotationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.keysTranslateObj = function (on) {\r\n this._isKeysTranslatingObj = on;\r\n};\r\n\r\nObjectControls.prototype.isEditingAltObj = function () {\r\n return ((this._state === STATE.ROTATE) || (this._state === STATE.TRANSLATE))\r\n && (this._affectedObj === this._altObj);\r\n};\r\n\r\n// convert page coords of mouse/touch to uniform coords with smaller side being [-0.5, 0.5]\r\n// (uniform coords keep direct proportion with screen distance travelled by mouse regardless of screen aspect ratio)\r\nObjectControls.prototype.convertMouseToOnCircle = function (coords, pageX, pageY) {\r\n const screenSize = Math.min(this.screen.width, this.screen.height);\r\n\r\n if (screenSize === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n ((pageX - this.screen.width * 0.5 - this.screen.left) / screenSize),\r\n ((0.5 * this.screen.height + this.screen.top - pageY) / screenSize),\r\n );\r\n};\r\n\r\n// convert page coords of mouse/touch to viewport coords with both sides being [-1, 1]\r\n// (those are non-uniform coords affected by screen aspect ratio)\r\nObjectControls.prototype.convertMouseToViewport = function (coords, pageX, pageY) {\r\n if (this.screen.width === 0 || this.screen.height === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n (2.0 * (pageX - this.screen.width * 0.5 - this.screen.left) / this.screen.width),\r\n (2.0 * (0.5 * this.screen.height + this.screen.top - pageY) / this.screen.height),\r\n );\r\n};\r\n\r\nObjectControls.prototype.stop = function () {\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n};\r\n\r\n// rotate object based on latest mouse/touch movement\r\nObjectControls.prototype.rotateByMouse = (function () {\r\n const quat = new THREE.Quaternion();\r\n\r\n return function (aboutZAxis) {\r\n this._affectedObj.rotate(quat, this._mousePrevPos, this._mouseCurPos, aboutZAxis);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n };\r\n}());\r\n\r\n// rotate object by specified quaternion\r\nObjectControls.prototype.rotate = function (quat) {\r\n this.object.quaternion.multiply(quat);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n};\r\n\r\n// get object's orientation\r\nObjectControls.prototype.getOrientation = function () {\r\n return this.object.quaternion;\r\n};\r\n\r\n// set object's orientation\r\nObjectControls.prototype.setOrientation = function (quat) {\r\n this.object.quaternion.copy(quat);\r\n};\r\n\r\n// translate object based on latest mouse/touch movement\r\nObjectControls.prototype.translate = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this._affectedObj.translate(delta);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n };\r\n}());\r\n\r\n// get object scale\r\nObjectControls.prototype.getScale = function () {\r\n return this.object.scale.x;\r\n};\r\n\r\n// set uniform object scale\r\nObjectControls.prototype.setScale = function (scale) {\r\n this.object.scale.set(scale, scale, scale);\r\n};\r\n\r\n// scale object by factor (factor should be greater than zero)\r\nObjectControls.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n return;\r\n }\r\n this.setScale(this.object.scale.x * factor);\r\n this.dispatchEvent({ type: 'change', action: 'zoom', factor });\r\n};\r\n\r\nObjectControls.prototype.update = (function () {\r\n const shift = new THREE.Vector2();\r\n\r\n return function () {\r\n const curTime = this._clock.getElapsedTime();\r\n const timeSinceLastUpdate = curTime - this._lastUpdateTime;\r\n\r\n // update object handler\r\n if (this._state === STATE.NONE) {\r\n const timeSinceMove = curTime - this._lastMouseMoveTime;\r\n if (this._mainObj.update(timeSinceLastUpdate, timeSinceMove)\r\n || this._altObj.update(timeSinceLastUpdate, timeSinceMove)) {\r\n this.dispatchEvent({ type: 'change', action: 'auto' });\r\n }\r\n }\r\n\r\n // apply arrow keys\r\n if (this._isKeysTranslatingObj) {\r\n const speedX = Number(this._pressedKeys[VK_RIGHT]) - Number(this._pressedKeys[VK_LEFT]);\r\n const speedY = Number(this._pressedKeys[VK_UP]) - Number(this._pressedKeys[VK_DOWN]);\r\n if (speedX !== 0.0 || speedY !== 0.0) {\r\n const delta = timeSinceLastUpdate;\r\n\r\n // update object translation\r\n const altObj = this.getAltObj();\r\n if (altObj.objects.length > 0) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n\r\n shift.set(delta * speedX, delta * speedY);\r\n this._altObj.translate(shift);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n }\r\n }\r\n }\r\n\r\n this._lastUpdateTime = curTime;\r\n };\r\n}());\r\n\r\nObjectControls.prototype.reset = function () {\r\n this._state = STATE.NONE;\r\n\r\n this.object.quaternion.copy(quaternion.set(0, 0, 0, 1));\r\n};\r\n\r\n// listeners\r\n\r\nObjectControls.prototype.mousedown = function (event) {\r\n if (this.enabled === false || this._state !== STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (this._state === STATE.NONE) {\r\n if (event.button === 0) {\r\n this._affectedObj.stop(); // can edit only one object at a time\r\n\r\n let workWithAltObj = false;\r\n\r\n if (event.altKey) {\r\n const altObj = this.getAltObj();\r\n workWithAltObj = (altObj.objects.length > 0);\r\n if (workWithAltObj) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n this._affectedObj = workWithAltObj ? this._altObj : this._mainObj;\r\n\r\n this._state = (workWithAltObj && event.ctrlKey && this._isTranslationAllowed) ? STATE.TRANSLATE : STATE.ROTATE;\r\n } else if (event.button === 2) {\r\n this._state = STATE.TRANSLATE_PIVOT;\r\n }\r\n }\r\n\r\n if (this._state === STATE.ROTATE) {\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n\r\n if (this._state === STATE.TRANSLATE || this._state === STATE.TRANSLATE_PIVOT) {\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousemove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this.rotateByMouse((event.altKey && !this._isAltObjFreeRotationAllowed) || event.shiftKey);\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.TRANSLATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translate();\r\n break;\r\n\r\n case STATE.TRANSLATE_PIVOT:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translatePivotByMouse();\r\n break;\r\n\r\n default: break;\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousewheel = function (event) {\r\n if (this.enabled === false || !settings.now.zooming || this._state !== STATE.NONE || event.shiftKey) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n\r\n let delta = 0;\r\n\r\n if (event.wheelDelta) {\r\n // WebKit / Opera / Explorer 9\r\n delta = event.wheelDelta / 40;\r\n } else if (event.detail) {\r\n // Firefox\r\n delta = -event.detail / 3;\r\n }\r\n\r\n let factor = 1.0 + delta * 0.05;\r\n factor = Math.max(factor, 0.01);\r\n this.scale(factor);\r\n};\r\n\r\nObjectControls.prototype.mouseup = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n this._state = STATE.NONE;\r\n\r\n if (this._clock.getElapsedTime() - this._lastMouseMoveTime > FULL_STOP_THRESHOLD) {\r\n this._affectedObj.stop();\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchstartend = function (event) {\r\n if (this.enabled === false) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (event.touches.length) {\r\n case 1:\r\n this._state = STATE.ROTATE;\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n break;\r\n\r\n case 2: {\r\n // prevent inertial rotation\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n\r\n this._state = STATE.SCALE;\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = this._touchDistanceStart = Math.sqrt(dx * dx + dy * dy);\r\n this._scaleStart = this.object.scale.x;\r\n break;\r\n }\r\n\r\n default:\r\n this._state = STATE.NONE;\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchmove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this.rotateByMouse(false);\r\n\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.SCALE:\r\n if (settings.now.zooming) {\r\n // update scale\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = Math.sqrt(dx * dx + dy * dy);\r\n const newScale = this._scaleStart * this._touchDistanceCur / this._touchDistanceStart;\r\n const factor = newScale / this.object.scale.x;\r\n this.scale(factor);\r\n }\r\n break;\r\n\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.keydownup = function (event) {\r\n if (this.enabled === false || this.hotkeysEnabled === false) {\r\n return;\r\n }\r\n\r\n switch (event.keyCode) {\r\n case VK_LEFT:\r\n case VK_UP:\r\n case VK_RIGHT:\r\n case VK_DOWN:\r\n this._pressedKeys[event.keyCode] = (event.type === 'keydown');\r\n event.preventDefault();\r\n event.stopPropagation();\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.getKeyBindObject = function () {\r\n return getTopWindow();\r\n};\r\n\r\nObjectControls.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nObjectControls.prototype.translatePivotByMouse = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this.translatePivotInWorld(settings.now.translationSpeed * delta.x, settings.now.translationSpeed * delta.y, 0);\r\n };\r\n}());\r\n\r\n// Translate in WorldCS, translation is scaled with root scale matrix\r\nObjectControls.prototype.translatePivotInWorld = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.applyMatrix4(this.object.matrixWorld);\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n pos.applyMatrix4(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Translate in ModelCS, x, y, z are Ang\r\nObjectControls.prototype.translatePivot = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Set pivot\r\nObjectControls.prototype.setPivot = function (newPivot) {\r\n this.objectPivot.position.copy(newPivot);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\nexport default ObjectControls;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\nimport Timer from '../Timer';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\n\r\nfunction Picker(gfxObj, camera, domElement) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.gfxObj = gfxObj;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n this._lastMousePos = new THREE.Vector2(0, 0);\r\n this._mouseTotalDist = 0.0;\r\n this._lastClickBeginTime = -1000.0;\r\n this._lastClickPos = new THREE.Vector2(0, 0);\r\n this._clickBeginTime = 0.0;\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstart(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchend(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n}\r\n\r\nPicker.prototype = Object.create(EventDispatcher.prototype);\r\nPicker.prototype.constructor = Picker;\r\n\r\nPicker.prototype.reset = function () {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n};\r\n\r\nPicker.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nPicker.prototype.pickObject = function (screenPos) {\r\n if (!this.gfxObj) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n const { gfxObj } = this;\r\n const rayCaster = new THREE.Raycaster();\r\n rayCaster.ray.origin.setFromMatrixPosition(this.camera.matrixWorld);\r\n rayCaster.ray.direction.set(screenPos.x, screenPos.y, 0.5).unproject(this.camera).sub(rayCaster.ray.origin).normalize();\r\n\r\n const clipPlane = (settings.now.draft.clipPlane && this.clipPlaneValue) ? this.clipPlaneValue : Infinity;\r\n const fogFarPlane = (settings.now.fog && this.fogFarValue) ? this.fogFarValue : Infinity;\r\n const point = rayCaster.intersectVisibleObject(gfxObj, this.camera, clipPlane, fogFarPlane);\r\n if (!point) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n let picked = {};\r\n if (point.residue || point.atom) {\r\n const residue = point.residue || point.atom.residue;\r\n if (settings.now.pick === 'chain') {\r\n picked = { chain: residue.getChain() };\r\n } else if (settings.now.pick === 'molecule') {\r\n picked = { molecule: residue.getMolecule() };\r\n } else if (point.residue || settings.now.pick === 'residue') {\r\n picked = { residue };\r\n } else if (point.atom) {\r\n picked = { atom: point.atom };\r\n }\r\n }\r\n this.picked = picked;\r\n this.dispatchEvent({ type: 'newpick', obj: picked });\r\n};\r\n\r\nPicker.prototype.getMouseInViewport = function (pageX, pageY) {\r\n return new THREE.Vector2(\r\n (pageX - this.screen.left) / this.screen.width * 2 - 1,\r\n -(pageY - this.screen.top) / this.screen.height * 2 + 1,\r\n );\r\n};\r\n\r\nPicker.prototype.mousedown = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n this._lastMousePos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist = 0.0;\r\n this._clickBeginTime = this._clock.getElapsedTime();\r\n }\r\n};\r\n\r\nPicker.prototype.mousemove = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n const pos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist += pos.sub(this._lastMousePos).length();\r\n};\r\n\r\nPicker.prototype.mouseup = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n if (this._mouseTotalDist < 0.01) {\r\n const curTime = this._clock.getElapsedTime();\r\n const curPos = this.getMouseInViewport(event.pageX, event.pageY);\r\n\r\n const timeSinceLastClickBegin = curTime - this._lastClickBeginTime;\r\n if (timeSinceLastClickBegin < 0.7) {\r\n const clickDist = new THREE.Vector2().subVectors(curPos, this._lastClickPos);\r\n if (clickDist.length() < 0.01) {\r\n // it's a double click\r\n this.dispatchEvent({ type: 'dblclick', obj: this.picked });\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = -1000; // this click cannot serve as first click in double-click\r\n return;\r\n }\r\n }\r\n\r\n setTimeout(() => {\r\n self.pickObject(curPos);\r\n }, 0);\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = this._clickBeginTime;\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.touchstart = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 1) {\r\n this._lastTouchdownPos = this.getMouseInViewport(event.touches[0].pageX, event.touches[0].pageY);\r\n }\r\n};\r\n\r\nPicker.prototype.touchend = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 0\r\n && event.changedTouches.length === 1) {\r\n const pos = this.getMouseInViewport(event.changedTouches[0].pageX, event.changedTouches[0].pageY);\r\n const dist = pos.sub(this._lastTouchdownPos).length();\r\n if (dist < 0.01) {\r\n setTimeout(() => {\r\n self.pickObject(self._lastTouchdownPos);\r\n }, 0);\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nexport default Picker;\r\n","import * as THREE from 'three';\r\n\r\nclass Axes {\r\n constructor(target, targetCamera) {\r\n this._target = target;\r\n this._targetCamera = targetCamera;\r\n this._camera = new THREE.PerspectiveCamera(targetCamera.fov, targetCamera.aspect, 1, 100);\r\n this._object = new THREE.AxesHelper(1);\r\n this._scene = new THREE.Scene();\r\n this._scene.add(this._object);\r\n this._full = new THREE.Vector2();\r\n\r\n this._update();\r\n }\r\n\r\n _update() {\r\n const { fov } = this._targetCamera;\r\n const camera = this._camera;\r\n camera.aspect = this._targetCamera.aspect;\r\n camera.setMinimalFov(fov);\r\n camera.setDistanceToFit(1.0, fov);\r\n camera.updateProjectionMatrix();\r\n\r\n this._object.quaternion.copy(this._target.quaternion);\r\n }\r\n\r\n render(renderer) {\r\n this._update();\r\n\r\n renderer.getSize(this._full);\r\n const width = this._full.width * 0.25;\r\n const height = this._full.height * 0.25;\r\n\r\n const { autoClear } = renderer;\r\n renderer.autoClear = false;\r\n renderer.setViewport(0.0, 0.0, width, height);\r\n renderer.clear(false, true, false);\r\n renderer.render(this._scene, this._camera);\r\n renderer.setViewport(0, 0, this._full.width, this._full.height);\r\n renderer.autoClear = autoClear;\r\n }\r\n}\r\nexport default Axes;\r\n","import * as THREE from 'three';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\n\r\nconst cDataOffset = 12;\r\nconst cFirstMask = 0x0FFFFF00;\r\nconst cFirstShift = 8;\r\nconst cSecMask1 = 0x000000FF;\r\nconst cSecShift1 = 12;\r\nconst cSecMask2 = 0xFFF00000;\r\nconst cSecShift2 = 20;\r\nconst cThirdMask = 0x000FFFFF;\r\nconst cStrMask = 0xF0000000;\r\nconst cStrShift = 28;\r\nconst c219 = 1 << 19;\r\nconst c220 = 1 << 20;\r\n\r\nconst cHelixIdx = 1;\r\nconst cSheetIdx = 2;\r\nconst secTypes = ['helix', 'strand'];\r\nconst cSecNames = ['fs', 'ps', 'ns', 'us'];\r\n\r\nfunction _createSecondary(strArray, complex) {\r\n const residues = complex._residues;\r\n const nRes = residues.length;\r\n const resid = new Uint8Array(nRes);\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, n = strArray.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n resid[atom.residue._index] = strArray[i];\r\n }\r\n\r\n const secondary = [];\r\n let rIdx = 0;\r\n while (rIdx < nRes) {\r\n if (resid[rIdx] !== 0) {\r\n const start = rIdx;\r\n const val = resid[rIdx];\r\n while (rIdx < nRes - 1 && resid[rIdx + 1] === val\r\n && residues[rIdx].isConnected(residues[rIdx + 1])) {\r\n ++rIdx;\r\n }\r\n secondary.push({ start, end: rIdx, type: secTypes[val - 1] });\r\n }\r\n ++rIdx;\r\n }\r\n return secondary;\r\n}\r\n\r\nfunction fromUInt20ToInt20(uint20) {\r\n return uint20 >= c219 ? uint20 - c220 : uint20;\r\n}\r\n\r\nclass FrameInfo {\r\n constructor(complex, payload, callbacks) {\r\n this._complex = complex;\r\n this._secondary = null;\r\n this.isLoading = false;\r\n this._framesRange = {\r\n start: 0,\r\n end: -1,\r\n };\r\n this.frameIsReady = false;\r\n this._buffer = null;\r\n this._frameRequest = null;\r\n this._callbacks = callbacks;\r\n if (typeof payload === 'function') {\r\n this._framesRequestLength = 1;\r\n this._downloadDataFn = payload;\r\n } else {\r\n this.parseBinaryData(payload, true);\r\n }\r\n this.reset();\r\n this.setFrame(0);\r\n }\r\n\r\n _prepareBuffer(framesStart, framesEnd) {\r\n if (framesStart === undefined || framesStart === null) {\r\n framesStart = 0;\r\n }\r\n if (framesEnd === undefined || framesEnd === null) {\r\n framesEnd = framesStart + this._framesRequestLength;\r\n }\r\n if (this._framesCount !== undefined) {\r\n framesEnd = Math.min(this._framesCount - 1, framesEnd);\r\n }\r\n if (this._downloadDataFn) {\r\n const self = this;\r\n const onDone = function (data) {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n self._buffer = {\r\n data,\r\n state: 'ready',\r\n start: framesStart,\r\n end: framesEnd,\r\n };\r\n if (self._frameRequest !== null) {\r\n const idx = self._frameRequest;\r\n self._frameRequest = null;\r\n self.setFrame(idx);\r\n }\r\n };\r\n const onFail = function () {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onError === 'function') {\r\n self._callbacks.onError('Streaming failed');\r\n }\r\n };\r\n if (!this._buffer) {\r\n this._buffer = {};\r\n }\r\n this._buffer.state = 'downloading';\r\n this.isLoading = true;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n this._downloadDataFn({ start: framesStart, end: framesEnd + 1 }, onDone, onFail);\r\n }\r\n }\r\n\r\n _parseBuffer() {\r\n if (this._buffer && this._buffer.state === 'ready') {\r\n this._framesRange = {\r\n start: this._buffer.start,\r\n end: this._buffer.end,\r\n };\r\n this.parseBinaryData(this._buffer.data, false);\r\n let _bufferRequestStart = (this._buffer.end + 1) % this._framesCount;\r\n if (_bufferRequestStart >= this._framesCount) {\r\n _bufferRequestStart = 0;\r\n }\r\n this._buffer = {\r\n state: 'none',\r\n };\r\n this._prepareBuffer(_bufferRequestStart, _bufferRequestStart + this._framesRequestLength);\r\n if (this._frameRequest !== null) {\r\n const idx = this._frameRequest;\r\n this._frameRequest = null;\r\n this.setFrame(idx);\r\n }\r\n }\r\n }\r\n\r\n parseBinaryData(arrayBuffer) {\r\n const dataView = new DataView(arrayBuffer);\r\n let offset = 0;\r\n const atomsCount = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const framesCount = dataView.getUint32(offset, true);\r\n this._framesCount = framesCount;\r\n this._framesRange.end = this._framesRange.end > 0\r\n ? Math.min(this._framesRange.end, framesCount - 1) : framesCount - 1;\r\n offset += 4;\r\n this._atomsCount = atomsCount;\r\n const maxSize = 1024 * 1024; // 1 MB\r\n this._framesRequestLength = Math.ceil(maxSize / (atomsCount * 8));\r\n const chunkedFramesCount = this._framesRange.end - this._framesRange.start + 1;\r\n if (atomsCount !== this._complex._atoms.length\r\n || arrayBuffer.byteLength !== cDataOffset + chunkedFramesCount * atomsCount * 8) {\r\n throw new Error();\r\n }\r\n const complex = this._complex;\r\n let timeStep = dataView.getUint32(offset, true);\r\n let iName = 0;\r\n while (timeStep > 1000 && iName < cSecNames.length - 1) {\r\n timeStep /= 1000;\r\n ++iName;\r\n }\r\n\r\n this._timeStep = `${timeStep.toString()} ${cSecNames[iName]}`;\r\n offset += 4;\r\n const secondary = [];\r\n const posData = new Float32Array(chunkedFramesCount * atomsCount * 3);\r\n let coordIdx = 0;\r\n const secondaryArr = new Int8Array(atomsCount);\r\n for (let j = 0; j < chunkedFramesCount; ++j) {\r\n for (let i = 0; i < atomsCount; ++i) {\r\n const hiWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const loWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const str = (loWord & cStrMask) >>> cStrShift;\r\n const x = fromUInt20ToInt20(((loWord & cFirstMask) >>> cFirstShift) >> 0);\r\n const y = fromUInt20ToInt20((((loWord & cSecMask1) << cSecShift1)\r\n | ((hiWord & cSecMask2) >>> cSecShift2)) >> 0);\r\n const z = fromUInt20ToInt20((hiWord & cThirdMask) >> 0);\r\n secondaryArr[i] = 0;\r\n if (str > 0 && str < 4) {\r\n secondaryArr[i] = cHelixIdx;\r\n } else if (str === 4) {\r\n secondaryArr[i] = cSheetIdx;\r\n }\r\n posData[coordIdx++] = x / 100;\r\n posData[coordIdx++] = y / 100;\r\n posData[coordIdx++] = z / 100;\r\n }\r\n secondary.push(_createSecondary(secondaryArr, complex));\r\n }\r\n this._secondaryData = secondary;\r\n this._data = posData;\r\n }\r\n\r\n nextFrame() {\r\n this.setFrame((this._currFrame + 1) % this._framesCount);\r\n }\r\n\r\n needsColorUpdate(colorer) {\r\n return colorer instanceof SecondaryStructureColorer;\r\n }\r\n\r\n getAtomColor(colorer, atom) {\r\n return colorer.getResidueColor(this._residues[atom.residue._index], this._complex);\r\n }\r\n\r\n getResidueColor(colorer, residue) {\r\n return colorer.getResidueColor(this._residues[residue._index], this._complex);\r\n }\r\n\r\n _updateSecondary() {\r\n let i;\r\n const myResidues = this._residues;\r\n let n = myResidues.length;\r\n for (i = 0; i < n; ++i) {\r\n myResidues[i]._secondary = null;\r\n }\r\n const sec = this._secondaryData[this._currFrame - this._framesRange.start];\r\n for (i = 0, n = sec.length; i < n; ++i) {\r\n const oldSec = sec[i];\r\n const { start, end } = oldSec;\r\n const nSec = {\r\n _start: myResidues[start],\r\n _end: myResidues[end],\r\n type: oldSec.type,\r\n generic: oldSec.generic,\r\n };\r\n for (let j = start; j <= end; ++j) {\r\n myResidues[j]._secondary = nSec;\r\n }\r\n }\r\n }\r\n\r\n reset() {\r\n const compRes = this._complex._residues;\r\n const n = compRes.length;\r\n this._residues = new Array(n);\r\n const myResidues = this._residues;\r\n const getSec = function () {\r\n return this._secondary;\r\n };\r\n for (let i = 0; i < n; ++i) {\r\n myResidues[i] = {\r\n _type: compRes[i]._type,\r\n _isValid: compRes[i]._isValid,\r\n _controlPoint: null,\r\n _wingVector: null,\r\n _secondary: null,\r\n getSecondary: getSec,\r\n };\r\n }\r\n }\r\n\r\n setFrame(frameIdx) {\r\n this.frameIsReady = false;\r\n if (frameIdx >= this._framesRange.start && frameIdx <= this._framesRange.end) {\r\n this._currFrame = frameIdx;\r\n this._cachedResidues = false;\r\n this._updateSecondary();\r\n this.frameIsReady = true;\r\n } else {\r\n this._frameRequest = frameIdx;\r\n if (!this._buffer) {\r\n this._prepareBuffer(frameIdx);\r\n } else {\r\n const self = this;\r\n switch (this._buffer.state) {\r\n case 'none':\r\n this._prepareBuffer(frameIdx);\r\n break;\r\n case 'ready':\r\n self._parseBuffer();\r\n break;\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n disableEvents() {\r\n this._callbacks = null;\r\n }\r\n\r\n /**\r\n * Returns link to atom pos vector, clone it if needed\r\n */\r\n\r\n static _vec = new THREE.Vector3();\r\n\r\n getAtomPos(atomIdx) {\r\n const vec = FrameInfo._vec;\r\n const self = this;\r\n const data = self._data;\r\n const idx = (self._atomsCount * (self._currFrame - self._framesRange.start) + atomIdx) * 3;\r\n vec.set(data[idx], data[idx + 1], data[idx + 2]);\r\n return vec;\r\n }\r\n\r\n getResidues() {\r\n if (this._cachedResidues) {\r\n return this._residues;\r\n }\r\n this._complex.updateToFrame(this);\r\n return this._residues;\r\n }\r\n}\r\nexport default FrameInfo;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\n\r\n/**\r\n * Create new scene object.\r\n *\r\n * @param {array=} params - Object required params.\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports SceneObject\r\n * @this SceneObject\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all scene objects that are not reps.\r\n */\r\nclass SceneObject {\r\n constructor(params, opts) {\r\n if (this.constructor === SceneObject) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Object's options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.params = params;\r\n this.opts = _.merge(utils.deriveDeep(settings.now.objects[this.type], true), opts);\r\n this.needsRebuild = false;\r\n this._mesh = null;\r\n this.id = null;\r\n }\r\n\r\n /**\r\n * Get object identification, probably with options.\r\n * @returns {Object} field type contains type information, params - object's formal parameters,\r\n * opts - changed options\r\n * Options are returned if they were changed during or after object creation.\r\n */\r\n identify() {\r\n const result = {\r\n type: this.type,\r\n params: this.params,\r\n };\r\n const diff = utils.objectsDiff(this.opts, settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n result.opts = diff;\r\n }\r\n return result;\r\n }\r\n\r\n toString() {\r\n const paramsStr = `o=${this.type},${this.params.join(',')}`;\r\n const optsStr = utils.compareOptionsWithDefaults(this.opts, settings.defaults.objects[this.type]);\r\n return paramsStr + optsStr;\r\n }\r\n\r\n getGeometry() {\r\n return this._mesh;\r\n }\r\n\r\n destroy() {\r\n if (this._mesh) {\r\n gfxutils.destroyObject(this._mesh);\r\n }\r\n }\r\n}\r\n\r\n/**\r\n * Scene object identifier.\r\n * @type {string}\r\n */\r\nSceneObject.prototype.type = '__';\r\n\r\nexport default SceneObject;\r\n","import * as THREE from 'three';\r\nimport SceneObject from './SceneObject';\r\nimport meshutils from '../meshutils';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\nimport meshes from '../meshes/meshes';\r\nimport settings from '../../settings';\r\n\r\nclass LinesObj extends SceneObject {\r\n constructor(params, opts) {\r\n super(params, opts);\r\n if (params.length < 2) {\r\n throw new Error('Wrong number of argumets on line object creation!');\r\n }\r\n [this._id1, this._id2] = params;\r\n }\r\n\r\n _getAtomFromName(complex, atomId) {\r\n const err = ' - Wrong atom format it must be \\'#CHAIN_NAME.#RESIDUE_NUMBER.#ATOM_NAME\\' (e.g. \\'A.38.CO1\\')';\r\n const atom1 = complex.getAtomByFullname(atomId);\r\n if (!atom1) {\r\n throw new Error(atomId + err);\r\n }\r\n return atom1;\r\n }\r\n\r\n build(complex) {\r\n const geom = new THREE.BufferGeometry();\r\n this._atom1 = this._getAtomFromName(complex, this._id1);\r\n this._atom2 = this._getAtomFromName(complex, this._id2);\r\n\r\n const p1 = this._atom1.position;\r\n const p2 = this._atom2.position;\r\n const vertices = new Float32Array([\r\n p1.x, p1.y, p1.z,\r\n p2.x, p2.y, p2.z,\r\n ]);\r\n\r\n geom.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n geom.computeBoundingBox();\r\n\r\n this._line = new meshes.Line(geom, new UberMaterial({\r\n lights: false,\r\n overrideColor: true,\r\n dashedLine: true,\r\n fogTransparent: settings.now.bg.transparent,\r\n }));\r\n this._line.computeLineDistances();\r\n this._line.material.setUberOptions({\r\n fixedColor: new THREE.Color(this.opts.color),\r\n dashedLineSize: this.opts.dashSize,\r\n dashedLinePeriod: this.opts.dashSize + this.opts.gapSize,\r\n });\r\n this._line.material.updateUniforms();\r\n\r\n this._line.raycast = function (_raycaster, _intersects) {};\r\n this._mesh = this._line;\r\n const transforms = complex.getTransforms();\r\n if (transforms.length > 0) {\r\n this._mesh = new THREE.Group();\r\n this._mesh.add(this._line);\r\n meshutils.applyTransformsToMeshes(this._mesh, transforms);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n if (!this._atom1 || !this._atom2 || !this._line) {\r\n return;\r\n }\r\n\r\n const geo = this._line.geometry;\r\n geo.vertices[0].copy(frameData.getAtomPos(this._atom1.index));\r\n geo.vertices[1].copy(frameData.getAtomPos(this._atom2.index));\r\n this._line.computeLineDistances();\r\n geo.computeBoundingSphere();\r\n\r\n geo.verticesNeedUpdate = true;\r\n }\r\n}\r\n\r\nLinesObj.prototype.constructor = LinesObj;\r\nLinesObj.prototype.type = 'line';\r\n\r\nexport default LinesObj;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Outline.frag';\r\n\r\nclass OutlineMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n // add depth outline\r\n super(params);\r\n\r\n const settings = {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcDepthTex: { type: 't', value: null },\r\n srcTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n color: { type: 'v3', value: null },\r\n threshold: { type: 'f', value: null },\r\n opacity: { type: 'f', value: 1.0 },\r\n thickness: { type: 'v2', value: new THREE.Vector2(1, 1) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: true,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n\r\n this.setValues(settings);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n const defines = {};\r\n\r\n if (this.depth) {\r\n defines.DEPTH_OUTLINE = 1;\r\n }\r\n\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nOutlineMaterial.prototype.depth = false;\r\n\r\nexport default OutlineMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './FXAA.frag';\r\n\r\nclass FXAAMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n bgColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.bgTransparent) {\r\n defines.BG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nFXAAMaterial.prototype.bgTransparent = false;\r\n\r\nexport default FXAAMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AO.frag';\r\nimport noise from '../noiseTexture';\r\n\r\nconst _samplesKernel = [\r\n // hemisphere samples adopted to sphere\r\n new THREE.Vector3(0.295184, 0.077723, 0.068429),\r\n new THREE.Vector3(-0.271976, -0.365221, 0.838363),\r\n new THREE.Vector3(0.547713, 0.467576, 0.488515),\r\n new THREE.Vector3(0.662808, -0.031733, 0.584758),\r\n new THREE.Vector3(-0.025717, 0.218955, 0.657094),\r\n new THREE.Vector3(-0.310153, -0.365223, 0.370701),\r\n new THREE.Vector3(-0.101407, -0.006313, 0.747665),\r\n new THREE.Vector3(-0.769138, 0.360399, 0.086847),\r\n new THREE.Vector3(-0.271988, -0.275140, 0.905353),\r\n new THREE.Vector3(0.096740, -0.566901, 0.700151),\r\n new THREE.Vector3(0.562872, -0.735136, 0.094647),\r\n new THREE.Vector3(0.379877, 0.359278, 0.190061),\r\n new THREE.Vector3(0.519064, -0.023055, 0.405068),\r\n new THREE.Vector3(-0.301036, 0.114696, 0.088885),\r\n new THREE.Vector3(-0.282922, 0.598305, 0.487214),\r\n new THREE.Vector3(-0.181859, 0.251670, 0.679702),\r\n new THREE.Vector3(-0.191463, -0.635818, 0.512919),\r\n new THREE.Vector3(-0.293655, 0.427423, 0.078921),\r\n new THREE.Vector3(-0.267983, 0.680534, 0.132880),\r\n new THREE.Vector3(0.139611, 0.319637, 0.477439),\r\n new THREE.Vector3(-0.352086, 0.311040, 0.653913),\r\n new THREE.Vector3(0.321032, 0.805279, 0.487345),\r\n new THREE.Vector3(0.073516, 0.820734, 0.414183),\r\n new THREE.Vector3(-0.155324, 0.589983, 0.411460),\r\n new THREE.Vector3(0.335976, 0.170782, 0.527627),\r\n new THREE.Vector3(0.463460, -0.355658, 0.167689),\r\n new THREE.Vector3(0.222654, 0.596550, 0.769406),\r\n new THREE.Vector3(0.922138, -0.042070, 0.147555),\r\n new THREE.Vector3(-0.727050, -0.329192, 0.369826),\r\n new THREE.Vector3(-0.090731, 0.533820, 0.463767),\r\n new THREE.Vector3(-0.323457, -0.876559, 0.238524),\r\n new THREE.Vector3(-0.663277, -0.372384, 0.342856),\r\n];\r\n\r\nclass AOMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n noiseTexture: { type: 't', value: noise.noiseTexture },\r\n noiseTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight) },\r\n diffuseTexture: { type: 't', value: null },\r\n normalTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n camNearFar: { type: 'v2', value: new THREE.Vector2(1.0, 10.0) },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n samplesKernel: { type: 'v3v', value: _samplesKernel },\r\n kernelRadius: { type: 'f', value: 1.0 },\r\n depthThreshold: { type: 'f', value: 1.0 },\r\n factor: { type: 'f', value: 1.0 },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOHorBlur.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOHorBlurMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOHorBlurMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOVertBlurWithBlend.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOVertBlurWithBlendMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n diffuseTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n fogNearFar: { type: 'v2', value: new THREE.Vector2(100.0, 100.0) },\r\n fogColor: { type: 'v4', value: new THREE.Vector4(0.0, 0.5, 0.0, 1.0) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.useFog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nAOVertBlurWithBlendMaterial.prototype.useFog = true;\r\nAOVertBlurWithBlendMaterial.prototype.fogTransparent = false;\r\n\r\nexport default AOVertBlurWithBlendMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Anaglyph.frag';\r\n\r\nclass AnaglyphMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n const settings = {\r\n uniforms: {\r\n srcL: { type: 't', value: null },\r\n srcR: { type: 't', value: null },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n this.setValues(settings);\r\n }\r\n}\r\n\r\nexport default AnaglyphMaterial;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\n\r\nclass View {\r\n constructor() {\r\n this.position = new THREE.Vector3(0, 0, 0);\r\n this.scale = 1;\r\n this.orientation = new THREE.Quaternion(0, 0, 0, 1);\r\n }\r\n\r\n set(position, scale, orientation) {\r\n this.position = position;\r\n this.scale = scale;\r\n this.orientation = orientation;\r\n }\r\n}\r\n\r\nconst _transitionTime = 1.5; // in seconds\r\n\r\nexport default class ViewInterpolator {\r\n setup(startView, endView) {\r\n this._startTime = undefined;\r\n this._endTime = undefined;\r\n this._isPaused = false;\r\n\r\n this._srcView = startView;\r\n this._dstView = endView;\r\n this._isMoving = false;\r\n }\r\n\r\n isMoving() {\r\n return this._isMoving;\r\n }\r\n\r\n wasStarted() {\r\n return typeof this._startTime !== 'undefined' && typeof this._endTime !== 'undefined';\r\n }\r\n\r\n start() {\r\n this._startTime = Date.now();\r\n const transTime = settings.now.interpolateViews ? _transitionTime * 1000 : 0;\r\n this._endTime = this._startTime + transTime;\r\n this._isMoving = true;\r\n }\r\n\r\n getCurrentView() {\r\n if (typeof this._srcView === 'undefined' || typeof this._dstView === 'undefined'\r\n || !this._isMoving || !this.wasStarted()) {\r\n return { success: false };\r\n }\r\n\r\n let view = this.createView();\r\n const time = Date.now();\r\n if (time > this._endTime) {\r\n view = this._dstView;\r\n this.reset();\r\n return { success: true, view };\r\n }\r\n\r\n const factor = (time - this._startTime) / (this._endTime - this._startTime);\r\n view.position.copy(this._srcView.position);\r\n view.position.lerp(this._dstView.position, factor);\r\n view.scale = (1 - factor) * this._srcView.scale + factor * this._dstView.scale;\r\n view.orientation.copy(this._srcView.orientation);\r\n view.orientation.slerp(this._dstView.orientation, factor);\r\n return { success: true, view };\r\n }\r\n\r\n reset() {\r\n this._startTime = this._endTime = 0;\r\n this._isMoving = false;\r\n }\r\n\r\n pause() {\r\n if (!this._isPaused) {\r\n this.setup(this.getCurrentView().view, this._dstView);\r\n this._isPaused = true;\r\n }\r\n }\r\n\r\n resume() {\r\n this._isPaused = false;\r\n }\r\n\r\n createView() {\r\n return new View();\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport makeContextDependent from './makeContextDependent';\r\n\r\nconst MAX_COOKIE_LEN = 4000;\r\nconst COUNT_SUFFIX = 'Cnt';\r\n\r\nfunction _chunkString(string, chunkLen) {\r\n const l = string.length;\r\n const chunks = [];\r\n for (let c = 0, lc = 0; lc < l; c++, lc += chunkLen) {\r\n chunks[c] = string.slice(lc, lc + chunkLen);\r\n }\r\n return chunks;\r\n}\r\n\r\n/**\r\n * Create new context dependent Cookie holder object.\r\n * @param context\r\n * @param {Object} opts - options\r\n * @param {string} opts.path - cookie path\r\n * @constructor\r\n */\r\nfunction Cookies(context, opts) {\r\n this.context = context;\r\n this._opts = _.merge({\r\n path: '/',\r\n }, opts);\r\n}\r\n\r\nmakeContextDependent(Cookies.prototype);\r\n\r\n/**\r\n * Remove cookie by the name.\r\n * @param key\r\n */\r\nCookies.prototype.removeCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n this._removeSimpleCookie(key);\r\n return;\r\n }\r\n this._removeSimpleCookie(cntKey);\r\n cntVal = parseInt(cntVal, 10);\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._removeSimpleCookie(key + i);\r\n }\r\n};\r\n\r\n/**\r\n * Set new cookie value. Automatically splits\r\n * values that are too large into multiple cookies.\r\n * @param key\r\n * @param value\r\n */\r\nCookies.prototype.setCookie = function (key, value) {\r\n this.removeCookie(key);\r\n value = encodeURIComponent(value);\r\n const values = _chunkString(value, MAX_COOKIE_LEN - key.length - 1);\r\n const cntVal = values.length;\r\n if (cntVal === 1) {\r\n this._setSimpleCookie(key, value);\r\n return;\r\n }\r\n const cntKey = this._toCount(key);\r\n this._setSimpleCookie(cntKey, cntVal.toString());\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._setSimpleCookie(key + i, values[i]);\r\n }\r\n};\r\n\r\n/**\r\n * Obtain the value of a compound cookie.\r\n * @param key\r\n */\r\nCookies.prototype.getCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n return this._getSimpleCookie(key);\r\n }\r\n cntVal = parseInt(cntVal, 10);\r\n const value = [];\r\n for (let i = 0; i < cntVal; ++i) {\r\n value[i] = this._getSimpleCookie(key + i);\r\n }\r\n return value.join('');\r\n};\r\n\r\nCookies.prototype._toCount = function (key) {\r\n return key + COUNT_SUFFIX;\r\n};\r\n\r\nCookies.prototype._removeSimpleCookie = function (key) {\r\n document.cookie = `${key}=; expires=Thu, 01 Jan 1970 00:00:01 GMT;`;\r\n};\r\n\r\nCookies.prototype._getExpirationDate = function () {\r\n const today = new Date();\r\n const EXP_PERIOD_YEARS = 10;\r\n today.setFullYear(today.getFullYear() + EXP_PERIOD_YEARS);\r\n return today;\r\n};\r\n\r\nCookies.prototype._setSimpleCookie = function (key, value) {\r\n document.cookie = `${key}=${value\r\n };expires=${this._getExpirationDate().toUTCString()\r\n };path=${this._opts.path}`;\r\n};\r\n\r\nCookies.prototype._getSimpleCookie = function (key) {\r\n const matches = document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n return matches ? decodeURIComponent(matches[1]) : '';\r\n};\r\n\r\nCookies.prototype._exists = function (key) {\r\n return document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n};\r\n\r\nexport default Cookies;\r\n","/*\r\n * Toggling WebVR is done through button.click because of limitations on calling requestPresent in webVR:\r\n * VRDisplay::requestPresent should be called from user gesture:\r\n * https://developer.mozilla.org/en-US/docs/Web/API/VRDisplay/requestPresent\r\n */\r\nexport default function (webVRPoC) {\r\n function showEnterVR(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'pointer';\r\n button.style.left = 'calc(50% - 50px)';\r\n button.style.width = '100px';\r\n\r\n button.textContent = 'ENTER VR';\r\n\r\n let currentSession = null;\r\n\r\n function onSessionEnded(/* event */) {\r\n currentSession.removeEventListener('end', onSessionEnded);\r\n button.textContent = 'ENTER VR';\r\n currentSession = null;\r\n }\r\n\r\n function onSessionStarted(session) {\r\n session.addEventListener('end', onSessionEnded);\r\n webVRPoC._gfx.renderer.xr.setReferenceSpaceType('local');\r\n webVRPoC._gfx.renderer.xr.setSession(session);\r\n button.textContent = 'EXIT VR';\r\n currentSession = session;\r\n }\r\n\r\n button.onmouseenter = function () { button.style.opacity = '1.0'; };\r\n button.onmouseleave = function () { button.style.opacity = '0.5'; };\r\n\r\n button.onclick = function () {\r\n if (currentSession === null) {\r\n // WebXR's requestReferenceSpace only works if the corresponding feature\r\n // was requested at session creation time. For simplicity, just ask for\r\n // the interesting ones as optional features, but be aware that the\r\n // requestReferenceSpace call will fail if it turns out to be unavailable.\r\n // ('local' is always available for immersive sessions and doesn't need to\r\n // be requested separately.)\r\n\r\n const sessionInit = { optionalFeatures: ['local-floor', 'bounded-floor'] };\r\n navigator.xr.requestSession('immersive-vr', sessionInit).then(onSessionStarted);\r\n webVRPoC.moveSceneBehindHeadset();\r\n } else {\r\n currentSession.end();\r\n }\r\n };\r\n }\r\n\r\n function showWebXRNotFound(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'auto';\r\n button.style.left = 'calc(50% - 75px)';\r\n button.style.width = '150px';\r\n button.textContent = 'VR NOT FOUND';\r\n button.onmouseenter = null;\r\n button.onmouseleave = null;\r\n button.onclick = null;\r\n }\r\n\r\n function stylizeElement(element) {\r\n element.style.position = 'absolute';\r\n element.style.bottom = '20px';\r\n element.style.padding = '12px 6px';\r\n element.style.border = '1px solid #fff';\r\n element.style.borderRadius = '4px';\r\n element.style.background = 'transparent';\r\n element.style.color = '#fff';\r\n element.style.font = 'normal 13px sans-serif';\r\n element.style.textAlign = 'center';\r\n element.style.opacity = '0.5';\r\n element.style.outline = 'none';\r\n element.style.zIndex = '999';\r\n }\r\n\r\n if ('xr' in navigator) {\r\n const button = document.createElement('button');\r\n button.style.display = 'none';\r\n stylizeElement(button);\r\n navigator.xr.isSessionSupported('immersive-vr').then((supported) => (\r\n supported ? showEnterVR(button) : showWebXRNotFound(button)\r\n ));\r\n return button;\r\n }\r\n const message = document.createElement('a');\r\n message.href = 'https://webvr.info';\r\n message.innerHTML = 'WEBXR NOT SUPPORTED';\r\n message.style.left = 'calc(50% - 90px)';\r\n message.style.width = '180px';\r\n message.style.textDecoration = 'none';\r\n stylizeElement(message);\r\n return message;\r\n}\r\n","import * as THREE from 'three';\r\nimport createWebVRButton from './createWebVRButton';\r\nimport gfxutils from '../gfxutils';\r\nimport logger from '../../utils/logger';\r\nimport settings from '../../settings';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default class WebVRPoC {\r\n constructor(onToggle) {\r\n this._mainCamera = new THREE.PerspectiveCamera();\r\n this._button = null;\r\n this._onToggle = onToggle;\r\n\r\n this._molContainer = new gfxutils.RCGroup();\r\n this._user = new gfxutils.RCGroup();\r\n this._scalingPivot = new THREE.Object3D();\r\n this._user.add(this._scalingPivot);\r\n\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n this._pressedGripsCounter = 0;\r\n this._distance = 0;\r\n\r\n this._gfx = null;\r\n }\r\n\r\n startScalingByControllers() {\r\n // reset scale\r\n this._distance = this._controller1.position.distanceTo(this._controller2.position);\r\n gfxutils.getMiddlePoint(this._controller1.position, this._controller2.position, this._scalingPivot.position);\r\n this._scalingPivot.scale.set(1, 1, 1);\r\n this._scalingPivot.updateMatrix();\r\n this._scalingPivot.updateMatrixWorld();\r\n // link molecule to pivot\r\n this._scalingPivot.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n stopScalingByControllers() {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n handleGripsDown(event) {\r\n this._pressedGripsCounter++;\r\n if (this._pressedGripsCounter === 2) {\r\n this.startScalingByControllers();\r\n } else if (this._pressedGripsCounter === 1) {\r\n event.target.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n handleGripsUp(event) {\r\n this._pressedGripsCounter--;\r\n if (this._pressedGripsCounter === 1) {\r\n this.stopScalingByControllers();\r\n // reattach molecule to other controller\r\n const anotherController = event.target === this._controller1 ? this._controller2 : this._controller1;\r\n anotherController.addSavingWorldTransform(this._molContainer);\r\n } else if (this._pressedGripsCounter === 0) {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n enable(gfx) {\r\n if (!gfx) {\r\n logger.warn('WebVR couldn\\'t be enabled, because gfx is not defined');\r\n return;\r\n }\r\n this._gfx = gfx;\r\n const { renderer, camera } = gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n if (!camera) {\r\n throw new Error('No camera is available to toggle WebVR');\r\n }\r\n\r\n // enable xr in renderer\r\n renderer.xr.enabled = true;\r\n // add button for turning vr mode\r\n if (!this._button) {\r\n this._button = createWebVRButton(this);\r\n document.body.appendChild(this._button);\r\n } else {\r\n this._button.style.display = 'block';\r\n }\r\n // store fog setting\r\n this._mainFog = settings.now.fog;\r\n settings.set('fog', false);\r\n\r\n this._plugVRNodesIntoScene(gfx, renderer);\r\n this._setControllersListeners();\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n _plugVRNodesIntoScene(gfx, renderer) {\r\n // store common scene camera\r\n this._mainCamera.copy(gfx.camera);\r\n // add hierarchical structure for webVR into scene\r\n gfx.scene.add(this._user);\r\n // turn on webvr transformation\r\n gfx.scene.add(this._molContainer);\r\n this._molContainer.add(gfx.root);\r\n\r\n this._controller1 = renderer.xr.getController(0);\r\n this._controller2 = renderer.xr.getController(1);\r\n const mesh = this._createControllerMesh();\r\n this._controller1.add(mesh);\r\n this._controller2.add(mesh.clone());\r\n this._user.add(this._controller1);\r\n this._user.add(this._controller2);\r\n }\r\n\r\n _setControllersListeners() {\r\n this._controller1.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n\r\n this._controller1.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n }\r\n\r\n disable() {\r\n if (!this._gfx) {\r\n return;\r\n }\r\n const { renderer, camera } = this._gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n\r\n // nullify webxr callback for animation frame\r\n renderer.setAnimationLoop(null);\r\n const session = renderer.xr.getSession();\r\n if (session) {\r\n session.end();\r\n }\r\n renderer.xr.enabled = false;\r\n // remove button of VR entering\r\n if (this._button) {\r\n this._button.style.display = 'none';\r\n }\r\n // restore fog param\r\n settings.set('fog', this._mainFog);\r\n\r\n this._unplugVRNodesFromScene(camera);\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(false);\r\n }\r\n }\r\n\r\n _unplugVRNodesFromScene(camera) {\r\n // restore common camera\r\n if (this._mainCamera && camera) {\r\n camera.copy(this._mainCamera);\r\n }\r\n // turn off webvr transformation\r\n const root = this._molContainer.children[0];\r\n if (root) {\r\n this._gfx.scene.add(root);\r\n }\r\n this._molContainer.parent.remove(this._molContainer);\r\n if (this._user) {\r\n this._gfx.scene.remove(this._user);\r\n }\r\n // free scene nodes\r\n this._molContainer = null;\r\n this._user = null;\r\n this._scalingPivot = null;\r\n this._user = null;\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n }\r\n\r\n _createControllerMesh() {\r\n // visualize controllers with cylinders\r\n const geometry = new THREE.CylinderGeometry(0.04, 0.04, 0.3);\r\n const material = new UberMaterial({ lights: false, overrideColor: true });\r\n material.setUberOptions({ fixedColor: new THREE.Color(0x4444ff) });\r\n material.updateUniforms();\r\n const cylinder = new THREE.Mesh(geometry, material);\r\n cylinder.rotateX(-Math.PI / 2);\r\n return cylinder;\r\n }\r\n\r\n updateMoleculeScale() {\r\n if (!this._controller1 || !this._controller2) {\r\n return;\r\n }\r\n\r\n const self = this;\r\n // update molecule scaling by controllers\r\n if (self._pressedGripsCounter === 2) {\r\n // recalc scaling pivot\r\n gfxutils.getMiddlePoint(self._controller1.position, self._controller2.position, self._scalingPivot.position);\r\n // recalc scaler\r\n const dist = self._controller1.position.distanceTo(self._controller2.position);\r\n const scaler = dist / self._distance;\r\n self._scalingPivot.scale.multiplyScalar(scaler);\r\n // save cur distance for next frame\r\n self._distance = dist;\r\n }\r\n }\r\n\r\n /**\r\n * Reposition molecule right before the camera.\r\n * @note The proper way is to initiate headset in the place of common Miew's camera.\r\n * But threejs limitations on setting new XRReferenceSpace enforce the molecule repositioning\r\n * Hope, something will change.\r\n */\r\n moveSceneBehindHeadset() {\r\n const gfx = this._gfx;\r\n const { camera } = gfx;\r\n\r\n // set container position in camera space\r\n const container = this._molContainer;\r\n container.matrix.identity();\r\n container.position.set(0, 0, -4.0);\r\n container.updateMatrix();\r\n\r\n // update container world matrix\r\n container.matrixWorld.multiplyMatrices(camera.matrixWorld, container.matrix);\r\n // readd to scene\r\n gfx.scene.addSavingWorldTransform(container);\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n getCanvas() {\r\n const gfx = this._gfx;\r\n return (gfx && gfx.renderer) ? gfx.renderer.domElement : null;\r\n }\r\n}\r\n","/* global PACKAGE_VERSION:false */\r\nimport _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport { Spinner } from 'spin.js';\r\nimport Stats from './gfx/Stats';\r\nimport utils from './utils';\r\nimport JobHandle from './utils/JobHandle';\r\nimport options from './options';\r\nimport settings from './settings';\r\nimport chem from './chem';\r\nimport Visual from './Visual';\r\nimport ComplexVisual from './ComplexVisual';\r\nimport Complex from './chem/Complex';\r\nimport VolumeVisual from './VolumeVisual';\r\nimport io from './io/io';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport CSS2DRenderer from './gfx/CSS2DRenderer';\r\nimport ObjectControls from './ui/ObjectControls';\r\nimport Picker from './ui/Picker';\r\nimport Axes from './gfx/Axes';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport meshutils from './gfx/meshutils';\r\nimport FrameInfo from './gfx/FrameInfo';\r\nimport meshes from './gfx/meshes/meshes';\r\nimport LinesObject from './gfx/objects/LinesObj';\r\nimport UberMaterial from './gfx/shaders/UberMaterial';\r\nimport OutlineMaterial from './gfx/shaders/OutlineMaterial';\r\nimport FXAAMaterial from './gfx/shaders/FXAAMaterial';\r\nimport AOMaterial from './gfx/shaders/AOMaterial';\r\nimport AOHorBlurMaterial from './gfx/shaders/AOHorBlurMaterial';\r\nimport AOVertBlurWithBlendMaterial from './gfx/shaders/AOVertBlurWithBlendMaterial';\r\nimport AnaglyphMaterial from './gfx/shaders/AnaglyphMaterial';\r\nimport VolumeMaterial from './gfx/shaders/VolumeMaterial';\r\nimport ViewInterpolator from './gfx/ViewInterpolator';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\nimport logger from './utils/logger';\r\nimport Cookies from './utils/Cookies';\r\nimport capabilities from './gfx/capabilities';\r\nimport WebVRPoC from './gfx/vr/WebVRPoC';\r\nimport vertexScreenQuadShader from './gfx/shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromDistTex from './gfx/shaders/ScreenQuadFromDistortionTex.frag';\r\nimport getTopWindow from './utils/getTopWindow';\r\n\r\nconst {\r\n selectors,\r\n Atom,\r\n Residue,\r\n Chain,\r\n Molecule,\r\n} = chem;\r\n\r\nconst EDIT_MODE = { COMPLEX: 0, COMPONENT: 1, FRAGMENT: 2 };\r\n\r\nconst LOADER_NOT_FOUND = 'Could not find suitable loader for this source';\r\nconst PARSER_NOT_FOUND = 'Could not find suitable parser for this source';\r\n\r\n// Color management changed a lot in threejs 152+ version.\r\n// To keep miew colors we disable the new color management system\r\nTHREE.ColorManagement.enabled = false;\r\n\r\nconst { createElement } = utils;\r\n\r\nfunction updateFogRange(fog, center, radius) {\r\n fog.near = center - radius * settings.now.fogNearFactor;\r\n fog.far = center + radius * settings.now.fogFarFactor;\r\n}\r\n\r\nfunction removeExtension(fileName) {\r\n const dot = fileName.lastIndexOf('.');\r\n if (dot >= 0) {\r\n fileName = fileName.substr(0, dot);\r\n }\r\n return fileName;\r\n}\r\n\r\nfunction hasValidResidues(complex) {\r\n let hasValidRes = false;\r\n complex.forEachComponent((component) => {\r\n component.forEachResidue((residue) => {\r\n if (residue._isValid) {\r\n hasValidRes = true;\r\n }\r\n });\r\n });\r\n return hasValidRes;\r\n}\r\n\r\nfunction reportProgress(log, action, percent) {\r\n const TOTAL_PERCENT = 100;\r\n if (percent !== undefined) {\r\n log.debug(`${action}... ${Math.floor(percent * TOTAL_PERCENT)}%`);\r\n } else {\r\n log.debug(`${action}...`);\r\n }\r\n}\r\n\r\nfunction chooseFogColor() {\r\n return settings.now.fogColorEnable ? settings.now.fogColor : settings.now.bg.color;\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\n/**\r\n * Main 3D Molecular Viewer class.\r\n *\r\n * @param {object} opts - Viewer options.\r\n * @param {HTMLElement=} opts.container - DOM element that serves as a viewer container.\r\n * @param {object=} opts.settings - An object with properties to override default settings.\r\n * @param {string=} opts.settingsCookie='settings' - The name of the cookie to save current settings to.\r\n * @param {string=} opts.cookiePath='/' - The path option for cookies. Defaults to root.\r\n *\r\n * @exports Miew\r\n * @constructor\r\n */\r\nfunction Miew(opts) {\r\n EventDispatcher.call(this);\r\n this._opts = _.merge({\r\n settingsCookie: 'settings',\r\n cookiePath: '/',\r\n }, opts);\r\n /** @type {?object} */\r\n this._gfx = null;\r\n /** @type {ViewInterpolator} */\r\n this._interpolator = new ViewInterpolator();\r\n /** @type {HTMLElement} */\r\n this._container = (opts && opts.container)\r\n || document.getElementById('miew-container')\r\n || _.head(document.getElementsByClassName('miew-container'))\r\n || document.body;\r\n /** @type {HTMLElement} */\r\n this._containerRoot = this._container;\r\n\r\n /** @type {boolean} */\r\n this._running = false;\r\n /** @type {boolean} */\r\n this._halting = false;\r\n /** @type {boolean} */\r\n this._building = false;\r\n /** @type {boolean} */\r\n this._needRender = true;\r\n /** @type {boolean} */\r\n this._hotKeysEnabled = true;\r\n\r\n /** @type {Settings} */\r\n this.settings = settings;\r\n const log = logger;\r\n log.console = DEBUG;\r\n log.level = DEBUG ? 'debug' : 'info';\r\n /**\r\n * @type {Logger}\r\n * @example\r\n * miew.logger.addEventListener('message', function _onLogMessage(evt) {\r\n * console.log(evt.message);\r\n * });\r\n */\r\n this.logger = log;\r\n\r\n this._cookies = new Cookies(this);\r\n this.restoreSettings();\r\n if (opts && opts.settings) {\r\n this.settings.set(opts.settings);\r\n }\r\n\r\n /** @type {?Spinner} */\r\n this._spinner = null;\r\n /** @type {JobHandle[]} */\r\n this._loading = [];\r\n /** @type {?number}\r\n * @deprecated until Animation system refactoring\r\n */\r\n this._animInterval = null;\r\n\r\n /** @type {object} */\r\n this._visuals = {};\r\n /** @type {?string} */\r\n this._curVisualName = null;\r\n\r\n /** @type {array} */\r\n this._objects = [];\r\n\r\n /** @type {object} */\r\n this._sourceWindow = null;\r\n\r\n this.reset();\r\n\r\n if (this._repr) {\r\n log.debug(`Selected ${this._repr.mode.name} mode with ${this._repr.colorer.name} colorer.`);\r\n }\r\n\r\n const self = this;\r\n Miew.registeredPlugins.forEach((plugin) => {\r\n plugin.call(self);\r\n });\r\n\r\n this._initOnSettingsChanged();\r\n}\r\n\r\nMiew.prototype = Object.create(EventDispatcher.prototype);\r\nMiew.prototype.constructor = Miew;\r\n\r\nMiew.prototype.getMaxRepresentationCount = function () {\r\n return ComplexVisual.NUM_REPRESENTATION_BITS;\r\n};\r\n\r\n/**\r\n * Replace viewer container contents with a DOM element.\r\n * @param {HTMLElement} container - parent container.\r\n * @param {HTMLElement} element - DOM element to show.\r\n * @private\r\n */\r\nfunction _setContainerContents(container, element) {\r\n const parent = container;\r\n while (parent.firstChild) {\r\n parent.removeChild(parent.firstChild);\r\n }\r\n parent.appendChild(element);\r\n}\r\n\r\n/**\r\n * Update Shadow Camera target position and frustum.\r\n * @private\r\n */\r\nMiew.prototype._updateShadowCamera = (function () {\r\n const shadowMatrix = new THREE.Matrix4();\r\n const direction = new THREE.Vector3();\r\n const OBB = { center: new THREE.Vector3(), halfSize: new THREE.Vector3() };\r\n\r\n return function () {\r\n this._gfx.scene.updateMatrixWorld();\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = this._gfx.scene.children[i];\r\n shadowMatrix.copy(light.shadow.camera.matrixWorldInverse);\r\n this.getOBB(shadowMatrix, OBB);\r\n\r\n direction.subVectors(light.target.position, light.position);\r\n light.position.subVectors(OBB.center, direction);\r\n light.target.position.copy(OBB.center);\r\n\r\n light.shadow.bias = 0.09;\r\n light.shadow.camera.bottom = -OBB.halfSize.y;\r\n light.shadow.camera.top = OBB.halfSize.y;\r\n light.shadow.camera.right = OBB.halfSize.x;\r\n light.shadow.camera.left = -OBB.halfSize.x;\r\n light.shadow.camera.near = direction.length() - OBB.halfSize.z;\r\n light.shadow.camera.far = direction.length() + OBB.halfSize.z;\r\n\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Initialize the viewer.\r\n * @returns {boolean} true on success.\r\n * @throws Forwards exception raised during initialization.\r\n * @see Miew#term\r\n */\r\nMiew.prototype.init = function () {\r\n const container = this._container;\r\n const elem = utils.createElement('div', { class: 'miew-canvas' });\r\n _setContainerContents(container, elem);\r\n this._container = elem;\r\n\r\n const frag = document.createDocumentFragment();\r\n frag.appendChild(this._msgMode = createElement(\r\n 'div',\r\n { class: 'mode-message overlay' },\r\n createElement('p', {}, 'COMPONENT EDIT MODE'),\r\n ));\r\n frag.appendChild(this._msgAtomInfo = createElement(\r\n 'div',\r\n { class: 'atom-info overlay' },\r\n createElement('p', {}, ''),\r\n ));\r\n container.appendChild(frag);\r\n\r\n if (this._gfx !== null) { // block double init\r\n return true;\r\n }\r\n\r\n const self = this;\r\n this._showMessage('Viewer is being initialized...');\r\n try {\r\n this._initGfx();\r\n\r\n this._initListeners();\r\n this._spinner = new Spinner({\r\n lines: 13,\r\n length: 28,\r\n width: 14,\r\n radius: 42,\r\n color: '#fff',\r\n zIndex: 700,\r\n });\r\n\r\n const target = getTopWindow();\r\n target.addEventListener('keydown', (event) => {\r\n self._onKeyDown(event);\r\n });\r\n\r\n target.addEventListener('keyup', (event) => {\r\n self._onKeyUp(event);\r\n });\r\n\r\n this._objectControls = new ObjectControls(\r\n this._gfx.root,\r\n this._gfx.pivot,\r\n this._gfx.camera,\r\n this._gfx.renderer.domElement,\r\n () => self._getAltObj(),\r\n );\r\n this._objectControls.addEventListener('change', (e) => {\r\n if (settings.now.shadow.on) {\r\n self._updateShadowCamera();\r\n }\r\n // route rotate, zoom, translate and translatePivot events to the external API\r\n switch (e.action) {\r\n case 'rotate':\r\n self.dispatchEvent({ type: 'rotate', quaternion: e.quaternion });\r\n break;\r\n case 'zoom':\r\n self.dispatchEvent({ type: 'zoom', factor: e.factor });\r\n break;\r\n default:\r\n self.dispatchEvent({ type: e.action });\r\n }\r\n self.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n });\r\n\r\n const gfx = this._gfx;\r\n this._picker = new Picker(gfx.root, gfx.camera, gfx.renderer.domElement);\r\n this._picker.addEventListener('newpick', (event) => {\r\n self._onPick(event);\r\n });\r\n this._picker.addEventListener('dblclick', (event) => {\r\n self.center(event);\r\n });\r\n } catch (error) {\r\n if (error.name === 'TypeError' && error.message === 'Cannot read property \\'getExtension\\' of null') {\r\n this._showMessage('Could not create WebGL context.');\r\n } else if (error.message.search(/webgl/i) > 1) {\r\n this._showMessage(error.message);\r\n } else {\r\n this._showMessage('Viewer initialization failed.');\r\n throw error;\r\n }\r\n return false;\r\n }\r\n\r\n // automatically load default file\r\n const file = this._opts && this._opts.load;\r\n if (file) {\r\n const type = this._opts && this._opts.type;\r\n this.load(file, { fileType: type, keepRepsInfo: true });\r\n }\r\n\r\n return true;\r\n};\r\n\r\n/**\r\n * Terminate the viewer completely.\r\n * @see Miew#init\r\n */\r\nMiew.prototype.term = function () {\r\n this._showMessage('Viewer has been terminated.');\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n this.halt();\r\n this._gfx = null;\r\n};\r\n\r\n/**\r\n * Display message inside the viewer container, hiding WebGL canvas.\r\n * @param {string} msg - Message to show.\r\n * @private\r\n */\r\nMiew.prototype._showMessage = function (msg) {\r\n const element = document.createElement('div');\r\n element.setAttribute('class', 'miew-message');\r\n element.appendChild(document.createElement('p')).appendChild(document.createTextNode(msg));\r\n _setContainerContents(this._container, element);\r\n};\r\n\r\n/**\r\n * Display WebGL canvas inside the viewer container, hiding any message shown.\r\n * @private\r\n */\r\nMiew.prototype._showCanvas = function () {\r\n _setContainerContents(this._container, this._gfx.renderer.domElement);\r\n};\r\n\r\nMiew.prototype._requestAnimationFrame = function (callback) {\r\n const { xr } = this._gfx.renderer;\r\n if (xr && xr.enabled) {\r\n this._gfx.renderer.setAnimationLoop(callback);\r\n return;\r\n }\r\n requestAnimationFrame(callback);\r\n};\r\n\r\nfunction arezSpritesSupported(context) {\r\n return context.getExtension('EXT_frag_depth');\r\n}\r\n\r\nfunction isAOSupported(context) {\r\n return (context.getExtension('WEBGL_depth_texture')\r\n && context.getExtension('WEBGL_draw_buffers'));\r\n}\r\n\r\n/**\r\n * Initialize WebGL and set 3D scene up.\r\n * @private\r\n */\r\nMiew.prototype._initGfx = function () {\r\n const gfx = {\r\n width: this._container.clientWidth,\r\n height: this._container.clientHeight,\r\n };\r\n\r\n const webGLOptions = { preserveDrawingBuffer: true, alpha: true, premultipliedAlpha: false };\r\n if (settings.now.antialias) {\r\n webGLOptions.antialias = true;\r\n }\r\n\r\n gfx.renderer2d = new CSS2DRenderer();\r\n\r\n gfx.renderer = new THREE.WebGL1Renderer(webGLOptions);\r\n gfx.renderer.shadowMap.enabled = settings.now.shadow.on;\r\n gfx.renderer.shadowMap.autoUpdate = false;\r\n gfx.renderer.shadowMap.type = THREE.PCFShadowMap;\r\n capabilities.init(gfx.renderer);\r\n\r\n // z-sprites and ambient occlusion possibility\r\n if (!arezSpritesSupported(gfx.renderer.getContext())) {\r\n settings.set('zSprites', false);\r\n }\r\n if (!isAOSupported(gfx.renderer.getContext())) {\r\n settings.set('ao', false);\r\n }\r\n\r\n gfx.renderer.autoClear = false;\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n gfx.camera = new THREE.PerspectiveCamera(\r\n settings.now.camFov,\r\n gfx.width / gfx.height,\r\n settings.now.camNear,\r\n settings.now.camFar,\r\n );\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.position.z = settings.now.camDistance;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n\r\n gfx.stereoCam = new THREE.StereoCamera();\r\n\r\n gfx.scene = new THREE.Scene();\r\n\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color, settings.now.camNear, settings.now.camFar);\r\n\r\n gfx.root = new gfxutils.RCGroup();\r\n gfx.scene.add(gfx.root);\r\n\r\n gfx.pivot = new gfxutils.RCGroup();\r\n gfx.root.add(gfx.pivot);\r\n\r\n gfx.selectionScene = new THREE.Scene();\r\n gfx.selectionRoot = new THREE.Group();\r\n gfx.selectionRoot.matrixAutoUpdate = false;\r\n gfx.selectionScene.add(gfx.selectionRoot);\r\n\r\n gfx.selectionPivot = new THREE.Group();\r\n gfx.selectionPivot.matrixAutoUpdate = false;\r\n gfx.selectionRoot.add(gfx.selectionPivot);\r\n\r\n const light12 = new THREE.DirectionalLight(0xffffff, 0.45);\r\n light12.position.set(0, 0.414, 1);\r\n light12.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n light12.castShadow = true;\r\n light12.shadow.bias = 0.09;\r\n light12.shadow.radius = settings.now.shadow.radius;\r\n light12.shadow.camera.layers.set(gfxutils.LAYERS.SHADOWMAP);\r\n\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n const shadowMapSize = Math.max(gfx.width, gfx.height) * pixelRatio;\r\n light12.shadow.mapSize.width = shadowMapSize;\r\n light12.shadow.mapSize.height = shadowMapSize;\r\n light12.target.position.set(0.0, 0.0, 0.0);\r\n gfx.scene.add(light12);\r\n gfx.scene.add(light12.target);\r\n\r\n const light3 = new THREE.AmbientLight(0x666666);\r\n light3.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.scene.add(light3);\r\n\r\n // add axes\r\n gfx.axes = new Axes(gfx.root, gfx.camera);\r\n const deviceWidth = gfx.width * pixelRatio;\r\n const deviceHeight = gfx.height * pixelRatio;\r\n\r\n gfx.offscreenBuf = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat, depthBuffer: true,\r\n },\r\n );\r\n\r\n if (gfx.renderer.getContext().getExtension('WEBGL_depth_texture')) {\r\n gfx.offscreenBuf.depthTexture = new THREE.DepthTexture();\r\n gfx.offscreenBuf.depthTexture.type = THREE.UnsignedShortType;\r\n }\r\n\r\n gfx.offscreenBuf2 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf3 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf4 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf3;\r\n gfx.volFFTex = gfx.offscreenBuf4;\r\n gfx.volWFFTex = gfx.offscreenBuf;\r\n\r\n // use float textures for volume rendering if possible\r\n if (gfx.renderer.getContext().getExtension('OES_texture_float')) {\r\n gfx.offscreenBuf5 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf6 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf7 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf5;\r\n gfx.volFFTex = gfx.offscreenBuf6;\r\n gfx.volWFFTex = gfx.offscreenBuf7;\r\n } else {\r\n this.logger.warn('Device doesn\\'t support OES_texture_float extension');\r\n }\r\n\r\n gfx.stereoBufL = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.stereoBufR = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n this._gfx = gfx;\r\n this._showCanvas();\r\n\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n\r\n this._container.appendChild(gfx.renderer2d.getElement());\r\n\r\n // add FPS counter\r\n const stats = new Stats();\r\n stats.domElement.style.position = 'absolute';\r\n stats.domElement.style.right = '0';\r\n stats.domElement.style.bottom = '0';\r\n this._container.appendChild(stats.domElement);\r\n this._fps = stats;\r\n this._fps.show(settings.now.fps);\r\n};\r\n\r\n/**\r\n * Setup event listeners.\r\n * @private\r\n */\r\nMiew.prototype._initListeners = function () {\r\n const self = this;\r\n window.addEventListener('resize', () => {\r\n self._onResize();\r\n });\r\n};\r\n\r\n/**\r\n * Try to add numbers to the base name to make it unique among visuals\r\n * @private\r\n */\r\nMiew.prototype._makeUniqueVisualName = function (baseName) {\r\n if (!baseName) {\r\n return Math.random().toString();\r\n }\r\n\r\n let name = baseName;\r\n let suffix = 1;\r\n while (this._visuals.hasOwnProperty(name)) {\r\n name = `${baseName} (${suffix.toString()})`;\r\n suffix++;\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Add visual to the viewer\r\n * @private\r\n */\r\nMiew.prototype._addVisual = function (visual) {\r\n if (!visual) {\r\n return null;\r\n }\r\n\r\n // change visual name in order to make it unique\r\n const name = this._makeUniqueVisualName(visual.name);\r\n visual.name = name;\r\n\r\n this._visuals[name] = visual;\r\n this._gfx.pivot.add(visual);\r\n if (visual.getSelectionGeo) {\r\n this._gfx.selectionPivot.add(visual.getSelectionGeo());\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Remove visual from the viewer\r\n * @private\r\n */\r\nMiew.prototype._removeVisual = function (visual) {\r\n let name = '';\r\n let obj = null;\r\n if (visual instanceof Visual) {\r\n ({ name } = visual);\r\n obj = visual;\r\n } else if (typeof visual === 'string') {\r\n name = visual;\r\n obj = this._visuals[name];\r\n }\r\n\r\n if (!obj || !this._visuals.hasOwnProperty(name) || this._visuals[name] !== obj) {\r\n return;\r\n }\r\n\r\n if (name === this._curVisualName) {\r\n this._curVisualName = undefined;\r\n }\r\n\r\n delete this._visuals[name];\r\n obj.release(); // removes nodes from scene\r\n\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Call specified function for each Visual\r\n * @private\r\n */\r\nMiew.prototype._forEachVisual = function (callback) {\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Release (destroy) all visuals in the scene\r\n * @private\r\n */\r\nMiew.prototype._releaseAllVisuals = function () {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n this._visuals[name].release();\r\n }\r\n }\r\n\r\n this._visuals = {};\r\n};\r\n\r\n/**\r\n * Call specified function for each ComplexVisual\r\n * @private\r\n */\r\nMiew.prototype._forEachComplexVisual = function (callback) {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)\r\n && this._visuals[name] instanceof ComplexVisual) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual with specified name, or current (if not found), or any, or null\r\n * @private\r\n */\r\nMiew.prototype._getComplexVisual = function (name) {\r\n name = name || this._curVisualName;\r\n let any = null;\r\n let named = null;\r\n this._forEachComplexVisual((visual) => {\r\n any = visual;\r\n if (visual.name === name) {\r\n named = visual;\r\n }\r\n });\r\n return named || any;\r\n};\r\n\r\n/**\r\n * Returns first found VolumeVisual (no more than one should be present actually)\r\n * @private\r\n */\r\nMiew.prototype._getVolumeVisual = function () {\r\n let any = null;\r\n this._forEachVisual((visual) => {\r\n if (visual instanceof VolumeVisual) {\r\n any = visual;\r\n }\r\n });\r\n return any;\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual corresponding to specified complex\r\n * @private\r\n */\r\nMiew.prototype._getVisualForComplex = function (complex) {\r\n if (!complex) {\r\n return null;\r\n }\r\n\r\n let found = null;\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getComplex() === complex) {\r\n found = visual;\r\n }\r\n });\r\n return found;\r\n};\r\n\r\n/*\r\n * Get a list of names of visuals currently shown by the viewer\r\n */\r\nMiew.prototype.getVisuals = function () {\r\n return Object.keys(this._visuals);\r\n};\r\n\r\n/*\r\n * Get complex visuals count\r\n */\r\nMiew.prototype.getComplexVisualsCount = function () {\r\n let count = 0;\r\n this._forEachComplexVisual(() => count++);\r\n return count;\r\n};\r\n\r\n/*\r\n * Get current visual\r\n */\r\nMiew.prototype.getCurrentVisual = function () {\r\n return this._curVisualName;\r\n};\r\n\r\n/*\r\n * Set current visual.\r\n * All further operations will be performed on this visual (complex) if not stated otherwise.\r\n */\r\nMiew.prototype.setCurrentVisual = function (name) {\r\n if (!this._visuals[name]) {\r\n return;\r\n }\r\n\r\n this._curVisualName = name;\r\n};\r\n\r\n/**\r\n * Run the viewer, start processing update/render frames periodically.\r\n * Has no effect if already running.\r\n * @see Miew#halt\r\n */\r\nMiew.prototype.run = function () {\r\n if (!this._running) {\r\n this._running = true;\r\n if (this._halting) {\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._objectControls.enable(true);\r\n this._interpolator.resume();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to stop.\r\n * Will be processed during the next frame.\r\n * @see Miew#run\r\n */\r\nMiew.prototype.halt = function () {\r\n if (this._running) {\r\n this._discardComponentEdit();\r\n this._discardFragmentEdit();\r\n this._objectControls.enable(false);\r\n this._interpolator.pause();\r\n this._halting = true;\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to start / stop responsing\r\n * on hot keys.\r\n * @param enabled - start (true) or stop (false) response on hot keys.\r\n */\r\nMiew.prototype.enableHotKeys = function (enabled) {\r\n this._hotKeysEnabled = enabled;\r\n this._objectControls.enableHotkeys(enabled);\r\n};\r\n\r\n/**\r\n * Callback which processes window resize.\r\n * @private\r\n */\r\nMiew.prototype._onResize = function () {\r\n const gfx = this._gfx;\r\n if (!gfx) {\r\n return;\r\n }\r\n\r\n this._needRender = true;\r\n\r\n gfx.width = this._container.clientWidth;\r\n gfx.height = this._container.clientHeight;\r\n\r\n gfx.camera.aspect = gfx.width / gfx.height;\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n this.dispatchEvent({ type: 'resize' });\r\n};\r\n\r\nMiew.prototype._resizeOffscreenBuffers = function (width, height, stereo) {\r\n const gfx = this._gfx;\r\n stereo = stereo || 'NONE';\r\n const isAnaglyph = (stereo === 'NONE' || stereo === 'ANAGLYPH');\r\n const multi = isAnaglyph ? 1 : 0.5;\r\n gfx.offscreenBuf.setSize(multi * width, height);\r\n gfx.offscreenBuf2.setSize(multi * width, height);\r\n gfx.offscreenBuf3.setSize(multi * width, height);\r\n gfx.offscreenBuf4.setSize(multi * width, height);\r\n if (gfx.offscreenBuf5) {\r\n gfx.offscreenBuf5.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf6) {\r\n gfx.offscreenBuf6.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf7) {\r\n gfx.offscreenBuf7.setSize(multi * width, height);\r\n }\r\n if (isAnaglyph) {\r\n gfx.stereoBufL.setSize(width, height);\r\n gfx.stereoBufR.setSize(width, height);\r\n }\r\n};\r\n\r\n/**\r\n * Callback which processes update/render frames.\r\n * @private\r\n */\r\nMiew.prototype._onTick = function () {\r\n if (this._halting) {\r\n this._running = false;\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._fps.update();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n\r\n this._onUpdate();\r\n if (this._needRender) {\r\n this._onRender();\r\n this._needRender = !settings.now.suspendRender || settings.now.stereo === 'WEBVR';\r\n }\r\n};\r\n\r\nMiew.prototype._getBSphereRadius = function () {\r\n // calculate radius that would include all visuals\r\n let radius = 0;\r\n this._forEachVisual((visual) => {\r\n radius = Math.max(radius, visual.getBoundaries().boundingSphere.radius);\r\n });\r\n return radius * this._objectControls.getScale();\r\n};\r\n\r\n/**\r\n * Calculate bounding box that would include all visuals and being axis aligned in world defined by\r\n * transformation matrix: matrix\r\n * @param {Matrix4} matrix - transformation matrix.\r\n * @param {object} OBB - calculating bounding box.\r\n * @param {Vector3} OBB.center - OBB center.\r\n * @param {Vector3} OBB.halfSize - half magnitude of OBB sizes.\r\n */\r\nMiew.prototype.getOBB = (function () {\r\n const _bSphereForOneVisual = new THREE.Sphere();\r\n const _bBoxForOneVisual = new THREE.Box3();\r\n const _bBox = new THREE.Box3();\r\n\r\n const _invMatrix = new THREE.Matrix4();\r\n\r\n const _points = [\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n ];\r\n\r\n return function (matrix, OBB) {\r\n _bBox.makeEmpty();\r\n\r\n this._forEachVisual((visual) => {\r\n _bSphereForOneVisual.copy(visual.getBoundaries().boundingSphere);\r\n _bSphereForOneVisual.applyMatrix4(visual.matrixWorld).applyMatrix4(matrix);\r\n _bSphereForOneVisual.getBoundingBox(_bBoxForOneVisual);\r\n _bBox.union(_bBoxForOneVisual);\r\n });\r\n _bBox.getCenter(OBB.center);\r\n\r\n _invMatrix.copy(matrix).invert();\r\n OBB.center.applyMatrix4(_invMatrix);\r\n\r\n const { min } = _bBox;\r\n const { max } = _bBox;\r\n _points[0].set(min.x, min.y, min.z); // 000\r\n _points[1].set(max.x, min.y, min.z); // 100\r\n _points[2].set(min.x, max.y, min.z); // 010\r\n _points[3].set(min.x, min.y, max.z); // 001\r\n for (let i = 0, l = _points.length; i < l; i++) {\r\n _points[i].applyMatrix4(_invMatrix);\r\n }\r\n\r\n OBB.halfSize.set(\r\n Math.abs(_points[0].x - _points[1].x),\r\n Math.abs(_points[0].y - _points[2].y),\r\n Math.abs(_points[0].z - _points[3].z),\r\n ).multiplyScalar(0.5);\r\n };\r\n}());\r\n\r\nMiew.prototype._updateFog = function () {\r\n const gfx = this._gfx;\r\n\r\n if (settings.now.fog) {\r\n if (typeof gfx.scene.fog === 'undefined' || gfx.scene.fog === null) {\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color);\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n updateFogRange(gfx.scene.fog, gfx.camera.position.z, this._getBSphereRadius());\r\n } else if (gfx.scene.fog) {\r\n gfx.scene.fog = undefined;\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n};\r\n\r\nMiew.prototype._onUpdate = function () {\r\n if (this.isScriptingCommandAvailable !== undefined && this.isScriptingCommandAvailable() && !this._building) {\r\n this.callNextCmd();\r\n }\r\n\r\n this._objectControls.update();\r\n\r\n this._forEachComplexVisual((visual) => {\r\n visual.getComplex().update();\r\n });\r\n\r\n if (settings.now.autobuild && !this._loading.length && !this._building && this._needRebuild()) {\r\n this.rebuild();\r\n }\r\n\r\n if (!this._loading.length && !this._building && !this._needRebuild()) {\r\n this._updateView();\r\n }\r\n\r\n this._updateFog();\r\n\r\n if (this._gfx.renderer.xr.enabled) {\r\n this.webVR.updateMoleculeScale();\r\n }\r\n};\r\n\r\nMiew.prototype._onRender = function () {\r\n const gfx = this._gfx;\r\n\r\n // update all matrices\r\n gfx.scene.updateMatrixWorld();\r\n gfx.camera.updateMatrixWorld();\r\n\r\n this._clipPlaneUpdateValue(this._getBSphereRadius());\r\n this._fogFarUpdateValue();\r\n\r\n gfx.renderer.setRenderTarget(null);\r\n gfx.renderer.clear();\r\n\r\n this._renderFrame(settings.now.stereo);\r\n};\r\n\r\nMiew.prototype._renderFrame = (function () {\r\n const _anaglyphMat = new AnaglyphMaterial();\r\n const _size = new THREE.Vector2();\r\n\r\n return function (stereo) {\r\n const gfx = this._gfx;\r\n const { renderer } = gfx;\r\n\r\n renderer.getSize(_size);\r\n\r\n if (stereo !== 'NONE') {\r\n gfx.camera.focus = gfx.camera.position.z; // set focus to the center of the object\r\n gfx.stereoCam.aspect = 1.0;\r\n\r\n // in anaglyph mode we render full-size image for each eye\r\n // while in other stereo modes only half-size (two images on the screen)\r\n if (stereo === 'ANAGLYPH') {\r\n gfx.stereoCam.update(gfx.camera);\r\n } else {\r\n gfx.stereoCam.updateHalfSized(gfx.camera, settings.now.camFov);\r\n }\r\n }\r\n\r\n // resize offscreen buffers to match the target\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n this._resizeOffscreenBuffers(_size.width * pixelRatio, _size.height * pixelRatio, stereo);\r\n\r\n this._renderShadowMap();\r\n\r\n switch (stereo) {\r\n case 'WEBVR':\r\n case 'NONE':\r\n this._renderScene(gfx.camera, false);\r\n break;\r\n case 'SIMPLE':\r\n case 'DISTORTED':\r\n renderer.setScissorTest(true);\r\n\r\n renderer.setScissor(0, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(0, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraL, stereo === 'DISTORTED');\r\n\r\n renderer.setScissor(_size.width / 2, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(_size.width / 2, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraR, stereo === 'DISTORTED');\r\n\r\n renderer.setScissorTest(false);\r\n break;\r\n case 'ANAGLYPH':\r\n this._renderScene(this._gfx.stereoCam.cameraL, false, gfx.stereoBufL);\r\n this._renderScene(this._gfx.stereoCam.cameraR, false, gfx.stereoBufR);\r\n renderer.setRenderTarget(null);\r\n _anaglyphMat.uniforms.srcL.value = gfx.stereoBufL.texture;\r\n _anaglyphMat.uniforms.srcR.value = gfx.stereoBufR.texture;\r\n gfx.renderer.renderScreenQuad(_anaglyphMat);\r\n break;\r\n default:\r\n }\r\n\r\n gfx.renderer2d.render(gfx.scene, gfx.camera);\r\n\r\n if (settings.now.axes && gfx.axes && !gfx.renderer.xr.enabled) {\r\n gfx.axes.render(renderer);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._onBgColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx) {\r\n if (gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onFogColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx && gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._setUberMaterialValues = function (values) {\r\n this._gfx.root.traverse((obj) => {\r\n if ((obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line)\r\n && obj.material instanceof UberMaterial) {\r\n obj.material.setValues(values);\r\n obj.material.needsUpdate = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) {\r\n const gfx = this._gfx;\r\n const gl = gfx.renderer.getContext();\r\n const ext = gl.getExtension('WEBGL_draw_buffers');\r\n const { properties } = gfx.renderer;\r\n\r\n if (!on) {\r\n ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, null]);\r\n return;\r\n }\r\n\r\n // take extra texture from Texture Buffer\r\n gfx.renderer.setRenderTarget(textureBuffer);\r\n const tx8 = properties.get(textureBuffer.texture).__webglTexture;\r\n gl.bindTexture(gl.TEXTURE_2D, tx8);\r\n\r\n // take texture and framebuffer from renderbuffer\r\n gfx.renderer.setRenderTarget(renderBuffer);\r\n const fb = properties.get(renderBuffer).__webglFramebuffer;\r\n const tx = properties.get(renderBuffer.texture).__webglTexture;\r\n\r\n // set framebuffer\r\n gl.bindFramebuffer(gl.FRAMEBUFFER, fb);\r\n fb.width = renderBuffer.width;\r\n fb.height = renderBuffer.height;\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT0, gl.TEXTURE_2D, tx, 0);\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, ext.COLOR_ATTACHMENT1_WEBGL, gl.TEXTURE_2D, tx8, 0);\r\n\r\n // mapping textures\r\n ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, ext.COLOR_ATTACHMENT1_WEBGL]);\r\n};\r\n\r\nMiew.prototype._renderScene = (function () {\r\n return function (camera, distortion, target) {\r\n distortion = distortion || false;\r\n target = target || null;\r\n\r\n const gfx = this._gfx;\r\n\r\n // render to offscreen buffer\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.clear();\r\n if (gfx.renderer.xr.enabled) {\r\n gfx.renderer.render(gfx.scene, camera);\r\n return;\r\n }\r\n\r\n // clean buffer for normals texture\r\n gfx.renderer.setClearColor(0x000000, 0.0);\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf4);\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.clear();\r\n\r\n const bHaveComplexes = (this._getComplexVisual() !== null);\r\n const volumeVisual = this._getVolumeVisual();\r\n const ssao = bHaveComplexes && settings.now.ao;\r\n\r\n if (ssao) {\r\n this._enableMRT(true, gfx.offscreenBuf, gfx.offscreenBuf4);\r\n }\r\n\r\n if (settings.now.transparency === 'prepass') {\r\n this._renderWithPrepassTransparency(camera, gfx.offscreenBuf);\r\n } else if (settings.now.transparency === 'standard') {\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n }\r\n\r\n if (ssao) {\r\n this._enableMRT(false, null, null);\r\n }\r\n\r\n // when fxaa we should get resulting image in temp off-screen buff2 for further postprocessing with fxaa filter\r\n // otherwise we render to canvas\r\n const outline = bHaveComplexes && settings.now.outline.on;\r\n const fxaa = bHaveComplexes && settings.now.fxaa;\r\n const volume = (volumeVisual !== null) && (volumeVisual.getMesh().material != null);\r\n let dstBuffer = (ssao || outline || volume || fxaa || distortion) ? gfx.offscreenBuf2 : target;\r\n let srcBuffer = gfx.offscreenBuf;\r\n\r\n if (ssao) {\r\n this._performAO(\r\n srcBuffer,\r\n gfx.offscreenBuf4,\r\n gfx.offscreenBuf.depthTexture,\r\n dstBuffer,\r\n gfx.offscreenBuf3,\r\n gfx.offscreenBuf2,\r\n );\r\n if (!fxaa && !distortion && !volume && !outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = target;\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n } else {\r\n // just copy color buffer to dst buffer\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n\r\n // outline\r\n if (outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = (volume || fxaa || distortion) ? gfx.offscreenBuf3 : target;\r\n if (srcBuffer != null) {\r\n this._renderOutline(camera, gfx.offscreenBuf, srcBuffer, dstBuffer);\r\n }\r\n }\r\n\r\n // render selected part with outline material\r\n this._renderSelection(camera, gfx.offscreenBuf, dstBuffer);\r\n\r\n if (volume) {\r\n // copy current picture to the buffer that retains depth-data of the original molecule render\r\n // so that volume renderer could use depth-test\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n dstBuffer = gfx.offscreenBuf;\r\n this._renderVolume(volumeVisual, camera, dstBuffer, gfx.volBFTex, gfx.volFFTex, gfx.volWFFTex);\r\n\r\n // if this is the last stage -- copy image to target\r\n if (!fxaa && !distortion) {\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n }\r\n }\r\n\r\n srcBuffer = dstBuffer;\r\n\r\n if (fxaa) {\r\n dstBuffer = distortion ? gfx.offscreenBuf4 : target;\r\n this._performFXAA(srcBuffer, dstBuffer);\r\n srcBuffer = dstBuffer;\r\n }\r\n\r\n if (distortion) {\r\n dstBuffer = target;\r\n this._performDistortion(srcBuffer, dstBuffer, true);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._performDistortion = (function () {\r\n const _scene = new THREE.Scene();\r\n const _camera = new THREE.OrthographicCamera(-1.0, 1.0, 1.0, -1.0, -500, 1000);\r\n\r\n const _material = new THREE.RawShaderMaterial({\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n aberration: { type: 'fv3', value: new THREE.Vector3(1.0) },\r\n },\r\n vertexShader: vertexScreenQuadShader,\r\n fragmentShader: fragmentScreenQuadFromDistTex,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n const _geo = gfxutils.buildDistorionMesh(10, 10, settings.now.debug.stereoBarrel);\r\n _scene.add(new meshes.Mesh(_geo, _material));\r\n\r\n return function (srcBuffer, targetBuffer, mesh) {\r\n this._gfx.renderer.setRenderTarget(targetBuffer);\r\n this._gfx.renderer.clear();\r\n\r\n if (mesh) {\r\n _material.uniforms.srcTex.value = srcBuffer.texture;\r\n _material.uniforms.aberration.value.set(0.995, 1.0, 1.01);\r\n this._gfx.renderer.render(_scene, _camera);\r\n } else {\r\n this._gfx.renderer.renderScreenQuadFromTexWithDistortion(srcBuffer, settings.now.debug.stereoBarrel);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._renderOutline = (function () {\r\n const _outlineMaterial = new OutlineMaterial({ depth: true });\r\n\r\n return function (camera, srcDepthBuffer, srcColorBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcColorBuffer.texture;\r\n _outlineMaterial.uniforms.srcDepthTex.value = srcDepthBuffer.depthTexture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcDepthBuffer.width, srcDepthBuffer.height);\r\n _outlineMaterial.uniforms.color.value = new THREE.Color(settings.now.outline.color);\r\n _outlineMaterial.uniforms.threshold.value = settings.now.outline.threshold;\r\n _outlineMaterial.uniforms.thickness.value = new THREE.Vector2(\r\n settings.now.outline.thickness,\r\n settings.now.outline.thickness,\r\n );\r\n\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._renderShadowMap = (function () {\r\n const pars = { minFilter: THREE.NearestFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat };\r\n\r\n return function () {\r\n if (!settings.now.shadow.on) {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n const currentRenderTarget = gfx.renderer.getRenderTarget();\r\n const activeCubeFace = gfx.renderer.getActiveCubeFace();\r\n const activeMipmapLevel = gfx.renderer.getActiveMipmapLevel();\r\n\r\n const _state = gfx.renderer.state;\r\n\r\n // Set GL state for depth map.\r\n _state.setBlending(THREE.NoBlending);\r\n _state.buffers.color.setClear(1, 1, 1, 1);\r\n _state.buffers.depth.setTest(true);\r\n _state.setScissorTest(false);\r\n\r\n for (let i = 0; i < gfx.scene.children.length; i++) {\r\n if (gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = gfx.scene.children[i];\r\n\r\n if (light.shadow.map == null) {\r\n light.shadow.map = new THREE.WebGLRenderTarget(light.shadow.mapSize.width, light.shadow.mapSize.height, pars);\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n light.shadow.updateMatrices(light);\r\n\r\n gfx.renderer.setRenderTarget(light.shadow.map);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.render(gfx.scene, light.shadow.camera);\r\n }\r\n }\r\n gfx.renderer.setRenderTarget(currentRenderTarget, activeCubeFace, activeMipmapLevel);\r\n };\r\n}());\r\n\r\n/**\r\n * Check if there is selection which must be rendered or not.\r\n * @private\r\n * @returns {boolean} true on existing selection to render\r\n */\r\nMiew.prototype._hasSelectionToRender = function () {\r\n const selPivot = this._gfx.selectionPivot;\r\n\r\n for (let i = 0; i < selPivot.children.length; i++) {\r\n const selPivotChild = selPivot.children[i];\r\n if (selPivotChild.children.length > 0) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n};\r\n\r\nMiew.prototype._renderSelection = (function () {\r\n const _outlineMaterial = new OutlineMaterial();\r\n\r\n return function (camera, srcBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // clear offscreen buffer (leave z-buffer intact)\r\n gfx.renderer.setClearColor('black', 0);\r\n\r\n // render selection to offscreen buffer\r\n gfx.renderer.setRenderTarget(srcBuffer);\r\n gfx.renderer.clear(true, false, false);\r\n if (self._hasSelectionToRender()) {\r\n gfx.selectionRoot.matrix = gfx.root.matrix;\r\n gfx.selectionPivot.matrix = gfx.pivot.matrix;\r\n gfx.renderer.render(gfx.selectionScene, camera);\r\n } else {\r\n // just render something to force \"target clear\" operation to finish\r\n gfx.renderer.renderDummyQuad();\r\n }\r\n\r\n // overlay to screen\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 0.6);\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcBuffer.width, srcBuffer.height);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._checkVolumeRenderingSupport = function (renderTarget) {\r\n if (!renderTarget) {\r\n return false;\r\n }\r\n const gfx = this._gfx;\r\n const oldRT = gfx.renderer.getRenderTarget();\r\n\r\n gfx.renderer.setRenderTarget(renderTarget);\r\n const context = gfx.renderer.getContext();\r\n const result = context.checkFramebufferStatus(context.FRAMEBUFFER);\r\n gfx.renderer.setRenderTarget(oldRT);\r\n if (result !== context.FRAMEBUFFER_COMPLETE) {\r\n // floatFrameBufferWarning = ;\r\n this.logger.warn('Device doesn\\'t support electron density rendering');\r\n return false;\r\n }\r\n return true;\r\n};\r\n\r\nMiew.prototype._renderVolume = (function () {\r\n const volumeBFMat = new VolumeMaterial.BackFacePosMaterial();\r\n const volumeFFMat = new VolumeMaterial.FrontFacePosMaterial();\r\n const cubeOffsetMat = new THREE.Matrix4().makeTranslation(0.5, 0.5, 0.5);\r\n const world2colorMat = new THREE.Matrix4();\r\n\r\n let volumeRenderingSupported;\r\n\r\n return function (volumeVisual, camera, dstBuf, tmpBuf1, tmpBuf2, tmpBuf3) {\r\n const gfx = this._gfx;\r\n\r\n if (typeof volumeRenderingSupported === 'undefined') {\r\n volumeRenderingSupported = this._checkVolumeRenderingSupport(tmpBuf1);\r\n }\r\n\r\n if (!volumeRenderingSupported) {\r\n return;\r\n }\r\n\r\n const mesh = volumeVisual.getMesh();\r\n\r\n mesh.rebuild(gfx.camera);\r\n\r\n // use main camera to prepare special textures to be used by volumetric rendering\r\n // these textures have the size of the window and are stored in offscreen buffers\r\n gfx.renderer.setClearColor('black', 0);\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n // draw plane with its own material, because it differs slightly from volumeBFMat\r\n camera.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeBFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeFFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.scene.overrideMaterial = null;\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n\r\n // prepare texture that contains molecule positions\r\n world2colorMat.copy(mesh.matrixWorld).invert();\r\n UberMaterial.prototype.uberOptions.world2colorMatrix.multiplyMatrices(cubeOffsetMat, world2colorMat);\r\n camera.layers.set(gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // render volume\r\n const vm = mesh.material;\r\n vm.uniforms._BFRight.value = tmpBuf1.texture;\r\n vm.uniforms._FFRight.value = tmpBuf2.texture;\r\n vm.uniforms._WFFRight.value = tmpBuf3.texture;\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.renderer.setRenderTarget(dstBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\n/* Render scene with 'ZPrepass transparency Effect'\r\n * Idea: transparent objects are rendered in two passes. The first one writes result only into depth buffer.\r\n * The second pass reads depth buffer and writes only to color buffer. The method results in\r\n * correct image of front part of the semi-transparent objects, but we can see only front transparent objects\r\n * and opaque objects inside, there is no transparent objects inside.\r\n * Notes: 1. Opaque objects should be rendered strictly before semi-transparent ones.\r\n * 2. Realization doesn't use camera layers because scene traversing is used for material changes and\r\n * we can use it to select needed meshes and don't complicate meshes builders with layers\r\n */\r\nMiew.prototype._renderWithPrepassTransparency = (function () {\r\n return function (camera, targetBuffer) {\r\n const gfx = this._gfx;\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n\r\n // opaque objects\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // transparent objects z prepass\r\n camera.layers.set(gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n gfx.renderer.getContext().colorMask(false, false, false, false); // don't update color buffer\r\n gfx.renderer.render(gfx.scene, camera);\r\n gfx.renderer.getContext().colorMask(true, true, true, true); // update color buffer\r\n\r\n // transparent objects color pass\r\n camera.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // restore default layer\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\nMiew.prototype._performFXAA = (function () {\r\n const _fxaaMaterial = new FXAAMaterial();\r\n\r\n return function (srcBuffer, targetBuffer) {\r\n if (typeof srcBuffer === 'undefined' || typeof targetBuffer === 'undefined') {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n\r\n // clear canvas\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.clear();\r\n\r\n // do fxaa processing of offscreen buff2\r\n _fxaaMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _fxaaMaterial.uniforms.srcTexelSize.value.set(1.0 / srcBuffer.width, 1.0 / srcBuffer.height);\r\n _fxaaMaterial.uniforms.bgColor.value.set(settings.now.bg.color);\r\n\r\n if (_fxaaMaterial.bgTransparent !== settings.now.bg.transparent) {\r\n _fxaaMaterial.setValues({ bgTransparent: settings.now.bg.transparent });\r\n _fxaaMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.renderScreenQuad(_fxaaMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._performAO = (function () {\r\n const _aoMaterial = new AOMaterial();\r\n const _horBlurMaterial = new AOHorBlurMaterial();\r\n const _vertBlurMaterial = new AOVertBlurWithBlendMaterial();\r\n\r\n const _scale = new THREE.Vector3();\r\n return function (srcColorBuffer, normalBuffer, srcDepthTexture, targetBuffer, tempBuffer, tempBuffer1) {\r\n if (!srcColorBuffer || !normalBuffer || !srcDepthTexture || !targetBuffer || !tempBuffer || !tempBuffer1) {\r\n return;\r\n }\r\n const gfx = this._gfx;\r\n const tanHalfFOV = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * gfx.camera.fov);\r\n\r\n _aoMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _aoMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _aoMaterial.uniforms.normalTexture.value = normalBuffer.texture;\r\n _aoMaterial.uniforms.srcTexelSize.value.set(1.0 / srcColorBuffer.width, 1.0 / srcColorBuffer.height);\r\n _aoMaterial.uniforms.camNearFar.value.set(gfx.camera.near, gfx.camera.far);\r\n _aoMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _aoMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _aoMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n gfx.root.matrix.extractScale(_scale);\r\n _aoMaterial.uniforms.kernelRadius.value = settings.now.debug.ssaoKernelRadius * _scale.x;\r\n _aoMaterial.uniforms.depthThreshold.value = 2.0 * this._getBSphereRadius(); // diameter\r\n _aoMaterial.uniforms.factor.value = settings.now.debug.ssaoFactor;\r\n // N: should be tempBuffer1 for proper use of buffers (see buffers using outside the function)\r\n gfx.renderer.setRenderTarget(tempBuffer1);\r\n gfx.renderer.renderScreenQuad(_aoMaterial);\r\n\r\n _horBlurMaterial.uniforms.aoMap.value = tempBuffer1.texture;\r\n _horBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer1.width, 1.0 / tempBuffer1.height);\r\n _horBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n gfx.renderer.setRenderTarget(tempBuffer);\r\n gfx.renderer.renderScreenQuad(_horBlurMaterial);\r\n\r\n _vertBlurMaterial.uniforms.aoMap.value = tempBuffer.texture;\r\n _vertBlurMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _vertBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer.width, 1.0 / tempBuffer.height);\r\n _vertBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _vertBlurMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _vertBlurMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _vertBlurMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n const { fog } = gfx.scene;\r\n if (fog) {\r\n _vertBlurMaterial.uniforms.fogNearFar.value.set(fog.near, fog.far);\r\n _vertBlurMaterial.uniforms.fogColor.value.set(fog.color.r, fog.color.g, fog.color.b, settings.now.fogAlpha);\r\n }\r\n if ((_vertBlurMaterial.useFog !== settings.now.fog)\r\n || (_vertBlurMaterial.fogTransparent !== settings.now.bg.transparent)) {\r\n _vertBlurMaterial.setValues({ useFog: settings.now.fog, fogTransparent: settings.now.bg.transparent });\r\n _vertBlurMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_vertBlurMaterial);\r\n };\r\n}());\r\n\r\n/**\r\n * Reset the viewer, unload molecules.\r\n * @param {boolean=} keepReps - Keep representations while resetting viewer state.\r\n */\r\nMiew.prototype.reset = function (/* keepReps */) {\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._lastPick = null;\r\n\r\n this._releaseAllVisuals();\r\n\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._resetObjects();\r\n\r\n if (this._gfx) {\r\n gfxutils.clearTree(this._gfx.pivot);\r\n this._gfx.renderer2d.reset();\r\n }\r\n\r\n this.setNeedRender();\r\n};\r\n\r\nMiew.prototype._resetScene = function () {\r\n this._objectControls.reset();\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n this.resetReps();\r\n this.resetPivot();\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype.resetView = function () {\r\n // reset controls\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._resetScene();\r\n\r\n // reset selection\r\n this._forEachComplexVisual((visual) => {\r\n visual.updateSelectionMask({});\r\n visual.rebuildSelectionGeometry();\r\n });\r\n};\r\n\r\nMiew.prototype._export = function (format) {\r\n const TheExporter = _.head(io.exporters.find({ format }));\r\n if (!TheExporter) {\r\n this.logger.error('Could not find suitable exporter for this source');\r\n return Promise.reject(new Error('Could not find suitable exporter for this source'));\r\n }\r\n this.dispatchEvent({ type: 'exporting' });\r\n\r\n if (this._visuals[this._curVisualName] instanceof ComplexVisual) {\r\n let dataSource = null;\r\n if (TheExporter.SourceClass === ComplexVisual) {\r\n dataSource = this._visuals[this._curVisualName];\r\n } else if (TheExporter.SourceClass === Complex) {\r\n dataSource = this._visuals[this._curVisualName]._complex;\r\n }\r\n const exporter = new TheExporter(dataSource, { miewVersion: Miew.VERSION });\r\n return exporter.export().then((data) => data);\r\n }\r\n if (this._visuals[this._curVisualName] instanceof VolumeVisual) {\r\n return Promise.reject(new Error('Sorry, exporter for volume data not implemented yet'));\r\n }\r\n return Promise.reject(new Error('Unexpected format of data'));\r\n};\r\n\r\nconst rePdbId = /^(?:(pdb|cif|ccp4|dsn6):\\s*)?(\\d[a-z\\d]{3})$/i;\r\nconst rePubchem = /^(?:pc|pubchem):\\s*([a-z]+)$/i;\r\nconst reUrlScheme = /^([a-z][a-z\\d\\-+.]*):/i;\r\n\r\nfunction resolveSourceShortcut(source, opts) {\r\n if (!_.isString(source)) {\r\n return source;\r\n }\r\n\r\n // e.g. \"cif:1CRN\"\r\n const matchesPdbId = rePdbId.exec(source);\r\n if (matchesPdbId) {\r\n let [, format = 'pdb', id] = matchesPdbId;\r\n\r\n format = format.toLowerCase();\r\n id = id.toUpperCase();\r\n\r\n switch (format) {\r\n case 'pdb':\r\n source = `https://files.rcsb.org/download/${id}.pdb`;\r\n break;\r\n case 'cif':\r\n source = `https://files.rcsb.org/download/${id}.cif`;\r\n break;\r\n case 'ccp4':\r\n source = `https://www.ebi.ac.uk/pdbe/coordinates/files/${id.toLowerCase()}.ccp4`;\r\n break;\r\n case 'dsn6':\r\n source = `https://edmaps.rcsb.org/maps/${id.toLowerCase()}_2fofc.dsn6`;\r\n break;\r\n default:\r\n throw new Error('Unexpected data format shortcut');\r\n }\r\n\r\n opts.fileType = format;\r\n opts.fileName = `${id}.${format}`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // e.g. \"pc:aspirin\"\r\n const matchesPubchem = rePubchem.exec(source);\r\n if (matchesPubchem) {\r\n const compound = matchesPubchem[1].toLowerCase();\r\n source = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${compound}/JSON?record_type=3d`;\r\n opts.fileType = 'pubchem';\r\n opts.fileName = `${compound}.json`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // otherwise is should be an URL\r\n if (opts.sourceType === 'url' || opts.sourceType === undefined) {\r\n opts.sourceType = 'url';\r\n\r\n // e.g. \"./data/1CRN.pdb\"\r\n if (!reUrlScheme.test(source)) {\r\n source = utils.resolveURL(source);\r\n }\r\n }\r\n\r\n return source;\r\n}\r\n\r\nfunction updateBinaryMode(opts) {\r\n let { binary } = opts;\r\n\r\n // detect by format\r\n if (opts.fileType !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n } else {\r\n throw new Error('Could not find suitable parser for this format');\r\n }\r\n }\r\n\r\n // detect by file extension\r\n if (binary === undefined && opts.fileExt !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ ext: opts.fileExt }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n }\r\n }\r\n\r\n // temporary workaround for animation\r\n if (opts.fileExt !== undefined && opts.fileExt.toLowerCase() === '.man') {\r\n opts.binary = true;\r\n opts.animation = true; // who cares?\r\n }\r\n\r\n // update if detected\r\n if (binary !== undefined) {\r\n if (opts.binary !== undefined && opts.binary !== binary) {\r\n opts.context.logger.warn('Overriding incorrect binary mode');\r\n }\r\n }\r\n\r\n opts.binary = binary || false;\r\n}\r\n\r\nfunction _fetchData(source, opts, job) {\r\n return new Promise(((resolve) => {\r\n if (job.shouldCancel()) {\r\n throw new Error('Operation cancelled');\r\n }\r\n job.notify({ type: 'fetching' });\r\n\r\n // allow for source shortcuts\r\n source = resolveSourceShortcut(source, opts);\r\n\r\n // detect a proper loader\r\n const TheLoader = _.head(io.loaders.find({ type: opts.sourceType, source }));\r\n if (!TheLoader) {\r\n throw new Error(LOADER_NOT_FOUND);\r\n }\r\n\r\n // split file name\r\n const fileName = opts.fileName || TheLoader.extractName(source);\r\n if (fileName) {\r\n const [name, fileExt] = utils.splitFileName(fileName);\r\n _.defaults(opts, { name, fileExt, fileName });\r\n }\r\n\r\n // should it be text or binary?\r\n updateBinaryMode(opts);\r\n\r\n // FIXME: All new settings retrieved from server are applied after the loading is complete. However, we need some\r\n // flags to alter the loading process itself. Here we apply them in advance. Dirty hack. Kill the server, remove\r\n // all hacks and everybody's happy.\r\n let newOptions = _.get(opts, 'preset.expression');\r\n if (!_.isUndefined(newOptions)) {\r\n newOptions = JSON.parse(newOptions);\r\n if (newOptions && newOptions.settings) {\r\n const keys = ['singleUnit'];\r\n for (let keyIndex = 0, keyCount = keys.length; keyIndex < keyCount; ++keyIndex) {\r\n const key = keys[keyIndex];\r\n const value = _.get(newOptions.settings, key);\r\n if (!_.isUndefined(value)) {\r\n settings.set(key, value);\r\n }\r\n }\r\n }\r\n }\r\n\r\n // create a loader\r\n const loader = new TheLoader(source, opts);\r\n loader.context = opts.context;\r\n job.addEventListener('cancel', () => loader.abort());\r\n\r\n loader.addEventListener('progress', (event) => {\r\n if (event.lengthComputable && event.total > 0) {\r\n reportProgress(loader.logger, 'Fetching', event.loaded / event.total);\r\n } else {\r\n reportProgress(loader.logger, 'Fetching');\r\n }\r\n });\r\n\r\n console.time('fetch');\r\n const promise = loader.load()\r\n .then((data) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.info('Fetching finished');\r\n job.notify({ type: 'fetchingDone', data });\r\n return data;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Fetching failed');\r\n job.notify({ type: 'fetchingDone', error });\r\n throw error;\r\n });\r\n resolve(promise);\r\n }));\r\n}\r\n\r\nfunction _parseData(data, opts, job) {\r\n if (job.shouldCancel()) {\r\n return Promise.reject(new Error('Operation cancelled'));\r\n }\r\n\r\n job.notify({ type: 'parsing' });\r\n\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType, ext: opts.fileExt, data }));\r\n if (!TheParser) {\r\n return Promise.reject(new Error('Could not find suitable parser'));\r\n }\r\n\r\n const parser = new TheParser(data, opts);\r\n parser.context = opts.context;\r\n job.addEventListener('cancel', () => parser.abort());\r\n\r\n console.time('parse');\r\n return parser.parse()\r\n .then((dataSet) => {\r\n console.timeEnd('parse');\r\n job.notify({ type: 'parsingDone', data: dataSet });\r\n return dataSet;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('parse');\r\n opts.error = error;\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Parsing failed');\r\n job.notify({ type: 'parsingDone', error });\r\n throw error;\r\n });\r\n}\r\n\r\n/**\r\n * Load molecule asynchronously.\r\n * @param {string|File} source - Molecule source to load (e.g. PDB ID, URL or File object).\r\n * @param {object=} opts - Options.\r\n * @param {string=} opts.sourceType - Data source type (e.g. 'url', 'file').\r\n * @param {string=} opts.fileType - Data contents type (e.g. 'pdb', 'cml').\r\n * @param {string=} opts.mdFile - .nc file path.\r\n * @param {boolean=} opts.keepRepsInfo - prevent reset of object and reps information.\r\n * @returns {Promise} name of the visual that was added to the viewer\r\n */\r\nMiew.prototype.load = function (source, opts) {\r\n opts = _.merge({}, opts, {\r\n context: this,\r\n });\r\n\r\n // for a single-file scenario\r\n if (!this.settings.now.use.multiFile) {\r\n // abort all loaders in progress\r\n if (this._loading.length) {\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n }\r\n\r\n // reset\r\n if (!opts.animation) { // FIXME: sometimes it is set AFTERWARDS!\r\n this.reset(true);\r\n }\r\n }\r\n\r\n this._interpolator.reset();\r\n\r\n this.dispatchEvent({ type: 'loading', options: opts, source });\r\n\r\n const job = new JobHandle();\r\n this._loading.push(job);\r\n job.addEventListener('notification', (e) => {\r\n this.dispatchEvent(e.slaveEvent);\r\n });\r\n\r\n this._spinner.spin(this._container);\r\n\r\n const onLoadEnd = (anything) => {\r\n const jobIndex = this._loading.indexOf(job);\r\n if (jobIndex !== -1) {\r\n this._loading.splice(jobIndex, 1);\r\n }\r\n this._spinner.stop();\r\n this._refreshTitle();\r\n job.notify({ type: 'loadingDone', anything });\r\n return anything;\r\n };\r\n\r\n return _fetchData(source, opts, job)\r\n .then((data) => _parseData(data, opts, job))\r\n .then((object) => {\r\n const name = this._onLoad(object, opts);\r\n return onLoadEnd(name);\r\n })\r\n .catch((err) => {\r\n this.logger.error('Could not load data');\r\n this.logger.debug(err);\r\n throw onLoadEnd(err);\r\n });\r\n};\r\n\r\n/**\r\n * Unload molecule (delete corresponding visual).\r\n * @param {string=} name - name of the visual\r\n */\r\nMiew.prototype.unload = function (name) {\r\n this._removeVisual(name || this.getCurrentVisual());\r\n this.resetPivot();\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n};\r\n\r\n/**\r\n * Start new animation. Now is broken.\r\n * @param fileData - new data to animate\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._startAnimation = function (fileData) {\r\n this._stopAnimation();\r\n const self = this;\r\n const visual = this._getComplexVisual();\r\n if (visual === null) {\r\n this.logger.error('Unable to start animation - no molecule is loaded.');\r\n return;\r\n }\r\n try {\r\n this._frameInfo = new FrameInfo(\r\n visual.getComplex(),\r\n fileData,\r\n {\r\n onLoadStatusChanged() {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo ? self._frameInfo.isLoading : true,\r\n },\r\n });\r\n },\r\n onError(message) {\r\n self._stopAnimation();\r\n self.logger.error(message);\r\n },\r\n },\r\n );\r\n } catch (e) {\r\n this.logger.error('Animation file does not fit to current complex!');\r\n return;\r\n }\r\n this._continueAnimation();\r\n};\r\n\r\n/**\r\n * Pause current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._pauseAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n this._isAnimating = false;\r\n clearInterval(this._animInterval);\r\n this._animInterval = null;\r\n if (this._frameInfo) {\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: this._isAnimating,\r\n isLoading: this._frameInfo.isLoading,\r\n },\r\n });\r\n }\r\n};\r\n\r\n/**\r\n * Continue current animation after pausing. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._continueAnimation = function () {\r\n this._isAnimating = true;\r\n let minFrameTime = 1000 / settings.now.maxfps;\r\n minFrameTime = Number.isNaN(minFrameTime) ? 0 : minFrameTime;\r\n const self = this;\r\n const { pivot } = self._gfx;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.resetSelectionMask();\r\n visual.rebuildSelectionGeometry();\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n }\r\n this._animInterval = setInterval(() => {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo.isLoading,\r\n },\r\n });\r\n if (self._frameInfo.frameIsReady) {\r\n pivot.updateToFrame(self._frameInfo);\r\n self._updateObjsToFrame(self._frameInfo);\r\n self._refreshTitle(` Frame ${self._frameInfo._currFrame} of ${self._frameInfo._framesCount\r\n } time interval - ${self._frameInfo._timeStep}`);\r\n try {\r\n self._frameInfo.nextFrame();\r\n } catch (e) {\r\n self.logger.error('Error during animation');\r\n self._stopAnimation();\r\n return;\r\n }\r\n self._needRender = true;\r\n }\r\n }, minFrameTime);\r\n};\r\n\r\n/**\r\n * Stop current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._stopAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n clearInterval(this._animInterval);\r\n this._frameInfo.disableEvents();\r\n this._frameInfo = null;\r\n this._animInterval = null;\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: null,\r\n });\r\n};\r\n\r\n/**\r\n * Invoked upon successful loading of some data source\r\n * @param {DataSource} dataSource - Data source for visualization (molecular complex or other)\r\n * @param {object} opts - Options.\r\n * @private\r\n */\r\nMiew.prototype._onLoad = function (dataSource, opts) {\r\n const gfx = this._gfx;\r\n let visualName = null;\r\n\r\n if (opts.animation) {\r\n this._refreshTitle();\r\n this._startAnimation(dataSource);\r\n return null;\r\n }\r\n this._stopAnimation();\r\n if (!opts || !opts.keepRepsInfo) {\r\n this._opts.reps = null;\r\n this._opts._objects = null;\r\n }\r\n\r\n if (dataSource.id === 'Complex') {\r\n const complex = dataSource;\r\n\r\n // update title\r\n if (opts.fileName) {\r\n complex.name = complex.name || removeExtension(opts.fileName).toUpperCase();\r\n } else if (opts.amberFileName) {\r\n complex.name = complex.name || removeExtension(opts.amberFileName).toUpperCase();\r\n } else {\r\n complex.name = `Dynamic ${opts.fileType} molecule`;\r\n }\r\n\r\n visualName = this._addVisual(new ComplexVisual(complex.name, complex));\r\n this._curVisualName = visualName;\r\n\r\n const desc = this.info();\r\n this.logger.info(`Parsed ${opts.fileName} (${\r\n desc.atoms} atoms, ${\r\n desc.bonds} bonds, ${\r\n desc.residues} residues, ${\r\n desc.chains} chains).`);\r\n\r\n if (_.isNumber(this._opts.unit)) {\r\n complex.setCurrentUnit(this._opts.unit);\r\n }\r\n\r\n if (opts.preset) {\r\n // ...removed server access...\r\n } else if (settings.now.autoPreset) {\r\n switch (opts.fileType) {\r\n case 'cml':\r\n this.resetReps('small');\r\n break;\r\n case 'pdb':\r\n case 'mmtf':\r\n case 'cif':\r\n if (hasValidResidues(complex)) {\r\n this.resetReps('macro');\r\n } else {\r\n this.resetReps('small');\r\n }\r\n break;\r\n default:\r\n this.resetReps('default');\r\n break;\r\n }\r\n } else {\r\n this.resetReps('default');\r\n }\r\n } else if (dataSource.id === 'Volume') {\r\n this.resetEd();\r\n visualName = this._onLoadEd(dataSource);\r\n }\r\n\r\n gfx.camera.updateProjectionMatrix();\r\n this._updateFog();\r\n\r\n // reset global transform\r\n gfx.root.resetTransform();\r\n this.resetPivot();\r\n\r\n // set scale to fit everything on the screen\r\n this._objectControls.setScale(settings.now.radiusToFit / this._getBSphereRadius());\r\n\r\n this._resetObjects();\r\n\r\n if (settings.now.autoResolution) {\r\n this._tweakResolution();\r\n }\r\n\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n this._refreshTitle();\r\n\r\n return visualName;\r\n};\r\n\r\nMiew.prototype.resetEd = function () {\r\n if (this._edLoader) {\r\n this._edLoader.abort();\r\n this._edLoader = null;\r\n }\r\n\r\n // free all resources\r\n this._removeVisual(this._getVolumeVisual());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype.loadEd = function (source) {\r\n this.resetEd();\r\n\r\n const TheLoader = _.head(io.loaders.find({ source }));\r\n if (!TheLoader) {\r\n this.logger.error(LOADER_NOT_FOUND);\r\n return Promise.reject(new Error(LOADER_NOT_FOUND));\r\n }\r\n\r\n const loader = this._edLoader = new TheLoader(source, { binary: true });\r\n loader.context = this;\r\n return loader.load().then((data) => {\r\n const TheParser = _.head(io.parsers.find({ format: 'ccp4' }));\r\n if (!TheParser) {\r\n throw new Error(PARSER_NOT_FOUND);\r\n }\r\n const parser = new TheParser(data);\r\n parser.context = this;\r\n return parser.parse().then((dataSource) => {\r\n this._onLoadEd(dataSource);\r\n });\r\n }).catch((error) => {\r\n this.logger.error('Could not load ED data');\r\n this.logger.debug(error);\r\n });\r\n};\r\n\r\nMiew.prototype._onLoadEd = function (dataSource) {\r\n dataSource.normalize();\r\n\r\n const volumeVisual = new VolumeVisual('volume', dataSource);\r\n volumeVisual.getMesh().layers.set(gfxutils.LAYERS.VOLUME); // volume mesh is not visible to common render\r\n const visualName = this._addVisual(volumeVisual);\r\n\r\n this._needRender = true;\r\n return visualName;\r\n};\r\n\r\nMiew.prototype._needRebuild = function () {\r\n let needsRebuild = false;\r\n this._forEachComplexVisual((visual) => {\r\n needsRebuild = needsRebuild || visual.needsRebuild();\r\n });\r\n return needsRebuild;\r\n};\r\n\r\nMiew.prototype._rebuildObjects = function () {\r\n const self = this;\r\n const gfx = this._gfx;\r\n let i;\r\n let n;\r\n\r\n // remove old object geometry\r\n const toRemove = [];\r\n for (i = 0; i < gfx.pivot.children.length; ++i) {\r\n const child = gfx.pivot.children[i];\r\n if (!(child instanceof Visual)) {\r\n toRemove.push(child);\r\n }\r\n }\r\n for (i = 0; i < toRemove.length; ++i) {\r\n toRemove[i].parent.remove(toRemove[i]);\r\n }\r\n\r\n setTimeout(() => {\r\n const objList = self._objects;\r\n for (i = 0, n = objList.length; i < n; ++i) {\r\n const obj = objList[i];\r\n if (obj.needsRebuild) {\r\n obj.build();\r\n }\r\n if (obj.getGeometry()) {\r\n gfx.pivot.add(obj.getGeometry());\r\n }\r\n }\r\n }, 10);\r\n};\r\n\r\nMiew.prototype.changeUnit = function (unitIdx, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n throw new Error('There is no complex to change!');\r\n }\r\n\r\n function currentUnitInfo() {\r\n const unit = visual ? visual.getComplex().getCurrentUnit() : 0;\r\n const type = unit > 0 ? (`Bio molecule ${unit}`) : 'Asymmetric unit';\r\n return `Current unit: ${unit} (${type})`;\r\n }\r\n\r\n if (unitIdx === undefined) {\r\n return currentUnitInfo();\r\n }\r\n if (_.isString(unitIdx)) {\r\n unitIdx = Math.max(parseInt(unitIdx, 10), 0);\r\n }\r\n if (visual.getComplex().setCurrentUnit(unitIdx)) {\r\n this._resetScene();\r\n this._updateInfoPanel();\r\n }\r\n return currentUnitInfo();\r\n};\r\n\r\n/**\r\n * Start to rebuild geometry asynchronously.\r\n */\r\nMiew.prototype.rebuild = function () {\r\n if (this._building) {\r\n this.logger.warn('Miew.rebuild(): already building!');\r\n return;\r\n }\r\n this._building = true;\r\n\r\n this.dispatchEvent({ type: 'rebuilding' });\r\n\r\n this._rebuildObjects();\r\n\r\n this._gfx.renderer2d.reset();\r\n\r\n const rebuildActions = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.needsRebuild()) {\r\n rebuildActions.push(visual.rebuild().then(() => new Promise(((resolve) => {\r\n visual.rebuildSelectionGeometry();\r\n resolve();\r\n }))));\r\n }\r\n });\r\n\r\n // Start asynchronous rebuild\r\n const self = this;\r\n this._spinner.spin(this._container);\r\n Promise.all(rebuildActions).then(() => {\r\n self._spinner.stop();\r\n\r\n self._needRender = true;\r\n\r\n self._refreshTitle();\r\n this.dispatchEvent({ type: 'buildingDone' });\r\n self._building = false;\r\n });\r\n};\r\n\r\n/** Mark all representations for rebuilding */\r\nMiew.prototype.rebuildAll = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setNeedsRebuild();\r\n });\r\n};\r\n\r\nMiew.prototype._refreshTitle = function (appendix) {\r\n let title;\r\n appendix = appendix === undefined ? '' : appendix;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n title = visual.getComplex().name;\r\n const rep = visual.repGet(visual.repCurrent());\r\n title += (rep ? ` – ${rep.mode.name} Mode` : '');\r\n } else {\r\n title = Object.keys(this._visuals).length > 0 ? 'Unknown' : 'No Data';\r\n }\r\n title += appendix;\r\n\r\n this.dispatchEvent({ type: 'titleChanged', data: title });\r\n};\r\n\r\nMiew.prototype.setNeedRender = function () {\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._extractRepresentation = function () {\r\n const changed = [];\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCount() === 0) {\r\n return;\r\n }\r\n\r\n const selector = visual.buildSelectorFromMask(1 << visual.getSelectionBit());\r\n const defPreset = settings.now.presets.default;\r\n const res = visual.repAdd({\r\n selector,\r\n mode: defPreset[0].mode.id,\r\n colorer: defPreset[0].colorer.id,\r\n material: defPreset[0].material.id,\r\n });\r\n if (!res) {\r\n if (visual.repCount() === ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n this.logger.warn(`Number of representations is limited to ${ComplexVisual.NUM_REPRESENTATION_BITS}`);\r\n }\r\n return;\r\n }\r\n\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n visual.repCurrent(res.index);\r\n\r\n changed.push(visual.name);\r\n });\r\n\r\n if (changed.length > 0) {\r\n this.logger.report(`New representation from selection for complexes: ${changed.join(', ')}`);\r\n }\r\n};\r\n\r\n/**\r\n * Change current representation list.\r\n * @param {array} reps - Representation list.\r\n */\r\nMiew.prototype._setReps = function (reps) {\r\n reps = reps || (this._opts && this._opts.reps) || [];\r\n this._forEachComplexVisual((visual) => visual.resetReps(reps));\r\n};\r\n\r\n/**\r\n * Apply existing preset to current scene.\r\n * @param preset\r\n */\r\nMiew.prototype.applyPreset = function (preset) {\r\n const { presets } = settings.now;\r\n const presList = [\r\n preset || settings.defaults.preset,\r\n settings.defaults.preset,\r\n Object.keys(presets)[0],\r\n ];\r\n let reps = null;\r\n for (let i = 0; !reps && i < presList.length; ++i) {\r\n settings.set('preset', presList[i]);\r\n reps = presets[settings.now.preset];\r\n if (!reps) {\r\n this.logger.warn(`Unknown preset \"${settings.now.preset}\"`);\r\n }\r\n }\r\n this._setReps(reps);\r\n};\r\n\r\n/**\r\n * Reset current representation list to initial values.\r\n * @param {string} [preset] - The source preset in case of uninitialized representation list.\r\n */\r\nMiew.prototype.resetReps = function (preset) {\r\n const reps = this._opts && this._opts.reps;\r\n if (reps) {\r\n this._setReps(reps);\r\n } else {\r\n this.applyPreset(preset);\r\n }\r\n};\r\n\r\n/**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\nMiew.prototype.repCount = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repCount() : 0;\r\n};\r\n\r\n/**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {string=} [name] - Complex name. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\nMiew.prototype.repCurrent = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n const newIdx = visual ? visual.repCurrent(index) : -1;\r\n if (index && newIdx !== index) {\r\n this.logger.warn(`Representation ${index} was not found. Current rep remains unchanged.`);\r\n }\r\n return newIdx;\r\n};\r\n\r\n/**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {?object} Representation description.\r\n */\r\nMiew.prototype.rep = function (index, rep) {\r\n const visual = this._getComplexVisual('');\r\n if (!visual) {\r\n return null;\r\n }\r\n const res = visual.rep(index, rep);\r\n if (res.status === 'created') {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n } else if (res.status === 'changed') {\r\n this.dispatchEvent({ type: 'repChanged', index: res.index, name: visual.name });\r\n }\r\n return res.desc;\r\n};\r\n\r\n/**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\nMiew.prototype.repGet = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repGet(index) : null;\r\n};\r\n\r\n/**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {number} Index of the new representation.\r\n */\r\nMiew.prototype.repAdd = function (rep, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return -1;\r\n }\r\n\r\n const res = visual.repAdd(rep);\r\n if (res) {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name });\r\n return res.index;\r\n }\r\n return -1;\r\n};\r\n\r\n/**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\nMiew.prototype.repRemove = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n visual.repRemove(index);\r\n this.dispatchEvent({ type: 'repRemoved', index, name });\r\n};\r\n\r\n/**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\nMiew.prototype.repHide = function (index, hide, name) {\r\n this._needRender = true;\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repHide(index, hide) : null;\r\n};\r\n\r\nMiew.prototype._setEditMode = function (mode) {\r\n this._editMode = mode;\r\n\r\n const elem = this._msgMode;\r\n if (elem) {\r\n elem.style.opacity = (mode === EDIT_MODE.COMPLEX) ? 0.0 : 1.0;\r\n\r\n if (mode !== EDIT_MODE.COMPLEX) {\r\n const t = elem.getElementsByTagName('p')[0];\r\n t.innerHTML = (mode === EDIT_MODE.COMPONENT) ? 'COMPONENT EDIT MODE' : 'FRAGMENT EDIT MODE';\r\n }\r\n }\r\n\r\n this.dispatchEvent({ type: 'editModeChanged', data: mode === EDIT_MODE.COMPLEX });\r\n};\r\n\r\nMiew.prototype._enterComponentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const editors = [];\r\n this._forEachComplexVisual((visual) => {\r\n const editor = visual.beginComponentEdit();\r\n if (editor) {\r\n editors.push(editor);\r\n }\r\n });\r\n\r\n if (editors === []) {\r\n return;\r\n }\r\n\r\n this._editors = editors;\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- ON');\r\n this._setEditMode(EDIT_MODE.COMPONENT);\r\n this._objectControls.keysTranslateObj(true);\r\n};\r\n\r\nMiew.prototype._applyComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._needRender = true;\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._enterFragmentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const selectedVisuals = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual instanceof ComplexVisual\r\n && visual.getSelectionCount() > 0) {\r\n selectedVisuals.push(visual);\r\n }\r\n });\r\n\r\n if (selectedVisuals.length !== 1) {\r\n // either we have no selection or\r\n // we have selected atoms in two or more visuals -- not supported\r\n return;\r\n }\r\n\r\n const editor = selectedVisuals[0].beginFragmentEdit();\r\n if (!editor) {\r\n return;\r\n }\r\n this._editors = [editor];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- ON (single bond)');\r\n this._setEditMode(EDIT_MODE.FRAGMENT);\r\n this._objectControls.allowTranslation(false);\r\n this._objectControls.allowAltObjFreeRotation(editor.isFreeRotationAllowed());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._applyFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onPick = function (event) {\r\n if (!settings.now.picking) {\r\n // picking is disabled\r\n return;\r\n }\r\n\r\n if (this._animInterval !== null) {\r\n // animation playback is on\r\n return;\r\n }\r\n\r\n if (this._editMode === EDIT_MODE.FRAGMENT) {\r\n // prevent picking in fragment edit mode\r\n return;\r\n }\r\n\r\n if (this._objectControls.isEditingAltObj()) {\r\n // prevent picking during component rotation\r\n return;\r\n }\r\n\r\n // update last pick & find complex\r\n let complex = null;\r\n if (event.obj.atom) {\r\n complex = event.obj.atom.residue.getChain().getComplex();\r\n this._lastPick = event.obj.atom;\r\n } else if (event.obj.residue) {\r\n complex = event.obj.residue.getChain().getComplex();\r\n this._lastPick = event.obj.residue;\r\n } else if (event.obj.chain) {\r\n complex = event.obj.chain.getComplex();\r\n this._lastPick = event.obj.chain;\r\n } else if (event.obj.molecule) {\r\n complex = event.obj.molecule.complex;\r\n this._lastPick = event.obj.molecule;\r\n } else {\r\n this._lastPick = null;\r\n }\r\n\r\n function _updateSelection(visual) {\r\n visual.updateSelectionMask(event.obj);\r\n visual.rebuildSelectionGeometry();\r\n }\r\n\r\n // update visual\r\n if (complex) {\r\n const visual = this._getVisualForComplex(complex);\r\n if (visual) {\r\n _updateSelection(visual);\r\n this._needRender = true;\r\n }\r\n } else {\r\n this._forEachComplexVisual(_updateSelection);\r\n this._needRender = true;\r\n }\r\n\r\n this._updateInfoPanel();\r\n this.dispatchEvent(event);\r\n};\r\n\r\nMiew.prototype._onKeyDown = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n // editing keys\r\n if (settings.now.editing) {\r\n switch (event.code) {\r\n case 'KeyC':\r\n this._enterComponentEditMode();\r\n break;\r\n case 'KeyF':\r\n this._enterFragmentEditMode();\r\n break;\r\n case 'KeyA':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._applyComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._applyFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n case 'KeyD':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._discardComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._discardFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n default:\r\n }\r\n }\r\n\r\n // other keys\r\n switch (event.code) {\r\n case 'NumpadAdd':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.expandSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n case 'NumpadSubtract':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.shrinkSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nMiew.prototype._onKeyUp = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n if (event.code === 'KeyX') {\r\n this._extractRepresentation();\r\n }\r\n};\r\n\r\nMiew.prototype._updateInfoPanel = function () {\r\n const info = this._msgAtomInfo.getElementsByTagName('p')[0];\r\n let atom;\r\n let residue;\r\n\r\n let count = 0;\r\n this._forEachComplexVisual((visual) => {\r\n count += visual.getSelectionCount();\r\n });\r\n\r\n while (info.firstChild) {\r\n info.removeChild(info.firstChild);\r\n }\r\n\r\n if (count === 0) {\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n return;\r\n }\r\n\r\n let firstLine = `${String(count)} atom${count !== 1 ? 's' : ''} selected`;\r\n if (this._lastPick !== null) {\r\n firstLine += ', the last pick:';\r\n }\r\n let secondLine = '';\r\n let aName = '';\r\n let coordLine = '';\r\n\r\n if (this._lastPick instanceof Atom) {\r\n atom = this._lastPick;\r\n residue = atom.residue;\r\n\r\n aName = atom.name;\r\n const location = (atom.location !== 32) ? String.fromCharCode(atom.location) : ''; // 32 is code of white-space\r\n secondLine = `${atom.element.fullName} #${atom.serial}${location}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}.`;\r\n secondLine += aName;\r\n\r\n coordLine = `Coord: (${atom.position.x.toFixed(2).toString()},\\\r\n ${atom.position.y.toFixed(2).toString()},\\\r\n ${atom.position.z.toFixed(2).toString()})`;\r\n } else if (this._lastPick instanceof Residue) {\r\n residue = this._lastPick;\r\n\r\n secondLine = `${residue._type._fullName}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}`;\r\n } else if (this._lastPick instanceof Chain) {\r\n secondLine = `chain ${this._lastPick._name}`;\r\n } else if (this._lastPick instanceof Molecule) {\r\n secondLine = `molecule ${this._lastPick._name}`;\r\n }\r\n\r\n info.appendChild(document.createTextNode(firstLine));\r\n\r\n if (secondLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(secondLine));\r\n }\r\n\r\n if (coordLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(coordLine));\r\n }\r\n\r\n this._msgAtomInfo.style.opacity = 1.0;\r\n};\r\n\r\nMiew.prototype._getAltObj = function () {\r\n if (this._editors) {\r\n let altObj = null;\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n const nextAltObj = this._editors[i].getAltObj();\r\n if (nextAltObj.objects.length > 0) {\r\n if (altObj) {\r\n // we have selected atoms in two or more visuals -- not supported\r\n altObj = null;\r\n break;\r\n }\r\n altObj = nextAltObj;\r\n }\r\n }\r\n if (altObj) {\r\n return altObj;\r\n }\r\n }\r\n\r\n return {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n};\r\n\r\nMiew.prototype.resetPivot = (function () {\r\n const boundingBox = new THREE.Box3();\r\n const center = new THREE.Vector3();\r\n\r\n return function () {\r\n boundingBox.makeEmpty();\r\n this._forEachVisual((visual) => {\r\n boundingBox.union(visual.getBoundaries().boundingBox);\r\n });\r\n\r\n boundingBox.getCenter(center);\r\n this._objectControls.setPivot(center.negate());\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotResidue = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (residue) {\r\n const visual = this._getVisualForComplex(residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n if (residue._controlPoint) {\r\n center.copy(residue._controlPoint);\r\n } else {\r\n let x = 0;\r\n let y = 0;\r\n let z = 0;\r\n const amount = residue._atoms.length;\r\n for (let i = 0; i < amount; ++i) {\r\n const p = residue._atoms[i].position;\r\n x += p.x / amount;\r\n y += p.y / amount;\r\n z += p.z / amount;\r\n }\r\n center.set(x, y, z);\r\n }\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotAtom = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (atom) {\r\n const visual = this._getVisualForComplex(atom.residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n center.copy(atom.position);\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.getSelectionCenter = (function () {\r\n const _centerInVisual = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n return function (center, includesAtom, selector) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCenter(_centerInVisual, includesAtom, selector || visual.getSelectionBit())) {\r\n center.add(_centerInVisual);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.negate();\r\n return true;\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotSubset = (function () {\r\n const _center = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n function _includesInCurSelection(atom, selectionBit) {\r\n return atom.mask & (1 << selectionBit);\r\n }\r\n\r\n function _includesInSelector(atom, selector) {\r\n return selector.selector.includesAtom(atom);\r\n }\r\n\r\n return function (selector) {\r\n const includesAtom = (selector) ? _includesInSelector : _includesInCurSelection;\r\n\r\n if (this.getSelectionCenter(_center, includesAtom, selector)) {\r\n this._objectControls.setPivot(_center);\r\n this.dispatchEvent({ type: 'transform' });\r\n } else {\r\n this.logger.warn('selection is empty. Center operation not performed');\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Makes a screenshot.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n * @returns {string} Data URL representing the image contents.\r\n */\r\nMiew.prototype.screenshot = function (width, height) {\r\n const gfx = this._gfx;\r\n const deviceWidth = gfx.renderer.domElement.width;\r\n const deviceHeight = gfx.renderer.domElement.height;\r\n\r\n function fov2Tan(fov) {\r\n return Math.tan(THREE.MathUtils.degToRad(0.5 * fov));\r\n }\r\n\r\n function tan2Fov(tan) {\r\n return THREE.MathUtils.radToDeg(Math.atan(tan)) * 2.0;\r\n }\r\n\r\n function getDataURL() {\r\n let dataURL;\r\n const currBrowser = utils.getBrowser();\r\n\r\n if (currBrowser === utils.browserType.SAFARI) {\r\n const canvas = document.createElement('canvas');\r\n const canvasContext = canvas.getContext('2d');\r\n\r\n canvas.width = width === undefined ? deviceWidth : width;\r\n canvas.height = height === undefined ? deviceHeight : height;\r\n\r\n canvasContext.drawImage(gfx.renderer.domElement, 0, 0, canvas.width, canvas.height);\r\n dataURL = canvas.toDataURL('image/png');\r\n } else {\r\n // Copy current canvas to screenshot\r\n dataURL = gfx.renderer.domElement.toDataURL('image/png');\r\n }\r\n return dataURL;\r\n }\r\n height = height || width;\r\n\r\n let screenshotURI;\r\n if ((width === undefined && height === undefined)\r\n || (width === deviceWidth && height === deviceHeight)) {\r\n // renderer.domElement.toDataURL('image/png') returns flipped image in Safari\r\n // It hasn't been resolved yet, but getScreenshotSafari()\r\n // fixes it using an extra canvas.\r\n screenshotURI = getDataURL();\r\n } else {\r\n const originalAspect = gfx.camera.aspect;\r\n const originalFov = gfx.camera.fov;\r\n const originalTanFov2 = fov2Tan(gfx.camera.fov);\r\n\r\n // screenshot should contain the principal area of interest (a centered square touching screen sides)\r\n const areaOfInterestSize = Math.min(gfx.width, gfx.height);\r\n const areaOfInterestTanFov2 = originalTanFov2 * areaOfInterestSize / gfx.height;\r\n\r\n // set appropriate camera aspect & FOV\r\n const shotAspect = width / height;\r\n gfx.renderer.setPixelRatio(1);\r\n gfx.camera.aspect = shotAspect;\r\n gfx.camera.fov = tan2Fov(areaOfInterestTanFov2 / Math.min(shotAspect, 1.0));\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n // resize canvas to the required size of screenshot\r\n gfx.renderer.setDrawingBufferSize(width, height, 1);\r\n\r\n // make screenshot\r\n this._renderFrame(settings.now.stereo);\r\n screenshotURI = getDataURL();\r\n\r\n // restore original camera & canvas proportions\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.camera.aspect = originalAspect;\r\n gfx.camera.fov = originalFov;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.renderer.setDrawingBufferSize(gfx.width, gfx.height, window.devicePixelRatio);\r\n this._needRender = true;\r\n }\r\n\r\n return screenshotURI;\r\n};\r\n\r\n/**\r\n * Makes screenshot and initiates a download.\r\n * @param {string} [filename] - Name of a file. Default to a 'screenshot-XXXXX.png', where XXXXX is a current\r\n * date/time in seconds.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n */\r\nMiew.prototype.screenshotSave = function (filename, width, height) {\r\n const uri = this.screenshot(width, height);\r\n utils.shotDownload(uri, filename);\r\n};\r\n\r\nMiew.prototype.save = function (opts) {\r\n this._export(opts.fileType).then((dataString) => {\r\n const filename = this._visuals[this._curVisualName]._complex.name;\r\n utils.download(dataString, filename, opts.fileType);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone' });\r\n }).catch((error) => {\r\n this.logger.error('Could not export data');\r\n this.logger.debug(error);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone', error });\r\n });\r\n};\r\n\r\nMiew.prototype._tweakResolution = function () {\r\n const maxPerf = [\r\n ['poor', 100],\r\n ['low', 500],\r\n ['medium', 1000],\r\n ['high', 5000],\r\n ['ultra', Number.MAX_VALUE],\r\n ];\r\n\r\n let atomCount = 0;\r\n this._forEachComplexVisual((visual) => {\r\n atomCount += visual.getComplex().getAtomCount();\r\n });\r\n\r\n if (atomCount > 0) {\r\n const performance = this._gfxScore * 10e5 / atomCount;\r\n // set resolution based on estimated performance\r\n for (let i = 0; i < maxPerf.length; ++i) {\r\n if (performance < maxPerf[i][1]) {\r\n this._autoChangeResolution(maxPerf[i][0]);\r\n break;\r\n }\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._autoChangeResolution = function (resolution) {\r\n if (resolution !== settings.now.resolution) {\r\n this.logger.report(`Your rendering resolution was changed to \"${resolution}\" for best performance.`);\r\n }\r\n settings.now.resolution = resolution;\r\n};\r\n\r\n/**\r\n * Save current settings to cookies.\r\n */\r\nMiew.prototype.saveSettings = function () {\r\n this._cookies.setCookie(this._opts.settingsCookie, JSON.stringify(this.settings.getDiffs(true)));\r\n};\r\n\r\n/**\r\n * Load settings from cookies.\r\n */\r\nMiew.prototype.restoreSettings = function () {\r\n try {\r\n const cookie = this._cookies.getCookie(this._opts.settingsCookie);\r\n const diffs = cookie ? JSON.parse(cookie) : {};\r\n this.settings.applyDiffs(diffs, true);\r\n } catch (e) {\r\n this.logger.error(`Cookies parse error: ${e.message}`);\r\n }\r\n};\r\n\r\n/**\r\n * Reset current settings to the defaults.\r\n */\r\nMiew.prototype.resetSettings = function () {\r\n this.settings.reset();\r\n};\r\n\r\n/*\r\n * DANGEROUS and TEMPORARY. The method should change or disappear in future versions.\r\n * @param {string|object} opts - See {@link Miew} constructor.\r\n * @see {@link Miew#set}, {@link Miew#repAdd}, {@link Miew#rep}.\r\n */\r\nMiew.prototype.setOptions = function (opts) {\r\n if (typeof opts === 'string') {\r\n opts = Miew.options.fromAttr(opts);\r\n }\r\n if (opts.reps) {\r\n this._opts.reps = null;\r\n }\r\n _.merge(this._opts, opts);\r\n if (opts.settings) {\r\n this.set(opts.settings);\r\n }\r\n\r\n this._opts._objects = opts._objects;\r\n this._resetObjects();\r\n\r\n if (opts.load) {\r\n this.load(opts.load, { fileType: opts.type });\r\n }\r\n\r\n if (opts.preset) {\r\n settings.now.preset = opts.preset;\r\n }\r\n\r\n if (opts.reps) {\r\n this.resetReps(opts.preset);\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.getComplex().resetCurrentUnit();\r\n if (_.isNumber(opts.unit)) {\r\n visual.getComplex().setCurrentUnit(opts.unit);\r\n }\r\n this.resetView();\r\n this.rebuildAll();\r\n }\r\n};\r\n\r\nMiew.prototype.info = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return {};\r\n }\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n return {\r\n id: metadata.id || complex.name || 'UNKNOWN',\r\n title: (metadata.title && metadata.title.join(' ')) || 'UNKNOWN DATA',\r\n atoms: complex.getAtomCount(),\r\n bonds: complex.getBondCount(),\r\n residues: complex.getResidueCount(),\r\n chains: complex.getChainCount(),\r\n };\r\n};\r\n\r\n/*\r\n * OBJECTS SEGMENT\r\n */\r\n\r\nMiew.prototype.addObject = function (objData, bThrow) {\r\n let Ctor = null;\r\n\r\n if (objData.type === LinesObject.prototype.type) {\r\n Ctor = LinesObject;\r\n }\r\n\r\n if (Ctor === null) {\r\n throw new Error(`Unknown scene object type - ${objData.type}`);\r\n }\r\n\r\n try {\r\n const newObj = new Ctor(objData.params, objData.opts);\r\n this._addSceneObject(newObj);\r\n } catch (error) {\r\n if (!bThrow) {\r\n this.logger.debug(`Error during scene object creation: ${error.message}`);\r\n } else {\r\n throw error;\r\n }\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._addSceneObject = function (sceneObject) {\r\n const visual = this._getComplexVisual();\r\n if (sceneObject.build && visual) {\r\n sceneObject.build(visual.getComplex());\r\n this._gfx.pivot.add(sceneObject.getGeometry());\r\n }\r\n const objects = this._objects;\r\n objects[objects.length] = sceneObject;\r\n};\r\n\r\nMiew.prototype._updateObjsToFrame = function (frameData) {\r\n const objs = this._objects;\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n if (objs[i].updateToFrame) {\r\n objs[i].updateToFrame(frameData);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._resetObjects = function () {\r\n const objs = this._opts._objects;\r\n\r\n this._objects = [];\r\n if (objs) {\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n this.addObject(objs[i], false);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype.removeObject = function (index) {\r\n const obj = this._objects[index];\r\n if (!obj) {\r\n throw new Error(`Scene object with index ${index} does not exist`);\r\n }\r\n obj.destroy();\r\n this._objects.splice(index, 1);\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Get a string with a URL to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {string} URL\r\n */\r\nMiew.prototype.getURL = function (opts) {\r\n return options.toURL(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n })));\r\n};\r\n\r\n/**\r\n * Get a string with a script to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=true] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=true] - when this flag is true, a view information is included\r\n * @returns {string} script\r\n */\r\nMiew.prototype.getScript = function (opts) {\r\n return options.toScript(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: true,\r\n view: true,\r\n })));\r\n};\r\n\r\n/*\r\n * Generates object that represents the current state of representations list\r\n * @param {boolean} compareWithDefaults - when this flag is true, reps list is compared (if possible)\r\n * to preset's defaults and only diffs are generated\r\n */\r\nMiew.prototype._compareReps = function (complexVisual, compareWithDefaults) {\r\n const ans = {};\r\n let repCount = 0;\r\n\r\n if (complexVisual) {\r\n repCount = complexVisual.repCount();\r\n }\r\n\r\n const currPreset = settings.defaults.presets[settings.now.preset];\r\n let compare = compareWithDefaults;\r\n if (currPreset === undefined || currPreset.length > repCount) {\r\n compare = false;\r\n ans.preset = 'empty';\r\n } else if (settings.now.preset !== settings.defaults.preset) {\r\n ans.preset = settings.now.preset;\r\n }\r\n\r\n const repsDiff = [];\r\n let emptyReps = true;\r\n for (let i = 0, n = repCount; i < n; ++i) {\r\n repsDiff[i] = complexVisual.repGet(i).compare(compare ? currPreset[i] : null);\r\n if (!_.isEmpty(repsDiff[i])) {\r\n emptyReps = false;\r\n }\r\n }\r\n if (!emptyReps) {\r\n ans.reps = repsDiff;\r\n }\r\n return ans;\r\n};\r\n\r\n/*\r\n * Obtain object that represents current state of miew (might be used as options in constructor).\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {Object} State object.\r\n */\r\nMiew.prototype.getState = function (opts) {\r\n const state = {};\r\n\r\n opts = _.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n });\r\n\r\n // load\r\n const visual = this._getComplexVisual();\r\n if (visual !== null) {\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n if (metadata.id) {\r\n const format = metadata.format ? `${metadata.format}:` : '';\r\n state.load = format + metadata.id;\r\n }\r\n const unit = complex.getCurrentUnit();\r\n if (unit !== 1) {\r\n state.unit = unit;\r\n }\r\n }\r\n\r\n // representations\r\n const repsInfo = this._compareReps(visual, opts.compact);\r\n if (repsInfo.preset) {\r\n state.preset = repsInfo.preset;\r\n }\r\n\r\n if (repsInfo.reps) {\r\n state.reps = repsInfo.reps;\r\n }\r\n\r\n // objects\r\n const objects = this._objects;\r\n const objectsState = [];\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n objectsState[i] = objects[i].identify();\r\n }\r\n if (objects.length > 0) {\r\n state._objects = objectsState;\r\n }\r\n\r\n // view\r\n if (opts.view) {\r\n state.view = this.view();\r\n }\r\n\r\n // settings\r\n if (opts.settings) {\r\n const diff = this.settings.getDiffs(false);\r\n if (!_.isEmpty(diff)) {\r\n state.settings = diff;\r\n }\r\n }\r\n\r\n return state;\r\n};\r\n\r\n/**\r\n * Get parameter value.\r\n * @param {string} param - Parameter name or path (e.g. 'modes.BS.atom').\r\n * @param {*=} value - Default value.\r\n * @returns {*} Parameter value.\r\n */\r\nMiew.prototype.get = function (param, value) {\r\n return settings.get(param, value);\r\n};\r\n\r\nMiew.prototype._clipPlaneUpdateValue = function (radius) {\r\n const clipPlaneValue = Math.max(\r\n this._gfx.camera.position.z - radius * settings.now.draft.clipPlaneFactor,\r\n settings.now.camNear,\r\n );\r\n\r\n const opts = { clipPlaneValue };\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions(opts);\r\n });\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setUberOptions(opts);\r\n }\r\n }\r\n if (this._picker !== null) {\r\n this._picker.clipPlaneValue = clipPlaneValue;\r\n }\r\n};\r\n\r\nMiew.prototype._fogFarUpdateValue = function () {\r\n if (this._picker !== null) {\r\n if (this._gfx.scene.fog) {\r\n this._picker.fogFarValue = this._gfx.scene.fog.far;\r\n } else {\r\n this._picker.fogFarValue = undefined;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._updateShadowmapMeshes = function (process) {\r\n this._forEachComplexVisual((visual) => {\r\n const reprList = visual._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n process(repr.geo, repr.material);\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._updateMaterials = function (values, needTraverse = false, process = undefined) {\r\n this._forEachComplexVisual((visual) => visual.setMaterialValues(values, needTraverse, process));\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setValues(values);\r\n obj._line.material.needsUpdate = true;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._fogAlphaChanged = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions({\r\n fogAlpha: settings.now.fogAlpha,\r\n });\r\n });\r\n};\r\n\r\nMiew.prototype._embedWebXR = function () {\r\n // switch off\r\n if (settings.now.stereo !== 'WEBVR') {\r\n if (this.webVR) {\r\n this.webVR.disable();\r\n }\r\n this.webVR = null;\r\n return;\r\n }\r\n // switch on\r\n if (!this.webVR) {\r\n this.webVR = new WebVRPoC(() => {\r\n this._requestAnimationFrame(() => this._onTick());\r\n this._needRender = true;\r\n this._onResize();\r\n });\r\n }\r\n this.webVR.enable(this._gfx);\r\n};\r\n\r\nMiew.prototype._initOnSettingsChanged = function () {\r\n const on = (props, func) => {\r\n props = _.isArray(props) ? props : [props];\r\n props.forEach((prop) => {\r\n this.settings.addEventListener(`change:${prop}`, func);\r\n });\r\n };\r\n\r\n on('modes.VD.frame', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.showFrame(settings.now.modes.VD.frame);\r\n this._needRender = true;\r\n });\r\n\r\n on('modes.VD.isoMode', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n });\r\n\r\n on('bg.color', () => {\r\n this._onBgColorChanged();\r\n });\r\n\r\n on('ao', () => {\r\n if (settings.now.ao && !isAOSupported(this._gfx.renderer.getContext())) {\r\n this.logger.warn('Your device or browser does not support ao');\r\n settings.set('ao', false);\r\n } else {\r\n const values = { normalsToGBuffer: settings.now.ao };\r\n this._setUberMaterialValues(values);\r\n }\r\n });\r\n\r\n on('zSprites', () => {\r\n if (settings.now.zSprites && !arezSpritesSupported(this._gfx.renderer.getContext())) {\r\n this.logger.warn('Your device or browser does not support zSprites');\r\n settings.set('zSprites', false);\r\n }\r\n this.rebuildAll();\r\n });\r\n\r\n on('fogColor', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('fogColorEnable', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('bg.transparent', (evt) => {\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n // update materials\r\n this._updateMaterials({ fogTransparent: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('draft.clipPlane', (evt) => {\r\n // update materials\r\n this._updateMaterials({ clipPlane: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('shadow.on', (evt) => {\r\n // update materials\r\n const values = { shadowmap: evt.value, shadowmapType: settings.now.shadow.type };\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.shadowMap.enabled = Boolean(values.shadowmap);\r\n }\r\n this._updateMaterials(values, true);\r\n if (values.shadowmap) {\r\n this._updateShadowCamera();\r\n this._updateShadowmapMeshes(meshutils.createShadowmapMaterial);\r\n } else {\r\n this._updateShadowmapMeshes(meshutils.removeShadowmapMaterial);\r\n }\r\n this._needRender = true;\r\n });\r\n\r\n on('shadow.type', (evt) => {\r\n // update materials if shadowmap is enable\r\n if (settings.now.shadow.on) {\r\n this._updateMaterials({ shadowmapType: evt.value }, true);\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on('shadow.radius', (evt) => {\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].shadow !== undefined) {\r\n const light = this._gfx.scene.children[i];\r\n light.shadow.radius = evt.value;\r\n this._needRender = true;\r\n }\r\n }\r\n });\r\n\r\n on('fps', () => {\r\n this._fps.show(settings.now.fps);\r\n });\r\n\r\n on(['fog', 'fogNearFactor', 'fogFarFactor'], () => {\r\n this._updateFog();\r\n this._needRender = true;\r\n });\r\n\r\n on('fogAlpha', () => {\r\n const { fogAlpha } = settings.now;\r\n if (fogAlpha < 0 || fogAlpha > 1) {\r\n this.logger.warn('fogAlpha must belong range [0,1]');\r\n }\r\n this._fogAlphaChanged();\r\n this._needRender = true;\r\n });\r\n\r\n on('autoResolution', (evt) => {\r\n if (evt.value && !this._gfxScore) {\r\n this.logger.warn('Benchmarks are missed, autoresolution will not work! '\r\n + 'Autoresolution should be set during miew startup.');\r\n }\r\n });\r\n\r\n on('stereo', () => {\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n this._needRender = true;\r\n });\r\n\r\n on(['transparency', 'palette'], () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('resolution', () => {\r\n // update complex visuals\r\n this.rebuildAll();\r\n\r\n // update volume visual\r\n const volume = this._getVolumeVisual();\r\n if (volume) {\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on(['axes', 'fxaa', 'ao',\r\n 'outline.on', 'outline.color', 'outline.threshold', 'outline.thickness'], () => {\r\n this._needRender = true;\r\n });\r\n};\r\n\r\n/**\r\n * Set parameter value.\r\n * @param {string|object} params - Parameter name or path (e.g. 'modes.BS.atom') or even settings object.\r\n * @param {*=} value - Value.\r\n */\r\nMiew.prototype.set = function (params, value) {\r\n settings.set(params, value);\r\n};\r\n\r\n/**\r\n * Select atoms with selection string.\r\n * @param {string} expression - string expression of selection\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\nMiew.prototype.select = function (expression, append) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n let sel = expression;\r\n if (_.isString(expression)) {\r\n sel = selectors.parse(expression).selector;\r\n }\r\n\r\n visual.select(sel, append);\r\n this._lastPick = null;\r\n\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n};\r\n\r\nconst VIEW_VERSION = '1';\r\n\r\n/**\r\n * Get or set view info packed into string.\r\n *\r\n * **Note:** view is stored for *left-handed* cs, euler angles are stored in radians and *ZXY-order*,\r\n *\r\n * @param {string=} expression - Optional string encoded the view\r\n */\r\nMiew.prototype.view = function (expression) {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n let transform = [];\r\n const eulerOrder = 'ZXY';\r\n\r\n function encode() {\r\n const pos = pivot.position;\r\n const scale = self._objectControls.getScale() / settings.now.radiusToFit;\r\n const euler = new THREE.Euler();\r\n euler.setFromQuaternion(self._objectControls.getOrientation(), eulerOrder);\r\n transform = [\r\n pos.x, pos.y, pos.z,\r\n scale,\r\n euler.x, euler.y, euler.z,\r\n ];\r\n return VIEW_VERSION + utils.arrayToBase64(transform, Float32Array);\r\n }\r\n\r\n function decode() {\r\n // backwards compatible: old non-versioned view is the 0th version\r\n if (expression.length === 40) {\r\n expression = `0${expression}`;\r\n }\r\n\r\n const version = expression[0];\r\n transform = utils.arrayFromBase64(expression.substr(1), Float32Array);\r\n\r\n // apply adapter for old versions\r\n if (version !== VIEW_VERSION) {\r\n if (version === '0') {\r\n // cancel radiusToFit included in old views\r\n transform[3] /= 8.0;\r\n } else {\r\n // do nothing\r\n self.logger.warn(`Encoded view version mismatch, stored as ${version} vs ${VIEW_VERSION} expected`);\r\n return;\r\n }\r\n }\r\n\r\n const interpolator = self._interpolator;\r\n const srcView = interpolator.createView();\r\n srcView.position.copy(pivot.position);\r\n srcView.scale = self._objectControls.getScale();\r\n srcView.orientation.copy(self._objectControls.getOrientation());\r\n\r\n const dstView = interpolator.createView();\r\n dstView.position.set(transform[0], transform[1], transform[2]);\r\n\r\n // hack to make preset views work after we moved centering offset to visual nodes\r\n // FIXME should only store main pivot offset in preset\r\n if (self._getComplexVisual()) {\r\n dstView.position.sub(self._getComplexVisual().position);\r\n }\r\n\r\n dstView.scale = transform[3]; // eslint-disable-line prefer-destructuring\r\n dstView.orientation.setFromEuler(new THREE.Euler(transform[4], transform[5], transform[6], eulerOrder));\r\n\r\n interpolator.setup(srcView, dstView);\r\n }\r\n\r\n if (typeof expression === 'undefined') {\r\n return encode();\r\n }\r\n decode();\r\n\r\n return expression;\r\n};\r\n\r\n/*\r\n * Update current view due to viewinterpolator state\r\n */\r\nMiew.prototype._updateView = function () {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n\r\n const interpolator = this._interpolator;\r\n if (!interpolator.wasStarted()) {\r\n interpolator.start();\r\n }\r\n\r\n if (!interpolator.isMoving()) {\r\n return;\r\n }\r\n\r\n const res = interpolator.getCurrentView();\r\n if (res.success) {\r\n const curr = res.view;\r\n pivot.position.copy(curr.position);\r\n self._objectControls.setScale(curr.scale * settings.now.radiusToFit);\r\n self._objectControls.setOrientation(curr.orientation);\r\n this.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n }\r\n};\r\n\r\n/**\r\n * Translate object by vector\r\n * @param {number} x - translation value (Ang) along model's X axis\r\n * @param {number} y - translation value (Ang) along model's Y axis\r\n * @param {number} z - translation value (Ang) along model's Z axis\r\n */\r\nMiew.prototype.translate = function (x, y, z) {\r\n this._objectControls.translatePivot(x, y, z);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Rotate object by Euler angles\r\n * @param {number} x - rotation angle around X axis in radians\r\n * @param {number} y - rotation angle around Y axis in radians\r\n * @param {number} z - rotation angle around Z axis in radians\r\n */\r\nMiew.prototype.rotate = function (x, y, z) {\r\n this._objectControls.rotate(new THREE.Quaternion().setFromEuler(new THREE.Euler(x, y, z, 'XYZ')));\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Scale object by factor\r\n * @param {number} factor - scale multiplier, should greater than zero\r\n */\r\nMiew.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n throw new RangeError('Scale should be greater than zero');\r\n }\r\n this._objectControls.scale(factor);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Center view on selection\r\n * @param {empty | subset | string} selector - defines part of molecule which must be centered (\r\n * empty - center on current selection;\r\n * subset - center on picked atom/residue/molecule;\r\n * string - center on atoms correspond to selection string)\r\n */\r\nMiew.prototype.center = function (selector) {\r\n // no arguments - center on current selection;\r\n if (selector === undefined) {\r\n this.setPivotSubset();\r\n this._needRender = true;\r\n return;\r\n }\r\n // subset with atom or residue - center on picked atom/residue;\r\n if (selector.obj !== undefined && ('atom' in selector.obj || 'residue' in selector.obj)) { // from event with selection\r\n if ('atom' in selector.obj) {\r\n this.setPivotAtom(selector.obj.atom);\r\n } else {\r\n this.setPivotResidue(selector.obj.residue);\r\n }\r\n this._needRender = true;\r\n return;\r\n }\r\n // string - center on atoms correspond to selection string\r\n if (selector.obj === undefined && selector !== '') {\r\n const sel = selectors.parse(selector);\r\n if (sel.error === undefined) {\r\n this.setPivotSubset(sel);\r\n this._needRender = true;\r\n return;\r\n }\r\n }\r\n // empty subset or incorrect/empty string - center on all molecule;\r\n this.resetPivot();\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\nMiew.prototype.within = function (selector, radius) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return selectors.None();\r\n }\r\n\r\n if (selector instanceof String) {\r\n selector = selectors.parse(selector);\r\n }\r\n\r\n const res = visual.within(selector, radius);\r\n if (res) {\r\n visual.rebuildSelectionGeometry();\r\n this._needRender = true;\r\n }\r\n return res;\r\n};\r\n\r\n/**\r\n * Get atom position in 2D canvas coords\r\n * @param {string} fullAtomName - full atom name, like A.38.CG\r\n * @returns {Object} {x, y} or false if atom not found\r\n */\r\nMiew.prototype.projected = function (fullAtomName, complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return false;\r\n }\r\n\r\n const atom = visual.getComplex().getAtomByFullname(fullAtomName);\r\n if (atom === null) {\r\n return false;\r\n }\r\n\r\n const pos = atom.position.clone();\r\n // we consider atom position to be affected only by common complex transform\r\n // ignoring any transformations that may add during editing\r\n this._gfx.pivot.updateMatrixWorldRecursive();\r\n this._gfx.camera.updateMatrixWorldRecursive();\r\n this._gfx.pivot.localToWorld(pos);\r\n pos.project(this._gfx.camera);\r\n\r\n return {\r\n x: (pos.x + 1.0) * 0.5 * this._gfx.width,\r\n y: (1.0 - pos.y) * 0.5 * this._gfx.height,\r\n };\r\n};\r\n\r\n/**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n *\r\n * @param {string=} complexName - complex name\r\n */\r\nMiew.prototype.dssp = function (complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return;\r\n }\r\n visual.getComplex().dssp();\r\n\r\n // rebuild dependent representations (cartoon or ss-colored)\r\n visual._reprList.forEach((rep) => {\r\n if (rep.mode.id === 'CA' || rep.colorer.id === 'SS') {\r\n rep.needsRebuild = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype.exportCML = function () {\r\n const self = this;\r\n\r\n function extractRotation(m) {\r\n const xAxis = new THREE.Vector3();\r\n const yAxis = new THREE.Vector3();\r\n const zAxis = new THREE.Vector3();\r\n m.extractBasis(xAxis, yAxis, zAxis);\r\n xAxis.normalize();\r\n yAxis.normalize();\r\n zAxis.normalize();\r\n const retMat = new THREE.Matrix4();\r\n retMat.identity();\r\n retMat.makeBasis(xAxis, yAxis, zAxis);\r\n return retMat;\r\n }\r\n\r\n function updateCMLData(complex) {\r\n const { root } = self._gfx;\r\n const mat = extractRotation(root.matrixWorld);\r\n const v4 = new THREE.Vector4(0, 0, 0, 0);\r\n const vCenter = new THREE.Vector4(0, 0, 0, 0);\r\n let xml = null;\r\n let ap = null;\r\n\r\n // update atoms in cml\r\n complex.forEachAtom((atom) => {\r\n if (atom.xmlNodeRef && atom.xmlNodeRef.xmlNode) {\r\n xml = atom.xmlNodeRef.xmlNode;\r\n ap = atom.position;\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n v4.applyMatrix4(mat);\r\n xml.setAttribute('x3', v4.x.toString());\r\n xml.setAttribute('y3', v4.y.toString());\r\n xml.setAttribute('z3', v4.z.toString());\r\n xml.removeAttribute('x2');\r\n xml.removeAttribute('y2');\r\n }\r\n });\r\n // update stereo groups in cml\r\n complex.forEachSGroup((sGroup) => {\r\n if (sGroup.xmlNodeRef && sGroup.xmlNodeRef.xmlNode) {\r\n xml = sGroup.xmlNodeRef.xmlNode;\r\n ap = sGroup.getPosition();\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n const cp = sGroup.getCentralPoint();\r\n if (cp === null) {\r\n v4.applyMatrix4(mat);\r\n } else {\r\n vCenter.set(cp.x, cp.y, cp.z, 0.0);\r\n v4.add(vCenter);\r\n v4.applyMatrix4(mat); // pos in global space\r\n vCenter.set(cp.x, cp.y, cp.z, 1.0);\r\n vCenter.applyMatrix4(mat);\r\n v4.sub(vCenter);\r\n }\r\n xml.setAttribute('x', v4.x.toString());\r\n xml.setAttribute('y', v4.y.toString());\r\n xml.setAttribute('z', v4.z.toString());\r\n }\r\n });\r\n }\r\n\r\n const visual = self._getComplexVisual();\r\n const complex = visual ? visual.getComplex() : null;\r\n if (complex && complex.originalCML) {\r\n updateCMLData(complex);\r\n\r\n // serialize xml structure to string\r\n const oSerializer = new XMLSerializer();\r\n return oSerializer.serializeToString(complex.originalCML);\r\n }\r\n\r\n return null;\r\n};\r\n\r\n/**\r\n * Reproduce the RCSB PDB Molecule of the Month style by David S. Goodsell\r\n *\r\n * @see http://pdb101.rcsb.org/motm/motm-about\r\n */\r\nMiew.prototype.motm = function () {\r\n settings.set({\r\n fogColorEnable: true,\r\n fogColor: 0x000000,\r\n outline: { on: true, threshold: 0.01 },\r\n bg: { color: 0xffffff },\r\n });\r\n\r\n this._forEachComplexVisual((visual) => {\r\n const rep = [];\r\n const complex = visual.getComplex();\r\n const palette = palettes.get(settings.now.palette);\r\n for (let i = 0; i < complex.getChainCount(); i++) {\r\n const curChainName = complex._chains[i]._name;\r\n const curChainColor = palette.getChainColor(curChainName);\r\n rep[i] = {\r\n selector: `chain ${curChainName}`,\r\n mode: 'VW',\r\n colorer: ['CB', { color: curChainColor, factor: 0.9 }],\r\n material: 'FL',\r\n };\r\n }\r\n visual.resetReps(rep);\r\n });\r\n};\r\n\r\nMiew.prototype.VERSION = (typeof PACKAGE_VERSION !== 'undefined' && PACKAGE_VERSION) || '0.0.0-dev';\r\n\r\n// Uncomment this to get debug trace:\r\n// Miew.prototype.debugTracer = new utils.DebugTracer(Miew.prototype);\r\n\r\n_.assign(Miew, /** @lends Miew */ {\r\n VERSION: Miew.prototype.VERSION,\r\n\r\n registeredPlugins: [],\r\n\r\n // export namespaces // TODO: WIP: refactoring external interface\r\n chem,\r\n io,\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n utils,\r\n gfx: {\r\n Representation,\r\n },\r\n\r\n /**\r\n * Third-party libraries packaged together with Miew.\r\n *\r\n * @property {object} lodash - [Lodash](https://lodash.com/), a modern JavaScript utility library delivering\r\n * modularity, performance & extras.\r\n * @property {object} three - [three.js](https://threejs.org/), JavaScript 3D library.\r\n *\r\n * @example\r\n * var _ = Miew.thirdParty.lodash;\r\n * var opts = _.merge({ ... }, Miew.options.fromURL(window.location.search));\r\n * var miew = new Miew(opts);\r\n */\r\n thirdParty: {\r\n lodash: _,\r\n three: THREE,\r\n },\r\n});\r\n\r\nexport default Miew;\r\n","import palettes from '../gfx/palettes';\r\nimport settings from '../settings';\r\n\r\nconst modeIdDesc = {\r\n $help: [\r\n 'Rendering mode shortcut',\r\n ' BS - balls and sticks mode',\r\n ' LN - lines mode',\r\n ' LC - licorice mode',\r\n ' VW - van der waals mode',\r\n ' TR - trace mode',\r\n ' TU - tube mode',\r\n ' CA - cartoon mode',\r\n ' SA - isosurface mode',\r\n ' QS - quick surface mode',\r\n ' SE - solvent excluded mode',\r\n ' TX - text mode',\r\n ],\r\n BS: {\r\n $help: [\r\n ' Balls and sticks',\r\n ' aromrad = #aromatic radius',\r\n ' atom = #atom radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n CA: {\r\n $help: [\r\n ' Cartoon',\r\n ' arrow = #arrow size',\r\n ' depth = #depth of surface',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = #',\r\n ' width = #secondary width\\n',\r\n ],\r\n },\r\n LN: {\r\n $help: [\r\n ' Lines',\r\n ' atom = #atom radius',\r\n ' chunkarom = ',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' offsarom = \\n',\r\n ],\r\n },\r\n LC: {\r\n $help: [\r\n ' Licorice',\r\n ' aromrad = #aromatic radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n VW: {\r\n $help: [\r\n ' Van der Waals',\r\n ' nothing\\n',\r\n ],\r\n },\r\n TR: {\r\n $help: [\r\n ' Trace',\r\n ' radius = #tube radius\\n',\r\n ],\r\n },\r\n TU: {\r\n $help: [\r\n ' Tube',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = \\n',\r\n ],\r\n },\r\n SA: {\r\n $help: [\r\n ' Surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n QS: {\r\n $help: [\r\n ' Quick surface',\r\n ' isoValue = ',\r\n ' scale = ',\r\n ' wireframe = ',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n SE: {\r\n $help: [\r\n ' Solvent excluded surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n TX: {\r\n $help: [\r\n ' Text mode',\r\n ' template = string that can include \"{{ id }}\"',\r\n ' it will be replaced by value, id can be one of next:',\r\n ' serial, name, type, sequence, residue, chain, hetatm, water\\n',\r\n ' horizontalAlign = {\"left\", \"right\", \"center\"}',\r\n ' verticalAlign = {\"top\", \"bottom\", \"middle\"}',\r\n ' dx = #offset along x',\r\n ' dy = #offset along y',\r\n ' dz = #offset along z',\r\n ' fg = #text color modificator',\r\n ' could be keyword, named color or hex',\r\n ' fg = #back color modificator',\r\n ' could be keyword, named color or hex',\r\n ' showBg = #if set show background',\r\n ' plate under text',\r\n ],\r\n },\r\n};\r\n\r\nconst colorDesc = {\r\n $help: [\r\n 'Coloring mode shortcut',\r\n ' EL - color by element',\r\n ' CH - color by chain',\r\n ' SQ - color by sequence',\r\n ' RT - color by residue type',\r\n ' SS - color by secondary structure',\r\n ' UN - uniform',\r\n ],\r\n UN: {\r\n $help: [\r\n 'Parameters of coloring modes customization',\r\n ' Uniform',\r\n ' color = #RGB->HEX->dec\\n',\r\n ],\r\n color: {\r\n $help: Object.keys(palettes.get(settings.now.palette).namedColors).sort().join('\\n'),\r\n },\r\n },\r\n};\r\n\r\nconst materialDesc = {\r\n $help: [\r\n 'Material shortcut',\r\n ' DF - diffuse',\r\n ' TR - transparent',\r\n ' SF - soft plastic',\r\n ' PL - glossy plastic',\r\n ' ME - metal',\r\n ' GL - glass',\r\n ],\r\n};\r\n\r\nconst addRepDesc = {\r\n $help: [\r\n 'Short (packed) representation description as a set of variables',\r\n ' s=',\r\n ' selector property',\r\n ' m=[!:[,...]]',\r\n ' render mode property',\r\n ' c=[!:[,...]]',\r\n ' color mode property',\r\n ' mt=',\r\n ' material property',\r\n ],\r\n s: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n m: modeIdDesc,\r\n c: colorDesc,\r\n mt: materialDesc,\r\n};\r\n\r\nconst setGetParameterDesc = {\r\n $help: [\r\n 'Parameters of rendering modes customization: modes',\r\n 'Parameters of colorer customization: colorers',\r\n 'Autobuild: autobuild = (|)',\r\n ],\r\n modes: modeIdDesc,\r\n colorers: colorDesc,\r\n};\r\n\r\nconst help = {\r\n $help: [\r\n 'help (| )',\r\n 'You can get detailed information about command options',\r\n ' using \"help cmd.opt.opt.[...]\"\\n',\r\n ' you can use one line comments',\r\n ' everything started from (#|//) will be skipped',\r\n ' Example: >build //some comment\\n',\r\n 'List of available commands:',\r\n ],\r\n reset: {\r\n $help: [\r\n 'Reload current object, delete all representations',\r\n ' Nothing will work until load new object',\r\n ],\r\n },\r\n load: {\r\n $help: [\r\n 'load (||-f [<*.NC FILE URL STRING>])',\r\n ' Load new pdb object from selected source',\r\n ],\r\n PDBID: {\r\n $help: 'pdb id in remote molecule database',\r\n },\r\n URL: {\r\n $help: 'url to source file',\r\n },\r\n f: {\r\n $help: [\r\n 'open file system dialog to fetch local file',\r\n 'optionally you can determine trajectory file',\r\n 'via URL for *.top model',\r\n ],\r\n },\r\n },\r\n clear: {\r\n $help: 'No args. Clear terminal',\r\n },\r\n add: {\r\n $help: [\r\n 'add [] []',\r\n ' Add new item to representation set with',\r\n ' default or params',\r\n ],\r\n REP_NAME: {\r\n $help: 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n rep: {\r\n $help: [\r\n 'rep [|] []',\r\n ' set current representation by name or index',\r\n ' edit current representation by ',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n remove: {\r\n $help: [\r\n 'remove (|)',\r\n 'Remove representation by name or index',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n },\r\n selector: {\r\n $help: [\r\n 'selector ',\r\n ' set selector from EXPRESSION to current representation',\r\n ],\r\n EXPRESSION: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n },\r\n mode: {\r\n $help: [\r\n 'mode [=...]',\r\n ' set rendering mode and apply parameters to current representation',\r\n ],\r\n MODE_ID: modeIdDesc,\r\n },\r\n color: {\r\n $help: [\r\n 'color [=...]',\r\n ' set colorer and apply parameters to current representation',\r\n ],\r\n COLORER_ID: colorDesc,\r\n },\r\n material: {\r\n $help: [\r\n 'material ',\r\n ' set material to current representation',\r\n ],\r\n MATERIAL_ID: materialDesc,\r\n },\r\n build: {\r\n $help: 'build help str',\r\n add: {\r\n $help: 'build.add',\r\n new: {\r\n $help: [\r\n 'add.new',\r\n 'add.new new line 1',\r\n 'add.new new line 2',\r\n 'add.new new line 3',\r\n ],\r\n },\r\n },\r\n del: {\r\n $help: 'build.del',\r\n },\r\n },\r\n list: {\r\n $help: [\r\n 'list [-e|-s||]',\r\n 'Print representations if no args print list of representations',\r\n ' -e expand list and show all representations',\r\n ' -s show all user-registered selectors',\r\n ' | show only current representation',\r\n ],\r\n },\r\n hide: {\r\n $help: [\r\n 'hide (|)',\r\n 'Hide representation referenced in args',\r\n ],\r\n },\r\n show: {\r\n $help: [\r\n 'show (|)',\r\n 'Show representation referenced in args',\r\n ],\r\n },\r\n get: {\r\n $help: [\r\n 'get ',\r\n 'Print value',\r\n ' - path to option use get.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set: {\r\n $help: [\r\n 'set ',\r\n 'Set with ',\r\n ' - path to option use set.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set_save: {\r\n $help: [\r\n 'set_save',\r\n 'Save current settings to cookie',\r\n ],\r\n },\r\n set_restore: {\r\n $help: [\r\n 'set_restore',\r\n 'Load and apply settings from cookie',\r\n ],\r\n },\r\n set_reset: {\r\n $help: [\r\n 'set_reset',\r\n 'Reset current settings to the defaults',\r\n ],\r\n },\r\n preset: {\r\n $help: [\r\n 'preset []',\r\n 'Reset current representation or set preset to ',\r\n ],\r\n PRESET: {\r\n $help: [\r\n 'default',\r\n 'wire',\r\n 'small',\r\n 'macro',\r\n ],\r\n },\r\n },\r\n unit: {\r\n $help: [\r\n 'unit []',\r\n 'Change current biological structure view. Zero value means asymmetric unit,',\r\n 'positive values set an assembly with corresponding number.',\r\n 'Being called with no parameters command prints current unit information.',\r\n ],\r\n },\r\n view: {\r\n $help: [\r\n 'view []',\r\n 'Get current encoded view or set if ENCODED_VIEW placed as argument',\r\n ],\r\n ENCODED_VIEW: {\r\n $help: [\r\n 'encoded view matrix string (binary code)',\r\n ],\r\n },\r\n },\r\n rotate: {\r\n $help: [\r\n 'rotate (x|y|z) [] [(x|y|z) []]...',\r\n 'Rotate scene',\r\n ],\r\n },\r\n scale: {\r\n $help: [\r\n 'scale ',\r\n 'Scale scene',\r\n ],\r\n },\r\n select: {\r\n $help: [\r\n 'select [as ]',\r\n 'Select atoms using selector defined in SELECTOR_STRING',\r\n ' and if SELECTOR_NAME is defined register it in viewer',\r\n ' you can use it later as a complex selector',\r\n ],\r\n },\r\n within: {\r\n $help: [\r\n 'within of as ',\r\n 'Build within named selector',\r\n ' DISTANCE ',\r\n ' SELECTOR_STRING ',\r\n ' SELECTOR_NAME ',\r\n ],\r\n },\r\n url: {\r\n $help: [\r\n 'url [-s] [-v]',\r\n 'Report URL encoded scene',\r\n ' if -s set that include settings in the URL',\r\n ' if -v set that include view in the URL',\r\n ],\r\n },\r\n screenshot: {\r\n $help: [\r\n 'screenshot [ []]',\r\n 'Make a screenshot of the scene',\r\n ' WIDTH in pixels',\r\n ' HEIGHT in pixels, equal to WIDTH by default',\r\n ],\r\n },\r\n line: {\r\n $help: [\r\n 'line [=]',\r\n 'Draw dashed line between two specified atoms',\r\n ],\r\n },\r\n removeobj: {\r\n $help: [\r\n 'removeobj ',\r\n 'Remove scene object by its index. Indices could be obtained by command',\r\n ],\r\n },\r\n listobj: {\r\n $help: [\r\n 'listobj',\r\n 'Display the list of all existing scene objects',\r\n ],\r\n },\r\n};\r\n\r\nexport default help;\r\n","import _ from 'lodash';\r\nimport Miew from './Miew';\r\nimport { parser as parsercli } from './utils/MiewCLIParser';\r\nimport clihelp from './utils/MiewCLIHelp';\r\nimport logger from './utils/logger';\r\nimport utils from './utils';\r\n\r\nconst {\r\n chem: { selectors },\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n} = Miew;\r\n\r\nfunction None() {\r\n}\r\n\r\nconst NULL = (function () {\r\n const obj = new None();\r\n return function () {\r\n return obj;\r\n };\r\n}());\r\n\r\nclass RepresentationMap {\r\n constructor() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n\r\n get(strId) {\r\n return this.representationMap[strId] || this.representationID[strId] || '';\r\n }\r\n\r\n add(strId, index) {\r\n if (strId === -1) {\r\n return 'Can not create representation: there is no data';\r\n }\r\n\r\n if (index !== undefined) {\r\n if (!this.representationMap.hasOwnProperty(strId)) {\r\n this.representationMap[strId.toString()] = index;\r\n this.representationID[index] = strId.toString();\r\n } else {\r\n return 'This name has already existed, registered without name';\r\n }\r\n }\r\n return `Representation ${strId} successfully added`;\r\n }\r\n\r\n remove(index) {\r\n if (index && this.representationID.hasOwnProperty(index)) {\r\n delete this.representationMap[this.representationID[index]];\r\n delete this.representationID[index];\r\n }\r\n\r\n const sortedKeys = Object.keys(this.representationID).sort();\r\n for (const i in sortedKeys) {\r\n if (sortedKeys.hasOwnProperty(i)) {\r\n const id = sortedKeys[i];\r\n if (id > index) {\r\n this.representationID[id - 1] = this.representationID[id];\r\n this.representationMap[this.representationID[id]] -= 1;\r\n delete this.representationID[id];\r\n }\r\n }\r\n }\r\n }\r\n\r\n clear() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n}\r\n\r\nconst representationsStorage = new RepresentationMap();\r\n\r\nfunction keyRemap(key) {\r\n const keys = {\r\n s: 'selector',\r\n m: 'mode',\r\n c: 'colorer',\r\n mt: 'material',\r\n mode: 'modes',\r\n color: 'colorers',\r\n colorer: 'colorers',\r\n select: 'selector',\r\n material: 'materials',\r\n selector: 'selector',\r\n };\r\n const ans = keys[key];\r\n return ans === undefined ? key : ans;\r\n}\r\n\r\nclass CLIUtils {\r\n list(miew, repMap, key) {\r\n let ret = '';\r\n if (miew && repMap !== undefined) {\r\n if (key === undefined || key === '-e') {\r\n const count = miew.repCount();\r\n\r\n for (let i = 0; i < count; i++) {\r\n ret += this.listRep(miew, repMap, i, key);\r\n }\r\n }\r\n }\r\n return ret;\r\n }\r\n\r\n listRep(miew, repMap, repIndex, key) {\r\n let ret = '';\r\n const rep = miew.repGet(repIndex);\r\n if (!rep) {\r\n logger.warn(`Rep ${repIndex} does not exist!`);\r\n return ret;\r\n }\r\n const index = repIndex;\r\n const repName = repMap.get(index);\r\n\r\n const { mode, colorer } = rep;\r\n const selectionStr = rep.selectorString;\r\n const material = rep.materialPreset;\r\n\r\n ret += `#${index} : ${mode.name}${repName === '' ? '' : `, ${repName}`}\\n`;\r\n\r\n if (key !== undefined) {\r\n ret += ` selection : \"${selectionStr}\"\\n`;\r\n ret += ` mode : (${mode.id}), ${mode.name}\\n`;\r\n ret += ` colorer : (${colorer.id}), ${colorer.name}\\n`;\r\n ret += ` material : (${material.id}), ${material.name}\\n`;\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listSelector(miew, context) {\r\n let ret = '';\r\n\r\n for (const k in context) {\r\n if (context.hasOwnProperty(k)) {\r\n ret += `${k} : \"${context[k]}\"\\n`;\r\n }\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listObjs(miew) {\r\n const objs = miew._objects;\r\n\r\n if (!objs || !Array.isArray(objs) || objs.length === 0) {\r\n return 'There are no objects on the scene';\r\n }\r\n\r\n const strList = [];\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n strList[i] = `${i}: ${objs[i].toString()}`;\r\n }\r\n\r\n return strList.join('\\n');\r\n }\r\n\r\n joinHelpStr(helpData) {\r\n if (helpData instanceof Array) {\r\n return helpData.join('\\n');\r\n }\r\n return helpData;\r\n }\r\n\r\n help(path) {\r\n if (_.isUndefined(path)) {\r\n return `${this.joinHelpStr(clihelp.$help)}\\n${_.slice(_.sortBy(_.keys(clihelp)), 1).join(', ')}\\n`;\r\n }\r\n\r\n const helpItem = _.get(clihelp, path);\r\n return _.isUndefined(helpItem) ? this.help() : `${this.joinHelpStr(helpItem.$help)}\\n`;\r\n }\r\n\r\n load(miew, arg) {\r\n if (miew === undefined || arg === undefined || arg === '-f') {\r\n return;\r\n }\r\n miew.awaitWhileCMDisInProcess();\r\n const finish = () => miew.finishAwaitingCMDInProcess();\r\n miew.load(arg).then(finish, finish);\r\n }\r\n\r\n checkArg(key, arg, modificate) {\r\n if (key !== undefined && arg !== undefined) {\r\n if (keyRemap(key) === 'selector') {\r\n const res = selectors.parse(arg);\r\n\r\n if (res.error !== undefined) {\r\n const selExc = { message: res.error };\r\n throw selExc;\r\n }\r\n\r\n if (modificate !== undefined && modificate) {\r\n return res.selector;\r\n }\r\n return arg;\r\n }\r\n\r\n const modificators = {\r\n colorers,\r\n modes,\r\n materials,\r\n };\r\n\r\n let modificator = key;\r\n let temp;\r\n while (modificator !== temp) {\r\n temp = modificator;\r\n modificator = keyRemap(temp);\r\n }\r\n\r\n if (modificators[modificator].get(arg) === undefined) {\r\n const exc = { message: `${arg} is not existed in ${modificator}` };\r\n throw exc;\r\n }\r\n return arg;\r\n }\r\n return NULL;\r\n }\r\n\r\n propagateProp(path, arg) {\r\n if (path !== undefined) {\r\n let argExc = {};\r\n const adapter = options.adapters[typeof _.get(settings.defaults, path)];\r\n if (adapter === undefined) {\r\n const pathExc = { message: `${path} is not existed` };\r\n throw pathExc;\r\n }\r\n\r\n if ((path.endsWith('.color') || path.endsWith('.baseColor')\r\n || path.endsWith('.EL.carbon')) && typeof arg !== 'number') {\r\n arg = palettes.get(settings.now.palette).getNamedColor(arg);\r\n }\r\n\r\n if (path.endsWith('.fg') || path.endsWith('.bg')) {\r\n if (typeof arg !== 'number') {\r\n const val = palettes.get(settings.now.palette).getNamedColor(arg, true);\r\n if (val !== undefined) {\r\n arg = `0x${val.toString(16)}`;\r\n }\r\n } else {\r\n arg = `0x${arg.toString(16)}`;\r\n }\r\n }\r\n\r\n if (path.endsWith('.template')) {\r\n arg = arg.replace(/\\\\n/g, '\\n');// NOSONAR\r\n }\r\n\r\n if (arg !== undefined && adapter(arg) !== arg && adapter(arg) !== (arg > 0)) {\r\n argExc = { message: `${path} must be a \"${typeof _.get(settings.defaults, path)}\"` };\r\n throw argExc;\r\n }\r\n }\r\n return arg;\r\n }\r\n\r\n unquoteString(value) {\r\n return utils.unquoteString(value);\r\n }\r\n}\r\n// repIndexOrRepMap could be RepresentationMap or index\r\n\r\nconst utilFunctions = new CLIUtils();\r\n\r\nfunction CreateObjectPair(a, b) {\r\n const obj = {};\r\n obj[a] = b;\r\n return obj;\r\n}\r\n\r\nfunction ArgList(arg) {\r\n if (arg instanceof this.constructor) {\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n}\r\n\r\nArgList.prototype.append = function (value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n};\r\n\r\nArgList.prototype.remove = function (value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n};\r\n\r\nArgList.prototype.toJSO = function (cliUtils, cmd, arg) {\r\n const res = {};\r\n\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n _.set(res, list[i].id, cliUtils.propagateProp(`${keyRemap(cmd)}.${arg}.${list[i].id}`, list[i].val));\r\n }\r\n\r\n return res;\r\n};\r\n\r\nfunction Arg(_id, _val) {\r\n this.id = _id;\r\n this.val = _val;\r\n}\r\n\r\nconst cliutils = Object.create({});\r\n\r\ncliutils.Arg = Arg;\r\ncliutils.ArgList = ArgList;\r\n\r\ncliutils.miew = null;\r\ncliutils.echo = null;\r\ncliutils.representations = representationsStorage;\r\ncliutils.utils = utilFunctions;\r\n\r\ncliutils._ = _;\r\ncliutils.CreateObjectPair = CreateObjectPair;\r\ncliutils.keyRemap = keyRemap;\r\ncliutils.Context = selectors.Context;\r\ncliutils.ClearContext = selectors.ClearContext;\r\n\r\ncliutils.NULL = NULL;\r\n\r\ncliutils.notimplemented = function () {\r\n return this.NULL;\r\n};\r\n\r\nMiew.prototype.script = function (script, _printCallback, _errorCallback) {\r\n parsercli.yy.miew = this;\r\n parsercli.yy.echo = _printCallback;\r\n parsercli.yy.error = _errorCallback;\r\n if (this.cmdQueue === undefined) {\r\n this.cmdQueue = [];\r\n }\r\n\r\n if (this.commandInAction === undefined) {\r\n this.commandInAction = false;\r\n }\r\n\r\n this.cmdQueue = this.cmdQueue.concat(script.split('\\n'));\r\n};\r\n\r\nMiew.prototype.awaitWhileCMDisInProcess = function () {\r\n this.commandInAction = true;\r\n};\r\n\r\nMiew.prototype.finishAwaitingCMDInProcess = function () {\r\n this.commandInAction = false;\r\n};\r\n\r\nMiew.prototype.isScriptingCommandAvailable = function () {\r\n return this.commandInAction !== undefined\r\n && !this.commandInAction\r\n && this.cmdQueue !== undefined\r\n && this.cmdQueue.length > 0;\r\n};\r\n\r\nMiew.prototype.callNextCmd = function () {\r\n if (this.isScriptingCommandAvailable()) {\r\n const cmd = this.cmdQueue.shift();\r\n\r\n const res = {};\r\n res.success = false;\r\n try {\r\n parsercli.parse(cmd);\r\n res.success = true;\r\n } catch (e) {\r\n res.error = e.message;\r\n parsercli.yy.error(res.error);\r\n this.finishAwaitingCMDInProcess();\r\n }\r\n return res;\r\n }\r\n return '';\r\n};\r\n\r\nparsercli.yy = cliutils;\r\n// workaround for incorrect JISON parser generator for AMD module\r\nparsercli.yy.parseError = parsercli.parseError;\r\n","import Miew from './Miew';\r\nimport './Miew-cli';\r\n\r\nexport default 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function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.miew.reset(false); yy.ClearContext(); yy.miew.resetReps(\"empty\");\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.miew.rebuild();\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.miew.rebuildAll(); yy.miew.rebuild();\r\nbreak;\r\ncase 6:\r\nthis.$ = yy.echo(yy.utils.help().toString());\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.echo(yy.utils.help($$[$0]).toString());\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.miew.motm();\r\nbreak;\r\ncase 10: case 11:\r\nthis.$ = yy.utils.propagateProp($$[$0]); yy.echo(yy.miew.get($$[$0]).toString());\r\nbreak;\r\ncase 12: case 13:\r\nthis.$ = yy.miew.set($$[$0-1], yy.utils.propagateProp($$[$0-1], $$[$0]));;\r\nbreak;\r\ncase 14:\r\nthis.$ = yy.miew.saveSettings();;\r\nbreak;\r\ncase 15:\r\nthis.$ = yy.miew.restoreSettings();;\r\nbreak;\r\ncase 16:\r\nthis.$ = yy.miew.resetSettings();;\r\nbreak;\r\ncase 17:\r\nthis.$ = yy.miew.resetReps();\r\nbreak;\r\ncase 18:\r\nthis.$ = yy.miew.applyPreset($$[$0]);\r\nbreak;\r\ncase 21:\r\nthis.$ = yy.miew.repRemove($$[$0]); yy.representations.remove($$[$0]);\r\nbreak;\r\ncase 22:\r\nthis.$ = yy.miew.repHide($$[$0]);\r\nbreak;\r\ncase 23:\r\nthis.$ = yy.miew.repHide($$[$0], false);\r\nbreak;\r\ncase 24:\r\nthis.$ = yy.echo(yy.utils.listRep(yy.miew, yy.representations, $$[$0], '-e'));\r\nbreak;\r\ncase 25:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations));\r\nbreak;\r\ncase 26:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations, $$[$0]));\r\nbreak;\r\ncase 27:\r\nthis.$ = yy.echo(yy.utils.listSelector(yy.miew, yy.Context));\r\nbreak;\r\ncase 28:\r\nthis.$ = yy.miew.select(yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0], true));\r\nbreak;\r\ncase 29:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.utils.checkArg($$[$0-3].toLowerCase(), $$[$0-2], true); yy.miew.select(yy.Context[$$[$0].toLowerCase()]);\r\nbreak;\r\ncase 30:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {selector : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0])});\r\nbreak;\r\ncase 31:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.miew.within(yy.utils.checkArg(\"select\", $$[$0-2], true), Number($$[$0-4]));\r\nbreak;\r\ncase 32:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {material : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 35:\r\nthis.$ = yy.echo(yy.miew.view());\r\nbreak;\r\ncase 36: case 37:\r\nthis.$ = yy.miew.view($$[$0]);\r\nbreak;\r\ncase 38:\r\nthis.$ = yy.echo(yy.miew.changeUnit());\r\nbreak;\r\ncase 39:\r\nthis.$ = yy.echo(yy.miew.changeUnit($$[$0]));\r\nbreak;\r\ncase 40:\r\nthis.$ = yy.miew.dssp();\r\nbreak;\r\ncase 41:\r\nthis.$ = yy.miew.scale($$[$0]);\r\nbreak;\r\ncase 42:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.rotate($$[$0][i]['x'] * Math.PI / 180.0, $$[$0][i]['y'] * Math.PI / 180.0, $$[$0][i]['z'] * Math.PI / 180.0)} \r\nbreak;\r\ncase 43:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.translate($$[$0][i]['x'] || 0, $$[$0][i]['y'] || 0, $$[$0][i]['z'] || 0)} \r\nbreak;\r\ncase 44:\r\nthis.$ = yy.miew.center();\r\nbreak;\r\ncase 45:\r\nthis.$ = yy.miew.center($$[$0]);\r\nbreak;\r\ncase 48: case 49:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-1], $$[$0]]}, true);\r\nbreak;\r\ncase 50: case 51:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-2], $$[$0-1]], opts:$$[$0].toJSO(yy.utils, 'objects', 'line')}, true);\r\nbreak;\r\ncase 52:\r\nthis.$ = yy.echo(yy.utils.listObjs(yy.miew));\r\nbreak;\r\ncase 53:\r\nthis.$ = yy.miew.removeObject($$[$0]);\r\nbreak;\r\ncase 54:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: false}));\r\nbreak;\r\ncase 55:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: true}));\r\nbreak;\r\ncase 56:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: false}));\r\nbreak;\r\ncase 57: case 58:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: true}));\r\nbreak;\r\ncase 59:\r\nthis.$ = yy.miew.screenshotSave();\r\nbreak;\r\ncase 60:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0]));\r\nbreak;\r\ncase 61:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0-1]), Number($$[$0]));\r\nbreak;\r\ncase 62: case 63: case 64:\r\nthis.$ = yy.utils.load(yy.miew, $$[$0]); yy.representations.clear();\r\nbreak;\r\ncase 65:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd()));\r\nbreak;\r\ncase 66:\r\nthis.$ = yy.echo(yy.representations.add($$[$0], yy.miew.repAdd()));\r\nbreak;\r\ncase 67:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 68:\r\nthis.$ = yy.echo(yy.representations.add($$[$0-1], yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 69:\r\nthis.$ = yy.miew.rep($$[$0]); yy.miew.repCurrent($$[$0]);\r\nbreak;\r\ncase 70:\r\nthis.$ = yy.miew.rep($$[$0-1], $$[$0]); yy.miew.repCurrent($$[$0-1]);\r\nbreak;\r\ncase 71:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 72:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 73:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 74:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 75:\r\nthis.$ = Number(yy.representations.get($$[$0]));\r\nbreak;\r\ncase 76: case 92:\r\nthis.$ = Number($$[$0]);\r\nbreak;\r\ncase 77:\r\nthis.$ = $$[$0];\r\nbreak;\r\ncase 78:\r\nthis.$ = yy._.assign($$[$0-1], $$[$0]);\r\nbreak;\r\ncase 79:\r\nthis.$ = yy._.assign($$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 80:\r\nthis.$ = yy._.assign($$[$0-3], $$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 81: case 82:\r\nthis.$ = yy.CreateObjectPair($$[$0].key, $$[$0].val);\r\nbreak;\r\ncase 83:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].key, new Array($$[$0-1].val, $$[$0].toJSO(yy.utils, $$[$0-1].key, $$[$0-1].val)));\r\nbreak;\r\ncase 84: case 85:\r\nthis.$ = Object.create({'key': yy.keyRemap($$[$0-2]), 'val': yy.utils.checkArg($$[$0-2], $$[$0])});\r\nbreak;\r\ncase 86:\r\nthis.$ = [$$[$0]];\r\nbreak;\r\ncase 87:\r\nthis.$ = $$[$0-1].concat($$[$0]);\r\nbreak;\r\ncase 88:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].toLowerCase(), Number($$[$0]));\r\nbreak;\r\ncase 89:\r\nthis.$ = new yy.ArgList($$[$0]);\r\nbreak;\r\ncase 90:\r\nthis.$ = $$[$0-1].append($$[$0]);\r\nbreak;\r\ncase 91:\r\nthis.$ = new yy.Arg($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 93:\r\nthis.$ = parseInt($$[$0]);\r\nbreak;\r\ncase 94:\r\nthis.$ = JSON.parse($$[$0]);\r\nbreak;\r\ncase 95: case 96:\r\nthis.$ = String($$[$0]);\r\nbreak;\r\ncase 157: case 158: case 161: case 162: case 163:\r\nthis.$ = $$[$0-2] + $$[$0-1] + $$[$0] //cause of could be color word in path;\r\nbreak;\r\ncase 166:\r\nthis.$ = $$[$0-2] = $$[$0-2] + $$[$0-1] + $$[$0];\r\nbreak;\r\n}\r\n},\r\ntable: 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,[2,90]),{14:$VS,16:197,35:$VT,38:$VU,77:$VV,78:$VW},{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,33:$Ve,34:$Vf,35:[1,199],37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,79:198,80:52,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN},o($V41,[2,84]),o($V31,[2,85]),{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,32:200,33:$Ve,34:$Vf,37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,70:$Vx,72:$Vy,74:$Vz,79:184,80:52,81:185,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN,96:$VO,97:$VP,98:$VQ,99:$VR},{5:[2,80]},o($V31,[2,91]),o($V61,[2,157]),o($V61,[2,158]),{5:[2,31]}],\r\ndefaultActions: {3:[2,2],4:[2,3],7:[2,8],8:[2,9],11:[2,14],12:[2,15],13:[2,16],15:[2,19],16:[2,20],25:[2,33],26:[2,34],29:[2,40],34:[2,46],35:[2,47],37:[2,52],46:[2,1],47:[2,5],107:[2,11],110:[2,18],116:[2,21],119:[2,22],120:[2,23],121:[2,24],122:[2,26],123:[2,27],125:[2,30],127:[2,32],128:[2,36],129:[2,37],130:[2,39],131:[2,41],136:[2,45],139:[2,53],140:[2,62],141:[2,63],142:[2,64],143:[2,164],145:[2,67],158:[2,12],159:[2,13],166:[2,68],174:[2,70],177:[2,57],178:[2,58],179:[2,61],183:[2,29],184:[2,99],185:[2,100],196:[2,80],200:[2,31]},\r\nparseError: function parseError (str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function(match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex () {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin (condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState () {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules () {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState (n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState (condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* ignore whitespace */\r\nbreak;\r\ncase 1:return '';\r\nbreak;\r\ncase 2:return '';\r\nbreak;\r\ncase 3:return 42;\r\nbreak;\r\ncase 4:return 35;\r\nbreak;\r\ncase 5:return 77;\r\nbreak;\r\ncase 6:return 78;\r\nbreak;\r\ncase 7:return 78;\r\nbreak;\r\ncase 8:return 8;\r\nbreak;\r\ncase 9:return 6;\r\nbreak;\r\ncase 10:return 82;\r\nbreak;\r\ncase 11:return 7;\r\nbreak;\r\ncase 12:return 9;\r\nbreak;\r\ncase 13:return 59;\r\nbreak;\r\ncase 14:return 13\r\nbreak;\r\ncase 15:return 15\r\nbreak;\r\ncase 16:return 17\r\nbreak;\r\ncase 17:return 18\r\nbreak;\r\ncase 18:return 19\r\nbreak;\r\ncase 19:return 20\r\nbreak;\r\ncase 20:return 11\r\nbreak;\r\ncase 21:return 62\r\nbreak;\r\ncase 22:return 64\r\nbreak;\r\ncase 23:return 23\r\nbreak;\r\ncase 24:return 25\r\nbreak;\r\ncase 25:return 26\r\nbreak;\r\ncase 26:return 27\r\nbreak;\r\ncase 27:return 30\r\nbreak;\r\ncase 28:return 34\r\nbreak;\r\ncase 29:return 33\r\nbreak;\r\ncase 30:return 65\r\nbreak;\r\ncase 31:return 66\r\nbreak;\r\ncase 32:return 37\r\nbreak;\r\ncase 33:return 41\r\nbreak;\r\ncase 34:return 43\r\nbreak;\r\ncase 35:return 52\r\nbreak;\r\ncase 36:return 54\r\nbreak;\r\ncase 37:return 55\r\nbreak;\r\ncase 38:return 46\r\nbreak;\r\ncase 39:return 48\r\nbreak;\r\ncase 40:return 45\r\nbreak;\r\ncase 41:return 49\r\nbreak;\r\ncase 42:return 56\r\nbreak;\r\ncase 43:return 58;\r\nbreak;\r\ncase 44:return 44\r\nbreak;\r\ncase 45:return 83\r\nbreak;\r\ncase 46:return 84\r\nbreak;\r\ncase 47:return 85\r\nbreak;\r\ncase 48:return 86\r\nbreak;\r\ncase 49:return 87\r\nbreak;\r\ncase 50:return 88\r\nbreak;\r\ncase 51:return 89\r\nbreak;\r\ncase 52:return 90\r\nbreak;\r\ncase 53:return 91\r\nbreak;\r\ncase 54:return 92\r\nbreak;\r\ncase 55:return 93\r\nbreak;\r\ncase 56:return 94\r\nbreak;\r\ncase 57:return 95\r\nbreak;\r\ncase 58:return 70\r\nbreak;\r\ncase 59:return 70\r\nbreak;\r\ncase 60:return 72\r\nbreak;\r\ncase 61:return 72\r\nbreak;\r\ncase 62:return 74\r\nbreak;\r\ncase 63:return 74\r\nbreak;\r\ncase 64:return 74\r\nbreak;\r\ncase 65:return 31\r\nbreak;\r\ncase 66:return 36\r\nbreak;\r\ncase 67:return 96\r\nbreak;\r\ncase 68:return 97\r\nbreak;\r\ncase 69:return 98\r\nbreak;\r\ncase 70:return 99\r\nbreak;\r\ncase 71:yy_.yytext = yy.utils.unquoteString(yy_.yytext); return 14;\r\nbreak;\r\ncase 72:return 38;\r\nbreak;\r\ncase 73:return 5;\r\nbreak;\r\ncase 74:return 101;\r\nbreak;\r\ncase 75:return 103;\r\nbreak;\r\ncase 76:return '\\\\';\r\nbreak;\r\ncase 77:return 28\r\nbreak;\r\ncase 78:return 61\r\nbreak;\r\ncase 79:return 29\r\nbreak;\r\ncase 80:return 57\r\nbreak;\r\ncase 81:return 71\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:[#].*)/i,/^(?:\\/\\/.*)/i,/^(?:([_A-Z0-9\\/\\+]+==))/i,/^(?:-?[0-9]+(\\.[0-9]+)?\\b)/i,/^(?:0[xX][0-9A-F]+\\b)/i,/^(?:false\\b)/i,/^(?:true\\b)/i,/^(?:all\\b)/i,/^(?:reset\\b)/i,/^(?:clear\\b)/i,/^(?:build\\b)/i,/^(?:help\\b)/i,/^(?:load\\b)/i,/^(?:get\\b)/i,/^(?:set\\b)/i,/^(?:set_save\\b)/i,/^(?:set_restore\\b)/i,/^(?:set_reset\\b)/i,/^(?:preset\\b)/i,/^(?:motm\\b)/i,/^(?:add\\b)/i,/^(?:rep\\b)/i,/^(?:remove\\b)/i,/^(?:hide\\b)/i,/^(?:show\\b)/i,/^(?:list\\b)/i,/^(?:select\\b)/i,/^(?:within\\b)/i,/^(?:selector\\b)/i,/^(?:mode\\b)/i,/^(?:color\\b)/i,/^(?:material\\b)/i,/^(?:view\\b)/i,/^(?:unit\\b)/i,/^(?:line\\b)/i,/^(?:listobj\\b)/i,/^(?:removeobj\\b)/i,/^(?:rotate\\b)/i,/^(?:translate\\b)/i,/^(?:scale\\b)/i,/^(?:center\\b)/i,/^(?:url\\b)/i,/^(?:screenshot\\b)/i,/^(?:dssp\\b)/i,/^(?:file_list\\b)/i,/^(?:file_register\\b)/i,/^(?:file_delete\\b)/i,/^(?:preset_add\\b)/i,/^(?:preset_delete\\b)/i,/^(?:preset_update\\b)/i,/^(?:preset_rename\\b)/i,/^(?:preset_open\\b)/i,/^(?:create_scenario\\b)/i,/^(?:reset_scenario\\b)/i,/^(?:delete_scenario\\b)/i,/^(?:add_scenario_item\\b)/i,/^(?:list_scenario\\b)/i,/^(?:s\\b)/i,/^(?:mt\\b)/i,/^(?:m\\b)/i,/^(?:c\\b)/i,/^(?:x\\b)/i,/^(?:y\\b)/i,/^(?:z\\b)/i,/^(?:as\\b)/i,/^(?:of\\b)/i,/^(?:pdb\\b)/i,/^(?:delay\\b)/i,/^(?:prst\\b)/i,/^(?:desc\\b)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:\\.)/i,/^(?:\\/)/i,/^(?:\\\\)/i,/^(?:-e\\b)/i,/^(?:-f\\b)/i,/^(?:-s\\b)/i,/^(?:-v\\b)/i,/^(?:=)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","/* eslint-disable */\r\n// DO NOT EDIT! Automatically generated from .jison\r\n/* parser generated by jison 0.4.18 */\r\n/*\r\n Returns a Parser object of the following structure:\r\n\r\n Parser: {\r\n yy: {}\r\n }\r\n\r\n Parser.prototype: {\r\n yy: {},\r\n trace: function(),\r\n symbols_: {associative list: name ==> number},\r\n terminals_: {associative list: number ==> name},\r\n productions_: [...],\r\n performAction: function anonymous(yytext, yyleng, yylineno, yy, yystate, $$, _$),\r\n table: [...],\r\n defaultActions: {...},\r\n parseError: function(str, hash),\r\n parse: function(input),\r\n\r\n lexer: {\r\n EOF: 1,\r\n parseError: function(str, hash),\r\n setInput: function(input),\r\n input: function(),\r\n unput: function(str),\r\n more: function(),\r\n less: function(n),\r\n pastInput: function(),\r\n upcomingInput: function(),\r\n showPosition: function(),\r\n test_match: function(regex_match_array, rule_index),\r\n next: function(),\r\n lex: function(),\r\n begin: function(condition),\r\n popState: function(),\r\n _currentRules: function(),\r\n topState: function(),\r\n pushState: function(condition),\r\n\r\n options: {\r\n ranges: boolean (optional: true ==> token location info will include a .range[] member)\r\n flex: boolean (optional: true ==> flex-like lexing behaviour where the rules are tested exhaustively to find the longest match)\r\n backtrack_lexer: boolean (optional: true ==> lexer regexes are tested in order and for each matching regex the action code is invoked; the lexer terminates the scan when a token is returned by the action code)\r\n },\r\n\r\n performAction: function(yy, yy_, $avoiding_name_collisions, YY_START),\r\n rules: [...],\r\n conditions: {associative list: name ==> set},\r\n }\r\n }\r\n\r\n\r\n token location info (@$, _$, etc.): {\r\n first_line: n,\r\n last_line: n,\r\n first_column: n,\r\n last_column: n,\r\n range: [start_number, end_number] (where the numbers are indexes into the input string, regular zero-based)\r\n }\r\n\r\n\r\n the parseError function receives a 'hash' object with these members for lexer and parser errors: {\r\n text: (matched text)\r\n token: (the produced terminal token, if any)\r\n line: (yylineno)\r\n }\r\n while parser (grammar) errors will also provide these members, i.e. parser errors deliver a superset of attributes: {\r\n loc: (yylloc)\r\n expected: (string describing the set of expected tokens)\r\n recoverable: (boolean: TRUE when the parser has a error recovery rule available for this particular error)\r\n }\r\n*/\r\nvar parser = (function(){\r\nvar o=function(k,v,o,l){for(o=o||{},l=k.length;l--;o[k[l]]=v);return o},$V0=[1,4],$V1=[1,5],$V2=[1,6],$V3=[1,7],$V4=[1,8],$V5=[1,9],$V6=[1,11],$V7=[1,12],$V8=[5,7,8,11],$V9=[1,17],$Va=[1,22],$Vb=[1,20],$Vc=[1,21],$Vd=[5,7,8,11,19];\r\nvar parser = {trace: function trace() { },\r\nyy: {},\r\nsymbols_: {\"error\":2,\"Program\":3,\"Expression\":4,\"EOF\":5,\"Selector\":6,\"OR\":7,\"AND\":8,\"NOT\":9,\"(\":10,\")\":11,\"SELECTOR\":12,\"NAMED_SELECTOR\":13,\"SELECTOR_RANGED\":14,\"RangeList\":15,\"SELECTOR_NAMED\":16,\"NameList\":17,\"Range\":18,\",\":19,\"NUMBER\":20,\":\":21,\"Name\":22,\"IDENTIFIER\":23,\"STRING\":24,\"$accept\":0,\"$end\":1},\r\nterminals_: {2:\"error\",5:\"EOF\",7:\"OR\",8:\"AND\",9:\"NOT\",10:\"(\",11:\")\",12:\"SELECTOR\",13:\"NAMED_SELECTOR\",14:\"SELECTOR_RANGED\",16:\"SELECTOR_NAMED\",19:\",\",20:\"NUMBER\",21:\":\",23:\"IDENTIFIER\",24:\"STRING\"},\r\nproductions_: [0,[3,2],[4,1],[4,3],[4,3],[4,2],[4,3],[6,1],[6,1],[6,2],[6,2],[15,1],[15,3],[18,1],[18,3],[17,1],[17,3],[22,1],[22,1],[22,1]],\r\nperformAction: function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.keyword('or')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.keyword('and')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.keyword('not')($$[$0]);\r\nbreak;\r\ncase 6:\r\nthis.$ = $$[$0-1];\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.keyword($$[$0])();\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.GetSelector($$[$0].toLowerCase().slice(1, $$[$0].length));\r\nbreak;\r\ncase 9: case 10:\r\nthis.$ = yy.keyword($$[$0-1])($$[$0]);\r\nbreak;\r\ncase 11:\r\nthis.$ = new yy.RangeList($$[$0]);\r\nbreak;\r\ncase 12: case 16:\r\nthis.$ = $$[$0-2].append($$[$0]);\r\nbreak;\r\ncase 13:\r\nthis.$ = new yy.Range(Number($$[$0]));\r\nbreak;\r\ncase 14:\r\nthis.$ = new yy.Range(Number($$[$0-2]), Number($$[$0]));\r\nbreak;\r\ncase 15:\r\nthis.$ = new yy.ValueList($$[$0]);\r\nbreak;\r\n}\r\n},\r\ntable: [{3:1,4:2,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{1:[3]},{5:[1,10],7:$V6,8:$V7},o($V8,[2,2]),{4:13,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:14,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,7]),o($V8,[2,8]),{15:15,18:16,20:$V9},{17:18,20:$Va,22:19,23:$Vb,24:$Vc},{1:[2,1]},{4:23,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:24,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,5]),{7:$V6,8:$V7,11:[1,25]},o($V8,[2,9],{19:[1,26]}),o($Vd,[2,11]),o($Vd,[2,13],{21:[1,27]}),o($V8,[2,10],{19:[1,28]}),o($Vd,[2,15]),o($Vd,[2,17]),o($Vd,[2,18]),o($Vd,[2,19]),o([5,7,11],[2,3],{8:$V7}),o($V8,[2,4]),o($V8,[2,6]),{18:29,20:$V9},{20:[1,30]},{20:$Va,22:31,23:$Vb,24:$Vc},o($Vd,[2,12]),o($Vd,[2,14]),o($Vd,[2,16])],\r\ndefaultActions: {10:[2,1]},\r\nparseError: function parseError(str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function (match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex() {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin(condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState() {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules() {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState(n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState(condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* skip whitespace */\r\nbreak;\r\ncase 1:return 20;\r\nbreak;\r\ncase 2:return 7;\r\nbreak;\r\ncase 3:return 8;\r\nbreak;\r\ncase 4:return 9;\r\nbreak;\r\ncase 5:return 12;\r\nbreak;\r\ncase 6:return 16;\r\nbreak;\r\ncase 7:return 14;\r\nbreak;\r\ncase 8:return 10;\r\nbreak;\r\ncase 9:return 11;\r\nbreak;\r\ncase 10:return 19;\r\nbreak;\r\ncase 11:return 21;\r\nbreak;\r\ncase 12:return '<=';\r\nbreak;\r\ncase 13:return '>=';\r\nbreak;\r\ncase 14:return '<';\r\nbreak;\r\ncase 15:return '>';\r\nbreak;\r\ncase 16:yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2); return 24;\r\nbreak;\r\ncase 17:return 13;\r\nbreak;\r\ncase 18:return 23;\r\nbreak;\r\ncase 19:return 5;\r\nbreak;\r\ncase 20:return 'INVALID';\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:(-?(?:[1-9][0-9]+|[0-9]))\\b)/i,/^(?:OR\\b)/i,/^(?:AND\\b)/i,/^(?:NOT\\b)/i,/^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\\b)/i,/^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\\b)/i,/^(?:((SERIAL|SEQUENCE|RESIDX))\\b)/i,/^(?:\\()/i,/^(?:\\))/i,/^(?:,)/i,/^(?::)/i,/^(?:<=)/i,/^(?:>=)/i,/^(?:<)/i,/^(?:>)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:(@[_A-Z0-9]+))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:.)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","\r\n/*\r\nSmooth.js version 0.1.7\r\n\r\nTurn arrays into smooth functions.\r\n\r\nCopyright 2012 Spencer Cohen\r\nLicensed under MIT license (see \"Smooth.js MIT license.txt\")\r\n*/\r\n\r\n/*Constants (these are accessible by Smooth.WHATEVER in user space)\r\n*/\r\n\r\n(function() {\r\n var AbstractInterpolator, CubicInterpolator, Enum, LinearInterpolator, NearestInterpolator, PI, SincFilterInterpolator, Smooth, clipClamp, clipMirror, clipPeriodic, defaultConfig, getColumn, getType, isValidNumber, k, makeLanczosWindow, makeScaledFunction, makeSincKernel, normalizeScaleTo, shallowCopy, sin, sinc, v, validateNumber, validateVector,\r\n __hasProp = Object.prototype.hasOwnProperty,\r\n __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor; child.__super__ = parent.prototype; return child; };\r\n\r\n Enum = {\r\n /*Interpolation methods\r\n */\r\n METHOD_NEAREST: 'nearest',\r\n METHOD_LINEAR: 'linear',\r\n METHOD_CUBIC: 'cubic',\r\n METHOD_LANCZOS: 'lanczos',\r\n METHOD_SINC: 'sinc',\r\n /*Input clipping modes\r\n */\r\n CLIP_CLAMP: 'clamp',\r\n CLIP_ZERO: 'zero',\r\n CLIP_PERIODIC: 'periodic',\r\n CLIP_MIRROR: 'mirror',\r\n /* Constants for control over the cubic interpolation tension\r\n */\r\n CUBIC_TENSION_DEFAULT: 0,\r\n CUBIC_TENSION_CATMULL_ROM: 0\r\n };\r\n\r\n defaultConfig = {\r\n method: Enum.METHOD_CUBIC,\r\n cubicTension: Enum.CUBIC_TENSION_DEFAULT,\r\n clip: Enum.CLIP_CLAMP,\r\n scaleTo: 0,\r\n sincFilterSize: 2,\r\n sincWindow: void 0\r\n };\r\n\r\n /*Index clipping functions\r\n */\r\n\r\n clipClamp = function(i, n) {\r\n return Math.max(0, Math.min(i, n - 1));\r\n };\r\n\r\n clipPeriodic = function(i, n) {\r\n i = i % n;\r\n if (i < 0) i += n;\r\n return i;\r\n };\r\n\r\n clipMirror = function(i, n) {\r\n var period;\r\n period = 2 * (n - 1);\r\n i = clipPeriodic(i, period);\r\n if (i > n - 1) i = period - i;\r\n return i;\r\n };\r\n\r\n /*\r\n Abstract scalar interpolation class which provides common functionality for all interpolators\r\n \r\n Subclasses must override interpolate().\r\n */\r\n\r\n AbstractInterpolator = (function() {\r\n\r\n function AbstractInterpolator(array, config) {\r\n this.array = array.slice(0);\r\n this.length = this.array.length;\r\n if (!(this.clipHelper = {\r\n clamp: this.clipHelperClamp,\r\n zero: this.clipHelperZero,\r\n periodic: this.clipHelperPeriodic,\r\n mirror: this.clipHelperMirror\r\n }[config.clip])) {\r\n throw \"Invalid clip: \" + config.clip;\r\n }\r\n }\r\n\r\n AbstractInterpolator.prototype.getClippedInput = function(i) {\r\n if ((0 <= i && i < this.length)) {\r\n return this.array[i];\r\n } else {\r\n return this.clipHelper(i);\r\n }\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperClamp = function(i) {\r\n return this.array[clipClamp(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperZero = function(i) {\r\n return 0;\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperPeriodic = function(i) {\r\n return this.array[clipPeriodic(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperMirror = function(i) {\r\n return this.array[clipMirror(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.interpolate = function(t) {\r\n throw 'Subclasses of AbstractInterpolator must override the interpolate() method.';\r\n };\r\n\r\n return AbstractInterpolator;\r\n\r\n })();\r\n\r\n NearestInterpolator = (function(_super) {\r\n\r\n __extends(NearestInterpolator, _super);\r\n\r\n function NearestInterpolator() {\r\n NearestInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n NearestInterpolator.prototype.interpolate = function(t) {\r\n return this.getClippedInput(Math.round(t));\r\n };\r\n\r\n return NearestInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n LinearInterpolator = (function(_super) {\r\n\r\n __extends(LinearInterpolator, _super);\r\n\r\n function LinearInterpolator() {\r\n LinearInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n LinearInterpolator.prototype.interpolate = function(t) {\r\n var k;\r\n k = Math.floor(t);\r\n t -= k;\r\n return (1 - t) * this.getClippedInput(k) + t * this.getClippedInput(k + 1);\r\n };\r\n\r\n return LinearInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n CubicInterpolator = (function(_super) {\r\n\r\n __extends(CubicInterpolator, _super);\r\n\r\n function CubicInterpolator(array, config) {\r\n this.tangentFactor = 1 - Math.max(-1, Math.min(1, config.cubicTension));\r\n CubicInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n CubicInterpolator.prototype.getTangent = function(k) {\r\n return this.tangentFactor * (this.getClippedInput(k + 1) - this.getClippedInput(k - 1)) / 2;\r\n };\r\n\r\n CubicInterpolator.prototype.interpolate = function(t) {\r\n var k, m, p, t2, t3;\r\n k = Math.floor(t);\r\n m = [this.getTangent(k), this.getTangent(k + 1)];\r\n p = [this.getClippedInput(k), this.getClippedInput(k + 1)];\r\n t -= k;\r\n t2 = t * t;\r\n t3 = t * t2;\r\n return (2 * t3 - 3 * t2 + 1) * p[0] + (t3 - 2 * t2 + t) * m[0] + (-2 * t3 + 3 * t2) * p[1] + (t3 - t2) * m[1];\r\n };\r\n\r\n return CubicInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n sin = Math.sin, PI = Math.PI;\r\n\r\n sinc = function(x) {\r\n if (x === 0) {\r\n return 1;\r\n } else {\r\n return sin(PI * x) / (PI * x);\r\n }\r\n };\r\n\r\n makeLanczosWindow = function(a) {\r\n return function(x) {\r\n return sinc(x / a);\r\n };\r\n };\r\n\r\n makeSincKernel = function(window) {\r\n return function(x) {\r\n return sinc(x) * window(x);\r\n };\r\n };\r\n\r\n SincFilterInterpolator = (function(_super) {\r\n\r\n __extends(SincFilterInterpolator, _super);\r\n\r\n function SincFilterInterpolator(array, config) {\r\n SincFilterInterpolator.__super__.constructor.apply(this, arguments);\r\n this.a = config.sincFilterSize;\r\n if (!config.sincWindow) throw 'No sincWindow provided';\r\n this.kernel = makeSincKernel(config.sincWindow);\r\n }\r\n\r\n SincFilterInterpolator.prototype.interpolate = function(t) {\r\n var k, n, sum, _ref, _ref2;\r\n k = Math.floor(t);\r\n sum = 0;\r\n for (n = _ref = k - this.a + 1, _ref2 = k + this.a; _ref <= _ref2 ? n <= _ref2 : n >= _ref2; _ref <= _ref2 ? n++ : n--) {\r\n sum += this.kernel(t - n) * this.getClippedInput(n);\r\n }\r\n return sum;\r\n };\r\n\r\n return SincFilterInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n getColumn = function(arr, i) {\r\n var row, _i, _len, _results;\r\n _results = [];\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n row = arr[_i];\r\n _results.push(row[i]);\r\n }\r\n return _results;\r\n };\r\n\r\n makeScaledFunction = function(f, baseScale, scaleRange) {\r\n var scaleFactor, translation;\r\n if (scaleRange.join === '0,1') {\r\n return f;\r\n } else {\r\n scaleFactor = baseScale / (scaleRange[1] - scaleRange[0]);\r\n translation = scaleRange[0];\r\n return function(t) {\r\n return f(scaleFactor * (t - translation));\r\n };\r\n }\r\n };\r\n\r\n getType = function(x) {\r\n return Object.prototype.toString.call(x).slice('[object '.length, -1);\r\n };\r\n\r\n validateNumber = function(n) {\r\n if (isNaN(n)) throw 'NaN in Smooth() input';\r\n if (getType(n) !== 'Number') throw 'Non-number in Smooth() input';\r\n if (!isFinite(n)) throw 'Infinity in Smooth() input';\r\n };\r\n\r\n validateVector = function(v, dimension) {\r\n var n, _i, _len;\r\n if (getType(v) !== 'Array') throw 'Non-vector in Smooth() input';\r\n if (v.length !== dimension) throw 'Inconsistent dimension in Smooth() input';\r\n for (_i = 0, _len = v.length; _i < _len; _i++) {\r\n n = v[_i];\r\n validateNumber(n);\r\n }\r\n };\r\n\r\n isValidNumber = function(n) {\r\n return (getType(n) === 'Number') && isFinite(n) && !isNaN(n);\r\n };\r\n\r\n normalizeScaleTo = function(s) {\r\n var invalidErr;\r\n invalidErr = \"scaleTo param must be number or array of two numbers\";\r\n switch (getType(s)) {\r\n case 'Number':\r\n if (!isValidNumber(s)) throw invalidErr;\r\n s = [0, s];\r\n break;\r\n case 'Array':\r\n if (s.length !== 2) throw invalidErr;\r\n if (!(isValidNumber(s[0]) && isValidNumber(s[1]))) throw invalidErr;\r\n break;\r\n default:\r\n throw invalidErr;\r\n }\r\n return s;\r\n };\r\n\r\n shallowCopy = function(obj) {\r\n var copy, k, v;\r\n copy = {};\r\n for (k in obj) {\r\n if (!__hasProp.call(obj, k)) continue;\r\n v = obj[k];\r\n copy[k] = v;\r\n }\r\n return copy;\r\n };\r\n\r\n Smooth = function(arr, config) {\r\n var baseDomainEnd, dimension, i, interpolator, interpolatorClass, interpolators, k, n, properties, smoothFunc, v;\r\n if (config == null) config = {};\r\n properties = {};\r\n config = shallowCopy(config);\r\n properties.config = shallowCopy(config);\r\n if (config.scaleTo == null) config.scaleTo = config.period;\r\n if (config.sincFilterSize == null) {\r\n config.sincFilterSize = config.lanczosFilterSize;\r\n }\r\n for (k in defaultConfig) {\r\n if (!__hasProp.call(defaultConfig, k)) continue;\r\n v = defaultConfig[k];\r\n if (config[k] == null) config[k] = v;\r\n }\r\n if (!(interpolatorClass = {\r\n nearest: NearestInterpolator,\r\n linear: LinearInterpolator,\r\n cubic: CubicInterpolator,\r\n lanczos: SincFilterInterpolator,\r\n sinc: SincFilterInterpolator\r\n }[config.method])) {\r\n throw \"Invalid method: \" + config.method;\r\n }\r\n if (config.method === 'lanczos') {\r\n config.sincWindow = makeLanczosWindow(config.sincFilterSize);\r\n }\r\n if (arr.length < 2) throw 'Array must have at least two elements';\r\n properties.count = arr.length;\r\n smoothFunc = (function() {\r\n var _i, _j, _len, _len2;\r\n switch (getType(arr[0])) {\r\n case 'Number':\r\n properties.dimension = 'scalar';\r\n if (Smooth.deepValidation) {\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n n = arr[_i];\r\n validateNumber(n);\r\n }\r\n }\r\n interpolator = new interpolatorClass(arr, config);\r\n return function(t) {\r\n return interpolator.interpolate(t);\r\n };\r\n case 'Array':\r\n properties.dimension = dimension = arr[0].length;\r\n if (!dimension) throw 'Vectors must be non-empty';\r\n if (Smooth.deepValidation) {\r\n for (_j = 0, _len2 = arr.length; _j < _len2; _j++) {\r\n v = arr[_j];\r\n validateVector(v, dimension);\r\n }\r\n }\r\n interpolators = (function() {\r\n var _results;\r\n _results = [];\r\n for (i = 0; 0 <= dimension ? i < dimension : i > dimension; 0 <= dimension ? i++ : i--) {\r\n _results.push(new interpolatorClass(getColumn(arr, i), config));\r\n }\r\n return _results;\r\n })();\r\n return function(t) {\r\n var interpolator, _k, _len3, _results;\r\n _results = [];\r\n for (_k = 0, _len3 = interpolators.length; _k < _len3; _k++) {\r\n interpolator = interpolators[_k];\r\n _results.push(interpolator.interpolate(t));\r\n }\r\n return _results;\r\n };\r\n default:\r\n throw \"Invalid element type: \" + (getType(arr[0]));\r\n }\r\n })();\r\n if (config.clip === 'periodic') {\r\n baseDomainEnd = arr.length;\r\n } else {\r\n baseDomainEnd = arr.length - 1;\r\n }\r\n config.scaleTo || (config.scaleTo = baseDomainEnd);\r\n properties.domain = normalizeScaleTo(config.scaleTo);\r\n smoothFunc = makeScaledFunction(smoothFunc, baseDomainEnd, properties.domain);\r\n properties.domain.sort();\r\n /*copy properties\r\n */\r\n for (k in properties) {\r\n if (!__hasProp.call(properties, k)) continue;\r\n v = properties[k];\r\n smoothFunc[k] = v;\r\n }\r\n return smoothFunc;\r\n };\r\n\r\n for (k in Enum) {\r\n if (!__hasProp.call(Enum, k)) continue;\r\n v = Enum[k];\r\n Smooth[k] = v;\r\n }\r\n\r\n Smooth.deepValidation = true;\r\n\r\n (typeof exports !== \"undefined\" && exports !== null ? exports : window).Smooth = Smooth;\r\n\r\n}).call(this);\r\n","!function(r,t){if(\"function\"==typeof define&&define.amd)define([\"exports\"],t);else if(\"object\"==typeof exports&&\"undefined\"!=typeof module)t(exports);else t(r.MMTF=r.MMTF||{})}(this,function(r){\"use strict\";function t(r,t,n){for(var e=(r.byteLength,0),i=n.length;i>e;e++){var o=n.charCodeAt(e);if(128>o)r.setUint8(t++,o>>>0&127|0);else if(2048>o)r.setUint8(t++,o>>>6&31|192),r.setUint8(t++,o>>>0&63|128);else if(65536>o)r.setUint8(t++,o>>>12&15|224),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128);else{if(!(1114112>o))throw new Error(\"bad codepoint \"+o);r.setUint8(t++,o>>>18&7|240),r.setUint8(t++,o>>>12&63|128),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128)}}}function n(r){for(var t=0,n=0,e=r.length;e>n;n++){var i=r.charCodeAt(n);if(128>i)t+=1;else if(2048>i)t+=2;else if(65536>i)t+=3;else{if(!(1114112>i))throw new Error(\"bad codepoint \"+i);t+=4}}return t}function e(r,i,o){var a=typeof r;if(\"string\"===a){var u=n(r);if(32>u)return i.setUint8(o,160|u),t(i,o+1,r),1+u;if(256>u)return i.setUint8(o,217),i.setUint8(o+1,u),t(i,o+2,r),2+u;if(65536>u)return 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zIndex: 2e9,\n className: 'spinner',\n top: '50%',\n left: '50%',\n shadow: '0 0 1px transparent', // prevent aliased lines\n position: 'absolute',\n};\nvar Spinner = /** @class */ (function () {\n function Spinner(opts) {\n if (opts === void 0) { opts = {}; }\n this.opts = __assign(__assign({}, defaults), opts);\n }\n /**\n * Adds the spinner to the given target element. If this instance is already\n * spinning, it is automatically removed from its previous target by calling\n * stop() internally.\n */\n Spinner.prototype.spin = function (target) {\n this.stop();\n this.el = document.createElement('div');\n this.el.className = this.opts.className;\n this.el.setAttribute('role', 'progressbar');\n this.el.style.position = this.opts.position;\n this.el.style.width = \"0\";\n this.el.style.zIndex = this.opts.zIndex.toString();\n this.el.style.left = this.opts.left;\n this.el.style.top = this.opts.top;\n this.el.style.transform = \"scale(\".concat(this.opts.scale, \")\");\n if (target) {\n target.insertBefore(this.el, target.firstChild || null);\n }\n drawLines(this.el, this.opts);\n return this;\n };\n /**\n * Stops and removes the Spinner.\n * Stopped spinners may be reused by calling spin() again.\n */\n Spinner.prototype.stop = function () {\n if (this.el) {\n if (this.el.parentNode) {\n this.el.parentNode.removeChild(this.el);\n }\n this.el = undefined;\n }\n return this;\n };\n return Spinner;\n}());\nexport { Spinner };\n/**\n * Returns the line color from the given string or array.\n */\nfunction getColor(color, idx) {\n return typeof color == 'string' ? color : color[idx % color.length];\n}\n/**\n * Internal method that draws the individual lines.\n */\nfunction drawLines(el, opts) {\n var borderRadius = (Math.round(opts.corners * opts.width * 500) / 1000) + 'px';\n var shadow = 'none';\n if (opts.shadow === true) {\n shadow = '0 2px 4px #000'; // default shadow\n }\n else if (typeof opts.shadow === 'string') {\n shadow = opts.shadow;\n }\n var shadows = parseBoxShadow(shadow);\n for (var i = 0; i < opts.lines; i++) {\n var degrees = ~~(360 / opts.lines * i + opts.rotate);\n var backgroundLine = document.createElement('div');\n backgroundLine.style.position = 'absolute';\n backgroundLine.style.top = \"\".concat(-opts.width / 2, \"px\");\n backgroundLine.style.width = (opts.length + opts.width) + 'px';\n backgroundLine.style.height = opts.width + 'px';\n backgroundLine.style.background = getColor(opts.fadeColor, i);\n backgroundLine.style.borderRadius = borderRadius;\n backgroundLine.style.transformOrigin = 'left';\n backgroundLine.style.transform = \"rotate(\".concat(degrees, \"deg) translateX(\").concat(opts.radius, \"px)\");\n var delay = i * opts.direction / opts.lines / opts.speed;\n delay -= 1 / opts.speed; // so initial animation state will include trail\n var line = document.createElement('div');\n line.style.width = '100%';\n line.style.height = '100%';\n line.style.background = getColor(opts.color, i);\n line.style.borderRadius = borderRadius;\n line.style.boxShadow = normalizeShadow(shadows, degrees);\n line.style.animation = \"\".concat(1 / opts.speed, \"s linear \").concat(delay, \"s infinite \").concat(opts.animation);\n backgroundLine.appendChild(line);\n el.appendChild(backgroundLine);\n }\n}\nfunction parseBoxShadow(boxShadow) {\n var regex = /^\\s*([a-zA-Z]+\\s+)?(-?\\d+(\\.\\d+)?)([a-zA-Z]*)\\s+(-?\\d+(\\.\\d+)?)([a-zA-Z]*)(.*)$/;\n var shadows = [];\n for (var _i = 0, _a = boxShadow.split(','); _i < _a.length; _i++) {\n var shadow = _a[_i];\n var matches = shadow.match(regex);\n if (matches === null) {\n continue; // invalid syntax\n }\n var x = +matches[2];\n var y = +matches[5];\n var xUnits = matches[4];\n var yUnits = matches[7];\n if (x === 0 && !xUnits) {\n xUnits = yUnits;\n }\n if (y === 0 && !yUnits) {\n yUnits = xUnits;\n }\n if (xUnits !== yUnits) {\n continue; // units must match to use as coordinates\n }\n shadows.push({\n prefix: matches[1] || '', // could have value of 'inset' or undefined\n x: x,\n y: y,\n xUnits: xUnits,\n yUnits: yUnits,\n end: matches[8],\n });\n }\n return shadows;\n}\n/**\n * Modify box-shadow x/y offsets to counteract rotation\n */\nfunction normalizeShadow(shadows, degrees) {\n var normalized = [];\n for (var _i = 0, shadows_1 = shadows; _i < shadows_1.length; _i++) {\n var shadow = shadows_1[_i];\n var xy = convertOffset(shadow.x, shadow.y, degrees);\n normalized.push(shadow.prefix + xy[0] + shadow.xUnits + ' ' + xy[1] + shadow.yUnits + shadow.end);\n }\n return normalized.join(', ');\n}\nfunction convertOffset(x, y, degrees) {\n var radians = degrees * Math.PI / 180;\n var sin = Math.sin(radians);\n var cos = Math.cos(radians);\n return [\n Math.round((x * cos + y * sin) * 1000) / 1000,\n Math.round((-x * sin + y * cos) * 1000) / 1000,\n ];\n}\n","//----------------------------------------------------------------------------\r\n// Timer\r\n\r\nexport default class Timer {\r\n constructor() {\r\n this.startTime = 0;\r\n this.oldTime = 0;\r\n this.elapsedTime = 0;\r\n this.running = false;\r\n }\r\n\r\n start() {\r\n this.startTime = Timer.now();\r\n this.oldTime = this.startTime;\r\n this.running = true;\r\n }\r\n\r\n stop() {\r\n this.getElapsedTime();\r\n this.running = false;\r\n }\r\n\r\n getElapsedTime() {\r\n this.update();\r\n return this.elapsedTime;\r\n }\r\n\r\n update() {\r\n let delta = 0;\r\n if (this.running) {\r\n const newTime = Timer.now();\r\n delta = 0.001 * (newTime - this.oldTime);\r\n this.oldTime = newTime;\r\n this.elapsedTime += delta;\r\n }\r\n\r\n return delta;\r\n }\r\n}\r\n\r\nTimer.now = (function () {\r\n const p = typeof window !== 'undefined' && window.performance;\r\n return (p && p.now) ? p.now.bind(p) : Date.now;\r\n}());\r\n","import Timer from '../Timer';\r\n\r\nconst { now } = Timer;\r\n\r\nfunction createElement(tag, id, css) {\r\n const element = document.createElement(tag);\r\n element.id = id;\r\n element.style.cssText = css;\r\n return element;\r\n}\r\n\r\nclass Stats {\r\n constructor() {\r\n this.domElement = createElement('div', 'stats', 'padding:8px');\r\n this._text = createElement('p', 'fps', 'margin:0;color:silver;font-size:large');\r\n this.domElement.appendChild(this._text);\r\n\r\n this._startTime = now();\r\n this._prevTime = this._startTime;\r\n\r\n this._deltas = new Array(20);\r\n this._index = 0;\r\n this._total = 0.0;\r\n this._count = 0;\r\n }\r\n\r\n end() {\r\n const time = now();\r\n const delta = time - this._startTime;\r\n\r\n if (this._count < this._deltas.length) {\r\n this._count++;\r\n } else {\r\n this._total -= this._deltas[this._index];\r\n }\r\n this._total += delta;\r\n this._deltas[this._index] = delta;\r\n this._index = (this._index + 1) % this._deltas.length;\r\n\r\n this.ms = this._total / this._count;\r\n this.fps = 1000 / this.ms;\r\n\r\n if (time > this._prevTime + 1000) {\r\n this._text.textContent = this.fps.toPrecision(2);\r\n this._prevTime = time;\r\n }\r\n\r\n return time;\r\n }\r\n\r\n update() {\r\n this._startTime = this.end();\r\n }\r\n\r\n show(on) {\r\n if (on === undefined) {\r\n on = true;\r\n }\r\n this.domElement.style.display = on ? 'block' : 'none';\r\n }\r\n}\r\n\r\nexport default Stats;\r\n","/**\r\n * This class introduces the simplest event system.\r\n */\r\n\r\nimport _ from 'lodash';\r\n\r\nfunction isUndefOrEqual(param, value) {\r\n return !param || param === value;\r\n}\r\n\r\n/**\r\n * Creates empty dispatcher.\r\n *\r\n * @exports EventDispatcher\r\n * @constructor\r\n */\r\nfunction EventDispatcher() {\r\n this._handlers = {};\r\n}\r\n\r\n/**\r\n * Binds callback on specific event type. Optional `context` parameter\r\n * could be used as 'this' for the `callback`.\r\n * @param {string} type Event name.\r\n * @param {function} callback Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.addEventListener = function (type, callback, context) {\r\n let handlers = this._handlers[type];\r\n\r\n if (!handlers) {\r\n this._handlers[type] = [];\r\n handlers = this._handlers[type];\r\n }\r\n\r\n const params = [callback, context];\r\n function _checkPar(par) {\r\n return par[0] === params[0] && par[1] === params[1];\r\n }\r\n\r\n if (_.find(handlers, _checkPar) === undefined) {\r\n handlers.push(params);\r\n }\r\n};\r\n\r\n/**\r\n * Removes a previously-bound callback function from an object.\r\n * If no `context` is specified, all versions of the `callback` with different\r\n * contexts will be removed.\r\n * If no `callback` is specified, all callbacks of the `type` will be removed.\r\n * If no `type` is specified, callbacks for all events will be removed.\r\n * @param {?string} [type] Event type.\r\n * @param {function} [callback] Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.removeEventListener = function (type, callback, context) {\r\n const self = this;\r\n _.forEach(self._handlers, (handler, ev) => {\r\n _.remove(handler, (values) => isUndefOrEqual(type, ev)\r\n && isUndefOrEqual(callback, values[0])\r\n && isUndefOrEqual(context, values[1] || self));\r\n });\r\n\r\n this._handlers = _.omitBy(self._handlers, (handler) => handler.length === 0);\r\n};\r\n\r\n/**\r\n * Makes all the callbacks for the specific `event` to trigger.\r\n * @param {Object} event Event.\r\n * @param {string} event.type Type of the event.\r\n */\r\nEventDispatcher.prototype.dispatchEvent = function (event) {\r\n const self = this;\r\n\r\n _.forEach(this._handlers[event.type], (callback) => {\r\n const context = callback[1] || self;\r\n callback[0].apply(context, [event]);\r\n });\r\n};\r\n\r\nexport default EventDispatcher;\r\n","/**\r\n * This module contains class for logging.\r\n * Returns an instance of a logger that have already been created.\r\n * Allows users to log messages for five different levels,\r\n * enable console output and catch signal on each message.\r\n */\r\nimport _ from 'lodash';\r\nimport EventDispatcher from './EventDispatcher';\r\n\r\nconst priorities = {\r\n debug: 0,\r\n info: 1,\r\n report: 2,\r\n warn: 3,\r\n error: 4,\r\n};\r\n\r\n/**\r\n * Create new Logger.\r\n *\r\n * @exports Logger\r\n * @extends EventDispatcher\r\n * @constructor\r\n */\r\nfunction Logger() {\r\n EventDispatcher.call(this);\r\n /** Boolean flag that toggles output to browser console.\r\n * @type {boolean}\r\n */\r\n this.console = false;\r\n this._priority = priorities.warn;\r\n}\r\n\r\nLogger.prototype = Object.create(EventDispatcher.prototype);\r\nLogger.prototype.constructor = Logger;\r\n\r\n/**\r\n * Create new clean instance of the logger.\r\n * @returns {Logger}\r\n */\r\nLogger.prototype.instantiate = function () {\r\n return new Logger();\r\n};\r\n\r\nfunction verify(number) {\r\n if (!_.isNumber(number)) {\r\n throw new Error('Wrong log level specified!');\r\n }\r\n return number;\r\n}\r\n\r\n/**\r\n * @property {string} current threshold for signals and console output.\r\n * @name Logger#level\r\n */\r\nObject.defineProperty(Logger.prototype, 'level', {\r\n get() {\r\n return _.findKey(priorities, (value) => value === this._priority);\r\n },\r\n set(level) {\r\n this._priority = verify(priorities[level]);\r\n },\r\n});\r\n\r\n/**\r\n * Returns the list of all possible level values.\r\n * @returns {Array}\r\n */\r\nLogger.prototype.levels = function () {\r\n return Object.keys(priorities);\r\n};\r\n\r\n/**\r\n * Add new message with specified level.\r\n * @param {string} level - level of the message, must be one of the\r\n * {'debug' | 'info' | 'report' | 'warn' | 'error'}\r\n * @param {string} message\r\n */\r\nLogger.prototype.message = function (level, message) {\r\n const priority = verify(priorities[level]);\r\n this._message(priority, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('debug', ...);\r\n * @param message\r\n */\r\nLogger.prototype.debug = function (message) {\r\n this._message(priorities.debug, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('info', ...);\r\n * @param message\r\n */\r\nLogger.prototype.info = function (message) {\r\n this._message(priorities.info, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('report', ...);\r\n * @param message\r\n */\r\nLogger.prototype.report = function (message) {\r\n this._message(priorities.report, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('warn', ...);\r\n * @param message\r\n */\r\nLogger.prototype.warn = function (message) {\r\n this._message(priorities.warn, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('error', ...);\r\n * @param message\r\n */\r\nLogger.prototype.error = function (message) {\r\n this._message(priorities.error, message);\r\n};\r\n\r\n/**\r\n * Add new message with specified priority.\r\n * @param {number} priority - priority of the message\r\n * @param {string} message\r\n * @private\r\n */\r\nLogger.prototype._message = function (priority, message) {\r\n if (priority < this._priority) {\r\n return;\r\n }\r\n const level = _.findKey(priorities, (value) => value === priority);\r\n message = String(message);\r\n if (this.console) {\r\n const output = `miew:${level}: ${message}`;\r\n if (level === 'error') {\r\n console.error(output); // NOSONAR\r\n } else if (level === 'warn') {\r\n console.warn(output); // NOSONAR\r\n } else {\r\n console.log(output); // NOSONAR\r\n }\r\n }\r\n this.dispatchEvent({ type: 'message', level, message });\r\n};\r\n\r\nexport default new Logger();\r\n","import _ from 'lodash';\r\nimport logger from './utils/logger';\r\n\r\nconst browserType = {\r\n DEFAULT: 0,\r\n SAFARI: 1,\r\n};\r\n//----------------------------------------------------------------------------\r\n// Query string\r\n\r\n/**\r\n * Escape only dangerous chars in a query string component, use a plus instead of a space.\r\n *\r\n * [RFC 3986](https://tools.ietf.org/html/rfc3986) allows the following chars in the query (see 3.4):\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! $ & ' ( ) * + , ; = : @ / ?\r\n *\r\n * For query string elements we need to escape ampersand, equal sign, and plus,\r\n * but encodeURIComponent() function encodes anything except for the following:\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! ' ( ) *\r\n *\r\n * @param {string} text - key or value to encode\r\n * @param {string} excludeExp - regexp for symbols to exclude from encoding\r\n * @returns {string} encoded string\r\n */\r\nfunction encodeQueryComponent(text, excludeExp) {\r\n const encode = (code) => String.fromCharCode(parseInt(code.substr(1), 16));\r\n return encodeURIComponent(text).replace(excludeExp, encode).replace(/%20/g, '+');\r\n}\r\n\r\n/**\r\n * Unescape dangerous chars in a query string component.\r\n *\r\n * @param {string} text - encoded key or value\r\n * @returns {string} decoded string\r\n * @see {@link encodeQueryComponent}\r\n */\r\nfunction decodeQueryComponent(text) {\r\n return decodeURIComponent(text.replace(/\\+/g, ' '));\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Array} array of (key, value) pairs.\r\n */\r\nfunction getUrlParameters(url) {\r\n url = url || window.location.search;\r\n\r\n const query = url.substring(url.indexOf('?') + 1);\r\n const search = /([^&=]+)=?([^&]*)/g;\r\n const result = [];\r\n let match;\r\n\r\n while ((match = search.exec(query)) !== null) { // eslint-disable-line no-cond-assign\r\n result.push([decodeQueryComponent(match[1]), decodeQueryComponent(match[2])]);\r\n }\r\n\r\n return result;\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters as a hash.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Object}\r\n */\r\nfunction getUrlParametersAsDict(url) {\r\n const result = {};\r\n const a = getUrlParameters(url);\r\n for (let i = 0; i < a.length; ++i) {\r\n const [key, value] = a[i];\r\n result[key] = value;\r\n }\r\n return result;\r\n}\r\n\r\nfunction resolveURL(str) {\r\n if (typeof URL !== 'undefined') {\r\n try {\r\n if (typeof window !== 'undefined') {\r\n return new URL(str, window.location).href;\r\n }\r\n return new URL(str).href;\r\n } catch {\r\n // IE 11 has a URL object with no constructor available so just try a different approach instead\r\n }\r\n }\r\n if (typeof document !== 'undefined') {\r\n const anchor = document.createElement('a');\r\n anchor.href = str;\r\n return anchor.href;\r\n }\r\n return str;\r\n}\r\n\r\n/**\r\n * Generates regular expression object that includes all symbols\r\n * listed in the argument\r\n * @param symbolStr {string} - String containing characters list.\r\n * @returns {RegExp} - Regular expression.\r\n */\r\nfunction generateRegExp(symbolStr) {\r\n const symbolList = [];\r\n\r\n for (let i = 0, n = symbolStr.length; i < n; ++i) {\r\n symbolList[symbolList.length] = symbolStr[i].charCodeAt(0).toString(16);\r\n }\r\n\r\n const listStr = symbolList.join('|');\r\n\r\n return new RegExp(`%(?:${listStr})`, 'gi');\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Create HTML element\r\n\r\nfunction createElement(tag, attrs, content) {\r\n const element = document.createElement(tag);\r\n let i;\r\n let n;\r\n if (attrs) {\r\n const keys = Object.keys(attrs);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n element.setAttribute(key, attrs[key]);\r\n }\r\n }\r\n if (content) {\r\n if (!(content instanceof Array)) {\r\n content = [content];\r\n }\r\n for (i = 0, n = content.length; i < n; ++i) {\r\n const child = content[i];\r\n if (typeof child === 'string') {\r\n element.appendChild(document.createTextNode(child));\r\n } else if (child instanceof HTMLElement) {\r\n element.appendChild(child);\r\n }\r\n }\r\n }\r\n return element;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Easy inheritance\r\n\r\n/**\r\n * Derive the class from the base.\r\n * @param cls {function} - Class (constructor) to derive.\r\n * @param base {function} - Class (constructor) to derive from.\r\n * @param members {object=} - Optional instance members to add.\r\n * @param statics {object=} - Optional static class members to add.\r\n * @returns {function} Original class.\r\n */\r\nfunction deriveClass(cls, base, members, statics) {\r\n cls.prototype = _.assign(Object.create(base.prototype), { constructor: cls }, members);\r\n if (statics) {\r\n _.assign(cls, statics);\r\n }\r\n return cls;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Deep prototyping\r\n\r\nfunction deriveDeep(obj, needZeroOwnProperties) {\r\n let res = obj;\r\n let i;\r\n let n;\r\n if (obj instanceof Array) {\r\n res = new Array(obj.length);\r\n for (i = 0, n = obj.length; i < n; ++i) {\r\n res[i] = deriveDeep(obj[i]);\r\n }\r\n } else if (obj instanceof Object) {\r\n res = Object.create(obj);\r\n const keys = Object.keys(obj);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = obj[key];\r\n const copy = deriveDeep(value);\r\n if (copy !== value) {\r\n res[key] = copy;\r\n }\r\n }\r\n if (needZeroOwnProperties && Object.keys(res).length > 0) {\r\n res = Object.create(res);\r\n }\r\n }\r\n return res;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Colors\r\n\r\nfunction hexColor(color) {\r\n const hex = (`0000000${color.toString(16)}`).substr(-6);\r\n return `#${hex}`;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Debug tracing\r\n\r\nfunction DebugTracer(namespace) {\r\n let enabled = false;\r\n\r\n this.enable = function (on) {\r\n enabled = on;\r\n };\r\n\r\n let indent = 0;\r\n const methods = Object.keys(namespace);\r\n\r\n function wrap(method_, name_) {\r\n return function (...args) {\r\n const spaces = DebugTracer.spaces.substr(0, indent * 2);\r\n if (enabled) {\r\n logger.debug(`${spaces + name_} {`);\r\n }\r\n indent++;\r\n const result = method_.apply(this, args);\r\n indent--;\r\n if (enabled) {\r\n logger.debug(`${spaces}} // ${name_}`);\r\n }\r\n return result;\r\n };\r\n }\r\n\r\n for (let i = 0, n = methods.length; i < n; ++i) {\r\n const name = methods[i];\r\n const method = namespace[name];\r\n if (method instanceof Function && name !== 'constructor') {\r\n namespace[name] = wrap(method, name);\r\n }\r\n }\r\n}\r\n\r\nDebugTracer.spaces = ' ';\r\n\r\nclass OutOfMemoryError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'OutOfMemoryError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction allocateTyped(TypedArrayName, size) {\r\n let result = null;\r\n try {\r\n result = new TypedArrayName(size);\r\n } catch (e) {\r\n if (e instanceof RangeError) {\r\n throw new OutOfMemoryError(e.message);\r\n } else {\r\n throw e;\r\n }\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Float array conversion\r\n\r\nfunction bytesToBase64(/** ArrayBuffer */ buffer) {\r\n const bytes = new Uint8Array(buffer);\r\n let binary = '';\r\n for (let i = 0; i < bytes.byteLength; i++) {\r\n binary += String.fromCharCode(bytes[i]);\r\n }\r\n return window.btoa(binary);\r\n}\r\n\r\nfunction bytesFromBase64(/** string */ str) {\r\n const binary = window.atob(str);\r\n const bytes = new Uint8Array(binary.length);\r\n for (let i = 0; i < bytes.length; ++i) {\r\n bytes[i] = binary[i].charCodeAt(0);\r\n }\r\n return bytes.buffer;\r\n}\r\n\r\nfunction arrayToBase64(/** number[] */ array, /** function */ TypedArrayClass) {\r\n return bytesToBase64(new TypedArrayClass(array).buffer);\r\n}\r\n\r\nfunction arrayFromBase64(/** string */ str, /** function */ TypedArrayClass) {\r\n return Array.prototype.slice.call(new TypedArrayClass(bytesFromBase64(str)));\r\n}\r\n\r\n// NOTE: this is 1-level comparison\r\nfunction compareOptionsWithDefaults(opts, defOpts) {\r\n const optsStr = [];\r\n if (defOpts && opts) {\r\n const keys = Object.keys(opts);\r\n for (let p = 0; p < keys.length; ++p) {\r\n const key = keys[p];\r\n const value = opts[key];\r\n // TODO add processing for tree structure\r\n if (!(value instanceof Object) && typeof defOpts[key] !== 'undefined' && defOpts[key] !== value) {\r\n optsStr.push(`${key}:${value}`);\r\n }\r\n }\r\n if (optsStr.length > 0) {\r\n return `!${optsStr.join()}`;\r\n }\r\n }\r\n return '';\r\n}\r\n\r\nfunction isAlmostPlainObject(o) {\r\n if (_.isPlainObject(o)) {\r\n return true;\r\n }\r\n const proto = o && Object.getPrototypeOf(o);\r\n return !!proto && !proto.hasOwnProperty('constructor') && isAlmostPlainObject(proto);\r\n}\r\n\r\n/**\r\n * Build an object that contains properties (and subproperties) of `src` different from those\r\n * in `dst`. Objects are parsed recursively, other values (including arrays) are compared for\r\n * equality using `_.isEqual()`.\r\n * @param {!object} src - a new object to compare, may contain changed or new properties\r\n * @param {!object} dst - an old reference object\r\n */\r\nfunction objectsDiff(src, dst) {\r\n const diff = {};\r\n _.forIn(src, (srcValue, key) => {\r\n const dstValue = dst[key];\r\n if (isAlmostPlainObject(srcValue) && isAlmostPlainObject(dstValue)) {\r\n const deepDiff = objectsDiff(srcValue, dstValue);\r\n if (!_.isEmpty(deepDiff)) {\r\n diff[key] = deepDiff;\r\n }\r\n } else if (!_.isEqual(srcValue, dstValue)) {\r\n diff[key] = srcValue;\r\n }\r\n });\r\n return diff;\r\n}\r\n\r\nfunction forInRecursive(object, callback) {\r\n function iterateThrough(obj, prefix) {\r\n _.forIn(obj, (value, key) => {\r\n const newPref = prefix + (prefix.length > 0 ? '.' : '');\r\n if (value instanceof Object) {\r\n iterateThrough(value, newPref + key);\r\n } else if (value !== undefined) {\r\n callback(value, newPref + key);\r\n }\r\n });\r\n }\r\n iterateThrough(object, '');\r\n}\r\n\r\nfunction enquoteString(value) {\r\n if (_.isString(value)) {\r\n return `\"${value.replace(/\"/g, '\\\\\"')}\"`;\r\n }\r\n return value;\r\n}\r\n\r\nfunction unquoteString(value) {\r\n if (!_.isString(value)) {\r\n return value;\r\n }\r\n if (value[0] === '\"' && value[value.length - 1] === '\"') {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\\"/g, '\"');\r\n }\r\n if (value[0] === \"'\" && value[value.length - 1] === \"'\") {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\'/g, \"'\");\r\n }\r\n throw new SyntaxError('Incorrect string format, can\\'t unqute it');\r\n}\r\n\r\nfunction getFileExtension(fileName) {\r\n return fileName.slice((Math.max(0, fileName.lastIndexOf('.')) || Infinity));\r\n}\r\n\r\nfunction splitFileName(fileName) {\r\n const ext = getFileExtension(fileName);\r\n const name = fileName.slice(0, fileName.length - ext.length);\r\n return [name, ext];\r\n}\r\n\r\nfunction dataUrlToBlob(url) {\r\n const parts = url.split(/[:;,]/);\r\n const partsCount = parts.length;\r\n if (partsCount >= 3 && parts[partsCount - 2] === 'base64') {\r\n return new Blob([bytesFromBase64(parts[partsCount - 1])]);\r\n }\r\n return null;\r\n}\r\n\r\nfunction getBrowser() {\r\n if (navigator.vendor && navigator.vendor.indexOf('Apple') > -1\r\n && navigator.userAgent\r\n && navigator.userAgent.indexOf('CriOS') === -1\r\n && navigator.userAgent.indexOf('FxiOS') === -1) {\r\n return browserType.SAFARI;\r\n }\r\n return browserType.DEFAULT;\r\n}\r\n\r\nfunction shotOpen(url) {\r\n if (typeof window !== 'undefined') {\r\n window.open().document.write(``);\r\n }\r\n}\r\n\r\nfunction shotDownload(dataUrl, filename) {\r\n if (!dataUrl || dataUrl.substr(0, 5) !== 'data:') {\r\n return;\r\n }\r\n if (!filename) {\r\n filename = ['screenshot-', +new Date(), '.png'].join('');\r\n }\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(dataUrlToBlob(dataUrl), filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(dataUrlToBlob(dataUrl));\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction download(data, filename, type) {\r\n const blobData = new Blob([data]);\r\n\r\n if (!filename) {\r\n filename = ['data', +new Date()].join('');\r\n }\r\n\r\n if (!type) {\r\n filename += blobData.type || '.bin';\r\n } else {\r\n filename += `.${type}`;\r\n }\r\n\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(blobData, filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(blobData);\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction copySubArrays(src, dst, indices, itemSize) {\r\n for (let i = 0, n = indices.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n dst[i * itemSize + j] = src[indices[i] * itemSize + j];\r\n }\r\n }\r\n}\r\n\r\nfunction shallowCloneNode(node) {\r\n const newNode = node.cloneNode(true);\r\n newNode.worldPos = node.worldPos;\r\n // .style property is readonly, so \"newNode.style = node.style;\" won't work (and we don't need it, right?)\r\n return newNode;\r\n}\r\n\r\nconst unquotedStringRE = /^[a-zA-Z0-9_]*$/;\r\nconst enquoteHelper = ['\"', '', '\"'];\r\n\r\n// verify and correct if needed selctor identifier\r\nfunction correctSelectorIdentifier(value) {\r\n if (unquotedStringRE.test(value)) {\r\n return value;\r\n }\r\n // quote incorrect identifier\r\n enquoteHelper[1] = value;\r\n return enquoteHelper.join('');\r\n}\r\n\r\n/**\r\n * Concatenates two TypedArray. Doesn't check null refs o type equality\r\n * Attention! It must be use very rarely because requires memory reallocation every time. Use MergeTypedArraysUnsafe to\r\n * unite array of subarrays.\r\n * @param{TypedArray} first - destination array\r\n * @param{TypedArray} second - source array\r\n * @returns{TypedArray} resulting concatenated array\r\n */\r\nfunction concatTypedArraysUnsafe(first, second) {\r\n const result = new first.constructor(first.length + second.length);\r\n result.set(first);\r\n result.set(second, first.length);\r\n return result;\r\n}\r\n\r\n/**\r\n * Merges array of TypedArray into TypedArray. Doesn't check null refs o type equality\r\n * @param{array} array - source array of subarrays\r\n * @returns{TypedArray} resulting merged array\r\n */\r\nfunction mergeTypedArraysUnsafe(array) {\r\n if (array.length <= 0) {\r\n return null;\r\n }\r\n // count the size\r\n const size = array.reduce((acc, cur) => acc + cur.length, 0);\r\n // create combined array\r\n const result = new array[0].constructor(size);\r\n for (let i = 0, start = 0; i < array.length; i++) {\r\n const count = array[i].length;\r\n result.set(array[i], start);\r\n start += count;\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Exports\r\n\r\nexport default {\r\n browserType,\r\n encodeQueryComponent,\r\n decodeQueryComponent,\r\n getUrlParameters,\r\n getUrlParametersAsDict,\r\n resolveURL,\r\n generateRegExp,\r\n createElement,\r\n deriveClass,\r\n deriveDeep,\r\n hexColor,\r\n DebugTracer,\r\n OutOfMemoryError,\r\n allocateTyped,\r\n bytesFromBase64,\r\n bytesToBase64,\r\n arrayFromBase64,\r\n arrayToBase64,\r\n compareOptionsWithDefaults,\r\n objectsDiff,\r\n forInRecursive,\r\n enquoteString,\r\n unquoteString,\r\n getBrowser,\r\n shotOpen,\r\n shotDownload,\r\n copySubArrays,\r\n shallowCloneNode,\r\n correctSelectorIdentifier,\r\n getFileExtension,\r\n splitFileName,\r\n download,\r\n concatTypedArraysUnsafe,\r\n mergeTypedArraysUnsafe,\r\n};\r\n","import EventDispatcher from './EventDispatcher';\r\n\r\nexport default class JobHandle extends EventDispatcher {\r\n constructor() {\r\n super();\r\n this._shouldCancel = false;\r\n }\r\n\r\n cancel() {\r\n this._shouldCancel = true;\r\n this.dispatchEvent({ type: 'cancel' });\r\n }\r\n\r\n shouldCancel() {\r\n return this._shouldCancel;\r\n }\r\n\r\n // slaves use this to notify master about their events\r\n // master routes these notifications to a single event slot\r\n notify(event) {\r\n this.dispatchEvent({ type: 'notification', slaveEvent: event });\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport utils from './utils';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\n\r\nconst VERSION = 0;\r\n\r\n//----------------------------------------------------------------------------\r\n// DEFAULT SETTINGS\r\n//----------------------------------------------------------------------------\r\n\r\n/**\r\n * Polygonal complexity settings.\r\n *\r\n * @typedef PolyComplexity\r\n * @property {number} poor\r\n * @property {number} low\r\n * @property {number} medium\r\n * @property {number} high\r\n * @property {number} ultra\r\n */\r\n\r\n/**\r\n * @alias SettingsObject\r\n * @namespace\r\n */\r\nconst defaults = {\r\n /**\r\n * Default options for all available modes.\r\n * Use {@link Mode.id} as a dictionary key to access mode options.\r\n *\r\n * Usually you don't need to override these settings. You may specify mode options as a parameter during\r\n * {@link Mode} construction.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {LinesModeOptions} LN - Lines mode options.\r\n * @property {LicoriceModeOptions} LC - Licorice mode options.\r\n * @property {BallsAndSticksModeOptions} BS - Balls and Sticks mode options.\r\n * @property {VanDerWaalsModeOptions} VW - Van der Waals mode options.\r\n * @property {TraceModeOptions} TR - Trace mode options.\r\n * @property {TubeModeOptions} TU - Tube mode options.\r\n * @property {CartoonModeOptions} CA - Cartoon mode options.\r\n * @property {QuickSurfaceModeOptions} QS - Contact Surface mode options.\r\n * @property {IsoSurfaceSASModeOptions} SA - Solvent Accessible Surface mode options.\r\n * @property {IsoSurfaceSESModeOptions} SE - Solvent Excluded Surface mode options.\r\n * @property {ContactSurfaceModeOptions} CS - Contact Surface mode options.\r\n * @property {TextModeOptions} TX - Text mode options.\r\n * @property {VolumeDensityModeOptions} VD - Volume Density mode options.\r\n */\r\n modes: {\r\n //----------------------------------------------------------------------------\r\n // BALLS AND STICKS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Balls and Sticks mode options.\r\n *\r\n * @typedef BallsAndSticksModeOptions\r\n *\r\n * @property {number} atom - Sphere radius as a fraction of Van der Waals atom radius.\r\n * @property {number} bond - Cylinder radius in angstroms.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n BS: {\r\n atom: 0.23,\r\n bond: 0.15,\r\n space: 0.5,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VAN DER WAALS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Van der Waals mode options.\r\n *\r\n * @typedef VanDerWaalsModeOptions\r\n *\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VW: {\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 8,\r\n high: 16,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LINES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Lines mode options.\r\n *\r\n * @typedef LinesModeOptions\r\n *\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {number} offsarom - Offset between bonds and aromatic cycle.\r\n * @property {number} chunkarom - Number of pieces in a-loop arc, corresponding to atom.\r\n * @property {number} atom - Collision radius for atoms picking.\r\n * @property {number} lineWidth - Line width in pixels (not used in thin lines).\r\n */\r\n LN: {\r\n multibond: true,\r\n showarom: true,\r\n offsarom: 0.2,\r\n chunkarom: 10,\r\n atom: 0.23,\r\n lineWidth: 2,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LICORICE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Licorice mode options.\r\n *\r\n * @typedef LicoriceModeOptions\r\n *\r\n * @property {number} bond - Bond cylinder radius.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Poly complexity values for render modes.\r\n */\r\n LC: {\r\n bond: 0.20,\r\n space: 0.0,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SAS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Accessible Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSASModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SA: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Excluded Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSESModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SE: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // QUICK SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Quick Surface mode options.\r\n *\r\n * @typedef QuickSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} scale - Radius scale for the surface being built.\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} gaussLim - Gauss lim for coloring the bigger the value, the smoother our colors are.\r\n * @property {PolyComplexity} gridSpacing - Poly complexity values for render modes. In this case the value\r\n * corresponds to the grid density.\r\n */\r\n QS: {\r\n isoValue: 0.5,\r\n gaussLim: {\r\n poor: 1.5,\r\n low: 2.0,\r\n medium: 2.5,\r\n high: 3.0,\r\n ultra: 4.0,\r\n },\r\n scale: 1.0,\r\n wireframe: false,\r\n gridSpacing: {\r\n poor: 2,\r\n low: 1.5,\r\n medium: 1,\r\n high: 0.5,\r\n ultra: 0.25,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CONTACT SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Contact Surface mode options.\r\n *\r\n * @typedef ContactSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} probeRadius - Probe radius.\r\n * @property {number} probePositions\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Radius scale for the surface being built.\r\n * Poly complexity values for render modes. In this case the value corresponds to the grid density.\r\n */\r\n CS: {\r\n probeRadius: 1.4,\r\n isoValue: 1.5,\r\n wireframe: false,\r\n probePositions: 30,\r\n polyComplexity: {\r\n poor: 0.5,\r\n low: 1.0,\r\n medium: 1.5,\r\n high: 1.75,\r\n ultra: 2.0,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TRACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Trace mode options.\r\n *\r\n * @typedef TraceModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n TR: {\r\n radius: 0.30,\r\n polyComplexity: {\r\n poor: 12,\r\n low: 16,\r\n medium: 32,\r\n high: 64,\r\n ultra: 64,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TUBE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Tube mode options.\r\n *\r\n * @typedef TubeModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {number} tension - Tension for interpolation.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n TU: {\r\n radius: 0.30,\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CARTOON\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Cartoon mode options.\r\n *\r\n * @typedef CartoonModeOptions\r\n *\r\n * @property {number} radius - Standard tube radius.\r\n * @property {number} depth - Height of the secondary structure ribbon.\r\n * @property {number} tension - Tension for interpolation.\r\n * @proprety {object} ss - Secondary structure parameters.\r\n * @proprety {object} ss.helix - Options for helices render.\r\n * @proprety {number} ss.helix.width - Width of the secondary structure ribbon.\r\n * @proprety {number} ss.helix.arrow - Secondary structure's arrow width.\r\n * @proprety {object} ss.strand - Options for strands render.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * polyComplexity must be even for producing symmetric arrows.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n CA: {\r\n radius: 0.30,\r\n depth: 0.25,\r\n ss: {\r\n helix: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n strand: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n },\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TEXT\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Text mode options.\r\n *\r\n * @typedef TextModeOptions\r\n *\r\n * @property {string} template - Format string for building output text.\r\n * @property {string} horizontalAlign - Text alignment ('left', 'right', 'center').\r\n * @property {string} verticalAlign - Vertical text box alignment ('top', 'bottom', 'middle').\r\n * @property {number} dx - Text offset x in angstroms.\r\n * @property {number} dy - Text offset y in angstroms.\r\n * @property {number} dz - Text offset z in angstroms.\r\n * @property {string} fg - Color rule for foreground.\r\n * @property {string} bg - Color rule for background.\r\n * @property {boolean} showBg - Flag, that toggles background rendering.\r\n *\r\n */\r\n TX: {\r\n template: '{{Chain}}.{{Residue}}{{Sequence}}.{{Name}}',\r\n horizontalAlign: 'center',\r\n verticalAlign: 'middle',\r\n dx: 0,\r\n dy: 0,\r\n dz: 1,\r\n fg: 'none',\r\n bg: '0x202020',\r\n showBg: true,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VOLUME DENSITY\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Volume density mode options.\r\n *\r\n * @typedef VolumeDensityModeOptions\r\n *\r\n * @property {number} kSigma - Noise threshold coefficient.\r\n * @property {boolean} frame - flag, that turns on box frame painting.\r\n * @property {boolean} isoMode - flag, that turns on IsoSurface mode instead of Volume Rendering.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VD: {\r\n kSigma: 1.0,\r\n kSigmaMed: 2.0,\r\n kSigmaMax: 4.0,\r\n frame: true,\r\n isoMode: false,\r\n polyComplexity: {\r\n poor: 2,\r\n low: 3,\r\n medium: 4,\r\n high: 8,\r\n ultra: 10,\r\n },\r\n },\r\n },\r\n\r\n /**\r\n * Default options for all available colorers.\r\n * Use {@link Colorer.id} as a dictionary key to access colorer options.\r\n *\r\n * Usually you don't need to override these settings. You may specify colorer options as a parameter during\r\n * {@link Colorer} construction.\r\n *\r\n * Not all colorers have options.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {ElementColorerOptions} EL - Element colorer options.\r\n * @property {SequenceColorerOptions} SQ - Sequence colorer options.\r\n * @property {MoleculeColorerOptions} MO - Molecule colorer options.\r\n * @property {UniformColorerOptions} UN - Uniform colorer options.\r\n * @property {ConditionalColorerOptions} CO - Conditional colorer options.\r\n * @property {TemperatureColorerOptions} TM - Temperature colorer options.\r\n * @property {OccupancyColorerOptions} OC - Occupancy colorer options.\r\n * @property {HydrophobicityColorerOptions} HY - Hydrophobicity colorer options.\r\n */\r\n colorers: {\r\n /**\r\n * Element colorer options.\r\n *\r\n * @typedef ElementColorerOptions\r\n *\r\n * @property {number} carbon - Carbon color or -1 to use default.\r\n */\r\n EL: {\r\n carbon: -1,\r\n },\r\n\r\n /**\r\n * Uniform colorer options.\r\n *\r\n * @typedef UniformColorerOptions\r\n *\r\n * @property {number} color - Single color to paint with.\r\n */\r\n UN: {\r\n color: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Conditional colorer options.\r\n *\r\n * @typedef ConditionalColorerOptions\r\n *\r\n * @property {string} subset - Selector string.\r\n * @property {number} color - Color of selected atoms.\r\n * @property {number} baseColor - Color of other atoms.\r\n */\r\n CO: {\r\n subset: 'charged',\r\n color: 0xFF0000,\r\n baseColor: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Carbon colorer options.\r\n *\r\n * @typedef CarbonColorerOptions\r\n *\r\n * @property {number} color - Single color to paint carbons\r\n * @property {number} factor - Color factor for not carbon atoms.\r\n */\r\n CB: {\r\n color: 0x909090,\r\n factor: 0.6,\r\n },\r\n\r\n /**\r\n * Sequence colorer options.\r\n *\r\n * @typedef SequenceColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n SQ: {\r\n gradient: 'rainbow',\r\n },\r\n\r\n /**\r\n * Temperature colorer options.\r\n *\r\n * @typedef TemperatureColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n * @property {number} min - Minimal temperature.\r\n * @property {number} max - Maximal temperature.\r\n */\r\n TM: {\r\n gradient: 'temp',\r\n min: 5,\r\n max: 40,\r\n },\r\n\r\n /**\r\n * Occupancy colorer options.\r\n *\r\n * @typedef OccupancyColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n OC: {\r\n gradient: 'reds',\r\n },\r\n\r\n /**\r\n * Hydrophobicity colorer options.\r\n *\r\n * @typedef HydrophobicityColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n HY: {\r\n gradient: 'blue-red',\r\n },\r\n\r\n /**\r\n * Molecule colorer options.\r\n *\r\n * @typedef MoleculeColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n MO: {\r\n gradient: 'rainbow',\r\n },\r\n },\r\n\r\n /*\r\n * Use antialiasing in WebGL.\r\n * @type {boolean}\r\n */\r\n antialias: true,\r\n\r\n /*\r\n * Camera field of view in degrees.\r\n * @type {number}\r\n */\r\n camFov: 45.0,\r\n\r\n /*\r\n * Camera near plane distance.\r\n * @type {number}\r\n */\r\n camNear: 0.5,\r\n\r\n /*\r\n * Camera far plane distance.\r\n * @type {number}\r\n */\r\n camFar: 100.0,\r\n\r\n camDistance: 2.5,\r\n\r\n radiusToFit: 1.0,\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogNearFactor: 0.5, // [0, 1]\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogFarFactor: 1, // [0, 1]\r\n fogAlpha: 1.0,\r\n fogColor: 0x000000,\r\n fogColorEnable: false,\r\n\r\n /**\r\n * Palette used for molecule coloring.\r\n * @type {string}\r\n */\r\n palette: 'JM',\r\n\r\n /*\r\n * Geometry resolution.\r\n * @type {string}\r\n */\r\n resolution: 'medium',\r\n\r\n autoResolution: false/* true */,\r\n\r\n autoPreset: true,\r\n\r\n preset: 'default', // TODO: remove 'preset' from settings, implement autodetection\r\n\r\n presets: {\r\n // Default\r\n default: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n empty: [],\r\n\r\n // Wireframe\r\n wire: [{\r\n mode: 'LN',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Small molecules\r\n small: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Proteins, nucleic acids etc.\r\n macro: [{\r\n mode: 'CA',\r\n colorer: 'SS',\r\n selector: 'not hetatm',\r\n material: 'SF',\r\n }, {\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'hetatm and not water',\r\n material: 'SF',\r\n }],\r\n },\r\n\r\n objects: {\r\n line: {\r\n color: 0xFFFFFFFF,\r\n dashSize: 0.3,\r\n gapSize: 0.05,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n\r\n bg: {\r\n color: 0x202020,\r\n transparent: false,\r\n },\r\n\r\n draft: {\r\n clipPlane: false,\r\n clipPlaneFactor: 0.5,\r\n clipPlaneSpeed: 0.00003,\r\n },\r\n\r\n /*\r\n * Separate group for plugins.\r\n * Each plugin handles its field by itself.\r\n */\r\n plugins: {\r\n\r\n },\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n axes: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fog: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fps: true,\r\n\r\n /**\r\n * Switch using of z-sprites for sphere and cylinder geometry\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zSprites: true,\r\n\r\n isoSurfaceFakeOpacity: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n suspendRender: true,\r\n\r\n nowater: false,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autobuild: true,\r\n\r\n /**\r\n * Anti-aliasing.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fxaa: true,\r\n /**\r\n * Outline depths\r\n * @type {boolean}\r\n * @instance\r\n */\r\n outline: {\r\n on: false,\r\n color: 0x000000,\r\n threshold: 0.1,\r\n thickness: 1,\r\n },\r\n\r\n /**\r\n * Ambient Occlusion special effect.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n ao: false,\r\n\r\n /**\r\n * Shadows options.\r\n *\r\n * @property {boolean} shadowMap - enable/disable.\r\n * @property {string} basic/percentage-closer filtering/non-uniform randomizing pcf.\r\n * @property {number} radius for percentage-closer filtering.\r\n */\r\n shadow: {\r\n on: false,\r\n type: 'random'/* basic, pcf, random */,\r\n radius: 1.0,\r\n },\r\n\r\n /**\r\n * Auto-rotation with constant speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n autoRotation: 0.0,\r\n\r\n /**\r\n * Set maximum fps for animation.\r\n * @type {number}\r\n * @instance\r\n */\r\n maxfps: 30,\r\n\r\n /**\r\n * Set fbx output precision.\r\n * @type {number}\r\n * @instance\r\n */\r\n fbxprec: 4,\r\n\r\n /**\r\n * Auto-rotation axis.\r\n *\r\n * - true: complex auto-rotation is about vertical axis\r\n * - false: rotation axis is defined by last user rotation\r\n *\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autoRotationAxisFixed: true,\r\n\r\n /**\r\n * Enable zooming with mouse wheel or pinch gesture.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zooming: true,\r\n\r\n /**\r\n * Enable picking atoms & residues with left mouse button or touch.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n picking: true,\r\n\r\n /**\r\n * Set picking mode ('atom', 'residue', 'chain', 'molecule').\r\n * @type {string}\r\n * @instance\r\n */\r\n pick: 'atom',\r\n\r\n /**\r\n * Make \"component\" and \"fragment\" editing modes available.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n editing: false,\r\n\r\n /**\r\n * Detect aromatic loops.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n aromatic: false,\r\n\r\n /**\r\n * Load only one biological unit from all those described in PDB file.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n singleUnit: true,\r\n\r\n /**\r\n * Set stereo mode ('NONE', 'SIMPLE', 'DISTORTED', 'ANAGLYPH', 'WEBVR').\r\n * @type {string}\r\n * @instance\r\n */\r\n stereo: 'NONE',\r\n\r\n /**\r\n * Enable smooth transition between views\r\n * @type {boolean}\r\n * @instance\r\n */\r\n interpolateViews: true,\r\n\r\n /**\r\n * Set transparency mode ('standard', 'prepass').\r\n * @type {string}\r\n * @instance\r\n */\r\n transparency: 'prepass',\r\n\r\n /**\r\n * Mouse translation speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n translationSpeed: 2,\r\n\r\n debug: {\r\n example: 3.5,\r\n text: 'hello!',\r\n good: true,\r\n ssaoKernelRadius: 0.7,\r\n ssaoFactor: 0.7,\r\n stereoBarrel: 0.25,\r\n },\r\n use: {\r\n multiFile: false,\r\n },\r\n};\r\n\r\n//----------------------------------------------------------------------------\r\n// SETTINGS CLASS\r\n//----------------------------------------------------------------------------\r\n\r\nfunction Settings() {\r\n EventDispatcher.call(this);\r\n\r\n this.old = null;\r\n this.now = {};\r\n this._changed = {};\r\n\r\n this.reset();\r\n}\r\n\r\nutils.deriveClass(Settings, EventDispatcher, {\r\n defaults,\r\n\r\n set(path, value) {\r\n if (_.isString(path)) {\r\n const oldValue = _.get(this.now, path);\r\n if (oldValue !== value) {\r\n _.set(this.now, path, value);\r\n this._notifyChange(path, value);\r\n }\r\n } else {\r\n const diff = utils.objectsDiff(path, this.now);\r\n if (!_.isEmpty(diff)) {\r\n _.merge(this.now, diff);\r\n this._notifyChanges(diff);\r\n }\r\n }\r\n },\r\n\r\n get(path, defaultValue) {\r\n return _.get(this.now, path, defaultValue);\r\n },\r\n\r\n reset() {\r\n const diff = utils.objectsDiff(defaults, this.now);\r\n this.now = _.cloneDeep(defaults);\r\n this.old = null;\r\n this._notifyChanges(diff);\r\n this._changed = {};\r\n },\r\n\r\n checkpoint() {\r\n this.old = _.cloneDeep(this.now);\r\n this._changed = {};\r\n },\r\n\r\n _notifyChange(path, value) {\r\n this._changed[path] = true;\r\n this.dispatchEvent({ type: `change:${path}`, value });\r\n },\r\n\r\n _notifyChanges(diff) {\r\n utils.forInRecursive(diff, (deepValue, deepPath) => {\r\n this._notifyChange(deepPath, deepValue);\r\n });\r\n },\r\n\r\n changed() {\r\n if (!this.old) {\r\n return [];\r\n }\r\n const { old, now } = this;\r\n const keys = _.filter(Object.keys(this._changed), (key) => _.get(old, key) !== _.get(now, key));\r\n return keys;\r\n },\r\n\r\n applyDiffs(diffs) {\r\n if (diffs.hasOwnProperty('VERSION') && diffs.VERSION !== VERSION) {\r\n throw new Error('Settings version does not match!');\r\n }\r\n // VERSION shouldn't be presented inside settings structure\r\n delete diffs.VERSION;\r\n this.reset();\r\n this.set(diffs);\r\n },\r\n\r\n getDiffs(versioned) {\r\n const diffs = utils.objectsDiff(this.now, defaults);\r\n if (versioned) {\r\n diffs.VERSION = VERSION;\r\n }\r\n return diffs;\r\n },\r\n\r\n setPluginOpts(plugin, opts) {\r\n defaults.plugins[plugin] = _.cloneDeep(opts);\r\n this.now.plugins[plugin] = _.cloneDeep(opts);\r\n },\r\n});\r\n\r\nexport default new Settings();\r\n","import _ from 'lodash';\r\nimport settings from './settings';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\n\r\nlet repIndex = 0;\r\n\r\nfunction asBoolean(value) {\r\n return !(!value || value === '0' || (_.isString(value) && value.toLowerCase() === 'false'));\r\n}\r\n\r\nconst adapters = {\r\n string: String,\r\n number: Number,\r\n boolean: asBoolean,\r\n};\r\n\r\n// Level 1 assignment symbol\r\nconst cL1Ass = '=';\r\n\r\nconst cOptsSep = '!';\r\n// Level 2 (options) assignment symbol\r\nconst cL2Ass = ':';\r\n// Level 2 (options) separator symbol\r\nconst cLSep = ',';\r\n\r\nconst cCommonIgnoreSymbols = '$;@/?';\r\n/**\r\n * We may (and should) leave as is for better readability:\r\n *\r\n * $ , ; : @ / ?\r\n */\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n */\r\nfunction getLevel1ExcludedExpr() {\r\n const cLevel1Ignores = ':,';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel1Ignores);\r\n}\r\n\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n * (options, etc, ..)\r\n */\r\nfunction getLevel2ExcludedExpr() {\r\n const cLevel2Ignores = ' ';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel2Ignores);\r\n}\r\n\r\nconst cL1ExclExpr = getLevel1ExcludedExpr();\r\nfunction encodeQueryComponentL1(value) {\r\n return utils.encodeQueryComponent(value, cL1ExclExpr);\r\n}\r\n\r\nconst cL2ExclExpr = getLevel2ExcludedExpr();\r\nfunction encodeQueryComponentL2(value) {\r\n return utils.encodeQueryComponent(value, cL2ExclExpr);\r\n}\r\n\r\nfunction ensureRepList(opts) {\r\n let { reps } = opts;\r\n if (!reps) {\r\n const { presets } = settings.now;\r\n let preset = opts.preset || settings.now.preset;\r\n reps = presets[preset];\r\n if (!reps) {\r\n logger.warn(`Unknown preset \"${preset}\"`);\r\n [preset] = Object.keys(presets);\r\n reps = presets[preset]; // fall back to any preset\r\n }\r\n opts.preset = preset;\r\n opts.reps = utils.deriveDeep(reps, true);\r\n }\r\n}\r\n\r\nfunction ensureRepAssign(opts, prop, value) {\r\n ensureRepList(opts);\r\n const rep = opts.reps[repIndex];\r\n // prop specified twice therefore start new rep by cloning the current\r\n if (rep.hasOwnProperty(prop)) {\r\n repIndex = opts.reps.length;\r\n opts.reps[repIndex] = utils.deriveDeep(rep, true);\r\n }\r\n if (value !== undefined) {\r\n opts.reps[repIndex][prop] = value;\r\n }\r\n}\r\n\r\nfunction addObject(opts, params, options) {\r\n if (opts._objects === undefined) {\r\n opts._objects = [];\r\n }\r\n\r\n const [type, newOpts] = options;\r\n const newObj = {\r\n type,\r\n params,\r\n };\r\n\r\n if (newOpts !== undefined) {\r\n newObj.opts = newOpts;\r\n }\r\n\r\n opts._objects[opts._objects.length] = newObj;\r\n}\r\n\r\nfunction parseParams(str, params) {\r\n const sep = str.indexOf(',');\r\n if (sep >= 0) {\r\n params.push(str.substr(sep + 1).split(','));\r\n return str.substr(0, sep);\r\n }\r\n // keep this untouched if no params were extracted\r\n return str;\r\n}\r\n\r\nfunction extractArgs(input, defaultsDict, params) {\r\n if (input) {\r\n const bang = input.indexOf(cOptsSep);\r\n const inputVal = parseParams(input.substr(0, bang >= 0 ? bang : undefined), params);\r\n if (bang >= 0) {\r\n const args = input.substr(bang + 1).split(cLSep);\r\n input = inputVal;\r\n if (defaultsDict) {\r\n const defaults = defaultsDict[input];\r\n const opts = utils.deriveDeep(defaults, true);\r\n args.forEach((arg) => {\r\n const pair = arg.split(cL2Ass, 2);\r\n const key = decodeURIComponent(pair[0]);\r\n const value = decodeURIComponent(pair[1]);\r\n const adapter = adapters[typeof _.get(defaults, key)];\r\n if (adapter) {\r\n _.set(opts, key, adapter(value));\r\n } else {\r\n logger.warn(`Unknown argument \"${key}\" for option \"${input}\"`);\r\n }\r\n });\r\n if (Object.keys(opts).length > 0) {\r\n input = [input, opts];\r\n }\r\n }\r\n } else {\r\n input = inputVal;\r\n }\r\n }\r\n return input;\r\n}\r\n\r\nconst actions = {\r\n\r\n l: 'load',\r\n load: String,\r\n t: 'type',\r\n type: String,\r\n v: 'view',\r\n view: String,\r\n u: 'unit',\r\n unit: Number,\r\n menu: asBoolean,\r\n\r\n // Commands\r\n\r\n o: 'object',\r\n object(value, opts) {\r\n const params = [];\r\n let options = extractArgs(value, settings.defaults.objects, params);\r\n if (!Array.isArray(options)) {\r\n options = [options];\r\n }\r\n addObject(opts, params[0], options);\r\n },\r\n\r\n p: 'preset',\r\n preset(value, opts) {\r\n opts.preset = value;\r\n opts.reps = null;\r\n ensureRepList(opts);\r\n },\r\n\r\n r: 'rep',\r\n rep(value, opts) {\r\n ensureRepList(opts);\r\n repIndex = Number(value);\r\n // clamp the index to one greater than the last\r\n repIndex = repIndex <= opts.reps.length ? (repIndex < 0 ? 0 : repIndex) : opts.reps.length;\r\n // create a new rep if it is adjacent to the existing ones\r\n if (repIndex === opts.reps.length) {\r\n // if there is no rep to derive from, derive from the first rep of the default\r\n opts.reps[repIndex] = repIndex > 0 ? utils.deriveDeep(opts.reps[repIndex - 1], true)\r\n : utils.deriveDeep(settings.defaults.presets.default[0], true);\r\n }\r\n },\r\n\r\n s: 'select',\r\n select(value, opts) {\r\n ensureRepAssign(opts, 'selector', value);\r\n },\r\n\r\n m: 'mode',\r\n mode(value, opts) {\r\n ensureRepAssign(opts, 'mode', extractArgs(value, settings.defaults.modes));\r\n },\r\n\r\n c: 'color',\r\n color(value, opts) {\r\n ensureRepAssign(opts, 'colorer', extractArgs(value, settings.defaults.colorers));\r\n },\r\n\r\n mt: 'material',\r\n material(value, opts) {\r\n ensureRepAssign(opts, 'material', extractArgs(value, settings.defaults.materials));\r\n },\r\n\r\n dup(value, opts) {\r\n ensureRepList(opts);\r\n const { reps } = opts;\r\n const rep = reps[repIndex];\r\n repIndex = reps.length;\r\n reps[repIndex] = utils.deriveDeep(rep, true);\r\n },\r\n\r\n // Settings shortcuts\r\n\r\n ar: 'autoResolution',\r\n};\r\n\r\nfunction _fromArray(entries) {\r\n repIndex = 0;\r\n\r\n const opts = {};\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const /** string[] */ entry = entries[i];\r\n let /** string? */ key = entry[0];\r\n const /** string? */ value = entry[1];\r\n let /** function|string? */ action = actions[key];\r\n\r\n // unwind shortcuts and aliases\r\n while (_.isString(action)) {\r\n key = action;\r\n action = actions[key];\r\n }\r\n\r\n // either set a property or use specialized parser\r\n if (!action) {\r\n const adapter = adapters[typeof _.get(settings.defaults, key)];\r\n if (adapter) {\r\n _.set(opts, `settings.${key}`, adapter(value));\r\n } else {\r\n logger.warn(`Unknown option \"${key}\"`);\r\n }\r\n } else if (_.isFunction(action)) {\r\n const result = action(value, opts);\r\n if (result !== undefined) {\r\n opts[key] = result;\r\n }\r\n }\r\n }\r\n\r\n return opts;\r\n}\r\n\r\nfunction fromAttr(attr) {\r\n return _fromArray(utils.getUrlParameters(`?${attr || ''}`));\r\n}\r\n\r\nfunction fromURL(url) {\r\n return _fromArray(utils.getUrlParameters(url));\r\n}\r\n\r\nfunction _processOptsForURL(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = encodeQueryComponentL2(key) + cL2Ass + encodeQueryComponentL2(value);\r\n });\r\n return str.join(cLSep);\r\n}\r\n\r\nfunction _processArgsForURL(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]}${cOptsSep}${_processOptsForURL(args[1])}`;\r\n}\r\n\r\nfunction _processObjForURL(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += `,${objOpts.params.join(',')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += cOptsSep + _processOptsForURL(objOpts.opts);\r\n }\r\n return res;\r\n}\r\n\r\nfunction toURL(opts) {\r\n const stringList = [];\r\n let idx = 0;\r\n\r\n function checkAndAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n stringList[idx++] = encodeQueryComponentL1(prefix)\r\n + cL1Ass + encodeQueryComponentL1(value);\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n if (_.isEmpty(repList[i])) {\r\n continue;\r\n }\r\n checkAndAdd('r', i);\r\n checkAndAdd('s', repList[i].selector);\r\n checkAndAdd('m', _processArgsForURL(repList[i].mode));\r\n checkAndAdd('c', _processArgsForURL(repList[i].colorer));\r\n checkAndAdd('mt', _processArgsForURL(repList[i].material));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('o', _processObjForURL(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('l', opts.load);\r\n checkAndAdd('u', opts.unit);\r\n checkAndAdd('p', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n checkAndAdd('v', opts.view);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(key, value);\r\n });\r\n\r\n let url = '';\r\n if (typeof window !== 'undefined') {\r\n const { location } = window;\r\n url = `${location.protocol}//${location.host}${location.pathname}`;\r\n }\r\n if (stringList.length > 0) {\r\n url += `?${stringList.join('&')}`;\r\n }\r\n\r\n return url;\r\n}\r\n\r\nfunction _processOptsForScript(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = `${key}=${utils.enquoteString(value)}`;\r\n });\r\n return str.join(' ');\r\n}\r\n\r\nfunction _processArgsForScript(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]} ${_processOptsForScript(args[1])}`;\r\n}\r\n\r\nfunction _processObjForScript(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += ` ${objOpts.params.map(utils.enquoteString).join(' ')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += ` ${_processOptsForScript(objOpts.opts)}`;\r\n }\r\n return res;\r\n}\r\n\r\nfunction _processRepsForScript(rep, index) {\r\n const repString = [];\r\n let strIdx = 0;\r\n function localAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n repString[strIdx++] = prefix + value;\r\n }\r\n }\r\n if (_.isEmpty(rep)) {\r\n return null;\r\n }\r\n localAdd('', index);\r\n localAdd('s=', utils.enquoteString(rep.selector));\r\n localAdd('m=', _processArgsForScript(rep.mode));\r\n localAdd('c=', _processArgsForScript(rep.colorer));\r\n localAdd('mt=', _processArgsForScript(rep.material));\r\n return repString.join(' ');\r\n}\r\n\r\nfunction toScript(opts) {\r\n const commandsList = [];\r\n let idx = 0;\r\n function checkAndAdd(command, value, saveQuotes) {\r\n if (value !== null && value !== undefined) {\r\n const quote = (typeof value === 'string' && saveQuotes) ? '\"' : '';\r\n commandsList[idx++] = `${command} ${quote}${value}${quote}`.trim();\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n checkAndAdd('rep', _processRepsForScript(repList[i], i));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('', _processObjForScript(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('set', 'autobuild false');\r\n checkAndAdd('load', opts.load, true);\r\n checkAndAdd('unit', opts.unit);\r\n checkAndAdd('preset', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(`set ${key}`, value, true);\r\n });\r\n checkAndAdd('view', opts.view);\r\n checkAndAdd('set', 'autobuild true');\r\n return commandsList.join('\\n');\r\n}\r\n\r\nexport default {\r\n fromURL,\r\n fromAttr,\r\n adapters,\r\n toURL,\r\n toScript,\r\n};\r\n","/**\r\n * Atom measurements.\r\n *\r\n * @param {Residue} residue - (required) Residue containing the atom\r\n * @param {string} name - (required) Name, unique in the residue\r\n * @param {Element} type - (required) Chemical element reference\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n *\r\n * @param {number} role - Role of atom inside monomer: Lead and wing are particularity interesting\r\n * @param {boolean} het - Non-standard residue indicator\r\n *\r\n * @param {number} serial - Serial number, unique in the model\r\n * @param {string} location - Alternative location indicator (usually space or A-Z)\r\n * @param {number} occupancy - Occupancy percentage, from 0 to 1\r\n * @param {number} temperature - Temperature\r\n * @param {number} charge - Charge\r\n *\r\n * @exports Atom\r\n * @constructor\r\n */\r\n\r\nclass Atom {\r\n constructor(residue, name, type, position, role, het, serial, location, occupancy, temperature, charge) {\r\n this.index = -1;\r\n this.residue = residue;\r\n this.name = name;\r\n this.element = type;\r\n this.position = position;\r\n this.role = role;\r\n this.mask = 1 | 0;\r\n\r\n this.het = het;\r\n\r\n this.serial = serial;\r\n this.location = (location || ' ').charCodeAt(0);\r\n this.occupancy = occupancy || 1;\r\n this.temperature = temperature;\r\n this.charge = charge;\r\n this.hydrogenCount = -1; // explicitly invalid\r\n this.radicalCount = 0;\r\n this.valence = -1; // explicitly invalid\r\n\r\n this.bonds = [];\r\n\r\n this.flags = 0x0000;\r\n if (type.name === 'H') {\r\n this.flags |= Atom.Flags.HYDROGEN;\r\n } else if (type.name === 'C') {\r\n this.flags |= Atom.Flags.CARBON;\r\n }\r\n }\r\n\r\n isHet() {\r\n return this.het;\r\n }\r\n\r\n isHydrogen() {\r\n return this.element.number === 1;\r\n }\r\n\r\n getVisualName() {\r\n const { name } = this;\r\n if (name.length > 0) {\r\n return name;\r\n }\r\n return this.element.name.trim();\r\n }\r\n\r\n forEachBond(process) {\r\n const { bonds } = this;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n getFullName() {\r\n let name = '';\r\n if (this.residue !== null) {\r\n if (this.residue._chain !== null) {\r\n name += `${this.residue._chain.getName()}.`;\r\n }\r\n name += `${this.residue._sequence}.`;\r\n }\r\n name += this.name;\r\n return name;\r\n }\r\n\r\n /**\r\n * Enumeration of atom flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n CARBON: 0x0001,\r\n // OXYGEN: 0x0002,\r\n // NITROGEN: 0x0004,\r\n HYDROGEN: 0x0008,\r\n /** Non-polar hydrogen (it is also a HYDROGEN) */\r\n NONPOLARH: 0x1008,\r\n };\r\n}\r\n\r\nexport default Atom;\r\n","class Element {\r\n constructor(number, name, fullName, weight, radius, radiusBonding, hValency) {\r\n this.number = number;\r\n this.name = name;\r\n this.fullName = fullName;\r\n this.weight = weight;\r\n this.radius = radius;\r\n this.radiusBonding = radiusBonding;\r\n this.hydrogenValency = hValency;\r\n }\r\n\r\n static Constants = {\r\n\r\n U1: 1,\r\n Lead: 2,\r\n U2: 3,\r\n Wing: 4,\r\n U18: 18,\r\n\r\n };\r\n\r\n static Role = {\r\n\r\n N: Element.Constants.U1,\r\n CA: Element.Constants.Lead,\r\n C: Element.Constants.U2,\r\n O: Element.Constants.Wing,\r\n SG: Element.Constants.U18,\r\n\r\n };\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByAtomicNumber = [\r\n\r\n null,\r\n new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]),\r\n new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]),\r\n new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]),\r\n new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]),\r\n new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]),\r\n new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]),\r\n new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]),\r\n new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]),\r\n new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]),\r\n new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]),\r\n new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]),\r\n new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]),\r\n new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]),\r\n new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]),\r\n new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]),\r\n new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]),\r\n new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]),\r\n new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]),\r\n new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]),\r\n new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]),\r\n new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]),\r\n new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]),\r\n new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]),\r\n new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]),\r\n new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]),\r\n new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]),\r\n new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]),\r\n new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]),\r\n new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]),\r\n new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]),\r\n new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]),\r\n new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]),\r\n new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]),\r\n new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]),\r\n new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]),\r\n new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]),\r\n new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]),\r\n new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]),\r\n new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]),\r\n new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]),\r\n new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]),\r\n new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]),\r\n new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]),\r\n new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]),\r\n new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]),\r\n new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]),\r\n new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]),\r\n new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]),\r\n new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]),\r\n new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]),\r\n new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]),\r\n new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]),\r\n new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]),\r\n new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]),\r\n new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]),\r\n new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]),\r\n new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]),\r\n new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]),\r\n new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]),\r\n new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]),\r\n new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]),\r\n new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]),\r\n new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]),\r\n new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]),\r\n new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]),\r\n new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]),\r\n new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]),\r\n new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]),\r\n new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]),\r\n new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]),\r\n new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]),\r\n new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]),\r\n new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]),\r\n new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]),\r\n new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]),\r\n new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]),\r\n new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]),\r\n new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]),\r\n new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]),\r\n new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]),\r\n new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]),\r\n new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]),\r\n new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]),\r\n new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]),\r\n new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]),\r\n new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]),\r\n new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]),\r\n new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]),\r\n new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]),\r\n new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]),\r\n new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]),\r\n new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]),\r\n new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]),\r\n new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]),\r\n new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]),\r\n new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]),\r\n new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]),\r\n new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]),\r\n new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]),\r\n new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]),\r\n new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]),\r\n new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]),\r\n new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]),\r\n new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]),\r\n new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]),\r\n new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]),\r\n new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]),\r\n new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]),\r\n new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0]),\r\n\r\n ];\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByName = {\r\n // Duplicate atomic numbers (isotopes)\r\n\r\n D: new Element(1, 'D', 'Deuterium', 2.014, 1.2, 0.23, [1]),\r\n T: new Element(1, 'T', 'Tritium', 3.016, 1.2, 0.23, [1]),\r\n\r\n // All regular elements will be added later, automatically\r\n };\r\n}\r\n\r\n(function () {\r\n const byAtomicNumber = Element.ByAtomicNumber;\r\n const byName = Element.ByName;\r\n for (let i = 0, n = byAtomicNumber.length; i < n; ++i) {\r\n const element = byAtomicNumber[i];\r\n if (element) {\r\n byName[element.name] = element;\r\n }\r\n }\r\n}());\r\n\r\n// find atom type by chemical element (or create if missing)\r\nElement.getByName = function (element) {\r\n let type = Element.ByName[element];\r\n if (!type) {\r\n type = Element.ByName[element] = new Element(0, element, 'Unknown', 0, 1.0, 0.01, [0]);\r\n }\r\n return type;\r\n};\r\n\r\nexport default Element;\r\n","const cBondTypes = {\r\n /** Was generated manually */\r\n UNKNOWN: 0,\r\n /** Simple covalent bond */\r\n COVALENT: 1,\r\n /** Aromatic bond */\r\n AROMATIC: 2,\r\n};\r\n\r\nfunction getAtomPos(atom) {\r\n return atom.position;\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Atom} left - The first atom.\r\n * @param {Atom} right - The second atom.\r\n * @param {number} order - Order of current bond.\r\n * @param {number} type - Bond type.\r\n * @param {boolean} fixed - Indicator of a pre-specified connection (in contrast with guessed one).\r\n *\r\n * @exports Bond\r\n * @constructor\r\n */\r\nclass Bond {\r\n constructor(left, right, order, type, fixed) {\r\n this._left = left;\r\n this._right = right;\r\n this._fixed = fixed;\r\n this._index = -1;\r\n if (left > right) {\r\n throw new Error('In a bond atom indices must be in increasing order');\r\n }\r\n this._order = order;\r\n this._type = type;\r\n }\r\n\r\n getLeft() {\r\n return this._left;\r\n }\r\n\r\n getRight() {\r\n return this._right;\r\n }\r\n\r\n getOrder() {\r\n return this._order;\r\n }\r\n\r\n calcLength() {\r\n return this._left.position.distanceTo(this._right.position);\r\n }\r\n\r\n _forEachNeighbour(currAtom, process) {\r\n const { bonds } = currAtom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]._left !== currAtom ? bonds[i]._left : bonds[i]._right);\r\n }\r\n }\r\n\r\n forEachLevelOne(process) {\r\n const left = this._left;\r\n const right = this._right;\r\n this._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n this._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n }\r\n\r\n forEachLevelTwo(process) {\r\n // TODO refactor this piece of an art?\r\n const left = this._left;\r\n const right = this._right;\r\n const self = this;\r\n self._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === left) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n self._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === right) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n }\r\n\r\n _fixDir(refPoint, currDir, posGetter) {\r\n // count atoms to the right and to the left of the current plane\r\n let rightCount = 0;\r\n let leftCount = 0;\r\n const tmpVec = refPoint.clone();\r\n function checkDir(atom) {\r\n tmpVec.copy(posGetter(atom));\r\n tmpVec.sub(refPoint);\r\n const dotProd = currDir.dot(tmpVec);\r\n if (dotProd > 0) {\r\n ++rightCount;\r\n } else {\r\n ++leftCount;\r\n }\r\n }\r\n function checkCarbon(atom) {\r\n if (atom.element.name === 'C') {\r\n checkDir(atom);\r\n }\r\n }\r\n // count all atoms to the left and right of our plane, start from level 1 and carbons\r\n const stages = [\r\n [this.forEachLevelOne, checkCarbon],\r\n [this.forEachLevelOne, checkDir],\r\n [this.forEachLevelTwo, checkCarbon],\r\n [this.forEachLevelTwo, checkDir],\r\n ];\r\n\r\n for (let stageId = 0; stageId < stages.length; ++stageId) {\r\n stages[stageId][0].call(this, stages[stageId][1]);\r\n if (leftCount > rightCount) {\r\n return currDir.multiplyScalar(-1);\r\n }\r\n if (leftCount < rightCount) {\r\n return currDir;\r\n }\r\n }\r\n return currDir;\r\n }\r\n\r\n calcNormalDir(posGetter) {\r\n const left = this._left;\r\n const right = this._right;\r\n let first = left;\r\n let second = right;\r\n posGetter = posGetter === undefined ? getAtomPos : posGetter;\r\n if (left.bonds.length > right.bonds.length) {\r\n first = right;\r\n second = left;\r\n }\r\n let third = first;\r\n let maxNeibs = 0;\r\n const { bonds } = second;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n let another = bonds[i]._left;\r\n if (bonds[i]._left === second) {\r\n another = bonds[i]._right;\r\n }\r\n if (another.bonds.length > maxNeibs && another !== first) {\r\n third = another;\r\n maxNeibs = another.bonds.length;\r\n }\r\n }\r\n const secondPos = posGetter(second);\r\n const firstV = posGetter(first).clone().sub(secondPos);\r\n const secondV = posGetter(third).clone().sub(secondPos);\r\n secondV.crossVectors(firstV, secondV);\r\n if (secondV.lengthSq() < 0.0001) {\r\n secondV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n secondV.normalize();\r\n firstV.crossVectors(secondV, firstV);\r\n if (firstV.lengthSq() < 0.0001) {\r\n firstV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n return this._fixDir(secondPos, firstV, posGetter);\r\n }\r\n\r\n static BondType = cBondTypes;\r\n}\r\n\r\nBond.prototype.BondType = cBondTypes;\r\n\r\nexport default Bond;\r\n","import * as THREE from 'three';\r\nimport Atom from './Atom';\r\nimport Element from './Element';\r\n\r\nconst cNucleicControlNames = ['C3\\'', 'C3*', 'P', 'H5T', 'H3T'];\r\nconst cNucleicWing1Names = ['OP1', 'O1P'];\r\nconst cNucleicWing2Names = ['OP2', 'O2P'];\r\n\r\nconst cCylinderSource = ['C3\\'', 'C3*', 'C1', 'C1\\'', 'C1*', 'P'];\r\nconst cCylinderTarget = [{\r\n types: ['A', 'DA', 'G', 'DG'],\r\n atoms: ['N1'],\r\n}, {\r\n types: ['C', 'DC'],\r\n atoms: ['N3'],\r\n}, {\r\n types: ['T', 'DT', 'U', 'DU'],\r\n atoms: ['O4'],\r\n}];\r\n\r\n/**\r\n * Residue instance.\r\n *\r\n * @param {Chain} chain - Chain this residue belongs to.\r\n * @param {ResidueType} type - Generic residue instance type.\r\n * @param {number} sequence - Sequence ID.\r\n * @param {string} icode - One character insertion code (usually space or A-Z).\r\n *\r\n * @exports Residue\r\n * @constructor\r\n */\r\nclass Residue {\r\n constructor(chain, type, sequence, icode) {\r\n this._chain = chain;\r\n this._component = null;\r\n this._type = type;\r\n this._sequence = sequence;\r\n this._icode = icode;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n\r\n this._atoms = [];\r\n this._secondary = null;\r\n this._firstAtom = null;\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n this._lastAtom = null;\r\n this._controlPoint = null;\r\n this._midPoint = null;\r\n this._wingVector = null;\r\n this._cylinders = null;\r\n this._isValid = true;\r\n this._het = false;\r\n this._molecule = null;\r\n this.temperature = null;\r\n this.occupancy = null;\r\n }\r\n\r\n // Getters and setters\r\n getChain() {\r\n return this._chain;\r\n }\r\n\r\n getMolecule() {\r\n return this._molecule;\r\n }\r\n\r\n getType() {\r\n return this._type;\r\n }\r\n\r\n getSequence() {\r\n return this._sequence;\r\n }\r\n\r\n getSecondary() {\r\n return this._secondary;\r\n }\r\n\r\n getICode() {\r\n return this._icode;\r\n }\r\n\r\n // Other methods\r\n\r\n addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge) {\r\n const atom = new Atom(this, name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n const complex = this._chain.getComplex();\r\n complex.addAtom(atom);\r\n this._atoms.push(atom);\r\n this._het = this._het || het;\r\n return atom;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (process(atoms[i])) {\r\n break;\r\n }\r\n }\r\n }\r\n\r\n _findAtomByName(name) {\r\n let res = null;\r\n this.forEachAtom((atom) => {\r\n if (atom.name === name) {\r\n res = atom;\r\n return true;\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _findFirstAtomInList(names) {\r\n let res = null;\r\n for (let i = 0; i < names.length; ++i) {\r\n res = this._findAtomByName(names[i]);\r\n if (res !== null) {\r\n return res;\r\n }\r\n }\r\n return res;\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n mask &= atoms[i].mask;\r\n }\r\n this._mask = mask;\r\n }\r\n\r\n getCylinderTargetList() {\r\n const type = this._type._name;\r\n for (let i = 0, n = cCylinderTarget.length; i < n; ++i) {\r\n for (let j = 0, m = cCylinderTarget[i].types.length; j < m; ++j) {\r\n if (type === cCylinderTarget[i].types[j]) {\r\n return cCylinderTarget[i].atoms;\r\n }\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n _detectLeadWing(dst, next, getAtomPosition) {\r\n const leadAtom = this._findFirstAtomInList(cNucleicControlNames);\r\n let wingStart = this._findFirstAtomInList(cNucleicWing1Names);\r\n let wingEnd = this._findFirstAtomInList(cNucleicWing2Names);\r\n\r\n if (wingStart === null && next !== null) {\r\n wingStart = next._findFirstAtomInList(cNucleicWing1Names);\r\n }\r\n\r\n if (wingEnd === null && next !== null) {\r\n wingEnd = next._findFirstAtomInList(cNucleicWing2Names);\r\n }\r\n\r\n if (leadAtom === null || wingStart === null || wingEnd === null) {\r\n return;\r\n }\r\n\r\n dst._leadAtom = leadAtom;\r\n dst._controlPoint = getAtomPosition(leadAtom);\r\n dst._wingVector = getAtomPosition(wingEnd).clone().sub(getAtomPosition(wingStart));\r\n dst._isValid = true;\r\n\r\n const cylSource = this._findFirstAtomInList(cCylinderSource);\r\n const targetList = this.getCylinderTargetList();\r\n const cylTarget = targetList !== null ? this._findFirstAtomInList(targetList) : null;\r\n if (cylSource === null || cylTarget === null) {\r\n return;\r\n }\r\n dst._cylinders = [getAtomPosition(cylSource), getAtomPosition(cylTarget)];\r\n }\r\n\r\n calcWing(prevLeadPos, currLeadPos, prevWingPos, prevWing) {\r\n const vectorA = currLeadPos.clone().sub(prevLeadPos);\r\n const vectorB = prevLeadPos.clone().sub(prevWingPos);\r\n vectorB.crossVectors(vectorA, vectorB);\r\n vectorB.crossVectors(vectorA, vectorB).normalize();\r\n if (prevWing !== null && prevWing.length() > 0.0001) {\r\n const needToNegate = vectorB.length() > 0.0001 && Math.abs(prevWing.angleTo(vectorB)) > Math.PI / 2;\r\n if (needToNegate) {\r\n vectorB.negate();\r\n }\r\n }\r\n return vectorB;\r\n }\r\n\r\n _innerFinalize(prevRes, prev, nextRes, dst, chainAsNucleic, getAtomPosition) {\r\n const bFirstInChain = prev === null;\r\n\r\n const lp = getAtomPosition(this._leadAtom);\r\n const currLeadPos = new THREE.Vector3(lp.x, lp.y, lp.z);\r\n if (chainAsNucleic) {\r\n this._detectLeadWing(dst, nextRes, getAtomPosition);\r\n return;\r\n }\r\n\r\n if (bFirstInChain) { // for first one in chain\r\n dst._midPoint = getAtomPosition(this._firstAtom).clone();\r\n } else {\r\n const prevLeadPos = prev._controlPoint; // lead point of previous monomer\r\n dst._midPoint = prevLeadPos.clone().lerp(currLeadPos, 0.5);\r\n dst._wingVector = this.calcWing(prevLeadPos, currLeadPos, getAtomPosition(prevRes._wingAtom), prev._wingVector);\r\n }\r\n dst._controlPoint = currLeadPos;\r\n }\r\n\r\n _finalize2(prev, next, asNucleic) {\r\n // Should be called AFTER first finalize\r\n this._innerFinalize(prev, prev, next, this, asNucleic, (atom) => atom.position);\r\n }\r\n\r\n isConnected(anotherResidue) {\r\n if (this._chain !== anotherResidue._chain) {\r\n return false;\r\n }\r\n if (this === anotherResidue) {\r\n return true;\r\n }\r\n let res = false;\r\n this.forEachAtom((atom) => {\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue === anotherResidue || bond._right.residue === anotherResidue) {\r\n res = true;\r\n return true;\r\n }\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _finalize() {\r\n const self = this;\r\n [this._firstAtom] = this._atoms;\r\n this._lastAtom = this._atoms[this._atoms.length - 1];\r\n\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n\r\n let tempCount = 0;\r\n let temperature = 0; // average temperature\r\n let occupCount = 0;\r\n let occupancy = 0; // average occupancy\r\n this.forEachAtom((a) => {\r\n if (self._leadAtom === null) {\r\n if (a.role === Element.Constants.Lead) {\r\n self._leadAtom = a;\r\n }\r\n }\r\n if (self._wingAtom === null) {\r\n if (a.role === Element.Constants.Wing) {\r\n self._wingAtom = a;\r\n }\r\n }\r\n if (a.temperature) {\r\n temperature += a.temperature;\r\n tempCount++;\r\n }\r\n if (a.occupancy) {\r\n occupancy += a.occupancy;\r\n occupCount++;\r\n }\r\n return (self._leadAtom !== null && self._wingAtom !== null);\r\n });\r\n\r\n if (tempCount > 0) {\r\n this.temperature = temperature / tempCount;\r\n }\r\n if (occupCount > 0) {\r\n this.occupancy = occupancy / occupCount;\r\n }\r\n\r\n // Still try to make monomer look valid\r\n if (this._leadAtom === null || this._wingAtom === null) {\r\n this._isValid = false;\r\n }\r\n if (this._leadAtom === null) {\r\n this._leadAtom = this._firstAtom;\r\n }\r\n if (this._wingAtom === null) {\r\n this._wingAtom = this._lastAtom;\r\n }\r\n }\r\n}\r\n\r\nexport default Residue;\r\n","/**\r\n * Residue type.\r\n *\r\n * Predefined acid or created with HET, HETNAM, etc.\r\n *\r\n * @param {string} name - Short name, either standard (ALA, MET, etc.) or non-standard one.\r\n * @param {string} fullName - Full residue name.\r\n * @param {string} letterCode - 1-letter symbol.\r\n *\r\n * @exports ResidueType\r\n * @constructor\r\n */\r\nclass ResidueType {\r\n constructor(name, fullName, letterCode) {\r\n this._name = name;\r\n this._fullName = fullName;\r\n this.letterCode = letterCode;\r\n this.flags = 0x0000;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\n static StandardTypes = {\r\n\r\n ALA: new ResidueType('ALA', 'Alanine', 'A'),\r\n ARG: new ResidueType('ARG', 'Arginine', 'R'),\r\n ASN: new ResidueType('ASN', 'Asparagine', 'N'),\r\n ASP: new ResidueType('ASP', 'Aspartic Acid', 'D'),\r\n CYS: new ResidueType('CYS', 'Cysteine', 'C'),\r\n GLN: new ResidueType('GLN', 'Glutamine', 'Q'),\r\n GLU: new ResidueType('GLU', 'Glutamic Acid', 'E'),\r\n GLY: new ResidueType('GLY', 'Glycine', 'G'),\r\n HIS: new ResidueType('HIS', 'Histidine', 'H'),\r\n ILE: new ResidueType('ILE', 'Isoleucine', 'I'),\r\n LEU: new ResidueType('LEU', 'Leucine', 'L'),\r\n LYS: new ResidueType('LYS', 'Lysine', 'K'),\r\n MET: new ResidueType('MET', 'Methionine', 'M'),\r\n PHE: new ResidueType('PHE', 'Phenylalanine', 'F'),\r\n PRO: new ResidueType('PRO', 'Proline', 'P'),\r\n PYL: new ResidueType('PYL', 'Pyrrolysine', 'O'),\r\n SEC: new ResidueType('SEC', 'Selenocysteine', 'U'),\r\n SER: new ResidueType('SER', 'Serine', 'S'),\r\n THR: new ResidueType('THR', 'Threonine', 'T'),\r\n TRP: new ResidueType('TRP', 'Tryptophan', 'W'),\r\n TYR: new ResidueType('TYR', 'Tyrosine', 'Y'),\r\n VAL: new ResidueType('VAL', 'Valine', 'V'),\r\n A: new ResidueType('A', 'Adenine', 'A'),\r\n C: new ResidueType('C', 'Cytosine', 'C'),\r\n G: new ResidueType('G', 'Guanine', 'G'),\r\n I: new ResidueType('I', 'Inosine', 'I'),\r\n T: new ResidueType('T', 'Thymine', 'T'),\r\n U: new ResidueType('U', 'Uracil', 'U'),\r\n DA: new ResidueType('DA', 'Adenine', 'A'),\r\n DC: new ResidueType('DC', 'Cytosine', 'C'),\r\n DG: new ResidueType('DG', 'Guanine', 'G'),\r\n DI: new ResidueType('DI', 'Inosine', 'I'),\r\n DT: new ResidueType('DT', 'Thymine', 'T'),\r\n DU: new ResidueType('DU', 'Uracil', 'U'),\r\n '+A': new ResidueType('+A', 'Adenine', 'A'),\r\n '+C': new ResidueType('+C', 'Cytosine', 'C'),\r\n '+G': new ResidueType('+G', 'Guanine', 'G'),\r\n '+I': new ResidueType('+I', 'Inosine', 'I'),\r\n '+T': new ResidueType('+T', 'Thymine', 'T'),\r\n '+U': new ResidueType('+U', 'Uracil', 'U'),\r\n WAT: new ResidueType('WAT', 'Water', ''),\r\n H2O: new ResidueType('H2O', 'Water', ''),\r\n HOH: new ResidueType('HOH', 'Water', ''),\r\n DOD: new ResidueType('DOD', 'Water', ''),\r\n UNK: new ResidueType('UNK', 'Unknown', ''),\r\n UNL: new ResidueType('UNL', 'Unknown Ligand', ''),\r\n\r\n };\r\n\r\n /**\r\n * Enumeration of residue flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n // Amino acids\r\n /** Amino acid residue */\r\n PROTEIN: 0x0001,\r\n /** Basic amino acid residue */\r\n BASIC: 0x0002,\r\n /** Acidic amino acid residue */\r\n ACIDIC: 0x0004,\r\n /** Polar uncharged side chain amino acid residue */\r\n POLAR: 0x0008,\r\n /** Non-polar hydrophobic side chain amino acid residue */\r\n NONPOLAR: 0x0010,\r\n /** Aromatic amino acid residue */\r\n AROMATIC: 0x0020,\r\n\r\n // Nucleic acids\r\n\r\n /** Nucleic residue */\r\n NUCLEIC: 0x0100,\r\n /** Purine nucleic residue */\r\n PURINE: 0x0200,\r\n /** Pyrimidine nucleic residue */\r\n PYRIMIDINE: 0x0400,\r\n /** DNA */\r\n DNA: 0x0800,\r\n /** RNA */\r\n RNA: 0x1000,\r\n\r\n /** Water */\r\n WATER: 0x10000,\r\n };\r\n}\r\n\r\n// Flag combinations\r\nfunction _addFlag(flag, list) {\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const res = ResidueType.StandardTypes[list[i]];\r\n if (res) {\r\n res.flags |= flag;\r\n }\r\n }\r\n}\r\n\r\nconst { Flags } = ResidueType;\r\n_addFlag(Flags.WATER, ['WAT', 'H2O', 'HOH', 'DOD']);\r\n\r\n_addFlag(Flags.PROTEIN, [\r\n 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLY', 'GLU', 'GLN', 'HIS', 'ILE',\r\n 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'PYL', 'SEC', 'SER', 'THR', 'TRP',\r\n 'TYR', 'VAL',\r\n]);\r\n_addFlag(Flags.BASIC, ['ARG', 'HIS', 'LYS']);\r\n_addFlag(Flags.ACIDIC, ['ASP', 'GLU']);\r\n_addFlag(Flags.POLAR, ['ASN', 'CYS', 'GLN', 'SER', 'THR', 'TYR']);\r\n_addFlag(Flags.NONPOLAR, ['ALA', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'VAL', 'GLY']);\r\n_addFlag(Flags.AROMATIC, ['PHE', 'TRP', 'TYR']);\r\n\r\n_addFlag(Flags.NUCLEIC, [\r\n 'A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I',\r\n 'C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U',\r\n]);\r\n_addFlag(Flags.PURINE, ['A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I']);\r\n_addFlag(Flags.PYRIMIDINE, ['C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U']);\r\n_addFlag(Flags.DNA, ['DA', 'DG', 'DI', 'DC', 'DT', 'DU']);\r\n_addFlag(Flags.RNA, ['A', 'G', 'I', 'C', 'T', 'U']);\r\n// Table of kdHydrophobicity\r\nconst hydro = {\r\n ILE: 4.5,\r\n VAL: 4.2,\r\n LEU: 3.8,\r\n PHE: 2.8,\r\n CYS: 2.5,\r\n MET: 1.9,\r\n ALA: 1.8,\r\n GLY: -0.4,\r\n THR: -0.7,\r\n SER: -0.8,\r\n TRP: -0.9,\r\n TYR: -1.3,\r\n PRO: -1.6,\r\n HIS: -3.2,\r\n GLU: -3.5,\r\n GLN: -3.5,\r\n ASP: -3.5,\r\n ASN: -3.5,\r\n LYS: -3.9,\r\n ARG: -4.5,\r\n};\r\n\r\nfunction _addParam(param, list) {\r\n const keys = Object.keys(list);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = list[key];\r\n ResidueType.StandardTypes[key][param] = value;\r\n }\r\n}\r\n\r\n_addParam('hydrophobicity', hydro);\r\n\r\nexport default ResidueType;\r\n","import * as THREE from 'three';\r\nimport Residue from './Residue';\r\nimport ResidueType from './ResidueType';\r\n\r\n/**\r\n * Residues in chain are either amino acid either nucleic acid (and water)\r\n * There might be some modified/mutated residues, which type could not be determined by their name (nucleic or amino); In this\r\n * case firstly program definites the chain type (by well-known residues) and then definites modified/mutated residues\r\n */\r\nconst ChainType = {\r\n UNKNOWN: 0,\r\n PROTEIN: 1,\r\n NUCLEIC: 2,\r\n};\r\n\r\n/**\r\n * Residue chain.\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n * @param {string} name - One character identifier (usually space, A-Z, 0-9, or a-z).\r\n *\r\n * @exports Chain\r\n * @constructor\r\n */\r\nclass Chain {\r\n constructor(complex, name) {\r\n this._complex = complex;\r\n this._name = name;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n this._residues = [];\r\n\r\n this.minSequence = Number.POSITIVE_INFINITY;\r\n this.maxSequence = Number.NEGATIVE_INFINITY;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n _determineType() {\r\n const residues = this._residues;\r\n\r\n const { PROTEIN, NUCLEIC } = ResidueType.Flags;\r\n\r\n this.type = ChainType.UNKNOWN;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const { flags } = residues[i]._type;\r\n\r\n if ((flags & NUCLEIC) !== 0) {\r\n this.type = ChainType.NUCLEIC;\r\n break;\r\n } else if ((flags & PROTEIN) !== 0) {\r\n this.type = ChainType.PROTEIN;\r\n break;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Finds thre residue with specified sequence number and inserion code\r\n * @param {Number} seqNum sequence number\r\n * @param {string} iCode insertion code\r\n * @returns {*} Residue or null if not found\r\n */\r\n findResidue(seqNum, iCode) {\r\n const residues = this._residues;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n if (res._sequence === seqNum && res._icode === iCode) {\r\n return [res, i];\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _finalize() {\r\n this._determineType();\r\n\r\n const residues = this._residues;\r\n\r\n let prev = null;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const next = (i + 1 < n) ? residues[i + 1] : null;\r\n const curr = residues[i];\r\n // TODO: skip invalid residues\r\n if (1 /* curr._isValid */) { // eslint-disable-line no-constant-condition\r\n curr._finalize2(prev, next, this.type === ChainType.NUCLEIC);\r\n prev = curr;\r\n }\r\n }\r\n\r\n // fix very first wing\r\n if (residues.length > 1 && residues[1]._wingVector) {\r\n const p = residues[1]._wingVector;\r\n residues[0]._wingVector = new THREE.Vector3(p.x, p.y, p.z);\r\n } else if (residues.length > 0) {\r\n residues[0]._wingVector = new THREE.Vector3(1, 0, 0);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const residues = this._residues;\r\n let prev = null;\r\n let prevData = null;\r\n const frameRes = frameData._residues;\r\n const n = residues.length;\r\n function getAtomPos(atom) {\r\n return frameData.getAtomPos(atom.index);\r\n }\r\n\r\n for (let i = 0; i < n; ++i) {\r\n const curr = residues[i];\r\n const currData = frameRes[curr._index];\r\n const nextRes = (i + 1 < n) ? residues[i + 1] : null;\r\n curr._innerFinalize(prev, prevData, nextRes, currData, this.type === ChainType.NUCLEIC, getAtomPos);\r\n prev = curr;\r\n prevData = currData;\r\n }\r\n\r\n frameRes[residues[0]._index]._wingVector = n > 1\r\n ? frameRes[residues[1]._index]._wingVector\r\n : new THREE.Vector3(1, 0, 0);\r\n }\r\n\r\n /**\r\n * Create a new residue.\r\n *\r\n * @param {string} name - Residue name.\r\n * @param {number} sequence - Residue sequence number.\r\n * @param {string} iCode - Insertion code.\r\n * @returns {Residue} - Newly created residue instance.\r\n */\r\n addResidue(name, sequence, iCode) {\r\n let type = this._complex.getResidueType(name);\r\n if (type === null) {\r\n type = this._complex.addResidueType(name);\r\n }\r\n const residue = new Residue(this, type, sequence, iCode);\r\n this._complex.addResidue(residue);\r\n this._residues.push(residue);\r\n\r\n if (type.flags & (ResidueType.Flags.NUCLEIC | ResidueType.Flags.PROTEIN)) {\r\n if (this.maxSequence < sequence) {\r\n this.maxSequence = sequence;\r\n }\r\n if (this.minSequence > sequence) {\r\n this.minSequence = sequence;\r\n }\r\n }\r\n\r\n return residue;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this._mask = mask;\r\n }\r\n}\r\n\r\nexport default Chain;\r\n","import Residue from './Residue';\r\n\r\n/** An element of protein secondary structure. */\r\nclass StructuralElement {\r\n /**\r\n * Create a secondary structural element of the specified type.\r\n *\r\n * @param {StructuralElement.Type} type Secondary structure type.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n */\r\n constructor(type, init, term) {\r\n /**\r\n * Secondary structure type.\r\n * @type {StructuralElement.Type}\r\n */\r\n this.type = type;\r\n /**\r\n * Generic secondary structure type.\r\n * @type {StructuralElement.Generic}\r\n */\r\n this.generic = StructuralElement.genericByType[this.type] || 'loop';\r\n /**\r\n * Initial residue.\r\n * @type Residue\r\n */\r\n this.init = init;\r\n /**\r\n * Terminal residue.\r\n * @type Residue\r\n */\r\n this.term = term;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n if (this.init instanceof Residue && this.term instanceof Residue) {\r\n return;\r\n }\r\n\r\n // Link all intermediate residues to this structural element\r\n const start = complex.splitUnifiedSerial(this.init);\r\n const end = complex.splitUnifiedSerial(this.term);\r\n for (let chainId = start.chain; chainId <= end.chain; chainId++) {\r\n for (let serialId = start.serial; serialId <= end.serial; serialId++) {\r\n for (let { iCode } = start; iCode <= end.iCode; iCode++) {\r\n const hashCode = complex.getUnifiedSerial(chainId, serialId, iCode);\r\n if (residueHash[hashCode]) {\r\n residueHash[hashCode]._secondary = this;\r\n }\r\n }\r\n }\r\n }\r\n\r\n // Replace unfined serials by objects\r\n this.init = residueHash[this.init];\r\n this.term = residueHash[this.term];\r\n }\r\n}\r\n\r\n/**\r\n * Specific type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Generic\r\n */\r\nStructuralElement.Type = {\r\n /** A strand of a [beta-sheet](https://en.wikipedia.org/wiki/Beta_sheet). */\r\n STRAND: 'E',\r\n /** An isolated beta-bridge (too small for a beta-sheet). */\r\n BRIDGE: 'B',\r\n\r\n /** A [3/10 helix](https://en.wikipedia.org/wiki/310_helix) (hydrogen bonding is 3 residues apart). */\r\n HELIX_310: 'G',\r\n /** An [alpha-helix](https://en.wikipedia.org/wiki/Alpha_helix) (hydrogen bonding is 4 residues apart). */\r\n HELIX_ALPHA: 'H',\r\n /** A [pi-helix](https://en.wikipedia.org/wiki/Pi_helix) (hydrogen bonding is 5 residues apart). */\r\n HELIX_PI: 'I',\r\n /** A generic helix of unspecified bonding distance. */\r\n HELIX: 'X',\r\n\r\n /** An isolated 3/10-like helical turn. */\r\n TURN_310: '3',\r\n /** An isolated alpha-like helical turn. */\r\n TURN_ALPHA: '4',\r\n /** An isolated pi-like helical turn. */\r\n TURN_PI: '5',\r\n /** An isolated helical [turn](https://en.wikipedia.org/wiki/Turn_(biochemistry)) of unspecified bonding distance. */\r\n TURN: 'T',\r\n\r\n /** A bend (a region of high curvature). */\r\n BEND: 'S',\r\n /** Just a protein section with no particular conformation. */\r\n COIL: 'C',\r\n};\r\n\r\n/**\r\n * Generic type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Type\r\n */\r\nStructuralElement.Generic = {\r\n /** A strand of a sheet. */\r\n STRAND: 'strand',\r\n /** A helix. */\r\n HELIX: 'helix',\r\n /** Just a protein section with no particular conformation. */\r\n LOOP: 'loop',\r\n};\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\nconst StructuralElementGeneric = StructuralElement.Generic;\r\n\r\n/**\r\n * A mapping from specific types to generic ones.\r\n * @type {Object}\r\n */\r\nStructuralElement.genericByType = {\r\n [StructuralElementType.STRAND]: StructuralElementGeneric.STRAND,\r\n [StructuralElementType.HELIX_310]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_ALPHA]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_PI]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX]: StructuralElementGeneric.HELIX,\r\n};\r\n\r\nexport default StructuralElement;\r\n","import StructuralElement from './StructuralElement';\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\nexport const typeByPDBHelixClass = {\r\n 1: StructuralElementType.HELIX_ALPHA,\r\n 3: StructuralElementType.HELIX_PI,\r\n 5: StructuralElementType.HELIX_310,\r\n};\r\n\r\n/**\r\n * Helical secondary structure of a protein.\r\n * @extends StructuralElement\r\n */\r\nclass Helix extends StructuralElement {\r\n /**\r\n * Create a helix.\r\n *\r\n * @param {number} helixClass A helix class according to the\r\n * [PDB Format](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX).\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} serial Serial number of the helix (see PDB Format).\r\n * @param {string} name Helix identifier (see PDB Format).\r\n * @param {string} comment Comment about this helix (see PDB Format).\r\n * @param {number} length Length of this helix, in residues (see PDB Format).\r\n */\r\n constructor(helixClass, init, term, serial, name, comment, length) {\r\n super(typeByPDBHelixClass[helixClass] || StructuralElement.Type.HELIX, init, term);\r\n\r\n /**\r\n * Serial number of the helix (see PDB Format).\r\n * @type {number}\r\n */\r\n this.serial = serial;\r\n /**\r\n * Helix identifier (see PDB Format).\r\n * @type {string}\r\n */\r\n this.name = name;\r\n /**\r\n * Comment about this helix (see PDB Format).\r\n * @type {string}\r\n */\r\n this.comment = comment;\r\n /**\r\n * Length of this helix, in residues (see PDB Format).\r\n * @type {number}\r\n */\r\n this.length = length;\r\n }\r\n}\r\n\r\nexport default Helix;\r\n","import StructuralElement from './StructuralElement';\r\n\r\n/**\r\n * A single strand of a sheet in a protein secondary structure.\r\n * @extends StructuralElement\r\n */\r\nclass Strand extends StructuralElement {\r\n /**\r\n * Create a strand.\r\n *\r\n * @param {Sheet} sheet Parent sheet this strand belongs to.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} sense Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @param {Atom} atomCur Atom in current strand (see PDB Format).\r\n * @param {Atom} atomPrev Atom in previous strand (see PDB Format).\r\n */\r\n constructor(sheet, init, term, sense, atomCur, atomPrev) {\r\n super(StructuralElement.Type.STRAND, init, term);\r\n\r\n /**\r\n * Parent sheet this strand belongs to.\r\n * @type {Sheet}\r\n */\r\n this.sheet = sheet;\r\n /**\r\n * Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @type {number}\r\n */\r\n this.sense = sense;\r\n /**\r\n * Atom in current strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomCur = atomCur;\r\n /**\r\n * Atom in previous strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomPrev = atomPrev;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n *\r\n * @override\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n super._finalize(serialAtomMap, residueHash, complex);\r\n\r\n let as = this.atomCur;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomCur = serialAtomMap[as];\r\n }\r\n as = this.atomPrev;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomPrev = serialAtomMap[as];\r\n }\r\n }\r\n}\r\n\r\nexport default Strand;\r\n","import Strand from './Strand';\r\n\r\n/**\r\n * Sheet secondary structure of a protein.\r\n *\r\n * @param {string} name -\r\n * @param {number} width -\r\n *\r\n * @exports Sheet\r\n * @constructor\r\n */\r\nclass Sheet {\r\n constructor(name, width) {\r\n this._name = name;\r\n this._width = width;\r\n\r\n this._strands = [];\r\n }\r\n\r\n // Getters and setters\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getWidth() {\r\n return this._width;\r\n }\r\n\r\n addStrand(strand) {\r\n this._strands.push(strand);\r\n this._width = this._strands.length;\r\n }\r\n\r\n addEmptyStrand() {\r\n this._strands.push(new Strand(null, null, null, null, null, null));\r\n }\r\n\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n const s = this._strands;\r\n for (let i = 0, n = s.length; i < n; ++i) {\r\n s[i]._finalize(serialAtomMap, residueHash, complex);\r\n }\r\n if (!this._width) {\r\n this._width = s.length;\r\n }\r\n if (s.length !== this._width) {\r\n throw new Error(`Sheet ${this._name} is inconsistent.`);\r\n }\r\n }\r\n}\r\n\r\nexport default Sheet;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Atom measurements.\r\n *\r\n * @param {string} id - SGroup id\r\n * @param {string} name - Name of the group\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n * @param {array} atoms - Atoms group consists of\r\n * @param {object} saveNode - XML node from file for saving\r\n *\r\n * @exports SGroup\r\n * @constructor\r\n */\r\nclass SGroup {\r\n constructor(id, name, position, atoms, saveNode) {\r\n this._id = id;\r\n this._name = name;\r\n this._position = position || new THREE.Vector3();\r\n this._atoms = atoms || [];\r\n this._charge = 0; // default group charge\r\n this._repeat = 1; // how many times group repeated: always > 0\r\n this._center = null;\r\n this.xmlNodeRef = saveNode || null;\r\n }\r\n\r\n /**\r\n * Get atom full name.\r\n * @returns {string} Atom full name.\r\n */\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getPosition() {\r\n return this._position;\r\n }\r\n\r\n getCentralPoint() {\r\n return this._center;\r\n }\r\n\r\n _rebuildSGroupOnAtomChange() {\r\n const nLimon = 100000000;\r\n if (this._center === null) {\r\n return; // nothing to do if we are not relative\r\n }\r\n\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n for (let j = 0, n = this._atoms.length; j < n; j++) {\r\n const aPos = this._atoms[j].position;\r\n bLow.set(Math.min(bLow.x, aPos.x), Math.min(bLow.y, aPos.y), Math.min(bLow.z, aPos.z));\r\n bHight.set(Math.max(bHight.x, aPos.x), Math.max(bHight.y, aPos.y), Math.max(bHight.z, aPos.z));\r\n }\r\n this._center.addVectors(bLow, bHight);\r\n this._center.multiplyScalar(0.5);\r\n }\r\n}\r\n\r\nexport default SGroup;\r\n","import utils from '../../utils';\r\n\r\n//----------------------------------------------------------------------------\r\nclass Range {\r\n constructor(min, max) {\r\n this.min = min;\r\n this.max = typeof max === 'undefined' ? min : max;\r\n }\r\n\r\n includes(value) {\r\n return this.min <= value && value <= this.max;\r\n }\r\n\r\n toString() {\r\n const { min, max } = this;\r\n return min === max ? String(min) : [min, max].join(':');\r\n }\r\n\r\n toJSON() {\r\n return [this.min, this.max];\r\n }\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\nclass List {\r\n constructor(arg) {\r\n if (arg instanceof this.constructor) {\r\n // delegate construction to a different class\r\n // eslint-disable-next-line no-constructor-return\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n }\r\n\r\n append(value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n }\r\n\r\n toString() {\r\n return this._values.join(',');\r\n }\r\n\r\n toJSON() {\r\n const values = this._values;\r\n const result = [];\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n result[i] = value.toJSON ? value.toJSON() : value;\r\n }\r\n return result;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nclass RangeList extends List {\r\n includes(value) {\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n if (list[i].includes(value)) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nconst valuesArray = [];\r\n\r\nclass ValueList extends List {\r\n constructor(arg, upperOnly) {\r\n const list = super(arg);\r\n if (upperOnly) {\r\n this.upperOnly = true;\r\n const values = list._values;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n if (typeof value === 'string') {\r\n values[i] = value.toUpperCase();\r\n }\r\n }\r\n } else {\r\n this.upperOnly = false;\r\n }\r\n // return constructed object\r\n // eslint-disable-next-line no-constructor-return\r\n return list;\r\n }\r\n\r\n includes(value) {\r\n // we do not convert to upper case here for perfomance reasons\r\n // if list is upper case only, value must be converted before it is sent up to here\r\n return this._values.indexOf(value) !== -1;\r\n }\r\n\r\n toString() {\r\n // Quote values that are not correct identifiers\r\n const values = this._values;\r\n valuesArray.length = 0;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n valuesArray[i] = utils.correctSelectorIdentifier(String(values[i]));\r\n }\r\n return valuesArray.join(',');\r\n }\r\n\r\n _validate(value) {\r\n return (this.upperOnly && typeof value === 'string') ? value.toUpperCase() : value;\r\n }\r\n\r\n append(value) {\r\n super.append(this._validate(value));\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n super.remove(this._validate(value));\r\n return this;\r\n }\r\n}\r\n\r\nexport {\r\n Range,\r\n List,\r\n RangeList,\r\n ValueList,\r\n};\r\n","import { RangeList, ValueList } from './selectArgs';\r\n\r\n/** Base class for atom selectors. */\r\nclass Selector {\r\n toString() {\r\n return this.keyword;\r\n }\r\n\r\n toJSON() {\r\n return [this.name];\r\n }\r\n}\r\n\r\nSelector.prototype.name = 'Error';\r\nSelector.prototype.keyword = 'error';\r\n\r\n/** Base class for list-based atom selectors. */\r\nclass ListSelector extends Selector {\r\n constructor(list) {\r\n super();\r\n this.list = list;\r\n }\r\n\r\n toString() {\r\n return `${this.keyword} ${this.list}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.list.toJSON()];\r\n }\r\n}\r\n\r\nclass RangeListSelector extends ListSelector {\r\n constructor(arg) {\r\n super(new RangeList(arg));\r\n }\r\n}\r\n\r\nclass ValueListSelector extends ListSelector {\r\n constructor(arg, caseSensitive) {\r\n super(new ValueList(arg, !caseSensitive));\r\n }\r\n}\r\n\r\nclass NoneSelector extends Selector {\r\n includesAtom(_atom) {\r\n return false;\r\n }\r\n}\r\n\r\nNoneSelector.prototype.name = 'None';\r\nNoneSelector.prototype.keyword = 'none';\r\n\r\nclass AllSelector extends Selector {\r\n includesAtom(_atom) {\r\n return true;\r\n }\r\n}\r\n\r\nAllSelector.prototype.name = 'All';\r\nAllSelector.prototype.keyword = 'all';\r\n\r\nexport {\r\n Selector,\r\n ListSelector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n};\r\n","import { Selector, NoneSelector } from './selectorsBase';\r\n\r\n//----------------------------------------------------------------------------\r\n// Operators\r\n//----------------------------------------------------------------------------\r\nconst none = new NoneSelector();\r\n\r\nclass PrefixOperator extends Selector {\r\n constructor(rhs) {\r\n super();\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nPrefixOperator.prototype.priority = 1;\r\n\r\nclass InfixOperator extends Selector {\r\n constructor(lhs, rhs) {\r\n super();\r\n this.lhs = lhs || none;\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const lhs = this.lhs.priority && this.lhs.priority > this.priority ? `(${this.lhs})` : this.lhs;\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${lhs} ${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.lhs.toJSON(), this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nInfixOperator.prototype.priority = 1000;\r\n\r\nexport { PrefixOperator, InfixOperator };\r\n","import Atom from './Atom';\r\nimport ResidueType from './ResidueType';\r\nimport { parser } from '../utils/SelectionParser';\r\nimport { Range, RangeList, ValueList } from './selectors/selectArgs';\r\nimport { PrefixOperator, InfixOperator } from './selectors/selectOps';\r\nimport {\r\n Selector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n} from './selectors/selectorsBase';\r\n\r\nconst keywords = {};\r\n\r\n//----------------------------------------------------------------------------\r\n// Named selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineSelector(name, SelectorClass) {\r\n const keyword = name.toLowerCase();\r\n SelectorClass.prototype.keyword = keyword;\r\n SelectorClass.prototype.name = name;\r\n\r\n const factory = ((...args) => new SelectorClass(...args));\r\n factory.SelectorClass = SelectorClass;\r\n keywords[keyword] = factory;\r\n\r\n return SelectorClass;\r\n}\r\n\r\ndefineSelector('Serial', class SerialSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.serial);\r\n }\r\n});\r\n\r\ndefineSelector('Name', class NameSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.name);\r\n }\r\n});\r\n\r\ndefineSelector('AltLoc', class AltLocSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(String.fromCharCode(atom.location));\r\n }\r\n});\r\n\r\ndefineSelector('Elem', class ElemSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.element.name);\r\n }\r\n});\r\n\r\ndefineSelector('Residue', class ResidueSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._type._name);\r\n }\r\n});\r\n\r\ndefineSelector('Sequence', class SequenceSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._sequence);\r\n }\r\n});\r\n\r\ndefineSelector('ICode', class ICodeSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._icode);\r\n }\r\n});\r\n\r\ndefineSelector('ResIdx', class ResIdxSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._index);\r\n }\r\n});\r\n\r\ndefineSelector('Chain', class ChainSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._chain._name);\r\n }\r\n});\r\n\r\ndefineSelector('Hetatm', class HetatmSelector extends Selector {\r\n includesAtom(atom) {\r\n return atom.het;\r\n }\r\n});\r\n\r\ndefineSelector('PolarH', class PolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.HYDROGEN;\r\n }\r\n});\r\n\r\ndefineSelector('NonPolarH', class NonPolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.NONPOLARH;\r\n }\r\n});\r\n\r\ndefineSelector('All', AllSelector);\r\n\r\ndefineSelector('None', NoneSelector);\r\n\r\nconst NULL_SELECTOR = keywords.none();\r\n\r\n//----------------------------------------------------------------------------\r\n// Named operators\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineOperator(name, priority, OperatorClass) {\r\n OperatorClass.prototype.priority = priority;\r\n return defineSelector(name, OperatorClass);\r\n}\r\ndefineOperator('Not', 1, class NotOperator extends PrefixOperator {\r\n includesAtom(atom) {\r\n return !this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('And', 2, class AndOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) && this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('Or', 3, class OrOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) || this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\n//----------------------------------------------------------------------------\r\n// Flag selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction byResidueTypeFlag(flag, name) {\r\n return defineSelector(name, class extends Selector {\r\n includesAtom(atom) {\r\n return (atom.residue._type.flags & flag) !== 0;\r\n }\r\n });\r\n}\r\n\r\nbyResidueTypeFlag(ResidueType.Flags.PROTEIN, 'Protein');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC, 'Basic');\r\nbyResidueTypeFlag(ResidueType.Flags.ACIDIC, 'Acidic');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC | ResidueType.Flags.ACIDIC, 'Charged');\r\nbyResidueTypeFlag(ResidueType.Flags.POLAR, 'Polar');\r\nbyResidueTypeFlag(ResidueType.Flags.NONPOLAR, 'NonPolar');\r\nbyResidueTypeFlag(ResidueType.Flags.AROMATIC, 'Aromatic');\r\nbyResidueTypeFlag(ResidueType.Flags.NUCLEIC, 'Nucleic');\r\nbyResidueTypeFlag(ResidueType.Flags.PURINE, 'Purine');\r\nbyResidueTypeFlag(ResidueType.Flags.PYRIMIDINE, 'Pyrimidine');\r\nbyResidueTypeFlag(ResidueType.Flags.WATER, 'Water');\r\n\r\n//----------------------------------------------------------------------------\r\nconst selectors = Object.create(keywords);\r\n\r\nselectors.Selector = Selector;\r\nselectors.RangeListSelector = RangeListSelector;\r\nselectors.ValueListSelector = ValueListSelector;\r\nselectors.Range = Range;\r\nselectors.RangeList = RangeList;\r\nselectors.ValueList = ValueList;\r\nselectors.PrefixOperator = PrefixOperator;\r\nselectors.InfixOperator = InfixOperator;\r\nselectors.Context = Object.create({});\r\n\r\nselectors.GetSelector = function (key) {\r\n if (!selectors.Context.hasOwnProperty(key)) {\r\n const exc = { message: `selector ${key} is not registered` };\r\n throw exc;\r\n }\r\n return selectors.Context[key] || NULL_SELECTOR;\r\n};\r\n\r\nselectors.ClearContext = function () {\r\n Object.keys(selectors.Context).forEach((k) => { delete selectors.Context[k]; });\r\n};\r\n\r\nselectors.keyword = function (key) {\r\n return keywords[key.toLowerCase()] || keywords.none;\r\n};\r\n\r\nselectors.parse = function (str) {\r\n const res = {};\r\n try {\r\n res.selector = parser.parse(str);\r\n } catch (e) {\r\n res.selector = NULL_SELECTOR;\r\n res.error = e.message;\r\n }\r\n return res;\r\n};\r\n\r\nparser.yy = selectors;\r\nparser.yy.parseError = parser.parseError; // workaround for incorrect JISON parser generator for AMD module\r\n\r\nexport default selectors;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\n\r\n/**\r\n * Basic biological unit class.\r\n *\r\n * @exports BiologicalUnit\r\n * @constructor\r\n */\r\nclass BiologicalUnit {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._selector = selectors.keyword('All')();\r\n this._boundaries = {\r\n boundingBox: new THREE.Box3(),\r\n boundingSphere: new THREE.Sphere(),\r\n };\r\n }\r\n\r\n computeBoundaries() {\r\n const atoms = this._complex._atoms;\r\n const n = atoms.length;\r\n const selector = this._selector;\r\n\r\n const { boundingBox } = this._boundaries;\r\n boundingBox.makeEmpty();\r\n if (n === 1) {\r\n boundingBox.expandByPoint(atoms[0].position);\r\n const bbc = new THREE.Vector3();\r\n boundingBox.getCenter(bbc);\r\n const s = 2 * atoms[0].element.radius;\r\n boundingBox.setFromCenterAndSize(bbc, new THREE.Vector3(s, s, s));\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (selector.includesAtom(atoms[i])) {\r\n boundingBox.expandByPoint(atoms[i].position);\r\n }\r\n }\r\n }\r\n\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n if (n === 1) {\r\n this._boundaries.boundingSphere.set(center, atoms[0].element.radius);\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (!selector.includesAtom(atoms[i])) {\r\n continue;\r\n }\r\n const pos = atoms[i].position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n this._boundaries.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n }\r\n\r\n getTransforms() {\r\n return [];\r\n }\r\n\r\n getSelector() {\r\n return this._selector;\r\n }\r\n\r\n getBoundaries() {\r\n return this._boundaries;\r\n }\r\n\r\n finalize() {\r\n }\r\n}\r\n\r\nexport default BiologicalUnit;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\nimport BiologicalUnit from './BiologicalUnit';\r\n\r\n/**\r\n * Biological assembly.\r\n *\r\n * @exports Assembly\r\n * @constructor\r\n */\r\n\r\nclass Assembly extends BiologicalUnit {\r\n constructor(complex) {\r\n super(complex);\r\n this.chains = [];\r\n this.matrices = [];\r\n }\r\n\r\n computeBoundaries() {\r\n super.computeBoundaries();\r\n // fix up the boundaries\r\n const { matrices } = this;\r\n const oldCenter = this._boundaries.boundingSphere.center;\r\n const oldRad = this._boundaries.boundingSphere.radius;\r\n const boundingBox = this._boundaries.boundingBox = new THREE.Box3();\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = matrices.length; i < n; ++i) {\r\n boundingBox.expandByPoint(oldCenter.clone().applyMatrix4(matrices[i]));\r\n }\r\n\r\n const newRad = boundingBox.max.distanceTo(boundingBox.min) / 2 + oldRad;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n this._boundaries.boundingSphere = new THREE.Sphere().set(center, newRad);\r\n boundingBox.max.addScalar(oldRad);\r\n boundingBox.min.subScalar(oldRad);\r\n }\r\n\r\n /**\r\n * Mark a chain as belonging to this biological assembly.\r\n * @param {string} chain - chain identifier, usually a single letter\r\n */\r\n addChain(chain) {\r\n this.chains[this.chains.length] = chain;\r\n }\r\n\r\n /**\r\n * Add a transformation matrix.\r\n * @param {THREE.Matrix4} matrix - transformation matrix\r\n */\r\n addMatrix(matrix) {\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n getTransforms() {\r\n return this.matrices;\r\n }\r\n\r\n finalize() {\r\n if (this.chains.length > 0) {\r\n this._selector = selectors.keyword('Chain')(this.chains);\r\n } else {\r\n this._selector = selectors.keyword('None')();\r\n }\r\n }\r\n}\r\n\r\nexport default Assembly;\r\n","/**\r\n * This class represents connected component as a part of a complex.\r\n * WARNING! The whole component entity is build under the assumption that residues\r\n * are placed in the chains and complex in ascending order of indices\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n *\r\n * @exports Component\r\n * @constructor\r\n */\r\nclass Component {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._index = -1;\r\n this._residueIndices = [];\r\n this._cycles = [];\r\n this._subDivs = [];\r\n this._residueCount = 0;\r\n }\r\n\r\n getResidues() {\r\n return this._complex._residues;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residueCount;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._complex._residues;\r\n const resIdc = this._residueIndices;\r\n for (let idIdc = 0, idCount = resIdc.length; idIdc < idCount; ++idIdc) {\r\n for (let idx = resIdc[idIdc].start, last = resIdc[idIdc].end; idx <= last; ++idx) {\r\n process(residues[idx]);\r\n }\r\n }\r\n }\r\n\r\n setSubDivs(subDivs) {\r\n this._subDivs = subDivs;\r\n let curr = 0;\r\n const resIdc = [];\r\n let resCnt = 0;\r\n for (let i = 0, n = subDivs.length; i < n; ++i) {\r\n if (i === n - 1 || subDivs[i].end + 1 !== subDivs[i + 1].start) {\r\n const { start } = subDivs[curr];\r\n const { end } = subDivs[i];\r\n resIdc[resIdc.length] = {\r\n start,\r\n end,\r\n };\r\n resCnt += end - start + 1;\r\n curr = i + 1;\r\n }\r\n }\r\n\r\n this._residueIndices = resIdc;\r\n this._residueCount = resCnt;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._complex._bonds;\r\n\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue._component === this) {\r\n process(bond);\r\n }\r\n }\r\n }\r\n\r\n update() {\r\n this.forEachCycle((cycle) => {\r\n cycle.update();\r\n });\r\n }\r\n\r\n forEachAtom(process) {\r\n this.forEachResidue((residue) => {\r\n residue.forEachAtom(process);\r\n });\r\n }\r\n\r\n addCycle(cycle) {\r\n this._cycles.push(cycle);\r\n }\r\n\r\n forEachCycle(process) {\r\n const cycles = this._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n process(cycles[i]);\r\n }\r\n }\r\n\r\n markResidues() {\r\n const self = this;\r\n self.forEachResidue((residue) => {\r\n residue._component = self;\r\n });\r\n }\r\n\r\n _forEachSubChain(mask, process) {\r\n const residues = this._complex._residues;\r\n const subs = this._subDivs;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let idx = subs[i].start, last = subs[i].end; idx <= last; ++idx) {\r\n const currRes = residues[idx];\r\n if (mask & currRes._mask && currRes._isValid) {\r\n let end = idx + 1;\r\n for (; end <= last; ++end) {\r\n const endRes = residues[end];\r\n if (!(mask & endRes._mask && endRes._isValid)) {\r\n break;\r\n }\r\n }\r\n process(i, idx, end - 1);\r\n idx = end;\r\n }\r\n }\r\n }\r\n }\r\n\r\n getMaskedSequences(mask) {\r\n const subs = [];\r\n let idx = 0;\r\n this._forEachSubChain(mask, (_subIdx, start, end) => {\r\n subs[idx++] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n\r\n getMaskedSubdivSequences(mask) {\r\n const subs = [];\r\n let currIdx = -1;\r\n let lastSubIdx = -1;\r\n const subDivs = this._subDivs;\r\n\r\n this._forEachSubChain(mask, (subIdx, start, end) => {\r\n if (lastSubIdx !== subIdx) {\r\n ++currIdx;\r\n subs[currIdx] = {\r\n arr: [],\r\n boundaries: subDivs[subIdx],\r\n };\r\n lastSubIdx = subIdx;\r\n }\r\n subs[currIdx].arr[subs[currIdx].arr.length] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n}\r\n\r\nexport default Component;\r\n","import utils from '../utils';\r\n\r\nconst cMaxPairsForHashCode = 32;\r\nconst cHashTableSize = 1024 * 1024;\r\nconst cNumbersPerPair = 4;\r\nconst cMaxNeighbours = 14;\r\nconst cInvalidVal = -1;\r\n// 89237 is a large simple number, can be used for pseudo random hash code create\r\nconst cBigPrime = 89237;\r\n\r\nclass AtomPairs {\r\n constructor(maxPairsEstimate) {\r\n this.numPairs = 0;\r\n this.numMaxPairs = maxPairsEstimate;\r\n this.intBuffer = utils.allocateTyped(Int32Array, maxPairsEstimate * cNumbersPerPair);\r\n for (let i = 0; i < maxPairsEstimate * cNumbersPerPair; i++) {\r\n this.intBuffer[i] = cInvalidVal;\r\n }\r\n this.hashBuffer = utils.allocateTyped(Int32Array, cHashTableSize * cMaxPairsForHashCode);\r\n for (let i = 0; i < cHashTableSize * cMaxPairsForHashCode; i++) {\r\n this.hashBuffer[i] = cInvalidVal;\r\n }\r\n }\r\n\r\n /**\r\n * Destroy all pairs memory\r\n */\r\n destroy() {\r\n this.intBuffer = null;\r\n this.hashBuffer = null;\r\n }\r\n\r\n /**\r\n * Add pair of atoms to collection\r\n * @param {number} indexA - Index of the 1st vertex.\r\n * @param {number} indexB - Index of the 2nd vertex.\r\n */\r\n addPair(indexA, indexB) {\r\n const ia = (indexA < indexB) ? indexA : indexB;\r\n const ib = (indexA > indexB) ? indexA : indexB;\r\n const codeToAdd = ia + (ib << cMaxNeighbours);\r\n\r\n const hashCode = (ia + (ib * cBigPrime)) & (cHashTableSize - 1);\r\n let j = hashCode * cMaxPairsForHashCode;\r\n let apI = 0;\r\n for (; apI < cMaxPairsForHashCode; apI++) {\r\n const code = this.hashBuffer[j + apI];\r\n if (code === cInvalidVal) {\r\n break;\r\n }\r\n if (code === codeToAdd) {\r\n return false;\r\n }\r\n }\r\n // add this new hash code\r\n if (apI >= cMaxPairsForHashCode) {\r\n throw new Error('addPair: increase cMaxPairsForHashCode');\r\n }\r\n this.hashBuffer[j + apI] = codeToAdd;\r\n\r\n // actually add\r\n if (this.numPairs >= this.numMaxPairs) {\r\n throw new Error('addPair: increase num pairs');\r\n }\r\n j = this.numPairs * cNumbersPerPair;\r\n this.intBuffer[j] = ia;\r\n this.intBuffer[j + 1] = ib;\r\n this.intBuffer[j + 2] = codeToAdd;\r\n this.numPairs++;\r\n return true;\r\n }\r\n}\r\n\r\nexport default AtomPairs;\r\n","import AtomPairs from './AtomPairs';\r\nimport Bond from './Bond';\r\n\r\nconst cProfileBondBuilder = false;\r\nconst cEstBondsMultiplier = 4;\r\nconst cSpaceCode = 32;\r\nconst cBondTolerance = 0.45;\r\nconst cVMDTolerance = 0.6;\r\nconst cBondRadInJMOL = true;\r\nconst cEpsilon = 0.001;\r\n\r\n/**\r\n * Get radius used for building bonds.\r\n *\r\n * @param {Atom} atom - Atom object.\r\n * @returns {number} special value for bonding radius for this atom\r\n */\r\nfunction _getBondingRadius(atom) {\r\n const { element } = atom;\r\n if (element) {\r\n return element.radiusBonding;\r\n }\r\n throw new Error('_getBondingRadius: Logic error.');\r\n}\r\n\r\nfunction _isAtomEligible(atom) {\r\n // build for all non-hetatm and for hetatm without bonds\r\n return !atom.isHet() || (atom.bonds && atom.bonds.length === 0);\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Complex} complex molecular complex\r\n\r\n * @exports AutoBond\r\n * @constructor\r\n */\r\nclass AutoBond {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._maxRad = 1.8;\r\n const bBox = this._complex.getDefaultBoundaries().boundingBox;\r\n this._vBoxMin = bBox.min.clone();\r\n this._vBoxMax = bBox.max.clone();\r\n\r\n this._pairCollection = null;\r\n }\r\n\r\n /**\r\n * Add existing pairs of connectors (from pdb file after its reading)\r\n * @returns {number} 0\r\n */\r\n _addExistingPairs() {\r\n const atoms = this._complex.getAtoms();\r\n const numAtoms = atoms.length;\r\n let aInd = 0;\r\n const collection = this._pairCollection;\r\n\r\n for (; aInd < numAtoms; aInd++) {\r\n const { bonds } = atoms[aInd];\r\n const numBondsForAtom = bonds.length;\r\n for (let bInd = 0; bInd < numBondsForAtom; bInd++) {\r\n const bond = bonds[bInd];\r\n const indTo = bond._left.index;\r\n if (indTo === aInd) {\r\n collection.addPair(aInd, bond._right.index);\r\n }\r\n } // for (b) all bonds in atom\r\n } // for (a)\r\n return 0;\r\n }\r\n\r\n _findPairs() {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const atoms = this._complex._atoms;\r\n const atomsNum = atoms.length;\r\n const self = this;\r\n\r\n let rA;\r\n let isHydrogenA;\r\n let posA;\r\n let locationA;\r\n let atomA;\r\n\r\n const processAtom = function (atomB) {\r\n if (isHydrogenA && atomB.isHydrogen()) {\r\n return;\r\n }\r\n\r\n const locationB = atomB.location;\r\n if ((locationA !== cSpaceCode)\r\n && (locationB !== cSpaceCode)\r\n && (locationA !== locationB)) {\r\n return;\r\n }\r\n\r\n const dist2 = posA.distanceToSquared(atomB.position);\r\n const rB = atomB.element.radiusBonding;\r\n const maxAcceptable = cBondRadInJMOL ? rA + rB + cBondTolerance : cVMDTolerance * (rA + rB);\r\n\r\n if (dist2 > (maxAcceptable * maxAcceptable)) {\r\n return;\r\n }\r\n\r\n if (dist2 < cEpsilon) {\r\n return;\r\n }\r\n\r\n self._pairCollection.addPair(atomA.index, atomB.index);\r\n };\r\n\r\n for (let i = 0; i < atomsNum; ++i) {\r\n atomA = atoms[i];\r\n if (!_isAtomEligible(atomA)) {\r\n continue;\r\n }\r\n\r\n rA = atomA.element.radiusBonding;\r\n isHydrogenA = atomA.isHydrogen();\r\n posA = atomA.position;\r\n locationA = atomA.location;\r\n\r\n vw.forEachAtomWithinRadius(posA, 2 * this._maxRad + cBondTolerance, processAtom);\r\n }\r\n }\r\n\r\n _addPairs() {\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0, k = 0; i < this._pairCollection.numPairs; i++, k += 4) {\r\n const iA = this._pairCollection.intBuffer[k];\r\n const iB = this._pairCollection.intBuffer[k + 1];\r\n this._addPair(atoms[iA], atoms[iB]);\r\n }\r\n }\r\n\r\n _addPair(atomA, atomB) {\r\n const bondsA = atomA.bonds;\r\n const indexA = atomA.index;\r\n const indexB = atomB.index;\r\n for (let j = 0, numBonds = bondsA.length; j < numBonds; ++j) {\r\n const bond = bondsA[j];\r\n if (bond._left.index === indexB || bond._right.index === indexB) {\r\n return;\r\n }\r\n }\r\n const left = indexA < indexB ? atomA : atomB;\r\n const right = indexA < indexB ? atomB : atomA;\r\n const newBond = this._complex.addBond(left, right, 0, Bond.BondType.UNKNOWN, false);\r\n bondsA.push(newBond);\r\n atomB.bonds.push(newBond);\r\n }\r\n\r\n build() {\r\n if (cProfileBondBuilder) {\r\n console.time('Bonds Builder');\r\n }\r\n this._buildInner();\r\n\r\n if (cProfileBondBuilder) {\r\n console.timeEnd('Bonds Builder');\r\n }\r\n }\r\n\r\n _buildInner() {\r\n const atoms = this._complex._atoms;\r\n if (atoms.length < 2) {\r\n return;\r\n }\r\n if (atoms[0].index < 0) {\r\n throw new Error('AutoBond: Atoms in complex were not indexed.');\r\n }\r\n\r\n this._calcBoundingBox();\r\n this._pairCollection = new AtomPairs(atoms.length * cEstBondsMultiplier);\r\n this._addExistingPairs();\r\n this._findPairs();\r\n this._addPairs();\r\n }\r\n\r\n _calcBoundingBox() {\r\n const atoms = this._complex._atoms;\r\n const nAtoms = atoms.length;\r\n let maxRad = _getBondingRadius(atoms[0]);\r\n for (let i = 1; i < nAtoms; ++i) {\r\n maxRad = Math.max(maxRad, _getBondingRadius(atoms[i]));\r\n }\r\n this._vBoxMax.addScalar(maxRad);\r\n this._vBoxMin.addScalar(-maxRad);\r\n this._maxRad = maxRad * 1.2;\r\n }\r\n\r\n destroy() {\r\n if (this._pairCollection) {\r\n this._pairCollection.destroy();\r\n }\r\n }\r\n}\r\n\r\nexport default AutoBond;\r\n","import * as THREE from 'three';\r\nimport Bond from './Bond';\r\nimport Element from './Element';\r\n\r\nconst cCrossThresh = 0.1;\r\nconst cAromaticType = Bond.BondType.AROMATIC;\r\nconst cAromaticAtoms = [\r\n Element.ByName.C.number,\r\n Element.ByName.N.number,\r\n // Element.ByName.O.number,\r\n // Element.ByName.S.number,\r\n];\r\n\r\n/** Conditions for bonds:\r\n * - Cross product with each subsequent bond to add is collinear and point to the same direction\r\n * - Each pair of a adjacent bonds belong to not more than one cycle\r\n * - If there is more than one candidates we try them in ascending order of angle values\r\n */\r\n\r\nconst _coDirVectors = (function () {\r\n const v1Tmp = new THREE.Vector3();\r\n const v2Tmp = new THREE.Vector3();\r\n const cp = new THREE.Vector3();\r\n return function (v1, v2) {\r\n v1Tmp.copy(v1).normalize();\r\n v2Tmp.copy(v2).normalize();\r\n cp.crossVectors(v1Tmp, v2Tmp);\r\n if (cp.length() > cCrossThresh) {\r\n return false;\r\n }\r\n // zero vector in out terms must be collinear to any\r\n return v1Tmp.dot(v2Tmp) >= 0;\r\n };\r\n}());\r\n\r\nfunction _insertAscending(arr, val) {\r\n let idx = 0;\r\n while (idx < arr.length && arr[idx] < val) {\r\n ++idx;\r\n }\r\n arr.splice(idx, 0, val);\r\n}\r\n\r\nfunction _anotherAtom(bond, currAtom) {\r\n return bond._left === currAtom ? bond._right : bond._left;\r\n}\r\n\r\nfunction _cosBetween(v1, v2) {\r\n const theta = v1.dot(v2) / (Math.sqrt(v1.lengthSq() * v2.lengthSq()));\r\n return THREE.MathUtils.clamp(theta, -1, 1);\r\n}\r\n\r\nfunction _markAromatic(bond) {\r\n bond._type = cAromaticType;\r\n}\r\n\r\nclass Cycle {\r\n constructor(atomsList) {\r\n this.atoms = atomsList;\r\n this.update();\r\n }\r\n\r\n update() {\r\n const { atoms } = this;\r\n const center = new THREE.Vector3();\r\n const nA = atoms.length;\r\n for (let j = 0; j < nA; ++j) {\r\n center.add(atoms[j].position);\r\n }\r\n center.multiplyScalar(1.0 / nA);\r\n this.center = center;\r\n this.radius = center.distanceTo(atoms[0].position.clone().lerp(atoms[1].position, 0.5));\r\n }\r\n\r\n forEachBond(process) {\r\n const { atoms } = this;\r\n const nA = atoms.length;\r\n let currAtom = atoms[0];\r\n let nextAtom;\r\n\r\n function checkBond(bond) {\r\n if (bond._left === nextAtom || bond._right === nextAtom) {\r\n process(bond);\r\n }\r\n }\r\n\r\n for (let i = 0; i < nA; ++i) {\r\n nextAtom = atoms[(i + 1) % nA];\r\n currAtom.forEachBond(checkBond);\r\n currAtom = nextAtom;\r\n }\r\n }\r\n}\r\n\r\nfunction _isAromatic(bond) {\r\n return bond._type === cAromaticType;\r\n}\r\n\r\nfunction _isPossibleAromatic(bond) {\r\n if (bond.type === cAromaticType) {\r\n return true;\r\n }\r\n const rightIdx = cAromaticAtoms.indexOf(bond._right.element.number);\r\n const leftIdx = cAromaticAtoms.indexOf(bond._left.element.number);\r\n return rightIdx !== -1 && leftIdx !== -1;\r\n}\r\n\r\nfunction _checkCycleSimple(cycle) {\r\n return cycle.length > 3;\r\n}\r\n\r\nfunction _checkCycleComplex(cycle) {\r\n console.assert(cycle.length > 2);\r\n return true;\r\n}\r\n\r\nclass AromaticLoopsMarker {\r\n constructor(complex) {\r\n this._complex = complex;\r\n const bondsData = new Array(complex._bonds.length);\r\n const bondMarks = new Array(complex._bonds.length);\r\n for (let i = 0, n = bondsData.length; i < n; ++i) {\r\n bondsData[i] = [];\r\n bondMarks[i] = false;\r\n }\r\n this._bondsData = bondsData;\r\n this._bondMarks = bondMarks;\r\n this._resetCycles();\r\n }\r\n\r\n _resetCycles() {\r\n this._cycles = [];\r\n this._currIdx = -1;\r\n }\r\n\r\n _haveSameCycle(bondsData, bond1, bond2) {\r\n const arr1 = bondsData[bond1._index];\r\n const arr2 = bondsData[bond2._index];\r\n const n1 = arr1.length;\r\n const n2 = arr2.length;\r\n let i1 = 0;\r\n let i2 = 0;\r\n while (i1 < n1 && i2 < n2) {\r\n if (arr1[i1] === arr2[i2]) {\r\n return true;\r\n }\r\n if (arr1[i1] > arr2[i2]) {\r\n ++i2;\r\n } else {\r\n ++i1;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _tryBond(prevBond, currRight, currDir) {\r\n const bondsOrder = [];\r\n const bondsData = this._bondsData;\r\n const currLeft = _anotherAtom(prevBond, currRight);\r\n const currVec = currRight.position.clone().sub(currLeft.position);\r\n const startAtomRef = this._currStart;\r\n const self = this;\r\n const bondMarks = this._bondMarks;\r\n let checkAromatic = this._checkBond;\r\n bondMarks[prevBond._index] = true;\r\n checkAromatic = checkAromatic === undefined ? _isAromatic : checkAromatic;\r\n currRight.forEachBond((newBond) => {\r\n if (!checkAromatic(newBond)\r\n || newBond === prevBond\r\n || bondMarks[newBond._index]\r\n || self._haveSameCycle(bondsData, prevBond, newBond)) {\r\n return;\r\n }\r\n const anotherAtom = _anotherAtom(newBond, currRight);\r\n const anotherVec = anotherAtom.position.clone().sub(currRight.position);\r\n const val = anotherAtom === startAtomRef ? -2.0 : 1 - _cosBetween(currVec, anotherVec);\r\n const newDir = anotherVec.cross(currVec);\r\n if (!_coDirVectors(newDir, currDir)) {\r\n return;\r\n }\r\n let idx = 0;\r\n while (idx < bondsOrder.length && bondsOrder[idx].val < val) {\r\n ++idx;\r\n }\r\n bondsOrder.splice(idx, 0, { bond: newBond, val, dir: newDir });\r\n });\r\n\r\n for (let i = 0, n = bondsOrder.length; i < n; ++i) {\r\n const { bond } = bondsOrder[i];\r\n const newRight = bond._left === currRight ? bond._right : bond._left;\r\n if (newRight === startAtomRef) {\r\n ++this._currIdx;\r\n this._cycles.push([currRight]);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n if (this._tryBond(bond, newRight, bondsOrder[i].dir)) {\r\n _insertAscending(bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(currRight);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n }\r\n bondMarks[prevBond._index] = false;\r\n return false;\r\n }\r\n\r\n _startCycle(bond) {\r\n // start from left to right\r\n this._currStart = bond._left;\r\n if (this._tryBond(bond, bond._right, new THREE.Vector3())) {\r\n _insertAscending(this._bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(bond._left);\r\n }\r\n }\r\n\r\n _findLoops(checkBond, checkCycle) {\r\n this._checkBond = checkBond;\r\n const complex = this._complex;\r\n const self = this;\r\n\r\n complex.forEachComponent((component) => {\r\n self._resetCycles();\r\n component.forEachBond((bond) => {\r\n if (checkBond(bond)) {\r\n self._startCycle(bond);\r\n }\r\n });\r\n const cycles = self._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n const cycle = cycles[i];\r\n if (!checkCycle(cycle)) {\r\n continue;\r\n }\r\n const newCycle = new Cycle(cycle);\r\n newCycle.forEachBond(_markAromatic);\r\n component.addCycle(newCycle);\r\n }\r\n });\r\n }\r\n\r\n markCycles() {\r\n this._findLoops(_isAromatic, _checkCycleSimple);\r\n }\r\n\r\n detectCycles() {\r\n this._findLoops(_isPossibleAromatic, _checkCycleComplex);\r\n }\r\n}\r\n\r\nexport default AromaticLoopsMarker;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\n/**\r\n * Calculate min & max radius of a sphere slice between zMin & zMax\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {number} zMin - lower bound of the slice\r\n * @param {number} zMax - upper bound of the slice\r\n */\r\nfunction _getSphereSliceRadiusRange(center, radius, zMin, zMax) {\r\n const dzMin = zMin - center.z;\r\n const dzMax = zMax - center.z;\r\n const rzMin = Math.sqrt(Math.max(radius * radius - dzMin * dzMin, 0.0));\r\n const rzMax = Math.sqrt(Math.max(radius * radius - dzMax * dzMax, 0.0));\r\n\r\n const rMin = Math.min(rzMin, rzMax);\r\n let rMax;\r\n\r\n if (zMin <= center.z && zMax >= center.z) {\r\n // sphere's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(rzMin, rzMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * Calculate min & max radius of a circle slice between yMin & yMax.\r\n *\r\n * To maintain analogy with _getSphereSliceRadiusRange we call radius what in fact is\r\n * half-width (along X axis) of the slice, i.e. 1D-sphere radius.\r\n *\r\n * @param {Vector3} center - center of the circle (z can be ignored)\r\n * @param {number} radius - circle radius\r\n * @param {number} yMin - lower bound of the slice\r\n * @param {number} yMax - upper bound of the slice\r\n * @returns {Array} - array of two numbers (min & max radius, or half-width)\r\n */\r\nfunction _getCircleSliceRadiusRange(center, radius, yMin, yMax) {\r\n const dyMin = yMin - center.y;\r\n const dyMax = yMax - center.y;\r\n const ryMin = Math.sqrt(Math.max(radius * radius - dyMin * dyMin, 0.0));\r\n const ryMax = Math.sqrt(Math.max(radius * radius - dyMax * dyMax, 0.0));\r\n\r\n const rMin = Math.min(ryMin, ryMax);\r\n let rMax;\r\n\r\n if (yMin <= center.y && yMax >= center.y) {\r\n // slice's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(ryMin, ryMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * VoxelWorld constructor\r\n *\r\n * @param {Box3} box - bounding box of the volume to be partitioned\r\n * @param {Vector3} vCellSizeHint - target voxel size (actual voxel size may differ from this)\r\n */\r\nclass VoxelWorld {\r\n constructor(box, vCellSizeHint) {\r\n this._box = box.clone();\r\n const size = new THREE.Vector3();\r\n box.getSize(size);\r\n this._count = size.clone().divide(vCellSizeHint).floor().max(new THREE.Vector3(1, 1, 1));\r\n this._last = this._count.clone().subScalar(1);\r\n this._cellSize = size.clone().divide(this._count);\r\n this._cellInnerR = 0.5 * Math.min(Math.min(this._cellSize.x, this._cellSize.y), this._cellSize.z);\r\n this._cellOuterR = 0.5 * Math.sqrt(this._cellSize.dot(this._cellSize));\r\n\r\n // array of voxels, each element contains index of first atom in voxel\r\n const numVoxels = this._count.x * this._count.y * this._count.z;\r\n this._voxels = utils.allocateTyped(Int32Array, numVoxels);\r\n for (let i = 0; i < numVoxels; ++i) {\r\n this._voxels[i] = -1;\r\n }\r\n\r\n // array of atoms that stores multiple single-linked lists\r\n // two elements for each atom: Atom ref, index of next atom (in this array\r\n this._atoms = [];\r\n }\r\n\r\n /**\r\n * Add all atoms from a complex to voxel world\r\n *\r\n * @param {Complex} complex - complex\r\n */\r\n addAtoms(complex) {\r\n const self = this;\r\n\r\n let idx = this._atoms.length;\r\n\r\n // resize array of atoms\r\n this._atoms.length += 2 * complex.getAtomCount();\r\n\r\n complex.forEachAtom((atom) => {\r\n // find which voxel contains this atom\r\n const voxelIdx = self._findVoxel(atom.position);\r\n\r\n // push current atom to the head of voxel's atom list\r\n self._atoms[idx] = atom;\r\n self._atoms[idx + 1] = self._voxels[voxelIdx];\r\n self._voxels[voxelIdx] = idx;\r\n\r\n idx += 2;\r\n });\r\n }\r\n\r\n /**\r\n * Get voxel that contains specified 3D point (we use clamp at the edges)\r\n *\r\n * @param {Vector3} point - a point in 3D\r\n * @returns {number} - index of voxel\r\n */\r\n static _zero = new THREE.Vector3(0, 0, 0);\r\n\r\n static _voxel = new THREE.Vector3();\r\n\r\n _findVoxel(point) {\r\n const zero = VoxelWorld._zero;\r\n const voxel = VoxelWorld._voxel;\r\n voxel.copy(point)\r\n .sub(this._box.min)\r\n .divide(this._cellSize)\r\n .floor()\r\n .clamp(zero, this._last);\r\n return voxel.x + this._count.x * (voxel.y + this._count.y * voxel.z);\r\n }\r\n\r\n /**\r\n * Call a function for each atom in voxel\r\n *\r\n * @param {number} voxel - index of voxel\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomInVoxel(voxel, process) {\r\n for (let i = this._voxels[voxel]; i >= 0; i = this._atoms[i + 1]) {\r\n process(this._atoms[i]);\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _xRange = new THREE.Vector2();\r\n\r\n static _yRange = new THREE.Vector2();\r\n\r\n static _zRange = new THREE.Vector2();\r\n\r\n _forEachVoxelWithinRadius(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n\r\n // switch to a faster method unless cell size is much smaller than sphere radius\r\n if (radius / this._cellInnerR < 10) {\r\n this._forEachVoxelWithinRadiusSimple(center, radius, process);\r\n return;\r\n }\r\n\r\n let rRangeXY;\r\n let rRangeX;\r\n let xVal;\r\n let yVal;\r\n let zVal;\r\n let isInsideX;\r\n let isInsideY;\r\n let isInsideZ;\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor()\r\n .clampScalar(0, this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n\r\n isInsideZ = (center.z - radius <= zVal[0]) && (zVal[1] <= center.z + radius);\r\n\r\n rRangeXY = _getSphereSliceRadiusRange(center, radius, zVal[0], zVal[1]);\r\n\r\n yRange.set(center.y - rRangeXY[1], center.y + rRangeXY[1]);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor()\r\n .clampScalar(0, this._count.y - 1);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n\r\n isInsideY = (center.y - rRangeXY[0] <= yVal[0]) && (yVal[1] <= center.y + rRangeXY[0]);\r\n\r\n rRangeX = _getCircleSliceRadiusRange(center, rRangeXY[1], yVal[0], yVal[1]);\r\n\r\n xRange.set(center.x - rRangeX[1], center.x + rRangeX[1]);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor()\r\n .clampScalar(0, this._count.x - 1);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n isInsideX = (center.x - rRangeX[0] <= xVal[0]) && (xVal[1] <= center.x + rRangeX[0]);\r\n\r\n process(x + this._count.x * (y + this._count.y * z), isInsideX && isInsideY && isInsideZ);\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n * This is a version of method that doesn't try to \"calculate\" what voxels fall inside radius\r\n * but instead just checks all voxels inside sphere's bounding box. This should be faster\r\n * unless cell size is much smaller than sphere radius.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _vCenter = new THREE.Vector3();\r\n\r\n _forEachVoxelWithinRadiusSimple(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n const vCenter = VoxelWorld._vCenter;\r\n\r\n const distTouch2 = (radius + this._cellOuterR) * (radius + this._cellOuterR);\r\n let distInside2 = -1.0;\r\n if (radius > this._cellOuterR) {\r\n distInside2 = (radius - this._cellOuterR) * (radius - this._cellOuterR);\r\n }\r\n\r\n // calculate bounding box for the sphere\r\n xRange.set(center.x - radius, center.x + radius);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor();\r\n xRange.x = Math.min(Math.max(xRange.x, 0), this._count.x - 1);\r\n xRange.y = Math.min(Math.max(xRange.y, 0), this._count.x - 1);\r\n\r\n yRange.set(center.y - radius, center.y + radius);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor();\r\n yRange.x = Math.min(Math.max(yRange.x, 0), this._count.y - 1);\r\n yRange.y = Math.min(Math.max(yRange.y, 0), this._count.y - 1);\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor();\r\n zRange.x = Math.min(Math.max(zRange.x, 0), this._count.z - 1);\r\n zRange.y = Math.min(Math.max(zRange.y, 0), this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n const zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n vCenter.z = 0.5 * (zVal[0] + zVal[1]);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n const yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n vCenter.y = 0.5 * (yVal[0] + yVal[1]);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n const xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n vCenter.x = 0.5 * (xVal[0] + xVal[1]);\r\n\r\n const d2 = center.distanceToSquared(vCenter);\r\n if (d2 <= distTouch2) {\r\n process(x + this._count.x * (y + this._count.y * z), d2 <= distInside2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each atom within given sphere\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinRadius(center, radius, process) {\r\n const self = this;\r\n const r2 = radius * radius;\r\n\r\n self._forEachVoxelWithinRadius(center, radius, (voxel, isInside) => {\r\n if (isInside) {\r\n self._forEachAtomInVoxel(voxel, process);\r\n } else {\r\n self._forEachAtomInVoxel(voxel, (atom) => {\r\n if (center.distanceToSquared(atom.position) <= r2) {\r\n process(atom);\r\n }\r\n });\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by mask\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} mask - bit mask\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromMasked(complex, mask, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by selector\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} selector - selector\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromSelected(complex, selector, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms\r\n *\r\n * @param {function} forEachAtom - enumerator of atoms in the group\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomWithinDistFromGroup(forEachAtom, dist, process) {\r\n const self = this;\r\n const r2 = dist * dist;\r\n\r\n const voxels = [];\r\n const atoms = [];\r\n let idx = 0;\r\n\r\n // build \"within radius\" atom list for each voxel\r\n forEachAtom((atom) => {\r\n self._forEachVoxelWithinRadius(atom.position, dist, (voxel, isInside) => {\r\n if (isInside) {\r\n // this voxel is inside circle -- no check will be required\r\n voxels[voxel] = -1;\r\n } else if (typeof voxels[voxel] === 'undefined') {\r\n // this voxel isn't covered yet -- start building list of atoms\r\n atoms.push(atom);\r\n atoms.push(-1);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n } else if (voxels[voxel] !== -1) {\r\n // this voxel has a list of atoms required for distance check -- add atom to the list\r\n atoms.push(atom);\r\n atoms.push(voxels[voxel]);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n }\r\n });\r\n });\r\n\r\n let voxel;\r\n\r\n const processIfWithin = function (atom) {\r\n if (typeof voxels[voxel] === 'undefined') {\r\n return;\r\n }\r\n\r\n idx = voxels[voxel];\r\n if (idx === -1) {\r\n // this voxel is fully covered\r\n process(atom);\r\n return;\r\n }\r\n\r\n // check distance to each atom within radius from this voxel\r\n for (; idx >= 0; idx = atoms[idx + 1]) {\r\n if (atom.position.distanceToSquared(atoms[idx].position) < r2) {\r\n process(atom);\r\n break;\r\n }\r\n }\r\n };\r\n\r\n // for each marked voxel\r\n for (voxel in voxels) {\r\n if (voxels.hasOwnProperty(voxel)) {\r\n self._forEachAtomInVoxel(voxel, processIfWithin);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default VoxelWorld;\r\n","import ResidueType from './ResidueType';\r\nimport PairCollection from './AtomPairs';\r\n\r\nconst MINIMAL_DISTANCE = 0.5;\r\nconst MIN_HBOND_ENERGY = -9.9;\r\nconst MAX_HBOND_ENERGY = -0.5;\r\nconst COUPLING_CONSTANT = -27.888; // = -332 * 0.42 * 0.2\r\nconst MAX_COUPLING_DISTANCE = 5.0; // how far is the closest atom of a potential partner residue from CA atom\r\nconst MAX_RESIDUES_THRESHOLD = 1000;\r\n\r\nexport default class HBondInfo {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._hbonds = []; // array of bond info for each residue\r\n if (this._complex._residues.length > MAX_RESIDUES_THRESHOLD) {\r\n this._buildVW(); // optimized version using voxel grid\r\n } else {\r\n this._build(); // test all pairs of residues\r\n }\r\n }\r\n\r\n isBond(from, to) {\r\n if (this._hbonds[from]) {\r\n const [acc0, acc1] = this._hbonds[from].acceptor;\r\n if (acc0 && acc0.residue === to && acc0.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n if (acc1 && acc1.residue === to && acc1.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n\r\n for (let i = 0; i < this._complex._residues.length - 1; ++i) {\r\n const ri = this._complex._residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let preri = null;\r\n if (i > 0 && (this._complex._residues[i - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && ri._sequence === this._complex._residues[i - 1]._sequence + 1) {\r\n preri = this._complex._residues[i - 1];\r\n }\r\n\r\n for (let j = i + 1; j < this._complex._residues.length; ++j) {\r\n const rj = this._complex._residues[j];\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = null;\r\n if ((this._complex._residues[j - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && rj._sequence === this._complex._residues[j - 1]._sequence + 1) {\r\n prerj = this._complex._residues[j - 1];\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (j !== i + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _buildVW() {\r\n const self = this;\r\n const residues = this._complex._residues;\r\n let ri;\r\n let preri;\r\n\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const pairs = new PairCollection(this._complex._residues.length * this._complex._residues.length / 2);\r\n\r\n function processAtom(atom) {\r\n const rj = atom.residue;\r\n\r\n if (rj._index === ri._index) {\r\n return;\r\n }\r\n\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n return;\r\n }\r\n\r\n if (!pairs.addPair(ri._index, rj._index)) {\r\n // we've seen this pair\r\n return;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = rj._index > 0 ? residues[rj._index - 1] : null;\r\n if (prerj\r\n && ((prerj.getType().flags & ResidueType.Flags.PROTEIN) === 0 || rj._sequence !== prerj._sequence + 1)) {\r\n prerj = null;\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (rj._index !== ri._index + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n\r\n for (let i = 0; i < residues.length - 1; ++i) {\r\n ri = residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n preri = i > 0 ? residues[i - 1] : null;\r\n if (preri\r\n && ((preri.getType().flags & ResidueType.Flags.PROTEIN) === 0 || ri._sequence !== preri._sequence + 1)) {\r\n preri = null;\r\n }\r\n\r\n vw.forEachAtomWithinRadius(this._residueGetCAlpha(ri), MAX_COUPLING_DISTANCE, processAtom);\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _residueGetCO(res) {\r\n let c = null;\r\n let o = null;\r\n\r\n res.forEachAtom((a) => {\r\n if (a.name === 'C') {\r\n c = a.position;\r\n } else if (a.name === 'O') {\r\n o = a.position;\r\n }\r\n });\r\n\r\n return [c, o];\r\n }\r\n\r\n // TODO Support hydrogen defined in complex\r\n _residueGetNH(prev, res) {\r\n const [c, o] = this._residueGetCO(prev);\r\n\r\n let n;\r\n res.forEachAtom((a) => {\r\n if (a.name === 'N') {\r\n n = a.position;\r\n }\r\n });\r\n\r\n if (c && o && n) {\r\n // calculate hydrogen position\r\n const h = c.clone();\r\n h.sub(o);\r\n h.multiplyScalar(1.0 / h.length());\r\n h.add(n);\r\n\r\n return [n, h];\r\n }\r\n\r\n return [null, null];\r\n }\r\n\r\n _calcHBondEnergy(predonor, donor, acceptor) {\r\n let result = 0;\r\n\r\n if (predonor === null) {\r\n return result;\r\n }\r\n\r\n if (donor.getType().getName() !== 'PRO') {\r\n const [n, h] = this._residueGetNH(predonor, donor);\r\n const [c, o] = this._residueGetCO(acceptor);\r\n\r\n if (n === null || h === null || c === null || o === null) {\r\n return result;\r\n }\r\n\r\n const distanceHO = h.distanceTo(o);\r\n const distanceHC = h.distanceTo(c);\r\n const distanceNC = n.distanceTo(c);\r\n const distanceNO = n.distanceTo(o);\r\n\r\n if (distanceHO < MINIMAL_DISTANCE || distanceHC < MINIMAL_DISTANCE\r\n || distanceNC < MINIMAL_DISTANCE || distanceNO < MINIMAL_DISTANCE) {\r\n result = MIN_HBOND_ENERGY;\r\n } else {\r\n result = COUPLING_CONSTANT / distanceHO - COUPLING_CONSTANT / distanceHC\r\n + COUPLING_CONSTANT / distanceNC - COUPLING_CONSTANT / distanceNO;\r\n }\r\n\r\n // DSSP compatibility mode:\r\n result = Math.round(result * 1000) / 1000;\r\n\r\n if (result < MIN_HBOND_ENERGY) {\r\n result = MIN_HBOND_ENERGY;\r\n }\r\n }\r\n\r\n // update donor\r\n if (typeof this._hbonds[donor._index] === 'undefined') {\r\n this._hbonds[donor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const donorInfo = this._hbonds[donor._index];\r\n\r\n if (donorInfo.acceptor.length < 2) {\r\n donorInfo.acceptor.push({\r\n residue: acceptor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (donorInfo.acceptor.length > 1) {\r\n if (result < donorInfo.acceptor[0].energy) {\r\n donorInfo.acceptor[1].residue = donorInfo.acceptor[0].residue;\r\n donorInfo.acceptor[1].energy = donorInfo.acceptor[0].energy;\r\n donorInfo.acceptor[0].residue = acceptor._index;\r\n donorInfo.acceptor[0].energy = result;\r\n } else if (result < donorInfo.acceptor[1].energy) {\r\n donorInfo.acceptor[1].residue = acceptor._index;\r\n donorInfo.acceptor[1].energy = result;\r\n }\r\n }\r\n\r\n // update acceptor\r\n if (typeof this._hbonds[acceptor._index] === 'undefined') {\r\n this._hbonds[acceptor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const accInfo = this._hbonds[acceptor._index];\r\n\r\n if (accInfo.donor.length < 2) {\r\n accInfo.donor.push({\r\n residue: donor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (accInfo.donor.length > 1) {\r\n if (result < accInfo.donor[0].energy) {\r\n accInfo.donor[1].residue = accInfo.donor[0].residue;\r\n accInfo.donor[1].energy = accInfo.donor[0].energy;\r\n accInfo.donor[0].residue = donor._index;\r\n accInfo.donor[0].energy = result;\r\n } else if (result < accInfo.donor[1].energy) {\r\n accInfo.donor[1].residue = donor._index;\r\n accInfo.donor[1].energy = result;\r\n }\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n","import HBondInfo from './HBondInfo';\r\nimport ResidueType from './ResidueType';\r\n\r\nconst BridgeType = Object.freeze({\r\n NO_BRIDGE: 0,\r\n PARALLEL: 1,\r\n ANTI_PARALLEL: 2,\r\n});\r\n\r\nconst HelixFlag = Object.freeze({\r\n START: 1,\r\n MIDDLE: 2,\r\n END: 3,\r\n START_AND_END: 4,\r\n});\r\n\r\nconst StructureType = Object.freeze({\r\n STRAND: 'E',\r\n BRIDGE: 'B',\r\n HELIX_310: 'G',\r\n HELIX_ALPHA: 'H',\r\n HELIX_PI: 'I',\r\n TURN: 'T',\r\n BEND: 'S',\r\n LOOP: ' ',\r\n});\r\n\r\nexport default class SecondaryStructureMap {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._build();\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n this._hbonds = new HBondInfo(this._complex);\r\n this._ss = []; // DSSP map by residue\r\n\r\n // auxilliary data\r\n this._sheet = [];\r\n this._betaPartners = [];\r\n this._bend = [];\r\n for (let i = 0; i < this._complex.getResidues().length; ++i) {\r\n this._betaPartners[i] = [];\r\n }\r\n this._helixFlags = [];\r\n this._helixFlags[3] = [];\r\n this._helixFlags[4] = [];\r\n this._helixFlags[5] = [];\r\n\r\n // calculate peptide chain lengths\r\n this._chainLengths = [];\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i].getResidues();\r\n let len = 0;\r\n for (; len < chain.length; ++len) {\r\n if ((chain[len].getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n break;\r\n }\r\n }\r\n this._chainLengths[i] = len;\r\n }\r\n\r\n this._buildBetaSheets();\r\n\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n self._buildAlphaHelices(this._complex._chains[i].getResidues(), this._chainLengths[i], false);\r\n }\r\n }\r\n\r\n _buildAlphaHelices(inResidues, chainLength, inPreferPiHelices) {\r\n // Helix and Turn\r\n for (let stride = 3; stride <= 5; ++stride) {\r\n if (inResidues.length < stride) {\r\n break;\r\n }\r\n\r\n for (let i = 0; i + stride < chainLength; ++i) {\r\n if (this._hbonds.isBond(inResidues[i + stride]._index, inResidues[i]._index)\r\n /* && NoChainBreak(res[i], res[i + stride]) */) {\r\n this._helixFlags[stride][inResidues[i + stride]._index] = HelixFlag.END;\r\n for (let j = i + 1; j < i + stride; ++j) {\r\n if (typeof this._helixFlags[stride][inResidues[j]._index] === 'undefined') {\r\n this._helixFlags[stride][inResidues[j]._index] = HelixFlag.MIDDLE;\r\n }\r\n }\r\n\r\n if (this._helixFlags[stride][inResidues[i]._index] === HelixFlag.END) {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START_AND_END;\r\n } else {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 2; i < chainLength - 2; ++i) {\r\n const kappa = this._kappa(inResidues[i - 2], inResidues[i], inResidues[i + 2]);\r\n this._bend[inResidues[i]._index] = (kappa !== 360 && kappa > 70);\r\n }\r\n\r\n for (let i = 1; i + 4 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 4) && this._isHelixStart(inResidues[i - 1]._index, 4)) {\r\n for (let j = i; j <= i + 3; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_ALPHA;\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 3 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 3) && this._isHelixStart(inResidues[i - 1]._index, 3)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 2; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_310;\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 2; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_310;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 5 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 5) && this._isHelixStart(inResidues[i - 1]._index, 5)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 4; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_PI\r\n || (inPreferPiHelices && this._ss[inResidues[j]._index] === StructureType.HELIX_ALPHA);\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 4; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_PI;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 1 < chainLength; ++i) {\r\n if (typeof this._ss[inResidues[i]._index] === 'undefined') {\r\n let isTurn = false;\r\n for (let stride = 3; stride <= 5 && !isTurn; ++stride) {\r\n for (let k = 1; k < stride && !isTurn; ++k) {\r\n isTurn = (i >= k) && this._isHelixStart(inResidues[i - k]._index, stride);\r\n }\r\n }\r\n\r\n if (isTurn) {\r\n this._ss[inResidues[i]._index] = StructureType.TURN;\r\n } else if (this._bend[inResidues[i]._index]) {\r\n this._ss[inResidues[i]._index] = StructureType.BEND;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _cosinusAngle(p1, p2, p3, p4) {\r\n const v12 = p1.clone().sub(p2);\r\n const v34 = p3.clone().sub(p4);\r\n\r\n let result = 0;\r\n\r\n const x = v12.dot(v12) * v34.dot(v34);\r\n if (x > 0) {\r\n result = v12.dot(v34) / Math.sqrt(x);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _kappa(prevPrev, res, nextNext) {\r\n const curCA = this._residueGetCAlpha(res);\r\n const ppCA = this._residueGetCAlpha(prevPrev);\r\n const nnCA = this._residueGetCAlpha(nextNext);\r\n if (curCA === null || ppCA === null || nnCA === null) {\r\n return 180;\r\n }\r\n\r\n const ckap = this._cosinusAngle(curCA, ppCA, nnCA, curCA);\r\n const skap = Math.sqrt(1 - ckap * ckap);\r\n return Math.atan2(skap, ckap) * 180 / Math.PI;\r\n }\r\n\r\n _isHelixStart(res, stride) {\r\n return (this._helixFlags[stride][res] === HelixFlag.START\r\n || this._helixFlags[stride][res] === HelixFlag.START_AND_END);\r\n }\r\n\r\n _buildBetaSheets() {\r\n // find bridges\r\n // check each chain against each other chain, and against itself\r\n const bridges = [];\r\n for (let a = 0; a < this._complex._chains.length; ++a) {\r\n const lenA = this._chainLengths[a];\r\n if (lenA <= 4) {\r\n continue;\r\n }\r\n\r\n const chainA = this._complex._chains[a].getResidues();\r\n\r\n for (let b = a; b < this._complex._chains.length; ++b) {\r\n const lenB = this._chainLengths[b];\r\n if (lenB <= 4) {\r\n continue;\r\n }\r\n\r\n const chainB = this._complex._chains[b].getResidues();\r\n\r\n for (let i = 1; i + 1 < lenA; ++i) {\r\n const ri = chainA[i];\r\n\r\n let j = 1;\r\n if (b === a) {\r\n j = i + 3; // check for self-bridges forward down the chain\r\n }\r\n\r\n for (; j + 1 < lenB; ++j) {\r\n const rj = chainB[j];\r\n\r\n const type = this._testBridge(chainA, i, chainB, j);\r\n if (type === BridgeType.NO_BRIDGE) {\r\n continue;\r\n }\r\n\r\n // there is a bridge, try to attach it to previously found sequence\r\n let found = false;\r\n for (const bridge of bridges) {\r\n if (type !== bridge.type || ri._index !== bridge.i[bridge.i.length - 1] + 1) {\r\n continue;\r\n }\r\n\r\n if (type === BridgeType.PARALLEL && bridge.j[bridge.j.length - 1] + 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.push(rj._index);\r\n found = true;\r\n break;\r\n }\r\n\r\n if (type === BridgeType.ANTI_PARALLEL && bridge.j[0] - 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.unshift(rj._index);\r\n found = true;\r\n break;\r\n }\r\n }\r\n\r\n // this bridge cannot be attached anywhere, start a new sequence\r\n if (!found) {\r\n bridges.push({\r\n type,\r\n i: [ri._index],\r\n chainI: ri.getChain()._index,\r\n j: [rj._index],\r\n chainJ: rj.getChain()._index,\r\n });\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // extend ladders\r\n bridges.sort((a, b) => {\r\n if (a.chainI < b.chainI || (a.chainI === b.chainI && a.i[0] < b.i[0])) {\r\n return -1;\r\n }\r\n return 1;\r\n });\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n for (let j = i + 1; j < bridges.length; ++j) {\r\n const ibi = bridges[i].i[0];\r\n const iei = bridges[i].i[bridges[i].i.length - 1];\r\n const jbi = bridges[i].j[0];\r\n const jei = bridges[i].j[bridges[i].j.length - 1];\r\n const ibj = bridges[j].i[0];\r\n const iej = bridges[j].i[bridges[j].i.length - 1];\r\n const jbj = bridges[j].j[0];\r\n const jej = bridges[j].j[bridges[j].j.length - 1];\r\n\r\n if (bridges[i].type !== bridges[j].type\r\n || this._hasChainBreak(Math.min(ibi, ibj), Math.max(iei, iej))\r\n || this._hasChainBreak(Math.min(jbi, jbj), Math.max(jei, jej))\r\n || ibj - iei >= 6 || (iei >= ibj && ibi <= iej)) {\r\n continue;\r\n }\r\n\r\n let bulge = false;\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bulge = ((jbj - jei < 6 && ibj - iei < 3) || (jbj - jei < 3));\r\n } else {\r\n bulge = ((jbi - jej < 6 && ibj - iei < 3) || (jbi - jej < 3));\r\n }\r\n\r\n if (bulge) {\r\n bridges[i].i = bridges[i].i.concat(bridges[j].i);\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bridges[i].j = bridges[i].j.concat(bridges[j].j);\r\n } else {\r\n bridges[i].j = bridges[j].j.concat(bridges[i].j);\r\n }\r\n bridges.splice(j--, 1);\r\n }\r\n }\r\n }\r\n\r\n // Sheet\r\n const ladderset = new Set();\r\n for (let i = 0; i < bridges.length; ++i) {\r\n ladderset.add(bridges[i]);\r\n }\r\n\r\n let sheet = 1;\r\n let ladder = 0;\r\n while (ladderset.size > 0) {\r\n let bridge = ladderset.values().next().value;\r\n ladderset.delete(bridge);\r\n\r\n const sheetset = new Set();\r\n sheetset.add(bridge);\r\n\r\n let toMove;\r\n do {\r\n toMove = new Set();\r\n for (const a of sheetset.values()) {\r\n for (const b of ladderset.values()) {\r\n if (this._areBridgesLinked(a, b)) {\r\n toMove.add(b);\r\n }\r\n }\r\n }\r\n for (bridge of toMove.values()) {\r\n sheetset.add(bridge);\r\n ladderset.delete(bridge);\r\n }\r\n } while (toMove.size > 0);\r\n\r\n for (bridge of sheetset.values()) {\r\n bridge.ladder = ladder;\r\n bridge.sheet = sheet;\r\n bridge.link = sheetset;\r\n ++ladder;\r\n }\r\n\r\n ++sheet;\r\n }\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n const bridge = bridges[i];\r\n\r\n // find out if any of the i and j set members already have\r\n // a bridge assigned, if so, we're assigning bridge 2\r\n\r\n let betai = 0;\r\n let betaj = 0;\r\n\r\n for (let l = 0; l < bridge.i.length; ++l) {\r\n if (this._betaPartners[bridge.i[l]][0]) {\r\n betai = 1;\r\n break;\r\n }\r\n }\r\n\r\n for (let l = 0; l < bridge.j.length; ++l) {\r\n if (this._betaPartners[bridge.j[l]][0]) {\r\n betaj = 1;\r\n break;\r\n }\r\n }\r\n\r\n let ss = StructureType.BRIDGE;\r\n if (bridge.i.length > 1) {\r\n ss = StructureType.STRAND;\r\n }\r\n\r\n if (bridge.type === BridgeType.PARALLEL) {\r\n let j = 0;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n\r\n j = 0;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n } else {\r\n let j = bridge.j.length - 1;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n\r\n j = bridge.i.length - 1;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n }\r\n\r\n for (let k = bridge.i[0]; k <= bridge.i[bridge.i.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n\r\n for (let k = bridge.j[0]; k <= bridge.j[bridge.j.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _testBridge(chainA, from, chainB, to) {\r\n let result = BridgeType.NO_BRIDGE;\r\n\r\n const a = chainA[from - 1]._index;\r\n const b = chainA[from]._index;\r\n const c = chainA[from + 1]._index;\r\n const d = chainB[to - 1]._index;\r\n const e = chainB[to]._index;\r\n const f = chainB[to + 1]._index;\r\n\r\n const isBond = this._hbonds.isBond.bind(this._hbonds);\r\n if ((isBond(c, e) && isBond(e, a)) || (isBond(f, b) && isBond(b, d))) {\r\n result = BridgeType.PARALLEL;\r\n } else if ((isBond(c, d) && isBond(f, a)) || (isBond(e, b) && isBond(b, e))) {\r\n result = BridgeType.ANTI_PARALLEL;\r\n }\r\n return result;\r\n }\r\n\r\n // return true if any of the residues in bridge a is identical to any of the residues in bridge b\r\n _areBridgesLinked(a, b) {\r\n const ai = new Set(a.i);\r\n const aj = new Set(a.j);\r\n\r\n for (const i of b.i) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n for (const i of b.j) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n }\r\n\r\n _hasChainBreak(from, to) {\r\n for (let i = from + 1; i <= to; ++i) {\r\n if (this._complex._residues[i]._sequence !== this._complex._residues[i - 1]._sequence + 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\nSecondaryStructureMap.StructureType = StructureType;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport Atom from './Atom';\r\nimport Chain from './Chain';\r\nimport Helix from './Helix';\r\nimport Strand from './Strand';\r\nimport Sheet from './Sheet';\r\nimport Component from './Component';\r\nimport ResidueType from './ResidueType';\r\nimport Bond from './Bond';\r\nimport AutoBond from './AutoBond';\r\nimport AromaticLoopsMarker from './AromaticLoopsMarker';\r\nimport BiologicalUnit from './BiologicalUnit';\r\nimport selectors from './selectors';\r\nimport VoxelWorld from './VoxelWorld';\r\nimport SecondaryStructureMap from './SecondaryStructureMap';\r\nimport StructuralElement from './StructuralElement';\r\n\r\nconst VOXEL_SIZE = 5.0;\r\n\r\nconst { StructureType } = SecondaryStructureMap;\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX\r\nconst helixClassMap = {\r\n [StructureType.HELIX_ALPHA]: 1,\r\n [StructureType.HELIX_PI]: 3,\r\n [StructureType.HELIX_310]: 5,\r\n};\r\n\r\nconst loopMap = {\r\n [StructureType.BRIDGE]: StructuralElementType.BRIDGE,\r\n [StructureType.TURN]: StructuralElementType.TURN,\r\n [StructureType.BEND]: StructuralElementType.BEND,\r\n [StructureType.LOOP]: StructuralElementType.COIL,\r\n};\r\n\r\n/**\r\n * The entire complex of the molecules under study.\r\n *\r\n * @exports Complex\r\n * @constructor\r\n */\r\nclass Complex {\r\n constructor() {\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n\r\n this._residueTypes = Object.create(ResidueType.StandardTypes);\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n this._molecules = [];\r\n this._maskNeedsUpdate = false;\r\n\r\n this.metadata = {};\r\n\r\n this.symmetry = [];\r\n this.units = [new BiologicalUnit(this)];\r\n this._currentUnit = 0; // default biological unit is the asymmetric unit\r\n }\r\n\r\n addAtom(atom) {\r\n const index = this._atoms.length;\r\n this._atoms.push(atom);\r\n return index;\r\n }\r\n\r\n addSheet(sheet) {\r\n const index = this._sheets.length;\r\n this._sheets.push(sheet);\r\n return index;\r\n }\r\n\r\n addHelix(helix) {\r\n const index = this._helices.length;\r\n this._helices.push(helix);\r\n return index;\r\n }\r\n\r\n getAtoms() {\r\n return this._atoms;\r\n }\r\n\r\n getBonds() {\r\n return this._bonds;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n addResidue(residue) {\r\n const index = this._residues.length;\r\n this._residues.push(residue);\r\n return index;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n this.forEachChain((chain) => {\r\n chain.updateToFrame(frameData);\r\n });\r\n }\r\n\r\n addResidueType(resName) {\r\n const rt = this._residueTypes[resName] = new ResidueType(resName, 'Unknown', '');\r\n return rt;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n getSGroupCount() {\r\n return this._sgroups.length;\r\n }\r\n\r\n getSGroups() {\r\n return this._sgroups;\r\n }\r\n\r\n /*\r\n Extract atom by its fullname: #chainName#.#residueId#.#atomName#\r\n */\r\n getAtomByFullname(fullName) {\r\n const parts = fullName.split('.');\r\n if (parts.length !== 3) {\r\n return null;\r\n }\r\n\r\n const chainName = parts[0];\r\n const resId = parseInt(parts[1], 10);\r\n if (Number.isNaN(resId)) {\r\n return null;\r\n }\r\n const atomName = parts[2].toUpperCase();\r\n\r\n let currAtom = null;\r\n this.forEachChain((chain) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (chain._name.localeCompare(chainName) === 0) {\r\n chain.forEachResidue((residue) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (residue._sequence === resId) {\r\n residue.forEachAtom((atom) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (atomName.localeCompare(atom.name) === 0) {\r\n currAtom = atom;\r\n }\r\n });\r\n }\r\n });\r\n }\r\n });\r\n\r\n return currAtom;\r\n }\r\n\r\n /**\r\n * Create a new chain.\r\n *\r\n * @param {string} name - Chain name.\r\n * @returns {Chain} - Newly created chain.\r\n */\r\n addChain(name) {\r\n const result = new Chain(this, name);\r\n this._chains.push(result);\r\n return result;\r\n }\r\n\r\n getChain(name) {\r\n for (let i = 0, n = this._chains.length; i < n; ++i) {\r\n const chain = this._chains[i];\r\n if (chain.getName() === name) {\r\n return chain;\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n getChainCount() {\r\n return this._chains.length;\r\n }\r\n\r\n getMolecules() {\r\n return this._molecules;\r\n }\r\n\r\n getMoleculeCount() {\r\n return this._molecules.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n process(atoms[i]);\r\n }\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._bonds;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n forEachChain(process) {\r\n const chains = this._chains;\r\n for (let i = 0, n = chains.length; i < n; ++i) {\r\n process(chains[i]);\r\n }\r\n }\r\n\r\n forEachMolecule(process) {\r\n const molecules = this._molecules;\r\n const n = molecules.length;\r\n for (let i = 0; i < n; ++i) {\r\n process(molecules[i]);\r\n }\r\n }\r\n\r\n forEachSGroup(process) {\r\n const groups = this._sgroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n process(groups[i]);\r\n }\r\n }\r\n\r\n forEachComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n forEachVisibleComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n addBond(left, right, order, type, fixed) {\r\n const bond = new Bond(left, right, order, type, fixed);\r\n this._bonds.push(bond);\r\n return bond;\r\n }\r\n\r\n getBondCount() {\r\n return this._bonds.length;\r\n }\r\n\r\n getResidueType(name) {\r\n return this._residueTypes[name] || null;\r\n }\r\n\r\n getUnifiedSerial(chain, serial, iCode) {\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n return serial + iCode * maxSerial + chain * chainShift;\r\n }\r\n\r\n splitUnifiedSerial(uniSerial) {\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n const chainId = Math.floor(uniSerial / chainShift);\r\n const remnant = uniSerial - chainId * chainShift;\r\n const insCode = Math.floor(remnant / maxSerial);\r\n const ser = remnant - insCode * maxSerial;\r\n return { chain: chainId, serial: ser, iCode: insCode };\r\n }\r\n\r\n _fillCmpEdit() {\r\n const self = this;\r\n const components = this._components;\r\n\r\n function addComp() {\r\n const comp = new Component(self);\r\n comp._index = components.length;\r\n components[comp._index] = comp;\r\n return comp;\r\n }\r\n\r\n this.forEachChain((chain) => {\r\n const residues = chain._residues;\r\n const resCount = residues.length;\r\n if (resCount < 1) {\r\n return;\r\n }\r\n let comp = addComp();\r\n let currStart = residues[0]._index;\r\n\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)\r\n || currRes._index !== nextRes._index - 1) {\r\n // the last condition is broken and incorrect\r\n // the refactoring of the Component is required in order to fix this issue\r\n comp.setSubDivs([{\r\n start: currStart,\r\n end: currRes._index,\r\n }]);\r\n if (nextRes) {\r\n currStart = nextRes._index;\r\n comp = addComp();\r\n }\r\n }\r\n }\r\n });\r\n }\r\n\r\n // This function was added in the moment of despair\r\n // It was the dark times for miew\r\n _fillCmpNoedit() {\r\n const comp = new Component(this);\r\n comp._index = 0;\r\n\r\n const residues = this._residues;\r\n const resCount = residues.length;\r\n if (resCount === 0) {\r\n return;\r\n }\r\n\r\n const currSubDivs = [];\r\n let currStart = 0;\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)) {\r\n // wrap up this interval\r\n currSubDivs[currSubDivs.length] = {\r\n start: currStart,\r\n end: i,\r\n };\r\n if (nextRes) {\r\n currStart = i + 1;\r\n }\r\n }\r\n }\r\n\r\n comp.setSubDivs(currSubDivs);\r\n this._components[comp._index] = comp;\r\n }\r\n\r\n /**\r\n * Fill components information.\r\n * @param {boolean} enableEditing - Restructure Complex to enable per-component editing.\r\n */\r\n _fillComponents(enableEditing) {\r\n if (enableEditing) {\r\n this._fillCmpEdit();\r\n } else {\r\n this._fillCmpNoedit();\r\n }\r\n }\r\n\r\n getCurrentUnit() {\r\n return this._currentUnit;\r\n }\r\n\r\n getDefaultBoundaries() {\r\n return this.units[0].getBoundaries();\r\n }\r\n\r\n getBoundaries() {\r\n return this.units[this._currentUnit].getBoundaries();\r\n }\r\n\r\n getTransforms() {\r\n return this.units[this._currentUnit].getTransforms();\r\n }\r\n\r\n getSelector() {\r\n return this.units[this._currentUnit].getSelector();\r\n }\r\n\r\n resetCurrentUnit() {\r\n this._currentUnit = 0;\r\n this.setCurrentUnit(1);\r\n }\r\n\r\n setCurrentUnit(newUnit) {\r\n if (newUnit !== null && newUnit !== undefined\r\n && newUnit !== this._currentUnit\r\n && newUnit >= 0\r\n && newUnit < this.units.length) {\r\n this._currentUnit = newUnit;\r\n return true;\r\n }\r\n return false;\r\n }\r\n\r\n _computeBounds() {\r\n const { units } = this;\r\n for (let i = 0, n = units.length; i < n; ++i) {\r\n units[i].computeBoundaries();\r\n }\r\n }\r\n\r\n onAtomPositionChanged() {\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n this.forEachComponent((c) => {\r\n c.update();\r\n });\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n this._finalizeBonds();\r\n this.forEachSGroup((s) => {\r\n s._rebuildSGroupOnAtomChange();\r\n });\r\n }\r\n\r\n update() {\r\n if (this._maskNeedsUpdate) {\r\n this.updateStructuresMask();\r\n this._maskNeedsUpdate = false;\r\n }\r\n }\r\n\r\n _finalizeBonds() {\r\n const bonds = this.getBonds();\r\n const n = bonds.length;\r\n for (let i = 0; i < n; ++i) {\r\n bonds[i]._index = i;\r\n }\r\n }\r\n\r\n /**\r\n * Finalizes complex's inner data(i.e. after parsing).\r\n * @param {objects} opts - Build bonds automatically.\r\n * @param {boolean} opts.needAutoBonding - Build bonds automatically.\r\n * @param {boolean} opts.detectAromaticLoops - Find/mark aromatic loops.\r\n * @param {boolean} opts.enableEditing - Restructure Complex to enable per-component editing.\r\n * @param {Array} [opts.serialAtomMap] - Array of atoms ordered by their serials.\r\n */\r\n finalize(opts) {\r\n opts = opts || {};\r\n // Put bonds into atoms\r\n const bonds = this._bonds;\r\n let i;\r\n let n;\r\n // remove invalid bonds\r\n for (i = bonds.length - 1; i >= 0; i--) {\r\n const bond = bonds[i];\r\n if (bond._left === null || bond._right === null) {\r\n bonds.splice(i, 1);\r\n } else {\r\n bond._left.bonds.push(bond);\r\n bond._right.bonds.push(bond);\r\n }\r\n }\r\n\r\n const residues = this._residues;\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._finalize();\r\n }\r\n\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n\r\n // WARNING! this MUST be done BEFORE computeBounds is called\r\n const { units } = this;\r\n for (i = 0, n = units.length; i < n; ++i) {\r\n units[i].finalize();\r\n }\r\n // try setting first biomolecule by defaults\r\n this.setCurrentUnit(1);\r\n\r\n const residueHash = {};\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n // This code is extremely dangerous for non-PDB formats\r\n residueHash[this.getUnifiedSerial(\r\n res.getChain().getName().charCodeAt(0),\r\n res.getSequence(),\r\n res.getICode().charCodeAt(0),\r\n )] = res;\r\n }\r\n\r\n const { structures } = this;\r\n for (i = 0, n = structures.length; i < n; ++i) {\r\n structures[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const helices = this._helices;\r\n for (i = 0, n = helices.length; i < n; ++i) {\r\n helices[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const sheets = this._sheets;\r\n for (i = 0, n = sheets.length; i < n; ++i) {\r\n sheets[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n\r\n const atoms = this._atoms;\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const currAtom = atoms[i];\r\n currAtom.index = i;\r\n }\r\n\r\n if (opts.needAutoBonding) {\r\n // Ignore errors during autobonding\r\n try {\r\n const autoConnector = new AutoBond(this);\r\n autoConnector.build();\r\n autoConnector.destroy();\r\n } catch (e) {\r\n console.warn('Autobonding failed:', e);\r\n }\r\n }\r\n\r\n const chains = this._chains;\r\n for (i = 0, n = chains.length; i < n; ++i) {\r\n chains[i]._index = i;\r\n }\r\n\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._index = i;\r\n }\r\n\r\n // mark non-polar hydrogens\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n if (atom.flags & Atom.Flags.HYDROGEN && atom.bonds.length === 1) {\r\n const bond = atom.bonds[0];\r\n const other = (bond._left !== atom && bond._left) || bond._right;\r\n if (other.flags & Atom.Flags.CARBON) {\r\n atom.flags |= Atom.Flags.NONPOLARH;\r\n }\r\n }\r\n }\r\n\r\n this._finalizeBonds();\r\n this._fillComponents(opts.enableEditing);\r\n\r\n const marker = new AromaticLoopsMarker(this);\r\n marker.markCycles();\r\n if (opts.detectAromaticLoops) { // TODO remove this condition clause, it is for debug purposes only!\r\n marker.detectCycles(); // TODO add conditional detection\r\n }\r\n\r\n this._finalizeMolecules();\r\n }\r\n\r\n _finalizeMolecules() {\r\n // add reference to molecule into residue\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const molecule = this._molecules[i];\r\n const count = molecule.residues.length;\r\n for (let j = 0; j < count; j++) {\r\n const residue = molecule.residues[j];\r\n residue._molecule = molecule;\r\n }\r\n }\r\n }\r\n\r\n updateStructuresMask() {\r\n const updater = (structure) => structure.collectMask();\r\n this.forEachResidue(updater);\r\n this.forEachChain(updater);\r\n this.forEachMolecule(updater);\r\n }\r\n\r\n countAtomsByMask(mask) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n getNumAtomsBySelector(selector) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n resetAtomMask(mask) {\r\n this.forEachAtom((atom) => {\r\n atom.mask = mask;\r\n });\r\n }\r\n\r\n markAtoms(selector, mask) {\r\n const setMask = mask;\r\n const clearMask = ~setMask;\r\n let count = 0;\r\n const totalSelector = selectors.keyword('And')(selector, this.getSelector());\r\n\r\n this.forEachAtom((atom) => {\r\n if (totalSelector.includesAtom(atom)) {\r\n atom.mask |= setMask;\r\n count++;\r\n } else {\r\n atom.mask &= clearMask;\r\n }\r\n });\r\n this._maskNeedsUpdate = true;\r\n\r\n return count;\r\n }\r\n\r\n markAtomsAdditionally(selector, mask) {\r\n const setMask = mask;\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom) && (atom.mask & mask) !== mask) {\r\n atom.mask |= setMask;\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n clearAtomBits(mask) {\r\n const clearMask = ~mask;\r\n this.forEachAtom((atom) => {\r\n atom.mask &= clearMask;\r\n });\r\n const reseter = (a) => {\r\n a._mask &= clearMask;\r\n };\r\n this.forEachAtom(reseter);\r\n this.forEachResidue(reseter);\r\n this.forEachChain(reseter);\r\n this.forEachMolecule(reseter);\r\n }\r\n\r\n getAtomNames() {\r\n if (this.hasOwnProperty('_atomNames')) {\r\n return this._atomNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.name] = 1;\r\n });\r\n this._atomNames = Object.keys(dict);\r\n\r\n return this._atomNames;\r\n }\r\n\r\n getElements() {\r\n if (this.hasOwnProperty('_elements')) {\r\n return this._elements;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.element.name] = 1;\r\n });\r\n this._elements = Object.keys(dict);\r\n\r\n return this._elements;\r\n }\r\n\r\n getResidueNames() {\r\n if (this.hasOwnProperty('_residueNames')) {\r\n return this._residueNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachResidue((res) => {\r\n dict[res._type._name] = 1;\r\n });\r\n this._residueNames = Object.keys(dict);\r\n\r\n return this._residueNames;\r\n }\r\n\r\n getChainNames() {\r\n if (this.hasOwnProperty('_chainNames')) {\r\n return this._chainNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachChain((chain) => {\r\n dict[chain._name] = 1;\r\n });\r\n this._chainNames = Object.keys(dict);\r\n\r\n return this._chainNames;\r\n }\r\n\r\n getAltLocNames() {\r\n if (this.hasOwnProperty('_altlocNames')) {\r\n return this._altlocNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[String.fromCharCode(atom.location)] = 1;\r\n });\r\n this._altlocNames = Object.keys(dict);\r\n\r\n return this._altlocNames;\r\n }\r\n\r\n getVoxelWorld() {\r\n if (!this.hasOwnProperty('_voxelWorld')) {\r\n try {\r\n this._voxelWorld = new VoxelWorld(\r\n this.getDefaultBoundaries().boundingBox,\r\n new THREE.Vector3(VOXEL_SIZE, VOXEL_SIZE, VOXEL_SIZE),\r\n );\r\n this._voxelWorld.addAtoms(this);\r\n } catch {\r\n logger.warn('Unable to create voxel world');\r\n this._voxelWorld = null;\r\n }\r\n }\r\n\r\n return this._voxelWorld;\r\n }\r\n\r\n /**\r\n * Simple function to make unified routine procedure without code duplication.\r\n * @param {Array} srcArray - Source chemical structure array (will be part of resulting chemical structure array).\r\n * @param {Array} dstArray - Resulting chemical structure array.\r\n * @param {number} param - Parameter for processor.\r\n * @param {function} functor - Processor for every element in array.\r\n */\r\n addElement(srcArray, dstArray, param, functor) {\r\n const { length } = srcArray;\r\n for (let i = 0; i < length; ++i) {\r\n const elem = srcArray[i];\r\n functor(elem, param);\r\n dstArray.push(elem);\r\n }\r\n }\r\n\r\n // this function joins multiple complexes into one (this)\r\n // atom, bond, ... objects are reused -- so input complexes are no longer valid\r\n joinComplexes(complexes) {\r\n // clear target complex\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n\r\n const self = this;\r\n let atomBias = 0;\r\n let bondBias = 0;\r\n let residueBias = 0;\r\n let chainBias = 0;\r\n let componentBias = 0;\r\n\r\n function processAtom(atom, bias) {\r\n atom.serial += bias;\r\n atom.index += bias;\r\n }\r\n\r\n function processBond(bond, bias) {\r\n bond._index += bias;\r\n }\r\n\r\n function processResidue(residue, bias) {\r\n residue._index += bias;\r\n }\r\n\r\n function processChain(chain, bias) {\r\n chain._complex = self;\r\n chain._index += bias;\r\n }\r\n\r\n function processComponent(component, bias) {\r\n component._complex = self;\r\n component._index += bias;\r\n }\r\n\r\n /**\r\n * Simple function to do nothing.\r\n */\r\n function doNothing() {\r\n }\r\n\r\n for (let i = 0; i < complexes.length; ++i) {\r\n const c = complexes[i];\r\n this.addElement(c._atoms, this._atoms, atomBias, processAtom);\r\n this.addElement(c._bonds, this._bonds, bondBias, processBond);\r\n this.addElement(c._residues, this._residues, residueBias, processResidue);\r\n this.addElement(c._chains, this._chains, chainBias, processChain);\r\n this.addElement(c._sheets, this._sheets, 0, doNothing);\r\n this.addElement(c._helices, this._helices, 0, doNothing);\r\n this.addElement(c._sgroups, this._sgroups, 0, doNothing);\r\n this.addElement(c._components, this._components, componentBias, processComponent);\r\n this.addElement(c.structures, this.structures, 0, doNothing);\r\n // merge residue types\r\n for (const rt in c._residueTypes) {\r\n if (c._residueTypes.hasOwnProperty(rt)) {\r\n this._residueTypes[rt] = c._residueTypes[rt];\r\n }\r\n }\r\n\r\n atomBias += c._atoms.length;\r\n bondBias += c._bonds.length;\r\n residueBias += c._residues.length;\r\n chainBias += c._chains.length;\r\n componentBias += c._components.length;\r\n }\r\n\r\n this._computeBounds();\r\n }\r\n\r\n /**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n */\r\n dssp() {\r\n const ssMap = new SecondaryStructureMap(this);\r\n\r\n const structures = this.structures = [];\r\n const helices = this._helices = [];\r\n const sheets = this._sheets = [];\r\n\r\n const getSheet = (index) => {\r\n let item = sheets[index];\r\n if (!item) {\r\n item = sheets[index] = new Sheet(String(index), 0);\r\n }\r\n return item;\r\n };\r\n\r\n let lastCode;\r\n let lastSheetIndex;\r\n let lastHelixIndex = 0;\r\n let curStructure = null;\r\n for (let i = 0, n = this._residues.length; i < n; ++i) {\r\n const curCode = ssMap._ss[i];\r\n const curResidue = this._residues[i];\r\n const curSheetIndex = ssMap._sheet[i];\r\n\r\n // expand the last structure\r\n if (curCode === lastCode && curSheetIndex === lastSheetIndex) {\r\n curResidue._secondary = curStructure;\r\n if (curStructure) {\r\n curStructure.term = curResidue;\r\n }\r\n if (curStructure instanceof Helix) {\r\n curStructure.length++;\r\n }\r\n continue;\r\n }\r\n\r\n // create a new structure\r\n const helixClass = helixClassMap[curCode];\r\n const loopType = loopMap[curCode];\r\n if (curCode === StructureType.STRAND) {\r\n const curSheet = getSheet(curSheetIndex);\r\n curStructure = new Strand(curSheet, curResidue, curResidue, 0, null, null);\r\n curSheet.addStrand(curStructure);\r\n } else if (helixClass !== undefined) {\r\n lastHelixIndex++;\r\n curStructure = new Helix(helixClass, curResidue, curResidue, lastHelixIndex, String(lastHelixIndex), '', 1);\r\n helices.push(curStructure);\r\n } else if (loopType !== undefined) {\r\n curStructure = new StructuralElement(loopType, curResidue, curResidue);\r\n } else {\r\n curStructure = null;\r\n }\r\n\r\n if (curStructure) {\r\n structures.push(curStructure);\r\n }\r\n\r\n curResidue._secondary = curStructure;\r\n\r\n lastCode = curCode;\r\n lastSheetIndex = curSheetIndex;\r\n }\r\n\r\n this._sheets = sheets.filter((_sheet) => true); // squeeze sheets array\r\n }\r\n}\r\n\r\nComplex.prototype.id = 'Complex';\r\nComplex.prototype.name = '';\r\n\r\nexport default Complex;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\nfunction pow2ceil(v) {\r\n let p = 2;\r\n v = (v - 1) >> 1;\r\n while (v) {\r\n p <<= 1;\r\n v >>= 1;\r\n }\r\n return p;\r\n}\r\n\r\n/**\r\n * Volume constructor\r\n *\r\n * @param {Object} type - Float32Array, Int8Array, etc...\r\n * @param {Object|Array} dimensions - number of data points on each axis (x, y, z)\r\n * @param {Box3} box - bounding box defining data place in metric space,\r\n * it's corners correspond to extreme data points\r\n * @param {Number} vecSize - dimension of the field data point (1 = scalar, 3 = 3D vector)\r\n * @param {Object} data - typed array of the same type as specified by the 1st parameter,\r\n * layout: point by point along X,\r\n * row by row along Y,\r\n * plane by plane along Z\r\n * @param {Number} volumeInfo - volume info values to define threshold to filter the noise\r\n */\r\n\r\nclass Volume {\r\n constructor(type, dimensions, box, vecSize, data, volumeInfo) {\r\n this._box = box.clone();\r\n this._dimVec = Math.max(Math.floor(vecSize || 1), 1);\r\n this._volumeInfo = volumeInfo;\r\n\r\n if (dimensions instanceof Array) {\r\n [this._dimX, this._dimY, this._dimZ] = dimensions;\r\n } else {\r\n this._dimX = dimensions.x;\r\n this._dimY = dimensions.y;\r\n this._dimZ = dimensions.z;\r\n }\r\n this._dimX = Math.max(Math.floor(this._dimX), 1);\r\n this._dimY = Math.max(Math.floor(this._dimY), 1);\r\n this._dimZ = Math.max(Math.floor(this._dimZ), 1);\r\n\r\n this._rowElements = this._dimVec * this._dimX;\r\n this._planeElements = this._rowElements * this._dimY;\r\n this._totalElements = this._planeElements * this._dimZ;\r\n\r\n this._data = data || utils.allocateTyped(type, this._totalElements);\r\n\r\n // override getter/setter for vector fields\r\n switch (this._dimVec) {\r\n case 1:\r\n break;\r\n\r\n case 2:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n };\r\n break;\r\n\r\n case 3:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1], this._data[idx + 2]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n this._data[idx + 2] = c;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n this._data[idx + 2] += c;\r\n };\r\n break;\r\n\r\n default:\r\n throw new Error('Volume: invalid vector dimension');\r\n }\r\n }\r\n\r\n // default getter assumes it's a scalar field\r\n getValue(x, y, z) {\r\n return this._data[x + y * this._rowElements + z * this._planeElements];\r\n }\r\n\r\n // default setter assumes it's a scalar field\r\n setValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] = val;\r\n }\r\n\r\n // default adder assumes it's a scalar field\r\n addValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] += val;\r\n }\r\n\r\n getDimensions() {\r\n return [this._dimX, this._dimY, this._dimZ];\r\n }\r\n\r\n getBox() {\r\n return this._box;\r\n }\r\n\r\n getVolumeInfo() {\r\n return this._volumeInfo;\r\n }\r\n\r\n getCellSize() {\r\n const boxSize = new THREE.Vector3();\r\n this._box.getSize(boxSize);\r\n const res = new THREE.Vector3();\r\n res.x = this._dimX > 1 ? boxSize.x / (this._dimX - 1) : 0;\r\n res.y = this._dimY > 1 ? boxSize.y / (this._dimY - 1) : 0;\r\n res.z = this._dimZ > 1 ? boxSize.z / (this._dimZ - 1) : 0;\r\n return res;\r\n }\r\n\r\n computeGradient() {\r\n if (this._dimVec !== 1) {\r\n // gradient can only be computed for scalar fields\r\n return null;\r\n }\r\n\r\n // create a 3D vector field of gradients\r\n const gradient = new Volume(Float32Array, [this._dimX, this._dimY, this._dimZ], this._box, 3);\r\n\r\n // calculate cell side lengths\r\n const vl = this.getCellSize();\r\n\r\n // gradient axis scaling values and averaging factors, to correctly\r\n // calculate the gradient for volumes with irregular cell spacing\r\n const vs = new THREE.Vector3(-0.5 / vl.x, -0.5 / vl.y, -0.5 / vl.z);\r\n\r\n // TODO Check for intended bug in VMD (min is zero)\r\n function clamp(val, min, max) {\r\n return Math.min(max, Math.max(min, val));\r\n }\r\n\r\n const xSize = this._dimX;\r\n const ySize = this._dimY;\r\n const zSize = this._dimZ;\r\n const volMap = this._data;\r\n\r\n function _voxelValue(x, y, z) {\r\n return volMap[z * xSize * ySize + y * xSize + x];\r\n }\r\n\r\n for (let zi = 0; zi < zSize; ++zi) {\r\n const zm = clamp(zi - 1, 0, zSize - 1);\r\n const zp = clamp(zi + 1, 0, zSize - 1);\r\n\r\n for (let yi = 0; yi < ySize; ++yi) {\r\n const ym = clamp(yi - 1, 0, ySize - 1);\r\n const yp = clamp(yi + 1, 0, ySize - 1);\r\n\r\n for (let xi = 0; xi < xSize; ++xi) {\r\n const xm = clamp(xi - 1, 0, xSize - 1);\r\n const xp = clamp(xi + 1, 0, xSize - 1);\r\n\r\n // Calculate the volume gradient at each grid cell.\r\n // Gradients are now stored unnormalized, since we need them in pure\r\n // form in order to draw field lines etc. Shading code will now have\r\n // to do renormalization for itself on-the-fly.\r\n\r\n // XXX this gradient is only correct for orthogonal grids, since\r\n // we're using the array index offsets rather to calculate the gradient\r\n // rather than voxel coordinate offsets. This will have to be\r\n // re-worked for non-orthogonal datasets.\r\n\r\n gradient.setValue(\r\n xi,\r\n yi,\r\n zi,\r\n (_voxelValue(xp, yi, zi) - _voxelValue(xm, yi, zi)) * vs.x,\r\n (_voxelValue(xi, yp, zi) - _voxelValue(xi, ym, zi)) * vs.y,\r\n (_voxelValue(xi, yi, zp) - _voxelValue(xi, yi, zm)) * vs.z,\r\n );\r\n }\r\n }\r\n }\r\n\r\n return gradient;\r\n }\r\n\r\n normalize() {\r\n const data = this._data;\r\n\r\n // get min/max\r\n let min = data[0];\r\n let max = data[0];\r\n for (let i = 1; i < data.length; ++i) {\r\n min = Math.min(min, data[i]);\r\n max = Math.max(max, data[i]);\r\n }\r\n\r\n const d = 1.0 / (max - min);\r\n if (d === 0) {\r\n return;\r\n }\r\n\r\n // normalize\r\n for (let i = 0; i < data.length; ++i) {\r\n data[i] = d * (data[i] - min);\r\n }\r\n }\r\n\r\n getTiledTextureStride() {\r\n return [this._dimX + 2, this._dimY + 2];\r\n }\r\n\r\n buildTiledTexture() {\r\n let tilesX = Math.ceil(Math.sqrt(this._dimZ * this._dimY / this._dimX));\r\n\r\n let width = tilesX * (this._dimX + 2) - 1;\r\n width = pow2ceil(width);\r\n tilesX = Math.floor(width / (this._dimX + 2));\r\n\r\n const tilesY = Math.ceil(this._dimZ / tilesX);\r\n let height = tilesY * (this._dimY + 2) - 1;\r\n height = pow2ceil(height);\r\n\r\n const data = new Uint8Array(width * height);\r\n\r\n let src;\r\n let dst;\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // process each pixel row of this tile row\r\n for (let row = 0; row < this._dimY; ++row) {\r\n src = tileRow * tilesX * this._planeElements + row * this._rowElements;\r\n dst = width * (tileRow * (this._dimY + 2) + row);\r\n // copy a series of rows through several XY planes\r\n for (let t = 0; t < tilesX; ++t) {\r\n // copy one row of one XY plane\r\n for (let x = 0; x < this._dimX; ++x) {\r\n data[dst++] = 255.0 * this._data[src++];\r\n }\r\n\r\n // repeat last pixel of previous tile\r\n data[dst++] = 255.0 * this._data[src - 1];\r\n\r\n if (t < tilesX - 1) {\r\n // skip to the same row of next XY plane\r\n src += this._planeElements - this._rowElements;\r\n // repeat first pixel of next tile\r\n data[dst++] = 255.0 * this._data[src];\r\n }\r\n }\r\n }\r\n }\r\n\r\n // fill pixels between tile rows with copy of edge pixels\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // copy last pixel row of this tile row to the following pixel row of the texture\r\n src = width * (tileRow * (this._dimY + 2) + this._dimY - 1);\r\n dst = src + width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n if (tileRow < tilesY - 1) {\r\n // copy first pixel row of next tile row to the preceding pixel row of the texture\r\n src = width * (tileRow + 1) * (this._dimY + 2);\r\n dst = src - width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n }\r\n }\r\n\r\n const texture = new THREE.DataTexture(\r\n data,\r\n width,\r\n height,\r\n THREE.RedFormat,\r\n THREE.UnsignedByteType,\r\n THREE.UVMapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.LinearFilter,\r\n THREE.LinearFilter,\r\n );\r\n texture.needsUpdate = true;\r\n return texture;\r\n }\r\n\r\n /* ********************************************************************************\r\n *\r\n * Methods that provide direct access to internal array (for better performance)\r\n *\r\n ******************************************************************************** */\r\n\r\n getData() {\r\n return this._data;\r\n }\r\n\r\n getDirectIdx(x, y, z) {\r\n return x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n }\r\n\r\n getStrideX() {\r\n return this._dimVec;\r\n }\r\n\r\n getStrideY() {\r\n return this._rowElements;\r\n }\r\n\r\n getStrideZ() {\r\n return this._planeElements;\r\n }\r\n}\r\n\r\nVolume.prototype.id = 'Volume';\r\n\r\nexport default Volume;\r\n","/**\r\n * Residue Molecule.\r\n *\r\n * @param {Complex} complex - Molecular complex this Molecule belongs to.\r\n * @param {String} name - Molecule's name.\r\n * @param {Integer} index - Molecule's index in file.\r\n *\r\n * @exports Molecule\r\n * @constructor\r\n */\r\nclass Molecule {\r\n constructor(complex, name, index) {\r\n this.complex = complex;\r\n this.name = name || '';\r\n this.residues = [];\r\n this.mask = 1 | 0;\r\n this.index = index || -1; // start with 1\r\n }\r\n\r\n forEachResidue(process) {\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this.mask = mask;\r\n }\r\n}\r\n\r\nexport default Molecule;\r\n","import Atom from './chem/Atom';\r\nimport Element from './chem/Element';\r\nimport Bond from './chem/Bond';\r\nimport Residue from './chem/Residue';\r\nimport ResidueType from './chem/ResidueType';\r\nimport Chain from './chem/Chain';\r\nimport Helix from './chem/Helix';\r\nimport Strand from './chem/Strand';\r\nimport Sheet from './chem/Sheet';\r\nimport SGroup from './chem/SGroup';\r\nimport Assembly from './chem/Assembly';\r\nimport Complex from './chem/Complex';\r\nimport Volume from './chem/Volume';\r\nimport VoxelWorld from './chem/VoxelWorld';\r\nimport selectors from './chem/selectors';\r\nimport Molecule from './chem/Molecule';\r\n\r\nexport default {\r\n Atom,\r\n Element,\r\n Bond,\r\n Residue,\r\n ResidueType,\r\n Chain,\r\n Helix,\r\n Strand,\r\n Sheet,\r\n SGroup,\r\n Assembly,\r\n Complex,\r\n Volume,\r\n VoxelWorld,\r\n selectors,\r\n Molecule,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\n\r\nclass CSS2DObject extends THREE.Object3D {\r\n constructor(element) {\r\n super();\r\n const self = this;\r\n this._element = element;\r\n this._element.style.position = 'absolute';\r\n this.addEventListener('removed', () => {\r\n if (self._element.parentNode !== null) {\r\n self._element.parentNode.removeChild(self._element);\r\n }\r\n });\r\n }\r\n\r\n getElement() {\r\n return this._element;\r\n }\r\n\r\n /**\r\n * Sets label transparency.\r\n *\r\n * @param {number} transp - in [0; 1] 1 means fully transparent\r\n */\r\n setTransparency(transp) {\r\n const el = this.getElement();\r\n if (el === null) {\r\n return;\r\n }\r\n if (transp === 1.0) {\r\n el.style.display = 'none';\r\n return;\r\n }\r\n el.style.display = 'inline';\r\n const op = 1.0 - transp;\r\n const top = op.toString();\r\n const op100 = op * 100;\r\n el.style.opacity = top;\r\n el.style.filter = `alpha(opacity=${op100})`; // IE fallback\r\n }\r\n\r\n clone() {\r\n const obj = new CSS2DObject(this._element);\r\n obj.copy(this);\r\n return obj;\r\n }\r\n}\r\n\r\nexport default CSS2DObject;\r\n","import * as THREE from 'three';\r\n\r\nclass RCGroup extends THREE.Group {\r\n raycast(raycaster, intersects) {\r\n if (!this.visible) {\r\n return;\r\n }\r\n\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n children[i].raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].enableSubset) {\r\n children[i].enableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].disableSubset) {\r\n children[i].disableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n isEmpty() {\r\n return this.children.length === 0;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].updateToFrame) {\r\n children[i].updateToFrame(frameData);\r\n }\r\n }\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n Array.prototype.push.apply(totalSubset, children[i].getSubset(mask, innerOnly));\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default RCGroup;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport CSS2DObject from './CSS2DObject';\r\nimport RCGroup from './RCGroup';\r\nimport vertexScreenQuadShader from './shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromTex from './shaders/ScreenQuadFromTex.frag';\r\nimport fragmentScreenQuadFromTexWithDistortion from './shaders/ScreenQuadFromTexWithDistortion.frag';\r\n\r\nconst LAYERS = {\r\n DEFAULT: 0, VOLUME: 1, TRANSPARENT: 2, PREPASS_TRANSPARENT: 3, VOLUME_BFPLANE: 4, COLOR_FROM_POSITION: 5, SHADOWMAP: 6,\r\n};\r\n\r\nconst SELECTION_LAYERS = [ // These layers, that are used in the selection by ray casting\r\n LAYERS.DEFAULT, LAYERS.TRANSPARENT,\r\n];\r\n\r\nTHREE.Object3D.prototype.resetTransform = function () {\r\n this.position.set(0, 0, 0);\r\n this.quaternion.set(0, 0, 0, 1);\r\n this.scale.set(1, 1, 1);\r\n};\r\n\r\n// update world matrix of this object and all its ancestors\r\nTHREE.Object3D.prototype.updateMatrixWorldRecursive = function () {\r\n if (this.parent != null) {\r\n this.parent.updateMatrixWorldRecursive();\r\n }\r\n this.updateMatrixWorld();\r\n};\r\n// add object to parent, saving objects' world transform\r\nTHREE.Object3D.prototype.addSavingWorldTransform = (function () {\r\n const _worldMatrixInverse = new THREE.Matrix4();\r\n\r\n return function (object) {\r\n if (object instanceof THREE.Object3D) {\r\n _worldMatrixInverse.copy(this.matrixWorld).invert();\r\n _worldMatrixInverse.multiply(object.matrixWorld);\r\n object.matrix.copy(_worldMatrixInverse);\r\n object.matrix.decompose(object.position, object.quaternion, object.scale);\r\n this.add(object);\r\n }\r\n };\r\n}());\r\n\r\n// render a tiny transparent quad in the center of the screen\r\nTHREE.WebGLRenderer.prototype.renderDummyQuad = (function () {\r\n const _material = new THREE.MeshBasicMaterial({ transparent: true, opacity: 0.0, depthWrite: false });\r\n\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(0.01, 0.01), _material);\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function () {\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuad = (function () {\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(1.0, 1.0));\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function (material) {\r\n _quad.material = material;\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.isIdentity = (function () {\r\n const identity = new THREE.Matrix4();\r\n return function () {\r\n return identity.equals(this);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.applyToPointsArray = function (array, stride, w) {\r\n if (!array || !stride || stride < 3) {\r\n return array;\r\n }\r\n w = w || 0; // use point as normal by default\r\n const e = this.elements;\r\n for (let i = 0; i < array.length; i += stride) {\r\n const x = array[i];\r\n const y = array[i + 1];\r\n const z = array[i + 2];\r\n\r\n const persp = 1 / (e[3] * x + e[7] * y + e[11] * z + e[15]);\r\n\r\n array[i] = (e[0] * x + e[4] * y + e[8] * z + e[12] * w) * persp;\r\n array[i + 1] = (e[1] * x + e[5] * y + e[9] * z + e[13] * w) * persp;\r\n array[i + 2] = (e[2] * x + e[6] * y + e[10] * z + e[14] * w) * persp;\r\n }\r\n return array;\r\n};\r\n\r\nclass ScreenQuadMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n if (params.uniforms === undefined) {\r\n params.uniforms = {};\r\n }\r\n params.uniforms.srcTex = { type: 't', value: null };\r\n params.vertexShader = vertexScreenQuadShader;\r\n params.transparent = false;\r\n params.depthTest = false;\r\n params.depthWrite = false;\r\n super(params);\r\n }\r\n}\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTex = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { opacity: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTex,\r\n transparent: true,\r\n });\r\n\r\n return function (srcTex, opacity) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.transparent = (opacity < 1.0);\r\n _material.uniforms.opacity.value = opacity;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTexWithDistortion = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { coef: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTexWithDistortion,\r\n });\r\n\r\n return function (srcTex, coef) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.uniforms.coef.value = coef;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\n/**\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setMinimalFov = function (angle) {\r\n if (this.aspect >= 1.0) {\r\n this.fov = angle;\r\n } else {\r\n this.fov = THREE.MathUtils.radToDeg(2 * Math.atan(Math.tan(THREE.MathUtils.degToRad(angle) * 0.5) / this.aspect));\r\n }\r\n};\r\n\r\n/**\r\n * @param {THREE.PerspectiveCamera} camera - Base camera for this stereo camera.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.StereoCamera.prototype.updateHalfSized = function (camera, angle) {\r\n const originalAspect = camera.aspect;\r\n const originalFov = camera.fov;\r\n\r\n camera.aspect = originalAspect / 2.0;\r\n camera.setMinimalFov(angle);\r\n camera.updateProjectionMatrix();\r\n\r\n this.update(camera);\r\n\r\n camera.aspect = originalAspect;\r\n camera.fov = originalFov;\r\n camera.updateProjectionMatrix();\r\n};\r\n\r\n/**\r\n * @param {number} radius - Radius of bounding sphere in angstroms to fit on screen.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setDistanceToFit = function (radius, angle) {\r\n this.position.z = radius / Math.sin(0.5 * THREE.MathUtils.degToRad(angle));\r\n};\r\n\r\n/**\r\n * @param {RCGroup} gfxObj - All objects on scene.\r\n * @param {THREE.PerspectiveCamera} camera - Camera used for rendering.\r\n * @param {number} clipPlane - Distance to clip plane.\r\n * @param {number} fogFarPlane - Distance to fog far plane.\r\n */\r\nTHREE.Raycaster.prototype.intersectVisibleObject = function (gfxObj, camera, clipPlane, fogFarPlane) {\r\n const intersects = this.intersectObject(gfxObj, false);\r\n if (intersects.length === 0) {\r\n return null;\r\n }\r\n\r\n // find point closest to camera that doesn't get clipped by camera near plane or clipPlane (if it exists)\r\n const nearPlane = Math.min(camera.near, clipPlane);\r\n let i;\r\n let p = intersects[0];\r\n const v = new THREE.Vector3();\r\n for (i = 0; i < intersects.length; ++i) {\r\n p = intersects[i];\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -nearPlane) {\r\n break;\r\n }\r\n }\r\n if (i === intersects.length) {\r\n return null;\r\n }\r\n\r\n // check that selected intersection point is not clipped by camera far plane or occluded by fog (if it exists)\r\n const farPlane = Math.min(camera.far, fogFarPlane);\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -farPlane) {\r\n return null;\r\n }\r\n return p;\r\n};\r\n\r\nTHREE.Matrix4.prototype.extractScale = (function () {\r\n const _v = new THREE.Vector3();\r\n\r\n return function (scale) {\r\n if (scale === undefined) {\r\n logger.debug('extractScale(): new is too expensive operation to do it on-the-fly');\r\n scale = _v.clone();\r\n }\r\n\r\n const te = this.elements;\r\n scale.x = _v.set(te[0], te[1], te[2]).length();\r\n scale.y = _v.set(te[4], te[5], te[6]).length();\r\n scale.z = _v.set(te[8], te[9], te[10]).length();\r\n\r\n // if determine is negative, we need to invert one scale\r\n const det = this.determinant();\r\n if (det < 0) {\r\n scale.x = -scale.x;\r\n }\r\n return scale;\r\n };\r\n}());\r\n\r\nfunction _calcCylinderMatrix(posBegin, posEnd, radius) {\r\n const posCenter = posBegin.clone().lerp(posEnd, 0.5);\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(radius, posBegin.distanceTo(posEnd), radius);\r\n\r\n const matRotHalf = new THREE.Matrix4();\r\n matRotHalf.makeRotationX(Math.PI / 2);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n const vUp = new THREE.Vector3(0, 1, 0);\r\n matRotLook.lookAt(posCenter, posEnd, vUp);\r\n\r\n matRotLook.multiply(matRotHalf);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(posCenter);\r\n return matRotLook;\r\n}\r\n\r\nfunction _calcChunkMatrix(eye, target, up, rad) {\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(rad.x, rad.y, 0);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n matRotLook.lookAt(eye, target, up);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(eye);\r\n\r\n return matRotLook;\r\n}\r\n\r\nfunction _groupHasGeometryToRender(group) {\r\n let hasGeoms = false;\r\n group.traverse((node) => {\r\n if (node.hasOwnProperty('geometry') || node instanceof CSS2DObject) {\r\n hasGeoms = true;\r\n }\r\n });\r\n return hasGeoms;\r\n}\r\n\r\nfunction _buildDistorionMesh(widthSegments, heightSegements, coef) {\r\n // solve equation r_u = r_d * (1 + k * r_d^2)\r\n // for r_d using iterations\r\n // takes: r_u^2\r\n // returns: r_d / r_u factor that can be used to distort point coords\r\n function calcInverseBarrel(r2) {\r\n const epsilon = 1e-5;\r\n let prevR2 = 0.0;\r\n let curR2 = r2;\r\n let dr = 1.0;\r\n while (Math.abs(curR2 - prevR2) > epsilon) {\r\n dr = 1.0 + coef * curR2;\r\n prevR2 = curR2;\r\n curR2 = r2 / (dr * dr);\r\n }\r\n\r\n return 1.0 / dr;\r\n }\r\n\r\n const geo = new THREE.PlaneGeometry(2.0, 2.0, widthSegments, heightSegements);\r\n\r\n const pos = geo.getAttribute('position');\r\n for (let i = 0; i < pos.count; ++i) {\r\n const x = pos.array[3 * i];\r\n const y = pos.array[3 * i + 1];\r\n const c = calcInverseBarrel(x * x + y * y);\r\n pos.setXY(i, c * x, c * y);\r\n }\r\n\r\n return geo;\r\n}\r\n\r\nTHREE.BufferAttribute.prototype.copyAtList = function (attribute, indexList) {\r\n console.assert(\r\n this.itemSize === attribute.itemSize,\r\n 'DEBUG: BufferAttribute.copyAtList buffers have different item size.',\r\n );\r\n const { itemSize } = this;\r\n for (let i = 0, n = indexList.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n this.array[i * itemSize + j] = attribute.array[indexList[i] * itemSize + j];\r\n }\r\n }\r\n return this;\r\n};\r\n\r\nfunction fillArray(array, value, startIndex, endIndex) {\r\n startIndex = (typeof startIndex !== 'undefined') ? startIndex : 0;\r\n endIndex = (typeof endIndex !== 'undefined') ? endIndex : array.length;\r\n for (let i = startIndex; i < endIndex; ++i) {\r\n array[i] = value;\r\n }\r\n}\r\n\r\n/** @param {THREE.Object3D} object - Parent object. */\r\nfunction removeChildren(object) {\r\n const { children } = object;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n child.parent = null;\r\n child.dispatchEvent({ type: 'removed' });\r\n }\r\n object.children = [];\r\n}\r\n\r\nfunction clearTree(object) {\r\n object.traverse((obj) => {\r\n if (obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line) {\r\n obj.geometry.dispose();\r\n }\r\n });\r\n removeChildren(object);\r\n}\r\n\r\nfunction destroyObject(object) {\r\n clearTree(object);\r\n if (object.parent) {\r\n object.parent.remove(object);\r\n } else {\r\n object.dispatchEvent({ type: 'removed' });\r\n }\r\n}\r\n\r\nfunction belongToSelectLayers(object) {\r\n for (let i = 0; i < SELECTION_LAYERS.length; i++) {\r\n if (((object.layers.mask >> SELECTION_LAYERS[i]) & 1) === 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n}\r\n\r\nfunction processObjRenderOrder(root, idMaterial) {\r\n // set renderOrder to 0 for Backdrop and to 1 in other cases to render Backdrop earlier all other materials\r\n const renderOrder = +(idMaterial !== 'BA');\r\n root.traverse((object) => {\r\n if (object.isGroup) {\r\n object.renderOrder = renderOrder;\r\n }\r\n });\r\n}\r\n\r\nfunction applySelectionMaterial(geo) {\r\n geo.traverse((node) => {\r\n if ('material' in node) {\r\n node.material = node.material.clone(true);\r\n // using z-offset to magically fix selection rendering artifact (on z-sprites)\r\n node.material.setValues({\r\n depthFunc: THREE.LessEqualDepth,\r\n overrideColor: true,\r\n fog: false,\r\n lights: false,\r\n shadowmap: false,\r\n });\r\n node.material.setUberOptions({ fixedColor: new THREE.Color(0xFFFF00), zOffset: -1e-6 });\r\n }\r\n });\r\n}\r\n\r\nfunction getMiddlePoint(point1, point2, optionalTarget) {\r\n const result = optionalTarget || new THREE.Vector3();\r\n\r\n result.set(0, 0, 0);\r\n result.addScaledVector(point1, 0.5);\r\n result.addScaledVector(point2, 0.5);\r\n\r\n return result;\r\n}\r\n\r\n// Monkey-patch for \"InstancedBufferGeometry.instanceCount becomes undefined after copy()\"\r\n// https://github.com/mrdoob/three.js/issues/22151\r\nconst _oldInstancedBufferGeometryCopy = THREE.InstancedBufferGeometry.prototype.copy;\r\n\r\nTHREE.InstancedBufferGeometry.prototype.copy = function (source) {\r\n _oldInstancedBufferGeometryCopy.call(this, source);\r\n if (this.instanceCount === undefined) {\r\n this.instanceCount = Infinity;\r\n }\r\n};\r\n\r\nexport default {\r\n calcCylinderMatrix: _calcCylinderMatrix,\r\n calcChunkMatrix: _calcChunkMatrix,\r\n groupHasGeometryToRender: _groupHasGeometryToRender,\r\n buildDistorionMesh: _buildDistorionMesh,\r\n RCGroup,\r\n fillArray,\r\n clearTree,\r\n destroyObject,\r\n belongToSelectLayers,\r\n processObjRenderOrder,\r\n applySelectionMaterial,\r\n getMiddlePoint,\r\n LAYERS,\r\n};\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfx/gfxutils';\r\n\r\nconst _defaultBoundaries = {\r\n boundingBox: new THREE.Box3(new THREE.Vector3(-1, -1, -1), new THREE.Vector3(1, 1, 1)),\r\n boundingSphere: new THREE.Sphere(new THREE.Vector3(0, 0, 0), 1),\r\n};\r\n\r\nclass Visual extends gfxutils.RCGroup {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this.name = name;\r\n this._dataSource = dataSource;\r\n }\r\n\r\n release() {\r\n if (this.parent) {\r\n this.parent.remove(this);\r\n }\r\n }\r\n\r\n getDataSource() {\r\n return this._dataSource;\r\n }\r\n\r\n getBoundaries() {\r\n return _defaultBoundaries;\r\n }\r\n}\r\n\r\nexport default Visual;\r\n","function _ensureArray(x) {\r\n if (x === null || x === undefined || Array.isArray(x)) {\r\n return x;\r\n }\r\n return [x];\r\n}\r\n\r\n/** An indexed list of objects or classes. */\r\nclass EntityList {\r\n /**\r\n * Create a list of objects.\r\n * The objects can be indexed by one or more properties for the later retrieval.\r\n *\r\n * @param {!Array=} entities A list of objects to automatically register at creation time.\r\n * @param {!Array=} indices A list of property names to use for case-insensitive indexing.\r\n * By default, a single `.id` property is used.\r\n * @see EntityList#register\r\n */\r\n constructor(entities = [], indices = ['id']) {\r\n this._list = [];\r\n this._dict = {};\r\n this._indices = [...indices];\r\n this._indices.forEach((index) => {\r\n this._dict[index] = {};\r\n });\r\n\r\n entities.forEach((entity) => this.register(entity));\r\n }\r\n\r\n /**\r\n * Add a value to the end of a list.\r\n * The list will contain only one copy of the value.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromList\r\n * @see EntityList.registerInDict\r\n */\r\n static registerInList(list, value) {\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n }\r\n\r\n /**\r\n * Remove a value from a list if it is there.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to remove.\r\n * @see EntityList.registerInList\r\n */\r\n static unregisterFromList(list, value) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n }\r\n\r\n /**\r\n * Add a value to a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromDict\r\n * @see EntityList.registerInList\r\n */\r\n static registerInDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key] = dict[key] || [];\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Remove a value from a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.registerInDict\r\n */\r\n static unregisterFromDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key];\r\n if (list) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n if (list.length === 0) {\r\n delete dict[key];\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Add an entity to this list.\r\n *\r\n * @param {!Object} entity An object or a class to register. The object must include all\r\n * properties specified as indices on construction.\r\n * @see EntityList#unregister\r\n */\r\n register(entity) {\r\n EntityList.registerInList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.registerInDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * Remove an entity from this list.\r\n *\r\n * @param {!Object} entity An object or a class to unregister. The object may be\r\n * missing from the list but it must include all properties specified as indices\r\n * on construction.\r\n * @see EntityList#register\r\n */\r\n unregister(entity) {\r\n EntityList.unregisterFromList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.unregisterFromDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * An ordered list of all registered entities.\r\n * It is a read-only copy, use {@link EntityList#register} and {@link EntityList#unregister}\r\n * to modify it.\r\n *\r\n * @type {!Array}\r\n */\r\n get all() {\r\n return [...this._list];\r\n }\r\n\r\n /**\r\n * The first registered entity.\r\n * Use it if you do not care which entity you are referring to.\r\n *\r\n * @type {Object=}\r\n */\r\n get first() {\r\n return this._list[0];\r\n }\r\n\r\n /**\r\n * Retrieve a list of keys for the index.\r\n *\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {!Array} An unordered list of keys in the index, i.e. particular property\r\n * values for all registered entities.\r\n */\r\n keys(index) {\r\n return Object.keys(this._dict[index || this._indices[0]]);\r\n }\r\n\r\n /**\r\n * Retrieve an entity by its key.\r\n *\r\n * @param {string} key A case-insensitive property value to look-up.\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {Object=} An object registered in the index under the key. If there are multiple\r\n * objects under the same key, the first one is returned.\r\n */\r\n get(key, index) {\r\n const dict = this._dict[index || this._indices[0]];\r\n if (dict) {\r\n const values = dict[key && key.toLowerCase()];\r\n return values && values.length > 0 ? values[0] : undefined;\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nexport default EntityList;\r\n","import settings from '../settings';\r\nimport logger from './logger';\r\n\r\nfunction makeContextDependent(prototype) {\r\n Object.defineProperties(prototype, {\r\n logger: {\r\n get() {\r\n return this.context && this.context.logger ? this.context.logger : logger;\r\n },\r\n },\r\n settings: {\r\n get() {\r\n return this.context && this.context.settings ? this.context.settings : settings;\r\n },\r\n },\r\n });\r\n}\r\n\r\nexport default makeContextDependent;\r\n","import * as THREE from 'three';\r\n\r\nclass CollisionSphere {\r\n constructor(position, radius) {\r\n this._position = position;\r\n this._radius = radius;\r\n }\r\n\r\n static _sphere = new THREE.Sphere();\r\n\r\n raycast(raycaster) {\r\n const sphere = CollisionSphere._sphere;\r\n sphere.set(this._position, this._radius);\r\n\r\n const p = new THREE.Vector3();\r\n if (raycaster.ray.intersectSphere(sphere, p)) {\r\n return {\r\n distance: raycaster.ray.origin.distanceTo(p),\r\n point: p,\r\n };\r\n }\r\n return null;\r\n }\r\n}\r\n\r\nconst SphereCollisionGeo = (base) => class extends base {\r\n constructor(count, ...args) {\r\n super(...args);\r\n this._objects = new Array(count);\r\n this.boundingSphere = null;\r\n this.boundingBox = null;\r\n }\r\n\r\n setSphere(idx, position, radius) {\r\n this._objects[idx] = new CollisionSphere(position, radius);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n // TODO raycast with bounding sphere? How to deal with updates?\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const inters = this._objects[i].raycast(raycaster);\r\n if (inters) {\r\n inters.chunkIdx = i;\r\n intersects.push(inters);\r\n }\r\n }\r\n }\r\n\r\n computeBoundingBox() {\r\n const objects = this._objects;\r\n let { boundingBox } = this;\r\n if (boundingBox === null) {\r\n this.boundingBox = boundingBox = new THREE.Box3();\r\n }\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n boundingBox.expandByPoint(objects[i]._position);\r\n }\r\n }\r\n\r\n computeBoundingSphere() {\r\n this.computeBoundingBox();\r\n const objects = this._objects;\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n const pos = objects[i]._position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n if (this.boundingSphere === null) {\r\n this.boundingSphere = new THREE.Sphere();\r\n }\r\n this.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n};\r\nexport default SphereCollisionGeo;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst tmpColor = new THREE.Color();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\nclass InstancedSpheresGeometry extends SphereCollisionGeo(THREE.InstancedBufferGeometry) {\r\n constructor(spheresCount, sphereComplexity, useZSprites) {\r\n super(spheresCount);\r\n this._sphGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new THREE.SphereGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI);\r\n this._init(spheresCount, this._sphGeometry);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n setArrayXYZW(this._offsets, itemIdx * OFFSET_SIZE, itemPos.x, itemPos.y, itemPos.z, itemRad);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n\r\n setColor(itemIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n setArrayXYZ(this._colors, itemIdx * COLOR_SIZE, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('offset').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[chunkIndices[i]] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._sphGeometry);\r\n\r\n copySubArrays(this._offsets, geom._offsets, chunkIndices, OFFSET_SIZE);\r\n copySubArrays(this._colors, geom._colors, chunkIndices, COLOR_SIZE);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(spheresCount, sphereGeo) {\r\n this.copy(sphereGeo);\r\n\r\n this._offsets = utils.allocateTyped(Float32Array, spheresCount * OFFSET_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, spheresCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('offset', new THREE.InstancedBufferAttribute(this._offsets, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._colors, COLOR_SIZE, false, 1));\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(alpha, 1, false, 1));\r\n }\r\n}\r\nexport default InstancedSpheresGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VEC_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n */\r\n\r\nclass ChunkedObjectsGeometry extends THREE.BufferGeometry {\r\n constructor(chunkGeo, chunksCount) {\r\n super();\r\n\r\n if (this.constructor === ChunkedObjectsGeometry) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n\r\n this._chunkGeo = chunkGeo;\r\n\r\n this._init(chunkGeo, chunksCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('normal').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n const idx = i * VEC_SIZE;\r\n colors[idx] = tmpColor.r;\r\n colors[idx + 1] = tmpColor.g;\r\n colors[idx + 2] = tmpColor.b;\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n _.fill(alphaArr, value, left, left + chunkSize);\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n // use THREE.Mesh raycasting interface for the Geometry. The Mesh is\r\n // created with existed geometry and default material, so it doesn't slowdown.\r\n const mesh = new THREE.Mesh();\r\n mesh.geometry = this;\r\n mesh.raycast(raycaster, inters);\r\n\r\n const facesPerChunk = this._chunkGeo.index.count / 3;\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('faceIndex')) {\r\n continue;\r\n }\r\n inters[i].chunkIdx = Math.floor(inters[i].faceIndex / facesPerChunk);\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.BufferGeometry();\r\n this._init.call(geom, this._chunkGeo, instanceCount);\r\n\r\n const srcPos = this._positions;\r\n const srcNorm = this._normals;\r\n const srcColor = this._colors;\r\n\r\n const dstPos = geom._positions;\r\n const dstNorm = geom._normals;\r\n const dstColor = geom._colors;\r\n\r\n const chunkSize = this._chunkSize * VEC_SIZE;\r\n\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const ptIdxBegin = chunkIndices[i] * chunkSize;\r\n const ptIdxEnd = ptIdxBegin + chunkSize;\r\n dstPos.set(srcPos.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstNorm.set(srcNorm.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstColor.set(srcColor.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n }\r\n\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(chunkGeo, chunksCount) {\r\n const chunkSize = this._chunkSize = chunkGeo.attributes.position.count;\r\n const chunkIndex = chunkGeo.index.array;\r\n const chunkIndexSize = chunkIndex.length;\r\n const pointsCount = this._chunkSize * chunksCount;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n const indexSize = chunkIndexSize * chunksCount;\r\n const index = this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, indexSize);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._normals = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n for (let i = 0; i < chunksCount; ++i) {\r\n const offset = i * chunkIndexSize;\r\n const posOffset = i * chunkSize;\r\n index.set(chunkIndex, offset);\r\n for (let j = 0; j < chunkIndexSize; ++j) {\r\n index[offset + j] += posOffset;\r\n }\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, VEC_SIZE));\r\n this.setAttribute('normal', new THREE.BufferAttribute(this._normals, VEC_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, VEC_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n }\r\n}\r\nexport default ChunkedObjectsGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst VEC_SIZE = 3;\r\n\r\nclass SimpleSpheresGeometry extends SphereCollisionGeo(ChunkedObjectsGeometry) {\r\n constructor(spheresCount, sphereComplexity) {\r\n const sphGeometry = new THREE.SphereGeometry(\r\n 1,\r\n sphereComplexity * 2,\r\n sphereComplexity,\r\n 0,\r\n Math.PI * 2,\r\n 0,\r\n Math.PI,\r\n );\r\n super(spheresCount, sphGeometry, spheresCount);\r\n\r\n const normals = this._normals;\r\n const geoNormals = sphGeometry.attributes.normal.array;\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._tmpPositions = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n for (let i = 0; i < spheresCount; ++i) {\r\n normals.set(geoNormals, chunkSize * VEC_SIZE * i);\r\n }\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n const tmpPos = this._tmpPositions;\r\n const chunkSize = this._chunkSize;\r\n const geoPos = this._chunkPos;\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n const idx = i * 3;\r\n tmpPos[idx] = itemPos.x + geoPos[idx] * itemRad;\r\n tmpPos[idx + 1] = itemPos.y + geoPos[idx + 1] * itemRad;\r\n tmpPos[idx + 2] = itemPos.z + geoPos[idx + 2] * itemRad;\r\n }\r\n\r\n this._positions.set(tmpPos, chunkSize * itemIdx * VEC_SIZE);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n}\r\nexport default SimpleSpheresGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst centerPos = new THREE.Vector3();\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass Simple2CCylindersGeometry extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, 2 * instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const firstOffset = chunkSize * 2 * itemIdx * VEC_SIZE;\r\n const secondOffset = firstOffset + chunkSize * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n centerPos.lerpVectors(botPos, topPos, 0.5);\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, centerPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, firstOffset);\r\n\r\n // now shift center to get another part of the cylinder\r\n centerPos.sub(botPos);\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpArray[idx] += centerPos.x;\r\n tmpArray[idx + 1] += centerPos.y;\r\n tmpArray[idx + 2] += centerPos.z;\r\n }\r\n this._positions.set(tmpArray, secondOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, firstOffset);\r\n this._normals.set(tmpArray, secondOffset);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const first = 2 * itemIdx;\r\n super.setColor(first, colorVal1);\r\n\r\n const second = first + 1;\r\n super.setColor(second, colorVal2);\r\n }\r\n}\r\n\r\nexport default Simple2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_POINTS_COUNT_16BIT = 65536;\r\nconst PTS_PER_TRIANGLE = 3;\r\n\r\nclass CylinderBufferGeometry extends THREE.BufferGeometry {\r\n constructor(\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n ) {\r\n super();\r\n\r\n const thetaStart = 0;\r\n const thetaLength = 2 * Math.PI;\r\n\r\n this.type = 'CylinderBufferGeometry';\r\n\r\n this.parameters = {\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n };\r\n\r\n const hasTop = openEnded === false && radiusTop > 0;\r\n const hasBottom = openEnded === false && radiusBottom > 0;\r\n const vertexCount = (heightSegments + 1) * radialSegments\r\n + hasTop * (radialSegments + 1)\r\n + hasBottom * (radialSegments + 1);\r\n const facesCount = (2 * heightSegments + hasTop + hasBottom) * radialSegments;\r\n\r\n const heightHalf = height / 2;\r\n\r\n const positions = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const normals = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const indices = new THREE.Uint16BufferAttribute(utils.allocateTyped(Uint16Array, facesCount * PTS_PER_TRIANGLE), 1);\r\n\r\n const uvs = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 2), 2);\r\n console.assert(vertexCount < MAX_POINTS_COUNT_16BIT, 'DEBUG: Cylinder Geometry has too many vertices (65536 max).');\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n const tanTheta = -(radiusBottom - radiusTop) / height;\r\n\r\n // setup cylinder data\r\n for (let y = 0; y <= heightSegments; y++) {\r\n // faces\r\n if (y !== heightSegments) {\r\n for (let i = 0; i < radialSegments; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + radialSegments + i;\r\n const v3 = currVtxIdx + radialSegments + ((i + 1) % radialSegments);\r\n const v4 = currVtxIdx + ((i + 1) % radialSegments);\r\n\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n // vertices\r\n const v = y / heightSegments;\r\n const radius = v * (radiusBottom - radiusTop) + radiusTop;\r\n\r\n for (let x = 0; x < radialSegments; x++) {\r\n const u = x / radialSegments;\r\n\r\n const vx = radius * Math.sin(u * thetaLength + thetaStart);\r\n const vy = v * height - heightHalf;\r\n const vz = radius * Math.cos(u * thetaLength + thetaStart);\r\n\r\n const normal = new THREE.Vector3(\r\n vx,\r\n Math.sqrt(vx * vx + vz * vz) * tanTheta,\r\n vz,\r\n ).normalize();\r\n\r\n positions.setXYZ(currVtxIdx, vx, vy, vz);\r\n normals.setXYZ(currVtxIdx, normal.x, normal.y, normal.z);\r\n uvs.setXY(currVtxIdx, u, v);\r\n ++currVtxIdx;\r\n }\r\n }\r\n\r\n // top cap\r\n if (hasTop) {\r\n const startTIdx = currVtxIdx;\r\n const lastIdx = currVtxIdx + radialSegments;\r\n for (let fTIdx = 0; fTIdx < radialSegments; ++fTIdx) {\r\n const currSrcIdx = currVtxIdx - radialSegments;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcIdx),\r\n positions.getY(currSrcIdx),\r\n positions.getZ(currSrcIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n\r\n const nextTVtx = startTIdx + ((fTIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, currVtxIdx, nextTVtx, lastIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n ++currVtxIdx;\r\n }\r\n\r\n // bottom cap\r\n if (hasBottom) {\r\n const startBIdx = currVtxIdx;\r\n const lastBIdx = currVtxIdx + radialSegments;\r\n for (let fBIdx = 0; fBIdx < radialSegments; ++fBIdx) {\r\n const currSrcBIdx = fBIdx;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcBIdx),\r\n positions.getY(currSrcBIdx),\r\n positions.getZ(currSrcBIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n\r\n const nextBVtx = startBIdx + ((fBIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, nextBVtx, currVtxIdx, lastBIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, -heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n }\r\n\r\n this.setIndex(indices);\r\n this.setAttribute('position', positions);\r\n this.setAttribute('normal', normals);\r\n this.setAttribute('uv', uvs);\r\n }\r\n\r\n clone() {\r\n const { parameters } = this;\r\n\r\n return new CylinderBufferGeometry(\r\n parameters.radiusTop,\r\n parameters.radiusBottom,\r\n parameters.height,\r\n parameters.radialSegments,\r\n parameters.heightSegments,\r\n parameters.openEnded,\r\n );\r\n }\r\n}\r\n\r\nexport default CylinderBufferGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport CylinderBufferGeometry from './CylinderBufferGeometry';\r\n\r\nconst tmpColor = new THREE.Color();\r\nconst invMatrix = new THREE.Matrix4();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction sortNumber(a, b) {\r\n return a - b;\r\n}\r\n\r\nfunction _prepareCylinderInfo(chunkIndices) {\r\n chunkIndices.sort(sortNumber);\r\n const chunksIdx = [];\r\n const cylinderInfo = [];\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const val = chunkIndices[i];\r\n const even = (val | 0) % 2 === 0;\r\n const newPar = {\r\n first: false,\r\n second: false,\r\n };\r\n if (even) {\r\n newPar.first = true;\r\n newPar.second = i + 1 < n && chunkIndices[i + 1] === chunkIndices[i] + 1;\r\n if (newPar.second) {\r\n ++i;\r\n }\r\n } else {\r\n newPar.second = true;\r\n }\r\n chunksIdx.push(Math.floor(val / 2));\r\n cylinderInfo.push(newPar);\r\n }\r\n return { indices: chunksIdx, cylinderInfo };\r\n}\r\n\r\nfunction _assignOpacity(cylinderInfo, color1, color2) {\r\n for (let i = 0, n = cylinderInfo.length; i < n; ++i) {\r\n const info = cylinderInfo[i];\r\n if (!info.first) {\r\n color1[COLOR_SIZE * i] = -0.5;\r\n }\r\n if (!info.second) {\r\n color2[COLOR_SIZE * i] = -0.5;\r\n }\r\n }\r\n}\r\nclass Instanced2CCylindersGeometry extends THREE.InstancedBufferGeometry {\r\n constructor(instanceCount, polyComplexity, useZSprites, openEnded) {\r\n super();\r\n this._useZSprites = useZSprites;\r\n this._cylGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new CylinderBufferGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, openEnded);\r\n this._init(instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n this._collisionGeo = new Simple2CCylindersGeometry(instanceCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const matrix = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n let me = matrix.elements;\r\n const mtxOffset = itemIdx * OFFSET_SIZE;\r\n\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, itemRad);\r\n setArrayXYZW(this._matVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._matVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._matVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n\r\n if (this._useZSprites) {\r\n invMatrix.copy(matrix).invert();\r\n me = invMatrix.elements;\r\n setArrayXYZW(this._invmatVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._invmatVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._invmatVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n }\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const colorIdx = itemIdx * COLOR_SIZE;\r\n tmpColor.set(colorVal1);\r\n setArrayXYZ(this._color1, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n tmpColor.set(colorVal2);\r\n setArrayXYZ(this._color2, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n computeBoundingSphere() {\r\n this._collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = this._collisionGeo.boundingSphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n this._collisionGeo.computeBoundingBox();\r\n this.boundingBox = this._collisionGeo.boundingBox;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('matVector1').needsUpdate = true;\r\n this.getAttribute('matVector2').needsUpdate = true;\r\n this.getAttribute('matVector3').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('color2').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n if (this._useZSprites) {\r\n this.getAttribute('invmatVector1').needsUpdate = true;\r\n this.getAttribute('invmatVector2').needsUpdate = true;\r\n this.getAttribute('invmatVector3').needsUpdate = true;\r\n }\r\n\r\n this._collisionGeo.finishUpdate();\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[Math.floor(chunkIndices[i] / 2)] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const info = _prepareCylinderInfo(chunkIndices);\r\n const cylinderIndices = info.indices;\r\n const instanceCount = cylinderIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n copySubArrays(this._matVector1, geom._matVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector2, geom._matVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector3, geom._matVector3, cylinderIndices, OFFSET_SIZE);\r\n\r\n if (this._useZSprites) {\r\n copySubArrays(this._invmatVector1, geom._invmatVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector2, geom._invmatVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector3, geom._invmatVector3, cylinderIndices, OFFSET_SIZE);\r\n }\r\n\r\n copySubArrays(this._color1, geom._color1, cylinderIndices, COLOR_SIZE);\r\n copySubArrays(this._color2, geom._color2, cylinderIndices, COLOR_SIZE);\r\n _assignOpacity(info.cylinderInfo, geom._color1, geom._color2);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n getGeoParams() {\r\n return this._cylGeometry.parameters;\r\n }\r\n\r\n _init(instanceCount, cylinderGeo, useZSprites) {\r\n this.copy(cylinderGeo);\r\n this._matVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._color1 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n this._color2 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, instanceCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('matVector1', new THREE.InstancedBufferAttribute(this._matVector1, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector2', new THREE.InstancedBufferAttribute(this._matVector2, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector3', new THREE.InstancedBufferAttribute(this._matVector3, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._color1, COLOR_SIZE, false, 1));\r\n this.setAttribute('color2', new THREE.InstancedBufferAttribute(this._color2, COLOR_SIZE, false, 1));\r\n\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(this._alpha, 1, false, 1));\r\n\r\n if (useZSprites) {\r\n this._invmatVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n\r\n this.setAttribute(\r\n 'invmatVector1',\r\n new THREE.InstancedBufferAttribute(this._invmatVector1, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector2',\r\n new THREE.InstancedBufferAttribute(this._invmatVector2, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector3',\r\n new THREE.InstancedBufferAttribute(this._invmatVector3, OFFSET_SIZE, false, 1),\r\n );\r\n }\r\n }\r\n}\r\n\r\nexport default Instanced2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst TRI_SIZE = 3;\r\nconst tmpPrev = new THREE.Vector3();\r\nconst tmpNext = new THREE.Vector3();\r\nconst tmpRes = new THREE.Vector3();\r\nconst simpleNormal = new THREE.Vector3(1.0, 0.0, 0.0);\r\nconst normalOnCut = new THREE.Vector3();\r\nconst nearRingPt = new THREE.Vector3();\r\n\r\nfunction _createExtrudedChunkGeometry(shape, ringsCount) {\r\n const geo = new THREE.BufferGeometry();\r\n const ptsCount = shape.length;\r\n const totalPts = ptsCount * ringsCount;\r\n const type = totalPts <= 65536 ? Uint16Array : Uint32Array;\r\n const facesPerChunk = (ringsCount - 1) * ptsCount * 2;\r\n const indices = new THREE.BufferAttribute(utils.allocateTyped(type, facesPerChunk * TRI_SIZE), 1);\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n for (let y = 0; y < ringsCount; y++) {\r\n // faces\r\n if (y !== ringsCount - 1) {\r\n for (let i = 0; i < ptsCount; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + ptsCount + i;\r\n const v3 = currVtxIdx + ptsCount + ((i + 1) % ptsCount);\r\n const v4 = currVtxIdx + ((i + 1) % ptsCount);\r\n\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n currVtxIdx += ptsCount;\r\n }\r\n\r\n geo.setIndex(indices);\r\n const pos = utils.allocateTyped(Float32Array, totalPts * VEC_SIZE);\r\n geo.setAttribute('position', new THREE.BufferAttribute(pos, VEC_SIZE));\r\n\r\n geo._positions = shape;\r\n\r\n return geo;\r\n}\r\n\r\nclass ExtrudedObjectsGeometry extends ChunkedObjectsGeometry {\r\n constructor(shape, ringsCount, chunksCount) {\r\n const chunkGeo = _createExtrudedChunkGeometry(shape, ringsCount);\r\n super(chunkGeo, chunksCount);\r\n this._ringsCount = ringsCount;\r\n\r\n const tmpShape = this._tmpShape = [];\r\n for (let i = 0; i < shape.length; ++i) {\r\n tmpShape[i] = new THREE.Vector3();\r\n }\r\n }\r\n\r\n setItem(itemIdx, matrices, hasSlope = false, hasCut = false) {\r\n const ptsCount = this._chunkGeo._positions.length;\r\n const ringsCount = this._ringsCount;\r\n const chunkStartIdx = ptsCount * this._ringsCount * itemIdx * VEC_SIZE;\r\n\r\n this._setPoints(matrices, ptsCount, ringsCount, chunkStartIdx);\r\n\r\n if (hasSlope) {\r\n this._setSlopeNormals(ptsCount, ringsCount, chunkStartIdx);\r\n } else {\r\n this._setBaseNormals(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n\r\n if (hasCut) {\r\n this._addCut(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n }\r\n\r\n _setPoints(matrices, ptsCount, ringsCount, chunkStartIdx) {\r\n const tmpShape = this._tmpShape;\r\n const positions = this._positions;\r\n const shape = this._chunkGeo._positions;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i) {\r\n const mtx = matrices[i];\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpShape[j].copy(shape[j]).applyMatrix4(mtx).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _setBaseNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, false);\r\n }\r\n }\r\n\r\n _setSlopeNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const normals = this._normals;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First ring\r\n // In all cases, besides cut, second ring is coincident to first. So values of first ring's normals doesn't\r\n // matter (In the cut case special handler will be applied later and will set them to correct values)\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n simpleNormal.toArray(normals, vtxIdx);\r\n }\r\n // second ring\r\n // If it isn't first Item we take normals' values from the last ring of the previous item (these rings are coincident)\r\n // else we count normals' values based on next ring information\r\n if (vtxIdx - 2 * nPtsInRing > 0) {\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(normals, vtxIdx - 2 * nPtsInRing).toArray(normals, vtxIdx);\r\n }\r\n } else {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, +nPtsInRing);\r\n vtxIdx += nPtsInRing;\r\n }\r\n // other rings\r\n // we count normals' values based on previous ring information\r\n for (let i = 2; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, -nPtsInRing);\r\n }\r\n }\r\n\r\n // Counting normals:\r\n // - Slope\r\n // Radius changes throught part => normals aren't parallel with the plane contains section points\r\n // normal = vTangentInSectionPlane x vToSuchPointInPrevSection (all vectors are scaled for being 1 in length)\r\n // - No slope\r\n // Radius doesn't change throught part => normals are parallel with the plane contains section points\r\n // normal = vToPrevPointInSection + vToNextPointInSection (all vectors are scaled for being 1 in length)\r\n _countNormalsInRing(ptsCount, vtxIdx, isSlope, shiftToExtraPt) {\r\n const tmpShape = this._tmpShape;\r\n const normals = this._normals;\r\n\r\n tmpShape[0].fromArray(this._positions, vtxIdx);\r\n tmpShape[ptsCount - 1].fromArray(this._positions, vtxIdx + (ptsCount - 1) * VEC_SIZE);\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n if (j < ptsCount - 1) {\r\n tmpShape[j + 1].fromArray(this._positions, vtxIdx + VEC_SIZE);\r\n }\r\n\r\n if (isSlope) {\r\n nearRingPt.fromArray(this._positions, vtxIdx + shiftToExtraPt);\r\n\r\n tmpPrev.subVectors(tmpShape[(j + ptsCount - 1) % ptsCount], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], nearRingPt).normalize();\r\n tmpRes.crossVectors(tmpNext, tmpPrev).normalize().toArray(normals, vtxIdx);\r\n } else {\r\n tmpPrev.subVectors(tmpShape[j], tmpShape[(j + ptsCount - 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpRes.addVectors(tmpPrev, tmpNext).normalize().toArray(normals, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _addCut(ptsCount, ringsCount, chunkStartIdx) {\r\n // Nothing to do if item is flat or only line\r\n if (ptsCount < 3 || ringsCount < 2) {\r\n return;\r\n }\r\n const positions = this._positions;\r\n const normals = this._normals;\r\n const tmpShape = this._tmpShape;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n // Normal to the cut plane is equal to cross product of two vectors which are lying in it\r\n tmpShape[0].fromArray(positions, chunkStartIdx);\r\n tmpShape[1].fromArray(positions, chunkStartIdx + VEC_SIZE);\r\n tmpShape[2].fromArray(positions, chunkStartIdx + 2 * VEC_SIZE);\r\n\r\n tmpPrev.subVectors(tmpShape[1], tmpShape[0]).normalize();\r\n tmpNext.subVectors(tmpShape[1], tmpShape[2]).normalize();\r\n normalOnCut.crossVectors(tmpPrev, tmpNext).normalize();\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First and second rings normals' values are equal to value of normal to the cutting plane\r\n for (let j = 0; j < ptsCount * 2; ++j, vtxIdx += VEC_SIZE) {\r\n normalOnCut.toArray(normals, vtxIdx);\r\n }\r\n if (ringsCount > 2) {\r\n // Third ring points are coincident to first ring points, but have different normals. It makes sharp angle near cut\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(positions, vtxIdx - nPtsInRing).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default ExtrudedObjectsGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VERTEX_PER_SEGMENT = 4;\r\nconst POS_SIZE = 4;\r\nconst DIR_SIZE = 3;\r\nconst COL_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\nconst direction = new THREE.Vector3();\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction getSubset(arr, startSegmentIdx, segmentsCount, elemSize) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT;\r\n const end = start + segmentsCount * VERTEX_PER_SEGMENT;\r\n return arr.subarray(start * elemSize, end * elemSize);\r\n}\r\n\r\n/**\r\n * This class represents lines geometry which consists of screen-aligned narrow quad of variable width.\r\n *\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * collision geometry.\r\n */\r\n\r\nclass ThickLinesGeometry extends THREE.BufferGeometry {\r\n constructor(segmentsCount) {\r\n super();\r\n this._initVertices(segmentsCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n this.getAttribute('direction').needsUpdate = true;\r\n }\r\n\r\n setColor(segmentIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n setSegment(segmentIdx, pos1, pos2) {\r\n direction.subVectors(pos1, pos2);\r\n direction.normalize();\r\n const positions = this._positions;\r\n const directions = this._directions;\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n let dirIdx = segmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n }\r\n\r\n setOpacity(startSegIdx, endSegIdx, value) {\r\n const start = startSegIdx * VERTEX_PER_SEGMENT;\r\n const end = endSegIdx * VERTEX_PER_SEGMENT;\r\n _.fill(this.alpha, value, end, start);\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubsetSegments(startSegmentIdx, segmentsCount) {\r\n return [\r\n getSubset(this._positions, startSegmentIdx, segmentsCount, POS_SIZE),\r\n getSubset(this._directions, startSegmentIdx, segmentsCount, DIR_SIZE),\r\n ];\r\n }\r\n\r\n getSubsetColors(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._colors, startSegmentIdx, segmentsCount, COL_SIZE);\r\n }\r\n\r\n getSubsetOpacities(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._alpha, startSegmentIdx, segmentsCount, 1);\r\n }\r\n\r\n getNumVertexPerSegment() {\r\n return VERTEX_PER_SEGMENT;\r\n }\r\n\r\n getPositionSize() {\r\n return POS_SIZE;\r\n }\r\n\r\n setSegments(startSegmentIdx, positions) {\r\n const startPos = startSegmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n if (positions instanceof Array && positions.length === 2) {\r\n this._positions.set(positions[0], startPos);\r\n const startDir = startSegmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n this._directions.set(positions[1], startDir); // dirs are geo part of vertex\r\n } else {\r\n this._positions.set(positions, startPos);\r\n }\r\n }\r\n\r\n setColors(startSegmentIdx, colors) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n this._colors.set(colors, start);\r\n }\r\n\r\n _initVertices(segmentsCount) {\r\n this._buffersSize = segmentsCount * VERTEX_PER_SEGMENT;\r\n const pointsCount = this._buffersSize;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, segmentsCount * 6);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * POS_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * COL_SIZE);\r\n this._directions = utils.allocateTyped(Float32Array, pointsCount * DIR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n const index = this._index;\r\n let indexOffset = 0;\r\n let pointOffset = 0;\r\n for (let j = 0; j < segmentsCount; j++, indexOffset += 6, pointOffset += VERTEX_PER_SEGMENT) {\r\n index[indexOffset] = pointOffset;\r\n index[indexOffset + 1] = pointOffset + 1;\r\n index[indexOffset + 2] = pointOffset + 3;\r\n index[indexOffset + 3] = pointOffset;\r\n index[indexOffset + 4] = pointOffset + 2;\r\n index[indexOffset + 5] = pointOffset + 3;\r\n }\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, POS_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, COL_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n this.setAttribute('direction', new THREE.BufferAttribute(this._directions, DIR_SIZE));\r\n }\r\n}\r\n\r\nexport default ThickLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport BaseLinesGeometry from './ThickLinesGeometry';\r\n\r\n/**\r\n * This class represents geometry which consists lines. This can build bounding volumes\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n */\r\nclass LinesGeometry extends BaseLinesGeometry {\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n if (boundingBox) {\r\n boundingBox.getCenter(center);\r\n }\r\n const positions = this._positions;\r\n const sphere = this.boundingSphere || new THREE.Sphere();\r\n const size = this._positions.length;\r\n const pos = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n pos.set(positions[i], positions[i + 1], positions[i + 2]);\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n sphere.set(center, Math.sqrt(radiusSquared));\r\n this.boundingSphere = sphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n const positions = this._positions;\r\n const box = new THREE.Box3();\r\n const size = this._positions.length;\r\n const tmpVec = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n tmpVec.set(positions[i], positions[i + 1], positions[i + 2]);\r\n box.expandByPoint(tmpVec);\r\n }\r\n this.boundingBox = box;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n}\r\n\r\nexport default LinesGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass CylinderCollisionGeo extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const itemOffset = chunkSize * itemIdx * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, itemOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, itemOffset);\r\n }\r\n}\r\nexport default CylinderCollisionGeo;\r\n","import LinesGeometry from './LinesGeometry';\r\nimport CylinderCollisionGeo from './CylinderCollisionGeo';\r\n\r\nconst COLLISION_RAD = 0.1;\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n *\r\n * @param {number} chunksCount Total chunks count.\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * @param {boolean} enableCollision Enable or disable collision where each segment is\r\n * a collidable cylinder.\r\n * collision geometry.\r\n */\r\nclass ChunkedLinesGeometry extends LinesGeometry {\r\n constructor(chunksCount, segmentsCount, enableCollision) {\r\n super(chunksCount * segmentsCount);\r\n this._init(segmentsCount);\r\n this._collisionGeo = enableCollision ? new CylinderCollisionGeo(chunksCount * segmentsCount, 3) : null;\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = collisionGeo.boundingSphere;\r\n return;\r\n }\r\n super.computeBoundingSphere();\r\n }\r\n\r\n computeBoundingBox() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingBox();\r\n this.boundingBox = collisionGeo.boundingBox;\r\n return;\r\n }\r\n super.computeBoundingBox();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const collisionGeo = this._collisionGeo;\r\n if (!collisionGeo) {\r\n return;\r\n }\r\n const segCount = this._chunkSize;\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n for (let i = 0, n = intersects.length; i < n; ++i) {\r\n let { chunkIdx } = intersects[i];\r\n if (chunkIdx === undefined) {\r\n continue;\r\n }\r\n chunkIdx = (chunkIdx / segCount) | 0;\r\n intersects[i].chunkIdx = chunkIdx;\r\n }\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n super.setColor(i, colorVal);\r\n }\r\n }\r\n\r\n setSegment(chunkIdx, segIdx, pos1, pos2) {\r\n const chunkSize = this._chunkSize;\r\n const idx = chunkIdx * chunkSize + segIdx;\r\n super.setSegment(idx, pos1, pos2);\r\n if (this._collisionGeo) {\r\n this._collisionGeo.setItem(chunkIdx * chunkSize + segIdx, pos1, pos2, COLLISION_RAD);\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n super.setOpacity(left, left + chunkSize - 1, value);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const chunkSize = this._chunkSize;\r\n const subset = new ChunkedLinesGeometry(instanceCount, chunkSize, false);\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const startSegIdx = chunkIndices[i] * chunkSize;\r\n subset.setSegments(dstPtOffset, this.getSubsetSegments(startSegIdx, chunkSize));\r\n subset.setColors(dstPtOffset, this.getSubsetColors(startSegIdx, chunkSize));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(chunkSize) {\r\n this._chunkSize = chunkSize;\r\n }\r\n}\r\n\r\nexport default ChunkedLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport LinesGeometry from './LinesGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\n\r\nconst COLLISION_RAD = 0.3;\r\nconst tmpVector = new THREE.Vector3();\r\n\r\nclass TwoColorLinesGeometry extends LinesGeometry {\r\n constructor(segmentsCount) {\r\n super(segmentsCount * 2);\r\n this._init(segmentsCount);\r\n this._collisionGeo = new Simple2CCylindersGeometry(segmentsCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos) {\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, COLLISION_RAD);\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n tmpVector.lerpVectors(botPos, topPos, 0.5);\r\n super.setSegment(offset, botPos, tmpVector);\r\n super.setSegment(offset + 1, tmpVector, topPos);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n super.setColor(offset, colorVal1);\r\n super.setColor(offset + 1, colorVal2);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n if (this._collisionGeo) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n getSubset(segmentIndices) {\r\n const instanceCount = segmentIndices.length;\r\n const subset = new TwoColorLinesGeometry(instanceCount, false);\r\n for (let i = 0, n = instanceCount; i < n; ++i) {\r\n const startSegIdx = segmentIndices[i];\r\n subset.setSegments(i, this.getSubsetSegments(startSegIdx, 1));\r\n subset.setColors(i, this.getSubsetColors(startSegIdx, 1));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(segmentsCount) {\r\n this._segCounts = segmentsCount * 2;\r\n }\r\n}\r\n// (???)parent = LinesGeometry.prototype;\r\n\r\nexport default TwoColorLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst vectors = [\r\n new THREE.Vector3(1, 0, 0),\r\n new THREE.Vector3(-1, 0, 0),\r\n new THREE.Vector3(0, 1, 0),\r\n new THREE.Vector3(0, -1, 0),\r\n new THREE.Vector3(0, 0, 1),\r\n new THREE.Vector3(0, 0, -1),\r\n];\r\nconst vecCount = vectors.length;\r\nconst tempPos1 = new THREE.Vector3();\r\nconst tempPos2 = new THREE.Vector3();\r\n\r\nclass CrossGeometry extends SphereCollisionGeo(ChunkedLinesGeometry) {\r\n constructor(chunksCount) {\r\n super(chunksCount, chunksCount, (vecCount / 2) | 0, false);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n\r\n for (let i = 0; i < vecCount / 2; ++i) {\r\n const first = i * 2;\r\n tempPos1.x = itemPos.x + vectors[first].x * itemRad;\r\n tempPos1.y = itemPos.y + vectors[first].y * itemRad;\r\n tempPos1.z = itemPos.z + vectors[first].z * itemRad;\r\n const second = first + 1;\r\n tempPos2.x = itemPos.x + vectors[second].x * itemRad;\r\n tempPos2.y = itemPos.y + vectors[second].y * itemRad;\r\n tempPos2.z = itemPos.z + vectors[second].z * itemRad;\r\n this.setSegment(itemIdx, i, tempPos1, tempPos2);\r\n }\r\n }\r\n}\r\nexport default CrossGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst POS_RAD_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This is a base class for isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\nclass IsoSurfaceGeometry extends THREE.BufferGeometry {\r\n constructor(spheresCount, opts) {\r\n super();\r\n\r\n this._opts = opts;\r\n this.zClip = this._opts.zClip;\r\n this._posRad = utils.allocateTyped(Float32Array, spheresCount * POS_RAD_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n }\r\n\r\n setItem(chunkIdx, pos, radius) {\r\n const posRad = this._posRad;\r\n let idx = POS_RAD_SIZE * chunkIdx;\r\n posRad[idx++] = pos.x;\r\n posRad[idx++] = pos.y;\r\n posRad[idx++] = pos.z;\r\n posRad[idx] = radius;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n let idx = COLOR_SIZE * chunkIdx;\r\n colors[idx++] = tmpColor.r;\r\n colors[idx++] = tmpColor.g;\r\n colors[idx] = tmpColor.b;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n finishUpdate() {\r\n this._build();\r\n }\r\n\r\n setOpacity() {\r\n // not implemented\r\n }\r\n\r\n raycast() {\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\nexport default IsoSurfaceGeometry;\r\n","import utils from '../../utils';\r\n\r\n/**\r\n * Class for marching cube\r\n * Stores 8 points and 8 float values are stored together in linear array\r\n * Int values for has intersection or not - in integer32 linear array\r\n * Int values for bits flags - in integer32 linear array\r\n *\r\n */\r\nclass IsoSurfaceMarchCube {\r\n constructor() {\r\n this.pointsValuesLinear = null;\r\n this.hasIntersection = null;\r\n this.bitsInside = null;\r\n }\r\n\r\n create(numCellsPerSide) {\r\n const vx7000000 = 0x7000000;\r\n const n3 = numCellsPerSide * numCellsPerSide * numCellsPerSide;\r\n if (n3 > vx7000000) {\r\n throw new Error('Too large cube dimension: lead to memory huge uasge');\r\n }\r\n this.pointsValuesLinear = utils.allocateTyped(Float32Array, (2 << (2 + 2)) * n3);\r\n this.hasIntersection = utils.allocateTyped(Int32Array, n3);\r\n this.bitsInside = utils.allocateTyped(Int32Array, n3);\r\n return 0;\r\n }\r\n\r\n destroy() {\r\n this.bitsInside = null;\r\n this.hasIntersection = null;\r\n this.pointsValuesLinear = null;\r\n }\r\n}\r\n\r\nIsoSurfaceMarchCube.prototype.striIndicesMarchCube = [\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 0, 2, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 8, 3, 2, 10, 8, 10, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 8, 11, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 2, 1, 9, 11, 9, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 1, 11, 10, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 10, 1, 0, 8, 10, 8, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 9, 0, 3, 11, 9, 11, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 7, 3, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 1, 9, 4, 7, 1, 7, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 4, 7, 3, 0, 4, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 9, 0, 2, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 8, 4, 7, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 4, 7, 11, 2, 4, 2, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 8, 4, 7, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1, -1, -1, -1, -1,\r\n 3, 10, 1, 3, 11, 10, 7, 8, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4, -1, -1, -1, -1,\r\n 4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 4, 7, 11, 4, 11, 9, 9, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 1, 5, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 5, 4, 8, 3, 5, 3, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 10, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 2, 10, 5, 4, 2, 4, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8, -1, -1, -1, -1,\r\n 9, 5, 4, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 0, 8, 11, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 0, 1, 5, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5, -1, -1, -1, -1,\r\n 10, 3, 11, 10, 1, 3, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10, -1, -1, -1, -1,\r\n 5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 5, 4, 8, 5, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 5, 7, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 3, 0, 9, 5, 3, 5, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 8, 0, 1, 7, 1, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 9, 5, 7, 10, 1, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3, -1, -1, -1, -1,\r\n 8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2, -1, -1, -1, -1,\r\n 2, 10, 5, 2, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 9, 5, 7, 8, 9, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7, -1, -1, -1, -1,\r\n 11, 2, 1, 11, 1, 7, 7, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11, -1, -1, -1, -1,\r\n 5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0, -1,\r\n 11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0, -1,\r\n 11, 10, 5, 7, 11, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 1, 9, 8, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 2, 6, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 1, 2, 6, 3, 0, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 6, 5, 9, 0, 6, 0, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 0, 8, 11, 2, 0, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11, -1, -1, -1, -1,\r\n 6, 3, 11, 6, 5, 3, 5, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9, -1, -1, -1, -1,\r\n 6, 5, 9, 6, 9, 11, 11, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 4, 7, 3, 6, 5, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 5, 10, 6, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 6, 1, 2, 6, 5, 1, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7, -1, -1, -1, -1,\r\n 8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6, -1, -1, -1, -1,\r\n 7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9, -1,\r\n 3, 11, 2, 7, 8, 4, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1,\r\n 9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6, -1,\r\n 8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11, -1,\r\n 0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7, -1,\r\n 6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9, -1, -1, -1, -1,\r\n 10, 4, 9, 6, 4, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 10, 6, 4, 9, 10, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 0, 1, 10, 6, 0, 6, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 1, 4, 9, 1, 2, 4, 2, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4, -1, -1, -1, -1,\r\n 0, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 2, 8, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 4, 9, 10, 6, 4, 11, 2, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6, -1, -1, -1, -1,\r\n 3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1, -1,\r\n 9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3, -1, -1, -1, -1,\r\n 8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1, -1,\r\n 3, 11, 6, 3, 6, 0, 0, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 4, 8, 11, 6, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 10, 6, 7, 8, 10, 8, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10, -1, -1, -1, -1,\r\n 10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0, -1, -1, -1, -1,\r\n 10, 6, 7, 10, 7, 1, 1, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9, -1,\r\n 7, 8, 0, 7, 0, 6, 6, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 3, 2, 6, 7, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7, -1,\r\n 1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11, -1,\r\n 11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1, -1, -1, -1, -1,\r\n 8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6, -1,\r\n 0, 9, 1, 11, 6, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0, -1, -1, -1, -1,\r\n 7, 11, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 9, 8, 3, 1, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 8, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 9, 0, 2, 10, 9, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8, -1, -1, -1, -1,\r\n 7, 2, 3, 6, 2, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 0, 8, 7, 6, 0, 6, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 7, 6, 2, 3, 7, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6, -1, -1, -1, -1,\r\n 10, 7, 6, 10, 1, 7, 1, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8, -1, -1, -1, -1,\r\n 0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7, -1, -1, -1, -1,\r\n 7, 6, 10, 7, 10, 8, 8, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 8, 4, 11, 8, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 3, 0, 6, 0, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 6, 11, 8, 4, 6, 9, 0, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6, -1, -1, -1, -1,\r\n 6, 8, 4, 6, 11, 8, 2, 10, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6, -1, -1, -1, -1,\r\n 4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9, -1, -1, -1, -1,\r\n 10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3, -1,\r\n 8, 2, 3, 8, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8, -1, -1, -1, -1,\r\n 1, 9, 4, 1, 4, 2, 2, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1, -1, -1, -1, -1,\r\n 10, 1, 0, 10, 0, 6, 6, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3, -1,\r\n 10, 9, 4, 6, 10, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 5, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 1, 5, 4, 0, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5, -1, -1, -1, -1,\r\n 9, 5, 4, 10, 1, 2, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5, -1, -1, -1, -1,\r\n 7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2, -1, -1, -1, -1,\r\n 3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6, -1,\r\n 7, 2, 3, 7, 6, 2, 5, 4, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7, -1, -1, -1, -1,\r\n 3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0, -1, -1, -1, -1,\r\n 6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8, -1,\r\n 9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7, -1, -1, -1, -1,\r\n 1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4, -1,\r\n 4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10, -1,\r\n 7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10, -1, -1, -1, -1,\r\n 6, 9, 5, 6, 11, 9, 11, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5, -1, -1, -1, -1,\r\n 0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11, -1, -1, -1, -1,\r\n 6, 11, 3, 6, 3, 5, 5, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6, -1, -1, -1, -1,\r\n 0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10, -1,\r\n 11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5, -1,\r\n 6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3, -1, -1, -1, -1,\r\n 5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2, -1, -1, -1, -1,\r\n 9, 5, 6, 9, 6, 0, 0, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8, -1,\r\n 1, 5, 6, 2, 1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6, -1,\r\n 10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0, -1, -1, -1, -1,\r\n 0, 3, 8, 5, 6, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 5, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 7, 5, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 11, 7, 5, 8, 3, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 11, 7, 5, 10, 11, 1, 9, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1, -1, -1, -1, -1,\r\n 11, 1, 2, 11, 7, 1, 7, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11, -1, -1, -1, -1,\r\n 9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7, -1, -1, -1, -1,\r\n 7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2, -1,\r\n 2, 5, 10, 2, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2, -1, -1, -1, -1,\r\n 9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2, -1,\r\n 1, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 7, 0, 7, 1, 1, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 3, 9, 3, 5, 5, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 7, 5, 9, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 8, 4, 5, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5, -1, -1, -1, -1,\r\n 10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4, -1,\r\n 2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8, -1, -1, -1, -1,\r\n 0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11, -1,\r\n 0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5, -1,\r\n 9, 4, 5, 2, 11, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4, -1, -1, -1, -1,\r\n 5, 10, 2, 5, 2, 4, 4, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9, -1,\r\n 5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 3, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 5, 1, 0, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5, -1, -1, -1, -1,\r\n 9, 4, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 11, 7, 4, 9, 11, 9, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11, -1, -1, -1, -1,\r\n 1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11, -1, -1, -1, -1,\r\n 3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4, -1,\r\n 4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2, -1, -1, -1, -1,\r\n 9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3, -1,\r\n 11, 7, 4, 11, 4, 2, 2, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4, -1, -1, -1, -1,\r\n 2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9, -1, -1, -1, -1,\r\n 9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7, -1,\r\n 3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10, -1,\r\n 1, 10, 2, 8, 7, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 7, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1, -1, -1, -1, -1,\r\n 4, 0, 3, 7, 4, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 8, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1,\r\n 0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1,\r\n 1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n];\r\n\r\nexport default IsoSurfaceMarchCube;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport utils from '../../utils';\r\n\r\nconst edgeTable = [\r\n 0x0, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c,\r\n 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00,\r\n 0x190, 0x99, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c,\r\n 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90,\r\n 0x230, 0x339, 0x33, 0x13a, 0x636, 0x73f, 0x435, 0x53c,\r\n 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30,\r\n 0x3a0, 0x2a9, 0x1a3, 0xaa, 0x7a6, 0x6af, 0x5a5, 0x4ac,\r\n 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0,\r\n 0x460, 0x569, 0x663, 0x76a, 0x66, 0x16f, 0x265, 0x36c,\r\n 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60,\r\n 0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0xff, 0x3f5, 0x2fc,\r\n 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0,\r\n 0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x55, 0x15c,\r\n 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950,\r\n 0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0xcc,\r\n 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0,\r\n 0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc,\r\n 0xcc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0,\r\n 0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c,\r\n 0x15c, 0x55, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650,\r\n 0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc,\r\n 0x2fc, 0x3f5, 0xff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0,\r\n 0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c,\r\n 0x36c, 0x265, 0x16f, 0x66, 0x76a, 0x663, 0x569, 0x460,\r\n 0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac,\r\n 0x4ac, 0x5a5, 0x6af, 0x7a6, 0xaa, 0x1a3, 0x2a9, 0x3a0,\r\n 0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c,\r\n 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x33, 0x339, 0x230,\r\n 0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c,\r\n 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x99, 0x190,\r\n 0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c,\r\n 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x0];\r\n\r\nfunction _voxelGradientFast(v, point, grad) {\r\n const g = v.getValue(point.x, point.y, point.z);\r\n grad.set(g[0], g[1], g[2]);\r\n}\r\n\r\n// Helper class GridCell\r\nclass GridCell {\r\n constructor() {\r\n this._arrSize = 8;\r\n this.p = new Array(this._arrSize);\r\n this.g = new Array(this._arrSize);\r\n this.val = new Array(this._arrSize);\r\n for (let i = 0; i < this._arrSize; ++i) {\r\n this.p[i] = new THREE.Vector3();\r\n this.g[i] = new THREE.Vector3();\r\n }\r\n this.cubeIndex = 0;\r\n }\r\n}\r\n\r\n// Helper class Triangle\r\nclass Triangle {\r\n constructor() {\r\n this.a = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.b = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.c = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n }\r\n}\r\n\r\nfunction createArray(arrSize) {\r\n const arr = new Array(arrSize);\r\n for (let i = 0; i < arrSize; ++i) {\r\n arr[i] = new THREE.Vector3();\r\n }\r\n\r\n return arr;\r\n}\r\n\r\nclass IsoSurface {\r\n constructor() {\r\n this._numTriangles = 0;\r\n this._numVertices = 0;\r\n this._position = [];\r\n this._normals = [];\r\n this._colors = null;\r\n this._indices = [];\r\n this._volumetricData = null;\r\n this._xAxis = new THREE.Vector3();\r\n this._yAxis = new THREE.Vector3();\r\n this._zAxis = new THREE.Vector3();\r\n this._xDir = new THREE.Vector3();\r\n this._yDir = new THREE.Vector3();\r\n this._zDir = new THREE.Vector3();\r\n }\r\n\r\n _prepareAxesAndDirs() {\r\n const volData = this._volumetricData;\r\n\r\n const cellSize = volData.getCellSize();\r\n\r\n // calculate cell axes\r\n const xAxis = this._xAxis;\r\n const yAxis = this._yAxis;\r\n const zAxis = this._zAxis;\r\n const xDir = this._xDir;\r\n const yDir = this._yDir;\r\n const zDir = this._zDir;\r\n\r\n xAxis.set(cellSize.x, 0, 0);\r\n yAxis.set(0, cellSize.y, 0);\r\n zAxis.set(0, 0, cellSize.z);\r\n\r\n xDir.set(1, 0, 0);\r\n yDir.set(0, 1, 0);\r\n zDir.set(0, 0, 1);\r\n\r\n // flip normals if coordinate system is in the wrong handedness\r\n const tmp = new THREE.Vector3();\r\n tmp.crossVectors(xDir, yDir);\r\n if (tmp.dot(zDir) < 0) {\r\n xDir.negate();\r\n yDir.negate();\r\n zDir.negate();\r\n }\r\n\r\n // check that the grid is in the all-positive octant of the coordinate system\r\n if (xDir.x < 0 || xDir.y < 0 || xDir.z < 0\r\n || yDir.x < 0 || yDir.y < 0 || yDir.z < 0\r\n || zDir.x < 0 || zDir.y < 0 || zDir.z < 0) {\r\n return false;\r\n }\r\n\r\n // check that the grid is axis-aligned\r\n const notZero = (axe) => Math.abs(axe) > Number.EPSILON;\r\n return !(notZero(xAxis.y) || notZero(xAxis.z)\r\n || notZero(yAxis.x) || notZero(yAxis.z)\r\n || notZero(zAxis.x) || notZero(zAxis.y));\r\n }\r\n\r\n _vertexInterp(isoLevel, grid, ind1, ind2, vertex, normal) {\r\n const p1 = grid.p[ind1];\r\n const p2 = grid.p[ind2];\r\n const n1 = grid.g[ind1];\r\n const n2 = grid.g[ind2];\r\n const valP1 = grid.val[ind1];\r\n const valP2 = grid.val[ind2];\r\n const isoDiffP1 = isoLevel - valP1;\r\n const diffValP2P1 = valP2 - valP1;\r\n\r\n let mu = 0.0;\r\n\r\n if (Math.abs(diffValP2P1) > 0.0) {\r\n mu = isoDiffP1 / diffValP2P1;\r\n }\r\n mu = mu > 1.0 ? 1.0 : mu;\r\n vertex.lerpVectors(p1, p2, mu);\r\n normal.lerpVectors(n1, n2, mu);\r\n }\r\n\r\n static _triTable = IsoSurfaceMarchCube.prototype.striIndicesMarchCube;\r\n\r\n static _arrSize = 12;\r\n\r\n static _firstIndices = [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3];\r\n\r\n static _secondIndices = [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7];\r\n\r\n static _vertexList = createArray(IsoSurface._arrSize);\r\n\r\n static _normalList = createArray(IsoSurface._arrSize);\r\n\r\n _polygonize(grid, isoLevel, triangles) {\r\n const { cubeIndex } = grid;\r\n let i = 0;\r\n const arrSize = IsoSurface._arrSize;\r\n const firstIndices = IsoSurface._firstIndices;\r\n const secondIndices = IsoSurface._secondIndices;\r\n const vertexList = IsoSurface._vertexList;\r\n const normalList = IsoSurface._normalList;\r\n\r\n for (; i < arrSize; ++i) {\r\n if (edgeTable[cubeIndex] & (1 << i)) {\r\n this._vertexInterp(\r\n isoLevel,\r\n grid,\r\n firstIndices[i],\r\n secondIndices[i],\r\n vertexList[i],\r\n normalList[i],\r\n );\r\n }\r\n }\r\n\r\n let triCount = 0;\r\n const triTblIdx = cubeIndex * 16;\r\n const triTable = IsoSurface._triTable;\r\n\r\n for (i = 0; triTable[triTblIdx + i] !== -1; i += 3) {\r\n triangles[triCount].a.p.copy(vertexList[triTable[triTblIdx + i]]);\r\n triangles[triCount].a.n.copy(normalList[triTable[triTblIdx + i]]);\r\n\r\n triangles[triCount].b.p.copy(vertexList[triTable[triTblIdx + i + 1]]);\r\n triangles[triCount].b.n.copy(normalList[triTable[triTblIdx + i + 1]]);\r\n\r\n triangles[triCount].c.p.copy(vertexList[triTable[triTblIdx + i + 2]]);\r\n triangles[triCount].c.n.copy(normalList[triTable[triTblIdx + i + 2]]);\r\n ++triCount;\r\n }\r\n\r\n return triCount;\r\n }\r\n\r\n _doGridPosNorms(isoValue, step, appendSimple) {\r\n const vol = this._volumetricData;\r\n const volData = this._volumetricData.getData();\r\n const dim = vol.getDimensions();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n const zSize = dim[2];\r\n const stepX = step * vol.getStrideX();\r\n const stepY = step * vol.getStrideY();\r\n const stepZ = step * vol.getStrideZ();\r\n\r\n const gc = new GridCell();\r\n const gcVal = gc.val;\r\n const gcValSize = gc.val.length;\r\n const additions = [\r\n new THREE.Vector3(0, 0, 0), // 0\r\n new THREE.Vector3(step, 0, 0), // 1\r\n new THREE.Vector3(step, step, 0), // 2\r\n new THREE.Vector3(0, step, 0), // 3\r\n new THREE.Vector3(0, 0, step), // 4\r\n new THREE.Vector3(step, 0, step), // 5\r\n new THREE.Vector3(step, step, step), // 6\r\n new THREE.Vector3(0, step, step), // 7\r\n ];\r\n\r\n const tmpTriCount = 5;\r\n const triangles = new Array(tmpTriCount);\r\n for (let j = 0; j < tmpTriCount; ++j) {\r\n triangles[j] = new Triangle();\r\n }\r\n\r\n let appendVertex;\r\n const self = this;\r\n const positions = this._position;\r\n const normals = this._normals;\r\n if (appendSimple) {\r\n // Special case for axis-aligned grid with positive unit vector normals\r\n appendVertex = (function () {\r\n const axis = new THREE.Vector3(self._xAxis.x, self._yAxis.y, self._zAxis.z);\r\n return function (triVertex) {\r\n const vertex = triVertex.p.clone();\r\n vertex.multiply(axis);\r\n positions.push(vertex.add(self._origin));\r\n normals.push(triVertex.n.clone());\r\n };\r\n }());\r\n } else {\r\n appendVertex = (function () {\r\n const posMtx = new THREE.Matrix3();\r\n posMtx.set(\r\n self._xAxis.x,\r\n self._yAxis.x,\r\n self._zAxis.x,\r\n self._xAxis.y,\r\n self._yAxis.y,\r\n self._zAxis.y,\r\n self._xAxis.z,\r\n self._yAxis.z,\r\n self._zAxis.z,\r\n );\r\n const normMtx = new THREE.Matrix3();\r\n normMtx.set(\r\n self._xDir.x,\r\n self._yDir.x,\r\n self._zDir.x,\r\n self._xDir.y,\r\n self._yDir.y,\r\n self._zDir.y,\r\n self._xDir.z,\r\n self._yDir.z,\r\n self._zDir.z,\r\n );\r\n\r\n return function (triVertex) {\r\n positions.push(triVertex.p.clone().applyMatrix3(posMtx).add(self._origin));\r\n normals.push(triVertex.n.clone().applyMatrix3(normMtx));\r\n };\r\n }());\r\n }\r\n const indices = this._indices;\r\n\r\n let globTriCount = 0;\r\n\r\n for (let z = 0; z < (zSize - step); z += step) {\r\n for (let y = 0; y < (ySize - step); y += step) {\r\n let idx = vol.getDirectIdx(0, y, z);\r\n for (let x = 0; x < (xSize - step); x += step, idx += stepX) {\r\n gcVal[0] = volData[idx];\r\n gcVal[1] = volData[idx + stepX];\r\n gcVal[3] = volData[idx + stepY];\r\n gcVal[2] = volData[idx + stepX + stepY];\r\n gcVal[4] = volData[idx + stepZ];\r\n gcVal[5] = volData[idx + stepX + stepZ];\r\n gcVal[7] = volData[idx + stepY + stepZ];\r\n gcVal[6] = volData[idx + stepX + stepY + stepZ];\r\n\r\n // Determine the index into the edge table which\r\n // tells us which vertices are inside of the surface\r\n let cubeIndex = 0;\r\n let i = 0;\r\n for (; i < gcValSize; ++i) {\r\n if (gcVal[i] < isoValue) {\r\n cubeIndex |= (1 << i);\r\n }\r\n }\r\n\r\n if (edgeTable[cubeIndex] === 0) {\r\n continue;\r\n }\r\n\r\n gc.cubeIndex = cubeIndex;\r\n for (i = 0; i < gcValSize; ++i) {\r\n gc.p[i].set(x + additions[i].x, y + additions[i].y, z + additions[i].z);\r\n _voxelGradientFast(this._gradient, gc.p[i], gc.g[i]);\r\n }\r\n\r\n // calculate vertices and facets for this cube,\r\n // calculate normals by interpolating between the negated\r\n // normalized volume gradients for the 8 reference voxels\r\n const triCount = this._polygonize(gc, isoValue, triangles);\r\n globTriCount += triCount;\r\n\r\n // append triangles using different techniques\r\n for (i = 0; i < triCount; ++i) {\r\n indices.push(this._numTriangles * 3);\r\n indices.push(this._numTriangles * 3 + 1);\r\n indices.push(this._numTriangles * 3 + 2);\r\n ++this._numTriangles;\r\n\r\n appendVertex(triangles[i].a);\r\n appendVertex(triangles[i].b);\r\n appendVertex(triangles[i].c);\r\n }\r\n }\r\n }\r\n }\r\n\r\n return globTriCount;\r\n }\r\n\r\n compute(volData, origin, isoValue, step) {\r\n this._volumetricData = volData;\r\n this._origin = origin;\r\n\r\n this._gradient = volData.computeGradient();\r\n\r\n this._doGridPosNorms(isoValue, step, this._prepareAxesAndDirs());\r\n }\r\n\r\n _remapIndices(vertexMap, idcCount) {\r\n const indices = this._indices;\r\n const newIndices = utils.allocateTyped(Uint32Array, idcCount);\r\n for (let i = 0; i < idcCount; ++i) {\r\n indices[i] = vertexMap[indices[i]];\r\n newIndices[i] = indices[i];\r\n }\r\n this._indices = newIndices;\r\n }\r\n\r\n _remapVertices(vertices, normals, count) {\r\n const newPositions = utils.allocateTyped(Float32Array, count * 3);\r\n const newNormals = utils.allocateTyped(Float32Array, count * 3);\r\n for (let i = 0; i < count; ++i) {\r\n const pos = vertices[i];\r\n newPositions[i * 3] = pos.x;\r\n newPositions[i * 3 + 1] = pos.y;\r\n newPositions[i * 3 + 2] = pos.z;\r\n const norm = normals[i].normalize();\r\n newNormals[i * 3] = norm.x;\r\n newNormals[i * 3 + 1] = norm.y;\r\n newNormals[i * 3 + 2] = norm.z;\r\n }\r\n this._position = newPositions;\r\n this._normals = newNormals;\r\n }\r\n\r\n vertexFusion(offset, len) {\r\n const faceVer = this._indices.length;\r\n const vertices = this._position;\r\n const normals = this._normals;\r\n const oldVerCount = vertices.length | 0;\r\n if (faceVer === 0 || oldVerCount === 0) {\r\n return;\r\n }\r\n const vMap = utils.allocateTyped(Uint32Array, oldVerCount);\r\n vMap[0] = 0;\r\n let newVer = 1;\r\n\r\n let i = 1;\r\n for (; i < oldVerCount; ++i) {\r\n const start = newVer - offset < 0 ? 0 : newVer - offset;\r\n const end = start + len > newVer ? newVer : start + len;\r\n let matchedIndex = -1;\r\n\r\n for (let j = start; j < end; ++j) {\r\n if (Math.abs(vertices[i] - vertices[j]) < Number.EPSILON) {\r\n matchedIndex = j;\r\n break;\r\n }\r\n }\r\n\r\n if (matchedIndex !== -1) {\r\n vMap[i] = matchedIndex;\r\n } else {\r\n vertices[newVer].copy(vertices[i]);\r\n normals[newVer].copy(normals[i]);\r\n vMap[i] = newVer;\r\n ++newVer;\r\n }\r\n }\r\n\r\n this._remapIndices(vMap, faceVer);\r\n this._remapVertices(vertices, normals, newVer);\r\n }\r\n\r\n // Assign per-vertex colors from a volumetric texture map (same dimensions as the original volumetric data).\r\n // Along with color dominating atom is determined for each vertex\r\n // and vertices with atom out of \"visible\" subset get filtered out.\r\n // XXX only handles orthogonal volumes currently\r\n setColorVolTex(colorMap, atomMap, atomWeightMap, visibilitySelector) {\r\n let i;\r\n let idx;\r\n const numVerts = this._position.length / 3;\r\n const vertices = this._position;\r\n const origin = this._origin;\r\n const dim = this._volumetricData.getDimensions();\r\n const xs = dim[0] - 1;\r\n const ys = dim[1] - 1;\r\n const zs = dim[2] - 1;\r\n\r\n const colorData = colorMap.getData();\r\n const strideX = colorMap.getStrideX();\r\n const strideY = colorMap.getStrideY();\r\n const strideZ = colorMap.getStrideZ();\r\n\r\n let atomWeightData;\r\n let atomStrideX;\r\n let atomStrideY;\r\n let atomStrideZ;\r\n\r\n if (visibilitySelector !== null) {\r\n atomWeightData = atomWeightMap.getData();\r\n atomStrideX = atomWeightMap.getStrideX();\r\n atomStrideY = atomWeightMap.getStrideY();\r\n atomStrideZ = atomWeightMap.getStrideZ();\r\n }\r\n\r\n const xInv = 1.0 / this._xAxis.x;\r\n const yInv = 1.0 / this._yAxis.y;\r\n const zInv = 1.0 / this._zAxis.z;\r\n\r\n let atomLookup = [];\r\n let atomWeights = [];\r\n const colors = utils.allocateTyped(Float32Array, numVerts * 3);\r\n\r\n function interp(mu, idx1, idx2, c) {\r\n c[0] = (1 - mu) * colorData[idx1] + mu * colorData[idx2];\r\n c[1] = (1 - mu) * colorData[idx1 + 1] + mu * colorData[idx2 + 1];\r\n c[2] = (1 - mu) * colorData[idx1 + 2] + mu * colorData[idx2 + 2];\r\n }\r\n\r\n function collectWeight(ai, coefX, coefY, coefZ) {\r\n const a = atomMap[ai]; // atomWeightMap is a scalar field, so index into atom map should be the same\r\n if (a != null) {\r\n atomLookup[a.index] = a;\r\n const w = coefX * coefY * coefZ * atomWeightData[ai];\r\n if (typeof atomWeights[a.index] === 'undefined') {\r\n atomWeights[a.index] = w;\r\n } else {\r\n atomWeights[a.index] += w;\r\n }\r\n }\r\n }\r\n\r\n const vMap = utils.allocateTyped(Int32Array, numVerts);\r\n let newVerCount = 0;\r\n\r\n for (i = 0; i < numVerts; i++) {\r\n const ind = i * 3;\r\n const vx = (vertices[ind] - origin.x) * xInv;\r\n const vy = (vertices[ind + 1] - origin.y) * yInv;\r\n const vz = (vertices[ind + 2] - origin.z) * zInv;\r\n const x = Math.min(Math.max(vx, 0), xs) | 0;\r\n const y = Math.min(Math.max(vy, 0), ys) | 0;\r\n const z = Math.min(Math.max(vz, 0), zs) | 0;\r\n\r\n const mux = (vx - x);\r\n const muy = (vy - y);\r\n const muz = (vz - z);\r\n\r\n if (visibilitySelector != null) {\r\n // collect atom weights\r\n atomLookup = [];\r\n atomWeights = [];\r\n idx = atomWeightMap.getDirectIdx(x, y, z);\r\n collectWeight(idx, 1 - mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideX, mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideY, 1 - mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideX + atomStrideY, mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideZ, 1 - mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideZ, mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideY + atomStrideZ, 1 - mux, muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideY + atomStrideZ, mux, muy, muz);\r\n\r\n // find dominant atom\r\n let maxWeight = 0.0;\r\n let dominantIdx = -1;\r\n for (const atomIdx in atomWeights) {\r\n if (atomWeights[atomIdx] > maxWeight) {\r\n dominantIdx = atomIdx;\r\n maxWeight = atomWeights[atomIdx];\r\n }\r\n }\r\n\r\n if (dominantIdx < 0 || !visibilitySelector.includesAtom(atomLookup[dominantIdx])) {\r\n // this vertex doesn't belong to visible subset and will be skipped\r\n vMap[i] = -1;\r\n continue;\r\n }\r\n }\r\n\r\n vMap[i] = newVerCount++;\r\n\r\n // color tri-linear interpolation\r\n const dx = (x < xs) ? strideX : 0;\r\n const dy = (y < ys) ? strideY : 0;\r\n const dz = (z < zs) ? strideZ : 0;\r\n\r\n const c0 = [0, 0, 0];\r\n const c1 = [0, 0, 0];\r\n const c2 = [0, 0, 0];\r\n const c3 = [0, 0, 0];\r\n\r\n idx = colorMap.getDirectIdx(x, y, z);\r\n interp(mux, idx, idx + dx, c0);\r\n interp(mux, idx + dy, idx + dx + dy, c1);\r\n interp(mux, idx + dz, idx + dx + dz, c2);\r\n interp(mux, idx + dy + dz, idx + dx + dy + dz, c3);\r\n\r\n const cz0 = [0, 0, 0];\r\n cz0[0] = (1 - muy) * c0[0] + muy * c1[0];\r\n cz0[1] = (1 - muy) * c0[1] + muy * c1[1];\r\n cz0[2] = (1 - muy) * c0[2] + muy * c1[2];\r\n\r\n const cz1 = [0, 0, 0];\r\n cz1[0] = (1 - muy) * c2[0] + muy * c3[0];\r\n cz1[1] = (1 - muy) * c2[1] + muy * c3[1];\r\n cz1[2] = (1 - muy) * c2[2] + muy * c3[2];\r\n\r\n colors[ind] = (1 - muz) * cz0[0] + muz * cz1[0];\r\n colors[ind + 1] = (1 - muz) * cz0[1] + muz * cz1[1];\r\n colors[ind + 2] = (1 - muz) * cz0[2] + muz * cz1[2];\r\n }\r\n this._colors = colors;\r\n\r\n if (visibilitySelector != null) {\r\n // shift visible vertices towards beginning of array\r\n for (i = 0; i < numVerts; ++i) {\r\n const j = vMap[i];\r\n if (j < 0) {\r\n continue;\r\n }\r\n\r\n // assert: j <= i\r\n this._position[j * 3] = this._position[i * 3];\r\n this._position[j * 3 + 1] = this._position[i * 3 + 1];\r\n this._position[j * 3 + 2] = this._position[i * 3 + 2];\r\n this._normals[j * 3] = this._normals[i * 3];\r\n this._normals[j * 3 + 1] = this._normals[i * 3 + 1];\r\n this._normals[j * 3 + 2] = this._normals[i * 3 + 2];\r\n this._colors[j * 3] = this._colors[i * 3];\r\n this._colors[j * 3 + 1] = this._colors[i * 3 + 1];\r\n this._colors[j * 3 + 2] = this._colors[i * 3 + 2];\r\n }\r\n\r\n // rebuild index list\r\n const numTriangles = this._indices.length / 3;\r\n let newTriCount = 0;\r\n for (i = 0; i < numTriangles; ++i) {\r\n const i0 = vMap[this._indices[3 * i]];\r\n const i1 = vMap[this._indices[3 * i + 1]];\r\n const i2 = vMap[this._indices[3 * i + 2]];\r\n if (i0 >= 0 && i1 >= 0 && i2 >= 0) {\r\n this._indices[3 * newTriCount] = i0;\r\n this._indices[3 * newTriCount + 1] = i1;\r\n this._indices[3 * newTriCount + 2] = i2;\r\n ++newTriCount;\r\n }\r\n }\r\n\r\n // shrink arrays to data size\r\n this._position = new Float32Array(this._position.buffer.slice(0, newVerCount * 3 * 4));\r\n this._normals = new Float32Array(this._normals.buffer.slice(0, newVerCount * 3 * 4));\r\n this._colors = new Float32Array(this._colors.buffer.slice(0, newVerCount * 3 * 4));\r\n this._indices = new Uint32Array(this._indices.buffer.slice(0, newTriCount * 3 * 4));\r\n }\r\n }\r\n\r\n toMesh() {\r\n const geo = new THREE.BufferGeometry();\r\n geo.setIndex(new THREE.BufferAttribute(this._indices, 1));\r\n geo.setAttribute('position', new THREE.BufferAttribute(this._position, 3));\r\n geo.setAttribute('normal', new THREE.BufferAttribute(this._normals, 3));\r\n geo.setAttribute('color', new THREE.BufferAttribute(this._colors, 3));\r\n geo.computeBoundingSphere();\r\n return geo;\r\n }\r\n}\r\nexport default IsoSurface;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurface from './IsoSurface';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * This is a base class for volumetric maps based isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass VolumeSurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n const params = this._opts;\r\n this.numVoxels = [128, 128, 128];\r\n this.xAxis = new THREE.Vector3(1.0, 0.0, 0.0);\r\n this.yAxis = new THREE.Vector3(0.0, 1.0, 0.0);\r\n this.zAxis = new THREE.Vector3(0.0, 0.0, 1.0);\r\n\r\n this.origin = new THREE.Vector3(0.0, 0.0, 0.0);\r\n this._visibilitySelector = params.visibilitySelector;\r\n\r\n this._calcSurface(params);\r\n }\r\n\r\n _findMinMax(posRadArray) {\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n const maxPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n const minPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n for (let i = 1; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n for (let itemIdx = 0; itemIdx < itemSize; ++itemIdx) {\r\n const tmpVal = posRadArray[ind + itemIdx];\r\n maxPosRad[itemIdx] = Math.max(tmpVal, maxPosRad[itemIdx]);\r\n minPosRad[itemIdx] = Math.min(tmpVal, minPosRad[itemIdx]);\r\n }\r\n }\r\n return { maxPosRad, minPosRad };\r\n }\r\n\r\n _findNumVoxels(posRadArray, params) {\r\n const { numVoxels } = this;\r\n const minMaxValues = this._findMinMax(posRadArray);\r\n const minCoordRad = minMaxValues.minPosRad;\r\n const maxCoordRad = minMaxValues.maxPosRad;\r\n\r\n // minrad\r\n if (minCoordRad[3] > 4.0) {\r\n params.gridSpacing *= minCoordRad[3];\r\n }\r\n\r\n let gridPadding = params.radScale * maxCoordRad[3] * 1.7;\r\n let padRad = gridPadding;\r\n padRad = 0.65 * Math.sqrt(4.0 / 3.0 * Math.PI * padRad * padRad * padRad);\r\n gridPadding = Math.max(gridPadding, padRad);\r\n\r\n let i = 0;\r\n for (; i < 3; ++i) {\r\n minCoordRad[i] -= gridPadding;\r\n maxCoordRad[i] += gridPadding;\r\n }\r\n\r\n for (i = 0; i < 3; ++i) {\r\n numVoxels[i] = Math.ceil((maxCoordRad[i] - minCoordRad[i]) / params.gridSpacing);\r\n }\r\n this.xAxis.x = (numVoxels[0] - 1) * params.gridSpacing;\r\n this.yAxis.y = (numVoxels[1] - 1) * params.gridSpacing;\r\n this.zAxis.z = (numVoxels[2] - 1) * params.gridSpacing;\r\n\r\n [this.origin.x, this.origin.y, this.origin.z] = minCoordRad;\r\n\r\n return { bbox: minMaxValues, dim: numVoxels };\r\n }\r\n\r\n _makeSurface(surface, params) {\r\n const isoSurf = new IsoSurface();\r\n isoSurf.compute(surface.volMap, this.origin, params.isoValue, 1);\r\n isoSurf.vertexFusion(9, 9);// normalization is included\r\n\r\n if (isoSurf._numTriangles > 0) {\r\n isoSurf.setColorVolTex(surface.volTexMap, surface.atomMap, surface.atomWeightMap, this._visibilitySelector);\r\n this.setIndex(new THREE.BufferAttribute(isoSurf._indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(isoSurf._position, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(isoSurf._normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(isoSurf._colors, 3));\r\n } else { // geometry should have at least empty position attributes to be processed in wireframe mode by three.js\r\n this.setAttribute('position', new THREE.BufferAttribute(utils.allocateTyped(Float32Array, 0), 3));\r\n }\r\n }\r\n\r\n _calcSurface(params) {\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n\r\n if (packedArrays.posRad.length === 0) {\r\n return;\r\n }\r\n const boundaries = this._findNumVoxels(packedArrays.posRad, params);\r\n\r\n const box = new THREE.Box3(\r\n this.origin,\r\n new THREE.Vector3(this.xAxis.x, this.yAxis.y, this.zAxis.z).add(this.origin),\r\n );\r\n const surface = this._computeSurface(packedArrays, box, boundaries, params);\r\n\r\n this._makeSurface(surface, params);\r\n }\r\n}\r\n\r\nexport default VolumeSurfaceGeometry;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass QuickSurfGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n // beware of shifting this multiple times!\r\n this._shiftByOrigin(packedArrays.posRad);\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3),\r\n };\r\n\r\n if (this._visibilitySelector != null) {\r\n surface.atomMap = [];\r\n surface.atomWeightMap = new Volume(Float32Array, this.numVoxels, box);\r\n }\r\n\r\n this.gaussdensity(surface, packedArrays, null, params);\r\n return surface;\r\n }\r\n\r\n gaussdensity(surface, packedArrays, atomicNum, params) {\r\n const numAtoms = packedArrays.posRad.length / 4;\r\n const { posRad, colors } = packedArrays;\r\n const { numVoxels } = this;\r\n const { radScale, gaussLim, gridSpacing } = params;\r\n const invIsoValue = 1.0 / params.isoValue;\r\n const invGridSpacing = 1.0 / gridSpacing;\r\n const maxVoxelX = numVoxels[0] - 1;\r\n const maxVoxelY = numVoxels[1] - 1;\r\n const maxVoxelZ = numVoxels[2] - 1;\r\n // TODO is densityMap and volTexMap initialized?\r\n\r\n const { volMap, volTexMap } = surface;\r\n const volData = volMap.getData();\r\n const strideX = volMap.getStrideX();\r\n\r\n const volTexData = volTexMap.getData();\r\n const texStrideX = volTexMap.getStrideX();\r\n\r\n let atomWeightData;\r\n if (this._visibilitySelector != null) {\r\n atomWeightData = surface.atomWeightMap.getData();\r\n }\r\n\r\n const { atomMap } = surface;\r\n\r\n for (let i = 0; i < numAtoms; ++i) {\r\n const ind = i * 4;\r\n const scaledRad = posRad[ind + 3] * radScale;\r\n const atomicNumFactor = atomicNum === null ? 1.0 : atomicNum[i];\r\n const radInv = 1 / (2 * scaledRad * scaledRad);\r\n let radLim = gaussLim * scaledRad;\r\n const radLim2 = radLim * radLim;\r\n radLim *= invGridSpacing;\r\n\r\n let tmp = posRad[ind] * invGridSpacing;\r\n const xMin = Math.max((tmp - radLim) | 0, 0);\r\n const xMax = Math.min((tmp + radLim) | 0, maxVoxelX);\r\n tmp = posRad[ind + 1] * invGridSpacing;\r\n const yMin = Math.max((tmp - radLim) | 0, 0);\r\n const yMax = Math.min((tmp + radLim) | 0, maxVoxelY);\r\n tmp = posRad[ind + 2] * invGridSpacing;\r\n const zMin = Math.max((tmp - radLim) | 0, 0);\r\n const zMax = Math.min((tmp + radLim) | 0, maxVoxelZ);\r\n\r\n let dz = zMin * gridSpacing - posRad[ind + 2];\r\n for (let z = zMin; z <= zMax; ++z, dz += gridSpacing) {\r\n let dy = yMin * gridSpacing - posRad[ind + 1];\r\n for (let y = yMin; y <= yMax; ++y, dy += gridSpacing) {\r\n const dy2dz2 = dy * dy + dz * dz;\r\n\r\n if (dy2dz2 >= radLim2) {\r\n continue;\r\n }\r\n\r\n let addr = volMap.getDirectIdx(xMin, y, z);\r\n let texAddr = volTexMap.getDirectIdx(xMin, y, z);\r\n let dx = xMin * gridSpacing - posRad[ind];\r\n for (let x = xMin; x <= xMax; ++x, dx += gridSpacing, addr += strideX, texAddr += texStrideX) {\r\n const r2 = dx * dx + dy2dz2;\r\n const expVal = -r2 * radInv;\r\n\r\n let density = Math.exp(expVal) * atomicNumFactor;\r\n\r\n // store most relevant atom (with highest density)\r\n if (this._visibilitySelector != null\r\n && density > atomWeightData[addr]) { // NOSONAR\r\n atomWeightData[addr] = density;\r\n // we use same index into atom map and atomWeightMap\r\n atomMap[addr] = packedArrays.atoms[i];\r\n }\r\n\r\n volData[addr] += density;\r\n\r\n // TODO check for volTexMap routine?\r\n density *= invIsoValue;\r\n const colInd = i * 3;\r\n volTexData[texAddr] += density * colors[colInd];\r\n volTexData[texAddr + 1] += density * colors[colInd + 1];\r\n volTexData[texAddr + 2] += density * colors[colInd + 2];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n _shiftByOrigin(posRadArray) {\r\n const originX = this.origin.x;\r\n const originY = this.origin.y;\r\n const originZ = this.origin.z;\r\n\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n for (let i = 0; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n posRadArray[ind] -= originX;\r\n posRadArray[ind + 1] -= originY;\r\n posRadArray[ind + 2] -= originZ;\r\n }\r\n }\r\n}\r\n\r\nexport default QuickSurfGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * Modifed from SpatialHash\r\n *\r\n * Main differences are:\r\n * - Optimized grid size to ensure we only ever need to look +/-1 cell\r\n * - Aware of atomic radii and will only output atoms within rAtom + rExtra\r\n * (see withinRadii method)\r\n *\r\n * (Uses rounding rather than bitshifting as consequence of arbitrary grid size)\r\n * @class\r\n * @param {Float32Array} posRad - x, y, z coordinates and radiuses\r\n * @param {Float32Array} min - xyz min coordinates\r\n * @param {Float32Array} max - xyz max coordinates\r\n * @param {number} maxDistance - max distance\r\n */\r\nfunction AVHash(posRad, min, max, maxDistance) {\r\n const itemSize = 4;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const minX = min[0];\r\n const minY = min[1];\r\n const minZ = min[2];\r\n\r\n const maxX = max[0];\r\n const maxY = max[1];\r\n const maxZ = max[2];\r\n\r\n function hashFunc(w, minW) {\r\n return Math.floor((w - minW) / maxDistance);\r\n }\r\n\r\n const iDim = hashFunc(maxX, minX) + 1;\r\n const jDim = hashFunc(maxY, minY) + 1;\r\n const kDim = hashFunc(maxZ, minZ) + 1;\r\n\r\n const nCells = iDim * jDim * kDim;\r\n\r\n const jkDim = jDim * kDim;\r\n\r\n /* Get cellID for cartesian x,y,z */\r\n const cellID = function (x, y, z) {\r\n return (((hashFunc(x, minX) * jDim) + hashFunc(y, minY)) * kDim) + hashFunc(z, minZ);\r\n };\r\n\r\n /* Initial building, could probably be optimized further */\r\n const preHash = [];\r\n let i;\r\n let cid;\r\n for (i = 0; i < nAtoms; i++) {\r\n const iIdx = itemSize * i;\r\n cid = cellID(posRad[iIdx], posRad[iIdx + 1], posRad[iIdx + 2]);\r\n\r\n if (preHash[cid] === undefined) {\r\n preHash[cid] = [i];\r\n } else {\r\n preHash[cid].push(i);\r\n }\r\n }\r\n\r\n const cellOffsets = utils.allocateTyped(Uint32Array, nCells);\r\n const cellLengths = utils.allocateTyped(Uint16Array, nCells);\r\n const data = utils.allocateTyped(Uint32Array, nAtoms);\r\n\r\n let offset = 0;\r\n let maxCellLength = 0;\r\n let j;\r\n for (i = 0; i < nCells; i++) {\r\n const start = cellOffsets[i] = offset;\r\n\r\n const subArray = preHash[i];\r\n\r\n if (subArray !== undefined) {\r\n for (j = 0; j < subArray.length; j++) {\r\n data[offset] = subArray[j];\r\n offset++;\r\n }\r\n }\r\n\r\n const cellLength = offset - start;\r\n cellLengths[i] = cellLength;\r\n\r\n if (cellLength > maxCellLength) {\r\n maxCellLength = cellLength;\r\n }\r\n }\r\n\r\n // Maximum number of neighbours we could ever produce (27 adjacent cells of equal population)\r\n this.neighbourListLength = (27 * maxCellLength) + 1;\r\n\r\n /**\r\n * Populate the supplied out array with atom indices that are within rAtom + rExtra\r\n * of x,y,z\r\n *\r\n * -1 in out array indicates the end of the list\r\n *\r\n * @param {number} x - x coordinate\r\n * @param {number} y - y coordinate\r\n * @param {number} z - z coordinate\r\n * @param {number} rExtra - additional radius\r\n * @param {Float32Array} out - pre-allocated output array\r\n * @return {undefined}\r\n */\r\n this.withinRadii = function (x, y, z, rExtra, out) {\r\n let outIdx = 0;\r\n\r\n const nearI = hashFunc(x, minX);\r\n const nearJ = hashFunc(y, minY);\r\n const nearK = hashFunc(z, minZ);\r\n\r\n const loI = Math.max(0, nearI - 1);\r\n const loJ = Math.max(0, nearJ - 1);\r\n const loK = Math.max(0, nearK - 1);\r\n\r\n const hiI = Math.min(iDim - 1, nearI + 1);\r\n const hiJ = Math.min(jDim - 1, nearJ + 1);\r\n const hiK = Math.min(kDim - 1, nearK + 1);\r\n\r\n for (i = loI; i <= hiI; ++i) {\r\n const iOffset = i * jkDim;\r\n\r\n for (j = loJ; j <= hiJ; ++j) {\r\n const jOffset = j * kDim;\r\n\r\n for (let k = loK; k <= hiK; ++k) {\r\n cid = iOffset + jOffset + k;\r\n\r\n const cellStart = cellOffsets[cid];\r\n const cellEnd = cellStart + cellLengths[cid];\r\n\r\n for (let dataIndex = cellStart; dataIndex < cellEnd; dataIndex++) {\r\n const atomIndex = data[dataIndex];\r\n const baseIndex = itemSize * atomIndex;\r\n const dx = posRad[baseIndex] - x;\r\n const dy = posRad[baseIndex + 1] - y;\r\n const dz = posRad[baseIndex + 2] - z;\r\n const rSum = posRad[baseIndex + 3] + rExtra;\r\n\r\n if ((dx * dx + dy * dy + dz * dz) <= (rSum * rSum)) {\r\n out[outIdx++] = data[dataIndex];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n // Add terminator\r\n out[outIdx] = -1;\r\n };\r\n}\r\nfunction ContactSurface(packedArrays, boundaries, params, _indexList) {\r\n // Field generation method adapted from AstexViewer (Mike Hartshorn)\r\n // by Fred Ludlow.\r\n // Other parts based heavily on NGL (Alexander Rose) EDT Surface class\r\n //\r\n // Should work as a drop-in alternative to EDTSurface (though some of\r\n // the EDT paramters are not relevant in this method).\r\n\r\n const itemSize = 4;\r\n const { posRad, colors, atoms } = packedArrays;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const { bbox } = boundaries;\r\n\r\n const min = bbox.minPosRad;\r\n const max = bbox.maxPosRad;\r\n\r\n let r2; // Atom positions, expanded radii (squared)\r\n let maxRadius;\r\n\r\n // Parameters\r\n let probeRadius;\r\n let scaleFactor;\r\n let probePositions;\r\n\r\n // Cache last value for obscured test\r\n let lastClip = -1;\r\n\r\n // Grid params\r\n let dim;\r\n let grid;\r\n let volTex;\r\n let weights;\r\n let weightsMap = null;\r\n let atomMap = null;\r\n let visibilitySelector = null;\r\n\r\n // grid indices -> xyz coords\r\n let gridx;\r\n let gridy;\r\n let gridz;\r\n\r\n // Lookup tables:\r\n let sinTable;\r\n let cosTable;\r\n\r\n // Spatial Hash\r\n let hash;\r\n\r\n // Neighbour array to be filled by hash\r\n let neighbours;\r\n\r\n // Vectors for Torus Projection\r\n const mid = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n1 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n2 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n let ngTorus;\r\n\r\n function uniformArray(TypeName, n, a) {\r\n const array = utils.allocateTyped(TypeName, n);\r\n for (let innI = 0; innI < n; ++innI) {\r\n array[innI] = a;\r\n }\r\n\r\n return array;\r\n }\r\n\r\n function fillGridDim(a, start, step) {\r\n for (let innI = 0; innI < a.length; innI++) {\r\n a[innI] = start + (step * innI);\r\n }\r\n }\r\n\r\n function initializeGrid() {\r\n ({ scaleFactor } = params);\r\n ({ dim } = boundaries);\r\n\r\n ngTorus = Math.min(5, 2 + Math.floor(probeRadius * scaleFactor));\r\n\r\n const gridSize = dim[0] * dim[1] * dim[2];\r\n grid = uniformArray(Float32Array, gridSize, -1001.0);\r\n volTex = utils.allocateTyped(Float32Array, gridSize * 3);\r\n weights = utils.allocateTyped(Float32Array, gridSize);\r\n if (visibilitySelector) {\r\n weightsMap = utils.allocateTyped(Float32Array, gridSize);\r\n atomMap = [];\r\n }\r\n\r\n gridx = utils.allocateTyped(Float32Array, dim[0]);\r\n gridy = utils.allocateTyped(Float32Array, dim[1]);\r\n gridz = utils.allocateTyped(Float32Array, dim[2]);\r\n\r\n fillGridDim(gridx, min[0], 1 / scaleFactor);\r\n fillGridDim(gridy, min[1], 1 / scaleFactor);\r\n fillGridDim(gridz, min[2], 1 / scaleFactor);\r\n }\r\n\r\n function initializeAngleTables() {\r\n let theta = 0.0;\r\n const step = 2 * Math.PI / probePositions;\r\n\r\n cosTable = utils.allocateTyped(Float32Array, probePositions);\r\n sinTable = utils.allocateTyped(Float32Array, probePositions);\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n cosTable[innI] = Math.cos(theta);\r\n sinTable[innI] = Math.sin(theta);\r\n theta += step;\r\n }\r\n }\r\n\r\n function initializeHash() {\r\n hash = new AVHash(posRad, min, max, 2.01 * maxRadius);\r\n neighbours = new Int32Array(hash.neighbourListLength);\r\n }\r\n\r\n function init() {\r\n ({\r\n probeRadius,\r\n scaleFactor,\r\n probePositions,\r\n visibilitySelector,\r\n } = params);\r\n r2 = utils.allocateTyped(Float32Array, nAtoms);\r\n maxRadius = 0;\r\n for (let innI = 0; innI < nAtoms; ++innI) {\r\n const rExt = posRad[innI * itemSize + 3] += probeRadius;\r\n if (rExt > maxRadius) {\r\n maxRadius = rExt;\r\n }\r\n r2[innI] = rExt * rExt;\r\n }\r\n\r\n initializeGrid();\r\n initializeAngleTables();\r\n initializeHash();\r\n\r\n lastClip = -1;\r\n }\r\n\r\n function singleAtomObscures(ai, innX, innY, innZ) {\r\n const innCI = itemSize * ai;\r\n const ra2 = r2[ai];\r\n const dx = posRad[innCI] - innX;\r\n const dy = posRad[innCI + 1] - innY;\r\n const dz = posRad[innCI + 2] - innZ;\r\n const d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n return d2 < ra2;\r\n }\r\n\r\n function obscured(innX, innY, innZ, a, b) {\r\n // Is the point at x,y,z obscured by any of the atoms\r\n // specifeid by indices in neighbours. Ignore indices\r\n // a and b (these are the relevant atoms in projectPoints/Torii)\r\n\r\n // Cache the last clipped atom (as very often the same one in\r\n // subsequent calls)\r\n let ai;\r\n\r\n if (lastClip !== -1) {\r\n ai = lastClip;\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n return ai;\r\n }\r\n lastClip = -1;\r\n }\r\n\r\n let ni = 0;\r\n ai = neighbours[ni];\r\n while (ai >= 0) {\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n lastClip = ai;\r\n return ai;\r\n }\r\n ai = neighbours[++ni];\r\n }\r\n\r\n lastClip = -1;\r\n\r\n return -1;\r\n }\r\n\r\n function projectPoints() {\r\n // For each atom:\r\n // Iterate over a subsection of the grid, for each point:\r\n // If current value < 0.0, unvisited, set positive\r\n //\r\n // In any case: Project this point onto surface of the atomic sphere\r\n // If this projected point is not obscured by any other atom\r\n // Calcualte delta distance and set grid value to minimum of\r\n // itself and delta\r\n\r\n // Should we alias frequently accessed closure constiables??\r\n // Assume JS engine capable of optimizing this\r\n // anyway...\r\n const maxRad = 4.0;\r\n const sigma = (maxRad) / 3;\r\n const sigma2Inv = 1 / (2 * sigma * sigma);\r\n\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innCI = itemSize * innI;\r\n const ax = posRad[innCI];\r\n const ay = posRad[innCI + 1];\r\n const az = posRad[innCI + 2];\r\n const ar = posRad[innCI + 3];\r\n const ar2 = r2[innI];\r\n\r\n hash.withinRadii(ax, ay, az, ar, neighbours);\r\n\r\n // Number of grid points, round this up...\r\n const ng = Math.ceil(ar * scaleFactor);\r\n\r\n // Center of the atom, mapped to grid points (take floor)\r\n const iax = Math.floor(scaleFactor * (ax - min[0]));\r\n const iay = Math.floor(scaleFactor * (ay - min[1]));\r\n const iaz = Math.floor(scaleFactor * (az - min[2]));\r\n\r\n // Extents of grid to consider for this atom\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n // Add two to these points:\r\n // - iax are floor'd values so this ensures coverage\r\n // - these are loop limits (exclusive)\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n const colIdx = innI * 3;\r\n const cr = colors[colIdx];\r\n const cg = colors[colIdx + 1];\r\n const cb = colors[colIdx + 2];\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n const dz = gridz[iz] - az;\r\n const zOffset = dim[1] * dim[0] * iz;\r\n\r\n for (let iy = miny; iy < maxy; iy++) {\r\n const dy = gridy[iy] - ay;\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n\r\n for (let ix = minx; ix < maxx; ix++) {\r\n const idx = ix + zyOffset;\r\n const dx = gridx[ix] - ax;\r\n const d2 = dzy2 + dx * dx;\r\n\r\n if (d2 < ar2) {\r\n const w = Math.exp(-d2 * sigma2Inv);\r\n const cIdx = idx * 3;\r\n volTex[cIdx] += cr * w;\r\n volTex[cIdx + 1] += cg * w;\r\n volTex[cIdx + 2] += cb * w;\r\n weights[idx] += w;\r\n if (visibilitySelector !== null && w > weightsMap[idx]) {\r\n weightsMap[idx] = w;\r\n atomMap[idx] = atoms[innI];\r\n }\r\n\r\n if (grid[idx] < 0.0) {\r\n // Unvisited, make positive\r\n grid[idx] = -grid[idx];\r\n }\r\n // Project on to the surface of the sphere\r\n // sp is the projected point ( dx, dy, dz ) * ( ra / d )\r\n const d = Math.sqrt(d2);\r\n const ap = ar / d;\r\n let spx = dx * ap;\r\n let spy = dy * ap;\r\n let spz = dz * ap;\r\n\r\n spx += ax;\r\n spy += ay;\r\n spz += az;\r\n\r\n if (obscured(spx, spy, spz, innI, -1) === -1) {\r\n const dd = ar - d;\r\n if (dd < grid[idx]) {\r\n grid[idx] = dd;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function normalToLine(out, p) {\r\n out.x = out.y = out.z = 1.0;\r\n if (p.x !== 0) {\r\n out.x = (p.y + p.z) / -p.x;\r\n } else if (p.y !== 0) {\r\n out.y = (p.x + p.z) / -p.y;\r\n } else if (p.z !== 0) {\r\n out.z = (p.x + p.y) / -p.z;\r\n }\r\n return out;\r\n }\r\n\r\n function projectTorus(a, b) {\r\n const aIdx = itemSize * a;\r\n const bIdx = itemSize * b;\r\n const xa = posRad[aIdx];\r\n const ya = posRad[aIdx + 1];\r\n const za = posRad[aIdx + 2];\r\n const r1 = posRad[aIdx + 3];\r\n let dx = mid.x = posRad[bIdx] - xa;\r\n let dy = mid.y = posRad[bIdx + 1] - ya;\r\n let dz = mid.z = posRad[bIdx + 2] - za;\r\n const innR2 = posRad[bIdx + 3];\r\n let d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n // This check now redundant as already done in AVHash.withinRadii\r\n // if( d2 > (( r1 + r2 ) * ( r1 + r2 )) ){ return; }\r\n\r\n const d = Math.sqrt(d2);\r\n\r\n // Find angle between a->b vector and the circle\r\n // of their intersection by cosine rule\r\n const cosA = (r1 * r1 + d * d - innR2 * innR2) / (2.0 * r1 * d);\r\n\r\n // distance along a->b at intersection\r\n const dmp = r1 * cosA;\r\n\r\n mid.normalize();\r\n\r\n // Create normal to line\r\n normalToLine(n1, mid);\r\n n1.normalize();\r\n\r\n // Cross together for second normal vector\r\n n2.crossVectors(mid, n1);\r\n n2.normalize();\r\n\r\n // r is radius of circle of intersection\r\n const rInt = Math.sqrt(r1 * r1 - dmp * dmp);\r\n\r\n n1.multiplyScalar(rInt);\r\n n2.multiplyScalar(rInt);\r\n mid.multiplyScalar(dmp);\r\n\r\n mid.x += xa;\r\n mid.y += ya;\r\n mid.z += za;\r\n\r\n lastClip = -1;\r\n\r\n const ng = ngTorus;\r\n\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n const cost = cosTable[innI];\r\n const sint = sinTable[innI];\r\n\r\n const px = mid.x + cost * n1.x + sint * n2.x;\r\n const py = mid.y + cost * n1.y + sint * n2.y;\r\n const pz = mid.z + cost * n1.z + sint * n2.z;\r\n\r\n if (obscured(px, py, pz, a, b) === -1) {\r\n // As above, iterate over our grid...\r\n // px, py, pz in grid coords\r\n const iax = Math.floor(scaleFactor * (px - min[0]));\r\n const iay = Math.floor(scaleFactor * (py - min[1]));\r\n const iaz = Math.floor(scaleFactor * (pz - min[2]));\r\n\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n dz = pz - gridz[iz];\r\n const zOffset = dim[1] * dim[0] * iz;\r\n for (let iy = miny; iy < maxy; iy++) {\r\n dy = py - gridy[iy];\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n for (let ix = minx; ix < maxx; ix++) {\r\n dx = px - gridx[ix];\r\n d2 = dzy2 + dx * dx;\r\n const idx = ix + zyOffset;\r\n const current = grid[idx];\r\n\r\n if (current > 0.0 && d2 < (current * current)) {\r\n grid[idx] = Math.sqrt(d2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function projectTorii() {\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innIdx = itemSize * innI;\r\n hash.withinRadii(\r\n posRad[innIdx],\r\n posRad[innIdx + 1],\r\n posRad[innIdx + 2],\r\n posRad[innIdx + 3],\r\n neighbours,\r\n );\r\n let ia = 0;\r\n let ni = neighbours[ia];\r\n while (ni >= 0) {\r\n if (innI < ni) {\r\n projectTorus(innI, ni);\r\n }\r\n ni = neighbours[++ia];\r\n }\r\n }\r\n }\r\n\r\n function fixNegatives() {\r\n for (let innI = 0, n = grid.length; innI < n; innI++) {\r\n if (grid[innI] < 0) grid[innI] = 0;\r\n let w = weights[innI];\r\n if (w > 0) {\r\n w = 1 / w;\r\n const innInnI = innI * 3;\r\n volTex[innInnI] *= w;\r\n volTex[innInnI + 1] *= w;\r\n volTex[innInnI + 2] *= w;\r\n }\r\n }\r\n }\r\n\r\n function getVolume() {\r\n // Basic steps are:\r\n // 1) Initialize\r\n // 2) Project points\r\n // 3) Project torii\r\n console.time('ContactSurface.getVolume');\r\n\r\n console.time('ContactSurface.init');\r\n init();\r\n console.timeEnd('ContactSurface.init');\r\n\r\n console.time('ContactSurface.projectPoints');\r\n projectPoints();\r\n console.timeEnd('ContactSurface.projectPoints');\r\n\r\n console.time('ContactSurface.projectTorii');\r\n projectTorii();\r\n console.timeEnd('ContactSurface.projectTorii');\r\n fixNegatives();\r\n console.timeEnd('ContactSurface.getVolume');\r\n }\r\n\r\n this.build = function () {\r\n // type and cutoff left in for compatibility with EDTSurface.getSurface\r\n // function signature\r\n getVolume();\r\n this.volTexMap = volTex;\r\n this.weightsMap = weightsMap;\r\n this.atomMap = atomMap;\r\n this.volMap = grid;\r\n };\r\n}\r\nexport default ContactSurface;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport ContactSurface from './ContactSurface';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'contact' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass ContactSurfaceGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n const contactSurface = new ContactSurface(packedArrays, boundaries, params);\r\n contactSurface.build();\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.volMap),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3, contactSurface.volTexMap),\r\n atomMap: contactSurface.atomMap,\r\n atomWeightMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.weightsMap),\r\n };\r\n return surface;\r\n }\r\n}\r\n\r\nexport default ContactSurfaceGeometry;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for colored atom. Need for atom structure clusterization\r\n *\r\n * @param {Vector3} vCenter Center of atom\r\n * @param {number} radiusAt Radius of atom\r\n */\r\nclass IsoSurfaceAtomColored {\r\n constructor(vCenter, radiusAt) {\r\n this.coord = new THREE.Vector3();\r\n this.coord.copy(vCenter);\r\n this.radius = radiusAt;\r\n this.colorX = 0.99999;\r\n this.colorY = 0.0;\r\n this.colorZ = 0.0;\r\n this.atomType = 0;\r\n this.srcAtom = null;\r\n }\r\n}\r\nexport default IsoSurfaceAtomColored;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n// suppress some JSHint warnings\r\n/* jshint bitwise: false */\r\n\r\n/**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numAtoms - Number of atoms in molecule\r\n * @param {Element} atoms - Array of atoms\r\n * @param {Vector3} vBoxMin - Bounding box min\r\n * @param {Vector3} vBoxMax - Bounding box max\r\n * @param {number} probeRadius - Normals for output\r\n *\r\n */\r\nclass IsosurfaceBuildNormals {\r\n constructor(numAtoms, atoms, vBoxMin, vBoxMax, probeRadius) {\r\n this._numAtoms = numAtoms;\r\n this._atoms = atoms;\r\n this._vBoxMin = new THREE.Vector3();\r\n this._vBoxMax = new THREE.Vector3();\r\n this._vBoxMin.copy(vBoxMin);\r\n this._vBoxMax.copy(vBoxMax);\r\n this._probeRadius = probeRadius;\r\n\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n }\r\n\r\n createVoxels() {\r\n let numAtomsRefs;\r\n let rad;\r\n const ATOM_VOXEL_REF_SCALE = 4.5;\r\n\r\n const numAtoms = this._numAtoms | 0;\r\n const atoms = this._atoms;\r\n const dx = this._vBoxMax.x - this._vBoxMin.x;\r\n const dy = this._vBoxMax.y - this._vBoxMin.y;\r\n const dz = this._vBoxMax.z - this._vBoxMin.z;\r\n let w = (dx < dy) ? dx : dy;\r\n w = (dz < w) ? dz : w;\r\n let maxRad = 0.0;\r\n let aveRad = 0.0;\r\n\r\n let i;\r\n for (i = 0; i < numAtoms; i++) {\r\n rad = (atoms[i].radius + this._probeRadius) * 2.0;\r\n maxRad = (rad > maxRad) ? rad : maxRad;\r\n aveRad += rad;\r\n }\r\n let numCells = Math.floor(w / maxRad);\r\n if (numCells < 2) {\r\n numCells = 2;\r\n }\r\n aveRad /= numAtoms;\r\n\r\n this._numCells = numCells;\r\n this._aveRad = aveRad;\r\n this._maxRad = maxRad;\r\n\r\n const side = numCells;\r\n const side2 = numCells * numCells;\r\n const side3 = numCells * numCells * numCells;\r\n\r\n const xScale = this._xScale = 1.0 / (this._vBoxMax.x - this._vBoxMin.x);\r\n const yScale = this._yScale = 1.0 / (this._vBoxMax.y - this._vBoxMin.y);\r\n const zScale = this._zScale = 1.0 / (this._vBoxMax.z - this._vBoxMin.z);\r\n\r\n // estimate number of individual atom refs in each voxel list\r\n let maxAtomsRefs = 0;\r\n\r\n const xNumVoxMult = xScale * numCells;\r\n const yNumVoxMult = yScale * numCells;\r\n const zNumVoxMult = zScale * numCells;\r\n\r\n for (i = 0; i < numAtoms; i++) {\r\n const radAffect = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n const diaAffect = radAffect * 2.0;\r\n let numVoxX = Math.floor(xNumVoxMult * diaAffect + 0.8);\r\n let numVoxY = Math.floor(yNumVoxMult * diaAffect + 0.8);\r\n let numVoxZ = Math.floor(zNumVoxMult * diaAffect + 0.8);\r\n // avoid case numVox? == 0\r\n // also use loop i <=\r\n numVoxX++;\r\n numVoxY++;\r\n numVoxZ++;\r\n maxAtomsRefs += numVoxX * numVoxY * numVoxZ;\r\n } // for (i)\r\n // maxAtomsRefs = numAtoms * MAX_ATOMS_IN_SINGLE_VOXEL;\r\n\r\n this._voxelList = utils.allocateTyped(Int32Array, side3);\r\n const atomsList = [];\r\n atomsList.length = maxAtomsRefs;\r\n if ((this._voxelList === null) || (atomsList === null)) {\r\n return 0 - 1;\r\n }\r\n // init voxel list\r\n for (i = 0; i < side3; i++) {\r\n this._voxelList[i] = -1;\r\n }\r\n numAtomsRefs = 0;\r\n\r\n // create voxel lists\r\n for (i = 0; i < numAtoms; i++) {\r\n // use multiplier 4 to locate this atom in different voxels\r\n rad = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n let xIndMin = Math.floor((atoms[i].coord.x - this._vBoxMin.x - rad) * numCells * xScale);\r\n let yIndMin = Math.floor((atoms[i].coord.y - this._vBoxMin.y - rad) * numCells * yScale);\r\n let zIndMin = Math.floor((atoms[i].coord.z - this._vBoxMin.z - rad) * numCells * zScale);\r\n let xIndMax = Math.floor((atoms[i].coord.x - this._vBoxMin.x + rad) * numCells * xScale);\r\n let yIndMax = Math.floor((atoms[i].coord.y - this._vBoxMin.y + rad) * numCells * yScale);\r\n let zIndMax = Math.floor((atoms[i].coord.z - this._vBoxMin.z + rad) * numCells * zScale);\r\n\r\n xIndMin = (xIndMin >= 0) ? xIndMin : 0;\r\n yIndMin = (yIndMin >= 0) ? yIndMin : 0;\r\n zIndMin = (zIndMin >= 0) ? zIndMin : 0;\r\n\r\n xIndMax = (xIndMax < numCells) ? xIndMax : (numCells - 1);\r\n yIndMax = (yIndMax < numCells) ? yIndMax : (numCells - 1);\r\n zIndMax = (zIndMax < numCells) ? zIndMax : (numCells - 1);\r\n\r\n for (let z = zIndMin; z <= zIndMax; z++) {\r\n for (let y = yIndMin; y <= yIndMax; y++) {\r\n for (let x = xIndMin; x <= xIndMax; x++) {\r\n // add atom with index \"i\" to this voxel list\r\n const indVoxel = x + y * side + z * side2;\r\n // assert indVoxel >= 0\r\n // assert indVoxel < side3\r\n\r\n // add first\r\n if (this._voxelList[indVoxel] < 0) {\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = 0 - 1;\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n numAtomsRefs++;\r\n // assert numAtomsRefs < maxAtomsRefs - 1\r\n continue;\r\n }\r\n // insert into head of list\r\n const indexNext = this._voxelList[indVoxel];\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = indexNext;\r\n numAtomsRefs++;\r\n } // for (x)\r\n } // for (y)\r\n } // for (z)\r\n } // for (i)\r\n\r\n // convert Array to Int32Array\r\n this._atomsList = Int32Array.from(atomsList);\r\n\r\n return 0;\r\n }\r\n\r\n destroyVoxels() {\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n\r\n this._atoms = null;\r\n this._vertices = null;\r\n this._vBoxMin = null;\r\n this._vBoxMax = null;\r\n }\r\n\r\n /**\r\n * Enumerate all atoms affecting specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n * @param {func(atom)} process - function to call for each atom\r\n */\r\n forEachRelatedAtom(point, process) {\r\n // find corresponding voxel\r\n const xInd = Math.floor((point.x - this._vBoxMin.x) * this._numCells * this._xScale);\r\n const yInd = Math.floor((point.y - this._vBoxMin.y) * this._numCells * this._yScale);\r\n const zInd = Math.floor((point.z - this._vBoxMin.z) * this._numCells * this._zScale);\r\n const indVoxel = xInd + yInd * this._numCells + zInd * this._numCells * this._numCells;\r\n\r\n // run through atoms affecting this voxel\r\n const atoms = this._atoms;\r\n for (let ref = this._voxelList[indVoxel]; ref >= 0; ref = this._atomsList[ref * 2 + 1]) {\r\n const indexAtom = this._atomsList[ref * 2];\r\n process(atoms[indexAtom]);\r\n }\r\n }\r\n\r\n /**\r\n * Get atom closest to specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n *\r\n * @returns {IsoSurfaceAtomColored} atom, or null if not found\r\n */\r\n getClosestAtom(point) {\r\n let closest = null;\r\n let minDist2 = Number.MAX_VALUE;\r\n\r\n this.forEachRelatedAtom(point, (atom) => {\r\n const dist2 = point.distanceToSquared(atom.coord);\r\n if (dist2 < minDist2) {\r\n minDist2 = dist2;\r\n closest = atom;\r\n }\r\n });\r\n\r\n return closest;\r\n }\r\n\r\n /**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} normals - Normals for output\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildNormals(numVertices, vertices, normals) {\r\n const self = this;\r\n let numCloseAtoms = 0;\r\n let vx = 0;\r\n let vy = 0;\r\n let vz = 0;\r\n let dist2;\r\n let vNormalX = 0;\r\n let vNormalY = 0;\r\n let vNormalZ = 0;\r\n let koef = 0;\r\n let w = 0;\r\n const r25 = 2.5;\r\n const r01 = 0.1;\r\n\r\n const maxRadAffect = this._aveRad * r25;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n const expScale = -this._aveRad * r01;\r\n\r\n // some stats\r\n // numSlowAtoms = 0;\r\n\r\n const gatherNormals = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = Math.exp(expScale * koef);\r\n\r\n vNormalX += dx * w;\r\n vNormalY += dy * w;\r\n vNormalZ += dz * w;\r\n numCloseAtoms++;\r\n };\r\n\r\n let maxClosedAtoms = 0;\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n numCloseAtoms = 0;\r\n vNormalX = vNormalY = vNormalZ = 0.0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherNormals);\r\n\r\n maxClosedAtoms = (numCloseAtoms > maxClosedAtoms) ? numCloseAtoms : maxClosedAtoms;\r\n\r\n // normalize vNormal\r\n dist2 = vNormalX * vNormalX + vNormalY * vNormalY + vNormalZ * vNormalZ;\r\n if (numCloseAtoms > 0) {\r\n koef = 1.0 / Math.sqrt(dist2);\r\n vNormalX *= koef;\r\n vNormalY *= koef;\r\n vNormalZ *= koef;\r\n }\r\n normals[i].x = vNormalX;\r\n normals[i].y = vNormalY;\r\n normals[i].z = vNormalZ;\r\n } // for (i) all vertices\r\n\r\n return 0;\r\n }\r\n\r\n /**\r\n * Build vertex colors for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} colors - Colors for output\r\n * @param {number} radiusColorSmoothness - Radius of smoothness sphere\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildColors(numVertices, vertices, colors, radiusColorSmoothness) {\r\n const self = this;\r\n let vx = 0.0;\r\n let vy = 0.0;\r\n let vz = 0.0;\r\n let koef = 0.0;\r\n let w = 0.0;\r\n const KOEF_ADD = 0.8;\r\n\r\n const maxRadAffect = radiusColorSmoothness;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n\r\n let colorsClose = [];\r\n let weights = [];\r\n let weightsSum = 0;\r\n\r\n const gatherColors = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = 1.0 / (KOEF_ADD + koef);\r\n\r\n colorsClose.push([atom.colorX, atom.colorY, atom.colorZ]);\r\n weights.push(w); // save weights for use\r\n weightsSum += w; // calc sum of weights fo further normalization\r\n };\r\n\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n colorsClose = [];\r\n weights = [];\r\n weightsSum = 0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherColors);\r\n\r\n // normalized weighted sum of colors\r\n for (let j = 0; j < colorsClose.length; ++j) {\r\n const weightNormalized = weights[j] / weightsSum;\r\n colors[i].x += colorsClose[j][0] * weightNormalized;\r\n colors[i].y += colorsClose[j][1] * weightNormalized;\r\n colors[i].z += colorsClose[j][2] * weightNormalized;\r\n }\r\n } // for (i) all vertices\r\n return 0;\r\n }\r\n}\r\nexport default IsosurfaceBuildNormals;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for geometry (triangle mesh) representation\r\n *\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices in mesh\r\n * @param {number} maxNumTriangles Maximum possible number of triangles in mesh\r\n * @param {boolean} needVertexColors Obvious\r\n */\r\nclass IsoSurfaceGeo {\r\n constructor(maxNumVertices, maxNumTriangles, needVertexColors) {\r\n this._maxNumVertices = maxNumVertices;\r\n this._maxNumTriangles = maxNumTriangles;\r\n this._vertices = new Array(maxNumVertices);\r\n this._normals = new Array(maxNumVertices);\r\n this._colors = null;\r\n if (needVertexColors) {\r\n this._colors = new Array(maxNumVertices);\r\n }\r\n this._indices = new Array(maxNumTriangles * (1 + 2));\r\n this._numVertices = 0;\r\n this._numTriangles = 0;\r\n\r\n let i;\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._vertices[i] = new THREE.Vector3();\r\n this._normals[i] = new THREE.Vector3();\r\n }\r\n for (i = 0; i < maxNumTriangles * (1 + 2); i++) {\r\n this._indices[i] = -1;\r\n }\r\n if (needVertexColors) {\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._colors[i] = new THREE.Vector3();\r\n }\r\n }\r\n }\r\n\r\n destroy() {\r\n this._vertices = null;\r\n this._normals = null;\r\n this._indices = null;\r\n }\r\n}\r\nexport default IsoSurfaceGeo;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurfaceAtomColored from './IsoSurfaceAtomColored';\r\nimport IsosurfaceBuildNormals from './IsosurfaceBuildNormals';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport IsoSurfaceGeo from './IsoSurfaceGeo';\r\nimport chem from '../../chem';\r\nimport utils from '../../utils';\r\n\r\nconst COLOR_SIZE = 3;\r\nconst HASH_SIZE = 32768;\r\nconst { Element } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass SSIsosurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n // convert geoOut into arrays of positions, indices, normals\r\n this._innerBuild();\r\n const geoOut = this.getGeo();\r\n this.destroy();\r\n this._fromGeo(geoOut);\r\n }\r\n\r\n _fromGeo(geoOut) {\r\n let colors = null;\r\n const positions = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n const normals = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n if (geoOut._colors !== null) {\r\n colors = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n }\r\n const indices = utils.allocateTyped(Uint32Array, (1 + 2) * geoOut._numTriangles);\r\n\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++) {\r\n positions[j + 0] = (geoOut._vertices[i].x);\r\n positions[j + 1] = (geoOut._vertices[i].y);\r\n positions[j + 2] = (geoOut._vertices[i].z);\r\n normals[j + 0] = geoOut._normals[i].x;\r\n normals[j + 1] = geoOut._normals[i].y;\r\n normals[j + 2] = geoOut._normals[i].z;\r\n j += 3;\r\n }\r\n if (colors !== null) {\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++, j += 3) {\r\n colors[j + 0] = geoOut._colors[i].x;\r\n colors[j + 1] = geoOut._colors[i].y;\r\n colors[j + 2] = geoOut._colors[i].z;\r\n }\r\n }\r\n\r\n const numTri3 = geoOut._numTriangles * (1 + 2);\r\n for (let i = 0; i < numTri3; i++) {\r\n indices[i] = geoOut._indices[i];\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(positions, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(colors, 3));\r\n this.computeBoundingBox();\r\n this.computeBoundingSphere();\r\n\r\n geoOut.destroy();\r\n }\r\n\r\n convertToAtomsColored(packedArrays, atomsColored) {\r\n const { atoms, colors } = packedArrays;\r\n for (let i = 0, numAtoms = atoms.length; i < numAtoms; i++) {\r\n const vCenter = atoms[i].position;\r\n const { radius } = atoms[i].element;\r\n atomsColored[i] = new IsoSurfaceAtomColored(vCenter, radius);\r\n const nm = atoms[i].element.number;\r\n atomsColored[i].atomType = this.getType(nm);\r\n let cIdx = COLOR_SIZE * i;\r\n atomsColored[i].colorX = colors[cIdx++];\r\n atomsColored[i].colorY = colors[cIdx++];\r\n atomsColored[i].colorZ = colors[cIdx];\r\n atomsColored[i].srcAtom = atoms[i];\r\n }\r\n }\r\n\r\n getGeo() {\r\n return this.geoOut;\r\n }\r\n\r\n destroy() {\r\n this.atoms = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n }\r\n\r\n /**\r\n * Calculates bounding box for array with spheres (atoms)\r\n *\r\n * @param {Object} atoms Atoms array\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n */\r\n getBoundingBox(atoms, vBoxMin, vBoxMax) {\r\n const bigNum = 10000000.0;\r\n\r\n vBoxMin.x = vBoxMin.y = vBoxMin.z = bigNum;\r\n vBoxMax.x = vBoxMax.y = vBoxMax.z = 0 - bigNum;\r\n\r\n const probeRadius2 = this.probeRadius * this.atomRadiusScale;\r\n let radMax = 0.0;\r\n for (let i = 0, num = atoms.length; i < num; i++) {\r\n const vCenter = atoms[i].coord;\r\n const rad = atoms[i].radius + probeRadius2;\r\n radMax = (rad > radMax) ? rad : radMax;\r\n if (vCenter.x - rad < vBoxMin.x) {\r\n vBoxMin.x = vCenter.x - rad;\r\n }\r\n if (vCenter.y - rad < vBoxMin.y) {\r\n vBoxMin.y = vCenter.y - rad;\r\n }\r\n if (vCenter.z - rad < vBoxMin.z) {\r\n vBoxMin.z = vCenter.z - rad;\r\n }\r\n if (vCenter.x + rad > vBoxMax.x) {\r\n vBoxMax.x = vCenter.x + rad;\r\n }\r\n if (vCenter.y + rad > vBoxMax.y) {\r\n vBoxMax.y = vCenter.y + rad;\r\n }\r\n if (vCenter.z + rad > vBoxMax.z) {\r\n vBoxMax.z = vCenter.z + rad;\r\n }\r\n }\r\n vBoxMin.x -= radMax;\r\n vBoxMin.y -= radMax;\r\n vBoxMin.z -= radMax;\r\n vBoxMax.x += radMax;\r\n vBoxMax.y += radMax;\r\n vBoxMax.z += radMax;\r\n }\r\n\r\n /**\r\n * Calculate (x,y,z) cordinate of the cell corner point\r\n *\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {number} x Cell integer x coordinate\r\n * @param {number} y Cell integer y coordinate\r\n * @param {number} z Cell integer z coordinate\r\n * @param {number} numPoints NUm points in cell on side\r\n * @param {Vector3} vOut Output vector\r\n */\r\n getCornerCoord(vBoxMin, vBoxMax, x, y, z, numPoints, vOut) {\r\n const invNP = 1.0 / (numPoints - 1.0);\r\n const tx = x * invNP;\r\n const ty = y * invNP;\r\n const tz = z * invNP;\r\n\r\n vOut.x = vBoxMin.x * (1.0 - tx) + vBoxMax.x * tx;\r\n vOut.y = vBoxMin.y * (1.0 - ty) + vBoxMax.y * ty;\r\n vOut.z = vBoxMin.z * (1.0 - tz) + vBoxMax.z * tz;\r\n }\r\n\r\n /**\r\n * Calculate point of intersection of sphere surface\r\n * and cell edge, given by [indexA, indexB] line\r\n *\r\n * @param {number} indexA Cell vertex index in [0..11]\r\n * @param {number} indexB Cell vertex index in [0..11]\r\n * @param {array} sign Sign array for all 8 vertices\r\n * @param {object} cube Cube\r\n * @param {number} indexPointValue for value placement\r\n * @param {Vector3} vOut Point of intersection\r\n */\r\n buildEdgePoint(indexA, indexB, sign, cube, indexPointValue, vOut) {\r\n if (sign[indexA] ^ sign[indexB]) {\r\n const cTwentyFour = 24;\r\n const t = (0 - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA])\r\n / (cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexB]\r\n - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA]);\r\n const xa = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 0];\r\n const ya = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 1];\r\n const za = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 2];\r\n const xb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 0];\r\n const yb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 1];\r\n const zb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 2];\r\n\r\n vOut.x = xa * (1.0 - t) + xb * t;\r\n vOut.y = ya * (1.0 - t) + yb * t;\r\n vOut.z = za * (1.0 - t) + zb * t;\r\n }\r\n }\r\n\r\n /**\r\n * Check if triangle is visible (vertices are close to atoms included in visibility set)\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} true if triangle is visible\r\n */\r\n isTriangleVisible(v0, v1, v2) {\r\n const a0 = this.voxelWorld.getClosestAtom(v0);\r\n const a1 = this.voxelWorld.getClosestAtom(v1);\r\n const a2 = this.voxelWorld.getClosestAtom(v2);\r\n if (a0 === null || a1 === null || a2 === null\r\n || a0.srcAtom === null || a1.srcAtom === null || a2.srcAtom === null) {\r\n return false;\r\n }\r\n\r\n return this.visibilitySelector.includesAtom(a0.srcAtom)\r\n && this.visibilitySelector.includesAtom(a1.srcAtom)\r\n && this.visibilitySelector.includesAtom(a2.srcAtom);\r\n }\r\n\r\n /**\r\n * Add triangle to result geometry\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} false if no more triangles can be added\r\n */\r\n addTriangle(v0, v1, v2) {\r\n if (this.visibilitySelector && !this.isTriangleVisible(v0, v1, v2)) {\r\n return true;\r\n }\r\n\r\n const geo = this.geoOut;\r\n\r\n if (geo._numTriangles >= this.maxNumTriangles) {\r\n return false;\r\n }\r\n\r\n // Add vertex with optimize\r\n const indInGeo0 = this.addVertexToGeo(geo, v0);\r\n const indInGeo1 = this.addVertexToGeo(geo, v1);\r\n const indInGeo2 = this.addVertexToGeo(geo, v2);\r\n if ((indInGeo0 | indInGeo1 | indInGeo2) < 0) {\r\n return false;\r\n }\r\n\r\n const itr = 3 * geo._numTriangles;\r\n geo._indices[itr + 0] = indInGeo0;\r\n geo._indices[itr + 1] = indInGeo1;\r\n geo._indices[itr + 2] = indInGeo2;\r\n geo._numTriangles++;\r\n return true;\r\n }\r\n\r\n /**\r\n * Build result geometry (triangle mesh) from marching cube cells\r\n *\r\n * @param {number} meshRes Marchnig cube vertex count on each side\r\n * @param {Vector3} vBoxMin Bounding box point min\r\n * @param {Vector3} vBoxMax Bounding box point max\r\n * @param {number} corners float values array for each cube point\r\n * @param {Vector3} vCellStep vector to next cube cell diagonal point\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} 0, if success (<0) is error\r\n */\r\n buildGeoFromCorners(meshRes, vBoxMin, vBoxMax, corners, vCellStep, cube) {\r\n const arrSize = 12;\r\n const cNumVerts = 8;\r\n const numCells = meshRes - 1;\r\n const side = meshRes;\r\n const side2 = meshRes * meshRes;\r\n\r\n const vaEdges = new Array(arrSize);\r\n for (let i = 0; i < arrSize; i++) {\r\n vaEdges[i] = new THREE.Vector3();\r\n }\r\n const sign = [];\r\n for (let i = 0; i < cNumVerts; i++) {\r\n sign[i] = 1.0;\r\n }\r\n const vCorner = new THREE.Vector3();\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n if (!cube.hasIntersection[indCell]) {\r\n // next cell\r\n indCell++;\r\n continue;\r\n }\r\n const bitsInside = cube.bitsInside[indCell];\r\n\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, meshRes, vCorner);\r\n\r\n const indPointValues = indCell * (2 << (2 + 2));\r\n for (let i = 0, j = 0; i < cNumVerts; i++) {\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.x;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.y;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.z;\r\n }\r\n\r\n cube.pointsValuesLinear[indPointValues + 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 2 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3] += vCellStep.x;\r\n\r\n cube.pointsValuesLinear[indPointValues + 2 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 3 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 2] += vCellStep.z;\r\n\r\n cube.pointsValuesLinear[indPointValues + 4 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 1] += vCellStep.y;\r\n\r\n // now current cell has intersections (from -x to +x) on some cube edges\r\n const indValues = indPointValues + 24;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n sign[i] = (cube.pointsValuesLinear[indValues + i] < 0.0) ? 1 : 0;\r\n }\r\n\r\n this.buildEdgePoint(0, 1, sign, cube, indPointValues, vaEdges[0]);\r\n this.buildEdgePoint(1, 2, sign, cube, indPointValues, vaEdges[1]);\r\n this.buildEdgePoint(2, 3, sign, cube, indPointValues, vaEdges[2]);\r\n this.buildEdgePoint(3, 0, sign, cube, indPointValues, vaEdges[3]);\r\n\r\n this.buildEdgePoint(4, 5, sign, cube, indPointValues, vaEdges[4]);\r\n this.buildEdgePoint(5, 6, sign, cube, indPointValues, vaEdges[5]);\r\n this.buildEdgePoint(6, 7, sign, cube, indPointValues, vaEdges[6]);\r\n this.buildEdgePoint(7, 4, sign, cube, indPointValues, vaEdges[7]);\r\n\r\n this.buildEdgePoint(0, 4, sign, cube, indPointValues, vaEdges[8]);\r\n this.buildEdgePoint(1, 5, sign, cube, indPointValues, vaEdges[9]);\r\n this.buildEdgePoint(2, 6, sign, cube, indPointValues, vaEdges[10]);\r\n this.buildEdgePoint(3, 7, sign, cube, indPointValues, vaEdges[11]);\r\n\r\n const offs = bitsInside * (2 << (1 + 2));\r\n for (let numTri = 0, indTri = 0; numTri < (2 + 2 + 2); numTri++, indTri += 3) {\r\n // s_triIndicesMarchCube is external array, defined in mold_ind.js\r\n const i0 = cube.striIndicesMarchCube[offs + indTri];\r\n if (i0 < 0) {\r\n break;\r\n }\r\n const i1 = cube.striIndicesMarchCube[offs + indTri + 1];\r\n const i2 = cube.striIndicesMarchCube[offs + indTri + 2];\r\n\r\n if (!this.addTriangle(vaEdges[i0], vaEdges[i1], vaEdges[i2])) {\r\n return 0 - 2;\r\n }\r\n } // for numTri\r\n\r\n // next cell (cube)\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return 0;\r\n }\r\n\r\n /**\r\n * Returns number of cell with intersection with at least one sphere.\r\n * Using this number, we can estimate required number of vertices\r\n * and triangles to build result mesh.\r\n *\r\n * @param {number} side Number of points in cube voxels\r\n * @param {number} numCells Number of cells in cube voxels (per direction)\r\n * @param {array} corners Array of float values for cube corner points\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} numIntersectedCells\r\n */\r\n getNumIntersectedCells(side, numCells, corners, cube) {\r\n const side2 = side * side;\r\n const cNumVerts = 8;\r\n let numIntersectedCells = 0;\r\n\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n const cubeValuesIndex = indCell * (2 << (2 + 2)) + 24;\r\n const indCorner = x + indZ + indY;\r\n\r\n cube.pointsValuesLinear[cubeValuesIndex] = corners[indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 1] = corners[indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 2] = corners[indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 3] = corners[indCorner + side];\r\n cube.pointsValuesLinear[cubeValuesIndex + 4] = corners[side2 + indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 5] = corners[side2 + indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 6] = corners[side2 + indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 7] = corners[side2 + indCorner + side];\r\n\r\n // check read exception\r\n // assert(side2 + indCorner + side + 1 < side3);\r\n\r\n // get bit flags inside\r\n let bitsInside = 0;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n if (cube.pointsValuesLinear[cubeValuesIndex + i] < 0.0) {\r\n bitsInside |= (1 << i);\r\n }\r\n }\r\n\r\n if ((bitsInside === 0) || (bitsInside === ((1 << cNumVerts) - 1))) {\r\n cube.hasIntersection[indCell] = false;\r\n } else {\r\n cube.hasIntersection[indCell] = true;\r\n numIntersectedCells++;\r\n }\r\n cube.bitsInside[indCell] = bitsInside;\r\n // next cell\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return numIntersectedCells;\r\n }\r\n\r\n getType(letter) {\r\n const atomT = [0, 0, 1, 1, 2, 6, 3, 6, 4, 6, 5, 6, 6, 0, 7, 3, 8, 2, 9, 6, 10, 6, 11, 6, 12, 6, 13, 6, 14, 6, 15, 4,\r\n 16, 5, 17, 6, 18, 6, 19, 6, 20, 6, 21, 6, 22, 6, 23, 6, 24, 6, 25, 6, 26, 6, 27, 6, 28, 6, 29, 6, 30, 6, 31, 6,\r\n 32, 6, 33, 6, 34, 6, 35, 6, 36, 6, 37, 6, 38, 6, 39, 6, 40, 6, 41, 6, 42, 6, 43, 6, 44, 6, 45, 6, 46, 6, 47, 6,\r\n 48, 6, 49, 6, 50, 6, 51, 6, 52, 6, 53, 6, 54, 6, 55, 6, 56, 6, 57, 6, 58, 6, 59, 6, 60, 6, 61, 6, 62, 6, 63, 6,\r\n 64, 6, 65, 6, 66, 6, 67, 6, 68, 6, 69, 6, 70, 6, 71, 6, 72, 6, 73, 6, 74, 6, 75, 6, 76, 6, 77, 6, 78, 6, 79, 6,\r\n 80, 6, 81, 6, 82, 6, 83, 6, 84, 6, 85, 6, 86, 6, 87, 6, 88, 6, 89, 6, 90, 6, 91, 6, 92, 6, 93, 6, 94, 6, 95, 6,\r\n 96, 6, 97, 6, 98, 6, 99, 6, 100, 6, 101, 6, 102, 6, 103, 6, 104, 6, 105, 6, 106, 6, 107, 6, 108, 6, 109, 6];\r\n\r\n if (letter < 1 || letter > atomT.length / 2\r\n || (Object.keys(Element.ByAtomicNumber).length * 2) !== atomT.length) {\r\n throw new Error('atomT.length should be equal Element.ByAtomicNumber.length * 2');\r\n }\r\n return atomT[letter * 2];\r\n }\r\n\r\n /**\r\n * Calculate values for marching cube grid points\r\n * positive values are outside sphere, negative - is inside\r\n *\r\n * @param {array} corners array of float values\r\n * @param {number} side Number of point in cube in 1 dimennsion\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {array} atoms Array of input atoms\r\n * @param {number} probeRad radius for atom probing\r\n */\r\n calculateGridCorners(corners, side, vBoxMin, vBoxMax, atoms, probeRad) {\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const vCorner = new THREE.Vector3();\r\n const vDif = new THREE.Vector3();\r\n\r\n const aLot = +1.0e12;\r\n\r\n for (let i = 0; i < side3; i++) {\r\n corners[i] = aLot; // to large value\r\n }\r\n\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n for (let s = 0, numAtoms = atoms.length; s < numAtoms; s++) {\r\n const atom = atoms[s];\r\n const radius = atom.radius + probeRad;\r\n\r\n const fx = ((atom.coord.x - radius) - vBoxMin.x) * xScale;\r\n const fy = ((atom.coord.y - radius) - vBoxMin.y) * yScale;\r\n const fz = ((atom.coord.z - radius) - vBoxMin.z) * zScale;\r\n\r\n const indXMin = Math.floor(fx);\r\n const indYMin = Math.floor(fy);\r\n const indZMin = Math.floor(fz);\r\n\r\n let indXMax = Math.floor(((atom.coord.x + radius) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((atom.coord.y + radius) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((atom.coord.z + radius) - vBoxMin.z) * zScale);\r\n\r\n indXMax++;\r\n indYMax++;\r\n indZMax++;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let y = indYMin; y <= indYMax; y++) {\r\n const indY = y * side2;\r\n for (let z = indZMin; z <= indZMax; z++) {\r\n const indZ = z * side;\r\n for (let x = indXMin; x <= indXMax; x++) {\r\n const ind = indY + indZ + x;\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, side, vCorner);\r\n vDif.x = vCorner.x - atom.coord.x;\r\n vDif.y = vCorner.y - atom.coord.y;\r\n vDif.z = vCorner.z - atom.coord.z;\r\n const distToSphere = Math.sqrt(vDif.x * vDif.x + vDif.y * vDif.y + vDif.z * vDif.z);\r\n // val: < 0, if inside sphere\r\n // val: > 0, if outside sphere\r\n const val = distToSphere - radius;\r\n if (val < corners[ind]) {\r\n corners[ind] = val;\r\n }\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n } // for (s)\r\n }\r\n\r\n /**\r\n * Create memory pool for vertex hash management\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices (that will be build)\r\n * @param {number} maxNumTriangles Maximum possible number of triangles (that will be build)\r\n * @returns {number} 0, if success. (<0) is non memory\r\n */\r\n createVertexHash(maxNumVertices, maxNumTriangles) {\r\n this.hashLines = utils.allocateTyped(Int32Array, HASH_SIZE * 2);\r\n if (this.hashLines === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < HASH_SIZE; i++) {\r\n this.hashLines[j++] = 0; // num vertices in this hash line\r\n this.hashLines[j++] = 0 - 1; // index of the first entry\r\n }\r\n\r\n this.maxNumVertices = maxNumVertices;\r\n this.maxNumTriangles = maxNumTriangles;\r\n\r\n this.numHashEtriesAllocated = maxNumVertices;\r\n this.hashEntries = utils.allocateTyped(Int32Array, 2 * this.numHashEtriesAllocated);\r\n if (this.hashEntries === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < this.numHashEtriesAllocated; i++) {\r\n this.hashEntries[j++] = 0 - 1; // index of vertex\r\n this.hashEntries[j++] = 0 - 1; // next hash entry index\r\n }\r\n this.numHashEntryIndex = 0;\r\n return 0;\r\n }\r\n\r\n /**\r\n * Allocate and return new hash entry. Just check possible amount.\r\n *\r\n * @returns {number} index of hash entry, that can be used for geometry add vertex functionality\r\n */\r\n getNewHashEntry() {\r\n if (this.numHashEntryIndex < this.numHashEtriesAllocated) {\r\n const i = this.numHashEntryIndex;\r\n this.numHashEntryIndex++;\r\n return i;\r\n }\r\n return 0 - 1;\r\n }\r\n\r\n /**\r\n * Add vertex to geometry structure\r\n * using vertex hash table to quickly check, is this vertex already exist in geometry\r\n *\r\n * @param {object} geoOut Geometry to build\r\n * @param {Vector3} vAdd Vertex to add\r\n * @returns {number} index of added (or existing) vertex in geometry.\r\n */\r\n addVertexToGeo(geoOut, vAdd) {\r\n let entry;\r\n const oneHynberes = 0.01;\r\n const n815851 = 815851;\r\n const n37633 = 37633;\r\n const n2453543 = 2453543;\r\n const r106 = 1.0e-6;\r\n\r\n const hashResolution = this.marCubeResoultion << 2;\r\n const v = new THREE.Vector3();\r\n const ix = Math.floor(hashResolution * (vAdd.x - this.vBoxMin.x) / (this.vBoxMax.x + oneHynberes - this.vBoxMin.x));\r\n const iy = Math.floor(hashResolution * (vAdd.y - this.vBoxMin.y) / (this.vBoxMax.y + oneHynberes - this.vBoxMin.y));\r\n const iz = Math.floor(hashResolution * (vAdd.z - this.vBoxMin.z) / (this.vBoxMax.z + oneHynberes - this.vBoxMin.z));\r\n let iHash = ix * n815851 + iz * n37633 + iy * n2453543;\r\n iHash &= (HASH_SIZE - 1);\r\n const hLineIndex = iHash + iHash;\r\n\r\n // search vertex via hash\r\n // search in hash list\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n for (entry = this.hashLines[hLineIndex + 1]; entry >= 0; entry = this.hashEntries[entry * 2 + 1]) {\r\n const ind = this.hashEntries[entry * 2 + 0]; // vertex index\r\n v.copy(geoOut._vertices[ind]);\r\n v.x -= vAdd.x;\r\n v.y -= vAdd.y;\r\n v.z -= vAdd.z;\r\n const dot2 = v.x * v.x + v.y * v.y + v.z * v.z;\r\n if (dot2 < r106) {\r\n return ind;\r\n } // if (found)\r\n } // for (entry)\r\n } // search\r\n\r\n // add new vertex to geometry\r\n if (geoOut._numVertices >= this.maxNumVertices) {\r\n return 0 - 1;\r\n }\r\n\r\n const iVertAdd = geoOut._numVertices;\r\n geoOut._vertices[iVertAdd].copy(vAdd);\r\n\r\n // add to hash\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n entry = this.getNewHashEntry();\r\n if (entry < 0) {\r\n return 0 - 1;\r\n }\r\n const entryFirst = this.hashLines[hLineIndex + 1];\r\n this.hashLines[hLineIndex + 1] = entry;\r\n this.hashEntries[entry * 2 + 0] = iVertAdd;\r\n this.hashEntries[entry * 2 + 1] = entryFirst;\r\n\r\n this.hashLines[hLineIndex + 0]++; // num vertices in line ++\r\n }\r\n geoOut._numVertices++;\r\n return iVertAdd;\r\n }\r\n\r\n /**\r\n *\r\n * @param {number} side some placeholder description\r\n * @param {number} probeSphereRadius some placeholder description\r\n * @param {object} vBoxMin some placeholder description\r\n * @param {object} vBoxMax some placeholder description\r\n * @param {object} geoOut some placeholder description\r\n * @param {object} corners some placeholder description\r\n * @returns {number} always 0\r\n */\r\n modifyExcludedFromGeo(\r\n side,\r\n probeSphereRadius,\r\n vBoxMin,\r\n vBoxMax,\r\n geoOut,\r\n corners,\r\n ) {\r\n let ind;\r\n let distToSphere;\r\n let distToBorder;\r\n const r11 = 1.1;\r\n\r\n function innerBlockWorkAround() {\r\n if (distToBorder > 0.0) {\r\n // point is inside probe sphere\r\n if (corners[ind] < 0.0) {\r\n corners[ind] = distToBorder; // was inside surface, now is oustide ( > 0)\r\n }\r\n if (distToBorder > corners[ind]) {\r\n corners[ind] = distToBorder; // find positive maximum\r\n }\r\n } else if (distToBorder > corners[ind]) { // point is outside sphere\r\n corners[ind] = distToBorder; // find negative maximum\r\n }\r\n }\r\n\r\n const side2 = side * side;\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n const probeSpRad2 = (probeSphereRadius * 2) * (probeSphereRadius * 2);\r\n const sideInv = 1.0 / (side - 1);\r\n\r\n for (let i = 0; i < geoOut._numVertices; i++) {\r\n const vCenter = geoOut._vertices[i];\r\n\r\n const radEst = probeSphereRadius * r11;\r\n\r\n let indXMin = Math.floor(((vCenter.x - radEst) - vBoxMin.x) * xScale);\r\n let indYMin = Math.floor(((vCenter.y - radEst) - vBoxMin.y) * yScale);\r\n let indZMin = Math.floor(((vCenter.z - radEst) - vBoxMin.z) * zScale);\r\n\r\n let indXMax = Math.floor(((vCenter.x + radEst) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((vCenter.y + radEst) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((vCenter.z + radEst) - vBoxMin.z) * zScale);\r\n\r\n indXMin = (indXMin >= 0) ? indXMin : 0;\r\n indYMin = (indYMin >= 0) ? indYMin : 0;\r\n indZMin = (indZMin >= 0) ? indZMin : 0;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let iy = indYMin; iy <= indYMax; iy++) {\r\n const indY = iy * side2;\r\n for (let iz = indZMin; iz <= indZMax; iz++) {\r\n const indZ = iz * side;\r\n for (let ix = indXMin; ix <= indXMax; ix++) {\r\n ind = indY + indZ + ix;\r\n // getCornerCoord(vBoxMin, vBoxMax, ix, iy, iz, side, &vCorner);\r\n let t = ix * sideInv;\r\n const xCorner = vBoxMin.x * (1.0 - t) + vBoxMax.x * t;\r\n t = iy * sideInv;\r\n const yCorner = vBoxMin.y * (1.0 - t) + vBoxMax.y * t;\r\n t = iz * sideInv;\r\n const zCorner = vBoxMin.z * (1.0 - t) + vBoxMax.z * t;\r\n\r\n const dx = xCorner - vCenter.x;\r\n const dy = yCorner - vCenter.y;\r\n const dz = zCorner - vCenter.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 < probeSpRad2) {\r\n distToSphere = Math.sqrt(dist2);\r\n distToBorder = -(distToSphere - probeSphereRadius);\r\n innerBlockWorkAround();\r\n } // if (dist from corner point to sphere center more 2 radiuses)\r\n } // for (ix)\r\n } // for (iz)\r\n } // for (iy)\r\n } // for (i) all geo vertices\r\n return 0;\r\n }\r\n\r\n _innerBuild() {\r\n let ok;\r\n const expandFactor = 1.2;\r\n\r\n // performance test\r\n // this.performanceTest();\r\n\r\n // Create temporary atoms (but colored)\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n this.complex = this._opts.parent;\r\n this.atoms = packedArrays.atoms;\r\n this.meshResolution = this._opts.gridSpacing;\r\n this.atomRadiusScale = this._opts.radScale;\r\n this.colorMode = this._opts.colorMode;\r\n this.probeRadius = this._opts.probeRadius;\r\n this.useVertexColors = true;\r\n this.excludeProbe = this._opts.excludeProbe;\r\n this.visibilitySelector = this._opts.visibilitySelector;\r\n\r\n this.geoOut = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n this.numHashEtriesAllocated = 0;\r\n this.numHashEntryIndex = 0;\r\n this.maxNumVertices = 0;\r\n this.maxNumTriangles = 0;\r\n\r\n const atomsColored = new Array(this.atoms.length);\r\n this.convertToAtomsColored(packedArrays, atomsColored);\r\n\r\n // find bbox for spheres scene\r\n const vBoxMin = this.vBoxMin = new THREE.Vector3();\r\n const vBoxMax = this.vBoxMax = new THREE.Vector3();\r\n this.getBoundingBox(atomsColored, vBoxMin, vBoxMax);\r\n\r\n const marCubeResoultion = this.marCubeResoultion = this.meshResolution * (2 + 2);\r\n\r\n // build grid corners for Marching cube algorithm\r\n const side = marCubeResoultion;\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const corners = utils.allocateTyped(Float32Array, side3);\r\n const rProbeRadius = this.probeRadius * this.atomRadiusScale;\r\n\r\n this.calculateGridCorners(corners, side, vBoxMin, vBoxMax, atomsColored, rProbeRadius);\r\n\r\n const numCells = marCubeResoultion - 1;\r\n const cube = new IsoSurfaceMarchCube();\r\n ok = cube.create(numCells);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // copy corners to cells\r\n const vCellStep = new THREE.Vector3();\r\n vCellStep.x = (vBoxMax.x - vBoxMin.x) / numCells;\r\n vCellStep.y = (vBoxMax.y - vBoxMin.y) / numCells;\r\n vCellStep.z = (vBoxMax.z - vBoxMin.z) / numCells;\r\n\r\n let numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n let maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n let maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n\r\n // build voxel world (used to check triangle-to-atom tie and to calculate normals and colors)\r\n let probeRadForNormalsColors = rProbeRadius;\r\n if (this.excludeProbe) {\r\n probeRadForNormalsColors = 0.01;\r\n }\r\n this.voxelWorld = new IsosurfaceBuildNormals(\r\n atomsColored.length,\r\n atomsColored,\r\n vBoxMin,\r\n vBoxMax,\r\n probeRadForNormalsColors,\r\n );\r\n this.voxelWorld.createVoxels();\r\n\r\n ok = this.buildGeoFromCorners(marCubeResoultion, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n if (this.excludeProbe) {\r\n // using 3d mesh (geoOut) as a surface points\r\n // move probe sphere and try to minimuze corners values\r\n this.modifyExcludedFromGeo(side, rProbeRadius, vBoxMin, vBoxMax, this.geoOut, corners);\r\n\r\n // delete old builded geo\r\n this.geoOut._vertices = null;\r\n this.geoOut._colors = null;\r\n this.geoOut._indices = null;\r\n this.geoOut._normals = null;\r\n this.geoOut._numVertices = 0;\r\n this.geoOut._numTriangles = 0;\r\n this.geoOut = null;\r\n\r\n // estimage geo vertices budget again\r\n numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n // creates empty new geometry\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // build vertices and triangles from corners values\r\n ok = this.buildGeoFromCorners(side, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n }\r\n\r\n // build vertex normals\r\n this.voxelWorld.buildNormals(this.geoOut._vertices.length, this.geoOut._vertices, this.geoOut._normals);\r\n // More value : more smooth color mixing\r\n // value about 0.7: very rough colors borders\r\n let radiusColorSmoothness = 6.5;\r\n if (this.excludeProbe) {\r\n radiusColorSmoothness -= 1.5;\r\n }\r\n if (this.useVertexColors) {\r\n this.voxelWorld.buildColors(\r\n this.geoOut._vertices.length,\r\n this.geoOut._vertices,\r\n this.geoOut._colors,\r\n radiusColorSmoothness,\r\n );\r\n }\r\n this.voxelWorld.destroyVoxels();\r\n this.voxelWorld = null;\r\n\r\n // remove objects\r\n cube.destroy();\r\n\r\n return ok;\r\n }\r\n}\r\n\r\n// All code below must be erased from every device and each developer's memory\r\n\r\nexport default SSIsosurfaceGeometry;\r\n","import * as THREE from 'three';\r\nimport EventDispatcher from '../../utils/EventDispatcher';\r\n\r\nfunction createLabel(fieldTxt, className) {\r\n const text = document.createElement('div');\r\n text.className = className;\r\n\r\n if (typeof fieldTxt === 'string') {\r\n const spanText = document.createElement('span');\r\n spanText.style.fontSize = '150%';\r\n const strings = fieldTxt.split('\\n');\r\n\r\n for (let i = 0, n = strings.length; i < n; ++i) {\r\n const spanNodeP = document.createElement('span');\r\n const spanNodeText = document.createTextNode(strings[i]);\r\n spanNodeP.appendChild(spanNodeText);\r\n spanText.appendChild(spanNodeP);\r\n if (i < n - 1) {\r\n spanText.appendChild(document.createElement('br'));\r\n }\r\n }\r\n\r\n text.appendChild(spanText);\r\n } else {\r\n text.appendChild(fieldTxt);\r\n }\r\n text.worldPos = new THREE.Vector3();\r\n return text;\r\n}\r\nclass LabelsGeometry extends EventDispatcher {\r\n constructor(instanceCount, opts) {\r\n super();\r\n this._opts = opts;\r\n this.items = [];\r\n this.needsUpdate = false;\r\n\r\n let xTranslation = -50;\r\n let yTranslation = -50;\r\n switch (opts.horizontalAlign) {\r\n case 'left':\r\n xTranslation = 0;\r\n break;\r\n case 'right':\r\n xTranslation = -100;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n switch (opts.verticalAlign) {\r\n case 'top':\r\n yTranslation = -100;\r\n break;\r\n case 'bottom':\r\n yTranslation = 0;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n const deltaPos = new THREE.Vector3(opts.dx || 0, opts.dy || 0, opts.dz || 0);\r\n this.userData = {\r\n translation: `translate(${xTranslation}%, ${yTranslation}%)`,\r\n offset: deltaPos,\r\n };\r\n }\r\n\r\n setItem(itemIdx, itemPos, fieldTxt) {\r\n const opts = this._opts;\r\n const text = this.items[itemIdx] || createLabel(fieldTxt, 'label');\r\n\r\n text.worldPos.copy(itemPos);\r\n text.style.textAlign = opts.horizontalAlign;\r\n text.style.verticalAlign = opts.verticalAlign;\r\n this.items[itemIdx] = text;\r\n }\r\n\r\n setColor(itemIdx, fColor, bColor) {\r\n const text = this.items[itemIdx];\r\n text.opts = {\r\n color: fColor,\r\n background: bColor,\r\n };\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.needsUpdate = true;\r\n this.dispatchEvent({ type: 'update' });\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n }\r\n\r\n // unimplemented functions\r\n raycast() {\r\n }\r\n\r\n setOpacity() {\r\n\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\n\r\nexport default LabelsGeometry;\r\n","import InstancedSpheresGeometry from './InstancedSpheresGeometry';\r\nimport SimpleSpheresGeometry from './SimpleSpheresGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport Instanced2CCylindersGeometry from './Instanced2CCylindersGeometry';\r\nimport ExtrudedObjectsGeometry from './ExtrudedObjectsGeometry';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport TwoColorLinesGeometry from './TwoColorLinesGeometry';\r\nimport CrossGeometry from './CrossGeometry';\r\nimport QuickSurfGeometry from './QuickSurfGeometry';\r\nimport ContactSurfaceGeometry from './ContactSurfaceGeometry';\r\nimport SSIsosurfaceGeometry from './SSIsosurfaceGeometry';\r\nimport LabelsGeometry from './LabelsGeometry';\r\n\r\nexport default {\r\n InstancedSpheresGeometry,\r\n SimpleSpheresGeometry,\r\n Simple2CCylindersGeometry,\r\n Instanced2CCylindersGeometry,\r\n ExtrudedObjectsGeometry,\r\n ChunkedLinesGeometry,\r\n TwoColorLinesGeometry,\r\n CrossGeometry,\r\n QuickSurfGeometry,\r\n ContactSurfaceGeometry,\r\n SSIsosurfaceGeometry,\r\n LabelsGeometry,\r\n};\r\n","export default {\r\n\r\n precision: 'mediump',\r\n\r\n /**\r\n *\r\n * @param {THREE.WebGLRenderer} renderer\r\n */\r\n init(renderer) {\r\n this.precision = renderer.capabilities.getMaxPrecision('highp');\r\n },\r\n};\r\n","import * as THREE from 'three';\r\n\r\nconst noiseWidth = 4;\r\nconst noiseHeight = 4;\r\nconst _noiseData = new Uint8Array([\r\n 24, 52, 0, 255, 254, 145, 0, 255, 122, 0, 0, 255, 7, 170, 0, 255,\r\n 34, 214, 0, 255, 173, 8, 0, 255, 86, 249, 0, 255, 160, 4, 0, 255,\r\n 226, 46, 0, 255, 224, 211, 0, 255, 3, 157, 0, 255, 174, 247, 0, 255,\r\n 12, 182, 0, 255, 220, 216, 0, 255, 1, 109, 0, 255, 253, 154, 0, 255,\r\n]);\r\nconst _noiseWrapS = THREE.RepeatWrapping;\r\nconst _noiseWrapT = THREE.RepeatWrapping;\r\nconst _noiseMinFilter = THREE.NearestFilter;\r\nconst _noiseMagFilter = THREE.NearestFilter;\r\nconst _noiseMapping = THREE.UVMapping;\r\nconst noiseTexture = new THREE.DataTexture(\r\n _noiseData,\r\n noiseWidth,\r\n noiseHeight,\r\n THREE.RGBAFormat,\r\n THREE.UnsignedByteType,\r\n _noiseMapping,\r\n _noiseWrapS,\r\n _noiseWrapT,\r\n _noiseMagFilter,\r\n _noiseMinFilter,\r\n 1,\r\n);\r\nnoiseTexture.needsUpdate = true;\r\n\r\nexport default {\r\n noiseWidth,\r\n noiseHeight,\r\n noiseTexture,\r\n};\r\n","import * as THREE from 'three';\r\nimport vertexShader from './Uber.vert';\r\nimport fragmentShader from './Uber.frag';\r\nimport capabilities from '../capabilities';\r\nimport noise from '../noiseTexture';\r\n\r\n// Length of _samplesKernel is used in Uber.frag\r\n// If you want to change length of _samplesKernel, please, remember change it in Uber.frag too.\r\n// You can easy find places for replace using word:_samplesKernel\r\nconst _samplesKernel = [\r\n new THREE.Vector2(-0.541978, 0.840393),\r\n new THREE.Vector2(0.125533, -0.992089),\r\n new THREE.Vector2(0.374329, 0.927296),\r\n new THREE.Vector2(-0.105475, 0.994422),\r\n];\r\n\r\nconst defaultUniforms = THREE.UniformsUtils.merge([\r\n\r\n THREE.UniformsLib.fog,\r\n THREE.UniformsLib.lights,\r\n\r\n {\r\n // are updated automatically by three.js (see THREE.ShaderLib.common)\r\n diffuse: { value: new THREE.Color(0xeeeeee) },\r\n opacity: { value: 1.0 },\r\n\r\n specular: { type: 'c', value: new THREE.Color(0x111111) },\r\n shininess: { type: 'f', value: 30 },\r\n fixedColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n zOffset: { type: 'f', value: 0.0 },\r\n zClipValue: { type: 'f', value: 0.0 },\r\n clipPlaneValue: { type: 'f', value: 0.0 },\r\n nearPlaneValue: { type: 'f', value: -0.5 },\r\n invModelViewMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n world2colorMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n dashedLineSize: { type: 'f', value: 0.1 },\r\n dashedLinePeriod: { type: 'f', value: 0.2 },\r\n projMatrixInv: { type: '4fv', value: new THREE.Matrix4() },\r\n viewport: { type: 'v2', value: new THREE.Vector2() },\r\n lineWidth: { type: 'f', value: 2.0 },\r\n // default value must be the same as settings\r\n fogAlpha: { type: 'f', value: 1.0 },\r\n samplesKernel: { type: 'v2v', value: null },\r\n noiseTex: { type: 't', value: null },\r\n noiseTexelSize: { type: 'v2', value: null },\r\n srcTexelSize: { type: 'v2', value: null },\r\n },\r\n\r\n]);\r\n\r\nconst uberOptionNames = [\r\n 'shininess',\r\n 'opacity',\r\n 'zOffset',\r\n 'diffuse',\r\n 'specular',\r\n 'fixedColor',\r\n 'zClipCoef',\r\n 'zClipValue',\r\n 'clipPlaneValue',\r\n 'world2colorMatrix',\r\n 'dashedLineSize',\r\n 'dashedLinePeriod',\r\n 'projMatrixInv',\r\n 'viewport',\r\n 'lineWidth',\r\n 'fogAlpha',\r\n 'samplesKernel',\r\n 'noiseTex',\r\n 'noiseTexelSize',\r\n 'srcTexelSize',\r\n];\r\n\r\n// properties that convert to uniforms\r\nconst uberOptions = {\r\n diffuse: new THREE.Color(0xffffff), // used in phong lighting\r\n specular: new THREE.Color(0x111111), // used in phong lighting\r\n shininess: 30, // used in phong lighting\r\n opacity: 1, // set mesh opacity\r\n fixedColor: new THREE.Color(0xffffff), // color to override (see OVERRIDE_COLOR)\r\n zOffset: 0.0, // used fo zsprites (see SPHERE_SPRITE CYLINDER_SPRITE)\r\n zClipCoef: 2.0, // use for Surfs clipping (mesh param, isn't used in shader) FIXME move to representation param\r\n zClipValue: 0.0, // value to clip Surfs in shader (see ZCLIP)\r\n clipPlaneValue: 0.0, // value to clip scene globally (see CLIPPLANE)\r\n world2colorMatrix: new THREE.Matrix4(),\r\n dashedLineSize: 0.1,\r\n dashedLinePeriod: 0.3,\r\n projMatrixInv: new THREE.Matrix4(),\r\n viewport: new THREE.Vector2(800, 600),\r\n lineWidth: 2.0,\r\n fogAlpha: 1.0,\r\n samplesKernel: _samplesKernel,\r\n noiseTex: noise.noiseTexture,\r\n noiseTexelSize: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight),\r\n srcTexelSize: new THREE.Vector2(1.0 / 800.0, 1.0 / 600.0),\r\n copy(source) {\r\n this.diffuse.copy(source.diffuse);\r\n this.specular.copy(source.specular);\r\n this.shininess = source.shininess;\r\n this.opacity = source.opacity;\r\n this.fixedColor.copy(source.fixedColor);\r\n this.zOffset = source.zOffset;\r\n this.zClipCoef = source.zClipCoef;\r\n this.zClipValue = source.zClipValue;\r\n this.clipPlaneValue = source.clipPlaneValue;\r\n this.world2colorMatrix.copy(source.world2colorMatrix);\r\n this.dashedLineSize = source.dashedLineSize;\r\n this.dashedLinePeriod = source.dashedLinePeriod;\r\n this.projMatrixInv = source.projMatrixInv;\r\n this.viewport = source.viewport;\r\n this.lineWidth = source.lineWidth; // used for thick lines only\r\n this.toonShading = source.toonShading;\r\n this.fogAlpha = source.fogAlpha;\r\n this.samplesKernel = source.samplesKernel;\r\n this.noiseTex = source.noiseTex;\r\n this.noiseTexelSize = source.noiseTexelSize;\r\n this.srcTexelSize = source.srcTexelSize;\r\n },\r\n};\r\n\r\nclass UberMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // add fog\r\n this.fog = true;\r\n // used for instanced geometry\r\n this.instancedPos = false;\r\n this.instancedMatrix = false;\r\n // atoms and links color\r\n this.attrColor = false;\r\n // second link color for cylinders\r\n this.attrColor2 = false;\r\n //\r\n this.attrAlphaColor = false;\r\n // overrides color for all vertices (used in selection)\r\n this.overrideColor = false;\r\n // zsrpites\r\n this.sphereSprite = false;\r\n this.cylinderSprite = false;\r\n // clip Surfs individually\r\n this.zClip = false;\r\n // clip scene with global clip plane\r\n this.clipPlane = false;\r\n // enable fake (chess-like) opacity\r\n this.fakeOpacity = false;\r\n // render only depth, don't take care about the pixel color (used for transparency depth prepass)\r\n this.prepassTransparancy = false;\r\n // used to render pixel positions\r\n this.colorFromPos = false;\r\n // used to render shadowmap\r\n this.shadowmap = false;\r\n // used to describe shadowmap type\r\n this.shadowmapType = 'random';\r\n // used to render pixel view deph\r\n this.colorFromDepth = false;\r\n // mark that rendering is for orthographic camera\r\n this.orthoCam = false;\r\n // used to render dashed line\r\n this.dashedLine = false;\r\n // mark as transparent\r\n this.transparent = true;\r\n // mark as thick lines\r\n this.thickLine = false;\r\n // makes fog begin transparency (required for transparent background)\r\n this.fogTransparent = false;\r\n // used to render surface normals to G buffer for ssao effect\r\n this.normalsToGBuffer = false;\r\n // used for toon material\r\n this.toonShading = false;\r\n\r\n // uber options of \"root\" materials are inherited from single uber-options object that resides in prototype\r\n this.uberOptions = Object.create(UberMaterial.prototype.uberOptions);\r\n\r\n // set default values\r\n super.setValues({\r\n glslVersion: THREE.GLSL3,\r\n vertexShader: this.precisionString() + vertexShader,\r\n fragmentShader: this.precisionString() + fragmentShader,\r\n uniforms: THREE.UniformsUtils.clone(defaultUniforms),\r\n lights: true,\r\n fog: true,\r\n side: THREE.DoubleSide,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n precisionString() {\r\n const { precision } = capabilities;\r\n const str = `precision ${precision} float;\\n`\r\n + `precision ${precision} int;\\n\\n`;\r\n return str;\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n\r\n this.fragmentShader = source.fragmentShader;\r\n this.vertexShader = source.vertexShader;\r\n\r\n this.uniforms = THREE.UniformsUtils.clone(source.uniforms);\r\n this.defines = { ...source.defines };\r\n this.extensions = source.extensions;\r\n\r\n this.fog = source.fog;\r\n this.instancedPos = source.instancedPos;\r\n this.instancedMatrix = source.instancedMatrix;\r\n this.attrColor = source.attrColor;\r\n this.attrColor2 = source.attrColor2;\r\n this.attrAlphaColor = source.attrAlphaColor;\r\n this.overrideColor = source.overrideColor;\r\n this.sphereSprite = source.sphereSprite;\r\n this.cylinderSprite = source.cylinderSprite;\r\n this.zClip = source.zClip;\r\n this.clipPlane = source.clipPlane;\r\n this.fakeOpacity = source.fakeOpacity;\r\n this.colorFromPos = source.colorFromPos;\r\n this.shadowmap = source.shadowmap;\r\n this.shadowmapType = source.shadowmapType;\r\n this.colorFromDepth = source.colorFromDepth;\r\n this.orthoCam = source.orthoCam;\r\n this.prepassTransparancy = source.prepassTransparancy;\r\n this.dashedLine = source.dashedLine;\r\n this.thickLine = source.thickLine;\r\n this.fogTransparent = source.fogTransparent;\r\n this.normalsToGBuffer = source.normalsToGBuffer;\r\n this.toonShading = source.toonShading;\r\n\r\n this.uberOptions.copy(source.uberOptions);\r\n\r\n return this;\r\n }\r\n\r\n // create copy of this material\r\n // its options are prototyped after this material's options\r\n createInstance() {\r\n const inst = new UberMaterial();\r\n inst.copy(this);\r\n inst.uberOptions = Object.create(this.uberOptions);\r\n return inst;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n const extensions = {};\r\n\r\n if (this.fog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.instancedPos) {\r\n defines.INSTANCED_POS = 1;\r\n }\r\n if (this.instancedMatrix) {\r\n defines.INSTANCED_MATRIX = 1;\r\n }\r\n if (this.attrColor) {\r\n defines.ATTR_COLOR = 1;\r\n }\r\n if (this.attrColor2) {\r\n defines.ATTR_COLOR2 = 1;\r\n }\r\n if (this.attrAlphaColor) {\r\n defines.ATTR_ALPHA_COLOR = 1;\r\n }\r\n if (this.overrideColor) {\r\n defines.OVERRIDE_COLOR = 1;\r\n }\r\n if (this.sphereSprite) {\r\n defines.SPHERE_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.cylinderSprite) {\r\n defines.CYLINDER_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.zClip) {\r\n defines.ZCLIP = 1;\r\n }\r\n if (this.clipPlane) {\r\n defines.CLIP_PLANE = 1;\r\n }\r\n if (this.fakeOpacity) {\r\n defines.FAKE_OPACITY = 1;\r\n }\r\n if (this.lights) {\r\n defines.USE_LIGHTS = 1;\r\n }\r\n if (this.colorFromPos) {\r\n defines.COLOR_FROM_POS = 1;\r\n }\r\n if (this.shadowmap) {\r\n defines.SHADOWMAP = 1;\r\n if (this.shadowmapType === 'pcf') {\r\n defines.SHADOWMAP_PCF_SHARP = 1;\r\n } else if (this.shadowmapType === 'random') {\r\n defines.SHADOWMAP_PCF_RAND = 1;\r\n } else {\r\n defines.SHADOWMAP_BASIC = 1;\r\n }\r\n }\r\n if (this.colorFromDepth) {\r\n defines.COLOR_FROM_DEPTH = 1;\r\n }\r\n if (this.orthoCam) {\r\n defines.ORTHOGRAPHIC_CAMERA = 1;\r\n }\r\n if (this.prepassTransparancy) {\r\n defines.PREPASS_TRANSP = 1;\r\n }\r\n if (this.dashedLine) {\r\n defines.DASHED_LINE = 1;\r\n }\r\n if (this.thickLine) {\r\n defines.THICK_LINE = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n if (this.normalsToGBuffer) {\r\n extensions.drawBuffers = true;\r\n defines.NORMALS_TO_G_BUFFER = 1;\r\n }\r\n if (this.toonShading) {\r\n defines.TOON_SHADING = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n this.extensions = extensions;\r\n }\r\n\r\n setUberOptions(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n for (const key in values) {\r\n if (!values.hasOwnProperty(key)) {\r\n continue;\r\n }\r\n\r\n if (this.uberOptions[key] instanceof THREE.Color) {\r\n this.uberOptions[key] = values[key].clone();\r\n } else {\r\n this.uberOptions[key] = values[key];\r\n }\r\n }\r\n }\r\n\r\n clone(shallow) {\r\n if (!shallow) {\r\n return super.clone();\r\n }\r\n return this.createInstance();\r\n }\r\n\r\n updateUniforms() {\r\n const self = this;\r\n\r\n uberOptionNames.forEach((p) => {\r\n if (self.uniforms.hasOwnProperty(p)) {\r\n if (self.uberOptions[p] instanceof THREE.Color\r\n || self.uberOptions[p] instanceof THREE.Matrix4) {\r\n self.uniforms[p].value = self.uberOptions[p].clone();\r\n } else {\r\n self.uniforms[p].value = self.uberOptions[p];\r\n }\r\n }\r\n });\r\n }\r\n}\r\n\r\nUberMaterial.prototype.uberOptions = uberOptions;\r\n\r\nexport default UberMaterial;\r\n","import UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default function (SuperClass) {\r\n class NewObjectType extends SuperClass {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.onBeforeRender = NewObjectType.prototype.onBeforeRender;\r\n }\r\n\r\n onBeforeRender(renderer, scene, camera, geometry, material, group) {\r\n this._onBeforeRender(renderer, scene, camera, geometry, material, group);\r\n this._update();\r\n }\r\n\r\n _onBeforeRender() {\r\n }\r\n\r\n _update() {\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material instanceof UberMaterial) {\r\n material.updateUniforms();\r\n }\r\n }\r\n }\r\n\r\n return NewObjectType;\r\n}\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZSpriteMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material.uniforms.invModelViewMatrix) {\r\n // NOTE: update of modelViewMatrix inside threejs is done after onBeforeRender call,\r\n // so we have to do it manually in that place\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n // get inverse matrix\r\n material.uniforms.invModelViewMatrix.value.copy(this.modelViewMatrix).invert();\r\n material.uniforms.nearPlaneValue.value = camera.near;\r\n material.uniformsNeedUpdate = true;\r\n }\r\n }\r\n}\r\n\r\nexport default ZSpriteMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZClippedMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n static _mvLength = new THREE.Vector3();\r\n\r\n static _center = new THREE.Vector3();\r\n\r\n static _modelView = new THREE.Matrix4();\r\n\r\n _onBeforeRender(renderer, scene, camera) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n\r\n const geo = this.geometry;\r\n const { material } = this;\r\n if (!geo.zClip || !material.uberOptions) {\r\n return;\r\n }\r\n\r\n const zClipCoef = 0.5;\r\n\r\n const modelView = ZClippedMesh._modelView;\r\n const mvLength = ZClippedMesh._mvLength;\r\n const center = ZClippedMesh._center;\r\n\r\n modelView.multiplyMatrices(this.matrixWorld, camera.matrixWorldInverse);\r\n const s = mvLength.setFromMatrixColumn(modelView, 0).length();\r\n center.copy(geo.boundingSphere.center);\r\n\r\n this.localToWorld(center);\r\n material.uberOptions.zClipValue = camera.position.z - center.z\r\n - s * (zClipCoef * geo.boundingSphere.radius);\r\n }\r\n}\r\n\r\nexport default ZClippedMesh;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from '../CSS2DObject';\r\nimport utils from '../../utils';\r\n\r\nclass TextMesh extends THREE.Group {\r\n constructor(geometry, _material) {\r\n super();\r\n this.geometry = geometry;\r\n\r\n const self = this;\r\n self.initialized = false;\r\n this.geometry.addEventListener('update', () => {\r\n self.update();\r\n });\r\n }\r\n\r\n init() {\r\n const { children } = this;\r\n for (let i = children.length - 1; i >= 0; --i) {\r\n this.remove(children[i]);\r\n }\r\n\r\n const { items, userData } = this.geometry;\r\n for (let i = 0, n = items.length; i < n; ++i) {\r\n const srcItem = items[i];\r\n if (!srcItem) {\r\n continue;\r\n }\r\n const item = utils.shallowCloneNode(srcItem);\r\n const label = new CSS2DObject(item);\r\n label.userData = _.clone(userData);\r\n const el = label.getElement();\r\n el.style.visibility = 'visible';\r\n label.source = srcItem;\r\n this.add(label);\r\n }\r\n this.initialized = true;\r\n }\r\n\r\n update() {\r\n const geo = this.geometry;\r\n if (!geo.needsUpdate) {\r\n return;\r\n }\r\n const { children } = this;\r\n if (!this.initialized) {\r\n this.init();\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n const item = child.source;\r\n child.position.copy(item.worldPos);\r\n child.userData.color = item.opts.color;\r\n child.userData.background = item.opts.background;\r\n }\r\n }\r\n}\r\n\r\nexport default TextMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass SimpleMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default SimpleMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\nconst _viewport = new THREE.Vector2();\r\n\r\nclass ThickLineMesh extends Mesh {\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!material.uberOptions) {\r\n return;\r\n }\r\n\r\n material.uberOptions.projMatrixInv.copy(camera.projectionMatrix).invert();\r\n renderer.getSize(_viewport);\r\n material.uberOptions.viewport.set(_viewport.width, _viewport.height);\r\n }\r\n}\r\n\r\nexport default ThickLineMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass InstancedMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default InstancedMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\nimport ZSpriteMesh from './ZSpriteMesh';\r\nimport ZClippedMesh from './ZClippedMesh';\r\nimport TextMesh from './TextMesh';\r\nimport SimpleMesh from './SimpleMesh';\r\nimport ThickLineMesh from './ThickLineMesh';\r\nimport InstancedMesh from './InstancedMesh';\r\n\r\nexport default {\r\n ZClipped: ZClippedMesh,\r\n ZSprite: ZSpriteMesh,\r\n Text: TextMesh,\r\n Line: UberObject(THREE.Line),\r\n LineSegments: UberObject(THREE.LineSegments),\r\n Mesh: SimpleMesh,\r\n ThickLineMesh,\r\n Instanced: InstancedMesh,\r\n};\r\n","import geometries from '../geometries/geometries';\r\nimport meshes from './meshes';\r\nimport ThickLinesGeometry from '../geometries/ThickLinesGeometry';\r\n\r\nfunction setMatParams(params, uniforms) {\r\n return function (material) {\r\n material.setValues(params);\r\n material.setUberOptions(uniforms);\r\n };\r\n}\r\n\r\nfunction _createInstancedCylinders(useZSprites, openEnded) {\r\n function Geometry(a, b) {\r\n return new geometries.Instanced2CCylindersGeometry(a, b, useZSprites, openEnded);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedMatrix: true,\r\n attrColor: true,\r\n attrColor2: true,\r\n attrAlphaColor: true,\r\n cylinderSprite: useZSprites,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createLineSegmentsGeoTriplet(geo, renderParams) {\r\n const thickLines = geo.prototype instanceof ThickLinesGeometry;\r\n const lineWidth = renderParams.lineWidth || 0;\r\n return {\r\n Geometry: geo,\r\n Object: thickLines ? meshes.ThickLineMesh : meshes.LineSegments,\r\n initMaterial: setMatParams({\r\n lights: false,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n thickLine: thickLines,\r\n }, {\r\n lineWidth,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createSimpleGeoTriplet(geoClass) {\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.Mesh,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createIsoSurfaceGeoTriplet(geoClass, caps, settings, renderParams) {\r\n const surfaceOpts = {\r\n wireframe: !!renderParams.wireframe,\r\n fakeOpacity: settings.now.isoSurfaceFakeOpacity,\r\n zClip: renderParams.zClip,\r\n };\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.ZClipped,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: false,\r\n wireframe: surfaceOpts.wireframe,\r\n fakeOpacity: surfaceOpts.fakeOpacity,\r\n zClip: surfaceOpts.zClip,\r\n }),\r\n };\r\n}\r\n\r\nclass MeshCreator {\r\n static createSpheres(caps, settings) {\r\n const useZSprites = settings.now.zSprites;\r\n function Geometry(a, b) {\r\n return new geometries.InstancedSpheresGeometry(a, b, useZSprites);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedPos: true,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n sphereSprite: useZSprites,\r\n }),\r\n };\r\n }\r\n\r\n static create2CClosedCylinders(_caps, _settings) {\r\n return _createInstancedCylinders(false, false);\r\n }\r\n\r\n static create2CCylinders(caps, settings) {\r\n return _createInstancedCylinders(settings.now.zSprites, true);\r\n }\r\n\r\n static create2CLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.TwoColorLinesGeometry, renderParams);\r\n }\r\n\r\n static createCrosses(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.CrossGeometry, renderParams);\r\n }\r\n\r\n static createExtrudedChains(_caps, _settings) {\r\n return _createSimpleGeoTriplet(geometries.ExtrudedObjectsGeometry);\r\n }\r\n\r\n static createChunkedLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.ChunkedLinesGeometry, renderParams);\r\n }\r\n\r\n static createQuickSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.QuickSurfGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createContactSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.ContactSurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createSASSES(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.SSIsosurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createLabels(_caps, _settings) {\r\n return {\r\n Geometry: geometries.LabelsGeometry,\r\n Object: meshes.Text,\r\n initMaterial() {\r\n },\r\n };\r\n }\r\n}\r\n\r\nexport default MeshCreator;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../gfxutils';\r\n\r\nclass TransformGroup extends THREE.Object3D {\r\n static _inverseMatrix = new THREE.Matrix4();\r\n\r\n static _ray = new THREE.Ray();\r\n\r\n constructor(geometry, geoParams, material, transforms) {\r\n super();\r\n this._geometry = geometry;\r\n this._geoParams = geoParams;\r\n const mat = material.createInstance();\r\n geoParams.initMaterial(mat);\r\n this._material = mat;\r\n this._transforms = transforms.length > 0 ? transforms : [new THREE.Matrix4()];\r\n const meshes = this._createMeshes(geometry);\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n this.add(meshes[i]);\r\n }\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const ray = TransformGroup._ray;\r\n const inverseMatrix = TransformGroup._inverseMatrix;\r\n const { children } = this;\r\n ray.copy(raycaster.ray);\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n\r\n if (!gfxutils.belongToSelectLayers(child)) {\r\n continue;\r\n }\r\n\r\n child.updateMatrixWorld();\r\n const mtx = child.matrixWorld;\r\n inverseMatrix.copy(mtx).invert();\r\n raycaster.ray.copy(ray).applyMatrix4(inverseMatrix);\r\n const childIntersects = [];\r\n this._geometry.raycast(raycaster, childIntersects);\r\n\r\n for (let j = 0, ciCount = childIntersects.length; j < ciCount; ++j) {\r\n const inters = childIntersects[j];\r\n if (inters.point) {\r\n inters.point.applyMatrix4(mtx);\r\n inters.distance = ray.origin.distanceTo(inters.point);\r\n }\r\n inters.object = child;\r\n intersects[intersects.length] = inters;\r\n }\r\n }\r\n raycaster.ray.copy(ray);\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const geos = this._geometry.getSubset(chunkIndices);\r\n const subset = [];\r\n let subIdx = 0;\r\n\r\n for (let i = 0, n = geos.length; i < n; ++i) {\r\n const meshes = this._createMeshes(geos[i]);\r\n for (let j = 0, meshCnt = meshes.length; j < meshCnt; ++j) {\r\n subset[subIdx++] = meshes[j];\r\n }\r\n }\r\n\r\n return subset;\r\n }\r\n\r\n _createMeshes(geometry) {\r\n const transforms = this._transforms;\r\n const Mesh = this._geoParams.Object;\r\n const material = this._material;\r\n const meshes = [];\r\n for (let i = 0, n = transforms.length; i < n; ++i) {\r\n const mesh = new Mesh(geometry, material);\r\n mesh.applyMatrix4(transforms[i]);\r\n meshes[i] = mesh;\r\n }\r\n\r\n return meshes;\r\n }\r\n}\r\n\r\nexport default TransformGroup;\r\n","import RCGroup from '../../RCGroup';\r\nimport TransformGroup from '../../meshes/TransformGroup';\r\n\r\nfunction wrapper(Name, args) {\r\n const params = [Name].concat(args);\r\n return Name.bind(...params);\r\n}\r\n\r\nclass ChemGroup extends RCGroup {\r\n constructor(geoParams, selection, colorer, mode, transforms, polyComplexity, material) {\r\n super();\r\n if (this.constructor === ChemGroup) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n this._selection = selection;\r\n this._mode = mode;\r\n this._colorer = colorer;\r\n this._chunksIdc = selection.chunks;\r\n this._polyComplexity = polyComplexity;\r\n this._geo = new (wrapper(geoParams.Geometry, this._makeGeoArgs()))();\r\n this._mesh = new TransformGroup(this._geo, geoParams, material, transforms);\r\n this.add(this._mesh);\r\n this._build();\r\n }\r\n\r\n _makeGeoArgs() {\r\n throw new Error('ChemGroup subclass must override _makeGeoArgs() method');\r\n }\r\n\r\n /**\r\n * Builds subset geometry by ATOMS index list\r\n *\r\n * @param {Number} mask - Representation mask\r\n * @param {Boolean} innerOnly - if true returns inner bonds only - without halves\r\n * @returns {Array} Subset geometry\r\n */\r\n getSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : false;\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return [];\r\n }\r\n return this._mesh.getSubset(chunksList);\r\n }\r\n\r\n _changeSubsetOpacity(mask, value, innerOnly) {\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return;\r\n }\r\n this._geo.setOpacity(chunksList, value);\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 1.0, innerOnly);\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 0.0, innerOnly);\r\n }\r\n}\r\n\r\nexport default ChemGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass AtomsGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { atoms } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const atomsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const atomIdx = atomsIdc[inters[i].chunkIdx];\r\n if (atomIdx < atoms.length) {\r\n inters[i].atom = atoms[atomIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { atoms } = this._selection;\r\n const atomsIdc = this._chunksIdc;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n if ((atom.mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default AtomsGroup;\r\n","import AtomsGroup from './AtomsGroup';\r\n\r\nclass AtomsSphereGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, atom.position, mode.calcAtomRadius(atom));\r\n geo.setColor(i, colorer.getAtomColor(atom, parent));\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), mode.calcAtomRadius(atom));\r\n if (updateColor) {\r\n geo.setColor(i, frameData.getAtomColor(colorer, atom));\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsSphereGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSurfaceGroup extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n return [n, opts];\r\n }\r\n}\r\nexport default AtomsSurfaceGroup;\r\n","/* This is a stub class keep it until SAS/SES is refactored */\r\n\r\nimport AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSASSESGroupStub extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n opts.selection = this._selection;\r\n opts.colorMode = this._colorer;\r\n return [n, opts];\r\n }\r\n}\r\n\r\nexport default AtomsSASSESGroupStub;\r\n","import AtomsGroup from './AtomsGroup';\r\nimport utils from '../../../utils';\r\n\r\nfunction adjustColor(color) {\r\n let r = (color >> 16) & 255;\r\n let g = (color >> 8) & 255;\r\n let b = color & 255;\r\n\r\n if (0.2126 * r + 0.7152 * g + 0.0722 * b > 127) {\r\n r = r * 3 / 10;\r\n g = g * 3 / 10;\r\n b = b * 3 / 10;\r\n } else {\r\n r = 255 - ((255 - r) * 3 / 10);\r\n g = 255 - ((255 - g) * 3 / 10);\r\n b = 255 - ((255 - b) * 3 / 10);\r\n }\r\n\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nfunction inverseColor(color) {\r\n const r = (color >> 16) & 255;\r\n const g = (color >> 8) & 255;\r\n const b = color & 255;\r\n\r\n return ((255 - r) << 16) | ((255 - g) << 8) | (255 - b);\r\n}\r\n\r\nfunction getAtomText(atom) {\r\n if (atom.name.getNode() !== null) {\r\n return atom.name.getNode();\r\n }\r\n\r\n return atom.getVisualName();\r\n}\r\n\r\nconst colorMappings = {\r\n none(c) {\r\n return c;\r\n },\r\n adjust: adjustColor,\r\n inverse: inverseColor,\r\n};\r\n\r\nfunction propagateColor(color, rule) {\r\n let result;\r\n if (colorMappings.hasOwnProperty(rule)) {\r\n result = utils.hexColor(colorMappings[rule](color));\r\n } else {\r\n const val = parseInt(rule, 16);\r\n if (!Number.isNaN(val) && rule.toLowerCase().startsWith('0x')) {\r\n result = utils.hexColor(val);\r\n } else {\r\n result = '#000000';\r\n }\r\n }\r\n return result;\r\n}\r\n\r\nconst templateMappings = {\r\n serial(a) {\r\n return a.serial;\r\n },\r\n name(a) {\r\n return a.getVisualName();\r\n },\r\n elem(a) {\r\n return a.element.name;\r\n },\r\n residue(a) {\r\n return a.residue.getType().getName();\r\n },\r\n sequence(a) {\r\n return a.residue.getSequence();\r\n },\r\n chain(a) {\r\n return a.residue.getChain().getName();\r\n },\r\n hetatm(a) {\r\n return a.isHet();\r\n },\r\n water(a) {\r\n return a.residue.getType().getName() === 'HOH' || a.residue.getType().getName() === 'WAT';\r\n },\r\n};\r\n\r\nconst parseTemplate = function (atom, str) {\r\n return str.replace(/\\{\\{(\\s*\\w+\\s*)\\}\\}/g, (m) => {\r\n let key = m.replace(/\\s+/g, '');\r\n key = key.substring(2, key.length - 2).toLowerCase();\r\n\r\n if (templateMappings.hasOwnProperty(key)) {\r\n return templateMappings[key](atom);\r\n }\r\n return 'null';\r\n });\r\n};\r\n\r\nclass AtomsTextGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n const opts = this._mode.getLabelOpts();\r\n return [this._selection.chunks.length, opts];\r\n }\r\n\r\n _build() {\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = colorer.getAtomColor(atom, parent);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, atom.position, text);\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = frameData.getAtomColor(colorer, atom);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), text);\r\n if (updateColor) {\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsTextGroup;\r\n","import * as THREE from 'three';\r\nimport AtomsGroup from './AtomsGroup';\r\n\r\nfunction _slerp(omega, v1, v2, t) {\r\n const oSin = Math.sin(omega);\r\n return v1.clone().multiplyScalar(Math.sin((1 - t) * omega) / oSin).addScaledVector(v2, Math.sin(t * omega) / oSin);\r\n}\r\n\r\nclass AromaticGroup extends AtomsGroup {\r\n _buildInner(radOffset, addChunk) {\r\n const chunksToIdx = this._selection.chunks;\r\n\r\n const prevVector = new THREE.Vector3();\r\n const currVector = new THREE.Vector3();\r\n const segmentsHeight = this._segmentsHeight;\r\n const leprStep = 1.0 / segmentsHeight;\r\n const colorer = this._colorer;\r\n\r\n const { cycles, parent } = this._selection;\r\n let chunkIdx = 0;\r\n let currAtomIdx = chunksToIdx[chunkIdx];\r\n\r\n for (let cIdx = 0, cCount = cycles.length; cIdx < cCount; ++cIdx) {\r\n const cycle = cycles[cIdx];\r\n const cycAtoms = cycle.atoms;\r\n const chunkPoints = [];\r\n const tmpDir = [];\r\n const { center } = cycle;\r\n const cycleRad = cycle.radius - radOffset;\r\n const n = cycAtoms.length;\r\n let i = 0;\r\n const prevPos = cycAtoms[n - 1].position;\r\n let currPos = cycAtoms[i].position;\r\n prevVector.subVectors(prevPos, center);\r\n currVector.subVectors(currPos, center);\r\n const upDir = currVector.clone().cross(prevVector).normalize();\r\n\r\n for (; i < n; ++i) {\r\n const omega = prevVector.angleTo(currVector);\r\n tmpDir[i] = _slerp(omega, prevVector, currVector, 0.5).normalize();\r\n currPos = cycAtoms[(i + 1) % n].position;\r\n prevVector.copy(currVector);\r\n currVector.subVectors(currPos, center);\r\n }\r\n\r\n for (i = 0; i < n; ++i) {\r\n if (cycAtoms[i].index !== currAtomIdx) {\r\n continue;\r\n }\r\n const start = tmpDir[i];\r\n const end = tmpDir[(i + 1) % n];\r\n const color = colorer.getAtomColor(cycAtoms[i], parent);\r\n const currAngle = start.angleTo(end);\r\n\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n chunkPoints[j] = _slerp(currAngle, start, end, j * leprStep).multiplyScalar(cycleRad).add(center);\r\n }\r\n\r\n addChunk(chunkIdx++, color, chunkPoints, center, upDir);\r\n currAtomIdx = chunksToIdx[chunkIdx];\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default AromaticGroup;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../../gfxutils';\r\nimport AromaticGroup from './AromaticGroup';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n for (let i = 0; i < parts; ++i) {\r\n const a = -2 * i / parts * Math.PI;\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\nconst { calcChunkMatrix } = gfxutils;\r\n\r\nclass AromaticTorusGroup extends AromaticGroup {\r\n _build() {\r\n const segmentsHeight = this._segmentsHeight;\r\n const torusRad = this._mode.getAromRadius();\r\n const radiusV = new THREE.Vector2(torusRad, torusRad);\r\n const radOffset = this._mode.calcStickRadius() + 2 * torusRad;\r\n const lookAtVector = new THREE.Vector3();\r\n const mtc = [];\r\n const geo = this._geo;\r\n this._buildInner(radOffset, (chunkIdx, color, points, center, upDir) => {\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n const currDir = currPoint.clone().sub(center).cross(upDir);\r\n lookAtVector.addVectors(currPoint, currDir);\r\n mtc[j] = calcChunkMatrix(currPoint, lookAtVector, upDir, radiusV);\r\n }\r\n geo.setItem(chunkIdx, mtc);\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._polyComplexity;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length];\r\n }\r\n}\r\n\r\nexport default AromaticTorusGroup;\r\n","import AromaticGroup from './AromaticGroup';\r\n\r\nclass AromaticLinesGroup extends AromaticGroup {\r\n _build() {\r\n const geo = this._geo;\r\n const radOffset = this._mode.getAromaticOffset();\r\n this._buildInner(radOffset, (chunkIdx, color, points) => {\r\n let prevPt = points[0];// do not replace with start\r\n for (let j = 1; j <= this._segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n geo.setSegment(chunkIdx, j - 1, prevPt, currPoint);\r\n prevPt = currPoint;\r\n }\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._mode.getAromaticArcChunks();\r\n return [this._selection.chunks.length, this._segmentsHeight, true];\r\n }\r\n}\r\n\r\nexport default AromaticLinesGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[inters[i].chunkIdx];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesGroup;\r\n","import ResiduesGroup from './ResiduesGroup';\r\n\r\nclass NucleicItemGroup extends ResiduesGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[Math.floor(inters[i].chunkIdx / 2)];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n let chunkIdx = 0;\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList[chunkIdx++] = 2 * i;\r\n chunksList[chunkIdx++] = 2 * i + 1;\r\n }\r\n }\r\n return chunksList;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finishUpdate();\r\n }\r\n}\r\n\r\nexport default NucleicItemGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicCylindersGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n geo.setItem(chunkIdx, cyl1, cyl2, stickRad);\r\n geo.setColor(chunkIdx, color, color);\r\n }\r\n}\r\n\r\nexport default NucleicCylindersGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicSpheresGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length * 2, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n let idx = chunkIdx * 2;\r\n geo.setItem(idx, cyl1, stickRad);\r\n geo.setColor(idx, color);\r\n idx++;\r\n geo.setItem(idx, cyl2, stickRad);\r\n geo.setColor(idx, color);\r\n }\r\n}\r\n\r\nexport default NucleicSpheresGroup;\r\n","import * as THREE from 'three';\r\nimport { Smooth } from '../../../../vendor/js/Smooth';\r\nimport gfxutils from '../../gfxutils';\r\nimport chem from '../../../chem';\r\n\r\nconst { ResidueType } = chem;\r\n\r\nconst calcMatrix = gfxutils.calcChunkMatrix;\r\n\r\nfunction _buildStructureInterpolator(points, tension) {\r\n const path = Smooth(points, {\r\n method: Smooth.METHOD_CUBIC,\r\n clip: Smooth.CLIP_CLAMP,\r\n cubicTension: tension,\r\n scaleTo: 1,\r\n });\r\n\r\n return function (t, argTrans) {\r\n let transformT = argTrans;\r\n if (transformT === null) {\r\n // map our range to the [second .. last but one]\r\n transformT = function (tt) {\r\n return (tt * ((points.length - 1) - 2) + 1) / (points.length - 1);\r\n };\r\n }\r\n const newt = transformT(t);\r\n const ans = path(newt);\r\n return new THREE.Vector3(ans[0], ans[1], ans[2]);\r\n };\r\n}\r\n\r\nfunction _addPoints(centerPoints, topPoints, idx, residue) {\r\n if (!residue._isValid) {\r\n centerPoints[idx] = centerPoints[idx - 1];\r\n topPoints[idx] = topPoints[idx - 1];\r\n return;\r\n }\r\n const cp = residue._controlPoint;\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n const tp = cp.clone().add(residue._wingVector);\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n}\r\n\r\nfunction _addPointsForLoneResidue(centerPoints, topPoints, idx, residue) {\r\n const nucleic = (residue._type.flags & ResidueType.Flags.NUCLEIC) !== 0;\r\n const nameFrom = nucleic ? 'C5\\'' : 'N';\r\n const nameTo = nucleic ? 'C3\\'' : 'C';\r\n\r\n let posFrom;\r\n let posTo;\r\n residue.forEachAtom((atom) => {\r\n const name = atom.getVisualName();\r\n if (!posFrom && name === nameFrom) {\r\n posFrom = atom.position;\r\n } else if (!posTo && name === nameTo) {\r\n posTo = atom.position;\r\n }\r\n });\r\n\r\n // provide a fallback for unknown residues\r\n if (!(posFrom && posTo)) {\r\n posFrom = residue._firstAtom.position;\r\n posTo = residue._lastAtom.position;\r\n }\r\n\r\n if (posFrom && posTo) {\r\n const shift = posTo.clone().sub(posFrom);\r\n\r\n const wing = residue._wingVector;\r\n const cp = residue._controlPoint;\r\n const tp = cp.clone().add(wing);\r\n\r\n const cpPrev = cp.clone().sub(shift);\r\n const tpPrev = cpPrev.clone().add(wing);\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n ++idx;\r\n\r\n const cpNext = cp.clone().add(shift);\r\n const tpNext = cpNext.clone().add(wing);\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n ++idx;\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n }\r\n}\r\n\r\nfunction _calcPoints(residues, firstIdx, lastIdx, boundaries) {\r\n const left = boundaries.start;\r\n const right = boundaries.end;\r\n function _prevIdx(idx) {\r\n return idx > left && residues[idx - 1]._isValid ? idx - 1 : idx;\r\n }\r\n function _nextIdx(idx) {\r\n return idx < right && residues[idx + 1]._isValid ? idx + 1 : idx;\r\n }\r\n\r\n const topPoints = [];\r\n const centerPoints = [];\r\n let arrIdx = 0;\r\n function _extrapolate2(currIdx, otherIdx) {\r\n const cp = residues[currIdx]._controlPoint.clone().lerp(residues[otherIdx]._controlPoint, -0.25);\r\n const tp = cp.clone().add(residues[currIdx]._wingVector);\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n }\r\n\r\n // a single disconnected residue\r\n const prevIdx = _prevIdx(firstIdx);\r\n const nextIdx = _nextIdx(lastIdx);\r\n if (prevIdx === nextIdx) {\r\n _addPointsForLoneResidue(centerPoints, topPoints, arrIdx, residues[firstIdx]);\r\n return { centerPoints, topPoints };\r\n }\r\n\r\n // Two points (prev-prev and next-next) are added to support edge conditions for cubic splines, they are ignored\r\n // Another two (prev and next) were added to support the outside of the sub chain\r\n\r\n // prev and prev-prev\r\n if (firstIdx === prevIdx) {\r\n // do the extrapolation\r\n _extrapolate2(firstIdx, _nextIdx(firstIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[_prevIdx(prevIdx)]);\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[prevIdx]);\r\n }\r\n\r\n // main loop\r\n for (let idx = firstIdx; idx <= lastIdx; ++idx) {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[idx]);\r\n }\r\n\r\n // next and next-next\r\n if (nextIdx === _nextIdx(nextIdx)) {\r\n // do the extrapolation\r\n _extrapolate2(lastIdx, _prevIdx(lastIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[nextIdx]);\r\n _addPoints(centerPoints, topPoints, arrIdx, residues[_nextIdx(nextIdx)]);\r\n }\r\n return { centerPoints, topPoints };\r\n}\r\n\r\nclass CartoonHelper {\r\n constructor(residues, startIdx, endIdx, segmentsCount, tension, boundaries) {\r\n const pointsArrays = _calcPoints(residues, startIdx, endIdx, boundaries);\r\n this._topInterp = _buildStructureInterpolator(pointsArrays.topPoints, tension);\r\n this._centerInterp = _buildStructureInterpolator(pointsArrays.centerPoints, tension);\r\n\r\n this._shift = 0.5 / (endIdx - startIdx + 2);\r\n this._valueStep = (1.0 - 2 * this._shift) / (2 * (endIdx - startIdx + 1) * (segmentsCount - 1));\r\n this._segmentsCount = segmentsCount;\r\n }\r\n\r\n prepareMatrices(idx, firstRad, secondRad) {\r\n const mtcCount = this._segmentsCount;\r\n const outMtc = new Array(mtcCount);\r\n const currRad = new THREE.Vector2(0, 0);\r\n\r\n const topInterp = this._topInterp;\r\n const cenInterp = this._centerInterp;\r\n\r\n let currentValue = this._shift + this._valueStep * (mtcCount - 1) * idx;\r\n\r\n for (let mtxIdx = 0; mtxIdx < mtcCount; ++mtxIdx) {\r\n const lerpVal = Math.min(1.0, mtxIdx / (mtcCount - 1));\r\n currRad.lerpVectors(firstRad, secondRad, lerpVal);\r\n\r\n const currTop = topInterp(currentValue, null);\r\n const currCenter = cenInterp(currentValue, null);\r\n currentValue += this._valueStep;\r\n const nextCenter = cenInterp(currentValue, null);\r\n\r\n outMtc[mtxIdx] = calcMatrix(currCenter.clone(), nextCenter.clone(), currTop.clone().sub(currCenter), currRad);\r\n }\r\n\r\n return outMtc;\r\n }\r\n}\r\n\r\nexport default CartoonHelper;\r\n","import * as THREE from 'three';\r\nimport ResiduesGroup from './ResiduesGroup';\r\nimport CartoonHelper from './CartoonHelper';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n\r\n for (let i = 0; i < parts; ++i) {\r\n // starts from pi/2 because it's important that points are lied on the angles of arrows (visual issues if not)\r\n const a = Math.PI / 2.0 - 2 * Math.PI * i / parts;\r\n\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\n\r\nfunction _loopThrough(subDiv, residues, segmentsHeight, tension, mode, callback) {\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n const { boundaries } = subDiv[subDivI];\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const idc = [subs[i].start, subs[i].end];\r\n const matrixHelper = new CartoonHelper(residues, idc[0], idc[1], segmentsHeight, tension, boundaries);\r\n let prevLast = null;\r\n const startIdx = subs[i].start * 2;\r\n const endIdx = subs[i].end * 2 + 1;\r\n let prevSecondRad = mode.getResidueRadius(residues[0], 0);\r\n for (let idx = startIdx; idx <= endIdx; ++idx) {\r\n const resIdx = (idx / 2 | 0);\r\n const currRes = residues[resIdx];\r\n const firstRad = mode.getResidueRadius(currRes, idx % 2);\r\n const secondRad = mode.getResidueRadius(currRes, 1 + (idx % 2));\r\n\r\n const mtc = matrixHelper.prepareMatrices(idx - idc[0] * 2, firstRad, secondRad);\r\n mtc.unshift(prevLast === null ? mtc[0] : prevLast);\r\n\r\n // Slope - radius is changed along this residue part\r\n const hasSlope = (firstRad.x !== secondRad.x) || (firstRad.y !== secondRad.y);\r\n // Cut - end radius of previous part not equal to start radius of this part. First section of this part lies in the orthogonal plane\r\n const hasCut = (firstRad.x !== prevSecondRad.x) || (firstRad.y !== prevSecondRad.y);\r\n\r\n callback(currRes, mtc, hasSlope, hasCut);\r\n\r\n prevLast = mtc[segmentsHeight];\r\n prevSecondRad = secondRad;\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ResiduesSubseqGroup extends ResiduesGroup {\r\n _makeGeoArgs() {\r\n const cmpMultiplier = this._mode.getHeightSegmentsRatio();\r\n this._segmentsHeight = this._polyComplexity * cmpMultiplier | 0;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length * 2];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, (currRes, mtc, hasSlope = false, hasCut = false) => {\r\n const color = colorer.getResidueColor(currRes, parent);\r\n chunkIdc[chunkIdx] = currRes._index;\r\n geo.setItem(chunkIdx, mtc, hasSlope, hasCut);\r\n geo.setColor(chunkIdx++, color);\r\n });\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n const frameRes = frameData.getResidues();\r\n let chunkIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n _loopThrough(this._selection.subdivs, frameRes, this._segmentsHeight, tension, mode, (currRes, mtc) => {\r\n geo.setItem(chunkIdx, mtc);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n });\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default ResiduesSubseqGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesTraceGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const subDiv = this._selection.subdivs;\r\n let chunksCount = 0;\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n chunksCount += subs[i].end - subs[i].start;\r\n }\r\n }\r\n return [chunksCount, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n chunkIdc[chunkIdx] = { first: prevRes._index, second: currRes._index };\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n geo.finalize();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n const { residues } = this._selection;\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksToIdx = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const chunk = chunksToIdx[Math.floor(chunkIdx / 2)];\r\n const resIdx = chunkIdx % 2 === 0 ? chunk.first : chunk.second;\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const chunksToIdx = this._chunksIdc;\r\n const { residues } = this._selection;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const chunk = chunksToIdx[i];\r\n if (residues[chunk.first]._mask & mask) {\r\n chunksList.push(i * 2);\r\n }\r\n if (residues[chunk.second]._mask & mask) {\r\n chunksList.push(i * 2 + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesTraceGroup;\r\n","import ChemGroup from './ChemGroup';\r\nimport Bond from '../../../chem/Bond';\r\n\r\nfunction getCylinderCount(bondOrder) {\r\n return bondOrder < 2 ? 1 : bondOrder;\r\n}\r\n\r\nclass BondsGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const drawMultiple = this._mode.drawMultiorderBonds();\r\n const showAromatic = this._mode.showAromaticLoops();\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n let bondsCount = 0;\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n bondsCount += this.getBondOrder(bonds[bondsIdc[i]], drawMultiple, showAromatic);\r\n }\r\n return [bondsCount, this._polyComplexity];\r\n }\r\n\r\n getBondOrder(bond, drawMultiple, showAromatic) {\r\n let bondOrder = 1;\r\n if (drawMultiple && (!showAromatic || bond._type !== Bond.BondType.AROMATIC)) {\r\n bondOrder = getCylinderCount(bond._order);\r\n }\r\n return bondOrder;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const { bonds } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const bondsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const bondIdx = bondsIdc[Math.floor(chunkIdx / 2)];\r\n if (bondIdx < bonds.length) {\r\n const bond = bonds[bondIdx];\r\n inters[i].atom = chunkIdx % 2 === 0 ? bond._left : bond._right;\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask, innerOnly) {\r\n const chunksList = [];\r\n const { bonds } = this._selection;\r\n const chunksToIdx = this._chunksIdc;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const bond = bonds[chunksToIdx[i]];\r\n if ((bond._left.mask & mask) && (!innerOnly || (bond._right.mask & mask))) {\r\n chunksList.push(2 * i);\r\n }\r\n if ((bond._right.mask & mask) && (!innerOnly || (bond._left.mask & mask))) {\r\n chunksList.push(2 * i + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default BondsGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nclass BondsCylinderGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsCylinderGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nconst STEP_SIZE = 0.15;\r\n\r\nclass BondsLinesGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsLinesGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\nimport AtomsSurfaceGroup from './AtomsSurfaceGroup';\r\nimport AtomsSASSESGroupStub from './AtomsSASSESGroupStub';\r\nimport AtomsTextGroup from './AtomsTextGroup';\r\nimport AromaticTorusGroup from './AromaticTorusGroup';\r\nimport AromaticLinesGroup from './AromaticLinesGroup';\r\nimport NucleicCylindersGroup from './NucleicCylindersGroup';\r\nimport NucleicSpheresGroup from './NucleicSpheresGroup';\r\nimport ResiduesSubseqGroup from './ResiduesSubseqGroup';\r\nimport ResiduesTraceGroup from './ResiduesTraceGroup';\r\nimport BondsCylinderGroup from './BondsCylinderGroup';\r\nimport BondsLinesGroup from './BondsLinesGroup';\r\n\r\nexport default {\r\n AtomsSphereGroup,\r\n AtomsSurfaceGroup,\r\n AtomsSASSESGroupStub,\r\n AtomsTextGroup,\r\n AromaticTorusGroup,\r\n AromaticLinesGroup,\r\n NucleicCylindersGroup,\r\n NucleicSpheresGroup,\r\n ResiduesSubseqGroup,\r\n ResiduesTraceGroup,\r\n BondsCylinderGroup,\r\n BondsLinesGroup,\r\n};\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AtomsProcessor extends RCGroup {\r\n constructor(AtomsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n this._mode = mode;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let atomCount = 0;\r\n component.forEachAtom((atom) => {\r\n if (!self._checkAtom(atom, mask)) {\r\n return;\r\n }\r\n atomsIdc[atomCount++] = atom.index;\r\n });\r\n if (atomCount === 0) {\r\n return;\r\n }\r\n const atomsGroup = new AtomsGroup(geoParams, {\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n _checkAtom(atom, mask) {\r\n return atom.mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AtomsProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\n\r\nclass OrphanAtomsProcessor extends AtomsProcessor {\r\n _checkAtom(atom, mask) {\r\n if (!(atom.mask & mask)) {\r\n return false;\r\n }\r\n\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n if ((bonds[i]._left.mask & mask) && (bonds[i]._right.mask & mask)) {\r\n return false;\r\n }\r\n }\r\n return true;\r\n }\r\n}\r\n\r\nexport default OrphanAtomsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass ResiduesProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n component.forEachResidue((residue) => {\r\n if (self._checkResidue(residue, mask)) {\r\n resIdc[chunksCount++] = residue._index;\r\n }\r\n });\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n checkResidue(residue, mask) {\r\n return residue._mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default ResiduesProcessor;\r\n","import ResidueProcessor from './ResiduesProcessor';\r\n\r\nclass NucleicProcessor extends ResidueProcessor {\r\n _checkResidue(residue, mask) {\r\n return mask & residue._mask && residue._cylinders !== null;\r\n }\r\n}\r\nexport default NucleicProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass SubseqsProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const subDivs = component.getMaskedSubdivSequences(mask);\r\n\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n for (let subDivI = 0, subDivN = subDivs.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDivs[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let j = subs[i].start, jEnd = subs[i].end; j <= jEnd; ++j) {\r\n resIdc[chunksCount++] = residues[j]._index;\r\n }\r\n }\r\n }\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n subdivs: subDivs,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default SubseqsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass BondsProcessor extends RCGroup {\r\n constructor(BondsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const bonds = complex.getBonds();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const bondsIdc = [];\r\n let bondsCount = 0;\r\n component.forEachBond((bond) => {\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n if (!(atom1.mask & mask) || !(atom2.mask & mask)) {\r\n return;\r\n }\r\n bondsIdc[bondsCount++] = bond._index;\r\n });\r\n if (bondsCount === 0) {\r\n return;\r\n }\r\n const bondsGroup = new BondsGroup(geoParams, {\r\n bonds,\r\n chunks: bondsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n bondsGroup._component = component;\r\n self.add(bondsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default BondsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AromaticProcessor extends RCGroup {\r\n constructor(AromaticGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n if (!mode.showAromaticLoops()) {\r\n return;\r\n }\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let chunksCount = 0;\r\n const cycles = [];\r\n let cycleIdx = 0;\r\n component.forEachCycle((cycle) => {\r\n const cycAtoms = cycle.atoms;\r\n let perCycle = 0;\r\n for (let i = 0, n = cycAtoms.length; i < n; ++i) {\r\n if ((cycAtoms[i].mask & mask) !== 0) {\r\n ++perCycle;\r\n atomsIdc[chunksCount++] = cycAtoms[i].index;\r\n }\r\n }\r\n if (perCycle > 0) {\r\n cycles[cycleIdx++] = cycle;\r\n }\r\n });\r\n\r\n const atomsGroup = new AromaticGroup(geoParams, {\r\n cycles,\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AromaticProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\nimport OrphanAtomsProcessor from './OrphanAtomsProcessor';\r\nimport ResiduesProcessor from './ResiduesProcessor';\r\nimport NucleicProcessor from './NucleicProcessor';\r\nimport SubseqsProcessor from './SubseqsProcessor';\r\nimport BondsProcessor from './BondsProcessor';\r\nimport AromaticProcessor from './AromaticProcessor';\r\n\r\nexport default {\r\n Atoms: AtomsProcessor,\r\n OrphanAtoms: OrphanAtomsProcessor,\r\n Residues: ResiduesProcessor,\r\n Nucleic: NucleicProcessor,\r\n Subseqs: SubseqsProcessor,\r\n Bonds: BondsProcessor,\r\n Aromatic: AromaticProcessor,\r\n};\r\n","import MeshCreator from '../../meshes/MeshCreator';\r\nimport groups from './groups';\r\nimport processors from '../processors/processors';\r\n\r\nfunction _bakeGroup(triplet, Processor, Group) {\r\n return function (complex, colorer, mode, polyComplexity, mask, material) {\r\n return new Processor(Group, triplet, complex, colorer, mode, polyComplexity, mask, material);\r\n };\r\n}\r\n\r\nclass GroupsFactory {\r\n static AtomsSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static OrphanedAtomsCrosses(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createCrosses(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.OrphanAtoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static BondsCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsCylinderGroup);\r\n }\r\n\r\n static BondsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.create2CLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsLinesGroup);\r\n }\r\n\r\n static CartoonChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesSubseqGroup);\r\n }\r\n\r\n static TraceChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CClosedCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesTraceGroup);\r\n }\r\n\r\n static NucleicSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicSpheresGroup);\r\n }\r\n\r\n static NucleicCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicCylindersGroup);\r\n }\r\n\r\n static ALoopsTorus(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticTorusGroup);\r\n }\r\n\r\n static ALoopsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createChunkedLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticLinesGroup);\r\n }\r\n\r\n static QuickSurfGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createQuickSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static ContactSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createContactSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static SASSESSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createSASSES(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSASSESGroupStub);\r\n }\r\n\r\n static TextLabelsGeo(caps, settings) {\r\n const gfxTriplet = MeshCreator.createLabels(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsTextGroup);\r\n }\r\n}\r\n\r\nexport default GroupsFactory;\r\n","import _ from 'lodash';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport factory from './groups/GroupsFactory';\r\n\r\n/**\r\n * Create new mode.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the mode after its creation.\r\n *\r\n * @exports Mode\r\n * @this Mode\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available modes used for building and displaying molecule geometry.\r\n */\r\nclass Mode {\r\n constructor(opts) {\r\n if (this.constructor === Mode) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Mode options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts);\r\n }\r\n\r\n /**\r\n * Get mode identification, probably with options.\r\n * @returns {string|Array} Mode identifier string ({@link Mode#id}) or two-element array containing both mode\r\n * identifier and options ({@link Mode#opts}).\r\n * Options are returned if they were changed during or after the mode creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, this.settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const polyComplexity = this.opts.polyComplexity ? this.opts.polyComplexity[this.settings.now.resolution] : 0;\r\n const groupList = this.depGroups;\r\n const groupCount = groupList.length;\r\n const group = new gfxutils.RCGroup();\r\n const self = this;\r\n for (let i = 0; i < groupCount; ++i) {\r\n let currGroup = groupList[i];\r\n let renderParams = {};\r\n if (_.isArray(currGroup)) {\r\n renderParams = currGroup[1].call(this);\r\n [currGroup] = currGroup;\r\n }\r\n const Group = factory[currGroup](null, this.settings, renderParams);\r\n const newGroup = new Group(complex, colorer, self, polyComplexity, mask, material);\r\n if (newGroup.children.length > 0) {\r\n group.add(newGroup);\r\n }\r\n }\r\n return group;\r\n }\r\n}\r\n\r\nmakeContextDependent(Mode.prototype);\r\n\r\n/**\r\n* Mode identifier.\r\n* @type {string}\r\n*/\r\nMode.prototype.id = '__';\r\n\r\n/**\r\n * Mode geo groups.\r\n * @type {Array}\r\n */\r\nMode.prototype.depGroups = [];\r\n\r\nexport default Mode;\r\n","import Mode from './Mode';\r\n\r\nfunction getRenderParams() {\r\n return {\r\n lineWidth: this.opts.lineWidth,\r\n };\r\n}\r\n\r\nclass LinesMode extends Mode {\r\n static id = 'LN';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const groups = this.depGroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n groups[i] = [groups[i], getRenderParams];\r\n }\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n\r\n calcAtomRadius() {\r\n return this.opts.atom;\r\n }\r\n\r\n getAromaticOffset() {\r\n return this.opts.offsarom;\r\n }\r\n\r\n getAromaticArcChunks() {\r\n return this.opts.chunkarom;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n}\r\n\r\nLinesMode.prototype.id = 'LN';\r\nLinesMode.prototype.name = 'Lines';\r\nLinesMode.prototype.shortName = 'Lines';\r\nLinesMode.prototype.depGroups = [\r\n 'ALoopsLines',\r\n 'BondsLines',\r\n 'OrphanedAtomsCrosses',\r\n];\r\n\r\nexport default LinesMode;\r\n","import Mode from './Mode';\r\n\r\nclass LicoriceMode extends Mode {\r\n static id = 'LC';\r\n\r\n calcAtomRadius(_atom) {\r\n return this.opts.bond;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nLicoriceMode.prototype.id = 'LC';\r\nLicoriceMode.prototype.name = 'Licorice';\r\nLicoriceMode.prototype.shortName = 'Licorice';\r\nLicoriceMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default LicoriceMode;\r\n","import Mode from './Mode';\r\n\r\nclass BallsAndSticksMode extends Mode {\r\n static id = 'BS';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius * this.opts.atom;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nBallsAndSticksMode.prototype.id = 'BS';\r\nBallsAndSticksMode.prototype.name = 'Balls and Sticks';\r\nBallsAndSticksMode.prototype.shortName = 'Balls';\r\nBallsAndSticksMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default BallsAndSticksMode;\r\n","import Mode from './Mode';\r\n\r\nclass VanDerWaalsMode extends Mode {\r\n static id = 'VW';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n}\r\n\r\nVanDerWaalsMode.prototype.id = 'VW';\r\nVanDerWaalsMode.prototype.name = 'Van der Waals';\r\nVanDerWaalsMode.prototype.shortName = 'VDW';\r\nVanDerWaalsMode.prototype.depGroups = ['AtomsSpheres'];\r\n\r\nexport default VanDerWaalsMode;\r\n","import Mode from './Mode';\r\n\r\nclass TraceMode extends Mode {\r\n static id = 'TR';\r\n\r\n calcStickRadius() {\r\n return this.opts.radius;\r\n }\r\n}\r\n\r\nTraceMode.prototype.id = 'TR';\r\nTraceMode.prototype.name = 'Trace';\r\nTraceMode.prototype.shortName = 'Trace';\r\nTraceMode.prototype.depGroups = ['TraceChains'];\r\n\r\nexport default TraceMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass TubeMode extends Mode {\r\n static id = 'TU';\r\n\r\n getResidueRadius(_residue) {\r\n return this.TUBE_RADIUS;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const rad = this.opts.radius;\r\n this.TUBE_RADIUS = new THREE.Vector2(rad, rad);\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nTubeMode.prototype.id = 'TU';\r\nTubeMode.prototype.name = 'Tube';\r\nTubeMode.prototype.shortName = 'Tube';\r\nTubeMode.prototype.depGroups = ['CartoonChains'];\r\n\r\nexport default TubeMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass CartoonMode extends Mode {\r\n static id = 'CA';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n // cache for secondary structure options\r\n this.secCache = {};\r\n }\r\n\r\n getResidueStartRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (!second || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return secOpts.start;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueEndRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (second === null || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return this.ARROW_END;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueRadius(residue, val) {\r\n const startRad = this.getResidueStartRadius(residue);\r\n if (val === 0) {\r\n return startRad;\r\n }\r\n\r\n const endRad = this.getResidueEndRadius(residue);\r\n if (val === 2) {\r\n return endRad;\r\n }\r\n\r\n return startRad.clone().lerp(endRad, val / 2.0);\r\n }\r\n\r\n calcStickRadius(_res) {\r\n return this.opts.radius;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const tubeRad = this.opts.radius;\r\n const secHeight = this.opts.depth;\r\n\r\n this.TUBE_RADIUS = new THREE.Vector2(tubeRad, tubeRad);\r\n this.ARROW_END = new THREE.Vector2(secHeight, tubeRad);\r\n const secCache = {};\r\n const secData = this.opts.ss;\r\n /* eslint-disable guard-for-in */\r\n for (const prop in secData) {\r\n secCache[prop] = {\r\n center: new THREE.Vector2(secHeight, secData[prop].width),\r\n start: new THREE.Vector2(secHeight, secData[prop].arrow),\r\n };\r\n }\r\n this.secCache = secCache;\r\n /* eslint-enable guard-for-in */\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nCartoonMode.prototype.id = 'CA';\r\nCartoonMode.prototype.name = 'Cartoon';\r\nCartoonMode.prototype.shortName = 'Cartoon';\r\nCartoonMode.prototype.depGroups = [\r\n 'CartoonChains',\r\n 'NucleicSpheres',\r\n 'NucleicCylinders',\r\n];\r\n\r\nexport default CartoonMode;\r\n","import chem from '../../chem';\r\nimport Mode from './Mode';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction getRenderParams() {\r\n return {\r\n wireframe: this.opts.wireframe,\r\n zClip: this.opts.zClip,\r\n };\r\n}\r\n\r\nclass SurfaceMode extends Mode {\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const surfaces = this.surfaceNames;\r\n const groups = this.depGroups;\r\n for (let i = 0, n = surfaces.length; i < n; ++i) {\r\n groups[groups.length] = [surfaces[i], getRenderParams];\r\n }\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getVisibilitySelector() {\r\n let visibilitySelector = null;\r\n if (this.opts.subset !== '') {\r\n const res = selectors.parse(this.opts.subset);\r\n if (!res.error) {\r\n visibilitySelector = res.selector;\r\n }\r\n }\r\n return visibilitySelector;\r\n }\r\n}\r\n\r\nSurfaceMode.prototype.isSurface = true;\r\nSurfaceMode.prototype.surfaceNames = [];\r\n\r\nexport default SurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass QuickSurfaceMode extends SurfaceMode {\r\n static id = 'QS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n useBeads: false,\r\n isoValue: this.opts.isoValue,\r\n gaussLim: this.opts.gaussLim[this.settings.now.resolution],\r\n radScale: this.opts.scale,\r\n gridSpacing: this.opts.gridSpacing[this.settings.now.resolution],\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nQuickSurfaceMode.prototype.id = 'QS';\r\nQuickSurfaceMode.prototype.name = 'Quick Surface';\r\nQuickSurfaceMode.prototype.shortName = 'Quick Surf';\r\nQuickSurfaceMode.prototype.surfaceNames = ['QuickSurfGeo'];\r\n\r\nexport default QuickSurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass IsoSurfaceMode extends SurfaceMode {\r\n constructor(excludeProbe, opts) {\r\n super(opts);\r\n this._excludeProbe = excludeProbe;\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getSurfaceOpts() {\r\n return {\r\n gridSpacing: this.opts.polyComplexity[this.settings.now.resolution],\r\n radScale: this._radScale,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n probeRadius: this.opts.probeRadius,\r\n excludeProbe: this._excludeProbe,\r\n };\r\n }\r\n}\r\n\r\nIsoSurfaceMode.prototype.id = 'SU';\r\nIsoSurfaceMode.prototype.name = 'Surface';\r\nIsoSurfaceMode.prototype.shortName = 'Surface';\r\nIsoSurfaceMode.prototype.surfaceNames = ['SASSESSurfaceGeo'];\r\n\r\nIsoSurfaceMode.prototype._radScale = 1;\r\nIsoSurfaceMode.prototype._excludeProbe = false;\r\n\r\nexport default IsoSurfaceMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSASMode extends IsoSurfaceMode {\r\n static id = 'SA';\r\n\r\n constructor(opts) {\r\n super(false, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSASMode.prototype.id = 'SA';\r\nIsoSurfaceSASMode.prototype.name = 'Solvent Accessible Surface';\r\nIsoSurfaceSASMode.prototype.shortName = 'SAS';\r\n\r\nexport default IsoSurfaceSASMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSESMode extends IsoSurfaceMode {\r\n static id = 'SE';\r\n\r\n constructor(opts) {\r\n super(true, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSESMode.prototype.id = 'SE';\r\nIsoSurfaceSESMode.prototype.name = 'Solvent Excluded Surface';\r\nIsoSurfaceSESMode.prototype.shortName = 'SES';\r\n\r\nexport default IsoSurfaceSESMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass ContactSurfaceMode extends SurfaceMode {\r\n static id = 'CS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n probeRadius: this.opts.probeRadius,\r\n radScale: this.opts.polyComplexity[this.settings.now.resolution],\r\n scaleFactor: this.opts.polyComplexity[this.settings.now.resolution],\r\n gridSpacing: 1.0 / this.opts.polyComplexity[this.settings.now.resolution],\r\n isoValue: this.opts.isoValue,\r\n probePositions: this.opts.probePositions,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nContactSurfaceMode.prototype.id = 'CS';\r\nContactSurfaceMode.prototype.name = 'Contact Surface';\r\nContactSurfaceMode.prototype.shortName = 'Contact Surf';\r\nContactSurfaceMode.prototype.isSurface = true;\r\nContactSurfaceMode.prototype.surfaceNames = ['ContactSurfaceGeo'];\r\n\r\nexport default ContactSurfaceMode;\r\n","import _ from 'lodash';\r\nimport Mode from './Mode';\r\n\r\nclass TextMode extends Mode {\r\n static id = 'TX';\r\n\r\n getTemplateOptions() {\r\n return this.opts.template;\r\n }\r\n\r\n getLabelOpts() {\r\n return _.merge(this.opts, {\r\n colors: true,\r\n adjustColor: true,\r\n transparent: true,\r\n });\r\n }\r\n}\r\n\r\nTextMode.prototype.id = 'TX';\r\nTextMode.prototype.name = 'Text mode';\r\nTextMode.prototype.shortName = 'Text';\r\nTextMode.prototype.depGroups = ['TextLabelsGeo'];\r\n\r\nexport default TextMode;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport LinesMode from './modes/LinesMode';\r\nimport LicoriceMode from './modes/LicoriceMode';\r\nimport BallsAndSticksMode from './modes/BallsAndSticksMode';\r\nimport VanDerWaalsMode from './modes/VanDerWaalsMode';\r\nimport TraceMode from './modes/TraceMode';\r\nimport TubeMode from './modes/TubeMode';\r\nimport CartoonMode from './modes/CartoonMode';\r\nimport QuickSurfaceMode from './modes/QuickSurfaceMode';\r\nimport IsoSurfaceSASMode from './modes/IsoSurfaceSASMode';\r\nimport IsoSurfaceSESMode from './modes/IsoSurfaceSESMode';\r\nimport ContactSurfaceMode from './modes/ContactSurfaceMode';\r\nimport TextMode from './modes/TextMode';\r\n\r\nconst modes = new EntityList([\r\n LinesMode,\r\n LicoriceMode,\r\n BallsAndSticksMode,\r\n VanDerWaalsMode,\r\n TraceMode,\r\n TubeMode,\r\n CartoonMode,\r\n QuickSurfaceMode,\r\n IsoSurfaceSASMode,\r\n IsoSurfaceSESMode,\r\n ContactSurfaceMode,\r\n TextMode,\r\n]);\r\n\r\nexport default modes;\r\n","import _ from 'lodash';\r\n\r\nfunction clamp(x, a, b) {\r\n return x <= b ? x < 0 ? 0 : x : b;\r\n}\r\n\r\nfunction lerpColor(c1, c2, alpha) {\r\n const beta = 1 - alpha;\r\n const r1 = (c1 >> 16) & 0xff;\r\n const g1 = (c1 >> 8) & 0xff;\r\n const b1 = c1 & 0xff;\r\n const r2 = (c2 >> 16) & 0xff;\r\n const g2 = (c2 >> 8) & 0xff;\r\n const b2 = c2 & 0xff;\r\n const r = beta * r1 + alpha * r2;\r\n const g = beta * g1 + alpha * g2;\r\n const b = beta * b1 + alpha * b2;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nclass Palette {\r\n constructor(name, id) {\r\n this.name = name || 'Custom';\r\n this.id = id || 'CP';\r\n }\r\n\r\n getElementColor(name, asIs = false) {\r\n const color = this.elementColors[name];\r\n return color === undefined && !asIs ? this.defaultElementColor : color;\r\n }\r\n\r\n getResidueColor(name, asIs = false) {\r\n const color = this.residueColors[name];\r\n return color === undefined && !asIs ? this.defaultResidueColor : color;\r\n }\r\n\r\n getChainColor(name) {\r\n let chain = name.charCodeAt(0);\r\n chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F)\r\n % this.chainColors.length;\r\n return this.chainColors[chain];\r\n }\r\n\r\n getSecondaryColor(type, asIs = false) {\r\n const color = this.secondaryColors[type];\r\n return color === undefined && !asIs ? this.defaultSecondaryColor : color;\r\n }\r\n\r\n getSequentialColor(index) {\r\n const { colors } = this;\r\n const len = colors.length;\r\n return index < 0 ? colors[(index % len) + len] : colors[index % len];\r\n }\r\n\r\n getGradientColor(value, gradientName) {\r\n const gradient = this.gradients[gradientName];\r\n if (!gradient) {\r\n return this.defaultNamedColor;\r\n }\r\n const count = gradient.length;\r\n const index = value * (count - 1);\r\n let left = Math.floor(index);\r\n const right = clamp(left + 1, 0, count - 1);\r\n left = clamp(left, 0, count - 1);\r\n return lerpColor(gradient[left], gradient[right], index - left);\r\n }\r\n\r\n getNamedColor(name, asIs = false) {\r\n const color = this.namedColors[name];\r\n return color === undefined && !asIs ? this.defaultNamedColor : color;\r\n }\r\n}\r\n\r\n_.assign(Palette.prototype, {\r\n colors: [0xFFFFFF, 0xFF0000, 0x00FF00, 0x0000FF, 0x808080],\r\n\r\n minRangeColor: 0x000000,\r\n midRangeColor: 0x7F7F7F,\r\n maxRangeColor: 0xFFFFFF,\r\n\r\n defaultElementColor: 0xFFFFFF,\r\n elementColors: {},\r\n\r\n defaultResidueColor: 0xFFFFFF,\r\n residueColors: {},\r\n\r\n chainColors: [0xFFFFFF],\r\n\r\n defaultSecondaryColor: 0xFFFFFF,\r\n secondaryColors: {},\r\n\r\n defaultGradientColor: 0x000000,\r\n\r\n defaultNamedColor: 0xFFFFFF,\r\n namedColorsArray: [\r\n /* eslint-disable no-multi-spaces */\r\n ['indianred', 0xcd5c5c],\r\n ['lightcoral', 0xf08080],\r\n ['salmon', 0xfa8072],\r\n ['darksalmon', 0xe9967a],\r\n ['lightsalmon', 0xffa07a],\r\n ['crimson', 0xdc143c],\r\n ['red', 0xff0000],\r\n ['firebrick', 0xb22222],\r\n ['darkred', 0x8b0000],\r\n ['pink', 0xffc0cb],\r\n ['lightpink', 0xffb6c1],\r\n ['hotpink', 0xff69b4],\r\n ['deeppink', 0xff1493],\r\n ['mediumvioletred', 0xc71585],\r\n ['palevioletred', 0xdb7093],\r\n ['coral', 0xff7f50],\r\n ['tomato', 0xff6347],\r\n ['orangered', 0xff4500],\r\n ['darkorange', 0xff8c00],\r\n ['orange', 0xffa500],\r\n ['gold', 0xffd700],\r\n ['yellow', 0xffff00],\r\n ['lightyellow', 0xffffe0],\r\n ['lemonchiffon', 0xfffacd],\r\n ['lightgoldenrodyellow', 0xfafad2],\r\n ['papayawhip', 0xffefd5],\r\n ['moccasin', 0xffe4b5],\r\n ['peachpuff', 0xffdab9],\r\n ['palegoldenrod', 0xeee8aa],\r\n ['khaki', 0xf0e68c],\r\n ['darkkhaki', 0xbdb76b],\r\n ['lavender', 0xe6e6fa],\r\n ['thistle', 0xd8bfd8],\r\n ['plum', 0xdda0dd],\r\n ['violet', 0xee82ee],\r\n ['orchid', 0xda70d6],\r\n ['fuchsia', 0xff00ff],\r\n ['magenta', 0xff00ff],\r\n ['mediumorchid', 0xba55d3],\r\n ['mediumpurple', 0x9370db],\r\n ['rebeccapurple', 0x663399],\r\n ['blueviolet', 0x8a2be2],\r\n ['darkviolet', 0x9400d3],\r\n ['darkorchid', 0x9932cc],\r\n ['darkmagenta', 0x8b008b],\r\n ['purple', 0x800080],\r\n ['indigo', 0x4b0082],\r\n ['slateblue', 0x6a5acd],\r\n ['mediumslateblue', 0x7b68ee],\r\n ['darkslateblue', 0x483d8b],\r\n ['greenyellow', 0xadff2f],\r\n ['chartreuse', 0x7fff00],\r\n ['lawngreen', 0x7cfc00],\r\n ['lime', 0x00ff00],\r\n ['limegreen', 0x32cd32],\r\n ['palegreen', 0x98fb98],\r\n ['lightgreen', 0x90ee90],\r\n ['mediumspringgreen', 0x00fa9a],\r\n ['springgreen', 0x00ff7f],\r\n ['mediumseagreen', 0x3cb371],\r\n ['seagreen', 0x2e8b57],\r\n ['forestgreen', 0x228b22],\r\n ['green', 0x008000],\r\n ['darkgreen', 0x006400],\r\n ['yellowgreen', 0x9acd32],\r\n ['olivedrab', 0x6b8e23],\r\n ['olive', 0x808000],\r\n ['darkolivegreen', 0x556b2f],\r\n ['mediumaquamarine', 0x66cdaa],\r\n ['darkseagreen', 0x8fbc8f],\r\n ['lightseagreen', 0x20b2aa],\r\n ['darkcyan', 0x008b8b],\r\n ['teal', 0x008080],\r\n ['aqua', 0x00ffff],\r\n ['cyan', 0x00ffff],\r\n ['lightcyan', 0xe0ffff],\r\n ['paleturquoise', 0xafeeee],\r\n ['aquamarine', 0x7fffd4],\r\n ['turquoise', 0x40e0d0],\r\n ['mediumturquoise', 0x48d1cc],\r\n ['darkturquoise', 0x00ced1],\r\n ['cadetblue', 0x5f9ea0],\r\n ['steelblue', 0x4682b4],\r\n ['lightsteelblue', 0xb0c4de],\r\n ['powderblue', 0xb0e0e6],\r\n ['lightblue', 0xadd8e6],\r\n ['skyblue', 0x87ceeb],\r\n ['lightskyblue', 0x87cefa],\r\n ['deepskyblue', 0x00bfff],\r\n ['dodgerblue', 0x1e90ff],\r\n ['cornflowerblue', 0x6495ed],\r\n ['royalblue', 0x4169e1],\r\n ['blue', 0x0000ff],\r\n ['mediumblue', 0x0000cd],\r\n ['darkblue', 0x00008b],\r\n ['navy', 0x000080],\r\n ['midnightblue', 0x191970],\r\n ['cornsilk', 0xfff8dc],\r\n ['blanchedalmond', 0xffebcd],\r\n ['bisque', 0xffe4c4],\r\n ['navajowhite', 0xffdead],\r\n ['wheat', 0xf5deb3],\r\n ['burlywood', 0xdeb887],\r\n ['tan', 0xd2b48c],\r\n ['rosybrown', 0xbc8f8f],\r\n ['sandybrown', 0xf4a460],\r\n ['goldenrod', 0xdaa520],\r\n ['darkgoldenrod', 0xb8860b],\r\n ['peru', 0xcd853f],\r\n ['chocolate', 0xd2691e],\r\n ['saddlebrown', 0x8b4513],\r\n ['sienna', 0xa0522d],\r\n ['brown', 0xa52a2a],\r\n ['maroon', 0x800000],\r\n ['white', 0xffffff],\r\n ['snow', 0xfffafa],\r\n ['honeydew', 0xf0fff0],\r\n ['mintcream', 0xf5fffa],\r\n ['azure', 0xf0ffff],\r\n ['aliceblue', 0xf0f8ff],\r\n ['ghostwhite', 0xf8f8ff],\r\n ['whitesmoke', 0xf5f5f5],\r\n ['seashell', 0xfff5ee],\r\n ['beige', 0xf5f5dc],\r\n ['oldlace', 0xfdf5e6],\r\n ['floralwhite', 0xfffaf0],\r\n ['ivory', 0xfffff0],\r\n ['antiquewhite', 0xfaebd7],\r\n ['linen', 0xfaf0e6],\r\n ['lavenderblush', 0xfff0f5],\r\n ['mistyrose', 0xffe4e1],\r\n ['gainsboro', 0xdcdcdc],\r\n ['lightgray', 0xd3d3d3],\r\n ['silver', 0xc0c0c0],\r\n ['darkgray', 0xa9a9a9],\r\n ['gray', 0x808080],\r\n ['dimgray', 0x696969],\r\n ['lightslategray', 0x778899],\r\n ['slategray', 0x708090],\r\n ['darkslategray', 0x2f4f4f],\r\n ['black', 0x000000],\r\n /* eslint-enable no-multi-spaces */\r\n ],\r\n\r\n namedColors: {},\r\n\r\n gradients: {\r\n rainbow: [\r\n 0x0000ff, // blue\r\n 0x00ffff, // cyan\r\n 0x00ff00, // green\r\n 0xffff00, // yellow\r\n 0xff0000, // red\r\n ],\r\n temp: [\r\n 0x0000ff, // blue\r\n 0x007fff, // light-blue\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n hot: [\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n cold: [\r\n 0xffffff, // white\r\n 0x007fff, // light-blue\r\n 0x0000ff, // blue\r\n ],\r\n 'blue-red': [\r\n 0x0000ff, // blue\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n reds: [\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n blues: [\r\n 0xffffff, // white\r\n 0x0000ff, // blue\r\n ],\r\n },\r\n});\r\n\r\nconst { namedColorsArray, namedColors } = Palette.prototype;\r\n\r\nfor (let i = 0, { length } = namedColorsArray; i < length; ++i) {\r\n const [name, value] = namedColorsArray[i];\r\n namedColors[name] = value;\r\n}\r\n\r\nexport default Palette;\r\n","import Palette from './Palette';\r\n\r\nconst palette = new Palette('CPK', 'CP');\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n C: 0x202020,\r\n N: 0x2060FF,\r\n O: 0xEE2010,\r\n F: 0x00FF00,\r\n P: 0x8020FF,\r\n S: 0xFFFF00,\r\n CL: 0x00BB00,\r\n FE: 0xD0D0D0,\r\n CO: 0xD0D0D0,\r\n NI: 0xD0D0D0,\r\n CU: 0xD0D0D0,\r\n BR: 0x008800,\r\n I: 0x005500,\r\n\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('Jmol', 'JM');\r\n\r\npalette.colors = [\r\n\r\n 0x0000FF, // blue\r\n 0x0055FF, //\r\n 0x00ABFF, //\r\n 0x00FFFF, // cyan\r\n 0x00FFAB, //\r\n 0x00FF55, //\r\n 0x00FF00, // green\r\n 0x55FF00, //\r\n 0xABFF00, //\r\n 0xFFFF00, // yellow\r\n 0xFFAB00, //\r\n 0xFF5500, //\r\n 0xFF0000, // red\r\n 0xFF0055, //\r\n 0xFF00AB, //\r\n 0xFF00FF, // magenta\r\n 0xAB00FF, //\r\n 0x5500FF, //\r\n\r\n];\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n D: 0xFFFFC0,\r\n T: 0xFFFFA0,\r\n HE: 0xD9FFFF,\r\n LI: 0xCC80FF,\r\n BE: 0xC2FF00,\r\n B: 0xFFB5B5,\r\n C: 0x909090,\r\n N: 0x3050F8,\r\n O: 0xFF0D0D,\r\n F: 0x90E050,\r\n NE: 0xB3E3F5,\r\n NA: 0xAB5CF2,\r\n MG: 0x8AFF00,\r\n AL: 0xBFA6A6,\r\n SI: 0xF0C8A0,\r\n P: 0xFF8000,\r\n S: 0xFFFF30,\r\n CL: 0x1FF01F,\r\n AR: 0x80D1E3,\r\n K: 0x8F40D4,\r\n CA: 0x3DFF00,\r\n SC: 0xE6E6E6,\r\n TI: 0xBFC2C7,\r\n V: 0xA6A6AB,\r\n CR: 0x8A99C7,\r\n MN: 0x9C7AC7,\r\n FE: 0xE06633,\r\n CO: 0xF090A0,\r\n NI: 0x50D050,\r\n CU: 0xC88033,\r\n ZN: 0x7D80B0,\r\n GA: 0xC28F8F,\r\n GE: 0x668F8F,\r\n AS: 0xBD80E3,\r\n SE: 0xFFA100,\r\n BR: 0xA62929,\r\n KR: 0x5CB8D1,\r\n RB: 0x702EB0,\r\n SR: 0x00FF00,\r\n Y: 0x94FFFF,\r\n ZR: 0x94E0E0,\r\n NB: 0x73C2C9,\r\n MO: 0x54B5B5,\r\n TC: 0x3B9E9E,\r\n RU: 0x248F8F,\r\n RH: 0x0A7D8C,\r\n PD: 0x006985,\r\n AG: 0xC0C0C0,\r\n CD: 0xFFD98F,\r\n IN: 0xA67573,\r\n SN: 0x668080,\r\n SB: 0x9E63B5,\r\n TE: 0xD47A00,\r\n I: 0x940094,\r\n XE: 0x429EB0,\r\n CS: 0x57178F,\r\n BA: 0x00C900,\r\n LA: 0x70D4FF,\r\n CE: 0xFFFFC7,\r\n PR: 0xD9FFC7,\r\n ND: 0xC7FFC7,\r\n PM: 0xA3FFC7,\r\n SM: 0x8FFFC7,\r\n EU: 0x61FFC7,\r\n GD: 0x45FFC7,\r\n TB: 0x30FFC7,\r\n DY: 0x1FFFC7,\r\n HO: 0x00FF9C,\r\n ER: 0x00E675,\r\n TM: 0x00D452,\r\n YB: 0x00BF38,\r\n LU: 0x00AB24,\r\n HF: 0x4DC2FF,\r\n TA: 0x4DA6FF,\r\n W: 0x2194D6,\r\n RE: 0x267DAB,\r\n OS: 0x266696,\r\n IR: 0x175487,\r\n PT: 0xD0D0E0,\r\n AU: 0xFFD123,\r\n HG: 0xB8B8D0,\r\n TL: 0xA6544D,\r\n PB: 0x575961,\r\n BI: 0x9E4FB5,\r\n PO: 0xAB5C00,\r\n AT: 0x754F45,\r\n RN: 0x428296,\r\n FR: 0x420066,\r\n RA: 0x007D00,\r\n AC: 0x70ABFA,\r\n TH: 0x00BAFF,\r\n PA: 0x00A1FF,\r\n U: 0x008FFF,\r\n NP: 0x0080FF,\r\n PU: 0x006BFF,\r\n AM: 0x545CF2,\r\n CM: 0x785CE3,\r\n BK: 0x8A4FE3,\r\n CF: 0xA136D4,\r\n ES: 0xB31FD4,\r\n FM: 0xB31FBA,\r\n MD: 0xB30DA6,\r\n NO: 0xBD0D87,\r\n LR: 0xC70066,\r\n RF: 0xCC0059,\r\n DB: 0xD1004F,\r\n SG: 0xD90045,\r\n BH: 0xE00038,\r\n HS: 0xE6002E,\r\n MT: 0xEB0026,\r\n\r\n};\r\n\r\npalette.defaultResidueColor = 0xBEA06E;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n\r\n ALA: 0xC8C8C8,\r\n ARG: 0x145AFF,\r\n ASN: 0x00DCDC,\r\n ASP: 0xE60A0A,\r\n CYS: 0xE6E600,\r\n GLN: 0x00DCDC,\r\n GLU: 0xE60A0A,\r\n GLY: 0xEBEBEB,\r\n HIS: 0x8282D2,\r\n ILE: 0x0F820F,\r\n LEU: 0x0F820F,\r\n LYS: 0x145AFF,\r\n MET: 0xE6E600,\r\n PHE: 0x3232AA,\r\n PRO: 0xDC9682,\r\n SER: 0xFA9600,\r\n THR: 0xFA9600,\r\n TRP: 0xB45AB4,\r\n TYR: 0x3232AA,\r\n VAL: 0x0F820F,\r\n A: 0xA0A0FF,\r\n C: 0xFF8C4B,\r\n G: 0xFF7070,\r\n I: 0x80FFFF,\r\n T: 0xA0FFA0,\r\n U: 0xFF8080,\r\n DA: 0xA0A0FF,\r\n DC: 0xFF8C4B,\r\n DG: 0xFF7070,\r\n DI: 0x80FFFF,\r\n DT: 0xA0FFA0,\r\n DU: 0xFF8080,\r\n '+A': 0xA0A0FF,\r\n '+C': 0xFF8C4B,\r\n '+G': 0xFF7070,\r\n '+I': 0x80FFFF,\r\n '+T': 0xA0FFA0,\r\n '+U': 0xFF8080,\r\n\r\n};\r\n\r\npalette.chainColors = [\r\n // ' '->0 'A'->1, 'B'->2\r\n 0xFFffffff, // ' ' & '0' white\r\n //\r\n 0xFFC0D0FF, // skyblue\r\n 0xFFB0FFB0, // pastel green\r\n 0xFFFFC0C8, // pink\r\n 0xFFFFFF80, // pastel yellow\r\n 0xFFFFC0FF, // pastel magenta\r\n 0xFFB0F0F0, // pastel cyan\r\n 0xFFFFD070, // pastel gold\r\n 0xFFF08080, // lightcoral\r\n\r\n 0xFFF5DEB3, // wheat\r\n 0xFF00BFFF, // deepskyblue\r\n 0xFFCD5C5C, // indianred\r\n 0xFF66CDAA, // mediumaquamarine\r\n 0xFF9ACD32, // yellowgreen\r\n 0xFFEE82EE, // violet\r\n 0xFF00CED1, // darkturquoise\r\n 0xFF00FF7F, // springgreen\r\n 0xFF3CB371, // mediumseagreen\r\n\r\n 0xFF00008B, // darkblue\r\n 0xFFBDB76B, // darkkhaki\r\n 0xFF006400, // darkgreen\r\n 0xFF800000, // maroon\r\n 0xFF808000, // olive\r\n 0xFF800080, // purple\r\n 0xFF008080, // teal\r\n 0xFFB8860B, // darkgoldenrod\r\n 0xFFB22222, // firebrick\r\n];\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xFF0080,\r\n [StructuralElementType.HELIX_PI]: 0x600080,\r\n [StructuralElementType.HELIX_310]: 0xA00080,\r\n [StructuralElementType.STRAND]: 0xFFC800,\r\n [StructuralElementType.TURN]: 0x6080FF,\r\n dna: 0xAE00FE,\r\n rna: 0xFD0162,\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('VMD', 'VM');\r\n\r\npalette.colors = [\r\n\r\n 0x0000FF, // blue\r\n 0xFF0000, // red\r\n 0x606060, // gray\r\n 0xFF8000, // orange\r\n 0xFFFF00, // yellow\r\n 0x808033, // tan\r\n 0x999999, // silver\r\n 0x00FF00, // green\r\n 0xFFFFFF, // white\r\n 0xFF9999, // pink\r\n 0x40C0C0, // cyan\r\n 0xA600A6, // purple\r\n 0x80E666, // lime\r\n 0xE666B3, // mauve\r\n 0x804D00, // ochre\r\n 0x8080C0, // ice blue\r\n\r\n];\r\n\r\npalette.defaultElementColor = 0x804D00;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n C: 0x40BFBF,\r\n N: 0x0000FF,\r\n O: 0xFF0000,\r\n P: 0x808033,\r\n S: 0xFFFF00,\r\n\r\n};\r\n\r\npalette.defaultResidueColor = 0x40C0C0;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n\r\n ALA: 0x0000FF,\r\n ARG: 0xFFFFFF,\r\n ASN: 0x808033,\r\n ASP: 0xFF0000,\r\n CYS: 0xFFFF00,\r\n GLN: 0xFF8000,\r\n GLU: 0xFF9999,\r\n GLY: 0xFFFFFF,\r\n HIS: 0x40C0C0,\r\n ILE: 0x00FF00,\r\n LEU: 0xFF9999,\r\n LYS: 0x40C0C0,\r\n MET: 0xFFFF00,\r\n PHE: 0xA600A6,\r\n PRO: 0x804C00,\r\n SER: 0xFFFF00,\r\n THR: 0xE666B3,\r\n TRP: 0x999999,\r\n TYR: 0x00FF00,\r\n VAL: 0x808033,\r\n A: 0x0000FF,\r\n C: 0xFF8000,\r\n G: 0xFFFF00,\r\n T: 0xA600A6,\r\n U: 0x00FF00,\r\n DA: 0x0000FF,\r\n DC: 0xFF8000,\r\n DG: 0xFFFF00,\r\n DT: 0xA600A6,\r\n DU: 0x00FF00,\r\n '+A': 0x0000FF,\r\n '+C': 0xFF8000,\r\n '+G': 0xFFFF00,\r\n '+T': 0xA600A6,\r\n '+U': 0x00FF00,\r\n WAT: 0x40C0C0,\r\n H2O: 0x40C0C0,\r\n HOH: 0x40C0C0,\r\n\r\n};\r\n\r\npalette.chainColors = [0xFFFFFF].concat(palette.colors);\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xA600A6,\r\n [StructuralElementType.HELIX_310]: 0x0000FF,\r\n [StructuralElementType.HELIX_PI]: 0xFF0000,\r\n [StructuralElementType.STRAND]: 0xFFFF00,\r\n [StructuralElementType.BRIDGE]: 0x808033,\r\n [StructuralElementType.TURN]: 0x40C0C0,\r\n};\r\n\r\nexport default palette;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport cpkPalette from './palettes/cpkPalette';\r\nimport jmolPalette from './palettes/jmolPalette';\r\nimport vmdPalette from './palettes/vmdPalette';\r\n\r\nconst palettes = new EntityList([\r\n cpkPalette,\r\n jmolPalette,\r\n vmdPalette,\r\n]);\r\n\r\nexport default palettes;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport palettes from '../palettes';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports Colorer\r\n * @this Colorer\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available coloring algorithms used for building and displaying molecule geometry.\r\n */\r\nclass Colorer {\r\n constructor(opts) {\r\n if (this.constructor === Colorer) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Colorer options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(settings.now.colorers[this.id], true), opts);\r\n /**\r\n * Palette in use.\r\n * @type {Palette}\r\n */\r\n this.palette = palettes.first;\r\n }\r\n\r\n /**\r\n * Get Colorer identification, probably with options.\r\n * @returns {string|Array} Colorer identifier string ({@link Colorer#id}) or two-element array containing both colorer\r\n * identifier and options ({@link Colorer#opts}).\r\n * Options are returned if they were changed during or after colorer creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, settings.now.colorers[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n}\r\n\r\n/**\r\n * Colorer identifier.\r\n * @type {string}\r\n */\r\n\r\nColorer.prototype.id = '__';\r\n\r\nexport default Colorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Element\r\n *\r\n * @exports ElementColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on chemical element.\r\n */\r\nclass ElementColorer extends Colorer {\r\n static id = 'EL';\r\n\r\n getAtomColor(atom, _complex) {\r\n const type = atom.element.name;\r\n if (type === 'C' && this.opts.carbon >= 0) {\r\n return this.opts.carbon;\r\n }\r\n return this.palette.getElementColor(type);\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nElementColorer.prototype.id = 'EL';\r\nElementColorer.prototype.name = 'Element';\r\nElementColorer.prototype.shortName = 'Element';\r\n\r\nexport default ElementColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Coloring algorithm based on residue type.\r\n *\r\n * @see ResidueType\r\n *\r\n * @exports ResidueTypeColorer\r\n * @constructor\r\n */\r\nclass ResidueTypeColorer extends Colorer {\r\n static id = 'RT';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getResidueColor(residue._type._name);\r\n }\r\n}\r\n\r\nResidueTypeColorer.prototype.id = 'RT';\r\nResidueTypeColorer.prototype.name = 'Residue Type';\r\nResidueTypeColorer.prototype.shortName = 'Residue';\r\n\r\nexport default ResidueTypeColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass SequenceColorer extends Colorer {\r\n static id = 'SQ';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const chain = residue._chain;\r\n if (chain.minSequence === Number.POSITIVE_INFINITY && chain.maxSequence === Number.NEGATIVE_INFINITY) {\r\n return this.palette.defaultNamedColor;\r\n }\r\n const min = chain.minSequence;\r\n const max = chain.maxSequence > min ? chain.maxSequence : min + 1;\r\n return this.palette.getGradientColor((residue._sequence - min) / (max - min), this.opts.gradient);\r\n }\r\n}\r\n\r\nSequenceColorer.prototype.id = 'SQ';\r\nSequenceColorer.prototype.name = 'Sequence';\r\nSequenceColorer.prototype.shortName = 'Sequence';\r\n\r\nexport default SequenceColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ChainColorer extends Colorer {\r\n static id = 'CH';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getChainColor(residue.getChain()._name);\r\n }\r\n}\r\n\r\nChainColorer.prototype.id = 'CH';\r\nChainColorer.prototype.name = 'Chain';\r\nChainColorer.prototype.shortName = 'Chain';\r\n\r\nexport default ChainColorer;\r\n","import Colorer from './Colorer';\r\nimport ResidueType from '../../chem/ResidueType';\r\n\r\nclass SecondaryStructureColorer extends Colorer {\r\n static id = 'SS';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n if (residue._type.flags & ResidueType.Flags.DNA) {\r\n return this.palette.getSecondaryColor('dna');\r\n }\r\n if (residue._type.flags & ResidueType.Flags.RNA) {\r\n return this.palette.getSecondaryColor('rna');\r\n }\r\n const secondary = residue.getSecondary();\r\n if (secondary) {\r\n let color = this.palette.getSecondaryColor(secondary.type, true);\r\n if (color === undefined) {\r\n color = this.palette.getSecondaryColor(secondary.generic);\r\n }\r\n return color;\r\n }\r\n return this.palette.defaultSecondaryColor;\r\n }\r\n}\r\n\r\nSecondaryStructureColorer.prototype.id = 'SS';\r\nSecondaryStructureColorer.prototype.name = 'Secondary Structure';\r\nSecondaryStructureColorer.prototype.shortName = 'Structure';\r\n\r\nexport default SecondaryStructureColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass UniformColorer extends Colorer {\r\n static id = 'UN';\r\n\r\n getAtomColor(_atom, _complex) {\r\n return this.opts.color;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nUniformColorer.prototype.id = 'UN';\r\nUniformColorer.prototype.name = 'Uniform';\r\nUniformColorer.prototype.shortName = 'Uniform';\r\n\r\nexport default UniformColorer;\r\n","import Colorer from './Colorer';\r\nimport selectors from '../../chem/selectors';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports ConditionalColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on a selector string used as a condition.\r\n */\r\nclass ConditionalColorer extends Colorer {\r\n static id = 'CO';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n const parsed = selectors.parse(this.opts.subset);\r\n this._subsetCached = parsed.error ? selectors.none() : parsed.selector;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n return this._subsetCached.includesAtom(atom) ? this.opts.color : this.opts.baseColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const subset = this._subsetCached;\r\n const atoms = residue._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (!subset.includesAtom(atoms[i])) {\r\n return this.opts.baseColor;\r\n }\r\n }\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nConditionalColorer.prototype.id = 'CO';\r\nConditionalColorer.prototype.name = 'Conditional';\r\nConditionalColorer.prototype.shortName = 'Conditional';\r\n\r\nexport default ConditionalColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ConformationColorer extends Colorer {\r\n static id = 'CF';\r\n\r\n getAtomColor(atom, _complex) {\r\n return this.palette.getChainColor(String.fromCharCode(atom.location));\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nConformationColorer.prototype.id = 'CF';\r\nConformationColorer.prototype.name = 'Conformation';\r\nConformationColorer.prototype.shortName = 'Conformation';\r\n\r\nexport default ConformationColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Temperature\r\n *\r\n * @exports TemperatureColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on temperature of chemical element.\r\n */\r\nclass TemperatureColorer extends Colorer {\r\n static id = 'TM';\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n let factor = 1;\r\n if (atom.temperature && opts) {\r\n if (opts.min === opts.max) {\r\n factor = atom.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (atom.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n if (!opts) {\r\n return this.palette.defaultGradientColor;\r\n }\r\n if (residue.temperature) {\r\n let factor = 0;\r\n if (opts.min === opts.max) {\r\n factor = residue.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (residue.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n}\r\n\r\nTemperatureColorer.prototype.id = 'TM'; // [T]e[M]perature\r\nTemperatureColorer.prototype.name = 'Temperature';\r\nTemperatureColorer.prototype.shortName = 'Temperature';\r\n\r\nexport default TemperatureColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Occupancy\r\n *\r\n * @exports OccupancyColorer\r\n * @augments Occupancy\r\n * @constructor\r\n * @classdesc Coloring algorithm based on occupancy of chemical element.\r\n */\r\nclass OccupancyColorer extends Colorer {\r\n static id = 'OC';\r\n\r\n _getColorByOccupancy(occupancy, opts) {\r\n if (occupancy !== undefined) {\r\n const factor = 1 - occupancy;\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(atom.occupancy, opts);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(residue.occupancy, opts);\r\n }\r\n}\r\n\r\nOccupancyColorer.prototype.id = 'OC'; // [OC]cupancy\r\nOccupancyColorer.prototype.name = 'Occupancy';\r\nOccupancyColorer.prototype.shortName = 'Occupancy';\r\n\r\nexport default OccupancyColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass HydrophobicityColorer extends Colorer {\r\n static id = 'HY';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n let color = this.palette.defaultResidueColor;\r\n if (residue._type.hydrophobicity !== undefined) {\r\n // Kyte Doolitle hydro [-4.5,4.5]->[0.1]\r\n const min = -4.5;\r\n const max = 4.5;\r\n color = this.palette.getGradientColor((residue._type.hydrophobicity - min) / (max - min), this.opts.gradient);\r\n }\r\n return color;\r\n }\r\n}\r\n\r\nHydrophobicityColorer.prototype.id = 'HY';\r\nHydrophobicityColorer.prototype.name = 'Hydrophobicity';\r\nHydrophobicityColorer.prototype.shortName = 'Hydrophobicity';\r\n\r\nexport default HydrophobicityColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass MoleculeColorer extends Colorer {\r\n static id = 'MO';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const molecule = residue._molecule;\r\n const count = _complex.getMoleculeCount();\r\n if (count > 1) {\r\n return this.palette.getGradientColor((molecule.index - 1) / (count - 1), this.opts.gradient);\r\n }\r\n return this.palette.getGradientColor(0, this.opts.gradient);\r\n }\r\n}\r\n\r\nMoleculeColorer.prototype.id = 'MO';\r\nMoleculeColorer.prototype.name = 'Molecule';\r\nMoleculeColorer.prototype.shortName = 'Molecule';\r\n\r\nexport default MoleculeColorer;\r\n","import Colorer from './Colorer';\r\nimport Atom from '../../chem/Atom';\r\n\r\nfunction scaleColor(c, factor) {\r\n const r1 = (c >> 16) & 0xff;\r\n const g1 = (c >> 8) & 0xff;\r\n const b1 = c & 0xff;\r\n const r = factor * r1;\r\n const g = factor * g1;\r\n const b = factor * b1;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports CarbonColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on selection carbon atoms.\r\n */\r\nclass CarbonColorer extends Colorer {\r\n static id = 'CB';\r\n\r\n getAtomColor(atom, _complex) {\r\n const colorCarbon = this.opts.color;\r\n const colorNotCarbon = scaleColor(colorCarbon, this.opts.factor);\r\n return (atom.flags & Atom.Flags.CARBON) ? colorCarbon : colorNotCarbon;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nCarbonColorer.prototype.id = 'CB';\r\nCarbonColorer.prototype.name = 'Carbon';\r\nCarbonColorer.prototype.shortName = 'Carbon';\r\n\r\nexport default CarbonColorer;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport ElementColorer from './colorers/ElementColorer';\r\nimport ResidueTypeColorer from './colorers/ResidueTypeColorer';\r\nimport SequenceColorer from './colorers/SequenceColorer';\r\nimport ChainColorer from './colorers/ChainColorer';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\nimport UniformColorer from './colorers/UniformColorer';\r\nimport ConditionalColorer from './colorers/ConditionalColorer';\r\nimport ConformationColorer from './colorers/ConformationColorer';\r\nimport TemperatureColorer from './colorers/TemperatureColorer';\r\nimport OccupancyColorer from './colorers/OccupancyColorer';\r\nimport HydrophobicityColorer from './colorers/HydrophobicityColorer';\r\nimport MoleculeColorer from './colorers/MoleculeColorer';\r\nimport CarbonColorer from './colorers/CarbonColorer';\r\n\r\nconst colorers = new EntityList([\r\n ElementColorer,\r\n ResidueTypeColorer,\r\n SequenceColorer,\r\n ChainColorer,\r\n SecondaryStructureColorer,\r\n UniformColorer,\r\n ConditionalColorer,\r\n ConformationColorer,\r\n TemperatureColorer,\r\n OccupancyColorer,\r\n HydrophobicityColorer,\r\n MoleculeColorer,\r\n CarbonColorer,\r\n]);\r\n\r\nexport default colorers;\r\n","import * as THREE from 'three';\r\nimport EntityList from '../utils/EntityList';\r\n\r\nfunction neutralColor(intensity) {\r\n return new THREE.Color(intensity, intensity, intensity);\r\n}\r\n\r\nconst materialList = [\r\n {\r\n id: 'DF',\r\n name: 'Diffuse',\r\n shortName: 'Diffuse',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'SF',\r\n name: 'Soft Plastic',\r\n shortName: 'Soft',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.1),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'PL',\r\n name: 'Glossy Plastic',\r\n shortName: 'Glossy',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.28),\r\n shininess: 100,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'ME',\r\n name: 'Metal',\r\n shortName: 'Metal',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.55),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TR',\r\n name: 'Transparent',\r\n shortName: 'Transparent',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'GL',\r\n name: 'Glass',\r\n shortName: 'Glass',\r\n uberOptions: {\r\n diffuse: neutralColor(0.50),\r\n specular: neutralColor(0.65),\r\n shininess: 100,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'BA',\r\n name: 'Backdrop',\r\n shortName: 'Backdrop',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: false,\r\n depthWrite: false,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TN',\r\n name: 'Toon',\r\n shortName: 'Toon',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: true,\r\n },\r\n }, {\r\n id: 'FL',\r\n name: 'Flat',\r\n shortName: 'Flat',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 0,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n },\r\n },\r\n];\r\n\r\nconst materials = new EntityList(materialList);\r\n\r\nexport default materials;\r\n","/**\r\n * Utils functions which is worked with meshes\r\n *\r\n * functions for doing something with all/specified meshes\r\n * functions for traversihg tree and create auxiliary meshes for transparency/shadowmaps...\r\n * functions for calculating data connected with meshes\r\n */\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _gatherObjects(root, meshTypes) {\r\n const meshes = [];\r\n root.traverse((object) => {\r\n for (let i = 0; i < meshTypes.length; i++) {\r\n if (object instanceof meshTypes[i]) {\r\n meshes[meshes.length] = object;\r\n break;\r\n }\r\n }\r\n });\r\n return meshes;\r\n}\r\n\r\n// new mesh with the same geometry and specified material values and layer\r\nfunction createDerivativeMesh(mesh, values, layer) {\r\n const material = mesh.material.createInstance();\r\n material.setValues(values);\r\n\r\n const newMesh = new mesh.constructor(mesh.geometry, material);\r\n newMesh.material.needsUpdate = true;\r\n newMesh.applyMatrix4(mesh.matrix);\r\n newMesh.layers.set(layer);\r\n return newMesh;\r\n}\r\n\r\nfunction traverseMeshes(root, meshTypes, func) {\r\n const meshes = _gatherObjects(root, meshTypes);\r\n\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n const mesh = meshes[i];\r\n if (!mesh.parent) {\r\n continue;\r\n }\r\n func(mesh);\r\n }\r\n}\r\n\r\nfunction applyTransformsToMeshes(root, mtc) {\r\n const mtcCount = mtc.length;\r\n if (mtcCount < 1) {\r\n return;\r\n }\r\n\r\n const meshTypes = [THREE.Mesh, THREE.LineSegments, THREE.Line];\r\n traverseMeshes(root, meshTypes, (mesh) => {\r\n mesh.applyMatrix4(mtc[0]);\r\n for (let j = 1; j < mtcCount; ++j) {\r\n const newMesh = new mesh.constructor(mesh.geometry, mesh.material);\r\n mesh.parent.add(newMesh);\r\n newMesh.applyMatrix4(mtc[j]);\r\n }\r\n });\r\n}\r\n\r\nconst processTransparentMaterial = (function () {\r\n const matValues = {\r\n prepassTransparancy: true,\r\n fakeOpacity: false,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n mesh.material.setValues({ prepassTransparancy: false, fakeOpacity: false });\r\n mesh.material.needsUpdate = true;\r\n mesh.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n\r\n const prepassTranspMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n mesh.parent.add(prepassTranspMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst processColFromPosMaterial = (function () {\r\n const matValues = {\r\n colorFromPos: true,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n overrideColor: false,\r\n fogTransparent: false,\r\n attrColor: false,\r\n attrColor2: false,\r\n attrAlphaColor: false,\r\n fakeOpacity: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n const colFromPosMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n mesh.parent.add(colFromPosMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst createShadowmapMaterial = (function () {\r\n const matValues = {\r\n colorFromDepth: true,\r\n orthoCam: true,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (!mesh.receiveShadow && mesh.material.shadowmap) { // remove shadow from non-receivers\r\n mesh.material.setValues({ shadowmap: false });\r\n }\r\n if (!mesh.material.lights) { // skip creating shadowmap meshes for materials without lighting\r\n return;\r\n }\r\n if (!mesh.castShadow) { // skip creating shadowmap meshes for non-casters\r\n return;\r\n }\r\n if (!gfxutils.belongToSelectLayers(mesh)) { // skip creating shadowmap meshes for selection layer\r\n return;\r\n }\r\n\r\n const shadowmapMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.SHADOWMAP);\r\n shadowmapMesh.isShadowmapMesh = true;\r\n mesh.parent.add(shadowmapMesh);\r\n });\r\n };\r\n}());\r\n\r\nfunction removeShadowmapMaterial(root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (mesh.isShadowmapMesh) {\r\n mesh.parent.remove(mesh);\r\n }\r\n });\r\n}\r\n\r\nfunction forEachMeshInGroup(group, process) {\r\n function processObj(object) {\r\n if (object instanceof THREE.Mesh) {\r\n process(object);\r\n }\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n processObj(object.children[i]);\r\n }\r\n }\r\n processObj(group);\r\n}\r\n\r\nfunction _countMeshTriangles(mesh) {\r\n const geom = mesh.geometry;\r\n if (geom instanceof THREE.InstancedBufferGeometry) {\r\n const attribs = geom.attributes;\r\n for (const property in attribs) {\r\n if (attribs.hasOwnProperty(property) && attribs[property] instanceof THREE.InstancedBufferAttribute) {\r\n const currAttr = attribs[property];\r\n const indexSize = geom.index ? geom.index.array.length / 3 : 0;\r\n return indexSize * currAttr.array.length / currAttr.itemSize;\r\n }\r\n }\r\n return 0;\r\n }\r\n if (geom instanceof THREE.BufferGeometry) {\r\n return geom.index ? geom.index.array.length / 3 : 0;\r\n }\r\n return geom.faces ? geom.faces.length : 0;\r\n}\r\n\r\nfunction countTriangles(group) {\r\n let totalCount = 0;\r\n forEachMeshInGroup(group, (mesh) => {\r\n totalCount += _countMeshTriangles(mesh);\r\n });\r\n return totalCount;\r\n}\r\n\r\nexport default {\r\n applyTransformsToMeshes,\r\n processTransparentMaterial,\r\n processColFromPosMaterial,\r\n createShadowmapMaterial,\r\n removeShadowmapMaterial,\r\n forEachMeshInGroup,\r\n countTriangles,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\nimport meshutils from './meshutils';\r\nimport settings from '../settings';\r\nimport materials from './materials';\r\nimport chem from '../chem';\r\n\r\nconst { selectors } = chem;\r\n\r\nclass Representation {\r\n constructor(index, mode, colorer, selector) {\r\n const startMaterialValues = {\r\n clipPlane: settings.now.draft.clipPlane,\r\n fogTransparent: settings.now.bg.transparent,\r\n shadowmap: settings.now.shadow.on,\r\n shadowmapType: settings.now.shadow.type,\r\n };\r\n this.index = index;\r\n this.mode = mode;\r\n this.colorer = colorer;\r\n this.selector = selector;\r\n this.selectorString = '';\r\n this.count = 0;\r\n this.material = new UberMaterial();\r\n this.material.setValues(startMaterialValues);\r\n this.material.setUberOptions({ fogAlpha: settings.now.fogAlpha });\r\n this.materialPreset = materials.first;\r\n this.needsRebuild = true;\r\n this.visible = true;\r\n\r\n // apply mode params & preset\r\n this.setMode(mode);\r\n }\r\n\r\n markAtoms(complex) {\r\n this.count = complex.markAtoms(this.selector, 1 << this.index);\r\n this.needsRebuild = true;\r\n return this.count;\r\n }\r\n\r\n unmarkAtoms(complex) {\r\n complex.clearAtomBits(1 << this.index);\r\n this.count = 0;\r\n }\r\n\r\n setMode(mode) {\r\n this.mode = mode;\r\n }\r\n\r\n setMaterialPreset(preset) {\r\n this.materialPreset = preset;\r\n this.material.setUberOptions(preset.uberOptions);\r\n this.material.setValues(preset.values);\r\n }\r\n\r\n reset() {\r\n this.geo = null;\r\n this.selectionGeo = null;\r\n }\r\n\r\n buildGeometry(complex) {\r\n this.reset();\r\n this.needsRebuild = false;\r\n\r\n if (settings.now.ao) {\r\n this.material.setValues({ normalsToGBuffer: settings.now.ao });\r\n }\r\n\r\n this.geo = this.mode.buildGeometry(complex, this.colorer, 1 << this.index, this.material);\r\n\r\n if (this.material.uberOptions.opacity < 0.99 && settings.now.transparency === 'prepass') {\r\n meshutils.processTransparentMaterial(this.geo, this.material);\r\n }\r\n this.geo.visible = this.visible;\r\n\r\n gfxutils.processObjRenderOrder(this.geo, this.materialPreset.id);\r\n meshutils.processColFromPosMaterial(this.geo, this.material);\r\n\r\n if (settings.now.shadow.on) {\r\n meshutils.createShadowmapMaterial(this.geo, this.material);\r\n }\r\n\r\n return this.geo;\r\n }\r\n\r\n buildSelectionGeometry(mask) {\r\n let sg = null;\r\n\r\n if (this.geo && ('getSubset' in this.geo)) {\r\n const meshes = this.geo.getSubset(mask);\r\n if (meshes && meshes.length > 0) {\r\n sg = new THREE.Group();\r\n sg.matrixAutoUpdate = false;\r\n sg.matrix = this.geo.matrix;\r\n\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n sg.add(m);\r\n }\r\n }\r\n }\r\n\r\n if (sg) {\r\n sg.visible = this.visible;\r\n }\r\n\r\n this.selectionGeo = sg;\r\n return this.selectionGeo;\r\n }\r\n\r\n /**\r\n * Create object that represents difference between current and another rep\r\n * anotherRep could be undefined. In this case everything is reported.\r\n */\r\n compare(repSettings) {\r\n const diff = {};\r\n\r\n const selStr = String(this.selector);\r\n if (!repSettings || selStr.valueOf() !== String(repSettings.selector).valueOf()) {\r\n diff.selector = selStr;\r\n }\r\n\r\n const modeDiff = this.mode.identify();\r\n if (!repSettings || Array.isArray(modeDiff) || modeDiff !== repSettings.mode) {\r\n diff.mode = modeDiff;\r\n }\r\n\r\n const colorerDiff = this.colorer.identify();\r\n if (!repSettings || Array.isArray(colorerDiff) || colorerDiff !== repSettings.colorer) {\r\n diff.colorer = colorerDiff;\r\n }\r\n\r\n if (!repSettings || this.materialPreset.id !== repSettings.material) {\r\n diff.material = this.materialPreset.id;\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n /**\r\n * Change representation. Write fields what was changed into new object, return it.\r\n */\r\n change(repSettings, complex, mode, color) {\r\n const diff = {};\r\n\r\n // modify selector\r\n if (repSettings.selector) {\r\n const newSelectorObject = selectors.parse(repSettings.selector).selector;\r\n const newSelector = String(newSelectorObject);\r\n if (this.selectorString !== newSelector) {\r\n diff.selector = newSelector;\r\n this.selectorString = newSelector;\r\n this.selector = newSelectorObject;\r\n this.markAtoms(complex);\r\n }\r\n }\r\n\r\n // modify mode\r\n if (repSettings.mode) {\r\n const newMode = repSettings.mode;\r\n if (!_.isEqual(this.mode.identify(), newMode)) {\r\n diff.mode = newMode;\r\n this.setMode(mode);\r\n }\r\n }\r\n\r\n // modify colorer\r\n if (repSettings.colorer) {\r\n const newColorer = repSettings.colorer;\r\n if (!_.isEqual(this.colorer.identify(), newColorer)) {\r\n diff.colorer = newColorer;\r\n this.colorer = color;\r\n }\r\n }\r\n\r\n // modify material\r\n if (repSettings.material) {\r\n const newMaterial = repSettings.material;\r\n if (!_.isEqual(this.materialPreset.id, newMaterial)) {\r\n diff.material = newMaterial;\r\n this.setMaterialPreset(materials.get(repSettings.material));\r\n }\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n show(visible) {\r\n this.visible = visible;\r\n if (this.geo) {\r\n this.geo.visible = visible;\r\n }\r\n if (this.selectionGeo) {\r\n this.selectionGeo.visible = visible;\r\n }\r\n }\r\n}\r\n\r\nexport default Representation;\r\n","import * as THREE from 'three';\r\nimport logger from './utils/logger';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport './gfx/modes';\r\n\r\nfunction _traverseComponentGroups(root, component, callback) {\r\n const { children } = root;\r\n if (!children) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n if (child._component === component) {\r\n callback(child);\r\n }\r\n if (child instanceof gfxutils.RCGroup) {\r\n _traverseComponentGroups(child, component, callback);\r\n }\r\n }\r\n}\r\n\r\nfunction ComplexEditor() {\r\n}\r\n\r\nclass ComplexComponentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n // init component matrices\r\n this._componentTransforms = [];\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n const component = complex._components[i];\r\n this._componentTransforms[component._index] = new THREE.Object3D();\r\n }\r\n\r\n this._inProgress = true;\r\n\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const complex = this._complexVisual.getComplex();\r\n\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n this._bakeComponentTransform(complex._components[i]);\r\n }\r\n\r\n complex.onAtomPositionChanged();\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n const visual = this._complexVisual;\r\n const component = visual.getSelectedComponent();\r\n\r\n if (component === null) {\r\n return res;\r\n }\r\n\r\n const selection = this._complexVisual.getSelectionGeo();\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n // find all geo nodes for this component\r\n _traverseComponentGroups(visual, component, (child) => {\r\n res.objects.push(child);\r\n });\r\n\r\n // find all selection nodes for this component\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component') && geo._component === component) {\r\n res.objects.push(geo);\r\n }\r\n }\r\n }\r\n\r\n // add dummy object that stores component transformation\r\n res.objects.push(this._componentTransforms[component._index]);\r\n\r\n const bbmin = new THREE.Vector3(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE);\r\n const bbmax = new THREE.Vector3(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE);\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (j = 0; j < atoms.length; ++j) {\r\n if (atoms[j].mask & selectionMask) {\r\n bbmin.min(atoms[j].position);\r\n bbmax.max(atoms[j].position);\r\n }\r\n }\r\n });\r\n\r\n res.pivot.lerpVectors(bbmin, bbmax, 0.5);\r\n return res;\r\n }\r\n\r\n _bakeComponentTransform(component) {\r\n const t = this._componentTransforms[component._index];\r\n if (t && (!(t.position.x === 0 && t.position.y === 0 && t.position.z === 0)\r\n || !(t.quaternion.x === 0 && t.quaternion.y === 0 && t.quaternion.z === 0 && t.quaternion.w === 1))) {\r\n t.updateMatrix();\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (let j = 0; j < atoms.length; ++j) {\r\n atoms[j].position.applyMatrix4(t.matrix);\r\n }\r\n });\r\n }\r\n }\r\n\r\n _resetComponentTransform() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n for (i = 0; i < this._componentTransforms.length; ++i) {\r\n geo = this._componentTransforms[i];\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n\r\n // reset all geo nodes\r\n for (i = 0; i < visual.children.length; ++i) {\r\n reprNode = visual.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n // reset all selection nodes\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ComplexFragmentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n const atoms = this._getSelectionBorderAtoms();\r\n if (atoms.length < 1 || atoms.length > 2) {\r\n logger.error('Can only edit fragments with one or two bound atoms.');\r\n return false;\r\n }\r\n\r\n this._fragmentBoundAtoms = atoms;\r\n\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n\r\n // hide selected fragment in main model\r\n visual.disableSubset(selectionMask, true);\r\n\r\n // hide selection geo in main model\r\n for (let k = 0; k < selection.children.length; ++k) {\r\n selection.children[k].visible = false;\r\n }\r\n\r\n // create visible fragment representation to rotate\r\n const pivotPos = atoms[0].position.clone();\r\n\r\n if (atoms.length === 2) {\r\n pivotPos.lerp(atoms[1].position, 0.5);\r\n }\r\n\r\n this._fragmentGeo = new THREE.Group();\r\n visual.add(this._fragmentGeo);\r\n this._fragmentGeo.position.copy(pivotPos);\r\n\r\n this._fragmentSelectionGeo = new THREE.Group();\r\n selection.add(this._fragmentSelectionGeo);\r\n this._fragmentSelectionGeo.position.copy(pivotPos);\r\n\r\n const offset = pivotPos.clone();\r\n offset.negate();\r\n\r\n for (let i = 0; i < visual.children.length; ++i) {\r\n const g = visual.children[i];\r\n if (!('getSubset' in g)) {\r\n continue;\r\n }\r\n\r\n const vg = new THREE.Group();\r\n this._fragmentGeo.add(vg);\r\n\r\n const sg = new THREE.Group();\r\n this._fragmentSelectionGeo.add(sg);\r\n\r\n const meshes = g.getSubset(selectionMask, true);\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n vg.add(m);\r\n m.position.copy(offset);\r\n }\r\n\r\n const smeshes = g.getSubset(selectionMask, true);\r\n for (let h = 0; h < smeshes.length; h++) {\r\n const sm = smeshes[h];\r\n sg.add(sm);\r\n sm.position.copy(offset);\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(this._fragmentSelectionGeo);\r\n\r\n this._inProgress = true;\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selectionBit = visual.getSelectionBit();\r\n\r\n const p = this._fragmentGeo.position;\r\n const m = this._fragmentGeo.matrix.clone();\r\n m.multiply(new THREE.Matrix4().makeTranslation(-p.x, -p.y, -p.z));\r\n\r\n this._bakeAtomTransform(m, 1 << selectionBit);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << selectionBit, true);\r\n\r\n visual.getComplex().onAtomPositionChanged();\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n this._fragmentGeo.parent.remove(this._fragmentGeo);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << visual.getSelectionBit(), true);\r\n\r\n // show selection geo in main model (+ remove fragment selection geo)\r\n for (let i = 0; i < selection.children.length; ++i) {\r\n const node = selection.children[i];\r\n if (node.visible) {\r\n selection.remove(node);\r\n } else {\r\n node.visible = true;\r\n }\r\n }\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n isFreeRotationAllowed() {\r\n return (this._fragmentBoundAtoms.length < 2);\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n res.objects.push(this._fragmentGeo, this._fragmentSelectionGeo);\r\n\r\n const boundAtoms = this._fragmentBoundAtoms;\r\n if (boundAtoms.length === 1) {\r\n if (boundAtoms[0].bonds.length === 1) {\r\n // single external bond allows rotation about bond axis\r\n const bond = boundAtoms[0].bonds[0];\r\n res.axis = new THREE.Vector3().subVectors(bond._right.position, bond._left.position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n } else if (boundAtoms.length === 2) {\r\n // two bound atoms allow rotation only about axis running through their centers\r\n res.axis = new THREE.Vector3().subVectors(boundAtoms[1].position, boundAtoms[0].position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _getSelectionBorderAtoms() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n const selectionMask = 1 << this._complexVisual.getSelectionBit();\r\n const atomHash = {};\r\n\r\n complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n atomHash[bond._left.index] = 1;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n atomHash[bond._right.index] = 1;\r\n }\r\n });\r\n\r\n const atoms = [];\r\n const keys = Object.keys(atomHash);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const idx = keys[i];\r\n atoms.push(complex._atoms[idx]);\r\n }\r\n\r\n return atoms;\r\n }\r\n\r\n _bakeAtomTransform(matrix, mask) {\r\n this._complexVisual.getComplex().forEachAtom((atom) => {\r\n if (atom.mask & mask) {\r\n atom.position.applyMatrix4(matrix);\r\n }\r\n });\r\n }\r\n}\r\n\r\nexport default {\r\n ComponentEditor: ComplexComponentEditor,\r\n FragmentEditor: ComplexFragmentEditor,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\nimport chem from './chem';\r\nimport settings from './settings';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport Visual from './Visual';\r\nimport ComplexVisualEdit from './ComplexVisualEdit';\r\nimport meshutils from './gfx/meshutils';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction lookupAndCreate(entityList, specs) {\r\n if (!Array.isArray(specs)) {\r\n specs = [specs];\r\n }\r\n const [id, opts] = specs;\r\n const Entity = entityList.get(id) || entityList.first;\r\n return new Entity(opts);\r\n}\r\n\r\nclass ComplexVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._complex = dataSource;\r\n\r\n /** @type {Representation[]} */\r\n this._reprList = [];\r\n /** @type {?Representation} */\r\n this._repr = null;\r\n this._reprListChanged = true;\r\n\r\n this._selectionBit = 0;\r\n this._reprUsedBits = 0;\r\n this._selectionCount = 0;\r\n\r\n this._selectionGeometry = new THREE.Group();\r\n }\r\n\r\n getBoundaries() {\r\n return this._complex.getBoundaries();\r\n }\r\n\r\n release() {\r\n if (this._selectionGeometry.parent) {\r\n this._selectionGeometry.remove(this._selectionGeometry);\r\n }\r\n Visual.prototype.release.call(this);\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getSelectionCount() {\r\n return this._selectionCount;\r\n }\r\n\r\n getSelectionGeo() {\r\n return this._selectionGeometry;\r\n }\r\n\r\n getSelectionBit() {\r\n return this._selectionBit;\r\n }\r\n\r\n getEditor() {\r\n return this._editor;\r\n }\r\n\r\n resetReps(reps) {\r\n // Create all necessary representations\r\n if (this._complex) {\r\n this._complex.clearAtomBits(~0);\r\n }\r\n this._reprListChanged = true;\r\n this._reprUsedBits = 0;\r\n this._reprList.length = reps.length;\r\n for (let i = 0, n = reps.length; i < n; ++i) {\r\n const rep = reps[i];\r\n\r\n let selector;\r\n let selectorString;\r\n if (typeof rep.selector === 'string') {\r\n selectorString = rep.selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else if (typeof rep.selector === 'undefined') {\r\n selectorString = settings.now.presets.default[0].selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else {\r\n ({ selector } = rep);\r\n selectorString = selector.toString();\r\n }\r\n const mode = lookupAndCreate(modes, rep.mode);\r\n const colorer = lookupAndCreate(colorers, rep.colorer);\r\n const material = materials.get(rep.material) || materials.first;\r\n\r\n this._reprList[i] = new Representation(i, mode, colorer, selector);\r\n this._reprList[i].setMaterialPreset(material);\r\n this._reprList[i].selectorString = selectorString;\r\n\r\n if (this._complex) {\r\n this._complex.markAtoms(selector, 1 << i);\r\n }\r\n\r\n this._reprUsedBits |= 1 << i;\r\n }\r\n this._repr = reps.length > 0 ? this._reprList[0] : null;\r\n\r\n this._selectionBit = reps.length;\r\n this._reprUsedBits |= 1 << this._selectionBit; // selection uses one bit\r\n this._selectionCount = 0;\r\n\r\n if (this._complex) {\r\n this._complex.update();\r\n }\r\n }\r\n\r\n /**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\n repCount() {\r\n return this._reprList.length;\r\n }\r\n\r\n /**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\n repCurrent(index) {\r\n if (index >= 0 && index < this._reprList.length) {\r\n this._repr = this._reprList[index];\r\n } else {\r\n index = this._reprList.indexOf(this._repr);\r\n }\r\n return index;\r\n }\r\n\r\n /**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {Object} {desc, index, status} field desc contains rep description, index - index of correspondent rep,\r\n * status - one of three strings: 'created', 'changed', ''. 'created' means new rep was created during this function,\r\n * 'changed' - rep was changed during this function. '' - something else.\r\n */\r\n rep(index, rep) {\r\n // if index is missing then it is the current\r\n if (!rep && (index === undefined || index instanceof Object)) {\r\n rep = index;\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index > this._reprList.length) {\r\n logger.error(`Rep ${index} does not exist!`);\r\n return null;\r\n }\r\n\r\n // a special case of adding just after the end\r\n if (index === this._reprList.length) {\r\n const res = this.repAdd(rep);\r\n logger.warn(`Rep ${index} does not exist! New representation was created.`);\r\n return { desc: res.desc, index, status: 'created' };\r\n }\r\n\r\n // gather description\r\n const target = this._reprList[index];\r\n const desc = {\r\n selector: target.selectorString,\r\n mode: target.mode.identify(),\r\n colorer: target.colorer.identify(),\r\n material: target.materialPreset.id,\r\n };\r\n\r\n // modification is requested\r\n if (rep) {\r\n // modify\r\n const diff = target.change(\r\n rep,\r\n this._complex,\r\n lookupAndCreate(modes, rep.mode),\r\n lookupAndCreate(colorers, rep.colorer),\r\n );\r\n\r\n // something was changed\r\n if (!_.isEmpty(diff)) {\r\n target.needsRebuild = true;\r\n for (const key in diff) {\r\n if (diff.hasOwnProperty(key)) {\r\n desc[key] = diff[key];\r\n logger.debug(`rep[${index}].${key} changed to ${diff[key]}`);\r\n }\r\n }\r\n\r\n // safety trick: lower resolution for surface modes\r\n if (diff.mode && target.mode.isSurface\r\n && (settings.now.resolution === 'ultra' || settings.now.resolution === 'high')) {\r\n logger.report('Surface resolution was changed to \"medium\" to avoid hang-ups.');\r\n settings.set('resolution', 'medium');\r\n }\r\n return { desc, index, status: 'changed' };\r\n }\r\n }\r\n return { desc, index, status: '' };\r\n }\r\n\r\n /**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\n repGet(index) {\r\n // if index is missing then it is the current\r\n if (index === undefined || index instanceof Object) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return null;\r\n }\r\n\r\n return this._reprList[index];\r\n }\r\n\r\n _getFreeReprIdx() {\r\n let bits = this._reprUsedBits;\r\n for (let i = 0; i <= ComplexVisual.NUM_REPRESENTATION_BITS; ++i, bits >>= 1) {\r\n if ((bits & 1) === 0) {\r\n return i;\r\n }\r\n }\r\n return -1;\r\n }\r\n\r\n /**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {Object} {desc, index} field desc contains added rep description, index - index of this rep.\r\n */\r\n repAdd(rep) {\r\n if (this._reprList.length >= ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n return null;\r\n }\r\n\r\n const newSelectionBit = this._getFreeReprIdx();\r\n if (newSelectionBit < 0) {\r\n return null; // no more slots for representations\r\n }\r\n\r\n const originalSelection = this.buildSelectorFromMask(1 << this._selectionBit);\r\n\r\n // Fill in default values\r\n const def = settings.now.presets.default[0];\r\n const desc = _.merge({\r\n selector: def.selector,\r\n mode: def.mode,\r\n colorer: def.colorer,\r\n material: def.material,\r\n }, rep);\r\n\r\n const selector = (typeof desc.selector === 'string') ? selectors.parse(desc.selector).selector : desc.selector;\r\n const target = new Representation(\r\n this._selectionBit,\r\n lookupAndCreate(modes, desc.mode),\r\n lookupAndCreate(colorers, desc.colorer),\r\n selector,\r\n );\r\n target.selectorString = selector.toString();\r\n target.setMaterialPreset(materials.get(desc.material));\r\n target.markAtoms(this._complex);\r\n this._reprList.push(target);\r\n\r\n // change selection bit\r\n this._selectionBit = newSelectionBit;\r\n this._reprUsedBits |= 1 << this._selectionBit;\r\n\r\n // restore selection using new selection bit\r\n this._complex.markAtoms(originalSelection, 1 << this._selectionBit);\r\n\r\n return { desc, index: this._reprList.length - 1 };\r\n }\r\n\r\n /**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\n repRemove(index) {\r\n if (index === undefined) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // catch out of bounds case\r\n let count = this._reprList.length;\r\n if (index < 0 || index >= count || count <= 1) { // do not allow to remove the single rep\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.unmarkAtoms(this._complex);\r\n this._reprUsedBits &= ~(1 << target.index);\r\n\r\n this._reprList.splice(index, 1);\r\n\r\n // update current rep\r\n if (target === this._repr) {\r\n --count;\r\n index = index < count ? index : count - 1;\r\n this._repr = this._reprList[index];\r\n }\r\n this._reprListChanged = true;\r\n }\r\n\r\n /**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\n repHide(index, hide) {\r\n if (hide === undefined) {\r\n hide = true;\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.show(!hide);\r\n }\r\n\r\n /**\r\n * Select atoms with selector\r\n * @param {Selector} selector - selector\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\n select(selector, append) {\r\n if (append) {\r\n this._selectionCount += this._complex.markAtomsAdditionally(selector, 1 << this._selectionBit);\r\n } else {\r\n this._selectionCount = this._complex.markAtoms(selector, 1 << this._selectionBit);\r\n }\r\n this._complex.updateStructuresMask();\r\n this.rebuildSelectionGeometry();\r\n }\r\n\r\n resetSelectionMask() {\r\n if (this._selectionCount !== 0) {\r\n this._selectionCount = 0;\r\n if (this._complex) {\r\n this._complex.clearAtomBits(1 << this._selectionBit);\r\n }\r\n }\r\n }\r\n\r\n updateSelectionMask(pickedObj) {\r\n const self = this;\r\n const { atom } = pickedObj;\r\n let { residue, chain, molecule } = pickedObj;\r\n const setMask = 1 << this._selectionBit;\r\n const clearMask = ~setMask;\r\n\r\n if (atom) {\r\n residue = atom.residue;\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (atom.mask & setMask) {\r\n atom.mask &= clearMask;\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n if (molecule) {\r\n molecule.mask &= clearMask;\r\n }\r\n this._selectionCount--;\r\n } else {\r\n atom.mask |= setMask;\r\n this._selectionCount++;\r\n\r\n // select residue if all atoms in it are selected\r\n residue.collectMask();\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (residue) {\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (residue._mask & setMask) {\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n residue.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n } else {\r\n residue._mask |= setMask;\r\n residue.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (chain || molecule) {\r\n const obj = chain || molecule;\r\n if (obj._mask & setMask) {\r\n obj._mask &= clearMask;\r\n obj.forEachResidue((r) => {\r\n if (r._mask & setMask) {\r\n r._mask &= clearMask;\r\n r.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n r._mask &= clearMask;\r\n }\r\n });\r\n } else {\r\n obj._mask |= setMask;\r\n obj.forEachResidue((r) => {\r\n if (!(r._mask & setMask)) {\r\n r._mask |= setMask;\r\n r.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n const otherObj = chain ? r.getMolecule() : r.getChain();\r\n if (otherObj) {\r\n otherObj.collectMask();\r\n }\r\n }\r\n });\r\n }\r\n } else {\r\n this.resetSelectionMask();\r\n }\r\n }\r\n\r\n expandSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms to add\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // select marked atoms\r\n const deselectionMask = ~tmpMask;\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask = (atom.mask & deselectionMask) | selectionMask;\r\n ++self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n shrinkSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms neighbouring to unselected ones\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // mark hanging atoms\r\n this._complex.forEachAtom((atom) => {\r\n if ((atom.mask & selectionMask) && (atom.bonds.length === 1)) {\r\n atom.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // deselect marked atoms\r\n const deselectionMask = ~(selectionMask | tmpMask);\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask &= deselectionMask;\r\n --self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n getSelectedComponent() {\r\n const selectionMask = 1 << this._selectionBit;\r\n\r\n let component = null;\r\n let multiple = false;\r\n\r\n // find which component is selected (exclusively)\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & selectionMask) {\r\n if (component === null) {\r\n component = atom.residue._component;\r\n } else if (component !== atom.residue._component) {\r\n multiple = true;\r\n }\r\n }\r\n });\r\n\r\n return multiple ? null : component;\r\n }\r\n\r\n getSelectionCenter(center, includesAtom, selRule) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._complex.forEachAtom((atom) => {\r\n if (includesAtom(atom, selRule)) {\r\n center.add(atom.position);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.applyMatrix4(this.matrix);\r\n return true;\r\n }\r\n\r\n needsRebuild() {\r\n if (this._reprListChanged) {\r\n return true;\r\n }\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n if (repr.needsRebuild) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n /**\r\n * Rebuild molecule geometry asynchronously.\r\n */\r\n rebuild() {\r\n const self = this;\r\n\r\n // Destroy current geometry\r\n gfxutils.clearTree(this);\r\n\r\n return new Promise(((resolve) => {\r\n // Nothing to do?\r\n const complex = self._complex;\r\n if (!complex) {\r\n resolve();\r\n return;\r\n }\r\n\r\n let errorOccured = false;\r\n setTimeout(() => {\r\n console.time('build');\r\n const reprList = self._reprList;\r\n const palette = palettes.get(settings.now.palette) || palettes.first;\r\n let hasGeometry = false;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n repr.colorer.palette = palette;\r\n\r\n if (repr.needsRebuild) {\r\n repr.reset();\r\n\r\n try {\r\n repr.buildGeometry(complex);\r\n } catch (e) {\r\n if (e instanceof utils.OutOfMemoryError) {\r\n repr.needsRebuild = false;\r\n repr.reset();\r\n logger.error(`Not enough memory to build geometry for representation ${repr.index + 1}`);\r\n errorOccured = true;\r\n } else {\r\n throw e;\r\n }\r\n }\r\n\r\n if (DEBUG && !errorOccured) {\r\n logger.debug(`Triangles count: ${meshutils.countTriangles(repr.geo)}`);\r\n }\r\n }\r\n\r\n hasGeometry = errorOccured || hasGeometry || gfxutils.groupHasGeometryToRender(repr.geo);\r\n\r\n if (repr.geo) {\r\n self.add(repr.geo);\r\n }\r\n }\r\n\r\n self._reprListChanged = false;\r\n\r\n console.timeEnd('build');\r\n resolve();\r\n }, 10);\r\n }));\r\n }\r\n\r\n setNeedsRebuild() {\r\n // invalidate all representations\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n reprList[i].needsRebuild = true;\r\n }\r\n }\r\n\r\n rebuildSelectionGeometry() {\r\n const mask = 1 << this._selectionBit;\r\n\r\n gfxutils.clearTree(this._selectionGeometry);\r\n\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const repr = this._reprList[i];\r\n const sg = repr.buildSelectionGeometry(mask);\r\n if (!sg) {\r\n continue;\r\n }\r\n\r\n this._selectionGeometry.add(sg);\r\n for (let j = 0; j < sg.children.length; j++) {\r\n const m = sg.children[j];\r\n\r\n // copy component transform (that's not applied yet)\r\n // TODO make this code obsolete, accessing editor is bad\r\n if (this._editor && this._editor._componentTransforms) {\r\n const t = this._editor._componentTransforms[m._component._index];\r\n if (t) {\r\n m.position.copy(t.position);\r\n m.quaternion.copy(t.quaternion);\r\n }\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(sg);\r\n }\r\n }\r\n\r\n _buildSelectorFromSortedLists(atoms, residues, chains) {\r\n const complex = this._complex;\r\n\r\n function optimizeList(list) {\r\n const result = [];\r\n let k = 0;\r\n let first = NaN;\r\n let last = NaN;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const value = list[i];\r\n if (value === last + 1) {\r\n last = value;\r\n } else {\r\n if (!Number.isNaN(first)) {\r\n result[k++] = new selectors.Range(first, last);\r\n }\r\n first = last = value;\r\n }\r\n }\r\n if (!Number.isNaN(first)) {\r\n result[k] = new selectors.Range(first, last);\r\n }\r\n return result;\r\n }\r\n\r\n let expression = null;\r\n if (chains.length === complex._chains.length) {\r\n expression = selectors.all();\r\n } else {\r\n let selector;\r\n if (chains.length > 0) {\r\n selector = selectors.chain(chains);\r\n expression = expression ? selectors.or(expression, selector) : selector;// NOSONAR\r\n }\r\n if (Object.keys(residues).length > 0) {\r\n for (const ch in residues) {\r\n if (residues.hasOwnProperty(ch)) {\r\n selector = selectors.and(\r\n selectors.chain(ch),\r\n selectors.residx(optimizeList(residues[ch])),\r\n );\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n }\r\n }\r\n if (atoms.length > 0) {\r\n selector = selectors.serial(optimizeList(atoms));\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n\r\n if (!expression) {\r\n expression = selectors.none();\r\n }\r\n }\r\n\r\n return expression;\r\n }\r\n\r\n buildSelectorFromMask(mask) {\r\n const complex = this._complex;\r\n const chains = [];\r\n const residues = {};\r\n const atoms = [];\r\n\r\n complex.forEachChain((chain) => {\r\n if (chain._mask & mask) {\r\n chains.push(chain._name);\r\n }\r\n });\r\n\r\n complex.forEachResidue((residue) => {\r\n if (residue._mask & mask && !(residue._chain._mask & mask)) {\r\n const c = residue._chain._name;\r\n if (!(c in residues)) {\r\n residues[c] = [residue._index];\r\n } else {\r\n residues[c].push(residue._index);\r\n }\r\n }\r\n });\r\n\r\n complex.forEachAtom((atom) => {\r\n if (atom.mask & mask && !(atom.residue._mask & mask)) {\r\n atoms.push(atom.serial);\r\n }\r\n });\r\n\r\n return this._buildSelectorFromSortedLists(atoms, residues, chains);\r\n }\r\n\r\n forSelectedResidues(process) {\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.forEachResidue((residue) => {\r\n if (residue._mask & selectionMask) {\r\n process(residue);\r\n }\r\n });\r\n }\r\n\r\n beginComponentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.ComponentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n beginFragmentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.FragmentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n // should only be called by editors\r\n finalizeEdit() {\r\n this._editor = null;\r\n }\r\n\r\n setMaterialValues(values, needTraverse = false, process = undefined) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setValues(values);\r\n if (needTraverse) {\r\n rep.geo.traverse((object) => {\r\n if (object instanceof THREE.Mesh) {\r\n object.material.setValues(values);\r\n\r\n if (process !== undefined) {\r\n process(object);\r\n }\r\n\r\n object.material.needsUpdate = true;\r\n }\r\n });\r\n }\r\n }\r\n }\r\n\r\n setUberOptions(values) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setUberOptions(values);\r\n }\r\n }\r\n\r\n /**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\n within(selector, radius) {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return false;\r\n }\r\n\r\n // mark atoms of the group as selected\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.markAtoms(selector, selectionMask);\r\n\r\n // mark all atoms within distance as selected\r\n if (vw) {\r\n vw.forEachAtomWithinDistFromMasked(this._complex, selectionMask, Number(radius), (atom) => {\r\n atom.mask |= selectionMask;\r\n });\r\n }\r\n\r\n // update selection count\r\n this._selectionCount = this._complex.countAtomsByMask(selectionMask);\r\n\r\n // update secondary structure mask\r\n this._complex.updateStructuresMask();\r\n\r\n return this.buildSelectorFromMask(selectionMask);\r\n }\r\n}\r\n// 32 bits = 30 bits for reps + 1 for selection + 1 for selection expansion\r\nComplexVisual.NUM_REPRESENTATION_BITS = 30;\r\n\r\nexport default ComplexVisual;\r\n","import * as THREE from 'three';\r\nimport vertexVolumeFaces from './VolumeFaces.vert';\r\nimport fragmentVolumeFaces from './VolumeFaces.frag';\r\nimport vertexVolume from './Volume.vert';\r\nimport fragmentVolume from './Volume.frag';\r\nimport vertexFarPlane from './VolumeFarPlane.vert';\r\nimport fragmentFarPlane from './VolumeFarPlane.frag';\r\nimport settings from '../../settings';\r\n\r\nconst volumeUniforms = THREE.UniformsUtils.merge([\r\n {\r\n volumeDim: { type: 'v3', value: new THREE.Vector3(512, 512, 512) },\r\n tileTex: { type: 't', value: null },\r\n tileTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n tileStride: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n\r\n boxAngles: { type: 'v3', value: new THREE.Vector3(1, 1, 1) },\r\n delta: { type: 'v3', value: new THREE.Vector3(0, 0, 0) },\r\n\r\n _isoLevel0: { type: 'v2', value: new THREE.Vector3(0.5, 0.75, 1.0) },\r\n _flipV: { type: 'f', value: 0.0 },\r\n _BFLeft: { type: 't', value: null },\r\n _BFRight: { type: 't', value: null },\r\n _FFLeft: { type: 't', value: null },\r\n _FFRight: { type: 't', value: null },\r\n _WFFLeft: { type: 't', value: null },\r\n _WFFRight: { type: 't', value: null },\r\n },\r\n]);\r\n\r\nfunction overrideUniforms(params, defUniforms) {\r\n const uniforms = THREE.UniformsUtils.clone(defUniforms);\r\n for (const p in params) {\r\n if (uniforms.hasOwnProperty(p)) {\r\n uniforms[p].value = params[p];\r\n }\r\n }\r\n return uniforms;\r\n}\r\n\r\nfunction facesPosMaterialParams(params, sideType) {\r\n return {\r\n uniforms: overrideUniforms(params, {}),\r\n vertexShader: vertexVolumeFaces,\r\n fragmentShader: fragmentVolumeFaces,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n side: sideType,\r\n };\r\n}\r\n\r\nclass BackFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const backFaceParams = facesPosMaterialParams(params, THREE.BackSide);\r\n super(backFaceParams);\r\n }\r\n}\r\n\r\nclass ShaderParams {\r\n constructor(params, uniforms, vertexShader, fragmentShader) {\r\n this.uniforms = overrideUniforms(params, uniforms);\r\n this.vertexShader = vertexShader;\r\n this.fragmentShader = fragmentShader;\r\n this.transparent = false;\r\n this.depthTest = false;\r\n this.depthWrite = false;\r\n this.side = THREE.FrontSide;\r\n }\r\n}\r\n\r\nclass BackFacePosMaterialFarPlane extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const matUniforms = THREE.UniformsUtils.merge([\r\n {\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n farZ: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n matWorld2Volume: { type: '4fv', value: new THREE.Matrix4() },\r\n },\r\n ]);\r\n\r\n const shaderParams = new ShaderParams(params, matUniforms, vertexFarPlane, fragmentFarPlane);\r\n super(shaderParams);\r\n }\r\n}\r\n\r\nclass FrontFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const frontFaceParams = facesPosMaterialParams(params, THREE.FrontSide);\r\n super(frontFaceParams);\r\n }\r\n}\r\n\r\nclass VolumeMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const shaderParams = new ShaderParams(params, volumeUniforms, vertexVolume, fragmentVolume);\r\n shaderParams.transparent = true;\r\n shaderParams.depthTest = true;\r\n\r\n super(shaderParams);\r\n this.updateDefines();\r\n }\r\n\r\n updateDefines() {\r\n this.defines = {\r\n ISO_MODE: settings.now.modes.VD.isoMode,\r\n STEPS_COUNT: settings.now.modes.VD.polyComplexity[settings.now.resolution] * 100,\r\n };\r\n this.needsUpdate = true;\r\n }\r\n}\r\n\r\nexport default {\r\n BackFacePosMaterial,\r\n BackFacePosMaterialFarPlane,\r\n FrontFacePosMaterial,\r\n VolumeMaterial,\r\n};\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport settings from '../settings';\r\n\r\nclass VolumeMesh extends THREE.Mesh {\r\n volumeInfo = {}; // data for noise filter\r\n\r\n constructor() {\r\n const geo = new THREE.BufferGeometry();\r\n super(geo);\r\n this.clipPlane = new THREE.Plane();\r\n const size = new THREE.Vector3(0.5, 0.5, 0.5);\r\n this.size = size;\r\n\r\n this.cullFlag = [\r\n true, true, true, true,\r\n true, true, true, true,\r\n false, false, false, false, false, false,\r\n ];\r\n\r\n this.faces = [\r\n { indices: [], norm: new THREE.Vector3(0, 0, -1) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 1) },\r\n { indices: [], norm: new THREE.Vector3(0, -1, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 1, 0) },\r\n { indices: [], norm: new THREE.Vector3(-1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 0) },\r\n ];\r\n\r\n this.vertices = [\r\n new THREE.Vector3(-size.x, -size.y, -size.z),\r\n new THREE.Vector3(-size.x, size.y, -size.z),\r\n new THREE.Vector3(size.x, -size.y, -size.z),\r\n new THREE.Vector3(size.x, size.y, -size.z),\r\n new THREE.Vector3(-size.x, -size.y, size.z),\r\n new THREE.Vector3(-size.x, size.y, size.z),\r\n new THREE.Vector3(size.x, -size.y, size.z),\r\n new THREE.Vector3(size.x, size.y, size.z),\r\n new THREE.Vector3(0.0, 0.0, 0.0), // Placeholder for section\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n ];\r\n\r\n geo.setAttribute('position', new THREE.BufferAttribute(new Float32Array(this.vertices.length * 3), 3));\r\n\r\n this.name = 'VolumeMesh';\r\n }\r\n\r\n static _corners = [\r\n // x, y, z, edge1, edge2, edge3\r\n [-1, -1, -1, 0, 4, 8],\r\n [1, -1, -1, 0, 5, 9],\r\n [1, 1, -1, 1, 5, 10],\r\n [-1, 1, -1, 1, 4, 11],\r\n [-1, -1, 1, 2, 6, 8],\r\n [1, -1, 1, 2, 7, 9],\r\n [1, 1, 1, 3, 7, 10],\r\n [-1, 1, 1, 3, 6, 11],\r\n ];\r\n\r\n static _edges = [\r\n // corner1, corner2, center_x, center_y, center_z\r\n [0, 1, 0, -1, -1],\r\n [2, 3, 0, 1, -1],\r\n [4, 5, 0, -1, 1],\r\n [6, 7, 0, 1, 1],\r\n [0, 3, -1, 0, -1],\r\n [1, 2, 1, 0, -1],\r\n [4, 7, -1, 0, 1],\r\n [5, 6, 1, 0, 1],\r\n [0, 4, -1, -1, 0],\r\n [1, 5, 1, -1, 0],\r\n [2, 6, -1, 1, 0],\r\n [3, 7, 1, 1, 0],\r\n ];\r\n\r\n static _edgeIntersections = (function () {\r\n const edgeIntersections = [];\r\n for (let j = 0; j < 12; ++j) {\r\n edgeIntersections.push(new THREE.Vector3());\r\n }\r\n return edgeIntersections;\r\n }());\r\n\r\n _updateVertices() {\r\n // Algorithm:\r\n // 1. Get plane parameters\r\n // 2. Compute culling flags for all vertices\r\n // 3. If intersection occurs => compute from 3 to 6 intersection points\r\n const corners = VolumeMesh._corners;\r\n const edges = VolumeMesh._edges;\r\n const edgeIntersections = VolumeMesh._edgeIntersections;\r\n\r\n let i;\r\n\r\n const norm = this.clipPlane.normal;\r\n const D = this.clipPlane.constant;\r\n\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n const cornerMark = [0, 0, 0, 0, 0, 0, 0, 0];\r\n const edgeMark = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1];\r\n\r\n const curEdge = new THREE.Vector3();\r\n let curEdgeInter = null;\r\n\r\n function CheckX() {\r\n if (norm.x === 0) return 0;\r\n const x = -(norm.dot(curEdge) + D) / norm.x;\r\n if (-size.x <= x && x <= size.x) {\r\n curEdgeInter.set(x, curEdge.y, curEdge.z);\r\n if (x === size.x) return 2;\r\n if (x === -size.x) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckY() {\r\n if (norm.y === 0) return 0;\r\n const y = -(norm.dot(curEdge) + D) / norm.y;\r\n if (-size.y <= y && y <= size.y) {\r\n curEdgeInter.set(curEdge.x, y, curEdge.z);\r\n if (y === size.y) return 2;\r\n if (y === -size.y) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckZ() {\r\n if (norm.z === 0) return 0;\r\n const z = -(norm.dot(curEdge) + D) / norm.z;\r\n if (-size.z <= z && z <= size.z) {\r\n curEdgeInter.set(curEdge.x, curEdge.y, z);\r\n if (z === size.z) return 2;\r\n if (z === -size.z) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n // for each edge\r\n for (let curEdgeIdx = 0; curEdgeIdx < 12; ++curEdgeIdx) {\r\n const curEdgeSource = edges[curEdgeIdx];\r\n curEdgeInter = edgeIntersections[curEdgeIdx];\r\n\r\n curEdge.set(curEdgeSource[2], curEdgeSource[3], curEdgeSource[4]);\r\n curEdge.multiply(size);\r\n\r\n // calculate intersection point\r\n let flag = 0;\r\n if (curEdgeSource[2] === 0) flag = CheckX();\r\n if (curEdgeSource[3] === 0) flag = CheckY();\r\n if (curEdgeSource[4] === 0) flag = CheckZ();\r\n\r\n // mark corresponding corner (if plane cuts through one)\r\n if (flag === -2) {\r\n cornerMark[curEdgeSource[0]] = 1;\r\n } else if (flag === 2) {\r\n cornerMark[curEdgeSource[1]] = 1;\r\n } else if (flag === 0) {\r\n // edge is not intersected by the plane (doesn't produce a vertex)\r\n edgeMark[curEdgeIdx] = 0;\r\n }\r\n }\r\n\r\n const face = {\r\n indices: [],\r\n norm: norm.clone().negate(),\r\n };\r\n\r\n let nextVertex = 8;\r\n\r\n // for each marked corner\r\n for (i = 0; i < 8; ++i) {\r\n if (cornerMark[i] === 1) {\r\n // add corner as vertex to the face\r\n vert[nextVertex].set(corners[i][0], corners[i][1], corners[i][2]).multiply(size);\r\n face.indices.push(nextVertex++);\r\n // skip adjacent edges\r\n edgeMark[corners[i][3]] = 0;\r\n edgeMark[corners[i][4]] = 0;\r\n edgeMark[corners[i][5]] = 0;\r\n }\r\n }\r\n\r\n // for each edge that has internal intersection\r\n for (i = 0; i < 12; ++i) {\r\n if (edgeMark[i] === 1) {\r\n // add intersection point as vertex to the face\r\n vert[nextVertex].copy(edgeIntersections[i]);\r\n face.indices.push(nextVertex++);\r\n }\r\n }\r\n\r\n this.faces[6] = face;\r\n\r\n const diff = new THREE.Vector3();\r\n const coplanarPoint = new THREE.Vector3();\r\n this.clipPlane.coplanarPoint(coplanarPoint);\r\n for (i = 0; i < vert.length; ++i) {\r\n this.cullFlag[i] = false;\r\n if (i < 8) {\r\n // corners should be culled by clipping plane\r\n diff.subVectors(vert[i], coplanarPoint);\r\n this.cullFlag[i] = (norm.dot(diff) >= 0.0);\r\n } else if (i < 8 + face.indices.length) {\r\n // cross section vertices don't get culled\r\n this.cullFlag[i] = true;\r\n }\r\n }\r\n\r\n // write data to vertex buffer\r\n const positions = this.geometry.getAttribute('position');\r\n let idx = 0;\r\n for (i = 0; i < vert.length; ++i) {\r\n positions.array[idx++] = vert[i].x;\r\n positions.array[idx++] = vert[i].y;\r\n positions.array[idx++] = vert[i].z;\r\n }\r\n positions.needsUpdate = true;\r\n }\r\n\r\n _collectVertices(face, filter) {\r\n let i;\r\n const vert = this.vertices;\r\n face.indices = [];\r\n for (i = 0; i < vert.length; ++i) {\r\n if (this.cullFlag[i] && filter(vert[i])) {\r\n face.indices.push(i);\r\n }\r\n }\r\n }\r\n\r\n _sortIndices(face, right) {\r\n let i;\r\n let j;\r\n const vert = this.vertices;\r\n const angle = [];\r\n\r\n const dir = new THREE.Vector3();\r\n for (i = 1; i < face.indices.length; ++i) {\r\n dir.subVectors(vert[face.indices[i]], vert[face.indices[0]]);\r\n dir.normalize();\r\n dir.cross(right);\r\n dir.negate();\r\n angle[i] = face.norm.dot(dir);\r\n }\r\n\r\n // Exchange sort\r\n for (i = 1; i < face.indices.length - 1; ++i) {\r\n for (j = i + 1; j < face.indices.length; ++j) {\r\n if (angle[j] < angle[i]) {\r\n // swap\r\n let t = angle[i];\r\n angle[i] = angle[j];\r\n angle[j] = t;\r\n\r\n t = face.indices[i];\r\n face.indices[i] = face.indices[j];\r\n face.indices[j] = t;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _updateIndices() {\r\n // Algorithm:\r\n // 1. Get plane vertices (from 3 to 6 vertices)\r\n // 2. Get \"right\" vector in plane\r\n // 3. Sort vertices using Graham-like method\r\n // 4. Create indices\r\n\r\n let i;\r\n let faceIdx;\r\n let face;\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n this._collectVertices(this.faces[0], (vertex) => vertex.z === -size.z);\r\n this._collectVertices(this.faces[1], (vertex) => vertex.z === size.z);\r\n this._collectVertices(this.faces[2], (vertex) => vertex.y === -size.y);\r\n this._collectVertices(this.faces[3], (vertex) => vertex.y === size.y);\r\n this._collectVertices(this.faces[4], (vertex) => vertex.x === -size.x);\r\n this._collectVertices(this.faces[5], (vertex) => vertex.x === size.x);\r\n\r\n const vCenter = new THREE.Vector3();\r\n const vRight = new THREE.Vector3();\r\n const vDir = new THREE.Vector3();\r\n\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n\r\n if (face.indices.length === 0) continue;\r\n\r\n vCenter.set(0, 0, 0);\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vCenter.add(vert[face.indices[i]]);\r\n }\r\n vCenter.multiplyScalar(1.0 / face.indices.length);\r\n vRight.subVectors(vert[face.indices[0]], vCenter);\r\n vRight.normalize();\r\n\r\n const rightProj = [];\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vDir.subVectors(vert[face.indices[i]], vCenter);\r\n rightProj[i] = vDir.dot(vRight);\r\n }\r\n for (i = 1; i < face.indices.length; ++i) {\r\n if (rightProj[i] < rightProj[0]) {\r\n // swap\r\n let t = rightProj[0];\r\n rightProj[0] = rightProj[i];\r\n rightProj[i] = t;\r\n\r\n [t] = face.indices;\r\n face.indices[0] = face.indices[i];\r\n face.indices[i] = t;\r\n }\r\n }\r\n\r\n this._sortIndices(face, vRight);\r\n }\r\n\r\n let numIndices = 0;\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n if (face.indices.length >= 3) {\r\n numIndices += 3 * (face.indices.length - 2);\r\n }\r\n }\r\n let offset = 0;\r\n const indices = new Uint16Array(numIndices);\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n for (i = 0; i < face.indices.length - 2; ++i) {\r\n indices[offset] = face.indices[0]; // eslint-disable-line prefer-destructuring\r\n indices[offset + 1] = face.indices[i + 1];\r\n indices[offset + 2] = face.indices[i + 2];\r\n offset += 3;\r\n }\r\n }\r\n\r\n this.geometry.setIndex(new THREE.BufferAttribute(indices, 1));\r\n }\r\n\r\n setDataSource(dataSource) {\r\n const vm = new VolumeMaterial.VolumeMaterial();\r\n const dim = dataSource.getDimensions();\r\n const stride = dataSource.getTiledTextureStride();\r\n const texture = dataSource.buildTiledTexture();\r\n const bbox = dataSource.getBox();\r\n vm.uniforms.volumeDim.value.set(dim[0], dim[1], dim[2]);\r\n vm.uniforms.tileTex.value = texture;\r\n vm.uniforms.tileTexSize.value.set(texture.image.width, texture.image.height);\r\n vm.uniforms.tileStride.value.set(stride[0], stride[1]);\r\n Object.assign(this.volumeInfo, dataSource.getVolumeInfo());\r\n\r\n const volInfo = this.volumeInfo;\r\n vm.uniforms.delta.value.copy(volInfo.delta);\r\n vm.uniforms.boxAngles.value.set(volInfo.obtuseAngle[0], volInfo.obtuseAngle[1], volInfo.obtuseAngle[2]);\r\n\r\n this.material = vm;\r\n\r\n bbox.getSize(this.scale);\r\n bbox.getCenter(this.position);\r\n }\r\n\r\n _updateIsoLevel() {\r\n const { kSigma, kSigmaMed, kSigmaMax } = settings.now.modes.VD;\r\n const volInfo = this.volumeInfo;\r\n const mean = volInfo.dmean - volInfo.dmin;\r\n const span = volInfo.dmax - volInfo.dmin;\r\n const level = (k) => (mean + k * volInfo.sd) / span;\r\n this.material.uniforms._isoLevel0.value.set(level(kSigma), level(kSigmaMed), level(kSigmaMax));\r\n }\r\n\r\n static _nearClipPlaneOffset = 0.2;\r\n\r\n static _pos = new THREE.Vector3();\r\n\r\n static _norm = new THREE.Vector3();\r\n\r\n static _norm4D = new THREE.Vector4();\r\n\r\n static _matrixWorldToLocal = new THREE.Matrix4();\r\n\r\n static _clipPlane = new THREE.Plane();\r\n\r\n rebuild(camera) {\r\n const nearClipPlaneOffset = VolumeMesh._nearClipPlaneOffset;\r\n const pos = VolumeMesh._pos;\r\n const norm = VolumeMesh._norm;\r\n const norm4D = VolumeMesh._norm4D;\r\n const matrixWorldToLocal = VolumeMesh._matrixWorldToLocal;\r\n const clipPlane = VolumeMesh._clipPlane;\r\n\r\n this._updateIsoLevel();\r\n\r\n // get clip plane in local space\r\n camera.getWorldDirection(norm);\r\n camera.getWorldPosition(pos);\r\n pos.addScaledVector(norm, camera.near + nearClipPlaneOffset);\r\n\r\n // transform pos to local CS\r\n matrixWorldToLocal.copy(this.matrixWorld).invert();\r\n pos.applyMatrix4(matrixWorldToLocal);\r\n\r\n // transform norm to local CS\r\n norm4D.set(norm.x, norm.y, norm.z, 0.0); // NOTE: use homogeneous norm for proper transformation\r\n norm4D.applyMatrix4(matrixWorldToLocal);\r\n norm.copy(norm4D);\r\n norm.normalize();\r\n\r\n clipPlane.setFromNormalAndCoplanarPoint(norm, pos);\r\n\r\n if (!this.clipPlane.equals(clipPlane)) {\r\n this.clipPlane = clipPlane.clone();\r\n this._updateVertices();\r\n this._updateIndices();\r\n }\r\n }\r\n}\r\n\r\nexport default VolumeMesh;\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _flattenArray(input) {\r\n const n = input.length;\r\n const output = new Float32Array(n * 3);\r\n for (let i = 0; i < n; ++i) {\r\n const j = 3 * i;\r\n const v = input[i];\r\n output[j] = v.x;\r\n output[j + 1] = v.y;\r\n output[j + 2] = v.z;\r\n }\r\n return output;\r\n}\r\n\r\nclass VolumeBounds {\r\n static _projectionTable = { // corresponds between (origin axes and angles between them) and between saving vector coordinates\r\n XY: ['x', 2],\r\n XZ: ['y', 1],\r\n YZ: ['z', 0],\r\n };\r\n\r\n constructor(bBox, volInfo) {\r\n const { delta } = volInfo; // {x: XY, y : XZ, z: YZ}\r\n const { obtuseAngle } = volInfo; // 1 - obtuse, 0 - acute\r\n\r\n const bSize = new THREE.Vector3();\r\n bBox.getSize(bSize);\r\n bSize.multiplyScalar(0.5);\r\n\r\n const offsetVert = this._getBaseVertices(delta, obtuseAngle);\r\n\r\n const geometry = new THREE.BufferGeometry();\r\n const vertices = [];\r\n\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(offsetVert[i].clone().multiply(bSize));\r\n vertices.push(offsetVert[(i + 1) % 4].clone().multiply(bSize));\r\n }\r\n const translation = new THREE.Vector3(2 * bSize.x * (1 - delta.x - delta.y), 0, 0);\r\n for (let i = 0; i < 8; i++) {\r\n vertices.push(vertices[i].clone().add(translation));\r\n }\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(vertices[i * 2].clone());\r\n vertices.push(vertices[i * 2 + 8].clone());\r\n }\r\n const center = new THREE.Vector3();\r\n bBox.getCenter(center);\r\n vertices.forEach((vertex) => vertex.add(center)); // pivot shift\r\n\r\n const flatVertices = _flattenArray(vertices);\r\n geometry.setAttribute('position', new THREE.BufferAttribute(flatVertices, 3));\r\n\r\n this._lines = new THREE.LineSegments(geometry, new THREE.LineBasicMaterial({ color: 0xFFFFFF }));\r\n this._lines.layers.set(gfxutils.LAYERS.VOLUME);\r\n }\r\n\r\n // Set one edge (4 points) of frame, from which with parallel transfer the rest of the frame points can be obtained\r\n _getBaseVertices(delta, obtuseAngle) {\r\n const projTable = VolumeBounds._projectionTable;\r\n\r\n const proj = ((index, inv) => { // tricky function to take account of projections: their position(related to box) and sign\r\n const currDelta = delta[projTable[index][0]];\r\n const angleValue = -0.5 * (inv - 1) + inv * obtuseAngle[projTable[index][1]];// inv = 1: alpha; inv = -1: 1 - alpha\r\n return angleValue * currDelta;\r\n });\r\n\r\n const offsetVert = [\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', 1)), -1 + 2 * proj('YZ', 1), -1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', 1)), -1 + 2 * proj('YZ', -1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', -1)), 1 - 2 * proj('YZ', 1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', -1)), 1 - 2 * proj('YZ', -1), -1),\r\n ];\r\n\r\n return offsetVert;\r\n }\r\n\r\n getMesh() {\r\n return this._lines;\r\n }\r\n}\r\n\r\nexport default VolumeBounds;\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport meshes from './meshes/meshes';\r\nimport gfxutils from './gfxutils';\r\n\r\n// Thes geometric far plane is required for correct filling in the BFTexture in case, when far plane cuts the volume\r\n// cube. In cut place of cube there is no correct data in BFTexture and volume rendering integral is calculated\r\n// with errors.\r\n// Far plane cuts the cube in case of large volume scale (zoom), because farplane doesn't change\r\nclass VolumeFarPlane {\r\n // create plane with unit corners coords (for future rescale in vshader according to camera properties)\r\n constructor(volume, width, height) {\r\n const planeGeo = this._initPlaneGeo(width, height);\r\n\r\n const mat = new VolumeMaterial.BackFacePosMaterialFarPlane();\r\n this._plane = new meshes.Mesh(planeGeo, mat);\r\n this._plane.frustumCulled = false;\r\n this._plane.doubleSided = true;\r\n const matWorldToVolume = new THREE.Matrix4();\r\n\r\n this._plane._onBeforeRender = function (_renderer, _scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!volume || !material) {\r\n return;\r\n }\r\n\r\n // count point in world at farplane place\r\n const planeCamPos = new THREE.Vector4(0, 0, -(camera.far - 0.1), 1);\r\n planeCamPos.applyMatrix4(camera.matrixWorld);\r\n\r\n // recalc matrices to make plane be placed as farplane in the World relative to camera\r\n this.matrix.identity();\r\n this.matrix.makeTranslation(planeCamPos.x, planeCamPos.y, planeCamPos.z);\r\n this.matrixWorld.copy(this.matrix);\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n this.normalMatrix.getNormalMatrix(this.modelViewMatrix);\r\n\r\n // build worldToVolume matrix to transform plane into volumeCS (volumeCS coords are written to BackFaceTexture)\r\n const volumeMatrix = volume.matrixWorld;\r\n matWorldToVolume.copy(volumeMatrix).invert();\r\n\r\n // update material props\r\n material.uniforms.aspectRatio.value = camera.aspect;\r\n material.uniforms.farZ.value = camera.far;\r\n material.uniforms.tanHalfFOV.value = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * camera.fov);\r\n material.uniforms.matWorld2Volume.value = matWorldToVolume;\r\n };\r\n\r\n // set it to special layer to draw only into BFTexture\r\n this._plane.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n }\r\n\r\n _initPlaneGeo(width, height) {\r\n const planeGeo = new THREE.BufferGeometry();\r\n\r\n width = width || 1;\r\n height = height || 1;\r\n\r\n const vertices = new Float32Array([\r\n -0.5 * width, 0.5 * height, 0,\r\n 0.5 * width, 0.5 * height, 0,\r\n -0.5 * width, -0.5 * height, 0,\r\n 0.5 * width, -0.5 * height, 0,\r\n ]);\r\n\r\n planeGeo.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n planeGeo.setIndex([0, 2, 1, 2, 3, 1]);\r\n\r\n return planeGeo;\r\n }\r\n\r\n getMesh() {\r\n return this._plane;\r\n }\r\n}\r\n\r\nexport default VolumeFarPlane;\r\n","import * as THREE from 'three';\r\nimport VolumeMesh from './gfx/VolumeMesh';\r\nimport VolumeBounds from './gfx/VolumeBounds';\r\nimport VolumeFarPlane from './gfx/VolumeFarPlane';\r\nimport Visual from './Visual';\r\nimport settings from './settings';\r\n\r\nclass VolumeVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._mesh = new VolumeMesh();\r\n this._mesh.setDataSource(dataSource);\r\n this.add(this._mesh);\r\n\r\n this._frame = new VolumeBounds(this.getBoundaries().boundingBox, this._mesh.volumeInfo);\r\n this.add(this._frame.getMesh());\r\n this.showFrame(settings.now.modes.VD.frame);\r\n\r\n this._farPlane = new VolumeFarPlane(this._mesh, 2, 2);\r\n this.add(this._farPlane.getMesh());\r\n }\r\n\r\n getBoundaries() {\r\n const box = this._dataSource.getBox();\r\n const sphere = new THREE.Sphere();\r\n box.getBoundingSphere(sphere);\r\n\r\n return {\r\n boundingBox: box,\r\n boundingSphere: sphere,\r\n };\r\n }\r\n\r\n getMesh() {\r\n return this._mesh;\r\n }\r\n\r\n showFrame(needShow) {\r\n this._frame.getMesh().material.visible = needShow;\r\n }\r\n}\r\n\r\nexport default VolumeVisual;\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available loaders.\r\n * @extends EntityList\r\n */\r\nclass LoaderList extends EntityList {\r\n /**\r\n * Create a list of loaders.\r\n * The loaders are indexed by supported source types (`.types` property of a Loader\r\n * subclass).\r\n * The loaders can be retrieved later by matching against specs (see {@link LoaderList#find}).\r\n *\r\n * @param {!Array=} someLoaders A list of {@link Loader} subclasses to\r\n * automatically register at creation time.\r\n * @see LoaderList#register\r\n */\r\n constructor(someLoaders = []) {\r\n super(someLoaders, ['types']);\r\n }\r\n\r\n /**\r\n * Find a suitable loader for a source type.\r\n *\r\n * @param {Object} specs Loader specifications.\r\n * @param {string=} specs.type Supported source type.\r\n * @param {*=} specs.source Source to load from.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.type) {\r\n list = this._dict.types[specs.type.toLowerCase()] || [];\r\n } else if (specs.source) {\r\n return this._list.filter((SomeLoader) => SomeLoader.canProbablyLoad && SomeLoader.canProbablyLoad(specs.source));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default LoaderList;\r\n","import EventDispatcher from '../../utils/EventDispatcher';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Loader extends EventDispatcher {\r\n constructor(source, options) {\r\n super();\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n this._agent = null;\r\n }\r\n\r\n load() {\r\n return Promise.reject(new Error('Loading from this source is not implemented'));\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n if (this._agent) {\r\n this._agent.abort();\r\n }\r\n }\r\n\r\n static extractName(_source) {\r\n return undefined;\r\n }\r\n}\r\n\r\nmakeContextDependent(Loader.prototype);\r\n","import Loader from './Loader';\r\n\r\nexport default class FileLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = options.binary === true;\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const blob = this._source;\r\n const reader = this._agent = new FileReader();\r\n\r\n reader.addEventListener('load', () => {\r\n resolve(reader.result);\r\n });\r\n reader.addEventListener('error', () => {\r\n reject(reader.error);\r\n });\r\n reader.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n reader.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n if (this._binary) {\r\n reader.readAsArrayBuffer(blob);\r\n } else {\r\n reader.readAsText(blob);\r\n }\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return (File && source instanceof File) || (Blob && source instanceof Blob);\r\n }\r\n\r\n static extractName(source) {\r\n return source && source.name;\r\n }\r\n}\r\n\r\nFileLoader.types = ['file', 'blob'];\r\n","import _ from 'lodash';\r\nimport Loader from './Loader';\r\n\r\n// we don't need to detect all kinds of URLs, just the evident ones\r\nconst urlStartRegexp = /^(https?|ftp):\\/\\//i;\r\n\r\nexport default class XHRLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = (options.binary === true);\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const url = this._source;\r\n const request = this._agent = new XMLHttpRequest();\r\n\r\n request.addEventListener('load', () => {\r\n if (request.status === 200) {\r\n resolve(request.response);\r\n } else {\r\n reject(new Error(`HTTP ${request.status} while fetching ${url}`));\r\n }\r\n });\r\n request.addEventListener('error', () => {\r\n reject(new Error('HTTP request failed'));\r\n });\r\n request.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n request.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n request.open('GET', url);\r\n if (this._binary) {\r\n request.responseType = 'arraybuffer';\r\n } else {\r\n request.responseType = 'text';\r\n }\r\n request.send();\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return _.isString(source) && urlStartRegexp.test(source);\r\n }\r\n\r\n static extractName(source) {\r\n if (source) {\r\n const last = (source.indexOf('?') + 1 || source.lastIndexOf('#') + 1 || source.length + 1) - 1;\r\n return source.slice(source.lastIndexOf('/', last) + 1, last);\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nXHRLoader.types = ['url'];\r\n","import Loader from './Loader';\r\n\r\nexport default class ImmediateLoader extends Loader {\r\n load() {\r\n return new Promise((resolve) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n resolve(this._source);\r\n });\r\n }\r\n\r\n static canProbablyLoad(_source) {\r\n return false;\r\n }\r\n}\r\n\r\nImmediateLoader.types = ['immediate'];\r\n","import LoaderList from './loaders/LoaderList';\r\n\r\nimport FileLoader from './loaders/FileLoader';\r\nimport XHRLoader from './loaders/XHRLoader';\r\nimport ImmediateLoader from './loaders/ImmediateLoader';\r\n\r\nexport default new LoaderList([\r\n // note: order might be important\r\n FileLoader,\r\n XHRLoader,\r\n ImmediateLoader,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available parsers.\r\n * @extends EntityList\r\n */\r\nclass ParserList extends EntityList {\r\n /**\r\n * Create a list of parsers.\r\n * The parsers are indexed by supported data formats and file extensions (`.formats` and\r\n * `.extensions` properties of a Parser subclass).\r\n * The parsers can be retrieved later by matching against specs (see {@link ParsrerList#find}).\r\n *\r\n * @param {!Array=} someParsers A list of {@link Parser} subclasses to\r\n * automatically register at creation time.\r\n * @see ParserList#register\r\n */\r\n constructor(someParsers = []) {\r\n super(someParsers, ['formats', 'extensions']);\r\n }\r\n\r\n /**\r\n * Find a suitable parser for data.\r\n *\r\n * @param {Object} specs Parser specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {string=} specs.ext Supported filename extension.\r\n * @param {*=} specs.data Data to parse.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n } else if (specs.ext) {\r\n list = this._dict.extensions[specs.ext.toLowerCase()] || [];\r\n }\r\n // autodetect only if no format is forced\r\n if (list.length === 0 && !specs.format && specs.data) {\r\n return this._list.filter((SomeParser) => SomeParser.canProbablyParse && SomeParser.canProbablyParse(specs.data));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ParserList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Parser {\r\n constructor(data, options) {\r\n this._data = data;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n parseSync() {\r\n throw new Error('Parsing this type of data is not implemented');\r\n }\r\n\r\n parse() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Parsing aborted'));\r\n }\r\n return resolve(this.parseSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n // only for volume Parsers\r\n getModel() {\r\n this.model._parseHeader(this._data);\r\n return this.model;\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Parser.prototype);\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 290\".\r\n *\r\n * @exports Remark290\r\n * @constructor\r\n */\r\nclass Remark290 {\r\n constructor() {\r\n /** @type {THREE.Matrix4[]} */\r\n this.matrices = [];\r\n\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (stream.readString(12, 18) === ' SMTRY') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === this.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n }\r\n }\r\n}\r\n\r\nRemark290.prototype.id = 290;\r\n\r\nexport default Remark290;\r\n","import * as THREE from 'three';\r\nimport chem from '../../../chem';\r\n\r\nconst { Assembly } = chem;\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 350\".\r\n *\r\n * @exports Remark350\r\n * @constructor\r\n */\r\nclass Remark350 {\r\n constructor(complex) {\r\n /** @type {Complex} */\r\n this._complex = complex;\r\n /** @type {Assembly[]} */\r\n this.assemblies = [];\r\n\r\n /** @type {?Assembly} */\r\n this._assembly = null;\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?Assembly} */\r\n let assembly = this._assembly;\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (assembly && stream.readString(12, 18) === ' BIOMT') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === assembly.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n } else if (assembly && stream.readString(35, 41) === 'CHAINS:') {\r\n const entries = stream.readString(42, 80).split(',');\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const chain = entries[i].trim();\r\n if (chain.length > 0) {\r\n assembly.addChain(chain);\r\n }\r\n }\r\n } else if (stream.readString(12, 23) === 'BIOMOLECULE:') {\r\n // assert molIndex === this.assemblies.length + 1\r\n this._matrix = null;\r\n this._matrixIndex = -1;\r\n this._assembly = assembly = new Assembly(this._complex);\r\n this.assemblies.push(assembly);\r\n }\r\n }\r\n}\r\n\r\nRemark350.prototype.id = 350;\r\n\r\nexport default Remark350;\r\n","/** Helper class for stream-like reading input files. */\r\nclass PDBStream {\r\n /**\r\n * Create a stream\r\n * @param {String} data Input data\r\n */\r\n constructor(data) {\r\n /** @type String */\r\n this._data = data; // Input file\r\n /** @type Number */\r\n this._start = 0; // Starting position of line\r\n /** @type Number */\r\n this._nextCR = -1; // Position of next CR (0x0D)\r\n /** @type Number */\r\n this._nextLF = -1; // Position of next LF (0x0A)\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n /** @type Number */\r\n this._end = data.length; // End of data\r\n\r\n this.next();\r\n }\r\n\r\n /**\r\n * Reading next line.\r\n * @returns {String} Next line in data (ending with LF or CR)\r\n */\r\n readLine() {\r\n return this._data.slice(this._start, this._next);\r\n }\r\n\r\n /**\r\n * Reading character from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {String} Character from position\r\n */\r\n readChar(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data[pos] : ' ';\r\n }\r\n\r\n /**\r\n * Reading character code from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {Number} Character code from position\r\n */\r\n readCharCode(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data.charCodeAt(pos) : 32;\r\n }\r\n\r\n /**\r\n * Reading string from begin to end points.\r\n * For a reason unknown, numbering assumed not to start from 0, but from 1.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {String} String from begin to end\r\n */\r\n readString(begin, end) {\r\n const from = this._start + begin - 1;\r\n const to = this._start + end;\r\n return this._data.slice(from, to < this._next ? to : this._next);\r\n }\r\n\r\n /**\r\n * Reading integer from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Integer from begin to end\r\n */\r\n readInt(begin, end) {\r\n return parseInt(this.readString(begin, end), 10);\r\n }\r\n\r\n /**\r\n * Reading float from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Float from begin to end\r\n */\r\n readFloat(begin, end) {\r\n return parseFloat(this.readString(begin, end));\r\n }\r\n\r\n /**\r\n * Checking for end of data.\r\n * @returns {boolean} True if data is ended, false otherwise\r\n */\r\n end() {\r\n return this._start >= this._end;\r\n }\r\n\r\n /**\r\n * Procedure to re-arrange current pointers in data.\r\n */\r\n next() {\r\n const start = this._next + 1;\r\n this._start = start < this._end ? start : this._end;\r\n\r\n // support CR, LF, CR+LF line endings\r\n // do not support LF+CR, CR+CR+LF, and other strange combinations\r\n\r\n if (this._start > this._nextCR) {\r\n this._nextCR = (this._data.indexOf('\\r', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n if (this._start > this._nextLF) {\r\n this._nextLF = (this._data.indexOf('\\n', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n this._next = this._nextCR + 1 < this._nextLF ? this._nextCR : this._nextLF;\r\n }\r\n}\r\n\r\nexport default PDBStream;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport Remark290 from './pdb/Remark290';\r\nimport Remark350 from './pdb/Remark350';\r\nimport PDBStream from './PDBStream';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst TAG_LENGTH = 6;\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\n// the most frequently used beginnings; although HEADER is mandatory, it is often missing in handmade files\r\nconst pdbStartRegexp = /^(HEADER\\s|COMPND\\s|REMARK\\s|ATOM {2}|HETATM|MODEL )/i;\r\n\r\nconst remarkParsers = {\r\n // NOTE: please forget the idea to build the method name in runtime, it can be obfuscated.\r\n 290: Remark290,\r\n 350: Remark350,\r\n};\r\n\r\nclass PDBParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._sheet = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._compaundFound = false;\r\n this._biomoleculeFound = false;\r\n this._allowedChainsIDs = null;\r\n this._lastMolId = -1;\r\n\r\n this._remarks = {};\r\n this._remark = null;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n this._compndCurrToken = '';\r\n\r\n this._options.fileType = 'pdb';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && pdbStartRegexp.test(data);\r\n }\r\n\r\n _finalize() {\r\n this._fixBondsArray();\r\n this._fixChains();\r\n\r\n // keep crystallographic symmetry transformations\r\n const remark290 = this._remarks[290];\r\n this._complex.symmetry = _.isUndefined(remark290) ? [] : remark290.matrices;\r\n\r\n // add loaded biological assemblies\r\n const remark350 = this._remarks[350];\r\n this._complex.units = this._complex.units.concat(_.isUndefined(remark350) ? [] : remark350.assemblies);\r\n\r\n // add loaded macromolecules\r\n this._finalizeMolecules();\r\n\r\n // create secondary structure etc.\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _finalizeMolecules() {\r\n // get chains from complex\r\n const chainDict = {};\r\n let i;\r\n const chains = this._complex._chains;\r\n for (i = 0; i < chains.length; ++i) {\r\n const chainObj = chains[i];\r\n const chainName = chainObj._name;\r\n chainDict[chainName] = chainObj;\r\n }\r\n\r\n // aggregate residues from chains\r\n for (i = 0; i < this._molecules.length; i++) {\r\n const m = this._molecules[i];\r\n let residues = [];\r\n for (let j = 0; j < m._chains.length; j++) {\r\n const name = m._chains[j];\r\n const chain = chainDict[name];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, m._name, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _fixChains() {\r\n const idChainMap = {};\r\n const complex = this._complex;\r\n\r\n // prepare\r\n for (let i = 0; i < complex._chains.length; i++) {\r\n const chain = complex._chains[i];\r\n idChainMap[chain._name.charCodeAt(0)] = chain;\r\n }\r\n }\r\n\r\n // FIXME: This function is redundant, CONECT records always follow ATOM and HETATM. Build the map online.\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseATOM(stream) {\r\n if (this._modelId !== 1) {\r\n return;\r\n }\r\n\r\n const het = stream.readCharCode(1) === 0x48;\r\n\r\n // field names according to wwPDB Format\r\n // NOTE: Chimera allows (nonstandard) use of columns 6-11 for the integer atom serial number in ATOM records.\r\n const serial = het ? stream.readInt(7, 11) : stream.readInt(6, 11);\r\n let name = stream.readString(13, 16);\r\n const altLoc = stream.readChar(17);\r\n const resName = stream.readString(18, 20).trim();\r\n const chainID = stream.readChar(22);\r\n const resSeq = stream.readInt(23, 26);\r\n const iCode = stream.readChar(27);\r\n const x = stream.readFloat(31, 38);\r\n const y = stream.readFloat(39, 46);\r\n const z = stream.readFloat(47, 54);\r\n const occupancy = stream.readFloat(55, 60);\r\n const tempFactor = stream.readFloat(61, 66);\r\n const element = stream.readString(77, 78).trim() || nameToElement(name);\r\n const charge = stream.readInt(79, 80) || 0;\r\n\r\n // skip waters (there may be lots of them)\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n // PDB uses positional system for atom names. It helps derive element type from the name\r\n // but names may include extra spaces. From this point on we don't need those spaces anymore.\r\n name = name.trim();\r\n\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name]; // FIXME: Maybe should use type as additional index (\" CA \" vs. \"CA \")\r\n\r\n // NOTE: Residues of a particular chain are not required to be listed next to each other.\r\n // https://github.com/biasmv/pv/commit/7319b898b7473ba380c26699e3b028b2b1a7e1a1\r\n let chain = this._chain;\r\n if (!chain || chain.getName() !== chainID) {\r\n this._chain = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n _parseENDMDL() {\r\n this._modelId += 1;\r\n }\r\n\r\n _parseCONECT(stream) {\r\n const serial0 = stream.readInt(7, 11);\r\n const serial1 = stream.readInt(12, 16);\r\n const serial2 = stream.readInt(17, 21);\r\n const serial3 = stream.readInt(22, 26);\r\n const serial4 = stream.readInt(27, 31);\r\n\r\n const complex = this._complex;\r\n\r\n // Keep bonds ordered by atom serial\r\n if (serial1 && serial1 > serial0) {\r\n complex.addBond(serial0, serial1, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial2 && serial2 > serial0) {\r\n complex.addBond(serial0, serial2, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial3 && serial3 > serial0) {\r\n complex.addBond(serial0, serial3, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial4 && serial4 > serial0) {\r\n complex.addBond(serial0, serial4, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n }\r\n\r\n _parseCOMPND(stream) {\r\n const str = stream.readString(11, 80);\r\n const tokenIdx = str.indexOf(':');\r\n this._compndCurrToken = tokenIdx > 0 ? str.substring(0, tokenIdx).trim() : this._compndCurrToken;\r\n\r\n // start reading new molecule\r\n if (this._compndCurrToken === 'MOL_ID') {\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = parseInt(str.substring(tokenIdx + 1, str.indexOf(';')), 10);\r\n this._molecules.push(this._molecule);\r\n // parse molecule name\r\n } else if (this._compndCurrToken === 'MOLECULE' && this._molecule != null) {\r\n this._molecule._name = str.substring(tokenIdx + 1, str.indexOf(';')).trim();\r\n // parse molecule chains\r\n } else if (this._compndCurrToken === 'CHAIN' && this._molecule != null) {\r\n let chainStr = str.substring(tokenIdx + 1, 80).trim();\r\n const lastChar = chainStr[chainStr.length - 1];\r\n if (lastChar === ';' || lastChar === ',') {\r\n chainStr = chainStr.slice(0, -1);\r\n }\r\n chainStr = chainStr.replace(/\\s+/g, '');\r\n const chains = chainStr.split(',');\r\n this._molecule._chains = this._molecule._chains.concat(chains);\r\n }\r\n }\r\n\r\n _parseREMARK(stream) {\r\n const remarkNum = stream.readInt(8, 10);\r\n\r\n // create remark parser if needed\r\n let remark = this._remarks[remarkNum];\r\n if (_.isUndefined(remark)) {\r\n const RemarkParser = remarkParsers[remarkNum];\r\n if (_.isFunction(RemarkParser)) {\r\n this._remarks[remarkNum] = remark = new RemarkParser(this._complex);\r\n }\r\n }\r\n\r\n // delegate parsing\r\n if (!_.isUndefined(remark)) {\r\n remark.parse(stream);\r\n }\r\n }\r\n\r\n _parseHELIX(stream) {\r\n const fields = [20, 22, 32, 34];\r\n\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addHelix(obj);\r\n this._complex.structures.push(obj);\r\n });\r\n }\r\n\r\n _parseSHEET(stream) {\r\n const fields = [22, 23, 33, 34];\r\n\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addSheet(obj);\r\n });\r\n }\r\n\r\n _parseSTRUCTURE(stream, pars, adder) {\r\n const startId = 0;\r\n const startIndex = 1;\r\n const endId = 2;\r\n const endIndex = 3;\r\n\r\n // identify fields: debugging and stuff\r\n\r\n const codeOfS = 0x53;\r\n const serialNumber = stream.readInt(8, 10);\r\n const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim()\r\n const comment = stream.readString(41, 70).trim();\r\n const helLength = stream.readInt(72, 76);\r\n const helixClass = stream.readInt(39, 40);\r\n const shWidth = stream.readInt(15, 16);\r\n const shCur = stream.readInt(42, 45);\r\n const shPrev = stream.readInt(57, 60);\r\n\r\n // file fields\r\n const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0);\r\n const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0);\r\n const startSequenceNumber = stream.readInt(pars[startIndex], pars[startIndex] + 3);\r\n let iCodeStr = stream.readString(pars[startIndex] + 4, pars[startIndex] + 4);\r\n let startICode = 0;\r\n\r\n if (iCodeStr.length > 0) {\r\n startICode = iCodeStr.charCodeAt(0);\r\n }\r\n const endSequenceNumber = stream.readInt(pars[endIndex], pars[endIndex] + 3);\r\n iCodeStr = stream.readString(pars[endIndex] + 4, pars[endIndex] + 4);\r\n let endICode = 0;\r\n if (iCodeStr.length > 0) {\r\n endICode = iCodeStr.charCodeAt(0);\r\n }\r\n\r\n let obj;\r\n let cs = this._sheet;\r\n if (stream.readCharCode(1) === codeOfS) {\r\n if (cs !== null && cs.getName() !== structureName) {\r\n cs = null;\r\n this._sheet = null;\r\n }\r\n if (cs === null) {\r\n this._sheet = obj = new Sheet(structureName, shWidth);\r\n adder(obj);\r\n } else {\r\n obj = cs;\r\n }\r\n const strand = new Strand(\r\n obj,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n helixClass,\r\n shCur,\r\n shPrev,\r\n );\r\n obj.addStrand(strand);\r\n this._complex.structures.push(strand);\r\n } else {\r\n obj = new Helix(\r\n helixClass,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n serialNumber,\r\n structureName,\r\n comment,\r\n helLength,\r\n );\r\n adder(obj);\r\n }\r\n }\r\n\r\n _parseHEADER(stream) {\r\n const { metadata } = this._complex;\r\n metadata.classification = stream.readString(11, 50).trim();\r\n metadata.date = stream.readString(51, 59).trim();\r\n\r\n const id = stream.readString(63, 66).trim();\r\n metadata.id = id;\r\n if (id) {\r\n this._complex.name = id;\r\n }\r\n metadata.format = 'pdb';\r\n }\r\n\r\n _parseTITLE(stream) {\r\n const { metadata } = this._complex;\r\n metadata.title = metadata.title || [];\r\n\r\n const line = stream.readInt(9, 10) || 1;\r\n metadata.title[line - 1] = stream.readString(11, 80).trim();\r\n }\r\n\r\n static tagParsers = {\r\n HEADER: PDBParser.prototype._parseHEADER,\r\n 'TITLE ': PDBParser.prototype._parseTITLE,\r\n 'ATOM ': PDBParser.prototype._parseATOM,\r\n HETATM: PDBParser.prototype._parseATOM,\r\n ENDMDL: PDBParser.prototype._parseENDMDL,\r\n CONECT: PDBParser.prototype._parseCONECT,\r\n COMPND: PDBParser.prototype._parseCOMPND,\r\n REMARK: PDBParser.prototype._parseREMARK,\r\n // 'SOURCE': PDBParser.prototype._parseSOURCE,\r\n 'HELIX ': PDBParser.prototype._parseHELIX,\r\n 'SHEET ': PDBParser.prototype._parseSHEET,\r\n\r\n // nonstandard extension to allow range 100,000 - 999,999\r\n 'ATOM 1': PDBParser.prototype._parseATOM,\r\n 'ATOM 2': PDBParser.prototype._parseATOM,\r\n 'ATOM 3': PDBParser.prototype._parseATOM,\r\n 'ATOM 4': PDBParser.prototype._parseATOM,\r\n 'ATOM 5': PDBParser.prototype._parseATOM,\r\n 'ATOM 6': PDBParser.prototype._parseATOM,\r\n 'ATOM 7': PDBParser.prototype._parseATOM,\r\n 'ATOM 8': PDBParser.prototype._parseATOM,\r\n 'ATOM 9': PDBParser.prototype._parseATOM,\r\n };\r\n\r\n parseSync() {\r\n const stream = new PDBStream(this._data);\r\n const result = this._complex = new Complex();\r\n\r\n // parse PDB line by line\r\n while (!stream.end()) {\r\n const tag = stream.readString(1, TAG_LENGTH);\r\n const func = PDBParser.tagParsers[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, stream);\r\n }\r\n stream.next();\r\n }\r\n\r\n // Resolve indices and serials to objects\r\n this._finalize();\r\n\r\n // cleanup\r\n this._serialAtomMap = null;\r\n this._sheet = null;\r\n this._residue = null;\r\n this._chain = null;\r\n this._complex = null;\r\n\r\n if (result.getAtomCount() === 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n\r\nPDBParser.formats = ['pdb'];\r\nPDBParser.extensions = ['.pdb', '.ent'];\r\n\r\nexport default PDBParser;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n SGroup,\r\n Bond,\r\n} = chem;\r\n\r\nconst cOrderCharCodes = {\r\n A: 0,\r\n S: 1,\r\n D: 2,\r\n T: 3,\r\n};\r\n\r\nconst cmlStartRegexp = /\\s*<\\?xml\\b[^?>]*\\?>\\s*<(?:cml|molecule)\\b/i;\r\n\r\nclass CMLParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._complex = null;\r\n this._residue = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._lastMolId = -1;\r\n this._readOnlyOneMolecule = false;\r\n this._options.fileType = 'cml';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && cmlStartRegexp.test(data);\r\n }\r\n\r\n _rebuidBondIndexes(atoms, bonds) {\r\n const count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n\r\n const countBonds = bonds.length;\r\n for (let j = 0; j < countBonds; j++) {\r\n const idxs = bonds[j].atomRefs2.split(' ');\r\n if (idxs[0] === atomId) {\r\n bonds[j].start = i;\r\n }\r\n\r\n if (idxs[1] === atomId) {\r\n bonds[j].end = i;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _createSGroup(molecule, moleculeArr) {\r\n const newGroup = new SGroup(\r\n molecule.id,\r\n molecule.fieldData,\r\n new THREE.Vector3(parseFloat(molecule.x), parseFloat(molecule.y), 0),\r\n molecule.atomRefs,\r\n molecule,\r\n );\r\n if (molecule.placement === 'Relative') {\r\n newGroup._center = new THREE.Vector3(0, 0, 0);\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_CHARGE') {\r\n newGroup._charge = parseInt(molecule.fieldData, 10) || 0;\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_COEFFICIENT') {\r\n newGroup._repeat = parseInt(molecule.fieldData, 10) || 1;\r\n }\r\n moleculeArr.push(newGroup);\r\n }\r\n\r\n _extractSGroup(molecule, moleculeArr) {\r\n if (!Array.isArray(moleculeArr)) {\r\n moleculeArr = [];\r\n }\r\n\r\n if (molecule) {\r\n if (Array.isArray(molecule)) {\r\n const count = molecule.length;\r\n for (let i = 0; i < count; i++) {\r\n if (molecule[i].molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule[i].molecule));\r\n }\r\n this._createSGroup(molecule[i], moleculeArr);\r\n }\r\n } else {\r\n if (molecule.molecule) {\r\n if (molecule.molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule.molecule));\r\n }\r\n }\r\n this._createSGroup(molecule, moleculeArr);\r\n }\r\n }\r\n\r\n return moleculeArr;\r\n }\r\n\r\n _extractSGroups(molecule, atoms) {\r\n const moleculeArr = this._extractSGroup(molecule);\r\n\r\n const count = atoms.length;\r\n let i;\r\n let j;\r\n\r\n for (i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n const firstAtomRef = moleculeArr[j]._atoms.split(' ')[0];\r\n if (firstAtomRef === atomId) {\r\n if (!atoms[i].sgroupRef) {\r\n atoms[i].sgroupRef = [];\r\n }\r\n atoms[i].sgroupRef.push(moleculeArr[j]);\r\n }\r\n }\r\n }\r\n // build sGroups centers\r\n let atomMap = {}; // sgrpmap cache\r\n let mapEntry = null;\r\n const nLimon = 100000000;\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n\r\n function cycleFuncInner(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n moleculeArr[j]._atoms.push(mapEntry.a);\r\n }\r\n }\r\n\r\n function cycleFunc(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n bLow.set(Math.min(bLow.x, mapEntry.x), Math.min(bLow.y, mapEntry.y), Math.min(bLow.z, mapEntry.z));\r\n bHight.set(Math.max(bHight.x, mapEntry.x), Math.max(bHight.y, mapEntry.y), Math.max(bHight.z, mapEntry.z));\r\n cycleFuncInner(e);\r\n }\r\n }\r\n\r\n for (i = 0; i < atoms.length; i++) {\r\n atomMap[atoms[i].id] = {};\r\n atomMap[atoms[i].id].x = atoms[i].x2;\r\n if (atoms[i].x3) {\r\n atomMap[atoms[i].id].x = atoms[i].x3;\r\n }\r\n atomMap[atoms[i].id].x = parseFloat(atomMap[atoms[i].id].x);\r\n atomMap[atoms[i].id].y = atoms[i].y2;\r\n if (atoms[i].y3) {\r\n atomMap[atoms[i].id].y = atoms[i].y3;\r\n }\r\n atomMap[atoms[i].id].y = parseFloat(atomMap[atoms[i].id].y);\r\n atomMap[atoms[i].id].z = '0.0';\r\n if (atoms[i].z3) {\r\n atomMap[atoms[i].id].z = atoms[i].z3;\r\n }\r\n atomMap[atoms[i].id].z = parseFloat(atomMap[atoms[i].id].z);\r\n atomMap[atoms[i].id].a = atoms[i];\r\n }\r\n\r\n let atomsRef;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n if (moleculeArr[j]._center !== null) {\r\n bLow.set(nLimon, nLimon, nLimon);\r\n bHight.set(-nLimon, -nLimon, -nLimon);\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFunc);\r\n\r\n moleculeArr[j]._center.addVectors(bLow, bHight);\r\n moleculeArr[j]._center.multiplyScalar(0.5);\r\n } else {\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFuncInner);\r\n }\r\n }\r\n atomMap = null;\r\n }\r\n\r\n _traverseData(dom) {\r\n function isArray(o) {\r\n return Object.prototype.toString.apply(o) === '[object Array]';\r\n }\r\n\r\n function parseNode(xmlNode, result) {\r\n if (xmlNode.nodeName === '#text' && xmlNode.nodeValue.trim() === '') {\r\n return;\r\n }\r\n\r\n const jsonNode = {};\r\n jsonNode.xmlNode = xmlNode;\r\n const existing = result[xmlNode.nodeName];\r\n if (existing) {\r\n if (!isArray(existing)) {\r\n result[xmlNode.nodeName] = [existing, jsonNode];\r\n } else {\r\n result[xmlNode.nodeName].push(jsonNode);\r\n }\r\n } else {\r\n result[xmlNode.nodeName] = jsonNode;\r\n }\r\n\r\n let length;\r\n let i;\r\n if (xmlNode.attributes) {\r\n ({ length } = xmlNode.attributes);\r\n for (i = 0; i < length; i++) {\r\n const attribute = xmlNode.attributes[i];\r\n jsonNode[attribute.nodeName] = attribute.nodeValue;\r\n }\r\n }\r\n\r\n ({ length } = xmlNode.childNodes);\r\n for (i = 0; i < length; i++) {\r\n parseNode(xmlNode.childNodes[i], jsonNode);\r\n }\r\n }\r\n\r\n const result = {};\r\n if (dom.childNodes.length) {\r\n parseNode(dom.childNodes[0], result);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _findSuitableMolecule(data, molSet) {\r\n for (const key in data) {\r\n if (key === 'xmlNode') {\r\n continue;\r\n } else if (key === 'molecule') {\r\n if (data.molecule) {\r\n if (data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n molSet.push(data);\r\n }\r\n if (Array.isArray(data.molecule)) {\r\n for (let i = 0; i < data.molecule.length; i++) {\r\n if (data.molecule[i].atomArray && data.molecule[i].atomArray.atom) {\r\n molSet.push({ molecule: data.molecule[i] });\r\n }\r\n }\r\n }\r\n }\r\n } else if (data[key] && data[key] !== null && typeof (data[key]) === 'object') {\r\n this._findSuitableMolecule(data[key], molSet);\r\n }\r\n }\r\n }\r\n\r\n _selectComponents(text) {\r\n const parser = new DOMParser();\r\n const doc = parser.parseFromString(text, 'application/xml');\r\n const traversedData = this._traverseData(doc);\r\n let rawData;\r\n const self = this;\r\n\r\n function prepareComponentCompound(data) {\r\n let atoms = [];\r\n if (data.molecule && data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n if (!Array.isArray(data.molecule.atomArray.atom)) {\r\n atoms.push(data.molecule.atomArray.atom);\r\n } else {\r\n atoms = data.molecule.atomArray.atom;\r\n }\r\n } else if (!data.molecule) {\r\n const ret = {};\r\n ret.atomLabels = null;\r\n ret.labelsCount = 1;\r\n return ret;\r\n }\r\n\r\n if (data.molecule.molecule) {\r\n self._extractSGroups(data.molecule.molecule, atoms);\r\n }\r\n\r\n let atom;\r\n let count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges = [];\r\n }\r\n\r\n let localBond = [];\r\n if (data.molecule.bondArray && data.molecule.bondArray.bond) {\r\n if (!Array.isArray(data.molecule.bondArray.bond)) {\r\n localBond.push(data.molecule.bondArray.bond);\r\n } else {\r\n localBond = data.molecule.bondArray.bond;\r\n }\r\n }\r\n let bond;\r\n count = localBond.length;\r\n self._rebuidBondIndexes(atoms, localBond);\r\n\r\n function addCurrBond(index) {\r\n bond = localBond[index];\r\n atom = atoms[bond.start];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.end);\r\n atom = atoms[bond.end];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.start);\r\n return true;\r\n }\r\n\r\n for (let i = 0; i < count; i++) {\r\n if (!addCurrBond(i)) {\r\n // ignore invalid bond\r\n continue;\r\n }\r\n const orderAttr = bond.xmlNode.getAttribute('order');\r\n const tc = parseInt(orderAttr, 10);\r\n // the default bond order is unknown\r\n localBond[i].order = 0;\r\n localBond[i].type = Bond.BondType.UNKNOWN;\r\n if (tc > 1) {\r\n localBond[i].order = tc;\r\n } else {\r\n // another option - bond order is a string\r\n const order = cOrderCharCodes[orderAttr];\r\n if (order !== undefined) {\r\n localBond[i].order = order;\r\n if (orderAttr === 'A') {\r\n localBond[i].type = Bond.BondType.AROMATIC;\r\n }\r\n }\r\n }\r\n }\r\n\r\n count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges.sort();\r\n }\r\n\r\n const labels = self._breadWidthSearch(atoms, 0); // for now\r\n\r\n const retStruct = {};\r\n retStruct.atoms = atoms;\r\n retStruct.bonds = localBond;\r\n retStruct.labels = labels.atomLabels;\r\n retStruct.count = Math.min(1, labels.labelsCount); // for now\r\n retStruct.curr = -1;\r\n retStruct.originalCML = doc;\r\n\r\n return retStruct;\r\n }\r\n\r\n if (traversedData.cml) {\r\n rawData = traversedData.cml;\r\n } else {\r\n rawData = traversedData;\r\n }\r\n const retData = [];\r\n const filteredData = [];\r\n this._findSuitableMolecule(rawData, filteredData);\r\n if (this._readOnlyOneMolecule && filteredData.length > 1) {\r\n filteredData.splice(1, filteredData.length - 1);\r\n }\r\n filteredData.forEach((d) => {\r\n const rd = prepareComponentCompound(d);\r\n if (rd.atoms.length > 0) {\r\n retData.push(rd);\r\n }\r\n });\r\n return retData;\r\n }\r\n\r\n _packLabel(compId, molId) {\r\n const shift = 16;\r\n return (molId << shift) + compId;\r\n }\r\n\r\n _unpackLabel(l) {\r\n const shift = 16;\r\n const mask = (1 << shift) - 1;\r\n return { molId: l >>> shift, compId: l & mask };\r\n }\r\n\r\n _breadWidthSearch(atoms, molID) {\r\n const atomLabels = new Array(atoms.length);\r\n\r\n let id;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n atomLabels[id] = this._packLabel(0, molID);\r\n }\r\n\r\n const breadthQueue = [];\r\n let componentID = 0;\r\n let labeledAtoms = atoms.length;\r\n\r\n while (labeledAtoms > 0) {\r\n componentID++;\r\n\r\n let startID = -1;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n if (this._unpackLabel(atomLabels[id]).compId === 0) {\r\n startID = id;\r\n break;\r\n }\r\n }\r\n\r\n if (startID < 0) {\r\n break;\r\n }\r\n\r\n // Bread first search\r\n breadthQueue.push(atoms[startID]);\r\n atomLabels[startID] = this._packLabel(componentID, molID);\r\n labeledAtoms--;\r\n\r\n while (breadthQueue.length > 0) {\r\n const curr = breadthQueue.shift();\r\n if (!curr) {\r\n continue;\r\n }\r\n\r\n for (let i = 0; i < curr.edges.length; i++) {\r\n if (atomLabels[curr.edges[i]] !== componentID) {\r\n breadthQueue.push(atoms[curr.edges[i]]);\r\n atomLabels[curr.edges[i]] = componentID;\r\n labeledAtoms--;\r\n }\r\n }\r\n }\r\n }\r\n const ret = {};\r\n ret.atomLabels = atomLabels;\r\n ret.labelsCount = componentID;\r\n return ret;\r\n }\r\n\r\n _parseBond(eAtom, mainAtom, order, type) {\r\n if (eAtom >= 0) {\r\n const h = [Math.min(eAtom, mainAtom), Math.max(eAtom, mainAtom)];\r\n this._complex.addBond(h[0], h[1], order, type, true);\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseSet(varData) {\r\n const complex = this._complex = new Complex();\r\n const data = varData;\r\n const currentLabel = data.curr;\r\n const { atoms, labels } = data;\r\n let atom = null;\r\n let i;\r\n let j;\r\n const count = atoms.length;\r\n\r\n function addFunc(a) {\r\n a.xmlNodeRef = atom;\r\n if (atom.x2) {\r\n atom.x3 = atom.x2;\r\n delete atom.x2;\r\n }\r\n if (atom.y2) {\r\n atom.y3 = atom.y2;\r\n delete atom.y2;\r\n }\r\n if (!(atom.z3)) {\r\n atom.z3 = '0.0';\r\n }\r\n atom.complexAtom = a;\r\n }\r\n\r\n let chains = {};\r\n // parse atoms in label order\r\n const reorder = [];\r\n for (i = 0; i < count; i++) {\r\n reorder.push(i);\r\n }\r\n reorder.sort((a, b) => labels[a] - labels[b]);\r\n for (i = 0; i < count; i++) {\r\n const atomCharge = 0;\r\n const lLabel = labels[reorder[i]];\r\n if (this._unpackLabel(lLabel).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[reorder[i]];\r\n const atomFullNameStruct = atom.elementType;\r\n\r\n if (atom.sgroupRef) {\r\n const countRef = atom.sgroupRef.length;\r\n for (let k = 0; k < countRef; ++k) {\r\n complex._sgroups.push(atom.sgroupRef[k]);\r\n }\r\n }\r\n\r\n if (atom.x3 || atom.x2) {\r\n const currAtomComp = this._unpackLabel(lLabel).compId;\r\n // use ' ' by default instead of synthetic creation of chain names\r\n const chainID = ' '; //= String.fromCharCode('A'.charCodeAt(0) + currAtomComp);\r\n const resSeq = currAtomComp;\r\n const iCode = ' ';\r\n let strLabel = currAtomComp.toString();\r\n if (strLabel.length === 1) {\r\n strLabel = `0${strLabel}`;\r\n }\r\n const resName = `N${strLabel}`;\r\n let chain = chains[chainID];\r\n if (!chain || chain.getName() !== chainID) {\r\n chains[chainID] = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n // _x, _y, _z, mname, mindex, atomNameFull, atomName, chainID, serial, isHet, atlLocInd, atomNameToTypeF\r\n let xyz = null;\r\n if (atom.x3) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x3), parseFloat(atom.y3), parseFloat(atom.z3));\r\n } else if (atom.x2) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x2), parseFloat(atom.y2), 0);\r\n }\r\n let element = Element.ByName[atom.elementType.toUpperCase()];\r\n if (!element) {\r\n element = (JSON.parse(JSON.stringify(Element.ByName[\r\n Object.keys(Element.ByName)[Object.keys(Element.ByName).length - 1]])));\r\n element.number += 1;\r\n element.name = atom.elementType.toUpperCase();\r\n element.fullName = 'Unknown';\r\n Element.ByName[atom.elementType.toUpperCase()] = element;\r\n }\r\n const atomSerial = parseInt(atom.id.replace(/[^0-9]/, ''), 10);\r\n const added = residue.addAtom(\r\n atomFullNameStruct,\r\n element,\r\n xyz,\r\n Element.Role.SG,\r\n true,\r\n atomSerial,\r\n ' ',\r\n 1.0,\r\n 0.0,\r\n atomCharge,\r\n );\r\n if (atom.hydrogenCount) {\r\n added.hydrogenCount = parseInt(atom.hydrogenCount, 10);\r\n }\r\n if (atom.mrvValence) {\r\n added.valence = parseInt(atom.mrvValence, 10);\r\n }\r\n addFunc(added);\r\n }\r\n }\r\n }\r\n chains = null;// NOSONAR\r\n for (i = 0; i < data.bonds.length; i++) {\r\n const cb = data.bonds[i];\r\n if (this._unpackLabel(labels[cb.start]).molId === this._unpackLabel(currentLabel).molId\r\n && this._unpackLabel(labels[cb.end]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[cb.start];\r\n if (!atom || !(atoms[cb.end])) {\r\n continue; // skip invalid\r\n }\r\n this._parseBond(\r\n parseInt(atom.id.replace(/[^0-9]/, ''), 10),\r\n parseInt(atoms[cb.end].id.replace(/[^0-9]/, ''), 10),\r\n cb.order,\r\n cb.type,\r\n );\r\n }\r\n }\r\n\r\n for (i = 0; i < this._complex.getSGroupCount(); i++) {\r\n const sGrp = this._complex.getSGroups()[i];\r\n for (j = 0; j < sGrp._atoms.length; j++) {\r\n sGrp._atoms[j] = sGrp._atoms[j].complexAtom;\r\n }\r\n }\r\n for (i = 0; i < count; i++) {\r\n if (this._unpackLabel(labels[i]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[i];\r\n atom.complexAtom = null;\r\n delete atom.complexAtom;\r\n }\r\n }\r\n this._complex.originalCML = data.originalCML;\r\n this._fixBondsArray();\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n this._serialAtomMap = null;\r\n this._complex = null;\r\n return complex;\r\n }\r\n\r\n parseSync() {\r\n const complexes = [];\r\n const self = this;\r\n const moleculaSet = this._selectComponents(this._data);\r\n moleculaSet.forEach((molSet) => {\r\n molSet.curr = 2;\r\n if (molSet.count === 0) {\r\n molSet.count = 1;\r\n }\r\n for (let i = 0; i < molSet.count; i++) {\r\n molSet.curr = (i + 1);\r\n complexes.push(self._parseSet(molSet, false));\r\n }\r\n });\r\n\r\n let totalAtomsParsed = 0;\r\n complexes.forEach((c) => {\r\n totalAtomsParsed += c.getAtomCount();\r\n });\r\n if (totalAtomsParsed <= 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n if (complexes.length > 1) {\r\n const joinedComplex = new Complex();\r\n joinedComplex.joinComplexes(complexes);\r\n joinedComplex.originalCML = complexes[0].originalCML;\r\n return joinedComplex;\r\n }\r\n if (complexes.length === 1) {\r\n return complexes[0];\r\n }\r\n return new Complex();\r\n }\r\n}\r\n\r\nCMLParser.formats = ['cml'];\r\nCMLParser.extensions = ['.cml'];\r\n\r\nexport default CMLParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport MMTF from '../../../vendor/js/mmtf';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst {\r\n Complex,\r\n Chain,\r\n Atom,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nclass ArrayComparator {\r\n constructor(original) {\r\n this._original = Array.from(original);\r\n this._original.sort();\r\n\r\n this._sum = 0;\r\n for (let i = 0; i < this._original.length; ++i) {\r\n this._sum += this._original[i];\r\n }\r\n }\r\n\r\n compare(candidate) {\r\n const len = candidate.length;\r\n if (len !== this._original.length) {\r\n return false;\r\n }\r\n\r\n let sum = 0;\r\n let i;\r\n for (i = 0; i < len; ++i) {\r\n sum += candidate[i];\r\n }\r\n\r\n if (sum !== this._sum) {\r\n return false;\r\n }\r\n\r\n const sorted = Array.from(candidate);\r\n sorted.sort();\r\n\r\n for (i = 0; i < len; ++i) {\r\n if (sorted[i] !== this._original[i]) {\r\n return false;\r\n }\r\n }\r\n\r\n return true;\r\n }\r\n}\r\n\r\nArrayComparator.prototype.constructor = ArrayComparator;\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see https://github.com/rcsb/mmtf-javascript/blob/master/src/mmtf-traverse.js\r\nconst secStructToType = [\r\n StructuralElementType.HELIX_PI, // 0\r\n StructuralElementType.BEND, // 1\r\n StructuralElementType.HELIX_ALPHA, // 2\r\n StructuralElementType.STRAND, // 3\r\n StructuralElementType.HELIX_310, // 4\r\n StructuralElementType.BRIDGE, // 5\r\n StructuralElementType.TURN, // 6\r\n StructuralElementType.COIL, // 7\r\n];\r\n\r\nfunction getFirstByte(buf) {\r\n const bytes = new Uint8Array(buf, 0, 1);\r\n return bytes[0];\r\n}\r\n\r\nclass MMTFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'mmtf';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n // check if it's binary MessagePack format containing a map (dictionary)\r\n // see https://github.com/msgpack/msgpack/blob/master/spec.md\r\n return _.isArrayBuffer(data) && ((getFirstByte(data) | 1) === 0xDF);\r\n }\r\n\r\n _onModel(_modelData) {\r\n }\r\n\r\n _onChain(chainData) {\r\n if (chainData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const chain = new Chain(this._complex, chainData.chainName);\r\n this._complex._chains[chainData.chainIndex] = chain;\r\n chain._index = chainData.chainIndex;\r\n }\r\n\r\n _onGroup(groupData) {\r\n if (groupData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n if (this.settings.now.nowater) {\r\n // skip water\r\n if (groupData.groupName === 'HOH' || groupData.groupName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n const chain = this._complex._chains[groupData.chainIndex];\r\n const icode = !groupData.insCode.charCodeAt(0) ? '' : groupData.insCode;\r\n const residue = chain.addResidue(groupData.groupName, groupData.groupId, icode);\r\n residue._index = groupData.groupIndex;\r\n\r\n this._updateSecStructure(this._complex, residue, groupData);\r\n }\r\n\r\n _onAtom(atomData) {\r\n if (atomData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const altLoc = !atomData.altLoc.charCodeAt(0) ? '' : atomData.altLoc;\r\n const atom = new Atom(\r\n atomData.groupIndex, // we store residue index here to replace it later with actual reference\r\n atomData.atomName,\r\n Element.getByName(atomData.element.toUpperCase()),\r\n new THREE.Vector3(atomData.xCoord, atomData.yCoord, atomData.zCoord),\r\n Element.Role[atomData.atomName],\r\n false, // hetero atoms will be marked later\r\n atomData.atomId,\r\n altLoc,\r\n atomData.occupancy,\r\n atomData.bFactor,\r\n atomData.formalCharge,\r\n );\r\n\r\n this._complex._atoms[atomData.atomIndex] = atom;\r\n atom.index = atomData.atomIndex;\r\n\r\n this._serialAtomMap[atomData.atomId] = atom;\r\n }\r\n\r\n _onBond(bondData) {\r\n const right = Math.max(bondData.atomIndex1, bondData.atomIndex2);\r\n if (right >= this._complex._atoms.length) {\r\n return;\r\n }\r\n const left = Math.min(bondData.atomIndex1, bondData.atomIndex2);\r\n this._complex.addBond(\r\n this._complex._atoms[left],\r\n this._complex._atoms[right],\r\n bondData.bondOrder,\r\n Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n\r\n _updateSecStructure(complex, residue, groupData) {\r\n const helixClasses = [3, -1, 1, -1, 5];\r\n\r\n if (!_.isUndefined(groupData) && groupData.secStruct === this._ssType) {\r\n residue._secondary = this._ssStruct;\r\n if (this._ssStruct) {\r\n this._ssStruct.term = residue;\r\n }\r\n return;\r\n }\r\n\r\n if (!_.isUndefined(groupData)) {\r\n // start new secondary structure\r\n const type = secStructToType[groupData.secStruct];\r\n this._ssType = groupData.secStruct;\r\n this._ssStart = residue;\r\n\r\n let struct = null;\r\n switch (this._ssType) {\r\n case -1: // undefined\r\n case 7: // coil\r\n break;\r\n case 0: // pi helix\r\n case 2: // alpha helix\r\n case 4: // 3-10 helix\r\n struct = new Helix(helixClasses[this._ssType], residue, residue, 0, '', '', 0);\r\n complex._helices.push(struct);\r\n break;\r\n case 3: { // extended\r\n const sheet = new Sheet('', 0);\r\n complex._sheets.push(sheet);\r\n struct = new Strand(sheet, residue, residue, 0, null, null);\r\n break;\r\n }\r\n default:\r\n if (type !== undefined) {\r\n struct = new StructuralElement(type, residue, residue);\r\n }\r\n break;\r\n }\r\n\r\n this._ssStruct = struct;\r\n residue._secondary = struct;\r\n if (struct) {\r\n complex.structures.push(struct);\r\n }\r\n }\r\n }\r\n\r\n _updateMolecules(mmtfData) {\r\n const entities = mmtfData.entityList;\r\n if (!entities) {\r\n return;\r\n }\r\n\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < entities.length; i++) {\r\n const entity = entities[i];\r\n const chains = entity.chainIndexList;\r\n let residues = [];\r\n for (let j = 0; j < chains.length; j++) {\r\n const chainIndex = chains[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, entity.description, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n // populate complex with chains, residues and atoms\r\n _traverse(mmtfData) {\r\n const self = this;\r\n\r\n // get metadata\r\n const { metadata } = this._complex;\r\n metadata.id = mmtfData.structureId;\r\n metadata.title = [];\r\n metadata.title[0] = mmtfData.title;\r\n metadata.date = mmtfData.releaseDate;\r\n metadata.format = 'mmtf';\r\n\r\n // create event callback functions\r\n const eventCallbacks = {\r\n onModel(modelData) {\r\n self._onModel(modelData);\r\n },\r\n onChain(chainData) {\r\n self._onChain(chainData);\r\n },\r\n onGroup(groupData) {\r\n self._onGroup(groupData);\r\n },\r\n onAtom(atomData) {\r\n self._onAtom(atomData);\r\n },\r\n onBond(bondData) {\r\n self._onBond(bondData);\r\n },\r\n };\r\n\r\n // temporary variables used during traversal to track secondary structures\r\n this._ssType = -1;\r\n this._ssStruct = null;\r\n this._ssStart = null;\r\n\r\n // traverse the structure and listen to the events\r\n MMTF.traverse(mmtfData, eventCallbacks);\r\n\r\n this._updateSecStructure(this._complex);\r\n this._updateMolecules(mmtfData);\r\n }\r\n\r\n // During traversal atoms and residues don't come sequentially\r\n // so a residue for certain atom can be unavailable. Thus we\r\n // store residue index in atom.\r\n // This function being called after traversal replaces the index\r\n // with actual reference, and also populates atom lists in residues.\r\n _linkAtomsToResidues() {\r\n for (let i = 0; i < this._complex._atoms.length; ++i) {\r\n const atom = this._complex._atoms[i];\r\n const residue = this._complex._residues[atom.residue];\r\n atom.residue = residue;\r\n residue._atoms.push(atom);\r\n }\r\n }\r\n\r\n _findSynonymousChains() {\r\n const named = {};\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!named.hasOwnProperty(name)) {\r\n named[name] = [];\r\n }\r\n\r\n named[name].push(chain._index);\r\n }\r\n\r\n return named;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _parseAssemblyInfo(mmtfData) {\r\n let i;\r\n let j;\r\n let k;\r\n const assemblies = [];\r\n const { logger } = this;\r\n\r\n for (i = 0; i < mmtfData.bioAssemblyList.length; ++i) {\r\n const baInfo = mmtfData.bioAssemblyList[i];\r\n if (baInfo.transformList.length === 0) {\r\n continue;\r\n }\r\n\r\n const chains = baInfo.transformList[0].chainIndexList;\r\n const chainListCheck = new ArrayComparator(chains);\r\n\r\n // build list of chain names\r\n const chainNames = {};\r\n for (j = 0; j < chains.length; ++j) {\r\n chainNames[this._complex._chains[chains[j]].getName()] = 1;\r\n }\r\n\r\n // all chains with the same name should belong to assembly if one of them belongs\r\n const allChains = [];\r\n let name;\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n // just concat arrays -- there should be no duplicates\r\n Array.prototype.push.apply(allChains, this._chainsByName[name]);\r\n }\r\n }\r\n if (!chainListCheck.compare(allChains)) {\r\n // assembly is missing some of the chains\r\n logger.debug('MMTF: Assembly is missing some of the synonymous chains. Skipping...');\r\n }\r\n\r\n const a = new Assembly(this._complex);\r\n\r\n // add chains to assembly\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n a.addChain(name);\r\n }\r\n }\r\n\r\n // add unique matrices to assembly\r\n a.addMatrix(new THREE.Matrix4().fromArray(baInfo.transformList[0].matrix).transpose());\r\n for (j = 1; j < baInfo.transformList.length; ++j) {\r\n const transform = baInfo.transformList[j];\r\n\r\n if (!chainListCheck.compare(transform.chainIndexList)) {\r\n // list of chains for this transform doesn't match that for other transforms\r\n // this is illegal in our structure\r\n logger.debug('MMTF: Chain lists differ for different transforms in one assembly. Skipping...');\r\n continue;\r\n }\r\n\r\n const m = new THREE.Matrix4().fromArray(transform.matrix).transpose();\r\n\r\n // check if matrix is already in the list\r\n for (k = 0; k < a.matrices.length; ++k) {\r\n if (a.matrices[k].equals(m)) {\r\n break;\r\n }\r\n }\r\n\r\n if (k === a.matrices.length) {\r\n a.addMatrix(m);\r\n }\r\n }\r\n\r\n a.finalize();\r\n assemblies.push(a);\r\n }\r\n\r\n return assemblies;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _markHeteroAtoms(mmtfData) {\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < mmtfData.entityList.length; ++i) {\r\n const entity = mmtfData.entityList[i];\r\n if (entity.type !== 'polymer') {\r\n for (let j = 0; j < entity.chainIndexList.length; ++j) {\r\n const chainIndex = entity.chainIndexList[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n for (let k = 0; k < chain._residues.length; ++k) {\r\n const res = chain._residues[k];\r\n for (let m = 0; m < res._atoms.length; ++m) {\r\n res._atoms[m].het = true;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // joins chains with the same name into single chain\r\n _joinSynonymousChains() {\r\n let i;\r\n let j;\r\n\r\n const primaryChainsArray = [];\r\n const primaryChainsHash = {};\r\n\r\n // join chains\r\n for (i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!primaryChainsHash.hasOwnProperty(name)) {\r\n // new name -- this is a primary chain\r\n primaryChainsHash[name] = chain;\r\n chain._index = primaryChainsArray.length; // update index as this array will later replace original chain list\r\n primaryChainsArray.push(chain);\r\n continue;\r\n }\r\n\r\n // this chain should be joined with the primary chain of the same name\r\n const primary = primaryChainsHash[name];\r\n for (j = 0; j < chain._residues.length; ++j) {\r\n const residue = chain._residues[j];\r\n primary._residues.push(residue);\r\n residue._chain = primary;\r\n }\r\n }\r\n\r\n // replace chains list with one containing only primary chains\r\n // dropping references to all chains but primary\r\n this._complex._chains = primaryChainsArray;\r\n }\r\n\r\n parseSync() {\r\n const mmtfData = MMTF.decode(this._data);\r\n\r\n this._complex = new Complex();\r\n this._serialAtomMap = {}; // filled during traversal\r\n\r\n this._traverse(mmtfData);\r\n this._linkAtomsToResidues();\r\n this._markHeteroAtoms(mmtfData);\r\n this._chainsByName = this._findSynonymousChains();\r\n Array.prototype.push.apply(this._complex.units, this._parseAssemblyInfo(mmtfData));\r\n this._joinSynonymousChains();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n return this._complex;\r\n }\r\n}\r\n\r\nMMTFParser.formats = ['mmtf'];\r\nMMTFParser.extensions = ['.mmtf'];\r\nMMTFParser.binary = true;\r\n\r\nexport default MMTFParser;\r\n","class ParsingError extends Error {\r\n constructor(message, line, column) {\r\n super(`data:${line}:${column}: ${message}`);\r\n\r\n if (Error.captureStackTrace) {\r\n Error.captureStackTrace(this, ParsingError);\r\n }\r\n\r\n this.name = 'ParsingError';\r\n this.parseLine = line;\r\n this.parseColumn = column;\r\n }\r\n}\r\n\r\nexport default ParsingError;\r\n","import _ from 'lodash';\r\nimport ParsingError from './ParsingError';\r\n\r\n// Implemented and being tested against: https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax\r\n\r\nfunction _isWhitespace(ch) {\r\n return ch === 32 || ch === 10 || ch === 13 || ch === 9;\r\n}\r\n\r\nfunction _inlineIndexOf(ch0, str, idx) {\r\n const len = str.length;\r\n let ch = -1;\r\n while (idx < len) {\r\n ch = str.charCodeAt(idx);\r\n if (ch === ch0 || ch === 10) {\r\n break;\r\n }\r\n ++idx;\r\n }\r\n return ch === ch0 ? idx : -1;\r\n}\r\n\r\nexport default function readCIF(source) {\r\n let i = 0;\r\n let j = 0;\r\n const n = source.length;\r\n let code = NaN;\r\n let newline = true;\r\n let line = 1;\r\n let column = 1;\r\n let begin;\r\n let state = 0; // 0 - start, 1 - block, 2 - item, 3 - loop, 4 - values, 5 - value\r\n const result = {};\r\n let block = {};\r\n let keys = [];\r\n let keysCount = 0;\r\n let key = '';\r\n let values = [];\r\n let valuesCount = 0;\r\n let value;\r\n\r\n function _parseValue() {\r\n let val;\r\n if ((code === 46 || code === 63) && (i + 1 >= n || _isWhitespace(source.charCodeAt(i + 1)))) { // '.' or '?' .....\r\n // it's a missing value\r\n ++column;\r\n ++i;\r\n return undefined;\r\n }\r\n if (newline && code === 59) { // ';' ......................................................................\r\n // parse multi-line string\r\n j = i;\r\n let lines = 0;\r\n do {\r\n j = _inlineIndexOf(10, source, j + 1); // '\\n'\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated text block found', line, column);\r\n }\r\n ++lines;\r\n } while ((j + 1 < n && source.charCodeAt(j + 1) !== code) || j + 1 >= n);\r\n val = source.substring(i + 1, j).replace(/\\r/g, '');\r\n i = j + 2;\r\n line += lines;\r\n column = 1;\r\n newline = false;\r\n return val;\r\n }\r\n if (code === 39 || code === 34) { // ''' or '\"' ...........................................................\r\n // parse quoted string\r\n j = i;\r\n do {\r\n j = _inlineIndexOf(code, source, j + 1);\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated quoted string found', line, column);\r\n }\r\n } while (j + 1 < n && !_isWhitespace(source.charCodeAt(j + 1)));\r\n val = source.substring(i + 1, j);\r\n column += j - i + 1;\r\n i = j + 1;\r\n return val;\r\n } // ......................................................................................................\r\n // parse until the first whitespace\r\n j = i;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n val = source.substring(i, j);\r\n column += j - i;\r\n i = j;\r\n // try to convert to a number\r\n const num = Number(val);\r\n if (!Number.isNaN(num)) {\r\n return num;\r\n }\r\n // or leave as an unquoted string\r\n return val;\r\n }\r\n\r\n function _storeKey(tag) {\r\n keys[keysCount++] = tag;\r\n }\r\n\r\n function _storeValue(val) {\r\n const keyIndex = valuesCount % keysCount;\r\n values[keyIndex].push(val);\r\n ++valuesCount;\r\n return val;\r\n }\r\n\r\n while (i <= n) {\r\n code = source.charCodeAt(i); // 'NaN' in place of ''\r\n if (code === 13) { // '\\r' .......................................................................................\r\n // just ignore\r\n } else if (code === 10) { // '\\n' ................................................................................\r\n // take note of new lines\r\n newline = true;\r\n ++line;\r\n column = 1;\r\n } else {\r\n // process inline characters\r\n if (code === 32 || code === 9) { // ' ' or '\\t' ................................................................\r\n // just ignore\r\n } else if (code === 35) { // '#' ...............................................................................\r\n // skip the comment until before the end of the line\r\n i = _inlineIndexOf(10, source, i + 1); // '\\n'\r\n if (i === -1) {\r\n break;\r\n } else {\r\n continue; // don't forget to process the new line\r\n }\r\n } else if (state === 0) { // start =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n j = i + 5;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new data block\r\n result[source.substring(begin, i)] = block = {};\r\n state = 1; // block\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Data block name missing', line, column);\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 1) { // block =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n continue; // parse again in a different state\r\n } else if (code === 95) { // '_' .............................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // start new item\r\n key = source.substring(begin, i);\r\n state = 2; // item\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n i += 5;\r\n column += 5;\r\n if (i < n && !_isWhitespace(source.charCodeAt(i))) {\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n } else {\r\n // start new loop\r\n keys = [];\r\n keysCount = 0;\r\n values = [];\r\n valuesCount = 0;\r\n state = 3; // loop\r\n continue; // don't forget to process the whitespace\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 2) { // item ==============================================================================\r\n if (Number.isNaN(code)) {\r\n break;\r\n }\r\n value = _parseValue();\r\n _.set(block, key, value);\r\n state = 1; // block\r\n continue;\r\n } else if (state === 3) { // loop ==============================================================================\r\n if (code === 95) { // '_' ....................................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new key\r\n _storeKey(source.substring(begin, i));\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else { // ..................................................................................................\r\n if (keysCount > 0) {\r\n for (let keyIndex = 0; keyIndex < keysCount; ++keyIndex) {\r\n value = [];\r\n values[keyIndex] = value;\r\n _.set(block, keys[keyIndex], value);\r\n }\r\n state = 4;\r\n continue; // parse again in a different state\r\n }\r\n throw new ParsingError('Data tags are missing inside a loop', line, column);\r\n }\r\n } else if (state === 4) { // values ============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n } else if (code === 95) { // '_' .............................................................................\r\n state = 1; // block\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n state = 1; // block\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n state = 0;\r\n } else { // ..................................................................................................\r\n _storeValue(_parseValue());\r\n }\r\n continue; // parse again in a different state\r\n } else { // ====================================================================================================\r\n throw new ParsingError(`Unexpected internal state ${state}`, line, column);\r\n }\r\n\r\n newline = false;\r\n ++column;\r\n }\r\n ++i;\r\n }\r\n\r\n if (state === 2) { // item\r\n throw new ParsingError(`Unexpected end of file in state ${state}`, line, column);\r\n }\r\n\r\n return result;\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\nimport readCIF from './readCIF';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nconst cRequiredAtomFields = [\r\n 'auth_seq_id',\r\n 'Cartn_x',\r\n 'Cartn_y',\r\n 'Cartn_z',\r\n 'label_atom_id',\r\n];\r\n\r\nconst cSecondaryCoding = {\r\n helx: 'helix',\r\n turn: 'turn',\r\n strn: 'strand',\r\n};\r\n\r\nfunction getTypeFromId(string) {\r\n const typeId = /[A-Za-z]+/.exec(string);\r\n if (!typeId) {\r\n return null;\r\n }\r\n\r\n return cSecondaryCoding[typeId[0].toLowerCase()];\r\n}\r\n\r\n/**\r\n * Make valid object an array\r\n * @param arrayLikeObject\r\n * @return {array, object} array or object\r\n */\r\nfunction arrize(arrayLikeObject) {\r\n if (arrayLikeObject === null || arrayLikeObject === undefined || _.isArray(arrayLikeObject)) {\r\n return arrayLikeObject;\r\n }\r\n return [arrayLikeObject];\r\n}\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\nclass AtomDataError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'AtomDataError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction _getOperations(operList) {\r\n if (!operList) {\r\n return null;\r\n }\r\n const idc = arrize(operList.id);\r\n const { matrix, vector } = operList;\r\n if (!idc || !matrix || !vector) {\r\n return null;\r\n }\r\n\r\n const ops = [];\r\n for (let i = 0, n = idc.length; i < n; ++i) {\r\n const mtx = new THREE.Matrix4();\r\n const { elements } = mtx;\r\n\r\n for (let row = 0; row < 3; ++row) {\r\n const matrixData = matrix[row + 1];\r\n elements[row] = arrize(matrixData[1])[i];\r\n elements[row + 4] = arrize(matrixData[2])[i];\r\n elements[row + 8] = arrize(matrixData[3])[i];\r\n elements[row + 12] = arrize(vector[row + 1])[i];\r\n }\r\n ops[idc[i]] = mtx;\r\n }\r\n return ops;\r\n}\r\n\r\nfunction _extractOperations(assemblyGen, opsDict) {\r\n assemblyGen = _.isString(assemblyGen) ? assemblyGen : `${assemblyGen}`;\r\n const l = assemblyGen.replace(/\\)\\s*\\(/g, '!').replace(/[()']/g, '');\r\n const groupStr = l.split('!');\r\n const gps = [];\r\n\r\n for (let grIdx = 0, grCount = groupStr.length; grIdx < grCount; ++grIdx) {\r\n const gr = groupStr[grIdx].split(',');\r\n const gp = [];\r\n let idx = 0;\r\n for (let i = 0, n = gr.length; i < n; ++i) {\r\n const s = gr[i];\r\n if (s.includes('-')) {\r\n const es = s.split('-');\r\n let j = parseInt(es[0], 10);\r\n const m = parseInt(es[1], 10);\r\n for (; j <= m; ++j) {\r\n gp[idx++] = opsDict[j];\r\n }\r\n } else {\r\n gp[idx++] = opsDict[s];\r\n }\r\n }\r\n gps.push(gp);\r\n }\r\n\r\n // traverse all groups from the end of array and make all mults\r\n const matrices = [];\r\n let cnt = 0;\r\n function traverse(level, mtx) {\r\n for (let ii = 0, nn = gps[level].length; ii < nn; ++ii) {\r\n const newMtx = mtx ? mtx.clone() : new THREE.Matrix4();\r\n newMtx.multiplyMatrices(gps[level][ii], newMtx);\r\n if (level === 0) {\r\n matrices[cnt++] = newMtx;\r\n } else {\r\n traverse(level - 1, newMtx);\r\n }\r\n }\r\n }\r\n traverse(gps.length - 1);\r\n return matrices;\r\n}\r\n\r\nclass CIFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this.asymDict = {};\r\n this.molecules = [];\r\n this._options.fileType = 'cif';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*data_/i.test(data);\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing CIF file..');\r\n const data = readCIF(this._data);\r\n return this._toComplex(data);\r\n }\r\n\r\n /**\r\n * Convert intermediate structure into our valid Complex object\r\n * @param cifData intermediate CIF object\r\n * @returns {Complex} complex\r\n * @private\r\n */\r\n _toComplex(cifData) {\r\n const complex = new Complex();\r\n const complexData = cifData[Object.keys(cifData)[0]];\r\n this._extractAtoms(complex, complexData);\r\n this._extractSecondary(complex, complexData);\r\n this._extractAssemblies(complex, complexData);\r\n this._extractMolecules(complex, complexData);\r\n this._extractMetadata(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n\r\n return complex;\r\n }\r\n\r\n /**\r\n * Extract metadata\r\n * @param complex structure to fill\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n\r\n _extractMetadata(complex, complexData) {\r\n const { metadata } = complex;\r\n metadata.id = complexData.entry.id;\r\n metadata.classification = complexData.struct_keywords.pdbx_keywords;\r\n const databaserev = complexData.database_PDB_rev;\r\n metadata.date = (databaserev && databaserev.date_original) ? databaserev.date_original : '';\r\n metadata.format = 'cif';\r\n metadata.title = [];\r\n metadata.title[0] = complexData.struct.title;\r\n }\r\n\r\n /**\r\n * Extract molecules information from CIF structure (should be called strictly after _extractAtoms)\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractMolecules(complex, complexData) {\r\n const molData = complexData.entity;\r\n const names = arrize(molData.pdbx_description);\r\n const count = names.length;\r\n let i;\r\n\r\n // molecules names from cif\r\n for (i = 0; i < count; i++) {\r\n if (this.molecules[i]) { // molecule was created during atoms processing\r\n this.molecules[i].name = names[i];\r\n } else { // molecule wasn't created, because there is no atom which is contained\r\n this.molecules[i] = { name: names[i], residues: [] };\r\n }\r\n }\r\n\r\n // reorganize molecules for complex and check chains\r\n const molecules = complex.getMolecules();\r\n for (i = 0; i < count; i++) {\r\n const molecule = this.molecules[i];\r\n molecules[i] = new Molecule(complex, molecule.name, i + 1);\r\n molecules[i].residues = molecule.residues;\r\n }\r\n }\r\n\r\n /**\r\n * Extract atom information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAtoms(complex, complexData) {\r\n const atomData = complexData.atom_site;\r\n if (!atomData) {\r\n throw new AtomDataError('CIF parsing error: atom_site is not specified!');\r\n }\r\n\r\n for (let f = 0, n = cRequiredAtomFields.length; f < n; ++f) {\r\n if (!atomData[cRequiredAtomFields[f]]) {\r\n throw new AtomDataError(`CIF parsing error: requires field ${cRequiredAtomFields[f]} not found!`);\r\n }\r\n }\r\n\r\n const { asymDict } = this;\r\n // required fields\r\n const resIdc = arrize(atomData.auth_seq_id);\r\n const x = arrize(atomData.Cartn_x);\r\n const y = arrize(atomData.Cartn_y);\r\n const z = arrize(atomData.Cartn_z);\r\n const names = arrize(atomData.label_atom_id);\r\n const count = names.length;\r\n // optional fields\r\n const group = arrize(atomData.group_PDB) || [];\r\n const chainIdc = arrize(atomData.auth_asym_id) || [];\r\n const chainLabelIdc = arrize(atomData.label_asym_id) || [];\r\n const serials = arrize(atomData.id) || [];\r\n const iCodes = arrize(atomData.pdbx_PDB_ins_code) || [];\r\n const resNames = arrize(atomData.label_comp_id) || [];\r\n const elements = arrize(atomData.type_symbol) || [];\r\n const tempFactors = arrize(atomData.B_iso_or_equiv) || [];\r\n const occupancies = arrize(atomData.occupancy) || [];\r\n const charges = arrize(atomData.pdbx_formal_charge) || [];\r\n const altLocs = arrize(atomData.label_alt_id) || [];\r\n const models = arrize(atomData.pdbx_PDB_model_num) || [];\r\n const molecules = arrize(atomData.label_entity_id) || [];\r\n\r\n let chain = null;\r\n let residue = null;\r\n for (let i = 0; i < count; ++i) {\r\n const model = models[i] || 1;\r\n if (model !== 1) {\r\n continue;\r\n }\r\n const chainID = String(chainIdc[i] || ' ');\r\n\r\n if (!chain || chain.getName() !== chainID) {\r\n chain = complex.getChain(chainID) || complex.addChain(chainID);\r\n }\r\n asymDict[String(chainLabelIdc[i] || ' ')] = chainID;\r\n const resSeq = resIdc[i];\r\n const iCode = String(iCodes[i] || ' ');\r\n const resName = String(resNames[i] || '');\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n residue = chain.addResidue(resName, resSeq, iCode);\r\n\r\n // store residue in appropriate molecule\r\n const moleculeIdx = molecules[i] - 1;\r\n let entity = this.molecules[moleculeIdx];\r\n if (!entity) { // create new molecule if it hasn't been created\r\n this.molecules[moleculeIdx] = { name: '', residues: [] };\r\n entity = this.molecules[moleculeIdx];\r\n }\r\n entity.residues.push(residue);\r\n }\r\n\r\n const name = names[i];\r\n const element = elements[i] || nameToElement(name);\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name.trim()];\r\n const xyz = new THREE.Vector3(x[i], y[i], z[i]);\r\n const het = group[i] === 'HETATM' || false;\r\n const serial = serials[i] || i;\r\n const tempFactor = tempFactors[i] || 0.0;\r\n const occupancy = occupancies[i] || 0.0;\r\n const altLoc = String(altLocs[i] || '');\r\n const charge = charges[i] || 0;\r\n\r\n residue.addAtom(\r\n name,\r\n type,\r\n xyz,\r\n role,\r\n het,\r\n serial,\r\n altLoc,\r\n occupancy,\r\n tempFactor,\r\n charge,\r\n );\r\n }\r\n }\r\n\r\n /**\r\n * Extracts secondary structure information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex - complex to fill\r\n * @param complexData - CIF complex data\r\n * @private\r\n */\r\n _extractSecondary(complex, complexData) {\r\n if (complexData.struct_conf) {\r\n this._extractConfs(complex, complexData.struct_conf);\r\n }\r\n if (complexData.struct_sheet_range) {\r\n this._extractSheets(complex, complexData.struct_sheet_range);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts sheets information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param sheetData\r\n * @private\r\n */\r\n _extractSheets(complex, sheetData) {\r\n const { asymDict } = this;\r\n if (!sheetData.sheet_id || !sheetData.id || !sheetData.beg_label_seq_id || !sheetData.end_label_seq_id\r\n || !sheetData.beg_label_asym_id) {\r\n return;\r\n }\r\n // Strand(sheet, start, end, sense, cur, prev)\r\n const sheets = complex._sheets;\r\n\r\n function getSheet(name) {\r\n const n = sheets.length;\r\n for (let i = 0; i < n; ++i) {\r\n if (sheets[i]._name === name) {\r\n return sheets[i];\r\n }\r\n }\r\n sheets[n] = new Sheet(name, 0);\r\n return sheets[n];\r\n }\r\n\r\n const sheetNames = arrize(sheetData.sheet_id);\r\n const strandNames = arrize(sheetData.id);\r\n const starts = arrize(sheetData.beg_auth_seq_id);\r\n const ends = arrize(sheetData.end_auth_seq_id);\r\n const chains = arrize(sheetData.beg_label_asym_id);\r\n const stICodes = arrize(sheetData.pdbx_beg_PDB_ins_code) || [];\r\n const endICodes = arrize(sheetData.pdbx_end_PDB_ins_code) || [];\r\n\r\n for (let i = 0, n = strandNames.length; i < n; ++i) {\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n const sheet = getSheet(sheetNames[i]);\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n\r\n const strand = new Strand(sheet, start[0], end[0], 0, null, null);\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = strand;\r\n }\r\n sheet.addStrand(strand);\r\n complex.structures.push(strand);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts helix/turn/strand(?) information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param helicesData\r\n * @private\r\n */\r\n _extractConfs(complex, helicesData) {\r\n const { asymDict } = this;\r\n if (!helicesData.conf_type_id || !helicesData.beg_label_seq_id || !helicesData.end_label_seq_id\r\n || !helicesData.beg_label_asym_id) {\r\n return;\r\n }\r\n\r\n const types = arrize(helicesData.conf_type_id);\r\n const starts = arrize(helicesData.beg_auth_seq_id);\r\n const stICodes = arrize(helicesData.pdbx_beg_PDB_ins_code) || [];\r\n const ends = arrize(helicesData.end_auth_seq_id);\r\n const endICodes = arrize(helicesData.pdbx_end_PDB_ins_code) || [];\r\n const comments = arrize(helicesData.details) || [];\r\n const lengths = arrize(helicesData.pdbx_PDB_helix_length) || [];\r\n const helixClasses = arrize(helicesData.pdbx_PDB_helix_class) || [];\r\n const names = arrize(helicesData.id) || [];\r\n const chains = arrize(helicesData.beg_label_asym_id);\r\n\r\n for (let i = 0, n = types.length; i < n; ++i) {\r\n const type = getTypeFromId(types[i]);\r\n if (!type) {\r\n continue;\r\n }\r\n const name = names[i] || types[i];\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n const comment = comments[i] || '';\r\n const length = lengths[i] || 0;\r\n const helixClass = helixClasses[i] || ' ';\r\n let struct;\r\n if (type === 'helix') {\r\n const idx = complex._helices.length;\r\n struct = new Helix(helixClass, start[0], end[0], idx, name, comment, length);\r\n complex.addHelix(struct);\r\n complex.structures.push(struct);\r\n } else if (type === 'turn') {\r\n struct = new StructuralElement(StructuralElement.Type.TURN, start[0], end[0]);\r\n complex.structures.push(struct);\r\n } else {\r\n struct = null;\r\n }\r\n if (!struct) {\r\n continue;\r\n }\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = struct;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Extract biological assemblies information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAssemblies(complex, complexData) {\r\n const { asymDict } = this;\r\n const asmGen = complexData.pdbx_struct_assembly_gen;\r\n if (!asmGen) {\r\n return;\r\n }\r\n\r\n const asmIdx = arrize(asmGen.assembly_id);\r\n const asmOper = arrize(asmGen.oper_expression);\r\n const asmList = arrize(asmGen.asym_id_list);\r\n if (!asmIdx || !asmOper || !asmList) {\r\n return;\r\n }\r\n\r\n const operList = _getOperations(complexData.pdbx_struct_oper_list);\r\n if (!operList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = asmIdx.length; i < n; ++i) {\r\n const asm = new Assembly(complex);\r\n const assemblyOps = _extractOperations(asmOper[i], operList);\r\n const entries = asmList[i].split(',');\r\n for (let ii = 0, nn = entries.length; ii < nn; ++ii) {\r\n const chain = entries[ii].trim();\r\n if (chain.length > 0) {\r\n asm.addChain(asymDict[chain]);\r\n }\r\n }\r\n asm.matrices = assemblyOps;\r\n complex.units.push(asm);\r\n }\r\n }\r\n}\r\n\r\nCIFParser.formats = ['cif', 'mmcif'];\r\nCIFParser.extensions = ['.cif', '.mmcif'];\r\n\r\nexport default CIFParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Volume from '../../chem/Volume';\r\n\r\nexport const valueType = {\r\n singular: 0,\r\n vector: 1,\r\n array: 2,\r\n buffer: 3,\r\n};\r\n\r\nclass VolumeModel {\r\n _xyz2crs = [];\r\n\r\n _origin = new THREE.Vector3(0, 0, 0);\r\n\r\n constructor() {\r\n this._header = {};\r\n this._boxSize = new THREE.Vector3();\r\n this._boxStart = new THREE.Vector3();\r\n this._header.delta = {};\r\n this._header.extent = [];\r\n this._header.nstart = [];\r\n this._header.grid = [];\r\n this._header.crs2xyz = [];\r\n this._header.cellDims = new THREE.Vector3();\r\n this._header.angles = [];\r\n this._header.origin = new THREE.Vector3(0, 0, 0);\r\n this._header.dmin = 0;\r\n this._header.dmean = 0;\r\n this._header.dmax = 0;\r\n }\r\n\r\n _typedCheck() {\r\n if (_.isTypedArray(this._buff)) {\r\n this._buff = this._buff.buffer;\r\n } else if (!_.isArrayBuffer(this._buff)) {\r\n throw new TypeError('Expected ArrayBuffer or TypedArray');\r\n }\r\n }\r\n\r\n _fillHeader(headerFormat, arrays) {\r\n for (const key in headerFormat) {\r\n if (headerFormat.hasOwnProperty(key)) {\r\n switch (headerFormat[key][0]) {\r\n case valueType.singular:\r\n this._header[key] = arrays[headerFormat[key][1]][headerFormat[key][2]];\r\n break;\r\n\r\n case valueType.array:\r\n this._parseArray(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.vector:\r\n this._parseVector(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.buffer:\r\n this._header[key] = new Uint8Array(\r\n arrays[headerFormat[key][1]],\r\n [headerFormat[key][2]] * 4,\r\n [headerFormat[key][3]] * 4,\r\n );\r\n break;\r\n\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _parseVector(vector, arr, pos) {\r\n [vector.x, vector.y, vector.z] = [arr[pos], arr[pos + 1], arr[pos + 2]];\r\n }\r\n\r\n _parseArray(vector, arr, pos) {\r\n vector[0] = arr[pos];\r\n vector[1] = arr[pos + 1];\r\n vector[2] = arr[pos + 2];\r\n }\r\n\r\n _parseHeader(_buffer) {}\r\n\r\n _setAxisIndices() {}\r\n\r\n _setOrigins() {}\r\n\r\n _getAxis() {\r\n const header = this._header;\r\n\r\n const xScale = header.cellDims.x / header.grid[0];\r\n const yScale = header.cellDims.y / header.grid[1];\r\n const zScale = header.cellDims.z / header.grid[2];\r\n\r\n const [alpha, beta, gamma] = header.angles;\r\n\r\n const z1 = Math.cos(beta);\r\n const z2 = (Math.cos(alpha) - Math.cos(beta)\r\n * Math.cos(gamma)) / Math.sin(gamma);\r\n const z3 = Math.sqrt(1.0 - z1 * z1 - z2 * z2);\r\n\r\n const xaxis = new THREE.Vector3(xScale, 0, 0);\r\n const yaxis = new THREE.Vector3(Math.cos(gamma) * yScale, Math.sin(gamma) * yScale, 0);\r\n const zaxis = new THREE.Vector3(z1 * zScale, z2 * zScale, z3 * zScale);\r\n\r\n return [xaxis, yaxis, zaxis];\r\n }\r\n\r\n _getXYZdim() {\r\n return [this._header.extent[this._xyz2crs[0]],\r\n this._header.extent[this._xyz2crs[1]],\r\n this._header.extent[this._xyz2crs[2]]];\r\n }\r\n\r\n _getVolumeInfo() {\r\n const volInfo = _.pick(this._header, ['dmean', 'dmin', 'dmax', 'sd', 'delta']);\r\n volInfo.obtuseAngle = this._header.angles.map((angle) => Number(angle >= (Math.PI / 2)));\r\n return volInfo;\r\n }\r\n\r\n _setBoxParams(xaxis, yaxis, zaxis) {\r\n // if axes are not orthogonal, the origins might not match with box coordinates - need to make shift\r\n let shiftX = 0;\r\n let shiftY = 0;\r\n const [alpha, beta, gamma] = this._header.angles;\r\n\r\n if (gamma >= Math.PI / 2) {\r\n shiftX += Math.abs(yaxis.x);\r\n }\r\n if (beta >= Math.PI / 2) {\r\n shiftX += Math.abs(zaxis.x);\r\n }\r\n if (alpha >= Math.PI / 2) {\r\n shiftY += Math.abs(zaxis.y);\r\n }\r\n\r\n this._boxStart = new THREE.Vector3(this._origin.x - shiftX, this._origin.y - shiftY, this._origin.z);\r\n this._boxSize = new THREE.Vector3(\r\n Math.abs(xaxis.x) + Math.abs(yaxis.x) + Math.abs(zaxis.x),\r\n Math.abs(yaxis.y) + Math.abs(zaxis.y),\r\n Math.abs(zaxis.z),\r\n );\r\n\r\n const delta = (axe, proj) => (Math.abs(axe[proj]) / this._boxSize[proj]);\r\n this._header.delta.x = delta(yaxis, 'x');\r\n this._header.delta.y = delta(zaxis, 'x');\r\n this._header.delta.z = delta(zaxis, 'y');\r\n }\r\n\r\n _getXYZbox() {\r\n return new THREE.Box3(this._boxStart.clone(), this._boxStart.clone().add(this._boxSize));\r\n }\r\n\r\n _toXYZData() {}\r\n\r\n parse(data) {\r\n this._parseHeader(data);\r\n this._setOrigins();\r\n return new Volume(Float32Array, this._getXYZdim(), this._getXYZbox(), 1, this._toXYZData(), this._getVolumeInfo());\r\n }\r\n}\r\n\r\nexport default VolumeModel;\r\n","import Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\nconst CCP4Header = {\r\n extent: [valueType.array, 'u32', 0],\r\n type: [valueType.singular, 'u32', 3],\r\n nstart: [valueType.array, 'i32', 4],\r\n grid: [valueType.array, 'u32', 7],\r\n cellDims: [valueType.vector, 'f32', 10],\r\n angles: [valueType.array, 'f32', 13],\r\n crs2xyz: [valueType.array, 'i32', 16],\r\n dmin: [valueType.singular, 'f32', 19],\r\n dmax: [valueType.singular, 'f32', 20],\r\n dmean: [valueType.singular, 'f32', 21],\r\n ispg: [valueType.singular, 'u32', 22],\r\n nsymbt: [valueType.singular, 'u32', 23],\r\n lksflg: [valueType.singular, 'u32', 24],\r\n customData: [valueType.buffer, 'buffer', 25, 9],\r\n origin: [valueType.vector, 'f32', 34],\r\n map: [valueType.buffer, 'buffer', 52, 1],\r\n machine: [valueType.singular, 'u32', 53],\r\n sd: [valueType.singular, 'f32', 54],\r\n nlabel: [valueType.singular, 'f32', 55],\r\n label: [valueType.buffer, 'buffer', 56, 200],\r\n};\r\n\r\nclass Ccp4Model extends VolumeModel {\r\n // read header (http://www.ccp4.ac.uk/html/maplib.html)\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n const arrays = {};\r\n arrays.u32 = new Uint32Array(this._buff, 0, 56);\r\n arrays.i32 = new Int32Array(this._buff, 0, 56);\r\n arrays.f32 = new Float32Array(this._buff, 0, 56);\r\n arrays.buffer = this._buff;\r\n const header = this._header;\r\n\r\n this._fillHeader(CCP4Header, arrays);\r\n\r\n // calculate non-orthogonal unit cell coordinates\r\n header.angles.forEach((angle, i, a) => { a[i] *= Math.PI / 180.0; });\r\n }\r\n\r\n _setAxisIndices() {\r\n const header = this._header;\r\n\r\n if (header.cellDims.x === 0.0 && header.cellDims.y === 0.0 && header.cellDims.z === 0.0) {\r\n header.cellDims.set(1.0, 1.0, 1.0);\r\n }\r\n // Apply header conversion\r\n // Mapping between CCP4 column, row, section and VMD x, y, z.\r\n const { crs2xyz } = this._header;\r\n if (crs2xyz[0] === 0 && crs2xyz[1] === 0 && crs2xyz[2] === 0) {\r\n crs2xyz[0] = 1;\r\n crs2xyz[1] = 2;\r\n crs2xyz[2] = 3;\r\n }\r\n\r\n const xyz2crs = this._xyz2crs;\r\n xyz2crs[crs2xyz[0] - 1] = 0; // column\r\n xyz2crs[crs2xyz[1] - 1] = 1; // row\r\n xyz2crs[crs2xyz[2] - 1] = 2; // section\r\n }\r\n\r\n _setOrigins() {\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n const header = this._header;\r\n const xyz2crs = this._xyz2crs;\r\n // Handle both MRC-2000 and older format maps\r\n if (header.origin.x === 0.0 && header.origin.y === 0.0 && header.origin.z === 0.0) {\r\n this._origin.addScaledVector(xaxis, header.nstart[xyz2crs[0]]);\r\n this._origin.addScaledVector(yaxis, header.nstart[xyz2crs[1]]);\r\n this._origin.addScaledVector(zaxis, header.nstart[xyz2crs[2]]);\r\n } else {\r\n this._origin = header.origin;\r\n // Use ORIGIN records rather than old n[xyz]start records\r\n // http://www2.mrc-lmb.cam.ac.uk/image2000.html\r\n // XXX the ORIGIN field is only used by the EM community, and\r\n // has undefined meaning for non-orthogonal maps and/or non-cubic voxels, etc.\r\n }\r\n xaxis.multiplyScalar(header.extent[xyz2crs[0]] - 1);\r\n yaxis.multiplyScalar(header.extent[xyz2crs[1]] - 1);\r\n zaxis.multiplyScalar(header.extent[xyz2crs[2]] - 1);\r\n\r\n if (header.type === 2) {\r\n this._data = new Float32Array(\r\n this._buff,\r\n 1024 + header.nsymbt,\r\n header.extent[0] * header.extent[1] * header.extent[2],\r\n );\r\n } else {\r\n throw new Error(`CCP4: Unsupported format ${header.type}`);\r\n }\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const data = this._data;\r\n const xyz2crs = this._xyz2crs;\r\n const xyzData = new Float32Array(data.length);\r\n\r\n const dim = this._getXYZdim();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n\r\n let crsIdx = 0;\r\n const coord = [];\r\n let x;\r\n let y;\r\n let z;\r\n for (coord[2] = 0; coord[2] < header.extent[2]; coord[2]++) { // Site\r\n for (coord[1] = 0; coord[1] < header.extent[1]; coord[1]++) { // Row\r\n for (coord[0] = 0; coord[0] < header.extent[0]; coord[0]++, crsIdx++) { // Column\r\n x = coord[xyz2crs[0]];\r\n y = coord[xyz2crs[1]];\r\n z = coord[xyz2crs[2]];\r\n xyzData[x + xSize * (y + ySize * z)] = data[crsIdx];\r\n }\r\n }\r\n }\r\n\r\n return xyzData;\r\n }\r\n}\r\n\r\nclass CCP4Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'ccp4';\r\n this.model = new Ccp4Model();\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false; // Autodetection is not implemented yet\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nCCP4Parser.formats = ['ccp4'];\r\nCCP4Parser.extensions = ['.ccp4', '.map', '.mrc'];\r\nCCP4Parser.binary = true;\r\n\r\nexport default CCP4Parser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element, Molecule } = chem;\r\n\r\nclass XYZParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n this._options.fileType = 'xyz';\r\n this._fileName = options.name;\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*\\d+ *\\n[^\\n]*\\n\\s*\\w{1,3}\\s+-?\\d/.test(data);\r\n }\r\n\r\n _parseToAtomsInf(source) {\r\n const endnAtoms = source.indexOf('\\n');\r\n const nAtoms = parseInt(source.substring(0, endnAtoms), 10);\r\n const endComment = source.indexOf('\\n', endnAtoms + 1);\r\n let comment = source.slice(endnAtoms + 1, endComment).trim();\r\n if (comment.length === 0) {\r\n comment = this._fileName;\r\n }\r\n\r\n const startAtomsInf = endComment + source.substring(endComment).search(/\\S/);\r\n this._atomsInf = source.substring(startAtomsInf).split(/[\\s,]*\\n[\\s,]*/);\r\n if (!Number.isNaN(nAtoms) && (this._atomsInf.length - 1 !== nAtoms)) {\r\n this._complex.error = {\r\n message: 'wrong number of atoms',\r\n };\r\n return;\r\n }\r\n\r\n this._complex.metadata.format = 'xyz';\r\n this._complex.name = comment;\r\n }\r\n\r\n _parseAtomsInf() {\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n\r\n const chain = this._complex.addChain('A');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0; i < this._atomsInf.length - 1; i++) {\r\n const words = this._atomsInf[i].split(/[\\s,]+/);\r\n\r\n if (words.length !== 4) {\r\n this._complex.error = {\r\n message: 'missed parameters',\r\n };\r\n break;\r\n }\r\n\r\n const serial = i + 1;\r\n const name = words[0];\r\n const xyz = new THREE.Vector3(parseFloat(words[1]), parseFloat(words[2]), parseFloat(words[3]));\r\n const type = Element.getByName(name);\r\n const role = undefined;\r\n\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n const molecule = new Molecule(this._complex, this._complex.name, 1);\r\n molecule.residues = residue;\r\n this._complex._molecules[0] = molecule;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n\r\n this._parseToAtomsInf(this._data);\r\n this._parseAtomsInf();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n return result;\r\n }\r\n\r\n static formats = ['xyz'];\r\n\r\n static extensions = ['.xyz'];\r\n}\r\n\r\nexport default XYZParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element } = chem;\r\n\r\nclass PubChemParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'pubchem+json';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && data[0] === '{';\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing PubChem JSON file...');\r\n return this._toComplex(JSON.parse(this._data));\r\n }\r\n\r\n _toComplex(jsonData) {\r\n const complex = new Complex();\r\n const complexData = jsonData.PC_Compounds && jsonData.PC_Compounds[0];\r\n if (complexData) {\r\n this._extractAtoms(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n }\r\n return complex;\r\n }\r\n\r\n _extractAtoms(complex, complexData) {\r\n let aids = complexData.atoms && complexData.atoms.aid;\r\n let elements = aids && complexData.atoms.element;\r\n if (!elements || aids.length !== elements.length) {\r\n throw new Error('Unable to parse atom elements');\r\n }\r\n elements = _.fromPairs(_.zip(aids, elements));\r\n const atoms = {};\r\n\r\n const coords = complexData.coords && complexData.coords[0];\r\n const model = coords && coords.conformers && coords.conformers[0];\r\n const xs = model && model.x;\r\n const ys = model && model.y;\r\n const zs = (model && model.z) || [];\r\n aids = coords && coords.aid;\r\n if (!aids || !xs || !ys) {\r\n throw new Error('Coordinates are not found in the file');\r\n }\r\n\r\n const chain = complex.addChain(' ');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0, n = aids.length; i < n; ++i) {\r\n const aid = aids[i];\r\n const element = Element.ByAtomicNumber[elements[aid]];\r\n const xyz = new THREE.Vector3(xs[i], ys[i], zs[i] || 0.0);\r\n atoms[aid] = residue.addAtom(element.name, element, xyz, undefined, true, aid, ' ', 1.0, 0.0, 0);\r\n }\r\n\r\n const aids1 = complexData.bonds && complexData.bonds.aid1;\r\n const aids2 = complexData.bonds && complexData.bonds.aid2;\r\n const orders = (complexData.bonds && complexData.bonds.order) || [];\r\n if (!aids1 || !aids2 || aids1.length !== aids2.length) {\r\n return;\r\n }\r\n\r\n for (let j = 0, m = aids1.length; j < m; ++j) {\r\n complex.addBond(atoms[aids1[j]], atoms[aids2[j]], orders[j] || 1, 0, true);\r\n }\r\n }\r\n}\r\n\r\nPubChemParser.formats = ['pubchem', 'pubchem+json', 'pc'];\r\nPubChemParser.extensions = ['.json'];\r\n\r\nexport default PubChemParser;\r\n","import _ from 'lodash';\r\n\r\nexport default class SDFStream {\r\n constructor(data) {\r\n this._strings = data.split(/\\r?\\n|\\r/);\r\n this._currentStart = 0;\r\n this._currentStringIndx = 0;\r\n }\r\n\r\n setStart(start) {\r\n if (start >= this._strings.length) {\r\n this._currentStart = this._strings.length - 1;\r\n this._currentStringIndx = this._strings.length - 1;\r\n } else {\r\n this._currentStart = start;\r\n this._currentStringIndx = start;\r\n }\r\n }\r\n\r\n getNextString() {\r\n return this._strings[++this._currentStringIndx];\r\n }\r\n\r\n getCurrentString() {\r\n return this._strings[this._currentStringIndx];\r\n }\r\n\r\n getStringFromStart(numb) {\r\n this._currentStringIndx = this._currentStart + numb;\r\n return this._strings[this._currentStart + numb];\r\n }\r\n\r\n findNextDataItem() {\r\n let curStr = this.getNextString();\r\n let res = false;\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n if (curStr.match(/>\\s+<(.*)>/)) {\r\n res = true;\r\n break;\r\n }\r\n curStr = this.getNextString();\r\n }\r\n\r\n return res;\r\n }\r\n\r\n findNextCompoundStart() {\r\n let curStr = this.getCurrentString();\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n curStr = this.getNextString();\r\n }\r\n this.setStart(++this._currentStringIndx);\r\n return this.probablyHaveDataToParse();\r\n }\r\n\r\n probablyHaveDataToParse() {\r\n return this._currentStringIndx < this._strings.length - 2;\r\n }\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport SDFStream from './SDFStream';\r\nimport Assembly from '../../chem/Assembly';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst chargeMap = [0, 3, 2, 1, 0, -1, -2, -3];\r\nconst orderMap = [0, 1, 2, 3, 1, 1, 1, 2];\r\nconst typeMap = [\r\n Bond.BondType.UNKNOWN, // 0 - error\r\n Bond.BondType.COVALENT, // 1 - single\r\n Bond.BondType.COVALENT, // 2 - double\r\n Bond.BondType.COVALENT, // 3 - triple\r\n Bond.BondType.AROMATIC, // 4 - aromatic\r\n Bond.BondType.UNKNOWN, // 5 - single or double\r\n Bond.BondType.AROMATIC, // 6 - single or aromatic\r\n Bond.BondType.AROMATIC, // 7 - double or aromatic\r\n // 8 - any\r\n // 9 - coordination\r\n // 10 - hydrogen\r\n];\r\n\r\nconst sdfAndMolRegexp = /.*(M\\s\\sEND).*|.*(^$$$$).*|.*>\\s+<(.+)>.*/;\r\nconst sdfRegExp = /.*($$$$).*|.*>\\s+<(.+)>.*/;\r\n\r\nconst fileFormat = { SDF: 'sdf', MOL: 'mol' };\r\n\r\nconst possibleNameTags = ['PUBCHEM_IUPAC_TRADITIONAL_NAME', /PUBCHEM_(.+)_NAME/, /(.+)name/, /(.+)NAME/];\r\nconst possibleIDTags = ['PUBCHEM_COMPOUND_CID', 'id', 'ID', /.*CID/, /.*ID/, /.*id/];\r\nconst possibleTitleTags = ['msg', 'MSG', 'message', 'title', 'description', 'desc'];\r\nconst tagsNames = ['name', 'id', 'title'];\r\nconst tags = { name: possibleNameTags, id: possibleIDTags, title: possibleTitleTags };\r\n\r\nfunction buildChainID(index) {\r\n if (!index) {\r\n return 'A';\r\n }\r\n\r\n const codes = [];\r\n while (index) {\r\n codes.push(65 + (index % 26));\r\n index = Math.trunc(index / 26);\r\n }\r\n if (codes.length > 1) {\r\n codes.reverse();\r\n codes[0] -= 1;\r\n }\r\n\r\n return String.fromCharCode(...codes);\r\n}\r\n\r\nexport default class SDFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._format = 'sdf';\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._molecules = null;\r\n this._metadata = {};\r\n this._metadata.molecules = [];\r\n this._currentMolProps = {};\r\n this._compoundIndx = -1;\r\n this._assemblies = [];\r\n this._atomsParsed = 0;\r\n this._atomsIndexes = [];\r\n }\r\n\r\n canProbablyParse(data) {\r\n return _.isString(data) && sdfAndMolRegexp.test(data);\r\n }\r\n\r\n _parseHeader(stream) {\r\n const molecule = {};\r\n molecule.name = stream.getStringFromStart(0);\r\n const date = parseInt(stream.getStringFromStart(1).substr(10, 6).trim(), 10);\r\n molecule.date = date.toString() || '';\r\n molecule.title = stream.getStringFromStart(2);\r\n this._metadata.molecules.push(molecule);\r\n }\r\n\r\n _parseAtoms(stream, atomsNum) {\r\n let curStr;\r\n let serial = this._atomsParsed;\r\n\r\n // each molecule = chain\\residue\r\n const chainID = buildChainID(this._compoundIndx);\r\n const resName = 'UNK';\r\n const resSeq = 1;\r\n\r\n this._chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = this._chain.addResidue(resName, resSeq, ' ');\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n curStr = stream.getNextString();\r\n serial++;\r\n const x = parseFloat(curStr.substr(0, 10));\r\n const y = parseFloat(curStr.substr(10, 10));\r\n const z = parseFloat(curStr.substr(20, 10));\r\n const charge = chargeMap[parseInt(curStr.substr(36, 3), 10)];\r\n const xyz = new THREE.Vector3(x, y, z);\r\n let name = curStr.substr(31, 3).trim().toUpperCase();\r\n const type = Element.getByName(name);\r\n if (!this._atomsIndexes[name]) {\r\n this._atomsIndexes[name] = 0;\r\n }\r\n this._atomsIndexes[name] += 1;\r\n name += this._atomsIndexes[name]; // every atom need to have unique name.\r\n\r\n this._residue.addAtom(name, type, xyz, undefined, true, serial, ' ', 1.0, 0.0, charge);\r\n }\r\n }\r\n\r\n _parseBonds(stream, bondsNum) {\r\n let curStr;\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n curStr = stream.getNextString();\r\n let atom1 = parseInt(curStr.substr(0, 3), 10) + this._atomsParsed;\r\n let atom2 = parseInt(curStr.substr(3, 3), 10) + this._atomsParsed;\r\n const bondType = parseInt(curStr.substr(6, 3), 10);\r\n\r\n if (atom1 > atom2) {\r\n [atom1, atom2] = [atom2, atom1];\r\n }\r\n this._complex.addBond(\r\n atom1,\r\n atom2,\r\n orderMap[bondType] || 1,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _parseMOL(stream) {\r\n this._compoundIndx++;\r\n\r\n this._parseHeader(stream);\r\n const countsLine = stream.getStringFromStart(3);\r\n const atomsNum = parseInt(countsLine.substr(0, 3), 10);\r\n const bondsNum = parseInt(countsLine.substr(3, 3), 10);\r\n this._parseAtoms(stream, atomsNum);\r\n this._parseBonds(stream, bondsNum);\r\n\r\n this._atomsParsed += atomsNum;\r\n\r\n this._metadata.molecules[this._compoundIndx]._residues = [];\r\n this._metadata.molecules[this._compoundIndx]._residues.push(this._residue);\r\n }\r\n\r\n _parseDataItem(stream) {\r\n const tag = stream.getCurrentString();\r\n\r\n let data = [];\r\n let curStr = stream.getNextString();\r\n\r\n // read data\r\n while (curStr.trim() !== '') {\r\n data.push(curStr);\r\n curStr = stream.getNextString();\r\n }\r\n if (data.length === 1) {\r\n [data] = data;\r\n }\r\n this._currentMolProps[tag.replace(/[<>]/g, '').trim()] = data;\r\n }\r\n\r\n _parseCompound(stream) {\r\n this._parseMOL(stream);\r\n\r\n // parse data items block\r\n if (this._format === fileFormat.SDF) {\r\n this._currentMolProps = {};\r\n while (stream.findNextDataItem()) {\r\n this._parseDataItem(stream);\r\n }\r\n if (Object.keys(this._currentMolProps).length !== 0) {\r\n const molecule = this._metadata.molecules[this._compoundIndx];\r\n molecule.props = this._currentMolProps;\r\n this._tryToUpdateMoleculeData(molecule);\r\n }\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n console.log('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _buildAssemblies() {\r\n const chains = this._complex._chains;\r\n\r\n if (chains.length === 1) {\r\n return this._assemblies;\r\n }\r\n\r\n for (let i = 0; i < chains.length; i++) {\r\n const assembly = new Assembly(this._complex);\r\n const matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n assembly.addChain(chains[i]._name);\r\n this._assemblies.push(assembly);\r\n }\r\n\r\n return this._assemblies;\r\n }\r\n\r\n _buildMolecules() {\r\n this._complex._molecules = [];\r\n const { molecules } = this._metadata;\r\n for (let i = 0; i < molecules.length; i++) {\r\n const molecule = new Molecule(this._complex, molecules[i].name, i + 1);\r\n molecule.residues = molecules[i]._residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n\r\n return this._complex._molecules;\r\n }\r\n\r\n _searchTag(tag, props) {\r\n for (let i = 0; i < props.length; i++) {\r\n if ((tag instanceof RegExp && tag.test(props[i].tag)) || tag === props[i].tag) {\r\n return props[i].data;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToFind(tagsList, props) {\r\n for (let j = 0; j < tagsList.length; j++) {\r\n const res = this._searchTag(tagsList[j], props);\r\n if (res) {\r\n return res;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToUpdateMoleculeData(molecule) {\r\n let res = false;\r\n for (let i = 0; i < tagsNames.length; i++) {\r\n const tagPossibleNames = tags[tagsNames[i]];\r\n const data = this._tryToFind(tagPossibleNames, molecule.props);\r\n if (data) {\r\n molecule[tagsNames[i]] = data;\r\n res = true;\r\n }\r\n }\r\n\r\n molecule.name = molecule.name || molecule.id;\r\n if (molecule.name.match(/^\\d+$/)) {\r\n molecule.name = `CID: ${molecule.name}`;\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _finalizeMetadata() {\r\n const { molecules } = this._metadata;\r\n const { metadata } = this._complex;\r\n const complex = this._complex;\r\n\r\n if (molecules.length === 1) {\r\n complex.name = molecules[0].name;\r\n metadata.title = molecules[0].title;\r\n metadata.date = molecules[0].date;\r\n metadata.properties = molecules[0].props;\r\n } else if (molecules.length > 1) {\r\n metadata.molecules = [];\r\n for (let i = 0; i < molecules.length; i++) {\r\n metadata.molecules.push({\r\n name: molecules[i].name, date: molecules[i].date, title: molecules[i].title, properties: molecules[i].props,\r\n });\r\n }\r\n }\r\n }\r\n\r\n _finalize() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n this._complex._finalizeBonds();\r\n this._fixBondsArray();\r\n this._finalizeMetadata();\r\n this._buildAssemblies();\r\n this._complex.units = this._complex.units.concat(this._assemblies);\r\n this._buildMolecules();\r\n this._complex.finalize({\r\n needAutoBonding: false, detectAromaticLoops: false, enableEditing: false, serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n defineFormat(data) {\r\n let format;\r\n if (sdfRegExp.test(data)) {\r\n format = fileFormat.SDF;\r\n } else {\r\n format = fileFormat.MOL;\r\n }\r\n\r\n return format;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const stream = new SDFStream(this._data);\r\n\r\n this._format = this.defineFormat(this._data);\r\n result.metadata.format = this._format;\r\n\r\n do {\r\n this._parseCompound(stream);\r\n } while (stream.findNextCompoundStart());\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nSDFParser.formats = ['mol', 'sdf'];\r\nSDFParser.extensions = ['.mol', '.sdf'];\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\n// http://www.uoxray.uoregon.edu/tnt/manual/node104.html\r\nconst DSN6Header = {\r\n nstart: [valueType.array, 'i16', 0],\r\n extent: [valueType.array, 'i16', 3],\r\n grid: [valueType.array, 'i16', 6],\r\n cellDims: [valueType.vector, 'i16', 9],\r\n angles: [valueType.array, 'i16', 12],\r\n div: [valueType.singular, 'i16', 15],\r\n adder: [valueType.singular, 'i16', 16],\r\n scaleFactor: [valueType.singular, 'i16', 17],\r\n};\r\n\r\nclass DSN6Model extends VolumeModel {\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n\r\n const arrays = {};\r\n arrays.i16 = new Int16Array(this._buff);\r\n\r\n // check and reverse if big endian\r\n if (arrays.i16[18] !== 100) {\r\n for (let i = 0, n = arrays.i16.length; i < n; ++i) {\r\n const val = arrays.i16[i];\r\n arrays.i16[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff);\r\n }\r\n }\r\n if (arrays.i16[18] !== 100) {\r\n throw new Error('DSN6: Incorrect format ');\r\n }\r\n\r\n const header = this._header;\r\n\r\n this._fillHeader(DSN6Header, arrays);\r\n header.cellDims.multiplyScalar(1.0 / header.scaleFactor);\r\n header.angles.forEach((angle, i, a) => { a[i] *= (Math.PI / 180.0) / header.scaleFactor; });\r\n header.div /= 100;\r\n }\r\n\r\n _setAxisIndices() {\r\n this._xyz2crs[0] = 0;\r\n this._xyz2crs[1] = 1;\r\n this._xyz2crs[2] = 2;\r\n }\r\n\r\n _setOrigins() {\r\n const header = this._header;\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n this._origin.addScaledVector(xaxis, header.nstart[0]);\r\n this._origin.addScaledVector(yaxis, header.nstart[1]);\r\n this._origin.addScaledVector(zaxis, header.nstart[2]);\r\n\r\n xaxis.multiplyScalar(header.extent[0]);\r\n yaxis.multiplyScalar(header.extent[1]);\r\n zaxis.multiplyScalar(header.extent[2]);\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _pointCalculate(xyzData, byteBuffer, z, y, x, pos, i) {\r\n const header = this._header;\r\n\r\n if (x < header.extent[0] && y < header.extent[1] && z < header.extent[2]) {\r\n const idx = x + header.extent[0] * (y + header.extent[1] * z);\r\n xyzData[idx] = (byteBuffer[pos.counter] - header.adder) / header.div;\r\n ++pos.counter;\r\n } else {\r\n pos.counter += 8 - i;\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n _blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos) {\r\n for (let k = 0; k < 8; ++k) {\r\n const z = 8 * zBlock + k;\r\n for (let j = 0; j < 8; ++j) {\r\n const y = 8 * yBlock + j;\r\n let inRange = true;\r\n let i = 0;\r\n while (inRange && i < 8) {\r\n const x = 8 * xBlock + i;\r\n inRange = this._pointCalculate(xyzData, byteBuffer, z, y, x, pos, i);\r\n i++;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const byteBuffer = new Uint8Array(this._buff);\r\n const xyzData = new Float32Array(header.extent[0] * header.extent[1] * header.extent[2]);\r\n\r\n const blocks = new THREE.Vector3(header.extent[0] / 8, header.extent[1] / 8, header.extent[2] / 8);\r\n\r\n const pos = {};\r\n pos.counter = 512;\r\n\r\n for (let zBlock = 0; zBlock < blocks.z; ++zBlock) {\r\n for (let yBlock = 0; yBlock < blocks.y; ++yBlock) {\r\n for (let xBlock = 0; xBlock < blocks.x; ++xBlock) {\r\n this._blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos);\r\n }\r\n }\r\n }\r\n this._calculateInfoParams(xyzData);\r\n return xyzData;\r\n }\r\n\r\n _calculateInfoParams(xyzData) {\r\n this._header.dmean /= xyzData.length;\r\n let dispersion = 0;\r\n let minDensity = xyzData[0];\r\n let maxDensity = xyzData[0];\r\n for (let j = 0; j < xyzData.length; j++) {\r\n dispersion += (this._header.dmean - xyzData[j]) ** 2;\r\n\r\n if (xyzData[j] < minDensity) {\r\n minDensity = xyzData[j];\r\n }\r\n if (xyzData[j] > maxDensity) {\r\n maxDensity = xyzData[j];\r\n }\r\n }\r\n this._header.sd = Math.sqrt(dispersion / xyzData.length);\r\n this._header.dmax = maxDensity;\r\n this._header.dmin = minDensity;\r\n }\r\n}\r\n\r\nclass DSN6Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'dsn6';\r\n this.model = new DSN6Model();\r\n }\r\n\r\n static canParse(data, options) {\r\n if (!data) {\r\n return false;\r\n }\r\n return data instanceof ArrayBuffer && Parser.checkDataTypeOptions(options, 'dsn6');\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false;\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nDSN6Parser.formats = ['dsn6'];\r\nDSN6Parser.extensions = ['.dsn6', '.omap'];\r\nDSN6Parser.binary = true;\r\n\r\nexport default DSN6Parser;\r\n","import PDBStream from './PDBStream';\r\n\r\n/**\r\n * Little helper class for GRO Parser usage.\r\n * @extends PDBStream\r\n */\r\nclass GROReader extends PDBStream {\r\n constructor(data) {\r\n super(data);\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n this.next();\r\n }\r\n\r\n /**\r\n * Getting end of string.\r\n * @returns {Number} Pointer to end of string\r\n */\r\n getNext() {\r\n return this._next;\r\n }\r\n}\r\n\r\nexport default GROReader;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport GROReader from './GROReader';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Molecule,\r\n} = chem;\r\n\r\n/**\r\n * Gromos87 file format parser.\r\n * @extends Parser\r\n */\r\nclass GROParser extends Parser {\r\n /**\r\n * Create parser for .gro file format\r\n *\r\n * @param {String} data Input file\r\n * @param {String} options Input options (optional field)\r\n */\r\n constructor(data, options) {\r\n super(data, options);\r\n /** @type Date */\r\n this._time = null; // Time in ps, optional field for animations\r\n /** @type Number */\r\n this._numAtoms = null; // Number of atoms in complex\r\n /** @type Number */\r\n this._residueNumber = null; // Number of exact residue\r\n /** @type String */\r\n this._residueName = ''; // Scientific name of exact residue\r\n /** @type String */\r\n this._atomName = ''; // Scientific name of exact atom\r\n /** @type Number */\r\n this._atomNumber = null; // Sorted number of exact atom\r\n /** @type Array */\r\n this._atomPosition = []; // Array which contains x, y, z position of exact atom\r\n /** @type Array */\r\n this._atomVelocity = []; // Array which contains x, y, z velocity of exact atom (optional)\r\n /** @type Complex */\r\n this._complex = null; // Complex structure for unified molecule representation\r\n /** @type Vector3 */\r\n this._molecules = []; // Molecules array\r\n /** @type Molecule */\r\n this._molecule = null; // Single molecule\r\n /** @type String */\r\n this._options.filetype = 'gro'; // Extension of data file.\r\n }\r\n\r\n /**\r\n * General check for possibility of parsing.\r\n * @param {String} data - Input file\r\n * @returns {boolean} true if this file is in ascii, false otherwise\r\n */\r\n canProbablyParse(data) {\r\n return _.isString(this._data) && /^\\s*[^\\n]*\\n\\s*\\d+ *\\n\\s*\\d+[^\\n\\d]{3}\\s*\\w+\\s*\\d+\\s*-?\\d/.test(data);\r\n }\r\n\r\n /**\r\n * Parsing title of molecule complex.\r\n * NOTE: that names are ESTIMATES, there is no strict rules in Gromos87 standard for first line in input file.\r\n * @param {GROReader} line - Line containing title and time.\r\n */\r\n _parseTitle(line) {\r\n const { metadata } = this._complex;\r\n metadata.id = line.readLine().trim();\r\n metadata.name = metadata.id.slice(metadata.id.lastIndexOf('\\\\') + 1, metadata.id.lastIndexOf('.'));\r\n metadata.format = 'gro';\r\n }\r\n\r\n /**\r\n * Parsing line containing number of atoms information.\r\n * @param {GROReader} line - Line containing number of atoms.\r\n */\r\n _parseNumberOfAtoms(line) {\r\n this._numAtoms = line.readInt(0, line.getNext());\r\n if (Number.isNaN(this._numAtoms)) {\r\n throw new Error('Line 2 is not representing atom number. Consider checking input file');\r\n }\r\n }\r\n\r\n /**\r\n * Parsing line containing information about residues, atoms etc. Also information about box vectors.\r\n * Format of atoms MUST (by Gromos87 standard) be this: (note that numbering starts not from 0, but from 1!)\r\n * ResidueNumber[1 - 5] ResidueName[6 - 10] AtomName[11 - 15] AtomNumber[16 - 20] Position[21 - 45] Velocity[46 - 69]\r\n * @param {GROReader} line - Line containing information about atom.\r\n */\r\n _parseAtom(line) {\r\n this._residueNumber = line.readInt(1, 5);\r\n this._residueName = line.readString(6, 10).trim();\r\n this._atomName = line.readString(11, 15).trim();\r\n this._atomNumber = line.readInt(16, 20);\r\n const positionX = line.readFloat(21, 28) * 10;\r\n const positionY = line.readFloat(29, 36) * 10;\r\n const positionZ = line.readFloat(37, 45) * 10;\r\n if (Number.isNaN(positionX) || Number.isNaN(positionY) || Number.isNaN(positionZ)) {\r\n this._complex.error = {\r\n message: `Atom position is invalid in \"${line.readLine()}\"`,\r\n };\r\n return;\r\n }\r\n /* const velocityX = line.readFloat(46, 53);\r\n const velocityY = line.readFloat(54, 61);\r\n const velocityZ = line.readFloat(62, 69); */\r\n /* Adding residue and atom to complex structure */\r\n const type = Element.getByName(this._atomName[0]); /* MAGIC 0. REASONS: This name is something like \"CA\", where\r\n C - is an element an A is something else. But what about Calcium? */\r\n if (type.fullName === 'Unknown') {\r\n this._complex.error = {\r\n message: `${this._atomName[0]} hasn't been recognised as an atom name.`,\r\n };\r\n return;\r\n }\r\n const role = Element.Role[this._atomName];\r\n /* Firstly, create a dummy chain */\r\n let chain = this._chain;\r\n if (!chain) {\r\n this._chain = chain = this._complex.addChain('A');\r\n }\r\n /* Secondly, add residue to that chain */\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== this._residueNumber) {\r\n this._residue = residue = chain.addResidue(this._residueName, this._residueNumber, ' ');\r\n }\r\n /* Lastly, add atom to that residue */\r\n this._atomPosition = new THREE.Vector3(positionX, positionY, positionZ);\r\n /* Adding default constants to correct atom addition process */\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n residue.addAtom(this._atomName, type, this._atomPosition, role, het, this._atomNumber, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n /**\r\n * Some finalizing procedures. In '.gro' file format there is only 1 chain and 1 molecule.\r\n */\r\n _finalize() {\r\n const molecule = new Molecule(this._complex, this._complex.metadata.name, 1);\r\n // aggregate residues from chain\r\n molecule.residues = this._chain._residues;\r\n molecule._chains = this._chain;\r\n this._complex._molecules[0] = molecule;\r\n this._molecules.push(molecule);\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n /**\r\n * Main parsing procedure.\r\n * @returns {Complex} Complex structure for visualizing.\r\n */\r\n parseSync() {\r\n /* Create \"Complex\" variable */\r\n const result = this._complex = new Complex();\r\n /* Parse input file line-by-line */\r\n const reader = new GROReader(this._data);\r\n let counter = 0; /* Simple counter regarding to format of .gro file */\r\n /* First two lines - technical information, other lines - Atoms */\r\n this._parseTitle(reader);\r\n reader.next();\r\n this._parseNumberOfAtoms(reader);\r\n reader.next();\r\n for (counter = 0; counter < this._numAtoms; ++counter) {\r\n if (!reader.end()) {\r\n this._parseAtom(reader);\r\n reader.next();\r\n } else break;\r\n }\r\n /* If number of atoms in second line is less then actual atoms in file */\r\n if (counter < this._numAtoms) {\r\n this._complex.error = {\r\n message: 'File ended unexpectedly.',\r\n };\r\n }\r\n /* Catch errors occurred in parsing process */\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n\r\n /* Finalizing data */\r\n this._finalize();\r\n\r\n /* Cleaning up */\r\n this._atomPosition = null;\r\n this._complex = null;\r\n this._molecules = null;\r\n this._molecule = null;\r\n\r\n /* Return resulting Complex variable */\r\n return result;\r\n }\r\n}\r\n\r\nGROParser.formats = ['gro'];\r\nGROParser.extensions = ['.gro'];\r\n\r\nexport default GROParser;\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst orderMap = {\r\n un: 0,\r\n 1: 1,\r\n 2: 2,\r\n 3: 3,\r\n ar: 1,\r\n am: 1,\r\n nc: 0,\r\n du: 1,\r\n};\r\nconst typeMap = {\r\n un: Bond.BondType.UNKNOWN, // unknown (cannot be determined from the parameter tables)\r\n 1: Bond.BondType.COVALENT, // single\r\n 2: Bond.BondType.COVALENT, // double\r\n 3: Bond.BondType.COVALENT, // triple\r\n ar: Bond.BondType.AROMATIC, // aromatic\r\n am: Bond.BondType.COVALENT, // amide\r\n nc: Bond.BondType.UNKNOWN, // not connected\r\n du: Bond.BondType.COVALENT, // dummy\r\n};\r\n\r\nconst resNumberRegex = /\\d+$/;\r\nconst spacesRegex = /\\s+/;\r\n\r\nfunction splitToFields(str) {\r\n return str.trim().split(spacesRegex);\r\n}\r\n/* There is no jsdoc documentation because of eslint corrections:\r\n * not all Parser methods are implemented\r\n */\r\n\r\nclass MOL2Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._compoundIndx = -1;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n\r\n this._currPosIdx = 0;\r\n this._currStartIdx = 0;\r\n\r\n this._serialAtomMap = {};\r\n\r\n this._options.fileType = 'mol2';\r\n }\r\n\r\n _parseRawStrings(data) {\r\n return data.split(/\\r?\\n|\\r/);\r\n }\r\n\r\n _toStringFromStart(numb, MOL2Data) {\r\n const newPosIdx = this._currStartIdx + numb;\r\n this._currPosIdx = (newPosIdx < MOL2Data.length) ? newPosIdx : this._currStartIdx;\r\n }\r\n\r\n _toHeaderString(header, MOL2Data) {\r\n this._toStringFromStart(0, MOL2Data);\r\n while (this._currPosIdx < MOL2Data.length) {\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`)) {\r\n return;\r\n }\r\n this._currPosIdx++;\r\n }\r\n this._toStringFromStart(0, MOL2Data);\r\n }\r\n\r\n _toStringFromHeader(header, numb, MOL2Data) {\r\n this._toHeaderString(header, MOL2Data);\r\n const newPosIdx = this._currPosIdx + numb;\r\n\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`) && newPosIdx < MOL2Data.length) {\r\n this._currPosIdx = newPosIdx;\r\n }\r\n }\r\n\r\n _setStart(startPos, MOL2Data) {\r\n if (startPos >= MOL2Data.length) {\r\n this._currStartIdx = this._currPosIdx = MOL2Data.length - 1;\r\n } else {\r\n this._currStartIdx = this._currPosIdx = startPos;\r\n }\r\n }\r\n\r\n _probablyHaveDataToParse(MOL2Data) {\r\n return this._currPosIdx < MOL2Data.length - 2;\r\n }\r\n\r\n _findNextCompoundStart(MOL2Data) {\r\n while (this._currPosIdx < MOL2Data.length && MOL2Data[this._currPosIdx].trim() !== '@MOLECULE>') {\r\n this._currPosIdx++;\r\n }\r\n this._setStart(++this._currPosIdx, MOL2Data);\r\n return this._probablyHaveDataToParse(MOL2Data);\r\n }\r\n\r\n _parseMolecule(MOL2Data) {\r\n this._toHeaderString('MOLECULE', MOL2Data);\r\n\r\n const { metadata } = this._complex;\r\n metadata.name = MOL2Data[++this._currPosIdx];\r\n metadata.format = 'mol2';\r\n\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = this._compoundIndx + 1;\r\n this._molecules.push(this._molecule);\r\n }\r\n\r\n /* Atom format description:\r\n * atomId atomName x y z element [resSeq [resName [charge [statusBit]]]]\r\n * statusBits is the internal SYBYL status bits associated with the atom.\r\n * These should never be set by the user.\r\n * Source: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf\r\n */\r\n _parseAtoms(atomsNum, MOL2Data) {\r\n this._toHeaderString('ATOM', MOL2Data);\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 6) {\r\n throw new Error('MOL2 parsing error: Not enough information to create atom!');\r\n }\r\n const atomId = parseInt(parsedStr[0], 10);\r\n const atomName = parsedStr[1];\r\n\r\n const x = parseFloat(parsedStr[2]);\r\n const y = parseFloat(parsedStr[3]);\r\n const z = parseFloat(parsedStr[4]);\r\n\r\n const element = parsedStr[5].split('.')[0].toUpperCase();\r\n\r\n let charge = 0;\r\n if (parsedStr.length >= 9) {\r\n charge = parseFloat(parsedStr[8]) || 0.0;\r\n }\r\n\r\n let chain = this._chain;\r\n if (!chain) {\r\n // .mol2 may contain information about multiple molecules, but they can't be visualized\r\n // at the same time now. There is no need to create different chain IDs then.\r\n this._chain = chain = this._complex.getChain('A') || this._complex.addChain('A');\r\n this._residue = null;\r\n }\r\n if (!this._setResidue(parsedStr)) {\r\n continue;\r\n }\r\n\r\n // These fields are not listed in mol2 format. Set them default.\r\n // Atoms and het atoms doesn't differ in .mol2,\r\n // but het atoms have special residues. It can be used in next updates\r\n const het = false;\r\n const altLoc = ' ';\r\n const occupancy = 1.0;\r\n const tempFactor = 0.0;\r\n const type = Element.getByName(element);\r\n const role = Element.Role[atomName];\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n this._residue.addAtom(atomName, type, xyz, role, het, atomId, altLoc, occupancy, tempFactor, charge);\r\n }\r\n }\r\n\r\n _setResidue(parsedStr) {\r\n let resSeq = 1;\r\n let resName = 'UNK'; // The same meaning has '<0>' in some mol2 files\r\n\r\n if (parsedStr.length >= 7) {\r\n resSeq = parseInt(parsedStr[6], 10);\r\n }\r\n if (parsedStr.length >= 8 && parsedStr[7] !== '<0>') {\r\n resName = parsedStr[7].replace(resNumberRegex, '');\r\n }\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return false;\r\n }\r\n }\r\n const residue = this._residue;\r\n const chain = this._chain;\r\n if (!residue || residue.getSequence() !== resSeq) {\r\n this._residue = chain.addResidue(resName, resSeq, 'A');\r\n }\r\n return true;\r\n }\r\n\r\n /* Bond format description\r\n * bondId originAtomId targetAtomId bondType [statusBits]\r\n */\r\n _parseBonds(bondsNum, MOL2Data) {\r\n this._toHeaderString('BOND', MOL2Data);\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 3) {\r\n throw new Error('MOL2 parsing error: Missing information about bonds!');\r\n }\r\n\r\n let originAtomId = parseInt(parsedStr[1], 10);\r\n let targetAtomId = parseInt(parsedStr[2], 10);\r\n const bondType = parsedStr[3];\r\n\r\n if (originAtomId > targetAtomId) {\r\n [originAtomId, targetAtomId] = [targetAtomId, originAtomId];\r\n }\r\n this._complex.addBond(\r\n originAtomId,\r\n targetAtomId,\r\n orderMap[bondType] || 0,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _fixSerialAtoms() {\r\n const atoms = this._complex._atoms;\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n this._serialAtomMap[atom.serial] = atom;\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n if (Object.keys(serialAtomMap).length === 0) {\r\n throw new Error('MOL2 parsing error: Missing atom information!');\r\n }\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _finalizeMolecules() {\r\n // Get chain from complex\r\n const chain = this._complex._chains[0];\r\n this._complex._molecules = [];\r\n\r\n // Aggregate residues from chains\r\n // (to be precise from the chain 'A')\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const currMolecule = this._molecules[i];\r\n const molResidues = chain._residues;\r\n const molecule = new Molecule(this._complex, currMolecule._name, i + 1);\r\n molecule.residues = molResidues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _finalize() {\r\n this._complex._finalizeBonds();\r\n this._fixSerialAtoms();\r\n this._fixBondsArray();\r\n this._finalizeMolecules();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _parseCompound(MOL2Data) {\r\n this._compoundIndx++;\r\n this._parseMolecule(MOL2Data);\r\n\r\n // Ignoring comments and everything before @MOLECULE block\r\n this._toStringFromHeader('MOLECULE', 2, MOL2Data);\r\n\r\n const parsedStr = MOL2Data[this._currPosIdx].trim().split(spacesRegex);\r\n const atomsNum = parsedStr[0];\r\n const bondsNum = parsedStr[1];\r\n\r\n this._parseAtoms(atomsNum, MOL2Data);\r\n this._parseBonds(bondsNum, MOL2Data);\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const MOL2Data = this._parseRawStrings(this._data);\r\n do {\r\n this._parseCompound(MOL2Data);\r\n } while (this._findNextCompoundStart(MOL2Data));\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nMOL2Parser.formats = ['mol2'];\r\nMOL2Parser.extensions = ['.mol2', '.ml2', '.sy2'];\r\n\r\nexport default MOL2Parser;\r\n","import ParserList from './parsers/ParserList';\r\n\r\nimport PDBParser from './parsers/PDBParser';\r\nimport CMLParser from './parsers/CMLParser';\r\nimport MMTFParser from './parsers/MMTFParser';\r\nimport CIFParser from './parsers/CIFParser';\r\nimport CCP4Parser from './parsers/CCP4Parser';\r\nimport XYZParser from './parsers/XYZParser';\r\nimport PubChemParser from './parsers/PubChemParser';\r\nimport SDFParser from './parsers/SDFParser';\r\nimport DSN6Parser from './parsers/DSN6Parser';\r\nimport GROParser from './parsers/GROParser';\r\nimport MOL2Parser from './parsers/MOL2Parser';\r\n\r\nexport default new ParserList([\r\n // note: order might be important\r\n PDBParser,\r\n CIFParser,\r\n MMTFParser,\r\n XYZParser,\r\n CMLParser,\r\n PubChemParser,\r\n SDFParser,\r\n CCP4Parser,\r\n DSN6Parser,\r\n GROParser,\r\n MOL2Parser,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available exporters.\r\n * @extends EntityList\r\n */\r\nclass ExporterList extends EntityList {\r\n /**\r\n * Create a list of exporters.\r\n * The exporters are indexed by supported data formats (`.formats` and\r\n * `.extensions` properties of a Exporter subclass).\r\n * The Exporters can be retrieved later by matching against specs (see {@link ExporterList#find}).\r\n *\r\n * @param {!Array=} someExporters A list of {@link Exporter} subclasses to\r\n * automatically register at creation time.\r\n * @see ExporterList#register\r\n */\r\n constructor(someExporters = []) {\r\n super(someExporters, ['formats']);\r\n }\r\n\r\n /**\r\n * Find a suitable exporter for data.\r\n *\r\n * @param {Object} specs Exporter specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {*=} specs.data Data to export.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ExporterList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Exporter {\r\n constructor(source, options) {\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n exportSync() {\r\n throw new Error('Exporting to this source is not implemented');\r\n }\r\n\r\n export() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Export aborted'));\r\n }\r\n return resolve(this.exportSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Exporter.prototype);\r\n","import _ from 'lodash';\r\nimport { Matrix4 } from 'three';\r\n\r\nexport default class PDBResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._currentStr = -1;\r\n this._tag = null;\r\n this._fixedNumeration = false;\r\n this._numeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n\r\n getResult() {\r\n this.writeString('\\n', 81, 81);\r\n return this._resultArray.join('');\r\n }\r\n\r\n _currentStrLength() {\r\n const curStr = this._resultArray[this._currentStr];\r\n return curStr ? curStr.length : 0;\r\n }\r\n\r\n // numeration can be number or boolean\r\n // if numeration is number then just put this number to 8-10 pos in string\r\n // if numeration is boolean then increase number for all new strings\r\n newTag(tag, numeration) {\r\n if (!tag) {\r\n this._tag = null;\r\n } else {\r\n this._tag = tag;\r\n }\r\n if (!_.isUndefined(numeration)) {\r\n if (_.isNumber(numeration)) {\r\n this._tagStrNum = numeration;\r\n this._numeration = true;\r\n this._fixedNumeration = true;\r\n } else if (_.isBoolean(numeration)) {\r\n this._tagStrNum = 0;\r\n this._numeration = numeration;\r\n this._fixedNumeration = false;\r\n }\r\n } else {\r\n this._numeration = false;\r\n this._fixedNumeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n }\r\n\r\n newString(tag) {\r\n this.writeString('\\n', 81, 81);\r\n this._currentStr++;\r\n this._resultArray.push('');\r\n\r\n if (tag) {\r\n this.writeString(tag, 1, 6);\r\n } else if (this._tag) {\r\n this.writeString(this._tag, 1, 6);\r\n }\r\n\r\n if (this._numeration) {\r\n if (!this._fixedNumeration) {\r\n this._tagStrNum++;\r\n }\r\n if (this._tagStrNum !== 1) {\r\n this.writeString(this._tagStrNum.toString(), 10, 8);\r\n }\r\n }\r\n }\r\n\r\n writeEntireString(string, maxStrPos, concat) {\r\n if (!maxStrPos) {\r\n maxStrPos = 81;\r\n }\r\n for (let j = 0; j < string.length; j++) {\r\n if (this._currentStrLength() === maxStrPos && j !== string.length - 1) {\r\n this.newString();\r\n if (concat) { // pretty hardcoddy\r\n this.writeString(concat.tag, concat.begin, concat.end);\r\n }\r\n }\r\n if (string[j] === '\\n') {\r\n this.newString();\r\n } else {\r\n this.writeString(string[j]);\r\n }\r\n }\r\n }\r\n\r\n writeString(string, begin, end) {\r\n let curStr = this._resultArray[this._currentStr];\r\n let str;\r\n\r\n const curStrLength = curStr ? curStr.length : 0;\r\n\r\n if (_.isUndefined(string)) {\r\n return;\r\n }\r\n\r\n if (!_.isNumber(begin)) {\r\n begin = curStrLength + 1;\r\n }\r\n\r\n if (!_.isNumber(end)) {\r\n end = curStrLength + string.length;\r\n }\r\n\r\n if (!_.isString(string)) {\r\n str = string.toString();\r\n } else {\r\n str = string;\r\n }\r\n\r\n const finish = begin < end ? end : begin;\r\n const start = begin < end ? begin : end;\r\n\r\n if (str.length > Math.abs(begin - end) + 1) {\r\n str = str.substr(0, Math.abs(begin - end + 1));\r\n }\r\n\r\n // spaces before start of new data\r\n if (start > curStrLength + 1) {\r\n this._resultArray[this._currentStr] += ' '.repeat(start - curStrLength - 1);\r\n } else if (start <= curStrLength) {\r\n const cStr = this._resultArray[this._currentStr];\r\n this._resultArray[this._currentStr] = cStr.slice(0, start - 1);\r\n }\r\n\r\n // if reverse order\r\n // reverse order of end and begin means that user wants to align text right\r\n if (end < begin) {\r\n const len = begin - end + 1;\r\n str = ' '.repeat(len - str.length) + str;\r\n }\r\n\r\n // some hardcode fix for space between string numeration and data\r\n // (see pdb file format description)\r\n if (start === 11 && this._numeration && this._tagStrNum !== 1) {\r\n str = ` ${str}`;\r\n }\r\n\r\n // append new data to string\r\n this._resultArray[this._currentStr] += str;\r\n curStr = this._resultArray[this._currentStr];\r\n\r\n if (finish > curStr.length) {\r\n this._resultArray[this._currentStr] += ' '.repeat(finish - curStr.length);\r\n }\r\n }\r\n\r\n writeBondsArray(bonds, atom) {\r\n const bondsArrays = this._getSubArrays(bonds, 4);\r\n\r\n for (let k = 0; k < bondsArrays.length; k++) {\r\n this.newString();\r\n this.writeString(atom.serial, 11, 7);\r\n\r\n for (let j = 0; j < bondsArrays[k].length; j++) {\r\n const serial = (bondsArrays[k][j]._left.serial === atom.serial)\r\n ? bondsArrays[k][j]._right.serial : bondsArrays[k][j]._left.serial;\r\n\r\n this.writeString(serial, 16 + 5 * j, 12 + 5 * j);\r\n }\r\n }\r\n }\r\n\r\n _getSubArrays(arr, subArraySize) {\r\n const subArrays = [];\r\n for (let i = 0; i < arr.length; i += subArraySize) {\r\n subArrays.push(arr.slice(i, i + subArraySize));\r\n }\r\n return subArrays;\r\n }\r\n\r\n // function for writing matrix in Remark290 and Remark350 tags\r\n // (see pdb file description)\r\n writeMatrix(matrix, matrixIndx, tag) {\r\n for (let j = 0; j < 3; j++) {\r\n this.newString();\r\n this.writeString(tag, 14, 18);\r\n this.writeString((j + 1).toString(), 19, 19);\r\n this.writeString(matrixIndx.toString(), 23, 20);\r\n for (let k = 0; k < 3; k++) {\r\n const numb = parseFloat(matrix.elements[j * 4 + k]).toFixed(6);\r\n this.writeString(numb.toString(), 33 + k * 10, 24 + k * 10);\r\n }\r\n\r\n const numb = parseFloat(matrix.elements[j * 4 + 3]).toFixed(5);\r\n this.writeString(numb.toString(), 68, 55);\r\n }\r\n }\r\n\r\n writeMatrices(matrices, string) {\r\n if (!matrices) {\r\n return;\r\n }\r\n const matrix = new Matrix4();\r\n for (let j = 0; j < matrices.length; j++) {\r\n matrix.copy(matrices[j]).transpose();\r\n this.writeMatrix(matrix, j + 1, string);\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport Complex from '../../chem/Complex';\r\nimport Exporter from './Exporter';\r\nimport PDBResult from './PDBResult';\r\nimport Assembly from '../../chem/Assembly';\r\nimport { typeByPDBHelixClass } from '../../chem/Helix';\r\n\r\nexport default class PDBExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n this._tags = ['HEADER', 'TITLE', 'COMPND', 'REMARK', 'HELIX', 'SHEET', 'ATOM and HETATM', 'CONECT'];\r\n this._result = null;\r\n this._tagExtractors = {\r\n HEADER: this._extractHEADER,\r\n TITLE: this._extractTITLE,\r\n 'ATOM and HETATM': this._extractATOM,\r\n CONECT: this._extractCONECT,\r\n COMPND: this._extractCOMPND,\r\n REMARK: this._extractREMARK,\r\n HELIX: this._extractHELIX,\r\n SHEET: this._extractSHEET,\r\n };\r\n this._stringForRemark350 = 'COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN\\n'\r\n + 'BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE\\n'\r\n + 'MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS\\n'\r\n + 'GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND\\n'\r\n + 'CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.';\r\n\r\n this._stringForRemark290 = 'CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS\\n'\r\n + 'THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM\\n'\r\n + 'RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY\\n'\r\n + 'RELATED MOLECULES.';\r\n }\r\n\r\n exportSync() {\r\n const result = new PDBResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n for (let i = 0; i < this._tags.length; i++) {\r\n const tag = this._tags[i];\r\n const func = this._tagExtractors[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, result);\r\n }\r\n }\r\n\r\n this._result = result.getResult();\r\n\r\n return this._result;\r\n }\r\n\r\n _extractHEADER(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n result.newTag('HEADER');\r\n result.newString();\r\n if (metadata.classification) {\r\n result.writeString(metadata.classification, 11, 50);\r\n }\r\n if (metadata.date) {\r\n result.writeString(metadata.date, 51, 59);\r\n }\r\n if (metadata.id) {\r\n result.writeString(metadata.id, 63, 66);\r\n }\r\n }\r\n\r\n _extractTITLE(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n if (!metadata.title) {\r\n return;\r\n }\r\n result.newTag('TITLE', true);\r\n for (let i = 0; i < metadata.title.length; i++) {\r\n result.newString();\r\n result.writeString(metadata.title[i], 11, 80);\r\n }\r\n }\r\n\r\n _extractCONECT(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n\r\n const atoms = this._source._atoms;\r\n result.newTag('CONECT');\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const fixedBonds = atoms[i].bonds.filter((bond) => bond._fixed);\r\n if (fixedBonds.length !== 0) {\r\n result.writeBondsArray(fixedBonds.reverse(), atoms[i]);\r\n }\r\n }\r\n }\r\n\r\n _extractSHEET(result) {\r\n if (!this._source._sheets) {\r\n return;\r\n }\r\n\r\n result.newTag('SHEET');\r\n\r\n const sheets = this._source._sheets;\r\n for (let i = 0; i < sheets.length; i++) {\r\n if (sheets[i]._strands) {\r\n const strands = sheets[i]._strands;\r\n for (let j = 0; j < strands.length; j++) {\r\n result.newString();\r\n result.writeString(j + 1, 10, 8);\r\n result.writeString(sheets[i]._name, 14, 12);\r\n result.writeString(strands.length, 16, 15);\r\n result.writeString(strands[j].init._type._name, 18, 20);\r\n result.writeString(strands[j].init._chain._name, 22, 22);\r\n result.writeString(strands[j].init._sequence, 26, 23);\r\n result.writeString(strands[j].init._icode, 27, 27);\r\n result.writeString(strands[j].term._type._name, 29, 31);\r\n result.writeString(strands[j].init._chain._name, 33, 33);\r\n result.writeString(strands[j].term._sequence, 37, 34);\r\n result.writeString(strands[j].term._icode, 38, 38);\r\n result.writeString(strands[j].sense, 40, 39);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _extractHELIX(result) {\r\n if (!this._source._helices) {\r\n return;\r\n }\r\n\r\n result.newTag('HELIX');\r\n const helices = this._source._helices;\r\n for (let i = 0; i < helices.length; i++) {\r\n const helix = helices[i];\r\n const helixClass = _.invert(typeByPDBHelixClass);\r\n result.newString();\r\n result.writeString(helix.serial, 10, 8);\r\n result.writeString(helix.name, 14, 12);\r\n result.writeString(helix.init._type._name, 16, 18);\r\n result.writeString(helix.init._chain._name, 20, 20);\r\n result.writeString(helix.init._sequence, 25, 22);\r\n result.writeString(helix.init._icode, 26, 26);\r\n result.writeString(helix.term._type._name, 28, 30);\r\n result.writeString(helix.term._chain._name, 32, 32);\r\n result.writeString(helix.term._sequence, 37, 34);\r\n result.writeString(helix.term._icode, 38, 38);\r\n result.writeString(helixClass[helix.type], 40, 39);\r\n result.writeString(helix.comment, 41, 70);\r\n result.writeString(helix.length, 76, 72);\r\n }\r\n }\r\n\r\n _extractATOM(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n const atoms = this._source._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const tag = atoms[i].het ? 'HETATM' : 'ATOM';\r\n result.newString(tag);\r\n const startIndx = (atoms[i].element.name.length > 1 || atoms[i].name.length > 3) ? 13 : 14;\r\n result.writeString(atoms[i].serial, 11, 7);\r\n result.writeString(atoms[i].name, startIndx, 16);\r\n result.writeString(String.fromCharCode(atoms[i].location), 17, 17);\r\n result.writeString(atoms[i].residue._type._name, 20, 18);\r\n result.writeString(atoms[i].residue._chain._name, 22, 22);\r\n result.writeString(atoms[i].residue._sequence, 26, 23);\r\n result.writeString(atoms[i].residue._icode, 27, 27);\r\n result.writeString(atoms[i].position.x.toFixed(3), 38, 31);\r\n result.writeString(atoms[i].position.y.toFixed(3), 46, 39);\r\n result.writeString(atoms[i].position.z.toFixed(3), 54, 47);\r\n result.writeString(atoms[i].occupancy.toFixed(2), 60, 55);\r\n result.writeString(atoms[i].temperature.toFixed(2), 66, 61);\r\n result.writeString(atoms[i].element.name, 78, 77);\r\n if (atoms[i].charge) {\r\n result.writeString(atoms[i].charge, 79, 80);\r\n }\r\n }\r\n }\r\n\r\n _extractCOMPND(result) {\r\n if (!this._source._molecules) {\r\n return;\r\n }\r\n const molecules = this._source._molecules;\r\n result.newTag('COMPND', true);\r\n\r\n for (let i = 0; i < molecules.length; i++) {\r\n const chains = this._getMoleculeChains(molecules[i]);\r\n result.newString();\r\n result.writeString(`MOL_ID: ${molecules[i].index};`, 11, 80);\r\n result.newString();\r\n result.writeString(`MOLECULE: ${molecules[i].name};`, 11, 80);\r\n result.newString();\r\n result.writeString('CHAIN: ', 11, 18);\r\n const chainsString = `${chains.join(', ')};`;\r\n result.writeEntireString(chainsString, 81);\r\n }\r\n }\r\n\r\n _extractREMARK(result) {\r\n this._Remark290(result);\r\n this._Remark350(result);\r\n }\r\n\r\n _Remark290(result) {\r\n if (!this._source.symmetry) {\r\n return;\r\n }\r\n\r\n if (this._source.symmetry.length !== 0) {\r\n const matrices = this._source.symmetry;\r\n result.newTag('REMARK', 290);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark290);\r\n result.writeMatrices(matrices, 'SMTRY');\r\n result.newString();\r\n result.newString();\r\n result.writeString('REMARK: NULL', 11, 80);\r\n }\r\n }\r\n\r\n _Remark350(result) {\r\n if (!this._source.units) {\r\n return;\r\n }\r\n const { units } = this._source;\r\n let biomolIndx = 0;\r\n\r\n result.newTag('REMARK', 350);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark350);\r\n\r\n const assemblies = units.filter((unit) => unit instanceof Assembly);\r\n\r\n for (let i = 0; i < assemblies.length; i++) {\r\n result.newString();\r\n result.newString();\r\n biomolIndx++;\r\n result.writeString(`BIOMOLECULE: ${biomolIndx}`, 11, 80);\r\n const chains = assemblies[i].chains.join(', ');\r\n result.newString();\r\n result.writeString('APPLY THE FOLLOWING TO CHAINS: ');\r\n result.writeEntireString(chains, 69, { tag: 'AND CHAINS: ', begin: 31, end: 42 });\r\n\r\n const { matrices } = assemblies[i];\r\n result.writeMatrices(matrices, 'BIOMT');\r\n }\r\n }\r\n\r\n _getMoleculeChains(molecule) {\r\n function getChainName(residue) {\r\n return residue._chain._name;\r\n }\r\n const chainNames = molecule.residues.map(getChainName);\r\n return chainNames.filter((item, pos) => chainNames.indexOf(item) === pos);\r\n }\r\n}\r\n\r\nPDBExporter.formats = ['pdb'];\r\nPDBExporter.SourceClass = Complex;\r\n","import * as THREE from 'three';\r\n\r\nconst FBX_POS_SIZE = 3;\r\nconst FBX_NORM_SIZE = 3;\r\nconst FBX_COL_SIZE = 4;\r\n\r\nfunction copyFbxPoint3(src, srcIdx, dst, dstIdx) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n}\r\n\r\nfunction copyFbxPoint4(src, srcIdx, dst, dstIdx, value) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n dst[dstIdx + 3] = value;\r\n}\r\n\r\nconst vector4 = new THREE.Vector4();\r\nfunction copyTransformedPoint3(src, srcIdx, dst, dstIdx, opts) {\r\n vector4.set(src[srcIdx], src[srcIdx + 1], src[srcIdx + 2], opts.w);\r\n vector4.applyMatrix4(opts.matrix);\r\n dst[dstIdx] = vector4.x;\r\n dst[dstIdx + 1] = vector4.y;\r\n dst[dstIdx + 2] = vector4.z;\r\n}\r\n\r\nfunction setSubArray(src, dst, count, copyFunctor, functorOpts) {\r\n if ((dst.array.length - dst.start) / dst.stride < count\r\n || (src.array.length - src.start) / src.stride < count) {\r\n return; // we've got no space\r\n }\r\n if (src.stride === dst.stride) { // stride is the same\r\n dst.array.set(src.array, dst.start);\r\n } else {\r\n let idx = dst.start;\r\n let arridx = src.start;\r\n for (let i = 0; i < count; ++i, idx += dst.stride, arridx += src.stride) {\r\n copyFunctor(src.array, arridx, dst.array, idx, functorOpts);\r\n }\r\n }\r\n}\r\n\r\nexport default class FBXModel {\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.lastPos = 0;\r\n this.lastNorm = 0;\r\n this.lastCol = 0;\r\n this.lastIdx = 0;\r\n }\r\n\r\n init(vertsCount, indsCount) {\r\n this.positions = new Float32Array(vertsCount * FBX_POS_SIZE);\r\n this.normals = new Float32Array(vertsCount * FBX_NORM_SIZE);\r\n this.colors = new Float32Array(vertsCount * FBX_COL_SIZE);\r\n this.indices = new Int32Array(indsCount);\r\n }\r\n\r\n setPositions(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.positions,\r\n start: this.lastPos,\r\n stride: FBX_POS_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setTransformedPositions(array, start, count, stride, matrix) {\r\n let idx = this.lastPos;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 1 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_POS_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.positions, idx, opts);\r\n }\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setNormals(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.normals,\r\n start: this.lastNorm,\r\n stride: FBX_NORM_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setTransformedNormals(array, start, count, stride, matrix) {\r\n let idx = this.lastNorm;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 0 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_NORM_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.normals, idx, opts);\r\n }\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setColors(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.colors,\r\n start: this.lastCol,\r\n stride: FBX_COL_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint4, 1);\r\n this.lastCol += count * FBX_COL_SIZE;\r\n }\r\n\r\n setIndices(array, start, count) {\r\n this.indices.set(array, this.lastIdx);\r\n this.lastIdx += count;\r\n }\r\n\r\n setShiftedIndices(array, count, shift) {\r\n const shifted = array.map((x) => x + shift);\r\n this.setIndices(shifted, 0, count);\r\n }\r\n\r\n getVerticesNumber() {\r\n return this.lastPos / FBX_POS_SIZE;\r\n }\r\n\r\n addInstance(matrix, geo) {\r\n // add indices at first to take old number of vertices for shift\r\n const currentCount = this.getVerticesNumber();\r\n this.setShiftedIndices(geo.indices, geo.indices.length, currentCount);\r\n // simply write vertices at empty space\r\n const size = geo.itemSize;\r\n this.setTransformedPositions(geo.positions, 0, geo.vertsCount, size.position, matrix);\r\n this.setTransformedNormals(geo.normals, 0, geo.vertsCount, size.normal, matrix);\r\n this.setColors(geo.colors, 0, geo.vertsCount, size.color);\r\n }\r\n}\r\n","/** Base class for fbx geometry contains simply organized attributes: positions+normals+colors, indices. */\r\nexport default class FBXGeometry {\r\n /**\r\n * Create a base geo with necessary members.\r\n */\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.vertsCount = 0;\r\n this.itemSize = null;\r\n }\r\n\r\n /**\r\n * Initialize base geo storing items info from attributes.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n const { attributes } = geo;\r\n // save item size\r\n this.itemSize = {\r\n position: attributes.position.itemSize,\r\n normal: attributes.normal.itemSize,\r\n color: attributes.color.itemSize,\r\n };\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes and creates colors filled with defined value.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX1CGeometry extends FBXGeometry {\r\n /**\r\n * Initialize geo storing positions, normals, indices and create colors.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n super.init(geo, _info);\r\n const {\r\n attributes: {\r\n position,\r\n normal,\r\n },\r\n index,\r\n } = geo;\r\n // copy vertices attributes\r\n this.vertsCount = position.count;\r\n this.positions = position.array;\r\n this.normals = normal.array;\r\n // create color array\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n // indices\r\n this.indices = index.array;\r\n }\r\n\r\n /**\r\n * Set defined color for all items in color attribute\r\n * @param {Object} color - THREE.Color.\r\n */\r\n setColors(color) {\r\n let offset = 0;\r\n for (let i = 0, l = this.colors.length, cl = this.itemSize.color; i < l; i += cl) {\r\n this.colors[offset++] = color.r;\r\n this.colors[offset++] = color.g;\r\n this.colors[offset++] = color.b;\r\n }\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes from cylinder geometry and creates colors filled with two\r\n * defined values.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX2CCylinder extends FBXGeometry {\r\n constructor() {\r\n super();\r\n this._cutRawStart = 0;\r\n this._cutRawEnd = 0;\r\n this._facesPerSlice = 0;\r\n }\r\n\r\n /**\r\n * Initialize geo by creating new attributes, because we extend number of vertices to make cylinder two-colored.\r\n * Indices remain the same. We process open- end close-ended cylinders and consider cylinders od 2 segments\r\n * in height ONLY.\r\n * NOTE: cylinder consists of 2 height segments and stores parts in the order: tube, topCap, bottomCap\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n * @param {Object} info - information needed for geo extend\r\n */\r\n init(geo, info) {\r\n super.init(geo, info);\r\n const {\r\n attributes: {\r\n position,\r\n },\r\n index,\r\n } = geo;\r\n // extend vertices arrays\r\n this.vertsCount = position.count + info.addPerCylinder;\r\n this._facesPerSlice = info.addPerCylinder;\r\n this.positions = new Float32Array(this.vertsCount * position.itemSize);\r\n this.normals = new Float32Array(this.vertsCount * this.itemSize.normal);\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n this._extendVertices(geo, info);\r\n // number of indices stays the same\r\n this.indices = new Uint32Array(index.count);\r\n this._extendIndices(geo, info);\r\n }\r\n\r\n /** Extend vertex attributes to have one more slice to make sharp middle startColor-endColor line. */\r\n _extendVertices(geo, info) {\r\n const { position } = geo.attributes;\r\n const { normal } = geo.attributes;\r\n const geoParams = geo.getGeoParams();\r\n const cutRaw = 1; // we expect cylinders of 2 segments in height => so half segment = 1\r\n this._cutRawStart = cutRaw * geoParams.radialSegments;\r\n this._cutRawEnd = this._cutRawStart + info.addPerCylinder;\r\n { // write first half of cylinder\r\n let temp = position.array.slice(0, this._cutRawEnd * position.itemSize);\r\n this.positions.set(temp, 0);\r\n temp = normal.array.slice(0, this._cutRawEnd * normal.itemSize);\r\n this.normals.set(temp, 0);\r\n }\r\n { // write second part of cylinder\r\n let temp = position.array.slice(this._cutRawStart * position.itemSize, position.array.length);\r\n this.positions.set(temp, this._cutRawEnd * position.itemSize);\r\n temp = normal.array.slice(this._cutRawStart * normal.itemSize, normal.array.length);\r\n this.normals.set(temp, this._cutRawEnd * normal.itemSize);\r\n }\r\n }\r\n\r\n /** Shift values of second part (+caps) indices by newly added vertices count. Number of faces remains the same. */\r\n _extendIndices(geo, info) {\r\n const { index } = geo;\r\n const indicesPerQuad = 6; // quad = 2 triangles => 6 indices\r\n const startToShift = info.addPerCylinder * indicesPerQuad;\r\n const shift = info.addPerCylinder;\r\n let shifted = index.array.slice(startToShift, index.count);\r\n shifted = shifted.map((x) => x + shift); // shift only the endings\r\n this.indices.set(index.array, 0);\r\n this.indices.set(shifted, startToShift);\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {number} start - start color index\r\n * @param {number} end - start color index\r\n * @param {array} array - array of colors\r\n * @param {array} color - color value components\r\n */\r\n _setColorRange(start, end, array, color) {\r\n const colorSize = color.length;\r\n for (let i = start; i < end; i += colorSize) {\r\n array.set(color, i);\r\n }\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {Object} color1 - THREE.Color.\r\n * @param {Object} color2 - THREE.Color.\r\n */\r\n setColors(color1, color2) {\r\n const colorSize = this.itemSize.color;\r\n const part1End = this._cutRawEnd * colorSize;\r\n const part2End = part1End * 2;\r\n this._setColorRange(0, part1End, this.colors, color1.toArray());\r\n this._setColorRange(part1End, part2End, this.colors, color2.toArray());\r\n if (part2End < this.colors.length) { // cylinder has caps, lets paint them\r\n const capSize = (this._facesPerSlice + 1) * colorSize;\r\n const cap1End = part2End + capSize;\r\n this._setColorRange(part2End, cap1End, this.colors, color2.toArray());\r\n const cap2End = cap1End + capSize; // should be equal to this.colors.length;\r\n this._setColorRange(cap1End, cap2End, this.colors, color1.toArray());\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\n\r\nimport utils from '../../../utils';\r\nimport gfxutils from '../../../gfx/gfxutils';\r\nimport logger from '../../../utils/logger';\r\n\r\nimport FBXModel from './FBXModel';\r\nimport ThickLineMesh from '../../../gfx/meshes/ThickLineMesh';\r\nimport ZSpriteMesh from '../../../gfx/meshes/ZSpriteMesh';\r\nimport InstancedSpheresGeometry from '../../../gfx/geometries/InstancedSpheresGeometry';\r\nimport Instanced2CCylindersGeometry from '../../../gfx/geometries/Instanced2CCylindersGeometry';\r\nimport FBX1CGeometry from './FBX1CGeometry';\r\nimport FBX2CCylinder from './FBX2CCylinder';\r\n\r\nexport default class FBXInfoExtractor {\r\n constructor() {\r\n this._materials = [];\r\n this._models = [];\r\n }\r\n\r\n process(data) {\r\n this._extractModelsAndMaterials(data);\r\n const models = this._flattenModels();\r\n\r\n return {\r\n name: data.name,\r\n models,\r\n materials: this._materials,\r\n };\r\n }\r\n\r\n /**\r\n * Extract fbx object information from ComplexVisual\r\n * @param {object} data - complexVisual to get geometry info from\r\n */\r\n _extractModelsAndMaterials(data) {\r\n const layersOfInterest = new THREE.Layers();\r\n layersOfInterest.set(gfxutils.LAYERS.DEFAULT);\r\n layersOfInterest.enable(gfxutils.LAYERS.TRANSPARENT);\r\n data.traverse((object) => {\r\n if (object instanceof THREE.Mesh && object.layers.test(layersOfInterest) && this.checkExportAbility(object)) {\r\n if (object.geometry.type === 'InstancedBufferGeometry') {\r\n this._collectInstancedGeoInfo(object);\r\n } else {\r\n this._collectGeoInfo(object);\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Reworking indices buffer, see https://banexdevblog.wordpress.com/2014/06/23/a-quick-tutorial-about-the-fbx-ascii-format/\r\n * basically, every triangle in Miew has been represented hat way (e.g.) : 0,1,7, but we must (for FBX) rework that\r\n * into: 0,1,-8.\r\n * @param {array} indices - belongs to [0, maxVertIndex]\r\n */\r\n _reworkIndices(indices) {\r\n const faceSize = 3;\r\n for (let i = faceSize - 1; i < indices.length; i += faceSize) {\r\n indices[i] *= -1;\r\n indices[i]--;\r\n }\r\n }\r\n\r\n /**\r\n * Combine geometry from several models having the same material into one Model and finally prepare indices\r\n * @returns {array} models, combined by material id\r\n */\r\n _flattenModels() {\r\n let overallVertsCount = 0;\r\n function shift(x) {\r\n return x + overallVertsCount;\r\n }\r\n const combined = [];\r\n // flatten models geometry\r\n for (let i = 0, n = this._models.length; i < n; i++) {\r\n const models = this._models[i];\r\n let indices = [];\r\n let positions = [];\r\n let normals = [];\r\n let colors = [];\r\n // reorganize every attributes as array of arrays\r\n overallVertsCount = 0;\r\n for (let j = 0; j < models.length; j++) {\r\n const m = models[j];\r\n indices.push(m.indices.map(shift));\r\n overallVertsCount += m.getVerticesNumber();\r\n positions.push(m.positions);\r\n normals.push(m.normals);\r\n colors.push(m.colors);\r\n }\r\n // join all subarrays into one\r\n indices = utils.mergeTypedArraysUnsafe(indices);\r\n this._reworkIndices(indices);\r\n positions = utils.mergeTypedArraysUnsafe(positions);\r\n normals = utils.mergeTypedArraysUnsafe(normals);\r\n colors = utils.mergeTypedArraysUnsafe(colors);\r\n combined.push({\r\n indices,\r\n positions,\r\n normals,\r\n colors,\r\n verticesCount: overallVertsCount,\r\n });\r\n }\r\n return combined;\r\n }\r\n\r\n /**\r\n * Check ability to export the kind of mesh.\r\n * @param {object} mesh - given mesh to check\r\n * @returns {boolean} result of check\r\n */\r\n checkExportAbility(mesh) {\r\n // check mesh on not being empty\r\n if (mesh.geometry.attributes.position.count === 0) {\r\n return false;\r\n }\r\n // check type of mesh\r\n // if (mesh.geometry.isInstancedBufferGeometry && settings.now.zSprites) {\r\n if (mesh instanceof ZSpriteMesh) {\r\n logger.warn('Currently we cannot export \\'sprites\\' modes, like BS, WV, LC. Please turn of settings \\'zSprites\\' and try again');\r\n return false;\r\n }\r\n if (mesh instanceof ThickLineMesh) {\r\n logger.warn('Currently we cannot export Lines mode');\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n /**\r\n * Save geometry info from common mesh, like Surface or Cartoon\r\n */\r\n _collectGeoInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n normal,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const vertCount = position.count;\r\n model.init(vertCount, index.count);\r\n if (matrix.isIdentity()) {\r\n model.setPositions(position.array, 0, vertCount, position.itemSize);\r\n model.setNormals(normal.array, 0, vertCount, normal.itemSize);\r\n } else {\r\n model.setTransformedPositions(position.array, 0, vertCount, position.itemSize, matrix);\r\n model.setTransformedNormals(normal.array, 0, vertCount, normal.itemSize, matrix);\r\n }\r\n model.setColors(color.array, 0, vertCount, color.itemSize);\r\n model.setIndices(index.array, 0, index.count);\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Collect instanced spheres geometry and materials.\r\n * @param {object} mesh - mesh with instanced spheres info\r\n */\r\n _collectSpheresInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount, instCount * indsCount);\r\n const geo = new FBX1CGeometry();\r\n geo.init(mesh.geometry);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const sphereColor = new THREE.Color();\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n sphereColor.fromArray(color.array, colorIdx);\r\n geo.setColors(sphereColor);\r\n // add instance to the model\r\n this._getSphereInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Getting all instanced cylinders from given mesh.\r\n * Divide cylinder (add additional vertexes) for prettiness therefore algorithm is a bit complicated\r\n * @param {object} mesh - given mesh with instanced cylinders\r\n */\r\n _collectCylindersInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n color2,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const oneCCylinder = new FBX1CGeometry();\r\n oneCCylinder.init(mesh.geometry);\r\n const splittingInfo = this._gatherCylindersColoringInfo(mesh.geometry);\r\n let twoCCylinder = null;\r\n if (splittingInfo.needToSplit > 0) {\r\n twoCCylinder = new FBX2CCylinder();\r\n twoCCylinder.init(mesh.geometry, splittingInfo);\r\n }\r\n const additionalVertsCount = splittingInfo.addPerCylinder * splittingInfo.needToSplit;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount + additionalVertsCount, instCount * indsCount);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const colorStart = new THREE.Color();\r\n const colorEnd = new THREE.Color();\r\n let geo = {};\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n if (splittingInfo.is2Colored[instanceIndex]) {\r\n // .color2 contains starting color, and .color contains starting color (see uber.frag ATTR_COLOR2)\r\n colorStart.fromArray(color2.array, colorIdx);\r\n colorEnd.fromArray(color.array, colorIdx);\r\n if (twoCCylinder) {\r\n twoCCylinder.setColors(colorStart, colorEnd);\r\n geo = twoCCylinder;\r\n }\r\n } else {\r\n // has one color per cylinder\r\n colorStart.fromArray(color.array, colorIdx);\r\n oneCCylinder.setColors(colorStart);\r\n geo = oneCCylinder;\r\n }\r\n // add instance to the model\r\n this._getCylinderInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Adding model to pool of models or extend existing ones\r\n * @param {object} model - model to add\r\n * @param {object} material - material to add\r\n */\r\n _addToPool(model, material) {\r\n const materialIdx = this._checkExistingMaterial(material);\r\n if (materialIdx < 0) { // new model-material pair\r\n this._models.push([model]);\r\n this._materials.push(material);\r\n } else { // add model to existing model-material pair\r\n const models = this._models[materialIdx];\r\n models.push(model);\r\n }\r\n }\r\n\r\n /**\r\n * Checking if given material already was registered in materials pool (no need to create new one)\r\n * @param {object} material - given material\r\n * @returns {number} number of model-material pair\r\n */\r\n _checkExistingMaterial(material) {\r\n return _.findIndex(this._materials, (m) => _.isEqual(m, material));\r\n }\r\n\r\n _gatherCylindersColoringInfo(geo) {\r\n const instCount = geo.instanceCount;\r\n const color1 = geo.attributes.color.array;\r\n const color2 = geo.attributes.color2.array;\r\n const stride = geo.attributes.color.itemSize;\r\n const is2Colored = new Array(instCount);\r\n // analyze color instance attributes\r\n let needToSplit = 0;\r\n let colIdx = 0;\r\n for (let i = 0; i < instCount; i++, colIdx += stride) {\r\n const differs = (Math.abs(color1[colIdx] - color2[colIdx]) > 0.0000001) // compare ending colors\r\n || (Math.abs(color1[colIdx + 1] - color2[colIdx + 1]) > 0.0000001)\r\n || (Math.abs(color1[colIdx + 2] - color2[colIdx + 2]) > 0.0000001);\r\n is2Colored[i] = differs;\r\n needToSplit += differs; // count number of 2-colored cylinders\r\n }\r\n // calc number of vertices to add into 2-colored\r\n const geoParams = geo.getGeoParams();\r\n const addPerCylinder = geoParams.radialSegments;\r\n return { is2Colored, needToSplit, addPerCylinder };\r\n }\r\n\r\n /**\r\n * Collect instanced models and materials.\r\n * @param {object} mesh - given mesh with instanced something (spheres or cylinders)\r\n */\r\n _collectInstancedGeoInfo(mesh) {\r\n if (mesh.geometry instanceof InstancedSpheresGeometry) {\r\n this._collectSpheresInfo(mesh);\r\n } else if (mesh.geometry instanceof Instanced2CCylindersGeometry) {\r\n this._collectCylindersInfo(mesh);\r\n }\r\n }\r\n\r\n /**\r\n * Collect Material info from given mesh.\r\n * @param {object} mesh - given mesh with material info\r\n * @returns {object} material\r\n */\r\n _collectMaterialInfo(mesh) {\r\n const { uberOptions } = mesh.material;\r\n return ({\r\n diffuse: uberOptions.diffuse.toArray(),\r\n opacity: uberOptions.opacity,\r\n shininess: uberOptions.shininess,\r\n specular: uberOptions.specular.toArray(),\r\n });\r\n }\r\n\r\n _getCylinderInstanceMatrix(geo, instIdx, matrix) {\r\n const matVector1 = geo.attributes.matVector1.array;\r\n const matVector2 = geo.attributes.matVector2.array;\r\n const matVector3 = geo.attributes.matVector3.array;\r\n const idxOffset = instIdx * 4; // used 4 because offset arrays are stored in quads\r\n matrix.set(\r\n matVector1[idxOffset],\r\n matVector1[idxOffset + 1],\r\n matVector1[idxOffset + 2],\r\n matVector1[idxOffset + 3],\r\n matVector2[idxOffset],\r\n matVector2[idxOffset + 1],\r\n matVector2[idxOffset + 2],\r\n matVector2[idxOffset + 3],\r\n matVector3[idxOffset],\r\n matVector3[idxOffset + 1],\r\n matVector3[idxOffset + 2],\r\n matVector3[idxOffset + 3],\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n\r\n _getSphereInstanceMatrix(geo, instIdx, matrix) {\r\n const { offset } = geo.attributes;\r\n const idx = instIdx * offset.itemSize;\r\n const x = offset.array[idx];\r\n const y = offset.array[idx + 1];\r\n const z = offset.array[idx + 2];\r\n const scale = offset.array[idx + 3];\r\n matrix.set(\r\n scale,\r\n 0,\r\n 0,\r\n x,\r\n 0,\r\n scale,\r\n 0,\r\n y,\r\n 0,\r\n 0,\r\n scale,\r\n z,\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n}\r\n","// Forming default definitions block\r\nconst defaultDefinitions = `\r\nDefinitions: {\r\n Version: 100\r\n Count: 3\r\n ObjectType: \"Model\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Geometry\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Material\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Pose\" {\r\n Count: 1\r\n }\r\n ObjectType: \"GlobalSettings\" {\r\n Count: 1\r\n }\r\n} `;\r\n\r\n// Default model properties\r\nconst defaultProperties = `Properties60: {\r\n Property: \"QuaternionInterpolate\", \"bool\", \"\",0\r\n Property: \"Visibility\", \"Visibility\", \"A\",1\r\n Property: \"Lcl Translation\", \"Lcl Translation\", \"A\",0.000000000000000,0.000000000000000,-1789.238037109375000\r\n Property: \"Lcl Rotation\", \"Lcl Rotation\", \"A\",0.000009334667643,-0.000000000000000,0.000000000000000\r\n Property: \"Lcl Scaling\", \"Lcl Scaling\", \"A\",1.000000000000000,1.000000000000000,1.000000000000000\r\n Property: \"RotationOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationActive\", \"bool\", \"\",0\r\n Property: \"TranslationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMinX\", \"bool\", \"\",0\r\n Property: \"TranslationMinY\", \"bool\", \"\",0\r\n Property: \"TranslationMinZ\", \"bool\", \"\",0\r\n Property: \"TranslationMaxX\", \"bool\", \"\",0\r\n Property: \"TranslationMaxY\", \"bool\", \"\",0\r\n Property: \"TranslationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationOrder\", \"enum\", \"\",0\r\n Property: \"RotationSpaceForLimitOnly\", \"bool\", \"\",0\r\n Property: \"AxisLen\", \"double\", \"\",10\r\n Property: \"PreRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"PostRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationActive\", \"bool\", \"\",0\r\n Property: \"RotationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMinX\", \"bool\", \"\",0\r\n Property: \"RotationMinY\", \"bool\", \"\",0\r\n Property: \"RotationMinZ\", \"bool\", \"\",0\r\n Property: \"RotationMaxX\", \"bool\", \"\",0\r\n Property: \"RotationMaxY\", \"bool\", \"\",0\r\n Property: \"RotationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationStiffnessX\", \"double\", \"\",0\r\n Property: \"RotationStiffnessY\", \"double\", \"\",0\r\n Property: \"RotationStiffnessZ\", \"double\", \"\",0\r\n Property: \"MinDampRangeX\", \"double\", \"\",0\r\n Property: \"MinDampRangeY\", \"double\", \"\",0\r\n Property: \"MinDampRangeZ\", \"double\", \"\",0\r\n Property: \"MaxDampRangeX\", \"double\", \"\",0\r\n Property: \"MaxDampRangeY\", \"double\", \"\",0\r\n Property: \"MaxDampRangeZ\", \"double\", \"\",0\r\n Property: \"MinDampStrengthX\", \"double\", \"\",0\r\n Property: \"MinDampStrengthY\", \"double\", \"\",0\r\n Property: \"MinDampStrengthZ\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthX\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthY\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthZ\", \"double\", \"\",0\r\n Property: \"PreferedAngleX\", \"double\", \"\",0\r\n Property: \"PreferedAngleY\", \"double\", \"\",0\r\n Property: \"PreferedAngleZ\", \"double\", \"\",0\r\n Property: \"InheritType\", \"enum\", \"\",0\r\n Property: \"ScalingActive\", \"bool\", \"\",0\r\n Property: \"ScalingMin\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMax\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMinX\", \"bool\", \"\",0\r\n Property: \"ScalingMinY\", \"bool\", \"\",0\r\n Property: \"ScalingMinZ\", \"bool\", \"\",0\r\n Property: \"ScalingMaxX\", \"bool\", \"\",0\r\n Property: \"ScalingMaxY\", \"bool\", \"\",0\r\n Property: \"ScalingMaxZ\", \"bool\", \"\",0\r\n Property: \"GeometricTranslation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricScaling\", \"Vector3D\", \"\",1,1,1\r\n Property: \"LookAtProperty\", \"object\", \"\"\r\n Property: \"UpVectorProperty\", \"object\", \"\"\r\n Property: \"Show\", \"bool\", \"\",1\r\n Property: \"NegativePercentShapeSupport\", \"bool\", \"\",1\r\n Property: \"DefaultAttributeIndex\", \"int\", \"\",0\r\n Property: \"Color\", \"Color\", \"A+\",0,0,0\r\n Property: \"Size\", \"double\", \"\",100\r\n Property: \"Look\", \"enum\", \"\",1\r\n }`;\r\n\r\n// Default materials layer\r\nconst defaultMaterialLayer = `\r\n LayerElementMaterial: 0 {\r\n Version: 101\r\n Name: \"\"\r\n MappingInformationType: \"AllSame\"\r\n ReferenceInformationType: \"Direct\"\r\n Materials: 0\r\n }`;\r\n\r\n// Default layers block\r\nconst defaultLayerBlock = `\r\n Layer: 0 {\r\n Version: 100\r\n LayerElement: {\r\n Type: \"LayerElementNormal\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementColor\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementMaterial\"\r\n TypedIndex: 0\r\n }\r\n }`;\r\n\r\n/**\r\n * globalSettings info in output file.\r\n */\r\nconst globalSettings = `GlobalSettings: {\r\n Version: 1000\r\n Properties60: {\r\n Property: \"UpAxis\", \"int\", \"\",1\r\n Property: \"UpAxisSign\", \"int\", \"\",1\r\n Property: \"FrontAxis\", \"int\", \"\",2\r\n Property: \"FrontAxisSign\", \"int\", \"\",1\r\n Property: \"CoordAxis\", \"int\", \"\",0\r\n Property: \"CoordAxisSign\", \"int\", \"\",1\r\n Property: \"UnitScaleFactor\", \"double\", \"\",1\r\n }\r\n }`;\r\n\r\nexport default class FBXResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._info = null;\r\n }\r\n\r\n getResult(info) {\r\n this._info = info;\r\n this._resultArray.push(this._writeHeader());\r\n this._resultArray.push(this._writeDefinitions());\r\n this._resultArray.push(this._writeObjects(info.models, info.materials));\r\n this._resultArray.push(this._writeRelations());\r\n this._resultArray.push(this._writeConnections()); // connections between models and materials)\r\n this._info = null;\r\n return this._resultArray.join('');\r\n }\r\n\r\n /**\r\n * Add FBXHeader info to output file.\r\n * Some fields are really confusing, but it seems that all listed fields are very informative\r\n */\r\n _writeHeader() {\r\n const FBXHeaderVersion = 1003; // 1003 is some number which appears to present in many 6.1 ASCII files\r\n const FBXVersion = 6100; // Mandatory and only supported version\r\n const date = new Date();\r\n const timeStampVersion = 1000;\r\n const creator = `Miew FBX Exporter v${this._info.version}`; // Supposed to be an engine\r\n\r\n return `; FBX 6.1.0 project file\r\n; Created by ${creator} Copyright (c) 2015-2026 EPAM Systems, Inc.\r\n; For support please contact miew@epam.com\r\n; ----------------------------------------------------\r\n\r\nFBXHeaderExtension: {\r\n FBXHeaderVersion: ${FBXHeaderVersion}\r\n FBXVersion: ${FBXVersion}\r\n CreationTimeStamp: {\r\n Version: ${timeStampVersion}\r\n Year: ${date.getFullYear()}\r\n Month: ${date.getMonth() + 1}\r\n Day: ${date.getDate()}\r\n Hour: ${date.getHours()}\r\n Minute: ${date.getMinutes()}\r\n Second: ${date.getSeconds()}\r\n Millisecond: ${date.getMilliseconds()}\r\n }\r\n Creator: \"${creator}\"\r\n OtherFlags: {\r\n FlagPLE: 0\r\n }\r\n}\r\nCreationTime: \"${date}\"\r\nCreator: \"${creator}\"\r\n`;\r\n }\r\n\r\n /**\r\n * Add Definitions info to output file.\r\n * Not exactly sure if this section is template section (as it is in 7.4+) or it should every time be like this\r\n */\r\n _writeDefinitions() {\r\n return `\r\n; Object definitions\r\n;------------------------------------------------------------------\r\n\r\n${defaultDefinitions}\r\n`;\r\n }\r\n\r\n /**\r\n * Adding gathered information about Models to resulting string.\r\n * Reminder - there may be more then 1 model in scene, but we must place materials after ALL models.\r\n * @returns {string} string containing all models (vertices, indices, colors, normals etc)\r\n */\r\n _models() {\r\n const modelVersion = 232;\r\n let allModels = '';\r\n const { models } = this._info;\r\n for (let i = 0; i < models.length; ++i) {\r\n const model = models[i];\r\n const vertCount = model.verticesCount;\r\n allModels += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n Version: ${modelVersion}\r\n ${defaultProperties}\r\n ${this._verticesIndices(model.positions, model.indices)}\r\n ${this._normalLayer(model.normals)}\r\n ${this._colorLayer(model.colors, vertCount)}\r\n ${defaultMaterialLayer}\r\n ${defaultLayerBlock}\r\n }`;\r\n }\r\n return allModels;\r\n }\r\n\r\n /**\r\n * Add Material info to result\r\n */\r\n _materials() {\r\n const materialVersion = 102;\r\n let allMaterials = '';\r\n const { materials } = this._info;\r\n for (let i = 0; i < materials.length; ++i) {\r\n const material = materials[i];\r\n allMaterials += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n Version: ${materialVersion}\r\n ShadingModel: \"lambert\"\r\n MultiLayer: 0\r\n ${this._materialProperties(material)}\r\n }`;\r\n }\r\n return allMaterials;\r\n }\r\n\r\n /**\r\n * Add Objects info to output file.\r\n */\r\n _writeObjects() {\r\n return `\r\n; Object properties\r\n;------------------------------------------------------------------\r\n\r\nObjects: {\r\n ${this._models()}\r\n ${this._materials()}\r\n ${globalSettings}\r\n}\r\n`;\r\n }\r\n\r\n /**\r\n * Add Relations info to output file.\r\n */\r\n _writeRelations() {\r\n let modelsList = '';\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n }`;\r\n }\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n }`;\r\n }\r\n\r\n return `\r\n; Object relations\r\n;------------------------------------------------------------------\r\n\r\nRelations: {\r\n ${modelsList}\r\n Model: \"Model::Producer Perspective\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Top\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Bottom\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Front\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Back\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Right\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Left\", \"Camera\" {\r\n }\r\n Model: \"Model::Camera Switcher\", \"CameraSwitcher\" {\r\n }\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Add Connections info to output file.\r\n */\r\n _writeConnections() {\r\n let modelsList = '';\r\n const { name } = this._info;\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Connect: \"OO\", \"Model::${name}_${i}\", \"Model::Scene\"`;\r\n }\r\n\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Connect: \"OO\", \"Material::${name}_${i}_default\", \"Model::${name}_${i}\"`;\r\n }\r\n\r\n return `\r\n; Object connections\r\n;------------------------------------------------------------------\r\n\r\nConnections: {\r\n ${modelsList}\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Write float array to string with limited precision\r\n * @param {Float32Array} array - array to be fixed\r\n * @returns {String} String with fixed floats\r\n */\r\n _floatArrayToString(array) {\r\n const str = [];\r\n for (let i = 0; i < array.length; ++i) {\r\n str[i] = array[i].toFixed(6);\r\n }\r\n return str.join(',');\r\n }\r\n\r\n /**\r\n * Adding color layer to resulting file\r\n * @param {Float32Array} colorArray attribute\r\n * @param {number} vertCount - number of vertices in the model\r\n * @returns {string} color layer info\r\n */\r\n _colorLayer(colorArray, vertCount) {\r\n const layerElementColorNumber = 0;\r\n const layerElementColorVersion = 101;\r\n const layerElementColorName = '';\r\n const colorsStr = this._floatArrayToString(colorArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n // As said [..Array(...)] - fastest and easiest way to produce [0, 1, .....] array\r\n const colorIndices = [...Array(vertCount).keys()];\r\n return `\r\n LayerElementColor: ${layerElementColorNumber} {\r\n Version: ${layerElementColorVersion}\r\n Name: \"${layerElementColorName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Colors: ${colorsStr}\r\n ColorIndex: ${colorIndices}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding normal layer to resulting file\r\n * @param {Float32Array} normalArray attribute\r\n * @returns {string} normal layer info\r\n */\r\n _normalLayer(normalArray) {\r\n const layerElementNormalNumber = 0;\r\n const layerElementNormalVersion = 101;\r\n const layerElementNormalName = '';\r\n const normalsStr = this._floatArrayToString(normalArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n return `\r\n LayerElementNormal: ${layerElementNormalNumber} {\r\n Version: ${layerElementNormalVersion}\r\n Name: \"${layerElementNormalName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Normals: ${normalsStr}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding vertices and indices to resulting string\r\n * @return {string} resulting string in FBX notation\r\n */\r\n _verticesIndices(positions, indices) {\r\n const multiLayer = 0;\r\n const multiTake = 1;\r\n const shading = 'Y';\r\n const culling = 'CullingOff';\r\n const geometryVersion = 124;\r\n const vertStr = this._floatArrayToString(positions);\r\n /* About _correctArrayNotation: Float32Arrays will contains only Float32 numbers, which implies that it will be floating points with 17 numbers after point.\r\n * We cannot (and it's logically incorrect) save all this information, so we convert this Float32Array into Array-like object with numbers with only 6 numbers after point\r\n * Reminder - this is big memory loss (as we must save at one moment two arrays with similar information) */\r\n return `MultiLayer: ${multiLayer}\r\n MultiTake: ${multiTake}\r\n Shading: ${shading}\r\n Culling: \"${culling}\"\r\n Vertices: ${vertStr}\r\n PolygonVertexIndex: ${indices}\r\n GeometryVersion: ${geometryVersion}`;\r\n }\r\n\r\n /**\r\n * Forming material properties block.\r\n * @param {Object} material - given material of model\r\n * @returns {String} material properties string\r\n */\r\n _materialProperties(material) {\r\n return `Properties60: {\r\n Property: \"ShadingModel\", \"KString\", \"\", \"Lambert\"\r\n Property: \"MultiLayer\", \"bool\", \"\",0\r\n Property: \"EmissiveColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"EmissiveFactor\", \"double\", \"\",0.0000\r\n Property: \"AmbientColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"AmbientFactor\", \"double\", \"\",0.0000\r\n Property: \"DiffuseColor\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"DiffuseFactor\", \"double\", \"\",1.0000\r\n Property: \"Bump\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TransparentColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"TransparencyFactor\", \"double\", \"\",0.0000\r\n Property: \"SpecularColor\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"SpecularFactor\", \"double\", \"\",1.0000\r\n Property: \"ShininessExponent\", \"double\", \"\",${material.shininess}\r\n Property: \"ReflectionColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"ReflectionFactor\", \"double\", \"\",1\r\n Property: \"Ambient\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"Diffuse\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"Specular\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"Shininess\", \"double\", \"\",${material.shininess}\r\n Property: \"Opacity\", \"double\", \"\",${material.opacity}\r\n Property: \"Reflectivity\", \"double\", \"\",0\r\n }`;\r\n }\r\n}\r\n","import Exporter from './Exporter';\r\nimport FBXInfoExtractor from './fbx/FBXInfoExtractor';\r\nimport FBXResult from './fbx/FBXResult';\r\nimport ComplexVisual from '../../ComplexVisual';\r\n\r\nexport default class FBXExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n // Data\r\n this._data = source;\r\n this._version = options.miewVersion || '0.0-UNSPECIFIED';\r\n this._extractor = new FBXInfoExtractor();\r\n }\r\n\r\n /**\r\n * Entry point to exporter.\r\n */\r\n exportSync() {\r\n // Creating mandatory blocks\r\n const result = new FBXResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n const info = this._extractor.process(this._data);\r\n info.version = this._version;\r\n this._result = result.getResult(info);\r\n return this._result;\r\n }\r\n}\r\n\r\nFBXExporter.formats = ['fbx'];\r\nFBXExporter.SourceClass = ComplexVisual;\r\n","import ExporterList from './exporters/ExporterList';\r\n\r\nimport PDBExporter from './exporters/PDBExporter';\r\nimport FBXExporter from './exporters/FBXExporter';\r\n\r\nexport default new ExporterList([\r\n PDBExporter,\r\n FBXExporter,\r\n]);\r\n","import loaders from './loaders';\r\nimport parsers from './parsers';\r\nimport exporters from './exporters';\r\n\r\nexport default {\r\n loaders,\r\n parsers,\r\n exporters,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from './CSS2DObject';\r\n\r\nconst tempColor = new THREE.Color();\r\n\r\nclass CSS2DRenderer {\r\n constructor() {\r\n this._width = 0;\r\n this._height = 0;\r\n this._widthHalf = 0;\r\n this._heightHalf = 0;\r\n\r\n this._vector = new THREE.Vector3();\r\n this._viewMatrix = new THREE.Matrix4();\r\n this._projectionMatrix = new THREE.Matrix4();\r\n\r\n this._domElement = document.createElement('div');\r\n this._domElement.style.overflow = 'hidden';\r\n this._domElement.style.position = 'absolute';\r\n this._domElement.style.top = '0';\r\n this._domElement.style.zIndex = '0'; // start a new Stacking Context to enclose all z-ordered children\r\n this._domElement.style.pointerEvents = 'none';\r\n }\r\n\r\n getElement() {\r\n return this._domElement;\r\n }\r\n\r\n reset() {\r\n const myNode = this.getElement();\r\n while (myNode.firstChild) {\r\n myNode.removeChild(myNode.firstChild);\r\n }\r\n }\r\n\r\n setSize(width, height) {\r\n this._width = width;\r\n this._height = height;\r\n\r\n this._widthHalf = this._width / 2;\r\n this._heightHalf = this._height / 2;\r\n\r\n this._domElement.style.width = `${width}px`;\r\n this._domElement.style.height = `${height}px`;\r\n }\r\n\r\n _renderObject(object, camera, scene) {\r\n function lerpColorAsHex(a, b, t) {\r\n tempColor.setHex(a);\r\n tempColor.lerp(b, t);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n function colorAsHex(a) {\r\n tempColor.setHex(a);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n if (object instanceof CSS2DObject) {\r\n this._vector.setFromMatrixPosition(object.matrixWorld);\r\n\r\n if (object.userData !== undefined && object.userData.offset !== undefined) {\r\n const localOffset = new THREE.Vector3(object.userData.offset.x, object.userData.offset.y, 0);\r\n this._vector.add(localOffset.multiplyScalar(object.matrixWorld.getMaxScaleOnAxis()));\r\n }\r\n\r\n this._vector.applyMatrix4(this._viewMatrix);\r\n\r\n const visibility = this._vector.z > -camera.near ? 'hidden' : 'visible';\r\n const zIndex = 10000 * (camera.far - (-this._vector.z)) / (camera.far - camera.near);\r\n\r\n const element = object.getElement();\r\n if (typeof scene.fog === 'undefined') {\r\n element.style.color = colorAsHex(object.userData.color);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = colorAsHex(object.userData.background);\r\n }\r\n } else {\r\n const fogFactor = THREE.MathUtils.smoothstep(-this._vector.z, scene.fog.near, scene.fog.far);\r\n element.style.color = lerpColorAsHex(object.userData.color, scene.fog.color, fogFactor);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = lerpColorAsHex(object.userData.background, scene.fog.color, fogFactor);\r\n }\r\n }\r\n\r\n this._vector.applyMatrix4(this._projectionMatrix);\r\n\r\n const style = `${object.userData !== {} ? object.userData.translation : 'translate(-50%, -50%) '\r\n }translate(${this._vector.x * this._widthHalf + this._widthHalf}px,${\r\n -this._vector.y * this._heightHalf + this._heightHalf}px)`;\r\n element.style.visibility = visibility;\r\n element.style.WebkitTransform = style;\r\n element.style.MozTransform = style;\r\n element.style.oTransform = style;\r\n element.style.transform = style;\r\n element.style.zIndex = Number(zIndex).toFixed(0);\r\n\r\n if (element.parentNode !== this._domElement) {\r\n this._domElement.appendChild(element);\r\n }\r\n }\r\n\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n this._renderObject(object.children[i], camera, scene);\r\n }\r\n }\r\n\r\n render(scene, camera) {\r\n scene.updateMatrixWorld();\r\n\r\n if (camera.parent === null) {\r\n camera.updateMatrixWorld();\r\n }\r\n\r\n camera.matrixWorldInverse.copy(camera.matrixWorld).invert();\r\n\r\n this._viewMatrix.copy(camera.matrixWorldInverse);\r\n this._projectionMatrix.copy(camera.projectionMatrix);\r\n\r\n this._renderObject(scene, camera, scene);\r\n }\r\n}\r\nexport default CSS2DRenderer;\r\n","export default function getTopWindow() {\r\n // intercept the exception if we have cross-origin iframe\r\n try {\r\n if (window.top.location.href !== undefined) {\r\n return window.top;\r\n }\r\n } catch {\r\n // provide fallback\r\n }\r\n return window;\r\n}\r\n","import * as THREE from 'three';\r\nimport Timer from '../Timer';\r\nimport settings from '../settings';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\nimport getTopWindow from '../utils/getTopWindow';\r\n\r\nconst VK_LEFT = 37;\r\nconst VK_UP = 38;\r\nconst VK_RIGHT = 39;\r\nconst VK_DOWN = 40;\r\n\r\nconst STATE = {\r\n NONE: -1, ROTATE: 0, TRANSLATE: 1, SCALE: 2, TRANSLATE_PIVOT: 3,\r\n};\r\n\r\n// pausing for this amount of time before releasing mouse button prevents inertial rotation (seconds)\r\nconst FULL_STOP_THRESHOLD = 0.1;\r\n\r\nconst quaternion = new THREE.Quaternion();\r\nconst matrix4 = new THREE.Matrix4();\r\n\r\n// pivot -- local offset of the rotation pivot point\r\nfunction ObjectHandler(objects, camera, pivot, options) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n this.camera = camera;\r\n this.pivot = pivot;\r\n this.axis = new THREE.Vector3(0, 0, 1);\r\n this.options = options;\r\n\r\n this.lastRotation = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n}\r\n\r\nObjectHandler.prototype._rotate = (function () {\r\n const p = new THREE.Vector3();\r\n const q = new THREE.Quaternion();\r\n const s = new THREE.Vector3();\r\n\r\n const m = new THREE.Matrix4();\r\n\r\n return function (quat) {\r\n const zeroPivot = (this.pivot.x === 0.0 && this.pivot.y === 0.0 && this.pivot.z === 0.0);\r\n\r\n m.copy(this.object.matrix);\r\n\r\n if (zeroPivot) {\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n } else {\r\n m.multiply(matrix4.makeTranslation(this.pivot.x, this.pivot.y, this.pivot.z));\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n m.multiply(matrix4.makeTranslation(-this.pivot.x, -this.pivot.y, -this.pivot.z));\r\n }\r\n\r\n m.decompose(p, q, s);\r\n\r\n // update objects\r\n if (!zeroPivot) {\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].position.copy(p);\r\n }\r\n }\r\n\r\n for (let j = 0; j < this.objects.length; ++j) {\r\n this.objects[j].quaternion.copy(q);\r\n this.objects[j].updateMatrix();\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.setObjects = function (objects) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n};\r\n\r\nObjectHandler.prototype.rotate = (function () {\r\n const rot = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n\r\n return function (quat, mousePrevPos, mouseCurPos, aboutAxis) {\r\n this.mouse2rotation(rot, mousePrevPos, mouseCurPos, aboutAxis);\r\n quat.setFromAxisAngle(rot.axis, rot.angle);\r\n\r\n if (rot.angle) {\r\n this._rotate(quat);\r\n }\r\n\r\n this.lastRotation = rot;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.translate = (function () {\r\n const dir = new THREE.Vector3();\r\n const pivot = new THREE.Vector3();\r\n\r\n return function (delta) {\r\n // reverse-project viewport movement to view coords (compensate for screen aspect ratio)\r\n dir.set(\r\n delta.x / this.camera.projectionMatrix.elements[0],\r\n delta.y / this.camera.projectionMatrix.elements[5],\r\n 0,\r\n );\r\n let dist = dir.length();\r\n dir.normalize();\r\n\r\n // transform movement direction to object local coords\r\n dir.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // visible translate distance shouldn't depend on camera-to-object distance\r\n pivot.copy(this.pivot);\r\n this.object.localToWorld(pivot);\r\n dist *= Math.abs(pivot.z - this.camera.position.z);\r\n\r\n // visible translate distance shouldn't depend on object scale\r\n dist /= this.object.matrixWorld.getMaxScaleOnAxis();\r\n\r\n // all objects are translated similar to principal object\r\n // (we assume they all have identical pivot and scale)\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].translateOnAxis(dir, dist);\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.update = (function () {\r\n const axis = new THREE.Vector3();\r\n\r\n return function (timeSinceLastUpdate, timeSinceMove) {\r\n if (settings.now.autoRotation !== 0.0) {\r\n // auto-rotation with constant speed\r\n\r\n // if rotation axis is fixed or hasn't been defined yet\r\n if (settings.now.autoRotationAxisFixed || this.lastRotation.axis.length() === 0.0) {\r\n // use Y-axis (transformed to local object coords)\r\n axis.set(0, 1, 0).transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n } else {\r\n // use axis defined by last user rotation\r\n axis.copy(this.lastRotation.axis);\r\n }\r\n\r\n this._rotate(quaternion.setFromAxisAngle(axis, settings.now.autoRotation * timeSinceLastUpdate));\r\n return true;\r\n }\r\n\r\n if (this.options.intertia && this.lastRotation.angle) {\r\n // inertial object rotation\r\n const angle = this.lastRotation.angle * ((1.0 - this.options.dynamicDampingFactor) ** (40.0 * timeSinceMove));\r\n\r\n if (Math.abs(angle) <= this.options.intertiaThreshold) {\r\n this.lastRotation.angle = 0.0;\r\n } else {\r\n this._rotate(quaternion.setFromAxisAngle(this.lastRotation.axis, angle));\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.stop = function () {\r\n this.lastRotation.angle = 0.0;\r\n};\r\n\r\n// calculate (axis, angle) pair from mouse/touch movement\r\nObjectHandler.prototype.mouse2rotation = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n const eye = new THREE.Vector3();\r\n const eyeDirection = new THREE.Vector3();\r\n\r\n const cameraUpDirection = new THREE.Vector3();\r\n const cameraSidewaysDirection = new THREE.Vector3();\r\n\r\n const moveDirection = new THREE.Vector3();\r\n\r\n const mouseDelta = new THREE.Vector2();\r\n\r\n return function (rot, mousePrev, mouseCur, aboutAxis) {\r\n if (aboutAxis) {\r\n rot.axis.copy(this.axis);\r\n rot.angle = this.options.axisRotateFactor * (mouseCur.y - mousePrev.y);\r\n\r\n /* cool method that allows rotation around Z axis to be \"tied\" to mouse cursor\r\n\r\n res.axis.copy(this.axis);\r\n\r\n var pivot = this.pivot.clone();\r\n this.object.localToWorld(pivot);\r\n pivot.project(this.camera);\r\n\r\n var v1 = new THREE.Vector3(mousePrev.x, mousePrev.y, this.camera.position.z);\r\n v1.sub(pivot);\r\n var v2 = new THREE.Vector3(mouseCur.x, mouseCur.y, this.camera.position.z);\r\n v2.sub(pivot);\r\n\r\n v1.sub(res.axis.clone().multiplyScalar(v1.dot(res.axis)));\r\n v2.sub(res.axis.clone().multiplyScalar(v2.dot(res.axis)));\r\n\r\n var abs = v1.length() * v2.length();\r\n if (abs > 0) {\r\n res.angle = res.axis.dot(v1.cross(v2)) / abs;\r\n }\r\n */\r\n } else {\r\n mouseDelta.subVectors(mouseCur, mousePrev);\r\n const angle = mouseDelta.length();\r\n if (angle === 0.0) {\r\n return;\r\n }\r\n\r\n center.copy(this.pivot);\r\n this.object.localToWorld(center);\r\n eye.subVectors(this.camera.position, center);\r\n eyeDirection.copy(eye).normalize();\r\n\r\n cameraUpDirection.copy(this.camera.up).normalize();\r\n cameraSidewaysDirection.crossVectors(cameraUpDirection, eyeDirection).normalize();\r\n\r\n cameraUpDirection.setLength(mouseDelta.y);\r\n cameraSidewaysDirection.setLength(mouseDelta.x);\r\n\r\n moveDirection.copy(cameraUpDirection.add(cameraSidewaysDirection));\r\n\r\n rot.axis.crossVectors(moveDirection, eye);\r\n\r\n rot.angle = -angle * this.options.rotateFactor;\r\n }\r\n\r\n rot.axis.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // make sure angle is always positive (thus 'axis' defines both axis and direction of rotation)\r\n if (rot.angle < 0.0) {\r\n rot.axis.negate();\r\n rot.angle = -rot.angle;\r\n }\r\n };\r\n}());\r\n\r\nfunction ObjectControls(object, objectPivot, camera, domElement, getAltObj) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.object = object;\r\n this.objectPivot = objectPivot;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.getAltObj = getAltObj;\r\n\r\n // API\r\n\r\n this.enabled = true;\r\n this.hotkeysEnabled = true;\r\n\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n\r\n this.options = {\r\n rotateFactor: Math.PI, // full screen slide (along short side) would roughly mean 180 deg. rotation\r\n axisRotateFactor: 4 * Math.PI, // full screen slide (along short side) would roughly mean 720 deg. rotation\r\n intertia: true,\r\n dynamicDampingFactor: 0.1,\r\n intertiaThreshold: 1e-3,\r\n };\r\n\r\n // internals\r\n\r\n this._state = STATE.NONE;\r\n\r\n this._mousePrevPos = new THREE.Vector2();\r\n this._mouseCurPos = new THREE.Vector2();\r\n\r\n this._mainObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._altObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._affectedObj = this._mainObj;\r\n this._isAltObjFreeRotationAllowed = true;\r\n this._isTranslationAllowed = true;\r\n this._isKeysTranslatingObj = false;\r\n\r\n this._pressedKeys = [];\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n this._lastUpdateTime = this._clock.getElapsedTime();\r\n\r\n // events\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousewheel',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'DOMMouseScroll',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseout',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchmove',\r\n handler(e) {\r\n self.touchmove(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keydown',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keyup',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'blur',\r\n handler() {\r\n self.resetKeys();\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'contextmenu',\r\n handler(e) {\r\n self.contextmenu(e);\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n\r\n this.resetKeys();\r\n\r\n // force an update at start\r\n this.update();\r\n}\r\n\r\n// methods\r\n\r\nObjectControls.prototype = Object.create(EventDispatcher.prototype);\r\nObjectControls.prototype.constructor = ObjectControls;\r\n\r\nObjectControls.prototype.resetKeys = function () {\r\n this._pressedKeys[VK_LEFT] = false;\r\n this._pressedKeys[VK_UP] = false;\r\n this._pressedKeys[VK_RIGHT] = false;\r\n this._pressedKeys[VK_DOWN] = false;\r\n};\r\n\r\nObjectControls.prototype.contextmenu = function (e) {\r\n e.stopPropagation();\r\n e.preventDefault();\r\n};\r\n\r\nObjectControls.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nObjectControls.prototype.enable = function (enable) {\r\n this.enabled = enable;\r\n};\r\n\r\nObjectControls.prototype.enableHotkeys = function (enable) {\r\n this.hotkeysEnabled = enable;\r\n};\r\n\r\nObjectControls.prototype.allowTranslation = function (allow) {\r\n this._isTranslationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.allowAltObjFreeRotation = function (allow) {\r\n this._isAltObjFreeRotationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.keysTranslateObj = function (on) {\r\n this._isKeysTranslatingObj = on;\r\n};\r\n\r\nObjectControls.prototype.isEditingAltObj = function () {\r\n return ((this._state === STATE.ROTATE) || (this._state === STATE.TRANSLATE))\r\n && (this._affectedObj === this._altObj);\r\n};\r\n\r\n// convert page coords of mouse/touch to uniform coords with smaller side being [-0.5, 0.5]\r\n// (uniform coords keep direct proportion with screen distance travelled by mouse regardless of screen aspect ratio)\r\nObjectControls.prototype.convertMouseToOnCircle = function (coords, pageX, pageY) {\r\n const screenSize = Math.min(this.screen.width, this.screen.height);\r\n\r\n if (screenSize === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n ((pageX - this.screen.width * 0.5 - this.screen.left) / screenSize),\r\n ((0.5 * this.screen.height + this.screen.top - pageY) / screenSize),\r\n );\r\n};\r\n\r\n// convert page coords of mouse/touch to viewport coords with both sides being [-1, 1]\r\n// (those are non-uniform coords affected by screen aspect ratio)\r\nObjectControls.prototype.convertMouseToViewport = function (coords, pageX, pageY) {\r\n if (this.screen.width === 0 || this.screen.height === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n (2.0 * (pageX - this.screen.width * 0.5 - this.screen.left) / this.screen.width),\r\n (2.0 * (0.5 * this.screen.height + this.screen.top - pageY) / this.screen.height),\r\n );\r\n};\r\n\r\nObjectControls.prototype.stop = function () {\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n};\r\n\r\n// rotate object based on latest mouse/touch movement\r\nObjectControls.prototype.rotateByMouse = (function () {\r\n const quat = new THREE.Quaternion();\r\n\r\n return function (aboutZAxis) {\r\n this._affectedObj.rotate(quat, this._mousePrevPos, this._mouseCurPos, aboutZAxis);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n };\r\n}());\r\n\r\n// rotate object by specified quaternion\r\nObjectControls.prototype.rotate = function (quat) {\r\n this.object.quaternion.multiply(quat);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n};\r\n\r\n// get object's orientation\r\nObjectControls.prototype.getOrientation = function () {\r\n return this.object.quaternion;\r\n};\r\n\r\n// set object's orientation\r\nObjectControls.prototype.setOrientation = function (quat) {\r\n this.object.quaternion.copy(quat);\r\n};\r\n\r\n// translate object based on latest mouse/touch movement\r\nObjectControls.prototype.translate = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this._affectedObj.translate(delta);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n };\r\n}());\r\n\r\n// get object scale\r\nObjectControls.prototype.getScale = function () {\r\n return this.object.scale.x;\r\n};\r\n\r\n// set uniform object scale\r\nObjectControls.prototype.setScale = function (scale) {\r\n this.object.scale.set(scale, scale, scale);\r\n};\r\n\r\n// scale object by factor (factor should be greater than zero)\r\nObjectControls.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n return;\r\n }\r\n this.setScale(this.object.scale.x * factor);\r\n this.dispatchEvent({ type: 'change', action: 'zoom', factor });\r\n};\r\n\r\nObjectControls.prototype.update = (function () {\r\n const shift = new THREE.Vector2();\r\n\r\n return function () {\r\n const curTime = this._clock.getElapsedTime();\r\n const timeSinceLastUpdate = curTime - this._lastUpdateTime;\r\n\r\n // update object handler\r\n if (this._state === STATE.NONE) {\r\n const timeSinceMove = curTime - this._lastMouseMoveTime;\r\n if (this._mainObj.update(timeSinceLastUpdate, timeSinceMove)\r\n || this._altObj.update(timeSinceLastUpdate, timeSinceMove)) {\r\n this.dispatchEvent({ type: 'change', action: 'auto' });\r\n }\r\n }\r\n\r\n // apply arrow keys\r\n if (this._isKeysTranslatingObj) {\r\n const speedX = Number(this._pressedKeys[VK_RIGHT]) - Number(this._pressedKeys[VK_LEFT]);\r\n const speedY = Number(this._pressedKeys[VK_UP]) - Number(this._pressedKeys[VK_DOWN]);\r\n if (speedX !== 0.0 || speedY !== 0.0) {\r\n const delta = timeSinceLastUpdate;\r\n\r\n // update object translation\r\n const altObj = this.getAltObj();\r\n if (altObj.objects.length > 0) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n\r\n shift.set(delta * speedX, delta * speedY);\r\n this._altObj.translate(shift);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n }\r\n }\r\n }\r\n\r\n this._lastUpdateTime = curTime;\r\n };\r\n}());\r\n\r\nObjectControls.prototype.reset = function () {\r\n this._state = STATE.NONE;\r\n\r\n this.object.quaternion.copy(quaternion.set(0, 0, 0, 1));\r\n};\r\n\r\n// listeners\r\n\r\nObjectControls.prototype.mousedown = function (event) {\r\n if (this.enabled === false || this._state !== STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (this._state === STATE.NONE) {\r\n if (event.button === 0) {\r\n this._affectedObj.stop(); // can edit only one object at a time\r\n\r\n let workWithAltObj = false;\r\n\r\n if (event.altKey) {\r\n const altObj = this.getAltObj();\r\n workWithAltObj = (altObj.objects.length > 0);\r\n if (workWithAltObj) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n this._affectedObj = workWithAltObj ? this._altObj : this._mainObj;\r\n\r\n this._state = (workWithAltObj && event.ctrlKey && this._isTranslationAllowed) ? STATE.TRANSLATE : STATE.ROTATE;\r\n } else if (event.button === 2) {\r\n this._state = STATE.TRANSLATE_PIVOT;\r\n }\r\n }\r\n\r\n if (this._state === STATE.ROTATE) {\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n\r\n if (this._state === STATE.TRANSLATE || this._state === STATE.TRANSLATE_PIVOT) {\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousemove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this.rotateByMouse((event.altKey && !this._isAltObjFreeRotationAllowed) || event.shiftKey);\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.TRANSLATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translate();\r\n break;\r\n\r\n case STATE.TRANSLATE_PIVOT:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translatePivotByMouse();\r\n break;\r\n\r\n default: break;\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousewheel = function (event) {\r\n if (this.enabled === false || !settings.now.zooming || this._state !== STATE.NONE || event.shiftKey) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n\r\n let delta = 0;\r\n\r\n if (event.wheelDelta) {\r\n // WebKit / Opera / Explorer 9\r\n delta = event.wheelDelta / 40;\r\n } else if (event.detail) {\r\n // Firefox\r\n delta = -event.detail / 3;\r\n }\r\n\r\n let factor = 1.0 + delta * 0.05;\r\n factor = Math.max(factor, 0.01);\r\n this.scale(factor);\r\n};\r\n\r\nObjectControls.prototype.mouseup = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n this._state = STATE.NONE;\r\n\r\n if (this._clock.getElapsedTime() - this._lastMouseMoveTime > FULL_STOP_THRESHOLD) {\r\n this._affectedObj.stop();\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchstartend = function (event) {\r\n if (this.enabled === false) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (event.touches.length) {\r\n case 1:\r\n this._state = STATE.ROTATE;\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n break;\r\n\r\n case 2: {\r\n // prevent inertial rotation\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n\r\n this._state = STATE.SCALE;\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = this._touchDistanceStart = Math.sqrt(dx * dx + dy * dy);\r\n this._scaleStart = this.object.scale.x;\r\n break;\r\n }\r\n\r\n default:\r\n this._state = STATE.NONE;\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchmove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this.rotateByMouse(false);\r\n\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.SCALE:\r\n if (settings.now.zooming) {\r\n // update scale\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = Math.sqrt(dx * dx + dy * dy);\r\n const newScale = this._scaleStart * this._touchDistanceCur / this._touchDistanceStart;\r\n const factor = newScale / this.object.scale.x;\r\n this.scale(factor);\r\n }\r\n break;\r\n\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.keydownup = function (event) {\r\n if (this.enabled === false || this.hotkeysEnabled === false) {\r\n return;\r\n }\r\n\r\n switch (event.keyCode) {\r\n case VK_LEFT:\r\n case VK_UP:\r\n case VK_RIGHT:\r\n case VK_DOWN:\r\n this._pressedKeys[event.keyCode] = (event.type === 'keydown');\r\n event.preventDefault();\r\n event.stopPropagation();\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.getKeyBindObject = function () {\r\n return getTopWindow();\r\n};\r\n\r\nObjectControls.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nObjectControls.prototype.translatePivotByMouse = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this.translatePivotInWorld(settings.now.translationSpeed * delta.x, settings.now.translationSpeed * delta.y, 0);\r\n };\r\n}());\r\n\r\n// Translate in WorldCS, translation is scaled with root scale matrix\r\nObjectControls.prototype.translatePivotInWorld = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.applyMatrix4(this.object.matrixWorld);\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n pos.applyMatrix4(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Translate in ModelCS, x, y, z are Ang\r\nObjectControls.prototype.translatePivot = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Set pivot\r\nObjectControls.prototype.setPivot = function (newPivot) {\r\n this.objectPivot.position.copy(newPivot);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\nexport default ObjectControls;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\nimport Timer from '../Timer';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\n\r\nfunction Picker(gfxObj, camera, domElement) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.gfxObj = gfxObj;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n this._lastMousePos = new THREE.Vector2(0, 0);\r\n this._mouseTotalDist = 0.0;\r\n this._lastClickBeginTime = -1000.0;\r\n this._lastClickPos = new THREE.Vector2(0, 0);\r\n this._clickBeginTime = 0.0;\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstart(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchend(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n}\r\n\r\nPicker.prototype = Object.create(EventDispatcher.prototype);\r\nPicker.prototype.constructor = Picker;\r\n\r\nPicker.prototype.reset = function () {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n};\r\n\r\nPicker.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nPicker.prototype.pickObject = function (screenPos) {\r\n if (!this.gfxObj) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n const { gfxObj } = this;\r\n const rayCaster = new THREE.Raycaster();\r\n rayCaster.ray.origin.setFromMatrixPosition(this.camera.matrixWorld);\r\n rayCaster.ray.direction.set(screenPos.x, screenPos.y, 0.5).unproject(this.camera).sub(rayCaster.ray.origin).normalize();\r\n\r\n const clipPlane = (settings.now.draft.clipPlane && this.clipPlaneValue) ? this.clipPlaneValue : Infinity;\r\n const fogFarPlane = (settings.now.fog && this.fogFarValue) ? this.fogFarValue : Infinity;\r\n const point = rayCaster.intersectVisibleObject(gfxObj, this.camera, clipPlane, fogFarPlane);\r\n if (!point) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n let picked = {};\r\n if (point.residue || point.atom) {\r\n const residue = point.residue || point.atom.residue;\r\n if (settings.now.pick === 'chain') {\r\n picked = { chain: residue.getChain() };\r\n } else if (settings.now.pick === 'molecule') {\r\n picked = { molecule: residue.getMolecule() };\r\n } else if (point.residue || settings.now.pick === 'residue') {\r\n picked = { residue };\r\n } else if (point.atom) {\r\n picked = { atom: point.atom };\r\n }\r\n }\r\n this.picked = picked;\r\n this.dispatchEvent({ type: 'newpick', obj: picked });\r\n};\r\n\r\nPicker.prototype.getMouseInViewport = function (pageX, pageY) {\r\n return new THREE.Vector2(\r\n (pageX - this.screen.left) / this.screen.width * 2 - 1,\r\n -(pageY - this.screen.top) / this.screen.height * 2 + 1,\r\n );\r\n};\r\n\r\nPicker.prototype.mousedown = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n this._lastMousePos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist = 0.0;\r\n this._clickBeginTime = this._clock.getElapsedTime();\r\n }\r\n};\r\n\r\nPicker.prototype.mousemove = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n const pos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist += pos.sub(this._lastMousePos).length();\r\n};\r\n\r\nPicker.prototype.mouseup = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n if (this._mouseTotalDist < 0.01) {\r\n const curTime = this._clock.getElapsedTime();\r\n const curPos = this.getMouseInViewport(event.pageX, event.pageY);\r\n\r\n const timeSinceLastClickBegin = curTime - this._lastClickBeginTime;\r\n if (timeSinceLastClickBegin < 0.7) {\r\n const clickDist = new THREE.Vector2().subVectors(curPos, this._lastClickPos);\r\n if (clickDist.length() < 0.01) {\r\n // it's a double click\r\n this.dispatchEvent({ type: 'dblclick', obj: this.picked });\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = -1000; // this click cannot serve as first click in double-click\r\n return;\r\n }\r\n }\r\n\r\n setTimeout(() => {\r\n self.pickObject(curPos);\r\n }, 0);\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = this._clickBeginTime;\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.touchstart = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 1) {\r\n this._lastTouchdownPos = this.getMouseInViewport(event.touches[0].pageX, event.touches[0].pageY);\r\n }\r\n};\r\n\r\nPicker.prototype.touchend = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 0\r\n && event.changedTouches.length === 1) {\r\n const pos = this.getMouseInViewport(event.changedTouches[0].pageX, event.changedTouches[0].pageY);\r\n const dist = pos.sub(this._lastTouchdownPos).length();\r\n if (dist < 0.01) {\r\n setTimeout(() => {\r\n self.pickObject(self._lastTouchdownPos);\r\n }, 0);\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nexport default Picker;\r\n","import * as THREE from 'three';\r\n\r\nclass Axes {\r\n constructor(target, targetCamera) {\r\n this._target = target;\r\n this._targetCamera = targetCamera;\r\n this._camera = new THREE.PerspectiveCamera(targetCamera.fov, targetCamera.aspect, 1, 100);\r\n this._object = new THREE.AxesHelper(1);\r\n this._scene = new THREE.Scene();\r\n this._scene.add(this._object);\r\n this._full = new THREE.Vector2();\r\n\r\n this._update();\r\n }\r\n\r\n _update() {\r\n const { fov } = this._targetCamera;\r\n const camera = this._camera;\r\n camera.aspect = this._targetCamera.aspect;\r\n camera.setMinimalFov(fov);\r\n camera.setDistanceToFit(1.0, fov);\r\n camera.updateProjectionMatrix();\r\n\r\n this._object.quaternion.copy(this._target.quaternion);\r\n }\r\n\r\n render(renderer) {\r\n this._update();\r\n\r\n renderer.getSize(this._full);\r\n const width = this._full.width * 0.25;\r\n const height = this._full.height * 0.25;\r\n\r\n const { autoClear } = renderer;\r\n renderer.autoClear = false;\r\n renderer.setViewport(0.0, 0.0, width, height);\r\n renderer.clear(false, true, false);\r\n renderer.render(this._scene, this._camera);\r\n renderer.setViewport(0, 0, this._full.width, this._full.height);\r\n renderer.autoClear = autoClear;\r\n }\r\n}\r\nexport default Axes;\r\n","import * as THREE from 'three';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\n\r\nconst cDataOffset = 12;\r\nconst cFirstMask = 0x0FFFFF00;\r\nconst cFirstShift = 8;\r\nconst cSecMask1 = 0x000000FF;\r\nconst cSecShift1 = 12;\r\nconst cSecMask2 = 0xFFF00000;\r\nconst cSecShift2 = 20;\r\nconst cThirdMask = 0x000FFFFF;\r\nconst cStrMask = 0xF0000000;\r\nconst cStrShift = 28;\r\nconst c219 = 1 << 19;\r\nconst c220 = 1 << 20;\r\n\r\nconst cHelixIdx = 1;\r\nconst cSheetIdx = 2;\r\nconst secTypes = ['helix', 'strand'];\r\nconst cSecNames = ['fs', 'ps', 'ns', 'us'];\r\n\r\nfunction _createSecondary(strArray, complex) {\r\n const residues = complex._residues;\r\n const nRes = residues.length;\r\n const resid = new Uint8Array(nRes);\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, n = strArray.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n resid[atom.residue._index] = strArray[i];\r\n }\r\n\r\n const secondary = [];\r\n let rIdx = 0;\r\n while (rIdx < nRes) {\r\n if (resid[rIdx] !== 0) {\r\n const start = rIdx;\r\n const val = resid[rIdx];\r\n while (rIdx < nRes - 1 && resid[rIdx + 1] === val\r\n && residues[rIdx].isConnected(residues[rIdx + 1])) {\r\n ++rIdx;\r\n }\r\n secondary.push({ start, end: rIdx, type: secTypes[val - 1] });\r\n }\r\n ++rIdx;\r\n }\r\n return secondary;\r\n}\r\n\r\nfunction fromUInt20ToInt20(uint20) {\r\n return uint20 >= c219 ? uint20 - c220 : uint20;\r\n}\r\n\r\nclass FrameInfo {\r\n constructor(complex, payload, callbacks) {\r\n this._complex = complex;\r\n this._secondary = null;\r\n this.isLoading = false;\r\n this._framesRange = {\r\n start: 0,\r\n end: -1,\r\n };\r\n this.frameIsReady = false;\r\n this._buffer = null;\r\n this._frameRequest = null;\r\n this._callbacks = callbacks;\r\n if (typeof payload === 'function') {\r\n this._framesRequestLength = 1;\r\n this._downloadDataFn = payload;\r\n } else {\r\n this.parseBinaryData(payload, true);\r\n }\r\n this.reset();\r\n this.setFrame(0);\r\n }\r\n\r\n _prepareBuffer(framesStart, framesEnd) {\r\n if (framesStart === undefined || framesStart === null) {\r\n framesStart = 0;\r\n }\r\n if (framesEnd === undefined || framesEnd === null) {\r\n framesEnd = framesStart + this._framesRequestLength;\r\n }\r\n if (this._framesCount !== undefined) {\r\n framesEnd = Math.min(this._framesCount - 1, framesEnd);\r\n }\r\n if (this._downloadDataFn) {\r\n const self = this;\r\n const onDone = function (data) {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n self._buffer = {\r\n data,\r\n state: 'ready',\r\n start: framesStart,\r\n end: framesEnd,\r\n };\r\n if (self._frameRequest !== null) {\r\n const idx = self._frameRequest;\r\n self._frameRequest = null;\r\n self.setFrame(idx);\r\n }\r\n };\r\n const onFail = function () {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onError === 'function') {\r\n self._callbacks.onError('Streaming failed');\r\n }\r\n };\r\n if (!this._buffer) {\r\n this._buffer = {};\r\n }\r\n this._buffer.state = 'downloading';\r\n this.isLoading = true;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n this._downloadDataFn({ start: framesStart, end: framesEnd + 1 }, onDone, onFail);\r\n }\r\n }\r\n\r\n _parseBuffer() {\r\n if (this._buffer && this._buffer.state === 'ready') {\r\n this._framesRange = {\r\n start: this._buffer.start,\r\n end: this._buffer.end,\r\n };\r\n this.parseBinaryData(this._buffer.data, false);\r\n let _bufferRequestStart = (this._buffer.end + 1) % this._framesCount;\r\n if (_bufferRequestStart >= this._framesCount) {\r\n _bufferRequestStart = 0;\r\n }\r\n this._buffer = {\r\n state: 'none',\r\n };\r\n this._prepareBuffer(_bufferRequestStart, _bufferRequestStart + this._framesRequestLength);\r\n if (this._frameRequest !== null) {\r\n const idx = this._frameRequest;\r\n this._frameRequest = null;\r\n this.setFrame(idx);\r\n }\r\n }\r\n }\r\n\r\n parseBinaryData(arrayBuffer) {\r\n const dataView = new DataView(arrayBuffer);\r\n let offset = 0;\r\n const atomsCount = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const framesCount = dataView.getUint32(offset, true);\r\n this._framesCount = framesCount;\r\n this._framesRange.end = this._framesRange.end > 0\r\n ? Math.min(this._framesRange.end, framesCount - 1) : framesCount - 1;\r\n offset += 4;\r\n this._atomsCount = atomsCount;\r\n const maxSize = 1024 * 1024; // 1 MB\r\n this._framesRequestLength = Math.ceil(maxSize / (atomsCount * 8));\r\n const chunkedFramesCount = this._framesRange.end - this._framesRange.start + 1;\r\n if (atomsCount !== this._complex._atoms.length\r\n || arrayBuffer.byteLength !== cDataOffset + chunkedFramesCount * atomsCount * 8) {\r\n throw new Error();\r\n }\r\n const complex = this._complex;\r\n let timeStep = dataView.getUint32(offset, true);\r\n let iName = 0;\r\n while (timeStep > 1000 && iName < cSecNames.length - 1) {\r\n timeStep /= 1000;\r\n ++iName;\r\n }\r\n\r\n this._timeStep = `${timeStep.toString()} ${cSecNames[iName]}`;\r\n offset += 4;\r\n const secondary = [];\r\n const posData = new Float32Array(chunkedFramesCount * atomsCount * 3);\r\n let coordIdx = 0;\r\n const secondaryArr = new Int8Array(atomsCount);\r\n for (let j = 0; j < chunkedFramesCount; ++j) {\r\n for (let i = 0; i < atomsCount; ++i) {\r\n const hiWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const loWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const str = (loWord & cStrMask) >>> cStrShift;\r\n const x = fromUInt20ToInt20(((loWord & cFirstMask) >>> cFirstShift) >> 0);\r\n const y = fromUInt20ToInt20((((loWord & cSecMask1) << cSecShift1)\r\n | ((hiWord & cSecMask2) >>> cSecShift2)) >> 0);\r\n const z = fromUInt20ToInt20((hiWord & cThirdMask) >> 0);\r\n secondaryArr[i] = 0;\r\n if (str > 0 && str < 4) {\r\n secondaryArr[i] = cHelixIdx;\r\n } else if (str === 4) {\r\n secondaryArr[i] = cSheetIdx;\r\n }\r\n posData[coordIdx++] = x / 100;\r\n posData[coordIdx++] = y / 100;\r\n posData[coordIdx++] = z / 100;\r\n }\r\n secondary.push(_createSecondary(secondaryArr, complex));\r\n }\r\n this._secondaryData = secondary;\r\n this._data = posData;\r\n }\r\n\r\n nextFrame() {\r\n this.setFrame((this._currFrame + 1) % this._framesCount);\r\n }\r\n\r\n needsColorUpdate(colorer) {\r\n return colorer instanceof SecondaryStructureColorer;\r\n }\r\n\r\n getAtomColor(colorer, atom) {\r\n return colorer.getResidueColor(this._residues[atom.residue._index], this._complex);\r\n }\r\n\r\n getResidueColor(colorer, residue) {\r\n return colorer.getResidueColor(this._residues[residue._index], this._complex);\r\n }\r\n\r\n _updateSecondary() {\r\n let i;\r\n const myResidues = this._residues;\r\n let n = myResidues.length;\r\n for (i = 0; i < n; ++i) {\r\n myResidues[i]._secondary = null;\r\n }\r\n const sec = this._secondaryData[this._currFrame - this._framesRange.start];\r\n for (i = 0, n = sec.length; i < n; ++i) {\r\n const oldSec = sec[i];\r\n const { start, end } = oldSec;\r\n const nSec = {\r\n _start: myResidues[start],\r\n _end: myResidues[end],\r\n type: oldSec.type,\r\n generic: oldSec.generic,\r\n };\r\n for (let j = start; j <= end; ++j) {\r\n myResidues[j]._secondary = nSec;\r\n }\r\n }\r\n }\r\n\r\n reset() {\r\n const compRes = this._complex._residues;\r\n const n = compRes.length;\r\n this._residues = new Array(n);\r\n const myResidues = this._residues;\r\n const getSec = function () {\r\n return this._secondary;\r\n };\r\n for (let i = 0; i < n; ++i) {\r\n myResidues[i] = {\r\n _type: compRes[i]._type,\r\n _isValid: compRes[i]._isValid,\r\n _controlPoint: null,\r\n _wingVector: null,\r\n _secondary: null,\r\n getSecondary: getSec,\r\n };\r\n }\r\n }\r\n\r\n setFrame(frameIdx) {\r\n this.frameIsReady = false;\r\n if (frameIdx >= this._framesRange.start && frameIdx <= this._framesRange.end) {\r\n this._currFrame = frameIdx;\r\n this._cachedResidues = false;\r\n this._updateSecondary();\r\n this.frameIsReady = true;\r\n } else {\r\n this._frameRequest = frameIdx;\r\n if (!this._buffer) {\r\n this._prepareBuffer(frameIdx);\r\n } else {\r\n const self = this;\r\n switch (this._buffer.state) {\r\n case 'none':\r\n this._prepareBuffer(frameIdx);\r\n break;\r\n case 'ready':\r\n self._parseBuffer();\r\n break;\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n disableEvents() {\r\n this._callbacks = null;\r\n }\r\n\r\n /**\r\n * Returns link to atom pos vector, clone it if needed\r\n */\r\n\r\n static _vec = new THREE.Vector3();\r\n\r\n getAtomPos(atomIdx) {\r\n const vec = FrameInfo._vec;\r\n const self = this;\r\n const data = self._data;\r\n const idx = (self._atomsCount * (self._currFrame - self._framesRange.start) + atomIdx) * 3;\r\n vec.set(data[idx], data[idx + 1], data[idx + 2]);\r\n return vec;\r\n }\r\n\r\n getResidues() {\r\n if (this._cachedResidues) {\r\n return this._residues;\r\n }\r\n this._complex.updateToFrame(this);\r\n return this._residues;\r\n }\r\n}\r\nexport default FrameInfo;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\n\r\n/**\r\n * Create new scene object.\r\n *\r\n * @param {array=} params - Object required params.\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports SceneObject\r\n * @this SceneObject\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all scene objects that are not reps.\r\n */\r\nclass SceneObject {\r\n constructor(params, opts) {\r\n if (this.constructor === SceneObject) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Object's options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.params = params;\r\n this.opts = _.merge(utils.deriveDeep(settings.now.objects[this.type], true), opts);\r\n this.needsRebuild = false;\r\n this._mesh = null;\r\n this.id = null;\r\n }\r\n\r\n /**\r\n * Get object identification, probably with options.\r\n * @returns {Object} field type contains type information, params - object's formal parameters,\r\n * opts - changed options\r\n * Options are returned if they were changed during or after object creation.\r\n */\r\n identify() {\r\n const result = {\r\n type: this.type,\r\n params: this.params,\r\n };\r\n const diff = utils.objectsDiff(this.opts, settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n result.opts = diff;\r\n }\r\n return result;\r\n }\r\n\r\n toString() {\r\n const paramsStr = `o=${this.type},${this.params.join(',')}`;\r\n const optsStr = utils.compareOptionsWithDefaults(this.opts, settings.defaults.objects[this.type]);\r\n return paramsStr + optsStr;\r\n }\r\n\r\n getGeometry() {\r\n return this._mesh;\r\n }\r\n\r\n destroy() {\r\n if (this._mesh) {\r\n gfxutils.destroyObject(this._mesh);\r\n }\r\n }\r\n}\r\n\r\n/**\r\n * Scene object identifier.\r\n * @type {string}\r\n */\r\nSceneObject.prototype.type = '__';\r\n\r\nexport default SceneObject;\r\n","import * as THREE from 'three';\r\nimport SceneObject from './SceneObject';\r\nimport meshutils from '../meshutils';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\nimport meshes from '../meshes/meshes';\r\nimport settings from '../../settings';\r\n\r\nclass LinesObj extends SceneObject {\r\n constructor(params, opts) {\r\n super(params, opts);\r\n if (params.length < 2) {\r\n throw new Error('Wrong number of argumets on line object creation!');\r\n }\r\n [this._id1, this._id2] = params;\r\n }\r\n\r\n _getAtomFromName(complex, atomId) {\r\n const err = ' - Wrong atom format it must be \\'#CHAIN_NAME.#RESIDUE_NUMBER.#ATOM_NAME\\' (e.g. \\'A.38.CO1\\')';\r\n const atom1 = complex.getAtomByFullname(atomId);\r\n if (!atom1) {\r\n throw new Error(atomId + err);\r\n }\r\n return atom1;\r\n }\r\n\r\n build(complex) {\r\n const geom = new THREE.BufferGeometry();\r\n this._atom1 = this._getAtomFromName(complex, this._id1);\r\n this._atom2 = this._getAtomFromName(complex, this._id2);\r\n\r\n const p1 = this._atom1.position;\r\n const p2 = this._atom2.position;\r\n const vertices = new Float32Array([\r\n p1.x, p1.y, p1.z,\r\n p2.x, p2.y, p2.z,\r\n ]);\r\n\r\n geom.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n geom.computeBoundingBox();\r\n\r\n this._line = new meshes.Line(geom, new UberMaterial({\r\n lights: false,\r\n overrideColor: true,\r\n dashedLine: true,\r\n fogTransparent: settings.now.bg.transparent,\r\n }));\r\n this._line.computeLineDistances();\r\n this._line.material.setUberOptions({\r\n fixedColor: new THREE.Color(this.opts.color),\r\n dashedLineSize: this.opts.dashSize,\r\n dashedLinePeriod: this.opts.dashSize + this.opts.gapSize,\r\n });\r\n this._line.material.updateUniforms();\r\n\r\n this._line.raycast = function (_raycaster, _intersects) {};\r\n this._mesh = this._line;\r\n const transforms = complex.getTransforms();\r\n if (transforms.length > 0) {\r\n this._mesh = new THREE.Group();\r\n this._mesh.add(this._line);\r\n meshutils.applyTransformsToMeshes(this._mesh, transforms);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n if (!this._atom1 || !this._atom2 || !this._line) {\r\n return;\r\n }\r\n\r\n const geo = this._line.geometry;\r\n geo.vertices[0].copy(frameData.getAtomPos(this._atom1.index));\r\n geo.vertices[1].copy(frameData.getAtomPos(this._atom2.index));\r\n this._line.computeLineDistances();\r\n geo.computeBoundingSphere();\r\n\r\n geo.verticesNeedUpdate = true;\r\n }\r\n}\r\n\r\nLinesObj.prototype.constructor = LinesObj;\r\nLinesObj.prototype.type = 'line';\r\n\r\nexport default LinesObj;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Outline.frag';\r\n\r\nclass OutlineMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n // add depth outline\r\n super(params);\r\n\r\n const settings = {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcDepthTex: { type: 't', value: null },\r\n srcTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n color: { type: 'v3', value: null },\r\n threshold: { type: 'f', value: null },\r\n opacity: { type: 'f', value: 1.0 },\r\n thickness: { type: 'v2', value: new THREE.Vector2(1, 1) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: true,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n\r\n this.setValues(settings);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n const defines = {};\r\n\r\n if (this.depth) {\r\n defines.DEPTH_OUTLINE = 1;\r\n }\r\n\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nOutlineMaterial.prototype.depth = false;\r\n\r\nexport default OutlineMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './FXAA.frag';\r\n\r\nclass FXAAMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n bgColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.bgTransparent) {\r\n defines.BG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nFXAAMaterial.prototype.bgTransparent = false;\r\n\r\nexport default FXAAMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AO.frag';\r\nimport noise from '../noiseTexture';\r\n\r\nconst _samplesKernel = [\r\n // hemisphere samples adopted to sphere\r\n new THREE.Vector3(0.295184, 0.077723, 0.068429),\r\n new THREE.Vector3(-0.271976, -0.365221, 0.838363),\r\n new THREE.Vector3(0.547713, 0.467576, 0.488515),\r\n new THREE.Vector3(0.662808, -0.031733, 0.584758),\r\n new THREE.Vector3(-0.025717, 0.218955, 0.657094),\r\n new THREE.Vector3(-0.310153, -0.365223, 0.370701),\r\n new THREE.Vector3(-0.101407, -0.006313, 0.747665),\r\n new THREE.Vector3(-0.769138, 0.360399, 0.086847),\r\n new THREE.Vector3(-0.271988, -0.275140, 0.905353),\r\n new THREE.Vector3(0.096740, -0.566901, 0.700151),\r\n new THREE.Vector3(0.562872, -0.735136, 0.094647),\r\n new THREE.Vector3(0.379877, 0.359278, 0.190061),\r\n new THREE.Vector3(0.519064, -0.023055, 0.405068),\r\n new THREE.Vector3(-0.301036, 0.114696, 0.088885),\r\n new THREE.Vector3(-0.282922, 0.598305, 0.487214),\r\n new THREE.Vector3(-0.181859, 0.251670, 0.679702),\r\n new THREE.Vector3(-0.191463, -0.635818, 0.512919),\r\n new THREE.Vector3(-0.293655, 0.427423, 0.078921),\r\n new THREE.Vector3(-0.267983, 0.680534, 0.132880),\r\n new THREE.Vector3(0.139611, 0.319637, 0.477439),\r\n new THREE.Vector3(-0.352086, 0.311040, 0.653913),\r\n new THREE.Vector3(0.321032, 0.805279, 0.487345),\r\n new THREE.Vector3(0.073516, 0.820734, 0.414183),\r\n new THREE.Vector3(-0.155324, 0.589983, 0.411460),\r\n new THREE.Vector3(0.335976, 0.170782, 0.527627),\r\n new THREE.Vector3(0.463460, -0.355658, 0.167689),\r\n new THREE.Vector3(0.222654, 0.596550, 0.769406),\r\n new THREE.Vector3(0.922138, -0.042070, 0.147555),\r\n new THREE.Vector3(-0.727050, -0.329192, 0.369826),\r\n new THREE.Vector3(-0.090731, 0.533820, 0.463767),\r\n new THREE.Vector3(-0.323457, -0.876559, 0.238524),\r\n new THREE.Vector3(-0.663277, -0.372384, 0.342856),\r\n];\r\n\r\nclass AOMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n noiseTexture: { type: 't', value: noise.noiseTexture },\r\n noiseTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight) },\r\n diffuseTexture: { type: 't', value: null },\r\n normalTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n camNearFar: { type: 'v2', value: new THREE.Vector2(1.0, 10.0) },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n samplesKernel: { type: 'v3v', value: _samplesKernel },\r\n kernelRadius: { type: 'f', value: 1.0 },\r\n depthThreshold: { type: 'f', value: 1.0 },\r\n factor: { type: 'f', value: 1.0 },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOHorBlur.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOHorBlurMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOHorBlurMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOVertBlurWithBlend.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOVertBlurWithBlendMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n diffuseTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n fogNearFar: { type: 'v2', value: new THREE.Vector2(100.0, 100.0) },\r\n fogColor: { type: 'v4', value: new THREE.Vector4(0.0, 0.5, 0.0, 1.0) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.useFog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nAOVertBlurWithBlendMaterial.prototype.useFog = true;\r\nAOVertBlurWithBlendMaterial.prototype.fogTransparent = false;\r\n\r\nexport default AOVertBlurWithBlendMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Anaglyph.frag';\r\n\r\nclass AnaglyphMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n const settings = {\r\n uniforms: {\r\n srcL: { type: 't', value: null },\r\n srcR: { type: 't', value: null },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n this.setValues(settings);\r\n }\r\n}\r\n\r\nexport default AnaglyphMaterial;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\n\r\nclass View {\r\n constructor() {\r\n this.position = new THREE.Vector3(0, 0, 0);\r\n this.scale = 1;\r\n this.orientation = new THREE.Quaternion(0, 0, 0, 1);\r\n }\r\n\r\n set(position, scale, orientation) {\r\n this.position = position;\r\n this.scale = scale;\r\n this.orientation = orientation;\r\n }\r\n}\r\n\r\nconst _transitionTime = 1.5; // in seconds\r\n\r\nexport default class ViewInterpolator {\r\n setup(startView, endView) {\r\n this._startTime = undefined;\r\n this._endTime = undefined;\r\n this._isPaused = false;\r\n\r\n this._srcView = startView;\r\n this._dstView = endView;\r\n this._isMoving = false;\r\n }\r\n\r\n isMoving() {\r\n return this._isMoving;\r\n }\r\n\r\n wasStarted() {\r\n return typeof this._startTime !== 'undefined' && typeof this._endTime !== 'undefined';\r\n }\r\n\r\n start() {\r\n this._startTime = Date.now();\r\n const transTime = settings.now.interpolateViews ? _transitionTime * 1000 : 0;\r\n this._endTime = this._startTime + transTime;\r\n this._isMoving = true;\r\n }\r\n\r\n getCurrentView() {\r\n if (typeof this._srcView === 'undefined' || typeof this._dstView === 'undefined'\r\n || !this._isMoving || !this.wasStarted()) {\r\n return { success: false };\r\n }\r\n\r\n let view = this.createView();\r\n const time = Date.now();\r\n if (time > this._endTime) {\r\n view = this._dstView;\r\n this.reset();\r\n return { success: true, view };\r\n }\r\n\r\n const factor = (time - this._startTime) / (this._endTime - this._startTime);\r\n view.position.copy(this._srcView.position);\r\n view.position.lerp(this._dstView.position, factor);\r\n view.scale = (1 - factor) * this._srcView.scale + factor * this._dstView.scale;\r\n view.orientation.copy(this._srcView.orientation);\r\n view.orientation.slerp(this._dstView.orientation, factor);\r\n return { success: true, view };\r\n }\r\n\r\n reset() {\r\n this._startTime = this._endTime = 0;\r\n this._isMoving = false;\r\n }\r\n\r\n pause() {\r\n if (!this._isPaused) {\r\n this.setup(this.getCurrentView().view, this._dstView);\r\n this._isPaused = true;\r\n }\r\n }\r\n\r\n resume() {\r\n this._isPaused = false;\r\n }\r\n\r\n createView() {\r\n return new View();\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport makeContextDependent from './makeContextDependent';\r\n\r\nconst MAX_COOKIE_LEN = 4000;\r\nconst COUNT_SUFFIX = 'Cnt';\r\n\r\nfunction _chunkString(string, chunkLen) {\r\n const l = string.length;\r\n const chunks = [];\r\n for (let c = 0, lc = 0; lc < l; c++, lc += chunkLen) {\r\n chunks[c] = string.slice(lc, lc + chunkLen);\r\n }\r\n return chunks;\r\n}\r\n\r\n/**\r\n * Create new context dependent Cookie holder object.\r\n * @param context\r\n * @param {Object} opts - options\r\n * @param {string} opts.path - cookie path\r\n * @constructor\r\n */\r\nfunction Cookies(context, opts) {\r\n this.context = context;\r\n this._opts = _.merge({\r\n path: '/',\r\n }, opts);\r\n}\r\n\r\nmakeContextDependent(Cookies.prototype);\r\n\r\n/**\r\n * Remove cookie by the name.\r\n * @param key\r\n */\r\nCookies.prototype.removeCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n this._removeSimpleCookie(key);\r\n return;\r\n }\r\n this._removeSimpleCookie(cntKey);\r\n cntVal = parseInt(cntVal, 10);\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._removeSimpleCookie(key + i);\r\n }\r\n};\r\n\r\n/**\r\n * Set new cookie value. Automatically splits\r\n * values that are too large into multiple cookies.\r\n * @param key\r\n * @param value\r\n */\r\nCookies.prototype.setCookie = function (key, value) {\r\n this.removeCookie(key);\r\n value = encodeURIComponent(value);\r\n const values = _chunkString(value, MAX_COOKIE_LEN - key.length - 1);\r\n const cntVal = values.length;\r\n if (cntVal === 1) {\r\n this._setSimpleCookie(key, value);\r\n return;\r\n }\r\n const cntKey = this._toCount(key);\r\n this._setSimpleCookie(cntKey, cntVal.toString());\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._setSimpleCookie(key + i, values[i]);\r\n }\r\n};\r\n\r\n/**\r\n * Obtain the value of a compound cookie.\r\n * @param key\r\n */\r\nCookies.prototype.getCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n return this._getSimpleCookie(key);\r\n }\r\n cntVal = parseInt(cntVal, 10);\r\n const value = [];\r\n for (let i = 0; i < cntVal; ++i) {\r\n value[i] = this._getSimpleCookie(key + i);\r\n }\r\n return value.join('');\r\n};\r\n\r\nCookies.prototype._toCount = function (key) {\r\n return key + COUNT_SUFFIX;\r\n};\r\n\r\nCookies.prototype._removeSimpleCookie = function (key) {\r\n document.cookie = `${key}=; expires=Thu, 01 Jan 1970 00:00:01 GMT;`;\r\n};\r\n\r\nCookies.prototype._getExpirationDate = function () {\r\n const today = new Date();\r\n const EXP_PERIOD_YEARS = 10;\r\n today.setFullYear(today.getFullYear() + EXP_PERIOD_YEARS);\r\n return today;\r\n};\r\n\r\nCookies.prototype._setSimpleCookie = function (key, value) {\r\n document.cookie = `${key}=${value\r\n };expires=${this._getExpirationDate().toUTCString()\r\n };path=${this._opts.path}`;\r\n};\r\n\r\nCookies.prototype._getSimpleCookie = function (key) {\r\n const matches = document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n return matches ? decodeURIComponent(matches[1]) : '';\r\n};\r\n\r\nCookies.prototype._exists = function (key) {\r\n return document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n};\r\n\r\nexport default Cookies;\r\n","/*\r\n * Toggling WebVR is done through button.click because of limitations on calling requestPresent in webVR:\r\n * VRDisplay::requestPresent should be called from user gesture:\r\n * https://developer.mozilla.org/en-US/docs/Web/API/VRDisplay/requestPresent\r\n */\r\nexport default function (webVRPoC) {\r\n function showEnterVR(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'pointer';\r\n button.style.left = 'calc(50% - 50px)';\r\n button.style.width = '100px';\r\n\r\n button.textContent = 'ENTER VR';\r\n\r\n let currentSession = null;\r\n\r\n function onSessionEnded(/* event */) {\r\n currentSession.removeEventListener('end', onSessionEnded);\r\n button.textContent = 'ENTER VR';\r\n currentSession = null;\r\n }\r\n\r\n function onSessionStarted(session) {\r\n session.addEventListener('end', onSessionEnded);\r\n webVRPoC._gfx.renderer.xr.setReferenceSpaceType('local');\r\n webVRPoC._gfx.renderer.xr.setSession(session);\r\n button.textContent = 'EXIT VR';\r\n currentSession = session;\r\n }\r\n\r\n button.onmouseenter = function () { button.style.opacity = '1.0'; };\r\n button.onmouseleave = function () { button.style.opacity = '0.5'; };\r\n\r\n button.onclick = function () {\r\n if (currentSession === null) {\r\n // WebXR's requestReferenceSpace only works if the corresponding feature\r\n // was requested at session creation time. For simplicity, just ask for\r\n // the interesting ones as optional features, but be aware that the\r\n // requestReferenceSpace call will fail if it turns out to be unavailable.\r\n // ('local' is always available for immersive sessions and doesn't need to\r\n // be requested separately.)\r\n\r\n const sessionInit = { optionalFeatures: ['local-floor', 'bounded-floor'] };\r\n navigator.xr.requestSession('immersive-vr', sessionInit).then(onSessionStarted);\r\n webVRPoC.moveSceneBehindHeadset();\r\n } else {\r\n currentSession.end();\r\n }\r\n };\r\n }\r\n\r\n function showWebXRNotFound(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'auto';\r\n button.style.left = 'calc(50% - 75px)';\r\n button.style.width = '150px';\r\n button.textContent = 'VR NOT FOUND';\r\n button.onmouseenter = null;\r\n button.onmouseleave = null;\r\n button.onclick = null;\r\n }\r\n\r\n function stylizeElement(element) {\r\n element.style.position = 'absolute';\r\n element.style.bottom = '20px';\r\n element.style.padding = '12px 6px';\r\n element.style.border = '1px solid #fff';\r\n element.style.borderRadius = '4px';\r\n element.style.background = 'transparent';\r\n element.style.color = '#fff';\r\n element.style.font = 'normal 13px sans-serif';\r\n element.style.textAlign = 'center';\r\n element.style.opacity = '0.5';\r\n element.style.outline = 'none';\r\n element.style.zIndex = '999';\r\n }\r\n\r\n if ('xr' in navigator) {\r\n const button = document.createElement('button');\r\n button.style.display = 'none';\r\n stylizeElement(button);\r\n navigator.xr.isSessionSupported('immersive-vr').then((supported) => (\r\n supported ? showEnterVR(button) : showWebXRNotFound(button)\r\n ));\r\n return button;\r\n }\r\n const message = document.createElement('a');\r\n message.href = 'https://webvr.info';\r\n message.innerHTML = 'WEBXR NOT SUPPORTED';\r\n message.style.left = 'calc(50% - 90px)';\r\n message.style.width = '180px';\r\n message.style.textDecoration = 'none';\r\n stylizeElement(message);\r\n return message;\r\n}\r\n","import * as THREE from 'three';\r\nimport createWebVRButton from './createWebVRButton';\r\nimport gfxutils from '../gfxutils';\r\nimport logger from '../../utils/logger';\r\nimport settings from '../../settings';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default class WebVRPoC {\r\n constructor(onToggle) {\r\n this._mainCamera = new THREE.PerspectiveCamera();\r\n this._button = null;\r\n this._onToggle = onToggle;\r\n\r\n this._molContainer = new gfxutils.RCGroup();\r\n this._user = new gfxutils.RCGroup();\r\n this._scalingPivot = new THREE.Object3D();\r\n this._user.add(this._scalingPivot);\r\n\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n this._pressedGripsCounter = 0;\r\n this._distance = 0;\r\n\r\n this._gfx = null;\r\n }\r\n\r\n startScalingByControllers() {\r\n // reset scale\r\n this._distance = this._controller1.position.distanceTo(this._controller2.position);\r\n gfxutils.getMiddlePoint(this._controller1.position, this._controller2.position, this._scalingPivot.position);\r\n this._scalingPivot.scale.set(1, 1, 1);\r\n this._scalingPivot.updateMatrix();\r\n this._scalingPivot.updateMatrixWorld();\r\n // link molecule to pivot\r\n this._scalingPivot.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n stopScalingByControllers() {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n handleGripsDown(event) {\r\n this._pressedGripsCounter++;\r\n if (this._pressedGripsCounter === 2) {\r\n this.startScalingByControllers();\r\n } else if (this._pressedGripsCounter === 1) {\r\n event.target.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n handleGripsUp(event) {\r\n this._pressedGripsCounter--;\r\n if (this._pressedGripsCounter === 1) {\r\n this.stopScalingByControllers();\r\n // reattach molecule to other controller\r\n const anotherController = event.target === this._controller1 ? this._controller2 : this._controller1;\r\n anotherController.addSavingWorldTransform(this._molContainer);\r\n } else if (this._pressedGripsCounter === 0) {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n enable(gfx) {\r\n if (!gfx) {\r\n logger.warn('WebVR couldn\\'t be enabled, because gfx is not defined');\r\n return;\r\n }\r\n this._gfx = gfx;\r\n const { renderer, camera } = gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n if (!camera) {\r\n throw new Error('No camera is available to toggle WebVR');\r\n }\r\n\r\n // enable xr in renderer\r\n renderer.xr.enabled = true;\r\n // add button for turning vr mode\r\n if (!this._button) {\r\n this._button = createWebVRButton(this);\r\n document.body.appendChild(this._button);\r\n } else {\r\n this._button.style.display = 'block';\r\n }\r\n // store fog setting\r\n this._mainFog = settings.now.fog;\r\n settings.set('fog', false);\r\n\r\n this._plugVRNodesIntoScene(gfx, renderer);\r\n this._setControllersListeners();\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n _plugVRNodesIntoScene(gfx, renderer) {\r\n // store common scene camera\r\n this._mainCamera.copy(gfx.camera);\r\n // add hierarchical structure for webVR into scene\r\n gfx.scene.add(this._user);\r\n // turn on webvr transformation\r\n gfx.scene.add(this._molContainer);\r\n this._molContainer.add(gfx.root);\r\n\r\n this._controller1 = renderer.xr.getController(0);\r\n this._controller2 = renderer.xr.getController(1);\r\n const mesh = this._createControllerMesh();\r\n this._controller1.add(mesh);\r\n this._controller2.add(mesh.clone());\r\n this._user.add(this._controller1);\r\n this._user.add(this._controller2);\r\n }\r\n\r\n _setControllersListeners() {\r\n this._controller1.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n\r\n this._controller1.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n }\r\n\r\n disable() {\r\n if (!this._gfx) {\r\n return;\r\n }\r\n const { renderer, camera } = this._gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n\r\n // nullify webxr callback for animation frame\r\n renderer.setAnimationLoop(null);\r\n const session = renderer.xr.getSession();\r\n if (session) {\r\n session.end();\r\n }\r\n renderer.xr.enabled = false;\r\n // remove button of VR entering\r\n if (this._button) {\r\n this._button.style.display = 'none';\r\n }\r\n // restore fog param\r\n settings.set('fog', this._mainFog);\r\n\r\n this._unplugVRNodesFromScene(camera);\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(false);\r\n }\r\n }\r\n\r\n _unplugVRNodesFromScene(camera) {\r\n // restore common camera\r\n if (this._mainCamera && camera) {\r\n camera.copy(this._mainCamera);\r\n }\r\n // turn off webvr transformation\r\n const root = this._molContainer.children[0];\r\n if (root) {\r\n this._gfx.scene.add(root);\r\n }\r\n this._molContainer.parent.remove(this._molContainer);\r\n if (this._user) {\r\n this._gfx.scene.remove(this._user);\r\n }\r\n // free scene nodes\r\n this._molContainer = null;\r\n this._user = null;\r\n this._scalingPivot = null;\r\n this._user = null;\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n }\r\n\r\n _createControllerMesh() {\r\n // visualize controllers with cylinders\r\n const geometry = new THREE.CylinderGeometry(0.04, 0.04, 0.3);\r\n const material = new UberMaterial({ lights: false, overrideColor: true });\r\n material.setUberOptions({ fixedColor: new THREE.Color(0x4444ff) });\r\n material.updateUniforms();\r\n const cylinder = new THREE.Mesh(geometry, material);\r\n cylinder.rotateX(-Math.PI / 2);\r\n return cylinder;\r\n }\r\n\r\n updateMoleculeScale() {\r\n if (!this._controller1 || !this._controller2) {\r\n return;\r\n }\r\n\r\n const self = this;\r\n // update molecule scaling by controllers\r\n if (self._pressedGripsCounter === 2) {\r\n // recalc scaling pivot\r\n gfxutils.getMiddlePoint(self._controller1.position, self._controller2.position, self._scalingPivot.position);\r\n // recalc scaler\r\n const dist = self._controller1.position.distanceTo(self._controller2.position);\r\n const scaler = dist / self._distance;\r\n self._scalingPivot.scale.multiplyScalar(scaler);\r\n // save cur distance for next frame\r\n self._distance = dist;\r\n }\r\n }\r\n\r\n /**\r\n * Reposition molecule right before the camera.\r\n * @note The proper way is to initiate headset in the place of common Miew's camera.\r\n * But threejs limitations on setting new XRReferenceSpace enforce the molecule repositioning\r\n * Hope, something will change.\r\n */\r\n moveSceneBehindHeadset() {\r\n const gfx = this._gfx;\r\n const { camera } = gfx;\r\n\r\n // set container position in camera space\r\n const container = this._molContainer;\r\n container.matrix.identity();\r\n container.position.set(0, 0, -4.0);\r\n container.updateMatrix();\r\n\r\n // update container world matrix\r\n container.matrixWorld.multiplyMatrices(camera.matrixWorld, container.matrix);\r\n // readd to scene\r\n gfx.scene.addSavingWorldTransform(container);\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n getCanvas() {\r\n const gfx = this._gfx;\r\n return (gfx && gfx.renderer) ? gfx.renderer.domElement : null;\r\n }\r\n}\r\n","/* global PACKAGE_VERSION:false */\r\nimport _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport { Spinner } from 'spin.js';\r\nimport Stats from './gfx/Stats';\r\nimport utils from './utils';\r\nimport JobHandle from './utils/JobHandle';\r\nimport options from './options';\r\nimport settings from './settings';\r\nimport chem from './chem';\r\nimport Visual from './Visual';\r\nimport ComplexVisual from './ComplexVisual';\r\nimport Complex from './chem/Complex';\r\nimport VolumeVisual from './VolumeVisual';\r\nimport io from './io/io';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport CSS2DRenderer from './gfx/CSS2DRenderer';\r\nimport ObjectControls from './ui/ObjectControls';\r\nimport Picker from './ui/Picker';\r\nimport Axes from './gfx/Axes';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport meshutils from './gfx/meshutils';\r\nimport FrameInfo from './gfx/FrameInfo';\r\nimport meshes from './gfx/meshes/meshes';\r\nimport LinesObject from './gfx/objects/LinesObj';\r\nimport UberMaterial from './gfx/shaders/UberMaterial';\r\nimport OutlineMaterial from './gfx/shaders/OutlineMaterial';\r\nimport FXAAMaterial from './gfx/shaders/FXAAMaterial';\r\nimport AOMaterial from './gfx/shaders/AOMaterial';\r\nimport AOHorBlurMaterial from './gfx/shaders/AOHorBlurMaterial';\r\nimport AOVertBlurWithBlendMaterial from './gfx/shaders/AOVertBlurWithBlendMaterial';\r\nimport AnaglyphMaterial from './gfx/shaders/AnaglyphMaterial';\r\nimport VolumeMaterial from './gfx/shaders/VolumeMaterial';\r\nimport ViewInterpolator from './gfx/ViewInterpolator';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\nimport logger from './utils/logger';\r\nimport Cookies from './utils/Cookies';\r\nimport capabilities from './gfx/capabilities';\r\nimport WebVRPoC from './gfx/vr/WebVRPoC';\r\nimport vertexScreenQuadShader from './gfx/shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromDistTex from './gfx/shaders/ScreenQuadFromDistortionTex.frag';\r\nimport getTopWindow from './utils/getTopWindow';\r\n\r\nconst {\r\n selectors,\r\n Atom,\r\n Residue,\r\n Chain,\r\n Molecule,\r\n} = chem;\r\n\r\nconst EDIT_MODE = { COMPLEX: 0, COMPONENT: 1, FRAGMENT: 2 };\r\n\r\nconst LOADER_NOT_FOUND = 'Could not find suitable loader for this source';\r\nconst PARSER_NOT_FOUND = 'Could not find suitable parser for this source';\r\n\r\n// Color management changed a lot in threejs 152+ version.\r\n// To keep miew colors we disable the new color management system\r\nTHREE.ColorManagement.enabled = false;\r\n\r\nconst { createElement } = utils;\r\n\r\nfunction updateFogRange(fog, center, radius) {\r\n fog.near = center - radius * settings.now.fogNearFactor;\r\n fog.far = center + radius * settings.now.fogFarFactor;\r\n}\r\n\r\nfunction removeExtension(fileName) {\r\n const dot = fileName.lastIndexOf('.');\r\n if (dot >= 0) {\r\n fileName = fileName.substr(0, dot);\r\n }\r\n return fileName;\r\n}\r\n\r\nfunction hasValidResidues(complex) {\r\n let hasValidRes = false;\r\n complex.forEachComponent((component) => {\r\n component.forEachResidue((residue) => {\r\n if (residue._isValid) {\r\n hasValidRes = true;\r\n }\r\n });\r\n });\r\n return hasValidRes;\r\n}\r\n\r\nfunction reportProgress(log, action, percent) {\r\n const TOTAL_PERCENT = 100;\r\n if (percent !== undefined) {\r\n log.debug(`${action}... ${Math.floor(percent * TOTAL_PERCENT)}%`);\r\n } else {\r\n log.debug(`${action}...`);\r\n }\r\n}\r\n\r\nfunction chooseFogColor() {\r\n return settings.now.fogColorEnable ? settings.now.fogColor : settings.now.bg.color;\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\n/**\r\n * Main 3D Molecular Viewer class.\r\n *\r\n * @param {object} opts - Viewer options.\r\n * @param {HTMLElement=} opts.container - DOM element that serves as a viewer container.\r\n * @param {object=} opts.settings - An object with properties to override default settings.\r\n * @param {string=} opts.settingsCookie='settings' - The name of the cookie to save current settings to.\r\n * @param {string=} opts.cookiePath='/' - The path option for cookies. Defaults to root.\r\n *\r\n * @exports Miew\r\n * @constructor\r\n */\r\nfunction Miew(opts) {\r\n EventDispatcher.call(this);\r\n this._opts = _.merge({\r\n settingsCookie: 'settings',\r\n cookiePath: '/',\r\n }, opts);\r\n /** @type {?object} */\r\n this._gfx = null;\r\n /** @type {ViewInterpolator} */\r\n this._interpolator = new ViewInterpolator();\r\n /** @type {HTMLElement} */\r\n this._container = (opts && opts.container)\r\n || document.getElementById('miew-container')\r\n || _.head(document.getElementsByClassName('miew-container'))\r\n || document.body;\r\n /** @type {HTMLElement} */\r\n this._containerRoot = this._container;\r\n\r\n /** @type {boolean} */\r\n this._running = false;\r\n /** @type {boolean} */\r\n this._halting = false;\r\n /** @type {boolean} */\r\n this._building = false;\r\n /** @type {boolean} */\r\n this._needRender = true;\r\n /** @type {boolean} */\r\n this._hotKeysEnabled = true;\r\n\r\n /** @type {Settings} */\r\n this.settings = settings;\r\n const log = logger;\r\n log.console = DEBUG;\r\n log.level = DEBUG ? 'debug' : 'info';\r\n /**\r\n * @type {Logger}\r\n * @example\r\n * miew.logger.addEventListener('message', function _onLogMessage(evt) {\r\n * console.log(evt.message);\r\n * });\r\n */\r\n this.logger = log;\r\n\r\n this._cookies = new Cookies(this);\r\n this.restoreSettings();\r\n if (opts && opts.settings) {\r\n this.settings.set(opts.settings);\r\n }\r\n\r\n /** @type {?Spinner} */\r\n this._spinner = null;\r\n /** @type {JobHandle[]} */\r\n this._loading = [];\r\n /** @type {?number}\r\n * @deprecated until Animation system refactoring\r\n */\r\n this._animInterval = null;\r\n\r\n /** @type {object} */\r\n this._visuals = {};\r\n /** @type {?string} */\r\n this._curVisualName = null;\r\n\r\n /** @type {array} */\r\n this._objects = [];\r\n\r\n /** @type {object} */\r\n this._sourceWindow = null;\r\n\r\n this.reset();\r\n\r\n if (this._repr) {\r\n log.debug(`Selected ${this._repr.mode.name} mode with ${this._repr.colorer.name} colorer.`);\r\n }\r\n\r\n const self = this;\r\n Miew.registeredPlugins.forEach((plugin) => {\r\n plugin.call(self);\r\n });\r\n\r\n this._initOnSettingsChanged();\r\n}\r\n\r\nMiew.prototype = Object.create(EventDispatcher.prototype);\r\nMiew.prototype.constructor = Miew;\r\n\r\nMiew.prototype.getMaxRepresentationCount = function () {\r\n return ComplexVisual.NUM_REPRESENTATION_BITS;\r\n};\r\n\r\n/**\r\n * Replace viewer container contents with a DOM element.\r\n * @param {HTMLElement} container - parent container.\r\n * @param {HTMLElement} element - DOM element to show.\r\n * @private\r\n */\r\nfunction _setContainerContents(container, element) {\r\n const parent = container;\r\n while (parent.firstChild) {\r\n parent.removeChild(parent.firstChild);\r\n }\r\n parent.appendChild(element);\r\n}\r\n\r\n/**\r\n * Update Shadow Camera target position and frustum.\r\n * @private\r\n */\r\nMiew.prototype._updateShadowCamera = (function () {\r\n const shadowMatrix = new THREE.Matrix4();\r\n const direction = new THREE.Vector3();\r\n const OBB = { center: new THREE.Vector3(), halfSize: new THREE.Vector3() };\r\n\r\n return function () {\r\n this._gfx.scene.updateMatrixWorld();\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = this._gfx.scene.children[i];\r\n shadowMatrix.copy(light.shadow.camera.matrixWorldInverse);\r\n this.getOBB(shadowMatrix, OBB);\r\n\r\n direction.subVectors(light.target.position, light.position);\r\n light.position.subVectors(OBB.center, direction);\r\n light.target.position.copy(OBB.center);\r\n\r\n light.shadow.bias = 0.09;\r\n light.shadow.camera.bottom = -OBB.halfSize.y;\r\n light.shadow.camera.top = OBB.halfSize.y;\r\n light.shadow.camera.right = OBB.halfSize.x;\r\n light.shadow.camera.left = -OBB.halfSize.x;\r\n light.shadow.camera.near = direction.length() - OBB.halfSize.z;\r\n light.shadow.camera.far = direction.length() + OBB.halfSize.z;\r\n\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Initialize the viewer.\r\n * @returns {boolean} true on success.\r\n * @throws Forwards exception raised during initialization.\r\n * @see Miew#term\r\n */\r\nMiew.prototype.init = function () {\r\n const container = this._container;\r\n const elem = utils.createElement('div', { class: 'miew-canvas' });\r\n _setContainerContents(container, elem);\r\n this._container = elem;\r\n\r\n const frag = document.createDocumentFragment();\r\n frag.appendChild(this._msgMode = createElement(\r\n 'div',\r\n { class: 'mode-message overlay' },\r\n createElement('p', {}, 'COMPONENT EDIT MODE'),\r\n ));\r\n frag.appendChild(this._msgAtomInfo = createElement(\r\n 'div',\r\n { class: 'atom-info overlay' },\r\n createElement('p', {}, ''),\r\n ));\r\n container.appendChild(frag);\r\n\r\n if (this._gfx !== null) { // block double init\r\n return true;\r\n }\r\n\r\n const self = this;\r\n this._showMessage('Viewer is being initialized...');\r\n try {\r\n this._initGfx();\r\n\r\n this._initListeners();\r\n this._spinner = new Spinner({\r\n lines: 13,\r\n length: 28,\r\n width: 14,\r\n radius: 42,\r\n color: '#fff',\r\n zIndex: 700,\r\n });\r\n\r\n const target = getTopWindow();\r\n target.addEventListener('keydown', (event) => {\r\n self._onKeyDown(event);\r\n });\r\n\r\n target.addEventListener('keyup', (event) => {\r\n self._onKeyUp(event);\r\n });\r\n\r\n this._objectControls = new ObjectControls(\r\n this._gfx.root,\r\n this._gfx.pivot,\r\n this._gfx.camera,\r\n this._gfx.renderer.domElement,\r\n () => self._getAltObj(),\r\n );\r\n this._objectControls.addEventListener('change', (e) => {\r\n if (settings.now.shadow.on) {\r\n self._updateShadowCamera();\r\n }\r\n // route rotate, zoom, translate and translatePivot events to the external API\r\n switch (e.action) {\r\n case 'rotate':\r\n self.dispatchEvent({ type: 'rotate', quaternion: e.quaternion });\r\n break;\r\n case 'zoom':\r\n self.dispatchEvent({ type: 'zoom', factor: e.factor });\r\n break;\r\n default:\r\n self.dispatchEvent({ type: e.action });\r\n }\r\n self.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n });\r\n\r\n const gfx = this._gfx;\r\n this._picker = new Picker(gfx.root, gfx.camera, gfx.renderer.domElement);\r\n this._picker.addEventListener('newpick', (event) => {\r\n self._onPick(event);\r\n });\r\n this._picker.addEventListener('dblclick', (event) => {\r\n self.center(event);\r\n });\r\n } catch (error) {\r\n if (error.name === 'TypeError' && error.message === 'Cannot read property \\'getExtension\\' of null') {\r\n this._showMessage('Could not create WebGL context.');\r\n } else if (error.message.search(/webgl/i) > 1) {\r\n this._showMessage(error.message);\r\n } else {\r\n this._showMessage('Viewer initialization failed.');\r\n throw error;\r\n }\r\n return false;\r\n }\r\n\r\n // automatically load default file\r\n const file = this._opts && this._opts.load;\r\n if (file) {\r\n const type = this._opts && this._opts.type;\r\n this.load(file, { fileType: type, keepRepsInfo: true });\r\n }\r\n\r\n return true;\r\n};\r\n\r\n/**\r\n * Terminate the viewer completely.\r\n * @see Miew#init\r\n */\r\nMiew.prototype.term = function () {\r\n this._showMessage('Viewer has been terminated.');\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n this.halt();\r\n this._gfx = null;\r\n};\r\n\r\n/**\r\n * Display message inside the viewer container, hiding WebGL canvas.\r\n * @param {string} msg - Message to show.\r\n * @private\r\n */\r\nMiew.prototype._showMessage = function (msg) {\r\n const element = document.createElement('div');\r\n element.setAttribute('class', 'miew-message');\r\n element.appendChild(document.createElement('p')).appendChild(document.createTextNode(msg));\r\n _setContainerContents(this._container, element);\r\n};\r\n\r\n/**\r\n * Display WebGL canvas inside the viewer container, hiding any message shown.\r\n * @private\r\n */\r\nMiew.prototype._showCanvas = function () {\r\n _setContainerContents(this._container, this._gfx.renderer.domElement);\r\n};\r\n\r\nMiew.prototype._requestAnimationFrame = function (callback) {\r\n const { xr } = this._gfx.renderer;\r\n if (xr && xr.enabled) {\r\n this._gfx.renderer.setAnimationLoop(callback);\r\n return;\r\n }\r\n requestAnimationFrame(callback);\r\n};\r\n\r\n/**\r\n * Initialize WebGL and set 3D scene up.\r\n * @private\r\n */\r\nMiew.prototype._initGfx = function () {\r\n const gfx = {\r\n width: this._container.clientWidth,\r\n height: this._container.clientHeight,\r\n };\r\n\r\n const webGLOptions = { preserveDrawingBuffer: true, alpha: true, premultipliedAlpha: false };\r\n if (settings.now.antialias) {\r\n webGLOptions.antialias = true;\r\n }\r\n\r\n gfx.renderer2d = new CSS2DRenderer();\r\n\r\n gfx.renderer = new THREE.WebGLRenderer(webGLOptions);\r\n gfx.renderer.shadowMap.enabled = settings.now.shadow.on;\r\n gfx.renderer.shadowMap.autoUpdate = false;\r\n gfx.renderer.shadowMap.type = THREE.PCFShadowMap;\r\n capabilities.init(gfx.renderer);\r\n\r\n gfx.renderer.autoClear = false;\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n gfx.camera = new THREE.PerspectiveCamera(\r\n settings.now.camFov,\r\n gfx.width / gfx.height,\r\n settings.now.camNear,\r\n settings.now.camFar,\r\n );\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.position.z = settings.now.camDistance;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n\r\n gfx.stereoCam = new THREE.StereoCamera();\r\n\r\n gfx.scene = new THREE.Scene();\r\n\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color, settings.now.camNear, settings.now.camFar);\r\n\r\n gfx.root = new gfxutils.RCGroup();\r\n gfx.scene.add(gfx.root);\r\n\r\n gfx.pivot = new gfxutils.RCGroup();\r\n gfx.root.add(gfx.pivot);\r\n\r\n gfx.selectionScene = new THREE.Scene();\r\n gfx.selectionRoot = new THREE.Group();\r\n gfx.selectionRoot.matrixAutoUpdate = false;\r\n gfx.selectionScene.add(gfx.selectionRoot);\r\n\r\n gfx.selectionPivot = new THREE.Group();\r\n gfx.selectionPivot.matrixAutoUpdate = false;\r\n gfx.selectionRoot.add(gfx.selectionPivot);\r\n\r\n const light12 = new THREE.DirectionalLight(0xffffff, 0.45);\r\n light12.position.set(0, 0.414, 1);\r\n light12.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n light12.castShadow = true;\r\n light12.shadow.bias = 0.09;\r\n light12.shadow.radius = settings.now.shadow.radius;\r\n light12.shadow.camera.layers.set(gfxutils.LAYERS.SHADOWMAP);\r\n\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n const shadowMapSize = Math.max(gfx.width, gfx.height) * pixelRatio;\r\n light12.shadow.mapSize.width = shadowMapSize;\r\n light12.shadow.mapSize.height = shadowMapSize;\r\n light12.target.position.set(0.0, 0.0, 0.0);\r\n gfx.scene.add(light12);\r\n gfx.scene.add(light12.target);\r\n\r\n const light3 = new THREE.AmbientLight(0x666666);\r\n light3.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.scene.add(light3);\r\n\r\n // add axes\r\n gfx.axes = new Axes(gfx.root, gfx.camera);\r\n const deviceWidth = gfx.width * pixelRatio;\r\n const deviceHeight = gfx.height * pixelRatio;\r\n\r\n gfx.offscreenBuf = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat, depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf.depthTexture = new THREE.DepthTexture();\r\n gfx.offscreenBuf.depthTexture.type = THREE.UnsignedShortType;\r\n\r\n gfx.offscreenBuf2 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf3 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf4 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf3;\r\n gfx.volFFTex = gfx.offscreenBuf4;\r\n gfx.volWFFTex = gfx.offscreenBuf;\r\n\r\n // use float textures for volume rendering (WebGL2 core feature)\r\n gfx.offscreenBuf5 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf6 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf7 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf5;\r\n gfx.volFFTex = gfx.offscreenBuf6;\r\n gfx.volWFFTex = gfx.offscreenBuf7;\r\n\r\n gfx.stereoBufL = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.stereoBufR = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n this._gfx = gfx;\r\n this._showCanvas();\r\n\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n\r\n this._container.appendChild(gfx.renderer2d.getElement());\r\n\r\n // add FPS counter\r\n const stats = new Stats();\r\n stats.domElement.style.position = 'absolute';\r\n stats.domElement.style.right = '0';\r\n stats.domElement.style.bottom = '0';\r\n this._container.appendChild(stats.domElement);\r\n this._fps = stats;\r\n this._fps.show(settings.now.fps);\r\n};\r\n\r\n/**\r\n * Setup event listeners.\r\n * @private\r\n */\r\nMiew.prototype._initListeners = function () {\r\n const self = this;\r\n window.addEventListener('resize', () => {\r\n self._onResize();\r\n });\r\n};\r\n\r\n/**\r\n * Try to add numbers to the base name to make it unique among visuals\r\n * @private\r\n */\r\nMiew.prototype._makeUniqueVisualName = function (baseName) {\r\n if (!baseName) {\r\n return Math.random().toString();\r\n }\r\n\r\n let name = baseName;\r\n let suffix = 1;\r\n while (this._visuals.hasOwnProperty(name)) {\r\n name = `${baseName} (${suffix.toString()})`;\r\n suffix++;\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Add visual to the viewer\r\n * @private\r\n */\r\nMiew.prototype._addVisual = function (visual) {\r\n if (!visual) {\r\n return null;\r\n }\r\n\r\n // change visual name in order to make it unique\r\n const name = this._makeUniqueVisualName(visual.name);\r\n visual.name = name;\r\n\r\n this._visuals[name] = visual;\r\n this._gfx.pivot.add(visual);\r\n if (visual.getSelectionGeo) {\r\n this._gfx.selectionPivot.add(visual.getSelectionGeo());\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Remove visual from the viewer\r\n * @private\r\n */\r\nMiew.prototype._removeVisual = function (visual) {\r\n let name = '';\r\n let obj = null;\r\n if (visual instanceof Visual) {\r\n ({ name } = visual);\r\n obj = visual;\r\n } else if (typeof visual === 'string') {\r\n name = visual;\r\n obj = this._visuals[name];\r\n }\r\n\r\n if (!obj || !this._visuals.hasOwnProperty(name) || this._visuals[name] !== obj) {\r\n return;\r\n }\r\n\r\n if (name === this._curVisualName) {\r\n this._curVisualName = undefined;\r\n }\r\n\r\n delete this._visuals[name];\r\n obj.release(); // removes nodes from scene\r\n\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Call specified function for each Visual\r\n * @private\r\n */\r\nMiew.prototype._forEachVisual = function (callback) {\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Release (destroy) all visuals in the scene\r\n * @private\r\n */\r\nMiew.prototype._releaseAllVisuals = function () {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n this._visuals[name].release();\r\n }\r\n }\r\n\r\n this._visuals = {};\r\n};\r\n\r\n/**\r\n * Call specified function for each ComplexVisual\r\n * @private\r\n */\r\nMiew.prototype._forEachComplexVisual = function (callback) {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)\r\n && this._visuals[name] instanceof ComplexVisual) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual with specified name, or current (if not found), or any, or null\r\n * @private\r\n */\r\nMiew.prototype._getComplexVisual = function (name) {\r\n name = name || this._curVisualName;\r\n let any = null;\r\n let named = null;\r\n this._forEachComplexVisual((visual) => {\r\n any = visual;\r\n if (visual.name === name) {\r\n named = visual;\r\n }\r\n });\r\n return named || any;\r\n};\r\n\r\n/**\r\n * Returns first found VolumeVisual (no more than one should be present actually)\r\n * @private\r\n */\r\nMiew.prototype._getVolumeVisual = function () {\r\n let any = null;\r\n this._forEachVisual((visual) => {\r\n if (visual instanceof VolumeVisual) {\r\n any = visual;\r\n }\r\n });\r\n return any;\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual corresponding to specified complex\r\n * @private\r\n */\r\nMiew.prototype._getVisualForComplex = function (complex) {\r\n if (!complex) {\r\n return null;\r\n }\r\n\r\n let found = null;\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getComplex() === complex) {\r\n found = visual;\r\n }\r\n });\r\n return found;\r\n};\r\n\r\n/*\r\n * Get a list of names of visuals currently shown by the viewer\r\n */\r\nMiew.prototype.getVisuals = function () {\r\n return Object.keys(this._visuals);\r\n};\r\n\r\n/*\r\n * Get complex visuals count\r\n */\r\nMiew.prototype.getComplexVisualsCount = function () {\r\n let count = 0;\r\n this._forEachComplexVisual(() => count++);\r\n return count;\r\n};\r\n\r\n/*\r\n * Get current visual\r\n */\r\nMiew.prototype.getCurrentVisual = function () {\r\n return this._curVisualName;\r\n};\r\n\r\n/*\r\n * Set current visual.\r\n * All further operations will be performed on this visual (complex) if not stated otherwise.\r\n */\r\nMiew.prototype.setCurrentVisual = function (name) {\r\n if (!this._visuals[name]) {\r\n return;\r\n }\r\n\r\n this._curVisualName = name;\r\n};\r\n\r\n/**\r\n * Run the viewer, start processing update/render frames periodically.\r\n * Has no effect if already running.\r\n * @see Miew#halt\r\n */\r\nMiew.prototype.run = function () {\r\n if (!this._running) {\r\n this._running = true;\r\n if (this._halting) {\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._objectControls.enable(true);\r\n this._interpolator.resume();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to stop.\r\n * Will be processed during the next frame.\r\n * @see Miew#run\r\n */\r\nMiew.prototype.halt = function () {\r\n if (this._running) {\r\n this._discardComponentEdit();\r\n this._discardFragmentEdit();\r\n this._objectControls.enable(false);\r\n this._interpolator.pause();\r\n this._halting = true;\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to start / stop responsing\r\n * on hot keys.\r\n * @param enabled - start (true) or stop (false) response on hot keys.\r\n */\r\nMiew.prototype.enableHotKeys = function (enabled) {\r\n this._hotKeysEnabled = enabled;\r\n this._objectControls.enableHotkeys(enabled);\r\n};\r\n\r\n/**\r\n * Callback which processes window resize.\r\n * @private\r\n */\r\nMiew.prototype._onResize = function () {\r\n const gfx = this._gfx;\r\n if (!gfx) {\r\n return;\r\n }\r\n\r\n this._needRender = true;\r\n\r\n gfx.width = this._container.clientWidth;\r\n gfx.height = this._container.clientHeight;\r\n\r\n gfx.camera.aspect = gfx.width / gfx.height;\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n this.dispatchEvent({ type: 'resize' });\r\n};\r\n\r\nMiew.prototype._resizeOffscreenBuffers = function (width, height, stereo) {\r\n const gfx = this._gfx;\r\n stereo = stereo || 'NONE';\r\n const isAnaglyph = (stereo === 'NONE' || stereo === 'ANAGLYPH');\r\n const multi = isAnaglyph ? 1 : 0.5;\r\n gfx.offscreenBuf.setSize(multi * width, height);\r\n gfx.offscreenBuf2.setSize(multi * width, height);\r\n gfx.offscreenBuf3.setSize(multi * width, height);\r\n gfx.offscreenBuf4.setSize(multi * width, height);\r\n if (gfx.offscreenBuf5) {\r\n gfx.offscreenBuf5.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf6) {\r\n gfx.offscreenBuf6.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf7) {\r\n gfx.offscreenBuf7.setSize(multi * width, height);\r\n }\r\n if (isAnaglyph) {\r\n gfx.stereoBufL.setSize(width, height);\r\n gfx.stereoBufR.setSize(width, height);\r\n }\r\n};\r\n\r\n/**\r\n * Callback which processes update/render frames.\r\n * @private\r\n */\r\nMiew.prototype._onTick = function () {\r\n if (this._halting) {\r\n this._running = false;\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._fps.update();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n\r\n this._onUpdate();\r\n if (this._needRender) {\r\n this._onRender();\r\n this._needRender = !settings.now.suspendRender || settings.now.stereo === 'WEBVR';\r\n }\r\n};\r\n\r\nMiew.prototype._getBSphereRadius = function () {\r\n // calculate radius that would include all visuals\r\n let radius = 0;\r\n this._forEachVisual((visual) => {\r\n radius = Math.max(radius, visual.getBoundaries().boundingSphere.radius);\r\n });\r\n return radius * this._objectControls.getScale();\r\n};\r\n\r\n/**\r\n * Calculate bounding box that would include all visuals and being axis aligned in world defined by\r\n * transformation matrix: matrix\r\n * @param {Matrix4} matrix - transformation matrix.\r\n * @param {object} OBB - calculating bounding box.\r\n * @param {Vector3} OBB.center - OBB center.\r\n * @param {Vector3} OBB.halfSize - half magnitude of OBB sizes.\r\n */\r\nMiew.prototype.getOBB = (function () {\r\n const _bSphereForOneVisual = new THREE.Sphere();\r\n const _bBoxForOneVisual = new THREE.Box3();\r\n const _bBox = new THREE.Box3();\r\n\r\n const _invMatrix = new THREE.Matrix4();\r\n\r\n const _points = [\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n ];\r\n\r\n return function (matrix, OBB) {\r\n _bBox.makeEmpty();\r\n\r\n this._forEachVisual((visual) => {\r\n _bSphereForOneVisual.copy(visual.getBoundaries().boundingSphere);\r\n _bSphereForOneVisual.applyMatrix4(visual.matrixWorld).applyMatrix4(matrix);\r\n _bSphereForOneVisual.getBoundingBox(_bBoxForOneVisual);\r\n _bBox.union(_bBoxForOneVisual);\r\n });\r\n _bBox.getCenter(OBB.center);\r\n\r\n _invMatrix.copy(matrix).invert();\r\n OBB.center.applyMatrix4(_invMatrix);\r\n\r\n const { min } = _bBox;\r\n const { max } = _bBox;\r\n _points[0].set(min.x, min.y, min.z); // 000\r\n _points[1].set(max.x, min.y, min.z); // 100\r\n _points[2].set(min.x, max.y, min.z); // 010\r\n _points[3].set(min.x, min.y, max.z); // 001\r\n for (let i = 0, l = _points.length; i < l; i++) {\r\n _points[i].applyMatrix4(_invMatrix);\r\n }\r\n\r\n OBB.halfSize.set(\r\n Math.abs(_points[0].x - _points[1].x),\r\n Math.abs(_points[0].y - _points[2].y),\r\n Math.abs(_points[0].z - _points[3].z),\r\n ).multiplyScalar(0.5);\r\n };\r\n}());\r\n\r\nMiew.prototype._updateFog = function () {\r\n const gfx = this._gfx;\r\n\r\n if (settings.now.fog) {\r\n if (typeof gfx.scene.fog === 'undefined' || gfx.scene.fog === null) {\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color);\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n updateFogRange(gfx.scene.fog, gfx.camera.position.z, this._getBSphereRadius());\r\n } else if (gfx.scene.fog) {\r\n gfx.scene.fog = undefined;\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n};\r\n\r\nMiew.prototype._onUpdate = function () {\r\n if (this.isScriptingCommandAvailable !== undefined && this.isScriptingCommandAvailable() && !this._building) {\r\n this.callNextCmd();\r\n }\r\n\r\n this._objectControls.update();\r\n\r\n this._forEachComplexVisual((visual) => {\r\n visual.getComplex().update();\r\n });\r\n\r\n if (settings.now.autobuild && !this._loading.length && !this._building && this._needRebuild()) {\r\n this.rebuild();\r\n }\r\n\r\n if (!this._loading.length && !this._building && !this._needRebuild()) {\r\n this._updateView();\r\n }\r\n\r\n this._updateFog();\r\n\r\n if (this._gfx.renderer.xr.enabled) {\r\n this.webVR.updateMoleculeScale();\r\n }\r\n};\r\n\r\nMiew.prototype._onRender = function () {\r\n const gfx = this._gfx;\r\n\r\n // update all matrices\r\n gfx.scene.updateMatrixWorld();\r\n gfx.camera.updateMatrixWorld();\r\n\r\n this._clipPlaneUpdateValue(this._getBSphereRadius());\r\n this._fogFarUpdateValue();\r\n\r\n gfx.renderer.setRenderTarget(null);\r\n gfx.renderer.clear();\r\n\r\n this._renderFrame(settings.now.stereo);\r\n};\r\n\r\nMiew.prototype._renderFrame = (function () {\r\n const _anaglyphMat = new AnaglyphMaterial();\r\n const _size = new THREE.Vector2();\r\n\r\n return function (stereo) {\r\n const gfx = this._gfx;\r\n const { renderer } = gfx;\r\n\r\n renderer.getSize(_size);\r\n\r\n if (stereo !== 'NONE') {\r\n gfx.camera.focus = gfx.camera.position.z; // set focus to the center of the object\r\n gfx.stereoCam.aspect = 1.0;\r\n\r\n // in anaglyph mode we render full-size image for each eye\r\n // while in other stereo modes only half-size (two images on the screen)\r\n if (stereo === 'ANAGLYPH') {\r\n gfx.stereoCam.update(gfx.camera);\r\n } else {\r\n gfx.stereoCam.updateHalfSized(gfx.camera, settings.now.camFov);\r\n }\r\n }\r\n\r\n // resize offscreen buffers to match the target\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n this._resizeOffscreenBuffers(_size.width * pixelRatio, _size.height * pixelRatio, stereo);\r\n\r\n this._renderShadowMap();\r\n\r\n switch (stereo) {\r\n case 'WEBVR':\r\n case 'NONE':\r\n this._renderScene(gfx.camera, false);\r\n break;\r\n case 'SIMPLE':\r\n case 'DISTORTED':\r\n renderer.setScissorTest(true);\r\n\r\n renderer.setScissor(0, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(0, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraL, stereo === 'DISTORTED');\r\n\r\n renderer.setScissor(_size.width / 2, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(_size.width / 2, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraR, stereo === 'DISTORTED');\r\n\r\n renderer.setScissorTest(false);\r\n break;\r\n case 'ANAGLYPH':\r\n this._renderScene(this._gfx.stereoCam.cameraL, false, gfx.stereoBufL);\r\n this._renderScene(this._gfx.stereoCam.cameraR, false, gfx.stereoBufR);\r\n renderer.setRenderTarget(null);\r\n _anaglyphMat.uniforms.srcL.value = gfx.stereoBufL.texture;\r\n _anaglyphMat.uniforms.srcR.value = gfx.stereoBufR.texture;\r\n gfx.renderer.renderScreenQuad(_anaglyphMat);\r\n break;\r\n default:\r\n }\r\n\r\n gfx.renderer2d.render(gfx.scene, gfx.camera);\r\n\r\n if (settings.now.axes && gfx.axes && !gfx.renderer.xr.enabled) {\r\n gfx.axes.render(renderer);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._onBgColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx) {\r\n if (gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onFogColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx && gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._setUberMaterialValues = function (values) {\r\n this._gfx.root.traverse((obj) => {\r\n if ((obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line)\r\n && obj.material instanceof UberMaterial) {\r\n obj.material.setValues(values);\r\n obj.material.needsUpdate = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) {\r\n const gfx = this._gfx;\r\n const gl = gfx.renderer.getContext();\r\n const { properties } = gfx.renderer;\r\n\r\n if (!on) {\r\n gl.drawBuffers([gl.COLOR_ATTACHMENT0, null]);\r\n return;\r\n }\r\n\r\n // take extra texture from Texture Buffer\r\n gfx.renderer.setRenderTarget(textureBuffer);\r\n const tx8 = properties.get(textureBuffer.texture).__webglTexture;\r\n gl.bindTexture(gl.TEXTURE_2D, tx8);\r\n\r\n // take texture and framebuffer from renderbuffer\r\n gfx.renderer.setRenderTarget(renderBuffer);\r\n const fb = properties.get(renderBuffer).__webglFramebuffer;\r\n const tx = properties.get(renderBuffer.texture).__webglTexture;\r\n\r\n // set framebuffer\r\n gl.bindFramebuffer(gl.FRAMEBUFFER, fb);\r\n fb.width = renderBuffer.width;\r\n fb.height = renderBuffer.height;\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT0, gl.TEXTURE_2D, tx, 0);\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT1, gl.TEXTURE_2D, tx8, 0);\r\n\r\n // mapping textures (MRT is core feature in WebGL2)\r\n gl.drawBuffers([gl.COLOR_ATTACHMENT0, gl.COLOR_ATTACHMENT1]);\r\n};\r\n\r\nMiew.prototype._renderScene = (function () {\r\n return function (camera, distortion, target) {\r\n distortion = distortion || false;\r\n target = target || null;\r\n\r\n const gfx = this._gfx;\r\n\r\n // render to offscreen buffer\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.clear();\r\n if (gfx.renderer.xr.enabled) {\r\n gfx.renderer.render(gfx.scene, camera);\r\n return;\r\n }\r\n\r\n // clean buffer for normals texture\r\n gfx.renderer.setClearColor(0x000000, 0.0);\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf4);\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.clear();\r\n\r\n const bHaveComplexes = (this._getComplexVisual() !== null);\r\n const volumeVisual = this._getVolumeVisual();\r\n const ssao = bHaveComplexes && settings.now.ao;\r\n\r\n if (ssao) {\r\n this._enableMRT(true, gfx.offscreenBuf, gfx.offscreenBuf4);\r\n }\r\n\r\n if (settings.now.transparency === 'prepass') {\r\n this._renderWithPrepassTransparency(camera, gfx.offscreenBuf);\r\n } else if (settings.now.transparency === 'standard') {\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n }\r\n\r\n if (ssao) {\r\n this._enableMRT(false, null, null);\r\n }\r\n\r\n // when fxaa we should get resulting image in temp off-screen buff2 for further postprocessing with fxaa filter\r\n // otherwise we render to canvas\r\n const outline = bHaveComplexes && settings.now.outline.on;\r\n const fxaa = bHaveComplexes && settings.now.fxaa;\r\n const volume = (volumeVisual !== null) && (volumeVisual.getMesh().material != null);\r\n let dstBuffer = (ssao || outline || volume || fxaa || distortion) ? gfx.offscreenBuf2 : target;\r\n let srcBuffer = gfx.offscreenBuf;\r\n\r\n if (ssao) {\r\n this._performAO(\r\n srcBuffer,\r\n gfx.offscreenBuf4,\r\n gfx.offscreenBuf.depthTexture,\r\n dstBuffer,\r\n gfx.offscreenBuf3,\r\n gfx.offscreenBuf2,\r\n );\r\n if (!fxaa && !distortion && !volume && !outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = target;\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n } else {\r\n // just copy color buffer to dst buffer\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n\r\n // outline\r\n if (outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = (volume || fxaa || distortion) ? gfx.offscreenBuf3 : target;\r\n if (srcBuffer != null) {\r\n this._renderOutline(camera, gfx.offscreenBuf, srcBuffer, dstBuffer);\r\n }\r\n }\r\n\r\n // render selected part with outline material\r\n this._renderSelection(camera, gfx.offscreenBuf, dstBuffer);\r\n\r\n if (volume) {\r\n // copy current picture to the buffer that retains depth-data of the original molecule render\r\n // so that volume renderer could use depth-test\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n dstBuffer = gfx.offscreenBuf;\r\n this._renderVolume(volumeVisual, camera, dstBuffer, gfx.volBFTex, gfx.volFFTex, gfx.volWFFTex);\r\n\r\n // if this is the last stage -- copy image to target\r\n if (!fxaa && !distortion) {\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n }\r\n }\r\n\r\n srcBuffer = dstBuffer;\r\n\r\n if (fxaa) {\r\n dstBuffer = distortion ? gfx.offscreenBuf4 : target;\r\n this._performFXAA(srcBuffer, dstBuffer);\r\n srcBuffer = dstBuffer;\r\n }\r\n\r\n if (distortion) {\r\n dstBuffer = target;\r\n this._performDistortion(srcBuffer, dstBuffer, true);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._performDistortion = (function () {\r\n const _scene = new THREE.Scene();\r\n const _camera = new THREE.OrthographicCamera(-1.0, 1.0, 1.0, -1.0, -500, 1000);\r\n\r\n const _material = new THREE.RawShaderMaterial({\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n aberration: { type: 'fv3', value: new THREE.Vector3(1.0) },\r\n },\r\n vertexShader: vertexScreenQuadShader,\r\n fragmentShader: fragmentScreenQuadFromDistTex,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n const _geo = gfxutils.buildDistorionMesh(10, 10, settings.now.debug.stereoBarrel);\r\n _scene.add(new meshes.Mesh(_geo, _material));\r\n\r\n return function (srcBuffer, targetBuffer, mesh) {\r\n this._gfx.renderer.setRenderTarget(targetBuffer);\r\n this._gfx.renderer.clear();\r\n\r\n if (mesh) {\r\n _material.uniforms.srcTex.value = srcBuffer.texture;\r\n _material.uniforms.aberration.value.set(0.995, 1.0, 1.01);\r\n this._gfx.renderer.render(_scene, _camera);\r\n } else {\r\n this._gfx.renderer.renderScreenQuadFromTexWithDistortion(srcBuffer, settings.now.debug.stereoBarrel);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._renderOutline = (function () {\r\n const _outlineMaterial = new OutlineMaterial({ depth: true });\r\n\r\n return function (camera, srcDepthBuffer, srcColorBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcColorBuffer.texture;\r\n _outlineMaterial.uniforms.srcDepthTex.value = srcDepthBuffer.depthTexture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcDepthBuffer.width, srcDepthBuffer.height);\r\n _outlineMaterial.uniforms.color.value = new THREE.Color(settings.now.outline.color);\r\n _outlineMaterial.uniforms.threshold.value = settings.now.outline.threshold;\r\n _outlineMaterial.uniforms.thickness.value = new THREE.Vector2(\r\n settings.now.outline.thickness,\r\n settings.now.outline.thickness,\r\n );\r\n\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._renderShadowMap = (function () {\r\n const pars = { minFilter: THREE.NearestFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat };\r\n\r\n return function () {\r\n if (!settings.now.shadow.on) {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n const currentRenderTarget = gfx.renderer.getRenderTarget();\r\n const activeCubeFace = gfx.renderer.getActiveCubeFace();\r\n const activeMipmapLevel = gfx.renderer.getActiveMipmapLevel();\r\n\r\n const _state = gfx.renderer.state;\r\n\r\n // Set GL state for depth map.\r\n _state.setBlending(THREE.NoBlending);\r\n _state.buffers.color.setClear(1, 1, 1, 1);\r\n _state.buffers.depth.setTest(true);\r\n _state.setScissorTest(false);\r\n\r\n for (let i = 0; i < gfx.scene.children.length; i++) {\r\n if (gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = gfx.scene.children[i];\r\n\r\n if (light.shadow.map == null) {\r\n light.shadow.map = new THREE.WebGLRenderTarget(light.shadow.mapSize.width, light.shadow.mapSize.height, pars);\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n light.shadow.updateMatrices(light);\r\n\r\n gfx.renderer.setRenderTarget(light.shadow.map);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.render(gfx.scene, light.shadow.camera);\r\n }\r\n }\r\n gfx.renderer.setRenderTarget(currentRenderTarget, activeCubeFace, activeMipmapLevel);\r\n };\r\n}());\r\n\r\n/**\r\n * Check if there is selection which must be rendered or not.\r\n * @private\r\n * @returns {boolean} true on existing selection to render\r\n */\r\nMiew.prototype._hasSelectionToRender = function () {\r\n const selPivot = this._gfx.selectionPivot;\r\n\r\n for (let i = 0; i < selPivot.children.length; i++) {\r\n const selPivotChild = selPivot.children[i];\r\n if (selPivotChild.children.length > 0) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n};\r\n\r\nMiew.prototype._renderSelection = (function () {\r\n const _outlineMaterial = new OutlineMaterial();\r\n\r\n return function (camera, srcBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // clear offscreen buffer (leave z-buffer intact)\r\n gfx.renderer.setClearColor('black', 0);\r\n\r\n // render selection to offscreen buffer\r\n gfx.renderer.setRenderTarget(srcBuffer);\r\n gfx.renderer.clear(true, false, false);\r\n if (self._hasSelectionToRender()) {\r\n gfx.selectionRoot.matrix = gfx.root.matrix;\r\n gfx.selectionPivot.matrix = gfx.pivot.matrix;\r\n gfx.renderer.render(gfx.selectionScene, camera);\r\n } else {\r\n // just render something to force \"target clear\" operation to finish\r\n gfx.renderer.renderDummyQuad();\r\n }\r\n\r\n // overlay to screen\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 0.6);\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcBuffer.width, srcBuffer.height);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._checkVolumeRenderingSupport = function (renderTarget) {\r\n if (!renderTarget) {\r\n return false;\r\n }\r\n const gfx = this._gfx;\r\n const oldRT = gfx.renderer.getRenderTarget();\r\n\r\n gfx.renderer.setRenderTarget(renderTarget);\r\n const context = gfx.renderer.getContext();\r\n const result = context.checkFramebufferStatus(context.FRAMEBUFFER);\r\n gfx.renderer.setRenderTarget(oldRT);\r\n if (result !== context.FRAMEBUFFER_COMPLETE) {\r\n // floatFrameBufferWarning = ;\r\n this.logger.warn('Device doesn\\'t support electron density rendering');\r\n return false;\r\n }\r\n return true;\r\n};\r\n\r\nMiew.prototype._renderVolume = (function () {\r\n const volumeBFMat = new VolumeMaterial.BackFacePosMaterial();\r\n const volumeFFMat = new VolumeMaterial.FrontFacePosMaterial();\r\n const cubeOffsetMat = new THREE.Matrix4().makeTranslation(0.5, 0.5, 0.5);\r\n const world2colorMat = new THREE.Matrix4();\r\n\r\n let volumeRenderingSupported;\r\n\r\n return function (volumeVisual, camera, dstBuf, tmpBuf1, tmpBuf2, tmpBuf3) {\r\n const gfx = this._gfx;\r\n\r\n if (typeof volumeRenderingSupported === 'undefined') {\r\n volumeRenderingSupported = this._checkVolumeRenderingSupport(tmpBuf1);\r\n }\r\n\r\n if (!volumeRenderingSupported) {\r\n return;\r\n }\r\n\r\n const mesh = volumeVisual.getMesh();\r\n\r\n mesh.rebuild(gfx.camera);\r\n\r\n // use main camera to prepare special textures to be used by volumetric rendering\r\n // these textures have the size of the window and are stored in offscreen buffers\r\n gfx.renderer.setClearColor('black', 0);\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n // draw plane with its own material, because it differs slightly from volumeBFMat\r\n camera.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeBFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeFFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.scene.overrideMaterial = null;\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n\r\n // prepare texture that contains molecule positions\r\n world2colorMat.copy(mesh.matrixWorld).invert();\r\n UberMaterial.prototype.uberOptions.world2colorMatrix.multiplyMatrices(cubeOffsetMat, world2colorMat);\r\n camera.layers.set(gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // render volume\r\n const vm = mesh.material;\r\n vm.uniforms._BFRight.value = tmpBuf1.texture;\r\n vm.uniforms._FFRight.value = tmpBuf2.texture;\r\n vm.uniforms._WFFRight.value = tmpBuf3.texture;\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.renderer.setRenderTarget(dstBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\n/* Render scene with 'ZPrepass transparency Effect'\r\n * Idea: transparent objects are rendered in two passes. The first one writes result only into depth buffer.\r\n * The second pass reads depth buffer and writes only to color buffer. The method results in\r\n * correct image of front part of the semi-transparent objects, but we can see only front transparent objects\r\n * and opaque objects inside, there is no transparent objects inside.\r\n * Notes: 1. Opaque objects should be rendered strictly before semi-transparent ones.\r\n * 2. Realization doesn't use camera layers because scene traversing is used for material changes and\r\n * we can use it to select needed meshes and don't complicate meshes builders with layers\r\n */\r\nMiew.prototype._renderWithPrepassTransparency = (function () {\r\n return function (camera, targetBuffer) {\r\n const gfx = this._gfx;\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n\r\n // opaque objects\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // transparent objects z prepass\r\n camera.layers.set(gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n gfx.renderer.getContext().colorMask(false, false, false, false); // don't update color buffer\r\n gfx.renderer.render(gfx.scene, camera);\r\n gfx.renderer.getContext().colorMask(true, true, true, true); // update color buffer\r\n\r\n // transparent objects color pass\r\n camera.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // restore default layer\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\nMiew.prototype._performFXAA = (function () {\r\n const _fxaaMaterial = new FXAAMaterial();\r\n\r\n return function (srcBuffer, targetBuffer) {\r\n if (typeof srcBuffer === 'undefined' || typeof targetBuffer === 'undefined') {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n\r\n // clear canvas\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.clear();\r\n\r\n // do fxaa processing of offscreen buff2\r\n _fxaaMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _fxaaMaterial.uniforms.srcTexelSize.value.set(1.0 / srcBuffer.width, 1.0 / srcBuffer.height);\r\n _fxaaMaterial.uniforms.bgColor.value.set(settings.now.bg.color);\r\n\r\n if (_fxaaMaterial.bgTransparent !== settings.now.bg.transparent) {\r\n _fxaaMaterial.setValues({ bgTransparent: settings.now.bg.transparent });\r\n _fxaaMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.renderScreenQuad(_fxaaMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._performAO = (function () {\r\n const _aoMaterial = new AOMaterial();\r\n const _horBlurMaterial = new AOHorBlurMaterial();\r\n const _vertBlurMaterial = new AOVertBlurWithBlendMaterial();\r\n\r\n const _scale = new THREE.Vector3();\r\n return function (srcColorBuffer, normalBuffer, srcDepthTexture, targetBuffer, tempBuffer, tempBuffer1) {\r\n if (!srcColorBuffer || !normalBuffer || !srcDepthTexture || !targetBuffer || !tempBuffer || !tempBuffer1) {\r\n return;\r\n }\r\n const gfx = this._gfx;\r\n const tanHalfFOV = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * gfx.camera.fov);\r\n\r\n _aoMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _aoMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _aoMaterial.uniforms.normalTexture.value = normalBuffer.texture;\r\n _aoMaterial.uniforms.srcTexelSize.value.set(1.0 / srcColorBuffer.width, 1.0 / srcColorBuffer.height);\r\n _aoMaterial.uniforms.camNearFar.value.set(gfx.camera.near, gfx.camera.far);\r\n _aoMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _aoMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _aoMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n gfx.root.matrix.extractScale(_scale);\r\n _aoMaterial.uniforms.kernelRadius.value = settings.now.debug.ssaoKernelRadius * _scale.x;\r\n _aoMaterial.uniforms.depthThreshold.value = 2.0 * this._getBSphereRadius(); // diameter\r\n _aoMaterial.uniforms.factor.value = settings.now.debug.ssaoFactor;\r\n // N: should be tempBuffer1 for proper use of buffers (see buffers using outside the function)\r\n gfx.renderer.setRenderTarget(tempBuffer1);\r\n gfx.renderer.renderScreenQuad(_aoMaterial);\r\n\r\n _horBlurMaterial.uniforms.aoMap.value = tempBuffer1.texture;\r\n _horBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer1.width, 1.0 / tempBuffer1.height);\r\n _horBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n gfx.renderer.setRenderTarget(tempBuffer);\r\n gfx.renderer.renderScreenQuad(_horBlurMaterial);\r\n\r\n _vertBlurMaterial.uniforms.aoMap.value = tempBuffer.texture;\r\n _vertBlurMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _vertBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer.width, 1.0 / tempBuffer.height);\r\n _vertBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _vertBlurMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _vertBlurMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _vertBlurMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n const { fog } = gfx.scene;\r\n if (fog) {\r\n _vertBlurMaterial.uniforms.fogNearFar.value.set(fog.near, fog.far);\r\n _vertBlurMaterial.uniforms.fogColor.value.set(fog.color.r, fog.color.g, fog.color.b, settings.now.fogAlpha);\r\n }\r\n if ((_vertBlurMaterial.useFog !== settings.now.fog)\r\n || (_vertBlurMaterial.fogTransparent !== settings.now.bg.transparent)) {\r\n _vertBlurMaterial.setValues({ useFog: settings.now.fog, fogTransparent: settings.now.bg.transparent });\r\n _vertBlurMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_vertBlurMaterial);\r\n };\r\n}());\r\n\r\n/**\r\n * Reset the viewer, unload molecules.\r\n * @param {boolean=} keepReps - Keep representations while resetting viewer state.\r\n */\r\nMiew.prototype.reset = function (/* keepReps */) {\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._lastPick = null;\r\n\r\n this._releaseAllVisuals();\r\n\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._resetObjects();\r\n\r\n if (this._gfx) {\r\n gfxutils.clearTree(this._gfx.pivot);\r\n this._gfx.renderer2d.reset();\r\n }\r\n\r\n this.setNeedRender();\r\n};\r\n\r\nMiew.prototype._resetScene = function () {\r\n this._objectControls.reset();\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n this.resetReps();\r\n this.resetPivot();\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype.resetView = function () {\r\n // reset controls\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._resetScene();\r\n\r\n // reset selection\r\n this._forEachComplexVisual((visual) => {\r\n visual.updateSelectionMask({});\r\n visual.rebuildSelectionGeometry();\r\n });\r\n};\r\n\r\nMiew.prototype._export = function (format) {\r\n const TheExporter = _.head(io.exporters.find({ format }));\r\n if (!TheExporter) {\r\n this.logger.error('Could not find suitable exporter for this source');\r\n return Promise.reject(new Error('Could not find suitable exporter for this source'));\r\n }\r\n this.dispatchEvent({ type: 'exporting' });\r\n\r\n if (this._visuals[this._curVisualName] instanceof ComplexVisual) {\r\n let dataSource = null;\r\n if (TheExporter.SourceClass === ComplexVisual) {\r\n dataSource = this._visuals[this._curVisualName];\r\n } else if (TheExporter.SourceClass === Complex) {\r\n dataSource = this._visuals[this._curVisualName]._complex;\r\n }\r\n const exporter = new TheExporter(dataSource, { miewVersion: Miew.VERSION });\r\n return exporter.export().then((data) => data);\r\n }\r\n if (this._visuals[this._curVisualName] instanceof VolumeVisual) {\r\n return Promise.reject(new Error('Sorry, exporter for volume data not implemented yet'));\r\n }\r\n return Promise.reject(new Error('Unexpected format of data'));\r\n};\r\n\r\nconst rePdbId = /^(?:(pdb|cif|ccp4|dsn6):\\s*)?(\\d[a-z\\d]{3})$/i;\r\nconst rePubchem = /^(?:pc|pubchem):\\s*([a-z]+)$/i;\r\nconst reUrlScheme = /^([a-z][a-z\\d\\-+.]*):/i;\r\n\r\nfunction resolveSourceShortcut(source, opts) {\r\n if (!_.isString(source)) {\r\n return source;\r\n }\r\n\r\n // e.g. \"cif:1CRN\"\r\n const matchesPdbId = rePdbId.exec(source);\r\n if (matchesPdbId) {\r\n let [, format = 'pdb', id] = matchesPdbId;\r\n\r\n format = format.toLowerCase();\r\n id = id.toUpperCase();\r\n\r\n switch (format) {\r\n case 'pdb':\r\n source = `https://files.rcsb.org/download/${id}.pdb`;\r\n break;\r\n case 'cif':\r\n source = `https://files.rcsb.org/download/${id}.cif`;\r\n break;\r\n case 'ccp4':\r\n source = `https://www.ebi.ac.uk/pdbe/coordinates/files/${id.toLowerCase()}.ccp4`;\r\n break;\r\n case 'dsn6':\r\n source = `https://edmaps.rcsb.org/maps/${id.toLowerCase()}_2fofc.dsn6`;\r\n break;\r\n default:\r\n throw new Error('Unexpected data format shortcut');\r\n }\r\n\r\n opts.fileType = format;\r\n opts.fileName = `${id}.${format}`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // e.g. \"pc:aspirin\"\r\n const matchesPubchem = rePubchem.exec(source);\r\n if (matchesPubchem) {\r\n const compound = matchesPubchem[1].toLowerCase();\r\n source = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${compound}/JSON?record_type=3d`;\r\n opts.fileType = 'pubchem';\r\n opts.fileName = `${compound}.json`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // otherwise is should be an URL\r\n if (opts.sourceType === 'url' || opts.sourceType === undefined) {\r\n opts.sourceType = 'url';\r\n\r\n // e.g. \"./data/1CRN.pdb\"\r\n if (!reUrlScheme.test(source)) {\r\n source = utils.resolveURL(source);\r\n }\r\n }\r\n\r\n return source;\r\n}\r\n\r\nfunction updateBinaryMode(opts) {\r\n let { binary } = opts;\r\n\r\n // detect by format\r\n if (opts.fileType !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n } else {\r\n throw new Error('Could not find suitable parser for this format');\r\n }\r\n }\r\n\r\n // detect by file extension\r\n if (binary === undefined && opts.fileExt !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ ext: opts.fileExt }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n }\r\n }\r\n\r\n // temporary workaround for animation\r\n if (opts.fileExt !== undefined && opts.fileExt.toLowerCase() === '.man') {\r\n opts.binary = true;\r\n opts.animation = true; // who cares?\r\n }\r\n\r\n // update if detected\r\n if (binary !== undefined) {\r\n if (opts.binary !== undefined && opts.binary !== binary) {\r\n opts.context.logger.warn('Overriding incorrect binary mode');\r\n }\r\n }\r\n\r\n opts.binary = binary || false;\r\n}\r\n\r\nfunction _fetchData(source, opts, job) {\r\n return new Promise(((resolve) => {\r\n if (job.shouldCancel()) {\r\n throw new Error('Operation cancelled');\r\n }\r\n job.notify({ type: 'fetching' });\r\n\r\n // allow for source shortcuts\r\n source = resolveSourceShortcut(source, opts);\r\n\r\n // detect a proper loader\r\n const TheLoader = _.head(io.loaders.find({ type: opts.sourceType, source }));\r\n if (!TheLoader) {\r\n throw new Error(LOADER_NOT_FOUND);\r\n }\r\n\r\n // split file name\r\n const fileName = opts.fileName || TheLoader.extractName(source);\r\n if (fileName) {\r\n const [name, fileExt] = utils.splitFileName(fileName);\r\n _.defaults(opts, { name, fileExt, fileName });\r\n }\r\n\r\n // should it be text or binary?\r\n updateBinaryMode(opts);\r\n\r\n // FIXME: All new settings retrieved from server are applied after the loading is complete. However, we need some\r\n // flags to alter the loading process itself. Here we apply them in advance. Dirty hack. Kill the server, remove\r\n // all hacks and everybody's happy.\r\n let newOptions = _.get(opts, 'preset.expression');\r\n if (!_.isUndefined(newOptions)) {\r\n newOptions = JSON.parse(newOptions);\r\n if (newOptions && newOptions.settings) {\r\n const keys = ['singleUnit'];\r\n for (let keyIndex = 0, keyCount = keys.length; keyIndex < keyCount; ++keyIndex) {\r\n const key = keys[keyIndex];\r\n const value = _.get(newOptions.settings, key);\r\n if (!_.isUndefined(value)) {\r\n settings.set(key, value);\r\n }\r\n }\r\n }\r\n }\r\n\r\n // create a loader\r\n const loader = new TheLoader(source, opts);\r\n loader.context = opts.context;\r\n job.addEventListener('cancel', () => loader.abort());\r\n\r\n loader.addEventListener('progress', (event) => {\r\n if (event.lengthComputable && event.total > 0) {\r\n reportProgress(loader.logger, 'Fetching', event.loaded / event.total);\r\n } else {\r\n reportProgress(loader.logger, 'Fetching');\r\n }\r\n });\r\n\r\n console.time('fetch');\r\n const promise = loader.load()\r\n .then((data) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.info('Fetching finished');\r\n job.notify({ type: 'fetchingDone', data });\r\n return data;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Fetching failed');\r\n job.notify({ type: 'fetchingDone', error });\r\n throw error;\r\n });\r\n resolve(promise);\r\n }));\r\n}\r\n\r\nfunction _parseData(data, opts, job) {\r\n if (job.shouldCancel()) {\r\n return Promise.reject(new Error('Operation cancelled'));\r\n }\r\n\r\n job.notify({ type: 'parsing' });\r\n\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType, ext: opts.fileExt, data }));\r\n if (!TheParser) {\r\n return Promise.reject(new Error('Could not find suitable parser'));\r\n }\r\n\r\n const parser = new TheParser(data, opts);\r\n parser.context = opts.context;\r\n job.addEventListener('cancel', () => parser.abort());\r\n\r\n console.time('parse');\r\n return parser.parse()\r\n .then((dataSet) => {\r\n console.timeEnd('parse');\r\n job.notify({ type: 'parsingDone', data: dataSet });\r\n return dataSet;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('parse');\r\n opts.error = error;\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Parsing failed');\r\n job.notify({ type: 'parsingDone', error });\r\n throw error;\r\n });\r\n}\r\n\r\n/**\r\n * Load molecule asynchronously.\r\n * @param {string|File} source - Molecule source to load (e.g. PDB ID, URL or File object).\r\n * @param {object=} opts - Options.\r\n * @param {string=} opts.sourceType - Data source type (e.g. 'url', 'file').\r\n * @param {string=} opts.fileType - Data contents type (e.g. 'pdb', 'cml').\r\n * @param {string=} opts.mdFile - .nc file path.\r\n * @param {boolean=} opts.keepRepsInfo - prevent reset of object and reps information.\r\n * @returns {Promise} name of the visual that was added to the viewer\r\n */\r\nMiew.prototype.load = function (source, opts) {\r\n opts = _.merge({}, opts, {\r\n context: this,\r\n });\r\n\r\n // for a single-file scenario\r\n if (!this.settings.now.use.multiFile) {\r\n // abort all loaders in progress\r\n if (this._loading.length) {\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n }\r\n\r\n // reset\r\n if (!opts.animation) { // FIXME: sometimes it is set AFTERWARDS!\r\n this.reset(true);\r\n }\r\n }\r\n\r\n this._interpolator.reset();\r\n\r\n this.dispatchEvent({ type: 'loading', options: opts, source });\r\n\r\n const job = new JobHandle();\r\n this._loading.push(job);\r\n job.addEventListener('notification', (e) => {\r\n this.dispatchEvent(e.slaveEvent);\r\n });\r\n\r\n this._spinner.spin(this._container);\r\n\r\n const onLoadEnd = (anything) => {\r\n const jobIndex = this._loading.indexOf(job);\r\n if (jobIndex !== -1) {\r\n this._loading.splice(jobIndex, 1);\r\n }\r\n this._spinner.stop();\r\n this._refreshTitle();\r\n job.notify({ type: 'loadingDone', anything });\r\n return anything;\r\n };\r\n\r\n return _fetchData(source, opts, job)\r\n .then((data) => _parseData(data, opts, job))\r\n .then((object) => {\r\n const name = this._onLoad(object, opts);\r\n return onLoadEnd(name);\r\n })\r\n .catch((err) => {\r\n this.logger.error('Could not load data');\r\n this.logger.debug(err);\r\n throw onLoadEnd(err);\r\n });\r\n};\r\n\r\n/**\r\n * Unload molecule (delete corresponding visual).\r\n * @param {string=} name - name of the visual\r\n */\r\nMiew.prototype.unload = function (name) {\r\n this._removeVisual(name || this.getCurrentVisual());\r\n this.resetPivot();\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n};\r\n\r\n/**\r\n * Start new animation. Now is broken.\r\n * @param fileData - new data to animate\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._startAnimation = function (fileData) {\r\n this._stopAnimation();\r\n const self = this;\r\n const visual = this._getComplexVisual();\r\n if (visual === null) {\r\n this.logger.error('Unable to start animation - no molecule is loaded.');\r\n return;\r\n }\r\n try {\r\n this._frameInfo = new FrameInfo(\r\n visual.getComplex(),\r\n fileData,\r\n {\r\n onLoadStatusChanged() {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo ? self._frameInfo.isLoading : true,\r\n },\r\n });\r\n },\r\n onError(message) {\r\n self._stopAnimation();\r\n self.logger.error(message);\r\n },\r\n },\r\n );\r\n } catch {\r\n this.logger.error('Animation file does not fit to current complex!');\r\n return;\r\n }\r\n this._continueAnimation();\r\n};\r\n\r\n/**\r\n * Pause current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._pauseAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n this._isAnimating = false;\r\n clearInterval(this._animInterval);\r\n this._animInterval = null;\r\n if (this._frameInfo) {\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: this._isAnimating,\r\n isLoading: this._frameInfo.isLoading,\r\n },\r\n });\r\n }\r\n};\r\n\r\n/**\r\n * Continue current animation after pausing. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._continueAnimation = function () {\r\n this._isAnimating = true;\r\n let minFrameTime = 1000 / settings.now.maxfps;\r\n minFrameTime = Number.isNaN(minFrameTime) ? 0 : minFrameTime;\r\n const self = this;\r\n const { pivot } = self._gfx;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.resetSelectionMask();\r\n visual.rebuildSelectionGeometry();\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n }\r\n this._animInterval = setInterval(() => {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo.isLoading,\r\n },\r\n });\r\n if (self._frameInfo.frameIsReady) {\r\n pivot.updateToFrame(self._frameInfo);\r\n self._updateObjsToFrame(self._frameInfo);\r\n self._refreshTitle(` Frame ${self._frameInfo._currFrame} of ${self._frameInfo._framesCount\r\n } time interval - ${self._frameInfo._timeStep}`);\r\n try {\r\n self._frameInfo.nextFrame();\r\n } catch {\r\n self.logger.error('Error during animation');\r\n self._stopAnimation();\r\n return;\r\n }\r\n self._needRender = true;\r\n }\r\n }, minFrameTime);\r\n};\r\n\r\n/**\r\n * Stop current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._stopAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n clearInterval(this._animInterval);\r\n this._frameInfo.disableEvents();\r\n this._frameInfo = null;\r\n this._animInterval = null;\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: null,\r\n });\r\n};\r\n\r\n/**\r\n * Invoked upon successful loading of some data source\r\n * @param {DataSource} dataSource - Data source for visualization (molecular complex or other)\r\n * @param {object} opts - Options.\r\n * @private\r\n */\r\nMiew.prototype._onLoad = function (dataSource, opts) {\r\n const gfx = this._gfx;\r\n let visualName = null;\r\n\r\n if (opts.animation) {\r\n this._refreshTitle();\r\n this._startAnimation(dataSource);\r\n return null;\r\n }\r\n this._stopAnimation();\r\n if (!opts || !opts.keepRepsInfo) {\r\n this._opts.reps = null;\r\n this._opts._objects = null;\r\n }\r\n\r\n if (dataSource.id === 'Complex') {\r\n const complex = dataSource;\r\n\r\n // update title\r\n if (opts.fileName) {\r\n complex.name = complex.name || removeExtension(opts.fileName).toUpperCase();\r\n } else if (opts.amberFileName) {\r\n complex.name = complex.name || removeExtension(opts.amberFileName).toUpperCase();\r\n } else {\r\n complex.name = `Dynamic ${opts.fileType} molecule`;\r\n }\r\n\r\n visualName = this._addVisual(new ComplexVisual(complex.name, complex));\r\n this._curVisualName = visualName;\r\n\r\n const desc = this.info();\r\n this.logger.info(`Parsed ${opts.fileName} (${\r\n desc.atoms} atoms, ${\r\n desc.bonds} bonds, ${\r\n desc.residues} residues, ${\r\n desc.chains} chains).`);\r\n\r\n if (_.isNumber(this._opts.unit)) {\r\n complex.setCurrentUnit(this._opts.unit);\r\n }\r\n\r\n if (opts.preset) {\r\n // ...removed server access...\r\n } else if (settings.now.autoPreset) {\r\n switch (opts.fileType) {\r\n case 'cml':\r\n this.resetReps('small');\r\n break;\r\n case 'pdb':\r\n case 'mmtf':\r\n case 'cif':\r\n if (hasValidResidues(complex)) {\r\n this.resetReps('macro');\r\n } else {\r\n this.resetReps('small');\r\n }\r\n break;\r\n default:\r\n this.resetReps('default');\r\n break;\r\n }\r\n } else {\r\n this.resetReps('default');\r\n }\r\n } else if (dataSource.id === 'Volume') {\r\n this.resetEd();\r\n visualName = this._onLoadEd(dataSource);\r\n }\r\n\r\n gfx.camera.updateProjectionMatrix();\r\n this._updateFog();\r\n\r\n // reset global transform\r\n gfx.root.resetTransform();\r\n this.resetPivot();\r\n\r\n // set scale to fit everything on the screen\r\n this._objectControls.setScale(settings.now.radiusToFit / this._getBSphereRadius());\r\n\r\n this._resetObjects();\r\n\r\n if (settings.now.autoResolution) {\r\n this._tweakResolution();\r\n }\r\n\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n this._refreshTitle();\r\n\r\n return visualName;\r\n};\r\n\r\nMiew.prototype.resetEd = function () {\r\n if (this._edLoader) {\r\n this._edLoader.abort();\r\n this._edLoader = null;\r\n }\r\n\r\n // free all resources\r\n this._removeVisual(this._getVolumeVisual());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype.loadEd = function (source) {\r\n this.resetEd();\r\n\r\n const TheLoader = _.head(io.loaders.find({ source }));\r\n if (!TheLoader) {\r\n this.logger.error(LOADER_NOT_FOUND);\r\n return Promise.reject(new Error(LOADER_NOT_FOUND));\r\n }\r\n\r\n const loader = this._edLoader = new TheLoader(source, { binary: true });\r\n loader.context = this;\r\n return loader.load().then((data) => {\r\n const TheParser = _.head(io.parsers.find({ format: 'ccp4' }));\r\n if (!TheParser) {\r\n throw new Error(PARSER_NOT_FOUND);\r\n }\r\n const parser = new TheParser(data);\r\n parser.context = this;\r\n return parser.parse().then((dataSource) => {\r\n this._onLoadEd(dataSource);\r\n });\r\n }).catch((error) => {\r\n this.logger.error('Could not load ED data');\r\n this.logger.debug(error);\r\n });\r\n};\r\n\r\nMiew.prototype._onLoadEd = function (dataSource) {\r\n dataSource.normalize();\r\n\r\n const volumeVisual = new VolumeVisual('volume', dataSource);\r\n volumeVisual.getMesh().layers.set(gfxutils.LAYERS.VOLUME); // volume mesh is not visible to common render\r\n const visualName = this._addVisual(volumeVisual);\r\n\r\n this._needRender = true;\r\n return visualName;\r\n};\r\n\r\nMiew.prototype._needRebuild = function () {\r\n let needsRebuild = false;\r\n this._forEachComplexVisual((visual) => {\r\n needsRebuild = needsRebuild || visual.needsRebuild();\r\n });\r\n return needsRebuild;\r\n};\r\n\r\nMiew.prototype._rebuildObjects = function () {\r\n const self = this;\r\n const gfx = this._gfx;\r\n let i;\r\n let n;\r\n\r\n // remove old object geometry\r\n const toRemove = [];\r\n for (i = 0; i < gfx.pivot.children.length; ++i) {\r\n const child = gfx.pivot.children[i];\r\n if (!(child instanceof Visual)) {\r\n toRemove.push(child);\r\n }\r\n }\r\n for (i = 0; i < toRemove.length; ++i) {\r\n toRemove[i].parent.remove(toRemove[i]);\r\n }\r\n\r\n setTimeout(() => {\r\n const objList = self._objects;\r\n for (i = 0, n = objList.length; i < n; ++i) {\r\n const obj = objList[i];\r\n if (obj.needsRebuild) {\r\n obj.build();\r\n }\r\n if (obj.getGeometry()) {\r\n gfx.pivot.add(obj.getGeometry());\r\n }\r\n }\r\n }, 10);\r\n};\r\n\r\nMiew.prototype.changeUnit = function (unitIdx, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n throw new Error('There is no complex to change!');\r\n }\r\n\r\n function currentUnitInfo() {\r\n const unit = visual ? visual.getComplex().getCurrentUnit() : 0;\r\n const type = unit > 0 ? (`Bio molecule ${unit}`) : 'Asymmetric unit';\r\n return `Current unit: ${unit} (${type})`;\r\n }\r\n\r\n if (unitIdx === undefined) {\r\n return currentUnitInfo();\r\n }\r\n if (_.isString(unitIdx)) {\r\n unitIdx = Math.max(parseInt(unitIdx, 10), 0);\r\n }\r\n if (visual.getComplex().setCurrentUnit(unitIdx)) {\r\n this._resetScene();\r\n this._updateInfoPanel();\r\n }\r\n return currentUnitInfo();\r\n};\r\n\r\n/**\r\n * Start to rebuild geometry asynchronously.\r\n */\r\nMiew.prototype.rebuild = function () {\r\n if (this._building) {\r\n this.logger.warn('Miew.rebuild(): already building!');\r\n return;\r\n }\r\n this._building = true;\r\n\r\n this.dispatchEvent({ type: 'rebuilding' });\r\n\r\n this._rebuildObjects();\r\n\r\n this._gfx.renderer2d.reset();\r\n\r\n const rebuildActions = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.needsRebuild()) {\r\n rebuildActions.push(visual.rebuild().then(() => new Promise(((resolve) => {\r\n visual.rebuildSelectionGeometry();\r\n resolve();\r\n }))));\r\n }\r\n });\r\n\r\n // Start asynchronous rebuild\r\n const self = this;\r\n this._spinner.spin(this._container);\r\n Promise.all(rebuildActions).then(() => {\r\n self._spinner.stop();\r\n\r\n self._needRender = true;\r\n\r\n self._refreshTitle();\r\n this.dispatchEvent({ type: 'buildingDone' });\r\n self._building = false;\r\n });\r\n};\r\n\r\n/** Mark all representations for rebuilding */\r\nMiew.prototype.rebuildAll = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setNeedsRebuild();\r\n });\r\n};\r\n\r\nMiew.prototype._refreshTitle = function (appendix) {\r\n let title;\r\n appendix = appendix === undefined ? '' : appendix;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n title = visual.getComplex().name;\r\n const rep = visual.repGet(visual.repCurrent());\r\n title += (rep ? ` – ${rep.mode.name} Mode` : '');\r\n } else {\r\n title = Object.keys(this._visuals).length > 0 ? 'Unknown' : 'No Data';\r\n }\r\n title += appendix;\r\n\r\n this.dispatchEvent({ type: 'titleChanged', data: title });\r\n};\r\n\r\nMiew.prototype.setNeedRender = function () {\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._extractRepresentation = function () {\r\n const changed = [];\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCount() === 0) {\r\n return;\r\n }\r\n\r\n const selector = visual.buildSelectorFromMask(1 << visual.getSelectionBit());\r\n const defPreset = settings.now.presets.default;\r\n const res = visual.repAdd({\r\n selector,\r\n mode: defPreset[0].mode.id,\r\n colorer: defPreset[0].colorer.id,\r\n material: defPreset[0].material.id,\r\n });\r\n if (!res) {\r\n if (visual.repCount() === ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n this.logger.warn(`Number of representations is limited to ${ComplexVisual.NUM_REPRESENTATION_BITS}`);\r\n }\r\n return;\r\n }\r\n\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n visual.repCurrent(res.index);\r\n\r\n changed.push(visual.name);\r\n });\r\n\r\n if (changed.length > 0) {\r\n this.logger.report(`New representation from selection for complexes: ${changed.join(', ')}`);\r\n }\r\n};\r\n\r\n/**\r\n * Change current representation list.\r\n * @param {array} reps - Representation list.\r\n */\r\nMiew.prototype._setReps = function (reps) {\r\n reps = reps || (this._opts && this._opts.reps) || [];\r\n this._forEachComplexVisual((visual) => visual.resetReps(reps));\r\n};\r\n\r\n/**\r\n * Apply existing preset to current scene.\r\n * @param preset\r\n */\r\nMiew.prototype.applyPreset = function (preset) {\r\n const { presets } = settings.now;\r\n const presList = [\r\n preset || settings.defaults.preset,\r\n settings.defaults.preset,\r\n Object.keys(presets)[0],\r\n ];\r\n let reps = null;\r\n for (let i = 0; !reps && i < presList.length; ++i) {\r\n settings.set('preset', presList[i]);\r\n reps = presets[settings.now.preset];\r\n if (!reps) {\r\n this.logger.warn(`Unknown preset \"${settings.now.preset}\"`);\r\n }\r\n }\r\n this._setReps(reps);\r\n};\r\n\r\n/**\r\n * Reset current representation list to initial values.\r\n * @param {string} [preset] - The source preset in case of uninitialized representation list.\r\n */\r\nMiew.prototype.resetReps = function (preset) {\r\n const reps = this._opts && this._opts.reps;\r\n if (reps) {\r\n this._setReps(reps);\r\n } else {\r\n this.applyPreset(preset);\r\n }\r\n};\r\n\r\n/**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\nMiew.prototype.repCount = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repCount() : 0;\r\n};\r\n\r\n/**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {string=} [name] - Complex name. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\nMiew.prototype.repCurrent = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n const newIdx = visual ? visual.repCurrent(index) : -1;\r\n if (index && newIdx !== index) {\r\n this.logger.warn(`Representation ${index} was not found. Current rep remains unchanged.`);\r\n }\r\n return newIdx;\r\n};\r\n\r\n/**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {?object} Representation description.\r\n */\r\nMiew.prototype.rep = function (index, rep) {\r\n const visual = this._getComplexVisual('');\r\n if (!visual) {\r\n return null;\r\n }\r\n const res = visual.rep(index, rep);\r\n if (res.status === 'created') {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n } else if (res.status === 'changed') {\r\n this.dispatchEvent({ type: 'repChanged', index: res.index, name: visual.name });\r\n }\r\n return res.desc;\r\n};\r\n\r\n/**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\nMiew.prototype.repGet = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repGet(index) : null;\r\n};\r\n\r\n/**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {number} Index of the new representation.\r\n */\r\nMiew.prototype.repAdd = function (rep, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return -1;\r\n }\r\n\r\n const res = visual.repAdd(rep);\r\n if (res) {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name });\r\n return res.index;\r\n }\r\n return -1;\r\n};\r\n\r\n/**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\nMiew.prototype.repRemove = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n visual.repRemove(index);\r\n this.dispatchEvent({ type: 'repRemoved', index, name });\r\n};\r\n\r\n/**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\nMiew.prototype.repHide = function (index, hide, name) {\r\n this._needRender = true;\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repHide(index, hide) : null;\r\n};\r\n\r\nMiew.prototype._setEditMode = function (mode) {\r\n this._editMode = mode;\r\n\r\n const elem = this._msgMode;\r\n if (elem) {\r\n elem.style.opacity = (mode === EDIT_MODE.COMPLEX) ? 0.0 : 1.0;\r\n\r\n if (mode !== EDIT_MODE.COMPLEX) {\r\n const t = elem.getElementsByTagName('p')[0];\r\n t.innerHTML = (mode === EDIT_MODE.COMPONENT) ? 'COMPONENT EDIT MODE' : 'FRAGMENT EDIT MODE';\r\n }\r\n }\r\n\r\n this.dispatchEvent({ type: 'editModeChanged', data: mode === EDIT_MODE.COMPLEX });\r\n};\r\n\r\nMiew.prototype._enterComponentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const editors = [];\r\n this._forEachComplexVisual((visual) => {\r\n const editor = visual.beginComponentEdit();\r\n if (editor) {\r\n editors.push(editor);\r\n }\r\n });\r\n\r\n if (editors.length === 0) {\r\n return;\r\n }\r\n\r\n this._editors = editors;\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- ON');\r\n this._setEditMode(EDIT_MODE.COMPONENT);\r\n this._objectControls.keysTranslateObj(true);\r\n};\r\n\r\nMiew.prototype._applyComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._needRender = true;\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._enterFragmentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const selectedVisuals = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual instanceof ComplexVisual\r\n && visual.getSelectionCount() > 0) {\r\n selectedVisuals.push(visual);\r\n }\r\n });\r\n\r\n if (selectedVisuals.length !== 1) {\r\n // either we have no selection or\r\n // we have selected atoms in two or more visuals -- not supported\r\n return;\r\n }\r\n\r\n const editor = selectedVisuals[0].beginFragmentEdit();\r\n if (!editor) {\r\n return;\r\n }\r\n this._editors = [editor];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- ON (single bond)');\r\n this._setEditMode(EDIT_MODE.FRAGMENT);\r\n this._objectControls.allowTranslation(false);\r\n this._objectControls.allowAltObjFreeRotation(editor.isFreeRotationAllowed());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._applyFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onPick = function (event) {\r\n if (!settings.now.picking) {\r\n // picking is disabled\r\n return;\r\n }\r\n\r\n if (this._animInterval !== null) {\r\n // animation playback is on\r\n return;\r\n }\r\n\r\n if (this._editMode === EDIT_MODE.FRAGMENT) {\r\n // prevent picking in fragment edit mode\r\n return;\r\n }\r\n\r\n if (this._objectControls.isEditingAltObj()) {\r\n // prevent picking during component rotation\r\n return;\r\n }\r\n\r\n // update last pick & find complex\r\n let complex = null;\r\n if (event.obj.atom) {\r\n complex = event.obj.atom.residue.getChain().getComplex();\r\n this._lastPick = event.obj.atom;\r\n } else if (event.obj.residue) {\r\n complex = event.obj.residue.getChain().getComplex();\r\n this._lastPick = event.obj.residue;\r\n } else if (event.obj.chain) {\r\n complex = event.obj.chain.getComplex();\r\n this._lastPick = event.obj.chain;\r\n } else if (event.obj.molecule) {\r\n complex = event.obj.molecule.complex;\r\n this._lastPick = event.obj.molecule;\r\n } else {\r\n this._lastPick = null;\r\n }\r\n\r\n function _updateSelection(visual) {\r\n visual.updateSelectionMask(event.obj);\r\n visual.rebuildSelectionGeometry();\r\n }\r\n\r\n // update visual\r\n if (complex) {\r\n const visual = this._getVisualForComplex(complex);\r\n if (visual) {\r\n _updateSelection(visual);\r\n this._needRender = true;\r\n }\r\n } else {\r\n this._forEachComplexVisual(_updateSelection);\r\n this._needRender = true;\r\n }\r\n\r\n this._updateInfoPanel();\r\n this.dispatchEvent(event);\r\n};\r\n\r\nMiew.prototype._onKeyDown = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n // editing keys\r\n if (settings.now.editing) {\r\n switch (event.code) {\r\n case 'KeyC':\r\n this._enterComponentEditMode();\r\n break;\r\n case 'KeyF':\r\n this._enterFragmentEditMode();\r\n break;\r\n case 'KeyA':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._applyComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._applyFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n case 'KeyD':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._discardComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._discardFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n default:\r\n }\r\n }\r\n\r\n // other keys\r\n switch (event.code) {\r\n case 'NumpadAdd':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.expandSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n case 'NumpadSubtract':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.shrinkSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nMiew.prototype._onKeyUp = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n if (event.code === 'KeyX') {\r\n this._extractRepresentation();\r\n }\r\n};\r\n\r\nMiew.prototype._updateInfoPanel = function () {\r\n const info = this._msgAtomInfo.getElementsByTagName('p')[0];\r\n let atom;\r\n let residue;\r\n\r\n let count = 0;\r\n this._forEachComplexVisual((visual) => {\r\n count += visual.getSelectionCount();\r\n });\r\n\r\n while (info.firstChild) {\r\n info.removeChild(info.firstChild);\r\n }\r\n\r\n if (count === 0) {\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n return;\r\n }\r\n\r\n let firstLine = `${String(count)} atom${count !== 1 ? 's' : ''} selected`;\r\n if (this._lastPick !== null) {\r\n firstLine += ', the last pick:';\r\n }\r\n let secondLine = '';\r\n let aName = '';\r\n let coordLine = '';\r\n\r\n if (this._lastPick instanceof Atom) {\r\n atom = this._lastPick;\r\n residue = atom.residue;\r\n\r\n aName = atom.name;\r\n const location = (atom.location !== 32) ? String.fromCharCode(atom.location) : ''; // 32 is code of white-space\r\n secondLine = `${atom.element.fullName} #${atom.serial}${location}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}.`;\r\n secondLine += aName;\r\n\r\n coordLine = `Coord: (${atom.position.x.toFixed(2).toString()},\\\r\n ${atom.position.y.toFixed(2).toString()},\\\r\n ${atom.position.z.toFixed(2).toString()})`;\r\n } else if (this._lastPick instanceof Residue) {\r\n residue = this._lastPick;\r\n\r\n secondLine = `${residue._type._fullName}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}`;\r\n } else if (this._lastPick instanceof Chain) {\r\n secondLine = `chain ${this._lastPick._name}`;\r\n } else if (this._lastPick instanceof Molecule) {\r\n secondLine = `molecule ${this._lastPick._name}`;\r\n }\r\n\r\n info.appendChild(document.createTextNode(firstLine));\r\n\r\n if (secondLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(secondLine));\r\n }\r\n\r\n if (coordLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(coordLine));\r\n }\r\n\r\n this._msgAtomInfo.style.opacity = 1.0;\r\n};\r\n\r\nMiew.prototype._getAltObj = function () {\r\n if (this._editors) {\r\n let altObj = null;\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n const nextAltObj = this._editors[i].getAltObj();\r\n if (nextAltObj.objects.length > 0) {\r\n if (altObj) {\r\n // we have selected atoms in two or more visuals -- not supported\r\n altObj = null;\r\n break;\r\n }\r\n altObj = nextAltObj;\r\n }\r\n }\r\n if (altObj) {\r\n return altObj;\r\n }\r\n }\r\n\r\n return {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n};\r\n\r\nMiew.prototype.resetPivot = (function () {\r\n const boundingBox = new THREE.Box3();\r\n const center = new THREE.Vector3();\r\n\r\n return function () {\r\n boundingBox.makeEmpty();\r\n this._forEachVisual((visual) => {\r\n boundingBox.union(visual.getBoundaries().boundingBox);\r\n });\r\n\r\n boundingBox.getCenter(center);\r\n this._objectControls.setPivot(center.negate());\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotResidue = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (residue) {\r\n const visual = this._getVisualForComplex(residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n if (residue._controlPoint) {\r\n center.copy(residue._controlPoint);\r\n } else {\r\n let x = 0;\r\n let y = 0;\r\n let z = 0;\r\n const amount = residue._atoms.length;\r\n for (let i = 0; i < amount; ++i) {\r\n const p = residue._atoms[i].position;\r\n x += p.x / amount;\r\n y += p.y / amount;\r\n z += p.z / amount;\r\n }\r\n center.set(x, y, z);\r\n }\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotAtom = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (atom) {\r\n const visual = this._getVisualForComplex(atom.residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n center.copy(atom.position);\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.getSelectionCenter = (function () {\r\n const _centerInVisual = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n return function (center, includesAtom, selector) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCenter(_centerInVisual, includesAtom, selector || visual.getSelectionBit())) {\r\n center.add(_centerInVisual);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.negate();\r\n return true;\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotSubset = (function () {\r\n const _center = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n function _includesInCurSelection(atom, selectionBit) {\r\n return atom.mask & (1 << selectionBit);\r\n }\r\n\r\n function _includesInSelector(atom, selector) {\r\n return selector.selector.includesAtom(atom);\r\n }\r\n\r\n return function (selector) {\r\n const includesAtom = (selector) ? _includesInSelector : _includesInCurSelection;\r\n\r\n if (this.getSelectionCenter(_center, includesAtom, selector)) {\r\n this._objectControls.setPivot(_center);\r\n this.dispatchEvent({ type: 'transform' });\r\n } else {\r\n this.logger.warn('selection is empty. Center operation not performed');\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Makes a screenshot.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n * @returns {string} Data URL representing the image contents.\r\n */\r\nMiew.prototype.screenshot = function (width, height) {\r\n const gfx = this._gfx;\r\n const deviceWidth = gfx.renderer.domElement.width;\r\n const deviceHeight = gfx.renderer.domElement.height;\r\n\r\n function fov2Tan(fov) {\r\n return Math.tan(THREE.MathUtils.degToRad(0.5 * fov));\r\n }\r\n\r\n function tan2Fov(tan) {\r\n return THREE.MathUtils.radToDeg(Math.atan(tan)) * 2.0;\r\n }\r\n\r\n function getDataURL() {\r\n let dataURL;\r\n const currBrowser = utils.getBrowser();\r\n\r\n if (currBrowser === utils.browserType.SAFARI) {\r\n const canvas = document.createElement('canvas');\r\n const canvasContext = canvas.getContext('2d');\r\n\r\n canvas.width = width === undefined ? deviceWidth : width;\r\n canvas.height = height === undefined ? deviceHeight : height;\r\n\r\n canvasContext.drawImage(gfx.renderer.domElement, 0, 0, canvas.width, canvas.height);\r\n dataURL = canvas.toDataURL('image/png');\r\n } else {\r\n // Copy current canvas to screenshot\r\n dataURL = gfx.renderer.domElement.toDataURL('image/png');\r\n }\r\n return dataURL;\r\n }\r\n height = height || width;\r\n\r\n let screenshotURI;\r\n if ((width === undefined && height === undefined)\r\n || (width === deviceWidth && height === deviceHeight)) {\r\n // renderer.domElement.toDataURL('image/png') returns flipped image in Safari\r\n // It hasn't been resolved yet, but getScreenshotSafari()\r\n // fixes it using an extra canvas.\r\n screenshotURI = getDataURL();\r\n } else {\r\n const originalAspect = gfx.camera.aspect;\r\n const originalFov = gfx.camera.fov;\r\n const originalTanFov2 = fov2Tan(gfx.camera.fov);\r\n\r\n // screenshot should contain the principal area of interest (a centered square touching screen sides)\r\n const areaOfInterestSize = Math.min(gfx.width, gfx.height);\r\n const areaOfInterestTanFov2 = originalTanFov2 * areaOfInterestSize / gfx.height;\r\n\r\n // set appropriate camera aspect & FOV\r\n const shotAspect = width / height;\r\n gfx.renderer.setPixelRatio(1);\r\n gfx.camera.aspect = shotAspect;\r\n gfx.camera.fov = tan2Fov(areaOfInterestTanFov2 / Math.min(shotAspect, 1.0));\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n // resize canvas to the required size of screenshot\r\n gfx.renderer.setDrawingBufferSize(width, height, 1);\r\n\r\n // make screenshot\r\n this._renderFrame(settings.now.stereo);\r\n screenshotURI = getDataURL();\r\n\r\n // restore original camera & canvas proportions\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.camera.aspect = originalAspect;\r\n gfx.camera.fov = originalFov;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.renderer.setDrawingBufferSize(gfx.width, gfx.height, window.devicePixelRatio);\r\n this._needRender = true;\r\n }\r\n\r\n return screenshotURI;\r\n};\r\n\r\n/**\r\n * Makes screenshot and initiates a download.\r\n * @param {string} [filename] - Name of a file. Default to a 'screenshot-XXXXX.png', where XXXXX is a current\r\n * date/time in seconds.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n */\r\nMiew.prototype.screenshotSave = function (filename, width, height) {\r\n const uri = this.screenshot(width, height);\r\n utils.shotDownload(uri, filename);\r\n};\r\n\r\nMiew.prototype.save = function (opts) {\r\n this._export(opts.fileType).then((dataString) => {\r\n const filename = this._visuals[this._curVisualName]._complex.name;\r\n utils.download(dataString, filename, opts.fileType);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone' });\r\n }).catch((error) => {\r\n this.logger.error('Could not export data');\r\n this.logger.debug(error);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone', error });\r\n });\r\n};\r\n\r\nMiew.prototype._tweakResolution = function () {\r\n const maxPerf = [\r\n ['poor', 100],\r\n ['low', 500],\r\n ['medium', 1000],\r\n ['high', 5000],\r\n ['ultra', Number.MAX_VALUE],\r\n ];\r\n\r\n let atomCount = 0;\r\n this._forEachComplexVisual((visual) => {\r\n atomCount += visual.getComplex().getAtomCount();\r\n });\r\n\r\n if (atomCount > 0) {\r\n const performance = this._gfxScore * 10e5 / atomCount;\r\n // set resolution based on estimated performance\r\n for (let i = 0; i < maxPerf.length; ++i) {\r\n if (performance < maxPerf[i][1]) {\r\n this._autoChangeResolution(maxPerf[i][0]);\r\n break;\r\n }\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._autoChangeResolution = function (resolution) {\r\n if (resolution !== settings.now.resolution) {\r\n this.logger.report(`Your rendering resolution was changed to \"${resolution}\" for best performance.`);\r\n }\r\n settings.now.resolution = resolution;\r\n};\r\n\r\n/**\r\n * Save current settings to cookies.\r\n */\r\nMiew.prototype.saveSettings = function () {\r\n this._cookies.setCookie(this._opts.settingsCookie, JSON.stringify(this.settings.getDiffs(true)));\r\n};\r\n\r\n/**\r\n * Load settings from cookies.\r\n */\r\nMiew.prototype.restoreSettings = function () {\r\n try {\r\n const cookie = this._cookies.getCookie(this._opts.settingsCookie);\r\n const diffs = cookie ? JSON.parse(cookie) : {};\r\n this.settings.applyDiffs(diffs, true);\r\n } catch (e) {\r\n this.logger.error(`Cookies parse error: ${e.message}`);\r\n }\r\n};\r\n\r\n/**\r\n * Reset current settings to the defaults.\r\n */\r\nMiew.prototype.resetSettings = function () {\r\n this.settings.reset();\r\n};\r\n\r\n/*\r\n * DANGEROUS and TEMPORARY. The method should change or disappear in future versions.\r\n * @param {string|object} opts - See {@link Miew} constructor.\r\n * @see {@link Miew#set}, {@link Miew#repAdd}, {@link Miew#rep}.\r\n */\r\nMiew.prototype.setOptions = function (opts) {\r\n if (typeof opts === 'string') {\r\n opts = Miew.options.fromAttr(opts);\r\n }\r\n if (opts.reps) {\r\n this._opts.reps = null;\r\n }\r\n _.merge(this._opts, opts);\r\n if (opts.settings) {\r\n this.set(opts.settings);\r\n }\r\n\r\n this._opts._objects = opts._objects;\r\n this._resetObjects();\r\n\r\n if (opts.load) {\r\n this.load(opts.load, { fileType: opts.type });\r\n }\r\n\r\n if (opts.preset) {\r\n settings.now.preset = opts.preset;\r\n }\r\n\r\n if (opts.reps) {\r\n this.resetReps(opts.preset);\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.getComplex().resetCurrentUnit();\r\n if (_.isNumber(opts.unit)) {\r\n visual.getComplex().setCurrentUnit(opts.unit);\r\n }\r\n this.resetView();\r\n this.rebuildAll();\r\n }\r\n};\r\n\r\nMiew.prototype.info = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return {};\r\n }\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n return {\r\n id: metadata.id || complex.name || 'UNKNOWN',\r\n title: (metadata.title && metadata.title.join(' ')) || 'UNKNOWN DATA',\r\n atoms: complex.getAtomCount(),\r\n bonds: complex.getBondCount(),\r\n residues: complex.getResidueCount(),\r\n chains: complex.getChainCount(),\r\n };\r\n};\r\n\r\n/*\r\n * OBJECTS SEGMENT\r\n */\r\n\r\nMiew.prototype.addObject = function (objData, bThrow) {\r\n let Ctor = null;\r\n\r\n if (objData.type === LinesObject.prototype.type) {\r\n Ctor = LinesObject;\r\n }\r\n\r\n if (Ctor === null) {\r\n throw new Error(`Unknown scene object type - ${objData.type}`);\r\n }\r\n\r\n try {\r\n const newObj = new Ctor(objData.params, objData.opts);\r\n this._addSceneObject(newObj);\r\n } catch (error) {\r\n if (!bThrow) {\r\n this.logger.debug(`Error during scene object creation: ${error.message}`);\r\n } else {\r\n throw error;\r\n }\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._addSceneObject = function (sceneObject) {\r\n const visual = this._getComplexVisual();\r\n if (sceneObject.build && visual) {\r\n sceneObject.build(visual.getComplex());\r\n this._gfx.pivot.add(sceneObject.getGeometry());\r\n }\r\n const objects = this._objects;\r\n objects[objects.length] = sceneObject;\r\n};\r\n\r\nMiew.prototype._updateObjsToFrame = function (frameData) {\r\n const objs = this._objects;\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n if (objs[i].updateToFrame) {\r\n objs[i].updateToFrame(frameData);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._resetObjects = function () {\r\n const objs = this._opts._objects;\r\n\r\n this._objects = [];\r\n if (objs) {\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n this.addObject(objs[i], false);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype.removeObject = function (index) {\r\n const obj = this._objects[index];\r\n if (!obj) {\r\n throw new Error(`Scene object with index ${index} does not exist`);\r\n }\r\n obj.destroy();\r\n this._objects.splice(index, 1);\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Get a string with a URL to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {string} URL\r\n */\r\nMiew.prototype.getURL = function (opts) {\r\n return options.toURL(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n })));\r\n};\r\n\r\n/**\r\n * Get a string with a script to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=true] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=true] - when this flag is true, a view information is included\r\n * @returns {string} script\r\n */\r\nMiew.prototype.getScript = function (opts) {\r\n return options.toScript(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: true,\r\n view: true,\r\n })));\r\n};\r\n\r\n/*\r\n * Generates object that represents the current state of representations list\r\n * @param {boolean} compareWithDefaults - when this flag is true, reps list is compared (if possible)\r\n * to preset's defaults and only diffs are generated\r\n */\r\nMiew.prototype._compareReps = function (complexVisual, compareWithDefaults) {\r\n const ans = {};\r\n let repCount = 0;\r\n\r\n if (complexVisual) {\r\n repCount = complexVisual.repCount();\r\n }\r\n\r\n const currPreset = settings.defaults.presets[settings.now.preset];\r\n let compare = compareWithDefaults;\r\n if (currPreset === undefined || currPreset.length > repCount) {\r\n compare = false;\r\n ans.preset = 'empty';\r\n } else if (settings.now.preset !== settings.defaults.preset) {\r\n ans.preset = settings.now.preset;\r\n }\r\n\r\n const repsDiff = [];\r\n let emptyReps = true;\r\n for (let i = 0, n = repCount; i < n; ++i) {\r\n repsDiff[i] = complexVisual.repGet(i).compare(compare ? currPreset[i] : null);\r\n if (!_.isEmpty(repsDiff[i])) {\r\n emptyReps = false;\r\n }\r\n }\r\n if (!emptyReps) {\r\n ans.reps = repsDiff;\r\n }\r\n return ans;\r\n};\r\n\r\n/*\r\n * Obtain object that represents current state of miew (might be used as options in constructor).\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {Object} State object.\r\n */\r\nMiew.prototype.getState = function (opts) {\r\n const state = {};\r\n\r\n opts = _.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n });\r\n\r\n // load\r\n const visual = this._getComplexVisual();\r\n if (visual !== null) {\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n if (metadata.id) {\r\n const format = metadata.format ? `${metadata.format}:` : '';\r\n state.load = format + metadata.id;\r\n }\r\n const unit = complex.getCurrentUnit();\r\n if (unit !== 1) {\r\n state.unit = unit;\r\n }\r\n }\r\n\r\n // representations\r\n const repsInfo = this._compareReps(visual, opts.compact);\r\n if (repsInfo.preset) {\r\n state.preset = repsInfo.preset;\r\n }\r\n\r\n if (repsInfo.reps) {\r\n state.reps = repsInfo.reps;\r\n }\r\n\r\n // objects\r\n const objects = this._objects;\r\n const objectsState = [];\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n objectsState[i] = objects[i].identify();\r\n }\r\n if (objects.length > 0) {\r\n state._objects = objectsState;\r\n }\r\n\r\n // view\r\n if (opts.view) {\r\n state.view = this.view();\r\n }\r\n\r\n // settings\r\n if (opts.settings) {\r\n const diff = this.settings.getDiffs(false);\r\n if (!_.isEmpty(diff)) {\r\n state.settings = diff;\r\n }\r\n }\r\n\r\n return state;\r\n};\r\n\r\n/**\r\n * Get parameter value.\r\n * @param {string} param - Parameter name or path (e.g. 'modes.BS.atom').\r\n * @param {*=} value - Default value.\r\n * @returns {*} Parameter value.\r\n */\r\nMiew.prototype.get = function (param, value) {\r\n return settings.get(param, value);\r\n};\r\n\r\nMiew.prototype._clipPlaneUpdateValue = function (radius) {\r\n const clipPlaneValue = Math.max(\r\n this._gfx.camera.position.z - radius * settings.now.draft.clipPlaneFactor,\r\n settings.now.camNear,\r\n );\r\n\r\n const opts = { clipPlaneValue };\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions(opts);\r\n });\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setUberOptions(opts);\r\n }\r\n }\r\n if (this._picker !== null) {\r\n this._picker.clipPlaneValue = clipPlaneValue;\r\n }\r\n};\r\n\r\nMiew.prototype._fogFarUpdateValue = function () {\r\n if (this._picker !== null) {\r\n if (this._gfx.scene.fog) {\r\n this._picker.fogFarValue = this._gfx.scene.fog.far;\r\n } else {\r\n this._picker.fogFarValue = undefined;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._updateShadowmapMeshes = function (process) {\r\n this._forEachComplexVisual((visual) => {\r\n const reprList = visual._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n process(repr.geo, repr.material);\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._updateMaterials = function (values, needTraverse = false, process = undefined) {\r\n this._forEachComplexVisual((visual) => visual.setMaterialValues(values, needTraverse, process));\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setValues(values);\r\n obj._line.material.needsUpdate = true;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._fogAlphaChanged = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions({\r\n fogAlpha: settings.now.fogAlpha,\r\n });\r\n });\r\n};\r\n\r\nMiew.prototype._embedWebXR = function () {\r\n // switch off\r\n if (settings.now.stereo !== 'WEBVR') {\r\n if (this.webVR) {\r\n this.webVR.disable();\r\n }\r\n this.webVR = null;\r\n return;\r\n }\r\n // switch on\r\n if (!this.webVR) {\r\n this.webVR = new WebVRPoC(() => {\r\n this._requestAnimationFrame(() => this._onTick());\r\n this._needRender = true;\r\n this._onResize();\r\n });\r\n }\r\n this.webVR.enable(this._gfx);\r\n};\r\n\r\nMiew.prototype._initOnSettingsChanged = function () {\r\n const on = (props, func) => {\r\n props = _.isArray(props) ? props : [props];\r\n props.forEach((prop) => {\r\n this.settings.addEventListener(`change:${prop}`, func);\r\n });\r\n };\r\n\r\n on('modes.VD.frame', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.showFrame(settings.now.modes.VD.frame);\r\n this._needRender = true;\r\n });\r\n\r\n on('modes.VD.isoMode', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n });\r\n\r\n on('bg.color', () => {\r\n this._onBgColorChanged();\r\n });\r\n\r\n on('ao', () => {\r\n const values = { normalsToGBuffer: settings.now.ao };\r\n this._setUberMaterialValues(values);\r\n });\r\n\r\n on('zSprites', () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('fogColor', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('fogColorEnable', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('bg.transparent', (evt) => {\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n // update materials\r\n this._updateMaterials({ fogTransparent: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('draft.clipPlane', (evt) => {\r\n // update materials\r\n this._updateMaterials({ clipPlane: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('shadow.on', (evt) => {\r\n // update materials\r\n const values = { shadowmap: evt.value, shadowmapType: settings.now.shadow.type };\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.shadowMap.enabled = Boolean(values.shadowmap);\r\n }\r\n this._updateMaterials(values, true);\r\n if (values.shadowmap) {\r\n this._updateShadowCamera();\r\n this._updateShadowmapMeshes(meshutils.createShadowmapMaterial);\r\n } else {\r\n this._updateShadowmapMeshes(meshutils.removeShadowmapMaterial);\r\n }\r\n this._needRender = true;\r\n });\r\n\r\n on('shadow.type', (evt) => {\r\n // update materials if shadowmap is enable\r\n if (settings.now.shadow.on) {\r\n this._updateMaterials({ shadowmapType: evt.value }, true);\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on('shadow.radius', (evt) => {\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].shadow !== undefined) {\r\n const light = this._gfx.scene.children[i];\r\n light.shadow.radius = evt.value;\r\n this._needRender = true;\r\n }\r\n }\r\n });\r\n\r\n on('fps', () => {\r\n this._fps.show(settings.now.fps);\r\n });\r\n\r\n on(['fog', 'fogNearFactor', 'fogFarFactor'], () => {\r\n this._updateFog();\r\n this._needRender = true;\r\n });\r\n\r\n on('fogAlpha', () => {\r\n const { fogAlpha } = settings.now;\r\n if (fogAlpha < 0 || fogAlpha > 1) {\r\n this.logger.warn('fogAlpha must belong range [0,1]');\r\n }\r\n this._fogAlphaChanged();\r\n this._needRender = true;\r\n });\r\n\r\n on('autoResolution', (evt) => {\r\n if (evt.value && !this._gfxScore) {\r\n this.logger.warn('Benchmarks are missed, autoresolution will not work! '\r\n + 'Autoresolution should be set during miew startup.');\r\n }\r\n });\r\n\r\n on('stereo', () => {\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n this._needRender = true;\r\n });\r\n\r\n on(['transparency', 'palette'], () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('resolution', () => {\r\n // update complex visuals\r\n this.rebuildAll();\r\n\r\n // update volume visual\r\n const volume = this._getVolumeVisual();\r\n if (volume) {\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on(['axes', 'fxaa', 'ao',\r\n 'outline.on', 'outline.color', 'outline.threshold', 'outline.thickness'], () => {\r\n this._needRender = true;\r\n });\r\n};\r\n\r\n/**\r\n * Set parameter value.\r\n * @param {string|object} params - Parameter name or path (e.g. 'modes.BS.atom') or even settings object.\r\n * @param {*=} value - Value.\r\n */\r\nMiew.prototype.set = function (params, value) {\r\n settings.set(params, value);\r\n};\r\n\r\n/**\r\n * Select atoms with selection string.\r\n * @param {string} expression - string expression of selection\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\nMiew.prototype.select = function (expression, append) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n let sel = expression;\r\n if (_.isString(expression)) {\r\n sel = selectors.parse(expression).selector;\r\n }\r\n\r\n visual.select(sel, append);\r\n this._lastPick = null;\r\n\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n};\r\n\r\nconst VIEW_VERSION = '1';\r\n\r\n/**\r\n * Get or set view info packed into string.\r\n *\r\n * **Note:** view is stored for *left-handed* cs, euler angles are stored in radians and *ZXY-order*,\r\n *\r\n * @param {string=} expression - Optional string encoded the view\r\n */\r\nMiew.prototype.view = function (expression) {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n let transform = [];\r\n const eulerOrder = 'ZXY';\r\n\r\n function encode() {\r\n const pos = pivot.position;\r\n const scale = self._objectControls.getScale() / settings.now.radiusToFit;\r\n const euler = new THREE.Euler();\r\n euler.setFromQuaternion(self._objectControls.getOrientation(), eulerOrder);\r\n transform = [\r\n pos.x, pos.y, pos.z,\r\n scale,\r\n euler.x, euler.y, euler.z,\r\n ];\r\n return VIEW_VERSION + utils.arrayToBase64(transform, Float32Array);\r\n }\r\n\r\n function decode() {\r\n // backwards compatible: old non-versioned view is the 0th version\r\n if (expression.length === 40) {\r\n expression = `0${expression}`;\r\n }\r\n\r\n const version = expression[0];\r\n transform = utils.arrayFromBase64(expression.substr(1), Float32Array);\r\n\r\n // apply adapter for old versions\r\n if (version !== VIEW_VERSION) {\r\n if (version === '0') {\r\n // cancel radiusToFit included in old views\r\n transform[3] /= 8.0;\r\n } else {\r\n // do nothing\r\n self.logger.warn(`Encoded view version mismatch, stored as ${version} vs ${VIEW_VERSION} expected`);\r\n return;\r\n }\r\n }\r\n\r\n const interpolator = self._interpolator;\r\n const srcView = interpolator.createView();\r\n srcView.position.copy(pivot.position);\r\n srcView.scale = self._objectControls.getScale();\r\n srcView.orientation.copy(self._objectControls.getOrientation());\r\n\r\n const dstView = interpolator.createView();\r\n dstView.position.set(transform[0], transform[1], transform[2]);\r\n\r\n // hack to make preset views work after we moved centering offset to visual nodes\r\n // FIXME should only store main pivot offset in preset\r\n if (self._getComplexVisual()) {\r\n dstView.position.sub(self._getComplexVisual().position);\r\n }\r\n\r\n dstView.scale = transform[3]; // eslint-disable-line prefer-destructuring\r\n dstView.orientation.setFromEuler(new THREE.Euler(transform[4], transform[5], transform[6], eulerOrder));\r\n\r\n interpolator.setup(srcView, dstView);\r\n }\r\n\r\n if (typeof expression === 'undefined') {\r\n return encode();\r\n }\r\n decode();\r\n\r\n return expression;\r\n};\r\n\r\n/*\r\n * Update current view due to viewinterpolator state\r\n */\r\nMiew.prototype._updateView = function () {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n\r\n const interpolator = this._interpolator;\r\n if (!interpolator.wasStarted()) {\r\n interpolator.start();\r\n }\r\n\r\n if (!interpolator.isMoving()) {\r\n return;\r\n }\r\n\r\n const res = interpolator.getCurrentView();\r\n if (res.success) {\r\n const curr = res.view;\r\n pivot.position.copy(curr.position);\r\n self._objectControls.setScale(curr.scale * settings.now.radiusToFit);\r\n self._objectControls.setOrientation(curr.orientation);\r\n this.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n }\r\n};\r\n\r\n/**\r\n * Translate object by vector\r\n * @param {number} x - translation value (Ang) along model's X axis\r\n * @param {number} y - translation value (Ang) along model's Y axis\r\n * @param {number} z - translation value (Ang) along model's Z axis\r\n */\r\nMiew.prototype.translate = function (x, y, z) {\r\n this._objectControls.translatePivot(x, y, z);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Rotate object by Euler angles\r\n * @param {number} x - rotation angle around X axis in radians\r\n * @param {number} y - rotation angle around Y axis in radians\r\n * @param {number} z - rotation angle around Z axis in radians\r\n */\r\nMiew.prototype.rotate = function (x, y, z) {\r\n this._objectControls.rotate(new THREE.Quaternion().setFromEuler(new THREE.Euler(x, y, z, 'XYZ')));\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Scale object by factor\r\n * @param {number} factor - scale multiplier, should greater than zero\r\n */\r\nMiew.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n throw new RangeError('Scale should be greater than zero');\r\n }\r\n this._objectControls.scale(factor);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Center view on selection\r\n * @param {empty | subset | string} selector - defines part of molecule which must be centered (\r\n * empty - center on current selection;\r\n * subset - center on picked atom/residue/molecule;\r\n * string - center on atoms correspond to selection string)\r\n */\r\nMiew.prototype.center = function (selector) {\r\n // no arguments - center on current selection;\r\n if (selector === undefined) {\r\n this.setPivotSubset();\r\n this._needRender = true;\r\n return;\r\n }\r\n // subset with atom or residue - center on picked atom/residue;\r\n if (selector.obj !== undefined && ('atom' in selector.obj || 'residue' in selector.obj)) { // from event with selection\r\n if ('atom' in selector.obj) {\r\n this.setPivotAtom(selector.obj.atom);\r\n } else {\r\n this.setPivotResidue(selector.obj.residue);\r\n }\r\n this._needRender = true;\r\n return;\r\n }\r\n // string - center on atoms correspond to selection string\r\n if (selector.obj === undefined && selector !== '') {\r\n const sel = selectors.parse(selector);\r\n if (sel.error === undefined) {\r\n this.setPivotSubset(sel);\r\n this._needRender = true;\r\n return;\r\n }\r\n }\r\n // empty subset or incorrect/empty string - center on all molecule;\r\n this.resetPivot();\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\nMiew.prototype.within = function (selector, radius) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return selectors.None();\r\n }\r\n\r\n if (selector instanceof String) {\r\n selector = selectors.parse(selector);\r\n }\r\n\r\n const res = visual.within(selector, radius);\r\n if (res) {\r\n visual.rebuildSelectionGeometry();\r\n this._needRender = true;\r\n }\r\n return res;\r\n};\r\n\r\n/**\r\n * Get atom position in 2D canvas coords\r\n * @param {string} fullAtomName - full atom name, like A.38.CG\r\n * @returns {Object} {x, y} or false if atom not found\r\n */\r\nMiew.prototype.projected = function (fullAtomName, complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return false;\r\n }\r\n\r\n const atom = visual.getComplex().getAtomByFullname(fullAtomName);\r\n if (atom === null) {\r\n return false;\r\n }\r\n\r\n const pos = atom.position.clone();\r\n // we consider atom position to be affected only by common complex transform\r\n // ignoring any transformations that may add during editing\r\n this._gfx.pivot.updateMatrixWorldRecursive();\r\n this._gfx.camera.updateMatrixWorldRecursive();\r\n this._gfx.pivot.localToWorld(pos);\r\n pos.project(this._gfx.camera);\r\n\r\n return {\r\n x: (pos.x + 1.0) * 0.5 * this._gfx.width,\r\n y: (1.0 - pos.y) * 0.5 * this._gfx.height,\r\n };\r\n};\r\n\r\n/**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n *\r\n * @param {string=} complexName - complex name\r\n */\r\nMiew.prototype.dssp = function (complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return;\r\n }\r\n visual.getComplex().dssp();\r\n\r\n // rebuild dependent representations (cartoon or ss-colored)\r\n visual._reprList.forEach((rep) => {\r\n if (rep.mode.id === 'CA' || rep.colorer.id === 'SS') {\r\n rep.needsRebuild = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype.exportCML = function () {\r\n const self = this;\r\n\r\n function extractRotation(m) {\r\n const xAxis = new THREE.Vector3();\r\n const yAxis = new THREE.Vector3();\r\n const zAxis = new THREE.Vector3();\r\n m.extractBasis(xAxis, yAxis, zAxis);\r\n xAxis.normalize();\r\n yAxis.normalize();\r\n zAxis.normalize();\r\n const retMat = new THREE.Matrix4();\r\n retMat.identity();\r\n retMat.makeBasis(xAxis, yAxis, zAxis);\r\n return retMat;\r\n }\r\n\r\n function updateCMLData(complex) {\r\n const { root } = self._gfx;\r\n const mat = extractRotation(root.matrixWorld);\r\n const v4 = new THREE.Vector4(0, 0, 0, 0);\r\n const vCenter = new THREE.Vector4(0, 0, 0, 0);\r\n let xml = null;\r\n let ap = null;\r\n\r\n // update atoms in cml\r\n complex.forEachAtom((atom) => {\r\n if (atom.xmlNodeRef && atom.xmlNodeRef.xmlNode) {\r\n xml = atom.xmlNodeRef.xmlNode;\r\n ap = atom.position;\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n v4.applyMatrix4(mat);\r\n xml.setAttribute('x3', v4.x.toString());\r\n xml.setAttribute('y3', v4.y.toString());\r\n xml.setAttribute('z3', v4.z.toString());\r\n xml.removeAttribute('x2');\r\n xml.removeAttribute('y2');\r\n }\r\n });\r\n // update stereo groups in cml\r\n complex.forEachSGroup((sGroup) => {\r\n if (sGroup.xmlNodeRef && sGroup.xmlNodeRef.xmlNode) {\r\n xml = sGroup.xmlNodeRef.xmlNode;\r\n ap = sGroup.getPosition();\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n const cp = sGroup.getCentralPoint();\r\n if (cp === null) {\r\n v4.applyMatrix4(mat);\r\n } else {\r\n vCenter.set(cp.x, cp.y, cp.z, 0.0);\r\n v4.add(vCenter);\r\n v4.applyMatrix4(mat); // pos in global space\r\n vCenter.set(cp.x, cp.y, cp.z, 1.0);\r\n vCenter.applyMatrix4(mat);\r\n v4.sub(vCenter);\r\n }\r\n xml.setAttribute('x', v4.x.toString());\r\n xml.setAttribute('y', v4.y.toString());\r\n xml.setAttribute('z', v4.z.toString());\r\n }\r\n });\r\n }\r\n\r\n const visual = self._getComplexVisual();\r\n const complex = visual ? visual.getComplex() : null;\r\n if (complex && complex.originalCML) {\r\n updateCMLData(complex);\r\n\r\n // serialize xml structure to string\r\n const oSerializer = new XMLSerializer();\r\n return oSerializer.serializeToString(complex.originalCML);\r\n }\r\n\r\n return null;\r\n};\r\n\r\n/**\r\n * Reproduce the RCSB PDB Molecule of the Month style by David S. Goodsell\r\n *\r\n * @see http://pdb101.rcsb.org/motm/motm-about\r\n */\r\nMiew.prototype.motm = function () {\r\n settings.set({\r\n fogColorEnable: true,\r\n fogColor: 0x000000,\r\n outline: { on: true, threshold: 0.01 },\r\n bg: { color: 0xffffff },\r\n });\r\n\r\n this._forEachComplexVisual((visual) => {\r\n const rep = [];\r\n const complex = visual.getComplex();\r\n const palette = palettes.get(settings.now.palette);\r\n for (let i = 0; i < complex.getChainCount(); i++) {\r\n const curChainName = complex._chains[i]._name;\r\n const curChainColor = palette.getChainColor(curChainName);\r\n rep[i] = {\r\n selector: `chain ${curChainName}`,\r\n mode: 'VW',\r\n colorer: ['CB', { color: curChainColor, factor: 0.9 }],\r\n material: 'FL',\r\n };\r\n }\r\n visual.resetReps(rep);\r\n });\r\n};\r\n\r\nMiew.prototype.VERSION = (typeof PACKAGE_VERSION !== 'undefined' && PACKAGE_VERSION) || '0.0.0-dev';\r\n\r\n// Uncomment this to get debug trace:\r\n// Miew.prototype.debugTracer = new utils.DebugTracer(Miew.prototype);\r\n\r\n_.assign(Miew, /** @lends Miew */ {\r\n VERSION: Miew.prototype.VERSION,\r\n\r\n registeredPlugins: [],\r\n\r\n // export namespaces // TODO: WIP: refactoring external interface\r\n chem,\r\n io,\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n utils,\r\n gfx: {\r\n Representation,\r\n },\r\n\r\n /**\r\n * Third-party libraries packaged together with Miew.\r\n *\r\n * @property {object} lodash - [Lodash](https://lodash.com/), a modern JavaScript utility library delivering\r\n * modularity, performance & extras.\r\n * @property {object} three - [three.js](https://threejs.org/), JavaScript 3D library.\r\n *\r\n * @example\r\n * var _ = Miew.thirdParty.lodash;\r\n * var opts = _.merge({ ... }, Miew.options.fromURL(window.location.search));\r\n * var miew = new Miew(opts);\r\n */\r\n thirdParty: {\r\n lodash: _,\r\n three: THREE,\r\n },\r\n});\r\n\r\nexport default Miew;\r\n","import palettes from '../gfx/palettes';\r\nimport settings from '../settings';\r\n\r\nconst modeIdDesc = {\r\n $help: [\r\n 'Rendering mode shortcut',\r\n ' BS - balls and sticks mode',\r\n ' LN - lines mode',\r\n ' LC - licorice mode',\r\n ' VW - van der waals mode',\r\n ' TR - trace mode',\r\n ' TU - tube mode',\r\n ' CA - cartoon mode',\r\n ' SA - isosurface mode',\r\n ' QS - quick surface mode',\r\n ' SE - solvent excluded mode',\r\n ' TX - text mode',\r\n ],\r\n BS: {\r\n $help: [\r\n ' Balls and sticks',\r\n ' aromrad = #aromatic radius',\r\n ' atom = #atom radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n CA: {\r\n $help: [\r\n ' Cartoon',\r\n ' arrow = #arrow size',\r\n ' depth = #depth of surface',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = #',\r\n ' width = #secondary width\\n',\r\n ],\r\n },\r\n LN: {\r\n $help: [\r\n ' Lines',\r\n ' atom = #atom radius',\r\n ' chunkarom = ',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' offsarom = \\n',\r\n ],\r\n },\r\n LC: {\r\n $help: [\r\n ' Licorice',\r\n ' aromrad = #aromatic radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n VW: {\r\n $help: [\r\n ' Van der Waals',\r\n ' nothing\\n',\r\n ],\r\n },\r\n TR: {\r\n $help: [\r\n ' Trace',\r\n ' radius = #tube radius\\n',\r\n ],\r\n },\r\n TU: {\r\n $help: [\r\n ' Tube',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = \\n',\r\n ],\r\n },\r\n SA: {\r\n $help: [\r\n ' Surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n QS: {\r\n $help: [\r\n ' Quick surface',\r\n ' isoValue = ',\r\n ' scale = ',\r\n ' wireframe = ',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n SE: {\r\n $help: [\r\n ' Solvent excluded surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n TX: {\r\n $help: [\r\n ' Text mode',\r\n ' template = string that can include \"{{ id }}\"',\r\n ' it will be replaced by value, id can be one of next:',\r\n ' serial, name, type, sequence, residue, chain, hetatm, water\\n',\r\n ' horizontalAlign = {\"left\", \"right\", \"center\"}',\r\n ' verticalAlign = {\"top\", \"bottom\", \"middle\"}',\r\n ' dx = #offset along x',\r\n ' dy = #offset along y',\r\n ' dz = #offset along z',\r\n ' fg = #text color modificator',\r\n ' could be keyword, named color or hex',\r\n ' fg = #back color modificator',\r\n ' could be keyword, named color or hex',\r\n ' showBg = #if set show background',\r\n ' plate under text',\r\n ],\r\n },\r\n};\r\n\r\nconst colorDesc = {\r\n $help: [\r\n 'Coloring mode shortcut',\r\n ' EL - color by element',\r\n ' CH - color by chain',\r\n ' SQ - color by sequence',\r\n ' RT - color by residue type',\r\n ' SS - color by secondary structure',\r\n ' UN - uniform',\r\n ],\r\n UN: {\r\n $help: [\r\n 'Parameters of coloring modes customization',\r\n ' Uniform',\r\n ' color = #RGB->HEX->dec\\n',\r\n ],\r\n color: {\r\n $help: Object.keys(palettes.get(settings.now.palette).namedColors).sort().join('\\n'),\r\n },\r\n },\r\n};\r\n\r\nconst materialDesc = {\r\n $help: [\r\n 'Material shortcut',\r\n ' DF - diffuse',\r\n ' TR - transparent',\r\n ' SF - soft plastic',\r\n ' PL - glossy plastic',\r\n ' ME - metal',\r\n ' GL - glass',\r\n ],\r\n};\r\n\r\nconst addRepDesc = {\r\n $help: [\r\n 'Short (packed) representation description as a set of variables',\r\n ' s=',\r\n ' selector property',\r\n ' m=[!:[,...]]',\r\n ' render mode property',\r\n ' c=[!:[,...]]',\r\n ' color mode property',\r\n ' mt=',\r\n ' material property',\r\n ],\r\n s: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n m: modeIdDesc,\r\n c: colorDesc,\r\n mt: materialDesc,\r\n};\r\n\r\nconst setGetParameterDesc = {\r\n $help: [\r\n 'Parameters of rendering modes customization: modes',\r\n 'Parameters of colorer customization: colorers',\r\n 'Autobuild: autobuild = (|)',\r\n ],\r\n modes: modeIdDesc,\r\n colorers: colorDesc,\r\n};\r\n\r\nconst help = {\r\n $help: [\r\n 'help (| )',\r\n 'You can get detailed information about command options',\r\n ' using \"help cmd.opt.opt.[...]\"\\n',\r\n ' you can use one line comments',\r\n ' everything started from (#|//) will be skipped',\r\n ' Example: >build //some comment\\n',\r\n 'List of available commands:',\r\n ],\r\n reset: {\r\n $help: [\r\n 'Reload current object, delete all representations',\r\n ' Nothing will work until load new object',\r\n ],\r\n },\r\n load: {\r\n $help: [\r\n 'load (||-f [<*.NC FILE URL STRING>])',\r\n ' Load new pdb object from selected source',\r\n ],\r\n PDBID: {\r\n $help: 'pdb id in remote molecule database',\r\n },\r\n URL: {\r\n $help: 'url to source file',\r\n },\r\n f: {\r\n $help: [\r\n 'open file system dialog to fetch local file',\r\n 'optionally you can determine trajectory file',\r\n 'via URL for *.top model',\r\n ],\r\n },\r\n },\r\n clear: {\r\n $help: 'No args. Clear terminal',\r\n },\r\n add: {\r\n $help: [\r\n 'add [] []',\r\n ' Add new item to representation set with',\r\n ' default or params',\r\n ],\r\n REP_NAME: {\r\n $help: 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n rep: {\r\n $help: [\r\n 'rep [|] []',\r\n ' set current representation by name or index',\r\n ' edit current representation by ',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n remove: {\r\n $help: [\r\n 'remove (|)',\r\n 'Remove representation by name or index',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n },\r\n selector: {\r\n $help: [\r\n 'selector ',\r\n ' set selector from EXPRESSION to current representation',\r\n ],\r\n EXPRESSION: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n },\r\n mode: {\r\n $help: [\r\n 'mode [=...]',\r\n ' set rendering mode and apply parameters to current representation',\r\n ],\r\n MODE_ID: modeIdDesc,\r\n },\r\n color: {\r\n $help: [\r\n 'color [=...]',\r\n ' set colorer and apply parameters to current representation',\r\n ],\r\n COLORER_ID: colorDesc,\r\n },\r\n material: {\r\n $help: [\r\n 'material ',\r\n ' set material to current representation',\r\n ],\r\n MATERIAL_ID: materialDesc,\r\n },\r\n build: {\r\n $help: 'build help str',\r\n add: {\r\n $help: 'build.add',\r\n new: {\r\n $help: [\r\n 'add.new',\r\n 'add.new new line 1',\r\n 'add.new new line 2',\r\n 'add.new new line 3',\r\n ],\r\n },\r\n },\r\n del: {\r\n $help: 'build.del',\r\n },\r\n },\r\n list: {\r\n $help: [\r\n 'list [-e|-s||]',\r\n 'Print representations if no args print list of representations',\r\n ' -e expand list and show all representations',\r\n ' -s show all user-registered selectors',\r\n ' | show only current representation',\r\n ],\r\n },\r\n hide: {\r\n $help: [\r\n 'hide (|)',\r\n 'Hide representation referenced in args',\r\n ],\r\n },\r\n show: {\r\n $help: [\r\n 'show (|)',\r\n 'Show representation referenced in args',\r\n ],\r\n },\r\n get: {\r\n $help: [\r\n 'get ',\r\n 'Print value',\r\n ' - path to option use get.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set: {\r\n $help: [\r\n 'set ',\r\n 'Set with ',\r\n ' - path to option use set.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set_save: {\r\n $help: [\r\n 'set_save',\r\n 'Save current settings to cookie',\r\n ],\r\n },\r\n set_restore: {\r\n $help: [\r\n 'set_restore',\r\n 'Load and apply settings from cookie',\r\n ],\r\n },\r\n set_reset: {\r\n $help: [\r\n 'set_reset',\r\n 'Reset current settings to the defaults',\r\n ],\r\n },\r\n preset: {\r\n $help: [\r\n 'preset []',\r\n 'Reset current representation or set preset to ',\r\n ],\r\n PRESET: {\r\n $help: [\r\n 'default',\r\n 'wire',\r\n 'small',\r\n 'macro',\r\n ],\r\n },\r\n },\r\n unit: {\r\n $help: [\r\n 'unit []',\r\n 'Change current biological structure view. Zero value means asymmetric unit,',\r\n 'positive values set an assembly with corresponding number.',\r\n 'Being called with no parameters command prints current unit information.',\r\n ],\r\n },\r\n view: {\r\n $help: [\r\n 'view []',\r\n 'Get current encoded view or set if ENCODED_VIEW placed as argument',\r\n ],\r\n ENCODED_VIEW: {\r\n $help: [\r\n 'encoded view matrix string (binary code)',\r\n ],\r\n },\r\n },\r\n rotate: {\r\n $help: [\r\n 'rotate (x|y|z) [] [(x|y|z) []]...',\r\n 'Rotate scene',\r\n ],\r\n },\r\n scale: {\r\n $help: [\r\n 'scale ',\r\n 'Scale scene',\r\n ],\r\n },\r\n select: {\r\n $help: [\r\n 'select [as ]',\r\n 'Select atoms using selector defined in SELECTOR_STRING',\r\n ' and if SELECTOR_NAME is defined register it in viewer',\r\n ' you can use it later as a complex selector',\r\n ],\r\n },\r\n within: {\r\n $help: [\r\n 'within of as ',\r\n 'Build within named selector',\r\n ' DISTANCE ',\r\n ' SELECTOR_STRING ',\r\n ' SELECTOR_NAME ',\r\n ],\r\n },\r\n url: {\r\n $help: [\r\n 'url [-s] [-v]',\r\n 'Report URL encoded scene',\r\n ' if -s set that include settings in the URL',\r\n ' if -v set that include view in the URL',\r\n ],\r\n },\r\n screenshot: {\r\n $help: [\r\n 'screenshot [ []]',\r\n 'Make a screenshot of the scene',\r\n ' WIDTH in pixels',\r\n ' HEIGHT in pixels, equal to WIDTH by default',\r\n ],\r\n },\r\n line: {\r\n $help: [\r\n 'line [=]',\r\n 'Draw dashed line between two specified atoms',\r\n ],\r\n },\r\n removeobj: {\r\n $help: [\r\n 'removeobj ',\r\n 'Remove scene object by its index. Indices could be obtained by command',\r\n ],\r\n },\r\n listobj: {\r\n $help: [\r\n 'listobj',\r\n 'Display the list of all existing scene objects',\r\n ],\r\n },\r\n};\r\n\r\nexport default help;\r\n","import _ from 'lodash';\r\nimport Miew from './Miew';\r\nimport { parser as parsercli } from './utils/MiewCLIParser';\r\nimport clihelp from './utils/MiewCLIHelp';\r\nimport logger from './utils/logger';\r\nimport utils from './utils';\r\n\r\nconst {\r\n chem: { selectors },\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n} = Miew;\r\n\r\nfunction None() {\r\n}\r\n\r\nconst NULL = (function () {\r\n const obj = new None();\r\n return function () {\r\n return obj;\r\n };\r\n}());\r\n\r\nclass RepresentationMap {\r\n constructor() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n\r\n get(strId) {\r\n return this.representationMap[strId] || this.representationID[strId] || '';\r\n }\r\n\r\n add(strId, index) {\r\n if (strId === -1) {\r\n return 'Can not create representation: there is no data';\r\n }\r\n\r\n if (index !== undefined) {\r\n if (!this.representationMap.hasOwnProperty(strId)) {\r\n this.representationMap[strId.toString()] = index;\r\n this.representationID[index] = strId.toString();\r\n } else {\r\n return 'This name has already existed, registered without name';\r\n }\r\n }\r\n return `Representation ${strId} successfully added`;\r\n }\r\n\r\n remove(index) {\r\n if (index && this.representationID.hasOwnProperty(index)) {\r\n delete this.representationMap[this.representationID[index]];\r\n delete this.representationID[index];\r\n }\r\n\r\n const sortedKeys = Object.keys(this.representationID).sort();\r\n for (const i in sortedKeys) {\r\n if (sortedKeys.hasOwnProperty(i)) {\r\n const id = sortedKeys[i];\r\n if (id > index) {\r\n this.representationID[id - 1] = this.representationID[id];\r\n this.representationMap[this.representationID[id]] -= 1;\r\n delete this.representationID[id];\r\n }\r\n }\r\n }\r\n }\r\n\r\n clear() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n}\r\n\r\nconst representationsStorage = new RepresentationMap();\r\n\r\nfunction keyRemap(key) {\r\n const keys = {\r\n s: 'selector',\r\n m: 'mode',\r\n c: 'colorer',\r\n mt: 'material',\r\n mode: 'modes',\r\n color: 'colorers',\r\n colorer: 'colorers',\r\n select: 'selector',\r\n material: 'materials',\r\n selector: 'selector',\r\n };\r\n const ans = keys[key];\r\n return ans === undefined ? key : ans;\r\n}\r\n\r\nclass CLIUtils {\r\n list(miew, repMap, key) {\r\n let ret = '';\r\n if (miew && repMap !== undefined) {\r\n if (key === undefined || key === '-e') {\r\n const count = miew.repCount();\r\n\r\n for (let i = 0; i < count; i++) {\r\n ret += this.listRep(miew, repMap, i, key);\r\n }\r\n }\r\n }\r\n return ret;\r\n }\r\n\r\n listRep(miew, repMap, repIndex, key) {\r\n let ret = '';\r\n const rep = miew.repGet(repIndex);\r\n if (!rep) {\r\n logger.warn(`Rep ${repIndex} does not exist!`);\r\n return ret;\r\n }\r\n const index = repIndex;\r\n const repName = repMap.get(index);\r\n\r\n const { mode, colorer } = rep;\r\n const selectionStr = rep.selectorString;\r\n const material = rep.materialPreset;\r\n\r\n ret += `#${index} : ${mode.name}${repName === '' ? '' : `, ${repName}`}\\n`;\r\n\r\n if (key !== undefined) {\r\n ret += ` selection : \"${selectionStr}\"\\n`;\r\n ret += ` mode : (${mode.id}), ${mode.name}\\n`;\r\n ret += ` colorer : (${colorer.id}), ${colorer.name}\\n`;\r\n ret += ` material : (${material.id}), ${material.name}\\n`;\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listSelector(miew, context) {\r\n let ret = '';\r\n\r\n for (const k in context) {\r\n if (context.hasOwnProperty(k)) {\r\n ret += `${k} : \"${context[k]}\"\\n`;\r\n }\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listObjs(miew) {\r\n const objs = miew._objects;\r\n\r\n if (!objs || !Array.isArray(objs) || objs.length === 0) {\r\n return 'There are no objects on the scene';\r\n }\r\n\r\n const strList = [];\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n strList[i] = `${i}: ${objs[i].toString()}`;\r\n }\r\n\r\n return strList.join('\\n');\r\n }\r\n\r\n joinHelpStr(helpData) {\r\n if (helpData instanceof Array) {\r\n return helpData.join('\\n');\r\n }\r\n return helpData;\r\n }\r\n\r\n help(path) {\r\n if (_.isUndefined(path)) {\r\n return `${this.joinHelpStr(clihelp.$help)}\\n${_.slice(_.sortBy(_.keys(clihelp)), 1).join(', ')}\\n`;\r\n }\r\n\r\n const helpItem = _.get(clihelp, path);\r\n return _.isUndefined(helpItem) ? this.help() : `${this.joinHelpStr(helpItem.$help)}\\n`;\r\n }\r\n\r\n load(miew, arg) {\r\n if (miew === undefined || arg === undefined || arg === '-f') {\r\n return;\r\n }\r\n miew.awaitWhileCMDisInProcess();\r\n const finish = () => miew.finishAwaitingCMDInProcess();\r\n miew.load(arg).then(finish, finish);\r\n }\r\n\r\n checkArg(key, arg, modificate) {\r\n if (key !== undefined && arg !== undefined) {\r\n if (keyRemap(key) === 'selector') {\r\n const res = selectors.parse(arg);\r\n\r\n if (res.error !== undefined) {\r\n const selExc = { message: res.error };\r\n throw selExc;\r\n }\r\n\r\n if (modificate !== undefined && modificate) {\r\n return res.selector;\r\n }\r\n return arg;\r\n }\r\n\r\n const modificators = {\r\n colorers,\r\n modes,\r\n materials,\r\n };\r\n\r\n let modificator = key;\r\n let temp;\r\n while (modificator !== temp) {\r\n temp = modificator;\r\n modificator = keyRemap(temp);\r\n }\r\n\r\n if (modificators[modificator].get(arg) === undefined) {\r\n const exc = { message: `${arg} is not existed in ${modificator}` };\r\n throw exc;\r\n }\r\n return arg;\r\n }\r\n return NULL;\r\n }\r\n\r\n propagateProp(path, arg) {\r\n if (path !== undefined) {\r\n let argExc = {};\r\n const adapter = options.adapters[typeof _.get(settings.defaults, path)];\r\n if (adapter === undefined) {\r\n const pathExc = { message: `${path} is not existed` };\r\n throw pathExc;\r\n }\r\n\r\n if ((path.endsWith('.color') || path.endsWith('.baseColor')\r\n || path.endsWith('.EL.carbon')) && typeof arg !== 'number') {\r\n arg = palettes.get(settings.now.palette).getNamedColor(arg);\r\n }\r\n\r\n if (path.endsWith('.fg') || path.endsWith('.bg')) {\r\n if (typeof arg !== 'number') {\r\n const val = palettes.get(settings.now.palette).getNamedColor(arg, true);\r\n if (val !== undefined) {\r\n arg = `0x${val.toString(16)}`;\r\n }\r\n } else {\r\n arg = `0x${arg.toString(16)}`;\r\n }\r\n }\r\n\r\n if (path.endsWith('.template')) {\r\n arg = arg.replace(/\\\\n/g, '\\n');// NOSONAR\r\n }\r\n\r\n if (arg !== undefined && adapter(arg) !== arg && adapter(arg) !== (arg > 0)) {\r\n argExc = { message: `${path} must be a \"${typeof _.get(settings.defaults, path)}\"` };\r\n throw argExc;\r\n }\r\n }\r\n return arg;\r\n }\r\n\r\n unquoteString(value) {\r\n return utils.unquoteString(value);\r\n }\r\n}\r\n// repIndexOrRepMap could be RepresentationMap or index\r\n\r\nconst utilFunctions = new CLIUtils();\r\n\r\nfunction CreateObjectPair(a, b) {\r\n const obj = {};\r\n obj[a] = b;\r\n return obj;\r\n}\r\n\r\nfunction ArgList(arg) {\r\n if (arg instanceof this.constructor) {\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n}\r\n\r\nArgList.prototype.append = function (value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n};\r\n\r\nArgList.prototype.remove = function (value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n};\r\n\r\nArgList.prototype.toJSO = function (cliUtils, cmd, arg) {\r\n const res = {};\r\n\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n _.set(res, list[i].id, cliUtils.propagateProp(`${keyRemap(cmd)}.${arg}.${list[i].id}`, list[i].val));\r\n }\r\n\r\n return res;\r\n};\r\n\r\nfunction Arg(_id, _val) {\r\n this.id = _id;\r\n this.val = _val;\r\n}\r\n\r\nconst cliutils = Object.create({});\r\n\r\ncliutils.Arg = Arg;\r\ncliutils.ArgList = ArgList;\r\n\r\ncliutils.miew = null;\r\ncliutils.echo = null;\r\ncliutils.representations = representationsStorage;\r\ncliutils.utils = utilFunctions;\r\n\r\ncliutils._ = _;\r\ncliutils.CreateObjectPair = CreateObjectPair;\r\ncliutils.keyRemap = keyRemap;\r\ncliutils.Context = selectors.Context;\r\ncliutils.ClearContext = selectors.ClearContext;\r\n\r\ncliutils.NULL = NULL;\r\n\r\ncliutils.notimplemented = function () {\r\n return this.NULL;\r\n};\r\n\r\nMiew.prototype.script = function (script, _printCallback, _errorCallback) {\r\n parsercli.yy.miew = this;\r\n parsercli.yy.echo = _printCallback;\r\n parsercli.yy.error = _errorCallback;\r\n if (this.cmdQueue === undefined) {\r\n this.cmdQueue = [];\r\n }\r\n\r\n if (this.commandInAction === undefined) {\r\n this.commandInAction = false;\r\n }\r\n\r\n this.cmdQueue = this.cmdQueue.concat(script.split('\\n'));\r\n};\r\n\r\nMiew.prototype.awaitWhileCMDisInProcess = function () {\r\n this.commandInAction = true;\r\n};\r\n\r\nMiew.prototype.finishAwaitingCMDInProcess = function () {\r\n this.commandInAction = false;\r\n};\r\n\r\nMiew.prototype.isScriptingCommandAvailable = function () {\r\n return this.commandInAction !== undefined\r\n && !this.commandInAction\r\n && this.cmdQueue !== undefined\r\n && this.cmdQueue.length > 0;\r\n};\r\n\r\nMiew.prototype.callNextCmd = function () {\r\n if (this.isScriptingCommandAvailable()) {\r\n const cmd = this.cmdQueue.shift();\r\n\r\n const res = {};\r\n res.success = false;\r\n try {\r\n parsercli.parse(cmd);\r\n res.success = true;\r\n } catch (e) {\r\n res.error = e.message;\r\n parsercli.yy.error(res.error);\r\n this.finishAwaitingCMDInProcess();\r\n }\r\n return res;\r\n }\r\n return '';\r\n};\r\n\r\nparsercli.yy = cliutils;\r\n// workaround for incorrect JISON parser generator for AMD module\r\nparsercli.yy.parseError = parsercli.parseError;\r\n","import Miew from './Miew';\r\nimport './Miew-cli';\r\n\r\nexport default 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this.yy=t||this.yy||{},this._input=e,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var e=this._input[0];return this.yytext+=e,this.yyleng++,this.offset++,this.match+=e,this.matched+=e,e.match(/(?:\r\n?|\n).*/g)?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),e},unput:function(e){var t=e.length,r=e.split(/(?:\r\n?|\n)/g);this._input=e+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-t),this.offset-=t;var n=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),r.length-1&&(this.yylineno-=r.length-1);var s=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:r?(r.length===n.length?this.yylloc.first_column:0)+n[n.length-r.length].length-r[0].length:this.yylloc.first_column-t},this.options.ranges&&(this.yylloc.range=[s[0],s[0]+this.yyleng-t]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){return this.options.backtrack_lexer?(this._backtrack=!0,this):this.parseError("Lexical error on line "+(this.yylineno+1)+". You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},less:function(e){this.unput(this.match.slice(e))},pastInput:function(){var e=this.matched.substr(0,this.matched.length-this.match.length);return(e.length>20?"...":"")+e.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var e=this.match;return e.length<20&&(e+=this._input.substr(0,20-e.length)),(e.substr(0,20)+(e.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var e=this.pastInput(),t=new Array(e.length+1).join("-");return e+this.upcomingInput()+"\n"+t+"^"},test_match:function(e,t){var r,n,s;if(this.options.backtrack_lexer&&(s={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(s.yylloc.range=this.yylloc.range.slice(0))),(n=e[0].match(/(?:\r\n?|\n).*/g))&&(this.yylineno+=n.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:n?n[n.length-1].length-n[n.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+e[0].length},this.yytext+=e[0],this.match+=e[0],this.matches=e,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(e[0].length),this.matched+=e[0],r=this.performAction.call(this,this.yy,this,t,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),r)return r;if(this._backtrack){for(var i in s)this[i]=s[i];return!1}return!1},next:function(){if(this.done)return this.EOF;var e,t,r,n;this._input||(this.done=!0),this._more||(this.yytext="",this.match="");for(var s=this._currentRules(),i=0;it[0].length)){if(t=r,n=i,this.options.backtrack_lexer){if(!1!==(e=this.test_match(r,s[i])))return e;if(this._backtrack){t=!1;continue}return!1}if(!this.options.flex)break}return t?!1!==(e=this.test_match(t,s[n]))&&e:""===this._input?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+". Unrecognized text.\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var e=this.next();return e||this.lex()},begin:function(e){this.conditionStack.push(e)},popState:function(){return this.conditionStack.length-1>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(e){return(e=this.conditionStack.length-1-Math.abs(e||0))>=0?this.conditionStack[e]:"INITIAL"},pushState:function(e){this.begin(e)},stateStackSize:function(){return this.conditionStack.length},options:{"case-insensitive":!0},performAction:function(e,t,r,n){switch(r){case 0:break;case 1:case 2:return"";case 3:return 42;case 4:return 35;case 5:return 77;case 6:case 7:return 78;case 8:return 8;case 9:return 6;case 10:return 82;case 11:return 7;case 12:return 9;case 13:return 59;case 14:return 13;case 15:return 15;case 16:return 17;case 17:return 18;case 18:return 19;case 19:return 20;case 20:return 11;case 21:return 62;case 22:return 64;case 23:return 23;case 24:return 25;case 25:return 26;case 26:return 27;case 27:return 30;case 28:return 34;case 29:return 33;case 30:return 65;case 31:return 66;case 32:return 37;case 33:return 41;case 34:return 43;case 35:return 52;case 36:return 54;case 37:return 55;case 38:return 46;case 39:return 48;case 40:return 45;case 41:return 49;case 42:return 56;case 43:return 58;case 44:return 44;case 45:return 83;case 46:return 84;case 47:return 85;case 48:return 86;case 49:return 87;case 50:return 88;case 51:return 89;case 52:return 90;case 53:return 91;case 54:return 92;case 55:return 93;case 56:return 94;case 57:return 95;case 58:case 59:return 70;case 60:case 61:return 72;case 62:case 63:case 64:return 74;case 65:return 31;case 66:return 36;case 67:return 96;case 68:return 97;case 69:return 98;case 70:return 99;case 71:return t.yytext=e.utils.unquoteString(t.yytext),14;case 72:return 38;case 73:return 5;case 74:return 101;case 75:return 103;case 76:return"\\";case 77:return 28;case 78:return 61;case 79:return 29;case 80:return 57;case 81:return 71}},rules:[/^(?:\s+)/i,/^(?:[#].*)/i,/^(?:\/\/.*)/i,/^(?:([_A-Z0-9\/\+]+==))/i,/^(?:-?[0-9]+(\.[0-9]+)?\b)/i,/^(?:0[xX][0-9A-F]+\b)/i,/^(?:false\b)/i,/^(?:true\b)/i,/^(?:all\b)/i,/^(?:reset\b)/i,/^(?:clear\b)/i,/^(?:build\b)/i,/^(?:help\b)/i,/^(?:load\b)/i,/^(?:get\b)/i,/^(?:set\b)/i,/^(?:set_save\b)/i,/^(?:set_restore\b)/i,/^(?:set_reset\b)/i,/^(?:preset\b)/i,/^(?:motm\b)/i,/^(?:add\b)/i,/^(?:rep\b)/i,/^(?:remove\b)/i,/^(?:hide\b)/i,/^(?:show\b)/i,/^(?:list\b)/i,/^(?:select\b)/i,/^(?:within\b)/i,/^(?:selector\b)/i,/^(?:mode\b)/i,/^(?:color\b)/i,/^(?:material\b)/i,/^(?:view\b)/i,/^(?:unit\b)/i,/^(?:line\b)/i,/^(?:listobj\b)/i,/^(?:removeobj\b)/i,/^(?:rotate\b)/i,/^(?:translate\b)/i,/^(?:scale\b)/i,/^(?:center\b)/i,/^(?:url\b)/i,/^(?:screenshot\b)/i,/^(?:dssp\b)/i,/^(?:file_list\b)/i,/^(?:file_register\b)/i,/^(?:file_delete\b)/i,/^(?:preset_add\b)/i,/^(?:preset_delete\b)/i,/^(?:preset_update\b)/i,/^(?:preset_rename\b)/i,/^(?:preset_open\b)/i,/^(?:create_scenario\b)/i,/^(?:reset_scenario\b)/i,/^(?:delete_scenario\b)/i,/^(?:add_scenario_item\b)/i,/^(?:list_scenario\b)/i,/^(?:s\b)/i,/^(?:mt\b)/i,/^(?:m\b)/i,/^(?:c\b)/i,/^(?:x\b)/i,/^(?:y\b)/i,/^(?:z\b)/i,/^(?:as\b)/i,/^(?:of\b)/i,/^(?:pdb\b)/i,/^(?:delay\b)/i,/^(?:prst\b)/i,/^(?:desc\b)/i,/^(?:((?:"(?:\\.|[^\\"])*"|'(?:\\.|[^\\'])*')))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:\.)/i,/^(?:\/)/i,/^(?:\\)/i,/^(?:-e\b)/i,/^(?:-f\b)/i,/^(?:-s\b)/i,/^(?:-v\b)/i,/^(?:=)/i],conditions:{INITIAL:{rules:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],inclusive:!0}}};function be(){this.yy={}}return ye.lexer=xe,be.prototype=ye,ye.Parser=be,new be}();e.exports={parser:t}},99:e=>{var t=function(){var e=function(e,t,r,n){for(r=r||{},n=e.length;n--;r[e[n]]=t);return r},t=[1,4],r=[1,5],n=[1,6],s=[1,7],i=[1,8],o=[1,9],a=[1,11],l=[1,12],c=[5,7,8,11],h=[1,17],u=[1,22],d=[1,20],p=[1,21],m=[5,7,8,11,19],f={trace:function(){},yy:{},symbols_:{error:2,Program:3,Expression:4,EOF:5,Selector:6,OR:7,AND:8,NOT:9,"(":10,")":11,SELECTOR:12,NAMED_SELECTOR:13,SELECTOR_RANGED:14,RangeList:15,SELECTOR_NAMED:16,NameList:17,Range:18,",":19,NUMBER:20,":":21,Name:22,IDENTIFIER:23,STRING:24,$accept:0,$end:1},terminals_:{2:"error",5:"EOF",7:"OR",8:"AND",9:"NOT",10:"(",11:")",12:"SELECTOR",13:"NAMED_SELECTOR",14:"SELECTOR_RANGED",16:"SELECTOR_NAMED",19:",",20:"NUMBER",21:":",23:"IDENTIFIER",24:"STRING"},productions_:[0,[3,2],[4,1],[4,3],[4,3],[4,2],[4,3],[6,1],[6,1],[6,2],[6,2],[15,1],[15,3],[18,1],[18,3],[17,1],[17,3],[22,1],[22,1],[22,1]],performAction:function(e,t,r,n,s,i,o){var a=i.length-1;switch(s){case 1:return i[a-1];case 3:this.$=n.keyword("or")(i[a-2],i[a]);break;case 4:this.$=n.keyword("and")(i[a-2],i[a]);break;case 5:this.$=n.keyword("not")(i[a]);break;case 6:this.$=i[a-1];break;case 7:this.$=n.keyword(i[a])();break;case 8:this.$=n.GetSelector(i[a].toLowerCase().slice(1,i[a].length));break;case 9:case 10:this.$=n.keyword(i[a-1])(i[a]);break;case 11:this.$=new n.RangeList(i[a]);break;case 12:case 16:this.$=i[a-2].append(i[a]);break;case 13:this.$=new n.Range(Number(i[a]));break;case 14:this.$=new n.Range(Number(i[a-2]),Number(i[a]));break;case 15:this.$=new n.ValueList(i[a])}},table:[{3:1,4:2,6:3,9:t,10:r,12:n,13:s,14:i,16:o},{1:[3]},{5:[1,10],7:a,8:l},e(c,[2,2]),{4:13,6:3,9:t,10:r,12:n,13:s,14:i,16:o},{4:14,6:3,9:t,10:r,12:n,13:s,14:i,16:o},e(c,[2,7]),e(c,[2,8]),{15:15,18:16,20:h},{17:18,20:u,22:19,23:d,24:p},{1:[2,1]},{4:23,6:3,9:t,10:r,12:n,13:s,14:i,16:o},{4:24,6:3,9:t,10:r,12:n,13:s,14:i,16:o},e(c,[2,5]),{7:a,8:l,11:[1,25]},e(c,[2,9],{19:[1,26]}),e(m,[2,11]),e(m,[2,13],{21:[1,27]}),e(c,[2,10],{19:[1,28]}),e(m,[2,15]),e(m,[2,17]),e(m,[2,18]),e(m,[2,19]),e([5,7,11],[2,3],{8:l}),e(c,[2,4]),e(c,[2,6]),{18:29,20:h},{20:[1,30]},{20:u,22:31,23:d,24:p},e(m,[2,12]),e(m,[2,14]),e(m,[2,16])],defaultActions:{10:[2,1]},parseError:function(e,t){if(!t.recoverable){var r=new Error(e);throw r.hash=t,r}this.trace(e)},parse:function(e){var t=this,r=[0],n=[],s=[null],i=[],o=this.table,a="",l=0,c=0,h=0,u=i.slice.call(arguments,1),d=Object.create(this.lexer),p={yy:{}};for(var m in this.yy)Object.prototype.hasOwnProperty.call(this.yy,m)&&(p.yy[m]=this.yy[m]);d.setInput(e,p.yy),p.yy.lexer=d,p.yy.parser=this,void 0===d.yylloc&&(d.yylloc={});var f=d.yylloc;i.push(f);var _=d.options&&d.options.ranges;"function"==typeof p.yy.parseError?this.parseError=p.yy.parseError:this.parseError=Object.getPrototypeOf(this).parseError;for(var g,y,x,b,w,S,v,C,A,E,T={};;){if(x=r[r.length-1],this.defaultActions[x]?b=this.defaultActions[x]:(null==g&&(E=void 0,"number"!=typeof(E=n.pop()||d.lex()||1)&&(E instanceof Array&&(E=(n=E).pop()),E=t.symbols_[E]||E),g=E),b=o[x]&&o[x][g]),void 0===b||!b.length||!b[0]){var R="";for(S in A=[],o[x])this.terminals_[S]&&S>2&&A.push("'"+this.terminals_[S]+"'");R=d.showPosition?"Parse error on line "+(l+1)+":\n"+d.showPosition()+"\nExpecting "+A.join(", ")+", got '"+(this.terminals_[g]||g)+"'":"Parse error on line "+(l+1)+": Unexpected "+(1==g?"end of input":"'"+(this.terminals_[g]||g)+"'"),this.parseError(R,{text:d.match,token:this.terminals_[g]||g,line:d.yylineno,loc:f,expected:A})}if(b[0]instanceof Array&&b.length>1)throw new Error("Parse Error: multiple actions possible at state: "+x+", token: "+g);switch(b[0]){case 1:r.push(g),s.push(d.yytext),i.push(d.yylloc),r.push(b[1]),g=null,y?(g=y,y=null):(c=d.yyleng,a=d.yytext,l=d.yylineno,f=d.yylloc,h>0&&h--);break;case 2:if(v=this.productions_[b[1]][1],T.$=s[s.length-v],T._$={first_line:i[i.length-(v||1)].first_line,last_line:i[i.length-1].last_line,first_column:i[i.length-(v||1)].first_column,last_column:i[i.length-1].last_column},_&&(T._$.range=[i[i.length-(v||1)].range[0],i[i.length-1].range[1]]),void 0!==(w=this.performAction.apply(T,[a,c,l,p.yy,b[1],s,i].concat(u))))return w;v&&(r=r.slice(0,-1*v*2),s=s.slice(0,-1*v),i=i.slice(0,-1*v)),r.push(this.productions_[b[1]][0]),s.push(T.$),i.push(T._$),C=o[r[r.length-2]][r[r.length-1]],r.push(C);break;case 3:return!0}}return!0}},_={EOF:1,parseError:function(e,t){if(!this.yy.parser)throw new Error(e);this.yy.parser.parseError(e,t)},setInput:function(e,t){return this.yy=t||this.yy||{},this._input=e,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var e=this._input[0];return this.yytext+=e,this.yyleng++,this.offset++,this.match+=e,this.matched+=e,e.match(/(?:\r\n?|\n).*/g)?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),e},unput:function(e){var t=e.length,r=e.split(/(?:\r\n?|\n)/g);this._input=e+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-t),this.offset-=t;var n=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),r.length-1&&(this.yylineno-=r.length-1);var s=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:r?(r.length===n.length?this.yylloc.first_column:0)+n[n.length-r.length].length-r[0].length:this.yylloc.first_column-t},this.options.ranges&&(this.yylloc.range=[s[0],s[0]+this.yyleng-t]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){return this.options.backtrack_lexer?(this._backtrack=!0,this):this.parseError("Lexical error on line "+(this.yylineno+1)+". You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},less:function(e){this.unput(this.match.slice(e))},pastInput:function(){var e=this.matched.substr(0,this.matched.length-this.match.length);return(e.length>20?"...":"")+e.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var e=this.match;return e.length<20&&(e+=this._input.substr(0,20-e.length)),(e.substr(0,20)+(e.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var e=this.pastInput(),t=new Array(e.length+1).join("-");return e+this.upcomingInput()+"\n"+t+"^"},test_match:function(e,t){var r,n,s;if(this.options.backtrack_lexer&&(s={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(s.yylloc.range=this.yylloc.range.slice(0))),(n=e[0].match(/(?:\r\n?|\n).*/g))&&(this.yylineno+=n.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:n?n[n.length-1].length-n[n.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+e[0].length},this.yytext+=e[0],this.match+=e[0],this.matches=e,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(e[0].length),this.matched+=e[0],r=this.performAction.call(this,this.yy,this,t,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),r)return r;if(this._backtrack){for(var i in s)this[i]=s[i];return!1}return!1},next:function(){if(this.done)return this.EOF;var e,t,r,n;this._input||(this.done=!0),this._more||(this.yytext="",this.match="");for(var s=this._currentRules(),i=0;it[0].length)){if(t=r,n=i,this.options.backtrack_lexer){if(!1!==(e=this.test_match(r,s[i])))return e;if(this._backtrack){t=!1;continue}return!1}if(!this.options.flex)break}return t?!1!==(e=this.test_match(t,s[n]))&&e:""===this._input?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+". Unrecognized text.\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var e=this.next();return e||this.lex()},begin:function(e){this.conditionStack.push(e)},popState:function(){return this.conditionStack.length-1>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(e){return(e=this.conditionStack.length-1-Math.abs(e||0))>=0?this.conditionStack[e]:"INITIAL"},pushState:function(e){this.begin(e)},stateStackSize:function(){return this.conditionStack.length},options:{"case-insensitive":!0},performAction:function(e,t,r,n){switch(r){case 0:break;case 1:return 20;case 2:return 7;case 3:return 8;case 4:return 9;case 5:return 12;case 6:return 16;case 7:return 14;case 8:return 10;case 9:return 11;case 10:return 19;case 11:return 21;case 12:return"<=";case 13:return">=";case 14:return"<";case 15:return">";case 16:return t.yytext=t.yytext.substr(1,t.yyleng-2),24;case 17:return 13;case 18:return 23;case 19:return 5;case 20:return"INVALID"}},rules:[/^(?:\s+)/i,/^(?:(-?(?:[1-9][0-9]+|[0-9]))\b)/i,/^(?:OR\b)/i,/^(?:AND\b)/i,/^(?:NOT\b)/i,/^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\b)/i,/^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\b)/i,/^(?:((SERIAL|SEQUENCE|RESIDX))\b)/i,/^(?:\()/i,/^(?:\))/i,/^(?:,)/i,/^(?::)/i,/^(?:<=)/i,/^(?:>=)/i,/^(?:<)/i,/^(?:>)/i,/^(?:((?:"(?:\\.|[^\\"])*"|'(?:\\.|[^\\'])*')))/i,/^(?:(@[_A-Z0-9]+))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:.)/i],conditions:{INITIAL:{rules:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],inclusive:!0}}};function g(){this.yy={}}return f.lexer=_,g.prototype=f,f.Parser=g,new g}();e.exports={parser:t}},690:function(e,t){ +/*! Miew - 3D Molecular Viewer v0.12.0 Copyright (c) 2015-2026 EPAM Systems, Inc. */ +!function(e,t){"object"==typeof exports&&"object"==typeof module?module.exports=t(require("lodash"),require("three")):"function"==typeof define&&define.amd?define(["lodash","three"],t):"object"==typeof exports?exports.Miew=t(require("lodash"),require("three")):e.Miew=t(e._,e.THREE)}(this,((e,t)=>(()=>{var r={89(e){var t=function(){var e=function(e,t,r,n){for(r=r||{},n=e.length;n--;r[e[n]]=t);return r},t=[1,60],r=[1,62],n=[1,63],s=[1,65],i=[1,66],o=[1,67],a=[1,68],l=[1,69],c=[1,80],h=[1,72],u=[1,73],d=[1,74],p=[1,75],m=[1,99],f=[1,76],_=[1,100],g=[1,79],y=[1,51],x=[1,81],b=[1,82],w=[1,84],S=[1,83],v=[1,85],C=[1,96],A=[1,97],E=[1,98],T=[1,86],R=[1,87],M=[1,64],P=[1,70],L=[1,71],N=[1,77],I=[1,78],O=[1,53],V=[1,54],D=[1,55],k=[1,61],z=[1,88],F=[1,89],B=[1,90],U=[1,91],G=[1,92],j=[1,93],H=[1,94],$=[1,95],W=[1,101],Y=[1,102],X=[1,103],q=[1,104],K=[1,105],Z=[1,56],Q=[1,57],J=[1,58],ee=[1,59],te=[1,115],re=[1,111],ne=[1,114],se=[1,112],ie=[1,113],oe=[1,118],ae=[1,117],le=[1,134],ce=[1,149],he=[1,150],ue=[1,157],de=[5,6,7,9,13,14,15,17,18,19,20,23,25,26,27,30,33,34,35,37,38,41,43,45,46,49,52,54,55,56,58,59,62,64,65,66,70,72,74,77,78,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,101],pe=[5,6,7,9,13,14,15,17,18,19,20,23,25,26,27,30,33,34,35,37,38,41,43,45,46,49,52,54,55,56,58,59,62,64,65,66,70,71,72,74,77,78,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,101],me=[5,6,7,9,13,15,17,18,19,20,23,25,26,27,30,33,34,37,38,41,43,45,46,49,52,54,55,56,58,59,62,64,65,66,70,72,82,83,84,85,86,87,88,89,90,91,92,93,94,95],fe=[5,70,72],_e=[5,74],ge=[71,101],ye={trace:function(){},yy:{},symbols_:{error:2,Program:3,Command:4,EOF:5,RESET:6,BUILD:7,ALL:8,HELP:9,Path:10,MOTM:11,OneArgCommand:12,GET:13,STRING:14,SET:15,Value:16,SET_SAVE:17,SET_RESTORE:18,SET_RESET:19,PRESET:20,AddRepresentation:21,EditRepresentation:22,REMOVE:23,RepresentationReference:24,HIDE:25,SHOW:26,LIST:27,EXPAND_KEY:28,SELECTOR_KEY:29,SELECT:30,AS:31,WordAll:32,SELECTOR:33,WITHIN:34,NUMBER:35,OF:36,MATERIAL:37,IDENTIFIER:38,ModeCMD:39,ColorCMD:40,VIEW:41,BASE_64:42,UNIT:43,DSSP:44,SCALE:45,ROTATE:46,AxesList:47,TRANSLATE:48,CENTER:49,GetURLBranch:50,Screenshot:51,LINE:52,ArgList:53,LISTOBJ:54,REMOVEOBJ:55,URL:56,VIEW_KEY:57,SCREENSHOT:58,LOAD:59,Url:60,FILE_KEY:61,ADD:62,Description:63,REP:64,MODE:65,COLOR:66,Descriptor:67,RepresentationOwnProperty:68,RepresentationOwnPropertyOpts:69,DESC_KEY:70,"=":71,DESC_KEY_OPTS:72,AxesArg:73,DESC_KEY_AXES:74,Arg:75,PathWoDescKey:76,HEX:77,BOOL:78,Word:79,CommandSetWoDESC_KEY:80,DescKeys:81,CLEAR:82,FILE_LIST:83,FILE_REGISTER:84,FILE_DELETE:85,PRESET_ADD:86,PRESET_DELETE:87,PRESET_UPDATE:88,PRESET_RENAME:89,PRESET_OPEN:90,CREATE_SCENARIO:91,RESET_SCENARIO:92,DELETE_SCENARIO:93,ADD_SCENARIO_ITEM:94,LIST_SCENARIO:95,PDB_KEY:96,DELAY_KEY:97,PRST_KEY:98,DESCRIPTION_KEY:99,CommandSet:100,".":101,PresetPath:102,"/":103,HexOrNumber:104,$accept:0,$end:1},terminals_:{2:"error",5:"EOF",6:"RESET",7:"BUILD",8:"ALL",9:"HELP",11:"MOTM",13:"GET",14:"STRING",15:"SET",17:"SET_SAVE",18:"SET_RESTORE",19:"SET_RESET",20:"PRESET",23:"REMOVE",25:"HIDE",26:"SHOW",27:"LIST",28:"EXPAND_KEY",29:"SELECTOR_KEY",30:"SELECT",31:"AS",33:"SELECTOR",34:"WITHIN",35:"NUMBER",36:"OF",37:"MATERIAL",38:"IDENTIFIER",41:"VIEW",42:"BASE_64",43:"UNIT",44:"DSSP",45:"SCALE",46:"ROTATE",48:"TRANSLATE",49:"CENTER",52:"LINE",54:"LISTOBJ",55:"REMOVEOBJ",56:"URL",57:"VIEW_KEY",58:"SCREENSHOT",59:"LOAD",61:"FILE_KEY",62:"ADD",64:"REP",65:"MODE",66:"COLOR",70:"DESC_KEY",71:"=",72:"DESC_KEY_OPTS",74:"DESC_KEY_AXES",77:"HEX",78:"BOOL",82:"CLEAR",83:"FILE_LIST",84:"FILE_REGISTER",85:"FILE_DELETE",86:"PRESET_ADD",87:"PRESET_DELETE",88:"PRESET_UPDATE",89:"PRESET_RENAME",90:"PRESET_OPEN",91:"CREATE_SCENARIO",92:"RESET_SCENARIO",93:"DELETE_SCENARIO",94:"ADD_SCENARIO_ITEM",95:"LIST_SCENARIO",96:"PDB_KEY",97:"DELAY_KEY",98:"PRST_KEY",99:"DESCRIPTION_KEY",101:".",103:"/"},productions_:[0,[3,2],[3,1],[4,1],[4,1],[4,2],[4,1],[4,2],[4,1],[4,1],[4,2],[4,2],[4,3],[4,3],[4,1],[4,1],[4,1],[4,1],[4,2],[4,1],[4,1],[4,2],[4,2],[4,2],[4,2],[4,1],[4,2],[4,2],[4,2],[4,4],[4,2],[4,6],[4,2],[4,1],[4,1],[4,1],[4,2],[4,2],[4,1],[4,2],[4,1],[4,2],[4,2],[4,2],[4,1],[4,2],[4,1],[4,1],[4,3],[4,3],[4,4],[4,4],[4,1],[4,2],[50,1],[50,2],[50,2],[50,3],[50,3],[51,1],[51,2],[51,3],[12,2],[12,2],[12,2],[21,1],[21,2],[21,2],[21,3],[22,2],[22,3],[39,2],[39,3],[40,2],[40,3],[24,1],[24,1],[63,1],[63,2],[63,3],[63,4],[67,1],[67,1],[67,2],[68,3],[69,3],[47,1],[47,2],[73,2],[53,1],[53,2],[75,3],[16,1],[16,1],[16,1],[16,1],[16,1],[79,1],[79,1],[32,1],[32,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[80,1],[81,1],[81,1],[81,1],[81,1],[81,1],[81,1],[81,1],[100,1],[100,1],[76,1],[76,3],[76,3],[10,1],[10,1],[10,3],[10,3],[10,3],[60,1],[102,1],[102,3],[104,1],[104,1]],performAction:function(e,t,r,n,s,i,o){var a=i.length-1;switch(s){case 1:return i[a-1];case 3:this.$=n.miew.reset(!1),n.ClearContext(),n.miew.resetReps("empty");break;case 4:this.$=n.miew.rebuild();break;case 5:this.$=n.miew.rebuildAll(),n.miew.rebuild();break;case 6:this.$=n.echo(n.utils.help().toString());break;case 7:this.$=n.echo(n.utils.help(i[a]).toString());break;case 8:this.$=n.miew.motm();break;case 10:case 11:this.$=n.utils.propagateProp(i[a]),n.echo(n.miew.get(i[a]).toString());break;case 12:case 13:this.$=n.miew.set(i[a-1],n.utils.propagateProp(i[a-1],i[a]));break;case 14:this.$=n.miew.saveSettings();break;case 15:this.$=n.miew.restoreSettings();break;case 16:this.$=n.miew.resetSettings();break;case 17:this.$=n.miew.resetReps();break;case 18:this.$=n.miew.applyPreset(i[a]);break;case 21:this.$=n.miew.repRemove(i[a]),n.representations.remove(i[a]);break;case 22:this.$=n.miew.repHide(i[a]);break;case 23:this.$=n.miew.repHide(i[a],!1);break;case 24:this.$=n.echo(n.utils.listRep(n.miew,n.representations,i[a],"-e"));break;case 25:this.$=n.echo(n.utils.list(n.miew,n.representations));break;case 26:this.$=n.echo(n.utils.list(n.miew,n.representations,i[a]));break;case 27:this.$=n.echo(n.utils.listSelector(n.miew,n.Context));break;case 28:this.$=n.miew.select(n.utils.checkArg(i[a-1].toLowerCase(),i[a],!0));break;case 29:this.$=n.Context[i[a].toLowerCase()]=n.utils.checkArg(i[a-3].toLowerCase(),i[a-2],!0),n.miew.select(n.Context[i[a].toLowerCase()]);break;case 30:this.$=n.miew.rep(n.miew.repCurrent(),{selector:n.utils.checkArg(i[a-1].toLowerCase(),i[a])});break;case 31:this.$=n.Context[i[a].toLowerCase()]=n.miew.within(n.utils.checkArg("select",i[a-2],!0),Number(i[a-4]));break;case 32:this.$=n.miew.rep(n.miew.repCurrent(),{material:n.utils.checkArg(i[a-1].toLowerCase(),i[a].toUpperCase())});break;case 35:this.$=n.echo(n.miew.view());break;case 36:case 37:this.$=n.miew.view(i[a]);break;case 38:this.$=n.echo(n.miew.changeUnit());break;case 39:this.$=n.echo(n.miew.changeUnit(i[a]));break;case 40:this.$=n.miew.dssp();break;case 41:this.$=n.miew.scale(i[a]);break;case 42:for(var l=0,c=i[a].length;l2&&A.push("'"+this.terminals_[S]+"'");R=d.showPosition?"Parse error on line "+(l+1)+":\n"+d.showPosition()+"\nExpecting "+A.join(", ")+", got '"+(this.terminals_[g]||g)+"'":"Parse error on line "+(l+1)+": Unexpected "+(1==g?"end of input":"'"+(this.terminals_[g]||g)+"'"),this.parseError(R,{text:d.match,token:this.terminals_[g]||g,line:d.yylineno,loc:f,expected:A})}if(b[0]instanceof Array&&b.length>1)throw new Error("Parse Error: multiple actions possible at state: "+x+", token: "+g);switch(b[0]){case 1:r.push(g),s.push(d.yytext),i.push(d.yylloc),r.push(b[1]),g=null,y?(g=y,y=null):(c=d.yyleng,a=d.yytext,l=d.yylineno,f=d.yylloc,h>0&&h--);break;case 2:if(v=this.productions_[b[1]][1],T.$=s[s.length-v],T._$={first_line:i[i.length-(v||1)].first_line,last_line:i[i.length-1].last_line,first_column:i[i.length-(v||1)].first_column,last_column:i[i.length-1].last_column},_&&(T._$.range=[i[i.length-(v||1)].range[0],i[i.length-1].range[1]]),void 0!==(w=this.performAction.apply(T,[a,c,l,p.yy,b[1],s,i].concat(u))))return w;v&&(r=r.slice(0,-1*v*2),s=s.slice(0,-1*v),i=i.slice(0,-1*v)),r.push(this.productions_[b[1]][0]),s.push(T.$),i.push(T._$),C=o[r[r.length-2]][r[r.length-1]],r.push(C);break;case 3:return!0}}return!0}},xe={EOF:1,parseError:function(e,t){if(!this.yy.parser)throw new Error(e);this.yy.parser.parseError(e,t)},setInput:function(e,t){return this.yy=t||this.yy||{},this._input=e,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var e=this._input[0];return this.yytext+=e,this.yyleng++,this.offset++,this.match+=e,this.matched+=e,e.match(/(?:\r\n?|\n).*/g)?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),e},unput:function(e){var t=e.length,r=e.split(/(?:\r\n?|\n)/g);this._input=e+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-t),this.offset-=t;var n=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),r.length-1&&(this.yylineno-=r.length-1);var s=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:r?(r.length===n.length?this.yylloc.first_column:0)+n[n.length-r.length].length-r[0].length:this.yylloc.first_column-t},this.options.ranges&&(this.yylloc.range=[s[0],s[0]+this.yyleng-t]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){return this.options.backtrack_lexer?(this._backtrack=!0,this):this.parseError("Lexical error on line "+(this.yylineno+1)+". You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},less:function(e){this.unput(this.match.slice(e))},pastInput:function(){var e=this.matched.substr(0,this.matched.length-this.match.length);return(e.length>20?"...":"")+e.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var e=this.match;return e.length<20&&(e+=this._input.substr(0,20-e.length)),(e.substr(0,20)+(e.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var e=this.pastInput(),t=new Array(e.length+1).join("-");return e+this.upcomingInput()+"\n"+t+"^"},test_match:function(e,t){var r,n,s;if(this.options.backtrack_lexer&&(s={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(s.yylloc.range=this.yylloc.range.slice(0))),(n=e[0].match(/(?:\r\n?|\n).*/g))&&(this.yylineno+=n.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:n?n[n.length-1].length-n[n.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+e[0].length},this.yytext+=e[0],this.match+=e[0],this.matches=e,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(e[0].length),this.matched+=e[0],r=this.performAction.call(this,this.yy,this,t,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),r)return r;if(this._backtrack){for(var i in s)this[i]=s[i];return!1}return!1},next:function(){if(this.done)return this.EOF;var e,t,r,n;this._input||(this.done=!0),this._more||(this.yytext="",this.match="");for(var s=this._currentRules(),i=0;it[0].length)){if(t=r,n=i,this.options.backtrack_lexer){if(!1!==(e=this.test_match(r,s[i])))return e;if(this._backtrack){t=!1;continue}return!1}if(!this.options.flex)break}return t?!1!==(e=this.test_match(t,s[n]))&&e:""===this._input?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+". Unrecognized text.\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var e=this.next();return e||this.lex()},begin:function(e){this.conditionStack.push(e)},popState:function(){return this.conditionStack.length-1>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(e){return(e=this.conditionStack.length-1-Math.abs(e||0))>=0?this.conditionStack[e]:"INITIAL"},pushState:function(e){this.begin(e)},stateStackSize:function(){return this.conditionStack.length},options:{"case-insensitive":!0},performAction:function(e,t,r,n){switch(r){case 0:break;case 1:case 2:return"";case 3:return 42;case 4:return 35;case 5:return 77;case 6:case 7:return 78;case 8:return 8;case 9:return 6;case 10:return 82;case 11:return 7;case 12:return 9;case 13:return 59;case 14:return 13;case 15:return 15;case 16:return 17;case 17:return 18;case 18:return 19;case 19:return 20;case 20:return 11;case 21:return 62;case 22:return 64;case 23:return 23;case 24:return 25;case 25:return 26;case 26:return 27;case 27:return 30;case 28:return 34;case 29:return 33;case 30:return 65;case 31:return 66;case 32:return 37;case 33:return 41;case 34:return 43;case 35:return 52;case 36:return 54;case 37:return 55;case 38:return 46;case 39:return 48;case 40:return 45;case 41:return 49;case 42:return 56;case 43:return 58;case 44:return 44;case 45:return 83;case 46:return 84;case 47:return 85;case 48:return 86;case 49:return 87;case 50:return 88;case 51:return 89;case 52:return 90;case 53:return 91;case 54:return 92;case 55:return 93;case 56:return 94;case 57:return 95;case 58:case 59:return 70;case 60:case 61:return 72;case 62:case 63:case 64:return 74;case 65:return 31;case 66:return 36;case 67:return 96;case 68:return 97;case 69:return 98;case 70:return 99;case 71:return t.yytext=e.utils.unquoteString(t.yytext),14;case 72:return 38;case 73:return 5;case 74:return 101;case 75:return 103;case 76:return"\\";case 77:return 28;case 78:return 61;case 79:return 29;case 80:return 57;case 81:return 71}},rules:[/^(?:\s+)/i,/^(?:[#].*)/i,/^(?:\/\/.*)/i,/^(?:([_A-Z0-9\/\+]+==))/i,/^(?:-?[0-9]+(\.[0-9]+)?\b)/i,/^(?:0[xX][0-9A-F]+\b)/i,/^(?:false\b)/i,/^(?:true\b)/i,/^(?:all\b)/i,/^(?:reset\b)/i,/^(?:clear\b)/i,/^(?:build\b)/i,/^(?:help\b)/i,/^(?:load\b)/i,/^(?:get\b)/i,/^(?:set\b)/i,/^(?:set_save\b)/i,/^(?:set_restore\b)/i,/^(?:set_reset\b)/i,/^(?:preset\b)/i,/^(?:motm\b)/i,/^(?:add\b)/i,/^(?:rep\b)/i,/^(?:remove\b)/i,/^(?:hide\b)/i,/^(?:show\b)/i,/^(?:list\b)/i,/^(?:select\b)/i,/^(?:within\b)/i,/^(?:selector\b)/i,/^(?:mode\b)/i,/^(?:color\b)/i,/^(?:material\b)/i,/^(?:view\b)/i,/^(?:unit\b)/i,/^(?:line\b)/i,/^(?:listobj\b)/i,/^(?:removeobj\b)/i,/^(?:rotate\b)/i,/^(?:translate\b)/i,/^(?:scale\b)/i,/^(?:center\b)/i,/^(?:url\b)/i,/^(?:screenshot\b)/i,/^(?:dssp\b)/i,/^(?:file_list\b)/i,/^(?:file_register\b)/i,/^(?:file_delete\b)/i,/^(?:preset_add\b)/i,/^(?:preset_delete\b)/i,/^(?:preset_update\b)/i,/^(?:preset_rename\b)/i,/^(?:preset_open\b)/i,/^(?:create_scenario\b)/i,/^(?:reset_scenario\b)/i,/^(?:delete_scenario\b)/i,/^(?:add_scenario_item\b)/i,/^(?:list_scenario\b)/i,/^(?:s\b)/i,/^(?:mt\b)/i,/^(?:m\b)/i,/^(?:c\b)/i,/^(?:x\b)/i,/^(?:y\b)/i,/^(?:z\b)/i,/^(?:as\b)/i,/^(?:of\b)/i,/^(?:pdb\b)/i,/^(?:delay\b)/i,/^(?:prst\b)/i,/^(?:desc\b)/i,/^(?:((?:"(?:\\.|[^\\"])*"|'(?:\\.|[^\\'])*')))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:\.)/i,/^(?:\/)/i,/^(?:\\)/i,/^(?:-e\b)/i,/^(?:-f\b)/i,/^(?:-s\b)/i,/^(?:-v\b)/i,/^(?:=)/i],conditions:{INITIAL:{rules:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],inclusive:!0}}};function be(){this.yy={}}return ye.lexer=xe,be.prototype=ye,ye.Parser=be,new be}();e.exports={parser:t}},99(e){var t=function(){var e=function(e,t,r,n){for(r=r||{},n=e.length;n--;r[e[n]]=t);return r},t=[1,4],r=[1,5],n=[1,6],s=[1,7],i=[1,8],o=[1,9],a=[1,11],l=[1,12],c=[5,7,8,11],h=[1,17],u=[1,22],d=[1,20],p=[1,21],m=[5,7,8,11,19],f={trace:function(){},yy:{},symbols_:{error:2,Program:3,Expression:4,EOF:5,Selector:6,OR:7,AND:8,NOT:9,"(":10,")":11,SELECTOR:12,NAMED_SELECTOR:13,SELECTOR_RANGED:14,RangeList:15,SELECTOR_NAMED:16,NameList:17,Range:18,",":19,NUMBER:20,":":21,Name:22,IDENTIFIER:23,STRING:24,$accept:0,$end:1},terminals_:{2:"error",5:"EOF",7:"OR",8:"AND",9:"NOT",10:"(",11:")",12:"SELECTOR",13:"NAMED_SELECTOR",14:"SELECTOR_RANGED",16:"SELECTOR_NAMED",19:",",20:"NUMBER",21:":",23:"IDENTIFIER",24:"STRING"},productions_:[0,[3,2],[4,1],[4,3],[4,3],[4,2],[4,3],[6,1],[6,1],[6,2],[6,2],[15,1],[15,3],[18,1],[18,3],[17,1],[17,3],[22,1],[22,1],[22,1]],performAction:function(e,t,r,n,s,i,o){var a=i.length-1;switch(s){case 1:return i[a-1];case 3:this.$=n.keyword("or")(i[a-2],i[a]);break;case 4:this.$=n.keyword("and")(i[a-2],i[a]);break;case 5:this.$=n.keyword("not")(i[a]);break;case 6:this.$=i[a-1];break;case 7:this.$=n.keyword(i[a])();break;case 8:this.$=n.GetSelector(i[a].toLowerCase().slice(1,i[a].length));break;case 9:case 10:this.$=n.keyword(i[a-1])(i[a]);break;case 11:this.$=new n.RangeList(i[a]);break;case 12:case 16:this.$=i[a-2].append(i[a]);break;case 13:this.$=new n.Range(Number(i[a]));break;case 14:this.$=new n.Range(Number(i[a-2]),Number(i[a]));break;case 15:this.$=new n.ValueList(i[a])}},table:[{3:1,4:2,6:3,9:t,10:r,12:n,13:s,14:i,16:o},{1:[3]},{5:[1,10],7:a,8:l},e(c,[2,2]),{4:13,6:3,9:t,10:r,12:n,13:s,14:i,16:o},{4:14,6:3,9:t,10:r,12:n,13:s,14:i,16:o},e(c,[2,7]),e(c,[2,8]),{15:15,18:16,20:h},{17:18,20:u,22:19,23:d,24:p},{1:[2,1]},{4:23,6:3,9:t,10:r,12:n,13:s,14:i,16:o},{4:24,6:3,9:t,10:r,12:n,13:s,14:i,16:o},e(c,[2,5]),{7:a,8:l,11:[1,25]},e(c,[2,9],{19:[1,26]}),e(m,[2,11]),e(m,[2,13],{21:[1,27]}),e(c,[2,10],{19:[1,28]}),e(m,[2,15]),e(m,[2,17]),e(m,[2,18]),e(m,[2,19]),e([5,7,11],[2,3],{8:l}),e(c,[2,4]),e(c,[2,6]),{18:29,20:h},{20:[1,30]},{20:u,22:31,23:d,24:p},e(m,[2,12]),e(m,[2,14]),e(m,[2,16])],defaultActions:{10:[2,1]},parseError:function(e,t){if(!t.recoverable){var r=new Error(e);throw r.hash=t,r}this.trace(e)},parse:function(e){var t=this,r=[0],n=[],s=[null],i=[],o=this.table,a="",l=0,c=0,h=0,u=i.slice.call(arguments,1),d=Object.create(this.lexer),p={yy:{}};for(var m in this.yy)Object.prototype.hasOwnProperty.call(this.yy,m)&&(p.yy[m]=this.yy[m]);d.setInput(e,p.yy),p.yy.lexer=d,p.yy.parser=this,void 0===d.yylloc&&(d.yylloc={});var f=d.yylloc;i.push(f);var _=d.options&&d.options.ranges;"function"==typeof p.yy.parseError?this.parseError=p.yy.parseError:this.parseError=Object.getPrototypeOf(this).parseError;for(var g,y,x,b,w,S,v,C,A,E,T={};;){if(x=r[r.length-1],this.defaultActions[x]?b=this.defaultActions[x]:(null==g&&(E=void 0,"number"!=typeof(E=n.pop()||d.lex()||1)&&(E instanceof Array&&(E=(n=E).pop()),E=t.symbols_[E]||E),g=E),b=o[x]&&o[x][g]),void 0===b||!b.length||!b[0]){var R="";for(S in A=[],o[x])this.terminals_[S]&&S>2&&A.push("'"+this.terminals_[S]+"'");R=d.showPosition?"Parse error on line "+(l+1)+":\n"+d.showPosition()+"\nExpecting "+A.join(", ")+", got '"+(this.terminals_[g]||g)+"'":"Parse error on line "+(l+1)+": Unexpected "+(1==g?"end of input":"'"+(this.terminals_[g]||g)+"'"),this.parseError(R,{text:d.match,token:this.terminals_[g]||g,line:d.yylineno,loc:f,expected:A})}if(b[0]instanceof Array&&b.length>1)throw new Error("Parse Error: multiple actions possible at state: "+x+", token: "+g);switch(b[0]){case 1:r.push(g),s.push(d.yytext),i.push(d.yylloc),r.push(b[1]),g=null,y?(g=y,y=null):(c=d.yyleng,a=d.yytext,l=d.yylineno,f=d.yylloc,h>0&&h--);break;case 2:if(v=this.productions_[b[1]][1],T.$=s[s.length-v],T._$={first_line:i[i.length-(v||1)].first_line,last_line:i[i.length-1].last_line,first_column:i[i.length-(v||1)].first_column,last_column:i[i.length-1].last_column},_&&(T._$.range=[i[i.length-(v||1)].range[0],i[i.length-1].range[1]]),void 0!==(w=this.performAction.apply(T,[a,c,l,p.yy,b[1],s,i].concat(u))))return w;v&&(r=r.slice(0,-1*v*2),s=s.slice(0,-1*v),i=i.slice(0,-1*v)),r.push(this.productions_[b[1]][0]),s.push(T.$),i.push(T._$),C=o[r[r.length-2]][r[r.length-1]],r.push(C);break;case 3:return!0}}return!0}},_={EOF:1,parseError:function(e,t){if(!this.yy.parser)throw new Error(e);this.yy.parser.parseError(e,t)},setInput:function(e,t){return this.yy=t||this.yy||{},this._input=e,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var e=this._input[0];return this.yytext+=e,this.yyleng++,this.offset++,this.match+=e,this.matched+=e,e.match(/(?:\r\n?|\n).*/g)?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),e},unput:function(e){var t=e.length,r=e.split(/(?:\r\n?|\n)/g);this._input=e+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-t),this.offset-=t;var n=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),r.length-1&&(this.yylineno-=r.length-1);var s=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:r?(r.length===n.length?this.yylloc.first_column:0)+n[n.length-r.length].length-r[0].length:this.yylloc.first_column-t},this.options.ranges&&(this.yylloc.range=[s[0],s[0]+this.yyleng-t]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){return this.options.backtrack_lexer?(this._backtrack=!0,this):this.parseError("Lexical error on line "+(this.yylineno+1)+". You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},less:function(e){this.unput(this.match.slice(e))},pastInput:function(){var e=this.matched.substr(0,this.matched.length-this.match.length);return(e.length>20?"...":"")+e.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var e=this.match;return e.length<20&&(e+=this._input.substr(0,20-e.length)),(e.substr(0,20)+(e.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var e=this.pastInput(),t=new Array(e.length+1).join("-");return e+this.upcomingInput()+"\n"+t+"^"},test_match:function(e,t){var r,n,s;if(this.options.backtrack_lexer&&(s={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(s.yylloc.range=this.yylloc.range.slice(0))),(n=e[0].match(/(?:\r\n?|\n).*/g))&&(this.yylineno+=n.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:n?n[n.length-1].length-n[n.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+e[0].length},this.yytext+=e[0],this.match+=e[0],this.matches=e,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(e[0].length),this.matched+=e[0],r=this.performAction.call(this,this.yy,this,t,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),r)return r;if(this._backtrack){for(var i in s)this[i]=s[i];return!1}return!1},next:function(){if(this.done)return this.EOF;var e,t,r,n;this._input||(this.done=!0),this._more||(this.yytext="",this.match="");for(var s=this._currentRules(),i=0;it[0].length)){if(t=r,n=i,this.options.backtrack_lexer){if(!1!==(e=this.test_match(r,s[i])))return e;if(this._backtrack){t=!1;continue}return!1}if(!this.options.flex)break}return t?!1!==(e=this.test_match(t,s[n]))&&e:""===this._input?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+". 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ue(79,"AU","Gold",196.97,1.66,1.5,[0]),new ue(80,"HG","Mercury",200.59,1.55,1.7,[0]),new ue(81,"TL","Thallium",204.38,1.96,1.55,[1,3]),new ue(82,"PB","Lead",207.2,2.02,1.54,[2,4]),new ue(83,"BI","Bismuth",208.98,1.7,1.54,[3,5]),new ue(84,"PO","Polonium",210,1.7,1.68,[2,4,6]),new ue(85,"AT","Astatine",210,1.7,1.7,[1,3,5,7]),new ue(86,"RN","Radon",222,1.7,2.4,[0]),new ue(87,"FR","Francium",223,1.7,2,[1]),new ue(88,"RA","Radium",226.03,1.7,1.9,[2]),new ue(89,"AC","Actinium",227.03,1.7,1.88,[0]),new ue(90,"TH","Thorium",232.04,1.7,1.79,[0]),new ue(91,"PA","Protactinium",231.04,1.7,1.61,[0]),new ue(92,"U","Uranium",238.03,1.86,1.58,[0]),new ue(93,"NP","Neptunium",237.05,1.7,1.55,[0]),new ue(94,"PU","Plutonium",239.1,1.7,1.53,[0]),new ue(95,"AM","Americium",243.1,1.7,1.51,[0]),new ue(96,"CM","Curium",247.1,1.7,1.5,[0]),new ue(97,"BK","Berkelium",247.1,1.7,1.5,[0]),new ue(98,"CF","Californium",252.1,1.7,1.5,[0]),new ue(99,"ES","Einsteinium",252.1,1.7,1.5,[0]),new ue(100,"FM","Fermium",257.1,1.7,1.5,[0]),new ue(101,"MD","Mendelevium",256.1,1.7,1.5,[0]),new ue(102,"NO","Nobelium",259.1,1.7,1.5,[0]),new ue(103,"LR","Lawrencium",260.1,1.7,1.5,[0]),new ue(104,"RF","Rutherfordium",261,1.7,1.6,[0]),new ue(105,"DB","Dubnium",262,1.7,1.6,[0]),new ue(106,"SG","Seaborgium",263,1.7,1.6,[0]),new ue(107,"BH","Bohrium",262,1.7,1.6,[0]),new ue(108,"HS","Hassium",265,1.7,1.6,[0]),new ue(109,"MT","Meitnerium",268,1.7,1.6,[0])])();static ByName=(()=>({D:new ue(1,"D","Deuterium",2.014,1.2,.23,[1]),T:new ue(1,"T","Tritium",3.016,1.2,.23,[1])}))()}!function(){const e=ue.ByAtomicNumber,t=ue.ByName;for(let r=0,n=e.length;rt)throw new Error("In a bond atom indices must be in increasing order");this._order=r,this._type=n}getLeft(){return this._left}getRight(){return this._right}getOrder(){return this._order}calcLength(){return this._left.position.distanceTo(this._right.position)}_forEachNeighbour(e,t){const{bonds:r}=e;for(let n=0,s=r.length;n{t!==r&&e(t)})),this._forEachNeighbour(r,(r=>{r!==t&&e(r)}))}forEachLevelTwo(e){const t=this._left,r=this._right,n=this;n._forEachNeighbour(t,(s=>{s!==r&&n._forEachNeighbour(s,(r=>{r!==t&&e(r)}))})),n._forEachNeighbour(r,(s=>{s!==t&&n._forEachNeighbour(s,(t=>{t!==r&&e(t)}))}))}_fixDir(e,t,r){let n=0,s=0;const i=e.clone();function o(o){i.copy(r(o)),i.sub(e);t.dot(i)>0?++n:++s}function a(e){"C"===e.element.name&&o(e)}const l=[[this.forEachLevelOne,a],[this.forEachLevelOne,o],[this.forEachLevelTwo,a],[this.forEachLevelTwo,o]];for(let e=0;en)return t.multiplyScalar(-1);if(sr.bonds.length&&(n=r,s=t);let i=n,o=0;const{bonds:a}=s;for(let e=0,t=a.length;eo&&t!==n&&(i=t,o=t.bonds.length)}const l=e(s),c=e(n).clone().sub(l),h=e(i).clone().sub(l);return h.crossVectors(c,h),h.lengthSq()<1e-4&&h.set(0,1,0),c.normalize(),h.normalize(),c.crossVectors(h,c),c.lengthSq()<1e-4&&c.set(0,1,0),c.normalize(),this._fixDir(l,c,e)}static BondType=(()=>pe)()}fe.prototype.BondType=pe;const _e=fe,ge=["C3'","C3*","P","H5T","H3T"],ye=["OP1","O1P"],xe=["OP2","O2P"],be=["C3'","C3*","C1","C1'","C1*","P"],we=[{types:["A","DA","G","DG"],atoms:["N1"]},{types:["C","DC"],atoms:["N3"]},{types:["T","DT","U","DU"],atoms:["O4"]}];const Se=class{constructor(e,t,r,n){this._chain=e,this._component=null,this._type=t,this._sequence=r,this._icode=n,this._mask=1,this._index=-1,this._atoms=[],this._secondary=null,this._firstAtom=null,this._leadAtom=null,this._wingAtom=null,this._lastAtom=null,this._controlPoint=null,this._midPoint=null,this._wingVector=null,this._cylinders=null,this._isValid=!0,this._het=!1,this._molecule=null,this.temperature=null,this.occupancy=null}getChain(){return this._chain}getMolecule(){return this._molecule}getType(){return this._type}getSequence(){return this._sequence}getSecondary(){return this._secondary}getICode(){return this._icode}addAtom(e,t,r,n,s,i,o,a,l,c){const h=new he(this,e,t,r,n,s,i,o,a,l,c);return this._chain.getComplex().addAtom(h),this._atoms.push(h),this._het=this._het||s,h}getAtomCount(){return this._atoms.length}forEachAtom(e){const t=this._atoms;for(let r=0,n=t.length;rr.name===e&&(t=r,!0))),t}_findFirstAtomInList(e){let t=null;for(let r=0;r1e-4){i.length()>1e-4&&Math.abs(n.angleTo(i))>Math.PI/2&&i.negate()}return i}_innerFinalize(e,t,n,s,i,o){const a=null===t,l=o(this._leadAtom),c=new r.Vector3(l.x,l.y,l.z);if(i)this._detectLeadWing(s,n,o);else{if(a)s._midPoint=o(this._firstAtom).clone();else{const r=t._controlPoint;s._midPoint=r.clone().lerp(c,.5),s._wingVector=this.calcWing(r,c,o(e._wingAtom),t._wingVector)}s._controlPoint=c}}_finalize2(e,t,r){this._innerFinalize(e,e,t,this,r,(e=>e.position))}isConnected(e){if(this._chain!==e._chain)return!1;if(this===e)return!0;let t=!1;return this.forEachAtom((r=>{const{bonds:n}=r;for(let r=0,s=n.length;r(null===e._leadAtom&&i.role===de.Constants.Lead&&(e._leadAtom=i),null===e._wingAtom&&i.role===de.Constants.Wing&&(e._wingAtom=i),i.temperature&&(r+=i.temperature,t++),i.occupancy&&(s+=i.occupancy,n++),null!==e._leadAtom&&null!==e._wingAtom))),t>0&&(this.temperature=r/t),n>0&&(this.occupancy=s/n),null!==this._leadAtom&&null!==this._wingAtom||(this._isValid=!1),null===this._leadAtom&&(this._leadAtom=this._firstAtom),null===this._wingAtom&&(this._wingAtom=this._lastAtom)}};class ve{constructor(e,t,r){this._name=e,this._fullName=t,this.letterCode=r,this.flags=0}getName(){return this._name}static StandardTypes=(()=>({ALA:new ve("ALA","Alanine","A"),ARG:new ve("ARG","Arginine","R"),ASN:new ve("ASN","Asparagine","N"),ASP:new ve("ASP","Aspartic Acid","D"),CYS:new ve("CYS","Cysteine","C"),GLN:new ve("GLN","Glutamine","Q"),GLU:new ve("GLU","Glutamic Acid","E"),GLY:new ve("GLY","Glycine","G"),HIS:new ve("HIS","Histidine","H"),ILE:new ve("ILE","Isoleucine","I"),LEU:new ve("LEU","Leucine","L"),LYS:new ve("LYS","Lysine","K"),MET:new ve("MET","Methionine","M"),PHE:new ve("PHE","Phenylalanine","F"),PRO:new ve("PRO","Proline","P"),PYL:new ve("PYL","Pyrrolysine","O"),SEC:new ve("SEC","Selenocysteine","U"),SER:new ve("SER","Serine","S"),THR:new ve("THR","Threonine","T"),TRP:new ve("TRP","Tryptophan","W"),TYR:new ve("TYR","Tyrosine","Y"),VAL:new ve("VAL","Valine","V"),A:new ve("A","Adenine","A"),C:new ve("C","Cytosine","C"),G:new ve("G","Guanine","G"),I:new ve("I","Inosine","I"),T:new ve("T","Thymine","T"),U:new ve("U","Uracil","U"),DA:new ve("DA","Adenine","A"),DC:new ve("DC","Cytosine","C"),DG:new ve("DG","Guanine","G"),DI:new ve("DI","Inosine","I"),DT:new ve("DT","Thymine","T"),DU:new ve("DU","Uracil","U"),"+A":new ve("+A","Adenine","A"),"+C":new ve("+C","Cytosine","C"),"+G":new ve("+G","Guanine","G"),"+I":new ve("+I","Inosine","I"),"+T":new ve("+T","Thymine","T"),"+U":new ve("+U","Uracil","U"),WAT:new ve("WAT","Water",""),H2O:new ve("H2O","Water",""),HOH:new ve("HOH","Water",""),DOD:new ve("DOD","Water",""),UNK:new ve("UNK","Unknown",""),UNL:new ve("UNL","Unknown Ligand","")}))();static Flags={PROTEIN:1,BASIC:2,ACIDIC:4,POLAR:8,NONPOLAR:16,AROMATIC:32,NUCLEIC:256,PURINE:512,PYRIMIDINE:1024,DNA:2048,RNA:4096,WATER:65536}}function Ce(e,t){for(let r=0,n=t.length;r1&&e[1]._wingVector){const t=e[1]._wingVector;e[0]._wingVector=new r.Vector3(t.x,t.y,t.z)}else e.length>0&&(e[0]._wingVector=new r.Vector3(1,0,0))}updateToFrame(e){const t=this._residues;let n=null,s=null;const i=e._residues,o=t.length;function a(t){return e.getAtomPos(t.index)}for(let e=0;e1?i[t[1]._index]._wingVector:new r.Vector3(1,0,0)}addResidue(e,t,r){let n=this._complex.getResidueType(e);null===n&&(n=this._complex.addResidueType(e));const s=new Se(this,n,t,r);return this._complex.addResidue(s),this._residues.push(s),n.flags&(Ee.Flags.NUCLEIC|Ee.Flags.PROTEIN)&&(this.maxSequencet&&(this.minSequence=t)),s}getResidueCount(){return this._residues.length}forEachResidue(e){const t=this._residues;for(let r=0,n=t.length;r=0&&t.splice(r,1),this}toString(){return this._values.join(",")}toJSON(){const e=this._values,t=[];for(let r=0,n=e.length;rthis.priority?`(${this.rhs})`:this.rhs;return`${this.keyword} ${e}`}toJSON(){return[this.name,this.rhs.toJSON()]}}Je.prototype.priority=1;class et extends We{constructor(e,t){super(),this.lhs=e||Qe,this.rhs=t||Qe}toString(){const e=this.lhs.priority&&this.lhs.priority>this.priority?`(${this.lhs})`:this.lhs,t=this.rhs.priority&&this.rhs.priority>this.priority?`(${this.rhs})`:this.rhs;return`${e} ${this.keyword} ${t}`}toJSON(){return[this.name,this.lhs.toJSON(),this.rhs.toJSON()]}}et.prototype.priority=1e3;const tt={};function rt(e,t){const r=e.toLowerCase();t.prototype.keyword=r,t.prototype.name=e;const n=function(){for(var e=arguments.length,r=new Array(e),n=0;n{delete ot.Context[e]}))},ot.keyword=function(e){return tt[e.toLowerCase()]||tt.none},ot.parse=function(e){const t={};try{t.selector=Ue.parser.parse(e)}catch(e){t.selector=nt,t.error=e.message}return t},Ue.parser.yy=ot,Ue.parser.yy.parseError=Ue.parser.parseError;const at=ot;const lt=class{constructor(e){this._complex=e,this._selector=at.keyword("All")(),this._boundaries={boundingBox:new r.Box3,boundingSphere:new r.Sphere}}computeBoundaries(){const e=this._complex._atoms,t=e.length,n=this._selector,{boundingBox:s}=this._boundaries;if(s.makeEmpty(),1===t){s.expandByPoint(e[0].position);const t=new r.Vector3;s.getCenter(t);const n=2*e[0].element.radius;s.setFromCenterAndSize(t,new r.Vector3(n,n,n))}else for(let r=0;r0?this._selector=at.keyword("Chain")(this.chains):this._selector=at.keyword("None")()}};const ht=class{constructor(e){this._complex=e,this._index=-1,this._residueIndices=[],this._cycles=[],this._subDivs=[],this._residueCount=0}getResidues(){return this._complex._residues}getResidueCount(){return this._residueCount}forEachResidue(e){const t=this._complex._residues,r=this._residueIndices;for(let n=0,s=r.length;n{e.update()}))}forEachAtom(e){this.forEachResidue((t=>{t.forEachAtom(e)}))}addCycle(e){this._cycles.push(e)}forEachCycle(e){const t=this._cycles;for(let r=0,n=t.length;r{t._component=e}))}_forEachSubChain(e,t){const r=this._complex._residues,n=this._subDivs;for(let s=0,i=n.length;s{t[r++]={start:n,end:s}})),t}getMaskedSubdivSequences(e){const t=[];let r=-1,n=-1;const s=this._subDivs;return this._forEachSubChain(e,((e,i,o)=>{n!==e&&(++r,t[r]={arr:[],boundaries:s[e]},n=e),t[r].arr[t[r].arr.length]={start:i,end:o}})),t}};const ut=class{constructor(e){this.numPairs=0,this.numMaxPairs=e,this.intBuffer=O.allocateTyped(Int32Array,4*e);for(let t=0;t<4*e;t++)this.intBuffer[t]=-1;this.hashBuffer=O.allocateTyped(Int32Array,33554432);for(let e=0;e<33554432;e++)this.hashBuffer[e]=-1}destroy(){this.intBuffer=null,this.hashBuffer=null}addPair(e,t){const r=et?e:t,s=r+(n<<14);let i=32*(r+89237*n&1048575),o=0;for(;o<32;o++){const e=this.hashBuffer[i+o];if(-1===e)break;if(e===s)return!1}if(o>=32)throw new Error("addPair: increase cMaxPairsForHashCode");if(this.hashBuffer[i+o]=s,this.numPairs>=this.numMaxPairs)throw new Error("addPair: increase num pairs");return i=4*this.numPairs,this.intBuffer[i]=r,this.intBuffer[i+1]=n,this.intBuffer[i+2]=s,this.numPairs++,!0}};function dt(e){const{element:t}=e;if(t)return t.radiusBonding;throw new Error("_getBondingRadius: Logic error.")}const pt=class{constructor(e){this._complex=e,this._maxRad=1.8;const t=this._complex.getDefaultBoundaries().boundingBox;this._vBoxMin=t.min.clone(),this._vBoxMax=t.max.clone(),this._pairCollection=null}_addExistingPairs(){const e=this._complex.getAtoms(),t=e.length;let r=0;const n=this._pairCollection;for(;rh*h||r<.001||n._pairCollection.addPair(l.index,e.index)};for(let n=0;n.1)&&e.dot(t)>=0}}();function gt(e,t){let r=0;for(;r3}function Ct(e){return!0}const At=class{constructor(e){this._complex=e;const t=new Array(e._bonds.length),r=new Array(e._bonds.length);for(let e=0,n=t.length;es[l]?++l:++a}return!1}_tryBond(e,t,n){const s=[],i=this._bondsData,o=yt(e,t),a=t.position.clone().sub(o.position),l=this._currStart,c=this,h=this._bondMarks;let u=this._checkBond;h[e._index]=!0,u=void 0===u?wt:u,t.forEachBond((o=>{if(!u(o)||o===e||h[o._index]||c._haveSameCycle(i,e,o))return;const d=yt(o,t),p=d.position.clone().sub(t.position),m=d===l?-2:1-function(e,t){const n=e.dot(t)/Math.sqrt(e.lengthSq()*t.lengthSq());return r.MathUtils.clamp(n,-1,1)}(a,p),f=p.cross(a);if(!_t(f,n))return;let _=0;for(;_{n._resetCycles(),r.forEachBond((t=>{e(t)&&n._startCycle(t)}));const s=n._cycles;for(let e=0,n=s.length;e=e.z?t:Math.max(o,a),[l,c]}function Tt(e,t,r,n){const s=r-e.y,i=n-e.y,o=Math.sqrt(Math.max(t*t-s*s,0)),a=Math.sqrt(Math.max(t*t-i*i,0)),l=Math.min(o,a);let c;return c=r<=e.y&&n>=e.y?t:Math.max(o,a),[l,c]}class Rt{constructor(e,t){this._box=e.clone();const n=new r.Vector3;e.getSize(n),this._count=n.clone().divide(t).floor().max(new r.Vector3(1,1,1)),this._last=this._count.clone().subScalar(1),this._cellSize=n.clone().divide(this._count),this._cellInnerR=.5*Math.min(Math.min(this._cellSize.x,this._cellSize.y),this._cellSize.z),this._cellOuterR=.5*Math.sqrt(this._cellSize.dot(this._cellSize));const s=this._count.x*this._count.y*this._count.z;this._voxels=O.allocateTyped(Int32Array,s);for(let e=0;e{const n=t._findVoxel(e.position);t._atoms[r]=e,t._atoms[r+1]=t._voxels[n],t._voxels[n]=r,r+=2}))}static _zero=(()=>new r.Vector3(0,0,0))();static _voxel=(()=>new r.Vector3)();_findVoxel(e){const t=Rt._zero,r=Rt._voxel;return r.copy(e).sub(this._box.min).divide(this._cellSize).floor().clamp(t,this._last),r.x+this._count.x*(r.y+this._count.y*r.z)}_forEachAtomInVoxel(e,t){for(let r=this._voxels[e];r>=0;r=this._atoms[r+1])t(this._atoms[r])}static _xRange=(()=>new r.Vector2)();static _yRange=(()=>new r.Vector2)();static _zRange=(()=>new r.Vector2)();_forEachVoxelWithinRadius(e,t,r){const n=Rt._xRange,s=Rt._yRange,i=Rt._zRange;if(t/this._cellInnerR<10)return void this._forEachVoxelWithinRadiusSimple(e,t,r);let o,a,l,c,h,u,d,p;i.set(e.z-t,e.z+t),i.subScalar(this._box.min.z).divideScalar(this._cellSize.z).floor().clampScalar(0,this._count.z-1);for(let m=i.x;m<=i.y;++m){h=[this._box.min.z+m*this._cellSize.z,this._box.min.z+(m+1)*this._cellSize.z],p=e.z-t<=h[0]&&h[1]<=e.z+t,o=Et(e,t,h[0],h[1]),s.set(e.y-o[1],e.y+o[1]),s.subScalar(this._box.min.y).divideScalar(this._cellSize.y).floor().clampScalar(0,this._count.y-1);for(let t=s.x;t<=s.y;++t){c=[this._box.min.y+t*this._cellSize.y,this._box.min.y+(t+1)*this._cellSize.y],d=e.y-o[0]<=c[0]&&c[1]<=e.y+o[0],a=Tt(e,o[1],c[0],c[1]),n.set(e.x-a[1],e.x+a[1]),n.subScalar(this._box.min.x).divideScalar(this._cellSize.x).floor().clampScalar(0,this._count.x-1);for(let{x:s}=n;s<=n.y;++s)l=[this._box.min.x+s*this._cellSize.x,this._box.min.x+(s+1)*this._cellSize.x],u=e.x-a[0]<=l[0]&&l[1]<=e.x+a[0],r(s+this._count.x*(t+this._count.y*m),u&&d&&p)}}}static _vCenter=(()=>new r.Vector3)();_forEachVoxelWithinRadiusSimple(e,t,r){const n=Rt._xRange,s=Rt._yRange,i=Rt._zRange,o=Rt._vCenter,a=(t+this._cellOuterR)*(t+this._cellOuterR);let l=-1;t>this._cellOuterR&&(l=(t-this._cellOuterR)*(t-this._cellOuterR)),n.set(e.x-t,e.x+t),n.subScalar(this._box.min.x).divideScalar(this._cellSize.x).floor(),n.x=Math.min(Math.max(n.x,0),this._count.x-1),n.y=Math.min(Math.max(n.y,0),this._count.x-1),s.set(e.y-t,e.y+t),s.subScalar(this._box.min.y).divideScalar(this._cellSize.y).floor(),s.x=Math.min(Math.max(s.x,0),this._count.y-1),s.y=Math.min(Math.max(s.y,0),this._count.y-1),i.set(e.z-t,e.z+t),i.subScalar(this._box.min.z).divideScalar(this._cellSize.z).floor(),i.x=Math.min(Math.max(i.x,0),this._count.z-1),i.y=Math.min(Math.max(i.y,0),this._count.z-1);for(let t=i.x;t<=i.y;++t){const i=[this._box.min.z+t*this._cellSize.z,this._box.min.z+(t+1)*this._cellSize.z];o.z=.5*(i[0]+i[1]);for(let i=s.x;i<=s.y;++i){const s=[this._box.min.y+i*this._cellSize.y,this._box.min.y+(i+1)*this._cellSize.y];o.y=.5*(s[0]+s[1]);for(let{x:s}=n;s<=n.y;++s){const n=[this._box.min.x+s*this._cellSize.x,this._box.min.x+(s+1)*this._cellSize.x];o.x=.5*(n[0]+n[1]);const c=e.distanceToSquared(o);c<=a&&r(s+this._count.x*(i+this._count.y*t),c<=l)}}}}forEachAtomWithinRadius(e,t,r){const n=this,s=t*t;n._forEachVoxelWithinRadius(e,t,((t,i)=>{i?n._forEachAtomInVoxel(t,r):n._forEachAtomInVoxel(t,(t=>{e.distanceToSquared(t.position)<=s&&r(t)}))}))}forEachAtomWithinDistFromMasked(e,t,r,n){this._forEachAtomWithinDistFromGroup((r=>{e.forEachAtom((e=>{0!=(e.mask&t)&&r(e)}))}),r,n)}forEachAtomWithinDistFromSelected(e,t,r,n){this._forEachAtomWithinDistFromGroup((r=>{e.forEachAtom((e=>{t.includesAtom(e)&&r(e)}))}),r,n)}_forEachAtomWithinDistFromGroup(e,t,r){const n=this,s=t*t,i=[],o=[];let a,l=0;e((e=>{n._forEachVoxelWithinRadius(e.position,t,((t,r)=>{r?i[t]=-1:void 0===i[t]?(o.push(e),o.push(-1),i[t]=l,l+=2):-1!==i[t]&&(o.push(e),o.push(i[t]),i[t]=l,l+=2)}))}));const c=function(e){if(void 0!==i[a])if(l=i[a],-1!==l){for(;l>=0;l=o[l+1])if(e.position.distanceToSquared(o[l].position)1e3?this._buildVW():this._build()}isBond(e,t){if(this._hbonds[e]){const[r,n]=this._hbonds[e].acceptor;if(r&&r.residue===t&&r.energy<-.5)return!0;if(n&&n.residue===t&&n.energy<-.5)return!0}return!1}_build(){const e=this;for(let t=0;t0&&this._complex._residues[t-1].getType().flags&Ee.Flags.PROTEIN&&r._sequence===this._complex._residues[t-1]._sequence+1&&(n=this._complex._residues[t-1]);for(let s=t+1;s0?t[o._index-1]:null;!a||0!=(a.getType().flags&Ee.Flags.PROTEIN)&&o._sequence===a._sequence+1||(a=null),e._calcHBondEnergy(n,r,o),o._index!==r._index+1&&e._calcHBondEnergy(a,o,r)}for(let e=0;e0?t[e-1]:null,!n||0!=(n.getType().flags&Ee.Flags.PROTEIN)&&r._sequence===n._sequence+1||(n=null),s.forEachAtomWithinRadius(this._residueGetCAlpha(r),5,o))}_residueGetCAlpha(e){for(let t=0;t{"C"===e.name?t=e.position:"O"===e.name&&(r=e.position)})),[t,r]}_residueGetNH(e,t){const[r,n]=this._residueGetCO(e);let s;if(t.forEachAtom((e=>{"N"===e.name&&(s=e.position)})),r&&n&&s){const e=r.clone();return e.sub(n),e.multiplyScalar(1/e.length()),e.add(s),[s,e]}return[null,null]}_calcHBondEnergy(e,t,r){let n=0;if(null===e)return n;if("PRO"!==t.getType().getName()){const[s,i]=this._residueGetNH(e,t),[o,a]=this._residueGetCO(r);if(null===s||null===i||null===o||null===a)return n;const l=i.distanceTo(a),c=i.distanceTo(o),h=s.distanceTo(o),u=s.distanceTo(a);n=l1&&(n1&&(n70}for(let r=1;r+4=s&&this._isHelixStart(e[r-s]._index,n);t?this._ss[e[r]._index]=Dt.TURN:this._bend[e[r]._index]&&(this._ss[e[r]._index]=Dt.BEND)}}_residueGetCAlpha(e){for(let t=0;t0&&(o=s.dot(i)/Math.sqrt(a)),o}_kappa(e,t,r){const n=this._residueGetCAlpha(t),s=this._residueGetCAlpha(e),i=this._residueGetCAlpha(r);if(null===n||null===s||null===i)return 180;const o=this._cosinusAngle(n,s,i,n),a=Math.sqrt(1-o*o);return 180*Math.atan2(a,o)/Math.PI}_isHelixStart(e,t){return this._helixFlags[t][e]===Vt.START||this._helixFlags[t][e]===Vt.START_AND_END}_buildBetaSheets(){const e=[];for(let t=0;te.chainI=6||s>=a&&n<=l)continue;let u=!1;u=e[t].type===Ot.PARALLEL?c-o<6&&a-s<3||c-o<3:i-h<6&&a-s<3||i-h<3,u&&(e[t].i=e[t].i.concat(e[r].i),e[t].type===Ot.PARALLEL?e[t].j=e[t].j.concat(e[r].j):e[t].j=e[r].j.concat(e[t].j),e.splice(r--,1))}const t=new Set;for(let r=0;r0;){let e=t.values().next().value;t.delete(e);const s=new Set;let i;s.add(e);do{i=new Set;for(const e of s.values())for(const r of t.values())this._areBridgesLinked(e,r)&&i.add(r);for(e of i.values())s.add(e),t.delete(e)}while(i.size>0);for(e of s.values())e.ladder=n,e.sheet=r,e.link=s,++n;++r}for(let t=0;t1&&(i=Dt.STRAND),r.type===Ot.PARALLEL){let e=0;for(let t=0;t{t.updateToFrame(e)}))}addResidueType(e){return this._residueTypes[e]=new Ee(e,"Unknown","")}getResidueCount(){return this._residues.length}getResidues(){return this._residues}getSGroupCount(){return this._sgroups.length}getSGroups(){return this._sgroups}getAtomByFullname(e){const t=e.split(".");if(3!==t.length)return null;const r=t[0],n=parseInt(t[1],10);if(Number.isNaN(n))return null;const s=t[2].toUpperCase();let i=null;return this.forEachChain((e=>{i||0===e._name.localeCompare(r)&&e.forEachResidue((e=>{i||e._sequence===n&&e.forEachAtom((e=>{i||0===s.localeCompare(e.name)&&(i=e)}))}))})),i}addChain(e){const t=new Pe(this,e);return this._chains.push(t),t}getChain(e){for(let t=0,r=this._chains.length;t{const t=e._residues,n=t.length;if(n<1)return;let s=r(),i=t[0]._index;for(let e=0;e=0&&e{e._finalize()})),this.forEachComponent((e=>{e.update()})),this._computeBounds(),this._finalizeBonds(),this.forEachSGroup((e=>{e._rebuildSGroupOnAtomChange()}))}update(){this._maskNeedsUpdate&&(this.updateStructuresMask(),this._maskNeedsUpdate=!1)}_finalizeBonds(){const e=this.getBonds(),t=e.length;for(let r=0;r=0;r--){const e=t[r];null===e._left||null===e._right?t.splice(r,1):(e._left.bonds.push(e),e._right.bonds.push(e))}const s=this._residues;for(r=0,n=s.length;r{e._finalize()}));const{units:i}=this;for(r=0,n=i.length;re.collectMask();this.forEachResidue(e),this.forEachChain(e),this.forEachMolecule(e)}countAtomsByMask(e){let t=0;return this.forEachAtom((r=>{0!=(r.mask&e)&&t++})),t}getNumAtomsBySelector(e){let t=0;return this.forEachAtom((r=>{e.includesAtom(r)&&t++})),t}resetAtomMask(e){this.forEachAtom((t=>{t.mask=e}))}markAtoms(e,t){const r=t,n=~r;let s=0;const i=at.keyword("And")(e,this.getSelector());return this.forEachAtom((e=>{i.includesAtom(e)?(e.mask|=r,s++):e.mask&=n})),this._maskNeedsUpdate=!0,s}markAtomsAdditionally(e,t){const r=t;let n=0;return this.forEachAtom((s=>{e.includesAtom(s)&&(s.mask&t)!==t&&(s.mask|=r,n++)})),n}clearAtomBits(e){const t=~e;this.forEachAtom((e=>{e.mask&=t}));const r=e=>{e._mask&=t};this.forEachAtom(r),this.forEachResidue(r),this.forEachChain(r),this.forEachMolecule(r)}getAtomNames(){if(this.hasOwnProperty("_atomNames"))return this._atomNames;const e={};return this.forEachAtom((t=>{e[t.name]=1})),this._atomNames=Object.keys(e),this._atomNames}getElements(){if(this.hasOwnProperty("_elements"))return this._elements;const e={};return this.forEachAtom((t=>{e[t.element.name]=1})),this._elements=Object.keys(e),this._elements}getResidueNames(){if(this.hasOwnProperty("_residueNames"))return this._residueNames;const e={};return this.forEachResidue((t=>{e[t._type._name]=1})),this._residueNames=Object.keys(e),this._residueNames}getChainNames(){if(this.hasOwnProperty("_chainNames"))return this._chainNames;const e={};return this.forEachChain((t=>{e[t._name]=1})),this._chainNames=Object.keys(e),this._chainNames}getAltLocNames(){if(this.hasOwnProperty("_altlocNames"))return this._altlocNames;const e={};return this.forEachAtom((t=>{e[String.fromCharCode(t.location)]=1})),this._altlocNames=Object.keys(e),this._altlocNames}getVoxelWorld(){if(!this.hasOwnProperty("_voxelWorld"))try{this._voxelWorld=new Mt(this.getDefaultBoundaries().boundingBox,new r.Vector3(5,5,5)),this._voxelWorld.addAtoms(this)}catch(e){w.warn("Unable to create voxel world"),this._voxelWorld=null}return this._voxelWorld}addElement(e,t,r,n){const{length:s}=e;for(let i=0;i{let t=n[e];return t||(t=n[e]=new Fe(String(e),0)),t};let i,o,a=0,l=null;for(let n=0,c=this._residues.length;n!0))}}Gt.prototype.id="Complex",Gt.prototype.name="";const jt=Gt;function Ht(e){let t=2;for(e=e-1>>1;e;)t<<=1,e>>=1;return t}class $t{constructor(e,t,r,n,s,i){switch(this._box=r.clone(),this._dimVec=Math.max(Math.floor(n||1),1),this._volumeInfo=i,t instanceof Array?[this._dimX,this._dimY,this._dimZ]=t:(this._dimX=t.x,this._dimY=t.y,this._dimZ=t.z),this._dimX=Math.max(Math.floor(this._dimX),1),this._dimY=Math.max(Math.floor(this._dimY),1),this._dimZ=Math.max(Math.floor(this._dimZ),1),this._rowElements=this._dimVec*this._dimX,this._planeElements=this._rowElements*this._dimY,this._totalElements=this._planeElements*this._dimZ,this._data=s||O.allocateTyped(e,this._totalElements),this._dimVec){case 1:break;case 2:this.getValue=function(e,t,r){const n=e*this._dimVec+t*this._rowElements+r*this._planeElements;return[this._data[n],this._data[n+1]]},this.setValue=function(e,t,r,n,s){const i=e*this._dimVec+t*this._rowElements+r*this._planeElements;this._data[i]=n,this._data[i+1]=s},this.addValue=function(e,t,r,n,s){const i=e*this._dimVec+t*this._rowElements+r*this._planeElements;this._data[i]+=n,this._data[i+1]+=s};break;case 3:this.getValue=function(e,t,r){const n=e*this._dimVec+t*this._rowElements+r*this._planeElements;return[this._data[n],this._data[n+1],this._data[n+2]]},this.setValue=function(e,t,r,n,s,i){const o=e*this._dimVec+t*this._rowElements+r*this._planeElements;this._data[o]=n,this._data[o+1]=s,this._data[o+2]=i},this.addValue=function(e,t,r,n,s,i){const o=e*this._dimVec+t*this._rowElements+r*this._planeElements;this._data[o]+=n,this._data[o+1]+=s,this._data[o+2]+=i};break;default:throw new Error("Volume: invalid vector dimension")}}getValue(e,t,r){return this._data[e+t*this._rowElements+r*this._planeElements]}setValue(e,t,r,n){this._data[e+t*this._rowElements+r*this._planeElements]=n}addValue(e,t,r,n){this._data[e+t*this._rowElements+r*this._planeElements]+=n}getDimensions(){return[this._dimX,this._dimY,this._dimZ]}getBox(){return this._box}getVolumeInfo(){return this._volumeInfo}getCellSize(){const e=new r.Vector3;this._box.getSize(e);const t=new r.Vector3;return t.x=this._dimX>1?e.x/(this._dimX-1):0,t.y=this._dimY>1?e.y/(this._dimY-1):0,t.z=this._dimZ>1?e.z/(this._dimZ-1):0,t}computeGradient(){if(1!==this._dimVec)return null;const e=new $t(Float32Array,[this._dimX,this._dimY,this._dimZ],this._box,3),t=this.getCellSize(),n=new r.Vector3(-.5/t.x,-.5/t.y,-.5/t.z);function s(e,t,r){return Math.min(r,Math.max(t,e))}const i=this._dimX,o=this._dimY,a=this._dimZ,l=this._data;function c(e,t,r){return l[r*i*o+t*i+e]}for(let t=0;t{null!==t._element.parentNode&&t._element.parentNode.removeChild(t._element)}))}getElement(){return this._element}setTransparency(e){const t=this.getElement();if(null===t)return;if(1===e)return void(t.style.display="none");t.style.display="inline";const r=1-e,n=r.toString(),s=100*r;t.style.opacity=n,t.style.filter=`alpha(opacity=${s})`}clone(){const e=new Xt(this._element);return e.copy(this),e}}const qt=Xt;class Zt extends r.Group{raycast(e,t){if(!this.visible)return;const{children:r}=this;for(let n=0,s=r.length;n{(e instanceof r.Mesh||e instanceof r.LineSegments||e instanceof r.Line)&&e.geometry.dispose()})),function(e){const{children:t}=e;for(let e=0,r=t.length;e=1?this.fov=e:this.fov=r.MathUtils.radToDeg(2*Math.atan(Math.tan(.5*r.MathUtils.degToRad(e))/this.aspect))},r.StereoCamera.prototype.updateHalfSized=function(e,t){const r=e.aspect,n=e.fov;e.aspect=r/2,e.setMinimalFov(t),e.updateProjectionMatrix(),this.update(e),e.aspect=r,e.fov=n,e.updateProjectionMatrix()},r.PerspectiveCamera.prototype.setDistanceToFit=function(e,t){this.position.z=e/Math.sin(.5*r.MathUtils.degToRad(t))},r.Raycaster.prototype.intersectVisibleObject=function(e,t,n,s){const i=this.intersectObject(e,!1);if(0===i.length)return null;const o=Math.min(t.near,n);let a,l=i[0];const c=new r.Vector3;for(a=0;a{(e.hasOwnProperty("geometry")||e instanceof qt)&&(t=!0)})),t},buildDistorionMesh:function(e,t,n){function s(e){let t=0,r=e,s=1;for(;Math.abs(r-t)>1e-5;)s=1+n*r,t=r,r=e/(s*s);return 1/s}const i=new r.PlaneGeometry(2,2,e,t),o=i.getAttribute("position");for(let e=0;e>er[t]&1))return!0;return!1},processObjRenderOrder:function(e,t){const r=+("BA"!==t);e.traverse((e=>{e.isGroup&&(e.renderOrder=r)}))},applySelectionMaterial:function(e){e.traverse((e=>{"material"in e&&(e.material=e.material.clone(!0),e.material.setValues({depthFunc:r.LessEqualDepth,overrideColor:!0,fog:!1,lights:!1,shadowmap:!1}),e.material.setUberOptions({fixedColor:new r.Color(16776960),zOffset:-1e-6}))}))},getMiddlePoint:function(e,t,n){const s=n||new r.Vector3;return s.set(0,0,0),s.addScaledVector(e,.5),s.addScaledVector(t,.5),s},LAYERS:Jt},ir={boundingBox:new r.Box3(new r.Vector3(-1,-1,-1),new r.Vector3(1,1,1)),boundingSphere:new r.Sphere(new r.Vector3(0,0,0),1)};class or extends sr.RCGroup{constructor(e,t){super(e,t),this.name=e,this._dataSource=t}release(){this.parent&&this.parent.remove(this)}getDataSource(){return this._dataSource}getBoundaries(){return ir}}const ar=or;function lr(e){return null==e||Array.isArray(e)?e:[e]}class cr{constructor(){let e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:[],t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:["id"];this._list=[],this._dict={},this._indices=[...t],this._indices.forEach((e=>{this._dict[e]={}})),e.forEach((e=>this.register(e)))}static registerInList(e,t){e.includes(t)||e.push(t)}static unregisterFromList(e,t){const r=e.indexOf(t);-1!==r&&e.splice(r,1)}static registerInDict(e,t,r){t.forEach((t=>{t=t.toLowerCase();const n=e[t]=e[t]||[];n.includes(r)||n.push(r)}))}static unregisterFromDict(e,t,r){t.forEach((t=>{t=t.toLowerCase();const n=e[t];if(n){const s=n.indexOf(r);-1!==s&&n.splice(s,1),0===n.length&&delete e[t]}}))}register(e){cr.registerInList(this._list,e),this._indices.forEach((t=>{cr.registerInDict(this._dict[t],lr(e[t]),e)}))}unregister(e){cr.unregisterFromList(this._list,e),this._indices.forEach((t=>{cr.unregisterFromDict(this._dict[t],lr(e[t]),e)}))}get all(){return[...this._list]}get first(){return this._list[0]}keys(e){return Object.keys(this._dict[e||this._indices[0]])}get(e,t){const r=this._dict[t||this._indices[0]];if(r){const t=r[e&&e.toLowerCase()];return t&&t.length>0?t[0]:void 0}}}const hr=cr;const ur=function(e){Object.defineProperties(e,{logger:{get(){return this.context&&this.context.logger?this.context.logger:w}},settings:{get(){return this.context&&this.context.settings?this.context.settings:z}}})};class dr{constructor(e,t){this._position=e,this._radius=t}static _sphere=(()=>new r.Sphere)();raycast(e){const t=dr._sphere;t.set(this._position,this._radius);const n=new r.Vector3;return e.ray.intersectSphere(t,n)?{distance:e.ray.origin.distanceTo(n),point:n}:null}}const pr=e=>class extends e{constructor(e){for(var t=arguments.length,r=new Array(t>1?t-1:0),n=1;n65535,c=o*n,h=this._index=O.allocateTyped(l?Uint32Array:Uint16Array,c);this._positions=O.allocateTyped(Float32Array,3*a),this._normals=O.allocateTyped(Float32Array,3*a),this._colors=O.allocateTyped(Float32Array,3*a);const u=this._alpha=O.allocateTyped(Float32Array,a);t().fill(u,1);for(let e=0;e0,c=!1===o&&t>0,h=(i+1)*s+l*(s+1)+c*(s+1),u=(2*i+l+c)*s,d=n/2,p=new r.BufferAttribute(O.allocateTyped(Float32Array,3*h),3),m=new r.BufferAttribute(O.allocateTyped(Float32Array,3*h),3),f=new r.Uint16BufferAttribute(O.allocateTyped(Uint16Array,3*u),1),_=new r.BufferAttribute(O.allocateTyped(Float32Array,2*h),2);let g=0,y=0;const x=-(t-e)/n;for(let o=0;o<=i;o++){if(o!==i)for(let e=0;e2&&void 0!==arguments[2]&&arguments[2],n=arguments.length>3&&void 0!==arguments[3]&&arguments[3];const s=this._chunkGeo._positions.length,i=this._ringsCount,o=s*this._ringsCount*e*3;this._setPoints(t,s,i,o),r?this._setSlopeNormals(s,i,o):this._setBaseNormals(s,i,o),n&&this._addCut(s,i,o)}_setPoints(e,t,r,n){const s=this._tmpShape,i=this._positions,o=this._chunkGeo._positions;for(let a=0,l=n;a0)for(let t=0;t2)for(let t=0;t65535;this._index=O.allocateTyped(s?Uint32Array:Uint16Array,6*e),this._positions=O.allocateTyped(Float32Array,4*n),this._colors=O.allocateTyped(Float32Array,3*n),this._directions=O.allocateTyped(Float32Array,3*n);const i=this._alpha=O.allocateTyped(Float32Array,n);t().fill(i,1);const o=this._index;let a=0,l=0;for(let t=0;t117440512)throw new Error("Too large cube dimension: lead to memory huge uasge");return this.pointsValuesLinear=O.allocateTyped(Float32Array,32*t),this.hasIntersection=O.allocateTyped(Int32Array,t),this.bitsInside=O.allocateTyped(Int32Array,t),0}destroy(){this.bitsInside=null,this.hasIntersection=null,this.pointsValuesLinear=null}}_n.prototype.striIndicesMarchCube=[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,8,3,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,1,9,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,8,3,9,8,1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,2,10,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,8,3,1,2,10,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,2,10,0,2,9,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,2,8,3,2,10,8,10,9,8,-1,-1,-1,-1,-1,-1,-1,3,11,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,11,2,8,11,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,9,0,2,3,11,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,11,2,1,9,11,9,8,11,-1,-1,-1,-1,-1,-1,-1,3,10,1,11,10,3,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,10,1,0,8,10,8,11,10,-1,-1,-1,-1,-1,-1,-1,3,9,0,3,11,9,11,10,9,-1,-1,-1,-1,-1,-1,-1,9,8,10,10,8,11,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,7,8,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,3,0,7,3,4,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,1,9,8,4,7,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,1,9,4,7,1,7,3,1,-1,-1,-1,-1,-1,-1,-1,1,2,10,8,4,7,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,3,4,7,3,0,4,1,2,10,-1,-1,-1,-1,-1,-1,-1,9,2,10,9,0,2,8,4,7,-1,-1,-1,-1,-1,-1,-1,2,10,9,2,9,7,2,7,3,7,9,4,-1,-1,-1,-1,8,4,7,3,11,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,11,4,7,11,2,4,2,0,4,-1,-1,-1,-1,-1,-1,-1,9,0,1,8,4,7,2,3,11,-1,-1,-1,-1,-1,-1,-1,4,7,11,9,4,11,9,11,2,9,2,1,-1,-1,-1,-1,3,10,1,3,11,10,7,8,4,-1,-1,-1,-1,-1,-1,-1,1,11,10,1,4,11,1,0,4,7,11,4,-1,-1,-1,-1,4,7,8,9,0,11,9,11,10,11,0,3,-1,-1,-1,-1,4,7,11,4,11,9,9,11,10,-1,-1,-1,-1,-1,-1,-1,9,5,4,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,5,4,0,8,3,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,5,4,1,5,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,8,5,4,8,3,5,3,1,5,-1,-1,-1,-1,-1,-1,-1,1,2,10,9,5,4,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,3,0,8,1,2,10,4,9,5,-1,-1,-1,-1,-1,-1,-1,5,2,10,5,4,2,4,0,2,-1,-1,-1,-1,-1,-1,-1,2,10,5,3,2,5,3,5,4,3,4,8,-1,-1,-1,-1,9,5,4,2,3,11,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,11,2,0,8,11,4,9,5,-1,-1,-1,-1,-1,-1,-1,0,5,4,0,1,5,2,3,11,-1,-1,-1,-1,-1,-1,-1,2,1,5,2,5,8,2,8,11,4,8,5,-1,-1,-1,-1,10,3,11,10,1,3,9,5,4,-1,-1,-1,-1,-1,-1,-1,4,9,5,0,8,1,8,10,1,8,11,10,-1,-1,-1,-1,5,4,0,5,0,11,5,11,10,11,0,3,-1,-1,-1,-1,5,4,8,5,8,10,10,8,11,-1,-1,-1,-1,-1,-1,-1,9,7,8,5,7,9,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,3,0,9,5,3,5,7,3,-1,-1,-1,-1,-1,-1,-1,0,7,8,0,1,7,1,5,7,-1,-1,-1,-1,-1,-1,-1,1,5,3,3,5,7,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,7,8,9,5,7,10,1,2,-1,-1,-1,-1,-1,-1,-1,10,1,2,9,5,0,5,3,0,5,7,3,-1,-1,-1,-1,8,0,2,8,2,5,8,5,7,10,5,2,-1,-1,-1,-1,2,10,5,2,5,3,3,5,7,-1,-1,-1,-1,-1,-1,-1,7,9,5,7,8,9,3,11,2,-1,-1,-1,-1,-1,-1,-1,9,5,7,9,7,2,9,2,0,2,7,11,-1,-1,-1,-1,2,3,11,0,1,8,1,7,8,1,5,7,-1,-1,-1,-1,11,2,1,11,1,7,7,1,5,-1,-1,-1,-1,-1,-1,-1,9,5,8,8,5,7,10,1,3,10,3,11,-1,-1,-1,-1,5,7,0,5,0,9,7,11,0,1,0,10,11,10,0,-1,11,10,0,11,0,3,10,5,0,8,0,7,5,7,0,-1,11,10,5,7,11,5,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,10,6,5,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,8,3,5,10,6,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,0,1,5,10,6,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,8,3,1,9,8,5,10,6,-1,-1,-1,-1,-1,-1,-1,1,6,5,2,6,1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,6,5,1,2,6,3,0,8,-1,-1,-1,-1,-1,-1,-1,9,6,5,9,0,6,0,2,6,-1,-1,-1,-1,-1,-1,-1,5,9,8,5,8,2,5,2,6,3,2,8,-1,-1,-1,-1,2,3,11,10,6,5,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,11,0,8,11,2,0,10,6,5,-1,-1,-1,-1,-1,-1,-1,0,1,9,2,3,11,5,10,6,-1,-1,-1,-1,-1,-1,-1,5,10,6,1,9,2,9,11,2,9,8,11,-1,-1,-1,-1,6,3,11,6,5,3,5,1,3,-1,-1,-1,-1,-1,-1,-1,0,8,11,0,11,5,0,5,1,5,11,6,-1,-1,-1,-1,3,11,6,0,3,6,0,6,5,0,5,9,-1,-1,-1,-1,6,5,9,6,9,11,11,9,8,-1,-1,-1,-1,-1,-1,-1,5,10,6,4,7,8,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,3,0,4,7,3,6,5,10,-1,-1,-1,-1,-1,-1,-1,1,9,0,5,10,6,8,4,7,-1,-1,-1,-1,-1,-1,-1,10,6,5,1,9,7,1,7,3,7,9,4,-1,-1,-1,-1,6,1,2,6,5,1,4,7,8,-1,-1,-1,-1,-1,-1,-1,1,2,5,5,2,6,3,0,4,3,4,7,-1,-1,-1,-1,8,4,7,9,0,5,0,6,5,0,2,6,-1,-1,-1,-1,7,3,9,7,9,4,3,2,9,5,9,6,2,6,9,-1,3,11,2,7,8,4,10,6,5,-1,-1,-1,-1,-1,-1,-1,5,10,6,4,7,2,4,2,0,2,7,11,-1,-1,-1,-1,0,1,9,4,7,8,2,3,11,5,10,6,-1,-1,-1,-1,9,2,1,9,11,2,9,4,11,7,11,4,5,10,6,-1,8,4,7,3,11,5,3,5,1,5,11,6,-1,-1,-1,-1,5,1,11,5,11,6,1,0,11,7,11,4,0,4,11,-1,0,5,9,0,6,5,0,3,6,11,6,3,8,4,7,-1,6,5,9,6,9,11,4,7,9,7,11,9,-1,-1,-1,-1,10,4,9,6,4,10,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,10,6,4,9,10,0,8,3,-1,-1,-1,-1,-1,-1,-1,10,0,1,10,6,0,6,4,0,-1,-1,-1,-1,-1,-1,-1,8,3,1,8,1,6,8,6,4,6,1,10,-1,-1,-1,-1,1,4,9,1,2,4,2,6,4,-1,-1,-1,-1,-1,-1,-1,3,0,8,1,2,9,2,4,9,2,6,4,-1,-1,-1,-1,0,2,4,4,2,6,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,8,3,2,8,2,4,4,2,6,-1,-1,-1,-1,-1,-1,-1,10,4,9,10,6,4,11,2,3,-1,-1,-1,-1,-1,-1,-1,0,8,2,2,8,11,4,9,10,4,10,6,-1,-1,-1,-1,3,11,2,0,1,6,0,6,4,6,1,10,-1,-1,-1,-1,6,4,1,6,1,10,4,8,1,2,1,11,8,11,1,-1,9,6,4,9,3,6,9,1,3,11,6,3,-1,-1,-1,-1,8,11,1,8,1,0,11,6,1,9,1,4,6,4,1,-1,3,11,6,3,6,0,0,6,4,-1,-1,-1,-1,-1,-1,-1,6,4,8,11,6,8,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,7,10,6,7,8,10,8,9,10,-1,-1,-1,-1,-1,-1,-1,0,7,3,0,10,7,0,9,10,6,7,10,-1,-1,-1,-1,10,6,7,1,10,7,1,7,8,1,8,0,-1,-1,-1,-1,10,6,7,10,7,1,1,7,3,-1,-1,-1,-1,-1,-1,-1,1,2,6,1,6,8,1,8,9,8,6,7,-1,-1,-1,-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gn=_n,yn=[0,265,515,778,1030,1295,1541,1804,2060,2309,2575,2822,3082,3331,3593,3840,400,153,915,666,1430,1183,1941,1692,2460,2197,2975,2710,3482,3219,3993,3728,560,825,51,314,1590,1855,1077,1340,2620,2869,2111,2358,3642,3891,3129,3376,928,681,419,170,1958,1711,1445,1196,2988,2725,2479,2214,4010,3747,3497,3232,1120,1385,1635,1898,102,367,613,876,3180,3429,3695,3942,2154,2403,2665,2912,1520,1273,2035,1786,502,255,1013,764,3580,3317,4095,3830,2554,2291,3065,2800,1616,1881,1107,1370,598,863,85,348,3676,3925,3167,3414,2650,2899,2137,2384,1984,1737,1475,1226,966,719,453,204,4044,3781,3535,3270,3018,2755,2505,2240,2240,2505,2755,3018,3270,3535,3781,4044,204,453,719,966,1226,1475,1737,1984,2384,2137,2899,2650,3414,3167,3925,3676,348,85,863,598,1370,1107,1881,1616,2800,3065,2291,2554,3830,4095,3317,3580,764,1013,255,502,1786,2035,1273,1520,2912,2665,2403,2154,3942,3695,3429,3180,876,613,367,102,1898,1635,1385,1120,3232,3497,3747,4010,2214,2479,2725,2988,1196,1445,1711,1958,170,419,681,928,3376,3129,3891,3642,2358,2111,2869,2620,1340,1077,1855,1590,314,51,825,560,3728,3993,3219,3482,2710,2975,2197,2460,1692,1941,1183,1430,666,915,153,400,3840,3593,3331,3082,2822,2575,2309,2060,1804,1541,1295,1030,778,515,265,0];function xn(e,t,r){const n=e.getValue(t.x,t.y,t.z);r.set(n[0],n[1],n[2])}class bn{constructor(){this._arrSize=8,this.p=new Array(this._arrSize),this.g=new Array(this._arrSize),this.val=new Array(this._arrSize);for(let e=0;eMath.abs(e)>Number.EPSILON;return!(c(t.y)||c(t.z)||c(n.x)||c(n.z)||c(s.x)||c(s.y))}_vertexInterp(e,t,r,n,s,i){const o=t.p[r],a=t.p[n],l=t.g[r],c=t.g[n],h=t.val[r],u=e-h,d=t.val[n]-h;let p=0;Math.abs(d)>0&&(p=u/d),p=p>1?1:p,s.lerpVectors(o,a,p),i.lerpVectors(l,c,p)}static _triTable=(()=>gn.prototype.striIndicesMarchCube)();static _arrSize=12;static _firstIndices=[0,1,2,3,4,5,6,7,0,1,2,3];static _secondIndices=[1,2,3,0,5,6,7,4,4,5,6,7];static _vertexList=(()=>Sn(vn._arrSize))();static _normalList=(()=>Sn(vn._arrSize))();_polygonize(e,t,r){const{cubeIndex:n}=e;let s=0;const i=vn._arrSize,o=vn._firstIndices,a=vn._secondIndices,l=vn._vertexList,c=vn._normalList;for(;sa?a:r+t;let c=-1;for(let e=r;ee&&(t=r,e=A[r]);if(t<0||!n.includesAtom(C[t])){M[s]=-1;continue}}M[s]=P++;const D=g=0&&r>=0&&n>=0&&(this._indices[3*t]=e,this._indices[3*t+1]=r,this._indices[3*t+2]=n,++t)}this._position=new Float32Array(this._position.buffer.slice(0,3*P*4)),this._normals=new Float32Array(this._normals.buffer.slice(0,3*P*4)),this._colors=new Float32Array(this._colors.buffer.slice(0,3*P*4)),this._indices=new Uint32Array(this._indices.buffer.slice(0,3*t*4))}}toMesh(){const e=new r.BufferGeometry;return e.setIndex(new r.BufferAttribute(this._indices,1)),e.setAttribute("position",new r.BufferAttribute(this._position,3)),e.setAttribute("normal",new r.BufferAttribute(this._normals,3)),e.setAttribute("color",new r.BufferAttribute(this._colors,3)),e.computeBoundingSphere(),e}}const Cn=vn;const An=class extends fn{_build(){const e=this._opts;this.numVoxels=[128,128,128],this.xAxis=new r.Vector3(1,0,0),this.yAxis=new r.Vector3(0,1,0),this.zAxis=new r.Vector3(0,0,1),this.origin=new r.Vector3(0,0,0),this._visibilitySelector=e.visibilitySelector,this._calcSurface(e)}_findMinMax(e){const t=e.length/4,r=[e[0],e[1],e[2],e[3]],n=[e[0],e[1],e[2],e[3]];for(let s=1;s4&&(t.gridSpacing*=s[3]);let o=t.radScale*i[3]*1.7,a=o;a=.65*Math.sqrt(4/3*Math.PI*a*a*a),o=Math.max(o,a);let l=0;for(;l<3;++l)s[l]-=o,i[l]+=o;for(l=0;l<3;++l)r[l]=Math.ceil((i[l]-s[l])/t.gridSpacing);return this.xAxis.x=(r[0]-1)*t.gridSpacing,this.yAxis.y=(r[1]-1)*t.gridSpacing,this.zAxis.z=(r[2]-1)*t.gridSpacing,[this.origin.x,this.origin.y,this.origin.z]=s,{bbox:n,dim:r}}_makeSurface(e,t){const n=new Cn;n.compute(e.volMap,this.origin,t.isoValue,1),n.vertexFusion(9,9),n._numTriangles>0?(n.setColorVolTex(e.volTexMap,e.atomMap,e.atomWeightMap,this._visibilitySelector),this.setIndex(new r.BufferAttribute(n._indices,1)),this.setAttribute("position",new r.BufferAttribute(n._position,3)),this.setAttribute("normal",new r.BufferAttribute(n._normals,3)),this.setAttribute("color",new r.BufferAttribute(n._colors,3))):this.setAttribute("position",new r.BufferAttribute(O.allocateTyped(Float32Array,0),3))}_calcSurface(e){const t={posRad:this._posRad,colors:this._colors,atoms:this._opts.atoms};if(0===t.posRad.length)return;const n=this._findNumVoxels(t.posRad,e),s=new r.Box3(this.origin,new r.Vector3(this.xAxis.x,this.yAxis.y,this.zAxis.z).add(this.origin)),i=this._computeSurface(t,s,n,e);this._makeSurface(i,e)}},{Volume:En}=Yt;const Tn=class extends An{_computeSurface(e,t,r,n){this._shiftByOrigin(e.posRad);const s={volMap:new En(Float32Array,this.numVoxels,t),volTexMap:new En(Float32Array,this.numVoxels,t,3)};return null!=this._visibilitySelector&&(s.atomMap=[],s.atomWeightMap=new En(Float32Array,this.numVoxels,t)),this.gaussdensity(s,e,null,n),s}gaussdensity(e,t,r,n){const s=t.posRad.length/4,{posRad:i,colors:o}=t,{numVoxels:a}=this,{radScale:l,gaussLim:c,gridSpacing:h}=n,u=1/n.isoValue,d=1/h,p=a[0]-1,m=a[1]-1,f=a[2]-1,{volMap:_,volTexMap:g}=e,y=_.getData(),x=_.getStrideX(),b=g.getData(),w=g.getStrideX();let S;null!=this._visibilitySelector&&(S=e.atomWeightMap.getData());const{atomMap:v}=e;for(let e=0;e=E)continue;let d=_.getDirectIdx(R,l,r),p=g.getDirectIdx(R,l,r),m=R*h-i[n];for(let r=R;r<=M;++r,m+=h,d+=x,p+=w){const r=-(m*m+c)*C;let n=Math.exp(r)*a;null!=this._visibilitySelector&&n>S[d]&&(S[d]=n,v[d]=t.atoms[e]),y[d]+=n,n*=u;const s=3*e;b[p]+=n*o[s],b[p+1]+=n*o[s+1],b[p+2]+=n*o[s+2]}}}}}_shiftByOrigin(e){const t=this.origin.x,r=this.origin.y,n=this.origin.z,s=e.length/4;for(let i=0;iR&&(R=r)}this.neighbourListLength=27*R+1,this.withinRadii=function(t,r,n,s,l){let c=0;const h=u(t,i),f=u(r,o),g=u(n,a),b=Math.max(0,h-1),w=Math.max(0,f-1),S=Math.max(0,g-1),T=Math.min(d-1,h+1),R=Math.min(p-1,f+1),M=Math.min(m-1,g+1);for(y=b;y<=T;++y){const i=y*_;for(E=w;E<=R;++E){const o=E*m;for(let a=S;a<=M;++a){x=i+o+a;const h=v[x],u=h+C[x];for(let i=h;im&&(m=t),p[e]=t*t}F(),function(){let e=0;const t=2*Math.PI/g;E=O.allocateTyped(Float32Array,g),A=O.allocateTyped(Float32Array,g);for(let r=0;r=0;){if(i!==n&&i!==s&&U(i,e,t,r))return M=i,i;i=R[++o]}return M=-1,-1}function j(e,t){const r=i*e,n=i*t,s=o[r],a=o[r+1],l=o[r+2],c=o[r+3];let h=I.x=o[n]-s,d=I.y=o[n+1]-a,p=I.z=o[n+2]-l;const m=o[n+3];let f=h*h+d*d+p*p;const b=Math.sqrt(f),w=c*((c*c+b*b-m*m)/(2*c*b));var T,R;I.normalize(),R=I,(T=V).x=T.y=T.z=1,0!==R.x?T.x=(R.y+R.z)/-R.x:0!==R.y?T.y=(R.x+R.z)/-R.y:0!==R.z&&(T.z=(R.x+R.y)/-R.z),V.normalize(),D.crossVectors(I,V),D.normalize();const P=Math.sqrt(c*c-w*w);V.multiplyScalar(P),D.multiplyScalar(P),I.multiplyScalar(w),I.x+=s,I.y+=a,I.z+=l,M=-1;const N=k;for(let r=0;r0&&fP[o]&&(P[o]=t,N[o]=l[e]),x[o]<0&&(x[o]=-x[o]);const u=Math.sqrt(m),d=c/u;let f=p*d,_=a*d,g=i*d;if(f+=r,_+=n,g+=s,-1===G(f,_,g,e,-1)){const e=c-u;e=0;)e0){t=1/t;const r=3*e;b[r]*=t,b[r+1]*=t,b[r+2]*=t}}}()}this.build=function(){H(),this.volTexMap=b,this.weightsMap=P,this.atomMap=N,this.volMap=x}},{Volume:Pn}=Yt;const Nn=class extends An{_computeSurface(e,t,r,n){const s=new Mn(e,r,n);s.build();return{volMap:new Pn(Float32Array,this.numVoxels,t,1,s.volMap),volTexMap:new Pn(Float32Array,this.numVoxels,t,3,s.volTexMap),atomMap:s.atomMap,atomWeightMap:new Pn(Float32Array,this.numVoxels,t,1,s.weightsMap)}}};const Ln=class{constructor(e,t){this.coord=new r.Vector3,this.coord.copy(e),this.radius=t,this.colorX=.99999,this.colorY=0,this.colorZ=0,this.atomType=0,this.srcAtom=null}};const In=class{constructor(e,t,n,s,i){this._numAtoms=e,this._atoms=t,this._vBoxMin=new r.Vector3,this._vBoxMax=new r.Vector3,this._vBoxMin.copy(n),this._vBoxMax.copy(s),this._probeRadius=i,this._atomsList=null,this._voxelList=null}createVoxels(){let e,t;const r=0|this._numAtoms,n=this._atoms,s=this._vBoxMax.x-this._vBoxMin.x,i=this._vBoxMax.y-this._vBoxMin.y,o=this._vBoxMax.z-this._vBoxMin.z;let a=sc?t:c,h+=t;let u=Math.floor(a/c);u<2&&(u=2),h/=r,this._numCells=u,this._aveRad=h,this._maxRad=c;const d=u,p=u*u,m=u*u*u,f=this._xScale=1/(this._vBoxMax.x-this._vBoxMin.x),_=this._yScale=1/(this._vBoxMax.y-this._vBoxMin.y),g=this._zScale=1/(this._vBoxMax.z-this._vBoxMin.z);let y=0;const x=f*u,b=_*u,w=g*u;for(l=0;l=0?r:0,s=s>=0?s:0,i=i>=0?i:0,o=o=0;e=this._atomsList[2*e+1]){t(o[this._atomsList[2*e]])}}getClosestAtom(e){let t=null,r=Number.MAX_VALUE;return this.forEachRelatedAtom(e,(n=>{const s=e.distanceToSquared(n.coord);sf)return;const g=e.radius+n._probeRadius;d=s-g*g,d<0&&(d=-d),p=Math.exp(_*d),c+=t*p,h+=r*p,u+=m*p,i++};let y=0;for(let n=0;ny?i:y,s=c*c+h*h+u*u,i>0&&(d=1/Math.sqrt(s),c*=d,h*=d,u*=d),r[n].x=c,r[n].y=h,r[n].z=u;return 0}buildColors(e,t,r,n){const s=this;let i=0,o=0,a=0,l=0,c=0;const h=n*n;let u=[],d=[],p=0;const m=function(e){const t=i-e.coord.x,r=o-e.coord.y,n=a-e.coord.z,m=t*t+r*r+n*n;if(m>h)return;const f=e.radius+s._probeRadius;l=m-f*f,l<0&&(l=-l),c=1/(.8+l),u.push([e.colorX,e.colorY,e.colorZ]),d.push(c),p+=c};for(let n=0;ni?a:i,o.x-ar.x&&(r.x=o.x+a),o.y+a>r.y&&(r.y=o.y+a),o.z+a>r.z&&(r.z=o.z+a)}t.x-=i,t.y-=i,t.z-=i,r.x+=i,r.y+=i,r.z+=i}getCornerCoord(e,t,r,n,s,i,o){const a=1/(i-1),l=r*a,c=n*a,h=s*a;o.x=e.x*(1-l)+t.x*l,o.y=e.y*(1-c)+t.y*c,o.z=e.z*(1-h)+t.z*h}buildEdgePoint(e,t,r,n,s,i){if(r[e]^r[t]){const r=24,o=(0-n.pointsValuesLinear[s+r+e])/(n.pointsValuesLinear[s+r+t]-n.pointsValuesLinear[s+r+e]),a=n.pointsValuesLinear[s+3*e+0],l=n.pointsValuesLinear[s+3*e+1],c=n.pointsValuesLinear[s+3*e+2],h=n.pointsValuesLinear[s+3*t+0],u=n.pointsValuesLinear[s+3*t+1],d=n.pointsValuesLinear[s+3*t+2];i.x=a*(1-o)+h*o,i.y=l*(1-o)+u*o,i.z=c*(1-o)+d*o}}isTriangleVisible(e,t,r){const n=this.voxelWorld.getClosestAtom(e),s=this.voxelWorld.getClosestAtom(t),i=this.voxelWorld.getClosestAtom(r);return null!==n&&null!==s&&null!==i&&null!==n.srcAtom&&null!==s.srcAtom&&null!==i.srcAtom&&(this.visibilitySelector.includesAtom(n.srcAtom)&&this.visibilitySelector.includesAtom(s.srcAtom)&&this.visibilitySelector.includesAtom(i.srcAtom))}addTriangle(e,t,r){if(this.visibilitySelector&&!this.isTriangleVisible(e,t,r))return!0;const n=this.geoOut;if(n._numTriangles>=this.maxNumTriangles)return!1;const s=this.addVertexToGeo(n,e),i=this.addVertexToGeo(n,t),o=this.addVertexToGeo(n,r);if((s|i|o)<0)return!1;const a=3*n._numTriangles;return n._indices[a+0]=s,n._indices[a+1]=i,n._indices[a+2]=o,n._numTriangles++,!0}buildGeoFromCorners(e,t,n,s,i,o){const a=e-1,l=e,c=e*e,h=new Array(12);for(let e=0;e<12;e++)h[e]=new r.Vector3;const u=[];for(let e=0;e<8;e++)u[e]=1;const d=new r.Vector3;let p=0,m=0;for(let r=0;rt.length/2||2*Object.keys(Dn.ByAtomicNumber).length!==t.length)throw new Error("atomT.length should be equal Element.ByAtomicNumber.length * 2");return t[2*e]}calculateGridCorners(e,t,n,s,i,o){const a=t*t,l=a*t,c=new r.Vector3,h=new r.Vector3;for(let t=0;t=0;n=this.hashEntries[2*n+1]){const r=this.hashEntries[2*n+0];o.copy(e._vertices[r]),o.x-=t.x,o.y-=t.y,o.z-=t.z;if(o.x*o.x+o.y*o.y+o.z*o.z<1e-6)return r}if(e._numVertices>=this.maxNumVertices)return-1;const u=e._numVertices;if(e._vertices[u].copy(t),null!==this.vBoxMin&&null!==this.vBoxMax){if(n=this.getNewHashEntry(),n<0)return-1;const e=this.hashLines[h+1];this.hashLines[h+1]=n,this.hashEntries[2*n+0]=u,this.hashEntries[2*n+1]=e,this.hashLines[h+0]++}return e._numVertices++,u}modifyExcludedFromGeo(e,t,r,n,s,i){let o,a,l;const c=e*e,h=(e-1)/(n.x-r.x),u=(e-1)/(n.y-r.y),d=(e-1)/(n.z-r.z),p=2*t*(2*t),m=1/(e-1);for(let f=0;f=0?y:0,x=x>=0?x:0,b=b>=0?b:0,w=w<=e-1?w:e-1,S=S<=e-1?S:e-1,v=v<=e-1?v:e-1;for(let s=x;s<=S;s++){const h=s*c;for(let c=b;c<=v;c++){const u=c*e;for(let e=y;e<=w;e++){o=h+u+e;let d=e*m;const f=r.x*(1-d)+n.x*d;d=s*m;const g=r.y*(1-d)+n.y*d;d=c*m;const y=r.z*(1-d)+n.z*d,x=f-_.x,b=g-_.y,w=y-_.z,S=x*x+b*b+w*w;S0?(i[o]<0&&(i[o]=l),l>i[o]&&(i[o]=l)):l>i[o]&&(i[o]=l))}}}}return 0}_innerBuild(){let e;const t=1.2,n={posRad:this._posRad,colors:this._colors,atoms:this._opts.atoms};this.complex=this._opts.parent,this.atoms=n.atoms,this.meshResolution=this._opts.gridSpacing,this.atomRadiusScale=this._opts.radScale,this.colorMode=this._opts.colorMode,this.probeRadius=this._opts.probeRadius,this.useVertexColors=!0,this.excludeProbe=this._opts.excludeProbe,this.visibilitySelector=this._opts.visibilitySelector,this.geoOut=null,this.hashLines=null,this.hashEntries=null,this.numHashEtriesAllocated=0,this.numHashEntryIndex=0,this.maxNumVertices=0,this.maxNumTriangles=0;const s=new Array(this.atoms.length);this.convertToAtomsColored(n,s);const i=this.vBoxMin=new r.Vector3,o=this.vBoxMax=new r.Vector3;this.getBoundingBox(s,i,o);const a=this.marCubeResoultion=4*this.meshResolution,l=a,c=l*l*l,h=O.allocateTyped(Float32Array,c),u=this.probeRadius*this.atomRadiusScale;this.calculateGridCorners(h,l,i,o,s,u);const d=a-1,p=new gn;if(e=p.create(d),e<0)return e;const m=new r.Vector3;m.x=(o.x-i.x)/d,m.y=(o.y-i.y)/d,m.z=(o.z-i.z)/d;let f=this.getNumIntersectedCells(l,d,h,p),_=Math.floor(f*t),g=Math.floor(f*t*2);if(this.geoOut=new On(_,g,this.useVertexColors),e=this.createVertexHash(_,g),e<0)return e;let y=u;if(this.excludeProbe&&(y=.01),this.voxelWorld=new In(s.length,s,i,o,y),this.voxelWorld.createVoxels(),e=this.buildGeoFromCorners(a,i,o,h,m,p),this.excludeProbe){if(this.modifyExcludedFromGeo(l,u,i,o,this.geoOut,h),this.geoOut._vertices=null,this.geoOut._colors=null,this.geoOut._indices=null,this.geoOut._normals=null,this.geoOut._numVertices=0,this.geoOut._numTriangles=0,this.geoOut=null,f=this.getNumIntersectedCells(l,d,h,p),_=Math.floor(f*t),g=Math.floor(f*t*2),this.geoOut=new On(_,g,this.useVertexColors),e=this.createVertexHash(_,g),e<0)return e;e=this.buildGeoFromCorners(l,i,o,h,m,p)}this.voxelWorld.buildNormals(this.geoOut._vertices.length,this.geoOut._vertices,this.geoOut._normals);let x=6.5;return this.excludeProbe&&(x-=1.5),this.useVertexColors&&this.voxelWorld.buildColors(this.geoOut._vertices.length,this.geoOut._vertices,this.geoOut._colors,x),this.voxelWorld.destroyVoxels(),this.voxelWorld=null,p.destroy(),e}};const zn={InstancedSpheresGeometry:gr,SimpleSpheresGeometry:Sr,Simple2CCylindersGeometry:Er,Instanced2CCylindersGeometry:Dr,ExtrudedObjectsGeometry:jr,ChunkedLinesGeometry:rn,TwoColorLinesGeometry:on,CrossGeometry:dn,QuickSurfGeometry:Tn,ContactSurfaceGeometry:Nn,SSIsosurfaceGeometry:kn,LabelsGeometry:class extends g{constructor(e,t){super(),this._opts=t,this.items=[],this.needsUpdate=!1;let n=-50,s=-50;switch(t.horizontalAlign){case"left":n=0;break;case"right":n=-100}switch(t.verticalAlign){case"top":s=-100;break;case"bottom":s=0}const i=new r.Vector3(t.dx||0,t.dy||0,t.dz||0);this.userData={translation:`translate(${n}%, ${s}%)`,offset:i}}setItem(e,t,n){const s=this._opts,i=this.items[e]||function(e,t){const n=document.createElement("div");if(n.className=t,"string"==typeof e){const t=document.createElement("span");t.style.fontSize="150%";const r=e.split("\n");for(let e=0,n=r.length;e 0\r\n\t\tuniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n attribute vec3 color;\r\n varying vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n attribute vec3 color2;\r\n varying vec3 vColor2;\r\n attribute vec2 uv;\r\n #ifndef CYLINDER_SPRITE\r\n varying vec2 vUv;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_POS\r\n attribute vec4 offset;\r\n #ifdef SPHERE_SPRITE\r\n varying vec4 instOffset;\r\n varying vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n attribute vec4 matVector1;\r\n attribute vec4 matVector2;\r\n attribute vec4 matVector3;\r\n attribute vec4 invmatVector1;\r\n attribute vec4 invmatVector2;\r\n attribute vec4 invmatVector3;\r\n\r\n #ifdef CYLINDER_SPRITE\r\n varying vec4 matVec1;\r\n varying vec4 matVec2;\r\n varying vec4 matVec3;\r\n varying vec4 invmatVec1;\r\n varying vec4 invmatVec2;\r\n varying vec4 invmatVec3;\r\n varying vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\nuniform mat4 modelViewMatrix; // optional\r\nuniform mat4 projectionMatrix; // optional\r\nuniform mat3 normalMatrix; // optional\r\nuniform mat4 modelMatrix; // optional\r\n\r\n#ifdef DASHED_LINE\r\n attribute float lineDistance;\r\n varying float vLineDistance;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n attribute vec3 direction;\r\n uniform mat4 projMatrixInv;\r\n uniform vec2 viewport;\r\n uniform float lineWidth;\r\n\r\n vec4 transform(vec4 coord){\r\n return projectionMatrix * modelViewMatrix * coord;\r\n }\r\n\r\n vec2 project(vec4 device){\r\n vec3 device_normal = device.xyz/device.w;\r\n vec2 clip_pos = (device_normal*0.5+0.5).xy;\r\n return clip_pos * viewport;\r\n }\r\n\r\n vec4 unproject(vec2 screen, float z, float w){\r\n vec2 clip_pos = screen/viewport;\r\n vec2 device_normal = clip_pos*2.0-1.0;\r\n return vec4(device_normal*w, z, w);\r\n }\r\n#endif\r\n\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n alphaCol = alphaColor;\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n vec3 objectNormal = vec3(\r\n dot(normal, matVector1.xyz),\r\n dot(normal, matVector2.xyz),\r\n dot(normal, matVector3.xyz));\r\n#else\r\n vec3 objectNormal = vec3( normal );\r\n#endif\r\n\r\nvec3 transformedNormal = normalMatrix * objectNormal;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n vNormal = normalize(transformedNormal);\r\n#endif\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n viewNormal = normalize(mat3(modelViewMatrix)*objectNormal);\r\n#endif\r\n\r\n vec4 localPos = vec4(position.xyz, 1.0);\r\n vec4 worldPos = modelMatrix * localPos;\r\n vec4 mvPosition = modelViewMatrix * localPos;\r\n\r\n// make thick line offset\r\n#ifdef THICK_LINE\r\n // get screen pos\r\n vec4 dPos = transform(vec4(position.xyz, 1.0));\r\n vec2 sPos = project(dPos);\r\n // move pos forward\r\n vec3 position2 = position.xyz + direction.xyz * 0.5;\r\n // get screen offset pos\r\n vec4 dPos2 = transform(vec4(position2.xyz, 1.0));\r\n vec2 sPos2 = project(dPos2);\r\n // screen line direction\r\n vec2 sDir = normalize(sPos2 - sPos);\r\n // vertex offset (orthogonal to line direction)\r\n vec2 offset1 = vec2(-sDir.y, sDir.x);\r\n // move screen vertex\r\n vec2 newPos = sPos + offset1 * position.w * lineWidth;\r\n // get moved pos in view space\r\n vec4 dNewPos = unproject(newPos, dPos.z, dPos.w);\r\n mvPosition.xyz = (projMatrixInv * dNewPos).xyz;\r\n#endif // THICK_LINE\r\n\r\n#ifdef INSTANCED_POS\r\n #ifdef SPHERE_SPRITE\r\n instOffset = offset;\r\n\r\n vec4 posEye = modelViewMatrix * vec4( offset.xyz, 1.0 );\r\n float scale = length(modelViewMatrix[0]);\r\n mvPosition = posEye + vec4( position.xyz * offset.w * scale * INSTANCED_SPRITE_OVERSCALE, 0.0 );\r\n posEye.w = offset.w * scale;\r\n\r\n spritePosEye = posEye;\r\n #else\r\n localPos = vec4( offset.xyz + position.xyz * offset.w, 1.0 );\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n #ifdef CYLINDER_SPRITE\r\n matVec1 = matVector1;\r\n matVec2 = matVector2;\r\n matVec3 = matVector3;\r\n invmatVec1 = invmatVector1;\r\n invmatVec2 = invmatVector2;\r\n invmatVec3 = invmatVector3;\r\n\r\n // calculate eye coords of cylinder endpoints\r\n vec4 v = vec4(0, -0.5, 0, 1);\r\n vec4 p1 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n v.y = 0.5;\r\n vec4 p2 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n\r\n // sprite is placed at the center of cylinder\r\n vec4 posEye;\r\n posEye.xyz = mix(p1.xyz, p2.xyz, 0.5);\r\n posEye.w = 1.0;\r\n spritePosEye = posEye;\r\n\r\n // cylinder radius in eye space\r\n float rad = length(modelViewMatrix[0]) * length(vec3(matVector1.x, matVector2.x, matVector3.x));\r\n vec2 spriteSize;\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // In ortho projection we skip z coordinate\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy - p1.xy);\r\n\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * (spriteSizeScreen + 2.0 * rad);\r\n #else\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy / p2.z - p1.xy / p1.z);\r\n\r\n // full sprite size in eye coords\r\n float minZ = min(abs(p1.z), abs(p2.z));\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * abs(posEye.z) * (spriteSizeScreen + 2.0 * rad / minZ);\r\n #endif\r\n\r\n mvPosition = posEye + vec4( position.xy * 0.5 * spriteSize, 0, 0 );\r\n #else\r\n localPos = vec4(dot(localPos, matVector1), dot(localPos, matVector2), dot(localPos, matVector3), 1.0);\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n gl_Position = projectionMatrix * mvPosition;\r\n\r\n vWorldPosition = worldPos.xyz;\r\n vViewPosition = - mvPosition.xyz;\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t vec4 worldPosition;\r\n\t // see THREE.WebGLProgram.unrollLoops\r\n\t #pragma unroll_loop_start\r\n\t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirectionalShadowCoord[ i ] = directionalShadowMatrix[ i ] * vec4(vWorldPosition, 1.0);\r\n vDirectionalShadowNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(objectNormal, 0.0))).xyz;\r\n\t }\r\n\t #pragma unroll_loop_end\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n vColor = color.xyz;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n vColor2 = color2;\r\n #ifndef CYLINDER_SPRITE\r\n vUv = uv;\r\n #endif\r\n#endif\r\n\r\n#ifdef DASHED_LINE\r\n vLineDistance = lineDistance;\r\n#endif\r\n}\r\n",fragmentShader:this.precisionString()+"#if defined (NORMALS_TO_G_BUFFER)\r\n #define fragColor gl_FragData[0]\r\n#else\r\n #define fragColor gl_FragColor\r\n#endif\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n varying float alphaCol;\r\n#endif\r\n\r\n#ifdef COLOR_FROM_POS\r\n uniform mat4 world2colorMatrix;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform sampler2D directionalShadowMap[ NUM_DIR_LIGHTS ];\r\n uniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ]; //only for sprites\r\n\t\tvarying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n vec4 vDirLightWorldCoord[ NUM_DIR_LIGHTS ];\r\n vec3 vDirLightWorldNormal[ NUM_DIR_LIGHTS ];\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n // We use 4 instead uniform variable or define because this value is used in for(... i < value; ...) with\r\n // unroll_loop and unroll_loop has pattern:\r\n // /#pragma unroll_loop[\\s]+?for \\( int i \\= (\\d+)\\; i < (\\d+)\\; i \\+\\+ \\) \\{([\\s\\S]+?)(?=\\})\\}/g\r\n uniform vec2 samplesKernel[4]; // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n uniform sampler2D noiseTex;\r\n uniform vec2 noiseTexelSize;\r\n uniform vec2 srcTexelSize;\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n varying vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n varying vec3 vColor2;\r\n #ifndef CYLINDER_SPRITE\r\n varying vec2 vUv;\r\n #endif\r\n#endif\r\n\r\nuniform vec3 diffuse;\r\nuniform vec3 emissive;\r\nuniform vec3 specular;\r\nuniform float shininess;\r\nuniform vec3 fixedColor;\r\nuniform float opacity;\r\nuniform float zClipValue;\r\nuniform float clipPlaneValue;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n varying vec3 viewNormal;\r\n#endif\r\n\r\n#define RECIPROCAL_PI 0.31830988618\r\n#define saturate(a) clamp( a, 0.0, 1.0 )\r\n\r\n#ifdef USE_FOG\r\n uniform vec3 fogColor;\r\n uniform float fogAlpha;\r\n uniform float fogNear;\r\n uniform float fogFar;\r\n#endif\r\n\r\nvarying vec3 vWorldPosition; // world position of the pixel (invalid when INSTANCED_SPRITE is defined)\r\nvarying vec3 vViewPosition;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n varying vec3 vNormal;\r\n#endif\r\n\r\n/////////////////////////////////////////// ZSprites ////////////////////////////////////////////////\r\n#if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n uniform float nearPlaneValue;\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n varying vec4 spritePosEye;\r\n#endif\r\n\r\n#if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n uniform float zOffset;\r\n\r\n #if !defined(USE_LIGHTS) || !defined(SHADOWMAP) || !defined(SHADOWMAP_PCF_RAND) || !(NUM_DIR_LIGHTS > 0)\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\r\n float calcDepthForSprites(vec4 pixelPosEye, float zOffset, mat4 projMatrix) {\r\n vec4 pixelPosScreen = projMatrix * pixelPosEye;\r\n return 0.5 * (pixelPosScreen.z / pixelPosScreen.w + 1.0) + zOffset;\r\n }\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n varying vec4 instOffset;\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n\r\n bool intersect_ray_sphere(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray, ray);\r\n float b = dot(ray, origin);\r\n float c = dot(origin, origin) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n // choose nearest point inside frustum\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all spheres the point with smaller 't' is visible\r\n // t1 is always smaller than t2 (from calculations)\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_sphere_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into sphere local coords\r\n origin = pixelPosEye.xyz - spritePosEye.xyz;\r\n origin = (invModelViewMatrix * vec4(origin, 0.0)).xyz / instOffset.w;\r\n\r\n // transform camera orientation vector into sphere local coords\r\n ray = (invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0)).xyz;\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n vec4 v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into sphere local coords\r\n v = invModelViewMatrix * v;\r\n origin = (v.xyz - instOffset.xyz) / instOffset.w;\r\n\r\n // transform vector from camera pos to curPixel into sphere local coords\r\n ray = (invModelViewMatrix * vec4(pixelPosEye, 0.0)).xyz;\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_sphere(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n varying vec4 matVec1;\r\n varying vec4 matVec2;\r\n varying vec4 matVec3;\r\n varying vec4 invmatVec1;\r\n varying vec4 invmatVec2;\r\n varying vec4 invmatVec3;\r\n\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n varying vec4 spritePosEye;\r\n\r\n bool intersect_ray_cylinder(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray.xz, ray.xz);\r\n float b = dot(ray.xz, origin.xz);\r\n float c = dot(origin.xz, origin.xz) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n float halfHeight = 0.5;\r\n\r\n // choose nearest point\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all cylinders the point with smaller 't' is visible\r\n // if it is not outside of cylinnder (t1 is always smaller than t2).\r\n if (p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0 && p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0 && p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_cylinder_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n vec4 v;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye.xyz - spritePosEye.xyz, 0.0);\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform camera orientation vector into cylinder local coords\r\n v = invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into cylinder local coords\r\n v = invModelViewMatrix * v;\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform vector from camera pos to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_cylinder(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n///////////////////////////////////// Pack and unpack ///////////////////////////////////////////////\r\nconst float PackUpscale = 256. / 255.; // fraction -> 0..1 (including 1)\r\nconst float UnpackDownscale = 255. / 256.; // 0..1 -> fraction (excluding 1)\r\n\r\nconst vec3 PackFactors = vec3( 256. * 256. * 256., 256. * 256., 256. );\r\nconst vec4 UnpackFactors = UnpackDownscale / vec4( PackFactors, 1. );\r\n\r\n\r\nconst float ShiftRight8 = 1. / 256.;\r\n\r\nvec4 packDepthToRGBA( const in float v ) {\r\n vec4 r = vec4( fract( v * PackFactors ), v );\r\n r.yzw -= r.xyz * ShiftRight8; // tidy overflow\r\n return r * PackUpscale;\r\n}\r\n\r\nfloat unpackRGBAToDepth( const in vec4 v ) {\r\n return dot( v, UnpackFactors );\r\n}\r\n\r\n////////////////////////////////////////// All Lighting /////////////////////////////////////////////////\r\n#ifdef TOON_SHADING\r\n #define LOW_TOON_BORDER 0.0\r\n #define MEDIUM_TOON_BORDER 0.7\r\n #define HIGH_TOON_BORDER 1.0\r\n\r\n #define MEDIUM_TOON_RANGE 0.5\r\n #define HIGH_TOON_RANGE 0.95\r\n#endif\r\n#if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n struct ReflectedLight {\r\n vec3 directDiffuse;\r\n vec3 directSpecular;\r\n vec3 indirectDiffuse;\r\n };\r\n\r\n struct BlinnPhongMaterial {\r\n vec3 diffuseColor;\r\n vec3 specularColor;\r\n float specularShininess;\r\n };\r\n\r\n struct GeometricContext {\r\n vec3 normal;\r\n vec3 viewDir;\r\n };\r\n\r\n struct DirectionalLight {\r\n vec3 direction;\r\n vec3 color;\r\n };\r\n uniform DirectionalLight directionalLights[ NUM_DIR_LIGHTS ];\r\n\r\n struct DirectionalLightShadow {\r\n vec2 shadowMapSize;\r\n float shadowBias;\r\n float shadowRadius;\r\n };\r\n uniform DirectionalLightShadow directionalLightShadows[ NUM_DIR_LIGHTS ];\r\n\r\n uniform vec3 ambientLightColor;\r\n\r\n /////////////////////////////////////////// Shadowmap ////////////////////////////////////////////////\r\n\r\n #if defined(SHADOWMAP)\r\n \tfloat texture2DCompare( sampler2D depths, vec2 uv, float compare ) {\r\n \t\treturn step( compare, unpackRGBAToDepth( texture2D( depths, uv ) ) );\r\n \t}\r\n\r\n float getShadow( sampler2D shadowMap, DirectionalLightShadow dirLight, vec4 shadowCoord, vec3 vViewPosition, vec3 vNormal ) {\r\n \t float shadow = 0.0;\r\n\r\n // When shadows for sprites will appear use here for them normals as it done for G-buffer\r\n shadowCoord.xyz += dirLight.shadowBias * vNormal;\r\n shadowCoord.xyz /= shadowCoord.w;\r\n\r\n bvec4 inFrustumVec = bvec4 ( shadowCoord.x >= 0.0, shadowCoord.x <= 1.0, shadowCoord.y >= 0.0, shadowCoord.y <= 1.0 );\r\n bool inFrustum = all( inFrustumVec );\r\n bvec2 frustumTestVec = bvec2( inFrustum, shadowCoord.z <= 1.0 );\r\n bool frustumTest = all( frustumTestVec );\r\n\r\n if ( frustumTest ) {\r\n #ifdef SHADOWMAP_BASIC\r\n \t shadow = texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z );\r\n \t#endif\r\n\r\n \t#ifdef SHADOWMAP_PCF_SHARP\r\n \t vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n float dx0 = - texelSize.x * dirLight.shadowRadius;\r\n float dy0 = - texelSize.y * dirLight.shadowRadius;\r\n float dx1 = + texelSize.x * dirLight.shadowRadius;\r\n float dy1 = + texelSize.y * dirLight.shadowRadius;\r\n\r\n shadow = (\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z )\r\n ) * ( 1.0 / 9.0 );\r\n #endif\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n vec4 vUv = ((projectionMatrix * vec4(vViewPosition, 1.0)) + 1.0) / 2.0;\r\n vec2 vUvNoise = vUv.xy / srcTexelSize * noiseTexelSize;\r\n\r\n vec2 noiseVec = normalize(texture2D(noiseTex, vUvNoise).rg);\r\n mat2 mNoise = mat2(noiseVec.x, noiseVec.y, -noiseVec.y, noiseVec.x);\r\n\r\n vec2 offset;\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < 4; i ++ ) { // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n offset = mNoise * ( normalize( samplesKernel[ i ]) * texelSize * dirLight.shadowRadius );\r\n shadow += texture2DCompare( shadowMap, shadowCoord.xy + offset, shadowCoord.z );\r\n }\r\n #pragma unroll_loop_end\r\n shadow /= float( 4 ); // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n #endif\r\n }\r\n return shadow;//(shadow != 1.0) ? 0.5 : 1.0;//vec4(shadow, shadow, shadow, 1.0);\r\n }\r\n #endif\r\n\r\n /////////////////////////////////////////// Lighting /////////////////////////////////////////////////\r\n\r\n vec3 BRDF_Diffuse_Lambert( const in vec3 diffuseColor ) {\r\n return RECIPROCAL_PI * diffuseColor;\r\n } // validated\r\n\r\n vec3 F_Schlick( const in vec3 specularColor, const in float dotLH ) {\r\n // Original approximation by Christophe Schlick '94\r\n //;float fresnel = pow( 1.0 - dotLH, 5.0 );\r\n // Optimized variant (presented by Epic at SIGGRAPH '13)\r\n float fresnel = exp2( ( -5.55473 * dotLH - 6.98316 ) * dotLH );\r\n return ( 1.0 - specularColor ) * fresnel + specularColor;\r\n } // validated\r\n\r\n float G_BlinnPhong_Implicit( /* const in float dotNL, const in float dotNV */ ) {\r\n // geometry term is (n dot l)(n dot v) / 4(n dot l)(n dot v)\r\n return 0.25;\r\n }\r\n\r\n float D_BlinnPhong( const in float shininess, const in float dotNH ) {\r\n return RECIPROCAL_PI * ( shininess * 0.5 + 1.0 ) * pow( dotNH, shininess );\r\n }\r\n\r\n vec3 BRDF_Specular_BlinnPhong( const in DirectionalLight incidentLight, const in GeometricContext geometry, const in vec3 specularColor, const in float shininess ) {\r\n vec3 halfDir = normalize( incidentLight.direction + geometry.viewDir );\r\n float dotNH = saturate(dot( geometry.normal, halfDir ));\r\n float dotLH = saturate(dot( incidentLight.direction, halfDir ));\r\n\r\n vec3 F = F_Schlick( specularColor, dotLH );\r\n float G = G_BlinnPhong_Implicit( /* dotNL, dotNV */ );\r\n float D = D_BlinnPhong( shininess, dotNH );\r\n\r\n return F * ( G * D );\r\n } // validated\r\n\r\n void RE_Direct_BlinnPhong( const in DirectionalLight directLight, const in GeometricContext geometry, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight, float penumbra ) {\r\n\r\n float dotNL = saturate( dot( geometry.normal, directLight.direction ));\r\n #ifdef TOON_SHADING\r\n if(dotNL < MEDIUM_TOON_RANGE){\r\n dotNL = LOW_TOON_BORDER;\r\n }\r\n else if(dotNL < HIGH_TOON_RANGE){\r\n dotNL = MEDIUM_TOON_BORDER;\r\n }\r\n else{\r\n dotNL = HIGH_TOON_BORDER;\r\n }\r\n #endif\r\n\r\n vec3 irradiance = dotNL * directLight.color;\r\n reflectedLight.directDiffuse += penumbra * irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n reflectedLight.directSpecular += penumbra * irradiance * BRDF_Specular_BlinnPhong( directLight, geometry, material.specularColor, material.specularShininess );\r\n }\r\n\r\n void RE_IndirectDiffuse_BlinnPhong( const in vec3 irradiance, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) {\r\n reflectedLight.indirectDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n }\r\n\r\n vec3 calcLighting(const in GeometricContext geometry, const in BlinnPhongMaterial material, vec3 vViewPosition) {\r\n ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ));\r\n vec3 irradiance = ambientLightColor;\r\n\r\n float shadowMask = 1.0;\r\n // see THREE.WebGLProgram.unrollLoops\r\n \t#pragma unroll_loop_start\r\n \t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n \t #ifdef SHADOWMAP\r\n \t shadowMask = getShadow( directionalShadowMap[ i ], directionalLightShadows[ i ], vDirLightWorldCoord[ i ], vViewPosition, vDirLightWorldNormal[ i ] );\r\n #endif\r\n\r\n \t\t if ( shadowMask > 0.0 ) RE_Direct_BlinnPhong( directionalLights[ i ], geometry, material, reflectedLight, shadowMask );\r\n \t\t}\r\n \t\t#pragma unroll_loop_end\r\n\r\n RE_IndirectDiffuse_BlinnPhong(irradiance, material, reflectedLight);\r\n\r\n return saturate(reflectedLight.indirectDiffuse + reflectedLight.directDiffuse + reflectedLight.directSpecular);\r\n }\r\n#endif\r\n\r\n/////////////////////////////////////////// Dashed Line ///////////////////////////////////////////////\r\n#ifdef DASHED_LINE\r\n uniform float dashedLineSize;\r\n uniform float dashedLinePeriod;\r\n varying float vLineDistance;\r\n#endif\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef CLIP_PLANE\r\n if (vViewPosition.z < clipPlaneValue) discard;\r\n#endif\r\n\r\n#ifdef ZCLIP\r\n if (vViewPosition.z < zClipValue) discard;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = vDirectionalShadowCoord[ i ];\r\n vDirLightWorldNormal[ i ] = vDirectionalShadowNormal[ i ];\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n#endif\r\n\r\n vec4 pixelPosWorld = vec4(vWorldPosition, 1.0);\r\n vec4 pixelPosEye;\r\n\r\n#ifdef SPHERE_SPRITE\r\n\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n vec3 normal;\r\n\r\n/* quick-and-dirty method\r\n normal.xy = ' + INSTANCED_SPRITE_OVERSCALE + ' * (2.0 * vUv - 1.0);\r\n float r2 = dot(normal.xy, normal.xy);\r\n if (r2 > 1.0) discard;\r\n float normalZ = sqrt(1.0 - r2);\r\n normal.z = normalZ;\r\n normal = normal * ( -1.0 + 2.0 * float( gl_FrontFacing ) );\r\n pixelPosEye = vec4(spritePosEye.xyz, 1.0);\r\n pixelPosEye.z += spritePosEye.w * normalZ;\r\n*/\r\n\r\n // ray-trace sphere surface\r\n {\r\n vec3 p;\r\n if (!get_sphere_point(-vViewPosition, p, frontFaced)) discard;\r\n vec4 v = vec4(instOffset.xyz + p * instOffset.w, 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n normal = normalize(normalMatrix * p);\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*p);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(p, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n vec3 normal;\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n float cylinderY = 0.0;\r\n\r\n // ray-trace cylinder surface\r\n {\r\n vec3 p;\r\n if (!get_cylinder_point(-vViewPosition, p, frontFaced)) discard;\r\n\r\n cylinderY = 0.5 * (p.y + 1.0);\r\n\r\n vec4 v = vec4(p, 1.0);\r\n v = vec4(dot(v, matVec1), dot(v, matVec2), dot(v, matVec3), 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n\r\n vec3 localNormal = normalize(vec3(p.x, 0.0, p.z));\r\n normal = vec3(\r\n dot(localNormal, matVec1.xyz),\r\n dot(localNormal, matVec2.xyz),\r\n dot(localNormal, matVec3.xyz));\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*normal);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(normal, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n\r\n normal = normalize(normalMatrix * normal);\r\n }\r\n#endif\r\n\r\n #ifdef ATTR_COLOR\r\n vec3 vertexColor = vColor;\r\n #else\r\n vec3 vertexColor = vec3(1.0, 1.0, 1.0);\r\n #endif\r\n\r\n #ifdef ATTR_COLOR2\r\n #ifdef CYLINDER_SPRITE\r\n float colorCoef = cylinderY; // cylinder parameter is calculated from ray-tracing\r\n #else\r\n float colorCoef = vUv.y; // cylinder parameter is interpolated as tex coord\r\n #endif\r\n // choose either color or color2\r\n vertexColor = mix(vColor2, vColor, step(0.5, colorCoef));\r\n #endif\r\n\r\n // negative red component is a special condition\r\n if (vertexColor.x < 0.0) discard;\r\n\r\n #ifdef DASHED_LINE\r\n if ( mod( vLineDistance, dashedLinePeriod ) > dashedLineSize ) discard;\r\n #endif\r\n\r\n // transparency prepass writes only z, so we don't need to calc the color\r\n #ifdef PREPASS_TRANSP\r\n fragColor = vec4(1.0, 1.0, 1.0, 1.0);\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n return;\r\n #endif\r\n\r\n float totalOpacity = opacity;\r\n\r\n #ifdef ATTR_ALPHA_COLOR\r\n totalOpacity *= alphaCol;\r\n #endif\r\n\r\n // discard fully transparent pixels\r\n if (totalOpacity == 0.0) discard;\r\n\r\n #ifdef FAKE_OPACITY\r\n // discard pixels in checker pattern\r\n vec2 dm_coord = floor(gl_FragCoord.xy);\r\n dm_coord = fract(dm_coord * 0.5);\r\n if (totalOpacity < 1.0 && (dm_coord.x < 0.5 ^^ dm_coord.y < 0.5)) discard;\r\n vec4 diffuseColor = vec4(diffuse, 1.0);\r\n #else\r\n vec4 diffuseColor = vec4(diffuse, totalOpacity);\r\n #endif\r\n\r\n float flipNormal;\r\n #if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n flipNormal = 1.0;\r\n #ifdef DOUBLE_SIDED\r\n flipNormal = float( gl_FrontFacing );\r\n #endif\r\n vec3 normal = normalize( vNormal ) * flipNormal;\r\n #endif\r\n\r\n diffuseColor.rgb *= vertexColor;\r\n\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n\r\n #ifdef NORMALS_TO_G_BUFFER\r\n #if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n vec3 viewNormaInColor = viewNormalSprites;\r\n #else\r\n vec3 viewNormaInColor = viewNormal;\r\n float frontFaced = float( gl_FrontFacing );\r\n #endif\r\n // [-1, 1] -> [0, 1]\r\n viewNormaInColor = 0.5 * viewNormaInColor + 0.5;\r\n gl_FragData[1] = vec4(viewNormaInColor, frontFaced);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n vec3 viewDir;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDir = -pixelPosEye.xyz;\r\n #else\r\n viewDir = vViewPosition;\r\n #endif\r\n GeometricContext geometry = GeometricContext(normal, normalize( viewDir ));\r\n BlinnPhongMaterial material = BlinnPhongMaterial(diffuseColor.rgb, specular, shininess);\r\n vec3 outgoingLight = calcLighting(geometry, material, viewDir);\r\n #else\r\n vec3 outgoingLight = diffuseColor.rgb;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_DEPTH\r\n float depth = 0.0;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n depth = gl_FragDepthEXT;\r\n #else\r\n depth = gl_FragCoord.z;\r\n #endif\r\n fragColor = packDepthToRGBA(depth);\r\n return;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_POS\r\n fragColor = world2colorMatrix * pixelPosWorld;\r\n #else\r\n #ifdef OVERRIDE_COLOR\r\n fragColor = vec4(fixedColor, diffuseColor.a);\r\n #else\r\n fragColor = vec4(outgoingLight, diffuseColor.a);//vec4(vNormal, 1.0);\r\n #endif\r\n\r\n #ifdef USE_FOG\r\n float viewDistance;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDistance = abs(pixelPosEye.z);\r\n #else\r\n viewDistance = vViewPosition.z;\r\n #endif\r\n float fogFactor = smoothstep( fogNear, fogFar, viewDistance) * fogAlpha;\r\n #ifdef FOG_TRANSPARENT\r\n fragColor.a = fragColor.a * (1.0 - fogFactor);\r\n #else\r\n fragColor.rgb = mix( fragColor.rgb, fogColor, fogFactor );\r\n #endif\r\n #endif\r\n\r\n #endif\r\n}\r\n",lights:!0,fog:!0,side:r.DoubleSide}),this.setValues(e)}precisionString(){const{precision:e}=Fn;return`precision ${e} float;\nprecision ${e} int;\n\n`}copy(e){return super.copy(e),this.fragmentShader=e.fragmentShader,this.vertexShader=e.vertexShader,this.uniforms=r.UniformsUtils.clone(e.uniforms),this.defines={...e.defines},this.extensions=e.extensions,this.fog=e.fog,this.instancedPos=e.instancedPos,this.instancedMatrix=e.instancedMatrix,this.attrColor=e.attrColor,this.attrColor2=e.attrColor2,this.attrAlphaColor=e.attrAlphaColor,this.overrideColor=e.overrideColor,this.sphereSprite=e.sphereSprite,this.cylinderSprite=e.cylinderSprite,this.zClip=e.zClip,this.clipPlane=e.clipPlane,this.fakeOpacity=e.fakeOpacity,this.colorFromPos=e.colorFromPos,this.shadowmap=e.shadowmap,this.shadowmapType=e.shadowmapType,this.colorFromDepth=e.colorFromDepth,this.orthoCam=e.orthoCam,this.prepassTransparancy=e.prepassTransparancy,this.dashedLine=e.dashedLine,this.thickLine=e.thickLine,this.fogTransparent=e.fogTransparent,this.normalsToGBuffer=e.normalsToGBuffer,this.toonShading=e.toonShading,this.uberOptions.copy(e.uberOptions),this}createInstance(){const e=new Qn;return e.copy(this),e.uberOptions=Object.create(this.uberOptions),e}setValues(e){if(void 0===e)return;super.setValues(e);const t={},r={};this.fog&&(t.USE_FOG=1),this.instancedPos&&(t.INSTANCED_POS=1),this.instancedMatrix&&(t.INSTANCED_MATRIX=1),this.attrColor&&(t.ATTR_COLOR=1),this.attrColor2&&(t.ATTR_COLOR2=1),this.attrAlphaColor&&(t.ATTR_ALPHA_COLOR=1),this.overrideColor&&(t.OVERRIDE_COLOR=1),this.sphereSprite&&(t.SPHERE_SPRITE=1,r.fragDepth=!0),this.cylinderSprite&&(t.CYLINDER_SPRITE=1,r.fragDepth=!0),this.zClip&&(t.ZCLIP=1),this.clipPlane&&(t.CLIP_PLANE=1),this.fakeOpacity&&(t.FAKE_OPACITY=1),this.lights&&(t.USE_LIGHTS=1),this.colorFromPos&&(t.COLOR_FROM_POS=1),this.shadowmap&&(t.SHADOWMAP=1,"pcf"===this.shadowmapType?t.SHADOWMAP_PCF_SHARP=1:"random"===this.shadowmapType?t.SHADOWMAP_PCF_RAND=1:t.SHADOWMAP_BASIC=1),this.colorFromDepth&&(t.COLOR_FROM_DEPTH=1),this.orthoCam&&(t.ORTHOGRAPHIC_CAMERA=1),this.prepassTransparancy&&(t.PREPASS_TRANSP=1),this.dashedLine&&(t.DASHED_LINE=1),this.thickLine&&(t.THICK_LINE=1),this.fogTransparent&&(t.FOG_TRANSPARENT=1),this.normalsToGBuffer&&(r.drawBuffers=!0,t.NORMALS_TO_G_BUFFER=1),this.toonShading&&(t.TOON_SHADING=1),this.defines=t,this.extensions=r}setUberOptions(e){if(void 0!==e)for(const t in e)e.hasOwnProperty(t)&&(this.uberOptions[t]instanceof r.Color?this.uberOptions[t]=e[t].clone():this.uberOptions[t]=e[t])}clone(e){return e?this.createInstance():super.clone()}updateUniforms(){const e=this;Zn.forEach((t=>{e.uniforms.hasOwnProperty(t)&&(e.uberOptions[t]instanceof r.Color||e.uberOptions[t]instanceof r.Matrix4?e.uniforms[t].value=e.uberOptions[t].clone():e.uniforms[t].value=e.uberOptions[t])}))}}Qn.prototype.uberOptions=Kn;const Jn=Qn;function es(e){class t extends e{constructor(){super(...arguments),this.onBeforeRender=t.prototype.onBeforeRender}onBeforeRender(e,t,r,n,s,i){this._onBeforeRender(e,t,r,n,s,i),this._update()}_onBeforeRender(){}_update(){const{material:e}=this;e&&e instanceof Jn&&e.updateUniforms()}}return t}const ts=es(r.Mesh);const rs=class extends ts{constructor(){super(...arguments),this.castShadow=!0,this.receiveShadow=!0}_onBeforeRender(e,t,r,n,s,i){ts.prototype._onBeforeRender.call(this,e,t,r);const{material:o}=this;o&&o.uniforms.invModelViewMatrix&&(this.modelViewMatrix.multiplyMatrices(r.matrixWorldInverse,this.matrixWorld),o.uniforms.invModelViewMatrix.value.copy(this.modelViewMatrix).invert(),o.uniforms.nearPlaneValue.value=r.near,o.uniformsNeedUpdate=!0)}},ns=es(r.Mesh);class ss extends ns{constructor(e,t){super(e,t),this.castShadow=!0,this.receiveShadow=!0}static _mvLength=(()=>new r.Vector3)();static _center=(()=>new r.Vector3)();static _modelView=(()=>new r.Matrix4)();_onBeforeRender(e,t,r){ns.prototype._onBeforeRender.call(this,e,t,r);const n=this.geometry,{material:s}=this;if(!n.zClip||!s.uberOptions)return;const i=ss._modelView,o=ss._mvLength,a=ss._center;i.multiplyMatrices(this.matrixWorld,r.matrixWorldInverse);const l=o.setFromMatrixColumn(i,0).length();a.copy(n.boundingSphere.center),this.localToWorld(a),s.uberOptions.zClipValue=r.position.z-a.z-l*(.5*n.boundingSphere.radius)}}const is=ss;class os extends r.Group{constructor(e,t){super(),this.geometry=e;const r=this;r.initialized=!1,this.geometry.addEventListener("update",(()=>{r.update()}))}init(){const{children:e}=this;for(let t=e.length-1;t>=0;--t)this.remove(e[t]);const{items:r,userData:n}=this.geometry;for(let e=0,s=r.length;enew r.Matrix4)();static _ray=(()=>new r.Ray)();constructor(e,t,n,s){super(),this._geometry=e,this._geoParams=t;const i=n.createInstance();t.initMaterial(i),this._material=i,this._transforms=s.length>0?s:[new r.Matrix4];const o=this._createMeshes(e);for(let e=0,t=o.length;ee,adjust:function(e){let t=e>>16&255,r=e>>8&255,n=255&e;return.2126*t+.7152*r+.0722*n>127?(t=3*t/10,r=3*r/10,n=3*n/10):(t=255-3*(255-t)/10,r=255-3*(255-r)/10,n=255-3*(255-n)/10),t<<16|r<<8|n},inverse:function(e){return 255-(e>>16&255)<<16|255-(e>>8&255)<<8|255-(255&e)}};function Ns(e,t){let r;if(Ps.hasOwnProperty(t))r=O.hexColor(Ps[t](e));else{const e=parseInt(t,16);r=!Number.isNaN(e)&&t.toLowerCase().startsWith("0x")?O.hexColor(e):"#000000"}return r}const Ls={serial:e=>e.serial,name:e=>e.getVisualName(),elem:e=>e.element.name,residue:e=>e.residue.getType().getName(),sequence:e=>e.residue.getSequence(),chain:e=>e.residue.getChain().getName(),hetatm:e=>e.isHet(),water:e=>"HOH"===e.residue.getType().getName()||"WAT"===e.residue.getType().getName()},Is=function(e,t){return t.replace(/\{\{(\s*\w+\s*)\}\}/g,(t=>{let r=t.replace(/\s+/g,"");return r=r.substring(2,r.length-2).toLowerCase(),Ls.hasOwnProperty(r)?Ls[r](e):"null"}))};const Os=class extends As{_makeGeoArgs(){const e=this._mode.getLabelOpts();return[this._selection.chunks.length,e]}_build(){const e=this._mode.getLabelOpts(),t=this._selection.chunks,{atoms:r,parent:n}=this._selection,s=this._colorer,i=this._geo;for(let o=0,a=t.length;o{for(let t=0;t<=e;++t){const e=s[t],r=e.clone().sub(l).cross(c);i.addVectors(e,r),o[t]=zs(e,i,c,n)}a.setItem(t,o),a.setColor(t,r)})),a.finalize()}_makeGeoArgs(){return this._segmentsHeight=this._polyComplexity,[ks(1,this._polyComplexity),this._segmentsHeight+1,this._selection.chunks.length]}};const Bs=class extends Ds{_build(){const e=this._geo,t=this._mode.getAromaticOffset();this._buildInner(t,((t,r,n)=>{let s=n[0];for(let r=1;r<=this._segmentsHeight;++r){const i=n[r];e.setSegment(t,r-1,s,i),s=i}e.setColor(t,r)})),e.finalize()}_makeGeoArgs(){return this._segmentsHeight=this._mode.getAromaticArcChunks(),[this._selection.chunks.length,this._segmentsHeight,!0]}};const Us=class extends Cs{raycast(e,t){const{residues:r}=this._selection,n=[];this._mesh.raycast(e,n);const s=this._chunksIdc;for(let e=0,i=n.length;es&&e[t-1]._isValid?t-1:t}function a(t){return t{const t=e.getVisualName();a||t!==i?l||t!==o||(l=e.position):a=e.position})),a&&l||(a=n._firstAtom.position,l=n._lastAtom.position),a&&l){const s=l.clone().sub(a),i=n._wingVector,o=n._controlPoint,c=o.clone().add(i),h=o.clone().sub(s),u=h.clone().add(i);e[r]=[h.x,h.y,h.z],t[r]=[u.x,u.y,u.z],e[++r]=[h.x,h.y,h.z],t[r]=[u.x,u.y,u.z],e[++r]=[o.x,o.y,o.z],t[r]=[c.x,c.y,c.z],++r;const d=o.clone().add(s),p=d.clone().add(i);e[r]=[d.x,d.y,d.z],t[r]=[p.x,p.y,p.z],e[++r]=[d.x,d.y,d.z],t[r]=[p.x,p.y,p.z]}}(c,l,h,e[t]),{centerPoints:c,topPoints:l};t===d?u(t,a(t)):(qs(c,l,h++,e[o(d)]),qs(c,l,h++,e[d]));for(let n=t;n<=r;++n)qs(c,l,h++,e[n]);return p===a(p)?u(r,o(r)):(qs(c,l,h++,e[p]),qs(c,l,h,e[a(p)])),{centerPoints:c,topPoints:l}}const Ks=class{constructor(e,t,r,n,s,i){const o=Zs(e,t,r,i);this._topInterp=Xs(o.topPoints,s),this._centerInterp=Xs(o.centerPoints,s),this._shift=.5/(r-t+2),this._valueStep=(1-2*this._shift)/(2*(r-t+1)*(n-1)),this._segmentsCount=n}prepareMatrices(e,t,n){const s=this._segmentsCount,i=new Array(s),o=new r.Vector2(0,0),a=this._topInterp,l=this._centerInterp;let c=this._shift+this._valueStep*(s-1)*e;for(let e=0;e2&&void 0!==arguments[2]&&arguments[2],l=arguments.length>3&&void 0!==arguments[3]&&arguments[3];const c=n.getResidueColor(e,t);a[o]=e._index,i.setItem(o,r,s,l),i.setColor(o++,c)})),this._chunksIdc=a,i.finalize()}updateToFrame(e){const{parent:t}=this._selection,r=this._mode,n=this._colorer,s=r.getTension(),i=this._geo,o=e.getResidues();let a=0;const l=e.needsColorUpdate(n);Js(this._selection.subdivs,o,this._segmentsHeight,s,r,((e,r)=>{i.setItem(a,r),l&&i.setColor(a,n.getResidueColor(e,t)),a++})),i.finalize()}};const ti=class extends Cs{_makeGeoArgs(){const e=this._selection.subdivs;let t=0;for(let r=0,n=e.length;r1&&0!==t&&(h.lerpVectors(_,g,si/b),u.lerpVectors(_,g,1-si/b)),t*=si,h.addScaledVector(w,t),u.addScaledVector(w,t),o.setItem(d,h,u),o.setColor(d++,i.getAtomColor(m,n),i.getAtomColor(f,n))}}o.finalize(),this._chunksIdc=p}updateToFrame(e){const t=this._selection.chunks,{bonds:n}=this._selection,s=this._mode,i=this._colorer,o=this._geo,a=s.drawMultiorderBonds(),l=s.showAromaticLoops(),c=new r.Vector3,h=new r.Vector3,u=new r.Vector3;let d=0;const p=e.needsColorUpdate(i);for(let r=0,s=t.length;r1&&0!==r&&(h.lerpVectors(_,g,si/b),u.lerpVectors(_,g,1-si/b)),r*=si,h.addScaledVector(w,r),u.addScaledVector(w,r),o.setItem(d,h,u),p&&o.setColor(d,e.getAtomColor(i,m),e.getAtomColor(i,f)),d++}}o.finalize()}}};const oi=class extends Kt{constructor(e,t,r,n,s,i,o,a){super();const l=this;this._complex=r,this._mode=s;const c=r.getAtoms(),h=r.getTransforms();r.forEachComponent((u=>{const d=[];let p=0;if(u.forEachAtom((e=>{l._checkAtom(e,o)&&(d[p++]=e.index)})),0===p)return;const m=new e(t,{atoms:c,chunks:d,parent:r},n,s,h,i,a);m._component=u,l.add(m)}))}_checkAtom(e,t){return e.mask&t}getSubset(e,t){const r=[],{children:n}=this;let s=0;for(let i=0,o=n.length;i{let d=0;const p=[];if(u.forEachResidue((e=>{l._checkResidue(e,o)&&(p[d++]=e._index)})),0===d)return;const m=new e(t,{residues:c,chunks:p,parent:r},n,s,h,i,a);m._component=u,l.add(m)}))}checkResidue(e,t){return e._mask&t}getSubset(e,t){const r=[],{children:n}=this;let s=0;for(let i=0,o=n.length;i{const d=u.getMaskedSubdivSequences(o);let p=0;const m=[];for(let e=0,t=d.length;e{const d=[];let p=0;if(u.forEachBond((e=>{const t=e._left,r=e._right;t.mask&o&&r.mask&o&&(d[p++]=e._index)})),0===p)return;const m=new e(t,{bonds:c,chunks:d,parent:r},n,s,h,i,a);m._component=u,l.add(m)}))}getSubset(e,t){const r=[],{children:n}=this;let s=0;for(let i=0,o=n.length;i{const d=[];let p=0;const m=[];let f=0;u.forEachCycle((e=>{const t=e.atoms;let r=0;for(let e=0,n=t.length;e0&&(m[f++]=e)}));const _=new e(t,{cycles:m,atoms:c,chunks:d,parent:r},n,s,h,i,a);_._component=u,l.add(_)}))}getSubset(e,t){const r=[],{children:n}=this;let s=0;for(let i=0,o=n.length;i0&&l.add(d)}return l}}ur(_i.prototype),_i.prototype.id="__",_i.prototype.depGroups=[];const gi=_i;function yi(){return{lineWidth:this.opts.lineWidth}}class xi extends gi{static id="LN";constructor(e){super(e),this.depGroups=this.depGroups.slice(0);const t=this.depGroups;for(let e=0,r=t.length;e1&&void 0!==arguments[1]&&arguments[1];const r=this.elementColors[e];return void 0!==r||t?r:this.defaultElementColor}getResidueColor(e){let t=arguments.length>1&&void 0!==arguments[1]&&arguments[1];const r=this.residueColors[e];return void 0!==r||t?r:this.defaultResidueColor}getChainColor(e){let t=e.charCodeAt(0);return t=(31&(t<0?0:t>=256?t-256:t))%this.chainColors.length,this.chainColors[t]}getSecondaryColor(e){let t=arguments.length>1&&void 0!==arguments[1]&&arguments[1];const r=this.secondaryColors[e];return void 0!==r||t?r:this.defaultSecondaryColor}getSequentialColor(e){const{colors:t}=this,r=t.length;return e<0?t[e%r+r]:t[e%r]}getGradientColor(e,t){const r=this.gradients[t];if(!r)return this.defaultNamedColor;const n=r.length,s=e*(n-1);let i=Math.floor(s);const o=qi(i+1,0,n-1);return i=qi(i,0,n-1),function(e,t,r){const n=1-r;return n*(e>>16&255)+r*(t>>16&255)<<16|n*(e>>8&255)+r*(t>>8&255)<<8|n*(255&e)+r*(255&t)}(r[i],r[o],s-i)}getNamedColor(e){let t=arguments.length>1&&void 0!==arguments[1]&&arguments[1];const r=this.namedColors[e];return void 0!==r||t?r:this.defaultNamedColor}}t().assign(Zi.prototype,{colors:[16777215,16711680,65280,255,8421504],minRangeColor:0,midRangeColor:8355711,maxRangeColor:16777215,defaultElementColor:16777215,elementColors:{},defaultResidueColor:16777215,residueColors:{},chainColors:[16777215],defaultSecondaryColor:16777215,secondaryColors:{},defaultGradientColor:0,defaultNamedColor:16777215,namedColorsArray:[["indianred",13458524],["lightcoral",15761536],["salmon",16416882],["darksalmon",15308410],["lightsalmon",16752762],["crimson",14423100],["red",16711680],["firebrick",11674146],["darkred",9109504],["pink",16761035],["lightpink",16758465],["hotpink",16738740],["deeppink",16716947],["mediumvioletred",13047173],["palevioletred",14381203],["coral",16744272],["tomato",16737095],["orangered",16729344],["darkorange",16747520],["orange",16753920],["gold",16766720],["yellow",16776960],["lightyellow",16777184],["lemonchiffon",16775885],["lightgoldenrodyellow",16448210],["papayawhip",16773077],["moccasin",16770229],["peachpuff",16767673],["palegoldenrod",15657130],["khaki",15787660],["darkkhaki",12433259],["lavender",15132410],["thistle",14204888],["plum",14524637],["violet",15631086],["orchid",14315734],["fuchsia",16711935],["magenta",16711935],["mediumorchid",12211667],["mediumpurple",9662683],["rebeccapurple",6697881],["blueviolet",9055202],["darkviolet",9699539],["darkorchid",10040012],["darkmagenta",9109643],["purple",8388736],["indigo",4915330],["slateblue",6970061],["mediumslateblue",8087790],["darkslateblue",4734347],["greenyellow",11403055],["chartreuse",8388352],["lawngreen",8190976],["lime",65280],["limegreen",3329330],["palegreen",10025880],["lightgreen",9498256],["mediumspringgreen",64154],["springgreen",65407],["mediumseagreen",3978097],["seagreen",3050327],["forestgreen",2263842],["green",32768],["darkgreen",25600],["yellowgreen",10145074],["olivedrab",7048739],["olive",8421376],["darkolivegreen",5597999],["mediumaquamarine",6737322],["darkseagreen",9419919],["lightseagreen",2142890],["darkcyan",35723],["teal",32896],["aqua",65535],["cyan",65535],["lightcyan",14745599],["paleturquoise",11529966],["aquamarine",8388564],["turquoise",4251856],["mediumturquoise",4772300],["darkturquoise",52945],["cadetblue",6266528],["steelblue",4620980],["lightsteelblue",11584734],["powderblue",11591910],["lightblue",11393254],["skyblue",8900331],["lightskyblue",8900346],["deepskyblue",49151],["dodgerblue",2003199],["cornflowerblue",6591981],["royalblue",4286945],["blue",255],["mediumblue",205],["darkblue",139],["navy",128],["midnightblue",1644912],["cornsilk",16775388],["blanchedalmond",16772045],["bisque",16770244],["navajowhite",16768685],["wheat",16113331],["burlywood",14596231],["tan",13808780],["rosybrown",12357519],["sandybrown",16032864],["goldenrod",14329120],["darkgoldenrod",12092939],["peru",13468991],["chocolate",13789470],["saddlebrown",9127187],["sienna",10506797],["brown",10824234],["maroon",8388608],["white",16777215],["snow",16775930],["honeydew",15794160],["mintcream",16121850],["azure",15794175],["aliceblue",15792383],["ghostwhite",16316671],["whitesmoke",16119285],["seashell",16774638],["beige",16119260],["oldlace",16643558],["floralwhite",16775920],["ivory",16777200],["antiquewhite",16444375],["linen",16445670],["lavenderblush",16773365],["mistyrose",16770273],["gainsboro",14474460],["lightgray",13882323],["silver",12632256],["darkgray",11119017],["gray",8421504],["dimgray",6908265],["lightslategray",7833753],["slategray",7372944],["darkslategray",3100495],["black",0]],namedColors:{},gradients:{rainbow:[255,65535,65280,16776960,16711680],temp:[255,32767,16777215,16744192,16711680],hot:[16777215,16744192,16711680],cold:[16777215,32767,255],"blue-red":[255,16777215,16711680],reds:[16777215,16711680],blues:[16777215,255]}});const{namedColorsArray:Ki,namedColors:Qi}=Zi.prototype;for(let e=0,{length:t}=Ki;e=0?this.opts.carbon:this.palette.getElementColor(r)}getResidueColor(e,t){return this.palette.defaultResidueColor}}ho.prototype.id="EL",ho.prototype.name="Element",ho.prototype.shortName="Element";const uo=ho;class po extends co{static id="RT";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){return this.palette.getResidueColor(e._type._name)}}po.prototype.id="RT",po.prototype.name="Residue Type",po.prototype.shortName="Residue";const mo=po;class fo extends co{static id="SQ";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){const r=e._chain;if(r.minSequence===Number.POSITIVE_INFINITY&&r.maxSequence===Number.NEGATIVE_INFINITY)return this.palette.defaultNamedColor;const n=r.minSequence,s=r.maxSequence>n?r.maxSequence:n+1;return this.palette.getGradientColor((e._sequence-n)/(s-n),this.opts.gradient)}}fo.prototype.id="SQ",fo.prototype.name="Sequence",fo.prototype.shortName="Sequence";const _o=fo;class go extends co{static id="CH";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){return this.palette.getChainColor(e.getChain()._name)}}go.prototype.id="CH",go.prototype.name="Chain",go.prototype.shortName="Chain";const yo=go;class xo extends co{static id="SS";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){if(e._type.flags&Ee.Flags.DNA)return this.palette.getSecondaryColor("dna");if(e._type.flags&Ee.Flags.RNA)return this.palette.getSecondaryColor("rna");const r=e.getSecondary();if(r){let e=this.palette.getSecondaryColor(r.type,!0);return void 0===e&&(e=this.palette.getSecondaryColor(r.generic)),e}return this.palette.defaultSecondaryColor}}xo.prototype.id="SS",xo.prototype.name="Secondary Structure",xo.prototype.shortName="Structure";const bo=xo;class wo extends co{static id="UN";getAtomColor(e,t){return this.opts.color}getResidueColor(e,t){return this.opts.color}}wo.prototype.id="UN",wo.prototype.name="Uniform",wo.prototype.shortName="Uniform";const So=wo;class vo extends co{static id="CO";constructor(e){super(e);const t=at.parse(this.opts.subset);this._subsetCached=t.error?at.none():t.selector}getAtomColor(e,t){return this._subsetCached.includesAtom(e)?this.opts.color:this.opts.baseColor}getResidueColor(e,t){const r=this._subsetCached,n=e._atoms;for(let e=0,t=n.length;er.max?1:0:(e.temperature-r.min)/(r.max-r.min),this.palette.getGradientColor(n,r.gradient)):this.palette.defaultGradientColor}getResidueColor(e,t){const{opts:r}=this;if(!r)return this.palette.defaultGradientColor;if(e.temperature){let t=0;return t=r.min===r.max?e.temperature>r.max?1:0:(e.temperature-r.min)/(r.max-r.min),this.palette.getGradientColor(t,r.gradient)}return this.palette.defaultGradientColor}}To.prototype.id="TM",To.prototype.name="Temperature",To.prototype.shortName="Temperature";const Ro=To;class Mo extends co{static id="OC";_getColorByOccupancy(e,t){if(void 0!==e){const r=1-e;return this.palette.getGradientColor(r,t.gradient)}return this.palette.defaultGradientColor}getAtomColor(e,t){const{opts:r}=this;return this._getColorByOccupancy(e.occupancy,r)}getResidueColor(e,t){const{opts:r}=this;return this._getColorByOccupancy(e.occupancy,r)}}Mo.prototype.id="OC",Mo.prototype.name="Occupancy",Mo.prototype.shortName="Occupancy";const Po=Mo;class No extends co{static id="HY";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){let r=this.palette.defaultResidueColor;if(void 0!==e._type.hydrophobicity){const t=-4.5,n=4.5;r=this.palette.getGradientColor((e._type.hydrophobicity-t)/(n-t),this.opts.gradient)}return r}}No.prototype.id="HY",No.prototype.name="Hydrophobicity",No.prototype.shortName="Hydrophobicity";const Lo=No;class Io extends co{static id="MO";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){const r=e._molecule,n=t.getMoleculeCount();return n>1?this.palette.getGradientColor((r.index-1)/(n-1),this.opts.gradient):this.palette.getGradientColor(0,this.opts.gradient)}}Io.prototype.id="MO",Io.prototype.name="Molecule",Io.prototype.shortName="Molecule";const Oo=Io;class Vo extends co{static id="CB";getAtomColor(e,t){const r=this.opts.color,n=(s=r,(i=this.opts.factor)*(s>>16&255)<<16|i*(s>>8&255)<<8|i*(255&s));var s,i;return e.flags&he.Flags.CARBON?r:n}getResidueColor(e,t){return this.opts.color}}Vo.prototype.id="CB",Vo.prototype.name="Carbon",Vo.prototype.shortName="Carbon";const Do=new hr([uo,mo,_o,yo,bo,So,Co,Eo,Ro,Po,Lo,Oo,Vo]);function ko(e){return new r.Color(e,e,e)}const zo=[{id:"DF",name:"Diffuse",shortName:"Diffuse",uberOptions:{diffuse:ko(1),specular:ko(0),shininess:1,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!1}},{id:"SF",name:"Soft Plastic",shortName:"Soft",uberOptions:{diffuse:ko(1),specular:ko(.1),shininess:30,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!1}},{id:"PL",name:"Glossy Plastic",shortName:"Glossy",uberOptions:{diffuse:ko(.56),specular:ko(.28),shininess:100,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!1}},{id:"ME",name:"Metal",shortName:"Metal",uberOptions:{diffuse:ko(.56),specular:ko(.55),shininess:30,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!1}},{id:"TR",name:"Transparent",shortName:"Transparent",uberOptions:{diffuse:ko(1),specular:ko(0),shininess:1,opacity:.5},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!0,toonShading:!1}},{id:"GL",name:"Glass",shortName:"Glass",uberOptions:{diffuse:ko(.5),specular:ko(.65),shininess:100,opacity:.5},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!0,toonShading:!1}},{id:"BA",name:"Backdrop",shortName:"Backdrop",uberOptions:{diffuse:ko(1),specular:ko(0),shininess:1,opacity:1},values:{lights:!1,fog:!1,depthWrite:!1,transparent:!1,toonShading:!1}},{id:"TN",name:"Toon",shortName:"Toon",uberOptions:{diffuse:ko(1),specular:ko(0),shininess:1,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!0}},{id:"FL",name:"Flat",shortName:"Flat",uberOptions:{diffuse:ko(1),specular:ko(0),shininess:0,opacity:1},values:{lights:!1,fog:!0,depthWrite:!0,transparent:!1}}],Fo=new hr(zo);function Bo(e,t,r){const n=e.material.createInstance();n.setValues(t);const s=new e.constructor(e.geometry,n);return s.material.needsUpdate=!0,s.applyMatrix4(e.matrix),s.layers.set(r),s}function Uo(e,t,r){const n=function(e,t){const r=[];return e.traverse((e=>{for(let n=0;n{e.applyMatrix4(t[0]);for(let r=1;r{t.material.setValues({prepassTransparancy:!1,fakeOpacity:!1}),t.material.needsUpdate=!0,t.layers.set(sr.LAYERS.TRANSPARENT);const r=Bo(t,e,sr.LAYERS.PREPASS_TRANSPARENT);t.parent.add(r)}))}}(),processColFromPosMaterial:function(){const e={colorFromPos:!0,transparent:!1,colorFromDepth:!1,lights:!1,shadowmap:!1,fog:!1,overrideColor:!1,fogTransparent:!1,attrColor:!1,attrColor2:!1,attrAlphaColor:!1,fakeOpacity:!1};return function(t,n){n instanceof Jn&&Uo(t,[r.Mesh,r.LineSegments],(t=>{const r=Bo(t,e,sr.LAYERS.COLOR_FROM_POSITION);t.parent.add(r)}))}}(),createShadowmapMaterial:function(){const e={colorFromDepth:!0,orthoCam:!0,lights:!1,shadowmap:!1,fog:!1};return function(t,n){n instanceof Jn&&Uo(t,[r.Mesh,r.LineSegments],(t=>{if(!t.receiveShadow&&t.material.shadowmap&&t.material.setValues({shadowmap:!1}),!t.material.lights)return;if(!t.castShadow)return;if(!sr.belongToSelectLayers(t))return;const r=Bo(t,e,sr.LAYERS.SHADOWMAP);r.isShadowmapMesh=!0,t.parent.add(r)}))}}(),removeShadowmapMaterial:function(e,t){t instanceof Jn&&Uo(e,[r.Mesh,r.LineSegments],(e=>{e.isShadowmapMesh&&e.parent.remove(e)}))},forEachMeshInGroup:Go,countTriangles:function(e){let t=0;return Go(e,(e=>{t+=function(e){const t=e.geometry;if(t instanceof r.InstancedBufferGeometry){const e=t.attributes;for(const n in e)if(e.hasOwnProperty(n)&&e[n]instanceof r.InstancedBufferAttribute){const r=e[n];return(t.index?t.index.array.length/3:0)*r.array.length/r.itemSize}return 0}return t instanceof r.BufferGeometry?t.index?t.index.array.length/3:0:t.faces?t.faces.length:0}(e)})),t}},{selectors:Ho}=Yt;const $o=class{constructor(e,t,r,n){const s={clipPlane:z.now.draft.clipPlane,fogTransparent:z.now.bg.transparent,shadowmap:z.now.shadow.on,shadowmapType:z.now.shadow.type};this.index=e,this.mode=t,this.colorer=r,this.selector=n,this.selectorString="",this.count=0,this.material=new Jn,this.material.setValues(s),this.material.setUberOptions({fogAlpha:z.now.fogAlpha}),this.materialPreset=Fo.first,this.needsRebuild=!0,this.visible=!0,this.setMode(t)}markAtoms(e){return this.count=e.markAtoms(this.selector,1<0){t=new r.Group,t.matrixAutoUpdate=!1,t.matrix=this.geo.matrix;for(let e=0;e{e.objects.push(t)})),o=0;o{const t=e._atoms;for(a=0;a{const r=e._atoms;for(let e=0;e2)return w.error("Can only edit fragments with one or two bound atoms."),!1;this._fragmentBoundAtoms=n;const s=1<{e._left.mask&t?0==(e._right.mask&t)&&(r[e._left.index]=1):e._right.mask&t&&(r[e._right.index]=1)}));const n=[],s=Object.keys(r);for(let t=0,r=s.length;t{r.mask&t&&r.position.applyMatrix4(e)}))}}},{selectors:qo}=Yt;function Zo(e,t){Array.isArray(t)||(t=[t]);const[r,n]=t;return new(e.get(r)||e.first)(n)}class Ko extends ar{constructor(e,t){super(e,t),this._complex=t,this._reprList=[],this._repr=null,this._reprListChanged=!0,this._selectionBit=0,this._reprUsedBits=0,this._selectionCount=0,this._selectionGeometry=new r.Group}getBoundaries(){return this._complex.getBoundaries()}release(){this._selectionGeometry.parent&&this._selectionGeometry.remove(this._selectionGeometry),ar.prototype.release.call(this)}getComplex(){return this._complex}getSelectionCount(){return this._selectionCount}getSelectionGeo(){return this._selectionGeometry}getSelectionBit(){return this._selectionBit}getEditor(){return this._editor}resetReps(e){this._complex&&this._complex.clearAtomBits(-1),this._reprListChanged=!0,this._reprUsedBits=0,this._reprList.length=e.length;for(let t=0,r=e.length;t0?this._reprList[0]:null,this._selectionBit=e.length,this._reprUsedBits|=1<=0&&ethis._reprList.length)return w.error(`Rep ${e} does not exist!`),null;if(e===this._reprList.length){const t=this.repAdd(r);return w.warn(`Rep ${e} does not exist! New representation was created.`),{desc:t.desc,index:e,status:"created"}}const n=this._reprList[e],s={selector:n.selectorString,mode:n.mode.identify(),colorer:n.colorer.identify(),material:n.materialPreset.id};if(r){const i=n.change(r,this._complex,Zo(Xi,r.mode),Zo(Do,r.colorer));if(!t().isEmpty(i)){n.needsRebuild=!0;for(const t in i)i.hasOwnProperty(t)&&(s[t]=i[t],w.debug(`rep[${e}].${t} changed to ${i[t]}`));return i.mode&&n.mode.isSurface&&("ultra"===z.now.resolution||"high"===z.now.resolution)&&(w.report('Surface resolution was changed to "medium" to avoid hang-ups.'),z.set("resolution","medium")),{desc:s,index:e,status:"changed"}}}return{desc:s,index:e,status:""}}repGet(e){return(void 0===e||e instanceof Object)&&(e=this.repCurrent()),e<0||e>=this._reprList.length?null:this._reprList[e]}_getFreeReprIdx(){let e=this._reprUsedBits;for(let t=0;t<=Ko.NUM_REPRESENTATION_BITS;++t,e>>=1)if(0==(1&e))return t;return-1}repAdd(e){if(this._reprList.length>=Ko.NUM_REPRESENTATION_BITS)return null;const r=this._getFreeReprIdx();if(r<0)return null;const n=this.buildSelectorFromMask(1<=t||t<=1)return;const r=this._reprList[e];r.unmarkAtoms(this._complex),this._reprUsedBits&=~(1<=this._reprList.length)return;this._reprList[e].show(!t)}select(e,t){t?this._selectionCount+=this._complex.markAtomsAdditionally(e,1<{e.mask&o&&(e.mask&=a,t._selectionCount--)}))):(n._mask|=o,n.forEachAtom((e=>{e.mask&o||(e.mask|=o,t._selectionCount++)})),s.collectMask(),i&&i.collectMask());else if(s||i){const e=s||i;e._mask&o?(e._mask&=a,e.forEachResidue((e=>{e._mask&o&&(e._mask&=a,e.forEachAtom((e=>{e.mask&o&&(e.mask&=a,t._selectionCount--)})),e._mask&=a)}))):(e._mask|=o,e.forEachResidue((e=>{if(!(e._mask&o)){e._mask|=o,e.forEachAtom((e=>{e.mask&o||(e.mask|=o,t._selectionCount++)}));const r=s?e.getMolecule():e.getChain();r&&r.collectMask()}})))}else this.resetSelectionMask()}expandSelection(){const e=this,t=1<{e._left.mask&t?0==(e._right.mask&t)&&(e._right.mask|=r):e._right.mask&t&&(e._left.mask|=r)}));this._complex.forEachAtom((n=>{n.mask&r&&(n.mask=2147483647&n.mask|t,++e._selectionCount)})),this._complex.updateStructuresMask()}shrinkSelection(){const e=this,t=1<{e._left.mask&t?0==(e._right.mask&t)&&(e._left.mask|=r):e._right.mask&t&&(e._right.mask|=r)})),this._complex.forEachAtom((e=>{e.mask&t&&1===e.bonds.length&&(e.mask|=r)}));const n=~(t|r);this._complex.forEachAtom((t=>{t.mask&r&&(t.mask&=n,--e._selectionCount)})),this._complex.updateStructuresMask()}getSelectedComponent(){const e=1<{n.mask&e&&(null===t?t=n.residue._component:t!==n.residue._component&&(r=!0))})),r?null:t}getSelectionCenter(e,t,r){e.set(0,0,0);let n=0;return this._complex.forEachAtom((s=>{t(s,r)&&(e.add(s.position),n++)})),0!==n&&(e.divideScalar(n),e.applyMatrix4(this.matrix),!0)}needsRebuild(){if(this._reprListChanged)return!0;const e=this._reprList;for(let t=0,r=e.length;t{const r=e._complex;if(!r)return void t();let n=!1;setTimeout((()=>{const s=e._reprList,i=ao.get(z.now.palette)||ao.first;let o=!1;for(let t=0,a=s.length;t0&&(n=qo.chain(r),i=i?qo.or(i,n):n),Object.keys(t).length>0)for(const e in t)t.hasOwnProperty(e)&&(n=qo.and(qo.chain(e),qo.residx(s(t[e]))),i=i?qo.or(i,n):n);e.length>0&&(n=qo.serial(s(e)),i=i?qo.or(i,n):n),i||(i=qo.none())}return i}buildSelectorFromMask(e){const t=this._complex,r=[],n={},s=[];return t.forEachChain((t=>{t._mask&e&&r.push(t._name)})),t.forEachResidue((t=>{if(t._mask&e&&!(t._chain._mask&e)){const e=t._chain._name;e in n?n[e].push(t._index):n[e]=[t._index]}})),t.forEachAtom((t=>{t.mask&e&&!(t.residue._mask&e)&&s.push(t.serial)})),this._buildSelectorFromSortedLists(s,n,r)}forSelectedResidues(e){const t=1<{r._mask&t&&e(r)}))}beginComponentEdit(){if(this._editor)return null;const e=new Xo.ComponentEditor(this);return e.begin()?(this._editor=e,e):null}beginFragmentEdit(){if(this._editor)return null;const e=new Xo.FragmentEditor(this);return e.begin()?(this._editor=e,e):null}finalizeEdit(){this._editor=null}setMaterialValues(e){let t=arguments.length>1&&void 0!==arguments[1]&&arguments[1],n=arguments.length>2&&void 0!==arguments[2]?arguments[2]:void 0;for(let s=0,i=this._reprList.length;s{t instanceof r.Mesh&&(t.material.setValues(e),void 0!==n&&n(t),t.material.needsUpdate=!0)}))}}setUberOptions(e){for(let t=0,r=this._reprList.length;t{e.mask|=n})),this._selectionCount=this._complex.countAtomsByMask(n),this._complex.updateStructuresMask(),this.buildSelectorFromMask(n)}}Ko.NUM_REPRESENTATION_BITS=30;const Qo=Ko,Jo=r.UniformsUtils.merge([{volumeDim:{type:"v3",value:new r.Vector3(512,512,512)},tileTex:{type:"t",value:null},tileTexSize:{type:"v2",value:new r.Vector2(512,512)},tileStride:{type:"v2",value:new r.Vector2(512,512)},boxAngles:{type:"v3",value:new r.Vector3(1,1,1)},delta:{type:"v3",value:new r.Vector3(0,0,0)},_isoLevel0:{type:"v2",value:new r.Vector3(.5,.75,1)},_flipV:{type:"f",value:0},_BFLeft:{type:"t",value:null},_BFRight:{type:"t",value:null},_FFLeft:{type:"t",value:null},_FFRight:{type:"t",value:null},_WFFLeft:{type:"t",value:null},_WFFRight:{type:"t",value:null}}]);function ea(e,t){const n=r.UniformsUtils.clone(t);for(const t in e)n.hasOwnProperty(t)&&(n[t].value=e[t]);return n}function ta(e,t){return{uniforms:ea(e,{}),vertexShader:"varying vec3 pos;\r\n\r\nvoid main() {\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n pos = position.xyz + 0.5;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n}",fragmentShader:"varying vec3 pos;\r\n\r\nvoid main() {\r\n gl_FragColor = vec4(pos, 0.5);\r\n}",transparent:!1,depthTest:!1,depthWrite:!1,side:t}}class ra extends r.ShaderMaterial{constructor(e){super(ta(e,r.BackSide))}}class na{constructor(e,t,n,s){this.uniforms=ea(e,t),this.vertexShader=n,this.fragmentShader=s,this.transparent=!1,this.depthTest=!1,this.depthWrite=!1,this.side=r.FrontSide}}class sa extends r.ShaderMaterial{constructor(e){const t=r.UniformsUtils.merge([{aspectRatio:{type:"f",value:0},farZ:{type:"f",value:0},tanHalfFOV:{type:"f",value:0},matWorld2Volume:{type:"4fv",value:new r.Matrix4}}]);super(new na(e,t,"varying vec4 volPos;\r\nuniform float aspectRatio;\r\nuniform float farZ;\r\nuniform float tanHalfFOV;\r\nuniform mat4 matWorld2Volume;\r\n\r\nvoid main() {\r\n // rescale plane to fill in the whole far plane area seen from camera\r\n vec3 pos = position.xyz;\r\n pos.x = pos.x * tanHalfFOV * farZ * aspectRatio;\r\n pos.y = pos.y * tanHalfFOV * farZ;\r\n // common transformation\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(pos, 1.0);\r\n // calc pos in volume CS\r\n volPos = matWorld2Volume * modelMatrix * vec4(pos, 1.0);\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n volPos = volPos + 0.5;\r\n volPos.w = 0.5;\r\n}\r\n","varying vec4 volPos;\r\n\r\nvoid main() {\r\n gl_FragColor = volPos;\r\n}"))}}class ia extends r.ShaderMaterial{constructor(e){super(ta(e,r.FrontSide))}}class oa extends r.ShaderMaterial{constructor(e){const t=new na(e,Jo,"varying vec4 screenSpacePos;\r\n\r\nvoid main() {\r\n screenSpacePos = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n gl_Position = screenSpacePos;\r\n}","uniform mat4 projectionMatrix;\r\n\r\n// 3D volume texture\r\nuniform vec3 volumeDim; // volume dimensions, pixels\r\nuniform sampler2D tileTex; // tiled texture containing all Z-slices of a 3D data\r\nuniform vec2 tileTexSize; // size of tiled texture, pixels\r\nuniform vec2 tileStride; // UV stride between slices in tile tex, pixels\r\n\r\nuniform vec3 boxAngles;//value of angles({x: alpha, y:beta, z:gamma}) types 1 - if angle is obtuse, 0 - if acute\r\nuniform vec3 delta; //Projection box delta's from non-orthogonal origin axes; {x: XY, y : XZ, z: YZ}\r\n\r\nuniform vec3 _isoLevel0;\r\nuniform float _flipV;\r\nuniform sampler2D _BFLeft;\r\nuniform sampler2D _BFRight;\r\nuniform sampler2D _FFLeft;\r\nuniform sampler2D _FFRight;\r\nuniform sampler2D _WFFLeft;\r\nuniform sampler2D _WFFRight;\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\n#define NO_COLOR vec4(0., 0., 0., 0.)\r\n\r\nvec4 sample3DTexture(vec3 texCoord) {\r\n // a pair of Z slices is determined by nearest slice border\r\n float zSliceBorder = floor(texCoord.z * volumeDim.z + 0.5);\r\n float zSliceNumber1 = max(zSliceBorder - 1.0, 0.0);\r\n float zSliceNumber2 = min(zSliceBorder, volumeDim.z - 1.0);\r\n\r\n float rowTiles = floor(tileTexSize.x / tileStride.x);\r\n\r\n // calculate coords in tile texture for both slices\r\n vec2 tileOffset = vec2(mod(zSliceNumber1, rowTiles), floor(zSliceNumber1 / rowTiles));\r\n vec2 texCoordSlice1 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n tileOffset = vec2(mod(zSliceNumber2, rowTiles), floor(zSliceNumber2 / rowTiles));\r\n vec2 texCoordSlice2 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n\r\n // bilinear filtering\r\n vec4 colorSlice1 = texture2D(tileTex, texCoordSlice1);\r\n vec4 colorSlice2 = texture2D(tileTex, texCoordSlice2);\r\n float weightSlice2 = texCoord.z * volumeDim.z - (zSliceNumber1 + 0.5);\r\n return mix(colorSlice1, colorSlice2, weightSlice2);\r\n}\r\n\r\nvec4 sample3DTextureInclined(vec3 boxCoord) { // delta:{ x: XY, y : XZ, z: YZ }\r\n vec3 textCoord = boxCoord;\r\n vec2 currDelta = mix(boxCoord.zz, vec2(1., 1.) - boxCoord.zz, boxAngles.yx) * delta.yz;\r\n\r\n textCoord.y = (boxCoord.y - currDelta.y) / (1. - delta.z);\r\n if (textCoord.y < 0.0 || textCoord.y > 1.0)\r\n return NO_COLOR;\r\n\r\n currDelta.x += mix(textCoord.y, 1.0 - textCoord.y, boxAngles.z) * delta.x;\r\n\r\n textCoord.x = (boxCoord.x - currDelta.x) / (1. - delta.x - delta.y);\r\n if (textCoord.x < 0.0 || textCoord.x > 1.0)\r\n return NO_COLOR;\r\n\r\n return sample3DTexture(textCoord);\r\n}\r\n\r\nfloat CalcColor(vec3 iter, vec3 dir) {\r\n float d = 1. / 128.;\r\n vec3 dx = vec3(d, 0.0, 0.0);\r\n vec3 dy = vec3(0.0, d, 0.0);\r\n vec3 dz = vec3(0.0, 0.0, d);\r\n\r\n // #Opt: coordInc.x:(iter + dx).x > 1. ? 0.: sample3DTextureInclined(iter + dx).x,\r\n vec3 coordInc = mix(\r\n vec3(\r\n sample3DTextureInclined(iter + dx).x,\r\n sample3DTextureInclined(iter + dy).x,\r\n sample3DTextureInclined(iter + dz).x\r\n ),\r\n vec3(0. ,0. , 0.),\r\n vec3(floor((iter + dx).x), floor((iter + dy).y), floor((iter + dz).z))\r\n );\r\n\r\n // #Opt: coordDec.x:(iter - dx).x < 0. ? 0.: sample3DTextureInclined(iter - dx).x,\r\n vec3 coordDec = mix(\r\n vec3(0. ,0. , 0.),\r\n vec3(\r\n sample3DTextureInclined(iter - dx).x,\r\n sample3DTextureInclined(iter - dy).x,\r\n sample3DTextureInclined(iter - dz).x\r\n ),\r\n vec3(ceil((iter - dx).x), ceil((iter - dy).y), ceil((iter - dz).z))\r\n );\r\n\r\n vec3 N = normalize(coordInc - coordDec);\r\n float dif = max(0.0, dot(N, dir));\r\n return dif;\r\n}\r\n\r\nvec3 AccuracyIso(vec3 left, vec3 right, float volLeft, float threshold) {\r\n for (int i = 0; i < 5; i++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if ((volLeft - threshold) * (vol - threshold) < 0.)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec3 CorrectIso(vec3 left, vec3 right, float tr) {\r\n for (int j = 0; j < 5; j++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if (vol < tr)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec4 GetIso1(vec3 start, vec3 back, float molDist, vec3 dir, float tr, int count) {\r\n float vol, stepSize = (float(count) + 2.) / float(STEPS_COUNT);\r\n vec3 step = stepSize * dir, iterator = start, left, right;\r\n vec4 acc = NO_COLOR;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n vol = sample3DTextureInclined(iterator).r;\r\n if (length(iterator - back) <= stepSize || (vol > tr))\r\n break;\r\n }\r\n\r\n if (vol > tr)\r\n acc = vec4(CorrectIso(iterator, iterator - step, tr).xyz, 1.);\r\n\r\n return acc;\r\n}\r\n\r\nfloat easeOut(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return 1.0 - (1.0 - t) * (1.0 - t);\r\n}\r\n\r\nfloat easeIn(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return t * t;\r\n}\r\n\r\nvec3 GetColSimple(float vol) {\r\n float t = easeOut(_isoLevel0.x, _isoLevel0.y, vol);\r\n float s = easeIn(_isoLevel0.y, _isoLevel0.z, vol);\r\n return vec3(0.5, 0.6, 0.7) * (1.0 - t) + 2.0 * vec3(s, 0, 0);\r\n}\r\n\r\nvec4 VolRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 acc = NO_COLOR, iso;\r\n vec3 iterator = start, sumColor = vec3(0., 0., 0.);\r\n float stepSize, alpha, sumAlpha = 0.0, vol, curStepSize, molD;\r\n vec3 step, col, colOld, right;\r\n float tr0 = _isoLevel0.x;\r\n float dif, r, kd, finish;\r\n int count = 0, stopMol = 0;\r\n\r\n for (int k = 0; k < 3; k++) {\r\n stepSize = (float(k) + 2.) / float(STEPS_COUNT);\r\n kd = 140. * tr0 * stepSize;\r\n r = 1. - kd;\r\n step = stepSize * dir;\r\n iso = GetIso1(iterator, back, molDist, dir, tr0, k);\r\n if (iso.a < 0.1 || length(iso.xyz - start) > molDist)\r\n break;\r\n iterator = iso.xyz;\r\n dif = 1.;// CalcColor(iterator, dir);\r\n colOld = GetColSimple(tr0);\r\n curStepSize = stepSize;\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n molD = length(iterator - start);\r\n vol = sample3DTextureInclined(iterator).r;\r\n finish = distance(iterator, back) - stepSize;\r\n if (finish < 0.0 || vol < tr0 || (sumAlpha > 0.97) || molD > molDist)\r\n break;\r\n alpha = (1. - r);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4.* colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n colOld = col;\r\n } // for i\r\n\r\n if (finish < 0.0 || sumAlpha > 0.97)\r\n break;\r\n\r\n if (molD > molDist) {\r\n curStepSize = stepSize - (molD - molDist);\r\n right = iterator - (molD - molDist) * dir;\r\n vol = sample3DTextureInclined(right).r;\r\n } else {\r\n vec3 left = iterator - step;\r\n right = CorrectIso(left, iterator, tr0);\r\n curStepSize = distance(left, right);\r\n vol = tr0;\r\n }\r\n\r\n alpha = (1. - r) * curStepSize / stepSize;\r\n dif = 1.;// CalcColor(right, dir);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * curStepSize / stepSize * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4. * colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n\r\n if (molD > molDist)\r\n break;\r\n } // for k\r\n acc.rgb = 1. * sumColor / sumAlpha;\r\n acc.a = sumAlpha;\r\n return acc;\r\n}\r\n\r\nvec4 VolRender1(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n float stepSize = 1.0 / float(STEPS_COUNT);\r\n float len = length(back - start);\r\n vec3 step = stepSize * dir;\r\n vec3 iterator = start;\r\n float acc = 0.0;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n if (float(i) * stepSize > len)\r\n break;\r\n iterator = iterator + step;\r\n if (sample3DTextureInclined(iterator).r > _isoLevel0.x)\r\n acc += 10. * sample3DTextureInclined(iterator).r / float(STEPS_COUNT);\r\n }\r\n\r\n return vec4(1.,1.,1., acc);\r\n}\r\n\r\nvec4 IsoRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 tst = GetIso1(start, back, 2., dir, _isoLevel0.x, 0);\r\n vec4 col = NO_COLOR;\r\n\r\n if (length(tst.xyz - start) < molDist && tst.a > 0.1) {\r\n float dif = CalcColor(tst.xyz, dir);\r\n dif = 0.9 * dif * dif;\r\n col = vec4(dif, dif, dif, 1);\r\n }\r\n return col;\r\n}\r\n\r\nvec4 VolRender2(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n return sample3DTexture(start);\r\n}\r\n\r\nvoid main() {\r\n vec3 tc = screenSpacePos.xyz / screenSpacePos.w * 0.5 + 0.5;\r\n\r\n if (_flipV > 0.0) {\r\n tc.y = 1.0 - tc.y;\r\n }\r\n\r\n vec3 start;\r\n vec3 back;\r\n vec3 molBack;\r\n if (projectionMatrix[0][2] < 0.0) {\r\n start = texture2D(_FFLeft, tc.xy).xyz;\r\n back = texture2D(_BFLeft, tc.xy).xyz;\r\n molBack = texture2D(_WFFLeft, tc.xy).xyz;\r\n } else {\r\n start = texture2D(_FFRight, tc.xy).xyz;\r\n back = texture2D(_BFRight, tc.xy).xyz;\r\n molBack = texture2D(_WFFRight, tc.xy).xyz;\r\n }\r\n\r\n vec3 dir = normalize(back - start);\r\n\r\n float molDist = 2.0;\r\n if (length(molBack) > 0.001) {\r\n molDist = distance(start, molBack);\r\n }\r\n\r\n #ifdef ISO_MODE\r\n gl_FragColor = IsoRender(start, back, molDist, dir);\r\n #else\r\n gl_FragColor = VolRender(start, back, molDist, dir);\r\n #endif\r\n}\r\n");t.transparent=!0,t.depthTest=!0,super(t),this.updateDefines()}updateDefines(){this.defines={ISO_MODE:z.now.modes.VD.isoMode,STEPS_COUNT:100*z.now.modes.VD.polyComplexity[z.now.resolution]},this.needsUpdate=!0}}const aa={BackFacePosMaterial:ra,BackFacePosMaterialFarPlane:sa,FrontFacePosMaterial:ia,VolumeMaterial:oa};class la extends r.Mesh{volumeInfo={};constructor(){const e=new r.BufferGeometry;super(e),this.clipPlane=new r.Plane;const t=new r.Vector3(.5,.5,.5);this.size=t,this.cullFlag=[!0,!0,!0,!0,!0,!0,!0,!0,!1,!1,!1,!1,!1,!1],this.faces=[{indices:[],norm:new r.Vector3(0,0,-1)},{indices:[],norm:new r.Vector3(0,0,1)},{indices:[],norm:new r.Vector3(0,-1,0)},{indices:[],norm:new r.Vector3(0,1,0)},{indices:[],norm:new r.Vector3(-1,0,0)},{indices:[],norm:new r.Vector3(1,0,0)},{indices:[],norm:new r.Vector3(0,0,0)}],this.vertices=[new r.Vector3(-t.x,-t.y,-t.z),new r.Vector3(-t.x,t.y,-t.z),new r.Vector3(t.x,-t.y,-t.z),new r.Vector3(t.x,t.y,-t.z),new r.Vector3(-t.x,-t.y,t.z),new r.Vector3(-t.x,t.y,t.z),new r.Vector3(t.x,-t.y,t.z),new r.Vector3(t.x,t.y,t.z),new r.Vector3(0,0,0),new r.Vector3(0,0,0),new r.Vector3(0,0,0),new r.Vector3(0,0,0),new r.Vector3(0,0,0),new r.Vector3(0,0,0)],e.setAttribute("position",new r.BufferAttribute(new Float32Array(3*this.vertices.length),3)),this.name="VolumeMesh"}static _corners=[[-1,-1,-1,0,4,8],[1,-1,-1,0,5,9],[1,1,-1,1,5,10],[-1,1,-1,1,4,11],[-1,-1,1,2,6,8],[1,-1,1,2,7,9],[1,1,1,3,7,10],[-1,1,1,3,6,11]];static _edges=[[0,1,0,-1,-1],[2,3,0,1,-1],[4,5,0,-1,1],[6,7,0,1,1],[0,3,-1,0,-1],[1,2,1,0,-1],[4,7,-1,0,1],[5,6,1,0,1],[0,4,-1,-1,0],[1,5,1,-1,0],[2,6,-1,1,0],[3,7,1,1,0]];static _edgeIntersections=function(){const e=[];for(let t=0;t<12;++t)e.push(new r.Vector3);return e}();_updateVertices(){const e=la._corners,t=la._edges,n=la._edgeIntersections;let s;const i=this.clipPlane.normal,o=this.clipPlane.constant,a=this.vertices,{size:l}=this,c=[0,0,0,0,0,0,0,0],h=[1,1,1,1,1,1,1,1,1,1,1,1],u=new r.Vector3;let d=null;function p(){if(0===i.x)return 0;const e=-(i.dot(u)+o)/i.x;return-l.x<=e&&e<=l.x?(d.set(e,u.y,u.z),e===l.x?2:e===-l.x?-2:1):0}function m(){if(0===i.y)return 0;const e=-(i.dot(u)+o)/i.y;return-l.y<=e&&e<=l.y?(d.set(u.x,e,u.z),e===l.y?2:e===-l.y?-2:1):0}function f(){if(0===i.z)return 0;const e=-(i.dot(u)+o)/i.z;return-l.z<=e&&e<=l.z?(d.set(u.x,u.y,e),e===l.z?2:e===-l.z?-2:1):0}for(let e=0;e<12;++e){const r=t[e];d=n[e],u.set(r[2],r[3],r[4]),u.multiply(l);let s=0;0===r[2]&&(s=p()),0===r[3]&&(s=m()),0===r[4]&&(s=f()),-2===s?c[r[0]]=1:2===s?c[r[1]]=1:0===s&&(h[e]=0)}const _={indices:[],norm:i.clone().negate()};let g=8;for(s=0;s<8;++s)1===c[s]&&(a[g].set(e[s][0],e[s][1],e[s][2]).multiply(l),_.indices.push(g++),h[e[s][3]]=0,h[e[s][4]]=0,h[e[s][5]]=0);for(s=0;s<12;++s)1===h[s]&&(a[g].copy(n[s]),_.indices.push(g++));this.faces[6]=_;const y=new r.Vector3,x=new r.Vector3;for(this.clipPlane.coplanarPoint(x),s=0;s=0):s<8+_.indices.length&&(this.cullFlag[s]=!0);const b=this.geometry.getAttribute("position");let w=0;for(s=0;se.z===-i.z)),this._collectVertices(this.faces[1],(e=>e.z===i.z)),this._collectVertices(this.faces[2],(e=>e.y===-i.y)),this._collectVertices(this.faces[3],(e=>e.y===i.y)),this._collectVertices(this.faces[4],(e=>e.x===-i.x)),this._collectVertices(this.faces[5],(e=>e.x===i.x));const o=new r.Vector3,a=new r.Vector3,l=new r.Vector3;for(t=0;t=3&&(c+=3*(n.indices.length-2));let h=0;const u=new Uint16Array(c);for(t=0;t(s+e*n.sd)/i;this.material.uniforms._isoLevel0.value.set(o(e),o(t),o(r))}static _nearClipPlaneOffset=.2;static _pos=(()=>new r.Vector3)();static _norm=(()=>new r.Vector3)();static _norm4D=(()=>new r.Vector4)();static _matrixWorldToLocal=(()=>new r.Matrix4)();static _clipPlane=(()=>new r.Plane)();rebuild(e){const t=la._nearClipPlaneOffset,r=la._pos,n=la._norm,s=la._norm4D,i=la._matrixWorldToLocal,o=la._clipPlane;this._updateIsoLevel(),e.getWorldDirection(n),e.getWorldPosition(r),r.addScaledVector(n,e.near+t),i.copy(this.matrixWorld).invert(),r.applyMatrix4(i),s.set(n.x,n.y,n.z,0),s.applyMatrix4(i),n.copy(s),n.normalize(),o.setFromNormalAndCoplanarPoint(n,r),this.clipPlane.equals(o)||(this.clipPlane=o.clone(),this._updateVertices(),this._updateIndices())}}const ca=la;class ha{static _projectionTable={XY:["x",2],XZ:["y",1],YZ:["z",0]};constructor(e,t){const{delta:n}=t,{obtuseAngle:s}=t,i=new r.Vector3;e.getSize(i),i.multiplyScalar(.5);const o=this._getBaseVertices(n,s),a=new r.BufferGeometry,l=[];for(let e=0;e<4;e++)l.push(o[e].clone().multiply(i)),l.push(o[(e+1)%4].clone().multiply(i));const c=new r.Vector3(2*i.x*(1-n.x-n.y),0,0);for(let e=0;e<8;e++)l.push(l[e].clone().add(c));for(let e=0;e<4;e++)l.push(l[2*e].clone()),l.push(l[2*e+8].clone());const h=new r.Vector3;e.getCenter(h),l.forEach((e=>e.add(h)));const u=function(e){const t=e.length,r=new Float32Array(3*t);for(let n=0;n{const i=e[n[r][0]];return(-.5*(s-1)+s*t[n[r][1]])*i};return[new r.Vector3(2*(s("XZ",1)+s("XY",1))-1,2*s("YZ",1)-1,-1),new r.Vector3(2*(s("XZ",-1)+s("XY",1))-1,2*s("YZ",-1)-1,1),new r.Vector3(2*(s("XZ",-1)+s("XY",-1))-1,1-2*s("YZ",1),1),new r.Vector3(2*(s("XZ",1)+s("XY",-1))-1,1-2*s("YZ",-1),-1)]}getMesh(){return this._lines}}const ua=ha;const da=class{constructor(e,t,n){const s=this._initPlaneGeo(t,n),i=new aa.BackFacePosMaterialFarPlane;this._plane=new fs.Mesh(s,i),this._plane.frustumCulled=!1,this._plane.doubleSided=!0;const o=new r.Matrix4;this._plane._onBeforeRender=function(t,n,s,i,a,l){const{material:c}=this;if(!e||!c)return;const h=new r.Vector4(0,0,-(s.far-.1),1);h.applyMatrix4(s.matrixWorld),this.matrix.identity(),this.matrix.makeTranslation(h.x,h.y,h.z),this.matrixWorld.copy(this.matrix),this.modelViewMatrix.multiplyMatrices(s.matrixWorldInverse,this.matrixWorld),this.normalMatrix.getNormalMatrix(this.modelViewMatrix);const u=e.matrixWorld;o.copy(u).invert(),c.uniforms.aspectRatio.value=s.aspect,c.uniforms.farZ.value=s.far,c.uniforms.tanHalfFOV.value=Math.tan(.5*r.MathUtils.DEG2RAD*s.fov),c.uniforms.matWorld2Volume.value=o},this._plane.layers.set(sr.LAYERS.VOLUME_BFPLANE)}_initPlaneGeo(e,t){const n=new r.BufferGeometry;e=e||1,t=t||1;const s=new Float32Array([-.5*e,.5*t,0,.5*e,.5*t,0,-.5*e,-.5*t,0,.5*e,-.5*t,0]);return n.setAttribute("position",new r.BufferAttribute(s,3)),n.setIndex([0,2,1,2,3,1]),n}getMesh(){return this._plane}};const pa=class extends ar{constructor(e,t){super(e,t),this._mesh=new ca,this._mesh.setDataSource(t),this.add(this._mesh),this._frame=new ua(this.getBoundaries().boundingBox,this._mesh.volumeInfo),this.add(this._frame.getMesh()),this.showFrame(z.now.modes.VD.frame),this._farPlane=new da(this._mesh,2,2),this.add(this._farPlane.getMesh())}getBoundaries(){const e=this._dataSource.getBox(),t=new r.Sphere;return e.getBoundingSphere(t),{boundingBox:e,boundingSphere:t}}getMesh(){return this._mesh}showFrame(e){this._frame.getMesh().material.visible=e}};const ma=class extends hr{constructor(){super(arguments.length>0&&void 0!==arguments[0]?arguments[0]:[],["types"])}find(e){let t=[];if(e.type)t=this._dict.types[e.type.toLowerCase()]||[];else if(e.source)return this._list.filter((t=>t.canProbablyLoad&&t.canProbablyLoad(e.source)));return[...t]}};class fa extends g{constructor(e,t){super(),this._source=e,this._options=t||{},this._abort=!1,this._agent=null}load(){return Promise.reject(new Error("Loading from this source is not implemented"))}abort(){this._abort=!0,this._agent&&this._agent.abort()}static extractName(e){}}ur(fa.prototype);class _a extends fa{constructor(e,t){super(e,t),t=this._options,this._binary=!0===t.binary}load(){return new Promise(((e,t)=>{if(this._abort)throw new Error("Loading aborted");const r=this._source,n=this._agent=new FileReader;n.addEventListener("load",(()=>{e(n.result)})),n.addEventListener("error",(()=>{t(n.error)})),n.addEventListener("abort",(()=>{t(new Error("Loading aborted"))})),n.addEventListener("progress",(e=>{this.dispatchEvent(e)})),this._binary?n.readAsArrayBuffer(r):n.readAsText(r)}))}static canProbablyLoad(e){return File&&e instanceof File||Blob&&e instanceof Blob}static extractName(e){return e&&e.name}}_a.types=["file","blob"];const ga=/^(https?|ftp):\/\//i;class ya extends fa{constructor(e,t){super(e,t),t=this._options,this._binary=!0===t.binary}load(){return new Promise(((e,t)=>{if(this._abort)throw new Error("Loading aborted");const r=this._source,n=this._agent=new XMLHttpRequest;n.addEventListener("load",(()=>{200===n.status?e(n.response):t(new Error(`HTTP ${n.status} while fetching ${r}`))})),n.addEventListener("error",(()=>{t(new Error("HTTP request failed"))})),n.addEventListener("abort",(()=>{t(new Error("Loading aborted"))})),n.addEventListener("progress",(e=>{this.dispatchEvent(e)})),n.open("GET",r),this._binary?n.responseType="arraybuffer":n.responseType="text",n.send()}))}static canProbablyLoad(e){return t().isString(e)&&ga.test(e)}static extractName(e){if(e){const t=(e.indexOf("?")+1||e.lastIndexOf("#")+1||e.length+1)-1;return e.slice(e.lastIndexOf("/",t)+1,t)}}}ya.types=["url"];class xa extends fa{load(){return new Promise((e=>{if(this._abort)throw new Error("Loading aborted");e(this._source)}))}static canProbablyLoad(e){return!1}}xa.types=["immediate"];const ba=new ma([_a,ya,xa]);const wa=class extends hr{constructor(){super(arguments.length>0&&void 0!==arguments[0]?arguments[0]:[],["formats","extensions"])}find(e){let t=[];return e.format?t=this._dict.formats[e.format.toLowerCase()]||[]:e.ext&&(t=this._dict.extensions[e.ext.toLowerCase()]||[]),0===t.length&&!e.format&&e.data?this._list.filter((t=>t.canProbablyParse&&t.canProbablyParse(e.data))):[...t]}};class Sa{constructor(e,t){this._data=e,this._options=t||{},this._abort=!1}parseSync(){throw new Error("Parsing this type of data is not implemented")}parse(){return new Promise(((e,t)=>{setTimeout((()=>{try{return this._abort?t(new Error("Parsing aborted")):e(this.parseSync())}catch(e){return t(e)}}))}))}getModel(){return this.model._parseHeader(this._data),this.model}abort(){this._abort=!0}}ur(Sa.prototype);class va{constructor(){this.matrices=[],this._matrix=null,this._matrixIndex=-1}parse(e){let t=this._matrix;if(" SMTRY"===e.readString(12,18)){const n=e.readCharCode(19)-49,s=e.readString(20,80).trim().split(/\s+/),i=parseInt(s[0],10);null!==this._matrix&&i===this._matrixIndex||(this._matrixIndex=i,this._matrix=t=new r.Matrix4,this.matrices[this.matrices.length]=t);const{elements:o}=t;o[n]=parseFloat(s[1]),o[n+4]=parseFloat(s[2]),o[n+8]=parseFloat(s[3]),o[n+12]=parseFloat(s[4])}}}va.prototype.id=290;const Ca=va,{Assembly:Aa}=Yt;class Ea{constructor(e){this._complex=e,this.assemblies=[],this._assembly=null,this._matrix=null,this._matrixIndex=-1}parse(e){let t=this._assembly,n=this._matrix;if(t&&" BIOMT"===e.readString(12,18)){const s=e.readCharCode(19)-49,i=e.readString(20,80).trim().split(/\s+/),o=parseInt(i[0],10);null!==this._matrix&&o===this._matrixIndex||(this._matrixIndex=o,this._matrix=n=new r.Matrix4,t.addMatrix(n));const{elements:a}=n;a[s]=parseFloat(i[1]),a[s+4]=parseFloat(i[2]),a[s+8]=parseFloat(i[3]),a[s+12]=parseFloat(i[4])}else if(t&&"CHAINS:"===e.readString(35,41)){const r=e.readString(42,80).split(",");for(let e=0,n=r.length;e0&&t.addChain(n)}}else"BIOMOLECULE:"===e.readString(12,23)&&(this._matrix=null,this._matrixIndex=-1,this._assembly=t=new Aa(this._complex),this.assemblies.push(t))}}Ea.prototype.id=350;const Ta=Ea;const Ra=class{constructor(e){this._data=e,this._start=0,this._nextCR=-1,this._nextLF=-1,this._next=-1,this._end=e.length,this.next()}readLine(){return this._data.slice(this._start,this._next)}readChar(e){return(e=this._start+e-1)=this._end}next(){const e=this._next+1;this._start=ethis._nextCR&&(this._nextCR=(this._data.indexOf("\r",this._start)+1||this._end+1)-1),this._start>this._nextLF&&(this._nextLF=(this._data.indexOf("\n",this._start)+1||this._end+1)-1),this._next=this._nextCR+1t&&o.addBond(t,r,0,Oa.BondType.UNKNOWN,!0),n&&n>t&&o.addBond(t,n,0,Oa.BondType.UNKNOWN,!0),s&&s>t&&o.addBond(t,s,0,Oa.BondType.UNKNOWN,!0),i&&i>t&&o.addBond(t,i,0,Oa.BondType.UNKNOWN,!0)}_parseCOMPND(e){const t=e.readString(11,80),r=t.indexOf(":");if(this._compndCurrToken=r>0?t.substring(0,r).trim():this._compndCurrToken,"MOL_ID"===this._compndCurrToken)this._molecule={_index:"",_chains:[]},this._molecule._index=parseInt(t.substring(r+1,t.indexOf(";")),10),this._molecules.push(this._molecule);else if("MOLECULE"===this._compndCurrToken&&null!=this._molecule)this._molecule._name=t.substring(r+1,t.indexOf(";")).trim();else if("CHAIN"===this._compndCurrToken&&null!=this._molecule){let e=t.substring(r+1,80).trim();const n=e[e.length-1];";"!==n&&","!==n||(e=e.slice(0,-1)),e=e.replace(/\s+/g,"");const s=e.split(",");this._molecule._chains=this._molecule._chains.concat(s)}}_parseREMARK(e){const r=e.readInt(8,10);let n=this._remarks[r];if(t().isUndefined(n)){const e=ka[r];t().isFunction(e)&&(this._remarks[r]=n=new e(this._complex))}t().isUndefined(n)||n.parse(e)}_parseHELIX(e){this._parseSTRUCTURE(e,[20,22,32,34],(e=>{this._complex.addHelix(e),this._complex.structures.push(e)}))}_parseSHEET(e){this._parseSTRUCTURE(e,[22,23,33,34],(e=>{this._complex.addSheet(e)}))}_parseSTRUCTURE(e,t,r){const n=e.readInt(8,10),s=e.readString(12,14).trim(),i=e.readString(41,70).trim(),o=e.readInt(72,76),a=e.readInt(39,40),l=e.readInt(15,16),c=e.readInt(42,45),h=e.readInt(57,60),u=e.readString(t[0],t[2]+1).charCodeAt(0),d=e.readString(t[2],t[2]+1).charCodeAt(0),p=e.readInt(t[1],t[1]+3);let m=e.readString(t[1]+4,t[1]+4),f=0;m.length>0&&(f=m.charCodeAt(0));const _=e.readInt(t[3],t[3]+3);m=e.readString(t[3]+4,t[3]+4);let g,y=0;m.length>0&&(y=m.charCodeAt(0));let x=this._sheet;if(83===e.readCharCode(1)){null!==x&&x.getName()!==s&&(x=null,this._sheet=null),null===x?(this._sheet=g=new La(s,l),r(g)):g=x;const e=new Ia(g,this._complex.getUnifiedSerial(u,p,f),this._complex.getUnifiedSerial(d,_,y),a,c,h);g.addStrand(e),this._complex.structures.push(e)}else g=new Na(a,this._complex.getUnifiedSerial(u,p,f),this._complex.getUnifiedSerial(d,_,y),n,s,i,o),r(g)}_parseHEADER(e){const{metadata:t}=this._complex;t.classification=e.readString(11,50).trim(),t.date=e.readString(51,59).trim();const r=e.readString(63,66).trim();t.id=r,r&&(this._complex.name=r),t.format="pdb"}_parseTITLE(e){const{metadata:t}=this._complex;t.title=t.title||[];const r=e.readInt(9,10)||1;t.title[r-1]=e.readString(11,80).trim()}static tagParsers=(()=>({HEADER:za.prototype._parseHEADER,"TITLE ":za.prototype._parseTITLE,"ATOM ":za.prototype._parseATOM,HETATM:za.prototype._parseATOM,ENDMDL:za.prototype._parseENDMDL,CONECT:za.prototype._parseCONECT,COMPND:za.prototype._parseCOMPND,REMARK:za.prototype._parseREMARK,"HELIX ":za.prototype._parseHELIX,"SHEET ":za.prototype._parseSHEET,"ATOM 1":za.prototype._parseATOM,"ATOM 2":za.prototype._parseATOM,"ATOM 3":za.prototype._parseATOM,"ATOM 4":za.prototype._parseATOM,"ATOM 5":za.prototype._parseATOM,"ATOM 6":za.prototype._parseATOM,"ATOM 7":za.prototype._parseATOM,"ATOM 8":za.prototype._parseATOM,"ATOM 9":za.prototype._parseATOM}))();parseSync(){const e=new Ra(this._data),r=this._complex=new Ma;for(;!e.end();){const r=e.readString(1,6),n=za.tagParsers[r];t().isFunction(n)&&n.call(this,e),e.next()}if(this._finalize(),this._serialAtomMap=null,this._sheet=null,this._residue=null,this._chain=null,this._complex=null,0===r.getAtomCount())throw new Error("The data does not contain valid atoms");return r}}za.formats=["pdb"],za.extensions=[".pdb",".ent"];const Fa=za,{Complex:Ba,Element:Ua,SGroup:Ga,Bond:ja}=Yt,Ha={A:0,S:1,D:2,T:3},$a=/\s*<\?xml\b[^?>]*\?>\s*<(?:cml|molecule)\b/i;class Wa extends Sa{constructor(e,t){super(e,t),this._complex=null,this._residue=null,this._serialAtomMap=null,this._modelId=1,this._lastMolId=-1,this._readOnlyOneMolecule=!1,this._options.fileType="cml"}static canProbablyParse(e){return t().isString(e)&&$a.test(e)}_rebuidBondIndexes(e,t){const r=e.length;for(let n=0;n1&&o.splice(1,o.length-1),o.forEach((e=>{const r=function(e){let r,n=[];if(e.molecule&&e.molecule.atomArray&&e.molecule.atomArray.atom)Array.isArray(e.molecule.atomArray.atom)?n=e.molecule.atomArray.atom:n.push(e.molecule.atomArray.atom);else if(!e.molecule){return{atomLabels:null,labelsCount:1}}e.molecule.molecule&&s._extractSGroups(e.molecule.molecule,n);let i=n.length;for(let e=0;e1)a[e].order=s;else{const r=Ha[t];void 0!==r&&(a[e].order=r,"A"===t&&(a[e].type=ja.BondType.AROMATIC))}}i=n.length;for(let e=0;e0&&i.push(r)})),i}_packLabel(e,t){return(t<<16)+e}_unpackLabel(e){return{molId:e>>>16,compId:65535&e}}_breadWidthSearch(e,t){const r=new Array(e.length);let n;for(n=0;n0;){i++;let a=-1;for(n=0;n0;){const t=s.shift();if(t)for(let n=0;n=0){const s=[Math.min(e,t),Math.max(e,t)];this._complex.addBond(s[0],s[1],r,n,!0)}}_fixBondsArray(){const e=this._serialAtomMap={},t=this._complex,r=t._atoms;for(let t=0,n=r.length;to[e]-o[t])),a=0;a{r.curr=2,0===r.count&&(r.count=1);for(let n=0;n{r+=e.getAtomCount()})),r<=0)throw new Error("The data does not contain valid atoms");if(e.length>1){const t=new Ba;return t.joinComplexes(e),t.originalCML=e[0].originalCML,t}return 1===e.length?e[0]:new Ba}}Wa.formats=["cml"],Wa.extensions=[".cml"];const Ya=Wa;var Xa=s(660),qa=s.n(Xa);const{Complex:Za,Chain:Ka,Atom:Qa,Element:Ja,Helix:el,Sheet:tl,Strand:rl,Bond:nl,Assembly:sl,Molecule:il}=Yt;class ol{constructor(e){this._original=Array.from(e),this._original.sort(),this._sum=0;for(let e=0;e=this._complex._atoms.length)return;const r=Math.min(e.atomIndex1,e.atomIndex2);this._complex.addBond(this._complex._atoms[r],this._complex._atoms[t],e.bondOrder,nl.BondType.UNKNOWN,!0)}_updateSecStructure(e,r,n){const s=[3,-1,1,-1,5];if(!t().isUndefined(n)&&n.secStruct===this._ssType)return r._secondary=this._ssStruct,void(this._ssStruct&&(this._ssStruct.term=r));if(!t().isUndefined(n)){const t=ll[n.secStruct];this._ssType=n.secStruct,this._ssStart=r;let i=null;switch(this._ssType){case-1:case 7:break;case 0:case 2:case 4:i=new el(s[this._ssType],r,r,0,"","",0),e._helices.push(i);break;case 3:{const t=new tl("",0);e._sheets.push(t),i=new rl(t,r,r,0,null,null);break}default:void 0!==t&&(i=new Oe(t,r,r))}this._ssStruct=i,r._secondary=i,i&&e.structures.push(i)}}_updateMolecules(e){const t=e.entityList;if(!t)return;const r=e.chainsPerModel[0];for(let e=0;e=r)continue;const n=this._complex._chains[t];i=i.concat(n._residues.slice())}const o=new il(this._complex,n.description,e+1);o.residues=i,this._complex._molecules[e]=o}}_traverse(e){const t=this,{metadata:r}=this._complex;r.id=e.structureId,r.title=[],r.title[0]=e.title,r.date=e.releaseDate,r.format="mmtf";const n={onModel(e){t._onModel(e)},onChain(e){t._onChain(e)},onGroup(e){t._onGroup(e)},onAtom(e){t._onAtom(e)},onBond(e){t._onBond(e)}};this._ssType=-1,this._ssStruct=null,this._ssStart=null,qa().traverse(e,n),this._updateSecStructure(this._complex),this._updateMolecules(e)}_linkAtomsToResidues(){for(let e=0;e=t)continue;const s=this._complex._chains[r];for(let e=0;e=s||pl(e.charCodeAt(r+1))))return++c,void++r;if(a&&59===o){n=r;let i=0;do{if(n=ml(10,e,n+1),-1===n)throw new dl("Unterminated text block found",l,c);++i}while(n+1=s);return t=e.substring(r+1,n).replace(/\r/g,""),r=n+2,l+=i,c=1,a=!1,t}if(39===o||34===o){n=r;do{if(n=ml(o,e,n+1),-1===n)throw new dl("Unterminated quoted string found",l,c)}while(n+10){for(let e=0;e0&&r.addChain(n[t])}r.matrices=s,e.units.push(r)}}}Ml.formats=["cif","mmcif"],Ml.extensions=[".cif",".mmcif"];const Pl=Ml,Nl=0,Ll=1,Il=2,Ol=3;const Vl=class{_xyz2crs=[];_origin=(()=>new r.Vector3(0,0,0))();constructor(){this._header={},this._boxSize=new r.Vector3,this._boxStart=new r.Vector3,this._header.delta={},this._header.extent=[],this._header.nstart=[],this._header.grid=[],this._header.crs2xyz=[],this._header.cellDims=new r.Vector3,this._header.angles=[],this._header.origin=new r.Vector3(0,0,0),this._header.dmin=0,this._header.dmean=0,this._header.dmax=0}_typedCheck(){if(t().isTypedArray(this._buff))this._buff=this._buff.buffer;else if(!t().isArrayBuffer(this._buff))throw new TypeError("Expected ArrayBuffer or TypedArray")}_fillHeader(e,t){for(const r in e)if(e.hasOwnProperty(r))switch(e[r][0]){case Nl:this._header[r]=t[e[r][1]][e[r][2]];break;case Il:this._parseArray(this._header[r],t[e[r][1]],e[r][2]);break;case Ll:this._parseVector(this._header[r],t[e[r][1]],e[r][2]);break;case Ol:this._header[r]=new Uint8Array(t[e[r][1]],4*[e[r][2]],4*[e[r][3]])}}_parseVector(e,t,r){[e.x,e.y,e.z]=[t[r],t[r+1],t[r+2]]}_parseArray(e,t,r){e[0]=t[r],e[1]=t[r+1],e[2]=t[r+2]}_parseHeader(e){}_setAxisIndices(){}_setOrigins(){}_getAxis(){const e=this._header,t=e.cellDims.x/e.grid[0],n=e.cellDims.y/e.grid[1],s=e.cellDims.z/e.grid[2],[i,o,a]=e.angles,l=Math.cos(o),c=(Math.cos(i)-Math.cos(o)*Math.cos(a))/Math.sin(a),h=Math.sqrt(1-l*l-c*c);return[new r.Vector3(t,0,0),new r.Vector3(Math.cos(a)*n,Math.sin(a)*n,0),new r.Vector3(l*s,c*s,h*s)]}_getXYZdim(){return[this._header.extent[this._xyz2crs[0]],this._header.extent[this._xyz2crs[1]],this._header.extent[this._xyz2crs[2]]]}_getVolumeInfo(){const e=t().pick(this._header,["dmean","dmin","dmax","sd","delta"]);return e.obtuseAngle=this._header.angles.map((e=>Number(e>=Math.PI/2))),e}_setBoxParams(e,t,n){let s=0,i=0;const[o,a,l]=this._header.angles;l>=Math.PI/2&&(s+=Math.abs(t.x)),a>=Math.PI/2&&(s+=Math.abs(n.x)),o>=Math.PI/2&&(i+=Math.abs(n.y)),this._boxStart=new r.Vector3(this._origin.x-s,this._origin.y-i,this._origin.z),this._boxSize=new r.Vector3(Math.abs(e.x)+Math.abs(t.x)+Math.abs(n.x),Math.abs(t.y)+Math.abs(n.y),Math.abs(n.z));const c=(e,t)=>Math.abs(e[t])/this._boxSize[t];this._header.delta.x=c(t,"x"),this._header.delta.y=c(n,"x"),this._header.delta.z=c(n,"y")}_getXYZbox(){return new r.Box3(this._boxStart.clone(),this._boxStart.clone().add(this._boxSize))}_toXYZData(){}parse(e){return this._parseHeader(e),this._setOrigins(),new Wt(Float32Array,this._getXYZdim(),this._getXYZbox(),1,this._toXYZData(),this._getVolumeInfo())}},Dl={extent:[Il,"u32",0],type:[Nl,"u32",3],nstart:[Il,"i32",4],grid:[Il,"u32",7],cellDims:[Ll,"f32",10],angles:[Il,"f32",13],crs2xyz:[Il,"i32",16],dmin:[Nl,"f32",19],dmax:[Nl,"f32",20],dmean:[Nl,"f32",21],ispg:[Nl,"u32",22],nsymbt:[Nl,"u32",23],lksflg:[Nl,"u32",24],customData:[Ol,"buffer",25,9],origin:[Ll,"f32",34],map:[Ol,"buffer",52,1],machine:[Nl,"u32",53],sd:[Nl,"f32",54],nlabel:[Nl,"f32",55],label:[Ol,"buffer",56,200]};class kl extends Vl{_parseHeader(e){this._buff=e,this._typedCheck();const t={};t.u32=new Uint32Array(this._buff,0,56),t.i32=new Int32Array(this._buff,0,56),t.f32=new Float32Array(this._buff,0,56),t.buffer=this._buff;const r=this._header;this._fillHeader(Dl,t),r.angles.forEach(((e,t,r)=>{r[t]*=Math.PI/180}))}_setAxisIndices(){const e=this._header;0===e.cellDims.x&&0===e.cellDims.y&&0===e.cellDims.z&&e.cellDims.set(1,1,1);const{crs2xyz:t}=this._header;0===t[0]&&0===t[1]&&0===t[2]&&(t[0]=1,t[1]=2,t[2]=3);const r=this._xyz2crs;r[t[0]-1]=0,r[t[1]-1]=1,r[t[2]-1]=2}_setOrigins(){const[e,t,r]=this._getAxis();this._setAxisIndices();const n=this._header,s=this._xyz2crs;if(0===n.origin.x&&0===n.origin.y&&0===n.origin.z?(this._origin.addScaledVector(e,n.nstart[s[0]]),this._origin.addScaledVector(t,n.nstart[s[1]]),this._origin.addScaledVector(r,n.nstart[s[2]])):this._origin=n.origin,e.multiplyScalar(n.extent[s[0]]-1),t.multiplyScalar(n.extent[s[1]]-1),r.multiplyScalar(n.extent[s[2]]-1),2!==n.type)throw new Error(`CCP4: Unsupported format ${n.type}`);this._data=new Float32Array(this._buff,1024+n.nsymbt,n.extent[0]*n.extent[1]*n.extent[2]),this._setBoxParams(e,t,r)}_toXYZData(){const e=this._header,t=this._data,r=this._xyz2crs,n=new Float32Array(t.length),s=this._getXYZdim(),i=s[0],o=s[1];let a=0;const l=[];let c,h,u;for(l[2]=0;l[2]=this._strings.length?(this._currentStart=this._strings.length-1,this._currentStringIndx=this._strings.length-1):(this._currentStart=e,this._currentStringIndx=e)}getNextString(){return this._strings[++this._currentStringIndx]}getCurrentString(){return this._strings[this._currentStringIndx]}getStringFromStart(e){return this._currentStringIndx=this._currentStart+e,this._strings[this._currentStart+e]}findNextDataItem(){let e=this.getNextString(),r=!1;for(;!t().isUndefined(e)&&"$$$$"!==e.trim();){if(e.match(/>\s+<(.*)>/)){r=!0;break}e=this.getNextString()}return r}findNextCompoundStart(){let e=this.getCurrentString();for(;!t().isUndefined(e)&&"$$$$"!==e.trim();)e=this.getNextString();return this.setStart(++this._currentStringIndx),this.probablyHaveDataToParse()}probablyHaveDataToParse(){return this._currentStringIndx\s+<(.+)>.*/,nc=/.*($$$$).*|.*>\s+<(.+)>.*/,sc="sdf",ic="mol",oc=["name","id","title"],ac={name:["PUBCHEM_IUPAC_TRADITIONAL_NAME",/PUBCHEM_(.+)_NAME/,/(.+)name/,/(.+)NAME/],id:["PUBCHEM_COMPOUND_CID","id","ID",/.*CID/,/.*ID/,/.*id/],title:["msg","MSG","message","title","description","desc"]};class lc extends Sa{constructor(e,t){super(e,t),this._format="sdf",this._complex=null,this._chain=null,this._residue=null,this._molecules=null,this._metadata={},this._metadata.molecules=[],this._currentMolProps={},this._compoundIndx=-1,this._assemblies=[],this._atomsParsed=0,this._atomsIndexes=[]}canProbablyParse(e){return t().isString(e)&&rc.test(e)}_parseHeader(e){const t={};t.name=e.getStringFromStart(0);const r=parseInt(e.getStringFromStart(1).substr(10,6).trim(),10);t.date=r.toString()||"",t.title=e.getStringFromStart(2),this._metadata.molecules.push(t)}_parseAtoms(e,t){let n,s=this._atomsParsed;const i=function(e){if(!e)return"A";const t=[];for(;e;)t.push(65+e%26),e=Math.trunc(e/26);return t.length>1&&(t.reverse(),t[0]-=1),String.fromCharCode(...t)}(this._compoundIndx);this._chain=this._complex.getChain(i)||this._complex.addChain(i),this._residue=this._chain.addResidue("UNK",1," ");for(let i=0;in&&([t,n]=[n,t]),this._complex.addBond(t,n,ec[s]||1,tc[s]||Kl.BondType.UNKNOWN,!0)}}_parseMOL(e){this._compoundIndx++,this._parseHeader(e);const t=e.getStringFromStart(3),r=parseInt(t.substr(0,3),10),n=parseInt(t.substr(3,3),10);this._parseAtoms(e,r),this._parseBonds(e,n),this._atomsParsed+=r,this._metadata.molecules[this._compoundIndx]._residues=[],this._metadata.molecules[this._compoundIndx]._residues.push(this._residue)}_parseDataItem(e){const t=e.getCurrentString();let r=[],n=e.getNextString();for(;""!==n.trim();)r.push(n),n=e.getNextString();1===r.length&&([r]=r),this._currentMolProps[t.replace(/[<>]/g,"").trim()]=r}_parseCompound(e){if(this._parseMOL(e),this._format===sc){for(this._currentMolProps={};e.findNextDataItem();)this._parseDataItem(e);if(0!==Object.keys(this._currentMolProps).length){const e=this._metadata.molecules[this._compoundIndx];e.props=this._currentMolProps,this._tryToUpdateMoleculeData(e)}}}_fixBondsArray(){const e=this._serialAtomMap,t=this._complex._bonds;for(let r=0;r1){t.molecules=[];for(let r=0;r>8&255}if(100!==t.i16[18])throw new Error("DSN6: Incorrect format ");const r=this._header;this._fillHeader(cc,t),r.cellDims.multiplyScalar(1/r.scaleFactor),r.angles.forEach(((e,t,n)=>{n[t]*=Math.PI/180/r.scaleFactor})),r.div/=100}_setAxisIndices(){this._xyz2crs[0]=0,this._xyz2crs[1]=1,this._xyz2crs[2]=2}_setOrigins(){const e=this._header,[t,r,n]=this._getAxis();this._setAxisIndices(),this._origin.addScaledVector(t,e.nstart[0]),this._origin.addScaledVector(r,e.nstart[1]),this._origin.addScaledVector(n,e.nstart[2]),t.multiplyScalar(e.extent[0]),r.multiplyScalar(e.extent[1]),n.multiplyScalar(e.extent[2]),this._setBoxParams(t,r,n)}_pointCalculate(e,t,r,n,s,i,o){const a=this._header;if(!(sn&&(n=e[s]);this._header.sd=Math.sqrt(t/e.length),this._header.dmax=n,this._header.dmin=r}}class uc extends Sa{constructor(e,t){super(e,t),this._options.fileType="dsn6",this.model=new hc}static canParse(e,t){return!!e&&(e instanceof ArrayBuffer&&Sa.checkDataTypeOptions(t,"dsn6"))}static canProbablyParse(e){return!1}parseSync(){return this.model.parse(this._data)}}uc.formats=["dsn6"],uc.extensions=[".dsn6",".omap"],uc.binary=!0;const dc=uc;const pc=class extends Ra{constructor(e){super(e),this._next=-1,this.next()}getNext(){return this._next}},{Complex:mc,Element:fc,Molecule:_c}=Yt;class gc extends Sa{constructor(e,t){super(e,t),this._time=null,this._numAtoms=null,this._residueNumber=null,this._residueName="",this._atomName="",this._atomNumber=null,this._atomPosition=[],this._atomVelocity=[],this._complex=null,this._molecules=[],this._molecule=null,this._options.filetype="gro"}canProbablyParse(e){return t().isString(this._data)&&/^\s*[^\n]*\n\s*\d+ *\n\s*\d+[^\n\d]{3}\s*\w+\s*\d+\s*-?\d/.test(e)}_parseTitle(e){const{metadata:t}=this._complex;t.id=e.readLine().trim(),t.name=t.id.slice(t.id.lastIndexOf("\\")+1,t.id.lastIndexOf(".")),t.format="gro"}_parseNumberOfAtoms(e){if(this._numAtoms=e.readInt(0,e.getNext()),Number.isNaN(this._numAtoms))throw new Error("Line 2 is not representing atom number. Consider checking input file")}_parseAtom(e){this._residueNumber=e.readInt(1,5),this._residueName=e.readString(6,10).trim(),this._atomName=e.readString(11,15).trim(),this._atomNumber=e.readInt(16,20);const t=10*e.readFloat(21,28),n=10*e.readFloat(29,36),s=10*e.readFloat(37,45);if(Number.isNaN(t)||Number.isNaN(n)||Number.isNaN(s))return void(this._complex.error={message:`Atom position is invalid in "${e.readLine()}"`});const i=fc.getByName(this._atomName[0]);if("Unknown"===i.fullName)return void(this._complex.error={message:`${this._atomName[0]} hasn't been recognised as an atom name.`});const o=fc.Role[this._atomName];let a=this._chain;a||(this._chain=a=this._complex.addChain("A"));let l=this._residue;l&&l.getSequence()===this._residueNumber||(this._residue=l=a.addResidue(this._residueName,this._residueNumber," ")),this._atomPosition=new r.Vector3(t,n,s);l.addAtom(this._atomName,i,this._atomPosition,o,!0,this._atomNumber," ",1,1,0)}_finalize(){const e=new _c(this._complex,this._complex.metadata.name,1);e.residues=this._chain._residues,e._chains=this._chain,this._complex._molecules[0]=e,this._molecules.push(e),this._complex.finalize({needAutoBonding:!0,detectAromaticLoops:this.settings.now.aromatic,enableEditing:this.settings.now.editing,serialAtomMap:this._serialAtomMap})}parseSync(){const e=this._complex=new mc,t=new pc(this._data);let r=0;for(this._parseTitle(t),t.next(),this._parseNumberOfAtoms(t),t.next(),r=0;r${e}`))return;this._currPosIdx++}this._toStringFromStart(0,t)}_toStringFromHeader(e,t,r){this._toHeaderString(e,r);const n=this._currPosIdx+t;r[this._currPosIdx].match(`@${e}`)&&n=t.length?this._currStartIdx=this._currPosIdx=t.length-1:this._currStartIdx=this._currPosIdx=e}_probablyHaveDataToParse(e){return this._currPosIdxMOLECULE>"!==e[this._currPosIdx].trim();)this._currPosIdx++;return this._setStart(++this._currPosIdx,e),this._probablyHaveDataToParse(e)}_parseMolecule(e){this._toHeaderString("MOLECULE",e);const{metadata:t}=this._complex;t.name=e[++this._currPosIdx],t.format="mol2",this._molecule={_index:"",_chains:[]},this._molecule._index=this._compoundIndx+1,this._molecules.push(this._molecule)}_parseAtoms(e,t){this._toHeaderString("ATOM",t);for(let n=0;n=9&&(c=parseFloat(e[8])||0);let h=this._chain;if(h||(this._chain=h=this._complex.getChain("A")||this._complex.addChain("A"),this._residue=null),!this._setResidue(e))continue;const u=!1,d=" ",p=1,m=0,f=bc.getByName(l),_=bc.Role[s],g=new r.Vector3(i,o,a);this._residue.addAtom(s,f,g,_,u,n,d,p,m,c)}}_setResidue(e){let t=1,r="UNK";if(e.length>=7&&(t=parseInt(e[6],10)),e.length>=8&&"<0>"!==e[7]&&(r=e[7].replace(Ac,"")),this.settings.now.nowater&&("HOH"===r||"WAT"===r))return!1;const n=this._residue,s=this._chain;return n&&n.getSequence()===t||(this._residue=s.addResidue(r,t,"A")),!0}_parseBonds(e,t){this._toHeaderString("BOND",t);for(let r=0;rn&&([r,n]=[n,r]),this._complex.addBond(r,n,vc[s]||0,Cc[s]||wc.BondType.UNKNOWN,!0)}}_fixSerialAtoms(){const e=this._complex._atoms;for(let t=0;t0&&void 0!==arguments[0]?arguments[0]:[],["formats"])}find(e){let t=[];return e.format&&(t=this._dict.formats[e.format.toLowerCase()]||[]),[...t]}};class Nc{constructor(e,t){this._source=e,this._options=t||{},this._abort=!1}exportSync(){throw new Error("Exporting to this source is not implemented")}export(){return new Promise(((e,t)=>{setTimeout((()=>{try{return this._abort?t(new Error("Export aborted")):e(this.exportSync())}catch(e){return t(e)}}))}))}abort(){this._abort=!0}}ur(Nc.prototype);class Lc{constructor(){this._resultArray=[],this._currentStr=-1,this._tag=null,this._fixedNumeration=!1,this._numeration=!1,this._tagStrNum=0}getResult(){return this.writeString("\n",81,81),this._resultArray.join("")}_currentStrLength(){const e=this._resultArray[this._currentStr];return e?e.length:0}newTag(e,r){this._tag=e||null,t().isUndefined(r)?(this._numeration=!1,this._fixedNumeration=!1,this._tagStrNum=0):t().isNumber(r)?(this._tagStrNum=r,this._numeration=!0,this._fixedNumeration=!0):t().isBoolean(r)&&(this._tagStrNum=0,this._numeration=r,this._fixedNumeration=!1)}newString(e){this.writeString("\n",81,81),this._currentStr++,this._resultArray.push(""),e?this.writeString(e,1,6):this._tag&&this.writeString(this._tag,1,6),this._numeration&&(this._fixedNumeration||this._tagStrNum++,1!==this._tagStrNum&&this.writeString(this._tagStrNum.toString(),10,8))}writeEntireString(e,t,r){t||(t=81);for(let n=0;nMath.abs(r-n)+1&&(s=s.substr(0,Math.abs(r-n+1))),l>o+1)this._resultArray[this._currentStr]+=" ".repeat(l-o-1);else if(l<=o){const e=this._resultArray[this._currentStr];this._resultArray[this._currentStr]=e.slice(0,l-1)}if(ni.length&&(this._resultArray[this._currentStr]+=" ".repeat(a-i.length))}writeBondsArray(e,t){const r=this._getSubArrays(e,4);for(let e=0;ee._fixed));0!==n.length&&e.writeBondsArray(n.reverse(),t[r])}}_extractSHEET(e){if(!this._source._sheets)return;e.newTag("SHEET");const t=this._source._sheets;for(let r=0;r1||t[r].name.length>3?13:14;e.writeString(t[r].serial,11,7),e.writeString(t[r].name,s,16),e.writeString(String.fromCharCode(t[r].location),17,17),e.writeString(t[r].residue._type._name,20,18),e.writeString(t[r].residue._chain._name,22,22),e.writeString(t[r].residue._sequence,26,23),e.writeString(t[r].residue._icode,27,27),e.writeString(t[r].position.x.toFixed(3),38,31),e.writeString(t[r].position.y.toFixed(3),46,39),e.writeString(t[r].position.z.toFixed(3),54,47),e.writeString(t[r].occupancy.toFixed(2),60,55),e.writeString(t[r].temperature.toFixed(2),66,61),e.writeString(t[r].element.name,78,77),t[r].charge&&e.writeString(t[r].charge,79,80)}}_extractCOMPND(e){if(!this._source._molecules)return;const t=this._source._molecules;e.newTag("COMPND",!0);for(let r=0;re instanceof ct));for(let t=0;tt.indexOf(e)===r))}}Ic.formats=["pdb"],Ic.SourceClass=jt;function Oc(e,t,r,n){r[n]=e[t],r[n+1]=e[t+1],r[n+2]=e[t+2]}function Vc(e,t,r,n,s){r[n]=e[t],r[n+1]=e[t+1],r[n+2]=e[t+2],r[n+3]=s}const Dc=new r.Vector4;function kc(e,t,r,n,s){Dc.set(e[t],e[t+1],e[t+2],s.w),Dc.applyMatrix4(s.matrix),r[n]=Dc.x,r[n+1]=Dc.y,r[n+2]=Dc.z}function zc(e,t,r,n,s){if(!((t.array.length-t.start)/t.stridee+r));this.setIndices(n,0,t)}getVerticesNumber(){return this.lastPos/3}addInstance(e,t){const r=this.getVerticesNumber();this.setShiftedIndices(t.indices,t.indices.length,r);const n=t.itemSize;this.setTransformedPositions(t.positions,0,t.vertsCount,n.position,e),this.setTransformedNormals(t.normals,0,t.vertsCount,n.normal,e),this.setColors(t.colors,0,t.vertsCount,n.color)}}class Bc{constructor(){this.positions=null,this.normals=null,this.colors=null,this.indices=null,this.vertsCount=0,this.itemSize=null}init(e,t){const{attributes:r}=e;this.itemSize={position:r.position.itemSize,normal:r.normal.itemSize,color:r.color.itemSize}}}class Uc extends Bc{init(e,t){super.init(e,t);const{attributes:{position:r,normal:n},index:s}=e;this.vertsCount=r.count,this.positions=r.array,this.normals=n.array,this.colors=new Float32Array(this.vertsCount*this.itemSize.color),this.indices=s.array}setColors(e){let t=0;for(let r=0,n=this.colors.length,s=this.itemSize.color;re+s)),this.indices.set(r.array,0),this.indices.set(i,n)}_setColorRange(e,t,r,n){const s=n.length;for(let i=e;i{e instanceof r.Mesh&&e.layers.test(t)&&this.checkExportAbility(e)&&("InstancedBufferGeometry"===e.geometry.type?this._collectInstancedGeoInfo(e):this._collectGeoInfo(e))}))}_reworkIndices(e){for(let t=2;t0&&(u=new Gc,u.init(e.geometry,h));const d=h.addPerCylinder*h.needToSplit,p=t.count,m=i.count;a.init(l*p+d,l*m);const f=new r.Matrix4,_=new r.Matrix4,g=new r.Color,y=new r.Color;let x={};for(let t=0;tt().isEqual(r,e)))}_gatherCylindersColoringInfo(e){const t=e.instanceCount,r=e.attributes.color.array,n=e.attributes.color2.array,s=e.attributes.color.itemSize,i=new Array(t);let o=0,a=0;for(let e=0;e1e-7||Math.abs(r[a+1]-n[a+1])>1e-7||Math.abs(r[a+2]-n[a+2])>1e-7;i[e]=t,o+=t}return{is2Colored:i,needToSplit:o,addPerCylinder:e.getGeoParams().radialSegments}}_collectInstancedGeoInfo(e){e.geometry instanceof gr?this._collectSpheresInfo(e):e.geometry instanceof Dr&&this._collectCylindersInfo(e)}_collectMaterialInfo(e){const{uberOptions:t}=e.material;return{diffuse:t.diffuse.toArray(),opacity:t.opacity,shininess:t.shininess,specular:t.specular.toArray()}}_getCylinderInstanceMatrix(e,t,r){const n=e.attributes.matVector1.array,s=e.attributes.matVector2.array,i=e.attributes.matVector3.array,o=4*t;r.set(n[o],n[o+1],n[o+2],n[o+3],s[o],s[o+1],s[o+2],s[o+3],i[o],i[o+1],i[o+2],i[o+3],0,0,0,1)}_getSphereInstanceMatrix(e,t,r){const{offset:n}=e.attributes,s=t*n.itemSize,i=n.array[s],o=n.array[s+1],a=n.array[s+2],l=n.array[s+3];r.set(l,0,0,i,0,l,0,o,0,0,l,a,0,0,0,1)}}class Hc{constructor(){this._resultArray=[],this._info=null}getResult(e){return this._info=e,this._resultArray.push(this._writeHeader()),this._resultArray.push(this._writeDefinitions()),this._resultArray.push(this._writeObjects(e.models,e.materials)),this._resultArray.push(this._writeRelations()),this._resultArray.push(this._writeConnections()),this._info=null,this._resultArray.join("")}_writeHeader(){const e=new Date,t=`Miew FBX Exporter v${this._info.version}`;return`; FBX 6.1.0 project file\n; Created by ${t} Copyright (c) 2015-2024 EPAM Systems, Inc.\n; For support please contact miew@epam.com\n; ----------------------------------------------------\n\nFBXHeaderExtension: {\n FBXHeaderVersion: 1003\n FBXVersion: 6100\n CreationTimeStamp: {\n Version: 1000\n Year: ${e.getFullYear()}\n Month: ${e.getMonth()+1}\n Day: ${e.getDate()}\n Hour: ${e.getHours()}\n Minute: ${e.getMinutes()}\n Second: ${e.getSeconds()}\n Millisecond: ${e.getMilliseconds()}\n }\n Creator: "${t}"\n OtherFlags: {\n FlagPLE: 0\n }\n}\nCreationTime: "${e}"\nCreator: "${t}"\n`}_writeDefinitions(){return'\n; Object definitions\n;------------------------------------------------------------------\n\n\nDefinitions: {\n Version: 100\n Count: 3\n ObjectType: "Model" {\n Count: 1\n }\n ObjectType: "Geometry" {\n Count: 1\n }\n ObjectType: "Material" {\n Count: 1\n }\n ObjectType: "Pose" {\n Count: 1\n }\n ObjectType: "GlobalSettings" {\n Count: 1\n }\n} \n'}_models(){let e="";const{models:t}=this._info;for(let r=0;r-t.near?"hidden":"visible",a=1e4*(t.far- -this._vector.z)/(t.far-t.near),l=e.getElement();if(void 0===n.fog)l.style.color=i(e.userData.color),"transparent"!==e.userData.background&&(l.style.background=i(e.userData.background));else{const t=r.MathUtils.smoothstep(-this._vector.z,n.fog.near,n.fog.far);l.style.color=s(e.userData.color,n.fog.color,t),"transparent"!==e.userData.background&&(l.style.background=s(e.userData.background,n.fog.color,t))}this._vector.applyMatrix4(this._projectionMatrix);const c=`${e.userData!=={}?e.userData.translation:"translate(-50%, -50%) "}translate(${this._vector.x*this._widthHalf+this._widthHalf}px,${-this._vector.y*this._heightHalf+this._heightHalf}px)`;l.style.visibility=o,l.style.WebkitTransform=c,l.style.MozTransform=c,l.style.oTransform=c,l.style.transform=c,l.style.zIndex=Number(a).toFixed(0),l.parentNode!==this._domElement&&this._domElement.appendChild(l)}for(let r=0,s=e.children.length;r0&&(this._altObj.setObjects(i.objects),this._altObj.pivot=i.pivot,"axis"in i?this._altObj.axis=i.axis.clone():this._altObj.axis.set(0,0,1),e.set(s*t,s*n),this._altObj.translate(e),this.dispatchEvent({type:"change",action:"translate"}))}}this._lastUpdateTime=t}}(),sh.prototype.reset=function(){this._state=Zc,this.object.quaternion.copy(th.set(0,0,0,1))},sh.prototype.mousedown=function(e){if(!1!==this.enabled&&this._state===Zc){if(e.preventDefault(),e.stopPropagation(),this._state===Zc)if(0===e.button){this._affectedObj.stop();let t=!1;if(e.altKey){const e=this.getAltObj();t=e.objects.length>0,t&&(this._altObj.setObjects(e.objects),this._altObj.pivot=e.pivot,"axis"in e?this._altObj.axis=e.axis.clone():this._altObj.axis.set(0,0,1))}this._affectedObj=t?this._altObj:this._mainObj,this._state=t&&e.ctrlKey&&this._isTranslationAllowed?Qc:Kc}else 2===e.button&&(this._state=eh);this._state===Kc&&(this.convertMouseToOnCircle(this._mouseCurPos,e.pageX,e.pageY),this._mousePrevPos.copy(this._mouseCurPos)),this._state!==Qc&&this._state!==eh||(this.convertMouseToViewport(this._mouseCurPos,e.pageX,e.pageY),this._mousePrevPos.copy(this._mouseCurPos))}},sh.prototype.mousemove=function(e){if(!1!==this.enabled&&this._state!==Zc)switch(e.preventDefault(),e.stopPropagation(),this._state){case Kc:this._mousePrevPos.copy(this._mouseCurPos),this.convertMouseToOnCircle(this._mouseCurPos,e.pageX,e.pageY),this.rotateByMouse(e.altKey&&!this._isAltObjFreeRotationAllowed||e.shiftKey),this._lastMouseMoveTime=this._clock.getElapsedTime();break;case Qc:this._mousePrevPos.copy(this._mouseCurPos),this.convertMouseToViewport(this._mouseCurPos,e.pageX,e.pageY),this.translate();break;case eh:this._mousePrevPos.copy(this._mouseCurPos),this.convertMouseToViewport(this._mouseCurPos,e.pageX,e.pageY),this.translatePivotByMouse()}},sh.prototype.mousewheel=function(e){if(!1===this.enabled||!z.now.zooming||this._state!==Zc||e.shiftKey)return;e.preventDefault();let t=0;e.wheelDelta?t=e.wheelDelta/40:e.detail&&(t=-e.detail/3);let r=1+.05*t;r=Math.max(r,.01),this.scale(r)},sh.prototype.mouseup=function(e){!1!==this.enabled&&this._state!==Zc&&(e.preventDefault(),e.stopPropagation(),this._state=Zc,this._clock.getElapsedTime()-this._lastMouseMoveTime>.1&&this._affectedObj.stop())},sh.prototype.touchstartend=function(e){if(!1!==this.enabled)switch(e.preventDefault(),e.stopPropagation(),e.touches.length){case 1:this._state=Kc,this.convertMouseToOnCircle(this._mouseCurPos,e.touches[0].pageX,e.touches[0].pageY),this._mousePrevPos.copy(this._mouseCurPos);break;case 2:{this._mainObj.stop(),this._altObj.stop(),this._state=Jc;const t=e.touches[0].pageX-e.touches[1].pageX,r=e.touches[0].pageY-e.touches[1].pageY;this._touchDistanceCur=this._touchDistanceStart=Math.sqrt(t*t+r*r),this._scaleStart=this.object.scale.x;break}default:this._state=Zc}},sh.prototype.touchmove=function(e){if(!1!==this.enabled&&this._state!==Zc)switch(e.preventDefault(),e.stopPropagation(),this._state){case Kc:this._mousePrevPos.copy(this._mouseCurPos),this.convertMouseToOnCircle(this._mouseCurPos,e.touches[0].pageX,e.touches[0].pageY),this.rotateByMouse(!1),this._lastMouseMoveTime=this._clock.getElapsedTime();break;case Jc:if(z.now.zooming){const t=e.touches[0].pageX-e.touches[1].pageX,r=e.touches[0].pageY-e.touches[1].pageY;this._touchDistanceCur=Math.sqrt(t*t+r*r);const n=this._scaleStart*this._touchDistanceCur/this._touchDistanceStart/this.object.scale.x;this.scale(n)}}},sh.prototype.keydownup=function(e){if(!1!==this.enabled&&!1!==this.hotkeysEnabled)switch(e.keyCode){case 37:case 38:case 39:case 40:this._pressedKeys[e.keyCode]="keydown"===e.type,e.preventDefault(),e.stopPropagation()}},sh.prototype.getKeyBindObject=function(){return qc()},sh.prototype.dispose=function(){for(let e=0;e{t.pickObject(s)}),0),this._lastClickPos=s,this._lastClickBeginTime=this._clickBeginTime}},oh.prototype.touchstart=function(e){e.preventDefault(),e.stopPropagation(),1===e.touches.length&&(this._lastTouchdownPos=this.getMouseInViewport(e.touches[0].pageX,e.touches[0].pageY))},oh.prototype.touchend=function(e){const t=this;if(e.preventDefault(),e.stopPropagation(),0===e.touches.length&&1===e.changedTouches.length){this.getMouseInViewport(e.changedTouches[0].pageX,e.changedTouches[0].pageY).sub(this._lastTouchdownPos).length()<.01&&setTimeout((()=>{t.pickObject(t._lastTouchdownPos)}),0)}},oh.prototype.dispose=function(){for(let e=0;e=524288?e-1048576:e}class ph{constructor(e,t,r){this._complex=e,this._secondary=null,this.isLoading=!1,this._framesRange={start:0,end:-1},this.frameIsReady=!1,this._buffer=null,this._frameRequest=null,this._callbacks=r,"function"==typeof t?(this._framesRequestLength=1,this._downloadDataFn=t):this.parseBinaryData(t,!0),this.reset(),this.setFrame(0)}_prepareBuffer(e,t){if(null==e&&(e=0),null==t&&(t=e+this._framesRequestLength),void 0!==this._framesCount&&(t=Math.min(this._framesCount-1,t)),this._downloadDataFn){const r=this,n=function(n){if(r.isLoading=!1,r._callbacks&&"function"==typeof r._callbacks.onLoadStatusChanged&&r._callbacks.onLoadStatusChanged(),r._buffer={data:n,state:"ready",start:e,end:t},null!==r._frameRequest){const e=r._frameRequest;r._frameRequest=null,r.setFrame(e)}},s=function(){r.isLoading=!1,r._callbacks&&"function"==typeof r._callbacks.onError&&r._callbacks.onError("Streaming failed")};this._buffer||(this._buffer={}),this._buffer.state="downloading",this.isLoading=!0,r._callbacks&&"function"==typeof r._callbacks.onLoadStatusChanged&&r._callbacks.onLoadStatusChanged(),this._downloadDataFn({start:e,end:t+1},n,s)}}_parseBuffer(){if(this._buffer&&"ready"===this._buffer.state){this._framesRange={start:this._buffer.start,end:this._buffer.end},this.parseBinaryData(this._buffer.data,!1);let e=(this._buffer.end+1)%this._framesCount;if(e>=this._framesCount&&(e=0),this._buffer={state:"none"},this._prepareBuffer(e,e+this._framesRequestLength),null!==this._frameRequest){const e=this._frameRequest;this._frameRequest=null,this.setFrame(e)}}}parseBinaryData(e){const t=new DataView(e);let r=0;const n=t.getUint32(r,!0);r+=4;const s=t.getUint32(r,!0);this._framesCount=s,this._framesRange.end=this._framesRange.end>0?Math.min(this._framesRange.end,s-1):s-1,r+=4,this._atomsCount=n;this._framesRequestLength=Math.ceil(1048576/(8*n));const i=this._framesRange.end-this._framesRange.start+1;if(n!==this._complex._atoms.length||e.byteLength!==12+i*n*8)throw new Error;const o=this._complex;let a=t.getUint32(r,!0),l=0;for(;a>1e3&&l>>28,o=dh((268435200&s)>>>8>>0),a=dh(((255&s)<<12|(4293918720&n)>>>20)>>0),l=dh((1048575&n)>>0);d[e]=0,i>0&&i<4?d[e]=1:4===i&&(d[e]=2),h[u++]=o/100,h[u++]=a/100,h[u++]=l/100}c.push(uh(d,o))}this._secondaryData=c,this._data=h}nextFrame(){this.setFrame((this._currFrame+1)%this._framesCount)}needsColorUpdate(e){return e instanceof bo}getAtomColor(e,t){return e.getResidueColor(this._residues[t.residue._index],this._complex)}getResidueColor(e,t){return e.getResidueColor(this._residues[t._index],this._complex)}_updateSecondary(){let e;const t=this._residues;let r=t.length;for(e=0;e=this._framesRange.start&&e<=this._framesRange.end)this._currFrame=e,this._cachedResidues=!1,this._updateSecondary(),this.frameIsReady=!0;else if(this._frameRequest=e,this._buffer){const t=this;switch(this._buffer.state){case"none":this._prepareBuffer(e);break;case"ready":t._parseBuffer()}}else this._prepareBuffer(e)}disableEvents(){this._callbacks=null}static _vec=(()=>new r.Vector3)();getAtomPos(e){const t=ph._vec,r=this,n=r._data,s=3*(r._atomsCount*(r._currFrame-r._framesRange.start)+e);return t.set(n[s],n[s+1],n[s+2]),t}getResidues(){return this._cachedResidues||this._complex.updateToFrame(this),this._residues}}const mh=ph;class fh{constructor(e,r){if(this.constructor===fh)throw new Error("Can not instantiate abstract class!");this.params=e,this.opts=t().merge(O.deriveDeep(z.now.objects[this.type],!0),r),this.needsRebuild=!1,this._mesh=null,this.id=null}identify(){const e={type:this.type,params:this.params},r=O.objectsDiff(this.opts,z.now.modes[this.id]);return t().isEmpty(r)||(e.opts=r),e}toString(){return`o=${this.type},${this.params.join(",")}`+O.compareOptionsWithDefaults(this.opts,z.defaults.objects[this.type])}getGeometry(){return this._mesh}destroy(){this._mesh&&sr.destroyObject(this._mesh)}}fh.prototype.type="__";const _h=fh;class gh extends _h{constructor(e,t){if(super(e,t),e.length<2)throw new Error("Wrong number of argumets on line object creation!");[this._id1,this._id2]=e}_getAtomFromName(e,t){const r=e.getAtomByFullname(t);if(!r)throw new Error(t+" - Wrong atom format it must be '#CHAIN_NAME.#RESIDUE_NUMBER.#ATOM_NAME' (e.g. 'A.38.CO1')");return r}build(e){const t=new r.BufferGeometry;this._atom1=this._getAtomFromName(e,this._id1),this._atom2=this._getAtomFromName(e,this._id2);const n=this._atom1.position,s=this._atom2.position,i=new Float32Array([n.x,n.y,n.z,s.x,s.y,s.z]);t.setAttribute("position",new r.BufferAttribute(i,3)),t.computeBoundingBox(),this._line=new fs.Line(t,new Jn({lights:!1,overrideColor:!0,dashedLine:!0,fogTransparent:z.now.bg.transparent})),this._line.computeLineDistances(),this._line.material.setUberOptions({fixedColor:new r.Color(this.opts.color),dashedLineSize:this.opts.dashSize,dashedLinePeriod:this.opts.dashSize+this.opts.gapSize}),this._line.material.updateUniforms(),this._line.raycast=function(e,t){},this._mesh=this._line;const o=e.getTransforms();o.length>0&&(this._mesh=new r.Group,this._mesh.add(this._line),jo.applyTransformsToMeshes(this._mesh,o))}updateToFrame(e){if(!this._atom1||!this._atom2||!this._line)return;const t=this._line.geometry;t.vertices[0].copy(e.getAtomPos(this._atom1.index)),t.vertices[1].copy(e.getAtomPos(this._atom2.index)),this._line.computeLineDistances(),t.computeBoundingSphere(),t.verticesNeedUpdate=!0}}gh.prototype.constructor=gh,gh.prototype.type="line";const yh=gh;class xh extends r.RawShaderMaterial{constructor(e){super(e);const t={uniforms:{srcTex:{type:"t",value:null},srcDepthTex:{type:"t",value:null},srcTexSize:{type:"v2",value:new r.Vector2(512,512)},color:{type:"v3",value:null},threshold:{type:"f",value:null},opacity:{type:"f",value:1},thickness:{type:"v2",value:new r.Vector2(1,1)}},vertexShader:Qt,fragmentShader:"precision highp float;\r\n\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexSize;\r\nuniform vec2 thickness;\r\nvarying vec2 vUv;\r\n\r\n#ifdef DEPTH_OUTLINE\r\n uniform sampler2D srcDepthTex; //depthTexture\r\n uniform vec3 color;\r\n uniform float threshold;\r\n#endif\r\n\r\nvoid main() {\r\n\r\n vec2 pixelSize = thickness / srcTexSize;\r\n\r\n #ifdef DEPTH_OUTLINE\r\n float c00 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,-pixelSize.y)).x;\r\n float c01 = texture2D(srcDepthTex, vUv + vec2(0,-pixelSize.y)).x;\r\n float c02 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,-pixelSize.y)).x;\r\n float c10 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,0)).x;\r\n float c12 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,0)).x;\r\n float c20 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,pixelSize.y)).x;\r\n float c21 = texture2D(srcDepthTex, vUv + vec2(0,pixelSize.y)).x;\r\n float c22 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,pixelSize.y)).x;\r\n\r\n float horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n float vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n float grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n\r\n gl_FragColor = ( grad > threshold ) ? vec4(color.rgb, 1.0) : gl_FragColor = texture2D(srcTex, vUv);\r\n\r\n #else\r\n vec4 c00 = texture2D(srcTex, vUv + vec2(-pixelSize.x,-pixelSize.y));\r\n vec4 c01 = texture2D(srcTex, vUv + vec2(0,-pixelSize.y));\r\n vec4 c02 = texture2D(srcTex, vUv + vec2(pixelSize.x,-pixelSize.y));\r\n vec4 c10 = texture2D(srcTex, vUv + vec2(-pixelSize.x,0));\r\n vec4 c12 = texture2D(srcTex, vUv + vec2(pixelSize.x,0));\r\n vec4 c20 = texture2D(srcTex, vUv + vec2(-pixelSize.x,pixelSize.y));\r\n vec4 c21 = texture2D(srcTex, vUv + vec2(0,pixelSize.y));\r\n vec4 c22 = texture2D(srcTex, vUv + vec2(pixelSize.x,pixelSize.y));\r\n\r\n vec4 horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n vec4 vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n vec4 grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n gl_FragColor = grad;\r\n #endif\r\n}\r\n",transparent:!0,depthTest:!1,depthWrite:!1};this.setValues(t)}copy(e){super.copy(e),this.depth=e.depth}setValues(e){if(void 0===e)return;super.setValues(e);const t={};this.depth&&(t.DEPTH_OUTLINE=1),this.defines=t}}xh.prototype.depth=!1;const bh=xh;class wh extends r.RawShaderMaterial{constructor(e){super(e),this.setValues.call(this,{uniforms:{srcTex:{type:"t",value:null},srcTexelSize:{type:"v2",value:new r.Vector2(1/512,1/512)},bgColor:{type:"c",value:new r.Color(16777215)}},vertexShader:Qt,fragmentShader:"precision highp float;\r\n\r\n// edge end finding algorithm parameters\r\n#define FXAA_QUALITY_PS 8\r\n#define FXAA_QUALITY_P0 1.0\r\n#define FXAA_QUALITY_P1 1.5\r\n#define FXAA_QUALITY_P2 2.0\r\n#define FXAA_QUALITY_P3 2.0\r\n#define FXAA_QUALITY_P4 2.0\r\n#define FXAA_QUALITY_P5 2.0\r\n#define FXAA_QUALITY_P6 4.0\r\n#define FXAA_QUALITY_P7 12.0\r\n// constants\r\nfloat fxaaQualityEdgeThreshold = 0.125;\r\nfloat fxaaQualityEdgeThresholdMin = 0.0625;\r\nfloat fxaaQualitySubpix = 0.7; //0.65;\r\n// global params\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexelSize;\r\nuniform vec3 bgColor;\r\n// from vs\r\nvarying vec2 vUv;\r\n//=====================================================================//\r\n// calc luminance from rgb\r\n//'float FxaaLuma(vec3 rgb) {return rgb.y * (0.587/0.299) + rgb.x; } // Lotte's idea about game luminance\r\nfloat FxaaLuma(vec3 rgb) {return dot(rgb, vec3(0.299, 0.587, 0.114)); } // real luminance calculation\r\n // for non-real scene rendering\r\n// texture sampling by pixel position(coords) and offset(in pixels)\r\n vec3 FxaaTex(sampler2D tex, vec2 pos, vec2 off, vec2 res ) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos + off * res );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos + off * res ).xyz;\r\n #endif\r\n}\r\nvec3 FxaaTexTop(sampler2D tex, vec2 pos) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos).xyz;\r\n #endif\r\n}\r\nvec4 FxaaTexTopAlpha(sampler2D tex, vec2 pos) {\r\n return texture2D( tex, pos);\r\n}\r\n\r\n//=====================================================================//\r\nvoid main() {\r\n // renaming\r\n vec2 posM = vUv;\r\n // get luminance for neighbours\r\n float lumaS = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, 1.0 ), srcTexelSize));\r\n float lumaE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 0.0 ), srcTexelSize));\r\n float lumaN = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, -1.0 ), srcTexelSize));\r\n float lumaW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 0.0 ), srcTexelSize));\r\n float lumaM = FxaaLuma(FxaaTexTop(srcTex, posM));\r\n // find max and min luminance\r\n float rangeMax = max(max(lumaN, lumaW), max(lumaE, max(lumaS, lumaM)));\r\n float rangeMin = min(min(lumaN, lumaW), min(lumaE, min(lumaS, lumaM)));\r\n // calc maximum non-edge range\r\n float rangeMaxScaled = rangeMax * fxaaQualityEdgeThreshold;\r\n float range = rangeMax - rangeMin;\r\n float rangeMaxClamped = max(fxaaQualityEdgeThresholdMin, rangeMaxScaled);\r\n // exit when luma contrast is small (is not edge)\r\n if(range < rangeMaxClamped){\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n return;\r\n }\r\n float subpixRcpRange = 1.0/range;\r\n // note: the sampling coordinates can be calculated in vertex shader but the approach doesn't affect performance\r\n // visibly, thus we decided to leave calculation here for better readability.\r\n // calc other neighbours luminance\r\n float lumaNE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, -1.0 ), srcTexelSize));\r\n float lumaSW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 1.0 ), srcTexelSize));\r\n float lumaSE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 1.0 ), srcTexelSize));\r\n float lumaNW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, -1.0 ), srcTexelSize));\r\n/*--------------span calculation and subpix amount calulation-----------------*/\r\n float lumaNS = lumaN + lumaS;\r\n float lumaWE = lumaW + lumaE;\r\n float subpixNSWE = lumaNS + lumaWE;\r\n float edgeHorz1 = (-2.0 * lumaM) + lumaNS;\r\n float edgeVert1 = (-2.0 * lumaM) + lumaWE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNESE = lumaNE + lumaSE;\r\n float lumaNWNE = lumaNW + lumaNE;\r\n float edgeHorz2 = (-2.0 * lumaE) + lumaNESE;\r\n float edgeVert2 = (-2.0 * lumaN) + lumaNWNE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNWSW = lumaNW + lumaSW;\r\n float lumaSWSE = lumaSW + lumaSE;\r\n float edgeHorz4 = (abs(edgeHorz1) * 2.0) + abs(edgeHorz2);\r\n float edgeVert4 = (abs(edgeVert1) * 2.0) + abs(edgeVert2);\r\n float edgeHorz3 = (-2.0 * lumaW) + lumaNWSW;\r\n float edgeVert3 = (-2.0 * lumaS) + lumaSWSE;\r\n float edgeHorz = abs(edgeHorz3) + edgeHorz4;\r\n float edgeVert = abs(edgeVert3) + edgeVert4;\r\n/*--------------------subpix amount calulation------------------------------*/\r\n float subpixNWSWNESE = lumaNWSW + lumaNESE;\r\n float lengthSign = srcTexelSize.x;\r\n bool horzSpan = edgeHorz >= edgeVert;\r\n // debug code edge span visualization\r\n/*' if (horzSpan)\r\n gl_FragColor = vec4(0.0, 0.0, 1.0, 1.0);\r\n else\r\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\r\n return;*/\r\n float subpixA = subpixNSWE * 2.0 + subpixNWSWNESE;\r\n/*--------------------------------------------------------------------------*/\r\n if(!horzSpan) lumaN = lumaW;\r\n if(!horzSpan) lumaS = lumaE;\r\n if(horzSpan) lengthSign = srcTexelSize.y;\r\n float subpixB = (subpixA * (1.0/12.0)) - lumaM;\r\n/*--------------------------------------------------------------------------*/\r\n float gradientN = lumaN - lumaM;\r\n float gradientS = lumaS - lumaM;\r\n float lumaNN = lumaN + lumaM;\r\n float lumaSS = lumaS + lumaM;\r\n bool pairN = abs(gradientN) >= abs(gradientS);\r\n float gradient = max(abs(gradientN), abs(gradientS));\r\n if(pairN) lengthSign = -lengthSign;\r\n float subpixC = clamp(abs(subpixB) * subpixRcpRange, 0.0, 1.0);\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posB;\r\n posB = posM;\r\n vec2 offNP;\r\n offNP.x = (!horzSpan) ? 0.0 : srcTexelSize.x;\r\n offNP.y = ( horzSpan) ? 0.0 : srcTexelSize.y;\r\n if(!horzSpan) posB.x += lengthSign * 0.5;\r\n if( horzSpan) posB.y += lengthSign * 0.5;\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posN;\r\n posN = posB - offNP * FXAA_QUALITY_P0;\r\n vec2 posP;\r\n posP = posB + offNP * FXAA_QUALITY_P0;\r\n float subpixD = ((-2.0)*subpixC) + 3.0;\r\n float lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN));\r\n float subpixE = subpixC * subpixC;\r\n float lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP));\r\n/*--------------------------------------------------------------------------*/\r\n if(!pairN) lumaNN = lumaSS;\r\n float gradientScaled = gradient * 1.0/4.0;\r\n float lumaMM = lumaM - lumaNN * 0.5;\r\n float subpixF = subpixD * subpixE;\r\n bool lumaMLTZero = lumaMM < 0.0;\r\n/*---------------------looped edge-end search-------------------------------*/\r\n lumaEndN -= lumaNN * 0.5;\r\n lumaEndP -= lumaNN * 0.5;\r\n bool doneN = abs(lumaEndN) >= gradientScaled;\r\n bool doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P1;\r\n bool doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P1;\r\n/*--------------------------------------------------------------------------*/\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P2;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P2;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 3)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P3;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P3;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 4)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P4;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P4;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 5)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P5;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P5;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 6)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P6;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P6;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 7)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P7;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P7;\r\n/*--------------------------------------------------------------------------*/\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n/*----------------calculate subpix offset due to edge ends-------------------*/\r\n float dstN = posM.x - posN.x;\r\n float dstP = posP.x - posM.x;\r\n if(!horzSpan) dstN = posM.y - posN.y;\r\n if(!horzSpan) dstP = posP.y - posM.y;\r\n/*--------------------------------------------------------------------------*/\r\n bool goodSpanN = (lumaEndN < 0.0) != lumaMLTZero;\r\n float spanLength = (dstP + dstN);\r\n bool goodSpanP = (lumaEndP < 0.0) != lumaMLTZero;\r\n float spanLengthRcp = 1.0 / spanLength;\r\n/*--------------------------------------------------------------------------*/\r\n bool directionN = dstN < dstP;\r\n float dst = min(dstN, dstP);\r\n bool goodSpan = directionN ? goodSpanN : goodSpanP;\r\n float subpixG = subpixF * subpixF;\r\n float pixelOffset = (dst * (-spanLengthRcp)) + 0.5;\r\n float subpixH = subpixG * fxaaQualitySubpix;\r\n/*-----------------calc texture offest using subpix-------------------------*/\r\n float pixelOffsetGood = goodSpan ? pixelOffset : 0.0;\r\n float pixelOffsetSubpix = max(pixelOffsetGood, subpixH);\r\n\r\n float offset = pixelOffsetSubpix * lengthSign;\r\n #ifdef BG_TRANSPARENT\r\n // get original texel\r\n vec4 rgbaA = FxaaTexTopAlpha(srcTex, posM);\r\n // calc step to blended texel\r\n vec2 step = sign((!horzSpan) ? vec2 (offset, 0.0) : vec2 (0.0, offset));\r\n // get neighboring texel\r\n vec4 rgbaB = FxaaTexTopAlpha(srcTex, posM + step * srcTexelSize);\r\n // calc blend factor from offset\r\n float f = (!horzSpan) ? offset / srcTexelSize.x : offset / srcTexelSize.y;\r\n f = abs(f);\r\n // calc alpha (special formula to emulate blending with bg)\r\n gl_FragColor.a = 1.0 - mix(1.0 - rgbaA.a, 1.0 - rgbaB.a, f);\r\n // calc color (special formula to emulate blending with bg)\r\n gl_FragColor.rgb = mix(rgbaA.rgb * rgbaA.a, rgbaB.rgb * rgbaB.a, f) / gl_FragColor.a;\r\n #else\r\n if(!horzSpan) {\r\n posM.x += offset;\r\n } else {\r\n posM.y += offset;\r\n }\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n #endif\r\n return;\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1}),this.setValues(e)}copy(e){super.copy(e),this.depth=e.depth}setValues(e){if(void 0===e)return;super.setValues(e);const t={};this.bgTransparent&&(t.BG_TRANSPARENT=1),this.defines=t}}wh.prototype.bgTransparent=!1;const Sh=wh,vh=[new r.Vector3(.295184,.077723,.068429),new r.Vector3(-.271976,-.365221,.838363),new r.Vector3(.547713,.467576,.488515),new r.Vector3(.662808,-.031733,.584758),new r.Vector3(-.025717,.218955,.657094),new r.Vector3(-.310153,-.365223,.370701),new r.Vector3(-.101407,-.006313,.747665),new r.Vector3(-.769138,.360399,.086847),new r.Vector3(-.271988,-.27514,.905353),new r.Vector3(.09674,-.566901,.700151),new r.Vector3(.562872,-.735136,.094647),new r.Vector3(.379877,.359278,.190061),new r.Vector3(.519064,-.023055,.405068),new r.Vector3(-.301036,.114696,.088885),new r.Vector3(-.282922,.598305,.487214),new r.Vector3(-.181859,.25167,.679702),new r.Vector3(-.191463,-.635818,.512919),new r.Vector3(-.293655,.427423,.078921),new r.Vector3(-.267983,.680534,.13288),new r.Vector3(.139611,.319637,.477439),new r.Vector3(-.352086,.31104,.653913),new r.Vector3(.321032,.805279,.487345),new r.Vector3(.073516,.820734,.414183),new r.Vector3(-.155324,.589983,.41146),new r.Vector3(.335976,.170782,.527627),new r.Vector3(.46346,-.355658,.167689),new r.Vector3(.222654,.59655,.769406),new r.Vector3(.922138,-.04207,.147555),new r.Vector3(-.72705,-.329192,.369826),new r.Vector3(-.090731,.53382,.463767),new r.Vector3(-.323457,-.876559,.238524),new r.Vector3(-.663277,-.372384,.342856)];class Ch extends r.RawShaderMaterial{constructor(){super(),this.setValues.call(this,{uniforms:{noiseTexture:{type:"t",value:Yn.noiseTexture},noiseTexelSize:{type:"v2",value:new r.Vector2(1/Yn.noiseWidth,1/Yn.noiseHeight)},diffuseTexture:{type:"t",value:null},normalTexture:{type:"t",value:null},depthTexture:{type:"t",value:null},srcTexelSize:{type:"v2",value:new r.Vector2(1/512,1/512)},camNearFar:{type:"v2",value:new r.Vector2(1,10)},projMatrix:{type:"mat4",value:new r.Matrix4},aspectRatio:{type:"f",value:0},tanHalfFOV:{type:"f",value:0},samplesKernel:{type:"v3v",value:vh},kernelRadius:{type:"f",value:1},depthThreshold:{type:"f",value:1},factor:{type:"f",value:1}},vertexShader:Qt,fragmentShader:"precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 32\r\nuniform vec3 samplesKernel[MAX_SAMPLES_COUNT];\r\nuniform sampler2D noiseTexture;\r\nuniform vec2 noiseTexelSize;\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D depthTexture;\r\nuniform sampler2D normalTexture;\r\nuniform vec2 srcTexelSize;\r\nuniform vec2 camNearFar;\r\nuniform mat4 projMatrix;\r\n\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\nuniform float kernelRadius;\r\nuniform float depthThreshold;\r\nuniform float factor;\r\n\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n // remap coordinates to prevent noise exture rescale\r\n vec2 vUvNoise = vUv / srcTexelSize * noiseTexelSize;\r\n vec4 normalData = texture2D(normalTexture, vUv);\r\n // return for background fragments (their normals are zero vectors)\r\n if (length(normalData.rgb) < EPSILON) {\r\n // 0.0 in alpha component means that it is background fragment\r\n gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);\r\n return;\r\n }\r\n //[0, 1] -> [-1, 1]\r\n vec3 normal = (normalData.rgb * 2.0 - 1.0);\r\n // normalData.a store 1.0 if normal was build for frontfaced surface\r\n // and 0.0 in other case\r\n if (normalData.a < EPSILON) {\r\n normal *= -1.0;\r\n }\r\n // get random vector for sampling sphere rotation\r\n vec3 randN = texture2D(noiseTexture, vUvNoise).rgb * 2.0 - 1.0;\r\n randN = normalize(randN);\r\n // build TBN (randomly rotated around normal)\r\n vec3 tangent = normalize(randN - normal * dot(randN, normal));\r\n vec3 bitangent = cross(tangent, normal);\r\n mat3 TBN = mat3(tangent, bitangent, normal);\r\n // calc AO value\r\n float AO = 0.0;\r\n for (int i = 0 ; i < MAX_SAMPLES_COUNT ; i++) {\r\n // rotate sampling kernel around normal\r\n vec3 reflectedSample = TBN * samplesKernel[i];\r\n // get sample\r\n vec3 samplePos = viewPos + reflectedSample * kernelRadius;\r\n\r\n // project sample to screen to get sample's screen pos\r\n vec4 SampleScrPos = vec4(samplePos, 1.0);\r\n // eye -> clip\r\n SampleScrPos = projMatrix * SampleScrPos;\r\n // normalize\r\n SampleScrPos.xy /= SampleScrPos.w;\r\n //[-1, 1] -> [0, 1]\r\n SampleScrPos.xy = (SampleScrPos.xy + vec2(1.0)) * 0.5;\r\n\r\n // get view z for sample projected to the objct surface\r\n float sampleDepth = CalcViewZ(SampleScrPos.xy);\r\n // calc occlusion made by object surface at the sample\r\n AO += step(samplePos.z, sampleDepth);\r\n }\r\n // calc result AO-map color\r\n AO = 1.0 - max(0.0, AO / float(MAX_SAMPLES_COUNT) * factor);\r\n // write value to AO-map\r\n gl_FragColor = vec4(AO, AO, AO, 1.0);\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1})}}const Ah=Ch,Eh=[-2,-1,0,1,2];class Th extends r.RawShaderMaterial{constructor(){super(),this.setValues.call(this,{uniforms:{depthTexture:{type:"t",value:null},srcTexelSize:{type:"v2",value:new r.Vector2(1/512,1/512)},aoMap:{type:"t",value:null},samplesOffsets:{type:"fv1",value:Eh}},vertexShader:Qt,fragmentShader:"precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = res;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x + samplesOffsets[i] * srcTexelSize.x, y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb = res.rgb / weightSum;\r\n gl_FragColor = res;\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1})}}const Rh=Th,Mh=[-2,-1,0,1,2];class Ph extends r.RawShaderMaterial{constructor(e){super(e),this.setValues.call(this,{uniforms:{diffuseTexture:{type:"t",value:null},depthTexture:{type:"t",value:null},srcTexelSize:{type:"v2",value:new r.Vector2(1/512,1/512)},aoMap:{type:"t",value:null},samplesOffsets:{type:"fv1",value:Mh},projMatrix:{type:"mat4",value:new r.Matrix4},aspectRatio:{type:"f",value:0},tanHalfFOV:{type:"f",value:0},fogNearFar:{type:"v2",value:new r.Vector2(100,100)},fogColor:{type:"v4",value:new r.Vector4(0,.5,0,1)}},vertexShader:Qt,fragmentShader:"precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nuniform mat4 projMatrix;\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\n#ifdef USE_FOG\r\n uniform vec2 fogNearFar;\r\n uniform vec4 fogColor;\r\n#endif\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 color = texture2D(diffuseTexture, vec2(x, y));\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = color;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x, y + samplesOffsets[i] * srcTexelSize.y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb /= weightSum;\r\n\r\n #if defined(USE_FOG) && !defined(FOG_TRANSPARENT)\r\n // Add fog to the result value\r\n // Proper way to get an image with fog and ao requires formula:\r\n // gl_FragColor = fragColor*AO*(1-fogFactor) + fogColor*fogFactor\r\n // But we have already fogged molecule to add AO too. Let's split the straight formula into our real steps!\r\n // We have: AO, fogFactor, fogColor,\r\n // color = fragColor*(1-fogFactor) + fogColor*fogFactor (it comes from diffuseTexture,\r\n // where molecule has been already drawn with fog)\r\n // Transform:\r\n // fragColor*AO*(1-fogFactor) + fogColor*fogFactor =\r\n // = [fragColor*(1-fogFactor) = color - fogColor*fogFactor] =\r\n // = (color - fogColor*fogFactor)*AO + fogColor*fogFactor =\r\n // = color*AO + fogColor*fogFactor*(1 - AO)\r\n // Result: gl_FragColor = color*AO + fogColor*fogFactor*(1 - AO)\r\n float fogFactor = smoothstep(fogNearFar.x, fogNearFar.y, - viewPos.z) * fogColor.a;\r\n gl_FragColor.rgb = color.rgb * res.rgb + fogColor.rgb * fogFactor *(vec3(1.0, 1.0, 1.0) - res.rgb);\r\n #else\r\n gl_FragColor.rgb = color.rgb * res.rgb;\r\n #endif\r\n gl_FragColor.a = color.a;\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1}),this.setValues(e)}setValues(e){if(void 0===e)return;super.setValues(e);const t={};this.useFog&&(t.USE_FOG=1),this.fogTransparent&&(t.FOG_TRANSPARENT=1),this.defines=t}}Ph.prototype.useFog=!0,Ph.prototype.fogTransparent=!1;const Nh=Ph;class Lh extends r.RawShaderMaterial{constructor(){super();const e={uniforms:{srcL:{type:"t",value:null},srcR:{type:"t",value:null}},vertexShader:Qt,fragmentShader:"precision highp float;\r\n\r\nuniform sampler2D srcL;\r\nuniform sampler2D srcR;\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vec4 l = texture2D(srcL, vUv);\r\n vec4 r = texture2D(srcR, vUv);\r\n gl_FragColor = vec4(l.r, r.g, r.b, 1.0);\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1};this.setValues(e)}}const Ih=Lh;class Oh{constructor(){this.position=new r.Vector3(0,0,0),this.scale=1,this.orientation=new r.Quaternion(0,0,0,1)}set(e,t,r){this.position=e,this.scale=t,this.orientation=r}}class Vh{setup(e,t){this._startTime=void 0,this._endTime=void 0,this._isPaused=!1,this._srcView=e,this._dstView=t,this._isMoving=!1}isMoving(){return this._isMoving}wasStarted(){return void 0!==this._startTime&&void 0!==this._endTime}start(){this._startTime=Date.now();const e=z.now.interpolateViews?1500:0;this._endTime=this._startTime+e,this._isMoving=!0}getCurrentView(){if(void 0===this._srcView||void 0===this._dstView||!this._isMoving||!this.wasStarted())return{success:!1};let e=this.createView();const t=Date.now();if(t>this._endTime)return e=this._dstView,this.reset(),{success:!0,view:e};const r=(t-this._startTime)/(this._endTime-this._startTime);return e.position.copy(this._srcView.position),e.position.lerp(this._dstView.position,r),e.scale=(1-r)*this._srcView.scale+r*this._dstView.scale,e.orientation.copy(this._srcView.orientation),e.orientation.slerp(this._dstView.orientation,r),{success:!0,view:e}}reset(){this._startTime=this._endTime=0,this._isMoving=!1}pause(){this._isPaused||(this.setup(this.getCurrentView().view,this._dstView),this._isPaused=!0)}resume(){this._isPaused=!1}createView(){return new Oh}}function Dh(e,r){this.context=e,this._opts=t().merge({path:"/"},r)}ur(Dh.prototype),Dh.prototype.removeCookie=function(e){const t=this._toCount(e);let r=this._getSimpleCookie(t);if(r){this._removeSimpleCookie(t),r=parseInt(r,10);for(let t=0;tt?function(t){t.style.display="",t.style.cursor="pointer",t.style.left="calc(50% - 50px)",t.style.width="100px",t.textContent="ENTER VR";let r=null;function n(){r.removeEventListener("end",n),t.textContent="ENTER VR",r=null}function s(s){s.addEventListener("end",n),e._gfx.renderer.xr.setReferenceSpaceType("local"),e._gfx.renderer.xr.setSession(s),t.textContent="EXIT VR",r=s}t.onmouseenter=function(){t.style.opacity="1.0"},t.onmouseleave=function(){t.style.opacity="0.5"},t.onclick=function(){if(null===r){const t={optionalFeatures:["local-floor","bounded-floor"]};navigator.xr.requestSession("immersive-vr",t).then(s),e.moveSceneBehindHeadset()}else r.end()}}(r):function(e){e.style.display="",e.style.cursor="auto",e.style.left="calc(50% - 75px)",e.style.width="150px",e.textContent="VR NOT FOUND",e.onmouseenter=null,e.onmouseleave=null,e.onclick=null}(r))),r}const r=document.createElement("a");return r.href="https://webvr.info",r.innerHTML="WEBXR NOT SUPPORTED",r.style.left="calc(50% - 90px)",r.style.width="180px",r.style.textDecoration="none",t(r),r}class Fh{constructor(e){this._mainCamera=new r.PerspectiveCamera,this._button=null,this._onToggle=e,this._molContainer=new sr.RCGroup,this._user=new sr.RCGroup,this._scalingPivot=new r.Object3D,this._user.add(this._scalingPivot),this._controller1=null,this._controller2=null,this._pressedGripsCounter=0,this._distance=0,this._gfx=null}startScalingByControllers(){this._distance=this._controller1.position.distanceTo(this._controller2.position),sr.getMiddlePoint(this._controller1.position,this._controller2.position,this._scalingPivot.position),this._scalingPivot.scale.set(1,1,1),this._scalingPivot.updateMatrix(),this._scalingPivot.updateMatrixWorld(),this._scalingPivot.addSavingWorldTransform(this._molContainer)}stopScalingByControllers(){this._gfx.scene.addSavingWorldTransform(this._molContainer)}handleGripsDown(e){this._pressedGripsCounter++,2===this._pressedGripsCounter?this.startScalingByControllers():1===this._pressedGripsCounter&&e.target.addSavingWorldTransform(this._molContainer)}handleGripsUp(e){if(this._pressedGripsCounter--,1===this._pressedGripsCounter){this.stopScalingByControllers();(e.target===this._controller1?this._controller2:this._controller1).addSavingWorldTransform(this._molContainer)}else 0===this._pressedGripsCounter&&this._gfx.scene.addSavingWorldTransform(this._molContainer)}enable(e){if(!e)return void w.warn("WebVR couldn't be enabled, because gfx is not defined");this._gfx=e;const{renderer:t,camera:r}=e;if(!t)throw new Error("No renderer is available to toggle WebVR");if(!r)throw new Error("No camera is available to toggle WebVR");t.xr.enabled=!0,this._button?this._button.style.display="block":(this._button=zh(this),document.body.appendChild(this._button)),this._mainFog=z.now.fog,z.set("fog",!1),this._plugVRNodesIntoScene(e,t),this._setControllersListeners(),this._onToggle&&this._onToggle(!0)}_plugVRNodesIntoScene(e,t){this._mainCamera.copy(e.camera),e.scene.add(this._user),e.scene.add(this._molContainer),this._molContainer.add(e.root),this._controller1=t.xr.getController(0),this._controller2=t.xr.getController(1);const r=this._createControllerMesh();this._controller1.add(r),this._controller2.add(r.clone()),this._user.add(this._controller1),this._user.add(this._controller2)}_setControllersListeners(){this._controller1.addEventListener("selectstart",(e=>{this.handleGripsDown(e)})),this._controller1.addEventListener("selectend",(e=>{this.handleGripsUp(e)})),this._controller2.addEventListener("selectstart",(e=>{this.handleGripsDown(e)})),this._controller2.addEventListener("selectend",(e=>{this.handleGripsUp(e)})),this._controller1.addEventListener("squeezestart",(e=>{this.handleGripsDown(e)})),this._controller1.addEventListener("squeezeend",(e=>{this.handleGripsUp(e)})),this._controller2.addEventListener("squeezestart",(e=>{this.handleGripsDown(e)})),this._controller2.addEventListener("squeezeend",(e=>{this.handleGripsUp(e)}))}disable(){if(!this._gfx)return;const{renderer:e,camera:t}=this._gfx;if(!e)throw new Error("No renderer is available to toggle WebVR");e.setAnimationLoop(null);const r=e.xr.getSession();r&&r.end(),e.xr.enabled=!1,this._button&&(this._button.style.display="none"),z.set("fog",this._mainFog),this._unplugVRNodesFromScene(t),this._onToggle&&this._onToggle(!1)}_unplugVRNodesFromScene(e){this._mainCamera&&e&&e.copy(this._mainCamera);const t=this._molContainer.children[0];t&&this._gfx.scene.add(t),this._molContainer.parent.remove(this._molContainer),this._user&&this._gfx.scene.remove(this._user),this._molContainer=null,this._user=null,this._scalingPivot=null,this._user=null,this._controller1=null,this._controller2=null}_createControllerMesh(){const e=new r.CylinderGeometry(.04,.04,.3),t=new Jn({lights:!1,overrideColor:!0});t.setUberOptions({fixedColor:new r.Color(4474111)}),t.updateUniforms();const n=new r.Mesh(e,t);return n.rotateX(-Math.PI/2),n}updateMoleculeScale(){if(!this._controller1||!this._controller2)return;const e=this;if(2===e._pressedGripsCounter){sr.getMiddlePoint(e._controller1.position,e._controller2.position,e._scalingPivot.position);const t=e._controller1.position.distanceTo(e._controller2.position),r=t/e._distance;e._scalingPivot.scale.multiplyScalar(r),e._distance=t}}moveSceneBehindHeadset(){const e=this._gfx,{camera:t}=e,r=this._molContainer;r.matrix.identity(),r.position.set(0,0,-4),r.updateMatrix(),r.matrixWorld.multiplyMatrices(t.matrixWorld,r.matrix),e.scene.addSavingWorldTransform(r),this._onToggle&&this._onToggle(!0)}getCanvas(){const e=this._gfx;return e&&e.renderer?e.renderer.domElement:null}}const{selectors:Bh,Atom:Uh,Residue:Gh,Chain:jh,Molecule:Hh}=Yt,$h=0,Wh=1,Yh=2,Xh="Could not find suitable loader for this source";r.ColorManagement.enabled=!1;const{createElement:qh}=O;function Zh(e){const t=e.lastIndexOf(".");return t>=0&&(e=e.substr(0,t)),e}function Kh(e,t,r){void 0!==r?e.debug(`${t}... ${Math.floor(100*r)}%`):e.debug(`${t}...`)}function Qh(){return z.now.fogColorEnable?z.now.fogColor:z.now.bg.color}function Jh(e){g.call(this),this._opts=t().merge({settingsCookie:"settings",cookiePath:"/"},e),this._gfx=null,this._interpolator=new Vh,this._container=e&&e.container||document.getElementById("miew-container")||t().head(document.getElementsByClassName("miew-container"))||document.body,this._containerRoot=this._container,this._running=!1,this._halting=!1,this._building=!1,this._needRender=!0,this._hotKeysEnabled=!0,this.settings=z;const r=w;r.console=!1,r.level="info",this.logger=r,this._cookies=new kh(this),this.restoreSettings(),e&&e.settings&&this.settings.set(e.settings),this._spinner=null,this._loading=[],this._animInterval=null,this._visuals={},this._curVisualName=null,this._objects=[],this._sourceWindow=null,this.reset(),this._repr&&r.debug(`Selected ${this._repr.mode.name} mode with ${this._repr.colorer.name} colorer.`);const n=this;Jh.registeredPlugins.forEach((e=>{e.call(n)})),this._initOnSettingsChanged()}function eu(e,t){const r=e;for(;r.firstChild;)r.removeChild(r.firstChild);r.appendChild(t)}function tu(e){return e.getExtension("EXT_frag_depth")}function ru(e){return e.getExtension("WEBGL_depth_texture")&&e.getExtension("WEBGL_draw_buffers")}Jh.prototype=Object.create(g.prototype),Jh.prototype.constructor=Jh,Jh.prototype.getMaxRepresentationCount=function(){return Qo.NUM_REPRESENTATION_BITS},Jh.prototype._updateShadowCamera=function(){const e=new r.Matrix4,t=new r.Vector3,n={center:new r.Vector3,halfSize:new r.Vector3};return function(){this._gfx.scene.updateMatrixWorld();for(let r=0;r{n._onKeyDown(e)})),e.addEventListener("keyup",(e=>{n._onKeyUp(e)})),this._objectControls=new ih(this._gfx.root,this._gfx.pivot,this._gfx.camera,this._gfx.renderer.domElement,(()=>n._getAltObj())),this._objectControls.addEventListener("change",(e=>{switch(z.now.shadow.on&&n._updateShadowCamera(),e.action){case"rotate":n.dispatchEvent({type:"rotate",quaternion:e.quaternion});break;case"zoom":n.dispatchEvent({type:"zoom",factor:e.factor});break;default:n.dispatchEvent({type:e.action})}n.dispatchEvent({type:"transform"}),n._needRender=!0}));const t=this._gfx;this._picker=new ah(t.root,t.camera,t.renderer.domElement),this._picker.addEventListener("newpick",(e=>{n._onPick(e)})),this._picker.addEventListener("dblclick",(e=>{n.center(e)}))}catch(e){if("TypeError"===e.name&&"Cannot read property 'getExtension' of null"===e.message)this._showMessage("Could not create WebGL context.");else{if(!(e.message.search(/webgl/i)>1))throw this._showMessage("Viewer initialization failed."),e;this._showMessage(e.message)}return!1}const s=this._opts&&this._opts.load;if(s){const e=this._opts&&this._opts.type;this.load(s,{fileType:e,keepRepsInfo:!0})}return!0},Jh.prototype.term=function(){this._showMessage("Viewer has been terminated."),this._loading.forEach((e=>{e.cancel()})),this._loading.length=0,this.halt(),this._gfx=null},Jh.prototype._showMessage=function(e){const t=document.createElement("div");t.setAttribute("class","miew-message"),t.appendChild(document.createElement("p")).appendChild(document.createTextNode(e)),eu(this._container,t)},Jh.prototype._showCanvas=function(){eu(this._container,this._gfx.renderer.domElement)},Jh.prototype._requestAnimationFrame=function(e){const{xr:t}=this._gfx.renderer;t&&t.enabled?this._gfx.renderer.setAnimationLoop(e):requestAnimationFrame(e)},Jh.prototype._initGfx=function(){const e={width:this._container.clientWidth,height:this._container.clientHeight},t={preserveDrawingBuffer:!0,alpha:!0,premultipliedAlpha:!1};z.now.antialias&&(t.antialias=!0),e.renderer2d=new Xc,e.renderer=new r.WebGL1Renderer(t),e.renderer.shadowMap.enabled=z.now.shadow.on,e.renderer.shadowMap.autoUpdate=!1,e.renderer.shadowMap.type=r.PCFShadowMap,Fn.init(e.renderer),tu(e.renderer.getContext())||z.set("zSprites",!1),ru(e.renderer.getContext())||z.set("ao",!1),e.renderer.autoClear=!1,e.renderer.setPixelRatio(window.devicePixelRatio),e.renderer.setSize(e.width,e.height),e.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),e.renderer.clearColor(),e.renderer2d.setSize(e.width,e.height),e.camera=new r.PerspectiveCamera(z.now.camFov,e.width/e.height,z.now.camNear,z.now.camFar),e.camera.setMinimalFov(z.now.camFov),e.camera.position.z=z.now.camDistance,e.camera.updateProjectionMatrix(),e.camera.layers.set(sr.LAYERS.DEFAULT),e.camera.layers.enable(sr.LAYERS.VOLUME),e.camera.layers.enable(sr.LAYERS.VOLUME_BFPLANE),e.stereoCam=new r.StereoCamera,e.scene=new r.Scene;const n=Qh();e.scene.fog=new r.Fog(n,z.now.camNear,z.now.camFar),e.root=new sr.RCGroup,e.scene.add(e.root),e.pivot=new sr.RCGroup,e.root.add(e.pivot),e.selectionScene=new r.Scene,e.selectionRoot=new r.Group,e.selectionRoot.matrixAutoUpdate=!1,e.selectionScene.add(e.selectionRoot),e.selectionPivot=new r.Group,e.selectionPivot.matrixAutoUpdate=!1,e.selectionRoot.add(e.selectionPivot);const s=new r.DirectionalLight(16777215,.45);s.position.set(0,.414,1),s.layers.enable(sr.LAYERS.TRANSPARENT),s.castShadow=!0,s.shadow.bias=.09,s.shadow.radius=z.now.shadow.radius,s.shadow.camera.layers.set(sr.LAYERS.SHADOWMAP);const i=e.renderer.getPixelRatio(),o=Math.max(e.width,e.height)*i;s.shadow.mapSize.width=o,s.shadow.mapSize.height=o,s.target.position.set(0,0,0),e.scene.add(s),e.scene.add(s.target);const a=new r.AmbientLight(6710886);a.layers.enable(sr.LAYERS.TRANSPARENT),e.scene.add(a),e.axes=new lh(e.root,e.camera);const l=e.width*i,c=e.height*i;e.offscreenBuf=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.NearestFilter,format:r.RGBAFormat,depthBuffer:!0}),e.renderer.getContext().getExtension("WEBGL_depth_texture")&&(e.offscreenBuf.depthTexture=new r.DepthTexture,e.offscreenBuf.depthTexture.type=r.UnsignedShortType),e.offscreenBuf2=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),e.offscreenBuf3=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),e.offscreenBuf4=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),e.volBFTex=e.offscreenBuf3,e.volFFTex=e.offscreenBuf4,e.volWFFTex=e.offscreenBuf,e.renderer.getContext().getExtension("OES_texture_float")?(e.offscreenBuf5=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,type:r.FloatType,depthBuffer:!1}),e.offscreenBuf6=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,type:r.FloatType,depthBuffer:!1}),e.offscreenBuf7=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,type:r.FloatType,depthBuffer:!0}),e.volBFTex=e.offscreenBuf5,e.volFFTex=e.offscreenBuf6,e.volWFFTex=e.offscreenBuf7):this.logger.warn("Device doesn't support OES_texture_float extension"),e.stereoBufL=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),e.stereoBufR=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),this._gfx=e,this._showCanvas(),this._embedWebXR("WEBVR"===z.now.stereo),this._container.appendChild(e.renderer2d.getElement());const h=new m;h.domElement.style.position="absolute",h.domElement.style.right="0",h.domElement.style.bottom="0",this._container.appendChild(h.domElement),this._fps=h,this._fps.show(z.now.fps)},Jh.prototype._initListeners=function(){const e=this;window.addEventListener("resize",(()=>{e._onResize()}))},Jh.prototype._makeUniqueVisualName=function(e){if(!e)return Math.random().toString();let t=e,r=1;for(;this._visuals.hasOwnProperty(t);)t=`${e} (${r.toString()})`,r++;return t},Jh.prototype._addVisual=function(e){if(!e)return null;const t=this._makeUniqueVisualName(e.name);return e.name=t,this._visuals[t]=e,this._gfx.pivot.add(e),e.getSelectionGeo&&this._gfx.selectionPivot.add(e.getSelectionGeo()),t},Jh.prototype._removeVisual=function(e){let t="",r=null;e instanceof ar?(({name:t}=e),r=e):"string"==typeof e&&(t=e,r=this._visuals[t]),r&&this._visuals.hasOwnProperty(t)&&this._visuals[t]===r&&(t===this._curVisualName&&(this._curVisualName=void 0),delete this._visuals[t],r.release(),this._needRender=!0)},Jh.prototype._forEachVisual=function(e){for(const t in this._visuals)this._visuals.hasOwnProperty(t)&&e(this._visuals[t])},Jh.prototype._releaseAllVisuals=function(){if(this._gfx&&this._gfx.pivot){for(const e in this._visuals)this._visuals.hasOwnProperty(e)&&this._visuals[e].release();this._visuals={}}},Jh.prototype._forEachComplexVisual=function(e){if(this._gfx&&this._gfx.pivot)for(const t in this._visuals)this._visuals.hasOwnProperty(t)&&this._visuals[t]instanceof Qo&&e(this._visuals[t])},Jh.prototype._getComplexVisual=function(e){e=e||this._curVisualName;let t=null,r=null;return this._forEachComplexVisual((n=>{t=n,n.name===e&&(r=n)})),r||t},Jh.prototype._getVolumeVisual=function(){let e=null;return this._forEachVisual((t=>{t instanceof pa&&(e=t)})),e},Jh.prototype._getVisualForComplex=function(e){if(!e)return null;let t=null;return this._forEachComplexVisual((r=>{r.getComplex()===e&&(t=r)})),t},Jh.prototype.getVisuals=function(){return Object.keys(this._visuals)},Jh.prototype.getComplexVisualsCount=function(){let e=0;return this._forEachComplexVisual((()=>e++)),e},Jh.prototype.getCurrentVisual=function(){return this._curVisualName},Jh.prototype.setCurrentVisual=function(e){this._visuals[e]&&(this._curVisualName=e)},Jh.prototype.run=function(){if(!this._running){if(this._running=!0,this._halting)return void(this._halting=!1);this._objectControls.enable(!0),this._interpolator.resume(),this._requestAnimationFrame((()=>this._onTick()))}},Jh.prototype.halt=function(){this._running&&(this._discardComponentEdit(),this._discardFragmentEdit(),this._objectControls.enable(!1),this._interpolator.pause(),this._halting=!0)},Jh.prototype.enableHotKeys=function(e){this._hotKeysEnabled=e,this._objectControls.enableHotkeys(e)},Jh.prototype._onResize=function(){const e=this._gfx;e&&(this._needRender=!0,e.width=this._container.clientWidth,e.height=this._container.clientHeight,e.camera.aspect=e.width/e.height,e.camera.setMinimalFov(z.now.camFov),e.camera.updateProjectionMatrix(),e.renderer.setSize(e.width,e.height),e.renderer2d.setSize(e.width,e.height),this.dispatchEvent({type:"resize"}))},Jh.prototype._resizeOffscreenBuffers=function(e,t,r){const n=this._gfx,s="NONE"===(r=r||"NONE")||"ANAGLYPH"===r,i=s?1:.5;n.offscreenBuf.setSize(i*e,t),n.offscreenBuf2.setSize(i*e,t),n.offscreenBuf3.setSize(i*e,t),n.offscreenBuf4.setSize(i*e,t),n.offscreenBuf5&&n.offscreenBuf5.setSize(i*e,t),n.offscreenBuf6&&n.offscreenBuf6.setSize(i*e,t),n.offscreenBuf7&&n.offscreenBuf7.setSize(i*e,t),s&&(n.stereoBufL.setSize(e,t),n.stereoBufR.setSize(e,t))},Jh.prototype._onTick=function(){if(this._halting)return this._running=!1,void(this._halting=!1);this._fps.update(),this._requestAnimationFrame((()=>this._onTick())),this._onUpdate(),this._needRender&&(this._onRender(),this._needRender=!z.now.suspendRender||"WEBVR"===z.now.stereo)},Jh.prototype._getBSphereRadius=function(){let e=0;return this._forEachVisual((t=>{e=Math.max(e,t.getBoundaries().boundingSphere.radius)})),e*this._objectControls.getScale()},Jh.prototype.getOBB=function(){const e=new r.Sphere,t=new r.Box3,n=new r.Box3,s=new r.Matrix4,i=[new r.Vector3,new r.Vector3,new r.Vector3,new r.Vector3];return function(r,o){n.makeEmpty(),this._forEachVisual((s=>{e.copy(s.getBoundaries().boundingSphere),e.applyMatrix4(s.matrixWorld).applyMatrix4(r),e.getBoundingBox(t),n.union(t)})),n.getCenter(o.center),s.copy(r).invert(),o.center.applyMatrix4(s);const{min:a}=n,{max:l}=n;i[0].set(a.x,a.y,a.z),i[1].set(l.x,a.y,a.z),i[2].set(a.x,l.y,a.z),i[3].set(a.x,a.y,l.z);for(let e=0,t=i.length;e{e.getComplex().update()})),z.now.autobuild&&!this._loading.length&&!this._building&&this._needRebuild()&&this.rebuild(),this._loading.length||this._building||this._needRebuild()||this._updateView(),this._updateFog(),this._gfx.renderer.xr.enabled&&this.webVR.updateMoleculeScale()},Jh.prototype._onRender=function(){const e=this._gfx;e.scene.updateMatrixWorld(),e.camera.updateMatrixWorld(),this._clipPlaneUpdateValue(this._getBSphereRadius()),this._fogFarUpdateValue(),e.renderer.setRenderTarget(null),e.renderer.clear(),this._renderFrame(z.now.stereo)},Jh.prototype._renderFrame=function(){const e=new Ih,t=new r.Vector2;return function(r){const n=this._gfx,{renderer:s}=n;s.getSize(t),"NONE"!==r&&(n.camera.focus=n.camera.position.z,n.stereoCam.aspect=1,"ANAGLYPH"===r?n.stereoCam.update(n.camera):n.stereoCam.updateHalfSized(n.camera,z.now.camFov));const i=n.renderer.getPixelRatio();switch(this._resizeOffscreenBuffers(t.width*i,t.height*i,r),this._renderShadowMap(),r){case"WEBVR":case"NONE":this._renderScene(n.camera,!1);break;case"SIMPLE":case"DISTORTED":s.setScissorTest(!0),s.setScissor(0,0,t.width/2,t.height),s.setViewport(0,0,t.width/2,t.height),this._renderScene(this._gfx.stereoCam.cameraL,"DISTORTED"===r),s.setScissor(t.width/2,0,t.width/2,t.height),s.setViewport(t.width/2,0,t.width/2,t.height),this._renderScene(this._gfx.stereoCam.cameraR,"DISTORTED"===r),s.setScissorTest(!1);break;case"ANAGLYPH":this._renderScene(this._gfx.stereoCam.cameraL,!1,n.stereoBufL),this._renderScene(this._gfx.stereoCam.cameraR,!1,n.stereoBufR),s.setRenderTarget(null),e.uniforms.srcL.value=n.stereoBufL.texture,e.uniforms.srcR.value=n.stereoBufR.texture,n.renderer.renderScreenQuad(e)}n.renderer2d.render(n.scene,n.camera),z.now.axes&&n.axes&&!n.renderer.xr.enabled&&n.axes.render(s)}}(),Jh.prototype._onBgColorChanged=function(){const e=this._gfx,t=Qh();e&&(e.scene.fog&&e.scene.fog.color.set(t),e.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent))),this._needRender=!0},Jh.prototype._onFogColorChanged=function(){const e=this._gfx,t=Qh();e&&e.scene.fog&&e.scene.fog.color.set(t),this._needRender=!0},Jh.prototype._setUberMaterialValues=function(e){this._gfx.root.traverse((t=>{(t instanceof r.Mesh||t instanceof r.LineSegments||t instanceof r.Line)&&t.material instanceof Jn&&(t.material.setValues(e),t.material.needsUpdate=!0)}))},Jh.prototype._enableMRT=function(e,t,r){const n=this._gfx,s=n.renderer.getContext(),i=s.getExtension("WEBGL_draw_buffers"),{properties:o}=n.renderer;if(!e)return void i.drawBuffersWEBGL([s.COLOR_ATTACHMENT0,null]);n.renderer.setRenderTarget(r);const a=o.get(r.texture).__webglTexture;s.bindTexture(s.TEXTURE_2D,a),n.renderer.setRenderTarget(t);const l=o.get(t).__webglFramebuffer,c=o.get(t.texture).__webglTexture;s.bindFramebuffer(s.FRAMEBUFFER,l),l.width=t.width,l.height=t.height,s.framebufferTexture2D(s.FRAMEBUFFER,s.COLOR_ATTACHMENT0,s.TEXTURE_2D,c,0),s.framebufferTexture2D(s.FRAMEBUFFER,i.COLOR_ATTACHMENT1_WEBGL,s.TEXTURE_2D,a,0),i.drawBuffersWEBGL([s.COLOR_ATTACHMENT0,i.COLOR_ATTACHMENT1_WEBGL])},Jh.prototype._renderScene=function(e,t,r){t=t||!1,r=r||null;const n=this._gfx;if(n.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),n.renderer.setRenderTarget(r),n.renderer.clear(),n.renderer.xr.enabled)return void n.renderer.render(n.scene,e);n.renderer.setClearColor(0,0),n.renderer.setRenderTarget(n.offscreenBuf4),n.renderer.clearColor(),n.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),n.renderer.setRenderTarget(n.offscreenBuf),n.renderer.clear();const s=null!==this._getComplexVisual(),i=this._getVolumeVisual(),o=s&&z.now.ao;o&&this._enableMRT(!0,n.offscreenBuf,n.offscreenBuf4),"prepass"===z.now.transparency?this._renderWithPrepassTransparency(e,n.offscreenBuf):"standard"===z.now.transparency&&(n.renderer.setRenderTarget(n.offscreenBuf),n.renderer.render(n.scene,e)),o&&this._enableMRT(!1,null,null);const a=s&&z.now.outline.on,l=s&&z.now.fxaa,c=null!==i&&null!=i.getMesh().material;let h=o||a||c||l||t?n.offscreenBuf2:r,u=n.offscreenBuf;o?(this._performAO(u,n.offscreenBuf4,n.offscreenBuf.depthTexture,h,n.offscreenBuf3,n.offscreenBuf2),l||t||c||a||(u=h,h=r,n.renderer.setRenderTarget(h),n.renderer.renderScreenQuadFromTex(u.texture,1))):(n.renderer.setRenderTarget(h),n.renderer.renderScreenQuadFromTex(u.texture,1)),a&&(u=h,h=c||l||t?n.offscreenBuf3:r,null!=u&&this._renderOutline(e,n.offscreenBuf,u,h)),this._renderSelection(e,n.offscreenBuf,h),c&&(n.renderer.setRenderTarget(n.offscreenBuf),n.renderer.renderScreenQuadFromTex(h.texture,1),h=n.offscreenBuf,this._renderVolume(i,e,h,n.volBFTex,n.volFFTex,n.volWFFTex),l||t||(n.renderer.setRenderTarget(r),n.renderer.renderScreenQuadFromTex(h.texture,1))),u=h,l&&(h=t?n.offscreenBuf4:r,this._performFXAA(u,h),u=h),t&&(h=r,this._performDistortion(u,h,!0))},Jh.prototype._performDistortion=function(){const e=new r.Scene,t=new r.OrthographicCamera(-1,1,1,-1,-500,1e3),n=new r.RawShaderMaterial({uniforms:{srcTex:{type:"t",value:null},aberration:{type:"fv3",value:new r.Vector3(1)}},vertexShader:Qt,fragmentShader:"precision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform vec3 aberration;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n \r\n gl_FragColor.r = texture2D(srcTex, 0.5 * (uv * aberration[0] + 1.0)).r;\r\n gl_FragColor.g = texture2D(srcTex, 0.5 * (uv * aberration[1] + 1.0)).g;\r\n gl_FragColor.b = texture2D(srcTex, 0.5 * (uv * aberration[2] + 1.0)).b;\r\n gl_FragColor.a = 1.0;\r\n}",transparent:!1,depthTest:!1,depthWrite:!1}),s=sr.buildDistorionMesh(10,10,z.now.debug.stereoBarrel);return e.add(new fs.Mesh(s,n)),function(r,s,i){this._gfx.renderer.setRenderTarget(s),this._gfx.renderer.clear(),i?(n.uniforms.srcTex.value=r.texture,n.uniforms.aberration.value.set(.995,1,1.01),this._gfx.renderer.render(e,t)):this._gfx.renderer.renderScreenQuadFromTexWithDistortion(r,z.now.debug.stereoBarrel)}}(),Jh.prototype._renderOutline=function(){const e=new bh({depth:!0});return function(t,n,s,i){const o=this._gfx;e.uniforms.srcTex.value=s.texture,e.uniforms.srcDepthTex.value=n.depthTexture,e.uniforms.srcTexSize.value.set(n.width,n.height),e.uniforms.color.value=new r.Color(z.now.outline.color),e.uniforms.threshold.value=z.now.outline.threshold,e.uniforms.thickness.value=new r.Vector2(z.now.outline.thickness,z.now.outline.thickness),o.renderer.setRenderTarget(i),o.renderer.renderScreenQuad(e)}}(),Jh.prototype._renderShadowMap=function(){const e={minFilter:r.NearestFilter,magFilter:r.NearestFilter,format:r.RGBAFormat};return function(){if(!z.now.shadow.on)return;const t=this._gfx,n=t.renderer.getRenderTarget(),s=t.renderer.getActiveCubeFace(),i=t.renderer.getActiveMipmapLevel(),o=t.renderer.state;o.setBlending(r.NoBlending),o.buffers.color.setClear(1,1,1,1),o.buffers.depth.setTest(!0),o.setScissorTest(!1);for(let n=0;n0)return!0}return!1},Jh.prototype._renderSelection=function(){const e=new bh;return function(t,r,n){const s=this._gfx;s.renderer.setClearColor("black",0),s.renderer.setRenderTarget(r),s.renderer.clear(!0,!1,!1),this._hasSelectionToRender()?(s.selectionRoot.matrix=s.root.matrix,s.selectionPivot.matrix=s.pivot.matrix,s.renderer.render(s.selectionScene,t)):s.renderer.renderDummyQuad(),s.renderer.setRenderTarget(n),s.renderer.renderScreenQuadFromTex(r.texture,.6),e.uniforms.srcTex.value=r.texture,e.uniforms.srcTexSize.value.set(r.width,r.height),s.renderer.renderScreenQuad(e)}}(),Jh.prototype._checkVolumeRenderingSupport=function(e){if(!e)return!1;const t=this._gfx,r=t.renderer.getRenderTarget();t.renderer.setRenderTarget(e);const n=t.renderer.getContext(),s=n.checkFramebufferStatus(n.FRAMEBUFFER);return t.renderer.setRenderTarget(r),s===n.FRAMEBUFFER_COMPLETE||(this.logger.warn("Device doesn't support electron density rendering"),!1)},Jh.prototype._renderVolume=function(){const e=new aa.BackFacePosMaterial,t=new aa.FrontFacePosMaterial,n=(new r.Matrix4).makeTranslation(.5,.5,.5),s=new r.Matrix4;let i;return function(r,o,a,l,c,h){const u=this._gfx;if(void 0===i&&(i=this._checkVolumeRenderingSupport(l)),!i)return;const d=r.getMesh();d.rebuild(u.camera),u.renderer.setClearColor("black",0),u.renderer.setRenderTarget(l),u.renderer.clear(),u.renderer.setRenderTarget(c),u.renderer.clear(),u.renderer.setRenderTarget(h),u.renderer.clear(),u.renderer.setRenderTarget(l),o.layers.set(sr.LAYERS.VOLUME_BFPLANE),u.renderer.render(u.scene,o),o.layers.set(sr.LAYERS.VOLUME),u.scene.overrideMaterial=e,u.renderer.render(u.scene,o),u.renderer.setRenderTarget(c),o.layers.set(sr.LAYERS.VOLUME),u.scene.overrideMaterial=t,u.renderer.render(u.scene,o),u.scene.overrideMaterial=null,o.layers.set(sr.LAYERS.DEFAULT),s.copy(d.matrixWorld).invert(),Jn.prototype.uberOptions.world2colorMatrix.multiplyMatrices(n,s),o.layers.set(sr.LAYERS.COLOR_FROM_POSITION),u.renderer.setRenderTarget(h),u.renderer.render(u.scene,o);const p=d.material;p.uniforms._BFRight.value=l.texture,p.uniforms._FFRight.value=c.texture,p.uniforms._WFFRight.value=h.texture,o.layers.set(sr.LAYERS.VOLUME),u.renderer.setRenderTarget(a),u.renderer.render(u.scene,o),o.layers.set(sr.LAYERS.DEFAULT)}}(),Jh.prototype._renderWithPrepassTransparency=function(e,t){const r=this._gfx;r.renderer.setRenderTarget(t),e.layers.set(sr.LAYERS.DEFAULT),r.renderer.render(r.scene,e),e.layers.set(sr.LAYERS.PREPASS_TRANSPARENT),r.renderer.getContext().colorMask(!1,!1,!1,!1),r.renderer.render(r.scene,e),r.renderer.getContext().colorMask(!0,!0,!0,!0),e.layers.set(sr.LAYERS.TRANSPARENT),r.renderer.render(r.scene,e),e.layers.set(sr.LAYERS.DEFAULT)},Jh.prototype._performFXAA=function(){const e=new Sh;return function(t,r){if(void 0===t||void 0===r)return;const n=this._gfx;n.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),n.renderer.setRenderTarget(r),n.renderer.clear(),e.uniforms.srcTex.value=t.texture,e.uniforms.srcTexelSize.value.set(1/t.width,1/t.height),e.uniforms.bgColor.value.set(z.now.bg.color),e.bgTransparent!==z.now.bg.transparent&&(e.setValues({bgTransparent:z.now.bg.transparent}),e.needsUpdate=!0),n.renderer.renderScreenQuad(e)}}(),Jh.prototype._performAO=function(){const e=new Ah,t=new Rh,n=new Nh,s=new r.Vector3;return function(i,o,a,l,c,h){if(!(i&&o&&a&&l&&c&&h))return;const u=this._gfx,d=Math.tan(.5*r.MathUtils.DEG2RAD*u.camera.fov);e.uniforms.diffuseTexture.value=i.texture,e.uniforms.depthTexture.value=a,e.uniforms.normalTexture.value=o.texture,e.uniforms.srcTexelSize.value.set(1/i.width,1/i.height),e.uniforms.camNearFar.value.set(u.camera.near,u.camera.far),e.uniforms.projMatrix.value=u.camera.projectionMatrix,e.uniforms.aspectRatio.value=u.camera.aspect,e.uniforms.tanHalfFOV.value=d,u.root.matrix.extractScale(s),e.uniforms.kernelRadius.value=z.now.debug.ssaoKernelRadius*s.x,e.uniforms.depthThreshold.value=2*this._getBSphereRadius(),e.uniforms.factor.value=z.now.debug.ssaoFactor,u.renderer.setRenderTarget(h),u.renderer.renderScreenQuad(e),t.uniforms.aoMap.value=h.texture,t.uniforms.srcTexelSize.value.set(1/h.width,1/h.height),t.uniforms.depthTexture.value=a,u.renderer.setRenderTarget(c),u.renderer.renderScreenQuad(t),n.uniforms.aoMap.value=c.texture,n.uniforms.diffuseTexture.value=i.texture,n.uniforms.srcTexelSize.value.set(1/c.width,1/c.height),n.uniforms.depthTexture.value=a,n.uniforms.projMatrix.value=u.camera.projectionMatrix,n.uniforms.aspectRatio.value=u.camera.aspect,n.uniforms.tanHalfFOV.value=d;const{fog:p}=u.scene;p&&(n.uniforms.fogNearFar.value.set(p.near,p.far),n.uniforms.fogColor.value.set(p.color.r,p.color.g,p.color.b,z.now.fogAlpha)),n.useFog===z.now.fog&&n.fogTransparent===z.now.bg.transparent||(n.setValues({useFog:z.now.fog,fogTransparent:z.now.bg.transparent}),n.needsUpdate=!0),u.renderer.setRenderTarget(l),u.renderer.renderScreenQuad(n)}}(),Jh.prototype.reset=function(){this._picker&&this._picker.reset(),this._lastPick=null,this._releaseAllVisuals(),this._setEditMode($h),this._resetObjects(),this._gfx&&(sr.clearTree(this._gfx.pivot),this._gfx.renderer2d.reset()),this.setNeedRender()},Jh.prototype._resetScene=function(){this._objectControls.reset(),this._objectControls.allowTranslation(!0),this._objectControls.allowAltObjFreeRotation(!0),this.resetReps(),this.resetPivot(),this.rebuildAll()},Jh.prototype.resetView=function(){this._picker&&this._picker.reset(),this._setEditMode($h),this._resetScene(),this._forEachComplexVisual((e=>{e.updateSelectionMask({}),e.rebuildSelectionGeometry()}))},Jh.prototype._export=function(e){const r=t().head(Wc.exporters.find({format:e}));if(!r)return this.logger.error("Could not find suitable exporter for this source"),Promise.reject(new Error("Could not find suitable exporter for this source"));if(this.dispatchEvent({type:"exporting"}),this._visuals[this._curVisualName]instanceof Qo){let e=null;r.SourceClass===Qo?e=this._visuals[this._curVisualName]:r.SourceClass===jt&&(e=this._visuals[this._curVisualName]._complex);return new r(e,{miewVersion:Jh.VERSION}).export().then((e=>e))}return this._visuals[this._curVisualName]instanceof pa?Promise.reject(new Error("Sorry, exporter for volume data not implemented yet")):Promise.reject(new Error("Unexpected format of data"))};const nu=/^(?:(pdb|cif|ccp4|dsn6):\s*)?(\d[a-z\d]{3})$/i,su=/^(?:pc|pubchem):\s*([a-z]+)$/i,iu=/^([a-z][a-z\d\-+.]*):/i;function ou(e,r,n){return new Promise((s=>{if(n.shouldCancel())throw new Error("Operation cancelled");n.notify({type:"fetching"}),e=function(e,r){if(!t().isString(e))return e;const n=nu.exec(e);if(n){let[,t="pdb",s]=n;switch(t=t.toLowerCase(),s=s.toUpperCase(),t){case"pdb":e=`https://files.rcsb.org/download/${s}.pdb`;break;case"cif":e=`https://files.rcsb.org/download/${s}.cif`;break;case"ccp4":e=`https://www.ebi.ac.uk/pdbe/coordinates/files/${s.toLowerCase()}.ccp4`;break;case"dsn6":e=`https://edmaps.rcsb.org/maps/${s.toLowerCase()}_2fofc.dsn6`;break;default:throw new Error("Unexpected data format shortcut")}return r.fileType=t,r.fileName=`${s}.${t}`,r.sourceType="url",e}const s=su.exec(e);if(s){const t=s[1].toLowerCase();return e=`https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${t}/JSON?record_type=3d`,r.fileType="pubchem",r.fileName=`${t}.json`,r.sourceType="url",e}return"url"!==r.sourceType&&void 0!==r.sourceType||(r.sourceType="url",iu.test(e)||(e=O.resolveURL(e))),e}(e,r);const i=t().head(Wc.loaders.find({type:r.sourceType,source:e}));if(!i)throw new Error(Xh);const o=r.fileName||i.extractName(e);if(o){const[e,n]=O.splitFileName(o);t().defaults(r,{name:e,fileExt:n,fileName:o})}!function(e){let{binary:r}=e;if(void 0!==e.fileType){const n=t().head(Wc.parsers.find({format:e.fileType}));if(!n)throw new Error("Could not find suitable parser for this format");r=n.binary||!1}if(void 0===r&&void 0!==e.fileExt){const n=t().head(Wc.parsers.find({ext:e.fileExt}));n&&(r=n.binary||!1)}void 0!==e.fileExt&&".man"===e.fileExt.toLowerCase()&&(e.binary=!0,e.animation=!0),void 0!==r&&void 0!==e.binary&&e.binary!==r&&e.context.logger.warn("Overriding incorrect binary mode"),e.binary=r||!1}(r);let a=t().get(r,"preset.expression");if(!t().isUndefined(a)&&(a=JSON.parse(a),a&&a.settings)){const e=["singleUnit"];for(let r=0,n=e.length;rl.abort())),l.addEventListener("progress",(e=>{e.lengthComputable&&e.total>0?Kh(l.logger,"Fetching",e.loaded/e.total):Kh(l.logger,"Fetching")}));s(l.load().then((e=>(r.context.logger.info("Fetching finished"),n.notify({type:"fetchingDone",data:e}),e))).catch((e=>{throw r.context.logger.debug(e.message),e.stack&&r.context.logger.debug(e.stack),r.context.logger.error("Fetching failed"),n.notify({type:"fetchingDone",error:e}),e})))}))}Jh.prototype.load=function(e,r){r=t().merge({},r,{context:this}),this.settings.now.use.multiFile||(this._loading.length&&(this._loading.forEach((e=>{e.cancel()})),this._loading.length=0),r.animation||this.reset(!0)),this._interpolator.reset(),this.dispatchEvent({type:"loading",options:r,source:e});const n=new V;this._loading.push(n),n.addEventListener("notification",(e=>{this.dispatchEvent(e.slaveEvent)})),this._spinner.spin(this._container);const s=e=>{const t=this._loading.indexOf(n);return-1!==t&&this._loading.splice(t,1),this._spinner.stop(),this._refreshTitle(),n.notify({type:"loadingDone",anything:e}),e};return ou(e,r,n).then((e=>function(e,r,n){if(n.shouldCancel())return Promise.reject(new Error("Operation cancelled"));n.notify({type:"parsing"});const s=t().head(Wc.parsers.find({format:r.fileType,ext:r.fileExt,data:e}));if(!s)return Promise.reject(new Error("Could not find suitable parser"));const i=new s(e,r);return i.context=r.context,n.addEventListener("cancel",(()=>i.abort())),i.parse().then((e=>(n.notify({type:"parsingDone",data:e}),e))).catch((e=>{throw r.error=e,r.context.logger.debug(e.message),e.stack&&r.context.logger.debug(e.stack),r.context.logger.error("Parsing failed"),n.notify({type:"parsingDone",error:e}),e}))}(e,r,n))).then((e=>{const t=this._onLoad(e,r);return s(t)})).catch((e=>{throw this.logger.error("Could not load data"),this.logger.debug(e),s(e)}))},Jh.prototype.unload=function(e){this._removeVisual(e||this.getCurrentVisual()),this.resetPivot(),z.now.shadow.on&&this._updateShadowCamera()},Jh.prototype._startAnimation=function(e){this._stopAnimation();const t=this,r=this._getComplexVisual();if(null!==r){try{this._frameInfo=new mh(r.getComplex(),e,{onLoadStatusChanged(){t.dispatchEvent({type:"mdPlayerStateChanged",state:{isPlaying:t._isAnimating,isLoading:!t._frameInfo||t._frameInfo.isLoading}})},onError(e){t._stopAnimation(),t.logger.error(e)}})}catch(e){return void this.logger.error("Animation file does not fit to current complex!")}this._continueAnimation()}else this.logger.error("Unable to start animation - no molecule is loaded.")},Jh.prototype._pauseAnimation=function(){null!==this._animInterval&&(this._isAnimating=!1,clearInterval(this._animInterval),this._animInterval=null,this._frameInfo&&this.dispatchEvent({type:"mdPlayerStateChanged",state:{isPlaying:this._isAnimating,isLoading:this._frameInfo.isLoading}}))},Jh.prototype._continueAnimation=function(){this._isAnimating=!0;let e=1e3/z.now.maxfps;e=Number.isNaN(e)?0:e;const t=this,{pivot:r}=t._gfx,n=this._getComplexVisual();n&&(n.resetSelectionMask(),n.rebuildSelectionGeometry(),this._msgAtomInfo.style.opacity=0),this._animInterval=setInterval((()=>{if(t.dispatchEvent({type:"mdPlayerStateChanged",state:{isPlaying:t._isAnimating,isLoading:t._frameInfo.isLoading}}),t._frameInfo.frameIsReady){r.updateToFrame(t._frameInfo),t._updateObjsToFrame(t._frameInfo),t._refreshTitle(` Frame ${t._frameInfo._currFrame} of ${t._frameInfo._framesCount} time interval - ${t._frameInfo._timeStep}`);try{t._frameInfo.nextFrame()}catch(e){return t.logger.error("Error during animation"),void t._stopAnimation()}t._needRender=!0}}),e)},Jh.prototype._stopAnimation=function(){null!==this._animInterval&&(clearInterval(this._animInterval),this._frameInfo.disableEvents(),this._frameInfo=null,this._animInterval=null,this.dispatchEvent({type:"mdPlayerStateChanged",state:null}))},Jh.prototype._onLoad=function(e,r){const n=this._gfx;let s=null;if(r.animation)return this._refreshTitle(),this._startAnimation(e),null;if(this._stopAnimation(),r&&r.keepRepsInfo||(this._opts.reps=null,this._opts._objects=null),"Complex"===e.id){const n=e;r.fileName?n.name=n.name||Zh(r.fileName).toUpperCase():r.amberFileName?n.name=n.name||Zh(r.amberFileName).toUpperCase():n.name=`Dynamic ${r.fileType} molecule`,s=this._addVisual(new Qo(n.name,n)),this._curVisualName=s;const i=this.info();if(this.logger.info(`Parsed ${r.fileName} (${i.atoms} atoms, ${i.bonds} bonds, ${i.residues} residues, ${i.chains} chains).`),t().isNumber(this._opts.unit)&&n.setCurrentUnit(this._opts.unit),r.preset);else if(z.now.autoPreset)switch(r.fileType){case"cml":this.resetReps("small");break;case"pdb":case"mmtf":case"cif":!function(e){let t=!1;return e.forEachComponent((e=>{e.forEachResidue((e=>{e._isValid&&(t=!0)}))})),t}(n)?this.resetReps("small"):this.resetReps("macro");break;default:this.resetReps("default")}else this.resetReps("default")}else"Volume"===e.id&&(this.resetEd(),s=this._onLoadEd(e));return n.camera.updateProjectionMatrix(),this._updateFog(),n.root.resetTransform(),this.resetPivot(),this._objectControls.setScale(z.now.radiusToFit/this._getBSphereRadius()),this._resetObjects(),z.now.autoResolution&&this._tweakResolution(),z.now.shadow.on&&this._updateShadowCamera(),this._opts.view&&(this.view(this._opts.view),delete this._opts.view),this._refreshTitle(),s},Jh.prototype.resetEd=function(){this._edLoader&&(this._edLoader.abort(),this._edLoader=null),this._removeVisual(this._getVolumeVisual()),this._needRender=!0},Jh.prototype.loadEd=function(e){this.resetEd();const r=t().head(Wc.loaders.find({source:e}));if(!r)return this.logger.error(Xh),Promise.reject(new Error(Xh));const n=this._edLoader=new r(e,{binary:!0});return n.context=this,n.load().then((e=>{const r=t().head(Wc.parsers.find({format:"ccp4"}));if(!r)throw new Error("Could not find suitable parser for this source");const n=new r(e);return n.context=this,n.parse().then((e=>{this._onLoadEd(e)}))})).catch((e=>{this.logger.error("Could not load ED data"),this.logger.debug(e)}))},Jh.prototype._onLoadEd=function(e){e.normalize();const t=new pa("volume",e);t.getMesh().layers.set(sr.LAYERS.VOLUME);const r=this._addVisual(t);return this._needRender=!0,r},Jh.prototype._needRebuild=function(){let e=!1;return this._forEachComplexVisual((t=>{e=e||t.needsRebuild()})),e},Jh.prototype._rebuildObjects=function(){const e=this,t=this._gfx;let r,n;const s=[];for(r=0;r{const s=e._objects;for(r=0,n=s.length;r0?`Bio molecule ${e}`:"Asymmetric unit"})`}return void 0===e||(t().isString(e)&&(e=Math.max(parseInt(e,10),0)),n.getComplex().setCurrentUnit(e)&&(this._resetScene(),this._updateInfoPanel())),s()},Jh.prototype.rebuild=function(){if(this._building)return void this.logger.warn("Miew.rebuild(): already building!");this._building=!0,this.dispatchEvent({type:"rebuilding"}),this._rebuildObjects(),this._gfx.renderer2d.reset();const e=[];this._forEachComplexVisual((t=>{t.needsRebuild()&&e.push(t.rebuild().then((()=>new Promise((e=>{t.rebuildSelectionGeometry(),e()})))))}));const t=this;this._spinner.spin(this._container),Promise.all(e).then((()=>{t._spinner.stop(),t._needRender=!0,t._refreshTitle(),this.dispatchEvent({type:"buildingDone"}),t._building=!1}))},Jh.prototype.rebuildAll=function(){this._forEachComplexVisual((e=>{e.setNeedsRebuild()}))},Jh.prototype._refreshTitle=function(e){let t;e=void 0===e?"":e;const r=this._getComplexVisual();if(r){t=r.getComplex().name;const e=r.repGet(r.repCurrent());t+=e?` – ${e.mode.name} Mode`:""}else t=Object.keys(this._visuals).length>0?"Unknown":"No Data";t+=e,this.dispatchEvent({type:"titleChanged",data:t})},Jh.prototype.setNeedRender=function(){this._needRender=!0},Jh.prototype._extractRepresentation=function(){const e=[];this._forEachComplexVisual((t=>{if(0===t.getSelectionCount())return;const r=t.buildSelectorFromMask(1<0&&this.logger.report(`New representation from selection for complexes: ${e.join(", ")}`)},Jh.prototype._setReps=function(e){e=e||this._opts&&this._opts.reps||[],this._forEachComplexVisual((t=>t.resetReps(e)))},Jh.prototype.applyPreset=function(e){const{presets:t}=z.now,r=[e||z.defaults.preset,z.defaults.preset,Object.keys(t)[0]];let n=null;for(let e=0;!n&&e{const r=t.beginComponentEdit();r&&e.push(r)})),e!==[]&&(this._editors=e,this.logger.info("COMPONENT EDIT MODE -- ON"),this._setEditMode(Wh),this._objectControls.keysTranslateObj(!0))},Jh.prototype._applyComponentEdit=function(){if(this._editMode===Wh){this._objectControls.stop(),this._objectControls.keysTranslateObj(!1);for(let e=0;e{t instanceof Qo&&t.getSelectionCount()>0&&e.push(t)})),1!==e.length)return;const t=e[0].beginFragmentEdit();t&&(this._editors=[t],this.logger.info("FRAGMENT EDIT MODE -- ON (single bond)"),this._setEditMode(Yh),this._objectControls.allowTranslation(!1),this._objectControls.allowAltObjFreeRotation(t.isFreeRotationAllowed()),this._needRender=!0)},Jh.prototype._applyFragmentEdit=function(){if(this._editMode===Yh){this._objectControls.stop();for(let e=0;e{e.expandSelection(),e.rebuildSelectionGeometry()})),this._updateInfoPanel(),this._needRender=!0);break;case"NumpadSubtract":e.altKey&&(e.preventDefault(),e.stopPropagation(),this._forEachComplexVisual((e=>{e.shrinkSelection(),e.rebuildSelectionGeometry()})),this._updateInfoPanel(),this._needRender=!0)}}},Jh.prototype._onKeyUp=function(e){this._running&&this._hotKeysEnabled&&"KeyX"===e.code&&this._extractRepresentation()},Jh.prototype._updateInfoPanel=function(){const e=this._msgAtomInfo.getElementsByTagName("p")[0];let t,r,n=0;for(this._forEachComplexVisual((e=>{n+=e.getSelectionCount()}));e.firstChild;)e.removeChild(e.firstChild);if(0===n)return void(this._msgAtomInfo.style.opacity=0);let s=`${String(n)} atom${1!==n?"s":""} selected`;null!==this._lastPick&&(s+=", the last pick:");let i="",o="",a="";if(this._lastPick instanceof Uh){t=this._lastPick,r=t.residue,o=t.name;const e=32!==t.location?String.fromCharCode(t.location):"";i=`${t.element.fullName} #${t.serial}${e}: ${r._chain._name}.${r._type._name}${r._sequence}${r._icode.trim()}.`,i+=o,a=`Coord: (${t.position.x.toFixed(2).toString()}, ${t.position.y.toFixed(2).toString()}, ${t.position.z.toFixed(2).toString()})`}else this._lastPick instanceof Gh?(r=this._lastPick,i=`${r._type._fullName}: ${r._chain._name}.${r._type._name}${r._sequence}${r._icode.trim()}`):this._lastPick instanceof jh?i=`chain ${this._lastPick._name}`:this._lastPick instanceof Hh&&(i=`molecule ${this._lastPick._name}`);e.appendChild(document.createTextNode(s)),""!==i&&(e.appendChild(document.createElement("br")),e.appendChild(document.createTextNode(i))),""!==a&&(e.appendChild(document.createElement("br")),e.appendChild(document.createTextNode(a))),this._msgAtomInfo.style.opacity=1},Jh.prototype._getAltObj=function(){if(this._editors){let e=null;for(let t=0;t0){if(e){e=null;break}e=r}}if(e)return e}return{objects:[],pivot:new r.Vector3(0,0,0)}},Jh.prototype.resetPivot=function(){const e=new r.Box3,t=new r.Vector3;return function(){e.makeEmpty(),this._forEachVisual((t=>{e.union(t.getBoundaries().boundingBox)})),e.getCenter(t),this._objectControls.setPivot(t.negate()),this.dispatchEvent({type:"transform"})}}(),Jh.prototype.setPivotResidue=function(){const e=new r.Vector3;return function(t){const r=this._getVisualForComplex(t.getChain().getComplex());if(r){if(t._controlPoint)e.copy(t._controlPoint);else{let r=0,n=0,s=0;const i=t._atoms.length;for(let e=0;e{i.getSelectionCenter(e,r,n||i.getSelectionBit())&&(t.add(e),s++)})),0!==s&&(t.divideScalar(s),t.negate(),!0)}}(),Jh.prototype.setPivotSubset=function(){const e=new r.Vector3(0,0,0);function t(e,t){return e.mask&1<{const r=this._visuals[this._curVisualName]._complex.name;O.download(t,r,e.fileType),this._refreshTitle(),this.dispatchEvent({type:"exportingDone"})})).catch((e=>{this.logger.error("Could not export data"),this.logger.debug(e),this._refreshTitle(),this.dispatchEvent({type:"exportingDone",error:e})}))},Jh.prototype._tweakResolution=function(){const e=[["poor",100],["low",500],["medium",1e3],["high",5e3],["ultra",Number.MAX_VALUE]];let t=0;if(this._forEachComplexVisual((e=>{t+=e.getComplex().getAtomCount()})),t>0){const r=1e6*this._gfxScore/t;for(let t=0;ts?(o=!1,n.preset="empty"):z.now.preset!==z.defaults.preset&&(n.preset=z.now.preset);const a=[];let l=!0;for(let r=0,n=s;r0&&(r._objects=o),e.view&&(r.view=this.view()),e.settings){const e=this.settings.getDiffs(!1);t().isEmpty(e)||(r.settings=e)}return r},Jh.prototype.get=function(e,t){return z.get(e,t)},Jh.prototype._clipPlaneUpdateValue=function(e){const t=Math.max(this._gfx.camera.position.z-e*z.now.draft.clipPlaneFactor,z.now.camNear),r={clipPlaneValue:t};this._forEachComplexVisual((e=>{e.setUberOptions(r)}));for(let e=0,t=this._objects.length;e{const r=t._reprList;for(let t=0,n=r.length;t1&&void 0!==arguments[1]&&arguments[1],r=arguments.length>2&&void 0!==arguments[2]?arguments[2]:void 0;this._forEachComplexVisual((n=>n.setMaterialValues(e,t,r)));for(let t=0,r=this._objects.length;t{e.setUberOptions({fogAlpha:z.now.fogAlpha})}))},Jh.prototype._embedWebXR=function(){if("WEBVR"!==z.now.stereo)return this.webVR&&this.webVR.disable(),void(this.webVR=null);this.webVR||(this.webVR=new Fh((()=>{this._requestAnimationFrame((()=>this._onTick())),this._needRender=!0,this._onResize()}))),this.webVR.enable(this._gfx)},Jh.prototype._initOnSettingsChanged=function(){const e=(e,r)=>{(e=t().isArray(e)?e:[e]).forEach((e=>{this.settings.addEventListener(`change:${e}`,r)}))};e("modes.VD.frame",(()=>{const e=this._getVolumeVisual();null!==e&&(e.showFrame(z.now.modes.VD.frame),this._needRender=!0)})),e("modes.VD.isoMode",(()=>{const e=this._getVolumeVisual();null!==e&&(e.getMesh().material.updateDefines(),this._needRender=!0)})),e("bg.color",(()=>{this._onBgColorChanged()})),e("ao",(()=>{if(z.now.ao&&!ru(this._gfx.renderer.getContext()))this.logger.warn("Your device or browser does not support ao"),z.set("ao",!1);else{const e={normalsToGBuffer:z.now.ao};this._setUberMaterialValues(e)}})),e("zSprites",(()=>{z.now.zSprites&&!tu(this._gfx.renderer.getContext())&&(this.logger.warn("Your device or browser does not support zSprites"),z.set("zSprites",!1)),this.rebuildAll()})),e("fogColor",(()=>{this._onFogColorChanged()})),e("fogColorEnable",(()=>{this._onFogColorChanged()})),e("bg.transparent",(e=>{const t=this._gfx;t&&t.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),this._updateMaterials({fogTransparent:e.value}),this.rebuildAll()})),e("draft.clipPlane",(e=>{this._updateMaterials({clipPlane:e.value}),this.rebuildAll()})),e("shadow.on",(e=>{const t={shadowmap:e.value,shadowmapType:z.now.shadow.type},r=this._gfx;r&&(r.renderer.shadowMap.enabled=Boolean(t.shadowmap)),this._updateMaterials(t,!0),t.shadowmap?(this._updateShadowCamera(),this._updateShadowmapMeshes(jo.createShadowmapMaterial)):this._updateShadowmapMeshes(jo.removeShadowmapMaterial),this._needRender=!0})),e("shadow.type",(e=>{z.now.shadow.on&&(this._updateMaterials({shadowmapType:e.value},!0),this._needRender=!0)})),e("shadow.radius",(e=>{for(let t=0;t{this._fps.show(z.now.fps)})),e(["fog","fogNearFactor","fogFarFactor"],(()=>{this._updateFog(),this._needRender=!0})),e("fogAlpha",(()=>{const{fogAlpha:e}=z.now;(e<0||e>1)&&this.logger.warn("fogAlpha must belong range [0,1]"),this._fogAlphaChanged(),this._needRender=!0})),e("autoResolution",(e=>{e.value&&!this._gfxScore&&this.logger.warn("Benchmarks are missed, autoresolution will not work! Autoresolution should be set during miew startup.")})),e("stereo",(()=>{this._embedWebXR("WEBVR"===z.now.stereo),this._needRender=!0})),e(["transparency","palette"],(()=>{this.rebuildAll()})),e("resolution",(()=>{this.rebuildAll();const e=this._getVolumeVisual();e&&(e.getMesh().material.updateDefines(),this._needRender=!0)})),e(["axes","fxaa","ao","outline.on","outline.color","outline.threshold","outline.thickness"],(()=>{this._needRender=!0}))},Jh.prototype.set=function(e,t){z.set(e,t)},Jh.prototype.select=function(e,r){const n=this._getComplexVisual();if(!n)return;let s=e;t().isString(e)&&(s=Bh.parse(e).selector),n.select(s,r),this._lastPick=null,this._updateInfoPanel(),this._needRender=!0};Jh.prototype.view=function(e){const t=this,{pivot:n}=this._gfx;let s=[];return void 0===e?function(){const e=n.position,i=t._objectControls.getScale()/z.now.radiusToFit,o=new r.Euler;return o.setFromQuaternion(t._objectControls.getOrientation(),"ZXY"),s=[e.x,e.y,e.z,i,o.x,o.y,o.z],"1"+O.arrayToBase64(s,Float32Array)}():(function(){40===e.length&&(e=`0${e}`);const i=e[0];if(s=O.arrayFromBase64(e.substr(1),Float32Array),"1"!==i){if("0"!==i)return void t.logger.warn(`Encoded view version mismatch, stored as ${i} vs 1 expected`);s[3]/=8}const o=t._interpolator,a=o.createView();a.position.copy(n.position),a.scale=t._objectControls.getScale(),a.orientation.copy(t._objectControls.getOrientation());const l=o.createView();l.position.set(s[0],s[1],s[2]),t._getComplexVisual()&&l.position.sub(t._getComplexVisual().position),l.scale=s[3],l.orientation.setFromEuler(new r.Euler(s[4],s[5],s[6],"ZXY")),o.setup(a,l)}(),e)},Jh.prototype._updateView=function(){const e=this,{pivot:t}=this._gfx,r=this._interpolator;if(r.wasStarted()||r.start(),!r.isMoving())return;const n=r.getCurrentView();if(n.success){const r=n.view;t.position.copy(r.position),e._objectControls.setScale(r.scale*z.now.radiusToFit),e._objectControls.setOrientation(r.orientation),this.dispatchEvent({type:"transform"}),e._needRender=!0}},Jh.prototype.translate=function(e,t,r){this._objectControls.translatePivot(e,t,r),this.dispatchEvent({type:"transform"}),this._needRender=!0},Jh.prototype.rotate=function(e,t,n){this._objectControls.rotate((new r.Quaternion).setFromEuler(new r.Euler(e,t,n,"XYZ"))),this.dispatchEvent({type:"transform"}),this._needRender=!0},Jh.prototype.scale=function(e){if(e<=0)throw new RangeError("Scale should be greater than zero");this._objectControls.scale(e),this.dispatchEvent({type:"transform"}),this._needRender=!0},Jh.prototype.center=function(e){if(void 0===e)return this.setPivotSubset(),void(this._needRender=!0);if(void 0!==e.obj&&("atom"in e.obj||"residue"in e.obj))return"atom"in e.obj?this.setPivotAtom(e.obj.atom):this.setPivotResidue(e.obj.residue),void(this._needRender=!0);if(void 0===e.obj&&""!==e){const t=Bh.parse(e);if(void 0===t.error)return this.setPivotSubset(t),void(this._needRender=!0)}this.resetPivot(),this._needRender=!0},Jh.prototype.within=function(e,t){const r=this._getComplexVisual();if(!r)return Bh.None();e instanceof String&&(e=Bh.parse(e));const n=r.within(e,t);return n&&(r.rebuildSelectionGeometry(),this._needRender=!0),n},Jh.prototype.projected=function(e,t){const r=this._getComplexVisual(t);if(!r)return!1;const n=r.getComplex().getAtomByFullname(e);if(null===n)return!1;const s=n.position.clone();return this._gfx.pivot.updateMatrixWorldRecursive(),this._gfx.camera.updateMatrixWorldRecursive(),this._gfx.pivot.localToWorld(s),s.project(this._gfx.camera),{x:.5*(s.x+1)*this._gfx.width,y:.5*(1-s.y)*this._gfx.height}},Jh.prototype.dssp=function(e){const t=this._getComplexVisual(e);t&&(t.getComplex().dssp(),t._reprList.forEach((e=>{"CA"!==e.mode.id&&"SS"!==e.colorer.id||(e.needsRebuild=!0)})))},Jh.prototype.exportCML=function(){const e=this;const t=e._getComplexVisual(),n=t?t.getComplex():null;if(n&&n.originalCML){!function(t){const{root:n}=e._gfx,s=function(e){const t=new r.Vector3,n=new r.Vector3,s=new r.Vector3;e.extractBasis(t,n,s),t.normalize(),n.normalize(),s.normalize();const i=new r.Matrix4;return i.identity(),i.makeBasis(t,n,s),i}(n.matrixWorld),i=new r.Vector4(0,0,0,0),o=new r.Vector4(0,0,0,0);let a=null,l=null;t.forEachAtom((e=>{e.xmlNodeRef&&e.xmlNodeRef.xmlNode&&(a=e.xmlNodeRef.xmlNode,l=e.position,i.set(l.x,l.y,l.z,1),i.applyMatrix4(s),a.setAttribute("x3",i.x.toString()),a.setAttribute("y3",i.y.toString()),a.setAttribute("z3",i.z.toString()),a.removeAttribute("x2"),a.removeAttribute("y2"))})),t.forEachSGroup((e=>{if(e.xmlNodeRef&&e.xmlNodeRef.xmlNode){a=e.xmlNodeRef.xmlNode,l=e.getPosition(),i.set(l.x,l.y,l.z,1);const t=e.getCentralPoint();null===t?i.applyMatrix4(s):(o.set(t.x,t.y,t.z,0),i.add(o),i.applyMatrix4(s),o.set(t.x,t.y,t.z,1),o.applyMatrix4(s),i.sub(o)),a.setAttribute("x",i.x.toString()),a.setAttribute("y",i.y.toString()),a.setAttribute("z",i.z.toString())}}))}(n);return(new XMLSerializer).serializeToString(n.originalCML)}return null},Jh.prototype.motm=function(){z.set({fogColorEnable:!0,fogColor:0,outline:{on:!0,threshold:.01},bg:{color:16777215}}),this._forEachComplexVisual((e=>{const t=[],r=e.getComplex(),n=ao.get(z.now.palette);for(let e=0;e #aromatic radius"," atom = #atom radius"," bond = #bond radius"," multibond = #use multibond"," showarom = #show aromatic"," space = #space value\n"]},CA:{$help:[" Cartoon"," arrow = #arrow size"," depth = #depth of surface"," heightSegmentsRatio = "," radius = #tube radius"," tension = #"," width = #secondary width\n"]},LN:{$help:[" Lines"," atom = #atom radius"," chunkarom = "," multibond = #use multibond"," showarom = #show aromatic"," offsarom = \n"]},LC:{$help:[" Licorice"," aromrad = #aromatic radius"," bond = #bond radius"," multibond = #use multibond"," showarom = #show aromatic"," space = #space value\n"]},VW:{$help:[" Van der Waals"," nothing\n"]},TR:{$help:[" Trace"," radius = #tube radius\n"]},TU:{$help:[" Tube"," heightSegmentsRatio = "," radius = #tube radius"," tension = \n"]},SA:{$help:[" Surface"," zClip = #clip z plane\n"]},QS:{$help:[" Quick surface"," isoValue = "," scale = "," wireframe = "," zClip = #clip z plane\n"]},SE:{$help:[" Solvent excluded surface"," zClip = #clip z plane\n"]},TX:{$help:[" Text mode",' template = string that can include "{{ id }}"'," it will be replaced by value, id can be one of next:"," serial, name, type, sequence, residue, chain, hetatm, water\n",' horizontalAlign = {"left", "right", "center"}',' verticalAlign = {"top", "bottom", "middle"}'," dx = #offset along x"," dy = #offset along y"," dz = #offset along z"," fg = #text color modificator"," could be keyword, named color or hex"," fg = #back color modificator"," could be keyword, named color or hex"," showBg = #if set show background"," plate under text"]}},hu={$help:["Coloring mode shortcut"," EL - color by element"," CH - color by chain"," SQ - color by sequence"," RT - color by residue type"," SS - color by secondary structure"," UN - uniform"],UN:{$help:["Parameters of coloring modes customization"," Uniform"," color = #RGB->HEX->dec\n"],color:{$help:Object.keys(ao.get(z.now.palette).namedColors).sort().join("\n")}}},uu={$help:["Material shortcut"," DF - diffuse"," TR - transparent"," SF - soft plastic"," PL - glossy plastic"," ME - metal"," GL - glass"]},du={$help:["Short (packed) representation description as a set of variables"," s="," selector property"," m=[!:[,...]]"," render mode property"," c=[!:[,...]]"," color mode property"," mt="," material property"],s:{$help:"Selection expression string as it is in menu->representations->selection"},m:cu,c:hu,mt:uu},pu={$help:["Parameters of rendering modes customization: modes","Parameters of colorer customization: colorers","Autobuild: autobuild = (|)"],modes:cu,colorers:hu},mu={$help:["help (| )","You can get detailed information about command options",' using "help cmd.opt.opt.[...]"\n'," you can use one line comments"," everything started from (#|//) will be skipped"," Example: >build //some comment\n","List of available commands:"],reset:{$help:["Reload current object, delete all representations"," Nothing will work until load new object"]},load:{$help:["load (||-f [<*.NC FILE URL STRING>])"," Load new pdb object from selected source"],PDBID:{$help:"pdb id in remote molecule database"},URL:{$help:"url to source file"},f:{$help:["open file system dialog to fetch local file","optionally you can determine trajectory file","via URL for *.top model"]}},clear:{$help:"No args. Clear terminal"},add:{$help:["add [] []"," Add new item to representation set with"," default or params"],REP_NAME:{$help:"Identifier string [_,a-z,A-Z,0-9] can not start from digit"},DESCRIPTION:du},rep:{$help:["rep [|] []"," set current representation by name or index"," edit current representation by "],REP_NAME:{$help:["Identifier string [_,a-z,A-Z,0-9] can not start from digit","Must be declared before"]},REP_INDEX:{$help:"Index of available representation"},DESCRIPTION:du},remove:{$help:["remove (|)","Remove representation by name or index"],REP_NAME:{$help:["Identifier string [_,a-z,A-Z,0-9] can not start from digit","Must be declared before"]},REP_INDEX:{$help:"Index of available representation"}},selector:{$help:["selector "," set selector from EXPRESSION to current representation"],EXPRESSION:{$help:"Selection expression string as it is in menu->representations->selection"}},mode:{$help:["mode [=...]"," set rendering mode and apply parameters to current representation"],MODE_ID:cu},color:{$help:["color [=...]"," set colorer and apply parameters to current representation"],COLORER_ID:hu},material:{$help:["material "," set material to current representation"],MATERIAL_ID:uu},build:{$help:"build help str",add:{$help:"build.add",new:{$help:["add.new","add.new new line 1","add.new new line 2","add.new new line 3"]}},del:{$help:"build.del"}},list:{$help:["list [-e|-s||]","Print representations if no args print list of representations"," -e expand list and show all representations"," -s show all user-registered selectors"," | show only current representation"]},hide:{$help:["hide (|)","Hide representation referenced in args"]},show:{$help:["show (|)","Show representation referenced in args"]},get:{$help:["get ","Print value"," - path to option use get.PARAMETER to get more info"],PARAMETER:pu},set:{$help:["set ","Set with "," - path to option use set.PARAMETER to get more info"],PARAMETER:pu},set_save:{$help:["set_save","Save current settings to cookie"]},set_restore:{$help:["set_restore","Load and apply settings from cookie"]},set_reset:{$help:["set_reset","Reset current settings to the defaults"]},preset:{$help:["preset []","Reset current representation or set preset to "],PRESET:{$help:["default","wire","small","macro"]}},unit:{$help:["unit []","Change current biological structure view. Zero value means asymmetric unit,","positive values set an assembly with corresponding number.","Being called with no parameters command prints current unit information."]},view:{$help:["view []","Get current encoded view or set if ENCODED_VIEW placed as argument"],ENCODED_VIEW:{$help:["encoded view matrix string (binary code)"]}},rotate:{$help:["rotate (x|y|z) [] [(x|y|z) []]...","Rotate scene"]},scale:{$help:["scale ","Scale scene"]},select:{$help:["select [as ]","Select atoms using selector defined in SELECTOR_STRING"," and if SELECTOR_NAME is defined register it in viewer"," you can use it later as a complex selector"]},within:{$help:["within of as ","Build within named selector"," DISTANCE "," SELECTOR_STRING "," SELECTOR_NAME "]},url:{$help:["url [-s] [-v]","Report URL encoded scene"," if -s set that include settings in the URL"," if -v set that include view in the URL"]},screenshot:{$help:["screenshot [ []]","Make a screenshot of the scene"," WIDTH in pixels"," HEIGHT in pixels, equal to WIDTH by default"]},line:{$help:["line [=]","Draw dashed line between two specified atoms"]},removeobj:{$help:["removeobj ","Remove scene object by its index. Indices could be obtained by command"]},listobj:{$help:["listobj","Display the list of all existing scene objects"]}},{chem:{selectors:fu},modes:_u,colorers:gu,materials:yu,palettes:xu,options:bu,settings:wu}=au;function Su(){}const vu=function(){const e=new Su;return function(){return e}}();const Cu=new class{constructor(){this.representationMap={},this.representationID={}}get(e){return this.representationMap[e]||this.representationID[e]||""}add(e,t){if(-1===e)return"Can not create representation: there is no data";if(void 0!==t){if(this.representationMap.hasOwnProperty(e))return"This name has already existed, registered without name";this.representationMap[e.toString()]=t,this.representationID[t]=e.toString()}return`Representation ${e} successfully added`}remove(e){e&&this.representationID.hasOwnProperty(e)&&(delete this.representationMap[this.representationID[e]],delete this.representationID[e]);const t=Object.keys(this.representationID).sort();for(const r in t)if(t.hasOwnProperty(r)){const n=t[r];n>e&&(this.representationID[n-1]=this.representationID[n],this.representationMap[this.representationID[n]]-=1,delete this.representationID[n])}}clear(){this.representationMap={},this.representationID={}}};function Au(e){const t={s:"selector",m:"mode",c:"colorer",mt:"material",mode:"modes",color:"colorers",colorer:"colorers",select:"selector",material:"materials",selector:"selector"}[e];return void 0===t?e:t}const Eu=new class{list(e,t,r){let n="";if(e&&void 0!==t&&(void 0===r||"-e"===r)){const s=e.repCount();for(let i=0;i"===a?"":`, ${a}`}\n`,void 0!==n&&(s+=` selection : "${h}"\n`,s+=` mode : (${l.id}), ${l.name}\n`,s+=` colorer : (${c.id}), ${c.name}\n`,s+=` material : (${u.id}), ${u.name}\n`),s}listSelector(e,t){let r="";for(const e in t)t.hasOwnProperty(e)&&(r+=`${e} : "${t[e]}"\n`);return r}listObjs(e){const t=e._objects;if(!t||!Array.isArray(t)||0===t.length)return"There are no objects on the scene";const r=[];for(let e=0,n=t.length;ee.finishAwaitingCMDInProcess();e.load(t).then(r,r)}checkArg(e,t,r){if(void 0!==e&&void 0!==t){if("selector"===Au(e)){const e=fu.parse(t);if(void 0!==e.error){throw{message:e.error}}return void 0!==r&&r?e.selector:t}const n={colorers:gu,modes:_u,materials:yu};let s,i=e;for(;i!==s;)s=i,i=Au(s);if(void 0===n[i].get(t)){throw{message:`${t} is not existed in ${i}`}}return t}return vu}propagateProp(e,r){if(void 0!==e){let n={};const s=bu.adapters[typeof t().get(wu.defaults,e)];if(void 0===s){throw{message:`${e} is not existed`}}if((e.endsWith(".color")||e.endsWith(".baseColor")||e.endsWith(".EL.carbon"))&&"number"!=typeof r&&(r=xu.get(wu.now.palette).getNamedColor(r)),e.endsWith(".fg")||e.endsWith(".bg"))if("number"!=typeof r){const e=xu.get(wu.now.palette).getNamedColor(r,!0);void 0!==e&&(r=`0x${e.toString(16)}`)}else r=`0x${r.toString(16)}`;if(e.endsWith(".template")&&(r=r.replace(/\\n/g,"\n")),void 0!==r&&s(r)!==r&&s(r)!==r>0)throw n={message:`${e} must be a "${typeof t().get(wu.defaults,e)}"`},n}return r}unquoteString(e){return O.unquoteString(e)}};function Tu(e){if(e instanceof this.constructor)return e;this._values=e instanceof Array?e.slice(0):e?[e]:[]}Tu.prototype.append=function(e){const t=this._values;return t[t.length]=e,this},Tu.prototype.remove=function(e){const t=this._values,r=t.indexOf(e);return r>=0&&t.splice(r,1),this},Tu.prototype.toJSO=function(e,r,n){const s={},i=this._values;for(let o=0,a=i.length;o0},au.prototype.callNextCmd=function(){if(this.isScriptingCommandAvailable()){const e=this.cmdQueue.shift(),t={success:!1};try{lu.parser.parse(e),t.success=!0}catch(e){t.error=e.message,lu.parser.yy.error(t.error),this.finishAwaitingCMDInProcess()}return t}return""},lu.parser.yy=Ru,lu.parser.yy.parseError=lu.parser.parseError;const Mu=au})(),i=i.default})())); +(function(){var e,r,n,s,i,o,a,l,c,h,u,d,p,m,f,_,g,y,x,b,w,S,v,C,A,E,T=Object.prototype.hasOwnProperty,R=function(e,t){for(var r in t)T.call(t,r)&&(e[r]=t[r]);function n(){this.constructor=e}return n.prototype=t.prototype,e.prototype=new n,e.__super__=t.prototype,e};for(_ in d={method:(n={METHOD_NEAREST:"nearest",METHOD_LINEAR:"linear",METHOD_CUBIC:"cubic",METHOD_LANCZOS:"lanczos",METHOD_SINC:"sinc",CLIP_CLAMP:"clamp",CLIP_ZERO:"zero",CLIP_PERIODIC:"periodic",CLIP_MIRROR:"mirror",CUBIC_TENSION_DEFAULT:0,CUBIC_TENSION_CATMULL_ROM:0}).METHOD_CUBIC,cubicTension:n.CUBIC_TENSION_DEFAULT,clip:n.CLIP_CLAMP,scaleTo:0,sincFilterSize:2,sincWindow:void 0},c=function(e,t){return Math.max(0,Math.min(e,t-1))},u=function(e,t){return(e%=t)<0&&(e+=t),e},h=function(e,t){var r;return(e=u(e,r=2*(t-1)))>t-1&&(e=r-e),e},e=function(){function e(e,t){if(this.array=e.slice(0),this.length=this.array.length,!(this.clipHelper={clamp:this.clipHelperClamp,zero:this.clipHelperZero,periodic:this.clipHelperPeriodic,mirror:this.clipHelperMirror}[t.clip]))throw"Invalid clip: "+t.clip}return e.prototype.getClippedInput=function(e){return 0<=e&&e=i;s<=i?r++:r--)n+=this.kernel(e-r)*this.getClippedInput(r);return n},t}(e),p=function(e,t){var r,n,s,i;for(i=[],n=0,s=e.length;no;0<=o?c++:c--)r.push(new u(p(e,c),t));return r}(),function(e){var t,r,n,s;for(s=[],r=0,n=f.length;rn;n++){var i=r.charCodeAt(n);if(128>i)e.setUint8(t++,i>>>0&127);else if(2048>i)e.setUint8(t++,i>>>6&31|192),e.setUint8(t++,i>>>0&63|128);else if(65536>i)e.setUint8(t++,i>>>12&15|224),e.setUint8(t++,i>>>6&63|128),e.setUint8(t++,i>>>0&63|128);else{if(!(1114112>i))throw new Error("bad codepoint "+i);e.setUint8(t++,i>>>18&7|240),e.setUint8(t++,i>>>12&63|128),e.setUint8(t++,i>>>6&63|128),e.setUint8(t++,i>>>0&63|128)}}}function r(e){for(var t=0,r=0,n=e.length;n>r;r++){var s=e.charCodeAt(r);if(128>s)t+=1;else if(2048>s)t+=2;else if(65536>s)t+=3;else{if(!(1114112>s))throw new Error("bad codepoint "+s);t+=4}}return t}function n(e,s,i){var o=typeof e;if("string"===o){if(32>(a=r(e)))return s.setUint8(i,160|a),t(s,i+1,e),1+a;if(256>a)return 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r=0;r1e-4){i.length()>1e-4&&Math.abs(n.angleTo(i))>Math.PI/2&&i.negate()}return i}_innerFinalize(e,t,n,s,i,o){const a=null===t,l=o(this._leadAtom),c=new r.Vector3(l.x,l.y,l.z);if(i)this._detectLeadWing(s,n,o);else{if(a)s._midPoint=o(this._firstAtom).clone();else{const r=t._controlPoint;s._midPoint=r.clone().lerp(c,.5),s._wingVector=this.calcWing(r,c,o(e._wingAtom),t._wingVector)}s._controlPoint=c}}_finalize2(e,t,r){this._innerFinalize(e,e,t,this,r,(e=>e.position))}isConnected(e){if(this._chain!==e._chain)return!1;if(this===e)return!0;let t=!1;return this.forEachAtom((r=>{const{bonds:n}=r;for(let 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be("LEU","Leucine","L"),LYS:new be("LYS","Lysine","K"),MET:new be("MET","Methionine","M"),PHE:new be("PHE","Phenylalanine","F"),PRO:new be("PRO","Proline","P"),PYL:new be("PYL","Pyrrolysine","O"),SEC:new be("SEC","Selenocysteine","U"),SER:new be("SER","Serine","S"),THR:new be("THR","Threonine","T"),TRP:new be("TRP","Tryptophan","W"),TYR:new be("TYR","Tyrosine","Y"),VAL:new be("VAL","Valine","V"),A:new be("A","Adenine","A"),C:new be("C","Cytosine","C"),G:new be("G","Guanine","G"),I:new be("I","Inosine","I"),T:new be("T","Thymine","T"),U:new be("U","Uracil","U"),DA:new be("DA","Adenine","A"),DC:new be("DC","Cytosine","C"),DG:new be("DG","Guanine","G"),DI:new be("DI","Inosine","I"),DT:new be("DT","Thymine","T"),DU:new be("DU","Uracil","U"),"+A":new be("+A","Adenine","A"),"+C":new be("+C","Cytosine","C"),"+G":new be("+G","Guanine","G"),"+I":new be("+I","Inosine","I"),"+T":new be("+T","Thymine","T"),"+U":new be("+U","Uracil","U"),WAT:new be("WAT","Water",""),H2O:new be("H2O","Water",""),HOH:new be("HOH","Water",""),DOD:new be("DOD","Water",""),UNK:new be("UNK","Unknown",""),UNL:new be("UNL","Unknown Ligand","")};static Flags={PROTEIN:1,BASIC:2,ACIDIC:4,POLAR:8,NONPOLAR:16,AROMATIC:32,NUCLEIC:256,PURINE:512,PYRIMIDINE:1024,DNA:2048,RNA:4096,WATER:65536}}function we(e,t){for(let r=0,n=t.length;r1&&e[1]._wingVector){const t=e[1]._wingVector;e[0]._wingVector=new r.Vector3(t.x,t.y,t.z)}else e.length>0&&(e[0]._wingVector=new r.Vector3(1,0,0))}updateToFrame(e){const t=this._residues;let n=null,s=null;const i=e._residues,o=t.length;function a(t){return e.getAtomPos(t.index)}for(let e=0;e1?i[t[1]._index]._wingVector:new r.Vector3(1,0,0)}addResidue(e,t,r){let n=this._complex.getResidueType(e);null===n&&(n=this._complex.addResidueType(e));const s=new xe(this,n,t,r);return this._complex.addResidue(s),this._residues.push(s),n.flags&(ve.Flags.NUCLEIC|ve.Flags.PROTEIN)&&(this.maxSequencet&&(this.minSequence=t)),s}getResidueCount(){return 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je{includesAtom(e){return(e.flags&ae.Flags.NONPOLARH)===ae.Flags.NONPOLARH}}),Je("All",Xe),Je("None",Ye);const et=Qe.none();function tt(e,t,r){return r.prototype.priority=t,Je(e,r)}function rt(e,t){return Je(t,class extends je{includesAtom(t){return 0!==(t.residue._type.flags&e)}})}tt("Not",1,class extends Ke{includesAtom(e){return!this.rhs.includesAtom(e)}}),tt("And",2,class extends Ze{includesAtom(e){return this.lhs.includesAtom(e)&&this.rhs.includesAtom(e)}}),tt("Or",3,class extends Ze{includesAtom(e){return this.lhs.includesAtom(e)||this.rhs.includesAtom(e)}}),rt(ve.Flags.PROTEIN,"Protein"),rt(ve.Flags.BASIC,"Basic"),rt(ve.Flags.ACIDIC,"Acidic"),rt(ve.Flags.BASIC|ve.Flags.ACIDIC,"Charged"),rt(ve.Flags.POLAR,"Polar"),rt(ve.Flags.NONPOLAR,"NonPolar"),rt(ve.Flags.AROMATIC,"Aromatic"),rt(ve.Flags.NUCLEIC,"Nucleic"),rt(ve.Flags.PURINE,"Purine"),rt(ve.Flags.PYRIMIDINE,"Pyrimidine"),rt(ve.Flags.WATER,"Water");const nt=Object.create(Qe);nt.Selector=je,nt.RangeListSelector=$e,nt.ValueListSelector=We,nt.Range=class{constructor(e,t){this.min=e,this.max=void 0===t?e:t}includes(e){return this.min<=e&&e<=this.max}toString(){const{min:e,max:t}=this;return e===t?String(e):[e,t].join(":")}toJSON(){return[this.min,this.max]}},nt.RangeList=Be,nt.ValueList=Ge,nt.PrefixOperator=Ke,nt.InfixOperator=Ze,nt.Context=Object.create({}),nt.GetSelector=function(e){if(!nt.Context.hasOwnProperty(e)){throw{message:`selector ${e} is not registered`}}return nt.Context[e]||et},nt.ClearContext=function(){Object.keys(nt.Context).forEach((e=>{delete nt.Context[e]}))},nt.keyword=function(e){return Qe[e.toLowerCase()]||Qe.none},nt.parse=function(e){const t={};try{t.selector=ze.parser.parse(e)}catch(e){t.selector=et,t.error=e.message}return t},ze.parser.yy=nt,ze.parser.yy.parseError=ze.parser.parseError;const st=nt;const it=class{constructor(e){this._complex=e,this._selector=st.keyword("All")(),this._boundaries={boundingBox:new r.Box3,boundingSphere:new r.Sphere}}computeBoundaries(){const e=this._complex._atoms,t=e.length,n=this._selector,{boundingBox:s}=this._boundaries;if(s.makeEmpty(),1===t){s.expandByPoint(e[0].position);const t=new r.Vector3;s.getCenter(t);const n=2*e[0].element.radius;s.setFromCenterAndSize(t,new r.Vector3(n,n,n))}else for(let r=0;r0?this._selector=st.keyword("Chain")(this.chains):this._selector=st.keyword("None")()}};const at=class{constructor(e){this._complex=e,this._index=-1,this._residueIndices=[],this._cycles=[],this._subDivs=[],this._residueCount=0}getResidues(){return this._complex._residues}getResidueCount(){return this._residueCount}forEachResidue(e){const t=this._complex._residues,r=this._residueIndices;for(let n=0,s=r.length;n{e.update()}))}forEachAtom(e){this.forEachResidue((t=>{t.forEachAtom(e)}))}addCycle(e){this._cycles.push(e)}forEachCycle(e){const t=this._cycles;for(let r=0,n=t.length;r{t._component=e}))}_forEachSubChain(e,t){const r=this._complex._residues,n=this._subDivs;for(let s=0,i=n.length;s{t[r++]={start:n,end:s}})),t}getMaskedSubdivSequences(e){const t=[];let r=-1,n=-1;const s=this._subDivs;return this._forEachSubChain(e,((e,i,o)=>{n!==e&&(++r,t[r]={arr:[],boundaries:s[e]},n=e),t[r].arr[t[r].arr.length]={start:i,end:o}})),t}};const lt=class{constructor(e){this.numPairs=0,this.numMaxPairs=e,this.intBuffer=O.allocateTyped(Int32Array,4*e);for(let t=0;t<4*e;t++)this.intBuffer[t]=-1;this.hashBuffer=O.allocateTyped(Int32Array,33554432);for(let e=0;e<33554432;e++)this.hashBuffer[e]=-1}destroy(){this.intBuffer=null,this.hashBuffer=null}addPair(e,t){const r=et?e:t,s=r+(n<<14);let i=32*(r+89237*n&1048575),o=0;for(;o<32;o++){const e=this.hashBuffer[i+o];if(-1===e)break;if(e===s)return!1}if(o>=32)throw new Error("addPair: increase cMaxPairsForHashCode");if(this.hashBuffer[i+o]=s,this.numPairs>=this.numMaxPairs)throw new Error("addPair: increase num pairs");return i=4*this.numPairs,this.intBuffer[i]=r,this.intBuffer[i+1]=n,this.intBuffer[i+2]=s,this.numPairs++,!0}};function ct(e){const{element:t}=e;if(t)return t.radiusBonding;throw new Error("_getBondingRadius: Logic error.")}const ht=class{constructor(e){this._complex=e,this._maxRad=1.8;const t=this._complex.getDefaultBoundaries().boundingBox;this._vBoxMin=t.min.clone(),this._vBoxMax=t.max.clone(),this._pairCollection=null}_addExistingPairs(){const e=this._complex.getAtoms(),t=e.length;let r=0;const n=this._pairCollection;for(;rh*h||r<.001||n._pairCollection.addPair(l.index,e.index)};for(let n=0;n.1)&&e.dot(t)>=0}}();function mt(e,t){let r=0;for(;r3}function wt(e){return!0}const St=class{constructor(e){this._complex=e;const t=new Array(e._bonds.length),r=new Array(e._bonds.length);for(let e=0,n=t.length;es[l]?++l:++a}return!1}_tryBond(e,t,n){const s=[],i=this._bondsData,o=ft(e,t),a=t.position.clone().sub(o.position),l=this._currStart,c=this,h=this._bondMarks;let u=this._checkBond;h[e._index]=!0,u=void 0===u?yt:u,t.forEachBond((o=>{if(!u(o)||o===e||h[o._index]||c._haveSameCycle(i,e,o))return;const d=ft(o,t),p=d.position.clone().sub(t.position),m=d===l?-2:1-function(e,t){const n=e.dot(t)/Math.sqrt(e.lengthSq()*t.lengthSq());return r.MathUtils.clamp(n,-1,1)}(a,p),f=p.cross(a);if(!pt(f,n))return;let _=0;for(;_{n._resetCycles(),r.forEachBond((t=>{e(t)&&n._startCycle(t)}));const s=n._cycles;for(let e=0,n=s.length;e=e.z?t:Math.max(o,a),[l,c]}function Ct(e,t,r,n){const s=r-e.y,i=n-e.y,o=Math.sqrt(Math.max(t*t-s*s,0)),a=Math.sqrt(Math.max(t*t-i*i,0)),l=Math.min(o,a);let c;return c=r<=e.y&&n>=e.y?t:Math.max(o,a),[l,c]}class At{constructor(e,t){this._box=e.clone();const n=new r.Vector3;e.getSize(n),this._count=n.clone().divide(t).floor().max(new r.Vector3(1,1,1)),this._last=this._count.clone().subScalar(1),this._cellSize=n.clone().divide(this._count),this._cellInnerR=.5*Math.min(Math.min(this._cellSize.x,this._cellSize.y),this._cellSize.z),this._cellOuterR=.5*Math.sqrt(this._cellSize.dot(this._cellSize));const s=this._count.x*this._count.y*this._count.z;this._voxels=O.allocateTyped(Int32Array,s);for(let e=0;e{const n=t._findVoxel(e.position);t._atoms[r]=e,t._atoms[r+1]=t._voxels[n],t._voxels[n]=r,r+=2}))}static _zero=new r.Vector3(0,0,0);static _voxel=new r.Vector3;_findVoxel(e){const t=At._zero,r=At._voxel;return r.copy(e).sub(this._box.min).divide(this._cellSize).floor().clamp(t,this._last),r.x+this._count.x*(r.y+this._count.y*r.z)}_forEachAtomInVoxel(e,t){for(let r=this._voxels[e];r>=0;r=this._atoms[r+1])t(this._atoms[r])}static _xRange=new r.Vector2;static _yRange=new r.Vector2;static _zRange=new r.Vector2;_forEachVoxelWithinRadius(e,t,r){const n=At._xRange,s=At._yRange,i=At._zRange;if(t/this._cellInnerR<10)return void this._forEachVoxelWithinRadiusSimple(e,t,r);let o,a,l,c,h,u,d,p;i.set(e.z-t,e.z+t),i.subScalar(this._box.min.z).divideScalar(this._cellSize.z).floor().clampScalar(0,this._count.z-1);for(let m=i.x;m<=i.y;++m){h=[this._box.min.z+m*this._cellSize.z,this._box.min.z+(m+1)*this._cellSize.z],p=e.z-t<=h[0]&&h[1]<=e.z+t,o=vt(e,t,h[0],h[1]),s.set(e.y-o[1],e.y+o[1]),s.subScalar(this._box.min.y).divideScalar(this._cellSize.y).floor().clampScalar(0,this._count.y-1);for(let t=s.x;t<=s.y;++t){c=[this._box.min.y+t*this._cellSize.y,this._box.min.y+(t+1)*this._cellSize.y],d=e.y-o[0]<=c[0]&&c[1]<=e.y+o[0],a=Ct(e,o[1],c[0],c[1]),n.set(e.x-a[1],e.x+a[1]),n.subScalar(this._box.min.x).divideScalar(this._cellSize.x).floor().clampScalar(0,this._count.x-1);for(let{x:s}=n;s<=n.y;++s)l=[this._box.min.x+s*this._cellSize.x,this._box.min.x+(s+1)*this._cellSize.x],u=e.x-a[0]<=l[0]&&l[1]<=e.x+a[0],r(s+this._count.x*(t+this._count.y*m),u&&d&&p)}}}static _vCenter=new r.Vector3;_forEachVoxelWithinRadiusSimple(e,t,r){const n=At._xRange,s=At._yRange,i=At._zRange,o=At._vCenter,a=(t+this._cellOuterR)*(t+this._cellOuterR);let l=-1;t>this._cellOuterR&&(l=(t-this._cellOuterR)*(t-this._cellOuterR)),n.set(e.x-t,e.x+t),n.subScalar(this._box.min.x).divideScalar(this._cellSize.x).floor(),n.x=Math.min(Math.max(n.x,0),this._count.x-1),n.y=Math.min(Math.max(n.y,0),this._count.x-1),s.set(e.y-t,e.y+t),s.subScalar(this._box.min.y).divideScalar(this._cellSize.y).floor(),s.x=Math.min(Math.max(s.x,0),this._count.y-1),s.y=Math.min(Math.max(s.y,0),this._count.y-1),i.set(e.z-t,e.z+t),i.subScalar(this._box.min.z).divideScalar(this._cellSize.z).floor(),i.x=Math.min(Math.max(i.x,0),this._count.z-1),i.y=Math.min(Math.max(i.y,0),this._count.z-1);for(let t=i.x;t<=i.y;++t){const i=[this._box.min.z+t*this._cellSize.z,this._box.min.z+(t+1)*this._cellSize.z];o.z=.5*(i[0]+i[1]);for(let i=s.x;i<=s.y;++i){const s=[this._box.min.y+i*this._cellSize.y,this._box.min.y+(i+1)*this._cellSize.y];o.y=.5*(s[0]+s[1]);for(let{x:s}=n;s<=n.y;++s){const n=[this._box.min.x+s*this._cellSize.x,this._box.min.x+(s+1)*this._cellSize.x];o.x=.5*(n[0]+n[1]);const c=e.distanceToSquared(o);c<=a&&r(s+this._count.x*(i+this._count.y*t),c<=l)}}}}forEachAtomWithinRadius(e,t,r){const n=this,s=t*t;n._forEachVoxelWithinRadius(e,t,((t,i)=>{i?n._forEachAtomInVoxel(t,r):n._forEachAtomInVoxel(t,(t=>{e.distanceToSquared(t.position)<=s&&r(t)}))}))}forEachAtomWithinDistFromMasked(e,t,r,n){this._forEachAtomWithinDistFromGroup((r=>{e.forEachAtom((e=>{0!==(e.mask&t)&&r(e)}))}),r,n)}forEachAtomWithinDistFromSelected(e,t,r,n){this._forEachAtomWithinDistFromGroup((r=>{e.forEachAtom((e=>{t.includesAtom(e)&&r(e)}))}),r,n)}_forEachAtomWithinDistFromGroup(e,t,r){const n=this,s=t*t,i=[],o=[];let a,l=0;e((e=>{n._forEachVoxelWithinRadius(e.position,t,((t,r)=>{r?i[t]=-1:void 0===i[t]?(o.push(e),o.push(-1),i[t]=l,l+=2):-1!==i[t]&&(o.push(e),o.push(i[t]),i[t]=l,l+=2)}))}));const c=function(e){if(void 0!==i[a])if(l=i[a],-1!==l){for(;l>=0;l=o[l+1])if(e.position.distanceToSquared(o[l].position)1e3?this._buildVW():this._build()}isBond(e,t){if(this._hbonds[e]){const[r,n]=this._hbonds[e].acceptor;if(r&&r.residue===t&&r.energy<-.5)return!0;if(n&&n.residue===t&&n.energy<-.5)return!0}return!1}_build(){const e=this;for(let t=0;t0&&this._complex._residues[t-1].getType().flags&ve.Flags.PROTEIN&&r._sequence===this._complex._residues[t-1]._sequence+1&&(n=this._complex._residues[t-1]);for(let s=t+1;s0?t[o._index-1]:null;!a||0!==(a.getType().flags&ve.Flags.PROTEIN)&&o._sequence===a._sequence+1||(a=null),e._calcHBondEnergy(n,r,o),o._index!==r._index+1&&e._calcHBondEnergy(a,o,r)}for(let e=0;e0?t[e-1]:null,!n||0!==(n.getType().flags&ve.Flags.PROTEIN)&&r._sequence===n._sequence+1||(n=null),s.forEachAtomWithinRadius(this._residueGetCAlpha(r),5,o))}_residueGetCAlpha(e){for(let t=0;t{"C"===e.name?t=e.position:"O"===e.name&&(r=e.position)})),[t,r]}_residueGetNH(e,t){const[r,n]=this._residueGetCO(e);let s;if(t.forEachAtom((e=>{"N"===e.name&&(s=e.position)})),r&&n&&s){const e=r.clone();return e.sub(n),e.multiplyScalar(1/e.length()),e.add(s),[s,e]}return[null,null]}_calcHBondEnergy(e,t,r){let n=0;if(null===e)return n;if("PRO"!==t.getType().getName()){const[s,i]=this._residueGetNH(e,t),[o,a]=this._residueGetCO(r);if(null===s||null===i||null===o||null===a)return n;const l=i.distanceTo(a),c=i.distanceTo(o),h=s.distanceTo(o),u=s.distanceTo(a);n=l1&&(n1&&(n70}for(let r=1;r+4=s&&this._isHelixStart(e[r-s]._index,n);t?this._ss[e[r]._index]=It.TURN:this._bend[e[r]._index]&&(this._ss[e[r]._index]=It.BEND)}}_residueGetCAlpha(e){for(let t=0;t0&&(o=s.dot(i)/Math.sqrt(a)),o}_kappa(e,t,r){const n=this._residueGetCAlpha(t),s=this._residueGetCAlpha(e),i=this._residueGetCAlpha(r);if(null===n||null===s||null===i)return 180;const o=this._cosinusAngle(n,s,i,n),a=Math.sqrt(1-o*o);return 180*Math.atan2(a,o)/Math.PI}_isHelixStart(e,t){return this._helixFlags[t][e]===Nt.START||this._helixFlags[t][e]===Nt.START_AND_END}_buildBetaSheets(){const e=[];for(let t=0;te.chainI=6||s>=a&&n<=l)continue;let u=!1;u=e[t].type===Lt.PARALLEL?c-o<6&&a-s<3||c-o<3:i-h<6&&a-s<3||i-h<3,u&&(e[t].i=e[t].i.concat(e[r].i),e[t].type===Lt.PARALLEL?e[t].j=e[t].j.concat(e[r].j):e[t].j=e[r].j.concat(e[t].j),e.splice(r--,1))}const t=new Set;for(let r=0;r0;){let e=t.values().next().value;t.delete(e);const s=new Set;let i;s.add(e);do{i=new Set;for(const e of s.values())for(const r of t.values())this._areBridgesLinked(e,r)&&i.add(r);for(e of i.values())s.add(e),t.delete(e)}while(i.size>0);for(e of s.values())e.ladder=n,e.sheet=r,e.link=s,++n;++r}for(let t=0;t1&&(i=It.STRAND),r.type===Lt.PARALLEL){let e=0;for(let t=0;t{t.updateToFrame(e)}))}addResidueType(e){return this._residueTypes[e]=new ve(e,"Unknown","")}getResidueCount(){return this._residues.length}getResidues(){return this._residues}getSGroupCount(){return this._sgroups.length}getSGroups(){return this._sgroups}getAtomByFullname(e){const t=e.split(".");if(3!==t.length)return null;const r=t[0],n=parseInt(t[1],10);if(Number.isNaN(n))return null;const s=t[2].toUpperCase();let i=null;return this.forEachChain((e=>{i||0===e._name.localeCompare(r)&&e.forEachResidue((e=>{i||e._sequence===n&&e.forEachAtom((e=>{i||0===s.localeCompare(e.name)&&(i=e)}))}))})),i}addChain(e){const t=new Te(this,e);return this._chains.push(t),t}getChain(e){for(let t=0,r=this._chains.length;t{const t=e._residues,n=t.length;if(n<1)return;let s=r(),i=t[0]._index;for(let e=0;e=0&&e{e._finalize()})),this.forEachComponent((e=>{e.update()})),this._computeBounds(),this._finalizeBonds(),this.forEachSGroup((e=>{e._rebuildSGroupOnAtomChange()}))}update(){this._maskNeedsUpdate&&(this.updateStructuresMask(),this._maskNeedsUpdate=!1)}_finalizeBonds(){const e=this.getBonds(),t=e.length;for(let r=0;r=0;r--){const e=t[r];null===e._left||null===e._right?t.splice(r,1):(e._left.bonds.push(e),e._right.bonds.push(e))}const s=this._residues;for(r=0,n=s.length;r{e._finalize()}));const{units:i}=this;for(r=0,n=i.length;re.collectMask();this.forEachResidue(e),this.forEachChain(e),this.forEachMolecule(e)}countAtomsByMask(e){let t=0;return this.forEachAtom((r=>{0!==(r.mask&e)&&t++})),t}getNumAtomsBySelector(e){let t=0;return this.forEachAtom((r=>{e.includesAtom(r)&&t++})),t}resetAtomMask(e){this.forEachAtom((t=>{t.mask=e}))}markAtoms(e,t){const r=t,n=~r;let s=0;const i=st.keyword("And")(e,this.getSelector());return this.forEachAtom((e=>{i.includesAtom(e)?(e.mask|=r,s++):e.mask&=n})),this._maskNeedsUpdate=!0,s}markAtomsAdditionally(e,t){const r=t;let n=0;return this.forEachAtom((s=>{e.includesAtom(s)&&(s.mask&t)!==t&&(s.mask|=r,n++)})),n}clearAtomBits(e){const t=~e;this.forEachAtom((e=>{e.mask&=t}));const r=e=>{e._mask&=t};this.forEachAtom(r),this.forEachResidue(r),this.forEachChain(r),this.forEachMolecule(r)}getAtomNames(){if(this.hasOwnProperty("_atomNames"))return this._atomNames;const e={};return this.forEachAtom((t=>{e[t.name]=1})),this._atomNames=Object.keys(e),this._atomNames}getElements(){if(this.hasOwnProperty("_elements"))return this._elements;const e={};return this.forEachAtom((t=>{e[t.element.name]=1})),this._elements=Object.keys(e),this._elements}getResidueNames(){if(this.hasOwnProperty("_residueNames"))return this._residueNames;const e={};return this.forEachResidue((t=>{e[t._type._name]=1})),this._residueNames=Object.keys(e),this._residueNames}getChainNames(){if(this.hasOwnProperty("_chainNames"))return this._chainNames;const e={};return this.forEachChain((t=>{e[t._name]=1})),this._chainNames=Object.keys(e),this._chainNames}getAltLocNames(){if(this.hasOwnProperty("_altlocNames"))return this._altlocNames;const e={};return this.forEachAtom((t=>{e[String.fromCharCode(t.location)]=1})),this._altlocNames=Object.keys(e),this._altlocNames}getVoxelWorld(){if(!this.hasOwnProperty("_voxelWorld"))try{this._voxelWorld=new Et(this.getDefaultBoundaries().boundingBox,new r.Vector3(5,5,5)),this._voxelWorld.addAtoms(this)}catch{w.warn("Unable to create voxel world"),this._voxelWorld=null}return this._voxelWorld}addElement(e,t,r,n){const{length:s}=e;for(let i=0;i{let t=n[e];return t||(t=n[e]=new De(String(e),0)),t};let i,o,a=0,l=null;for(let n=0,c=this._residues.length;n!0))}}Ft.prototype.id="Complex",Ft.prototype.name="";const Bt=Ft;function Ut(e){let t=2;for(e=e-1>>1;e;)t<<=1,e>>=1;return t}class Gt{constructor(e,t,r,n,s,i){switch(this._box=r.clone(),this._dimVec=Math.max(Math.floor(n||1),1),this._volumeInfo=i,t instanceof Array?[this._dimX,this._dimY,this._dimZ]=t:(this._dimX=t.x,this._dimY=t.y,this._dimZ=t.z),this._dimX=Math.max(Math.floor(this._dimX),1),this._dimY=Math.max(Math.floor(this._dimY),1),this._dimZ=Math.max(Math.floor(this._dimZ),1),this._rowElements=this._dimVec*this._dimX,this._planeElements=this._rowElements*this._dimY,this._totalElements=this._planeElements*this._dimZ,this._data=s||O.allocateTyped(e,this._totalElements),this._dimVec){case 1:break;case 2:this.getValue=function(e,t,r){const n=e*this._dimVec+t*this._rowElements+r*this._planeElements;return[this._data[n],this._data[n+1]]},this.setValue=function(e,t,r,n,s){const i=e*this._dimVec+t*this._rowElements+r*this._planeElements;this._data[i]=n,this._data[i+1]=s},this.addValue=function(e,t,r,n,s){const i=e*this._dimVec+t*this._rowElements+r*this._planeElements;this._data[i]+=n,this._data[i+1]+=s};break;case 3:this.getValue=function(e,t,r){const n=e*this._dimVec+t*this._rowElements+r*this._planeElements;return[this._data[n],this._data[n+1],this._data[n+2]]},this.setValue=function(e,t,r,n,s,i){const o=e*this._dimVec+t*this._rowElements+r*this._planeElements;this._data[o]=n,this._data[o+1]=s,this._data[o+2]=i},this.addValue=function(e,t,r,n,s,i){const o=e*this._dimVec+t*this._rowElements+r*this._planeElements;this._data[o]+=n,this._data[o+1]+=s,this._data[o+2]+=i};break;default:throw new Error("Volume: invalid vector dimension")}}getValue(e,t,r){return this._data[e+t*this._rowElements+r*this._planeElements]}setValue(e,t,r,n){this._data[e+t*this._rowElements+r*this._planeElements]=n}addValue(e,t,r,n){this._data[e+t*this._rowElements+r*this._planeElements]+=n}getDimensions(){return[this._dimX,this._dimY,this._dimZ]}getBox(){return this._box}getVolumeInfo(){return this._volumeInfo}getCellSize(){const e=new r.Vector3;this._box.getSize(e);const t=new r.Vector3;return t.x=this._dimX>1?e.x/(this._dimX-1):0,t.y=this._dimY>1?e.y/(this._dimY-1):0,t.z=this._dimZ>1?e.z/(this._dimZ-1):0,t}computeGradient(){if(1!==this._dimVec)return null;const e=new Gt(Float32Array,[this._dimX,this._dimY,this._dimZ],this._box,3),t=this.getCellSize(),n=new r.Vector3(-.5/t.x,-.5/t.y,-.5/t.z);function s(e,t,r){return Math.min(r,Math.max(t,e))}const i=this._dimX,o=this._dimY,a=this._dimZ,l=this._data;function c(e,t,r){return l[r*i*o+t*i+e]}for(let t=0;t{null!==t._element.parentNode&&t._element.parentNode.removeChild(t._element)}))}getElement(){return this._element}setTransparency(e){const t=this.getElement();if(null===t)return;if(1===e)return void(t.style.display="none");t.style.display="inline";const r=1-e,n=r.toString(),s=100*r;t.style.opacity=n,t.style.filter=`alpha(opacity=${s})`}clone(){const e=new $t(this._element);return e.copy(this),e}}const Wt=$t;class Yt extends r.Group{raycast(e,t){if(!this.visible)return;const{children:r}=this;for(let n=0,s=r.length;n{(e instanceof r.Mesh||e instanceof r.LineSegments||e instanceof r.Line)&&e.geometry.dispose()})),function(e){const{children:t}=e;for(let e=0,r=t.length;e=1?this.fov=e:this.fov=r.MathUtils.radToDeg(2*Math.atan(Math.tan(.5*r.MathUtils.degToRad(e))/this.aspect))},r.StereoCamera.prototype.updateHalfSized=function(e,t){const r=e.aspect,n=e.fov;e.aspect=r/2,e.setMinimalFov(t),e.updateProjectionMatrix(),this.update(e),e.aspect=r,e.fov=n,e.updateProjectionMatrix()},r.PerspectiveCamera.prototype.setDistanceToFit=function(e,t){this.position.z=e/Math.sin(.5*r.MathUtils.degToRad(t))},r.Raycaster.prototype.intersectVisibleObject=function(e,t,n,s){const i=this.intersectObject(e,!1);if(0===i.length)return null;const o=Math.min(t.near,n);let a,l=i[0];const c=new r.Vector3;for(a=0;a{(e.hasOwnProperty("geometry")||e instanceof Wt)&&(t=!0)})),t},buildDistorionMesh:function(e,t,n){function s(e){let t=0,r=e,s=1;for(;Math.abs(r-t)>1e-5;)s=1+n*r,t=r,r=e/(s*s);return 1/s}const i=new r.PlaneGeometry(2,2,e,t),o=i.getAttribute("position");for(let e=0;e>Zt[t]&1))return!0;return!1},processObjRenderOrder:function(e,t){const r=+("BA"!==t);e.traverse((e=>{e.isGroup&&(e.renderOrder=r)}))},applySelectionMaterial:function(e){e.traverse((e=>{"material"in e&&(e.material=e.material.clone(!0),e.material.setValues({depthFunc:r.LessEqualDepth,overrideColor:!0,fog:!1,lights:!1,shadowmap:!1}),e.material.setUberOptions({fixedColor:new r.Color(16776960),zOffset:-1e-6}))}))},getMiddlePoint:function(e,t,n){const s=n||new r.Vector3;return s.set(0,0,0),s.addScaledVector(e,.5),s.addScaledVector(t,.5),s},LAYERS:Kt},rr={boundingBox:new r.Box3(new r.Vector3(-1,-1,-1),new r.Vector3(1,1,1)),boundingSphere:new r.Sphere(new r.Vector3(0,0,0),1)};class nr extends tr.RCGroup{constructor(e,t){super(e,t),this.name=e,this._dataSource=t}release(){this.parent&&this.parent.remove(this)}getDataSource(){return this._dataSource}getBoundaries(){return rr}}const sr=nr;function ir(e){return null==e||Array.isArray(e)?e:[e]}class or{constructor(e=[],t=["id"]){this._list=[],this._dict={},this._indices=[...t],this._indices.forEach((e=>{this._dict[e]={}})),e.forEach((e=>this.register(e)))}static registerInList(e,t){e.includes(t)||e.push(t)}static unregisterFromList(e,t){const r=e.indexOf(t);-1!==r&&e.splice(r,1)}static registerInDict(e,t,r){t.forEach((t=>{t=t.toLowerCase();const n=e[t]=e[t]||[];n.includes(r)||n.push(r)}))}static unregisterFromDict(e,t,r){t.forEach((t=>{t=t.toLowerCase();const n=e[t];if(n){const s=n.indexOf(r);-1!==s&&n.splice(s,1),0===n.length&&delete e[t]}}))}register(e){or.registerInList(this._list,e),this._indices.forEach((t=>{or.registerInDict(this._dict[t],ir(e[t]),e)}))}unregister(e){or.unregisterFromList(this._list,e),this._indices.forEach((t=>{or.unregisterFromDict(this._dict[t],ir(e[t]),e)}))}get all(){return[...this._list]}get first(){return this._list[0]}keys(e){return Object.keys(this._dict[e||this._indices[0]])}get(e,t){const r=this._dict[t||this._indices[0]];if(r){const t=r[e&&e.toLowerCase()];return t&&t.length>0?t[0]:void 0}}}const ar=or;const lr=function(e){Object.defineProperties(e,{logger:{get(){return this.context&&this.context.logger?this.context.logger:w}},settings:{get(){return this.context&&this.context.settings?this.context.settings:z}}})};class cr{constructor(e,t){this._position=e,this._radius=t}static _sphere=new r.Sphere;raycast(e){const t=cr._sphere;t.set(this._position,this._radius);const n=new r.Vector3;return e.ray.intersectSphere(t,n)?{distance:e.ray.origin.distanceTo(n),point:n}:null}}const hr=e=>class extends e{constructor(e,...t){super(...t),this._objects=new Array(e),this.boundingSphere=null,this.boundingBox=null}setSphere(e,t,r){this._objects[e]=new cr(t,r)}raycast(e,t){for(let r=0,n=this._objects.length;r65535,c=o*n,h=this._index=O.allocateTyped(l?Uint32Array:Uint16Array,c);this._positions=O.allocateTyped(Float32Array,3*a),this._normals=O.allocateTyped(Float32Array,3*a),this._colors=O.allocateTyped(Float32Array,3*a);const u=this._alpha=O.allocateTyped(Float32Array,a);t().fill(u,1);for(let e=0;e0,c=!1===o&&t>0,h=(i+1)*s+l*(s+1)+c*(s+1),u=(2*i+l+c)*s,d=n/2,p=new r.BufferAttribute(O.allocateTyped(Float32Array,3*h),3),m=new r.BufferAttribute(O.allocateTyped(Float32Array,3*h),3),f=new r.Uint16BufferAttribute(O.allocateTyped(Uint16Array,3*u),1),_=new r.BufferAttribute(O.allocateTyped(Float32Array,2*h),2);let g=0,y=0;const x=-(t-e)/n;for(let o=0;o<=i;o++){if(o!==i)for(let e=0;e0)for(let t=0;t2)for(let t=0;t65535;this._index=O.allocateTyped(s?Uint32Array:Uint16Array,6*e),this._positions=O.allocateTyped(Float32Array,4*n),this._colors=O.allocateTyped(Float32Array,3*n),this._directions=O.allocateTyped(Float32Array,3*n);const i=this._alpha=O.allocateTyped(Float32Array,n);t().fill(i,1);const o=this._index;let a=0,l=0;for(let t=0;t117440512)throw new Error("Too large cube dimension: lead to memory huge uasge");return this.pointsValuesLinear=O.allocateTyped(Float32Array,32*t),this.hasIntersection=O.allocateTyped(Int32Array,t),this.bitsInside=O.allocateTyped(Int32Array,t),0}destroy(){this.bitsInside=null,this.hasIntersection=null,this.pointsValuesLinear=null}}pn.prototype.striIndicesMarchCube=[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,8,3,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,1,9,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,8,3,9,8,1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,2,10,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,8,3,1,2,10,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,2,10,0,2,9,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,2,8,3,2,10,8,10,9,8,-1,-1,-1,-1,-1,-1,-1,3,11,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,11,2,8,11,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,9,0,2,3,11,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,11,2,1,9,11,9,8,11,-1,-1,-1,-1,-1,-1,-1,3,10,1,11,10,3,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,10,1,0,8,10,8,11,10,-1,-1,-1,-1,-1,-1,-1,3,9,0,3,11,9,11,10,9,-1,-1,-1,-1,-1,-1,-1,9,8,10,10,8,11,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,7,8,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,3,0,7,3,4,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,1,9,8,4,7,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,1,9,4,7,1,7,3,1,-1,-1,-1,-1,-1,-1,-1,1,2,10,8,4,7,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,3,4,7,3,0,4,1,2,10,-1,-1,-1,-1,-1,-1,-1,9,2,10,9,0,2,8,4,7,-1,-1,-1,-1,-1,-1,-1,2,10,9,2,9,7,2,7,3,7,9,4,-1,-1,-1,-1,8,4,7,3,11,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,11,4,7,11,2,4,2,0,4,-1,-1,-1,-1,-1,-1,-1,9,0,1,8,4,7,2,3,11,-1,-1,-1,-1,-1,-1,-1,4,7,11,9,4,11,9,11,2,9,2,1,-1,-1,-1,-1,3,10,1,3,11,10,7,8,4,-1,-1,-1,-1,-1,-1,-1,1,11,10,1,4,11,1,0,4,7,11,4,-1,-1,-1,-1,4,7,8,9,0,11,9,11,10,11,0,3,-1,-1,-1,-1,4,7,11,4,11,9,9,11,10,-1,-1,-1,-1,-1,-1,-1,9,5,4,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,5,4,0,8,3,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,5,4,1,5,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,8,5,4,8,3,5,3,1,5,-1,-1,-1,-1,-1,-1,-1,1,2,10,9,5,4,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,3,0,8,1,2,10,4,9,5,-1,-1,-1,-1,-1,-1,-1,5,2,10,5,4,2,4,0,2,-1,-1,-1,-1,-1,-1,-1,2,10,5,3,2,5,3,5,4,3,4,8,-1,-1,-1,-1,9,5,4,2,3,11,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,11,2,0,8,11,4,9,5,-1,-1,-1,-1,-1,-1,-1,0,5,4,0,1,5,2,3,11,-1,-1,-1,-1,-1,-1,-1,2,1,5,2,5,8,2,8,11,4,8,5,-1,-1,-1,-1,10,3,11,10,1,3,9,5,4,-1,-1,-1,-1,-1,-1,-1,4,9,5,0,8,1,8,10,1,8,11,10,-1,-1,-1,-1,5,4,0,5,0,11,5,11,10,11,0,3,-1,-1,-1,-1,5,4,8,5,8,10,10,8,11,-1,-1,-1,-1,-1,-1,-1,9,7,8,5,7,9,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,3,0,9,5,3,5,7,3,-1,-1,-1,-1,-1,-1,-1,0,7,8,0,1,7,1,5,7,-1,-1,-1,-1,-1,-1,-1,1,5,3,3,5,7,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,7,8,9,5,7,10,1,2,-1,-1,-1,-1,-1,-1,-1,10,1,2,9,5,0,5,3,0,5,7,3,-1,-1,-1,-1,8,0,2,8,2,5,8,5,7,10,5,2,-1,-1,-1,-1,2,10,5,2,5,3,3,5,7,-1,-1,-1,-1,-1,-1,-1,7,9,5,7,8,9,3,11,2,-1,-1,-1,-1,-1,-1,-1,9,5,7,9,7,2,9,2,0,2,7,11,-1,-1,-1,-1,2,3,11,0,1,8,1,7,8,1,5,7,-1,-1,-1,-1,11,2,1,11,1,7,7,1,5,-1,-1,-1,-1,-1,-1,-1,9,5,8,8,5,7,10,1,3,10,3,11,-1,-1,-1,-1,5,7,0,5,0,9,7,11,0,1,0,10,11,10,0,-1,11,10,0,11,0,3,10,5,0,8,0,7,5,7,0,-1,11,10,5,7,11,5,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,10,6,5,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,8,3,5,10,6,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,9,0,1,5,10,6,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,8,3,1,9,8,5,10,6,-1,-1,-1,-1,-1,-1,-1,1,6,5,2,6,1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,6,5,1,2,6,3,0,8,-1,-1,-1,-1,-1,-1,-1,9,6,5,9,0,6,0,2,6,-1,-1,-1,-1,-1,-1,-1,5,9,8,5,8,2,5,2,6,3,2,8,-1,-1,-1,-1,2,3,11,10,6,5,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,11,0,8,11,2,0,10,6,5,-1,-1,-1,-1,-1,-1,-1,0,1,9,2,3,11,5,10,6,-1,-1,-1,-1,-1,-1,-1,5,10,6,1,9,2,9,11,2,9,8,11,-1,-1,-1,-1,6,3,11,6,5,3,5,1,3,-1,-1,-1,-1,-1,-1,-1,0,8,11,0,11,5,0,5,1,5,11,6,-1,-1,-1,-1,3,11,6,0,3,6,0,6,5,0,5,9,-1,-1,-1,-1,6,5,9,6,9,11,11,9,8,-1,-1,-1,-1,-1,-1,-1,5,10,6,4,7,8,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,3,0,4,7,3,6,5,10,-1,-1,-1,-1,-1,-1,-1,1,9,0,5,10,6,8,4,7,-1,-1,-1,-1,-1,-1,-1,10,6,5,1,9,7,1,7,3,7,9,4,-1,-1,-1,-1,6,1,2,6,5,1,4,7,8,-1,-1,-1,-1,-1,-1,-1,1,2,5,5,2,6,3,0,4,3,4,7,-1,-1,-1,-1,8,4,7,9,0,5,0,6,5,0,2,6,-1,-1,-1,-1,7,3,9,7,9,4,3,2,9,5,9,6,2,6,9,-1,3,11,2,7,8,4,10,6,5,-1,-1,-1,-1,-1,-1,-1,5,10,6,4,7,2,4,2,0,2,7,11,-1,-1,-1,-1,0,1,9,4,7,8,2,3,11,5,10,6,-1,-1,-1,-1,9,2,1,9,11,2,9,4,11,7,11,4,5,10,6,-1,8,4,7,3,11,5,3,5,1,5,11,6,-1,-1,-1,-1,5,1,11,5,11,6,1,0,11,7,11,4,0,4,11,-1,0,5,9,0,6,5,0,3,6,11,6,3,8,4,7,-1,6,5,9,6,9,11,4,7,9,7,11,9,-1,-1,-1,-1,10,4,9,6,4,10,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,4,10,6,4,9,10,0,8,3,-1,-1,-1,-1,-1,-1,-1,10,0,1,10,6,0,6,4,0,-1,-1,-1,-1,-1,-1,-1,8,3,1,8,1,6,8,6,4,6,1,10,-1,-1,-1,-1,1,4,9,1,2,4,2,6,4,-1,-1,-1,-1,-1,-1,-1,3,0,8,1,2,9,2,4,9,2,6,4,-1,-1,-1,-1,0,2,4,4,2,6,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,8,3,2,8,2,4,4,2,6,-1,-1,-1,-1,-1,-1,-1,10,4,9,10,6,4,11,2,3,-1,-1,-1,-1,-1,-1,-1,0,8,2,2,8,11,4,9,10,4,10,6,-1,-1,-1,-1,3,11,2,0,1,6,0,6,4,6,1,10,-1,-1,-1,-1,6,4,1,6,1,10,4,8,1,2,1,11,8,11,1,-1,9,6,4,9,3,6,9,1,3,11,6,3,-1,-1,-1,-1,8,11,1,8,1,0,11,6,1,9,1,4,6,4,1,-1,3,11,6,3,6,0,0,6,4,-1,-1,-1,-1,-1,-1,-1,6,4,8,11,6,8,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,7,10,6,7,8,10,8,9,10,-1,-1,-1,-1,-1,-1,-1,0,7,3,0,10,7,0,9,10,6,7,10,-1,-1,-1,-1,10,6,7,1,10,7,1,7,8,1,8,0,-1,-1,-1,-1,10,6,7,10,7,1,1,7,3,-1,-1,-1,-1,-1,-1,-1,1,2,6,1,6,8,1,8,9,8,6,7,-1,-1,-1,-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9,9,11,8,-1,-1,-1,-1,-1,-1,-1,3,0,9,3,9,11,1,2,9,2,11,9,-1,-1,-1,-1,0,2,11,8,0,11,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,3,2,11,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,2,3,8,2,8,10,10,8,9,-1,-1,-1,-1,-1,-1,-1,9,10,2,0,9,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,2,3,8,2,8,10,0,1,8,1,10,8,-1,-1,-1,-1,1,10,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,3,8,9,1,8,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,9,1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,3,8,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1];const mn=pn,fn=[0,265,515,778,1030,1295,1541,1804,2060,2309,2575,2822,3082,3331,3593,3840,400,153,915,666,1430,1183,1941,1692,2460,2197,2975,2710,3482,3219,3993,3728,560,825,51,314,1590,1855,1077,1340,2620,2869,2111,2358,3642,3891,3129,3376,928,681,419,170,1958,1711,1445,1196,2988,2725,2479,2214,4010,3747,3497,3232,1120,1385,1635,1898,102,367,613,876,3180,3429,3695,3942,2154,2403,2665,2912,1520,1273,2035,1786,502,255,1013,764,3580,3317,4095,3830,2554,2291,3065,2800,1616,1881,1107,1370,598,863,85,348,3676,3925,3167,3414,2650,2899,2137,2384,1984,1737,1475,1226,966,719,453,204,4044,3781,3535,3270,3018,2755,2505,2240,2240,2505,2755,3018,3270,3535,3781,4044,204,453,719,966,1226,1475,1737,1984,2384,2137,2899,2650,3414,3167,3925,3676,348,85,863,598,1370,1107,1881,1616,2800,3065,2291,2554,3830,4095,3317,3580,764,1013,255,502,1786,2035,1273,1520,2912,2665,2403,2154,3942,3695,3429,3180,876,613,367,102,1898,1635,1385,1120,3232,3497,3747,4010,2214,2479,2725,2988,1196,1445,1711,1958,170,419,681,928,3376,3129,3891,3642,2358,2111,2869,2620,1340,1077,1855,1590,314,51,825,560,3728,3993,3219,3482,2710,2975,2197,2460,1692,1941,1183,1430,666,915,153,400,3840,3593,3331,3082,2822,2575,2309,2060,1804,1541,1295,1030,778,515,265,0];function _n(e,t,r){const n=e.getValue(t.x,t.y,t.z);r.set(n[0],n[1],n[2])}class gn{constructor(){this._arrSize=8,this.p=new Array(this._arrSize),this.g=new Array(this._arrSize),this.val=new Array(this._arrSize);for(let e=0;eMath.abs(e)>Number.EPSILON;return!(c(t.y)||c(t.z)||c(n.x)||c(n.z)||c(s.x)||c(s.y))}_vertexInterp(e,t,r,n,s,i){const o=t.p[r],a=t.p[n],l=t.g[r],c=t.g[n],h=t.val[r],u=e-h,d=t.val[n]-h;let p=0;Math.abs(d)>0&&(p=u/d),p=p>1?1:p,s.lerpVectors(o,a,p),i.lerpVectors(l,c,p)}static _triTable=mn.prototype.striIndicesMarchCube;static _arrSize=12;static _firstIndices=[0,1,2,3,4,5,6,7,0,1,2,3];static _secondIndices=[1,2,3,0,5,6,7,4,4,5,6,7];static _vertexList=xn(bn._arrSize);static _normalList=xn(bn._arrSize);_polygonize(e,t,r){const{cubeIndex:n}=e;let s=0;const i=bn._arrSize,o=bn._firstIndices,a=bn._secondIndices,l=bn._vertexList,c=bn._normalList;for(;sa?a:r+t;let c=-1;for(let e=r;ee&&(t=r,e=A[r]);if(t<0||!n.includesAtom(C[t])){M[s]=-1;continue}}M[s]=P++;const D=g=0&&r>=0&&n>=0&&(this._indices[3*t]=e,this._indices[3*t+1]=r,this._indices[3*t+2]=n,++t)}this._position=new Float32Array(this._position.buffer.slice(0,3*P*4)),this._normals=new Float32Array(this._normals.buffer.slice(0,3*P*4)),this._colors=new Float32Array(this._colors.buffer.slice(0,3*P*4)),this._indices=new Uint32Array(this._indices.buffer.slice(0,3*t*4))}}toMesh(){const e=new r.BufferGeometry;return e.setIndex(new r.BufferAttribute(this._indices,1)),e.setAttribute("position",new r.BufferAttribute(this._position,3)),e.setAttribute("normal",new r.BufferAttribute(this._normals,3)),e.setAttribute("color",new r.BufferAttribute(this._colors,3)),e.computeBoundingSphere(),e}}const wn=bn;const Sn=class extends dn{_build(){const e=this._opts;this.numVoxels=[128,128,128],this.xAxis=new r.Vector3(1,0,0),this.yAxis=new r.Vector3(0,1,0),this.zAxis=new r.Vector3(0,0,1),this.origin=new r.Vector3(0,0,0),this._visibilitySelector=e.visibilitySelector,this._calcSurface(e)}_findMinMax(e){const t=e.length/4,r=[e[0],e[1],e[2],e[3]],n=[e[0],e[1],e[2],e[3]];for(let s=1;s4&&(t.gridSpacing*=s[3]);let o=t.radScale*i[3]*1.7,a=o;a=.65*Math.sqrt(4/3*Math.PI*a*a*a),o=Math.max(o,a);let l=0;for(;l<3;++l)s[l]-=o,i[l]+=o;for(l=0;l<3;++l)r[l]=Math.ceil((i[l]-s[l])/t.gridSpacing);return this.xAxis.x=(r[0]-1)*t.gridSpacing,this.yAxis.y=(r[1]-1)*t.gridSpacing,this.zAxis.z=(r[2]-1)*t.gridSpacing,[this.origin.x,this.origin.y,this.origin.z]=s,{bbox:n,dim:r}}_makeSurface(e,t){const n=new wn;n.compute(e.volMap,this.origin,t.isoValue,1),n.vertexFusion(9,9),n._numTriangles>0?(n.setColorVolTex(e.volTexMap,e.atomMap,e.atomWeightMap,this._visibilitySelector),this.setIndex(new r.BufferAttribute(n._indices,1)),this.setAttribute("position",new r.BufferAttribute(n._position,3)),this.setAttribute("normal",new r.BufferAttribute(n._normals,3)),this.setAttribute("color",new r.BufferAttribute(n._colors,3))):this.setAttribute("position",new r.BufferAttribute(O.allocateTyped(Float32Array,0),3))}_calcSurface(e){const t={posRad:this._posRad,colors:this._colors,atoms:this._opts.atoms};if(0===t.posRad.length)return;const n=this._findNumVoxels(t.posRad,e),s=new r.Box3(this.origin,new r.Vector3(this.xAxis.x,this.yAxis.y,this.zAxis.z).add(this.origin)),i=this._computeSurface(t,s,n,e);this._makeSurface(i,e)}},{Volume:vn}=Ht;const Cn=class extends Sn{_computeSurface(e,t,r,n){this._shiftByOrigin(e.posRad);const s={volMap:new vn(Float32Array,this.numVoxels,t),volTexMap:new vn(Float32Array,this.numVoxels,t,3)};return null!=this._visibilitySelector&&(s.atomMap=[],s.atomWeightMap=new vn(Float32Array,this.numVoxels,t)),this.gaussdensity(s,e,null,n),s}gaussdensity(e,t,r,n){const s=t.posRad.length/4,{posRad:i,colors:o}=t,{numVoxels:a}=this,{radScale:l,gaussLim:c,gridSpacing:h}=n,u=1/n.isoValue,d=1/h,p=a[0]-1,m=a[1]-1,f=a[2]-1,{volMap:_,volTexMap:g}=e,y=_.getData(),x=_.getStrideX(),b=g.getData(),w=g.getStrideX();let S;null!=this._visibilitySelector&&(S=e.atomWeightMap.getData());const{atomMap:v}=e;for(let e=0;e=E)continue;let d=_.getDirectIdx(R,l,r),p=g.getDirectIdx(R,l,r),m=R*h-i[n];for(let r=R;r<=M;++r,m+=h,d+=x,p+=w){const r=-(m*m+c)*C;let n=Math.exp(r)*a;null!=this._visibilitySelector&&n>S[d]&&(S[d]=n,v[d]=t.atoms[e]),y[d]+=n,n*=u;const s=3*e;b[p]+=n*o[s],b[p+1]+=n*o[s+1],b[p+2]+=n*o[s+2]}}}}}_shiftByOrigin(e){const t=this.origin.x,r=this.origin.y,n=this.origin.z,s=e.length/4;for(let i=0;iR&&(R=r)}this.neighbourListLength=27*R+1,this.withinRadii=function(t,r,n,s,l){let c=0;const h=u(t,i),f=u(r,o),g=u(n,a),b=Math.max(0,h-1),w=Math.max(0,f-1),S=Math.max(0,g-1),T=Math.min(d-1,h+1),R=Math.min(p-1,f+1),M=Math.min(m-1,g+1);for(y=b;y<=T;++y){const i=y*_;for(E=w;E<=R;++E){const o=E*m;for(let a=S;a<=M;++a){x=i+o+a;const h=v[x],u=h+C[x];for(let i=h;ip&&(p=t),d[e]=t*t}z(),function(){let e=0;const t=2*Math.PI/_;A=O.allocateTyped(Float32Array,_),C=O.allocateTyped(Float32Array,_);for(let r=0;r<_;r++)A[r]=Math.cos(e),C[r]=Math.sin(e),e+=t}(),E=new An(i,h,u,2.01*p),T=new Int32Array(E.neighbourListLength),R=-1}function B(e,t,r,n){const s=4*e,o=d[e],a=i[s]-t,l=i[s+1]-r,c=i[s+2]-n;return a*a+l*l+c*c=0;){if(i!==n&&i!==s&&B(i,e,t,r))return R=i,i;i=T[++o]}return R=-1,-1}function G(e,t){const r=4*e,n=4*t,s=i[r],o=i[r+1],a=i[r+2],l=i[r+3];let c=N.x=i[n]-s,u=N.y=i[n+1]-o,d=N.z=i[n+2]-a;const p=i[n+3];let m=c*c+u*u+d*d;const x=Math.sqrt(m),b=l*((l*l+x*x-p*p)/(2*l*x));var E,T;N.normalize(),T=N,(E=I).x=E.y=E.z=1,0!==T.x?E.x=(T.y+T.z)/-T.x:0!==T.y?E.y=(T.x+T.z)/-T.y:0!==T.z&&(E.z=(T.x+T.y)/-T.z),I.normalize(),V.crossVectors(N,I),V.normalize();const M=Math.sqrt(l*l-b*b);I.multiplyScalar(M),V.multiplyScalar(M),N.multiplyScalar(b),N.x+=s,N.y+=o,N.z+=a,R=-1;const P=D;for(let r=0;r<_;r++){const n=A[r],s=C[r],i=N.x+n*I.x+s*V.x,o=N.y+n*I.y+s*V.y,a=N.z+n*I.z+s*V.z;if(-1===U(i,o,a,e,t)){const e=Math.floor(f*(i-h[0])),t=Math.floor(f*(o-h[1])),r=Math.floor(f*(a-h[2])),n=Math.max(0,e-P),s=Math.max(0,t-P),l=Math.max(0,r-P),p=Math.min(g[0],e+P+2),_=Math.min(g[1],t+P+2),x=Math.min(g[2],r+P+2);for(let e=l;e0&&mM[o]&&(M[o]=t,P[o]=a[e]),y[o]<0&&(y[o]=-y[o]);const u=Math.sqrt(m),d=l/u;let f=p*d,_=h*d,g=i*d;if(f+=r,_+=n,g+=s,-1===U(f,_,g,e,-1)){const e=l-u;e=0;)e0){t=1/t;const r=3*e;x[r]*=t,x[r+1]*=t,x[r+2]*=t}}}()}this.build=function(){j(),this.volTexMap=x,this.weightsMap=M,this.atomMap=P,this.volMap=y}},{Volume:Tn}=Ht;const Rn=class extends Sn{_computeSurface(e,t,r,n){const s=new En(e,r,n);s.build();return{volMap:new Tn(Float32Array,this.numVoxels,t,1,s.volMap),volTexMap:new Tn(Float32Array,this.numVoxels,t,3,s.volTexMap),atomMap:s.atomMap,atomWeightMap:new Tn(Float32Array,this.numVoxels,t,1,s.weightsMap)}}};const Mn=class{constructor(e,t){this.coord=new r.Vector3,this.coord.copy(e),this.radius=t,this.colorX=.99999,this.colorY=0,this.colorZ=0,this.atomType=0,this.srcAtom=null}};const Pn=class{constructor(e,t,n,s,i){this._numAtoms=e,this._atoms=t,this._vBoxMin=new r.Vector3,this._vBoxMax=new r.Vector3,this._vBoxMin.copy(n),this._vBoxMax.copy(s),this._probeRadius=i,this._atomsList=null,this._voxelList=null}createVoxels(){let e,t;const r=0|this._numAtoms,n=this._atoms,s=this._vBoxMax.x-this._vBoxMin.x,i=this._vBoxMax.y-this._vBoxMin.y,o=this._vBoxMax.z-this._vBoxMin.z;let a=sc?t:c,h+=t;let u=Math.floor(a/c);u<2&&(u=2),h/=r,this._numCells=u,this._aveRad=h,this._maxRad=c;const d=u,p=u*u,m=u*u*u,f=this._xScale=1/(this._vBoxMax.x-this._vBoxMin.x),_=this._yScale=1/(this._vBoxMax.y-this._vBoxMin.y),g=this._zScale=1/(this._vBoxMax.z-this._vBoxMin.z);let y=0;const x=f*u,b=_*u,w=g*u;for(l=0;l=0?r:0,s=s>=0?s:0,i=i>=0?i:0,o=o=0;e=this._atomsList[2*e+1]){t(o[this._atomsList[2*e]])}}getClosestAtom(e){let t=null,r=Number.MAX_VALUE;return this.forEachRelatedAtom(e,(n=>{const s=e.distanceToSquared(n.coord);sf)return;const g=e.radius+n._probeRadius;d=s-g*g,d<0&&(d=-d),p=Math.exp(_*d),c+=t*p,h+=r*p,u+=m*p,i++};let y=0;for(let n=0;ny?i:y,s=c*c+h*h+u*u,i>0&&(d=1/Math.sqrt(s),c*=d,h*=d,u*=d),r[n].x=c,r[n].y=h,r[n].z=u;return 0}buildColors(e,t,r,n){const s=this;let i=0,o=0,a=0,l=0,c=0;const h=n*n;let u=[],d=[],p=0;const m=function(e){const t=i-e.coord.x,r=o-e.coord.y,n=a-e.coord.z,m=t*t+r*r+n*n;if(m>h)return;const f=e.radius+s._probeRadius;l=m-f*f,l<0&&(l=-l),c=1/(.8+l),u.push([e.colorX,e.colorY,e.colorZ]),d.push(c),p+=c};for(let n=0;ni?a:i,o.x-ar.x&&(r.x=o.x+a),o.y+a>r.y&&(r.y=o.y+a),o.z+a>r.z&&(r.z=o.z+a)}t.x-=i,t.y-=i,t.z-=i,r.x+=i,r.y+=i,r.z+=i}getCornerCoord(e,t,r,n,s,i,o){const a=1/(i-1),l=r*a,c=n*a,h=s*a;o.x=e.x*(1-l)+t.x*l,o.y=e.y*(1-c)+t.y*c,o.z=e.z*(1-h)+t.z*h}buildEdgePoint(e,t,r,n,s,i){if(r[e]^r[t]){const r=24,o=(0-n.pointsValuesLinear[s+r+e])/(n.pointsValuesLinear[s+r+t]-n.pointsValuesLinear[s+r+e]),a=n.pointsValuesLinear[s+3*e+0],l=n.pointsValuesLinear[s+3*e+1],c=n.pointsValuesLinear[s+3*e+2],h=n.pointsValuesLinear[s+3*t+0],u=n.pointsValuesLinear[s+3*t+1],d=n.pointsValuesLinear[s+3*t+2];i.x=a*(1-o)+h*o,i.y=l*(1-o)+u*o,i.z=c*(1-o)+d*o}}isTriangleVisible(e,t,r){const n=this.voxelWorld.getClosestAtom(e),s=this.voxelWorld.getClosestAtom(t),i=this.voxelWorld.getClosestAtom(r);return null!==n&&null!==s&&null!==i&&null!==n.srcAtom&&null!==s.srcAtom&&null!==i.srcAtom&&(this.visibilitySelector.includesAtom(n.srcAtom)&&this.visibilitySelector.includesAtom(s.srcAtom)&&this.visibilitySelector.includesAtom(i.srcAtom))}addTriangle(e,t,r){if(this.visibilitySelector&&!this.isTriangleVisible(e,t,r))return!0;const n=this.geoOut;if(n._numTriangles>=this.maxNumTriangles)return!1;const s=this.addVertexToGeo(n,e),i=this.addVertexToGeo(n,t),o=this.addVertexToGeo(n,r);if((s|i|o)<0)return!1;const a=3*n._numTriangles;return n._indices[a+0]=s,n._indices[a+1]=i,n._indices[a+2]=o,n._numTriangles++,!0}buildGeoFromCorners(e,t,n,s,i,o){const a=e-1,l=e,c=e*e,h=new Array(12);for(let e=0;e<12;e++)h[e]=new r.Vector3;const u=[];for(let e=0;e<8;e++)u[e]=1;const d=new r.Vector3;let p=0,m=0;for(let r=0;rt.length/2||2*Object.keys(In.ByAtomicNumber).length!==t.length)throw new Error("atomT.length should be equal Element.ByAtomicNumber.length * 2");return t[2*e]}calculateGridCorners(e,t,n,s,i,o){const a=t*t,l=a*t,c=new r.Vector3,h=new r.Vector3;for(let t=0;t=0;n=this.hashEntries[2*n+1]){const r=this.hashEntries[2*n+0];o.copy(e._vertices[r]),o.x-=t.x,o.y-=t.y,o.z-=t.z;if(o.x*o.x+o.y*o.y+o.z*o.z<1e-6)return r}if(e._numVertices>=this.maxNumVertices)return-1;const u=e._numVertices;if(e._vertices[u].copy(t),null!==this.vBoxMin&&null!==this.vBoxMax){if(n=this.getNewHashEntry(),n<0)return-1;const e=this.hashLines[h+1];this.hashLines[h+1]=n,this.hashEntries[2*n+0]=u,this.hashEntries[2*n+1]=e,this.hashLines[h+0]++}return e._numVertices++,u}modifyExcludedFromGeo(e,t,r,n,s,i){let o,a,l;const c=e*e,h=(e-1)/(n.x-r.x),u=(e-1)/(n.y-r.y),d=(e-1)/(n.z-r.z),p=2*t*(2*t),m=1/(e-1);for(let f=0;f=0?y:0,x=x>=0?x:0,b=b>=0?b:0,w=w<=e-1?w:e-1,S=S<=e-1?S:e-1,v=v<=e-1?v:e-1;for(let s=x;s<=S;s++){const h=s*c;for(let c=b;c<=v;c++){const u=c*e;for(let e=y;e<=w;e++){o=h+u+e;let d=e*m;const f=r.x*(1-d)+n.x*d;d=s*m;const g=r.y*(1-d)+n.y*d;d=c*m;const y=r.z*(1-d)+n.z*d,x=f-_.x,b=g-_.y,w=y-_.z,S=x*x+b*b+w*w;S0?(i[o]<0&&(i[o]=l),l>i[o]&&(i[o]=l)):l>i[o]&&(i[o]=l))}}}}return 0}_innerBuild(){let e;const t=1.2,n={posRad:this._posRad,colors:this._colors,atoms:this._opts.atoms};this.complex=this._opts.parent,this.atoms=n.atoms,this.meshResolution=this._opts.gridSpacing,this.atomRadiusScale=this._opts.radScale,this.colorMode=this._opts.colorMode,this.probeRadius=this._opts.probeRadius,this.useVertexColors=!0,this.excludeProbe=this._opts.excludeProbe,this.visibilitySelector=this._opts.visibilitySelector,this.geoOut=null,this.hashLines=null,this.hashEntries=null,this.numHashEtriesAllocated=0,this.numHashEntryIndex=0,this.maxNumVertices=0,this.maxNumTriangles=0;const s=new Array(this.atoms.length);this.convertToAtomsColored(n,s);const i=this.vBoxMin=new r.Vector3,o=this.vBoxMax=new r.Vector3;this.getBoundingBox(s,i,o);const a=this.marCubeResoultion=4*this.meshResolution,l=a,c=l*l*l,h=O.allocateTyped(Float32Array,c),u=this.probeRadius*this.atomRadiusScale;this.calculateGridCorners(h,l,i,o,s,u);const d=a-1,p=new mn;if(e=p.create(d),e<0)return e;const m=new r.Vector3;m.x=(o.x-i.x)/d,m.y=(o.y-i.y)/d,m.z=(o.z-i.z)/d;let f=this.getNumIntersectedCells(l,d,h,p),_=Math.floor(f*t),g=Math.floor(f*t*2);if(this.geoOut=new Ln(_,g,this.useVertexColors),e=this.createVertexHash(_,g),e<0)return e;let y=u;if(this.excludeProbe&&(y=.01),this.voxelWorld=new Pn(s.length,s,i,o,y),this.voxelWorld.createVoxels(),e=this.buildGeoFromCorners(a,i,o,h,m,p),this.excludeProbe){if(this.modifyExcludedFromGeo(l,u,i,o,this.geoOut,h),this.geoOut._vertices=null,this.geoOut._colors=null,this.geoOut._indices=null,this.geoOut._normals=null,this.geoOut._numVertices=0,this.geoOut._numTriangles=0,this.geoOut=null,f=this.getNumIntersectedCells(l,d,h,p),_=Math.floor(f*t),g=Math.floor(f*t*2),this.geoOut=new Ln(_,g,this.useVertexColors),e=this.createVertexHash(_,g),e<0)return e;e=this.buildGeoFromCorners(l,i,o,h,m,p)}this.voxelWorld.buildNormals(this.geoOut._vertices.length,this.geoOut._vertices,this.geoOut._normals);let x=6.5;return this.excludeProbe&&(x-=1.5),this.useVertexColors&&this.voxelWorld.buildColors(this.geoOut._vertices.length,this.geoOut._vertices,this.geoOut._colors,x),this.voxelWorld.destroyVoxels(),this.voxelWorld=null,p.destroy(),e}};const Vn={InstancedSpheresGeometry:mr,SimpleSpheresGeometry:xr,Simple2CCylindersGeometry:vr,Instanced2CCylindersGeometry:Ir,ExtrudedObjectsGeometry:Br,ChunkedLinesGeometry:Jr,TwoColorLinesGeometry:rn,CrossGeometry:cn,QuickSurfGeometry:Cn,ContactSurfaceGeometry:Rn,SSIsosurfaceGeometry:On,LabelsGeometry:class extends g{constructor(e,t){super(),this._opts=t,this.items=[],this.needsUpdate=!1;let n=-50,s=-50;switch(t.horizontalAlign){case"left":n=0;break;case"right":n=-100}switch(t.verticalAlign){case"top":s=-100;break;case"bottom":s=0}const i=new r.Vector3(t.dx||0,t.dy||0,t.dz||0);this.userData={translation:`translate(${n}%, ${s}%)`,offset:i}}setItem(e,t,n){const s=this._opts,i=this.items[e]||function(e,t){const n=document.createElement("div");if(n.className=t,"string"==typeof e){const t=document.createElement("span");t.style.fontSize="150%";const r=e.split("\n");for(let e=0,n=r.length;e 0\r\n\t\tuniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ];\r\n\t\tout vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tout vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n in vec3 color;\r\n out vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n in vec3 color2;\r\n out vec3 vColor2;\r\n in vec2 uv;\r\n #ifndef CYLINDER_SPRITE\r\n out vec2 vUv;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_POS\r\n in vec4 offset;\r\n #ifdef SPHERE_SPRITE\r\n out vec4 instOffset;\r\n out vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n in vec4 matVector1;\r\n in vec4 matVector2;\r\n in vec4 matVector3;\r\n in vec4 invmatVector1;\r\n in vec4 invmatVector2;\r\n in vec4 invmatVector3;\r\n\r\n #ifdef CYLINDER_SPRITE\r\n out vec4 matVec1;\r\n out vec4 matVec2;\r\n out vec4 matVec3;\r\n out vec4 invmatVec1;\r\n out vec4 invmatVec2;\r\n out vec4 invmatVec3;\r\n out vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\nuniform mat4 modelViewMatrix; // optional\r\nuniform mat4 projectionMatrix; // optional\r\nuniform mat3 normalMatrix; // optional\r\nuniform mat4 modelMatrix; // optional\r\n\r\n#ifdef DASHED_LINE\r\n in float lineDistance;\r\n out float vLineDistance;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n in vec3 direction;\r\n uniform mat4 projMatrixInv;\r\n uniform vec2 viewport;\r\n uniform float lineWidth;\r\n\r\n vec4 transform(vec4 coord){\r\n return projectionMatrix * modelViewMatrix * coord;\r\n }\r\n\r\n vec2 project(vec4 device){\r\n vec3 device_normal = device.xyz/device.w;\r\n vec2 clip_pos = (device_normal*0.5+0.5).xy;\r\n return clip_pos * viewport;\r\n }\r\n\r\n vec4 unproject(vec2 screen, float z, float w){\r\n vec2 clip_pos = screen/viewport;\r\n vec2 device_normal = clip_pos*2.0-1.0;\r\n return vec4(device_normal*w, z, w);\r\n }\r\n#endif\r\n\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n alphaCol = alphaColor;\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n vec3 objectNormal = vec3(\r\n dot(normal, matVector1.xyz),\r\n dot(normal, matVector2.xyz),\r\n dot(normal, matVector3.xyz));\r\n#else\r\n vec3 objectNormal = vec3( normal );\r\n#endif\r\n\r\nvec3 transformedNormal = normalMatrix * objectNormal;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n vNormal = normalize(transformedNormal);\r\n#endif\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n viewNormal = normalize(mat3(modelViewMatrix)*objectNormal);\r\n#endif\r\n\r\n vec4 localPos = vec4(position.xyz, 1.0);\r\n vec4 worldPos = modelMatrix * localPos;\r\n vec4 mvPosition = modelViewMatrix * localPos;\r\n\r\n// make thick line offset\r\n#ifdef THICK_LINE\r\n // get screen pos\r\n vec4 dPos = transform(vec4(position.xyz, 1.0));\r\n vec2 sPos = project(dPos);\r\n // move pos forward\r\n vec3 position2 = position.xyz + direction.xyz * 0.5;\r\n // get screen offset pos\r\n vec4 dPos2 = transform(vec4(position2.xyz, 1.0));\r\n vec2 sPos2 = project(dPos2);\r\n // screen line direction\r\n vec2 sDir = normalize(sPos2 - sPos);\r\n // vertex offset (orthogonal to line direction)\r\n vec2 offset1 = vec2(-sDir.y, sDir.x);\r\n // move screen vertex\r\n vec2 newPos = sPos + offset1 * position.w * lineWidth;\r\n // get moved pos in view space\r\n vec4 dNewPos = unproject(newPos, dPos.z, dPos.w);\r\n mvPosition.xyz = (projMatrixInv * dNewPos).xyz;\r\n#endif // THICK_LINE\r\n\r\n#ifdef INSTANCED_POS\r\n #ifdef SPHERE_SPRITE\r\n instOffset = offset;\r\n\r\n vec4 posEye = modelViewMatrix * vec4( offset.xyz, 1.0 );\r\n float scale = length(modelViewMatrix[0]);\r\n mvPosition = posEye + vec4( position.xyz * offset.w * scale * INSTANCED_SPRITE_OVERSCALE, 0.0 );\r\n posEye.w = offset.w * scale;\r\n\r\n spritePosEye = posEye;\r\n #else\r\n localPos = vec4( offset.xyz + position.xyz * offset.w, 1.0 );\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n #ifdef CYLINDER_SPRITE\r\n matVec1 = matVector1;\r\n matVec2 = matVector2;\r\n matVec3 = matVector3;\r\n invmatVec1 = invmatVector1;\r\n invmatVec2 = invmatVector2;\r\n invmatVec3 = invmatVector3;\r\n\r\n // calculate eye coords of cylinder endpoints\r\n vec4 v = vec4(0, -0.5, 0, 1);\r\n vec4 p1 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n v.y = 0.5;\r\n vec4 p2 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n\r\n // sprite is placed at the center of cylinder\r\n vec4 posEye;\r\n posEye.xyz = mix(p1.xyz, p2.xyz, 0.5);\r\n posEye.w = 1.0;\r\n spritePosEye = posEye;\r\n\r\n // cylinder radius in eye space\r\n float rad = length(modelViewMatrix[0]) * length(vec3(matVector1.x, matVector2.x, matVector3.x));\r\n vec2 spriteSize;\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // In ortho projection we skip z coordinate\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy - p1.xy);\r\n\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * (spriteSizeScreen + 2.0 * rad);\r\n #else\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy / p2.z - p1.xy / p1.z);\r\n\r\n // full sprite size in eye coords\r\n float minZ = min(abs(p1.z), abs(p2.z));\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * abs(posEye.z) * (spriteSizeScreen + 2.0 * rad / minZ);\r\n #endif\r\n\r\n mvPosition = posEye + vec4( position.xy * 0.5 * spriteSize, 0, 0 );\r\n #else\r\n localPos = vec4(dot(localPos, matVector1), dot(localPos, matVector2), dot(localPos, matVector3), 1.0);\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n gl_Position = projectionMatrix * mvPosition;\r\n\r\n vWorldPosition = worldPos.xyz;\r\n vViewPosition = - mvPosition.xyz;\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t vec4 worldPosition;\r\n\t // see THREE.WebGLProgram.unrollLoops\r\n\t #pragma unroll_loop_start\r\n\t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirectionalShadowCoord[ i ] = directionalShadowMatrix[ i ] * vec4(vWorldPosition, 1.0);\r\n vDirectionalShadowNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(objectNormal, 0.0))).xyz;\r\n\t }\r\n\t #pragma unroll_loop_end\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n vColor = color.xyz;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n vColor2 = color2;\r\n #ifndef CYLINDER_SPRITE\r\n vUv = uv;\r\n #endif\r\n#endif\r\n\r\n#ifdef DASHED_LINE\r\n vLineDistance = lineDistance;\r\n#endif\r\n}\r\n",fragmentShader:this.precisionString()+"/*\r\n * GLSL Version: ES 3.00 (WebGL 2.0 compatible)\r\n * No #version directive in this file (injected by Three.js).\r\n * Use GLSL3 semantics (`in`/`out`, `layout(location=...)`, `texture`).\r\n * Set `glslVersion: THREE.GLSL3` in ShaderMaterial/RawShaderMaterial.\r\n */\r\n\r\n#if defined (NORMALS_TO_G_BUFFER)\r\n layout(location = 0) out vec4 fragColor;\r\n layout(location = 1) out vec4 fragNormal;\r\n#else\r\n out vec4 fragColor;\r\n#endif\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n in float alphaCol;\r\n#endif\r\n\r\n#ifdef COLOR_FROM_POS\r\n uniform mat4 world2colorMatrix;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform sampler2D directionalShadowMap[ NUM_DIR_LIGHTS ];\r\n uniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ]; //only for sprites\r\n\t\tin vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tin vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n vec4 vDirLightWorldCoord[ NUM_DIR_LIGHTS ];\r\n vec3 vDirLightWorldNormal[ NUM_DIR_LIGHTS ];\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n // We use 4 instead uniform variable or define because this value is used in for(... i < value; ...) with\r\n // unroll_loop and unroll_loop has pattern:\r\n // /#pragma unroll_loop[\\s]+?for \\( int i \\= (\\d+)\\; i < (\\d+)\\; i \\+\\+ \\) \\{([\\s\\S]+?)(?=\\})\\}/g\r\n uniform vec2 samplesKernel[4]; // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n uniform sampler2D noiseTex;\r\n uniform vec2 noiseTexelSize;\r\n uniform vec2 srcTexelSize;\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n in vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n in vec3 vColor2;\r\n #ifndef CYLINDER_SPRITE\r\n in vec2 vUv;\r\n #endif\r\n#endif\r\n\r\nuniform vec3 diffuse;\r\nuniform vec3 emissive;\r\nuniform vec3 specular;\r\nuniform float shininess;\r\nuniform vec3 fixedColor;\r\nuniform float opacity;\r\nuniform float zClipValue;\r\nuniform float clipPlaneValue;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n in vec3 viewNormal;\r\n#endif\r\n\r\n#define RECIPROCAL_PI 0.31830988618\r\n#define saturate(a) clamp( a, 0.0, 1.0 )\r\n\r\n#ifdef USE_FOG\r\n uniform vec3 fogColor;\r\n uniform float fogAlpha;\r\n uniform float fogNear;\r\n uniform float fogFar;\r\n#endif\r\n\r\nin vec3 vWorldPosition; // world position of the pixel (invalid when INSTANCED_SPRITE is defined)\r\nin vec3 vViewPosition;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n in vec3 vNormal;\r\n#endif\r\n\r\n/////////////////////////////////////////// ZSprites ////////////////////////////////////////////////\r\n#if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n uniform float nearPlaneValue;\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n in vec4 spritePosEye;\r\n#endif\r\n\r\n#if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n uniform float zOffset;\r\n\r\n #if !defined(USE_LIGHTS) || !defined(SHADOWMAP) || !defined(SHADOWMAP_PCF_RAND) || !(NUM_DIR_LIGHTS > 0)\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\r\n float calcDepthForSprites(vec4 pixelPosEye, float zOffset, mat4 projMatrix) {\r\n vec4 pixelPosScreen = projMatrix * pixelPosEye;\r\n return 0.5 * (pixelPosScreen.z / pixelPosScreen.w + 1.0) + zOffset;\r\n }\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n in vec4 instOffset;\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n\r\n bool intersect_ray_sphere(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray, ray);\r\n float b = dot(ray, origin);\r\n float c = dot(origin, origin) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n // choose nearest point inside frustum\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all spheres the point with smaller 't' is visible\r\n // t1 is always smaller than t2 (from calculations)\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_sphere_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into sphere local coords\r\n origin = pixelPosEye.xyz - spritePosEye.xyz;\r\n origin = (invModelViewMatrix * vec4(origin, 0.0)).xyz / instOffset.w;\r\n\r\n // transform camera orientation vector into sphere local coords\r\n ray = (invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0)).xyz;\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n vec4 v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into sphere local coords\r\n v = invModelViewMatrix * v;\r\n origin = (v.xyz - instOffset.xyz) / instOffset.w;\r\n\r\n // transform vector from camera pos to curPixel into sphere local coords\r\n ray = (invModelViewMatrix * vec4(pixelPosEye, 0.0)).xyz;\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_sphere(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n in vec4 matVec1;\r\n in vec4 matVec2;\r\n in vec4 matVec3;\r\n in vec4 invmatVec1;\r\n in vec4 invmatVec2;\r\n in vec4 invmatVec3;\r\n\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n in vec4 spritePosEye;\r\n\r\n bool intersect_ray_cylinder(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray.xz, ray.xz);\r\n float b = dot(ray.xz, origin.xz);\r\n float c = dot(origin.xz, origin.xz) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n float halfHeight = 0.5;\r\n\r\n // choose nearest point\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all cylinders the point with smaller 't' is visible\r\n // if it is not outside of cylinnder (t1 is always smaller than t2).\r\n if (p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0 && p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0 && p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_cylinder_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n vec4 v;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye.xyz - spritePosEye.xyz, 0.0);\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform camera orientation vector into cylinder local coords\r\n v = invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into cylinder local coords\r\n v = invModelViewMatrix * v;\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform vector from camera pos to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_cylinder(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n///////////////////////////////////// Pack and unpack ///////////////////////////////////////////////\r\nconst float PackUpscale = 256. / 255.; // fraction -> 0..1 (including 1)\r\nconst float UnpackDownscale = 255. / 256.; // 0..1 -> fraction (excluding 1)\r\n\r\nconst vec3 PackFactors = vec3( 256. * 256. * 256., 256. * 256., 256. );\r\nconst vec4 UnpackFactors = UnpackDownscale / vec4( PackFactors, 1. );\r\n\r\n\r\nconst float ShiftRight8 = 1. / 256.;\r\n\r\nvec4 packDepthToRGBA( const in float v ) {\r\n vec4 r = vec4( fract( v * PackFactors ), v );\r\n r.yzw -= r.xyz * ShiftRight8; // tidy overflow\r\n return r * PackUpscale;\r\n}\r\n\r\nfloat unpackRGBAToDepth( const in vec4 v ) {\r\n return dot( v, UnpackFactors );\r\n}\r\n\r\n////////////////////////////////////////// All Lighting /////////////////////////////////////////////////\r\n#ifdef TOON_SHADING\r\n #define LOW_TOON_BORDER 0.0\r\n #define MEDIUM_TOON_BORDER 0.7\r\n #define HIGH_TOON_BORDER 1.0\r\n\r\n #define MEDIUM_TOON_RANGE 0.5\r\n #define HIGH_TOON_RANGE 0.95\r\n#endif\r\n#if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n struct ReflectedLight {\r\n vec3 directDiffuse;\r\n vec3 directSpecular;\r\n vec3 indirectDiffuse;\r\n };\r\n\r\n struct BlinnPhongMaterial {\r\n vec3 diffuseColor;\r\n vec3 specularColor;\r\n float specularShininess;\r\n };\r\n\r\n struct GeometricContext {\r\n vec3 normal;\r\n vec3 viewDir;\r\n };\r\n\r\n struct DirectionalLight {\r\n vec3 direction;\r\n vec3 color;\r\n };\r\n uniform DirectionalLight directionalLights[ NUM_DIR_LIGHTS ];\r\n\r\n struct DirectionalLightShadow {\r\n vec2 shadowMapSize;\r\n float shadowBias;\r\n float shadowRadius;\r\n };\r\n uniform DirectionalLightShadow directionalLightShadows[ NUM_DIR_LIGHTS ];\r\n\r\n uniform vec3 ambientLightColor;\r\n\r\n /////////////////////////////////////////// Shadowmap ////////////////////////////////////////////////\r\n\r\n #if defined(SHADOWMAP)\r\n \tfloat texture2DCompare( sampler2D depths, vec2 uv, float compare ) {\r\n \t\treturn step( compare, unpackRGBAToDepth( texture( depths, uv ) ) );\r\n \t}\r\n\r\n float getShadow( sampler2D shadowMap, DirectionalLightShadow dirLight, vec4 shadowCoord, vec3 vViewPosition, vec3 vNormal ) {\r\n \t float shadow = 0.0;\r\n\r\n // When shadows for sprites will appear use here for them normals as it done for G-buffer\r\n shadowCoord.xyz += dirLight.shadowBias * vNormal;\r\n shadowCoord.xyz /= shadowCoord.w;\r\n\r\n bvec4 inFrustumVec = bvec4 ( shadowCoord.x >= 0.0, shadowCoord.x <= 1.0, shadowCoord.y >= 0.0, shadowCoord.y <= 1.0 );\r\n bool inFrustum = all( inFrustumVec );\r\n bvec2 frustumTestVec = bvec2( inFrustum, shadowCoord.z <= 1.0 );\r\n bool frustumTest = all( frustumTestVec );\r\n\r\n if ( frustumTest ) {\r\n #ifdef SHADOWMAP_BASIC\r\n \t shadow = texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z );\r\n \t#endif\r\n\r\n \t#ifdef SHADOWMAP_PCF_SHARP\r\n \t vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n float dx0 = - texelSize.x * dirLight.shadowRadius;\r\n float dy0 = - texelSize.y * dirLight.shadowRadius;\r\n float dx1 = + texelSize.x * dirLight.shadowRadius;\r\n float dy1 = + texelSize.y * dirLight.shadowRadius;\r\n\r\n shadow = (\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z )\r\n ) * ( 1.0 / 9.0 );\r\n #endif\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n vec4 vUv = ((projectionMatrix * vec4(vViewPosition, 1.0)) + 1.0) / 2.0;\r\n vec2 vUvNoise = vUv.xy / srcTexelSize * noiseTexelSize;\r\n\r\n vec2 noiseVec = normalize(texture(noiseTex, vUvNoise).rg);\r\n mat2 mNoise = mat2(noiseVec.x, noiseVec.y, -noiseVec.y, noiseVec.x);\r\n\r\n vec2 offset;\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < 4; i ++ ) { // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n offset = mNoise * ( normalize( samplesKernel[ i ]) * texelSize * dirLight.shadowRadius );\r\n shadow += texture2DCompare( shadowMap, shadowCoord.xy + offset, shadowCoord.z );\r\n }\r\n #pragma unroll_loop_end\r\n shadow /= float( 4 ); // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n #endif\r\n }\r\n return shadow;//(shadow != 1.0) ? 0.5 : 1.0;//vec4(shadow, shadow, shadow, 1.0);\r\n }\r\n #endif\r\n\r\n /////////////////////////////////////////// Lighting /////////////////////////////////////////////////\r\n\r\n vec3 BRDF_Diffuse_Lambert( const in vec3 diffuseColor ) {\r\n return RECIPROCAL_PI * diffuseColor;\r\n } // validated\r\n\r\n vec3 F_Schlick( const in vec3 specularColor, const in float dotLH ) {\r\n // Original approximation by Christophe Schlick '94\r\n //;float fresnel = pow( 1.0 - dotLH, 5.0 );\r\n // Optimized variant (presented by Epic at SIGGRAPH '13)\r\n float fresnel = exp2( ( -5.55473 * dotLH - 6.98316 ) * dotLH );\r\n return ( 1.0 - specularColor ) * fresnel + specularColor;\r\n } // validated\r\n\r\n float G_BlinnPhong_Implicit( /* const in float dotNL, const in float dotNV */ ) {\r\n // geometry term is (n dot l)(n dot v) / 4(n dot l)(n dot v)\r\n return 0.25;\r\n }\r\n\r\n float D_BlinnPhong( const in float shininess, const in float dotNH ) {\r\n return RECIPROCAL_PI * ( shininess * 0.5 + 1.0 ) * pow( dotNH, shininess );\r\n }\r\n\r\n vec3 BRDF_Specular_BlinnPhong( const in DirectionalLight incidentLight, const in GeometricContext geometry, const in vec3 specularColor, const in float shininess ) {\r\n vec3 halfDir = normalize( incidentLight.direction + geometry.viewDir );\r\n float dotNH = saturate(dot( geometry.normal, halfDir ));\r\n float dotLH = saturate(dot( incidentLight.direction, halfDir ));\r\n\r\n vec3 F = F_Schlick( specularColor, dotLH );\r\n float G = G_BlinnPhong_Implicit( /* dotNL, dotNV */ );\r\n float D = D_BlinnPhong( shininess, dotNH );\r\n\r\n return F * ( G * D );\r\n } // validated\r\n\r\n void RE_Direct_BlinnPhong( const in DirectionalLight directLight, const in GeometricContext geometry, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight, float penumbra ) {\r\n\r\n float dotNL = saturate( dot( geometry.normal, directLight.direction ));\r\n #ifdef TOON_SHADING\r\n if(dotNL < MEDIUM_TOON_RANGE){\r\n dotNL = LOW_TOON_BORDER;\r\n }\r\n else if(dotNL < HIGH_TOON_RANGE){\r\n dotNL = MEDIUM_TOON_BORDER;\r\n }\r\n else{\r\n dotNL = HIGH_TOON_BORDER;\r\n }\r\n #endif\r\n\r\n vec3 irradiance = dotNL * directLight.color;\r\n reflectedLight.directDiffuse += penumbra * irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n reflectedLight.directSpecular += penumbra * irradiance * BRDF_Specular_BlinnPhong( directLight, geometry, material.specularColor, material.specularShininess );\r\n }\r\n\r\n void RE_IndirectDiffuse_BlinnPhong( const in vec3 irradiance, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) {\r\n reflectedLight.indirectDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n }\r\n\r\n vec3 calcLighting(const in GeometricContext geometry, const in BlinnPhongMaterial material, vec3 vViewPosition) {\r\n ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ));\r\n vec3 irradiance = ambientLightColor;\r\n\r\n float shadowMask = 1.0;\r\n // see THREE.WebGLProgram.unrollLoops\r\n \t#pragma unroll_loop_start\r\n \t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n \t #ifdef SHADOWMAP\r\n \t shadowMask = getShadow( directionalShadowMap[ i ], directionalLightShadows[ i ], vDirLightWorldCoord[ i ], vViewPosition, vDirLightWorldNormal[ i ] );\r\n #endif\r\n\r\n \t\t if ( shadowMask > 0.0 ) RE_Direct_BlinnPhong( directionalLights[ i ], geometry, material, reflectedLight, shadowMask );\r\n \t\t}\r\n \t\t#pragma unroll_loop_end\r\n\r\n RE_IndirectDiffuse_BlinnPhong(irradiance, material, reflectedLight);\r\n\r\n return saturate(reflectedLight.indirectDiffuse + reflectedLight.directDiffuse + reflectedLight.directSpecular);\r\n }\r\n#endif\r\n\r\n/////////////////////////////////////////// Dashed Line ///////////////////////////////////////////////\r\n#ifdef DASHED_LINE\r\n uniform float dashedLineSize;\r\n uniform float dashedLinePeriod;\r\n in float vLineDistance;\r\n#endif\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef CLIP_PLANE\r\n if (vViewPosition.z < clipPlaneValue) discard;\r\n#endif\r\n\r\n#ifdef ZCLIP\r\n if (vViewPosition.z < zClipValue) discard;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = vDirectionalShadowCoord[ i ];\r\n vDirLightWorldNormal[ i ] = vDirectionalShadowNormal[ i ];\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n#endif\r\n\r\n vec4 pixelPosWorld = vec4(vWorldPosition, 1.0);\r\n vec4 pixelPosEye;\r\n\r\n#ifdef SPHERE_SPRITE\r\n\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n vec3 normal;\r\n\r\n/* quick-and-dirty method\r\n normal.xy = ' + INSTANCED_SPRITE_OVERSCALE + ' * (2.0 * vUv - 1.0);\r\n float r2 = dot(normal.xy, normal.xy);\r\n if (r2 > 1.0) discard;\r\n float normalZ = sqrt(1.0 - r2);\r\n normal.z = normalZ;\r\n normal = normal * ( -1.0 + 2.0 * float( gl_FrontFacing ) );\r\n pixelPosEye = vec4(spritePosEye.xyz, 1.0);\r\n pixelPosEye.z += spritePosEye.w * normalZ;\r\n*/\r\n\r\n // ray-trace sphere surface\r\n {\r\n vec3 p;\r\n if (!get_sphere_point(-vViewPosition, p, frontFaced)) discard;\r\n vec4 v = vec4(instOffset.xyz + p * instOffset.w, 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n normal = normalize(normalMatrix * p);\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*p);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(p, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n vec3 normal;\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n float cylinderY = 0.0;\r\n\r\n // ray-trace cylinder surface\r\n {\r\n vec3 p;\r\n if (!get_cylinder_point(-vViewPosition, p, frontFaced)) discard;\r\n\r\n cylinderY = 0.5 * (p.y + 1.0);\r\n\r\n vec4 v = vec4(p, 1.0);\r\n v = vec4(dot(v, matVec1), dot(v, matVec2), dot(v, matVec3), 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n\r\n vec3 localNormal = normalize(vec3(p.x, 0.0, p.z));\r\n normal = vec3(\r\n dot(localNormal, matVec1.xyz),\r\n dot(localNormal, matVec2.xyz),\r\n dot(localNormal, matVec3.xyz));\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*normal);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(normal, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n\r\n normal = normalize(normalMatrix * normal);\r\n }\r\n#endif\r\n\r\n #ifdef ATTR_COLOR\r\n vec3 vertexColor = vColor;\r\n #else\r\n vec3 vertexColor = vec3(1.0, 1.0, 1.0);\r\n #endif\r\n\r\n #ifdef ATTR_COLOR2\r\n #ifdef CYLINDER_SPRITE\r\n float colorCoef = cylinderY; // cylinder parameter is calculated from ray-tracing\r\n #else\r\n float colorCoef = vUv.y; // cylinder parameter is interpolated as tex coord\r\n #endif\r\n // choose either color or color2\r\n vertexColor = mix(vColor2, vColor, step(0.5, colorCoef));\r\n #endif\r\n\r\n // negative red component is a special condition\r\n if (vertexColor.x < 0.0) discard;\r\n\r\n #ifdef DASHED_LINE\r\n if ( mod( vLineDistance, dashedLinePeriod ) > dashedLineSize ) discard;\r\n #endif\r\n\r\n // transparency prepass writes only z, so we don't need to calc the color\r\n #ifdef PREPASS_TRANSP\r\n fragColor = vec4(1.0, 1.0, 1.0, 1.0);\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n return;\r\n #endif\r\n\r\n float totalOpacity = opacity;\r\n\r\n #ifdef ATTR_ALPHA_COLOR\r\n totalOpacity *= alphaCol;\r\n #endif\r\n\r\n // discard fully transparent pixels\r\n if (totalOpacity == 0.0) discard;\r\n\r\n #ifdef FAKE_OPACITY\r\n // discard pixels in checker pattern\r\n vec2 dm_coord = floor(gl_FragCoord.xy);\r\n dm_coord = fract(dm_coord * 0.5);\r\n if (totalOpacity < 1.0 && (dm_coord.x < 0.5 ^^ dm_coord.y < 0.5)) discard;\r\n vec4 diffuseColor = vec4(diffuse, 1.0);\r\n #else\r\n vec4 diffuseColor = vec4(diffuse, totalOpacity);\r\n #endif\r\n\r\n float flipNormal;\r\n #if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n flipNormal = 1.0;\r\n #ifdef DOUBLE_SIDED\r\n flipNormal = float( gl_FrontFacing );\r\n #endif\r\n vec3 normal = normalize( vNormal ) * flipNormal;\r\n #endif\r\n\r\n diffuseColor.rgb *= vertexColor;\r\n\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n\r\n #ifdef NORMALS_TO_G_BUFFER\r\n #if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n vec3 viewNormaInColor = viewNormalSprites;\r\n #else\r\n vec3 viewNormaInColor = viewNormal;\r\n float frontFaced = float( gl_FrontFacing );\r\n #endif\r\n // [-1, 1] -> [0, 1]\r\n viewNormaInColor = 0.5 * viewNormaInColor + 0.5;\r\n fragNormal = vec4(viewNormaInColor, frontFaced);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n vec3 viewDir;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDir = -pixelPosEye.xyz;\r\n #else\r\n viewDir = vViewPosition;\r\n #endif\r\n GeometricContext geometry = GeometricContext(normal, normalize( viewDir ));\r\n BlinnPhongMaterial material = BlinnPhongMaterial(diffuseColor.rgb, specular, shininess);\r\n vec3 outgoingLight = calcLighting(geometry, material, viewDir);\r\n #else\r\n vec3 outgoingLight = diffuseColor.rgb;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_DEPTH\r\n float depth = 0.0;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n depth = gl_FragDepth;\r\n #else\r\n depth = gl_FragCoord.z;\r\n #endif\r\n fragColor = packDepthToRGBA(depth);\r\n return;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_POS\r\n fragColor = world2colorMatrix * pixelPosWorld;\r\n #else\r\n #ifdef OVERRIDE_COLOR\r\n fragColor = vec4(fixedColor, diffuseColor.a);\r\n #else\r\n fragColor = vec4(outgoingLight, diffuseColor.a);//vec4(vNormal, 1.0);\r\n #endif\r\n\r\n #ifdef USE_FOG\r\n float viewDistance;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDistance = abs(pixelPosEye.z);\r\n #else\r\n viewDistance = vViewPosition.z;\r\n #endif\r\n float fogFactor = smoothstep( fogNear, fogFar, viewDistance) * fogAlpha;\r\n #ifdef FOG_TRANSPARENT\r\n fragColor.a = fragColor.a * (1.0 - fogFactor);\r\n #else\r\n fragColor.rgb = mix( fragColor.rgb, fogColor, fogFactor );\r\n #endif\r\n #endif\r\n\r\n #endif\r\n}\r\n",uniforms:r.UniformsUtils.clone(Wn),lights:!0,fog:!0,side:r.DoubleSide}),this.setValues(e)}precisionString(){const{precision:e}=Dn;return`precision ${e} float;\nprecision ${e} int;\n\n`}copy(e){return super.copy(e),this.fragmentShader=e.fragmentShader,this.vertexShader=e.vertexShader,this.uniforms=r.UniformsUtils.clone(e.uniforms),this.defines={...e.defines},this.extensions=e.extensions,this.fog=e.fog,this.instancedPos=e.instancedPos,this.instancedMatrix=e.instancedMatrix,this.attrColor=e.attrColor,this.attrColor2=e.attrColor2,this.attrAlphaColor=e.attrAlphaColor,this.overrideColor=e.overrideColor,this.sphereSprite=e.sphereSprite,this.cylinderSprite=e.cylinderSprite,this.zClip=e.zClip,this.clipPlane=e.clipPlane,this.fakeOpacity=e.fakeOpacity,this.colorFromPos=e.colorFromPos,this.shadowmap=e.shadowmap,this.shadowmapType=e.shadowmapType,this.colorFromDepth=e.colorFromDepth,this.orthoCam=e.orthoCam,this.prepassTransparancy=e.prepassTransparancy,this.dashedLine=e.dashedLine,this.thickLine=e.thickLine,this.fogTransparent=e.fogTransparent,this.normalsToGBuffer=e.normalsToGBuffer,this.toonShading=e.toonShading,this.uberOptions.copy(e.uberOptions),this}createInstance(){const e=new qn;return e.copy(this),e.uberOptions=Object.create(this.uberOptions),e}setValues(e){if(void 0===e)return;super.setValues(e);const t={},r={};this.fog&&(t.USE_FOG=1),this.instancedPos&&(t.INSTANCED_POS=1),this.instancedMatrix&&(t.INSTANCED_MATRIX=1),this.attrColor&&(t.ATTR_COLOR=1),this.attrColor2&&(t.ATTR_COLOR2=1),this.attrAlphaColor&&(t.ATTR_ALPHA_COLOR=1),this.overrideColor&&(t.OVERRIDE_COLOR=1),this.sphereSprite&&(t.SPHERE_SPRITE=1,r.fragDepth=!0),this.cylinderSprite&&(t.CYLINDER_SPRITE=1,r.fragDepth=!0),this.zClip&&(t.ZCLIP=1),this.clipPlane&&(t.CLIP_PLANE=1),this.fakeOpacity&&(t.FAKE_OPACITY=1),this.lights&&(t.USE_LIGHTS=1),this.colorFromPos&&(t.COLOR_FROM_POS=1),this.shadowmap&&(t.SHADOWMAP=1,"pcf"===this.shadowmapType?t.SHADOWMAP_PCF_SHARP=1:"random"===this.shadowmapType?t.SHADOWMAP_PCF_RAND=1:t.SHADOWMAP_BASIC=1),this.colorFromDepth&&(t.COLOR_FROM_DEPTH=1),this.orthoCam&&(t.ORTHOGRAPHIC_CAMERA=1),this.prepassTransparancy&&(t.PREPASS_TRANSP=1),this.dashedLine&&(t.DASHED_LINE=1),this.thickLine&&(t.THICK_LINE=1),this.fogTransparent&&(t.FOG_TRANSPARENT=1),this.normalsToGBuffer&&(r.drawBuffers=!0,t.NORMALS_TO_G_BUFFER=1),this.toonShading&&(t.TOON_SHADING=1),this.defines=t,this.extensions=r}setUberOptions(e){if(void 0!==e)for(const t in e)e.hasOwnProperty(t)&&(this.uberOptions[t]instanceof r.Color?this.uberOptions[t]=e[t].clone():this.uberOptions[t]=e[t])}clone(e){return e?this.createInstance():super.clone()}updateUniforms(){const e=this;Yn.forEach((t=>{e.uniforms.hasOwnProperty(t)&&(e.uberOptions[t]instanceof r.Color||e.uberOptions[t]instanceof r.Matrix4?e.uniforms[t].value=e.uberOptions[t].clone():e.uniforms[t].value=e.uberOptions[t])}))}}qn.prototype.uberOptions=Xn;const Kn=qn;function Zn(e){class t extends e{constructor(...e){super(...e),this.onBeforeRender=t.prototype.onBeforeRender}onBeforeRender(e,t,r,n,s,i){this._onBeforeRender(e,t,r,n,s,i),this._update()}_onBeforeRender(){}_update(){const{material:e}=this;e&&e instanceof Kn&&e.updateUniforms()}}return t}const Qn=Zn(r.Mesh);const Jn=class extends Qn{constructor(...e){super(...e),this.castShadow=!0,this.receiveShadow=!0}_onBeforeRender(e,t,r,n,s,i){Qn.prototype._onBeforeRender.call(this,e,t,r);const{material:o}=this;o&&o.uniforms.invModelViewMatrix&&(this.modelViewMatrix.multiplyMatrices(r.matrixWorldInverse,this.matrixWorld),o.uniforms.invModelViewMatrix.value.copy(this.modelViewMatrix).invert(),o.uniforms.nearPlaneValue.value=r.near,o.uniformsNeedUpdate=!0)}},es=Zn(r.Mesh);class ts extends es{constructor(e,t){super(e,t),this.castShadow=!0,this.receiveShadow=!0}static _mvLength=new r.Vector3;static _center=new r.Vector3;static _modelView=new r.Matrix4;_onBeforeRender(e,t,r){es.prototype._onBeforeRender.call(this,e,t,r);const n=this.geometry,{material:s}=this;if(!n.zClip||!s.uberOptions)return;const i=ts._modelView,o=ts._mvLength,a=ts._center;i.multiplyMatrices(this.matrixWorld,r.matrixWorldInverse);const l=o.setFromMatrixColumn(i,0).length();a.copy(n.boundingSphere.center),this.localToWorld(a),s.uberOptions.zClipValue=r.position.z-a.z-l*(.5*n.boundingSphere.radius)}}const rs=ts;class ns extends r.Group{constructor(e,t){super(),this.geometry=e;const r=this;r.initialized=!1,this.geometry.addEventListener("update",(()=>{r.update()}))}init(){const{children:e}=this;for(let t=e.length-1;t>=0;--t)this.remove(e[t]);const{items:r,userData:n}=this.geometry;for(let e=0,s=r.length;e0?s:[new r.Matrix4];const o=this._createMeshes(e);for(let e=0,t=o.length;ee,adjust:function(e){let t=e>>16&255,r=e>>8&255,n=255&e;return.2126*t+.7152*r+.0722*n>127?(t=3*t/10,r=3*r/10,n=3*n/10):(t=255-3*(255-t)/10,r=255-3*(255-r)/10,n=255-3*(255-n)/10),t<<16|r<<8|n},inverse:function(e){return 255-(e>>16&255)<<16|255-(e>>8&255)<<8|255-(255&e)}};function Rs(e,t){let r;if(Ts.hasOwnProperty(t))r=O.hexColor(Ts[t](e));else{const e=parseInt(t,16);r=!Number.isNaN(e)&&t.toLowerCase().startsWith("0x")?O.hexColor(e):"#000000"}return r}const Ms={serial:e=>e.serial,name:e=>e.getVisualName(),elem:e=>e.element.name,residue:e=>e.residue.getType().getName(),sequence:e=>e.residue.getSequence(),chain:e=>e.residue.getChain().getName(),hetatm:e=>e.isHet(),water:e=>"HOH"===e.residue.getType().getName()||"WAT"===e.residue.getType().getName()},Ps=function(e,t){return t.replace(/\{\{(\s*\w+\s*)\}\}/g,(t=>{let r=t.replace(/\s+/g,"");return r=r.substring(2,r.length-2).toLowerCase(),Ms.hasOwnProperty(r)?Ms[r](e):"null"}))};const Ls=class extends Ss{_makeGeoArgs(){const e=this._mode.getLabelOpts();return[this._selection.chunks.length,e]}_build(){const e=this._mode.getLabelOpts(),t=this._selection.chunks,{atoms:r,parent:n}=this._selection,s=this._colorer,i=this._geo;for(let o=0,a=t.length;o{for(let t=0;t<=e;++t){const e=s[t],r=e.clone().sub(l).cross(c);i.addVectors(e,r),o[t]=Vs(e,i,c,n)}a.setItem(t,o),a.setColor(t,r)})),a.finalize()}_makeGeoArgs(){return this._segmentsHeight=this._polyComplexity,[Os(1,this._polyComplexity),this._segmentsHeight+1,this._selection.chunks.length]}};const ks=class extends Is{_build(){const e=this._geo,t=this._mode.getAromaticOffset();this._buildInner(t,((t,r,n)=>{let s=n[0];for(let r=1;r<=this._segmentsHeight;++r){const i=n[r];e.setSegment(t,r-1,s,i),s=i}e.setColor(t,r)})),e.finalize()}_makeGeoArgs(){return this._segmentsHeight=this._mode.getAromaticArcChunks(),[this._selection.chunks.length,this._segmentsHeight,!0]}};const zs=class extends ws{raycast(e,t){const{residues:r}=this._selection,n=[];this._mesh.raycast(e,n);const s=this._chunksIdc;for(let e=0,i=n.length;es&&e[t-1]._isValid?t-1:t}function a(t){return t{const t=e.getVisualName();a||t!==i?l||t!==o||(l=e.position):a=e.position})),a&&l||(a=n._firstAtom.position,l=n._lastAtom.position),a&&l){const s=l.clone().sub(a),i=n._wingVector,o=n._controlPoint,c=o.clone().add(i),h=o.clone().sub(s),u=h.clone().add(i);e[r]=[h.x,h.y,h.z],t[r]=[u.x,u.y,u.z],e[++r]=[h.x,h.y,h.z],t[r]=[u.x,u.y,u.z],e[++r]=[o.x,o.y,o.z],t[r]=[c.x,c.y,c.z],++r;const d=o.clone().add(s),p=d.clone().add(i);e[r]=[d.x,d.y,d.z],t[r]=[p.x,p.y,p.z],e[++r]=[d.x,d.y,d.z],t[r]=[p.x,p.y,p.z]}}(c,l,h,e[t]),{centerPoints:c,topPoints:l};t===d?u(t,a(t)):(Ws(c,l,h++,e[o(d)]),Ws(c,l,h++,e[d]));for(let n=t;n<=r;++n)Ws(c,l,h++,e[n]);return p===a(p)?u(r,o(r)):(Ws(c,l,h++,e[p]),Ws(c,l,h,e[a(p)])),{centerPoints:c,topPoints:l}}const Xs=class{constructor(e,t,r,n,s,i){const o=Ys(e,t,r,i);this._topInterp=$s(o.topPoints,s),this._centerInterp=$s(o.centerPoints,s),this._shift=.5/(r-t+2),this._valueStep=(1-2*this._shift)/(2*(r-t+1)*(n-1)),this._segmentsCount=n}prepareMatrices(e,t,n){const s=this._segmentsCount,i=new Array(s),o=new r.Vector2(0,0),a=this._topInterp,l=this._centerInterp;let c=this._shift+this._valueStep*(s-1)*e;for(let e=0;e{const c=n.getResidueColor(e,t);a[o]=e._index,i.setItem(o,r,s,l),i.setColor(o++,c)})),this._chunksIdc=a,i.finalize()}updateToFrame(e){const{parent:t}=this._selection,r=this._mode,n=this._colorer,s=r.getTension(),i=this._geo,o=e.getResidues();let a=0;const l=e.needsColorUpdate(n);Ks(this._selection.subdivs,o,this._segmentsHeight,s,r,((e,r)=>{i.setItem(a,r),l&&i.setColor(a,n.getResidueColor(e,t)),a++})),i.finalize()}};const Qs=class extends ws{_makeGeoArgs(){const e=this._selection.subdivs;let t=0;for(let r=0,n=e.length;r1&&0!==t&&(h.lerpVectors(_,g,ti/b),u.lerpVectors(_,g,1-ti/b)),t*=ti,h.addScaledVector(w,t),u.addScaledVector(w,t),o.setItem(d,h,u),o.setColor(d++,i.getAtomColor(m,n),i.getAtomColor(f,n))}}o.finalize(),this._chunksIdc=p}updateToFrame(e){const t=this._selection.chunks,{bonds:n}=this._selection,s=this._mode,i=this._colorer,o=this._geo,a=s.drawMultiorderBonds(),l=s.showAromaticLoops(),c=new r.Vector3,h=new r.Vector3,u=new r.Vector3;let d=0;const p=e.needsColorUpdate(i);for(let r=0,s=t.length;r1&&0!==r&&(h.lerpVectors(_,g,ti/b),u.lerpVectors(_,g,1-ti/b)),r*=ti,h.addScaledVector(w,r),u.addScaledVector(w,r),o.setItem(d,h,u),p&&o.setColor(d,e.getAtomColor(i,m),e.getAtomColor(i,f)),d++}}o.finalize()}}};const ni=class extends Xt{constructor(e,t,r,n,s,i,o,a){super();const l=this;this._complex=r,this._mode=s;const c=r.getAtoms(),h=r.getTransforms();r.forEachComponent((u=>{const d=[];let p=0;if(u.forEachAtom((e=>{l._checkAtom(e,o)&&(d[p++]=e.index)})),0===p)return;const m=new e(t,{atoms:c,chunks:d,parent:r},n,s,h,i,a);m._component=u,l.add(m)}))}_checkAtom(e,t){return e.mask&t}getSubset(e,t){const r=[],{children:n}=this;let s=0;for(let i=0,o=n.length;i{let d=0;const p=[];if(u.forEachResidue((e=>{l._checkResidue(e,o)&&(p[d++]=e._index)})),0===d)return;const m=new e(t,{residues:c,chunks:p,parent:r},n,s,h,i,a);m._component=u,l.add(m)}))}checkResidue(e,t){return e._mask&t}getSubset(e,t){const r=[],{children:n}=this;let s=0;for(let i=0,o=n.length;i{const d=u.getMaskedSubdivSequences(o);let p=0;const m=[];for(let e=0,t=d.length;e{const d=[];let p=0;if(u.forEachBond((e=>{const t=e._left,r=e._right;t.mask&o&&r.mask&o&&(d[p++]=e._index)})),0===p)return;const m=new e(t,{bonds:c,chunks:d,parent:r},n,s,h,i,a);m._component=u,l.add(m)}))}getSubset(e,t){const r=[],{children:n}=this;let s=0;for(let i=0,o=n.length;i{const d=[];let p=0;const m=[];let f=0;u.forEachCycle((e=>{const t=e.atoms;let r=0;for(let e=0,n=t.length;e0&&(m[f++]=e)}));const _=new e(t,{cycles:m,atoms:c,chunks:d,parent:r},n,s,h,i,a);_._component=u,l.add(_)}))}getSubset(e,t){const r=[],{children:n}=this;let s=0;for(let i=0,o=n.length;i0&&l.add(d)}return l}}lr(pi.prototype),pi.prototype.id="__",pi.prototype.depGroups=[];const mi=pi;function fi(){return{lineWidth:this.opts.lineWidth}}class _i extends mi{static id="LN";constructor(e){super(e),this.depGroups=this.depGroups.slice(0);const t=this.depGroups;for(let e=0,r=t.length;e=256?t-256:t))%this.chainColors.length,this.chainColors[t]}getSecondaryColor(e,t=!1){const r=this.secondaryColors[e];return void 0!==r||t?r:this.defaultSecondaryColor}getSequentialColor(e){const{colors:t}=this,r=t.length;return e<0?t[e%r+r]:t[e%r]}getGradientColor(e,t){const r=this.gradients[t];if(!r)return this.defaultNamedColor;const n=r.length,s=e*(n-1);let i=Math.floor(s);const o=Wi(i+1,0,n-1);return i=Wi(i,0,n-1),function(e,t,r){const n=1-r;return n*(e>>16&255)+r*(t>>16&255)<<16|n*(e>>8&255)+r*(t>>8&255)<<8|n*(255&e)+r*(255&t)}(r[i],r[o],s-i)}getNamedColor(e,t=!1){const r=this.namedColors[e];return void 0!==r||t?r:this.defaultNamedColor}}t().assign(Yi.prototype,{colors:[16777215,16711680,65280,255,8421504],minRangeColor:0,midRangeColor:8355711,maxRangeColor:16777215,defaultElementColor:16777215,elementColors:{},defaultResidueColor:16777215,residueColors:{},chainColors:[16777215],defaultSecondaryColor:16777215,secondaryColors:{},defaultGradientColor:0,defaultNamedColor:16777215,namedColorsArray:[["indianred",13458524],["lightcoral",15761536],["salmon",16416882],["darksalmon",15308410],["lightsalmon",16752762],["crimson",14423100],["red",16711680],["firebrick",11674146],["darkred",9109504],["pink",16761035],["lightpink",16758465],["hotpink",16738740],["deeppink",16716947],["mediumvioletred",13047173],["palevioletred",14381203],["coral",16744272],["tomato",16737095],["orangered",16729344],["darkorange",16747520],["orange",16753920],["gold",16766720],["yellow",16776960],["lightyellow",16777184],["lemonchiffon",16775885],["lightgoldenrodyellow",16448210],["papayawhip",16773077],["moccasin",16770229],["peachpuff",16767673],["palegoldenrod",15657130],["khaki",15787660],["darkkhaki",12433259],["lavender",15132410],["thistle",14204888],["plum",14524637],["violet",15631086],["orchid",14315734],["fuchsia",16711935],["magenta",16711935],["mediumorchid",12211667],["mediumpurple",9662683],["rebeccapurple",6697881],["blueviolet",9055202],["darkviolet",9699539],["darkorchid",10040012],["darkmagenta",9109643],["purple",8388736],["indigo",4915330],["slateblue",6970061],["mediumslateblue",8087790],["darkslateblue",4734347],["greenyellow",11403055],["chartreuse",8388352],["lawngreen",8190976],["lime",65280],["limegreen",3329330],["palegreen",10025880],["lightgreen",9498256],["mediumspringgreen",64154],["springgreen",65407],["mediumseagreen",3978097],["seagreen",3050327],["forestgreen",2263842],["green",32768],["darkgreen",25600],["yellowgreen",10145074],["olivedrab",7048739],["olive",8421376],["darkolivegreen",5597999],["mediumaquamarine",6737322],["darkseagreen",9419919],["lightseagreen",2142890],["darkcyan",35723],["teal",32896],["aqua",65535],["cyan",65535],["lightcyan",14745599],["paleturquoise",11529966],["aquamarine",8388564],["turquoise",4251856],["mediumturquoise",4772300],["darkturquoise",52945],["cadetblue",6266528],["steelblue",4620980],["lightsteelblue",11584734],["powderblue",11591910],["lightblue",11393254],["skyblue",8900331],["lightskyblue",8900346],["deepskyblue",49151],["dodgerblue",2003199],["cornflowerblue",6591981],["royalblue",4286945],["blue",255],["mediumblue",205],["darkblue",139],["navy",128],["midnightblue",1644912],["cornsilk",16775388],["blanchedalmond",16772045],["bisque",16770244],["navajowhite",16768685],["wheat",16113331],["burlywood",14596231],["tan",13808780],["rosybrown",12357519],["sandybrown",16032864],["goldenrod",14329120],["darkgoldenrod",12092939],["peru",13468991],["chocolate",13789470],["saddlebrown",9127187],["sienna",10506797],["brown",10824234],["maroon",8388608],["white",16777215],["snow",16775930],["honeydew",15794160],["mintcream",16121850],["azure",15794175],["aliceblue",15792383],["ghostwhite",16316671],["whitesmoke",16119285],["seashell",16774638],["beige",16119260],["oldlace",16643558],["floralwhite",16775920],["ivory",16777200],["antiquewhite",16444375],["linen",16445670],["lavenderblush",16773365],["mistyrose",16770273],["gainsboro",14474460],["lightgray",13882323],["silver",12632256],["darkgray",11119017],["gray",8421504],["dimgray",6908265],["lightslategray",7833753],["slategray",7372944],["darkslategray",3100495],["black",0]],namedColors:{},gradients:{rainbow:[255,65535,65280,16776960,16711680],temp:[255,32767,16777215,16744192,16711680],hot:[16777215,16744192,16711680],cold:[16777215,32767,255],"blue-red":[255,16777215,16711680],reds:[16777215,16711680],blues:[16777215,255]}});const{namedColorsArray:Xi,namedColors:qi}=Yi.prototype;for(let e=0,{length:t}=Xi;e=0?this.opts.carbon:this.palette.getElementColor(r)}getResidueColor(e,t){return this.palette.defaultResidueColor}}ao.prototype.id="EL",ao.prototype.name="Element",ao.prototype.shortName="Element";const lo=ao;class co extends oo{static id="RT";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){return this.palette.getResidueColor(e._type._name)}}co.prototype.id="RT",co.prototype.name="Residue Type",co.prototype.shortName="Residue";const ho=co;class uo extends oo{static id="SQ";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){const r=e._chain;if(r.minSequence===Number.POSITIVE_INFINITY&&r.maxSequence===Number.NEGATIVE_INFINITY)return this.palette.defaultNamedColor;const n=r.minSequence,s=r.maxSequence>n?r.maxSequence:n+1;return this.palette.getGradientColor((e._sequence-n)/(s-n),this.opts.gradient)}}uo.prototype.id="SQ",uo.prototype.name="Sequence",uo.prototype.shortName="Sequence";const po=uo;class mo extends oo{static id="CH";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){return this.palette.getChainColor(e.getChain()._name)}}mo.prototype.id="CH",mo.prototype.name="Chain",mo.prototype.shortName="Chain";const fo=mo;class _o extends oo{static id="SS";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){if(e._type.flags&ve.Flags.DNA)return this.palette.getSecondaryColor("dna");if(e._type.flags&ve.Flags.RNA)return this.palette.getSecondaryColor("rna");const r=e.getSecondary();if(r){let e=this.palette.getSecondaryColor(r.type,!0);return void 0===e&&(e=this.palette.getSecondaryColor(r.generic)),e}return this.palette.defaultSecondaryColor}}_o.prototype.id="SS",_o.prototype.name="Secondary Structure",_o.prototype.shortName="Structure";const go=_o;class yo extends oo{static id="UN";getAtomColor(e,t){return this.opts.color}getResidueColor(e,t){return this.opts.color}}yo.prototype.id="UN",yo.prototype.name="Uniform",yo.prototype.shortName="Uniform";const xo=yo;class bo extends oo{static id="CO";constructor(e){super(e);const t=st.parse(this.opts.subset);this._subsetCached=t.error?st.none():t.selector}getAtomColor(e,t){return this._subsetCached.includesAtom(e)?this.opts.color:this.opts.baseColor}getResidueColor(e,t){const r=this._subsetCached,n=e._atoms;for(let e=0,t=n.length;er.max?1:0:(e.temperature-r.min)/(r.max-r.min),this.palette.getGradientColor(n,r.gradient)):this.palette.defaultGradientColor}getResidueColor(e,t){const{opts:r}=this;if(!r)return this.palette.defaultGradientColor;if(e.temperature){let t=0;return t=r.min===r.max?e.temperature>r.max?1:0:(e.temperature-r.min)/(r.max-r.min),this.palette.getGradientColor(t,r.gradient)}return this.palette.defaultGradientColor}}Co.prototype.id="TM",Co.prototype.name="Temperature",Co.prototype.shortName="Temperature";const Ao=Co;class Eo extends oo{static id="OC";_getColorByOccupancy(e,t){if(void 0!==e){const r=1-e;return this.palette.getGradientColor(r,t.gradient)}return this.palette.defaultGradientColor}getAtomColor(e,t){const{opts:r}=this;return this._getColorByOccupancy(e.occupancy,r)}getResidueColor(e,t){const{opts:r}=this;return this._getColorByOccupancy(e.occupancy,r)}}Eo.prototype.id="OC",Eo.prototype.name="Occupancy",Eo.prototype.shortName="Occupancy";const To=Eo;class Ro extends oo{static id="HY";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){let r=this.palette.defaultResidueColor;if(void 0!==e._type.hydrophobicity){const t=-4.5,n=4.5;r=this.palette.getGradientColor((e._type.hydrophobicity-t)/(n-t),this.opts.gradient)}return r}}Ro.prototype.id="HY",Ro.prototype.name="Hydrophobicity",Ro.prototype.shortName="Hydrophobicity";const Mo=Ro;class Po extends oo{static id="MO";getAtomColor(e,t){return this.getResidueColor(e.residue,t)}getResidueColor(e,t){const r=e._molecule,n=t.getMoleculeCount();return n>1?this.palette.getGradientColor((r.index-1)/(n-1),this.opts.gradient):this.palette.getGradientColor(0,this.opts.gradient)}}Po.prototype.id="MO",Po.prototype.name="Molecule",Po.prototype.shortName="Molecule";const Lo=Po;class No extends oo{static id="CB";getAtomColor(e,t){const r=this.opts.color,n=(s=r,(i=this.opts.factor)*(s>>16&255)<<16|i*(s>>8&255)<<8|i*(255&s));var s,i;return e.flags&ae.Flags.CARBON?r:n}getResidueColor(e,t){return this.opts.color}}No.prototype.id="CB",No.prototype.name="Carbon",No.prototype.shortName="Carbon";const Io=new ar([lo,ho,po,fo,go,xo,wo,vo,Ao,To,Mo,Lo,No]);function Oo(e){return new r.Color(e,e,e)}const Vo=[{id:"DF",name:"Diffuse",shortName:"Diffuse",uberOptions:{diffuse:Oo(1),specular:Oo(0),shininess:1,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!1}},{id:"SF",name:"Soft Plastic",shortName:"Soft",uberOptions:{diffuse:Oo(1),specular:Oo(.1),shininess:30,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!1}},{id:"PL",name:"Glossy Plastic",shortName:"Glossy",uberOptions:{diffuse:Oo(.56),specular:Oo(.28),shininess:100,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!1}},{id:"ME",name:"Metal",shortName:"Metal",uberOptions:{diffuse:Oo(.56),specular:Oo(.55),shininess:30,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!1}},{id:"TR",name:"Transparent",shortName:"Transparent",uberOptions:{diffuse:Oo(1),specular:Oo(0),shininess:1,opacity:.5},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!0,toonShading:!1}},{id:"GL",name:"Glass",shortName:"Glass",uberOptions:{diffuse:Oo(.5),specular:Oo(.65),shininess:100,opacity:.5},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!0,toonShading:!1}},{id:"BA",name:"Backdrop",shortName:"Backdrop",uberOptions:{diffuse:Oo(1),specular:Oo(0),shininess:1,opacity:1},values:{lights:!1,fog:!1,depthWrite:!1,transparent:!1,toonShading:!1}},{id:"TN",name:"Toon",shortName:"Toon",uberOptions:{diffuse:Oo(1),specular:Oo(0),shininess:1,opacity:1},values:{lights:!0,fog:!0,depthWrite:!0,transparent:!1,toonShading:!0}},{id:"FL",name:"Flat",shortName:"Flat",uberOptions:{diffuse:Oo(1),specular:Oo(0),shininess:0,opacity:1},values:{lights:!1,fog:!0,depthWrite:!0,transparent:!1}}],Do=new ar(Vo);function ko(e,t,r){const n=e.material.createInstance();n.setValues(t);const s=new e.constructor(e.geometry,n);return s.material.needsUpdate=!0,s.applyMatrix4(e.matrix),s.layers.set(r),s}function zo(e,t,r){const n=function(e,t){const r=[];return e.traverse((e=>{for(let n=0;n{e.applyMatrix4(t[0]);for(let r=1;r{t.material.setValues({prepassTransparancy:!1,fakeOpacity:!1}),t.material.needsUpdate=!0,t.layers.set(tr.LAYERS.TRANSPARENT);const r=ko(t,e,tr.LAYERS.PREPASS_TRANSPARENT);t.parent.add(r)}))}}(),processColFromPosMaterial:function(){const e={colorFromPos:!0,transparent:!1,colorFromDepth:!1,lights:!1,shadowmap:!1,fog:!1,overrideColor:!1,fogTransparent:!1,attrColor:!1,attrColor2:!1,attrAlphaColor:!1,fakeOpacity:!1};return function(t,n){n instanceof Kn&&zo(t,[r.Mesh,r.LineSegments],(t=>{const r=ko(t,e,tr.LAYERS.COLOR_FROM_POSITION);t.parent.add(r)}))}}(),createShadowmapMaterial:function(){const e={colorFromDepth:!0,orthoCam:!0,lights:!1,shadowmap:!1,fog:!1};return function(t,n){n instanceof Kn&&zo(t,[r.Mesh,r.LineSegments],(t=>{if(!t.receiveShadow&&t.material.shadowmap&&t.material.setValues({shadowmap:!1}),!t.material.lights)return;if(!t.castShadow)return;if(!tr.belongToSelectLayers(t))return;const r=ko(t,e,tr.LAYERS.SHADOWMAP);r.isShadowmapMesh=!0,t.parent.add(r)}))}}(),removeShadowmapMaterial:function(e,t){t instanceof Kn&&zo(e,[r.Mesh,r.LineSegments],(e=>{e.isShadowmapMesh&&e.parent.remove(e)}))},forEachMeshInGroup:Fo,countTriangles:function(e){let t=0;return Fo(e,(e=>{t+=function(e){const t=e.geometry;if(t instanceof r.InstancedBufferGeometry){const e=t.attributes;for(const n in e)if(e.hasOwnProperty(n)&&e[n]instanceof r.InstancedBufferAttribute){const r=e[n];return(t.index?t.index.array.length/3:0)*r.array.length/r.itemSize}return 0}return t instanceof r.BufferGeometry?t.index?t.index.array.length/3:0:t.faces?t.faces.length:0}(e)})),t}},{selectors:Uo}=Ht;const Go=class{constructor(e,t,r,n){const s={clipPlane:z.now.draft.clipPlane,fogTransparent:z.now.bg.transparent,shadowmap:z.now.shadow.on,shadowmapType:z.now.shadow.type};this.index=e,this.mode=t,this.colorer=r,this.selector=n,this.selectorString="",this.count=0,this.material=new Kn,this.material.setValues(s),this.material.setUberOptions({fogAlpha:z.now.fogAlpha}),this.materialPreset=Do.first,this.needsRebuild=!0,this.visible=!0,this.setMode(t)}markAtoms(e){return this.count=e.markAtoms(this.selector,1<0){t=new r.Group,t.matrixAutoUpdate=!1,t.matrix=this.geo.matrix;for(let e=0;e{e.objects.push(t)})),o=0;o{const t=e._atoms;for(a=0;a{const r=e._atoms;for(let e=0;e2)return w.error("Can only edit fragments with one or two bound atoms."),!1;this._fragmentBoundAtoms=n;const s=1<{e._left.mask&t?0===(e._right.mask&t)&&(r[e._left.index]=1):e._right.mask&t&&(r[e._right.index]=1)}));const n=[],s=Object.keys(r);for(let t=0,r=s.length;t{r.mask&t&&r.position.applyMatrix4(e)}))}}},{selectors:Wo}=Ht;function Yo(e,t){Array.isArray(t)||(t=[t]);const[r,n]=t;return new(e.get(r)||e.first)(n)}class Xo extends sr{constructor(e,t){super(e,t),this._complex=t,this._reprList=[],this._repr=null,this._reprListChanged=!0,this._selectionBit=0,this._reprUsedBits=0,this._selectionCount=0,this._selectionGeometry=new r.Group}getBoundaries(){return this._complex.getBoundaries()}release(){this._selectionGeometry.parent&&this._selectionGeometry.remove(this._selectionGeometry),sr.prototype.release.call(this)}getComplex(){return this._complex}getSelectionCount(){return this._selectionCount}getSelectionGeo(){return this._selectionGeometry}getSelectionBit(){return this._selectionBit}getEditor(){return this._editor}resetReps(e){this._complex&&this._complex.clearAtomBits(-1),this._reprListChanged=!0,this._reprUsedBits=0,this._reprList.length=e.length;for(let t=0,r=e.length;t0?this._reprList[0]:null,this._selectionBit=e.length,this._reprUsedBits|=1<=0&&ethis._reprList.length)return w.error(`Rep ${e} does not exist!`),null;if(e===this._reprList.length){const t=this.repAdd(r);return w.warn(`Rep ${e} does not exist! New representation was created.`),{desc:t.desc,index:e,status:"created"}}const n=this._reprList[e],s={selector:n.selectorString,mode:n.mode.identify(),colorer:n.colorer.identify(),material:n.materialPreset.id};if(r){const i=n.change(r,this._complex,Yo($i,r.mode),Yo(Io,r.colorer));if(!t().isEmpty(i)){n.needsRebuild=!0;for(const t in i)i.hasOwnProperty(t)&&(s[t]=i[t],w.debug(`rep[${e}].${t} changed to ${i[t]}`));return i.mode&&n.mode.isSurface&&("ultra"===z.now.resolution||"high"===z.now.resolution)&&(w.report('Surface resolution was changed to "medium" to avoid hang-ups.'),z.set("resolution","medium")),{desc:s,index:e,status:"changed"}}}return{desc:s,index:e,status:""}}repGet(e){return(void 0===e||e instanceof Object)&&(e=this.repCurrent()),e<0||e>=this._reprList.length?null:this._reprList[e]}_getFreeReprIdx(){let e=this._reprUsedBits;for(let t=0;t<=Xo.NUM_REPRESENTATION_BITS;++t,e>>=1)if(!(1&e))return t;return-1}repAdd(e){if(this._reprList.length>=Xo.NUM_REPRESENTATION_BITS)return null;const r=this._getFreeReprIdx();if(r<0)return null;const n=this.buildSelectorFromMask(1<=t||t<=1)return;const r=this._reprList[e];r.unmarkAtoms(this._complex),this._reprUsedBits&=~(1<=this._reprList.length)return;this._reprList[e].show(!t)}select(e,t){t?this._selectionCount+=this._complex.markAtomsAdditionally(e,1<{e.mask&o&&(e.mask&=a,t._selectionCount--)}))):(n._mask|=o,n.forEachAtom((e=>{e.mask&o||(e.mask|=o,t._selectionCount++)})),s.collectMask(),i&&i.collectMask());else if(s||i){const e=s||i;e._mask&o?(e._mask&=a,e.forEachResidue((e=>{e._mask&o&&(e._mask&=a,e.forEachAtom((e=>{e.mask&o&&(e.mask&=a,t._selectionCount--)})),e._mask&=a)}))):(e._mask|=o,e.forEachResidue((e=>{if(!(e._mask&o)){e._mask|=o,e.forEachAtom((e=>{e.mask&o||(e.mask|=o,t._selectionCount++)}));const r=s?e.getMolecule():e.getChain();r&&r.collectMask()}})))}else this.resetSelectionMask()}expandSelection(){const e=this,t=1<{e._left.mask&t?0===(e._right.mask&t)&&(e._right.mask|=r):e._right.mask&t&&(e._left.mask|=r)}));const n=~r;this._complex.forEachAtom((s=>{s.mask&r&&(s.mask=s.mask&n|t,++e._selectionCount)})),this._complex.updateStructuresMask()}shrinkSelection(){const e=this,t=1<{e._left.mask&t?0===(e._right.mask&t)&&(e._left.mask|=r):e._right.mask&t&&(e._right.mask|=r)})),this._complex.forEachAtom((e=>{e.mask&t&&1===e.bonds.length&&(e.mask|=r)}));const n=~(t|r);this._complex.forEachAtom((t=>{t.mask&r&&(t.mask&=n,--e._selectionCount)})),this._complex.updateStructuresMask()}getSelectedComponent(){const e=1<{n.mask&e&&(null===t?t=n.residue._component:t!==n.residue._component&&(r=!0))})),r?null:t}getSelectionCenter(e,t,r){e.set(0,0,0);let n=0;return this._complex.forEachAtom((s=>{t(s,r)&&(e.add(s.position),n++)})),0!==n&&(e.divideScalar(n),e.applyMatrix4(this.matrix),!0)}needsRebuild(){if(this._reprListChanged)return!0;const e=this._reprList;for(let t=0,r=e.length;t{const r=e._complex;if(!r)return void t();let n=!1;setTimeout((()=>{const s=e._reprList,i=so.get(z.now.palette)||so.first;let o=!1;for(let t=0,a=s.length;t0&&(n=Wo.chain(r),i=i?Wo.or(i,n):n),Object.keys(t).length>0)for(const e in t)t.hasOwnProperty(e)&&(n=Wo.and(Wo.chain(e),Wo.residx(s(t[e]))),i=i?Wo.or(i,n):n);e.length>0&&(n=Wo.serial(s(e)),i=i?Wo.or(i,n):n),i||(i=Wo.none())}return i}buildSelectorFromMask(e){const t=this._complex,r=[],n={},s=[];return t.forEachChain((t=>{t._mask&e&&r.push(t._name)})),t.forEachResidue((t=>{if(t._mask&e&&!(t._chain._mask&e)){const e=t._chain._name;e in n?n[e].push(t._index):n[e]=[t._index]}})),t.forEachAtom((t=>{t.mask&e&&!(t.residue._mask&e)&&s.push(t.serial)})),this._buildSelectorFromSortedLists(s,n,r)}forSelectedResidues(e){const t=1<{r._mask&t&&e(r)}))}beginComponentEdit(){if(this._editor)return null;const e=new $o.ComponentEditor(this);return e.begin()?(this._editor=e,e):null}beginFragmentEdit(){if(this._editor)return null;const e=new $o.FragmentEditor(this);return e.begin()?(this._editor=e,e):null}finalizeEdit(){this._editor=null}setMaterialValues(e,t=!1,n=void 0){for(let s=0,i=this._reprList.length;s{t instanceof r.Mesh&&(t.material.setValues(e),void 0!==n&&n(t),t.material.needsUpdate=!0)}))}}setUberOptions(e){for(let t=0,r=this._reprList.length;t{e.mask|=n})),this._selectionCount=this._complex.countAtomsByMask(n),this._complex.updateStructuresMask(),this.buildSelectorFromMask(n)}}Xo.NUM_REPRESENTATION_BITS=30;const qo=Xo,Ko=r.UniformsUtils.merge([{volumeDim:{type:"v3",value:new r.Vector3(512,512,512)},tileTex:{type:"t",value:null},tileTexSize:{type:"v2",value:new r.Vector2(512,512)},tileStride:{type:"v2",value:new r.Vector2(512,512)},boxAngles:{type:"v3",value:new r.Vector3(1,1,1)},delta:{type:"v3",value:new r.Vector3(0,0,0)},_isoLevel0:{type:"v2",value:new r.Vector3(.5,.75,1)},_flipV:{type:"f",value:0},_BFLeft:{type:"t",value:null},_BFRight:{type:"t",value:null},_FFLeft:{type:"t",value:null},_FFRight:{type:"t",value:null},_WFFLeft:{type:"t",value:null},_WFFRight:{type:"t",value:null}}]);function Zo(e,t){const n=r.UniformsUtils.clone(t);for(const t in e)n.hasOwnProperty(t)&&(n[t].value=e[t]);return n}function Qo(e,t){return{uniforms:Zo(e,{}),vertexShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec3 pos;\r\n\r\nvoid main() {\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n pos = position.xyz + 0.5;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n}",fragmentShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec3 pos;\r\n\r\nvoid main() {\r\n gl_FragColor = vec4(pos, 0.5);\r\n}",transparent:!1,depthTest:!1,depthWrite:!1,side:t}}class Jo extends r.ShaderMaterial{constructor(e){super(Qo(e,r.BackSide))}}class ea{constructor(e,t,n,s){this.uniforms=Zo(e,t),this.vertexShader=n,this.fragmentShader=s,this.transparent=!1,this.depthTest=!1,this.depthWrite=!1,this.side=r.FrontSide}}class ta extends r.ShaderMaterial{constructor(e){const t=r.UniformsUtils.merge([{aspectRatio:{type:"f",value:0},farZ:{type:"f",value:0},tanHalfFOV:{type:"f",value:0},matWorld2Volume:{type:"4fv",value:new r.Matrix4}}]);super(new ea(e,t,"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 volPos;\r\nuniform float aspectRatio;\r\nuniform float farZ;\r\nuniform float tanHalfFOV;\r\nuniform mat4 matWorld2Volume;\r\n\r\nvoid main() {\r\n // rescale plane to fill in the whole far plane area seen from camera\r\n vec3 pos = position.xyz;\r\n pos.x = pos.x * tanHalfFOV * farZ * aspectRatio;\r\n pos.y = pos.y * tanHalfFOV * farZ;\r\n // common transformation\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(pos, 1.0);\r\n // calc pos in volume CS\r\n volPos = matWorld2Volume * modelMatrix * vec4(pos, 1.0);\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n volPos = volPos + 0.5;\r\n volPos.w = 0.5;\r\n}\r\n","/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 volPos;\r\n\r\nvoid main() {\r\n gl_FragColor = volPos;\r\n}"))}}class ra extends r.ShaderMaterial{constructor(e){super(Qo(e,r.FrontSide))}}class na extends r.ShaderMaterial{constructor(e){const t=new ea(e,Ko,"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\nvoid main() {\r\n screenSpacePos = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n gl_Position = screenSpacePos;\r\n}","/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nuniform mat4 projectionMatrix;\r\n\r\n// 3D volume texture\r\nuniform vec3 volumeDim; // volume dimensions, pixels\r\nuniform sampler2D tileTex; // tiled texture containing all Z-slices of a 3D data\r\nuniform vec2 tileTexSize; // size of tiled texture, pixels\r\nuniform vec2 tileStride; // UV stride between slices in tile tex, pixels\r\n\r\nuniform vec3 boxAngles;//value of angles({x: alpha, y:beta, z:gamma}) types 1 - if angle is obtuse, 0 - if acute\r\nuniform vec3 delta; //Projection box delta's from non-orthogonal origin axes; {x: XY, y : XZ, z: YZ}\r\n\r\nuniform vec3 _isoLevel0;\r\nuniform float _flipV;\r\nuniform sampler2D _BFLeft;\r\nuniform sampler2D _BFRight;\r\nuniform sampler2D _FFLeft;\r\nuniform sampler2D _FFRight;\r\nuniform sampler2D _WFFLeft;\r\nuniform sampler2D _WFFRight;\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\n#define NO_COLOR vec4(0., 0., 0., 0.)\r\n\r\nvec4 sample3DTexture(vec3 texCoord) {\r\n // a pair of Z slices is determined by nearest slice border\r\n float zSliceBorder = floor(texCoord.z * volumeDim.z + 0.5);\r\n float zSliceNumber1 = max(zSliceBorder - 1.0, 0.0);\r\n float zSliceNumber2 = min(zSliceBorder, volumeDim.z - 1.0);\r\n\r\n float rowTiles = floor(tileTexSize.x / tileStride.x);\r\n\r\n // calculate coords in tile texture for both slices\r\n vec2 tileOffset = vec2(mod(zSliceNumber1, rowTiles), floor(zSliceNumber1 / rowTiles));\r\n vec2 texCoordSlice1 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n tileOffset = vec2(mod(zSliceNumber2, rowTiles), floor(zSliceNumber2 / rowTiles));\r\n vec2 texCoordSlice2 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n\r\n // bilinear filtering\r\n vec4 colorSlice1 = texture2D(tileTex, texCoordSlice1);\r\n vec4 colorSlice2 = texture2D(tileTex, texCoordSlice2);\r\n float weightSlice2 = texCoord.z * volumeDim.z - (zSliceNumber1 + 0.5);\r\n return mix(colorSlice1, colorSlice2, weightSlice2);\r\n}\r\n\r\nvec4 sample3DTextureInclined(vec3 boxCoord) { // delta:{ x: XY, y : XZ, z: YZ }\r\n vec3 textCoord = boxCoord;\r\n vec2 currDelta = mix(boxCoord.zz, vec2(1., 1.) - boxCoord.zz, boxAngles.yx) * delta.yz;\r\n\r\n textCoord.y = (boxCoord.y - currDelta.y) / (1. - delta.z);\r\n if (textCoord.y < 0.0 || textCoord.y > 1.0)\r\n return NO_COLOR;\r\n\r\n currDelta.x += mix(textCoord.y, 1.0 - textCoord.y, boxAngles.z) * delta.x;\r\n\r\n textCoord.x = (boxCoord.x - currDelta.x) / (1. - delta.x - delta.y);\r\n if (textCoord.x < 0.0 || textCoord.x > 1.0)\r\n return NO_COLOR;\r\n\r\n return sample3DTexture(textCoord);\r\n}\r\n\r\nfloat CalcColor(vec3 iter, vec3 dir) {\r\n float d = 1. / 128.;\r\n vec3 dx = vec3(d, 0.0, 0.0);\r\n vec3 dy = vec3(0.0, d, 0.0);\r\n vec3 dz = vec3(0.0, 0.0, d);\r\n\r\n // #Opt: coordInc.x:(iter + dx).x > 1. ? 0.: sample3DTextureInclined(iter + dx).x,\r\n vec3 coordInc = mix(\r\n vec3(\r\n sample3DTextureInclined(iter + dx).x,\r\n sample3DTextureInclined(iter + dy).x,\r\n sample3DTextureInclined(iter + dz).x\r\n ),\r\n vec3(0. ,0. , 0.),\r\n vec3(floor((iter + dx).x), floor((iter + dy).y), floor((iter + dz).z))\r\n );\r\n\r\n // #Opt: coordDec.x:(iter - dx).x < 0. ? 0.: sample3DTextureInclined(iter - dx).x,\r\n vec3 coordDec = mix(\r\n vec3(0. ,0. , 0.),\r\n vec3(\r\n sample3DTextureInclined(iter - dx).x,\r\n sample3DTextureInclined(iter - dy).x,\r\n sample3DTextureInclined(iter - dz).x\r\n ),\r\n vec3(ceil((iter - dx).x), ceil((iter - dy).y), ceil((iter - dz).z))\r\n );\r\n\r\n vec3 N = normalize(coordInc - coordDec);\r\n float dif = max(0.0, dot(N, dir));\r\n return dif;\r\n}\r\n\r\nvec3 AccuracyIso(vec3 left, vec3 right, float volLeft, float threshold) {\r\n for (int i = 0; i < 5; i++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if ((volLeft - threshold) * (vol - threshold) < 0.)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec3 CorrectIso(vec3 left, vec3 right, float tr) {\r\n for (int j = 0; j < 5; j++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if (vol < tr)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec4 GetIso1(vec3 start, vec3 back, float molDist, vec3 dir, float tr, int count) {\r\n float vol, stepSize = (float(count) + 2.) / float(STEPS_COUNT);\r\n vec3 step = stepSize * dir, iterator = start, left, right;\r\n vec4 acc = NO_COLOR;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n vol = sample3DTextureInclined(iterator).r;\r\n if (length(iterator - back) <= stepSize || (vol > tr))\r\n break;\r\n }\r\n\r\n if (vol > tr)\r\n acc = vec4(CorrectIso(iterator, iterator - step, tr).xyz, 1.);\r\n\r\n return acc;\r\n}\r\n\r\nfloat easeOut(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return 1.0 - (1.0 - t) * (1.0 - t);\r\n}\r\n\r\nfloat easeIn(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return t * t;\r\n}\r\n\r\nvec3 GetColSimple(float vol) {\r\n float t = easeOut(_isoLevel0.x, _isoLevel0.y, vol);\r\n float s = easeIn(_isoLevel0.y, _isoLevel0.z, vol);\r\n return vec3(0.5, 0.6, 0.7) * (1.0 - t) + 2.0 * vec3(s, 0, 0);\r\n}\r\n\r\nvec4 VolRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 acc = NO_COLOR, iso;\r\n vec3 iterator = start, sumColor = vec3(0., 0., 0.);\r\n float stepSize, alpha, sumAlpha = 0.0, vol, curStepSize, molD;\r\n vec3 step, col, colOld, right;\r\n float tr0 = _isoLevel0.x;\r\n float dif, r, kd, finish;\r\n int count = 0, stopMol = 0;\r\n\r\n for (int k = 0; k < 3; k++) {\r\n stepSize = (float(k) + 2.) / float(STEPS_COUNT);\r\n kd = 140. * tr0 * stepSize;\r\n r = 1. - kd;\r\n step = stepSize * dir;\r\n iso = GetIso1(iterator, back, molDist, dir, tr0, k);\r\n if (iso.a < 0.1 || length(iso.xyz - start) > molDist)\r\n break;\r\n iterator = iso.xyz;\r\n dif = 1.;// CalcColor(iterator, dir);\r\n colOld = GetColSimple(tr0);\r\n curStepSize = stepSize;\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n molD = length(iterator - start);\r\n vol = sample3DTextureInclined(iterator).r;\r\n finish = distance(iterator, back) - stepSize;\r\n if (finish < 0.0 || vol < tr0 || (sumAlpha > 0.97) || molD > molDist)\r\n break;\r\n alpha = (1. - r);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4.* colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n colOld = col;\r\n } // for i\r\n\r\n if (finish < 0.0 || sumAlpha > 0.97)\r\n break;\r\n\r\n if (molD > molDist) {\r\n curStepSize = stepSize - (molD - molDist);\r\n right = iterator - (molD - molDist) * dir;\r\n vol = sample3DTextureInclined(right).r;\r\n } else {\r\n vec3 left = iterator - step;\r\n right = CorrectIso(left, iterator, tr0);\r\n curStepSize = distance(left, right);\r\n vol = tr0;\r\n }\r\n\r\n alpha = (1. - r) * curStepSize / stepSize;\r\n dif = 1.;// CalcColor(right, dir);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * curStepSize / stepSize * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4. * colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n\r\n if (molD > molDist)\r\n break;\r\n } // for k\r\n acc.rgb = 1. * sumColor / sumAlpha;\r\n acc.a = sumAlpha;\r\n return acc;\r\n}\r\n\r\nvec4 VolRender1(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n float stepSize = 1.0 / float(STEPS_COUNT);\r\n float len = length(back - start);\r\n vec3 step = stepSize * dir;\r\n vec3 iterator = start;\r\n float acc = 0.0;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n if (float(i) * stepSize > len)\r\n break;\r\n iterator = iterator + step;\r\n if (sample3DTextureInclined(iterator).r > _isoLevel0.x)\r\n acc += 10. * sample3DTextureInclined(iterator).r / float(STEPS_COUNT);\r\n }\r\n\r\n return vec4(1.,1.,1., acc);\r\n}\r\n\r\nvec4 IsoRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 tst = GetIso1(start, back, 2., dir, _isoLevel0.x, 0);\r\n vec4 col = NO_COLOR;\r\n\r\n if (length(tst.xyz - start) < molDist && tst.a > 0.1) {\r\n float dif = CalcColor(tst.xyz, dir);\r\n dif = 0.9 * dif * dif;\r\n col = vec4(dif, dif, dif, 1);\r\n }\r\n return col;\r\n}\r\n\r\nvec4 VolRender2(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n return sample3DTexture(start);\r\n}\r\n\r\nvoid main() {\r\n vec3 tc = screenSpacePos.xyz / screenSpacePos.w * 0.5 + 0.5;\r\n\r\n if (_flipV > 0.0) {\r\n tc.y = 1.0 - tc.y;\r\n }\r\n\r\n vec3 start;\r\n vec3 back;\r\n vec3 molBack;\r\n if (projectionMatrix[0][2] < 0.0) {\r\n start = texture2D(_FFLeft, tc.xy).xyz;\r\n back = texture2D(_BFLeft, tc.xy).xyz;\r\n molBack = texture2D(_WFFLeft, tc.xy).xyz;\r\n } else {\r\n start = texture2D(_FFRight, tc.xy).xyz;\r\n back = texture2D(_BFRight, tc.xy).xyz;\r\n molBack = texture2D(_WFFRight, tc.xy).xyz;\r\n }\r\n\r\n vec3 dir = normalize(back - start);\r\n\r\n float molDist = 2.0;\r\n if (length(molBack) > 0.001) {\r\n molDist = distance(start, molBack);\r\n }\r\n\r\n #ifdef ISO_MODE\r\n gl_FragColor = IsoRender(start, back, molDist, dir);\r\n #else\r\n gl_FragColor = VolRender(start, back, molDist, dir);\r\n #endif\r\n}\r\n");t.transparent=!0,t.depthTest=!0,super(t),this.updateDefines()}updateDefines(){this.defines={ISO_MODE:z.now.modes.VD.isoMode,STEPS_COUNT:100*z.now.modes.VD.polyComplexity[z.now.resolution]},this.needsUpdate=!0}}const sa={BackFacePosMaterial:Jo,BackFacePosMaterialFarPlane:ta,FrontFacePosMaterial:ra,VolumeMaterial:na};class ia extends r.Mesh{volumeInfo={};constructor(){const e=new r.BufferGeometry;super(e),this.clipPlane=new r.Plane;const t=new r.Vector3(.5,.5,.5);this.size=t,this.cullFlag=[!0,!0,!0,!0,!0,!0,!0,!0,!1,!1,!1,!1,!1,!1],this.faces=[{indices:[],norm:new r.Vector3(0,0,-1)},{indices:[],norm:new r.Vector3(0,0,1)},{indices:[],norm:new r.Vector3(0,-1,0)},{indices:[],norm:new r.Vector3(0,1,0)},{indices:[],norm:new r.Vector3(-1,0,0)},{indices:[],norm:new r.Vector3(1,0,0)},{indices:[],norm:new r.Vector3(0,0,0)}],this.vertices=[new r.Vector3(-t.x,-t.y,-t.z),new r.Vector3(-t.x,t.y,-t.z),new r.Vector3(t.x,-t.y,-t.z),new r.Vector3(t.x,t.y,-t.z),new r.Vector3(-t.x,-t.y,t.z),new r.Vector3(-t.x,t.y,t.z),new r.Vector3(t.x,-t.y,t.z),new r.Vector3(t.x,t.y,t.z),new r.Vector3(0,0,0),new r.Vector3(0,0,0),new r.Vector3(0,0,0),new r.Vector3(0,0,0),new r.Vector3(0,0,0),new r.Vector3(0,0,0)],e.setAttribute("position",new r.BufferAttribute(new Float32Array(3*this.vertices.length),3)),this.name="VolumeMesh"}static _corners=[[-1,-1,-1,0,4,8],[1,-1,-1,0,5,9],[1,1,-1,1,5,10],[-1,1,-1,1,4,11],[-1,-1,1,2,6,8],[1,-1,1,2,7,9],[1,1,1,3,7,10],[-1,1,1,3,6,11]];static _edges=[[0,1,0,-1,-1],[2,3,0,1,-1],[4,5,0,-1,1],[6,7,0,1,1],[0,3,-1,0,-1],[1,2,1,0,-1],[4,7,-1,0,1],[5,6,1,0,1],[0,4,-1,-1,0],[1,5,1,-1,0],[2,6,-1,1,0],[3,7,1,1,0]];static _edgeIntersections=function(){const e=[];for(let t=0;t<12;++t)e.push(new r.Vector3);return e}();_updateVertices(){const e=ia._corners,t=ia._edges,n=ia._edgeIntersections;let s;const i=this.clipPlane.normal,o=this.clipPlane.constant,a=this.vertices,{size:l}=this,c=[0,0,0,0,0,0,0,0],h=[1,1,1,1,1,1,1,1,1,1,1,1],u=new r.Vector3;let d=null;function p(){if(0===i.x)return 0;const e=-(i.dot(u)+o)/i.x;return-l.x<=e&&e<=l.x?(d.set(e,u.y,u.z),e===l.x?2:e===-l.x?-2:1):0}function m(){if(0===i.y)return 0;const e=-(i.dot(u)+o)/i.y;return-l.y<=e&&e<=l.y?(d.set(u.x,e,u.z),e===l.y?2:e===-l.y?-2:1):0}function f(){if(0===i.z)return 0;const e=-(i.dot(u)+o)/i.z;return-l.z<=e&&e<=l.z?(d.set(u.x,u.y,e),e===l.z?2:e===-l.z?-2:1):0}for(let e=0;e<12;++e){const r=t[e];d=n[e],u.set(r[2],r[3],r[4]),u.multiply(l);let s=0;0===r[2]&&(s=p()),0===r[3]&&(s=m()),0===r[4]&&(s=f()),-2===s?c[r[0]]=1:2===s?c[r[1]]=1:0===s&&(h[e]=0)}const _={indices:[],norm:i.clone().negate()};let g=8;for(s=0;s<8;++s)1===c[s]&&(a[g].set(e[s][0],e[s][1],e[s][2]).multiply(l),_.indices.push(g++),h[e[s][3]]=0,h[e[s][4]]=0,h[e[s][5]]=0);for(s=0;s<12;++s)1===h[s]&&(a[g].copy(n[s]),_.indices.push(g++));this.faces[6]=_;const y=new r.Vector3,x=new r.Vector3;for(this.clipPlane.coplanarPoint(x),s=0;s=0):s<8+_.indices.length&&(this.cullFlag[s]=!0);const b=this.geometry.getAttribute("position");let w=0;for(s=0;se.z===-i.z)),this._collectVertices(this.faces[1],(e=>e.z===i.z)),this._collectVertices(this.faces[2],(e=>e.y===-i.y)),this._collectVertices(this.faces[3],(e=>e.y===i.y)),this._collectVertices(this.faces[4],(e=>e.x===-i.x)),this._collectVertices(this.faces[5],(e=>e.x===i.x));const o=new r.Vector3,a=new r.Vector3,l=new r.Vector3;for(t=0;t=3&&(c+=3*(n.indices.length-2));let h=0;const u=new Uint16Array(c);for(t=0;t(s+e*n.sd)/i;this.material.uniforms._isoLevel0.value.set(o(e),o(t),o(r))}static _nearClipPlaneOffset=.2;static _pos=new r.Vector3;static _norm=new r.Vector3;static _norm4D=new r.Vector4;static _matrixWorldToLocal=new r.Matrix4;static _clipPlane=new r.Plane;rebuild(e){const t=ia._nearClipPlaneOffset,r=ia._pos,n=ia._norm,s=ia._norm4D,i=ia._matrixWorldToLocal,o=ia._clipPlane;this._updateIsoLevel(),e.getWorldDirection(n),e.getWorldPosition(r),r.addScaledVector(n,e.near+t),i.copy(this.matrixWorld).invert(),r.applyMatrix4(i),s.set(n.x,n.y,n.z,0),s.applyMatrix4(i),n.copy(s),n.normalize(),o.setFromNormalAndCoplanarPoint(n,r),this.clipPlane.equals(o)||(this.clipPlane=o.clone(),this._updateVertices(),this._updateIndices())}}const oa=ia;class aa{static _projectionTable={XY:["x",2],XZ:["y",1],YZ:["z",0]};constructor(e,t){const{delta:n}=t,{obtuseAngle:s}=t,i=new r.Vector3;e.getSize(i),i.multiplyScalar(.5);const o=this._getBaseVertices(n,s),a=new r.BufferGeometry,l=[];for(let e=0;e<4;e++)l.push(o[e].clone().multiply(i)),l.push(o[(e+1)%4].clone().multiply(i));const c=new r.Vector3(2*i.x*(1-n.x-n.y),0,0);for(let e=0;e<8;e++)l.push(l[e].clone().add(c));for(let e=0;e<4;e++)l.push(l[2*e].clone()),l.push(l[2*e+8].clone());const h=new r.Vector3;e.getCenter(h),l.forEach((e=>e.add(h)));const u=function(e){const t=e.length,r=new Float32Array(3*t);for(let n=0;n{const i=e[n[r][0]];return(-.5*(s-1)+s*t[n[r][1]])*i};return[new r.Vector3(2*(s("XZ",1)+s("XY",1))-1,2*s("YZ",1)-1,-1),new r.Vector3(2*(s("XZ",-1)+s("XY",1))-1,2*s("YZ",-1)-1,1),new r.Vector3(2*(s("XZ",-1)+s("XY",-1))-1,1-2*s("YZ",1),1),new r.Vector3(2*(s("XZ",1)+s("XY",-1))-1,1-2*s("YZ",-1),-1)]}getMesh(){return this._lines}}const la=aa;const ca=class{constructor(e,t,n){const s=this._initPlaneGeo(t,n),i=new sa.BackFacePosMaterialFarPlane;this._plane=new ds.Mesh(s,i),this._plane.frustumCulled=!1,this._plane.doubleSided=!0;const o=new r.Matrix4;this._plane._onBeforeRender=function(t,n,s,i,a,l){const{material:c}=this;if(!e||!c)return;const h=new r.Vector4(0,0,-(s.far-.1),1);h.applyMatrix4(s.matrixWorld),this.matrix.identity(),this.matrix.makeTranslation(h.x,h.y,h.z),this.matrixWorld.copy(this.matrix),this.modelViewMatrix.multiplyMatrices(s.matrixWorldInverse,this.matrixWorld),this.normalMatrix.getNormalMatrix(this.modelViewMatrix);const u=e.matrixWorld;o.copy(u).invert(),c.uniforms.aspectRatio.value=s.aspect,c.uniforms.farZ.value=s.far,c.uniforms.tanHalfFOV.value=Math.tan(.5*r.MathUtils.DEG2RAD*s.fov),c.uniforms.matWorld2Volume.value=o},this._plane.layers.set(tr.LAYERS.VOLUME_BFPLANE)}_initPlaneGeo(e,t){const n=new r.BufferGeometry;e=e||1,t=t||1;const s=new Float32Array([-.5*e,.5*t,0,.5*e,.5*t,0,-.5*e,-.5*t,0,.5*e,-.5*t,0]);return n.setAttribute("position",new r.BufferAttribute(s,3)),n.setIndex([0,2,1,2,3,1]),n}getMesh(){return this._plane}};const ha=class extends sr{constructor(e,t){super(e,t),this._mesh=new oa,this._mesh.setDataSource(t),this.add(this._mesh),this._frame=new la(this.getBoundaries().boundingBox,this._mesh.volumeInfo),this.add(this._frame.getMesh()),this.showFrame(z.now.modes.VD.frame),this._farPlane=new ca(this._mesh,2,2),this.add(this._farPlane.getMesh())}getBoundaries(){const e=this._dataSource.getBox(),t=new r.Sphere;return e.getBoundingSphere(t),{boundingBox:e,boundingSphere:t}}getMesh(){return this._mesh}showFrame(e){this._frame.getMesh().material.visible=e}};const ua=class extends ar{constructor(e=[]){super(e,["types"])}find(e){let t=[];if(e.type)t=this._dict.types[e.type.toLowerCase()]||[];else if(e.source)return this._list.filter((t=>t.canProbablyLoad&&t.canProbablyLoad(e.source)));return[...t]}};class da extends g{constructor(e,t){super(),this._source=e,this._options=t||{},this._abort=!1,this._agent=null}load(){return Promise.reject(new Error("Loading from this source is not implemented"))}abort(){this._abort=!0,this._agent&&this._agent.abort()}static extractName(e){}}lr(da.prototype);class pa extends da{constructor(e,t){super(e,t),t=this._options,this._binary=!0===t.binary}load(){return new Promise(((e,t)=>{if(this._abort)throw new Error("Loading aborted");const r=this._source,n=this._agent=new FileReader;n.addEventListener("load",(()=>{e(n.result)})),n.addEventListener("error",(()=>{t(n.error)})),n.addEventListener("abort",(()=>{t(new Error("Loading aborted"))})),n.addEventListener("progress",(e=>{this.dispatchEvent(e)})),this._binary?n.readAsArrayBuffer(r):n.readAsText(r)}))}static canProbablyLoad(e){return File&&e instanceof File||Blob&&e instanceof Blob}static extractName(e){return e&&e.name}}pa.types=["file","blob"];const ma=/^(https?|ftp):\/\//i;class fa extends da{constructor(e,t){super(e,t),t=this._options,this._binary=!0===t.binary}load(){return new Promise(((e,t)=>{if(this._abort)throw new Error("Loading aborted");const r=this._source,n=this._agent=new XMLHttpRequest;n.addEventListener("load",(()=>{200===n.status?e(n.response):t(new Error(`HTTP ${n.status} while fetching ${r}`))})),n.addEventListener("error",(()=>{t(new Error("HTTP request failed"))})),n.addEventListener("abort",(()=>{t(new Error("Loading aborted"))})),n.addEventListener("progress",(e=>{this.dispatchEvent(e)})),n.open("GET",r),this._binary?n.responseType="arraybuffer":n.responseType="text",n.send()}))}static canProbablyLoad(e){return t().isString(e)&&ma.test(e)}static extractName(e){if(e){const t=(e.indexOf("?")+1||e.lastIndexOf("#")+1||e.length+1)-1;return e.slice(e.lastIndexOf("/",t)+1,t)}}}fa.types=["url"];class _a extends da{load(){return new Promise((e=>{if(this._abort)throw new Error("Loading aborted");e(this._source)}))}static canProbablyLoad(e){return!1}}_a.types=["immediate"];const ga=new ua([pa,fa,_a]);const ya=class extends ar{constructor(e=[]){super(e,["formats","extensions"])}find(e){let t=[];return e.format?t=this._dict.formats[e.format.toLowerCase()]||[]:e.ext&&(t=this._dict.extensions[e.ext.toLowerCase()]||[]),0===t.length&&!e.format&&e.data?this._list.filter((t=>t.canProbablyParse&&t.canProbablyParse(e.data))):[...t]}};class xa{constructor(e,t){this._data=e,this._options=t||{},this._abort=!1}parseSync(){throw new Error("Parsing this type of data is not implemented")}parse(){return new Promise(((e,t)=>{setTimeout((()=>{try{return this._abort?t(new Error("Parsing aborted")):e(this.parseSync())}catch(e){return t(e)}}))}))}getModel(){return this.model._parseHeader(this._data),this.model}abort(){this._abort=!0}}lr(xa.prototype);class ba{constructor(){this.matrices=[],this._matrix=null,this._matrixIndex=-1}parse(e){let t=this._matrix;if(" SMTRY"===e.readString(12,18)){const n=e.readCharCode(19)-49,s=e.readString(20,80).trim().split(/\s+/),i=parseInt(s[0],10);null!==this._matrix&&i===this._matrixIndex||(this._matrixIndex=i,this._matrix=t=new r.Matrix4,this.matrices[this.matrices.length]=t);const{elements:o}=t;o[n]=parseFloat(s[1]),o[n+4]=parseFloat(s[2]),o[n+8]=parseFloat(s[3]),o[n+12]=parseFloat(s[4])}}}ba.prototype.id=290;const wa=ba,{Assembly:Sa}=Ht;class va{constructor(e){this._complex=e,this.assemblies=[],this._assembly=null,this._matrix=null,this._matrixIndex=-1}parse(e){let t=this._assembly,n=this._matrix;if(t&&" BIOMT"===e.readString(12,18)){const s=e.readCharCode(19)-49,i=e.readString(20,80).trim().split(/\s+/),o=parseInt(i[0],10);null!==this._matrix&&o===this._matrixIndex||(this._matrixIndex=o,this._matrix=n=new r.Matrix4,t.addMatrix(n));const{elements:a}=n;a[s]=parseFloat(i[1]),a[s+4]=parseFloat(i[2]),a[s+8]=parseFloat(i[3]),a[s+12]=parseFloat(i[4])}else if(t&&"CHAINS:"===e.readString(35,41)){const r=e.readString(42,80).split(",");for(let e=0,n=r.length;e0&&t.addChain(n)}}else"BIOMOLECULE:"===e.readString(12,23)&&(this._matrix=null,this._matrixIndex=-1,this._assembly=t=new Sa(this._complex),this.assemblies.push(t))}}va.prototype.id=350;const Ca=va;const Aa=class{constructor(e){this._data=e,this._start=0,this._nextCR=-1,this._nextLF=-1,this._next=-1,this._end=e.length,this.next()}readLine(){return this._data.slice(this._start,this._next)}readChar(e){return(e=this._start+e-1)=this._end}next(){const e=this._next+1;this._start=ethis._nextCR&&(this._nextCR=(this._data.indexOf("\r",this._start)+1||this._end+1)-1),this._start>this._nextLF&&(this._nextLF=(this._data.indexOf("\n",this._start)+1||this._end+1)-1),this._next=this._nextCR+1t&&o.addBond(t,r,0,La.BondType.UNKNOWN,!0),n&&n>t&&o.addBond(t,n,0,La.BondType.UNKNOWN,!0),s&&s>t&&o.addBond(t,s,0,La.BondType.UNKNOWN,!0),i&&i>t&&o.addBond(t,i,0,La.BondType.UNKNOWN,!0)}_parseCOMPND(e){const t=e.readString(11,80),r=t.indexOf(":");if(this._compndCurrToken=r>0?t.substring(0,r).trim():this._compndCurrToken,"MOL_ID"===this._compndCurrToken)this._molecule={_index:"",_chains:[]},this._molecule._index=parseInt(t.substring(r+1,t.indexOf(";")),10),this._molecules.push(this._molecule);else if("MOLECULE"===this._compndCurrToken&&null!=this._molecule)this._molecule._name=t.substring(r+1,t.indexOf(";")).trim();else if("CHAIN"===this._compndCurrToken&&null!=this._molecule){let e=t.substring(r+1,80).trim();const n=e[e.length-1];";"!==n&&","!==n||(e=e.slice(0,-1)),e=e.replace(/\s+/g,"");const s=e.split(",");this._molecule._chains=this._molecule._chains.concat(s)}}_parseREMARK(e){const r=e.readInt(8,10);let n=this._remarks[r];if(t().isUndefined(n)){const e=Oa[r];t().isFunction(e)&&(this._remarks[r]=n=new e(this._complex))}t().isUndefined(n)||n.parse(e)}_parseHELIX(e){this._parseSTRUCTURE(e,[20,22,32,34],(e=>{this._complex.addHelix(e),this._complex.structures.push(e)}))}_parseSHEET(e){this._parseSTRUCTURE(e,[22,23,33,34],(e=>{this._complex.addSheet(e)}))}_parseSTRUCTURE(e,t,r){const n=e.readInt(8,10),s=e.readString(12,14).trim(),i=e.readString(41,70).trim(),o=e.readInt(72,76),a=e.readInt(39,40),l=e.readInt(15,16),c=e.readInt(42,45),h=e.readInt(57,60),u=e.readString(t[0],t[2]+1).charCodeAt(0),d=e.readString(t[2],t[2]+1).charCodeAt(0),p=e.readInt(t[1],t[1]+3);let m=e.readString(t[1]+4,t[1]+4),f=0;m.length>0&&(f=m.charCodeAt(0));const _=e.readInt(t[3],t[3]+3);m=e.readString(t[3]+4,t[3]+4);let g,y=0;m.length>0&&(y=m.charCodeAt(0));let x=this._sheet;if(83===e.readCharCode(1)){null!==x&&x.getName()!==s&&(x=null,this._sheet=null),null===x?(this._sheet=g=new Ma(s,l),r(g)):g=x;const e=new Pa(g,this._complex.getUnifiedSerial(u,p,f),this._complex.getUnifiedSerial(d,_,y),a,c,h);g.addStrand(e),this._complex.structures.push(e)}else g=new Ra(a,this._complex.getUnifiedSerial(u,p,f),this._complex.getUnifiedSerial(d,_,y),n,s,i,o),r(g)}_parseHEADER(e){const{metadata:t}=this._complex;t.classification=e.readString(11,50).trim(),t.date=e.readString(51,59).trim();const r=e.readString(63,66).trim();t.id=r,r&&(this._complex.name=r),t.format="pdb"}_parseTITLE(e){const{metadata:t}=this._complex;t.title=t.title||[];const r=e.readInt(9,10)||1;t.title[r-1]=e.readString(11,80).trim()}static tagParsers={HEADER:Va.prototype._parseHEADER,"TITLE ":Va.prototype._parseTITLE,"ATOM ":Va.prototype._parseATOM,HETATM:Va.prototype._parseATOM,ENDMDL:Va.prototype._parseENDMDL,CONECT:Va.prototype._parseCONECT,COMPND:Va.prototype._parseCOMPND,REMARK:Va.prototype._parseREMARK,"HELIX ":Va.prototype._parseHELIX,"SHEET ":Va.prototype._parseSHEET,"ATOM 1":Va.prototype._parseATOM,"ATOM 2":Va.prototype._parseATOM,"ATOM 3":Va.prototype._parseATOM,"ATOM 4":Va.prototype._parseATOM,"ATOM 5":Va.prototype._parseATOM,"ATOM 6":Va.prototype._parseATOM,"ATOM 7":Va.prototype._parseATOM,"ATOM 8":Va.prototype._parseATOM,"ATOM 9":Va.prototype._parseATOM};parseSync(){const e=new Aa(this._data),r=this._complex=new Ea;for(;!e.end();){const r=e.readString(1,6),n=Va.tagParsers[r];t().isFunction(n)&&n.call(this,e),e.next()}if(this._finalize(),this._serialAtomMap=null,this._sheet=null,this._residue=null,this._chain=null,this._complex=null,0===r.getAtomCount())throw new Error("The data does not contain valid atoms");return r}}Va.formats=["pdb"],Va.extensions=[".pdb",".ent"];const Da=Va,{Complex:ka,Element:za,SGroup:Fa,Bond:Ba}=Ht,Ua={A:0,S:1,D:2,T:3},Ga=/\s*<\?xml\b[^?>]*\?>\s*<(?:cml|molecule)\b/i;class ja extends xa{constructor(e,t){super(e,t),this._complex=null,this._residue=null,this._serialAtomMap=null,this._modelId=1,this._lastMolId=-1,this._readOnlyOneMolecule=!1,this._options.fileType="cml"}static canProbablyParse(e){return t().isString(e)&&Ga.test(e)}_rebuidBondIndexes(e,t){const r=e.length;for(let n=0;n1&&o.splice(1,o.length-1),o.forEach((e=>{const r=function(e){let r,n=[];if(e.molecule&&e.molecule.atomArray&&e.molecule.atomArray.atom)Array.isArray(e.molecule.atomArray.atom)?n=e.molecule.atomArray.atom:n.push(e.molecule.atomArray.atom);else if(!e.molecule){return{atomLabels:null,labelsCount:1}}e.molecule.molecule&&s._extractSGroups(e.molecule.molecule,n);let i=n.length;for(let e=0;e1)a[e].order=s;else{const r=Ua[t];void 0!==r&&(a[e].order=r,"A"===t&&(a[e].type=Ba.BondType.AROMATIC))}}i=n.length;for(let e=0;e0&&i.push(r)})),i}_packLabel(e,t){return(t<<16)+e}_unpackLabel(e){return{molId:e>>>16,compId:65535&e}}_breadWidthSearch(e,t){const r=new Array(e.length);let n;for(n=0;n0;){i++;let a=-1;for(n=0;n0;){const t=s.shift();if(t)for(let n=0;n=0){const s=[Math.min(e,t),Math.max(e,t)];this._complex.addBond(s[0],s[1],r,n,!0)}}_fixBondsArray(){const e=this._serialAtomMap={},t=this._complex,r=t._atoms;for(let t=0,n=r.length;to[e]-o[t])),a=0;a{r.curr=2,0===r.count&&(r.count=1);for(let n=0;n{r+=e.getAtomCount()})),r<=0)throw new Error("The data does not contain valid atoms");if(e.length>1){const t=new ka;return t.joinComplexes(e),t.originalCML=e[0].originalCML,t}return 1===e.length?e[0]:new ka}}ja.formats=["cml"],ja.extensions=[".cml"];const Ha=ja;var $a=s(660),Wa=s.n($a);const{Complex:Ya,Chain:Xa,Atom:qa,Element:Ka,Helix:Za,Sheet:Qa,Strand:Ja,Bond:el,Assembly:tl,Molecule:rl}=Ht;class nl{constructor(e){this._original=Array.from(e),this._original.sort(),this._sum=0;for(let e=0;e=this._complex._atoms.length)return;const r=Math.min(e.atomIndex1,e.atomIndex2);this._complex.addBond(this._complex._atoms[r],this._complex._atoms[t],e.bondOrder,el.BondType.UNKNOWN,!0)}_updateSecStructure(e,r,n){const s=[3,-1,1,-1,5];if(!t().isUndefined(n)&&n.secStruct===this._ssType)return r._secondary=this._ssStruct,void(this._ssStruct&&(this._ssStruct.term=r));if(!t().isUndefined(n)){const t=il[n.secStruct];this._ssType=n.secStruct,this._ssStart=r;let i=null;switch(this._ssType){case-1:case 7:break;case 0:case 2:case 4:i=new Za(s[this._ssType],r,r,0,"","",0),e._helices.push(i);break;case 3:{const t=new Qa("",0);e._sheets.push(t),i=new Ja(t,r,r,0,null,null);break}default:void 0!==t&&(i=new Le(t,r,r))}this._ssStruct=i,r._secondary=i,i&&e.structures.push(i)}}_updateMolecules(e){const t=e.entityList;if(!t)return;const r=e.chainsPerModel[0];for(let e=0;e=r)continue;const n=this._complex._chains[t];i=i.concat(n._residues.slice())}const o=new rl(this._complex,n.description,e+1);o.residues=i,this._complex._molecules[e]=o}}_traverse(e){const t=this,{metadata:r}=this._complex;r.id=e.structureId,r.title=[],r.title[0]=e.title,r.date=e.releaseDate,r.format="mmtf";const n={onModel(e){t._onModel(e)},onChain(e){t._onChain(e)},onGroup(e){t._onGroup(e)},onAtom(e){t._onAtom(e)},onBond(e){t._onBond(e)}};this._ssType=-1,this._ssStruct=null,this._ssStart=null,Wa().traverse(e,n),this._updateSecStructure(this._complex),this._updateMolecules(e)}_linkAtomsToResidues(){for(let e=0;e=t)continue;const s=this._complex._chains[r];for(let e=0;e=s||hl(e.charCodeAt(r+1))))return++c,void++r;if(a&&59===o){n=r;let i=0;do{if(n=ul(10,e,n+1),-1===n)throw new cl("Unterminated text block found",l,c);++i}while(n+1=s);return t=e.substring(r+1,n).replace(/\r/g,""),r=n+2,l+=i,c=1,a=!1,t}if(39===o||34===o){n=r;do{if(n=ul(o,e,n+1),-1===n)throw new cl("Unterminated quoted string found",l,c)}while(n+10){for(let e=0;e0&&r.addChain(n[t])}r.matrices=s,e.units.push(r)}}}El.formats=["cif","mmcif"],El.extensions=[".cif",".mmcif"];const Tl=El,Rl=0,Ml=1,Pl=2,Ll=3;const Nl=class{_xyz2crs=[];_origin=new r.Vector3(0,0,0);constructor(){this._header={},this._boxSize=new r.Vector3,this._boxStart=new r.Vector3,this._header.delta={},this._header.extent=[],this._header.nstart=[],this._header.grid=[],this._header.crs2xyz=[],this._header.cellDims=new r.Vector3,this._header.angles=[],this._header.origin=new r.Vector3(0,0,0),this._header.dmin=0,this._header.dmean=0,this._header.dmax=0}_typedCheck(){if(t().isTypedArray(this._buff))this._buff=this._buff.buffer;else if(!t().isArrayBuffer(this._buff))throw new TypeError("Expected ArrayBuffer or TypedArray")}_fillHeader(e,t){for(const r in e)if(e.hasOwnProperty(r))switch(e[r][0]){case Rl:this._header[r]=t[e[r][1]][e[r][2]];break;case Pl:this._parseArray(this._header[r],t[e[r][1]],e[r][2]);break;case Ml:this._parseVector(this._header[r],t[e[r][1]],e[r][2]);break;case Ll:this._header[r]=new Uint8Array(t[e[r][1]],4*[e[r][2]],4*[e[r][3]])}}_parseVector(e,t,r){[e.x,e.y,e.z]=[t[r],t[r+1],t[r+2]]}_parseArray(e,t,r){e[0]=t[r],e[1]=t[r+1],e[2]=t[r+2]}_parseHeader(e){}_setAxisIndices(){}_setOrigins(){}_getAxis(){const e=this._header,t=e.cellDims.x/e.grid[0],n=e.cellDims.y/e.grid[1],s=e.cellDims.z/e.grid[2],[i,o,a]=e.angles,l=Math.cos(o),c=(Math.cos(i)-Math.cos(o)*Math.cos(a))/Math.sin(a),h=Math.sqrt(1-l*l-c*c);return[new r.Vector3(t,0,0),new r.Vector3(Math.cos(a)*n,Math.sin(a)*n,0),new r.Vector3(l*s,c*s,h*s)]}_getXYZdim(){return[this._header.extent[this._xyz2crs[0]],this._header.extent[this._xyz2crs[1]],this._header.extent[this._xyz2crs[2]]]}_getVolumeInfo(){const e=t().pick(this._header,["dmean","dmin","dmax","sd","delta"]);return e.obtuseAngle=this._header.angles.map((e=>Number(e>=Math.PI/2))),e}_setBoxParams(e,t,n){let s=0,i=0;const[o,a,l]=this._header.angles;l>=Math.PI/2&&(s+=Math.abs(t.x)),a>=Math.PI/2&&(s+=Math.abs(n.x)),o>=Math.PI/2&&(i+=Math.abs(n.y)),this._boxStart=new r.Vector3(this._origin.x-s,this._origin.y-i,this._origin.z),this._boxSize=new r.Vector3(Math.abs(e.x)+Math.abs(t.x)+Math.abs(n.x),Math.abs(t.y)+Math.abs(n.y),Math.abs(n.z));const c=(e,t)=>Math.abs(e[t])/this._boxSize[t];this._header.delta.x=c(t,"x"),this._header.delta.y=c(n,"x"),this._header.delta.z=c(n,"y")}_getXYZbox(){return new r.Box3(this._boxStart.clone(),this._boxStart.clone().add(this._boxSize))}_toXYZData(){}parse(e){return this._parseHeader(e),this._setOrigins(),new jt(Float32Array,this._getXYZdim(),this._getXYZbox(),1,this._toXYZData(),this._getVolumeInfo())}},Il={extent:[Pl,"u32",0],type:[Rl,"u32",3],nstart:[Pl,"i32",4],grid:[Pl,"u32",7],cellDims:[Ml,"f32",10],angles:[Pl,"f32",13],crs2xyz:[Pl,"i32",16],dmin:[Rl,"f32",19],dmax:[Rl,"f32",20],dmean:[Rl,"f32",21],ispg:[Rl,"u32",22],nsymbt:[Rl,"u32",23],lksflg:[Rl,"u32",24],customData:[Ll,"buffer",25,9],origin:[Ml,"f32",34],map:[Ll,"buffer",52,1],machine:[Rl,"u32",53],sd:[Rl,"f32",54],nlabel:[Rl,"f32",55],label:[Ll,"buffer",56,200]};class Ol extends Nl{_parseHeader(e){this._buff=e,this._typedCheck();const t={};t.u32=new Uint32Array(this._buff,0,56),t.i32=new Int32Array(this._buff,0,56),t.f32=new Float32Array(this._buff,0,56),t.buffer=this._buff;const r=this._header;this._fillHeader(Il,t),r.angles.forEach(((e,t,r)=>{r[t]*=Math.PI/180}))}_setAxisIndices(){const e=this._header;0===e.cellDims.x&&0===e.cellDims.y&&0===e.cellDims.z&&e.cellDims.set(1,1,1);const{crs2xyz:t}=this._header;0===t[0]&&0===t[1]&&0===t[2]&&(t[0]=1,t[1]=2,t[2]=3);const r=this._xyz2crs;r[t[0]-1]=0,r[t[1]-1]=1,r[t[2]-1]=2}_setOrigins(){const[e,t,r]=this._getAxis();this._setAxisIndices();const n=this._header,s=this._xyz2crs;if(0===n.origin.x&&0===n.origin.y&&0===n.origin.z?(this._origin.addScaledVector(e,n.nstart[s[0]]),this._origin.addScaledVector(t,n.nstart[s[1]]),this._origin.addScaledVector(r,n.nstart[s[2]])):this._origin=n.origin,e.multiplyScalar(n.extent[s[0]]-1),t.multiplyScalar(n.extent[s[1]]-1),r.multiplyScalar(n.extent[s[2]]-1),2!==n.type)throw new Error(`CCP4: Unsupported format ${n.type}`);this._data=new Float32Array(this._buff,1024+n.nsymbt,n.extent[0]*n.extent[1]*n.extent[2]),this._setBoxParams(e,t,r)}_toXYZData(){const e=this._header,t=this._data,r=this._xyz2crs,n=new Float32Array(t.length),s=this._getXYZdim(),i=s[0],o=s[1];let a=0;const l=[];let c,h,u;for(l[2]=0;l[2]=this._strings.length?(this._currentStart=this._strings.length-1,this._currentStringIndx=this._strings.length-1):(this._currentStart=e,this._currentStringIndx=e)}getNextString(){return this._strings[++this._currentStringIndx]}getCurrentString(){return this._strings[this._currentStringIndx]}getStringFromStart(e){return this._currentStringIndx=this._currentStart+e,this._strings[this._currentStart+e]}findNextDataItem(){let e=this.getNextString(),r=!1;for(;!t().isUndefined(e)&&"$$$$"!==e.trim();){if(e.match(/>\s+<(.*)>/)){r=!0;break}e=this.getNextString()}return r}findNextCompoundStart(){let e=this.getCurrentString();for(;!t().isUndefined(e)&&"$$$$"!==e.trim();)e=this.getNextString();return this.setStart(++this._currentStringIndx),this.probablyHaveDataToParse()}probablyHaveDataToParse(){return this._currentStringIndx\s+<(.+)>.*/,ec=/.*($$$$).*|.*>\s+<(.+)>.*/,tc="sdf",rc="mol",nc=["name","id","title"],sc={name:["PUBCHEM_IUPAC_TRADITIONAL_NAME",/PUBCHEM_(.+)_NAME/,/(.+)name/,/(.+)NAME/],id:["PUBCHEM_COMPOUND_CID","id","ID",/.*CID/,/.*ID/,/.*id/],title:["msg","MSG","message","title","description","desc"]};class ic extends xa{constructor(e,t){super(e,t),this._format="sdf",this._complex=null,this._chain=null,this._residue=null,this._molecules=null,this._metadata={},this._metadata.molecules=[],this._currentMolProps={},this._compoundIndx=-1,this._assemblies=[],this._atomsParsed=0,this._atomsIndexes=[]}canProbablyParse(e){return t().isString(e)&&Jl.test(e)}_parseHeader(e){const t={};t.name=e.getStringFromStart(0);const r=parseInt(e.getStringFromStart(1).substr(10,6).trim(),10);t.date=r.toString()||"",t.title=e.getStringFromStart(2),this._metadata.molecules.push(t)}_parseAtoms(e,t){let n,s=this._atomsParsed;const i=function(e){if(!e)return"A";const t=[];for(;e;)t.push(65+e%26),e=Math.trunc(e/26);return t.length>1&&(t.reverse(),t[0]-=1),String.fromCharCode(...t)}(this._compoundIndx);this._chain=this._complex.getChain(i)||this._complex.addChain(i),this._residue=this._chain.addResidue("UNK",1," ");for(let i=0;in&&([t,n]=[n,t]),this._complex.addBond(t,n,Zl[s]||1,Ql[s]||Xl.BondType.UNKNOWN,!0)}}_parseMOL(e){this._compoundIndx++,this._parseHeader(e);const t=e.getStringFromStart(3),r=parseInt(t.substr(0,3),10),n=parseInt(t.substr(3,3),10);this._parseAtoms(e,r),this._parseBonds(e,n),this._atomsParsed+=r,this._metadata.molecules[this._compoundIndx]._residues=[],this._metadata.molecules[this._compoundIndx]._residues.push(this._residue)}_parseDataItem(e){const t=e.getCurrentString();let r=[],n=e.getNextString();for(;""!==n.trim();)r.push(n),n=e.getNextString();1===r.length&&([r]=r),this._currentMolProps[t.replace(/[<>]/g,"").trim()]=r}_parseCompound(e){if(this._parseMOL(e),this._format===tc){for(this._currentMolProps={};e.findNextDataItem();)this._parseDataItem(e);if(0!==Object.keys(this._currentMolProps).length){const e=this._metadata.molecules[this._compoundIndx];e.props=this._currentMolProps,this._tryToUpdateMoleculeData(e)}}}_fixBondsArray(){const e=this._serialAtomMap,t=this._complex._bonds;for(let r=0;r1){t.molecules=[];for(let r=0;r>8&255}if(100!==t.i16[18])throw new Error("DSN6: Incorrect format ");const r=this._header;this._fillHeader(oc,t),r.cellDims.multiplyScalar(1/r.scaleFactor),r.angles.forEach(((e,t,n)=>{n[t]*=Math.PI/180/r.scaleFactor})),r.div/=100}_setAxisIndices(){this._xyz2crs[0]=0,this._xyz2crs[1]=1,this._xyz2crs[2]=2}_setOrigins(){const e=this._header,[t,r,n]=this._getAxis();this._setAxisIndices(),this._origin.addScaledVector(t,e.nstart[0]),this._origin.addScaledVector(r,e.nstart[1]),this._origin.addScaledVector(n,e.nstart[2]),t.multiplyScalar(e.extent[0]),r.multiplyScalar(e.extent[1]),n.multiplyScalar(e.extent[2]),this._setBoxParams(t,r,n)}_pointCalculate(e,t,r,n,s,i,o){const a=this._header;if(!(sn&&(n=e[s]);this._header.sd=Math.sqrt(t/e.length),this._header.dmax=n,this._header.dmin=r}}class lc extends xa{constructor(e,t){super(e,t),this._options.fileType="dsn6",this.model=new ac}static canParse(e,t){return!!e&&(e instanceof ArrayBuffer&&xa.checkDataTypeOptions(t,"dsn6"))}static canProbablyParse(e){return!1}parseSync(){return this.model.parse(this._data)}}lc.formats=["dsn6"],lc.extensions=[".dsn6",".omap"],lc.binary=!0;const cc=lc;const hc=class extends Aa{constructor(e){super(e),this._next=-1,this.next()}getNext(){return this._next}},{Complex:uc,Element:dc,Molecule:pc}=Ht;class mc extends xa{constructor(e,t){super(e,t),this._time=null,this._numAtoms=null,this._residueNumber=null,this._residueName="",this._atomName="",this._atomNumber=null,this._atomPosition=[],this._atomVelocity=[],this._complex=null,this._molecules=[],this._molecule=null,this._options.filetype="gro"}canProbablyParse(e){return t().isString(this._data)&&/^\s*[^\n]*\n\s*\d+ *\n\s*\d+[^\n\d]{3}\s*\w+\s*\d+\s*-?\d/.test(e)}_parseTitle(e){const{metadata:t}=this._complex;t.id=e.readLine().trim(),t.name=t.id.slice(t.id.lastIndexOf("\\")+1,t.id.lastIndexOf(".")),t.format="gro"}_parseNumberOfAtoms(e){if(this._numAtoms=e.readInt(0,e.getNext()),Number.isNaN(this._numAtoms))throw new Error("Line 2 is not representing atom number. Consider checking input file")}_parseAtom(e){this._residueNumber=e.readInt(1,5),this._residueName=e.readString(6,10).trim(),this._atomName=e.readString(11,15).trim(),this._atomNumber=e.readInt(16,20);const t=10*e.readFloat(21,28),n=10*e.readFloat(29,36),s=10*e.readFloat(37,45);if(Number.isNaN(t)||Number.isNaN(n)||Number.isNaN(s))return void(this._complex.error={message:`Atom position is invalid in "${e.readLine()}"`});const i=dc.getByName(this._atomName[0]);if("Unknown"===i.fullName)return void(this._complex.error={message:`${this._atomName[0]} hasn't been recognised as an atom name.`});const o=dc.Role[this._atomName];let a=this._chain;a||(this._chain=a=this._complex.addChain("A"));let l=this._residue;l&&l.getSequence()===this._residueNumber||(this._residue=l=a.addResidue(this._residueName,this._residueNumber," ")),this._atomPosition=new r.Vector3(t,n,s);l.addAtom(this._atomName,i,this._atomPosition,o,!0,this._atomNumber," ",1,1,0)}_finalize(){const e=new pc(this._complex,this._complex.metadata.name,1);e.residues=this._chain._residues,e._chains=this._chain,this._complex._molecules[0]=e,this._molecules.push(e),this._complex.finalize({needAutoBonding:!0,detectAromaticLoops:this.settings.now.aromatic,enableEditing:this.settings.now.editing,serialAtomMap:this._serialAtomMap})}parseSync(){const e=this._complex=new uc,t=new hc(this._data);let r=0;for(this._parseTitle(t),t.next(),this._parseNumberOfAtoms(t),t.next(),r=0;r${e}`))return;this._currPosIdx++}this._toStringFromStart(0,t)}_toStringFromHeader(e,t,r){this._toHeaderString(e,r);const n=this._currPosIdx+t;r[this._currPosIdx].match(`@${e}`)&&n=t.length?this._currStartIdx=this._currPosIdx=t.length-1:this._currStartIdx=this._currPosIdx=e}_probablyHaveDataToParse(e){return this._currPosIdxMOLECULE>"!==e[this._currPosIdx].trim();)this._currPosIdx++;return this._setStart(++this._currPosIdx,e),this._probablyHaveDataToParse(e)}_parseMolecule(e){this._toHeaderString("MOLECULE",e);const{metadata:t}=this._complex;t.name=e[++this._currPosIdx],t.format="mol2",this._molecule={_index:"",_chains:[]},this._molecule._index=this._compoundIndx+1,this._molecules.push(this._molecule)}_parseAtoms(e,t){this._toHeaderString("ATOM",t);for(let n=0;n=9&&(c=parseFloat(e[8])||0);let h=this._chain;if(h||(this._chain=h=this._complex.getChain("A")||this._complex.addChain("A"),this._residue=null),!this._setResidue(e))continue;const u=!1,d=" ",p=1,m=0,f=gc.getByName(l),_=gc.Role[s],g=new r.Vector3(i,o,a);this._residue.addAtom(s,f,g,_,u,n,d,p,m,c)}}_setResidue(e){let t=1,r="UNK";if(e.length>=7&&(t=parseInt(e[6],10)),e.length>=8&&"<0>"!==e[7]&&(r=e[7].replace(Sc,"")),this.settings.now.nowater&&("HOH"===r||"WAT"===r))return!1;const n=this._residue,s=this._chain;return n&&n.getSequence()===t||(this._residue=s.addResidue(r,t,"A")),!0}_parseBonds(e,t){this._toHeaderString("BOND",t);for(let r=0;rn&&([r,n]=[n,r]),this._complex.addBond(r,n,bc[s]||0,wc[s]||yc.BondType.UNKNOWN,!0)}}_fixSerialAtoms(){const e=this._complex._atoms;for(let t=0;t{setTimeout((()=>{try{return this._abort?t(new Error("Export aborted")):e(this.exportSync())}catch(e){return t(e)}}))}))}abort(){this._abort=!0}}lr(Rc.prototype);class Mc{constructor(){this._resultArray=[],this._currentStr=-1,this._tag=null,this._fixedNumeration=!1,this._numeration=!1,this._tagStrNum=0}getResult(){return this.writeString("\n",81,81),this._resultArray.join("")}_currentStrLength(){const e=this._resultArray[this._currentStr];return e?e.length:0}newTag(e,r){this._tag=e||null,t().isUndefined(r)?(this._numeration=!1,this._fixedNumeration=!1,this._tagStrNum=0):t().isNumber(r)?(this._tagStrNum=r,this._numeration=!0,this._fixedNumeration=!0):t().isBoolean(r)&&(this._tagStrNum=0,this._numeration=r,this._fixedNumeration=!1)}newString(e){this.writeString("\n",81,81),this._currentStr++,this._resultArray.push(""),e?this.writeString(e,1,6):this._tag&&this.writeString(this._tag,1,6),this._numeration&&(this._fixedNumeration||this._tagStrNum++,1!==this._tagStrNum&&this.writeString(this._tagStrNum.toString(),10,8))}writeEntireString(e,t,r){t||(t=81);for(let n=0;nMath.abs(r-n)+1&&(s=s.substr(0,Math.abs(r-n+1))),l>o+1)this._resultArray[this._currentStr]+=" ".repeat(l-o-1);else if(l<=o){const e=this._resultArray[this._currentStr];this._resultArray[this._currentStr]=e.slice(0,l-1)}if(ni.length&&(this._resultArray[this._currentStr]+=" ".repeat(a-i.length))}writeBondsArray(e,t){const r=this._getSubArrays(e,4);for(let e=0;ee._fixed));0!==n.length&&e.writeBondsArray(n.reverse(),t[r])}}_extractSHEET(e){if(!this._source._sheets)return;e.newTag("SHEET");const t=this._source._sheets;for(let r=0;r1||t[r].name.length>3?13:14;e.writeString(t[r].serial,11,7),e.writeString(t[r].name,s,16),e.writeString(String.fromCharCode(t[r].location),17,17),e.writeString(t[r].residue._type._name,20,18),e.writeString(t[r].residue._chain._name,22,22),e.writeString(t[r].residue._sequence,26,23),e.writeString(t[r].residue._icode,27,27),e.writeString(t[r].position.x.toFixed(3),38,31),e.writeString(t[r].position.y.toFixed(3),46,39),e.writeString(t[r].position.z.toFixed(3),54,47),e.writeString(t[r].occupancy.toFixed(2),60,55),e.writeString(t[r].temperature.toFixed(2),66,61),e.writeString(t[r].element.name,78,77),t[r].charge&&e.writeString(t[r].charge,79,80)}}_extractCOMPND(e){if(!this._source._molecules)return;const t=this._source._molecules;e.newTag("COMPND",!0);for(let r=0;re instanceof ot));for(let t=0;tt.indexOf(e)===r))}}Pc.formats=["pdb"],Pc.SourceClass=Bt;function Lc(e,t,r,n){r[n]=e[t],r[n+1]=e[t+1],r[n+2]=e[t+2]}function Nc(e,t,r,n,s){r[n]=e[t],r[n+1]=e[t+1],r[n+2]=e[t+2],r[n+3]=s}const Ic=new r.Vector4;function Oc(e,t,r,n,s){Ic.set(e[t],e[t+1],e[t+2],s.w),Ic.applyMatrix4(s.matrix),r[n]=Ic.x,r[n+1]=Ic.y,r[n+2]=Ic.z}function Vc(e,t,r,n,s){if(!((t.array.length-t.start)/t.stridee+r));this.setIndices(n,0,t)}getVerticesNumber(){return this.lastPos/3}addInstance(e,t){const r=this.getVerticesNumber();this.setShiftedIndices(t.indices,t.indices.length,r);const n=t.itemSize;this.setTransformedPositions(t.positions,0,t.vertsCount,n.position,e),this.setTransformedNormals(t.normals,0,t.vertsCount,n.normal,e),this.setColors(t.colors,0,t.vertsCount,n.color)}}class kc{constructor(){this.positions=null,this.normals=null,this.colors=null,this.indices=null,this.vertsCount=0,this.itemSize=null}init(e,t){const{attributes:r}=e;this.itemSize={position:r.position.itemSize,normal:r.normal.itemSize,color:r.color.itemSize}}}class zc extends kc{init(e,t){super.init(e,t);const{attributes:{position:r,normal:n},index:s}=e;this.vertsCount=r.count,this.positions=r.array,this.normals=n.array,this.colors=new Float32Array(this.vertsCount*this.itemSize.color),this.indices=s.array}setColors(e){let t=0;for(let r=0,n=this.colors.length,s=this.itemSize.color;re+s)),this.indices.set(r.array,0),this.indices.set(i,n)}_setColorRange(e,t,r,n){const s=n.length;for(let i=e;i{e instanceof r.Mesh&&e.layers.test(t)&&this.checkExportAbility(e)&&("InstancedBufferGeometry"===e.geometry.type?this._collectInstancedGeoInfo(e):this._collectGeoInfo(e))}))}_reworkIndices(e){for(let t=2;t0&&(u=new Fc,u.init(e.geometry,h));const d=h.addPerCylinder*h.needToSplit,p=t.count,m=i.count;a.init(l*p+d,l*m);const f=new r.Matrix4,_=new r.Matrix4,g=new r.Color,y=new r.Color;let x={};for(let t=0;tt().isEqual(r,e)))}_gatherCylindersColoringInfo(e){const t=e.instanceCount,r=e.attributes.color.array,n=e.attributes.color2.array,s=e.attributes.color.itemSize,i=new Array(t);let o=0,a=0;for(let e=0;e1e-7||Math.abs(r[a+1]-n[a+1])>1e-7||Math.abs(r[a+2]-n[a+2])>1e-7;i[e]=t,o+=t}return{is2Colored:i,needToSplit:o,addPerCylinder:e.getGeoParams().radialSegments}}_collectInstancedGeoInfo(e){e.geometry instanceof mr?this._collectSpheresInfo(e):e.geometry instanceof Ir&&this._collectCylindersInfo(e)}_collectMaterialInfo(e){const{uberOptions:t}=e.material;return{diffuse:t.diffuse.toArray(),opacity:t.opacity,shininess:t.shininess,specular:t.specular.toArray()}}_getCylinderInstanceMatrix(e,t,r){const n=e.attributes.matVector1.array,s=e.attributes.matVector2.array,i=e.attributes.matVector3.array,o=4*t;r.set(n[o],n[o+1],n[o+2],n[o+3],s[o],s[o+1],s[o+2],s[o+3],i[o],i[o+1],i[o+2],i[o+3],0,0,0,1)}_getSphereInstanceMatrix(e,t,r){const{offset:n}=e.attributes,s=t*n.itemSize,i=n.array[s],o=n.array[s+1],a=n.array[s+2],l=n.array[s+3];r.set(l,0,0,i,0,l,0,o,0,0,l,a,0,0,0,1)}}class Uc{constructor(){this._resultArray=[],this._info=null}getResult(e){return this._info=e,this._resultArray.push(this._writeHeader()),this._resultArray.push(this._writeDefinitions()),this._resultArray.push(this._writeObjects(e.models,e.materials)),this._resultArray.push(this._writeRelations()),this._resultArray.push(this._writeConnections()),this._info=null,this._resultArray.join("")}_writeHeader(){const e=new Date,t=`Miew FBX Exporter v${this._info.version}`;return`; FBX 6.1.0 project file\n; Created by ${t} Copyright (c) 2015-2026 EPAM Systems, Inc.\n; For support please contact miew@epam.com\n; ----------------------------------------------------\n\nFBXHeaderExtension: {\n FBXHeaderVersion: 1003\n FBXVersion: 6100\n CreationTimeStamp: {\n Version: 1000\n Year: ${e.getFullYear()}\n Month: ${e.getMonth()+1}\n Day: ${e.getDate()}\n Hour: ${e.getHours()}\n Minute: ${e.getMinutes()}\n Second: ${e.getSeconds()}\n Millisecond: ${e.getMilliseconds()}\n }\n Creator: "${t}"\n OtherFlags: {\n FlagPLE: 0\n }\n}\nCreationTime: "${e}"\nCreator: "${t}"\n`}_writeDefinitions(){return'\n; Object definitions\n;------------------------------------------------------------------\n\n\nDefinitions: {\n Version: 100\n Count: 3\n ObjectType: "Model" {\n Count: 1\n }\n ObjectType: "Geometry" {\n Count: 1\n }\n ObjectType: "Material" {\n Count: 1\n }\n ObjectType: "Pose" {\n Count: 1\n }\n ObjectType: "GlobalSettings" {\n Count: 1\n }\n} \n'}_models(){let e="";const{models:t}=this._info;for(let r=0;r-t.near?"hidden":"visible",a=1e4*(t.far- -this._vector.z)/(t.far-t.near),l=e.getElement();if(void 0===n.fog)l.style.color=i(e.userData.color),"transparent"!==e.userData.background&&(l.style.background=i(e.userData.background));else{const t=r.MathUtils.smoothstep(-this._vector.z,n.fog.near,n.fog.far);l.style.color=s(e.userData.color,n.fog.color,t),"transparent"!==e.userData.background&&(l.style.background=s(e.userData.background,n.fog.color,t))}this._vector.applyMatrix4(this._projectionMatrix);const c=`${e.userData!=={}?e.userData.translation:"translate(-50%, -50%) "}translate(${this._vector.x*this._widthHalf+this._widthHalf}px,${-this._vector.y*this._heightHalf+this._heightHalf}px)`;l.style.visibility=o,l.style.WebkitTransform=c,l.style.MozTransform=c,l.style.oTransform=c,l.style.transform=c,l.style.zIndex=Number(a).toFixed(0),l.parentNode!==this._domElement&&this._domElement.appendChild(l)}for(let r=0,s=e.children.length;r0&&(this._altObj.setObjects(i.objects),this._altObj.pivot=i.pivot,"axis"in i?this._altObj.axis=i.axis.clone():this._altObj.axis.set(0,0,1),e.set(s*t,s*n),this._altObj.translate(e),this.dispatchEvent({type:"change",action:"translate"}))}}this._lastUpdateTime=t}}(),th.prototype.reset=function(){this._state=Yc,this.object.quaternion.copy(Qc.set(0,0,0,1))},th.prototype.mousedown=function(e){if(!1!==this.enabled&&this._state===Yc){if(e.preventDefault(),e.stopPropagation(),this._state===Yc)if(0===e.button){this._affectedObj.stop();let t=!1;if(e.altKey){const e=this.getAltObj();t=e.objects.length>0,t&&(this._altObj.setObjects(e.objects),this._altObj.pivot=e.pivot,"axis"in e?this._altObj.axis=e.axis.clone():this._altObj.axis.set(0,0,1))}this._affectedObj=t?this._altObj:this._mainObj,this._state=t&&e.ctrlKey&&this._isTranslationAllowed?qc:Xc}else 2===e.button&&(this._state=Zc);this._state===Xc&&(this.convertMouseToOnCircle(this._mouseCurPos,e.pageX,e.pageY),this._mousePrevPos.copy(this._mouseCurPos)),this._state!==qc&&this._state!==Zc||(this.convertMouseToViewport(this._mouseCurPos,e.pageX,e.pageY),this._mousePrevPos.copy(this._mouseCurPos))}},th.prototype.mousemove=function(e){if(!1!==this.enabled&&this._state!==Yc)switch(e.preventDefault(),e.stopPropagation(),this._state){case Xc:this._mousePrevPos.copy(this._mouseCurPos),this.convertMouseToOnCircle(this._mouseCurPos,e.pageX,e.pageY),this.rotateByMouse(e.altKey&&!this._isAltObjFreeRotationAllowed||e.shiftKey),this._lastMouseMoveTime=this._clock.getElapsedTime();break;case qc:this._mousePrevPos.copy(this._mouseCurPos),this.convertMouseToViewport(this._mouseCurPos,e.pageX,e.pageY),this.translate();break;case Zc:this._mousePrevPos.copy(this._mouseCurPos),this.convertMouseToViewport(this._mouseCurPos,e.pageX,e.pageY),this.translatePivotByMouse()}},th.prototype.mousewheel=function(e){if(!1===this.enabled||!z.now.zooming||this._state!==Yc||e.shiftKey)return;e.preventDefault();let t=0;e.wheelDelta?t=e.wheelDelta/40:e.detail&&(t=-e.detail/3);let r=1+.05*t;r=Math.max(r,.01),this.scale(r)},th.prototype.mouseup=function(e){!1!==this.enabled&&this._state!==Yc&&(e.preventDefault(),e.stopPropagation(),this._state=Yc,this._clock.getElapsedTime()-this._lastMouseMoveTime>.1&&this._affectedObj.stop())},th.prototype.touchstartend=function(e){if(!1!==this.enabled)switch(e.preventDefault(),e.stopPropagation(),e.touches.length){case 1:this._state=Xc,this.convertMouseToOnCircle(this._mouseCurPos,e.touches[0].pageX,e.touches[0].pageY),this._mousePrevPos.copy(this._mouseCurPos);break;case 2:{this._mainObj.stop(),this._altObj.stop(),this._state=Kc;const t=e.touches[0].pageX-e.touches[1].pageX,r=e.touches[0].pageY-e.touches[1].pageY;this._touchDistanceCur=this._touchDistanceStart=Math.sqrt(t*t+r*r),this._scaleStart=this.object.scale.x;break}default:this._state=Yc}},th.prototype.touchmove=function(e){if(!1!==this.enabled&&this._state!==Yc)switch(e.preventDefault(),e.stopPropagation(),this._state){case Xc:this._mousePrevPos.copy(this._mouseCurPos),this.convertMouseToOnCircle(this._mouseCurPos,e.touches[0].pageX,e.touches[0].pageY),this.rotateByMouse(!1),this._lastMouseMoveTime=this._clock.getElapsedTime();break;case Kc:if(z.now.zooming){const t=e.touches[0].pageX-e.touches[1].pageX,r=e.touches[0].pageY-e.touches[1].pageY;this._touchDistanceCur=Math.sqrt(t*t+r*r);const n=this._scaleStart*this._touchDistanceCur/this._touchDistanceStart/this.object.scale.x;this.scale(n)}}},th.prototype.keydownup=function(e){if(!1!==this.enabled&&!1!==this.hotkeysEnabled)switch(e.keyCode){case 37:case 38:case 39:case 40:this._pressedKeys[e.keyCode]="keydown"===e.type,e.preventDefault(),e.stopPropagation()}},th.prototype.getKeyBindObject=function(){return Wc()},th.prototype.dispose=function(){for(let e=0;e{t.pickObject(s)}),0),this._lastClickPos=s,this._lastClickBeginTime=this._clickBeginTime}},nh.prototype.touchstart=function(e){e.preventDefault(),e.stopPropagation(),1===e.touches.length&&(this._lastTouchdownPos=this.getMouseInViewport(e.touches[0].pageX,e.touches[0].pageY))},nh.prototype.touchend=function(e){const t=this;if(e.preventDefault(),e.stopPropagation(),0===e.touches.length&&1===e.changedTouches.length){this.getMouseInViewport(e.changedTouches[0].pageX,e.changedTouches[0].pageY).sub(this._lastTouchdownPos).length()<.01&&setTimeout((()=>{t.pickObject(t._lastTouchdownPos)}),0)}},nh.prototype.dispose=function(){for(let e=0;e=524288?e-1048576:e}class hh{constructor(e,t,r){this._complex=e,this._secondary=null,this.isLoading=!1,this._framesRange={start:0,end:-1},this.frameIsReady=!1,this._buffer=null,this._frameRequest=null,this._callbacks=r,"function"==typeof t?(this._framesRequestLength=1,this._downloadDataFn=t):this.parseBinaryData(t,!0),this.reset(),this.setFrame(0)}_prepareBuffer(e,t){if(null==e&&(e=0),null==t&&(t=e+this._framesRequestLength),void 0!==this._framesCount&&(t=Math.min(this._framesCount-1,t)),this._downloadDataFn){const r=this,n=function(n){if(r.isLoading=!1,r._callbacks&&"function"==typeof r._callbacks.onLoadStatusChanged&&r._callbacks.onLoadStatusChanged(),r._buffer={data:n,state:"ready",start:e,end:t},null!==r._frameRequest){const e=r._frameRequest;r._frameRequest=null,r.setFrame(e)}},s=function(){r.isLoading=!1,r._callbacks&&"function"==typeof r._callbacks.onError&&r._callbacks.onError("Streaming failed")};this._buffer||(this._buffer={}),this._buffer.state="downloading",this.isLoading=!0,r._callbacks&&"function"==typeof r._callbacks.onLoadStatusChanged&&r._callbacks.onLoadStatusChanged(),this._downloadDataFn({start:e,end:t+1},n,s)}}_parseBuffer(){if(this._buffer&&"ready"===this._buffer.state){this._framesRange={start:this._buffer.start,end:this._buffer.end},this.parseBinaryData(this._buffer.data,!1);let e=(this._buffer.end+1)%this._framesCount;if(e>=this._framesCount&&(e=0),this._buffer={state:"none"},this._prepareBuffer(e,e+this._framesRequestLength),null!==this._frameRequest){const e=this._frameRequest;this._frameRequest=null,this.setFrame(e)}}}parseBinaryData(e){const t=new DataView(e);let r=0;const n=t.getUint32(r,!0);r+=4;const s=t.getUint32(r,!0);this._framesCount=s,this._framesRange.end=this._framesRange.end>0?Math.min(this._framesRange.end,s-1):s-1,r+=4,this._atomsCount=n;this._framesRequestLength=Math.ceil(1048576/(8*n));const i=this._framesRange.end-this._framesRange.start+1;if(n!==this._complex._atoms.length||e.byteLength!==12+i*n*8)throw new Error;const o=this._complex;let a=t.getUint32(r,!0),l=0;for(;a>1e3&&l>>28,o=ch((268435200&s)>>>8|0),a=ch((255&s)<<12|(4293918720&n)>>>20),l=ch(1048575&n);d[e]=0,i>0&&i<4?d[e]=1:4===i&&(d[e]=2),h[u++]=o/100,h[u++]=a/100,h[u++]=l/100}c.push(lh(d,o))}this._secondaryData=c,this._data=h}nextFrame(){this.setFrame((this._currFrame+1)%this._framesCount)}needsColorUpdate(e){return e instanceof go}getAtomColor(e,t){return e.getResidueColor(this._residues[t.residue._index],this._complex)}getResidueColor(e,t){return e.getResidueColor(this._residues[t._index],this._complex)}_updateSecondary(){let e;const t=this._residues;let r=t.length;for(e=0;e=this._framesRange.start&&e<=this._framesRange.end)this._currFrame=e,this._cachedResidues=!1,this._updateSecondary(),this.frameIsReady=!0;else if(this._frameRequest=e,this._buffer){const t=this;switch(this._buffer.state){case"none":this._prepareBuffer(e);break;case"ready":t._parseBuffer()}}else this._prepareBuffer(e)}disableEvents(){this._callbacks=null}static _vec=new r.Vector3;getAtomPos(e){const t=hh._vec,r=this,n=r._data,s=3*(r._atomsCount*(r._currFrame-r._framesRange.start)+e);return t.set(n[s],n[s+1],n[s+2]),t}getResidues(){return this._cachedResidues||this._complex.updateToFrame(this),this._residues}}const uh=hh;class dh{constructor(e,r){if(this.constructor===dh)throw new Error("Can not instantiate abstract class!");this.params=e,this.opts=t().merge(O.deriveDeep(z.now.objects[this.type],!0),r),this.needsRebuild=!1,this._mesh=null,this.id=null}identify(){const e={type:this.type,params:this.params},r=O.objectsDiff(this.opts,z.now.modes[this.id]);return t().isEmpty(r)||(e.opts=r),e}toString(){return`o=${this.type},${this.params.join(",")}`+O.compareOptionsWithDefaults(this.opts,z.defaults.objects[this.type])}getGeometry(){return this._mesh}destroy(){this._mesh&&tr.destroyObject(this._mesh)}}dh.prototype.type="__";const ph=dh;class mh extends ph{constructor(e,t){if(super(e,t),e.length<2)throw new Error("Wrong number of argumets on line object creation!");[this._id1,this._id2]=e}_getAtomFromName(e,t){const r=e.getAtomByFullname(t);if(!r)throw new Error(t+" - Wrong atom format it must be '#CHAIN_NAME.#RESIDUE_NUMBER.#ATOM_NAME' (e.g. 'A.38.CO1')");return r}build(e){const t=new r.BufferGeometry;this._atom1=this._getAtomFromName(e,this._id1),this._atom2=this._getAtomFromName(e,this._id2);const n=this._atom1.position,s=this._atom2.position,i=new Float32Array([n.x,n.y,n.z,s.x,s.y,s.z]);t.setAttribute("position",new r.BufferAttribute(i,3)),t.computeBoundingBox(),this._line=new ds.Line(t,new Kn({lights:!1,overrideColor:!0,dashedLine:!0,fogTransparent:z.now.bg.transparent})),this._line.computeLineDistances(),this._line.material.setUberOptions({fixedColor:new r.Color(this.opts.color),dashedLineSize:this.opts.dashSize,dashedLinePeriod:this.opts.dashSize+this.opts.gapSize}),this._line.material.updateUniforms(),this._line.raycast=function(e,t){},this._mesh=this._line;const o=e.getTransforms();o.length>0&&(this._mesh=new r.Group,this._mesh.add(this._line),Bo.applyTransformsToMeshes(this._mesh,o))}updateToFrame(e){if(!this._atom1||!this._atom2||!this._line)return;const t=this._line.geometry;t.vertices[0].copy(e.getAtomPos(this._atom1.index)),t.vertices[1].copy(e.getAtomPos(this._atom2.index)),this._line.computeLineDistances(),t.computeBoundingSphere(),t.verticesNeedUpdate=!0}}mh.prototype.constructor=mh,mh.prototype.type="line";const fh=mh;class _h extends r.RawShaderMaterial{constructor(e){super(e);const t={uniforms:{srcTex:{type:"t",value:null},srcDepthTex:{type:"t",value:null},srcTexSize:{type:"v2",value:new r.Vector2(512,512)},color:{type:"v3",value:null},threshold:{type:"f",value:null},opacity:{type:"f",value:1},thickness:{type:"v2",value:new r.Vector2(1,1)}},vertexShader:qt,fragmentShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexSize;\r\nuniform vec2 thickness;\r\nvarying vec2 vUv;\r\n\r\n#ifdef DEPTH_OUTLINE\r\n uniform sampler2D srcDepthTex; //depthTexture\r\n uniform vec3 color;\r\n uniform float threshold;\r\n#endif\r\n\r\nvoid main() {\r\n\r\n vec2 pixelSize = thickness / srcTexSize;\r\n\r\n #ifdef DEPTH_OUTLINE\r\n float c00 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,-pixelSize.y)).x;\r\n float c01 = texture2D(srcDepthTex, vUv + vec2(0,-pixelSize.y)).x;\r\n float c02 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,-pixelSize.y)).x;\r\n float c10 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,0)).x;\r\n float c12 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,0)).x;\r\n float c20 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,pixelSize.y)).x;\r\n float c21 = texture2D(srcDepthTex, vUv + vec2(0,pixelSize.y)).x;\r\n float c22 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,pixelSize.y)).x;\r\n\r\n float horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n float vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n float grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n\r\n gl_FragColor = ( grad > threshold ) ? vec4(color.rgb, 1.0) : gl_FragColor = texture2D(srcTex, vUv);\r\n\r\n #else\r\n vec4 c00 = texture2D(srcTex, vUv + vec2(-pixelSize.x,-pixelSize.y));\r\n vec4 c01 = texture2D(srcTex, vUv + vec2(0,-pixelSize.y));\r\n vec4 c02 = texture2D(srcTex, vUv + vec2(pixelSize.x,-pixelSize.y));\r\n vec4 c10 = texture2D(srcTex, vUv + vec2(-pixelSize.x,0));\r\n vec4 c12 = texture2D(srcTex, vUv + vec2(pixelSize.x,0));\r\n vec4 c20 = texture2D(srcTex, vUv + vec2(-pixelSize.x,pixelSize.y));\r\n vec4 c21 = texture2D(srcTex, vUv + vec2(0,pixelSize.y));\r\n vec4 c22 = texture2D(srcTex, vUv + vec2(pixelSize.x,pixelSize.y));\r\n\r\n vec4 horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n vec4 vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n vec4 grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n gl_FragColor = grad;\r\n #endif\r\n}\r\n",transparent:!0,depthTest:!1,depthWrite:!1};this.setValues(t)}copy(e){super.copy(e),this.depth=e.depth}setValues(e){if(void 0===e)return;super.setValues(e);const t={};this.depth&&(t.DEPTH_OUTLINE=1),this.defines=t}}_h.prototype.depth=!1;const gh=_h;class yh extends r.RawShaderMaterial{constructor(e){super(e),this.setValues.call(this,{uniforms:{srcTex:{type:"t",value:null},srcTexelSize:{type:"v2",value:new r.Vector2(1/512,1/512)},bgColor:{type:"c",value:new r.Color(16777215)}},vertexShader:qt,fragmentShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\n// edge end finding algorithm parameters\r\n#define FXAA_QUALITY_PS 8\r\n#define FXAA_QUALITY_P0 1.0\r\n#define FXAA_QUALITY_P1 1.5\r\n#define FXAA_QUALITY_P2 2.0\r\n#define FXAA_QUALITY_P3 2.0\r\n#define FXAA_QUALITY_P4 2.0\r\n#define FXAA_QUALITY_P5 2.0\r\n#define FXAA_QUALITY_P6 4.0\r\n#define FXAA_QUALITY_P7 12.0\r\n// constants\r\nfloat fxaaQualityEdgeThreshold = 0.125;\r\nfloat fxaaQualityEdgeThresholdMin = 0.0625;\r\nfloat fxaaQualitySubpix = 0.7; //0.65;\r\n// global params\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexelSize;\r\nuniform vec3 bgColor;\r\n// from vs\r\nvarying vec2 vUv;\r\n//=====================================================================//\r\n// calc luminance from rgb\r\n//'float FxaaLuma(vec3 rgb) {return rgb.y * (0.587/0.299) + rgb.x; } // Lotte's idea about game luminance\r\nfloat FxaaLuma(vec3 rgb) {return dot(rgb, vec3(0.299, 0.587, 0.114)); } // real luminance calculation\r\n // for non-real scene rendering\r\n// texture sampling by pixel position(coords) and offset(in pixels)\r\n vec3 FxaaTex(sampler2D tex, vec2 pos, vec2 off, vec2 res ) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos + off * res );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos + off * res ).xyz;\r\n #endif\r\n}\r\nvec3 FxaaTexTop(sampler2D tex, vec2 pos) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos).xyz;\r\n #endif\r\n}\r\nvec4 FxaaTexTopAlpha(sampler2D tex, vec2 pos) {\r\n return texture2D( tex, pos);\r\n}\r\n\r\n//=====================================================================//\r\nvoid main() {\r\n // renaming\r\n vec2 posM = vUv;\r\n // get luminance for neighbours\r\n float lumaS = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, 1.0 ), srcTexelSize));\r\n float lumaE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 0.0 ), srcTexelSize));\r\n float lumaN = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, -1.0 ), srcTexelSize));\r\n float lumaW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 0.0 ), srcTexelSize));\r\n float lumaM = FxaaLuma(FxaaTexTop(srcTex, posM));\r\n // find max and min luminance\r\n float rangeMax = max(max(lumaN, lumaW), max(lumaE, max(lumaS, lumaM)));\r\n float rangeMin = min(min(lumaN, lumaW), min(lumaE, min(lumaS, lumaM)));\r\n // calc maximum non-edge range\r\n float rangeMaxScaled = rangeMax * fxaaQualityEdgeThreshold;\r\n float range = rangeMax - rangeMin;\r\n float rangeMaxClamped = max(fxaaQualityEdgeThresholdMin, rangeMaxScaled);\r\n // exit when luma contrast is small (is not edge)\r\n if(range < rangeMaxClamped){\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n return;\r\n }\r\n float subpixRcpRange = 1.0/range;\r\n // note: the sampling coordinates can be calculated in vertex shader but the approach doesn't affect performance\r\n // visibly, thus we decided to leave calculation here for better readability.\r\n // calc other neighbours luminance\r\n float lumaNE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, -1.0 ), srcTexelSize));\r\n float lumaSW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 1.0 ), srcTexelSize));\r\n float lumaSE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 1.0 ), srcTexelSize));\r\n float lumaNW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, -1.0 ), srcTexelSize));\r\n/*--------------span calculation and subpix amount calulation-----------------*/\r\n float lumaNS = lumaN + lumaS;\r\n float lumaWE = lumaW + lumaE;\r\n float subpixNSWE = lumaNS + lumaWE;\r\n float edgeHorz1 = (-2.0 * lumaM) + lumaNS;\r\n float edgeVert1 = (-2.0 * lumaM) + lumaWE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNESE = lumaNE + lumaSE;\r\n float lumaNWNE = lumaNW + lumaNE;\r\n float edgeHorz2 = (-2.0 * lumaE) + lumaNESE;\r\n float edgeVert2 = (-2.0 * lumaN) + lumaNWNE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNWSW = lumaNW + lumaSW;\r\n float lumaSWSE = lumaSW + lumaSE;\r\n float edgeHorz4 = (abs(edgeHorz1) * 2.0) + abs(edgeHorz2);\r\n float edgeVert4 = (abs(edgeVert1) * 2.0) + abs(edgeVert2);\r\n float edgeHorz3 = (-2.0 * lumaW) + lumaNWSW;\r\n float edgeVert3 = (-2.0 * lumaS) + lumaSWSE;\r\n float edgeHorz = abs(edgeHorz3) + edgeHorz4;\r\n float edgeVert = abs(edgeVert3) + edgeVert4;\r\n/*--------------------subpix amount calulation------------------------------*/\r\n float subpixNWSWNESE = lumaNWSW + lumaNESE;\r\n float lengthSign = srcTexelSize.x;\r\n bool horzSpan = edgeHorz >= edgeVert;\r\n // debug code edge span visualization\r\n/*' if (horzSpan)\r\n gl_FragColor = vec4(0.0, 0.0, 1.0, 1.0);\r\n else\r\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\r\n return;*/\r\n float subpixA = subpixNSWE * 2.0 + subpixNWSWNESE;\r\n/*--------------------------------------------------------------------------*/\r\n if(!horzSpan) lumaN = lumaW;\r\n if(!horzSpan) lumaS = lumaE;\r\n if(horzSpan) lengthSign = srcTexelSize.y;\r\n float subpixB = (subpixA * (1.0/12.0)) - lumaM;\r\n/*--------------------------------------------------------------------------*/\r\n float gradientN = lumaN - lumaM;\r\n float gradientS = lumaS - lumaM;\r\n float lumaNN = lumaN + lumaM;\r\n float lumaSS = lumaS + lumaM;\r\n bool pairN = abs(gradientN) >= abs(gradientS);\r\n float gradient = max(abs(gradientN), abs(gradientS));\r\n if(pairN) lengthSign = -lengthSign;\r\n float subpixC = clamp(abs(subpixB) * subpixRcpRange, 0.0, 1.0);\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posB;\r\n posB = posM;\r\n vec2 offNP;\r\n offNP.x = (!horzSpan) ? 0.0 : srcTexelSize.x;\r\n offNP.y = ( horzSpan) ? 0.0 : srcTexelSize.y;\r\n if(!horzSpan) posB.x += lengthSign * 0.5;\r\n if( horzSpan) posB.y += lengthSign * 0.5;\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posN;\r\n posN = posB - offNP * FXAA_QUALITY_P0;\r\n vec2 posP;\r\n posP = posB + offNP * FXAA_QUALITY_P0;\r\n float subpixD = ((-2.0)*subpixC) + 3.0;\r\n float lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN));\r\n float subpixE = subpixC * subpixC;\r\n float lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP));\r\n/*--------------------------------------------------------------------------*/\r\n if(!pairN) lumaNN = lumaSS;\r\n float gradientScaled = gradient * 1.0/4.0;\r\n float lumaMM = lumaM - lumaNN * 0.5;\r\n float subpixF = subpixD * subpixE;\r\n bool lumaMLTZero = lumaMM < 0.0;\r\n/*---------------------looped edge-end search-------------------------------*/\r\n lumaEndN -= lumaNN * 0.5;\r\n lumaEndP -= lumaNN * 0.5;\r\n bool doneN = abs(lumaEndN) >= gradientScaled;\r\n bool doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P1;\r\n bool doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P1;\r\n/*--------------------------------------------------------------------------*/\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P2;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P2;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 3)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P3;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P3;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 4)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P4;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P4;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 5)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P5;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P5;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 6)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P6;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P6;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 7)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P7;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P7;\r\n/*--------------------------------------------------------------------------*/\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n/*----------------calculate subpix offset due to edge ends-------------------*/\r\n float dstN = posM.x - posN.x;\r\n float dstP = posP.x - posM.x;\r\n if(!horzSpan) dstN = posM.y - posN.y;\r\n if(!horzSpan) dstP = posP.y - posM.y;\r\n/*--------------------------------------------------------------------------*/\r\n bool goodSpanN = (lumaEndN < 0.0) != lumaMLTZero;\r\n float spanLength = (dstP + dstN);\r\n bool goodSpanP = (lumaEndP < 0.0) != lumaMLTZero;\r\n float spanLengthRcp = 1.0 / spanLength;\r\n/*--------------------------------------------------------------------------*/\r\n bool directionN = dstN < dstP;\r\n float dst = min(dstN, dstP);\r\n bool goodSpan = directionN ? goodSpanN : goodSpanP;\r\n float subpixG = subpixF * subpixF;\r\n float pixelOffset = (dst * (-spanLengthRcp)) + 0.5;\r\n float subpixH = subpixG * fxaaQualitySubpix;\r\n/*-----------------calc texture offest using subpix-------------------------*/\r\n float pixelOffsetGood = goodSpan ? pixelOffset : 0.0;\r\n float pixelOffsetSubpix = max(pixelOffsetGood, subpixH);\r\n\r\n float offset = pixelOffsetSubpix * lengthSign;\r\n #ifdef BG_TRANSPARENT\r\n // get original texel\r\n vec4 rgbaA = FxaaTexTopAlpha(srcTex, posM);\r\n // calc step to blended texel\r\n vec2 step = sign((!horzSpan) ? vec2 (offset, 0.0) : vec2 (0.0, offset));\r\n // get neighboring texel\r\n vec4 rgbaB = FxaaTexTopAlpha(srcTex, posM + step * srcTexelSize);\r\n // calc blend factor from offset\r\n float f = (!horzSpan) ? offset / srcTexelSize.x : offset / srcTexelSize.y;\r\n f = abs(f);\r\n // calc alpha (special formula to emulate blending with bg)\r\n gl_FragColor.a = 1.0 - mix(1.0 - rgbaA.a, 1.0 - rgbaB.a, f);\r\n // calc color (special formula to emulate blending with bg)\r\n gl_FragColor.rgb = mix(rgbaA.rgb * rgbaA.a, rgbaB.rgb * rgbaB.a, f) / gl_FragColor.a;\r\n #else\r\n if(!horzSpan) {\r\n posM.x += offset;\r\n } else {\r\n posM.y += offset;\r\n }\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n #endif\r\n return;\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1}),this.setValues(e)}copy(e){super.copy(e),this.depth=e.depth}setValues(e){if(void 0===e)return;super.setValues(e);const t={};this.bgTransparent&&(t.BG_TRANSPARENT=1),this.defines=t}}yh.prototype.bgTransparent=!1;const xh=yh,bh=[new r.Vector3(.295184,.077723,.068429),new r.Vector3(-.271976,-.365221,.838363),new r.Vector3(.547713,.467576,.488515),new r.Vector3(.662808,-.031733,.584758),new r.Vector3(-.025717,.218955,.657094),new r.Vector3(-.310153,-.365223,.370701),new r.Vector3(-.101407,-.006313,.747665),new r.Vector3(-.769138,.360399,.086847),new r.Vector3(-.271988,-.27514,.905353),new r.Vector3(.09674,-.566901,.700151),new r.Vector3(.562872,-.735136,.094647),new r.Vector3(.379877,.359278,.190061),new r.Vector3(.519064,-.023055,.405068),new r.Vector3(-.301036,.114696,.088885),new r.Vector3(-.282922,.598305,.487214),new r.Vector3(-.181859,.25167,.679702),new r.Vector3(-.191463,-.635818,.512919),new r.Vector3(-.293655,.427423,.078921),new r.Vector3(-.267983,.680534,.13288),new r.Vector3(.139611,.319637,.477439),new r.Vector3(-.352086,.31104,.653913),new r.Vector3(.321032,.805279,.487345),new r.Vector3(.073516,.820734,.414183),new r.Vector3(-.155324,.589983,.41146),new r.Vector3(.335976,.170782,.527627),new r.Vector3(.46346,-.355658,.167689),new r.Vector3(.222654,.59655,.769406),new r.Vector3(.922138,-.04207,.147555),new r.Vector3(-.72705,-.329192,.369826),new r.Vector3(-.090731,.53382,.463767),new r.Vector3(-.323457,-.876559,.238524),new r.Vector3(-.663277,-.372384,.342856)];class wh extends r.RawShaderMaterial{constructor(){super(),this.setValues.call(this,{uniforms:{noiseTexture:{type:"t",value:Hn.noiseTexture},noiseTexelSize:{type:"v2",value:new r.Vector2(1/Hn.noiseWidth,1/Hn.noiseHeight)},diffuseTexture:{type:"t",value:null},normalTexture:{type:"t",value:null},depthTexture:{type:"t",value:null},srcTexelSize:{type:"v2",value:new r.Vector2(1/512,1/512)},camNearFar:{type:"v2",value:new r.Vector2(1,10)},projMatrix:{type:"mat4",value:new r.Matrix4},aspectRatio:{type:"f",value:0},tanHalfFOV:{type:"f",value:0},samplesKernel:{type:"v3v",value:bh},kernelRadius:{type:"f",value:1},depthThreshold:{type:"f",value:1},factor:{type:"f",value:1}},vertexShader:qt,fragmentShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 32\r\nuniform vec3 samplesKernel[MAX_SAMPLES_COUNT];\r\nuniform sampler2D noiseTexture;\r\nuniform vec2 noiseTexelSize;\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D depthTexture;\r\nuniform sampler2D normalTexture;\r\nuniform vec2 srcTexelSize;\r\nuniform vec2 camNearFar;\r\nuniform mat4 projMatrix;\r\n\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\nuniform float kernelRadius;\r\nuniform float depthThreshold;\r\nuniform float factor;\r\n\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n // remap coordinates to prevent noise exture rescale\r\n vec2 vUvNoise = vUv / srcTexelSize * noiseTexelSize;\r\n vec4 normalData = texture2D(normalTexture, vUv);\r\n // return for background fragments (their normals are zero vectors)\r\n if (length(normalData.rgb) < EPSILON) {\r\n // 0.0 in alpha component means that it is background fragment\r\n gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);\r\n return;\r\n }\r\n //[0, 1] -> [-1, 1]\r\n vec3 normal = (normalData.rgb * 2.0 - 1.0);\r\n // normalData.a store 1.0 if normal was build for frontfaced surface\r\n // and 0.0 in other case\r\n if (normalData.a < EPSILON) {\r\n normal *= -1.0;\r\n }\r\n // get random vector for sampling sphere rotation\r\n vec3 randN = texture2D(noiseTexture, vUvNoise).rgb * 2.0 - 1.0;\r\n randN = normalize(randN);\r\n // build TBN (randomly rotated around normal)\r\n vec3 tangent = normalize(randN - normal * dot(randN, normal));\r\n vec3 bitangent = cross(tangent, normal);\r\n mat3 TBN = mat3(tangent, bitangent, normal);\r\n // calc AO value\r\n float AO = 0.0;\r\n for (int i = 0 ; i < MAX_SAMPLES_COUNT ; i++) {\r\n // rotate sampling kernel around normal\r\n vec3 reflectedSample = TBN * samplesKernel[i];\r\n // get sample\r\n vec3 samplePos = viewPos + reflectedSample * kernelRadius;\r\n\r\n // project sample to screen to get sample's screen pos\r\n vec4 SampleScrPos = vec4(samplePos, 1.0);\r\n // eye -> clip\r\n SampleScrPos = projMatrix * SampleScrPos;\r\n // normalize\r\n SampleScrPos.xy /= SampleScrPos.w;\r\n //[-1, 1] -> [0, 1]\r\n SampleScrPos.xy = (SampleScrPos.xy + vec2(1.0)) * 0.5;\r\n\r\n // get view z for sample projected to the objct surface\r\n float sampleDepth = CalcViewZ(SampleScrPos.xy);\r\n // calc occlusion made by object surface at the sample\r\n AO += step(samplePos.z, sampleDepth);\r\n }\r\n // calc result AO-map color\r\n AO = 1.0 - max(0.0, AO / float(MAX_SAMPLES_COUNT) * factor);\r\n // write value to AO-map\r\n gl_FragColor = vec4(AO, AO, AO, 1.0);\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1})}}const Sh=wh,vh=[-2,-1,0,1,2];class Ch extends r.RawShaderMaterial{constructor(){super(),this.setValues.call(this,{uniforms:{depthTexture:{type:"t",value:null},srcTexelSize:{type:"v2",value:new r.Vector2(1/512,1/512)},aoMap:{type:"t",value:null},samplesOffsets:{type:"fv1",value:vh}},vertexShader:qt,fragmentShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = res;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x + samplesOffsets[i] * srcTexelSize.x, y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb = res.rgb / weightSum;\r\n gl_FragColor = res;\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1})}}const Ah=Ch,Eh=[-2,-1,0,1,2];class Th extends r.RawShaderMaterial{constructor(e){super(e),this.setValues.call(this,{uniforms:{diffuseTexture:{type:"t",value:null},depthTexture:{type:"t",value:null},srcTexelSize:{type:"v2",value:new r.Vector2(1/512,1/512)},aoMap:{type:"t",value:null},samplesOffsets:{type:"fv1",value:Eh},projMatrix:{type:"mat4",value:new r.Matrix4},aspectRatio:{type:"f",value:0},tanHalfFOV:{type:"f",value:0},fogNearFar:{type:"v2",value:new r.Vector2(100,100)},fogColor:{type:"v4",value:new r.Vector4(0,.5,0,1)}},vertexShader:qt,fragmentShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nuniform mat4 projMatrix;\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\n#ifdef USE_FOG\r\n uniform vec2 fogNearFar;\r\n uniform vec4 fogColor;\r\n#endif\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 color = texture2D(diffuseTexture, vec2(x, y));\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = color;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x, y + samplesOffsets[i] * srcTexelSize.y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb /= weightSum;\r\n\r\n #if defined(USE_FOG) && !defined(FOG_TRANSPARENT)\r\n // Add fog to the result value\r\n // Proper way to get an image with fog and ao requires formula:\r\n // gl_FragColor = fragColor*AO*(1-fogFactor) + fogColor*fogFactor\r\n // But we have already fogged molecule to add AO too. Let's split the straight formula into our real steps!\r\n // We have: AO, fogFactor, fogColor,\r\n // color = fragColor*(1-fogFactor) + fogColor*fogFactor (it comes from diffuseTexture,\r\n // where molecule has been already drawn with fog)\r\n // Transform:\r\n // fragColor*AO*(1-fogFactor) + fogColor*fogFactor =\r\n // = [fragColor*(1-fogFactor) = color - fogColor*fogFactor] =\r\n // = (color - fogColor*fogFactor)*AO + fogColor*fogFactor =\r\n // = color*AO + fogColor*fogFactor*(1 - AO)\r\n // Result: gl_FragColor = color*AO + fogColor*fogFactor*(1 - AO)\r\n float fogFactor = smoothstep(fogNearFar.x, fogNearFar.y, - viewPos.z) * fogColor.a;\r\n gl_FragColor.rgb = color.rgb * res.rgb + fogColor.rgb * fogFactor *(vec3(1.0, 1.0, 1.0) - res.rgb);\r\n #else\r\n gl_FragColor.rgb = color.rgb * res.rgb;\r\n #endif\r\n gl_FragColor.a = color.a;\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1}),this.setValues(e)}setValues(e){if(void 0===e)return;super.setValues(e);const t={};this.useFog&&(t.USE_FOG=1),this.fogTransparent&&(t.FOG_TRANSPARENT=1),this.defines=t}}Th.prototype.useFog=!0,Th.prototype.fogTransparent=!1;const Rh=Th;class Mh extends r.RawShaderMaterial{constructor(){super();const e={uniforms:{srcL:{type:"t",value:null},srcR:{type:"t",value:null}},vertexShader:qt,fragmentShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nuniform sampler2D srcL;\r\nuniform sampler2D srcR;\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vec4 l = texture2D(srcL, vUv);\r\n vec4 r = texture2D(srcR, vUv);\r\n gl_FragColor = vec4(l.r, r.g, r.b, 1.0);\r\n}\r\n",transparent:!1,depthTest:!1,depthWrite:!1};this.setValues(e)}}const Ph=Mh;class Lh{constructor(){this.position=new r.Vector3(0,0,0),this.scale=1,this.orientation=new r.Quaternion(0,0,0,1)}set(e,t,r){this.position=e,this.scale=t,this.orientation=r}}class Nh{setup(e,t){this._startTime=void 0,this._endTime=void 0,this._isPaused=!1,this._srcView=e,this._dstView=t,this._isMoving=!1}isMoving(){return this._isMoving}wasStarted(){return void 0!==this._startTime&&void 0!==this._endTime}start(){this._startTime=Date.now();const e=z.now.interpolateViews?1500:0;this._endTime=this._startTime+e,this._isMoving=!0}getCurrentView(){if(void 0===this._srcView||void 0===this._dstView||!this._isMoving||!this.wasStarted())return{success:!1};let e=this.createView();const t=Date.now();if(t>this._endTime)return e=this._dstView,this.reset(),{success:!0,view:e};const r=(t-this._startTime)/(this._endTime-this._startTime);return e.position.copy(this._srcView.position),e.position.lerp(this._dstView.position,r),e.scale=(1-r)*this._srcView.scale+r*this._dstView.scale,e.orientation.copy(this._srcView.orientation),e.orientation.slerp(this._dstView.orientation,r),{success:!0,view:e}}reset(){this._startTime=this._endTime=0,this._isMoving=!1}pause(){this._isPaused||(this.setup(this.getCurrentView().view,this._dstView),this._isPaused=!0)}resume(){this._isPaused=!1}createView(){return new Lh}}function Ih(e,r){this.context=e,this._opts=t().merge({path:"/"},r)}lr(Ih.prototype),Ih.prototype.removeCookie=function(e){const t=this._toCount(e);let r=this._getSimpleCookie(t);if(r){this._removeSimpleCookie(t),r=parseInt(r,10);for(let t=0;tt?function(t){t.style.display="",t.style.cursor="pointer",t.style.left="calc(50% - 50px)",t.style.width="100px",t.textContent="ENTER VR";let r=null;function n(){r.removeEventListener("end",n),t.textContent="ENTER VR",r=null}function s(s){s.addEventListener("end",n),e._gfx.renderer.xr.setReferenceSpaceType("local"),e._gfx.renderer.xr.setSession(s),t.textContent="EXIT VR",r=s}t.onmouseenter=function(){t.style.opacity="1.0"},t.onmouseleave=function(){t.style.opacity="0.5"},t.onclick=function(){if(null===r){const t={optionalFeatures:["local-floor","bounded-floor"]};navigator.xr.requestSession("immersive-vr",t).then(s),e.moveSceneBehindHeadset()}else r.end()}}(r):function(e){e.style.display="",e.style.cursor="auto",e.style.left="calc(50% - 75px)",e.style.width="150px",e.textContent="VR NOT FOUND",e.onmouseenter=null,e.onmouseleave=null,e.onclick=null}(r))),r}const r=document.createElement("a");return r.href="https://webvr.info",r.innerHTML="WEBXR NOT SUPPORTED",r.style.left="calc(50% - 90px)",r.style.width="180px",r.style.textDecoration="none",t(r),r}class Dh{constructor(e){this._mainCamera=new r.PerspectiveCamera,this._button=null,this._onToggle=e,this._molContainer=new tr.RCGroup,this._user=new tr.RCGroup,this._scalingPivot=new r.Object3D,this._user.add(this._scalingPivot),this._controller1=null,this._controller2=null,this._pressedGripsCounter=0,this._distance=0,this._gfx=null}startScalingByControllers(){this._distance=this._controller1.position.distanceTo(this._controller2.position),tr.getMiddlePoint(this._controller1.position,this._controller2.position,this._scalingPivot.position),this._scalingPivot.scale.set(1,1,1),this._scalingPivot.updateMatrix(),this._scalingPivot.updateMatrixWorld(),this._scalingPivot.addSavingWorldTransform(this._molContainer)}stopScalingByControllers(){this._gfx.scene.addSavingWorldTransform(this._molContainer)}handleGripsDown(e){this._pressedGripsCounter++,2===this._pressedGripsCounter?this.startScalingByControllers():1===this._pressedGripsCounter&&e.target.addSavingWorldTransform(this._molContainer)}handleGripsUp(e){if(this._pressedGripsCounter--,1===this._pressedGripsCounter){this.stopScalingByControllers();(e.target===this._controller1?this._controller2:this._controller1).addSavingWorldTransform(this._molContainer)}else 0===this._pressedGripsCounter&&this._gfx.scene.addSavingWorldTransform(this._molContainer)}enable(e){if(!e)return void w.warn("WebVR couldn't be enabled, because gfx is not defined");this._gfx=e;const{renderer:t,camera:r}=e;if(!t)throw new Error("No renderer is available to toggle WebVR");if(!r)throw new Error("No camera is available to toggle WebVR");t.xr.enabled=!0,this._button?this._button.style.display="block":(this._button=Vh(this),document.body.appendChild(this._button)),this._mainFog=z.now.fog,z.set("fog",!1),this._plugVRNodesIntoScene(e,t),this._setControllersListeners(),this._onToggle&&this._onToggle(!0)}_plugVRNodesIntoScene(e,t){this._mainCamera.copy(e.camera),e.scene.add(this._user),e.scene.add(this._molContainer),this._molContainer.add(e.root),this._controller1=t.xr.getController(0),this._controller2=t.xr.getController(1);const r=this._createControllerMesh();this._controller1.add(r),this._controller2.add(r.clone()),this._user.add(this._controller1),this._user.add(this._controller2)}_setControllersListeners(){this._controller1.addEventListener("selectstart",(e=>{this.handleGripsDown(e)})),this._controller1.addEventListener("selectend",(e=>{this.handleGripsUp(e)})),this._controller2.addEventListener("selectstart",(e=>{this.handleGripsDown(e)})),this._controller2.addEventListener("selectend",(e=>{this.handleGripsUp(e)})),this._controller1.addEventListener("squeezestart",(e=>{this.handleGripsDown(e)})),this._controller1.addEventListener("squeezeend",(e=>{this.handleGripsUp(e)})),this._controller2.addEventListener("squeezestart",(e=>{this.handleGripsDown(e)})),this._controller2.addEventListener("squeezeend",(e=>{this.handleGripsUp(e)}))}disable(){if(!this._gfx)return;const{renderer:e,camera:t}=this._gfx;if(!e)throw new Error("No renderer is available to toggle WebVR");e.setAnimationLoop(null);const r=e.xr.getSession();r&&r.end(),e.xr.enabled=!1,this._button&&(this._button.style.display="none"),z.set("fog",this._mainFog),this._unplugVRNodesFromScene(t),this._onToggle&&this._onToggle(!1)}_unplugVRNodesFromScene(e){this._mainCamera&&e&&e.copy(this._mainCamera);const t=this._molContainer.children[0];t&&this._gfx.scene.add(t),this._molContainer.parent.remove(this._molContainer),this._user&&this._gfx.scene.remove(this._user),this._molContainer=null,this._user=null,this._scalingPivot=null,this._user=null,this._controller1=null,this._controller2=null}_createControllerMesh(){const e=new r.CylinderGeometry(.04,.04,.3),t=new Kn({lights:!1,overrideColor:!0});t.setUberOptions({fixedColor:new r.Color(4474111)}),t.updateUniforms();const n=new r.Mesh(e,t);return n.rotateX(-Math.PI/2),n}updateMoleculeScale(){if(!this._controller1||!this._controller2)return;const e=this;if(2===e._pressedGripsCounter){tr.getMiddlePoint(e._controller1.position,e._controller2.position,e._scalingPivot.position);const t=e._controller1.position.distanceTo(e._controller2.position),r=t/e._distance;e._scalingPivot.scale.multiplyScalar(r),e._distance=t}}moveSceneBehindHeadset(){const e=this._gfx,{camera:t}=e,r=this._molContainer;r.matrix.identity(),r.position.set(0,0,-4),r.updateMatrix(),r.matrixWorld.multiplyMatrices(t.matrixWorld,r.matrix),e.scene.addSavingWorldTransform(r),this._onToggle&&this._onToggle(!0)}getCanvas(){const e=this._gfx;return e&&e.renderer?e.renderer.domElement:null}}const{selectors:kh,Atom:zh,Residue:Fh,Chain:Bh,Molecule:Uh}=Ht,Gh=0,jh=1,Hh=2,$h="Could not find suitable loader for this source";r.ColorManagement.enabled=!1;const{createElement:Wh}=O;function Yh(e){const t=e.lastIndexOf(".");return t>=0&&(e=e.substr(0,t)),e}function Xh(e,t,r){void 0!==r?e.debug(`${t}... ${Math.floor(100*r)}%`):e.debug(`${t}...`)}function qh(){return z.now.fogColorEnable?z.now.fogColor:z.now.bg.color}function Kh(e){g.call(this),this._opts=t().merge({settingsCookie:"settings",cookiePath:"/"},e),this._gfx=null,this._interpolator=new Nh,this._container=e&&e.container||document.getElementById("miew-container")||t().head(document.getElementsByClassName("miew-container"))||document.body,this._containerRoot=this._container,this._running=!1,this._halting=!1,this._building=!1,this._needRender=!0,this._hotKeysEnabled=!0,this.settings=z;const r=w;r.console=!1,r.level="info",this.logger=r,this._cookies=new Oh(this),this.restoreSettings(),e&&e.settings&&this.settings.set(e.settings),this._spinner=null,this._loading=[],this._animInterval=null,this._visuals={},this._curVisualName=null,this._objects=[],this._sourceWindow=null,this.reset(),this._repr&&r.debug(`Selected ${this._repr.mode.name} mode with ${this._repr.colorer.name} colorer.`);const n=this;Kh.registeredPlugins.forEach((e=>{e.call(n)})),this._initOnSettingsChanged()}function Zh(e,t){const r=e;for(;r.firstChild;)r.removeChild(r.firstChild);r.appendChild(t)}Kh.prototype=Object.create(g.prototype),Kh.prototype.constructor=Kh,Kh.prototype.getMaxRepresentationCount=function(){return qo.NUM_REPRESENTATION_BITS},Kh.prototype._updateShadowCamera=function(){const e=new r.Matrix4,t=new r.Vector3,n={center:new r.Vector3,halfSize:new r.Vector3};return function(){this._gfx.scene.updateMatrixWorld();for(let r=0;r{n._onKeyDown(e)})),e.addEventListener("keyup",(e=>{n._onKeyUp(e)})),this._objectControls=new rh(this._gfx.root,this._gfx.pivot,this._gfx.camera,this._gfx.renderer.domElement,(()=>n._getAltObj())),this._objectControls.addEventListener("change",(e=>{switch(z.now.shadow.on&&n._updateShadowCamera(),e.action){case"rotate":n.dispatchEvent({type:"rotate",quaternion:e.quaternion});break;case"zoom":n.dispatchEvent({type:"zoom",factor:e.factor});break;default:n.dispatchEvent({type:e.action})}n.dispatchEvent({type:"transform"}),n._needRender=!0}));const t=this._gfx;this._picker=new sh(t.root,t.camera,t.renderer.domElement),this._picker.addEventListener("newpick",(e=>{n._onPick(e)})),this._picker.addEventListener("dblclick",(e=>{n.center(e)}))}catch(e){if("TypeError"===e.name&&"Cannot read property 'getExtension' of null"===e.message)this._showMessage("Could not create WebGL context.");else{if(!(e.message.search(/webgl/i)>1))throw this._showMessage("Viewer initialization failed."),e;this._showMessage(e.message)}return!1}const s=this._opts&&this._opts.load;if(s){const e=this._opts&&this._opts.type;this.load(s,{fileType:e,keepRepsInfo:!0})}return!0},Kh.prototype.term=function(){this._showMessage("Viewer has been terminated."),this._loading.forEach((e=>{e.cancel()})),this._loading.length=0,this.halt(),this._gfx=null},Kh.prototype._showMessage=function(e){const t=document.createElement("div");t.setAttribute("class","miew-message"),t.appendChild(document.createElement("p")).appendChild(document.createTextNode(e)),Zh(this._container,t)},Kh.prototype._showCanvas=function(){Zh(this._container,this._gfx.renderer.domElement)},Kh.prototype._requestAnimationFrame=function(e){const{xr:t}=this._gfx.renderer;t&&t.enabled?this._gfx.renderer.setAnimationLoop(e):requestAnimationFrame(e)},Kh.prototype._initGfx=function(){const e={width:this._container.clientWidth,height:this._container.clientHeight},t={preserveDrawingBuffer:!0,alpha:!0,premultipliedAlpha:!1};z.now.antialias&&(t.antialias=!0),e.renderer2d=new $c,e.renderer=new r.WebGLRenderer(t),e.renderer.shadowMap.enabled=z.now.shadow.on,e.renderer.shadowMap.autoUpdate=!1,e.renderer.shadowMap.type=r.PCFShadowMap,Dn.init(e.renderer),e.renderer.autoClear=!1,e.renderer.setPixelRatio(window.devicePixelRatio),e.renderer.setSize(e.width,e.height),e.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),e.renderer.clearColor(),e.renderer2d.setSize(e.width,e.height),e.camera=new r.PerspectiveCamera(z.now.camFov,e.width/e.height,z.now.camNear,z.now.camFar),e.camera.setMinimalFov(z.now.camFov),e.camera.position.z=z.now.camDistance,e.camera.updateProjectionMatrix(),e.camera.layers.set(tr.LAYERS.DEFAULT),e.camera.layers.enable(tr.LAYERS.VOLUME),e.camera.layers.enable(tr.LAYERS.VOLUME_BFPLANE),e.stereoCam=new r.StereoCamera,e.scene=new r.Scene;const n=qh();e.scene.fog=new r.Fog(n,z.now.camNear,z.now.camFar),e.root=new tr.RCGroup,e.scene.add(e.root),e.pivot=new tr.RCGroup,e.root.add(e.pivot),e.selectionScene=new r.Scene,e.selectionRoot=new r.Group,e.selectionRoot.matrixAutoUpdate=!1,e.selectionScene.add(e.selectionRoot),e.selectionPivot=new r.Group,e.selectionPivot.matrixAutoUpdate=!1,e.selectionRoot.add(e.selectionPivot);const s=new r.DirectionalLight(16777215,.45);s.position.set(0,.414,1),s.layers.enable(tr.LAYERS.TRANSPARENT),s.castShadow=!0,s.shadow.bias=.09,s.shadow.radius=z.now.shadow.radius,s.shadow.camera.layers.set(tr.LAYERS.SHADOWMAP);const i=e.renderer.getPixelRatio(),o=Math.max(e.width,e.height)*i;s.shadow.mapSize.width=o,s.shadow.mapSize.height=o,s.target.position.set(0,0,0),e.scene.add(s),e.scene.add(s.target);const a=new r.AmbientLight(6710886);a.layers.enable(tr.LAYERS.TRANSPARENT),e.scene.add(a),e.axes=new ih(e.root,e.camera);const l=e.width*i,c=e.height*i;e.offscreenBuf=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.NearestFilter,format:r.RGBAFormat,depthBuffer:!0}),e.offscreenBuf.depthTexture=new r.DepthTexture,e.offscreenBuf.depthTexture.type=r.UnsignedShortType,e.offscreenBuf2=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),e.offscreenBuf3=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),e.offscreenBuf4=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),e.volBFTex=e.offscreenBuf3,e.volFFTex=e.offscreenBuf4,e.volWFFTex=e.offscreenBuf,e.offscreenBuf5=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,type:r.FloatType,depthBuffer:!1}),e.offscreenBuf6=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,type:r.FloatType,depthBuffer:!1}),e.offscreenBuf7=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,type:r.FloatType,depthBuffer:!0}),e.volBFTex=e.offscreenBuf5,e.volFFTex=e.offscreenBuf6,e.volWFFTex=e.offscreenBuf7,e.stereoBufL=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),e.stereoBufR=new r.WebGLRenderTarget(l,c,{minFilter:r.LinearFilter,magFilter:r.LinearFilter,format:r.RGBAFormat,depthBuffer:!1}),this._gfx=e,this._showCanvas(),this._embedWebXR("WEBVR"===z.now.stereo),this._container.appendChild(e.renderer2d.getElement());const h=new m;h.domElement.style.position="absolute",h.domElement.style.right="0",h.domElement.style.bottom="0",this._container.appendChild(h.domElement),this._fps=h,this._fps.show(z.now.fps)},Kh.prototype._initListeners=function(){const e=this;window.addEventListener("resize",(()=>{e._onResize()}))},Kh.prototype._makeUniqueVisualName=function(e){if(!e)return Math.random().toString();let t=e,r=1;for(;this._visuals.hasOwnProperty(t);)t=`${e} (${r.toString()})`,r++;return t},Kh.prototype._addVisual=function(e){if(!e)return null;const t=this._makeUniqueVisualName(e.name);return e.name=t,this._visuals[t]=e,this._gfx.pivot.add(e),e.getSelectionGeo&&this._gfx.selectionPivot.add(e.getSelectionGeo()),t},Kh.prototype._removeVisual=function(e){let t="",r=null;e instanceof sr?(({name:t}=e),r=e):"string"==typeof e&&(t=e,r=this._visuals[t]),r&&this._visuals.hasOwnProperty(t)&&this._visuals[t]===r&&(t===this._curVisualName&&(this._curVisualName=void 0),delete this._visuals[t],r.release(),this._needRender=!0)},Kh.prototype._forEachVisual=function(e){for(const t in this._visuals)this._visuals.hasOwnProperty(t)&&e(this._visuals[t])},Kh.prototype._releaseAllVisuals=function(){if(this._gfx&&this._gfx.pivot){for(const e in this._visuals)this._visuals.hasOwnProperty(e)&&this._visuals[e].release();this._visuals={}}},Kh.prototype._forEachComplexVisual=function(e){if(this._gfx&&this._gfx.pivot)for(const t in this._visuals)this._visuals.hasOwnProperty(t)&&this._visuals[t]instanceof qo&&e(this._visuals[t])},Kh.prototype._getComplexVisual=function(e){e=e||this._curVisualName;let t=null,r=null;return this._forEachComplexVisual((n=>{t=n,n.name===e&&(r=n)})),r||t},Kh.prototype._getVolumeVisual=function(){let e=null;return this._forEachVisual((t=>{t instanceof ha&&(e=t)})),e},Kh.prototype._getVisualForComplex=function(e){if(!e)return null;let t=null;return this._forEachComplexVisual((r=>{r.getComplex()===e&&(t=r)})),t},Kh.prototype.getVisuals=function(){return Object.keys(this._visuals)},Kh.prototype.getComplexVisualsCount=function(){let e=0;return this._forEachComplexVisual((()=>e++)),e},Kh.prototype.getCurrentVisual=function(){return this._curVisualName},Kh.prototype.setCurrentVisual=function(e){this._visuals[e]&&(this._curVisualName=e)},Kh.prototype.run=function(){if(!this._running){if(this._running=!0,this._halting)return void(this._halting=!1);this._objectControls.enable(!0),this._interpolator.resume(),this._requestAnimationFrame((()=>this._onTick()))}},Kh.prototype.halt=function(){this._running&&(this._discardComponentEdit(),this._discardFragmentEdit(),this._objectControls.enable(!1),this._interpolator.pause(),this._halting=!0)},Kh.prototype.enableHotKeys=function(e){this._hotKeysEnabled=e,this._objectControls.enableHotkeys(e)},Kh.prototype._onResize=function(){const e=this._gfx;e&&(this._needRender=!0,e.width=this._container.clientWidth,e.height=this._container.clientHeight,e.camera.aspect=e.width/e.height,e.camera.setMinimalFov(z.now.camFov),e.camera.updateProjectionMatrix(),e.renderer.setSize(e.width,e.height),e.renderer2d.setSize(e.width,e.height),this.dispatchEvent({type:"resize"}))},Kh.prototype._resizeOffscreenBuffers=function(e,t,r){const n=this._gfx,s="NONE"===(r=r||"NONE")||"ANAGLYPH"===r,i=s?1:.5;n.offscreenBuf.setSize(i*e,t),n.offscreenBuf2.setSize(i*e,t),n.offscreenBuf3.setSize(i*e,t),n.offscreenBuf4.setSize(i*e,t),n.offscreenBuf5&&n.offscreenBuf5.setSize(i*e,t),n.offscreenBuf6&&n.offscreenBuf6.setSize(i*e,t),n.offscreenBuf7&&n.offscreenBuf7.setSize(i*e,t),s&&(n.stereoBufL.setSize(e,t),n.stereoBufR.setSize(e,t))},Kh.prototype._onTick=function(){if(this._halting)return this._running=!1,void(this._halting=!1);this._fps.update(),this._requestAnimationFrame((()=>this._onTick())),this._onUpdate(),this._needRender&&(this._onRender(),this._needRender=!z.now.suspendRender||"WEBVR"===z.now.stereo)},Kh.prototype._getBSphereRadius=function(){let e=0;return this._forEachVisual((t=>{e=Math.max(e,t.getBoundaries().boundingSphere.radius)})),e*this._objectControls.getScale()},Kh.prototype.getOBB=function(){const e=new r.Sphere,t=new r.Box3,n=new r.Box3,s=new r.Matrix4,i=[new r.Vector3,new r.Vector3,new r.Vector3,new r.Vector3];return function(r,o){n.makeEmpty(),this._forEachVisual((s=>{e.copy(s.getBoundaries().boundingSphere),e.applyMatrix4(s.matrixWorld).applyMatrix4(r),e.getBoundingBox(t),n.union(t)})),n.getCenter(o.center),s.copy(r).invert(),o.center.applyMatrix4(s);const{min:a}=n,{max:l}=n;i[0].set(a.x,a.y,a.z),i[1].set(l.x,a.y,a.z),i[2].set(a.x,l.y,a.z),i[3].set(a.x,a.y,l.z);for(let e=0,t=i.length;e{e.getComplex().update()})),z.now.autobuild&&!this._loading.length&&!this._building&&this._needRebuild()&&this.rebuild(),this._loading.length||this._building||this._needRebuild()||this._updateView(),this._updateFog(),this._gfx.renderer.xr.enabled&&this.webVR.updateMoleculeScale()},Kh.prototype._onRender=function(){const e=this._gfx;e.scene.updateMatrixWorld(),e.camera.updateMatrixWorld(),this._clipPlaneUpdateValue(this._getBSphereRadius()),this._fogFarUpdateValue(),e.renderer.setRenderTarget(null),e.renderer.clear(),this._renderFrame(z.now.stereo)},Kh.prototype._renderFrame=function(){const e=new Ph,t=new r.Vector2;return function(r){const n=this._gfx,{renderer:s}=n;s.getSize(t),"NONE"!==r&&(n.camera.focus=n.camera.position.z,n.stereoCam.aspect=1,"ANAGLYPH"===r?n.stereoCam.update(n.camera):n.stereoCam.updateHalfSized(n.camera,z.now.camFov));const i=n.renderer.getPixelRatio();switch(this._resizeOffscreenBuffers(t.width*i,t.height*i,r),this._renderShadowMap(),r){case"WEBVR":case"NONE":this._renderScene(n.camera,!1);break;case"SIMPLE":case"DISTORTED":s.setScissorTest(!0),s.setScissor(0,0,t.width/2,t.height),s.setViewport(0,0,t.width/2,t.height),this._renderScene(this._gfx.stereoCam.cameraL,"DISTORTED"===r),s.setScissor(t.width/2,0,t.width/2,t.height),s.setViewport(t.width/2,0,t.width/2,t.height),this._renderScene(this._gfx.stereoCam.cameraR,"DISTORTED"===r),s.setScissorTest(!1);break;case"ANAGLYPH":this._renderScene(this._gfx.stereoCam.cameraL,!1,n.stereoBufL),this._renderScene(this._gfx.stereoCam.cameraR,!1,n.stereoBufR),s.setRenderTarget(null),e.uniforms.srcL.value=n.stereoBufL.texture,e.uniforms.srcR.value=n.stereoBufR.texture,n.renderer.renderScreenQuad(e)}n.renderer2d.render(n.scene,n.camera),z.now.axes&&n.axes&&!n.renderer.xr.enabled&&n.axes.render(s)}}(),Kh.prototype._onBgColorChanged=function(){const e=this._gfx,t=qh();e&&(e.scene.fog&&e.scene.fog.color.set(t),e.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent))),this._needRender=!0},Kh.prototype._onFogColorChanged=function(){const e=this._gfx,t=qh();e&&e.scene.fog&&e.scene.fog.color.set(t),this._needRender=!0},Kh.prototype._setUberMaterialValues=function(e){this._gfx.root.traverse((t=>{(t instanceof r.Mesh||t instanceof r.LineSegments||t instanceof r.Line)&&t.material instanceof Kn&&(t.material.setValues(e),t.material.needsUpdate=!0)}))},Kh.prototype._enableMRT=function(e,t,r){const n=this._gfx,s=n.renderer.getContext(),{properties:i}=n.renderer;if(!e)return void s.drawBuffers([s.COLOR_ATTACHMENT0,null]);n.renderer.setRenderTarget(r);const o=i.get(r.texture).__webglTexture;s.bindTexture(s.TEXTURE_2D,o),n.renderer.setRenderTarget(t);const a=i.get(t).__webglFramebuffer,l=i.get(t.texture).__webglTexture;s.bindFramebuffer(s.FRAMEBUFFER,a),a.width=t.width,a.height=t.height,s.framebufferTexture2D(s.FRAMEBUFFER,s.COLOR_ATTACHMENT0,s.TEXTURE_2D,l,0),s.framebufferTexture2D(s.FRAMEBUFFER,s.COLOR_ATTACHMENT1,s.TEXTURE_2D,o,0),s.drawBuffers([s.COLOR_ATTACHMENT0,s.COLOR_ATTACHMENT1])},Kh.prototype._renderScene=function(e,t,r){t=t||!1,r=r||null;const n=this._gfx;if(n.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),n.renderer.setRenderTarget(r),n.renderer.clear(),n.renderer.xr.enabled)return void n.renderer.render(n.scene,e);n.renderer.setClearColor(0,0),n.renderer.setRenderTarget(n.offscreenBuf4),n.renderer.clearColor(),n.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),n.renderer.setRenderTarget(n.offscreenBuf),n.renderer.clear();const s=null!==this._getComplexVisual(),i=this._getVolumeVisual(),o=s&&z.now.ao;o&&this._enableMRT(!0,n.offscreenBuf,n.offscreenBuf4),"prepass"===z.now.transparency?this._renderWithPrepassTransparency(e,n.offscreenBuf):"standard"===z.now.transparency&&(n.renderer.setRenderTarget(n.offscreenBuf),n.renderer.render(n.scene,e)),o&&this._enableMRT(!1,null,null);const a=s&&z.now.outline.on,l=s&&z.now.fxaa,c=null!==i&&null!=i.getMesh().material;let h=o||a||c||l||t?n.offscreenBuf2:r,u=n.offscreenBuf;o?(this._performAO(u,n.offscreenBuf4,n.offscreenBuf.depthTexture,h,n.offscreenBuf3,n.offscreenBuf2),l||t||c||a||(u=h,h=r,n.renderer.setRenderTarget(h),n.renderer.renderScreenQuadFromTex(u.texture,1))):(n.renderer.setRenderTarget(h),n.renderer.renderScreenQuadFromTex(u.texture,1)),a&&(u=h,h=c||l||t?n.offscreenBuf3:r,null!=u&&this._renderOutline(e,n.offscreenBuf,u,h)),this._renderSelection(e,n.offscreenBuf,h),c&&(n.renderer.setRenderTarget(n.offscreenBuf),n.renderer.renderScreenQuadFromTex(h.texture,1),h=n.offscreenBuf,this._renderVolume(i,e,h,n.volBFTex,n.volFFTex,n.volWFFTex),l||t||(n.renderer.setRenderTarget(r),n.renderer.renderScreenQuadFromTex(h.texture,1))),u=h,l&&(h=t?n.offscreenBuf4:r,this._performFXAA(u,h),u=h),t&&(h=r,this._performDistortion(u,h,!0))},Kh.prototype._performDistortion=function(){const e=new r.Scene,t=new r.OrthographicCamera(-1,1,1,-1,-500,1e3),n=new r.RawShaderMaterial({uniforms:{srcTex:{type:"t",value:null},aberration:{type:"fv3",value:new r.Vector3(1)}},vertexShader:qt,fragmentShader:"/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform vec3 aberration;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n \r\n gl_FragColor.r = texture2D(srcTex, 0.5 * (uv * aberration[0] + 1.0)).r;\r\n gl_FragColor.g = texture2D(srcTex, 0.5 * (uv * aberration[1] + 1.0)).g;\r\n gl_FragColor.b = texture2D(srcTex, 0.5 * (uv * aberration[2] + 1.0)).b;\r\n gl_FragColor.a = 1.0;\r\n}",transparent:!1,depthTest:!1,depthWrite:!1}),s=tr.buildDistorionMesh(10,10,z.now.debug.stereoBarrel);return e.add(new ds.Mesh(s,n)),function(r,s,i){this._gfx.renderer.setRenderTarget(s),this._gfx.renderer.clear(),i?(n.uniforms.srcTex.value=r.texture,n.uniforms.aberration.value.set(.995,1,1.01),this._gfx.renderer.render(e,t)):this._gfx.renderer.renderScreenQuadFromTexWithDistortion(r,z.now.debug.stereoBarrel)}}(),Kh.prototype._renderOutline=function(){const e=new gh({depth:!0});return function(t,n,s,i){const o=this._gfx;e.uniforms.srcTex.value=s.texture,e.uniforms.srcDepthTex.value=n.depthTexture,e.uniforms.srcTexSize.value.set(n.width,n.height),e.uniforms.color.value=new r.Color(z.now.outline.color),e.uniforms.threshold.value=z.now.outline.threshold,e.uniforms.thickness.value=new r.Vector2(z.now.outline.thickness,z.now.outline.thickness),o.renderer.setRenderTarget(i),o.renderer.renderScreenQuad(e)}}(),Kh.prototype._renderShadowMap=function(){const e={minFilter:r.NearestFilter,magFilter:r.NearestFilter,format:r.RGBAFormat};return function(){if(!z.now.shadow.on)return;const t=this._gfx,n=t.renderer.getRenderTarget(),s=t.renderer.getActiveCubeFace(),i=t.renderer.getActiveMipmapLevel(),o=t.renderer.state;o.setBlending(r.NoBlending),o.buffers.color.setClear(1,1,1,1),o.buffers.depth.setTest(!0),o.setScissorTest(!1);for(let n=0;n0)return!0}return!1},Kh.prototype._renderSelection=function(){const e=new gh;return function(t,r,n){const s=this._gfx;s.renderer.setClearColor("black",0),s.renderer.setRenderTarget(r),s.renderer.clear(!0,!1,!1),this._hasSelectionToRender()?(s.selectionRoot.matrix=s.root.matrix,s.selectionPivot.matrix=s.pivot.matrix,s.renderer.render(s.selectionScene,t)):s.renderer.renderDummyQuad(),s.renderer.setRenderTarget(n),s.renderer.renderScreenQuadFromTex(r.texture,.6),e.uniforms.srcTex.value=r.texture,e.uniforms.srcTexSize.value.set(r.width,r.height),s.renderer.renderScreenQuad(e)}}(),Kh.prototype._checkVolumeRenderingSupport=function(e){if(!e)return!1;const t=this._gfx,r=t.renderer.getRenderTarget();t.renderer.setRenderTarget(e);const n=t.renderer.getContext(),s=n.checkFramebufferStatus(n.FRAMEBUFFER);return t.renderer.setRenderTarget(r),s===n.FRAMEBUFFER_COMPLETE||(this.logger.warn("Device doesn't support electron density rendering"),!1)},Kh.prototype._renderVolume=function(){const e=new sa.BackFacePosMaterial,t=new sa.FrontFacePosMaterial,n=(new r.Matrix4).makeTranslation(.5,.5,.5),s=new r.Matrix4;let i;return function(r,o,a,l,c,h){const u=this._gfx;if(void 0===i&&(i=this._checkVolumeRenderingSupport(l)),!i)return;const d=r.getMesh();d.rebuild(u.camera),u.renderer.setClearColor("black",0),u.renderer.setRenderTarget(l),u.renderer.clear(),u.renderer.setRenderTarget(c),u.renderer.clear(),u.renderer.setRenderTarget(h),u.renderer.clear(),u.renderer.setRenderTarget(l),o.layers.set(tr.LAYERS.VOLUME_BFPLANE),u.renderer.render(u.scene,o),o.layers.set(tr.LAYERS.VOLUME),u.scene.overrideMaterial=e,u.renderer.render(u.scene,o),u.renderer.setRenderTarget(c),o.layers.set(tr.LAYERS.VOLUME),u.scene.overrideMaterial=t,u.renderer.render(u.scene,o),u.scene.overrideMaterial=null,o.layers.set(tr.LAYERS.DEFAULT),s.copy(d.matrixWorld).invert(),Kn.prototype.uberOptions.world2colorMatrix.multiplyMatrices(n,s),o.layers.set(tr.LAYERS.COLOR_FROM_POSITION),u.renderer.setRenderTarget(h),u.renderer.render(u.scene,o);const p=d.material;p.uniforms._BFRight.value=l.texture,p.uniforms._FFRight.value=c.texture,p.uniforms._WFFRight.value=h.texture,o.layers.set(tr.LAYERS.VOLUME),u.renderer.setRenderTarget(a),u.renderer.render(u.scene,o),o.layers.set(tr.LAYERS.DEFAULT)}}(),Kh.prototype._renderWithPrepassTransparency=function(e,t){const r=this._gfx;r.renderer.setRenderTarget(t),e.layers.set(tr.LAYERS.DEFAULT),r.renderer.render(r.scene,e),e.layers.set(tr.LAYERS.PREPASS_TRANSPARENT),r.renderer.getContext().colorMask(!1,!1,!1,!1),r.renderer.render(r.scene,e),r.renderer.getContext().colorMask(!0,!0,!0,!0),e.layers.set(tr.LAYERS.TRANSPARENT),r.renderer.render(r.scene,e),e.layers.set(tr.LAYERS.DEFAULT)},Kh.prototype._performFXAA=function(){const e=new xh;return function(t,r){if(void 0===t||void 0===r)return;const n=this._gfx;n.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),n.renderer.setRenderTarget(r),n.renderer.clear(),e.uniforms.srcTex.value=t.texture,e.uniforms.srcTexelSize.value.set(1/t.width,1/t.height),e.uniforms.bgColor.value.set(z.now.bg.color),e.bgTransparent!==z.now.bg.transparent&&(e.setValues({bgTransparent:z.now.bg.transparent}),e.needsUpdate=!0),n.renderer.renderScreenQuad(e)}}(),Kh.prototype._performAO=function(){const e=new Sh,t=new Ah,n=new Rh,s=new r.Vector3;return function(i,o,a,l,c,h){if(!(i&&o&&a&&l&&c&&h))return;const u=this._gfx,d=Math.tan(.5*r.MathUtils.DEG2RAD*u.camera.fov);e.uniforms.diffuseTexture.value=i.texture,e.uniforms.depthTexture.value=a,e.uniforms.normalTexture.value=o.texture,e.uniforms.srcTexelSize.value.set(1/i.width,1/i.height),e.uniforms.camNearFar.value.set(u.camera.near,u.camera.far),e.uniforms.projMatrix.value=u.camera.projectionMatrix,e.uniforms.aspectRatio.value=u.camera.aspect,e.uniforms.tanHalfFOV.value=d,u.root.matrix.extractScale(s),e.uniforms.kernelRadius.value=z.now.debug.ssaoKernelRadius*s.x,e.uniforms.depthThreshold.value=2*this._getBSphereRadius(),e.uniforms.factor.value=z.now.debug.ssaoFactor,u.renderer.setRenderTarget(h),u.renderer.renderScreenQuad(e),t.uniforms.aoMap.value=h.texture,t.uniforms.srcTexelSize.value.set(1/h.width,1/h.height),t.uniforms.depthTexture.value=a,u.renderer.setRenderTarget(c),u.renderer.renderScreenQuad(t),n.uniforms.aoMap.value=c.texture,n.uniforms.diffuseTexture.value=i.texture,n.uniforms.srcTexelSize.value.set(1/c.width,1/c.height),n.uniforms.depthTexture.value=a,n.uniforms.projMatrix.value=u.camera.projectionMatrix,n.uniforms.aspectRatio.value=u.camera.aspect,n.uniforms.tanHalfFOV.value=d;const{fog:p}=u.scene;p&&(n.uniforms.fogNearFar.value.set(p.near,p.far),n.uniforms.fogColor.value.set(p.color.r,p.color.g,p.color.b,z.now.fogAlpha)),n.useFog===z.now.fog&&n.fogTransparent===z.now.bg.transparent||(n.setValues({useFog:z.now.fog,fogTransparent:z.now.bg.transparent}),n.needsUpdate=!0),u.renderer.setRenderTarget(l),u.renderer.renderScreenQuad(n)}}(),Kh.prototype.reset=function(){this._picker&&this._picker.reset(),this._lastPick=null,this._releaseAllVisuals(),this._setEditMode(Gh),this._resetObjects(),this._gfx&&(tr.clearTree(this._gfx.pivot),this._gfx.renderer2d.reset()),this.setNeedRender()},Kh.prototype._resetScene=function(){this._objectControls.reset(),this._objectControls.allowTranslation(!0),this._objectControls.allowAltObjFreeRotation(!0),this.resetReps(),this.resetPivot(),this.rebuildAll()},Kh.prototype.resetView=function(){this._picker&&this._picker.reset(),this._setEditMode(Gh),this._resetScene(),this._forEachComplexVisual((e=>{e.updateSelectionMask({}),e.rebuildSelectionGeometry()}))},Kh.prototype._export=function(e){const r=t().head(jc.exporters.find({format:e}));if(!r)return this.logger.error("Could not find suitable exporter for this source"),Promise.reject(new Error("Could not find suitable exporter for this source"));if(this.dispatchEvent({type:"exporting"}),this._visuals[this._curVisualName]instanceof qo){let e=null;r.SourceClass===qo?e=this._visuals[this._curVisualName]:r.SourceClass===Bt&&(e=this._visuals[this._curVisualName]._complex);return new r(e,{miewVersion:Kh.VERSION}).export().then((e=>e))}return this._visuals[this._curVisualName]instanceof ha?Promise.reject(new Error("Sorry, exporter for volume data not implemented yet")):Promise.reject(new Error("Unexpected format of data"))};const Qh=/^(?:(pdb|cif|ccp4|dsn6):\s*)?(\d[a-z\d]{3})$/i,Jh=/^(?:pc|pubchem):\s*([a-z]+)$/i,eu=/^([a-z][a-z\d\-+.]*):/i;function tu(e,r,n){return new Promise((s=>{if(n.shouldCancel())throw new Error("Operation cancelled");n.notify({type:"fetching"}),e=function(e,r){if(!t().isString(e))return e;const n=Qh.exec(e);if(n){let[,t="pdb",s]=n;switch(t=t.toLowerCase(),s=s.toUpperCase(),t){case"pdb":e=`https://files.rcsb.org/download/${s}.pdb`;break;case"cif":e=`https://files.rcsb.org/download/${s}.cif`;break;case"ccp4":e=`https://www.ebi.ac.uk/pdbe/coordinates/files/${s.toLowerCase()}.ccp4`;break;case"dsn6":e=`https://edmaps.rcsb.org/maps/${s.toLowerCase()}_2fofc.dsn6`;break;default:throw new Error("Unexpected data format shortcut")}return r.fileType=t,r.fileName=`${s}.${t}`,r.sourceType="url",e}const s=Jh.exec(e);if(s){const t=s[1].toLowerCase();return e=`https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${t}/JSON?record_type=3d`,r.fileType="pubchem",r.fileName=`${t}.json`,r.sourceType="url",e}return"url"!==r.sourceType&&void 0!==r.sourceType||(r.sourceType="url",eu.test(e)||(e=O.resolveURL(e))),e}(e,r);const i=t().head(jc.loaders.find({type:r.sourceType,source:e}));if(!i)throw new Error($h);const o=r.fileName||i.extractName(e);if(o){const[e,n]=O.splitFileName(o);t().defaults(r,{name:e,fileExt:n,fileName:o})}!function(e){let{binary:r}=e;if(void 0!==e.fileType){const n=t().head(jc.parsers.find({format:e.fileType}));if(!n)throw new Error("Could not find suitable parser for this format");r=n.binary||!1}if(void 0===r&&void 0!==e.fileExt){const n=t().head(jc.parsers.find({ext:e.fileExt}));n&&(r=n.binary||!1)}void 0!==e.fileExt&&".man"===e.fileExt.toLowerCase()&&(e.binary=!0,e.animation=!0),void 0!==r&&void 0!==e.binary&&e.binary!==r&&e.context.logger.warn("Overriding incorrect binary mode"),e.binary=r||!1}(r);let a=t().get(r,"preset.expression");if(!t().isUndefined(a)&&(a=JSON.parse(a),a&&a.settings)){const e=["singleUnit"];for(let r=0,n=e.length;rl.abort())),l.addEventListener("progress",(e=>{e.lengthComputable&&e.total>0?Xh(l.logger,"Fetching",e.loaded/e.total):Xh(l.logger,"Fetching")}));s(l.load().then((e=>(r.context.logger.info("Fetching finished"),n.notify({type:"fetchingDone",data:e}),e))).catch((e=>{throw r.context.logger.debug(e.message),e.stack&&r.context.logger.debug(e.stack),r.context.logger.error("Fetching failed"),n.notify({type:"fetchingDone",error:e}),e})))}))}Kh.prototype.load=function(e,r){r=t().merge({},r,{context:this}),this.settings.now.use.multiFile||(this._loading.length&&(this._loading.forEach((e=>{e.cancel()})),this._loading.length=0),r.animation||this.reset(!0)),this._interpolator.reset(),this.dispatchEvent({type:"loading",options:r,source:e});const n=new V;this._loading.push(n),n.addEventListener("notification",(e=>{this.dispatchEvent(e.slaveEvent)})),this._spinner.spin(this._container);const s=e=>{const t=this._loading.indexOf(n);return-1!==t&&this._loading.splice(t,1),this._spinner.stop(),this._refreshTitle(),n.notify({type:"loadingDone",anything:e}),e};return tu(e,r,n).then((e=>function(e,r,n){if(n.shouldCancel())return Promise.reject(new Error("Operation cancelled"));n.notify({type:"parsing"});const s=t().head(jc.parsers.find({format:r.fileType,ext:r.fileExt,data:e}));if(!s)return Promise.reject(new Error("Could not find suitable parser"));const i=new s(e,r);return i.context=r.context,n.addEventListener("cancel",(()=>i.abort())),i.parse().then((e=>(n.notify({type:"parsingDone",data:e}),e))).catch((e=>{throw r.error=e,r.context.logger.debug(e.message),e.stack&&r.context.logger.debug(e.stack),r.context.logger.error("Parsing failed"),n.notify({type:"parsingDone",error:e}),e}))}(e,r,n))).then((e=>{const t=this._onLoad(e,r);return s(t)})).catch((e=>{throw this.logger.error("Could not load data"),this.logger.debug(e),s(e)}))},Kh.prototype.unload=function(e){this._removeVisual(e||this.getCurrentVisual()),this.resetPivot(),z.now.shadow.on&&this._updateShadowCamera()},Kh.prototype._startAnimation=function(e){this._stopAnimation();const t=this,r=this._getComplexVisual();if(null!==r){try{this._frameInfo=new uh(r.getComplex(),e,{onLoadStatusChanged(){t.dispatchEvent({type:"mdPlayerStateChanged",state:{isPlaying:t._isAnimating,isLoading:!t._frameInfo||t._frameInfo.isLoading}})},onError(e){t._stopAnimation(),t.logger.error(e)}})}catch{return void this.logger.error("Animation file does not fit to current complex!")}this._continueAnimation()}else this.logger.error("Unable to start animation - no molecule is loaded.")},Kh.prototype._pauseAnimation=function(){null!==this._animInterval&&(this._isAnimating=!1,clearInterval(this._animInterval),this._animInterval=null,this._frameInfo&&this.dispatchEvent({type:"mdPlayerStateChanged",state:{isPlaying:this._isAnimating,isLoading:this._frameInfo.isLoading}}))},Kh.prototype._continueAnimation=function(){this._isAnimating=!0;let e=1e3/z.now.maxfps;e=Number.isNaN(e)?0:e;const t=this,{pivot:r}=t._gfx,n=this._getComplexVisual();n&&(n.resetSelectionMask(),n.rebuildSelectionGeometry(),this._msgAtomInfo.style.opacity=0),this._animInterval=setInterval((()=>{if(t.dispatchEvent({type:"mdPlayerStateChanged",state:{isPlaying:t._isAnimating,isLoading:t._frameInfo.isLoading}}),t._frameInfo.frameIsReady){r.updateToFrame(t._frameInfo),t._updateObjsToFrame(t._frameInfo),t._refreshTitle(` Frame ${t._frameInfo._currFrame} of ${t._frameInfo._framesCount} time interval - ${t._frameInfo._timeStep}`);try{t._frameInfo.nextFrame()}catch{return t.logger.error("Error during animation"),void t._stopAnimation()}t._needRender=!0}}),e)},Kh.prototype._stopAnimation=function(){null!==this._animInterval&&(clearInterval(this._animInterval),this._frameInfo.disableEvents(),this._frameInfo=null,this._animInterval=null,this.dispatchEvent({type:"mdPlayerStateChanged",state:null}))},Kh.prototype._onLoad=function(e,r){const n=this._gfx;let s=null;if(r.animation)return this._refreshTitle(),this._startAnimation(e),null;if(this._stopAnimation(),r&&r.keepRepsInfo||(this._opts.reps=null,this._opts._objects=null),"Complex"===e.id){const n=e;r.fileName?n.name=n.name||Yh(r.fileName).toUpperCase():r.amberFileName?n.name=n.name||Yh(r.amberFileName).toUpperCase():n.name=`Dynamic ${r.fileType} molecule`,s=this._addVisual(new qo(n.name,n)),this._curVisualName=s;const i=this.info();if(this.logger.info(`Parsed ${r.fileName} (${i.atoms} atoms, ${i.bonds} bonds, ${i.residues} residues, ${i.chains} chains).`),t().isNumber(this._opts.unit)&&n.setCurrentUnit(this._opts.unit),r.preset);else if(z.now.autoPreset)switch(r.fileType){case"cml":this.resetReps("small");break;case"pdb":case"mmtf":case"cif":!function(e){let t=!1;return e.forEachComponent((e=>{e.forEachResidue((e=>{e._isValid&&(t=!0)}))})),t}(n)?this.resetReps("small"):this.resetReps("macro");break;default:this.resetReps("default")}else this.resetReps("default")}else"Volume"===e.id&&(this.resetEd(),s=this._onLoadEd(e));return n.camera.updateProjectionMatrix(),this._updateFog(),n.root.resetTransform(),this.resetPivot(),this._objectControls.setScale(z.now.radiusToFit/this._getBSphereRadius()),this._resetObjects(),z.now.autoResolution&&this._tweakResolution(),z.now.shadow.on&&this._updateShadowCamera(),this._opts.view&&(this.view(this._opts.view),delete this._opts.view),this._refreshTitle(),s},Kh.prototype.resetEd=function(){this._edLoader&&(this._edLoader.abort(),this._edLoader=null),this._removeVisual(this._getVolumeVisual()),this._needRender=!0},Kh.prototype.loadEd=function(e){this.resetEd();const r=t().head(jc.loaders.find({source:e}));if(!r)return this.logger.error($h),Promise.reject(new Error($h));const n=this._edLoader=new r(e,{binary:!0});return n.context=this,n.load().then((e=>{const r=t().head(jc.parsers.find({format:"ccp4"}));if(!r)throw new Error("Could not find suitable parser for this source");const n=new r(e);return n.context=this,n.parse().then((e=>{this._onLoadEd(e)}))})).catch((e=>{this.logger.error("Could not load ED data"),this.logger.debug(e)}))},Kh.prototype._onLoadEd=function(e){e.normalize();const t=new ha("volume",e);t.getMesh().layers.set(tr.LAYERS.VOLUME);const r=this._addVisual(t);return this._needRender=!0,r},Kh.prototype._needRebuild=function(){let e=!1;return this._forEachComplexVisual((t=>{e=e||t.needsRebuild()})),e},Kh.prototype._rebuildObjects=function(){const e=this,t=this._gfx;let r,n;const s=[];for(r=0;r{const s=e._objects;for(r=0,n=s.length;r0?`Bio molecule ${e}`:"Asymmetric unit"})`}return void 0===e||(t().isString(e)&&(e=Math.max(parseInt(e,10),0)),n.getComplex().setCurrentUnit(e)&&(this._resetScene(),this._updateInfoPanel())),s()},Kh.prototype.rebuild=function(){if(this._building)return void this.logger.warn("Miew.rebuild(): already building!");this._building=!0,this.dispatchEvent({type:"rebuilding"}),this._rebuildObjects(),this._gfx.renderer2d.reset();const e=[];this._forEachComplexVisual((t=>{t.needsRebuild()&&e.push(t.rebuild().then((()=>new Promise((e=>{t.rebuildSelectionGeometry(),e()})))))}));const t=this;this._spinner.spin(this._container),Promise.all(e).then((()=>{t._spinner.stop(),t._needRender=!0,t._refreshTitle(),this.dispatchEvent({type:"buildingDone"}),t._building=!1}))},Kh.prototype.rebuildAll=function(){this._forEachComplexVisual((e=>{e.setNeedsRebuild()}))},Kh.prototype._refreshTitle=function(e){let t;e=void 0===e?"":e;const r=this._getComplexVisual();if(r){t=r.getComplex().name;const e=r.repGet(r.repCurrent());t+=e?` – ${e.mode.name} Mode`:""}else t=Object.keys(this._visuals).length>0?"Unknown":"No Data";t+=e,this.dispatchEvent({type:"titleChanged",data:t})},Kh.prototype.setNeedRender=function(){this._needRender=!0},Kh.prototype._extractRepresentation=function(){const e=[];this._forEachComplexVisual((t=>{if(0===t.getSelectionCount())return;const r=t.buildSelectorFromMask(1<0&&this.logger.report(`New representation from selection for complexes: ${e.join(", ")}`)},Kh.prototype._setReps=function(e){e=e||this._opts&&this._opts.reps||[],this._forEachComplexVisual((t=>t.resetReps(e)))},Kh.prototype.applyPreset=function(e){const{presets:t}=z.now,r=[e||z.defaults.preset,z.defaults.preset,Object.keys(t)[0]];let n=null;for(let e=0;!n&&e{const r=t.beginComponentEdit();r&&e.push(r)})),0!==e.length&&(this._editors=e,this.logger.info("COMPONENT EDIT MODE -- ON"),this._setEditMode(jh),this._objectControls.keysTranslateObj(!0))},Kh.prototype._applyComponentEdit=function(){if(this._editMode===jh){this._objectControls.stop(),this._objectControls.keysTranslateObj(!1);for(let e=0;e{t instanceof qo&&t.getSelectionCount()>0&&e.push(t)})),1!==e.length)return;const t=e[0].beginFragmentEdit();t&&(this._editors=[t],this.logger.info("FRAGMENT EDIT MODE -- ON (single bond)"),this._setEditMode(Hh),this._objectControls.allowTranslation(!1),this._objectControls.allowAltObjFreeRotation(t.isFreeRotationAllowed()),this._needRender=!0)},Kh.prototype._applyFragmentEdit=function(){if(this._editMode===Hh){this._objectControls.stop();for(let e=0;e{e.expandSelection(),e.rebuildSelectionGeometry()})),this._updateInfoPanel(),this._needRender=!0);break;case"NumpadSubtract":e.altKey&&(e.preventDefault(),e.stopPropagation(),this._forEachComplexVisual((e=>{e.shrinkSelection(),e.rebuildSelectionGeometry()})),this._updateInfoPanel(),this._needRender=!0)}}},Kh.prototype._onKeyUp=function(e){this._running&&this._hotKeysEnabled&&"KeyX"===e.code&&this._extractRepresentation()},Kh.prototype._updateInfoPanel=function(){const e=this._msgAtomInfo.getElementsByTagName("p")[0];let t,r,n=0;for(this._forEachComplexVisual((e=>{n+=e.getSelectionCount()}));e.firstChild;)e.removeChild(e.firstChild);if(0===n)return void(this._msgAtomInfo.style.opacity=0);let s=`${String(n)} atom${1!==n?"s":""} selected`;null!==this._lastPick&&(s+=", the last pick:");let i="",o="",a="";if(this._lastPick instanceof zh){t=this._lastPick,r=t.residue,o=t.name;const e=32!==t.location?String.fromCharCode(t.location):"";i=`${t.element.fullName} #${t.serial}${e}: ${r._chain._name}.${r._type._name}${r._sequence}${r._icode.trim()}.`,i+=o,a=`Coord: (${t.position.x.toFixed(2).toString()}, ${t.position.y.toFixed(2).toString()}, ${t.position.z.toFixed(2).toString()})`}else this._lastPick instanceof Fh?(r=this._lastPick,i=`${r._type._fullName}: ${r._chain._name}.${r._type._name}${r._sequence}${r._icode.trim()}`):this._lastPick instanceof Bh?i=`chain ${this._lastPick._name}`:this._lastPick instanceof Uh&&(i=`molecule ${this._lastPick._name}`);e.appendChild(document.createTextNode(s)),""!==i&&(e.appendChild(document.createElement("br")),e.appendChild(document.createTextNode(i))),""!==a&&(e.appendChild(document.createElement("br")),e.appendChild(document.createTextNode(a))),this._msgAtomInfo.style.opacity=1},Kh.prototype._getAltObj=function(){if(this._editors){let e=null;for(let t=0;t0){if(e){e=null;break}e=r}}if(e)return e}return{objects:[],pivot:new r.Vector3(0,0,0)}},Kh.prototype.resetPivot=function(){const e=new r.Box3,t=new r.Vector3;return function(){e.makeEmpty(),this._forEachVisual((t=>{e.union(t.getBoundaries().boundingBox)})),e.getCenter(t),this._objectControls.setPivot(t.negate()),this.dispatchEvent({type:"transform"})}}(),Kh.prototype.setPivotResidue=function(){const e=new r.Vector3;return function(t){const r=this._getVisualForComplex(t.getChain().getComplex());if(r){if(t._controlPoint)e.copy(t._controlPoint);else{let r=0,n=0,s=0;const i=t._atoms.length;for(let e=0;e{i.getSelectionCenter(e,r,n||i.getSelectionBit())&&(t.add(e),s++)})),0!==s&&(t.divideScalar(s),t.negate(),!0)}}(),Kh.prototype.setPivotSubset=function(){const e=new r.Vector3(0,0,0);function t(e,t){return e.mask&1<{const r=this._visuals[this._curVisualName]._complex.name;O.download(t,r,e.fileType),this._refreshTitle(),this.dispatchEvent({type:"exportingDone"})})).catch((e=>{this.logger.error("Could not export data"),this.logger.debug(e),this._refreshTitle(),this.dispatchEvent({type:"exportingDone",error:e})}))},Kh.prototype._tweakResolution=function(){const e=[["poor",100],["low",500],["medium",1e3],["high",5e3],["ultra",Number.MAX_VALUE]];let t=0;if(this._forEachComplexVisual((e=>{t+=e.getComplex().getAtomCount()})),t>0){const r=1e6*this._gfxScore/t;for(let t=0;ts?(o=!1,n.preset="empty"):z.now.preset!==z.defaults.preset&&(n.preset=z.now.preset);const a=[];let l=!0;for(let r=0,n=s;r0&&(r._objects=o),e.view&&(r.view=this.view()),e.settings){const e=this.settings.getDiffs(!1);t().isEmpty(e)||(r.settings=e)}return r},Kh.prototype.get=function(e,t){return z.get(e,t)},Kh.prototype._clipPlaneUpdateValue=function(e){const t=Math.max(this._gfx.camera.position.z-e*z.now.draft.clipPlaneFactor,z.now.camNear),r={clipPlaneValue:t};this._forEachComplexVisual((e=>{e.setUberOptions(r)}));for(let e=0,t=this._objects.length;e{const r=t._reprList;for(let t=0,n=r.length;tn.setMaterialValues(e,t,r)));for(let t=0,r=this._objects.length;t{e.setUberOptions({fogAlpha:z.now.fogAlpha})}))},Kh.prototype._embedWebXR=function(){if("WEBVR"!==z.now.stereo)return this.webVR&&this.webVR.disable(),void(this.webVR=null);this.webVR||(this.webVR=new Dh((()=>{this._requestAnimationFrame((()=>this._onTick())),this._needRender=!0,this._onResize()}))),this.webVR.enable(this._gfx)},Kh.prototype._initOnSettingsChanged=function(){const e=(e,r)=>{(e=t().isArray(e)?e:[e]).forEach((e=>{this.settings.addEventListener(`change:${e}`,r)}))};e("modes.VD.frame",(()=>{const e=this._getVolumeVisual();null!==e&&(e.showFrame(z.now.modes.VD.frame),this._needRender=!0)})),e("modes.VD.isoMode",(()=>{const e=this._getVolumeVisual();null!==e&&(e.getMesh().material.updateDefines(),this._needRender=!0)})),e("bg.color",(()=>{this._onBgColorChanged()})),e("ao",(()=>{const e={normalsToGBuffer:z.now.ao};this._setUberMaterialValues(e)})),e("zSprites",(()=>{this.rebuildAll()})),e("fogColor",(()=>{this._onFogColorChanged()})),e("fogColorEnable",(()=>{this._onFogColorChanged()})),e("bg.transparent",(e=>{const t=this._gfx;t&&t.renderer.setClearColor(z.now.bg.color,Number(!z.now.bg.transparent)),this._updateMaterials({fogTransparent:e.value}),this.rebuildAll()})),e("draft.clipPlane",(e=>{this._updateMaterials({clipPlane:e.value}),this.rebuildAll()})),e("shadow.on",(e=>{const t={shadowmap:e.value,shadowmapType:z.now.shadow.type},r=this._gfx;r&&(r.renderer.shadowMap.enabled=Boolean(t.shadowmap)),this._updateMaterials(t,!0),t.shadowmap?(this._updateShadowCamera(),this._updateShadowmapMeshes(Bo.createShadowmapMaterial)):this._updateShadowmapMeshes(Bo.removeShadowmapMaterial),this._needRender=!0})),e("shadow.type",(e=>{z.now.shadow.on&&(this._updateMaterials({shadowmapType:e.value},!0),this._needRender=!0)})),e("shadow.radius",(e=>{for(let t=0;t{this._fps.show(z.now.fps)})),e(["fog","fogNearFactor","fogFarFactor"],(()=>{this._updateFog(),this._needRender=!0})),e("fogAlpha",(()=>{const{fogAlpha:e}=z.now;(e<0||e>1)&&this.logger.warn("fogAlpha must belong range [0,1]"),this._fogAlphaChanged(),this._needRender=!0})),e("autoResolution",(e=>{e.value&&!this._gfxScore&&this.logger.warn("Benchmarks are missed, autoresolution will not work! Autoresolution should be set during miew startup.")})),e("stereo",(()=>{this._embedWebXR("WEBVR"===z.now.stereo),this._needRender=!0})),e(["transparency","palette"],(()=>{this.rebuildAll()})),e("resolution",(()=>{this.rebuildAll();const e=this._getVolumeVisual();e&&(e.getMesh().material.updateDefines(),this._needRender=!0)})),e(["axes","fxaa","ao","outline.on","outline.color","outline.threshold","outline.thickness"],(()=>{this._needRender=!0}))},Kh.prototype.set=function(e,t){z.set(e,t)},Kh.prototype.select=function(e,r){const n=this._getComplexVisual();if(!n)return;let s=e;t().isString(e)&&(s=kh.parse(e).selector),n.select(s,r),this._lastPick=null,this._updateInfoPanel(),this._needRender=!0};Kh.prototype.view=function(e){const t=this,{pivot:n}=this._gfx;let s=[];return void 0===e?function(){const e=n.position,i=t._objectControls.getScale()/z.now.radiusToFit,o=new r.Euler;return o.setFromQuaternion(t._objectControls.getOrientation(),"ZXY"),s=[e.x,e.y,e.z,i,o.x,o.y,o.z],"1"+O.arrayToBase64(s,Float32Array)}():(function(){40===e.length&&(e=`0${e}`);const i=e[0];if(s=O.arrayFromBase64(e.substr(1),Float32Array),"1"!==i){if("0"!==i)return void t.logger.warn(`Encoded view version mismatch, stored as ${i} vs 1 expected`);s[3]/=8}const o=t._interpolator,a=o.createView();a.position.copy(n.position),a.scale=t._objectControls.getScale(),a.orientation.copy(t._objectControls.getOrientation());const l=o.createView();l.position.set(s[0],s[1],s[2]),t._getComplexVisual()&&l.position.sub(t._getComplexVisual().position),l.scale=s[3],l.orientation.setFromEuler(new r.Euler(s[4],s[5],s[6],"ZXY")),o.setup(a,l)}(),e)},Kh.prototype._updateView=function(){const e=this,{pivot:t}=this._gfx,r=this._interpolator;if(r.wasStarted()||r.start(),!r.isMoving())return;const n=r.getCurrentView();if(n.success){const r=n.view;t.position.copy(r.position),e._objectControls.setScale(r.scale*z.now.radiusToFit),e._objectControls.setOrientation(r.orientation),this.dispatchEvent({type:"transform"}),e._needRender=!0}},Kh.prototype.translate=function(e,t,r){this._objectControls.translatePivot(e,t,r),this.dispatchEvent({type:"transform"}),this._needRender=!0},Kh.prototype.rotate=function(e,t,n){this._objectControls.rotate((new r.Quaternion).setFromEuler(new r.Euler(e,t,n,"XYZ"))),this.dispatchEvent({type:"transform"}),this._needRender=!0},Kh.prototype.scale=function(e){if(e<=0)throw new RangeError("Scale should be greater than zero");this._objectControls.scale(e),this.dispatchEvent({type:"transform"}),this._needRender=!0},Kh.prototype.center=function(e){if(void 0===e)return this.setPivotSubset(),void(this._needRender=!0);if(void 0!==e.obj&&("atom"in e.obj||"residue"in e.obj))return"atom"in e.obj?this.setPivotAtom(e.obj.atom):this.setPivotResidue(e.obj.residue),void(this._needRender=!0);if(void 0===e.obj&&""!==e){const t=kh.parse(e);if(void 0===t.error)return this.setPivotSubset(t),void(this._needRender=!0)}this.resetPivot(),this._needRender=!0},Kh.prototype.within=function(e,t){const r=this._getComplexVisual();if(!r)return kh.None();e instanceof String&&(e=kh.parse(e));const n=r.within(e,t);return n&&(r.rebuildSelectionGeometry(),this._needRender=!0),n},Kh.prototype.projected=function(e,t){const r=this._getComplexVisual(t);if(!r)return!1;const n=r.getComplex().getAtomByFullname(e);if(null===n)return!1;const s=n.position.clone();return this._gfx.pivot.updateMatrixWorldRecursive(),this._gfx.camera.updateMatrixWorldRecursive(),this._gfx.pivot.localToWorld(s),s.project(this._gfx.camera),{x:.5*(s.x+1)*this._gfx.width,y:.5*(1-s.y)*this._gfx.height}},Kh.prototype.dssp=function(e){const t=this._getComplexVisual(e);t&&(t.getComplex().dssp(),t._reprList.forEach((e=>{"CA"!==e.mode.id&&"SS"!==e.colorer.id||(e.needsRebuild=!0)})))},Kh.prototype.exportCML=function(){const e=this;const t=e._getComplexVisual(),n=t?t.getComplex():null;if(n&&n.originalCML){!function(t){const{root:n}=e._gfx,s=function(e){const t=new r.Vector3,n=new r.Vector3,s=new r.Vector3;e.extractBasis(t,n,s),t.normalize(),n.normalize(),s.normalize();const i=new r.Matrix4;return i.identity(),i.makeBasis(t,n,s),i}(n.matrixWorld),i=new r.Vector4(0,0,0,0),o=new r.Vector4(0,0,0,0);let a=null,l=null;t.forEachAtom((e=>{e.xmlNodeRef&&e.xmlNodeRef.xmlNode&&(a=e.xmlNodeRef.xmlNode,l=e.position,i.set(l.x,l.y,l.z,1),i.applyMatrix4(s),a.setAttribute("x3",i.x.toString()),a.setAttribute("y3",i.y.toString()),a.setAttribute("z3",i.z.toString()),a.removeAttribute("x2"),a.removeAttribute("y2"))})),t.forEachSGroup((e=>{if(e.xmlNodeRef&&e.xmlNodeRef.xmlNode){a=e.xmlNodeRef.xmlNode,l=e.getPosition(),i.set(l.x,l.y,l.z,1);const t=e.getCentralPoint();null===t?i.applyMatrix4(s):(o.set(t.x,t.y,t.z,0),i.add(o),i.applyMatrix4(s),o.set(t.x,t.y,t.z,1),o.applyMatrix4(s),i.sub(o)),a.setAttribute("x",i.x.toString()),a.setAttribute("y",i.y.toString()),a.setAttribute("z",i.z.toString())}}))}(n);return(new XMLSerializer).serializeToString(n.originalCML)}return null},Kh.prototype.motm=function(){z.set({fogColorEnable:!0,fogColor:0,outline:{on:!0,threshold:.01},bg:{color:16777215}}),this._forEachComplexVisual((e=>{const t=[],r=e.getComplex(),n=so.get(z.now.palette);for(let e=0;e #aromatic radius"," atom = #atom radius"," bond = #bond radius"," multibond = #use multibond"," showarom = #show aromatic"," space = #space value\n"]},CA:{$help:[" Cartoon"," arrow = #arrow size"," depth = #depth of surface"," heightSegmentsRatio = "," radius = #tube radius"," tension = #"," width = #secondary width\n"]},LN:{$help:[" Lines"," atom = #atom radius"," chunkarom = "," multibond = #use multibond"," showarom = #show aromatic"," offsarom = \n"]},LC:{$help:[" Licorice"," aromrad = #aromatic radius"," bond = #bond radius"," multibond = #use multibond"," showarom = #show aromatic"," space = #space value\n"]},VW:{$help:[" Van der Waals"," nothing\n"]},TR:{$help:[" Trace"," radius = #tube radius\n"]},TU:{$help:[" Tube"," heightSegmentsRatio = "," radius = #tube radius"," tension = \n"]},SA:{$help:[" Surface"," zClip = #clip z plane\n"]},QS:{$help:[" Quick surface"," isoValue = "," scale = "," wireframe = "," zClip = #clip z plane\n"]},SE:{$help:[" Solvent excluded surface"," zClip = #clip z plane\n"]},TX:{$help:[" Text mode",' template = string that can include "{{ id }}"'," it will be replaced by value, id can be one of next:"," serial, name, type, sequence, residue, chain, hetatm, water\n",' horizontalAlign = {"left", "right", "center"}',' verticalAlign = {"top", "bottom", "middle"}'," dx = #offset along x"," dy = #offset along y"," dz = #offset along z"," fg = #text color modificator"," could be keyword, named color or hex"," fg = #back color modificator"," could be keyword, named color or hex"," showBg = #if set show background"," plate under text"]}},iu={$help:["Coloring mode shortcut"," EL - color by element"," CH - color by chain"," SQ - color by sequence"," RT - color by residue type"," SS - color by secondary structure"," UN - uniform"],UN:{$help:["Parameters of coloring modes customization"," Uniform"," color = #RGB->HEX->dec\n"],color:{$help:Object.keys(so.get(z.now.palette).namedColors).sort().join("\n")}}},ou={$help:["Material shortcut"," DF - diffuse"," TR - transparent"," SF - soft plastic"," PL - glossy plastic"," ME - metal"," GL - glass"]},au={$help:["Short (packed) representation description as a set of variables"," s="," selector property"," m=[!:[,...]]"," render mode property"," c=[!:[,...]]"," color mode property"," mt="," material property"],s:{$help:"Selection expression string as it is in menu->representations->selection"},m:su,c:iu,mt:ou},lu={$help:["Parameters of rendering modes customization: modes","Parameters of colorer customization: colorers","Autobuild: autobuild = (|)"],modes:su,colorers:iu},cu={$help:["help (| )","You can get detailed information about command options",' using "help cmd.opt.opt.[...]"\n'," you can use one line comments"," everything started from (#|//) will be skipped"," Example: >build //some comment\n","List of available commands:"],reset:{$help:["Reload current object, delete all representations"," Nothing will work until load new object"]},load:{$help:["load (||-f [<*.NC FILE URL STRING>])"," Load new pdb object from selected source"],PDBID:{$help:"pdb id in remote molecule database"},URL:{$help:"url to source file"},f:{$help:["open file system dialog to fetch local file","optionally you can determine trajectory file","via URL for *.top model"]}},clear:{$help:"No args. Clear terminal"},add:{$help:["add [] []"," Add new item to representation set with"," default or params"],REP_NAME:{$help:"Identifier string [_,a-z,A-Z,0-9] can not start from digit"},DESCRIPTION:au},rep:{$help:["rep [|] []"," set current representation by name or index"," edit current representation by "],REP_NAME:{$help:["Identifier string [_,a-z,A-Z,0-9] can not start from digit","Must be declared before"]},REP_INDEX:{$help:"Index of available representation"},DESCRIPTION:au},remove:{$help:["remove (|)","Remove representation by name or index"],REP_NAME:{$help:["Identifier string [_,a-z,A-Z,0-9] can not start from digit","Must be declared before"]},REP_INDEX:{$help:"Index of available representation"}},selector:{$help:["selector "," set selector from EXPRESSION to current representation"],EXPRESSION:{$help:"Selection expression string as it is in menu->representations->selection"}},mode:{$help:["mode [=...]"," set rendering mode and apply parameters to current representation"],MODE_ID:su},color:{$help:["color [=...]"," set colorer and apply parameters to current representation"],COLORER_ID:iu},material:{$help:["material "," set material to current representation"],MATERIAL_ID:ou},build:{$help:"build help str",add:{$help:"build.add",new:{$help:["add.new","add.new new line 1","add.new new line 2","add.new new line 3"]}},del:{$help:"build.del"}},list:{$help:["list [-e|-s||]","Print representations if no args print list of representations"," -e expand list and show all representations"," -s show all user-registered selectors"," | show only current representation"]},hide:{$help:["hide (|)","Hide representation referenced in args"]},show:{$help:["show (|)","Show representation referenced in args"]},get:{$help:["get ","Print value"," - path to option use get.PARAMETER to get more info"],PARAMETER:lu},set:{$help:["set ","Set with "," - path to option use set.PARAMETER to get more info"],PARAMETER:lu},set_save:{$help:["set_save","Save current settings to cookie"]},set_restore:{$help:["set_restore","Load and apply settings from cookie"]},set_reset:{$help:["set_reset","Reset current settings to the defaults"]},preset:{$help:["preset []","Reset current representation or set preset to "],PRESET:{$help:["default","wire","small","macro"]}},unit:{$help:["unit []","Change current biological structure view. Zero value means asymmetric unit,","positive values set an assembly with corresponding number.","Being called with no parameters command prints current unit information."]},view:{$help:["view []","Get current encoded view or set if ENCODED_VIEW placed as argument"],ENCODED_VIEW:{$help:["encoded view matrix string (binary code)"]}},rotate:{$help:["rotate (x|y|z) [] [(x|y|z) []]...","Rotate scene"]},scale:{$help:["scale ","Scale scene"]},select:{$help:["select [as ]","Select atoms using selector defined in SELECTOR_STRING"," and if SELECTOR_NAME is defined register it in viewer"," you can use it later as a complex selector"]},within:{$help:["within of as ","Build within named selector"," DISTANCE "," SELECTOR_STRING "," SELECTOR_NAME "]},url:{$help:["url [-s] [-v]","Report URL encoded scene"," if -s set that include settings in the URL"," if -v set that include view in the URL"]},screenshot:{$help:["screenshot [ []]","Make a screenshot of the scene"," WIDTH in pixels"," HEIGHT in pixels, equal to WIDTH by default"]},line:{$help:["line [=]","Draw dashed line between two specified atoms"]},removeobj:{$help:["removeobj ","Remove scene object by its index. Indices could be obtained by command"]},listobj:{$help:["listobj","Display the list of all existing scene objects"]}},{chem:{selectors:hu},modes:uu,colorers:du,materials:pu,palettes:mu,options:fu,settings:_u}=ru;function gu(){}const yu=function(){const e=new gu;return function(){return e}}();const xu=new class{constructor(){this.representationMap={},this.representationID={}}get(e){return this.representationMap[e]||this.representationID[e]||""}add(e,t){if(-1===e)return"Can not create representation: there is no data";if(void 0!==t){if(this.representationMap.hasOwnProperty(e))return"This name has already existed, registered without name";this.representationMap[e.toString()]=t,this.representationID[t]=e.toString()}return`Representation ${e} successfully added`}remove(e){e&&this.representationID.hasOwnProperty(e)&&(delete this.representationMap[this.representationID[e]],delete this.representationID[e]);const t=Object.keys(this.representationID).sort();for(const r in t)if(t.hasOwnProperty(r)){const n=t[r];n>e&&(this.representationID[n-1]=this.representationID[n],this.representationMap[this.representationID[n]]-=1,delete this.representationID[n])}}clear(){this.representationMap={},this.representationID={}}};function bu(e){const t={s:"selector",m:"mode",c:"colorer",mt:"material",mode:"modes",color:"colorers",colorer:"colorers",select:"selector",material:"materials",selector:"selector"}[e];return void 0===t?e:t}const wu=new class{list(e,t,r){let n="";if(e&&void 0!==t&&(void 0===r||"-e"===r)){const s=e.repCount();for(let i=0;i"===a?"":`, ${a}`}\n`,void 0!==n&&(s+=` selection : "${h}"\n`,s+=` mode : (${l.id}), ${l.name}\n`,s+=` colorer : (${c.id}), ${c.name}\n`,s+=` material : (${u.id}), ${u.name}\n`),s}listSelector(e,t){let r="";for(const e in t)t.hasOwnProperty(e)&&(r+=`${e} : "${t[e]}"\n`);return r}listObjs(e){const t=e._objects;if(!t||!Array.isArray(t)||0===t.length)return"There are no objects on the scene";const r=[];for(let e=0,n=t.length;ee.finishAwaitingCMDInProcess();e.load(t).then(r,r)}checkArg(e,t,r){if(void 0!==e&&void 0!==t){if("selector"===bu(e)){const e=hu.parse(t);if(void 0!==e.error){throw{message:e.error}}return void 0!==r&&r?e.selector:t}const n={colorers:du,modes:uu,materials:pu};let s,i=e;for(;i!==s;)s=i,i=bu(s);if(void 0===n[i].get(t)){throw{message:`${t} is not existed in ${i}`}}return t}return yu}propagateProp(e,r){if(void 0!==e){let n={};const s=fu.adapters[typeof t().get(_u.defaults,e)];if(void 0===s){throw{message:`${e} is not existed`}}if((e.endsWith(".color")||e.endsWith(".baseColor")||e.endsWith(".EL.carbon"))&&"number"!=typeof r&&(r=mu.get(_u.now.palette).getNamedColor(r)),e.endsWith(".fg")||e.endsWith(".bg"))if("number"!=typeof r){const e=mu.get(_u.now.palette).getNamedColor(r,!0);void 0!==e&&(r=`0x${e.toString(16)}`)}else r=`0x${r.toString(16)}`;if(e.endsWith(".template")&&(r=r.replace(/\\n/g,"\n")),void 0!==r&&s(r)!==r&&s(r)!==r>0)throw n={message:`${e} must be a "${typeof 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function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.miew.reset(false); yy.ClearContext(); yy.miew.resetReps(\"empty\");\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.miew.rebuild();\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.miew.rebuildAll(); yy.miew.rebuild();\r\nbreak;\r\ncase 6:\r\nthis.$ = yy.echo(yy.utils.help().toString());\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.echo(yy.utils.help($$[$0]).toString());\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.miew.motm();\r\nbreak;\r\ncase 10: case 11:\r\nthis.$ = yy.utils.propagateProp($$[$0]); yy.echo(yy.miew.get($$[$0]).toString());\r\nbreak;\r\ncase 12: case 13:\r\nthis.$ = yy.miew.set($$[$0-1], yy.utils.propagateProp($$[$0-1], $$[$0]));;\r\nbreak;\r\ncase 14:\r\nthis.$ = yy.miew.saveSettings();;\r\nbreak;\r\ncase 15:\r\nthis.$ = yy.miew.restoreSettings();;\r\nbreak;\r\ncase 16:\r\nthis.$ = yy.miew.resetSettings();;\r\nbreak;\r\ncase 17:\r\nthis.$ = yy.miew.resetReps();\r\nbreak;\r\ncase 18:\r\nthis.$ = yy.miew.applyPreset($$[$0]);\r\nbreak;\r\ncase 21:\r\nthis.$ = yy.miew.repRemove($$[$0]); yy.representations.remove($$[$0]);\r\nbreak;\r\ncase 22:\r\nthis.$ = yy.miew.repHide($$[$0]);\r\nbreak;\r\ncase 23:\r\nthis.$ = yy.miew.repHide($$[$0], false);\r\nbreak;\r\ncase 24:\r\nthis.$ = yy.echo(yy.utils.listRep(yy.miew, yy.representations, $$[$0], '-e'));\r\nbreak;\r\ncase 25:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations));\r\nbreak;\r\ncase 26:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations, $$[$0]));\r\nbreak;\r\ncase 27:\r\nthis.$ = yy.echo(yy.utils.listSelector(yy.miew, yy.Context));\r\nbreak;\r\ncase 28:\r\nthis.$ = yy.miew.select(yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0], true));\r\nbreak;\r\ncase 29:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.utils.checkArg($$[$0-3].toLowerCase(), $$[$0-2], true); yy.miew.select(yy.Context[$$[$0].toLowerCase()]);\r\nbreak;\r\ncase 30:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {selector : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0])});\r\nbreak;\r\ncase 31:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.miew.within(yy.utils.checkArg(\"select\", $$[$0-2], true), Number($$[$0-4]));\r\nbreak;\r\ncase 32:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {material : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 35:\r\nthis.$ = yy.echo(yy.miew.view());\r\nbreak;\r\ncase 36: case 37:\r\nthis.$ = yy.miew.view($$[$0]);\r\nbreak;\r\ncase 38:\r\nthis.$ = yy.echo(yy.miew.changeUnit());\r\nbreak;\r\ncase 39:\r\nthis.$ = yy.echo(yy.miew.changeUnit($$[$0]));\r\nbreak;\r\ncase 40:\r\nthis.$ = yy.miew.dssp();\r\nbreak;\r\ncase 41:\r\nthis.$ = yy.miew.scale($$[$0]);\r\nbreak;\r\ncase 42:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.rotate($$[$0][i]['x'] * Math.PI / 180.0, $$[$0][i]['y'] * Math.PI / 180.0, $$[$0][i]['z'] * Math.PI / 180.0)} \r\nbreak;\r\ncase 43:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.translate($$[$0][i]['x'] || 0, $$[$0][i]['y'] || 0, $$[$0][i]['z'] || 0)} \r\nbreak;\r\ncase 44:\r\nthis.$ = yy.miew.center();\r\nbreak;\r\ncase 45:\r\nthis.$ = yy.miew.center($$[$0]);\r\nbreak;\r\ncase 48: case 49:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-1], $$[$0]]}, true);\r\nbreak;\r\ncase 50: case 51:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-2], $$[$0-1]], opts:$$[$0].toJSO(yy.utils, 'objects', 'line')}, true);\r\nbreak;\r\ncase 52:\r\nthis.$ = yy.echo(yy.utils.listObjs(yy.miew));\r\nbreak;\r\ncase 53:\r\nthis.$ = yy.miew.removeObject($$[$0]);\r\nbreak;\r\ncase 54:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: false}));\r\nbreak;\r\ncase 55:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: true}));\r\nbreak;\r\ncase 56:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: false}));\r\nbreak;\r\ncase 57: case 58:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: true}));\r\nbreak;\r\ncase 59:\r\nthis.$ = yy.miew.screenshotSave();\r\nbreak;\r\ncase 60:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0]));\r\nbreak;\r\ncase 61:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0-1]), Number($$[$0]));\r\nbreak;\r\ncase 62: case 63: case 64:\r\nthis.$ = yy.utils.load(yy.miew, $$[$0]); yy.representations.clear();\r\nbreak;\r\ncase 65:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd()));\r\nbreak;\r\ncase 66:\r\nthis.$ = yy.echo(yy.representations.add($$[$0], yy.miew.repAdd()));\r\nbreak;\r\ncase 67:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 68:\r\nthis.$ = yy.echo(yy.representations.add($$[$0-1], yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 69:\r\nthis.$ = yy.miew.rep($$[$0]); yy.miew.repCurrent($$[$0]);\r\nbreak;\r\ncase 70:\r\nthis.$ = yy.miew.rep($$[$0-1], $$[$0]); yy.miew.repCurrent($$[$0-1]);\r\nbreak;\r\ncase 71:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 72:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 73:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 74:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 75:\r\nthis.$ = Number(yy.representations.get($$[$0]));\r\nbreak;\r\ncase 76: case 92:\r\nthis.$ = Number($$[$0]);\r\nbreak;\r\ncase 77:\r\nthis.$ = $$[$0];\r\nbreak;\r\ncase 78:\r\nthis.$ = yy._.assign($$[$0-1], $$[$0]);\r\nbreak;\r\ncase 79:\r\nthis.$ = yy._.assign($$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 80:\r\nthis.$ = yy._.assign($$[$0-3], $$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 81: case 82:\r\nthis.$ = yy.CreateObjectPair($$[$0].key, $$[$0].val);\r\nbreak;\r\ncase 83:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].key, new Array($$[$0-1].val, $$[$0].toJSO(yy.utils, $$[$0-1].key, $$[$0-1].val)));\r\nbreak;\r\ncase 84: case 85:\r\nthis.$ = Object.create({'key': yy.keyRemap($$[$0-2]), 'val': yy.utils.checkArg($$[$0-2], $$[$0])});\r\nbreak;\r\ncase 86:\r\nthis.$ = [$$[$0]];\r\nbreak;\r\ncase 87:\r\nthis.$ = $$[$0-1].concat($$[$0]);\r\nbreak;\r\ncase 88:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].toLowerCase(), Number($$[$0]));\r\nbreak;\r\ncase 89:\r\nthis.$ = new yy.ArgList($$[$0]);\r\nbreak;\r\ncase 90:\r\nthis.$ = $$[$0-1].append($$[$0]);\r\nbreak;\r\ncase 91:\r\nthis.$ = new yy.Arg($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 93:\r\nthis.$ = parseInt($$[$0]);\r\nbreak;\r\ncase 94:\r\nthis.$ = JSON.parse($$[$0]);\r\nbreak;\r\ncase 95: case 96:\r\nthis.$ = String($$[$0]);\r\nbreak;\r\ncase 157: case 158: case 161: case 162: case 163:\r\nthis.$ = $$[$0-2] + $$[$0-1] + $$[$0] //cause of could be color word in path;\r\nbreak;\r\ncase 166:\r\nthis.$ = $$[$0-2] = $$[$0-2] + $$[$0-1] + $$[$0];\r\nbreak;\r\n}\r\n},\r\ntable: 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,[2,90]),{14:$VS,16:197,35:$VT,38:$VU,77:$VV,78:$VW},{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,33:$Ve,34:$Vf,35:[1,199],37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,79:198,80:52,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN},o($V41,[2,84]),o($V31,[2,85]),{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,32:200,33:$Ve,34:$Vf,37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,70:$Vx,72:$Vy,74:$Vz,79:184,80:52,81:185,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN,96:$VO,97:$VP,98:$VQ,99:$VR},{5:[2,80]},o($V31,[2,91]),o($V61,[2,157]),o($V61,[2,158]),{5:[2,31]}],\r\ndefaultActions: {3:[2,2],4:[2,3],7:[2,8],8:[2,9],11:[2,14],12:[2,15],13:[2,16],15:[2,19],16:[2,20],25:[2,33],26:[2,34],29:[2,40],34:[2,46],35:[2,47],37:[2,52],46:[2,1],47:[2,5],107:[2,11],110:[2,18],116:[2,21],119:[2,22],120:[2,23],121:[2,24],122:[2,26],123:[2,27],125:[2,30],127:[2,32],128:[2,36],129:[2,37],130:[2,39],131:[2,41],136:[2,45],139:[2,53],140:[2,62],141:[2,63],142:[2,64],143:[2,164],145:[2,67],158:[2,12],159:[2,13],166:[2,68],174:[2,70],177:[2,57],178:[2,58],179:[2,61],183:[2,29],184:[2,99],185:[2,100],196:[2,80],200:[2,31]},\r\nparseError: function parseError (str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function(match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex () {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin (condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState () {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules () {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState (n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState (condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* ignore whitespace */\r\nbreak;\r\ncase 1:return '';\r\nbreak;\r\ncase 2:return '';\r\nbreak;\r\ncase 3:return 42;\r\nbreak;\r\ncase 4:return 35;\r\nbreak;\r\ncase 5:return 77;\r\nbreak;\r\ncase 6:return 78;\r\nbreak;\r\ncase 7:return 78;\r\nbreak;\r\ncase 8:return 8;\r\nbreak;\r\ncase 9:return 6;\r\nbreak;\r\ncase 10:return 82;\r\nbreak;\r\ncase 11:return 7;\r\nbreak;\r\ncase 12:return 9;\r\nbreak;\r\ncase 13:return 59;\r\nbreak;\r\ncase 14:return 13\r\nbreak;\r\ncase 15:return 15\r\nbreak;\r\ncase 16:return 17\r\nbreak;\r\ncase 17:return 18\r\nbreak;\r\ncase 18:return 19\r\nbreak;\r\ncase 19:return 20\r\nbreak;\r\ncase 20:return 11\r\nbreak;\r\ncase 21:return 62\r\nbreak;\r\ncase 22:return 64\r\nbreak;\r\ncase 23:return 23\r\nbreak;\r\ncase 24:return 25\r\nbreak;\r\ncase 25:return 26\r\nbreak;\r\ncase 26:return 27\r\nbreak;\r\ncase 27:return 30\r\nbreak;\r\ncase 28:return 34\r\nbreak;\r\ncase 29:return 33\r\nbreak;\r\ncase 30:return 65\r\nbreak;\r\ncase 31:return 66\r\nbreak;\r\ncase 32:return 37\r\nbreak;\r\ncase 33:return 41\r\nbreak;\r\ncase 34:return 43\r\nbreak;\r\ncase 35:return 52\r\nbreak;\r\ncase 36:return 54\r\nbreak;\r\ncase 37:return 55\r\nbreak;\r\ncase 38:return 46\r\nbreak;\r\ncase 39:return 48\r\nbreak;\r\ncase 40:return 45\r\nbreak;\r\ncase 41:return 49\r\nbreak;\r\ncase 42:return 56\r\nbreak;\r\ncase 43:return 58;\r\nbreak;\r\ncase 44:return 44\r\nbreak;\r\ncase 45:return 83\r\nbreak;\r\ncase 46:return 84\r\nbreak;\r\ncase 47:return 85\r\nbreak;\r\ncase 48:return 86\r\nbreak;\r\ncase 49:return 87\r\nbreak;\r\ncase 50:return 88\r\nbreak;\r\ncase 51:return 89\r\nbreak;\r\ncase 52:return 90\r\nbreak;\r\ncase 53:return 91\r\nbreak;\r\ncase 54:return 92\r\nbreak;\r\ncase 55:return 93\r\nbreak;\r\ncase 56:return 94\r\nbreak;\r\ncase 57:return 95\r\nbreak;\r\ncase 58:return 70\r\nbreak;\r\ncase 59:return 70\r\nbreak;\r\ncase 60:return 72\r\nbreak;\r\ncase 61:return 72\r\nbreak;\r\ncase 62:return 74\r\nbreak;\r\ncase 63:return 74\r\nbreak;\r\ncase 64:return 74\r\nbreak;\r\ncase 65:return 31\r\nbreak;\r\ncase 66:return 36\r\nbreak;\r\ncase 67:return 96\r\nbreak;\r\ncase 68:return 97\r\nbreak;\r\ncase 69:return 98\r\nbreak;\r\ncase 70:return 99\r\nbreak;\r\ncase 71:yy_.yytext = yy.utils.unquoteString(yy_.yytext); return 14;\r\nbreak;\r\ncase 72:return 38;\r\nbreak;\r\ncase 73:return 5;\r\nbreak;\r\ncase 74:return 101;\r\nbreak;\r\ncase 75:return 103;\r\nbreak;\r\ncase 76:return '\\\\';\r\nbreak;\r\ncase 77:return 28\r\nbreak;\r\ncase 78:return 61\r\nbreak;\r\ncase 79:return 29\r\nbreak;\r\ncase 80:return 57\r\nbreak;\r\ncase 81:return 71\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:[#].*)/i,/^(?:\\/\\/.*)/i,/^(?:([_A-Z0-9\\/\\+]+==))/i,/^(?:-?[0-9]+(\\.[0-9]+)?\\b)/i,/^(?:0[xX][0-9A-F]+\\b)/i,/^(?:false\\b)/i,/^(?:true\\b)/i,/^(?:all\\b)/i,/^(?:reset\\b)/i,/^(?:clear\\b)/i,/^(?:build\\b)/i,/^(?:help\\b)/i,/^(?:load\\b)/i,/^(?:get\\b)/i,/^(?:set\\b)/i,/^(?:set_save\\b)/i,/^(?:set_restore\\b)/i,/^(?:set_reset\\b)/i,/^(?:preset\\b)/i,/^(?:motm\\b)/i,/^(?:add\\b)/i,/^(?:rep\\b)/i,/^(?:remove\\b)/i,/^(?:hide\\b)/i,/^(?:show\\b)/i,/^(?:list\\b)/i,/^(?:select\\b)/i,/^(?:within\\b)/i,/^(?:selector\\b)/i,/^(?:mode\\b)/i,/^(?:color\\b)/i,/^(?:material\\b)/i,/^(?:view\\b)/i,/^(?:unit\\b)/i,/^(?:line\\b)/i,/^(?:listobj\\b)/i,/^(?:removeobj\\b)/i,/^(?:rotate\\b)/i,/^(?:translate\\b)/i,/^(?:scale\\b)/i,/^(?:center\\b)/i,/^(?:url\\b)/i,/^(?:screenshot\\b)/i,/^(?:dssp\\b)/i,/^(?:file_list\\b)/i,/^(?:file_register\\b)/i,/^(?:file_delete\\b)/i,/^(?:preset_add\\b)/i,/^(?:preset_delete\\b)/i,/^(?:preset_update\\b)/i,/^(?:preset_rename\\b)/i,/^(?:preset_open\\b)/i,/^(?:create_scenario\\b)/i,/^(?:reset_scenario\\b)/i,/^(?:delete_scenario\\b)/i,/^(?:add_scenario_item\\b)/i,/^(?:list_scenario\\b)/i,/^(?:s\\b)/i,/^(?:mt\\b)/i,/^(?:m\\b)/i,/^(?:c\\b)/i,/^(?:x\\b)/i,/^(?:y\\b)/i,/^(?:z\\b)/i,/^(?:as\\b)/i,/^(?:of\\b)/i,/^(?:pdb\\b)/i,/^(?:delay\\b)/i,/^(?:prst\\b)/i,/^(?:desc\\b)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:\\.)/i,/^(?:\\/)/i,/^(?:\\\\)/i,/^(?:-e\\b)/i,/^(?:-f\\b)/i,/^(?:-s\\b)/i,/^(?:-v\\b)/i,/^(?:=)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","/* eslint-disable */\r\n// DO NOT EDIT! Automatically generated from .jison\r\n/* parser generated by jison 0.4.18 */\r\n/*\r\n Returns a Parser object of the following structure:\r\n\r\n Parser: {\r\n yy: {}\r\n }\r\n\r\n Parser.prototype: {\r\n yy: {},\r\n trace: function(),\r\n symbols_: {associative list: name ==> number},\r\n terminals_: {associative list: number ==> name},\r\n productions_: [...],\r\n performAction: function anonymous(yytext, yyleng, yylineno, yy, yystate, $$, _$),\r\n table: [...],\r\n defaultActions: {...},\r\n parseError: function(str, hash),\r\n parse: function(input),\r\n\r\n lexer: {\r\n EOF: 1,\r\n parseError: function(str, hash),\r\n setInput: function(input),\r\n input: function(),\r\n unput: function(str),\r\n more: function(),\r\n less: function(n),\r\n pastInput: function(),\r\n upcomingInput: function(),\r\n showPosition: function(),\r\n test_match: function(regex_match_array, rule_index),\r\n next: function(),\r\n lex: function(),\r\n begin: function(condition),\r\n popState: function(),\r\n _currentRules: function(),\r\n topState: function(),\r\n pushState: function(condition),\r\n\r\n options: {\r\n ranges: boolean (optional: true ==> token location info will include a .range[] member)\r\n flex: boolean (optional: true ==> flex-like lexing behaviour where the rules are tested exhaustively to find the longest match)\r\n backtrack_lexer: boolean (optional: true ==> lexer regexes are tested in order and for each matching regex the action code is invoked; the lexer terminates the scan when a token is returned by the action code)\r\n },\r\n\r\n performAction: function(yy, yy_, $avoiding_name_collisions, YY_START),\r\n rules: [...],\r\n conditions: {associative list: name ==> set},\r\n }\r\n }\r\n\r\n\r\n token location info (@$, _$, etc.): {\r\n first_line: n,\r\n last_line: n,\r\n first_column: n,\r\n last_column: n,\r\n range: [start_number, end_number] (where the numbers are indexes into the input string, regular zero-based)\r\n }\r\n\r\n\r\n the parseError function receives a 'hash' object with these members for lexer and parser errors: {\r\n text: (matched text)\r\n token: (the produced terminal token, if any)\r\n line: (yylineno)\r\n }\r\n while parser (grammar) errors will also provide these members, i.e. parser errors deliver a superset of attributes: {\r\n loc: (yylloc)\r\n expected: (string describing the set of expected tokens)\r\n recoverable: (boolean: TRUE when the parser has a error recovery rule available for this particular error)\r\n }\r\n*/\r\nvar parser = (function(){\r\nvar o=function(k,v,o,l){for(o=o||{},l=k.length;l--;o[k[l]]=v);return o},$V0=[1,4],$V1=[1,5],$V2=[1,6],$V3=[1,7],$V4=[1,8],$V5=[1,9],$V6=[1,11],$V7=[1,12],$V8=[5,7,8,11],$V9=[1,17],$Va=[1,22],$Vb=[1,20],$Vc=[1,21],$Vd=[5,7,8,11,19];\r\nvar parser = {trace: function trace() { },\r\nyy: {},\r\nsymbols_: {\"error\":2,\"Program\":3,\"Expression\":4,\"EOF\":5,\"Selector\":6,\"OR\":7,\"AND\":8,\"NOT\":9,\"(\":10,\")\":11,\"SELECTOR\":12,\"NAMED_SELECTOR\":13,\"SELECTOR_RANGED\":14,\"RangeList\":15,\"SELECTOR_NAMED\":16,\"NameList\":17,\"Range\":18,\",\":19,\"NUMBER\":20,\":\":21,\"Name\":22,\"IDENTIFIER\":23,\"STRING\":24,\"$accept\":0,\"$end\":1},\r\nterminals_: {2:\"error\",5:\"EOF\",7:\"OR\",8:\"AND\",9:\"NOT\",10:\"(\",11:\")\",12:\"SELECTOR\",13:\"NAMED_SELECTOR\",14:\"SELECTOR_RANGED\",16:\"SELECTOR_NAMED\",19:\",\",20:\"NUMBER\",21:\":\",23:\"IDENTIFIER\",24:\"STRING\"},\r\nproductions_: [0,[3,2],[4,1],[4,3],[4,3],[4,2],[4,3],[6,1],[6,1],[6,2],[6,2],[15,1],[15,3],[18,1],[18,3],[17,1],[17,3],[22,1],[22,1],[22,1]],\r\nperformAction: function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.keyword('or')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.keyword('and')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.keyword('not')($$[$0]);\r\nbreak;\r\ncase 6:\r\nthis.$ = $$[$0-1];\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.keyword($$[$0])();\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.GetSelector($$[$0].toLowerCase().slice(1, $$[$0].length));\r\nbreak;\r\ncase 9: case 10:\r\nthis.$ = yy.keyword($$[$0-1])($$[$0]);\r\nbreak;\r\ncase 11:\r\nthis.$ = new yy.RangeList($$[$0]);\r\nbreak;\r\ncase 12: case 16:\r\nthis.$ = $$[$0-2].append($$[$0]);\r\nbreak;\r\ncase 13:\r\nthis.$ = new yy.Range(Number($$[$0]));\r\nbreak;\r\ncase 14:\r\nthis.$ = new yy.Range(Number($$[$0-2]), Number($$[$0]));\r\nbreak;\r\ncase 15:\r\nthis.$ = new yy.ValueList($$[$0]);\r\nbreak;\r\n}\r\n},\r\ntable: [{3:1,4:2,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{1:[3]},{5:[1,10],7:$V6,8:$V7},o($V8,[2,2]),{4:13,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:14,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,7]),o($V8,[2,8]),{15:15,18:16,20:$V9},{17:18,20:$Va,22:19,23:$Vb,24:$Vc},{1:[2,1]},{4:23,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:24,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,5]),{7:$V6,8:$V7,11:[1,25]},o($V8,[2,9],{19:[1,26]}),o($Vd,[2,11]),o($Vd,[2,13],{21:[1,27]}),o($V8,[2,10],{19:[1,28]}),o($Vd,[2,15]),o($Vd,[2,17]),o($Vd,[2,18]),o($Vd,[2,19]),o([5,7,11],[2,3],{8:$V7}),o($V8,[2,4]),o($V8,[2,6]),{18:29,20:$V9},{20:[1,30]},{20:$Va,22:31,23:$Vb,24:$Vc},o($Vd,[2,12]),o($Vd,[2,14]),o($Vd,[2,16])],\r\ndefaultActions: {10:[2,1]},\r\nparseError: function parseError(str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function (match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex() {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin(condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState() {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules() {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState(n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState(condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* skip whitespace */\r\nbreak;\r\ncase 1:return 20;\r\nbreak;\r\ncase 2:return 7;\r\nbreak;\r\ncase 3:return 8;\r\nbreak;\r\ncase 4:return 9;\r\nbreak;\r\ncase 5:return 12;\r\nbreak;\r\ncase 6:return 16;\r\nbreak;\r\ncase 7:return 14;\r\nbreak;\r\ncase 8:return 10;\r\nbreak;\r\ncase 9:return 11;\r\nbreak;\r\ncase 10:return 19;\r\nbreak;\r\ncase 11:return 21;\r\nbreak;\r\ncase 12:return '<=';\r\nbreak;\r\ncase 13:return '>=';\r\nbreak;\r\ncase 14:return '<';\r\nbreak;\r\ncase 15:return '>';\r\nbreak;\r\ncase 16:yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2); return 24;\r\nbreak;\r\ncase 17:return 13;\r\nbreak;\r\ncase 18:return 23;\r\nbreak;\r\ncase 19:return 5;\r\nbreak;\r\ncase 20:return 'INVALID';\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:(-?(?:[1-9][0-9]+|[0-9]))\\b)/i,/^(?:OR\\b)/i,/^(?:AND\\b)/i,/^(?:NOT\\b)/i,/^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\\b)/i,/^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\\b)/i,/^(?:((SERIAL|SEQUENCE|RESIDX))\\b)/i,/^(?:\\()/i,/^(?:\\))/i,/^(?:,)/i,/^(?::)/i,/^(?:<=)/i,/^(?:>=)/i,/^(?:<)/i,/^(?:>)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:(@[_A-Z0-9]+))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:.)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","\r\n/*\r\nSmooth.js version 0.1.7\r\n\r\nTurn arrays into smooth functions.\r\n\r\nCopyright 2012 Spencer Cohen\r\nLicensed under MIT license (see \"Smooth.js MIT license.txt\")\r\n*/\r\n\r\n/*Constants (these are accessible by Smooth.WHATEVER in user space)\r\n*/\r\n\r\n(function() {\r\n var AbstractInterpolator, CubicInterpolator, Enum, LinearInterpolator, NearestInterpolator, PI, SincFilterInterpolator, Smooth, clipClamp, clipMirror, clipPeriodic, defaultConfig, getColumn, getType, isValidNumber, k, makeLanczosWindow, makeScaledFunction, makeSincKernel, normalizeScaleTo, shallowCopy, sin, sinc, v, validateNumber, validateVector,\r\n __hasProp = Object.prototype.hasOwnProperty,\r\n __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor; child.__super__ = parent.prototype; return child; };\r\n\r\n Enum = {\r\n /*Interpolation methods\r\n */\r\n METHOD_NEAREST: 'nearest',\r\n METHOD_LINEAR: 'linear',\r\n METHOD_CUBIC: 'cubic',\r\n METHOD_LANCZOS: 'lanczos',\r\n METHOD_SINC: 'sinc',\r\n /*Input clipping modes\r\n */\r\n CLIP_CLAMP: 'clamp',\r\n CLIP_ZERO: 'zero',\r\n CLIP_PERIODIC: 'periodic',\r\n CLIP_MIRROR: 'mirror',\r\n /* Constants for control over the cubic interpolation tension\r\n */\r\n CUBIC_TENSION_DEFAULT: 0,\r\n CUBIC_TENSION_CATMULL_ROM: 0\r\n };\r\n\r\n defaultConfig = {\r\n method: Enum.METHOD_CUBIC,\r\n cubicTension: Enum.CUBIC_TENSION_DEFAULT,\r\n clip: Enum.CLIP_CLAMP,\r\n scaleTo: 0,\r\n sincFilterSize: 2,\r\n sincWindow: void 0\r\n };\r\n\r\n /*Index clipping functions\r\n */\r\n\r\n clipClamp = function(i, n) {\r\n return Math.max(0, Math.min(i, n - 1));\r\n };\r\n\r\n clipPeriodic = function(i, n) {\r\n i = i % n;\r\n if (i < 0) i += n;\r\n return i;\r\n };\r\n\r\n clipMirror = function(i, n) {\r\n var period;\r\n period = 2 * (n - 1);\r\n i = clipPeriodic(i, period);\r\n if (i > n - 1) i = period - i;\r\n return i;\r\n };\r\n\r\n /*\r\n Abstract scalar interpolation class which provides common functionality for all interpolators\r\n \r\n Subclasses must override interpolate().\r\n */\r\n\r\n AbstractInterpolator = (function() {\r\n\r\n function AbstractInterpolator(array, config) {\r\n this.array = array.slice(0);\r\n this.length = this.array.length;\r\n if (!(this.clipHelper = {\r\n clamp: this.clipHelperClamp,\r\n zero: this.clipHelperZero,\r\n periodic: this.clipHelperPeriodic,\r\n mirror: this.clipHelperMirror\r\n }[config.clip])) {\r\n throw \"Invalid clip: \" + config.clip;\r\n }\r\n }\r\n\r\n AbstractInterpolator.prototype.getClippedInput = function(i) {\r\n if ((0 <= i && i < this.length)) {\r\n return this.array[i];\r\n } else {\r\n return this.clipHelper(i);\r\n }\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperClamp = function(i) {\r\n return this.array[clipClamp(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperZero = function(i) {\r\n return 0;\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperPeriodic = function(i) {\r\n return this.array[clipPeriodic(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperMirror = function(i) {\r\n return this.array[clipMirror(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.interpolate = function(t) {\r\n throw 'Subclasses of AbstractInterpolator must override the interpolate() method.';\r\n };\r\n\r\n return AbstractInterpolator;\r\n\r\n })();\r\n\r\n NearestInterpolator = (function(_super) {\r\n\r\n __extends(NearestInterpolator, _super);\r\n\r\n function NearestInterpolator() {\r\n NearestInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n NearestInterpolator.prototype.interpolate = function(t) {\r\n return this.getClippedInput(Math.round(t));\r\n };\r\n\r\n return NearestInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n LinearInterpolator = (function(_super) {\r\n\r\n __extends(LinearInterpolator, _super);\r\n\r\n function LinearInterpolator() {\r\n LinearInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n LinearInterpolator.prototype.interpolate = function(t) {\r\n var k;\r\n k = Math.floor(t);\r\n t -= k;\r\n return (1 - t) * this.getClippedInput(k) + t * this.getClippedInput(k + 1);\r\n };\r\n\r\n return LinearInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n CubicInterpolator = (function(_super) {\r\n\r\n __extends(CubicInterpolator, _super);\r\n\r\n function CubicInterpolator(array, config) {\r\n this.tangentFactor = 1 - Math.max(-1, Math.min(1, config.cubicTension));\r\n CubicInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n CubicInterpolator.prototype.getTangent = function(k) {\r\n return this.tangentFactor * (this.getClippedInput(k + 1) - this.getClippedInput(k - 1)) / 2;\r\n };\r\n\r\n CubicInterpolator.prototype.interpolate = function(t) {\r\n var k, m, p, t2, t3;\r\n k = Math.floor(t);\r\n m = [this.getTangent(k), this.getTangent(k + 1)];\r\n p = [this.getClippedInput(k), this.getClippedInput(k + 1)];\r\n t -= k;\r\n t2 = t * t;\r\n t3 = t * t2;\r\n return (2 * t3 - 3 * t2 + 1) * p[0] + (t3 - 2 * t2 + t) * m[0] + (-2 * t3 + 3 * t2) * p[1] + (t3 - t2) * m[1];\r\n };\r\n\r\n return CubicInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n sin = Math.sin, PI = Math.PI;\r\n\r\n sinc = function(x) {\r\n if (x === 0) {\r\n return 1;\r\n } else {\r\n return sin(PI * x) / (PI * x);\r\n }\r\n };\r\n\r\n makeLanczosWindow = function(a) {\r\n return function(x) {\r\n return sinc(x / a);\r\n };\r\n };\r\n\r\n makeSincKernel = function(window) {\r\n return function(x) {\r\n return sinc(x) * window(x);\r\n };\r\n };\r\n\r\n SincFilterInterpolator = (function(_super) {\r\n\r\n __extends(SincFilterInterpolator, _super);\r\n\r\n function SincFilterInterpolator(array, config) {\r\n SincFilterInterpolator.__super__.constructor.apply(this, arguments);\r\n this.a = config.sincFilterSize;\r\n if (!config.sincWindow) throw 'No sincWindow provided';\r\n this.kernel = makeSincKernel(config.sincWindow);\r\n }\r\n\r\n SincFilterInterpolator.prototype.interpolate = function(t) {\r\n var k, n, sum, _ref, _ref2;\r\n k = Math.floor(t);\r\n sum = 0;\r\n for (n = _ref = k - this.a + 1, _ref2 = k + this.a; _ref <= _ref2 ? n <= _ref2 : n >= _ref2; _ref <= _ref2 ? n++ : n--) {\r\n sum += this.kernel(t - n) * this.getClippedInput(n);\r\n }\r\n return sum;\r\n };\r\n\r\n return SincFilterInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n getColumn = function(arr, i) {\r\n var row, _i, _len, _results;\r\n _results = [];\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n row = arr[_i];\r\n _results.push(row[i]);\r\n }\r\n return _results;\r\n };\r\n\r\n makeScaledFunction = function(f, baseScale, scaleRange) {\r\n var scaleFactor, translation;\r\n if (scaleRange.join === '0,1') {\r\n return f;\r\n } else {\r\n scaleFactor = baseScale / (scaleRange[1] - scaleRange[0]);\r\n translation = scaleRange[0];\r\n return function(t) {\r\n return f(scaleFactor * (t - translation));\r\n };\r\n }\r\n };\r\n\r\n getType = function(x) {\r\n return Object.prototype.toString.call(x).slice('[object '.length, -1);\r\n };\r\n\r\n validateNumber = function(n) {\r\n if (isNaN(n)) throw 'NaN in Smooth() input';\r\n if (getType(n) !== 'Number') throw 'Non-number in Smooth() input';\r\n if (!isFinite(n)) throw 'Infinity in Smooth() input';\r\n };\r\n\r\n validateVector = function(v, dimension) {\r\n var n, _i, _len;\r\n if (getType(v) !== 'Array') throw 'Non-vector in Smooth() input';\r\n if (v.length !== dimension) throw 'Inconsistent dimension in Smooth() input';\r\n for (_i = 0, _len = v.length; _i < _len; _i++) {\r\n n = v[_i];\r\n validateNumber(n);\r\n }\r\n };\r\n\r\n isValidNumber = function(n) {\r\n return (getType(n) === 'Number') && isFinite(n) && !isNaN(n);\r\n };\r\n\r\n normalizeScaleTo = function(s) {\r\n var invalidErr;\r\n invalidErr = \"scaleTo param must be number or array of two numbers\";\r\n switch (getType(s)) {\r\n case 'Number':\r\n if (!isValidNumber(s)) throw invalidErr;\r\n s = [0, s];\r\n break;\r\n case 'Array':\r\n if (s.length !== 2) throw invalidErr;\r\n if (!(isValidNumber(s[0]) && isValidNumber(s[1]))) throw invalidErr;\r\n break;\r\n default:\r\n throw invalidErr;\r\n }\r\n return s;\r\n };\r\n\r\n shallowCopy = function(obj) {\r\n var copy, k, v;\r\n copy = {};\r\n for (k in obj) {\r\n if (!__hasProp.call(obj, k)) continue;\r\n v = obj[k];\r\n copy[k] = v;\r\n }\r\n return copy;\r\n };\r\n\r\n Smooth = function(arr, config) {\r\n var baseDomainEnd, dimension, i, interpolator, interpolatorClass, interpolators, k, n, properties, smoothFunc, v;\r\n if (config == null) config = {};\r\n properties = {};\r\n config = shallowCopy(config);\r\n properties.config = shallowCopy(config);\r\n if (config.scaleTo == null) config.scaleTo = config.period;\r\n if (config.sincFilterSize == null) {\r\n config.sincFilterSize = config.lanczosFilterSize;\r\n }\r\n for (k in defaultConfig) {\r\n if (!__hasProp.call(defaultConfig, k)) continue;\r\n v = defaultConfig[k];\r\n if (config[k] == null) config[k] = v;\r\n }\r\n if (!(interpolatorClass = {\r\n nearest: NearestInterpolator,\r\n linear: LinearInterpolator,\r\n cubic: CubicInterpolator,\r\n lanczos: SincFilterInterpolator,\r\n sinc: SincFilterInterpolator\r\n }[config.method])) {\r\n throw \"Invalid method: \" + config.method;\r\n }\r\n if (config.method === 'lanczos') {\r\n config.sincWindow = makeLanczosWindow(config.sincFilterSize);\r\n }\r\n if (arr.length < 2) throw 'Array must have at least two elements';\r\n properties.count = arr.length;\r\n smoothFunc = (function() {\r\n var _i, _j, _len, _len2;\r\n switch (getType(arr[0])) {\r\n case 'Number':\r\n properties.dimension = 'scalar';\r\n if (Smooth.deepValidation) {\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n n = arr[_i];\r\n validateNumber(n);\r\n }\r\n }\r\n interpolator = new interpolatorClass(arr, config);\r\n return function(t) {\r\n return interpolator.interpolate(t);\r\n };\r\n case 'Array':\r\n properties.dimension = dimension = arr[0].length;\r\n if (!dimension) throw 'Vectors must be non-empty';\r\n if (Smooth.deepValidation) {\r\n for (_j = 0, _len2 = arr.length; _j < _len2; _j++) {\r\n v = arr[_j];\r\n validateVector(v, dimension);\r\n }\r\n }\r\n interpolators = (function() {\r\n var _results;\r\n _results = [];\r\n for (i = 0; 0 <= dimension ? i < dimension : i > dimension; 0 <= dimension ? i++ : i--) {\r\n _results.push(new interpolatorClass(getColumn(arr, i), config));\r\n }\r\n return _results;\r\n })();\r\n return function(t) {\r\n var interpolator, _k, _len3, _results;\r\n _results = [];\r\n for (_k = 0, _len3 = interpolators.length; _k < _len3; _k++) {\r\n interpolator = interpolators[_k];\r\n _results.push(interpolator.interpolate(t));\r\n }\r\n return _results;\r\n };\r\n default:\r\n throw \"Invalid element type: \" + (getType(arr[0]));\r\n }\r\n })();\r\n if (config.clip === 'periodic') {\r\n baseDomainEnd = arr.length;\r\n } else {\r\n baseDomainEnd = arr.length - 1;\r\n }\r\n config.scaleTo || (config.scaleTo = baseDomainEnd);\r\n properties.domain = normalizeScaleTo(config.scaleTo);\r\n smoothFunc = makeScaledFunction(smoothFunc, baseDomainEnd, properties.domain);\r\n properties.domain.sort();\r\n /*copy properties\r\n */\r\n for (k in properties) {\r\n if (!__hasProp.call(properties, k)) continue;\r\n v = properties[k];\r\n smoothFunc[k] = v;\r\n }\r\n return smoothFunc;\r\n };\r\n\r\n for (k in Enum) {\r\n if (!__hasProp.call(Enum, k)) continue;\r\n v = Enum[k];\r\n Smooth[k] = v;\r\n }\r\n\r\n Smooth.deepValidation = true;\r\n\r\n (typeof exports !== \"undefined\" && exports !== null ? exports : window).Smooth = Smooth;\r\n\r\n}).call(this);\r\n","!function(r,t){if(\"function\"==typeof define&&define.amd)define([\"exports\"],t);else if(\"object\"==typeof exports&&\"undefined\"!=typeof module)t(exports);else t(r.MMTF=r.MMTF||{})}(this,function(r){\"use strict\";function t(r,t,n){for(var e=(r.byteLength,0),i=n.length;i>e;e++){var o=n.charCodeAt(e);if(128>o)r.setUint8(t++,o>>>0&127|0);else if(2048>o)r.setUint8(t++,o>>>6&31|192),r.setUint8(t++,o>>>0&63|128);else if(65536>o)r.setUint8(t++,o>>>12&15|224),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128);else{if(!(1114112>o))throw new Error(\"bad codepoint \"+o);r.setUint8(t++,o>>>18&7|240),r.setUint8(t++,o>>>12&63|128),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128)}}}function n(r){for(var t=0,n=0,e=r.length;e>n;n++){var i=r.charCodeAt(n);if(128>i)t+=1;else if(2048>i)t+=2;else if(65536>i)t+=3;else{if(!(1114112>i))throw new Error(\"bad codepoint \"+i);t+=4}}return t}function e(r,i,o){var a=typeof r;if(\"string\"===a){var u=n(r);if(32>u)return i.setUint8(o,160|u),t(i,o+1,r),1+u;if(256>u)return i.setUint8(o,217),i.setUint8(o+1,u),t(i,o+2,r),2+u;if(65536>u)return 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zIndex: 2e9,\n className: 'spinner',\n top: '50%',\n left: '50%',\n shadow: '0 0 1px transparent', // prevent aliased lines\n position: 'absolute',\n};\nvar Spinner = /** @class */ (function () {\n function Spinner(opts) {\n if (opts === void 0) { opts = {}; }\n this.opts = __assign(__assign({}, defaults), opts);\n }\n /**\n * Adds the spinner to the given target element. If this instance is already\n * spinning, it is automatically removed from its previous target by calling\n * stop() internally.\n */\n Spinner.prototype.spin = function (target) {\n this.stop();\n this.el = document.createElement('div');\n this.el.className = this.opts.className;\n this.el.setAttribute('role', 'progressbar');\n this.el.style.position = this.opts.position;\n this.el.style.width = \"0\";\n this.el.style.zIndex = this.opts.zIndex.toString();\n this.el.style.left = this.opts.left;\n this.el.style.top = this.opts.top;\n this.el.style.transform = \"scale(\".concat(this.opts.scale, \")\");\n if (target) {\n target.insertBefore(this.el, target.firstChild || null);\n }\n drawLines(this.el, this.opts);\n return this;\n };\n /**\n * Stops and removes the Spinner.\n * Stopped spinners may be reused by calling spin() again.\n */\n Spinner.prototype.stop = function () {\n if (this.el) {\n if (this.el.parentNode) {\n this.el.parentNode.removeChild(this.el);\n }\n this.el = undefined;\n }\n return this;\n };\n return Spinner;\n}());\nexport { Spinner };\n/**\n * Returns the line color from the given string or array.\n */\nfunction getColor(color, idx) {\n return typeof color == 'string' ? color : color[idx % color.length];\n}\n/**\n * Internal method that draws the individual lines.\n */\nfunction drawLines(el, opts) {\n var borderRadius = (Math.round(opts.corners * opts.width * 500) / 1000) + 'px';\n var shadow = 'none';\n if (opts.shadow === true) {\n shadow = '0 2px 4px #000'; // default shadow\n }\n else if (typeof opts.shadow === 'string') {\n shadow = opts.shadow;\n }\n var shadows = parseBoxShadow(shadow);\n for (var i = 0; i < opts.lines; i++) {\n var degrees = ~~(360 / opts.lines * i + opts.rotate);\n var backgroundLine = document.createElement('div');\n backgroundLine.style.position = 'absolute';\n backgroundLine.style.top = \"\".concat(-opts.width / 2, \"px\");\n backgroundLine.style.width = (opts.length + opts.width) + 'px';\n backgroundLine.style.height = opts.width + 'px';\n backgroundLine.style.background = getColor(opts.fadeColor, i);\n backgroundLine.style.borderRadius = borderRadius;\n backgroundLine.style.transformOrigin = 'left';\n backgroundLine.style.transform = \"rotate(\".concat(degrees, \"deg) translateX(\").concat(opts.radius, \"px)\");\n var delay = i * opts.direction / opts.lines / opts.speed;\n delay -= 1 / opts.speed; // so initial animation state will include trail\n var line = document.createElement('div');\n line.style.width = '100%';\n line.style.height = '100%';\n line.style.background = getColor(opts.color, i);\n line.style.borderRadius = borderRadius;\n line.style.boxShadow = normalizeShadow(shadows, degrees);\n line.style.animation = \"\".concat(1 / opts.speed, \"s linear \").concat(delay, \"s infinite \").concat(opts.animation);\n backgroundLine.appendChild(line);\n el.appendChild(backgroundLine);\n }\n}\nfunction parseBoxShadow(boxShadow) {\n var regex = /^\\s*([a-zA-Z]+\\s+)?(-?\\d+(\\.\\d+)?)([a-zA-Z]*)\\s+(-?\\d+(\\.\\d+)?)([a-zA-Z]*)(.*)$/;\n var shadows = [];\n for (var _i = 0, _a = boxShadow.split(','); _i < _a.length; _i++) {\n var shadow = _a[_i];\n var matches = shadow.match(regex);\n if (matches === null) {\n continue; // invalid syntax\n }\n var x = +matches[2];\n var y = +matches[5];\n var xUnits = matches[4];\n var yUnits = matches[7];\n if (x === 0 && !xUnits) {\n xUnits = yUnits;\n }\n if (y === 0 && !yUnits) {\n yUnits = xUnits;\n }\n if (xUnits !== yUnits) {\n continue; // units must match to use as coordinates\n }\n shadows.push({\n prefix: matches[1] || '', // could have value of 'inset' or undefined\n x: x,\n y: y,\n xUnits: xUnits,\n yUnits: yUnits,\n end: matches[8],\n });\n }\n return shadows;\n}\n/**\n * Modify box-shadow x/y offsets to counteract rotation\n */\nfunction normalizeShadow(shadows, degrees) {\n var normalized = [];\n for (var _i = 0, shadows_1 = shadows; _i < shadows_1.length; _i++) {\n var shadow = shadows_1[_i];\n var xy = convertOffset(shadow.x, shadow.y, degrees);\n normalized.push(shadow.prefix + xy[0] + shadow.xUnits + ' ' + xy[1] + shadow.yUnits + shadow.end);\n }\n return normalized.join(', ');\n}\nfunction convertOffset(x, y, degrees) {\n var radians = degrees * Math.PI / 180;\n var sin = Math.sin(radians);\n var cos = Math.cos(radians);\n return [\n Math.round((x * cos + y * sin) * 1000) / 1000,\n Math.round((-x * sin + y * cos) * 1000) / 1000,\n ];\n}\n","//----------------------------------------------------------------------------\r\n// Timer\r\n\r\nexport default class Timer {\r\n constructor() {\r\n this.startTime = 0;\r\n this.oldTime = 0;\r\n this.elapsedTime = 0;\r\n this.running = false;\r\n }\r\n\r\n start() {\r\n this.startTime = Timer.now();\r\n this.oldTime = this.startTime;\r\n this.running = true;\r\n }\r\n\r\n stop() {\r\n this.getElapsedTime();\r\n this.running = false;\r\n }\r\n\r\n getElapsedTime() {\r\n this.update();\r\n return this.elapsedTime;\r\n }\r\n\r\n update() {\r\n let delta = 0;\r\n if (this.running) {\r\n const newTime = Timer.now();\r\n delta = 0.001 * (newTime - this.oldTime);\r\n this.oldTime = newTime;\r\n this.elapsedTime += delta;\r\n }\r\n\r\n return delta;\r\n }\r\n}\r\n\r\nTimer.now = (function () {\r\n const p = typeof window !== 'undefined' && window.performance;\r\n return (p && p.now) ? p.now.bind(p) : Date.now;\r\n}());\r\n","import Timer from '../Timer';\r\n\r\nconst { now } = Timer;\r\n\r\nfunction createElement(tag, id, css) {\r\n const element = document.createElement(tag);\r\n element.id = id;\r\n element.style.cssText = css;\r\n return element;\r\n}\r\n\r\nclass Stats {\r\n constructor() {\r\n this.domElement = createElement('div', 'stats', 'padding:8px');\r\n this._text = createElement('p', 'fps', 'margin:0;color:silver;font-size:large');\r\n this.domElement.appendChild(this._text);\r\n\r\n this._startTime = now();\r\n this._prevTime = this._startTime;\r\n\r\n this._deltas = new Array(20);\r\n this._index = 0;\r\n this._total = 0.0;\r\n this._count = 0;\r\n }\r\n\r\n end() {\r\n const time = now();\r\n const delta = time - this._startTime;\r\n\r\n if (this._count < this._deltas.length) {\r\n this._count++;\r\n } else {\r\n this._total -= this._deltas[this._index];\r\n }\r\n this._total += delta;\r\n this._deltas[this._index] = delta;\r\n this._index = (this._index + 1) % this._deltas.length;\r\n\r\n this.ms = this._total / this._count;\r\n this.fps = 1000 / this.ms;\r\n\r\n if (time > this._prevTime + 1000) {\r\n this._text.textContent = this.fps.toPrecision(2);\r\n this._prevTime = time;\r\n }\r\n\r\n return time;\r\n }\r\n\r\n update() {\r\n this._startTime = this.end();\r\n }\r\n\r\n show(on) {\r\n if (on === undefined) {\r\n on = true;\r\n }\r\n this.domElement.style.display = on ? 'block' : 'none';\r\n }\r\n}\r\n\r\nexport default Stats;\r\n","/**\r\n * This class introduces the simplest event system.\r\n */\r\n\r\nimport _ from 'lodash';\r\n\r\nfunction isUndefOrEqual(param, value) {\r\n return !param || param === value;\r\n}\r\n\r\n/**\r\n * Creates empty dispatcher.\r\n *\r\n * @exports EventDispatcher\r\n * @constructor\r\n */\r\nfunction EventDispatcher() {\r\n this._handlers = {};\r\n}\r\n\r\n/**\r\n * Binds callback on specific event type. Optional `context` parameter\r\n * could be used as 'this' for the `callback`.\r\n * @param {string} type Event name.\r\n * @param {function} callback Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.addEventListener = function (type, callback, context) {\r\n let handlers = this._handlers[type];\r\n\r\n if (!handlers) {\r\n this._handlers[type] = [];\r\n handlers = this._handlers[type];\r\n }\r\n\r\n const params = [callback, context];\r\n function _checkPar(par) {\r\n return par[0] === params[0] && par[1] === params[1];\r\n }\r\n\r\n if (_.find(handlers, _checkPar) === undefined) {\r\n handlers.push(params);\r\n }\r\n};\r\n\r\n/**\r\n * Removes a previously-bound callback function from an object.\r\n * If no `context` is specified, all versions of the `callback` with different\r\n * contexts will be removed.\r\n * If no `callback` is specified, all callbacks of the `type` will be removed.\r\n * If no `type` is specified, callbacks for all events will be removed.\r\n * @param {?string} [type] Event type.\r\n * @param {function} [callback] Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.removeEventListener = function (type, callback, context) {\r\n const self = this;\r\n _.forEach(self._handlers, (handler, ev) => {\r\n _.remove(handler, (values) => isUndefOrEqual(type, ev)\r\n && isUndefOrEqual(callback, values[0])\r\n && isUndefOrEqual(context, values[1] || self));\r\n });\r\n\r\n this._handlers = _.omitBy(self._handlers, (handler) => handler.length === 0);\r\n};\r\n\r\n/**\r\n * Makes all the callbacks for the specific `event` to trigger.\r\n * @param {Object} event Event.\r\n * @param {string} event.type Type of the event.\r\n */\r\nEventDispatcher.prototype.dispatchEvent = function (event) {\r\n const self = this;\r\n\r\n _.forEach(this._handlers[event.type], (callback) => {\r\n const context = callback[1] || self;\r\n callback[0].apply(context, [event]);\r\n });\r\n};\r\n\r\nexport default EventDispatcher;\r\n","/**\r\n * This module contains class for logging.\r\n * Returns an instance of a logger that have already been created.\r\n * Allows users to log messages for five different levels,\r\n * enable console output and catch signal on each message.\r\n */\r\nimport _ from 'lodash';\r\nimport EventDispatcher from './EventDispatcher';\r\n\r\nconst priorities = {\r\n debug: 0,\r\n info: 1,\r\n report: 2,\r\n warn: 3,\r\n error: 4,\r\n};\r\n\r\n/**\r\n * Create new Logger.\r\n *\r\n * @exports Logger\r\n * @extends EventDispatcher\r\n * @constructor\r\n */\r\nfunction Logger() {\r\n EventDispatcher.call(this);\r\n /** Boolean flag that toggles output to browser console.\r\n * @type {boolean}\r\n */\r\n this.console = false;\r\n this._priority = priorities.warn;\r\n}\r\n\r\nLogger.prototype = Object.create(EventDispatcher.prototype);\r\nLogger.prototype.constructor = Logger;\r\n\r\n/**\r\n * Create new clean instance of the logger.\r\n * @returns {Logger}\r\n */\r\nLogger.prototype.instantiate = function () {\r\n return new Logger();\r\n};\r\n\r\nfunction verify(number) {\r\n if (!_.isNumber(number)) {\r\n throw new Error('Wrong log level specified!');\r\n }\r\n return number;\r\n}\r\n\r\n/**\r\n * @property {string} current threshold for signals and console output.\r\n * @name Logger#level\r\n */\r\nObject.defineProperty(Logger.prototype, 'level', {\r\n get() {\r\n return _.findKey(priorities, (value) => value === this._priority);\r\n },\r\n set(level) {\r\n this._priority = verify(priorities[level]);\r\n },\r\n});\r\n\r\n/**\r\n * Returns the list of all possible level values.\r\n * @returns {Array}\r\n */\r\nLogger.prototype.levels = function () {\r\n return Object.keys(priorities);\r\n};\r\n\r\n/**\r\n * Add new message with specified level.\r\n * @param {string} level - level of the message, must be one of the\r\n * {'debug' | 'info' | 'report' | 'warn' | 'error'}\r\n * @param {string} message\r\n */\r\nLogger.prototype.message = function (level, message) {\r\n const priority = verify(priorities[level]);\r\n this._message(priority, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('debug', ...);\r\n * @param message\r\n */\r\nLogger.prototype.debug = function (message) {\r\n this._message(priorities.debug, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('info', ...);\r\n * @param message\r\n */\r\nLogger.prototype.info = function (message) {\r\n this._message(priorities.info, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('report', ...);\r\n * @param message\r\n */\r\nLogger.prototype.report = function (message) {\r\n this._message(priorities.report, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('warn', ...);\r\n * @param message\r\n */\r\nLogger.prototype.warn = function (message) {\r\n this._message(priorities.warn, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('error', ...);\r\n * @param message\r\n */\r\nLogger.prototype.error = function (message) {\r\n this._message(priorities.error, message);\r\n};\r\n\r\n/**\r\n * Add new message with specified priority.\r\n * @param {number} priority - priority of the message\r\n * @param {string} message\r\n * @private\r\n */\r\nLogger.prototype._message = function (priority, message) {\r\n if (priority < this._priority) {\r\n return;\r\n }\r\n const level = _.findKey(priorities, (value) => value === priority);\r\n message = String(message);\r\n if (this.console) {\r\n const output = `miew:${level}: ${message}`;\r\n if (level === 'error') {\r\n console.error(output); // NOSONAR\r\n } else if (level === 'warn') {\r\n console.warn(output); // NOSONAR\r\n } else {\r\n console.log(output); // NOSONAR\r\n }\r\n }\r\n this.dispatchEvent({ type: 'message', level, message });\r\n};\r\n\r\nexport default new Logger();\r\n","import _ from 'lodash';\r\nimport logger from './utils/logger';\r\n\r\nconst browserType = {\r\n DEFAULT: 0,\r\n SAFARI: 1,\r\n};\r\n//----------------------------------------------------------------------------\r\n// Query string\r\n\r\n/**\r\n * Escape only dangerous chars in a query string component, use a plus instead of a space.\r\n *\r\n * [RFC 3986](https://tools.ietf.org/html/rfc3986) allows the following chars in the query (see 3.4):\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! $ & ' ( ) * + , ; = : @ / ?\r\n *\r\n * For query string elements we need to escape ampersand, equal sign, and plus,\r\n * but encodeURIComponent() function encodes anything except for the following:\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! ' ( ) *\r\n *\r\n * @param {string} text - key or value to encode\r\n * @param {string} excludeExp - regexp for symbols to exclude from encoding\r\n * @returns {string} encoded string\r\n */\r\nfunction encodeQueryComponent(text, excludeExp) {\r\n const encode = (code) => String.fromCharCode(parseInt(code.substr(1), 16));\r\n return encodeURIComponent(text).replace(excludeExp, encode).replace(/%20/g, '+');\r\n}\r\n\r\n/**\r\n * Unescape dangerous chars in a query string component.\r\n *\r\n * @param {string} text - encoded key or value\r\n * @returns {string} decoded string\r\n * @see {@link encodeQueryComponent}\r\n */\r\nfunction decodeQueryComponent(text) {\r\n return decodeURIComponent(text.replace(/\\+/g, ' '));\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Array} array of (key, value) pairs.\r\n */\r\nfunction getUrlParameters(url) {\r\n url = url || window.location.search;\r\n\r\n const query = url.substring(url.indexOf('?') + 1);\r\n const search = /([^&=]+)=?([^&]*)/g;\r\n const result = [];\r\n let match;\r\n\r\n while ((match = search.exec(query)) !== null) { // eslint-disable-line no-cond-assign\r\n result.push([decodeQueryComponent(match[1]), decodeQueryComponent(match[2])]);\r\n }\r\n\r\n return result;\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters as a hash.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Object}\r\n */\r\nfunction getUrlParametersAsDict(url) {\r\n const result = {};\r\n const a = getUrlParameters(url);\r\n for (let i = 0; i < a.length; ++i) {\r\n const [key, value] = a[i];\r\n result[key] = value;\r\n }\r\n return result;\r\n}\r\n\r\nfunction resolveURL(str) {\r\n if (typeof URL !== 'undefined') {\r\n try {\r\n if (typeof window !== 'undefined') {\r\n return new URL(str, window.location).href;\r\n }\r\n return new URL(str).href;\r\n } catch (error) {\r\n // IE 11 has a URL object with no constructor available so just try a different approach instead\r\n }\r\n }\r\n if (typeof document !== 'undefined') {\r\n const anchor = document.createElement('a');\r\n anchor.href = str;\r\n return anchor.href;\r\n }\r\n return str;\r\n}\r\n\r\n/**\r\n * Generates regular expression object that includes all symbols\r\n * listed in the argument\r\n * @param symbolStr {string} - String containing characters list.\r\n * @returns {RegExp} - Regular expression.\r\n */\r\nfunction generateRegExp(symbolStr) {\r\n const symbolList = [];\r\n\r\n for (let i = 0, n = symbolStr.length; i < n; ++i) {\r\n symbolList[symbolList.length] = symbolStr[i].charCodeAt(0).toString(16);\r\n }\r\n\r\n const listStr = symbolList.join('|');\r\n\r\n return new RegExp(`%(?:${listStr})`, 'gi');\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Create HTML element\r\n\r\nfunction createElement(tag, attrs, content) {\r\n const element = document.createElement(tag);\r\n let i;\r\n let n;\r\n if (attrs) {\r\n const keys = Object.keys(attrs);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n element.setAttribute(key, attrs[key]);\r\n }\r\n }\r\n if (content) {\r\n if (!(content instanceof Array)) {\r\n content = [content];\r\n }\r\n for (i = 0, n = content.length; i < n; ++i) {\r\n const child = content[i];\r\n if (typeof child === 'string') {\r\n element.appendChild(document.createTextNode(child));\r\n } else if (child instanceof HTMLElement) {\r\n element.appendChild(child);\r\n }\r\n }\r\n }\r\n return element;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Easy inheritance\r\n\r\n/**\r\n * Derive the class from the base.\r\n * @param cls {function} - Class (constructor) to derive.\r\n * @param base {function} - Class (constructor) to derive from.\r\n * @param members {object=} - Optional instance members to add.\r\n * @param statics {object=} - Optional static class members to add.\r\n * @returns {function} Original class.\r\n */\r\nfunction deriveClass(cls, base, members, statics) {\r\n cls.prototype = _.assign(Object.create(base.prototype), { constructor: cls }, members);\r\n if (statics) {\r\n _.assign(cls, statics);\r\n }\r\n return cls;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Deep prototyping\r\n\r\nfunction deriveDeep(obj, needZeroOwnProperties) {\r\n let res = obj;\r\n let i;\r\n let n;\r\n if (obj instanceof Array) {\r\n res = new Array(obj.length);\r\n for (i = 0, n = obj.length; i < n; ++i) {\r\n res[i] = deriveDeep(obj[i]);\r\n }\r\n } else if (obj instanceof Object) {\r\n res = Object.create(obj);\r\n const keys = Object.keys(obj);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = obj[key];\r\n const copy = deriveDeep(value);\r\n if (copy !== value) {\r\n res[key] = copy;\r\n }\r\n }\r\n if (needZeroOwnProperties && Object.keys(res).length > 0) {\r\n res = Object.create(res);\r\n }\r\n }\r\n return res;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Colors\r\n\r\nfunction hexColor(color) {\r\n const hex = (`0000000${color.toString(16)}`).substr(-6);\r\n return `#${hex}`;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Debug tracing\r\n\r\nfunction DebugTracer(namespace) {\r\n let enabled = false;\r\n\r\n this.enable = function (on) {\r\n enabled = on;\r\n };\r\n\r\n let indent = 0;\r\n const methods = Object.keys(namespace);\r\n\r\n function wrap(method_, name_) {\r\n return function (...args) {\r\n const spaces = DebugTracer.spaces.substr(0, indent * 2);\r\n if (enabled) {\r\n logger.debug(`${spaces + name_} {`);\r\n }\r\n indent++;\r\n const result = method_.apply(this, args); // eslint-disable-line no-invalid-this\r\n indent--;\r\n if (enabled) {\r\n logger.debug(`${spaces}} // ${name_}`);\r\n }\r\n return result;\r\n };\r\n }\r\n\r\n for (let i = 0, n = methods.length; i < n; ++i) {\r\n const name = methods[i];\r\n const method = namespace[name];\r\n if (method instanceof Function && name !== 'constructor') {\r\n namespace[name] = wrap(method, name);\r\n }\r\n }\r\n}\r\n\r\nDebugTracer.spaces = ' ';\r\n\r\nclass OutOfMemoryError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'OutOfMemoryError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction allocateTyped(TypedArrayName, size) {\r\n let result = null;\r\n try {\r\n result = new TypedArrayName(size);\r\n } catch (e) {\r\n if (e instanceof RangeError) {\r\n throw new OutOfMemoryError(e.message);\r\n } else {\r\n throw e;\r\n }\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Float array conversion\r\n\r\nfunction bytesToBase64(/** ArrayBuffer */ buffer) {\r\n const bytes = new Uint8Array(buffer);\r\n let binary = '';\r\n for (let i = 0; i < bytes.byteLength; i++) {\r\n binary += String.fromCharCode(bytes[i]);\r\n }\r\n return window.btoa(binary);\r\n}\r\n\r\nfunction bytesFromBase64(/** string */ str) {\r\n const binary = window.atob(str);\r\n const bytes = new Uint8Array(binary.length);\r\n for (let i = 0; i < bytes.length; ++i) {\r\n bytes[i] = binary[i].charCodeAt(0);\r\n }\r\n return bytes.buffer;\r\n}\r\n\r\nfunction arrayToBase64(/** number[] */ array, /** function */ TypedArrayClass) {\r\n return bytesToBase64(new TypedArrayClass(array).buffer);\r\n}\r\n\r\nfunction arrayFromBase64(/** string */ str, /** function */ TypedArrayClass) {\r\n return Array.prototype.slice.call(new TypedArrayClass(bytesFromBase64(str)));\r\n}\r\n\r\n// NOTE: this is 1-level comparison\r\nfunction compareOptionsWithDefaults(opts, defOpts) {\r\n const optsStr = [];\r\n if (defOpts && opts) {\r\n const keys = Object.keys(opts);\r\n for (let p = 0; p < keys.length; ++p) {\r\n const key = keys[p];\r\n const value = opts[key];\r\n // TODO add processing for tree structure\r\n if (!(value instanceof Object) && typeof defOpts[key] !== 'undefined' && defOpts[key] !== value) {\r\n optsStr.push(`${key}:${value}`);\r\n }\r\n }\r\n if (optsStr.length > 0) {\r\n return `!${optsStr.join()}`;\r\n }\r\n }\r\n return '';\r\n}\r\n\r\nfunction isAlmostPlainObject(o) {\r\n if (_.isPlainObject(o)) {\r\n return true;\r\n }\r\n const proto = o && Object.getPrototypeOf(o);\r\n return !!proto && !proto.hasOwnProperty('constructor') && isAlmostPlainObject(proto);\r\n}\r\n\r\n/**\r\n * Build an object that contains properties (and subproperties) of `src` different from those\r\n * in `dst`. Objects are parsed recursively, other values (including arrays) are compared for\r\n * equality using `_.isEqual()`.\r\n * @param {!object} src - a new object to compare, may contain changed or new properties\r\n * @param {!object} dst - an old reference object\r\n */\r\nfunction objectsDiff(src, dst) {\r\n const diff = {};\r\n _.forIn(src, (srcValue, key) => {\r\n const dstValue = dst[key];\r\n if (isAlmostPlainObject(srcValue) && isAlmostPlainObject(dstValue)) {\r\n const deepDiff = objectsDiff(srcValue, dstValue);\r\n if (!_.isEmpty(deepDiff)) {\r\n diff[key] = deepDiff;\r\n }\r\n } else if (!_.isEqual(srcValue, dstValue)) {\r\n diff[key] = srcValue;\r\n }\r\n });\r\n return diff;\r\n}\r\n\r\nfunction forInRecursive(object, callback) {\r\n function iterateThrough(obj, prefix) {\r\n _.forIn(obj, (value, key) => {\r\n const newPref = prefix + (prefix.length > 0 ? '.' : '');\r\n if (value instanceof Object) {\r\n iterateThrough(value, newPref + key);\r\n } else if (value !== undefined) {\r\n callback(value, newPref + key);\r\n }\r\n });\r\n }\r\n iterateThrough(object, '');\r\n}\r\n\r\nfunction enquoteString(value) {\r\n if (_.isString(value)) {\r\n return `\"${value.replace(/\"/g, '\\\\\"')}\"`;\r\n }\r\n return value;\r\n}\r\n\r\nfunction unquoteString(value) {\r\n if (!_.isString(value)) {\r\n return value;\r\n }\r\n if (value[0] === '\"' && value[value.length - 1] === '\"') {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\\"/g, '\"');\r\n }\r\n if (value[0] === \"'\" && value[value.length - 1] === \"'\") {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\'/g, \"'\");\r\n }\r\n throw new SyntaxError('Incorrect string format, can\\'t unqute it');\r\n}\r\n\r\nfunction getFileExtension(fileName) {\r\n return fileName.slice((Math.max(0, fileName.lastIndexOf('.')) || Infinity));\r\n}\r\n\r\nfunction splitFileName(fileName) {\r\n const ext = getFileExtension(fileName);\r\n const name = fileName.slice(0, fileName.length - ext.length);\r\n return [name, ext];\r\n}\r\n\r\nfunction dataUrlToBlob(url) {\r\n const parts = url.split(/[:;,]/);\r\n const partsCount = parts.length;\r\n if (partsCount >= 3 && parts[partsCount - 2] === 'base64') {\r\n return new Blob([bytesFromBase64(parts[partsCount - 1])]);\r\n }\r\n return null;\r\n}\r\n\r\nfunction getBrowser() {\r\n if (navigator.vendor && navigator.vendor.indexOf('Apple') > -1\r\n && navigator.userAgent\r\n && navigator.userAgent.indexOf('CriOS') === -1\r\n && navigator.userAgent.indexOf('FxiOS') === -1) {\r\n return browserType.SAFARI;\r\n }\r\n return browserType.DEFAULT;\r\n}\r\n\r\nfunction shotOpen(url) {\r\n if (typeof window !== 'undefined') {\r\n window.open().document.write(``);\r\n }\r\n}\r\n\r\nfunction shotDownload(dataUrl, filename) {\r\n if (!dataUrl || dataUrl.substr(0, 5) !== 'data:') {\r\n return;\r\n }\r\n if (!filename) {\r\n filename = ['screenshot-', +new Date(), '.png'].join('');\r\n }\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(dataUrlToBlob(dataUrl), filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(dataUrlToBlob(dataUrl));\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction download(data, filename, type) {\r\n const blobData = new Blob([data]);\r\n\r\n if (!filename) {\r\n filename = ['data', +new Date()].join('');\r\n }\r\n\r\n if (!type) {\r\n filename += blobData.type || '.bin';\r\n } else {\r\n filename += `.${type}`;\r\n }\r\n\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(blobData, filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(blobData);\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction copySubArrays(src, dst, indices, itemSize) {\r\n for (let i = 0, n = indices.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n dst[i * itemSize + j] = src[indices[i] * itemSize + j];\r\n }\r\n }\r\n}\r\n\r\nfunction shallowCloneNode(node) {\r\n const newNode = node.cloneNode(true);\r\n newNode.worldPos = node.worldPos;\r\n // .style property is readonly, so \"newNode.style = node.style;\" won't work (and we don't need it, right?)\r\n return newNode;\r\n}\r\n\r\nconst unquotedStringRE = /^[a-zA-Z0-9_]*$/;\r\nconst enquoteHelper = ['\"', '', '\"'];\r\n\r\n// verify and correct if needed selctor identifier\r\nfunction correctSelectorIdentifier(value) {\r\n if (unquotedStringRE.test(value)) {\r\n return value;\r\n }\r\n // quote incorrect identifier\r\n enquoteHelper[1] = value;\r\n return enquoteHelper.join('');\r\n}\r\n\r\n/**\r\n * Concatenates two TypedArray. Doesn't check null refs o type equality\r\n * Attention! It must be use very rarely because requires memory reallocation every time. Use MergeTypedArraysUnsafe to\r\n * unite array of subarrays.\r\n * @param{TypedArray} first - destination array\r\n * @param{TypedArray} second - source array\r\n * @returns{TypedArray} resulting concatenated array\r\n */\r\nfunction concatTypedArraysUnsafe(first, second) {\r\n const result = new first.constructor(first.length + second.length);\r\n result.set(first);\r\n result.set(second, first.length);\r\n return result;\r\n}\r\n\r\n/**\r\n * Merges array of TypedArray into TypedArray. Doesn't check null refs o type equality\r\n * @param{array} array - source array of subarrays\r\n * @returns{TypedArray} resulting merged array\r\n */\r\nfunction mergeTypedArraysUnsafe(array) {\r\n if (array.length <= 0) {\r\n return null;\r\n }\r\n // count the size\r\n const size = array.reduce((acc, cur) => acc + cur.length, 0);\r\n // create combined array\r\n const result = new array[0].constructor(size);\r\n for (let i = 0, start = 0; i < array.length; i++) {\r\n const count = array[i].length;\r\n result.set(array[i], start);\r\n start += count;\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Exports\r\n\r\nexport default {\r\n browserType,\r\n encodeQueryComponent,\r\n decodeQueryComponent,\r\n getUrlParameters,\r\n getUrlParametersAsDict,\r\n resolveURL,\r\n generateRegExp,\r\n createElement,\r\n deriveClass,\r\n deriveDeep,\r\n hexColor,\r\n DebugTracer,\r\n OutOfMemoryError,\r\n allocateTyped,\r\n bytesFromBase64,\r\n bytesToBase64,\r\n arrayFromBase64,\r\n arrayToBase64,\r\n compareOptionsWithDefaults,\r\n objectsDiff,\r\n forInRecursive,\r\n enquoteString,\r\n unquoteString,\r\n getBrowser,\r\n shotOpen,\r\n shotDownload,\r\n copySubArrays,\r\n shallowCloneNode,\r\n correctSelectorIdentifier,\r\n getFileExtension,\r\n splitFileName,\r\n download,\r\n concatTypedArraysUnsafe,\r\n mergeTypedArraysUnsafe,\r\n};\r\n","import EventDispatcher from './EventDispatcher';\r\n\r\nexport default class JobHandle extends EventDispatcher {\r\n constructor() {\r\n super();\r\n this._shouldCancel = false;\r\n }\r\n\r\n cancel() {\r\n this._shouldCancel = true;\r\n this.dispatchEvent({ type: 'cancel' });\r\n }\r\n\r\n shouldCancel() {\r\n return this._shouldCancel;\r\n }\r\n\r\n // slaves use this to notify master about their events\r\n // master routes these notifications to a single event slot\r\n notify(event) {\r\n this.dispatchEvent({ type: 'notification', slaveEvent: event });\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport utils from './utils';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\n\r\nconst VERSION = 0;\r\n\r\n//----------------------------------------------------------------------------\r\n// DEFAULT SETTINGS\r\n//----------------------------------------------------------------------------\r\n\r\n/**\r\n * Polygonal complexity settings.\r\n *\r\n * @typedef PolyComplexity\r\n * @property {number} poor\r\n * @property {number} low\r\n * @property {number} medium\r\n * @property {number} high\r\n * @property {number} ultra\r\n */\r\n\r\n/**\r\n * @alias SettingsObject\r\n * @namespace\r\n */\r\nconst defaults = {\r\n /**\r\n * Default options for all available modes.\r\n * Use {@link Mode.id} as a dictionary key to access mode options.\r\n *\r\n * Usually you don't need to override these settings. You may specify mode options as a parameter during\r\n * {@link Mode} construction.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {LinesModeOptions} LN - Lines mode options.\r\n * @property {LicoriceModeOptions} LC - Licorice mode options.\r\n * @property {BallsAndSticksModeOptions} BS - Balls and Sticks mode options.\r\n * @property {VanDerWaalsModeOptions} VW - Van der Waals mode options.\r\n * @property {TraceModeOptions} TR - Trace mode options.\r\n * @property {TubeModeOptions} TU - Tube mode options.\r\n * @property {CartoonModeOptions} CA - Cartoon mode options.\r\n * @property {QuickSurfaceModeOptions} QS - Contact Surface mode options.\r\n * @property {IsoSurfaceSASModeOptions} SA - Solvent Accessible Surface mode options.\r\n * @property {IsoSurfaceSESModeOptions} SE - Solvent Excluded Surface mode options.\r\n * @property {ContactSurfaceModeOptions} CS - Contact Surface mode options.\r\n * @property {TextModeOptions} TX - Text mode options.\r\n * @property {VolumeDensityModeOptions} VD - Volume Density mode options.\r\n */\r\n modes: {\r\n //----------------------------------------------------------------------------\r\n // BALLS AND STICKS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Balls and Sticks mode options.\r\n *\r\n * @typedef BallsAndSticksModeOptions\r\n *\r\n * @property {number} atom - Sphere radius as a fraction of Van der Waals atom radius.\r\n * @property {number} bond - Cylinder radius in angstroms.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n BS: {\r\n atom: 0.23,\r\n bond: 0.15,\r\n space: 0.5,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VAN DER WAALS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Van der Waals mode options.\r\n *\r\n * @typedef VanDerWaalsModeOptions\r\n *\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VW: {\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 8,\r\n high: 16,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LINES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Lines mode options.\r\n *\r\n * @typedef LinesModeOptions\r\n *\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {number} offsarom - Offset between bonds and aromatic cycle.\r\n * @property {number} chunkarom - Number of pieces in a-loop arc, corresponding to atom.\r\n * @property {number} atom - Collision radius for atoms picking.\r\n * @property {number} lineWidth - Line width in pixels (not used in thin lines).\r\n */\r\n LN: {\r\n multibond: true,\r\n showarom: true,\r\n offsarom: 0.2,\r\n chunkarom: 10,\r\n atom: 0.23,\r\n lineWidth: 2,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LICORICE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Licorice mode options.\r\n *\r\n * @typedef LicoriceModeOptions\r\n *\r\n * @property {number} bond - Bond cylinder radius.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Poly complexity values for render modes.\r\n */\r\n LC: {\r\n bond: 0.20,\r\n space: 0.0,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SAS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Accessible Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSASModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SA: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Excluded Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSESModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SE: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // QUICK SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Quick Surface mode options.\r\n *\r\n * @typedef QuickSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} scale - Radius scale for the surface being built.\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} gaussLim - Gauss lim for coloring the bigger the value, the smoother our colors are.\r\n * @property {PolyComplexity} gridSpacing - Poly complexity values for render modes. In this case the value\r\n * corresponds to the grid density.\r\n */\r\n QS: {\r\n isoValue: 0.5,\r\n gaussLim: {\r\n poor: 1.5,\r\n low: 2.0,\r\n medium: 2.5,\r\n high: 3.0,\r\n ultra: 4.0,\r\n },\r\n scale: 1.0,\r\n wireframe: false,\r\n gridSpacing: {\r\n poor: 2,\r\n low: 1.5,\r\n medium: 1,\r\n high: 0.5,\r\n ultra: 0.25,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CONTACT SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Contact Surface mode options.\r\n *\r\n * @typedef ContactSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} probeRadius - Probe radius.\r\n * @property {number} probePositions\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Radius scale for the surface being built.\r\n * Poly complexity values for render modes. In this case the value corresponds to the grid density.\r\n */\r\n CS: {\r\n probeRadius: 1.4,\r\n isoValue: 1.5,\r\n wireframe: false,\r\n probePositions: 30,\r\n polyComplexity: {\r\n poor: 0.5,\r\n low: 1.0,\r\n medium: 1.5,\r\n high: 1.75,\r\n ultra: 2.0,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TRACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Trace mode options.\r\n *\r\n * @typedef TraceModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n TR: {\r\n radius: 0.30,\r\n polyComplexity: {\r\n poor: 12,\r\n low: 16,\r\n medium: 32,\r\n high: 64,\r\n ultra: 64,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TUBE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Tube mode options.\r\n *\r\n * @typedef TubeModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {number} tension - Tension for interpolation.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n TU: {\r\n radius: 0.30,\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CARTOON\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Cartoon mode options.\r\n *\r\n * @typedef CartoonModeOptions\r\n *\r\n * @property {number} radius - Standard tube radius.\r\n * @property {number} depth - Height of the secondary structure ribbon.\r\n * @property {number} tension - Tension for interpolation.\r\n * @proprety {object} ss - Secondary structure parameters.\r\n * @proprety {object} ss.helix - Options for helices render.\r\n * @proprety {number} ss.helix.width - Width of the secondary structure ribbon.\r\n * @proprety {number} ss.helix.arrow - Secondary structure's arrow width.\r\n * @proprety {object} ss.strand - Options for strands render.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * polyComplexity must be even for producing symmetric arrows.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n CA: {\r\n radius: 0.30,\r\n depth: 0.25,\r\n ss: {\r\n helix: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n strand: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n },\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TEXT\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Text mode options.\r\n *\r\n * @typedef TextModeOptions\r\n *\r\n * @property {string} template - Format string for building output text.\r\n * @property {string} horizontalAlign - Text alignment ('left', 'right', 'center').\r\n * @property {string} verticalAlign - Vertical text box alignment ('top', 'bottom', 'middle').\r\n * @property {number} dx - Text offset x in angstroms.\r\n * @property {number} dy - Text offset y in angstroms.\r\n * @property {number} dz - Text offset z in angstroms.\r\n * @property {string} fg - Color rule for foreground.\r\n * @property {string} bg - Color rule for background.\r\n * @property {boolean} showBg - Flag, that toggles background rendering.\r\n *\r\n */\r\n TX: {\r\n template: '{{Chain}}.{{Residue}}{{Sequence}}.{{Name}}',\r\n horizontalAlign: 'center',\r\n verticalAlign: 'middle',\r\n dx: 0,\r\n dy: 0,\r\n dz: 1,\r\n fg: 'none',\r\n bg: '0x202020',\r\n showBg: true,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VOLUME DENSITY\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Volume density mode options.\r\n *\r\n * @typedef VolumeDensityModeOptions\r\n *\r\n * @property {number} kSigma - Noise threshold coefficient.\r\n * @property {boolean} frame - flag, that turns on box frame painting.\r\n * @property {boolean} isoMode - flag, that turns on IsoSurface mode instead of Volume Rendering.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VD: {\r\n kSigma: 1.0,\r\n kSigmaMed: 2.0,\r\n kSigmaMax: 4.0,\r\n frame: true,\r\n isoMode: false,\r\n polyComplexity: {\r\n poor: 2,\r\n low: 3,\r\n medium: 4,\r\n high: 8,\r\n ultra: 10,\r\n },\r\n },\r\n },\r\n\r\n /**\r\n * Default options for all available colorers.\r\n * Use {@link Colorer.id} as a dictionary key to access colorer options.\r\n *\r\n * Usually you don't need to override these settings. You may specify colorer options as a parameter during\r\n * {@link Colorer} construction.\r\n *\r\n * Not all colorers have options.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {ElementColorerOptions} EL - Element colorer options.\r\n * @property {SequenceColorerOptions} SQ - Sequence colorer options.\r\n * @property {MoleculeColorerOptions} MO - Molecule colorer options.\r\n * @property {UniformColorerOptions} UN - Uniform colorer options.\r\n * @property {ConditionalColorerOptions} CO - Conditional colorer options.\r\n * @property {TemperatureColorerOptions} TM - Temperature colorer options.\r\n * @property {OccupancyColorerOptions} OC - Occupancy colorer options.\r\n * @property {HydrophobicityColorerOptions} HY - Hydrophobicity colorer options.\r\n */\r\n colorers: {\r\n /**\r\n * Element colorer options.\r\n *\r\n * @typedef ElementColorerOptions\r\n *\r\n * @property {number} carbon - Carbon color or -1 to use default.\r\n */\r\n EL: {\r\n carbon: -1,\r\n },\r\n\r\n /**\r\n * Uniform colorer options.\r\n *\r\n * @typedef UniformColorerOptions\r\n *\r\n * @property {number} color - Single color to paint with.\r\n */\r\n UN: {\r\n color: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Conditional colorer options.\r\n *\r\n * @typedef ConditionalColorerOptions\r\n *\r\n * @property {string} subset - Selector string.\r\n * @property {number} color - Color of selected atoms.\r\n * @property {number} baseColor - Color of other atoms.\r\n */\r\n CO: {\r\n subset: 'charged',\r\n color: 0xFF0000,\r\n baseColor: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Carbon colorer options.\r\n *\r\n * @typedef CarbonColorerOptions\r\n *\r\n * @property {number} color - Single color to paint carbons\r\n * @property {number} factor - Color factor for not carbon atoms.\r\n */\r\n CB: {\r\n color: 0x909090,\r\n factor: 0.6,\r\n },\r\n\r\n /**\r\n * Sequence colorer options.\r\n *\r\n * @typedef SequenceColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n SQ: {\r\n gradient: 'rainbow',\r\n },\r\n\r\n /**\r\n * Temperature colorer options.\r\n *\r\n * @typedef TemperatureColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n * @property {number} min - Minimal temperature.\r\n * @property {number} max - Maximal temperature.\r\n */\r\n TM: {\r\n gradient: 'temp',\r\n min: 5,\r\n max: 40,\r\n },\r\n\r\n /**\r\n * Occupancy colorer options.\r\n *\r\n * @typedef OccupancyColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n OC: {\r\n gradient: 'reds',\r\n },\r\n\r\n /**\r\n * Hydrophobicity colorer options.\r\n *\r\n * @typedef HydrophobicityColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n HY: {\r\n gradient: 'blue-red',\r\n },\r\n\r\n /**\r\n * Molecule colorer options.\r\n *\r\n * @typedef MoleculeColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n MO: {\r\n gradient: 'rainbow',\r\n },\r\n },\r\n\r\n /*\r\n * Use antialiasing in WebGL.\r\n * @type {boolean}\r\n */\r\n antialias: true,\r\n\r\n /*\r\n * Camera field of view in degrees.\r\n * @type {number}\r\n */\r\n camFov: 45.0,\r\n\r\n /*\r\n * Camera near plane distance.\r\n * @type {number}\r\n */\r\n camNear: 0.5,\r\n\r\n /*\r\n * Camera far plane distance.\r\n * @type {number}\r\n */\r\n camFar: 100.0,\r\n\r\n camDistance: 2.5,\r\n\r\n radiusToFit: 1.0,\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogNearFactor: 0.5, // [0, 1]\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogFarFactor: 1, // [0, 1]\r\n fogAlpha: 1.0,\r\n fogColor: 0x000000,\r\n fogColorEnable: false,\r\n\r\n /**\r\n * Palette used for molecule coloring.\r\n * @type {string}\r\n */\r\n palette: 'JM',\r\n\r\n /*\r\n * Geometry resolution.\r\n * @type {string}\r\n */\r\n resolution: 'medium',\r\n\r\n autoResolution: false/* true */,\r\n\r\n autoPreset: true,\r\n\r\n preset: 'default', // TODO: remove 'preset' from settings, implement autodetection\r\n\r\n presets: {\r\n // Default\r\n default: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n empty: [],\r\n\r\n // Wireframe\r\n wire: [{\r\n mode: 'LN',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Small molecules\r\n small: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Proteins, nucleic acids etc.\r\n macro: [{\r\n mode: 'CA',\r\n colorer: 'SS',\r\n selector: 'not hetatm',\r\n material: 'SF',\r\n }, {\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'hetatm and not water',\r\n material: 'SF',\r\n }],\r\n },\r\n\r\n objects: {\r\n line: {\r\n color: 0xFFFFFFFF,\r\n dashSize: 0.3,\r\n gapSize: 0.05,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n\r\n bg: {\r\n color: 0x202020,\r\n transparent: false,\r\n },\r\n\r\n draft: {\r\n clipPlane: false,\r\n clipPlaneFactor: 0.5,\r\n clipPlaneSpeed: 0.00003,\r\n },\r\n\r\n /*\r\n * Separate group for plugins.\r\n * Each plugin handles its field by itself.\r\n */\r\n plugins: {\r\n\r\n },\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n axes: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fog: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fps: true,\r\n\r\n /**\r\n * Switch using of z-sprites for sphere and cylinder geometry\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zSprites: true,\r\n\r\n isoSurfaceFakeOpacity: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n suspendRender: true,\r\n\r\n nowater: false,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autobuild: true,\r\n\r\n /**\r\n * Anti-aliasing.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fxaa: true,\r\n /**\r\n * Outline depths\r\n * @type {boolean}\r\n * @instance\r\n */\r\n outline: {\r\n on: false,\r\n color: 0x000000,\r\n threshold: 0.1,\r\n thickness: 1,\r\n },\r\n\r\n /**\r\n * Ambient Occlusion special effect.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n ao: false,\r\n\r\n /**\r\n * Shadows options.\r\n *\r\n * @property {boolean} shadowMap - enable/disable.\r\n * @property {string} basic/percentage-closer filtering/non-uniform randomizing pcf.\r\n * @property {number} radius for percentage-closer filtering.\r\n */\r\n shadow: {\r\n on: false,\r\n type: 'random'/* basic, pcf, random */,\r\n radius: 1.0,\r\n },\r\n\r\n /**\r\n * Auto-rotation with constant speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n autoRotation: 0.0,\r\n\r\n /**\r\n * Set maximum fps for animation.\r\n * @type {number}\r\n * @instance\r\n */\r\n maxfps: 30,\r\n\r\n /**\r\n * Set fbx output precision.\r\n * @type {number}\r\n * @instance\r\n */\r\n fbxprec: 4,\r\n\r\n /**\r\n * Auto-rotation axis.\r\n *\r\n * - true: complex auto-rotation is about vertical axis\r\n * - false: rotation axis is defined by last user rotation\r\n *\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autoRotationAxisFixed: true,\r\n\r\n /**\r\n * Enable zooming with mouse wheel or pinch gesture.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zooming: true,\r\n\r\n /**\r\n * Enable picking atoms & residues with left mouse button or touch.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n picking: true,\r\n\r\n /**\r\n * Set picking mode ('atom', 'residue', 'chain', 'molecule').\r\n * @type {string}\r\n * @instance\r\n */\r\n pick: 'atom',\r\n\r\n /**\r\n * Make \"component\" and \"fragment\" editing modes available.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n editing: false,\r\n\r\n /**\r\n * Detect aromatic loops.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n aromatic: false,\r\n\r\n /**\r\n * Load only one biological unit from all those described in PDB file.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n singleUnit: true,\r\n\r\n /**\r\n * Set stereo mode ('NONE', 'SIMPLE', 'DISTORTED', 'ANAGLYPH', 'WEBVR').\r\n * @type {string}\r\n * @instance\r\n */\r\n stereo: 'NONE',\r\n\r\n /**\r\n * Enable smooth transition between views\r\n * @type {boolean}\r\n * @instance\r\n */\r\n interpolateViews: true,\r\n\r\n /**\r\n * Set transparency mode ('standard', 'prepass').\r\n * @type {string}\r\n * @instance\r\n */\r\n transparency: 'prepass',\r\n\r\n /**\r\n * Mouse translation speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n translationSpeed: 2,\r\n\r\n debug: {\r\n example: 3.5,\r\n text: 'hello!',\r\n good: true,\r\n ssaoKernelRadius: 0.7,\r\n ssaoFactor: 0.7,\r\n stereoBarrel: 0.25,\r\n },\r\n use: {\r\n multiFile: false,\r\n },\r\n};\r\n\r\n//----------------------------------------------------------------------------\r\n// SETTINGS CLASS\r\n//----------------------------------------------------------------------------\r\n\r\nfunction Settings() {\r\n EventDispatcher.call(this);\r\n\r\n this.old = null;\r\n this.now = {};\r\n this._changed = {};\r\n\r\n this.reset();\r\n}\r\n\r\nutils.deriveClass(Settings, EventDispatcher, {\r\n defaults,\r\n\r\n set(path, value) {\r\n if (_.isString(path)) {\r\n const oldValue = _.get(this.now, path);\r\n if (oldValue !== value) {\r\n _.set(this.now, path, value);\r\n this._notifyChange(path, value);\r\n }\r\n } else {\r\n const diff = utils.objectsDiff(path, this.now);\r\n if (!_.isEmpty(diff)) {\r\n _.merge(this.now, diff);\r\n this._notifyChanges(diff);\r\n }\r\n }\r\n },\r\n\r\n get(path, defaultValue) {\r\n return _.get(this.now, path, defaultValue);\r\n },\r\n\r\n reset() {\r\n const diff = utils.objectsDiff(defaults, this.now);\r\n this.now = _.cloneDeep(defaults);\r\n this.old = null;\r\n this._notifyChanges(diff);\r\n this._changed = {};\r\n },\r\n\r\n checkpoint() {\r\n this.old = _.cloneDeep(this.now);\r\n this._changed = {};\r\n },\r\n\r\n _notifyChange(path, value) {\r\n this._changed[path] = true;\r\n this.dispatchEvent({ type: `change:${path}`, value });\r\n },\r\n\r\n _notifyChanges(diff) {\r\n utils.forInRecursive(diff, (deepValue, deepPath) => {\r\n this._notifyChange(deepPath, deepValue);\r\n });\r\n },\r\n\r\n changed() {\r\n if (!this.old) {\r\n return [];\r\n }\r\n const { old, now } = this;\r\n const keys = _.filter(Object.keys(this._changed), (key) => _.get(old, key) !== _.get(now, key));\r\n return keys;\r\n },\r\n\r\n applyDiffs(diffs) {\r\n if (diffs.hasOwnProperty('VERSION') && diffs.VERSION !== VERSION) {\r\n throw new Error('Settings version does not match!');\r\n }\r\n // VERSION shouldn't be presented inside settings structure\r\n delete diffs.VERSION;\r\n this.reset();\r\n this.set(diffs);\r\n },\r\n\r\n getDiffs(versioned) {\r\n const diffs = utils.objectsDiff(this.now, defaults);\r\n if (versioned) {\r\n diffs.VERSION = VERSION;\r\n }\r\n return diffs;\r\n },\r\n\r\n setPluginOpts(plugin, opts) {\r\n defaults.plugins[plugin] = _.cloneDeep(opts);\r\n this.now.plugins[plugin] = _.cloneDeep(opts);\r\n },\r\n});\r\n\r\nexport default new Settings();\r\n","import _ from 'lodash';\r\nimport settings from './settings';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\n\r\nlet repIndex = 0;\r\n\r\nfunction asBoolean(value) {\r\n return !(!value || value === '0' || (_.isString(value) && value.toLowerCase() === 'false'));\r\n}\r\n\r\nconst adapters = {\r\n string: String,\r\n number: Number,\r\n boolean: asBoolean,\r\n};\r\n\r\n// Level 1 assignment symbol\r\nconst cL1Ass = '=';\r\n\r\nconst cOptsSep = '!';\r\n// Level 2 (options) assignment symbol\r\nconst cL2Ass = ':';\r\n// Level 2 (options) separator symbol\r\nconst cLSep = ',';\r\n\r\nconst cCommonIgnoreSymbols = '$;@/?';\r\n/**\r\n * We may (and should) leave as is for better readability:\r\n *\r\n * $ , ; : @ / ?\r\n */\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n */\r\nfunction getLevel1ExcludedExpr() {\r\n const cLevel1Ignores = ':,';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel1Ignores);\r\n}\r\n\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n * (options, etc, ..)\r\n */\r\nfunction getLevel2ExcludedExpr() {\r\n const cLevel2Ignores = ' ';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel2Ignores);\r\n}\r\n\r\nconst cL1ExclExpr = getLevel1ExcludedExpr();\r\nfunction encodeQueryComponentL1(value) {\r\n return utils.encodeQueryComponent(value, cL1ExclExpr);\r\n}\r\n\r\nconst cL2ExclExpr = getLevel2ExcludedExpr();\r\nfunction encodeQueryComponentL2(value) {\r\n return utils.encodeQueryComponent(value, cL2ExclExpr);\r\n}\r\n\r\nfunction ensureRepList(opts) {\r\n let { reps } = opts;\r\n if (!reps) {\r\n const { presets } = settings.now;\r\n let preset = opts.preset || settings.now.preset;\r\n reps = presets[preset];\r\n if (!reps) {\r\n logger.warn(`Unknown preset \"${preset}\"`);\r\n [preset] = Object.keys(presets);\r\n reps = presets[preset]; // fall back to any preset\r\n }\r\n opts.preset = preset;\r\n opts.reps = utils.deriveDeep(reps, true);\r\n }\r\n}\r\n\r\nfunction ensureRepAssign(opts, prop, value) {\r\n ensureRepList(opts);\r\n const rep = opts.reps[repIndex];\r\n // prop specified twice therefore start new rep by cloning the current\r\n if (rep.hasOwnProperty(prop)) {\r\n repIndex = opts.reps.length;\r\n opts.reps[repIndex] = utils.deriveDeep(rep, true);\r\n }\r\n if (value !== undefined) {\r\n opts.reps[repIndex][prop] = value;\r\n }\r\n}\r\n\r\nfunction addObject(opts, params, options) {\r\n if (opts._objects === undefined) {\r\n opts._objects = [];\r\n }\r\n\r\n const [type, newOpts] = options;\r\n const newObj = {\r\n type,\r\n params,\r\n };\r\n\r\n if (newOpts !== undefined) {\r\n newObj.opts = newOpts;\r\n }\r\n\r\n opts._objects[opts._objects.length] = newObj;\r\n}\r\n\r\nfunction parseParams(str, params) {\r\n const sep = str.indexOf(',');\r\n if (sep >= 0) {\r\n params.push(str.substr(sep + 1).split(','));\r\n return str.substr(0, sep);\r\n }\r\n // keep this untouched if no params were extracted\r\n return str;\r\n}\r\n\r\nfunction extractArgs(input, defaultsDict, params) {\r\n if (input) {\r\n const bang = input.indexOf(cOptsSep);\r\n const inputVal = parseParams(input.substr(0, bang >= 0 ? bang : undefined), params);\r\n if (bang >= 0) {\r\n const args = input.substr(bang + 1).split(cLSep);\r\n input = inputVal;\r\n if (defaultsDict) {\r\n const defaults = defaultsDict[input];\r\n const opts = utils.deriveDeep(defaults, true);\r\n args.forEach((arg) => {\r\n const pair = arg.split(cL2Ass, 2);\r\n const key = decodeURIComponent(pair[0]);\r\n const value = decodeURIComponent(pair[1]);\r\n const adapter = adapters[typeof _.get(defaults, key)];\r\n if (adapter) {\r\n _.set(opts, key, adapter(value));\r\n } else {\r\n logger.warn(`Unknown argument \"${key}\" for option \"${input}\"`);\r\n }\r\n });\r\n if (Object.keys(opts).length > 0) {\r\n input = [input, opts];\r\n }\r\n }\r\n } else {\r\n input = inputVal;\r\n }\r\n }\r\n return input;\r\n}\r\n\r\nconst actions = {\r\n\r\n l: 'load',\r\n load: String,\r\n t: 'type',\r\n type: String,\r\n v: 'view',\r\n view: String,\r\n u: 'unit',\r\n unit: Number,\r\n menu: asBoolean,\r\n\r\n // Commands\r\n\r\n o: 'object',\r\n object(value, opts) {\r\n const params = [];\r\n let options = extractArgs(value, settings.defaults.objects, params);\r\n if (!Array.isArray(options)) {\r\n options = [options];\r\n }\r\n addObject(opts, params[0], options);\r\n },\r\n\r\n p: 'preset',\r\n preset(value, opts) {\r\n opts.preset = value;\r\n opts.reps = null;\r\n ensureRepList(opts);\r\n },\r\n\r\n r: 'rep',\r\n rep(value, opts) {\r\n ensureRepList(opts);\r\n repIndex = Number(value);\r\n // clamp the index to one greater than the last\r\n repIndex = repIndex <= opts.reps.length ? (repIndex < 0 ? 0 : repIndex) : opts.reps.length;\r\n // create a new rep if it is adjacent to the existing ones\r\n if (repIndex === opts.reps.length) {\r\n // if there is no rep to derive from, derive from the first rep of the default\r\n opts.reps[repIndex] = repIndex > 0 ? utils.deriveDeep(opts.reps[repIndex - 1], true)\r\n : utils.deriveDeep(settings.defaults.presets.default[0], true);\r\n }\r\n },\r\n\r\n s: 'select',\r\n select(value, opts) {\r\n ensureRepAssign(opts, 'selector', value);\r\n },\r\n\r\n m: 'mode',\r\n mode(value, opts) {\r\n ensureRepAssign(opts, 'mode', extractArgs(value, settings.defaults.modes));\r\n },\r\n\r\n c: 'color',\r\n color(value, opts) {\r\n ensureRepAssign(opts, 'colorer', extractArgs(value, settings.defaults.colorers));\r\n },\r\n\r\n mt: 'material',\r\n material(value, opts) {\r\n ensureRepAssign(opts, 'material', extractArgs(value, settings.defaults.materials));\r\n },\r\n\r\n dup(value, opts) {\r\n ensureRepList(opts);\r\n const { reps } = opts;\r\n const rep = reps[repIndex];\r\n repIndex = reps.length;\r\n reps[repIndex] = utils.deriveDeep(rep, true);\r\n },\r\n\r\n // Settings shortcuts\r\n\r\n ar: 'autoResolution',\r\n};\r\n\r\nfunction _fromArray(entries) {\r\n repIndex = 0;\r\n\r\n const opts = {};\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const /** string[] */ entry = entries[i];\r\n let /** string? */ key = entry[0];\r\n const /** string? */ value = entry[1];\r\n let /** function|string? */ action = actions[key];\r\n\r\n // unwind shortcuts and aliases\r\n while (_.isString(action)) {\r\n key = action;\r\n action = actions[key];\r\n }\r\n\r\n // either set a property or use specialized parser\r\n if (!action) {\r\n const adapter = adapters[typeof _.get(settings.defaults, key)];\r\n if (adapter) {\r\n _.set(opts, `settings.${key}`, adapter(value));\r\n } else {\r\n logger.warn(`Unknown option \"${key}\"`);\r\n }\r\n } else if (_.isFunction(action)) {\r\n const result = action(value, opts);\r\n if (result !== undefined) {\r\n opts[key] = result;\r\n }\r\n }\r\n }\r\n\r\n return opts;\r\n}\r\n\r\nfunction fromAttr(attr) {\r\n return _fromArray(utils.getUrlParameters(`?${attr || ''}`));\r\n}\r\n\r\nfunction fromURL(url) {\r\n return _fromArray(utils.getUrlParameters(url));\r\n}\r\n\r\nfunction _processOptsForURL(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = encodeQueryComponentL2(key) + cL2Ass + encodeQueryComponentL2(value);\r\n });\r\n return str.join(cLSep);\r\n}\r\n\r\nfunction _processArgsForURL(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]}${cOptsSep}${_processOptsForURL(args[1])}`;\r\n}\r\n\r\nfunction _processObjForURL(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += `,${objOpts.params.join(',')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += cOptsSep + _processOptsForURL(objOpts.opts);\r\n }\r\n return res;\r\n}\r\n\r\nfunction toURL(opts) {\r\n const stringList = [];\r\n let idx = 0;\r\n\r\n function checkAndAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n stringList[idx++] = encodeQueryComponentL1(prefix)\r\n + cL1Ass + encodeQueryComponentL1(value);\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n if (_.isEmpty(repList[i])) {\r\n continue;\r\n }\r\n checkAndAdd('r', i);\r\n checkAndAdd('s', repList[i].selector);\r\n checkAndAdd('m', _processArgsForURL(repList[i].mode));\r\n checkAndAdd('c', _processArgsForURL(repList[i].colorer));\r\n checkAndAdd('mt', _processArgsForURL(repList[i].material));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('o', _processObjForURL(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('l', opts.load);\r\n checkAndAdd('u', opts.unit);\r\n checkAndAdd('p', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n checkAndAdd('v', opts.view);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(key, value);\r\n });\r\n\r\n let url = '';\r\n if (typeof window !== 'undefined') {\r\n const { location } = window;\r\n url = `${location.protocol}//${location.host}${location.pathname}`;\r\n }\r\n if (stringList.length > 0) {\r\n url += `?${stringList.join('&')}`;\r\n }\r\n\r\n return url;\r\n}\r\n\r\nfunction _processOptsForScript(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = `${key}=${utils.enquoteString(value)}`;\r\n });\r\n return str.join(' ');\r\n}\r\n\r\nfunction _processArgsForScript(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]} ${_processOptsForScript(args[1])}`;\r\n}\r\n\r\nfunction _processObjForScript(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += ` ${objOpts.params.map(utils.enquoteString).join(' ')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += ` ${_processOptsForScript(objOpts.opts)}`;\r\n }\r\n return res;\r\n}\r\n\r\nfunction _processRepsForScript(rep, index) {\r\n const repString = [];\r\n let strIdx = 0;\r\n function localAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n repString[strIdx++] = prefix + value;\r\n }\r\n }\r\n if (_.isEmpty(rep)) {\r\n return null;\r\n }\r\n localAdd('', index);\r\n localAdd('s=', utils.enquoteString(rep.selector));\r\n localAdd('m=', _processArgsForScript(rep.mode));\r\n localAdd('c=', _processArgsForScript(rep.colorer));\r\n localAdd('mt=', _processArgsForScript(rep.material));\r\n return repString.join(' ');\r\n}\r\n\r\nfunction toScript(opts) {\r\n const commandsList = [];\r\n let idx = 0;\r\n function checkAndAdd(command, value, saveQuotes) {\r\n if (value !== null && value !== undefined) {\r\n const quote = (typeof value === 'string' && saveQuotes) ? '\"' : '';\r\n commandsList[idx++] = `${command} ${quote}${value}${quote}`.trim();\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n checkAndAdd('rep', _processRepsForScript(repList[i], i));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('', _processObjForScript(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('set', 'autobuild false');\r\n checkAndAdd('load', opts.load, true);\r\n checkAndAdd('unit', opts.unit);\r\n checkAndAdd('preset', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(`set ${key}`, value, true);\r\n });\r\n checkAndAdd('view', opts.view);\r\n checkAndAdd('set', 'autobuild true');\r\n return commandsList.join('\\n');\r\n}\r\n\r\nexport default {\r\n fromURL,\r\n fromAttr,\r\n adapters,\r\n toURL,\r\n toScript,\r\n};\r\n","/**\r\n * Atom measurements.\r\n *\r\n * @param {Residue} residue - (required) Residue containing the atom\r\n * @param {string} name - (required) Name, unique in the residue\r\n * @param {Element} type - (required) Chemical element reference\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n *\r\n * @param {number} role - Role of atom inside monomer: Lead and wing are particularity interesting\r\n * @param {boolean} het - Non-standard residue indicator\r\n *\r\n * @param {number} serial - Serial number, unique in the model\r\n * @param {string} location - Alternative location indicator (usually space or A-Z)\r\n * @param {number} occupancy - Occupancy percentage, from 0 to 1\r\n * @param {number} temperature - Temperature\r\n * @param {number} charge - Charge\r\n *\r\n * @exports Atom\r\n * @constructor\r\n */\r\n\r\nclass Atom {\r\n constructor(residue, name, type, position, role, het, serial, location, occupancy, temperature, charge) {\r\n this.index = -1;\r\n this.residue = residue;\r\n this.name = name;\r\n this.element = type;\r\n this.position = position;\r\n this.role = role;\r\n this.mask = 1 | 0;\r\n\r\n this.het = het;\r\n\r\n this.serial = serial;\r\n this.location = (location || ' ').charCodeAt(0);\r\n this.occupancy = occupancy || 1;\r\n this.temperature = temperature;\r\n this.charge = charge;\r\n this.hydrogenCount = -1; // explicitly invalid\r\n this.radicalCount = 0;\r\n this.valence = -1; // explicitly invalid\r\n\r\n this.bonds = [];\r\n\r\n this.flags = 0x0000;\r\n if (type.name === 'H') {\r\n this.flags |= Atom.Flags.HYDROGEN;\r\n } else if (type.name === 'C') {\r\n this.flags |= Atom.Flags.CARBON;\r\n }\r\n }\r\n\r\n isHet() {\r\n return this.het;\r\n }\r\n\r\n isHydrogen() {\r\n return this.element.number === 1;\r\n }\r\n\r\n getVisualName() {\r\n const { name } = this;\r\n if (name.length > 0) {\r\n return name;\r\n }\r\n return this.element.name.trim();\r\n }\r\n\r\n forEachBond(process) {\r\n const { bonds } = this;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n getFullName() {\r\n let name = '';\r\n if (this.residue !== null) {\r\n if (this.residue._chain !== null) {\r\n name += `${this.residue._chain.getName()}.`;\r\n }\r\n name += `${this.residue._sequence}.`;\r\n }\r\n name += this.name;\r\n return name;\r\n }\r\n\r\n /**\r\n * Enumeration of atom flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n CARBON: 0x0001,\r\n // OXYGEN: 0x0002,\r\n // NITROGEN: 0x0004,\r\n HYDROGEN: 0x0008,\r\n /** Non-polar hydrogen (it is also a HYDROGEN) */\r\n NONPOLARH: 0x1008,\r\n };\r\n}\r\n\r\nexport default Atom;\r\n","class Element {\r\n constructor(number, name, fullName, weight, radius, radiusBonding, hValency) {\r\n this.number = number;\r\n this.name = name;\r\n this.fullName = fullName;\r\n this.weight = weight;\r\n this.radius = radius;\r\n this.radiusBonding = radiusBonding;\r\n this.hydrogenValency = hValency;\r\n }\r\n\r\n static Constants = {\r\n /* eslint-disable no-magic-numbers */\r\n U1: 1,\r\n Lead: 2,\r\n U2: 3,\r\n Wing: 4,\r\n U18: 18,\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n static Role = {\r\n /* eslint-disable no-magic-numbers */\r\n N: Element.Constants.U1,\r\n CA: Element.Constants.Lead,\r\n C: Element.Constants.U2,\r\n O: Element.Constants.Wing,\r\n SG: Element.Constants.U18,\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByAtomicNumber = [\r\n /* eslint-disable no-magic-numbers */\r\n null,\r\n new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]),\r\n new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]),\r\n new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]),\r\n new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]),\r\n new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]),\r\n new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]),\r\n new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]),\r\n new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]),\r\n new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]),\r\n new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]),\r\n new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]),\r\n new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]),\r\n new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]),\r\n new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]),\r\n new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]),\r\n new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]),\r\n new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]),\r\n new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]),\r\n new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]),\r\n new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]),\r\n new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]),\r\n new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]),\r\n new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]),\r\n new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]),\r\n new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]),\r\n new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]),\r\n new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]),\r\n new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]),\r\n new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]),\r\n new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]),\r\n new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]),\r\n new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]),\r\n new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]),\r\n new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]),\r\n new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]),\r\n new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]),\r\n new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]),\r\n new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]),\r\n new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]),\r\n new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]),\r\n new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]),\r\n new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]),\r\n new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]),\r\n new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]),\r\n new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]),\r\n new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]),\r\n new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]),\r\n new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]),\r\n new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]),\r\n new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]),\r\n new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]),\r\n new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]),\r\n new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]),\r\n new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]),\r\n new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]),\r\n new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]),\r\n new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]),\r\n new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]),\r\n new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]),\r\n new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]),\r\n new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]),\r\n new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]),\r\n new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]),\r\n new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]),\r\n new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]),\r\n new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]),\r\n new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]),\r\n new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]),\r\n new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]),\r\n new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]),\r\n new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]),\r\n new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]),\r\n new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]),\r\n new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]),\r\n new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]),\r\n new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]),\r\n new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]),\r\n new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]),\r\n new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]),\r\n new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]),\r\n new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]),\r\n new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]),\r\n new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]),\r\n new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]),\r\n new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]),\r\n new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]),\r\n new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]),\r\n new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]),\r\n new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]),\r\n new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]),\r\n new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]),\r\n new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]),\r\n new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]),\r\n new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]),\r\n new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]),\r\n new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]),\r\n new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]),\r\n new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]),\r\n new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]),\r\n new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]),\r\n new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]),\r\n new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]),\r\n new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]),\r\n new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]),\r\n new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]),\r\n new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]),\r\n new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]),\r\n new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]),\r\n new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0]),\r\n /* eslint-enable no-magic-numbers */\r\n ];\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByName = {\r\n // Duplicate atomic numbers (isotopes)\r\n /* eslint-disable no-magic-numbers */\r\n D: new Element(1, 'D', 'Deuterium', 2.014, 1.2, 0.23, [1]),\r\n T: new Element(1, 'T', 'Tritium', 3.016, 1.2, 0.23, [1]),\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // All regular elements will be added later, automatically\r\n };\r\n}\r\n\r\n(function () {\r\n const byAtomicNumber = Element.ByAtomicNumber;\r\n const byName = Element.ByName;\r\n for (let i = 0, n = byAtomicNumber.length; i < n; ++i) {\r\n const element = byAtomicNumber[i];\r\n if (element) {\r\n byName[element.name] = element;\r\n }\r\n }\r\n}());\r\n\r\n// find atom type by chemical element (or create if missing)\r\nElement.getByName = function (element) {\r\n let type = Element.ByName[element];\r\n if (!type) {\r\n type = Element.ByName[element] = new Element(0, element, 'Unknown', 0, 1.0, 0.01, [0]);\r\n }\r\n return type;\r\n};\r\n\r\nexport default Element;\r\n","const cBondTypes = {\r\n /** Was generated manually */\r\n UNKNOWN: 0,\r\n /** Simple covalent bond */\r\n COVALENT: 1,\r\n /** Aromatic bond */\r\n AROMATIC: 2,\r\n};\r\n\r\nfunction getAtomPos(atom) {\r\n return atom.position;\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Atom} left - The first atom.\r\n * @param {Atom} right - The second atom.\r\n * @param {number} order - Order of current bond.\r\n * @param {number} type - Bond type.\r\n * @param {boolean} fixed - Indicator of a pre-specified connection (in contrast with guessed one).\r\n *\r\n * @exports Bond\r\n * @constructor\r\n */\r\nclass Bond {\r\n constructor(left, right, order, type, fixed) {\r\n this._left = left;\r\n this._right = right;\r\n this._fixed = fixed;\r\n this._index = -1;\r\n if (left > right) {\r\n throw new Error('In a bond atom indices must be in increasing order');\r\n }\r\n this._order = order;\r\n this._type = type;\r\n }\r\n\r\n getLeft() {\r\n return this._left;\r\n }\r\n\r\n getRight() {\r\n return this._right;\r\n }\r\n\r\n getOrder() {\r\n return this._order;\r\n }\r\n\r\n calcLength() {\r\n return this._left.position.distanceTo(this._right.position);\r\n }\r\n\r\n _forEachNeighbour(currAtom, process) {\r\n const { bonds } = currAtom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]._left !== currAtom ? bonds[i]._left : bonds[i]._right);\r\n }\r\n }\r\n\r\n forEachLevelOne(process) {\r\n const left = this._left;\r\n const right = this._right;\r\n this._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n this._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n }\r\n\r\n forEachLevelTwo(process) {\r\n // TODO refactor this piece of an art?\r\n const left = this._left;\r\n const right = this._right;\r\n const self = this;\r\n self._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === left) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n self._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === right) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n }\r\n\r\n _fixDir(refPoint, currDir, posGetter) {\r\n // count atoms to the right and to the left of the current plane\r\n let rightCount = 0;\r\n let leftCount = 0;\r\n const tmpVec = refPoint.clone();\r\n function checkDir(atom) {\r\n tmpVec.copy(posGetter(atom));\r\n tmpVec.sub(refPoint);\r\n const dotProd = currDir.dot(tmpVec);\r\n if (dotProd > 0) {\r\n ++rightCount;\r\n } else {\r\n ++leftCount;\r\n }\r\n }\r\n function checkCarbon(atom) {\r\n if (atom.element.name === 'C') {\r\n checkDir(atom);\r\n }\r\n }\r\n // count all atoms to the left and right of our plane, start from level 1 and carbons\r\n const stages = [\r\n [this.forEachLevelOne, checkCarbon],\r\n [this.forEachLevelOne, checkDir],\r\n [this.forEachLevelTwo, checkCarbon],\r\n [this.forEachLevelTwo, checkDir],\r\n ];\r\n\r\n for (let stageId = 0; stageId < stages.length; ++stageId) {\r\n stages[stageId][0].call(this, stages[stageId][1]);\r\n if (leftCount > rightCount) {\r\n return currDir.multiplyScalar(-1);\r\n }\r\n if (leftCount < rightCount) {\r\n return currDir;\r\n }\r\n }\r\n return currDir;\r\n }\r\n\r\n calcNormalDir(posGetter) {\r\n const left = this._left;\r\n const right = this._right;\r\n let first = left;\r\n let second = right;\r\n posGetter = posGetter === undefined ? getAtomPos : posGetter;\r\n if (left.bonds.length > right.bonds.length) {\r\n first = right;\r\n second = left;\r\n }\r\n let third = first;\r\n let maxNeibs = 0;\r\n const { bonds } = second;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n let another = bonds[i]._left;\r\n if (bonds[i]._left === second) {\r\n another = bonds[i]._right;\r\n }\r\n if (another.bonds.length > maxNeibs && another !== first) {\r\n third = another;\r\n maxNeibs = another.bonds.length;\r\n }\r\n }\r\n const secondPos = posGetter(second);\r\n const firstV = posGetter(first).clone().sub(secondPos);\r\n const secondV = posGetter(third).clone().sub(secondPos);\r\n secondV.crossVectors(firstV, secondV);\r\n if (secondV.lengthSq() < 0.0001) {\r\n secondV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n secondV.normalize();\r\n firstV.crossVectors(secondV, firstV);\r\n if (firstV.lengthSq() < 0.0001) {\r\n firstV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n return this._fixDir(secondPos, firstV, posGetter);\r\n }\r\n\r\n static BondType = cBondTypes;\r\n}\r\n\r\nBond.prototype.BondType = cBondTypes;\r\n\r\nexport default Bond;\r\n","import * as THREE from 'three';\r\nimport Atom from './Atom';\r\nimport Element from './Element';\r\n\r\nconst cNucleicControlNames = ['C3\\'', 'C3*', 'P', 'H5T', 'H3T'];\r\nconst cNucleicWing1Names = ['OP1', 'O1P'];\r\nconst cNucleicWing2Names = ['OP2', 'O2P'];\r\n\r\nconst cCylinderSource = ['C3\\'', 'C3*', 'C1', 'C1\\'', 'C1*', 'P'];\r\nconst cCylinderTarget = [{\r\n types: ['A', 'DA', 'G', 'DG'],\r\n atoms: ['N1'],\r\n}, {\r\n types: ['C', 'DC'],\r\n atoms: ['N3'],\r\n}, {\r\n types: ['T', 'DT', 'U', 'DU'],\r\n atoms: ['O4'],\r\n}];\r\n\r\n/**\r\n * Residue instance.\r\n *\r\n * @param {Chain} chain - Chain this residue belongs to.\r\n * @param {ResidueType} type - Generic residue instance type.\r\n * @param {number} sequence - Sequence ID.\r\n * @param {string} icode - One character insertion code (usually space or A-Z).\r\n *\r\n * @exports Residue\r\n * @constructor\r\n */\r\nclass Residue {\r\n constructor(chain, type, sequence, icode) {\r\n this._chain = chain;\r\n this._component = null;\r\n this._type = type;\r\n this._sequence = sequence;\r\n this._icode = icode;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n\r\n this._atoms = [];\r\n this._secondary = null;\r\n this._firstAtom = null;\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n this._lastAtom = null;\r\n this._controlPoint = null;\r\n this._midPoint = null;\r\n this._wingVector = null;\r\n this._cylinders = null;\r\n this._isValid = true;\r\n this._het = false;\r\n this._molecule = null;\r\n this.temperature = null;\r\n this.occupancy = null;\r\n }\r\n\r\n // Getters and setters\r\n getChain() {\r\n return this._chain;\r\n }\r\n\r\n getMolecule() {\r\n return this._molecule;\r\n }\r\n\r\n getType() {\r\n return this._type;\r\n }\r\n\r\n getSequence() {\r\n return this._sequence;\r\n }\r\n\r\n getSecondary() {\r\n return this._secondary;\r\n }\r\n\r\n getICode() {\r\n return this._icode;\r\n }\r\n\r\n // Other methods\r\n\r\n addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge) {\r\n const atom = new Atom(this, name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n const complex = this._chain.getComplex();\r\n complex.addAtom(atom);\r\n this._atoms.push(atom);\r\n this._het = this._het || het;\r\n return atom;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (process(atoms[i])) {\r\n break;\r\n }\r\n }\r\n }\r\n\r\n _findAtomByName(name) {\r\n let res = null;\r\n this.forEachAtom((atom) => {\r\n if (atom.name === name) {\r\n res = atom;\r\n return true;\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _findFirstAtomInList(names) {\r\n let res = null;\r\n for (let i = 0; i < names.length; ++i) {\r\n res = this._findAtomByName(names[i]);\r\n if (res !== null) {\r\n return res;\r\n }\r\n }\r\n return res;\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n mask &= atoms[i].mask;\r\n }\r\n this._mask = mask;\r\n }\r\n\r\n getCylinderTargetList() {\r\n const type = this._type._name;\r\n for (let i = 0, n = cCylinderTarget.length; i < n; ++i) {\r\n for (let j = 0, m = cCylinderTarget[i].types.length; j < m; ++j) {\r\n if (type === cCylinderTarget[i].types[j]) {\r\n return cCylinderTarget[i].atoms;\r\n }\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n _detectLeadWing(dst, next, getAtomPosition) {\r\n const leadAtom = this._findFirstAtomInList(cNucleicControlNames);\r\n let wingStart = this._findFirstAtomInList(cNucleicWing1Names);\r\n let wingEnd = this._findFirstAtomInList(cNucleicWing2Names);\r\n\r\n if (wingStart === null && next !== null) {\r\n wingStart = next._findFirstAtomInList(cNucleicWing1Names);\r\n }\r\n\r\n if (wingEnd === null && next !== null) {\r\n wingEnd = next._findFirstAtomInList(cNucleicWing2Names);\r\n }\r\n\r\n if (leadAtom === null || wingStart === null || wingEnd === null) {\r\n return;\r\n }\r\n\r\n dst._leadAtom = leadAtom;\r\n dst._controlPoint = getAtomPosition(leadAtom);\r\n dst._wingVector = getAtomPosition(wingEnd).clone().sub(getAtomPosition(wingStart));\r\n dst._isValid = true;\r\n\r\n const cylSource = this._findFirstAtomInList(cCylinderSource);\r\n const targetList = this.getCylinderTargetList();\r\n const cylTarget = targetList !== null ? this._findFirstAtomInList(targetList) : null;\r\n if (cylSource === null || cylTarget === null) {\r\n return;\r\n }\r\n dst._cylinders = [getAtomPosition(cylSource), getAtomPosition(cylTarget)];\r\n }\r\n\r\n calcWing(prevLeadPos, currLeadPos, prevWingPos, prevWing) {\r\n const vectorA = currLeadPos.clone().sub(prevLeadPos);\r\n const vectorB = prevLeadPos.clone().sub(prevWingPos);\r\n vectorB.crossVectors(vectorA, vectorB);\r\n vectorB.crossVectors(vectorA, vectorB).normalize();\r\n if (prevWing !== null && prevWing.length() > 0.0001) {\r\n const needToNegate = vectorB.length() > 0.0001 && Math.abs(prevWing.angleTo(vectorB)) > Math.PI / 2;\r\n if (needToNegate) {\r\n vectorB.negate();\r\n }\r\n }\r\n return vectorB;\r\n }\r\n\r\n _innerFinalize(prevRes, prev, nextRes, dst, chainAsNucleic, getAtomPosition) {\r\n const bFirstInChain = prev === null;\r\n\r\n const lp = getAtomPosition(this._leadAtom);\r\n const currLeadPos = new THREE.Vector3(lp.x, lp.y, lp.z);\r\n if (chainAsNucleic) {\r\n this._detectLeadWing(dst, nextRes, getAtomPosition);\r\n return;\r\n }\r\n\r\n if (bFirstInChain) { // for first one in chain\r\n dst._midPoint = getAtomPosition(this._firstAtom).clone();\r\n } else {\r\n const prevLeadPos = prev._controlPoint; // lead point of previous monomer\r\n dst._midPoint = prevLeadPos.clone().lerp(currLeadPos, 0.5);\r\n dst._wingVector = this.calcWing(prevLeadPos, currLeadPos, getAtomPosition(prevRes._wingAtom), prev._wingVector);\r\n }\r\n dst._controlPoint = currLeadPos;\r\n }\r\n\r\n _finalize2(prev, next, asNucleic) {\r\n // Should be called AFTER first finalize\r\n this._innerFinalize(prev, prev, next, this, asNucleic, (atom) => atom.position);\r\n }\r\n\r\n isConnected(anotherResidue) {\r\n if (this._chain !== anotherResidue._chain) {\r\n return false;\r\n }\r\n if (this === anotherResidue) {\r\n return true;\r\n }\r\n let res = false;\r\n this.forEachAtom((atom) => {\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue === anotherResidue || bond._right.residue === anotherResidue) {\r\n res = true;\r\n return true;\r\n }\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _finalize() {\r\n const self = this;\r\n [this._firstAtom] = this._atoms;\r\n this._lastAtom = this._atoms[this._atoms.length - 1];\r\n\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n\r\n let tempCount = 0;\r\n let temperature = 0; // average temperature\r\n let occupCount = 0;\r\n let occupancy = 0; // average occupancy\r\n this.forEachAtom((a) => {\r\n if (self._leadAtom === null) {\r\n if (a.role === Element.Constants.Lead) {\r\n self._leadAtom = a;\r\n }\r\n }\r\n if (self._wingAtom === null) {\r\n if (a.role === Element.Constants.Wing) {\r\n self._wingAtom = a;\r\n }\r\n }\r\n if (a.temperature) {\r\n temperature += a.temperature;\r\n tempCount++;\r\n }\r\n if (a.occupancy) {\r\n occupancy += a.occupancy;\r\n occupCount++;\r\n }\r\n return (self._leadAtom !== null && self._wingAtom !== null);\r\n });\r\n\r\n if (tempCount > 0) {\r\n this.temperature = temperature / tempCount;\r\n }\r\n if (occupCount > 0) {\r\n this.occupancy = occupancy / occupCount;\r\n }\r\n\r\n // Still try to make monomer look valid\r\n if (this._leadAtom === null || this._wingAtom === null) {\r\n this._isValid = false;\r\n }\r\n if (this._leadAtom === null) {\r\n this._leadAtom = this._firstAtom;\r\n }\r\n if (this._wingAtom === null) {\r\n this._wingAtom = this._lastAtom;\r\n }\r\n }\r\n}\r\n\r\nexport default Residue;\r\n","/**\r\n * Residue type.\r\n *\r\n * Predefined acid or created with HET, HETNAM, etc.\r\n *\r\n * @param {string} name - Short name, either standard (ALA, MET, etc.) or non-standard one.\r\n * @param {string} fullName - Full residue name.\r\n * @param {string} letterCode - 1-letter symbol.\r\n *\r\n * @exports ResidueType\r\n * @constructor\r\n */\r\nclass ResidueType {\r\n constructor(name, fullName, letterCode) {\r\n this._name = name;\r\n this._fullName = fullName;\r\n this.letterCode = letterCode;\r\n this.flags = 0x0000;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\n static StandardTypes = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: new ResidueType('ALA', 'Alanine', 'A'),\r\n ARG: new ResidueType('ARG', 'Arginine', 'R'),\r\n ASN: new ResidueType('ASN', 'Asparagine', 'N'),\r\n ASP: new ResidueType('ASP', 'Aspartic Acid', 'D'),\r\n CYS: new ResidueType('CYS', 'Cysteine', 'C'),\r\n GLN: new ResidueType('GLN', 'Glutamine', 'Q'),\r\n GLU: new ResidueType('GLU', 'Glutamic Acid', 'E'),\r\n GLY: new ResidueType('GLY', 'Glycine', 'G'),\r\n HIS: new ResidueType('HIS', 'Histidine', 'H'),\r\n ILE: new ResidueType('ILE', 'Isoleucine', 'I'),\r\n LEU: new ResidueType('LEU', 'Leucine', 'L'),\r\n LYS: new ResidueType('LYS', 'Lysine', 'K'),\r\n MET: new ResidueType('MET', 'Methionine', 'M'),\r\n PHE: new ResidueType('PHE', 'Phenylalanine', 'F'),\r\n PRO: new ResidueType('PRO', 'Proline', 'P'),\r\n PYL: new ResidueType('PYL', 'Pyrrolysine', 'O'),\r\n SEC: new ResidueType('SEC', 'Selenocysteine', 'U'),\r\n SER: new ResidueType('SER', 'Serine', 'S'),\r\n THR: new ResidueType('THR', 'Threonine', 'T'),\r\n TRP: new ResidueType('TRP', 'Tryptophan', 'W'),\r\n TYR: new ResidueType('TYR', 'Tyrosine', 'Y'),\r\n VAL: new ResidueType('VAL', 'Valine', 'V'),\r\n A: new ResidueType('A', 'Adenine', 'A'),\r\n C: new ResidueType('C', 'Cytosine', 'C'),\r\n G: new ResidueType('G', 'Guanine', 'G'),\r\n I: new ResidueType('I', 'Inosine', 'I'),\r\n T: new ResidueType('T', 'Thymine', 'T'),\r\n U: new ResidueType('U', 'Uracil', 'U'),\r\n DA: new ResidueType('DA', 'Adenine', 'A'),\r\n DC: new ResidueType('DC', 'Cytosine', 'C'),\r\n DG: new ResidueType('DG', 'Guanine', 'G'),\r\n DI: new ResidueType('DI', 'Inosine', 'I'),\r\n DT: new ResidueType('DT', 'Thymine', 'T'),\r\n DU: new ResidueType('DU', 'Uracil', 'U'),\r\n '+A': new ResidueType('+A', 'Adenine', 'A'),\r\n '+C': new ResidueType('+C', 'Cytosine', 'C'),\r\n '+G': new ResidueType('+G', 'Guanine', 'G'),\r\n '+I': new ResidueType('+I', 'Inosine', 'I'),\r\n '+T': new ResidueType('+T', 'Thymine', 'T'),\r\n '+U': new ResidueType('+U', 'Uracil', 'U'),\r\n WAT: new ResidueType('WAT', 'Water', ''),\r\n H2O: new ResidueType('H2O', 'Water', ''),\r\n HOH: new ResidueType('HOH', 'Water', ''),\r\n DOD: new ResidueType('DOD', 'Water', ''),\r\n UNK: new ResidueType('UNK', 'Unknown', ''),\r\n UNL: new ResidueType('UNL', 'Unknown Ligand', ''),\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n /**\r\n * Enumeration of residue flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n // Amino acids\r\n /** Amino acid residue */\r\n PROTEIN: 0x0001,\r\n /** Basic amino acid residue */\r\n BASIC: 0x0002,\r\n /** Acidic amino acid residue */\r\n ACIDIC: 0x0004,\r\n /** Polar uncharged side chain amino acid residue */\r\n POLAR: 0x0008,\r\n /** Non-polar hydrophobic side chain amino acid residue */\r\n NONPOLAR: 0x0010,\r\n /** Aromatic amino acid residue */\r\n AROMATIC: 0x0020,\r\n\r\n // Nucleic acids\r\n\r\n /** Nucleic residue */\r\n NUCLEIC: 0x0100,\r\n /** Purine nucleic residue */\r\n PURINE: 0x0200,\r\n /** Pyrimidine nucleic residue */\r\n PYRIMIDINE: 0x0400,\r\n /** DNA */\r\n DNA: 0x0800,\r\n /** RNA */\r\n RNA: 0x1000,\r\n\r\n /** Water */\r\n WATER: 0x10000,\r\n };\r\n}\r\n\r\n// Flag combinations\r\nfunction _addFlag(flag, list) {\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const res = ResidueType.StandardTypes[list[i]];\r\n if (res) {\r\n res.flags |= flag;\r\n }\r\n }\r\n}\r\n\r\nconst { Flags } = ResidueType;\r\n_addFlag(Flags.WATER, ['WAT', 'H2O', 'HOH', 'DOD']);\r\n\r\n_addFlag(Flags.PROTEIN, [\r\n 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLY', 'GLU', 'GLN', 'HIS', 'ILE',\r\n 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'PYL', 'SEC', 'SER', 'THR', 'TRP',\r\n 'TYR', 'VAL',\r\n]);\r\n_addFlag(Flags.BASIC, ['ARG', 'HIS', 'LYS']);\r\n_addFlag(Flags.ACIDIC, ['ASP', 'GLU']);\r\n_addFlag(Flags.POLAR, ['ASN', 'CYS', 'GLN', 'SER', 'THR', 'TYR']);\r\n_addFlag(Flags.NONPOLAR, ['ALA', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'VAL', 'GLY']);\r\n_addFlag(Flags.AROMATIC, ['PHE', 'TRP', 'TYR']);\r\n\r\n_addFlag(Flags.NUCLEIC, [\r\n 'A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I',\r\n 'C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U',\r\n]);\r\n_addFlag(Flags.PURINE, ['A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I']);\r\n_addFlag(Flags.PYRIMIDINE, ['C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U']);\r\n_addFlag(Flags.DNA, ['DA', 'DG', 'DI', 'DC', 'DT', 'DU']);\r\n_addFlag(Flags.RNA, ['A', 'G', 'I', 'C', 'T', 'U']);\r\n// Table of kdHydrophobicity\r\nconst hydro = {\r\n ILE: 4.5,\r\n VAL: 4.2,\r\n LEU: 3.8,\r\n PHE: 2.8,\r\n CYS: 2.5,\r\n MET: 1.9,\r\n ALA: 1.8,\r\n GLY: -0.4,\r\n THR: -0.7,\r\n SER: -0.8,\r\n TRP: -0.9,\r\n TYR: -1.3,\r\n PRO: -1.6,\r\n HIS: -3.2,\r\n GLU: -3.5,\r\n GLN: -3.5,\r\n ASP: -3.5,\r\n ASN: -3.5,\r\n LYS: -3.9,\r\n ARG: -4.5,\r\n};\r\n\r\nfunction _addParam(param, list) {\r\n const keys = Object.keys(list);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = list[key];\r\n ResidueType.StandardTypes[key][param] = value;\r\n }\r\n}\r\n\r\n_addParam('hydrophobicity', hydro);\r\n\r\nexport default ResidueType;\r\n","import * as THREE from 'three';\r\nimport Residue from './Residue';\r\nimport ResidueType from './ResidueType';\r\n\r\n/**\r\n * Residues in chain are either amino acid either nucleic acid (and water)\r\n * There might be some modified/mutated residues, which type could not be determined by their name (nucleic or amino); In this\r\n * case firstly program definites the chain type (by well-known residues) and then definites modified/mutated residues\r\n */\r\nconst ChainType = {\r\n UNKNOWN: 0,\r\n PROTEIN: 1,\r\n NUCLEIC: 2,\r\n};\r\n\r\n/**\r\n * Residue chain.\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n * @param {string} name - One character identifier (usually space, A-Z, 0-9, or a-z).\r\n *\r\n * @exports Chain\r\n * @constructor\r\n */\r\nclass Chain {\r\n constructor(complex, name) {\r\n this._complex = complex;\r\n this._name = name;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n this._residues = [];\r\n\r\n this.minSequence = Number.POSITIVE_INFINITY;\r\n this.maxSequence = Number.NEGATIVE_INFINITY;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n _determineType() {\r\n const residues = this._residues;\r\n\r\n const { PROTEIN, NUCLEIC } = ResidueType.Flags;\r\n\r\n this.type = ChainType.UNKNOWN;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const { flags } = residues[i]._type;\r\n\r\n if ((flags & NUCLEIC) !== 0) {\r\n this.type = ChainType.NUCLEIC;\r\n break;\r\n } else if ((flags & PROTEIN) !== 0) {\r\n this.type = ChainType.PROTEIN;\r\n break;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Finds thre residue with specified sequence number and inserion code\r\n * @param {Number} seqNum sequence number\r\n * @param {string} iCode insertion code\r\n * @returns {*} Residue or null if not found\r\n */\r\n findResidue(seqNum, iCode) {\r\n const residues = this._residues;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n if (res._sequence === seqNum && res._icode === iCode) {\r\n return [res, i];\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _finalize() {\r\n this._determineType();\r\n\r\n const residues = this._residues;\r\n\r\n let prev = null;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const next = (i + 1 < n) ? residues[i + 1] : null;\r\n const curr = residues[i];\r\n // TODO: skip invalid residues\r\n if (1 /* curr._isValid */) { // eslint-disable-line no-constant-condition\r\n curr._finalize2(prev, next, this.type === ChainType.NUCLEIC);\r\n prev = curr;\r\n }\r\n }\r\n\r\n // fix very first wing\r\n if (residues.length > 1 && residues[1]._wingVector) {\r\n const p = residues[1]._wingVector;\r\n residues[0]._wingVector = new THREE.Vector3(p.x, p.y, p.z);\r\n } else if (residues.length > 0) {\r\n residues[0]._wingVector = new THREE.Vector3(1, 0, 0);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const residues = this._residues;\r\n let prev = null;\r\n let prevData = null;\r\n const frameRes = frameData._residues;\r\n const n = residues.length;\r\n function getAtomPos(atom) {\r\n return frameData.getAtomPos(atom.index);\r\n }\r\n\r\n for (let i = 0; i < n; ++i) {\r\n const curr = residues[i];\r\n const currData = frameRes[curr._index];\r\n const nextRes = (i + 1 < n) ? residues[i + 1] : null;\r\n curr._innerFinalize(prev, prevData, nextRes, currData, this.type === ChainType.NUCLEIC, getAtomPos);\r\n prev = curr;\r\n prevData = currData;\r\n }\r\n\r\n frameRes[residues[0]._index]._wingVector = n > 1\r\n ? frameRes[residues[1]._index]._wingVector\r\n : new THREE.Vector3(1, 0, 0);\r\n }\r\n\r\n /**\r\n * Create a new residue.\r\n *\r\n * @param {string} name - Residue name.\r\n * @param {number} sequence - Residue sequence number.\r\n * @param {string} iCode - Insertion code.\r\n * @returns {Residue} - Newly created residue instance.\r\n */\r\n addResidue(name, sequence, iCode) {\r\n let type = this._complex.getResidueType(name);\r\n if (type === null) {\r\n type = this._complex.addResidueType(name);\r\n }\r\n const residue = new Residue(this, type, sequence, iCode);\r\n this._complex.addResidue(residue);\r\n this._residues.push(residue);\r\n\r\n if (type.flags & (ResidueType.Flags.NUCLEIC | ResidueType.Flags.PROTEIN)) {\r\n if (this.maxSequence < sequence) {\r\n this.maxSequence = sequence;\r\n }\r\n if (this.minSequence > sequence) {\r\n this.minSequence = sequence;\r\n }\r\n }\r\n\r\n return residue;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this._mask = mask;\r\n }\r\n}\r\n\r\nexport default Chain;\r\n","import Residue from './Residue';\r\n\r\n/** An element of protein secondary structure. */\r\nclass StructuralElement {\r\n /**\r\n * Create a secondary structural element of the specified type.\r\n *\r\n * @param {StructuralElement.Type} type Secondary structure type.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n */\r\n constructor(type, init, term) {\r\n /**\r\n * Secondary structure type.\r\n * @type {StructuralElement.Type}\r\n */\r\n this.type = type;\r\n /**\r\n * Generic secondary structure type.\r\n * @type {StructuralElement.Generic}\r\n */\r\n this.generic = StructuralElement.genericByType[this.type] || 'loop';\r\n /**\r\n * Initial residue.\r\n * @type Residue\r\n */\r\n this.init = init;\r\n /**\r\n * Terminal residue.\r\n * @type Residue\r\n */\r\n this.term = term;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n if (this.init instanceof Residue && this.term instanceof Residue) {\r\n return;\r\n }\r\n\r\n // Link all intermediate residues to this structural element\r\n const start = complex.splitUnifiedSerial(this.init);\r\n const end = complex.splitUnifiedSerial(this.term);\r\n for (let chainId = start.chain; chainId <= end.chain; chainId++) {\r\n for (let serialId = start.serial; serialId <= end.serial; serialId++) {\r\n for (let { iCode } = start; iCode <= end.iCode; iCode++) {\r\n const hashCode = complex.getUnifiedSerial(chainId, serialId, iCode);\r\n if (residueHash[hashCode]) {\r\n residueHash[hashCode]._secondary = this;\r\n }\r\n }\r\n }\r\n }\r\n\r\n // Replace unfined serials by objects\r\n this.init = residueHash[this.init];\r\n this.term = residueHash[this.term];\r\n }\r\n}\r\n\r\n/**\r\n * Specific type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Generic\r\n */\r\nStructuralElement.Type = {\r\n /** A strand of a [beta-sheet](https://en.wikipedia.org/wiki/Beta_sheet). */\r\n STRAND: 'E',\r\n /** An isolated beta-bridge (too small for a beta-sheet). */\r\n BRIDGE: 'B',\r\n\r\n /** A [3/10 helix](https://en.wikipedia.org/wiki/310_helix) (hydrogen bonding is 3 residues apart). */\r\n HELIX_310: 'G',\r\n /** An [alpha-helix](https://en.wikipedia.org/wiki/Alpha_helix) (hydrogen bonding is 4 residues apart). */\r\n HELIX_ALPHA: 'H',\r\n /** A [pi-helix](https://en.wikipedia.org/wiki/Pi_helix) (hydrogen bonding is 5 residues apart). */\r\n HELIX_PI: 'I',\r\n /** A generic helix of unspecified bonding distance. */\r\n HELIX: 'X',\r\n\r\n /** An isolated 3/10-like helical turn. */\r\n TURN_310: '3',\r\n /** An isolated alpha-like helical turn. */\r\n TURN_ALPHA: '4',\r\n /** An isolated pi-like helical turn. */\r\n TURN_PI: '5',\r\n /** An isolated helical [turn](https://en.wikipedia.org/wiki/Turn_(biochemistry)) of unspecified bonding distance. */\r\n TURN: 'T',\r\n\r\n /** A bend (a region of high curvature). */\r\n BEND: 'S',\r\n /** Just a protein section with no particular conformation. */\r\n COIL: 'C',\r\n};\r\n\r\n/**\r\n * Generic type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Type\r\n */\r\nStructuralElement.Generic = {\r\n /** A strand of a sheet. */\r\n STRAND: 'strand',\r\n /** A helix. */\r\n HELIX: 'helix',\r\n /** Just a protein section with no particular conformation. */\r\n LOOP: 'loop',\r\n};\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\nconst StructuralElementGeneric = StructuralElement.Generic;\r\n\r\n/**\r\n * A mapping from specific types to generic ones.\r\n * @type {Object}\r\n */\r\nStructuralElement.genericByType = {\r\n [StructuralElementType.STRAND]: StructuralElementGeneric.STRAND,\r\n [StructuralElementType.HELIX_310]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_ALPHA]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_PI]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX]: StructuralElementGeneric.HELIX,\r\n};\r\n\r\nexport default StructuralElement;\r\n","import StructuralElement from './StructuralElement';\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\nexport const typeByPDBHelixClass = {\r\n 1: StructuralElementType.HELIX_ALPHA,\r\n 3: StructuralElementType.HELIX_PI,\r\n 5: StructuralElementType.HELIX_310,\r\n};\r\n\r\n/**\r\n * Helical secondary structure of a protein.\r\n * @extends StructuralElement\r\n */\r\nclass Helix extends StructuralElement {\r\n /**\r\n * Create a helix.\r\n *\r\n * @param {number} helixClass A helix class according to the\r\n * [PDB Format](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX).\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} serial Serial number of the helix (see PDB Format).\r\n * @param {string} name Helix identifier (see PDB Format).\r\n * @param {string} comment Comment about this helix (see PDB Format).\r\n * @param {number} length Length of this helix, in residues (see PDB Format).\r\n */\r\n constructor(helixClass, init, term, serial, name, comment, length) {\r\n super(typeByPDBHelixClass[helixClass] || StructuralElement.Type.HELIX, init, term);\r\n\r\n /**\r\n * Serial number of the helix (see PDB Format).\r\n * @type {number}\r\n */\r\n this.serial = serial;\r\n /**\r\n * Helix identifier (see PDB Format).\r\n * @type {string}\r\n */\r\n this.name = name;\r\n /**\r\n * Comment about this helix (see PDB Format).\r\n * @type {string}\r\n */\r\n this.comment = comment;\r\n /**\r\n * Length of this helix, in residues (see PDB Format).\r\n * @type {number}\r\n */\r\n this.length = length;\r\n }\r\n}\r\n\r\nexport default Helix;\r\n","import StructuralElement from './StructuralElement';\r\n\r\n/**\r\n * A single strand of a sheet in a protein secondary structure.\r\n * @extends StructuralElement\r\n */\r\nclass Strand extends StructuralElement {\r\n /**\r\n * Create a strand.\r\n *\r\n * @param {Sheet} sheet Parent sheet this strand belongs to.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} sense Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @param {Atom} atomCur Atom in current strand (see PDB Format).\r\n * @param {Atom} atomPrev Atom in previous strand (see PDB Format).\r\n */\r\n constructor(sheet, init, term, sense, atomCur, atomPrev) {\r\n super(StructuralElement.Type.STRAND, init, term);\r\n\r\n /**\r\n * Parent sheet this strand belongs to.\r\n * @type {Sheet}\r\n */\r\n this.sheet = sheet;\r\n /**\r\n * Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @type {number}\r\n */\r\n this.sense = sense;\r\n /**\r\n * Atom in current strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomCur = atomCur;\r\n /**\r\n * Atom in previous strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomPrev = atomPrev;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n *\r\n * @override\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n super._finalize(serialAtomMap, residueHash, complex);\r\n\r\n let as = this.atomCur;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomCur = serialAtomMap[as];\r\n }\r\n as = this.atomPrev;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomPrev = serialAtomMap[as];\r\n }\r\n }\r\n}\r\n\r\nexport default Strand;\r\n","import Strand from './Strand';\r\n\r\n/**\r\n * Sheet secondary structure of a protein.\r\n *\r\n * @param {string} name -\r\n * @param {number} width -\r\n *\r\n * @exports Sheet\r\n * @constructor\r\n */\r\nclass Sheet {\r\n constructor(name, width) {\r\n this._name = name;\r\n this._width = width;\r\n\r\n this._strands = [];\r\n }\r\n\r\n // Getters and setters\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getWidth() {\r\n return this._width;\r\n }\r\n\r\n addStrand(strand) {\r\n this._strands.push(strand);\r\n this._width = this._strands.length;\r\n }\r\n\r\n addEmptyStrand() {\r\n this._strands.push(new Strand(null, null, null, null, null, null));\r\n }\r\n\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n const s = this._strands;\r\n for (let i = 0, n = s.length; i < n; ++i) {\r\n s[i]._finalize(serialAtomMap, residueHash, complex);\r\n }\r\n if (!this._width) {\r\n this._width = s.length;\r\n }\r\n if (s.length !== this._width) {\r\n throw new Error(`Sheet ${this._name} is inconsistent.`);\r\n }\r\n }\r\n}\r\n\r\nexport default Sheet;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Atom measurements.\r\n *\r\n * @param {string} id - SGroup id\r\n * @param {string} name - Name of the group\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n * @param {array} atoms - Atoms group consists of\r\n * @param {object} saveNode - XML node from file for saving\r\n *\r\n * @exports SGroup\r\n * @constructor\r\n */\r\nclass SGroup {\r\n constructor(id, name, position, atoms, saveNode) {\r\n this._id = id;\r\n this._name = name;\r\n this._position = position || new THREE.Vector3();\r\n this._atoms = atoms || [];\r\n this._charge = 0; // default group charge\r\n this._repeat = 1; // how many times group repeated: always > 0\r\n this._center = null;\r\n this.xmlNodeRef = saveNode || null;\r\n }\r\n\r\n /**\r\n * Get atom full name.\r\n * @returns {string} Atom full name.\r\n */\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getPosition() {\r\n return this._position;\r\n }\r\n\r\n getCentralPoint() {\r\n return this._center;\r\n }\r\n\r\n _rebuildSGroupOnAtomChange() {\r\n const nLimon = 100000000;\r\n if (this._center === null) {\r\n return; // nothing to do if we are not relative\r\n }\r\n\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n for (let j = 0, n = this._atoms.length; j < n; j++) {\r\n const aPos = this._atoms[j].position;\r\n bLow.set(Math.min(bLow.x, aPos.x), Math.min(bLow.y, aPos.y), Math.min(bLow.z, aPos.z));\r\n bHight.set(Math.max(bHight.x, aPos.x), Math.max(bHight.y, aPos.y), Math.max(bHight.z, aPos.z));\r\n }\r\n this._center.addVectors(bLow, bHight);\r\n this._center.multiplyScalar(0.5);\r\n }\r\n}\r\n\r\nexport default SGroup;\r\n","import utils from '../../utils';\r\n\r\n//----------------------------------------------------------------------------\r\nclass Range {\r\n constructor(min, max) {\r\n this.min = min;\r\n this.max = typeof max === 'undefined' ? min : max;\r\n }\r\n\r\n includes(value) {\r\n return this.min <= value && value <= this.max;\r\n }\r\n\r\n toString() {\r\n const { min, max } = this;\r\n return min === max ? String(min) : [min, max].join(':');\r\n }\r\n\r\n toJSON() {\r\n return [this.min, this.max];\r\n }\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\nclass List {\r\n constructor(arg) {\r\n if (arg instanceof this.constructor) {\r\n // delegate construction to a different class\r\n // eslint-disable-next-line no-constructor-return\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n }\r\n\r\n append(value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n }\r\n\r\n toString() {\r\n return this._values.join(',');\r\n }\r\n\r\n toJSON() {\r\n const values = this._values;\r\n const result = [];\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n result[i] = value.toJSON ? value.toJSON() : value;\r\n }\r\n return result;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nclass RangeList extends List {\r\n includes(value) {\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n if (list[i].includes(value)) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nconst valuesArray = [];\r\n\r\nclass ValueList extends List {\r\n constructor(arg, upperOnly) {\r\n const list = super(arg);\r\n if (upperOnly) {\r\n this.upperOnly = true;\r\n const values = list._values;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n if (typeof value === 'string') {\r\n values[i] = value.toUpperCase();\r\n }\r\n }\r\n } else {\r\n this.upperOnly = false;\r\n }\r\n // return constructed object\r\n // eslint-disable-next-line no-constructor-return\r\n return list;\r\n }\r\n\r\n includes(value) {\r\n // we do not convert to upper case here for perfomance reasons\r\n // if list is upper case only, value must be converted before it is sent up to here\r\n return this._values.indexOf(value) !== -1;\r\n }\r\n\r\n toString() {\r\n // Quote values that are not correct identifiers\r\n const values = this._values;\r\n valuesArray.length = 0;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n valuesArray[i] = utils.correctSelectorIdentifier(String(values[i]));\r\n }\r\n return valuesArray.join(',');\r\n }\r\n\r\n _validate(value) {\r\n return (this.upperOnly && typeof value === 'string') ? value.toUpperCase() : value;\r\n }\r\n\r\n append(value) {\r\n super.append(this._validate(value));\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n super.remove(this._validate(value));\r\n return this;\r\n }\r\n}\r\n\r\nexport {\r\n Range,\r\n List,\r\n RangeList,\r\n ValueList,\r\n};\r\n","import { RangeList, ValueList } from './selectArgs';\r\n\r\n/** Base class for atom selectors. */\r\nclass Selector {\r\n toString() {\r\n return this.keyword;\r\n }\r\n\r\n toJSON() {\r\n return [this.name];\r\n }\r\n}\r\n\r\nSelector.prototype.name = 'Error';\r\nSelector.prototype.keyword = 'error';\r\n\r\n/** Base class for list-based atom selectors. */\r\nclass ListSelector extends Selector {\r\n constructor(list) {\r\n super();\r\n this.list = list;\r\n }\r\n\r\n toString() {\r\n return `${this.keyword} ${this.list}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.list.toJSON()];\r\n }\r\n}\r\n\r\nclass RangeListSelector extends ListSelector {\r\n constructor(arg) {\r\n super(new RangeList(arg));\r\n }\r\n}\r\n\r\nclass ValueListSelector extends ListSelector {\r\n constructor(arg, caseSensitive) {\r\n super(new ValueList(arg, !caseSensitive));\r\n }\r\n}\r\n\r\nclass NoneSelector extends Selector {\r\n includesAtom(_atom) {\r\n return false;\r\n }\r\n}\r\n\r\nNoneSelector.prototype.name = 'None';\r\nNoneSelector.prototype.keyword = 'none';\r\n\r\nclass AllSelector extends Selector {\r\n includesAtom(_atom) {\r\n return true;\r\n }\r\n}\r\n\r\nAllSelector.prototype.name = 'All';\r\nAllSelector.prototype.keyword = 'all';\r\n\r\nexport {\r\n Selector,\r\n ListSelector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n};\r\n","import { Selector, NoneSelector } from './selectorsBase';\r\n\r\n//----------------------------------------------------------------------------\r\n// Operators\r\n//----------------------------------------------------------------------------\r\nconst none = new NoneSelector();\r\n\r\nclass PrefixOperator extends Selector {\r\n constructor(rhs) {\r\n super();\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nPrefixOperator.prototype.priority = 1;\r\n\r\nclass InfixOperator extends Selector {\r\n constructor(lhs, rhs) {\r\n super();\r\n this.lhs = lhs || none;\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const lhs = this.lhs.priority && this.lhs.priority > this.priority ? `(${this.lhs})` : this.lhs;\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${lhs} ${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.lhs.toJSON(), this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nInfixOperator.prototype.priority = 1000;\r\n\r\nexport { PrefixOperator, InfixOperator };\r\n","import Atom from './Atom';\r\nimport ResidueType from './ResidueType';\r\nimport { parser } from '../utils/SelectionParser';\r\nimport { Range, RangeList, ValueList } from './selectors/selectArgs';\r\nimport { PrefixOperator, InfixOperator } from './selectors/selectOps';\r\nimport {\r\n Selector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n} from './selectors/selectorsBase';\r\n\r\nconst keywords = {};\r\n\r\n//----------------------------------------------------------------------------\r\n// Named selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineSelector(name, SelectorClass) {\r\n const keyword = name.toLowerCase();\r\n SelectorClass.prototype.keyword = keyword;\r\n SelectorClass.prototype.name = name;\r\n\r\n const factory = ((...args) => new SelectorClass(...args));\r\n factory.SelectorClass = SelectorClass;\r\n keywords[keyword] = factory;\r\n\r\n return SelectorClass;\r\n}\r\n\r\ndefineSelector('Serial', class SerialSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.serial);\r\n }\r\n});\r\n\r\ndefineSelector('Name', class NameSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.name);\r\n }\r\n});\r\n\r\ndefineSelector('AltLoc', class AltLocSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(String.fromCharCode(atom.location));\r\n }\r\n});\r\n\r\ndefineSelector('Elem', class ElemSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.element.name);\r\n }\r\n});\r\n\r\ndefineSelector('Residue', class ResidueSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._type._name);\r\n }\r\n});\r\n\r\ndefineSelector('Sequence', class SequenceSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._sequence);\r\n }\r\n});\r\n\r\ndefineSelector('ICode', class ICodeSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._icode);\r\n }\r\n});\r\n\r\ndefineSelector('ResIdx', class ResIdxSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._index);\r\n }\r\n});\r\n\r\ndefineSelector('Chain', class ChainSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._chain._name);\r\n }\r\n});\r\n\r\ndefineSelector('Hetatm', class HetatmSelector extends Selector {\r\n includesAtom(atom) {\r\n return atom.het;\r\n }\r\n});\r\n\r\ndefineSelector('PolarH', class PolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.HYDROGEN;\r\n }\r\n});\r\n\r\ndefineSelector('NonPolarH', class NonPolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.NONPOLARH;\r\n }\r\n});\r\n\r\ndefineSelector('All', AllSelector);\r\n\r\ndefineSelector('None', NoneSelector);\r\n\r\nconst NULL_SELECTOR = keywords.none();\r\n\r\n//----------------------------------------------------------------------------\r\n// Named operators\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineOperator(name, priority, OperatorClass) {\r\n OperatorClass.prototype.priority = priority;\r\n return defineSelector(name, OperatorClass);\r\n}\r\ndefineOperator('Not', 1, class NotOperator extends PrefixOperator {\r\n includesAtom(atom) {\r\n return !this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('And', 2, class AndOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) && this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('Or', 3, class OrOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) || this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\n//----------------------------------------------------------------------------\r\n// Flag selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction byResidueTypeFlag(flag, name) {\r\n return defineSelector(name, class extends Selector {\r\n includesAtom(atom) {\r\n return (atom.residue._type.flags & flag) !== 0;\r\n }\r\n });\r\n}\r\n\r\nbyResidueTypeFlag(ResidueType.Flags.PROTEIN, 'Protein');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC, 'Basic');\r\nbyResidueTypeFlag(ResidueType.Flags.ACIDIC, 'Acidic');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC | ResidueType.Flags.ACIDIC, 'Charged');\r\nbyResidueTypeFlag(ResidueType.Flags.POLAR, 'Polar');\r\nbyResidueTypeFlag(ResidueType.Flags.NONPOLAR, 'NonPolar');\r\nbyResidueTypeFlag(ResidueType.Flags.AROMATIC, 'Aromatic');\r\nbyResidueTypeFlag(ResidueType.Flags.NUCLEIC, 'Nucleic');\r\nbyResidueTypeFlag(ResidueType.Flags.PURINE, 'Purine');\r\nbyResidueTypeFlag(ResidueType.Flags.PYRIMIDINE, 'Pyrimidine');\r\nbyResidueTypeFlag(ResidueType.Flags.WATER, 'Water');\r\n\r\n//----------------------------------------------------------------------------\r\nconst selectors = Object.create(keywords);\r\n\r\nselectors.Selector = Selector;\r\nselectors.RangeListSelector = RangeListSelector;\r\nselectors.ValueListSelector = ValueListSelector;\r\nselectors.Range = Range;\r\nselectors.RangeList = RangeList;\r\nselectors.ValueList = ValueList;\r\nselectors.PrefixOperator = PrefixOperator;\r\nselectors.InfixOperator = InfixOperator;\r\nselectors.Context = Object.create({});\r\n\r\nselectors.GetSelector = function (key) {\r\n if (!selectors.Context.hasOwnProperty(key)) {\r\n const exc = { message: `selector ${key} is not registered` };\r\n throw exc;\r\n }\r\n return selectors.Context[key] || NULL_SELECTOR;\r\n};\r\n\r\nselectors.ClearContext = function () {\r\n Object.keys(selectors.Context).forEach((k) => { delete selectors.Context[k]; });\r\n};\r\n\r\nselectors.keyword = function (key) {\r\n return keywords[key.toLowerCase()] || keywords.none;\r\n};\r\n\r\nselectors.parse = function (str) {\r\n const res = {};\r\n try {\r\n res.selector = parser.parse(str);\r\n } catch (e) {\r\n res.selector = NULL_SELECTOR;\r\n res.error = e.message;\r\n }\r\n return res;\r\n};\r\n\r\nparser.yy = selectors;\r\nparser.yy.parseError = parser.parseError; // workaround for incorrect JISON parser generator for AMD module\r\n\r\nexport default selectors;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\n\r\n/**\r\n * Basic biological unit class.\r\n *\r\n * @exports BiologicalUnit\r\n * @constructor\r\n */\r\nclass BiologicalUnit {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._selector = selectors.keyword('All')();\r\n this._boundaries = {\r\n boundingBox: new THREE.Box3(),\r\n boundingSphere: new THREE.Sphere(),\r\n };\r\n }\r\n\r\n computeBoundaries() {\r\n const atoms = this._complex._atoms;\r\n const n = atoms.length;\r\n const selector = this._selector;\r\n\r\n const { boundingBox } = this._boundaries;\r\n boundingBox.makeEmpty();\r\n if (n === 1) {\r\n boundingBox.expandByPoint(atoms[0].position);\r\n const bbc = new THREE.Vector3();\r\n boundingBox.getCenter(bbc);\r\n const s = 2 * atoms[0].element.radius;\r\n boundingBox.setFromCenterAndSize(bbc, new THREE.Vector3(s, s, s));\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (selector.includesAtom(atoms[i])) {\r\n boundingBox.expandByPoint(atoms[i].position);\r\n }\r\n }\r\n }\r\n\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n if (n === 1) {\r\n this._boundaries.boundingSphere.set(center, atoms[0].element.radius);\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (!selector.includesAtom(atoms[i])) {\r\n continue;\r\n }\r\n const pos = atoms[i].position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n this._boundaries.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n }\r\n\r\n getTransforms() {\r\n return [];\r\n }\r\n\r\n getSelector() {\r\n return this._selector;\r\n }\r\n\r\n getBoundaries() {\r\n return this._boundaries;\r\n }\r\n\r\n finalize() {\r\n }\r\n}\r\n\r\nexport default BiologicalUnit;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\nimport BiologicalUnit from './BiologicalUnit';\r\n\r\n/**\r\n * Biological assembly.\r\n *\r\n * @exports Assembly\r\n * @constructor\r\n */\r\n\r\nclass Assembly extends BiologicalUnit {\r\n constructor(complex) {\r\n super(complex);\r\n this.chains = [];\r\n this.matrices = [];\r\n }\r\n\r\n computeBoundaries() {\r\n super.computeBoundaries();\r\n // fix up the boundaries\r\n const { matrices } = this;\r\n const oldCenter = this._boundaries.boundingSphere.center;\r\n const oldRad = this._boundaries.boundingSphere.radius;\r\n const boundingBox = this._boundaries.boundingBox = new THREE.Box3();\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = matrices.length; i < n; ++i) {\r\n boundingBox.expandByPoint(oldCenter.clone().applyMatrix4(matrices[i]));\r\n }\r\n\r\n const newRad = boundingBox.max.distanceTo(boundingBox.min) / 2 + oldRad;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n this._boundaries.boundingSphere = new THREE.Sphere().set(center, newRad);\r\n boundingBox.max.addScalar(oldRad);\r\n boundingBox.min.subScalar(oldRad);\r\n }\r\n\r\n /**\r\n * Mark a chain as belonging to this biological assembly.\r\n * @param {string} chain - chain identifier, usually a single letter\r\n */\r\n addChain(chain) {\r\n this.chains[this.chains.length] = chain;\r\n }\r\n\r\n /**\r\n * Add a transformation matrix.\r\n * @param {THREE.Matrix4} matrix - transformation matrix\r\n */\r\n addMatrix(matrix) {\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n getTransforms() {\r\n return this.matrices;\r\n }\r\n\r\n finalize() {\r\n if (this.chains.length > 0) {\r\n this._selector = selectors.keyword('Chain')(this.chains);\r\n } else {\r\n this._selector = selectors.keyword('None')();\r\n }\r\n }\r\n}\r\n\r\nexport default Assembly;\r\n","/**\r\n * This class represents connected component as a part of a complex.\r\n * WARNING! The whole component entity is build under the assumption that residues\r\n * are placed in the chains and complex in ascending order of indices\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n *\r\n * @exports Component\r\n * @constructor\r\n */\r\nclass Component {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._index = -1;\r\n this._residueIndices = [];\r\n this._cycles = [];\r\n this._subDivs = [];\r\n this._residueCount = 0;\r\n }\r\n\r\n getResidues() {\r\n return this._complex._residues;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residueCount;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._complex._residues;\r\n const resIdc = this._residueIndices;\r\n for (let idIdc = 0, idCount = resIdc.length; idIdc < idCount; ++idIdc) {\r\n for (let idx = resIdc[idIdc].start, last = resIdc[idIdc].end; idx <= last; ++idx) {\r\n process(residues[idx]);\r\n }\r\n }\r\n }\r\n\r\n setSubDivs(subDivs) {\r\n this._subDivs = subDivs;\r\n let curr = 0;\r\n const resIdc = [];\r\n let resCnt = 0;\r\n for (let i = 0, n = subDivs.length; i < n; ++i) {\r\n if (i === n - 1 || subDivs[i].end + 1 !== subDivs[i + 1].start) {\r\n const { start } = subDivs[curr];\r\n const { end } = subDivs[i];\r\n resIdc[resIdc.length] = {\r\n start,\r\n end,\r\n };\r\n resCnt += end - start + 1;\r\n curr = i + 1;\r\n }\r\n }\r\n\r\n this._residueIndices = resIdc;\r\n this._residueCount = resCnt;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._complex._bonds;\r\n\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue._component === this) {\r\n process(bond);\r\n }\r\n }\r\n }\r\n\r\n update() {\r\n this.forEachCycle((cycle) => {\r\n cycle.update();\r\n });\r\n }\r\n\r\n forEachAtom(process) {\r\n this.forEachResidue((residue) => {\r\n residue.forEachAtom(process);\r\n });\r\n }\r\n\r\n addCycle(cycle) {\r\n this._cycles.push(cycle);\r\n }\r\n\r\n forEachCycle(process) {\r\n const cycles = this._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n process(cycles[i]);\r\n }\r\n }\r\n\r\n markResidues() {\r\n const self = this;\r\n self.forEachResidue((residue) => {\r\n residue._component = self;\r\n });\r\n }\r\n\r\n _forEachSubChain(mask, process) {\r\n const residues = this._complex._residues;\r\n const subs = this._subDivs;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let idx = subs[i].start, last = subs[i].end; idx <= last; ++idx) {\r\n const currRes = residues[idx];\r\n if (mask & currRes._mask && currRes._isValid) {\r\n let end = idx + 1;\r\n for (; end <= last; ++end) {\r\n const endRes = residues[end];\r\n if (!(mask & endRes._mask && endRes._isValid)) {\r\n break;\r\n }\r\n }\r\n process(i, idx, end - 1);\r\n idx = end;\r\n }\r\n }\r\n }\r\n }\r\n\r\n getMaskedSequences(mask) {\r\n const subs = [];\r\n let idx = 0;\r\n this._forEachSubChain(mask, (_subIdx, start, end) => {\r\n subs[idx++] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n\r\n getMaskedSubdivSequences(mask) {\r\n const subs = [];\r\n let currIdx = -1;\r\n let lastSubIdx = -1;\r\n const subDivs = this._subDivs;\r\n\r\n this._forEachSubChain(mask, (subIdx, start, end) => {\r\n if (lastSubIdx !== subIdx) {\r\n ++currIdx;\r\n subs[currIdx] = {\r\n arr: [],\r\n boundaries: subDivs[subIdx],\r\n };\r\n lastSubIdx = subIdx;\r\n }\r\n subs[currIdx].arr[subs[currIdx].arr.length] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n}\r\n\r\nexport default Component;\r\n","import utils from '../utils';\r\n\r\nconst cMaxPairsForHashCode = 32;\r\nconst cHashTableSize = 1024 * 1024;\r\nconst cNumbersPerPair = 4;\r\nconst cMaxNeighbours = 14;\r\nconst cInvalidVal = -1;\r\n// 89237 is a large simple number, can be used for pseudo random hash code create\r\nconst cBigPrime = 89237;\r\n\r\nclass AtomPairs {\r\n constructor(maxPairsEstimate) {\r\n this.numPairs = 0;\r\n this.numMaxPairs = maxPairsEstimate;\r\n this.intBuffer = utils.allocateTyped(Int32Array, maxPairsEstimate * cNumbersPerPair);\r\n for (let i = 0; i < maxPairsEstimate * cNumbersPerPair; i++) {\r\n this.intBuffer[i] = cInvalidVal;\r\n }\r\n this.hashBuffer = utils.allocateTyped(Int32Array, cHashTableSize * cMaxPairsForHashCode);\r\n for (let i = 0; i < cHashTableSize * cMaxPairsForHashCode; i++) {\r\n this.hashBuffer[i] = cInvalidVal;\r\n }\r\n }\r\n\r\n /**\r\n * Destroy all pairs memory\r\n */\r\n destroy() {\r\n this.intBuffer = null;\r\n this.hashBuffer = null;\r\n }\r\n\r\n /**\r\n * Add pair of atoms to collection\r\n * @param {number} indexA - Index of the 1st vertex.\r\n * @param {number} indexB - Index of the 2nd vertex.\r\n */\r\n addPair(indexA, indexB) {\r\n const ia = (indexA < indexB) ? indexA : indexB;\r\n const ib = (indexA > indexB) ? indexA : indexB;\r\n const codeToAdd = ia + (ib << cMaxNeighbours);\r\n\r\n const hashCode = (ia + (ib * cBigPrime)) & (cHashTableSize - 1);\r\n let j = hashCode * cMaxPairsForHashCode;\r\n let apI = 0;\r\n for (; apI < cMaxPairsForHashCode; apI++) {\r\n const code = this.hashBuffer[j + apI];\r\n if (code === cInvalidVal) {\r\n break;\r\n }\r\n if (code === codeToAdd) {\r\n return false;\r\n }\r\n }\r\n // add this new hash code\r\n if (apI >= cMaxPairsForHashCode) {\r\n throw new Error('addPair: increase cMaxPairsForHashCode');\r\n }\r\n this.hashBuffer[j + apI] = codeToAdd;\r\n\r\n // actually add\r\n if (this.numPairs >= this.numMaxPairs) {\r\n throw new Error('addPair: increase num pairs');\r\n }\r\n j = this.numPairs * cNumbersPerPair;\r\n this.intBuffer[j] = ia;\r\n this.intBuffer[j + 1] = ib;\r\n this.intBuffer[j + 2] = codeToAdd;\r\n this.numPairs++;\r\n return true;\r\n }\r\n}\r\n\r\nexport default AtomPairs;\r\n","import AtomPairs from './AtomPairs';\r\nimport Bond from './Bond';\r\n\r\nconst cProfileBondBuilder = false;\r\nconst cEstBondsMultiplier = 4;\r\nconst cSpaceCode = 32;\r\nconst cBondTolerance = 0.45;\r\nconst cVMDTolerance = 0.6;\r\nconst cBondRadInJMOL = true;\r\nconst cEpsilon = 0.001;\r\n\r\n/**\r\n * Get radius used for building bonds.\r\n *\r\n * @param {Atom} atom - Atom object.\r\n * @returns {number} special value for bonding radius for this atom\r\n */\r\nfunction _getBondingRadius(atom) {\r\n const { element } = atom;\r\n if (element) {\r\n return element.radiusBonding;\r\n }\r\n throw new Error('_getBondingRadius: Logic error.');\r\n}\r\n\r\nfunction _isAtomEligible(atom) {\r\n // build for all non-hetatm and for hetatm without bonds\r\n return !atom.isHet() || (atom.bonds && atom.bonds.length === 0);\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Complex} complex molecular complex\r\n\r\n * @exports AutoBond\r\n * @constructor\r\n */\r\nclass AutoBond {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._maxRad = 1.8;\r\n const bBox = this._complex.getDefaultBoundaries().boundingBox;\r\n this._vBoxMin = bBox.min.clone();\r\n this._vBoxMax = bBox.max.clone();\r\n\r\n this._pairCollection = null;\r\n }\r\n\r\n /**\r\n * Add existing pairs of connectors (from pdb file after its reading)\r\n * @returns {number} 0\r\n */\r\n _addExistingPairs() {\r\n const atoms = this._complex.getAtoms();\r\n const numAtoms = atoms.length;\r\n let aInd = 0;\r\n const collection = this._pairCollection;\r\n\r\n for (; aInd < numAtoms; aInd++) {\r\n const { bonds } = atoms[aInd];\r\n const numBondsForAtom = bonds.length;\r\n for (let bInd = 0; bInd < numBondsForAtom; bInd++) {\r\n const bond = bonds[bInd];\r\n const indTo = bond._left.index;\r\n if (indTo === aInd) {\r\n collection.addPair(aInd, bond._right.index);\r\n }\r\n } // for (b) all bonds in atom\r\n } // for (a)\r\n return 0;\r\n }\r\n\r\n _findPairs() {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const atoms = this._complex._atoms;\r\n const atomsNum = atoms.length;\r\n const self = this;\r\n\r\n let rA;\r\n let isHydrogenA;\r\n let posA;\r\n let locationA;\r\n let atomA;\r\n\r\n const processAtom = function (atomB) {\r\n if (isHydrogenA && atomB.isHydrogen()) {\r\n return;\r\n }\r\n\r\n const locationB = atomB.location;\r\n if ((locationA !== cSpaceCode)\r\n && (locationB !== cSpaceCode)\r\n && (locationA !== locationB)) {\r\n return;\r\n }\r\n\r\n const dist2 = posA.distanceToSquared(atomB.position);\r\n const rB = atomB.element.radiusBonding;\r\n const maxAcceptable = cBondRadInJMOL ? rA + rB + cBondTolerance : cVMDTolerance * (rA + rB);\r\n\r\n if (dist2 > (maxAcceptable * maxAcceptable)) {\r\n return;\r\n }\r\n\r\n if (dist2 < cEpsilon) {\r\n return;\r\n }\r\n\r\n self._pairCollection.addPair(atomA.index, atomB.index);\r\n };\r\n\r\n for (let i = 0; i < atomsNum; ++i) {\r\n atomA = atoms[i];\r\n if (!_isAtomEligible(atomA)) {\r\n continue;\r\n }\r\n\r\n rA = atomA.element.radiusBonding;\r\n isHydrogenA = atomA.isHydrogen();\r\n posA = atomA.position;\r\n locationA = atomA.location;\r\n\r\n vw.forEachAtomWithinRadius(posA, 2 * this._maxRad + cBondTolerance, processAtom);\r\n }\r\n }\r\n\r\n _addPairs() {\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0, k = 0; i < this._pairCollection.numPairs; i++, k += 4) {\r\n const iA = this._pairCollection.intBuffer[k];\r\n const iB = this._pairCollection.intBuffer[k + 1];\r\n this._addPair(atoms[iA], atoms[iB]);\r\n }\r\n }\r\n\r\n _addPair(atomA, atomB) {\r\n const bondsA = atomA.bonds;\r\n const indexA = atomA.index;\r\n const indexB = atomB.index;\r\n for (let j = 0, numBonds = bondsA.length; j < numBonds; ++j) {\r\n const bond = bondsA[j];\r\n if (bond._left.index === indexB || bond._right.index === indexB) {\r\n return;\r\n }\r\n }\r\n const left = indexA < indexB ? atomA : atomB;\r\n const right = indexA < indexB ? atomB : atomA;\r\n const newBond = this._complex.addBond(left, right, 0, Bond.BondType.UNKNOWN, false);\r\n bondsA.push(newBond);\r\n atomB.bonds.push(newBond);\r\n }\r\n\r\n build() {\r\n if (cProfileBondBuilder) {\r\n console.time('Bonds Builder');\r\n }\r\n this._buildInner();\r\n\r\n if (cProfileBondBuilder) {\r\n console.timeEnd('Bonds Builder');\r\n }\r\n }\r\n\r\n _buildInner() {\r\n const atoms = this._complex._atoms;\r\n if (atoms.length < 2) {\r\n return;\r\n }\r\n if (atoms[0].index < 0) {\r\n throw new Error('AutoBond: Atoms in complex were not indexed.');\r\n }\r\n\r\n this._calcBoundingBox();\r\n this._pairCollection = new AtomPairs(atoms.length * cEstBondsMultiplier);\r\n this._addExistingPairs();\r\n this._findPairs();\r\n this._addPairs();\r\n }\r\n\r\n _calcBoundingBox() {\r\n const atoms = this._complex._atoms;\r\n const nAtoms = atoms.length;\r\n let maxRad = _getBondingRadius(atoms[0]);\r\n for (let i = 1; i < nAtoms; ++i) {\r\n maxRad = Math.max(maxRad, _getBondingRadius(atoms[i]));\r\n }\r\n this._vBoxMax.addScalar(maxRad);\r\n this._vBoxMin.addScalar(-maxRad);\r\n this._maxRad = maxRad * 1.2;\r\n }\r\n\r\n destroy() {\r\n if (this._pairCollection) {\r\n this._pairCollection.destroy();\r\n }\r\n }\r\n}\r\n\r\nexport default AutoBond;\r\n","import * as THREE from 'three';\r\nimport Bond from './Bond';\r\nimport Element from './Element';\r\n\r\nconst cCrossThresh = 0.1;\r\nconst cAromaticType = Bond.BondType.AROMATIC;\r\nconst cAromaticAtoms = [\r\n Element.ByName.C.number,\r\n Element.ByName.N.number,\r\n // Element.ByName.O.number,\r\n // Element.ByName.S.number,\r\n];\r\n\r\n/** Conditions for bonds:\r\n * - Cross product with each subsequent bond to add is collinear and point to the same direction\r\n * - Each pair of a adjacent bonds belong to not more than one cycle\r\n * - If there is more than one candidates we try them in ascending order of angle values\r\n */\r\n\r\nconst _coDirVectors = (function () {\r\n const v1Tmp = new THREE.Vector3();\r\n const v2Tmp = new THREE.Vector3();\r\n const cp = new THREE.Vector3();\r\n return function (v1, v2) {\r\n v1Tmp.copy(v1).normalize();\r\n v2Tmp.copy(v2).normalize();\r\n cp.crossVectors(v1Tmp, v2Tmp);\r\n if (cp.length() > cCrossThresh) {\r\n return false;\r\n }\r\n // zero vector in out terms must be collinear to any\r\n return v1Tmp.dot(v2Tmp) >= 0;\r\n };\r\n}());\r\n\r\nfunction _insertAscending(arr, val) {\r\n let idx = 0;\r\n while (idx < arr.length && arr[idx] < val) {\r\n ++idx;\r\n }\r\n arr.splice(idx, 0, val);\r\n}\r\n\r\nfunction _anotherAtom(bond, currAtom) {\r\n return bond._left === currAtom ? bond._right : bond._left;\r\n}\r\n\r\nfunction _cosBetween(v1, v2) {\r\n const theta = v1.dot(v2) / (Math.sqrt(v1.lengthSq() * v2.lengthSq()));\r\n return THREE.MathUtils.clamp(theta, -1, 1);\r\n}\r\n\r\nfunction _markAromatic(bond) {\r\n bond._type = cAromaticType;\r\n}\r\n\r\nclass Cycle {\r\n constructor(atomsList) {\r\n this.atoms = atomsList;\r\n this.update();\r\n }\r\n\r\n update() {\r\n const { atoms } = this;\r\n const center = new THREE.Vector3();\r\n const nA = atoms.length;\r\n for (let j = 0; j < nA; ++j) {\r\n center.add(atoms[j].position);\r\n }\r\n center.multiplyScalar(1.0 / nA);\r\n this.center = center;\r\n this.radius = center.distanceTo(atoms[0].position.clone().lerp(atoms[1].position, 0.5));\r\n }\r\n\r\n forEachBond(process) {\r\n const { atoms } = this;\r\n const nA = atoms.length;\r\n let currAtom = atoms[0];\r\n let nextAtom;\r\n\r\n function checkBond(bond) {\r\n if (bond._left === nextAtom || bond._right === nextAtom) {\r\n process(bond);\r\n }\r\n }\r\n\r\n for (let i = 0; i < nA; ++i) {\r\n nextAtom = atoms[(i + 1) % nA];\r\n currAtom.forEachBond(checkBond);\r\n currAtom = nextAtom;\r\n }\r\n }\r\n}\r\n\r\nfunction _isAromatic(bond) {\r\n return bond._type === cAromaticType;\r\n}\r\n\r\nfunction _isPossibleAromatic(bond) {\r\n if (bond.type === cAromaticType) {\r\n return true;\r\n }\r\n const rightIdx = cAromaticAtoms.indexOf(bond._right.element.number);\r\n const leftIdx = cAromaticAtoms.indexOf(bond._left.element.number);\r\n return rightIdx !== -1 && leftIdx !== -1;\r\n}\r\n\r\nfunction _checkCycleSimple(cycle) {\r\n return cycle.length > 3;\r\n}\r\n\r\nfunction _checkCycleComplex(cycle) {\r\n console.assert(cycle.length > 2);\r\n return true;\r\n}\r\n\r\nclass AromaticLoopsMarker {\r\n constructor(complex) {\r\n this._complex = complex;\r\n const bondsData = new Array(complex._bonds.length);\r\n const bondMarks = new Array(complex._bonds.length);\r\n for (let i = 0, n = bondsData.length; i < n; ++i) {\r\n bondsData[i] = [];\r\n bondMarks[i] = false;\r\n }\r\n this._bondsData = bondsData;\r\n this._bondMarks = bondMarks;\r\n this._resetCycles();\r\n }\r\n\r\n _resetCycles() {\r\n this._cycles = [];\r\n this._currIdx = -1;\r\n }\r\n\r\n _haveSameCycle(bondsData, bond1, bond2) {\r\n const arr1 = bondsData[bond1._index];\r\n const arr2 = bondsData[bond2._index];\r\n const n1 = arr1.length;\r\n const n2 = arr2.length;\r\n let i1 = 0;\r\n let i2 = 0;\r\n while (i1 < n1 && i2 < n2) {\r\n if (arr1[i1] === arr2[i2]) {\r\n return true;\r\n }\r\n if (arr1[i1] > arr2[i2]) {\r\n ++i2;\r\n } else {\r\n ++i1;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _tryBond(prevBond, currRight, currDir) {\r\n const bondsOrder = [];\r\n const bondsData = this._bondsData;\r\n const currLeft = _anotherAtom(prevBond, currRight);\r\n const currVec = currRight.position.clone().sub(currLeft.position);\r\n const startAtomRef = this._currStart;\r\n const self = this;\r\n const bondMarks = this._bondMarks;\r\n let checkAromatic = this._checkBond;\r\n bondMarks[prevBond._index] = true;\r\n checkAromatic = checkAromatic === undefined ? _isAromatic : checkAromatic;\r\n currRight.forEachBond((newBond) => {\r\n if (!checkAromatic(newBond)\r\n || newBond === prevBond\r\n || bondMarks[newBond._index]\r\n || self._haveSameCycle(bondsData, prevBond, newBond)) {\r\n return;\r\n }\r\n const anotherAtom = _anotherAtom(newBond, currRight);\r\n const anotherVec = anotherAtom.position.clone().sub(currRight.position);\r\n const val = anotherAtom === startAtomRef ? -2.0 : 1 - _cosBetween(currVec, anotherVec);\r\n const newDir = anotherVec.cross(currVec);\r\n if (!_coDirVectors(newDir, currDir)) {\r\n return;\r\n }\r\n let idx = 0;\r\n while (idx < bondsOrder.length && bondsOrder[idx].val < val) {\r\n ++idx;\r\n }\r\n bondsOrder.splice(idx, 0, { bond: newBond, val, dir: newDir });\r\n });\r\n\r\n for (let i = 0, n = bondsOrder.length; i < n; ++i) {\r\n const { bond } = bondsOrder[i];\r\n const newRight = bond._left === currRight ? bond._right : bond._left;\r\n if (newRight === startAtomRef) {\r\n ++this._currIdx;\r\n this._cycles.push([currRight]);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n if (this._tryBond(bond, newRight, bondsOrder[i].dir)) {\r\n _insertAscending(bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(currRight);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n }\r\n bondMarks[prevBond._index] = false;\r\n return false;\r\n }\r\n\r\n _startCycle(bond) {\r\n // start from left to right\r\n this._currStart = bond._left;\r\n if (this._tryBond(bond, bond._right, new THREE.Vector3())) {\r\n _insertAscending(this._bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(bond._left);\r\n }\r\n }\r\n\r\n _findLoops(checkBond, checkCycle) {\r\n this._checkBond = checkBond;\r\n const complex = this._complex;\r\n const self = this;\r\n\r\n complex.forEachComponent((component) => {\r\n self._resetCycles();\r\n component.forEachBond((bond) => {\r\n if (checkBond(bond)) {\r\n self._startCycle(bond);\r\n }\r\n });\r\n const cycles = self._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n const cycle = cycles[i];\r\n if (!checkCycle(cycle)) {\r\n continue;\r\n }\r\n const newCycle = new Cycle(cycle);\r\n newCycle.forEachBond(_markAromatic);\r\n component.addCycle(newCycle);\r\n }\r\n });\r\n }\r\n\r\n markCycles() {\r\n this._findLoops(_isAromatic, _checkCycleSimple);\r\n }\r\n\r\n detectCycles() {\r\n this._findLoops(_isPossibleAromatic, _checkCycleComplex);\r\n }\r\n}\r\n\r\nexport default AromaticLoopsMarker;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\n/**\r\n * Calculate min & max radius of a sphere slice between zMin & zMax\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {number} zMin - lower bound of the slice\r\n * @param {number} zMax - upper bound of the slice\r\n */\r\nfunction _getSphereSliceRadiusRange(center, radius, zMin, zMax) {\r\n const dzMin = zMin - center.z;\r\n const dzMax = zMax - center.z;\r\n const rzMin = Math.sqrt(Math.max(radius * radius - dzMin * dzMin, 0.0));\r\n const rzMax = Math.sqrt(Math.max(radius * radius - dzMax * dzMax, 0.0));\r\n\r\n const rMin = Math.min(rzMin, rzMax);\r\n let rMax;\r\n\r\n if (zMin <= center.z && zMax >= center.z) {\r\n // sphere's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(rzMin, rzMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * Calculate min & max radius of a circle slice between yMin & yMax.\r\n *\r\n * To maintain analogy with _getSphereSliceRadiusRange we call radius what in fact is\r\n * half-width (along X axis) of the slice, i.e. 1D-sphere radius.\r\n *\r\n * @param {Vector3} center - center of the circle (z can be ignored)\r\n * @param {number} radius - circle radius\r\n * @param {number} yMin - lower bound of the slice\r\n * @param {number} yMax - upper bound of the slice\r\n * @returns {Array} - array of two numbers (min & max radius, or half-width)\r\n */\r\nfunction _getCircleSliceRadiusRange(center, radius, yMin, yMax) {\r\n const dyMin = yMin - center.y;\r\n const dyMax = yMax - center.y;\r\n const ryMin = Math.sqrt(Math.max(radius * radius - dyMin * dyMin, 0.0));\r\n const ryMax = Math.sqrt(Math.max(radius * radius - dyMax * dyMax, 0.0));\r\n\r\n const rMin = Math.min(ryMin, ryMax);\r\n let rMax;\r\n\r\n if (yMin <= center.y && yMax >= center.y) {\r\n // slice's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(ryMin, ryMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * VoxelWorld constructor\r\n *\r\n * @param {Box3} box - bounding box of the volume to be partitioned\r\n * @param {Vector3} vCellSizeHint - target voxel size (actual voxel size may differ from this)\r\n */\r\nclass VoxelWorld {\r\n constructor(box, vCellSizeHint) {\r\n this._box = box.clone();\r\n const size = new THREE.Vector3();\r\n box.getSize(size);\r\n this._count = size.clone().divide(vCellSizeHint).floor().max(new THREE.Vector3(1, 1, 1));\r\n this._last = this._count.clone().subScalar(1);\r\n this._cellSize = size.clone().divide(this._count);\r\n this._cellInnerR = 0.5 * Math.min(Math.min(this._cellSize.x, this._cellSize.y), this._cellSize.z);\r\n this._cellOuterR = 0.5 * Math.sqrt(this._cellSize.dot(this._cellSize));\r\n\r\n // array of voxels, each element contains index of first atom in voxel\r\n const numVoxels = this._count.x * this._count.y * this._count.z;\r\n this._voxels = utils.allocateTyped(Int32Array, numVoxels);\r\n for (let i = 0; i < numVoxels; ++i) {\r\n this._voxels[i] = -1;\r\n }\r\n\r\n // array of atoms that stores multiple single-linked lists\r\n // two elements for each atom: Atom ref, index of next atom (in this array\r\n this._atoms = [];\r\n }\r\n\r\n /**\r\n * Add all atoms from a complex to voxel world\r\n *\r\n * @param {Complex} complex - complex\r\n */\r\n addAtoms(complex) {\r\n const self = this;\r\n\r\n let idx = this._atoms.length;\r\n\r\n // resize array of atoms\r\n this._atoms.length += 2 * complex.getAtomCount();\r\n\r\n complex.forEachAtom((atom) => {\r\n // find which voxel contains this atom\r\n const voxelIdx = self._findVoxel(atom.position);\r\n\r\n // push current atom to the head of voxel's atom list\r\n self._atoms[idx] = atom;\r\n self._atoms[idx + 1] = self._voxels[voxelIdx];\r\n self._voxels[voxelIdx] = idx;\r\n\r\n idx += 2;\r\n });\r\n }\r\n\r\n /**\r\n * Get voxel that contains specified 3D point (we use clamp at the edges)\r\n *\r\n * @param {Vector3} point - a point in 3D\r\n * @returns {number} - index of voxel\r\n */\r\n static _zero = new THREE.Vector3(0, 0, 0);\r\n\r\n static _voxel = new THREE.Vector3();\r\n\r\n _findVoxel(point) {\r\n const zero = VoxelWorld._zero;\r\n const voxel = VoxelWorld._voxel;\r\n voxel.copy(point)\r\n .sub(this._box.min)\r\n .divide(this._cellSize)\r\n .floor()\r\n .clamp(zero, this._last);\r\n return voxel.x + this._count.x * (voxel.y + this._count.y * voxel.z);\r\n }\r\n\r\n /**\r\n * Call a function for each atom in voxel\r\n *\r\n * @param {number} voxel - index of voxel\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomInVoxel(voxel, process) {\r\n for (let i = this._voxels[voxel]; i >= 0; i = this._atoms[i + 1]) {\r\n process(this._atoms[i]);\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _xRange = new THREE.Vector2();\r\n\r\n static _yRange = new THREE.Vector2();\r\n\r\n static _zRange = new THREE.Vector2();\r\n\r\n _forEachVoxelWithinRadius(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n\r\n // switch to a faster method unless cell size is much smaller than sphere radius\r\n if (radius / this._cellInnerR < 10) {\r\n this._forEachVoxelWithinRadiusSimple(center, radius, process);\r\n return;\r\n }\r\n\r\n let rRangeXY;\r\n let rRangeX;\r\n let xVal;\r\n let yVal;\r\n let zVal;\r\n let isInsideX;\r\n let isInsideY;\r\n let isInsideZ;\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor()\r\n .clampScalar(0, this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n\r\n isInsideZ = (center.z - radius <= zVal[0]) && (zVal[1] <= center.z + radius);\r\n\r\n rRangeXY = _getSphereSliceRadiusRange(center, radius, zVal[0], zVal[1]);\r\n\r\n yRange.set(center.y - rRangeXY[1], center.y + rRangeXY[1]);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor()\r\n .clampScalar(0, this._count.y - 1);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n\r\n isInsideY = (center.y - rRangeXY[0] <= yVal[0]) && (yVal[1] <= center.y + rRangeXY[0]);\r\n\r\n rRangeX = _getCircleSliceRadiusRange(center, rRangeXY[1], yVal[0], yVal[1]);\r\n\r\n xRange.set(center.x - rRangeX[1], center.x + rRangeX[1]);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor()\r\n .clampScalar(0, this._count.x - 1);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n isInsideX = (center.x - rRangeX[0] <= xVal[0]) && (xVal[1] <= center.x + rRangeX[0]);\r\n\r\n process(x + this._count.x * (y + this._count.y * z), isInsideX && isInsideY && isInsideZ);\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n * This is a version of method that doesn't try to \"calculate\" what voxels fall inside radius\r\n * but instead just checks all voxels inside sphere's bounding box. This should be faster\r\n * unless cell size is much smaller than sphere radius.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _vCenter = new THREE.Vector3();\r\n\r\n _forEachVoxelWithinRadiusSimple(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n const vCenter = VoxelWorld._vCenter;\r\n\r\n const distTouch2 = (radius + this._cellOuterR) * (radius + this._cellOuterR);\r\n let distInside2 = -1.0;\r\n if (radius > this._cellOuterR) {\r\n distInside2 = (radius - this._cellOuterR) * (radius - this._cellOuterR);\r\n }\r\n\r\n // calculate bounding box for the sphere\r\n xRange.set(center.x - radius, center.x + radius);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor();\r\n xRange.x = Math.min(Math.max(xRange.x, 0), this._count.x - 1);\r\n xRange.y = Math.min(Math.max(xRange.y, 0), this._count.x - 1);\r\n\r\n yRange.set(center.y - radius, center.y + radius);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor();\r\n yRange.x = Math.min(Math.max(yRange.x, 0), this._count.y - 1);\r\n yRange.y = Math.min(Math.max(yRange.y, 0), this._count.y - 1);\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor();\r\n zRange.x = Math.min(Math.max(zRange.x, 0), this._count.z - 1);\r\n zRange.y = Math.min(Math.max(zRange.y, 0), this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n const zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n vCenter.z = 0.5 * (zVal[0] + zVal[1]);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n const yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n vCenter.y = 0.5 * (yVal[0] + yVal[1]);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n const xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n vCenter.x = 0.5 * (xVal[0] + xVal[1]);\r\n\r\n const d2 = center.distanceToSquared(vCenter);\r\n if (d2 <= distTouch2) {\r\n process(x + this._count.x * (y + this._count.y * z), d2 <= distInside2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each atom within given sphere\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinRadius(center, radius, process) {\r\n const self = this;\r\n const r2 = radius * radius;\r\n\r\n self._forEachVoxelWithinRadius(center, radius, (voxel, isInside) => {\r\n if (isInside) {\r\n self._forEachAtomInVoxel(voxel, process);\r\n } else {\r\n self._forEachAtomInVoxel(voxel, (atom) => {\r\n if (center.distanceToSquared(atom.position) <= r2) {\r\n process(atom);\r\n }\r\n });\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by mask\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} mask - bit mask\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromMasked(complex, mask, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by selector\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} selector - selector\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromSelected(complex, selector, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms\r\n *\r\n * @param {function} forEachAtom - enumerator of atoms in the group\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomWithinDistFromGroup(forEachAtom, dist, process) {\r\n const self = this;\r\n const r2 = dist * dist;\r\n\r\n const voxels = [];\r\n const atoms = [];\r\n let idx = 0;\r\n\r\n // build \"within radius\" atom list for each voxel\r\n forEachAtom((atom) => {\r\n self._forEachVoxelWithinRadius(atom.position, dist, (voxel, isInside) => {\r\n if (isInside) {\r\n // this voxel is inside circle -- no check will be required\r\n voxels[voxel] = -1;\r\n } else if (typeof voxels[voxel] === 'undefined') {\r\n // this voxel isn't covered yet -- start building list of atoms\r\n atoms.push(atom);\r\n atoms.push(-1);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n } else if (voxels[voxel] !== -1) {\r\n // this voxel has a list of atoms required for distance check -- add atom to the list\r\n atoms.push(atom);\r\n atoms.push(voxels[voxel]);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n }\r\n });\r\n });\r\n\r\n let voxel;\r\n\r\n const processIfWithin = function (atom) {\r\n if (typeof voxels[voxel] === 'undefined') {\r\n return;\r\n }\r\n\r\n idx = voxels[voxel];\r\n if (idx === -1) {\r\n // this voxel is fully covered\r\n process(atom);\r\n return;\r\n }\r\n\r\n // check distance to each atom within radius from this voxel\r\n for (; idx >= 0; idx = atoms[idx + 1]) {\r\n if (atom.position.distanceToSquared(atoms[idx].position) < r2) {\r\n process(atom);\r\n break;\r\n }\r\n }\r\n };\r\n\r\n // for each marked voxel\r\n for (voxel in voxels) {\r\n if (voxels.hasOwnProperty(voxel)) {\r\n self._forEachAtomInVoxel(voxel, processIfWithin);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default VoxelWorld;\r\n","import ResidueType from './ResidueType';\r\nimport PairCollection from './AtomPairs';\r\n\r\nconst MINIMAL_DISTANCE = 0.5;\r\nconst MIN_HBOND_ENERGY = -9.9;\r\nconst MAX_HBOND_ENERGY = -0.5;\r\nconst COUPLING_CONSTANT = -27.888; // = -332 * 0.42 * 0.2\r\nconst MAX_COUPLING_DISTANCE = 5.0; // how far is the closest atom of a potential partner residue from CA atom\r\nconst MAX_RESIDUES_THRESHOLD = 1000;\r\n\r\nexport default class HBondInfo {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._hbonds = []; // array of bond info for each residue\r\n if (this._complex._residues.length > MAX_RESIDUES_THRESHOLD) {\r\n this._buildVW(); // optimized version using voxel grid\r\n } else {\r\n this._build(); // test all pairs of residues\r\n }\r\n }\r\n\r\n isBond(from, to) {\r\n if (this._hbonds[from]) {\r\n const [acc0, acc1] = this._hbonds[from].acceptor;\r\n if (acc0 && acc0.residue === to && acc0.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n if (acc1 && acc1.residue === to && acc1.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n\r\n for (let i = 0; i < this._complex._residues.length - 1; ++i) {\r\n const ri = this._complex._residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let preri = null;\r\n if (i > 0 && (this._complex._residues[i - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && ri._sequence === this._complex._residues[i - 1]._sequence + 1) {\r\n preri = this._complex._residues[i - 1];\r\n }\r\n\r\n for (let j = i + 1; j < this._complex._residues.length; ++j) {\r\n const rj = this._complex._residues[j];\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = null;\r\n if ((this._complex._residues[j - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && rj._sequence === this._complex._residues[j - 1]._sequence + 1) {\r\n prerj = this._complex._residues[j - 1];\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (j !== i + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _buildVW() {\r\n const self = this;\r\n const residues = this._complex._residues;\r\n let ri;\r\n let preri;\r\n\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const pairs = new PairCollection(this._complex._residues.length * this._complex._residues.length / 2);\r\n\r\n function processAtom(atom) {\r\n const rj = atom.residue;\r\n\r\n if (rj._index === ri._index) {\r\n return;\r\n }\r\n\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n return;\r\n }\r\n\r\n if (!pairs.addPair(ri._index, rj._index)) {\r\n // we've seen this pair\r\n return;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = rj._index > 0 ? residues[rj._index - 1] : null;\r\n if (prerj\r\n && ((prerj.getType().flags & ResidueType.Flags.PROTEIN) === 0 || rj._sequence !== prerj._sequence + 1)) {\r\n prerj = null;\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (rj._index !== ri._index + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n\r\n for (let i = 0; i < residues.length - 1; ++i) {\r\n ri = residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n preri = i > 0 ? residues[i - 1] : null;\r\n if (preri\r\n && ((preri.getType().flags & ResidueType.Flags.PROTEIN) === 0 || ri._sequence !== preri._sequence + 1)) {\r\n preri = null;\r\n }\r\n\r\n vw.forEachAtomWithinRadius(this._residueGetCAlpha(ri), MAX_COUPLING_DISTANCE, processAtom);\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _residueGetCO(res) {\r\n let c = null;\r\n let o = null;\r\n\r\n res.forEachAtom((a) => {\r\n if (a.name === 'C') {\r\n c = a.position;\r\n } else if (a.name === 'O') {\r\n o = a.position;\r\n }\r\n });\r\n\r\n return [c, o];\r\n }\r\n\r\n // TODO Support hydrogen defined in complex\r\n _residueGetNH(prev, res) {\r\n const [c, o] = this._residueGetCO(prev);\r\n\r\n let n;\r\n res.forEachAtom((a) => {\r\n if (a.name === 'N') {\r\n n = a.position;\r\n }\r\n });\r\n\r\n if (c && o && n) {\r\n // calculate hydrogen position\r\n const h = c.clone();\r\n h.sub(o);\r\n h.multiplyScalar(1.0 / h.length());\r\n h.add(n);\r\n\r\n return [n, h];\r\n }\r\n\r\n return [null, null];\r\n }\r\n\r\n _calcHBondEnergy(predonor, donor, acceptor) {\r\n let result = 0;\r\n\r\n if (predonor === null) {\r\n return result;\r\n }\r\n\r\n if (donor.getType().getName() !== 'PRO') {\r\n const [n, h] = this._residueGetNH(predonor, donor);\r\n const [c, o] = this._residueGetCO(acceptor);\r\n\r\n if (n === null || h === null || c === null || o === null) {\r\n return result;\r\n }\r\n\r\n const distanceHO = h.distanceTo(o);\r\n const distanceHC = h.distanceTo(c);\r\n const distanceNC = n.distanceTo(c);\r\n const distanceNO = n.distanceTo(o);\r\n\r\n if (distanceHO < MINIMAL_DISTANCE || distanceHC < MINIMAL_DISTANCE\r\n || distanceNC < MINIMAL_DISTANCE || distanceNO < MINIMAL_DISTANCE) {\r\n result = MIN_HBOND_ENERGY;\r\n } else {\r\n result = COUPLING_CONSTANT / distanceHO - COUPLING_CONSTANT / distanceHC\r\n + COUPLING_CONSTANT / distanceNC - COUPLING_CONSTANT / distanceNO;\r\n }\r\n\r\n // DSSP compatibility mode:\r\n result = Math.round(result * 1000) / 1000;\r\n\r\n if (result < MIN_HBOND_ENERGY) {\r\n result = MIN_HBOND_ENERGY;\r\n }\r\n }\r\n\r\n // update donor\r\n if (typeof this._hbonds[donor._index] === 'undefined') {\r\n this._hbonds[donor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const donorInfo = this._hbonds[donor._index];\r\n\r\n if (donorInfo.acceptor.length < 2) {\r\n donorInfo.acceptor.push({\r\n residue: acceptor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (donorInfo.acceptor.length > 1) {\r\n if (result < donorInfo.acceptor[0].energy) {\r\n donorInfo.acceptor[1].residue = donorInfo.acceptor[0].residue;\r\n donorInfo.acceptor[1].energy = donorInfo.acceptor[0].energy;\r\n donorInfo.acceptor[0].residue = acceptor._index;\r\n donorInfo.acceptor[0].energy = result;\r\n } else if (result < donorInfo.acceptor[1].energy) {\r\n donorInfo.acceptor[1].residue = acceptor._index;\r\n donorInfo.acceptor[1].energy = result;\r\n }\r\n }\r\n\r\n // update acceptor\r\n if (typeof this._hbonds[acceptor._index] === 'undefined') {\r\n this._hbonds[acceptor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const accInfo = this._hbonds[acceptor._index];\r\n\r\n if (accInfo.donor.length < 2) {\r\n accInfo.donor.push({\r\n residue: donor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (accInfo.donor.length > 1) {\r\n if (result < accInfo.donor[0].energy) {\r\n accInfo.donor[1].residue = accInfo.donor[0].residue;\r\n accInfo.donor[1].energy = accInfo.donor[0].energy;\r\n accInfo.donor[0].residue = donor._index;\r\n accInfo.donor[0].energy = result;\r\n } else if (result < accInfo.donor[1].energy) {\r\n accInfo.donor[1].residue = donor._index;\r\n accInfo.donor[1].energy = result;\r\n }\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n","import HBondInfo from './HBondInfo';\r\nimport ResidueType from './ResidueType';\r\n\r\nconst BridgeType = Object.freeze({\r\n NO_BRIDGE: 0,\r\n PARALLEL: 1,\r\n ANTI_PARALLEL: 2,\r\n});\r\n\r\nconst HelixFlag = Object.freeze({\r\n START: 1,\r\n MIDDLE: 2,\r\n END: 3,\r\n START_AND_END: 4,\r\n});\r\n\r\nconst StructureType = Object.freeze({\r\n STRAND: 'E',\r\n BRIDGE: 'B',\r\n HELIX_310: 'G',\r\n HELIX_ALPHA: 'H',\r\n HELIX_PI: 'I',\r\n TURN: 'T',\r\n BEND: 'S',\r\n LOOP: ' ',\r\n});\r\n\r\nexport default class SecondaryStructureMap {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._build();\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n this._hbonds = new HBondInfo(this._complex);\r\n this._ss = []; // DSSP map by residue\r\n\r\n // auxilliary data\r\n this._sheet = [];\r\n this._betaPartners = [];\r\n this._bend = [];\r\n for (let i = 0; i < this._complex.getResidues().length; ++i) {\r\n this._betaPartners[i] = [];\r\n }\r\n this._helixFlags = [];\r\n this._helixFlags[3] = [];\r\n this._helixFlags[4] = [];\r\n this._helixFlags[5] = [];\r\n\r\n // calculate peptide chain lengths\r\n this._chainLengths = [];\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i].getResidues();\r\n let len = 0;\r\n for (; len < chain.length; ++len) {\r\n if ((chain[len].getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n break;\r\n }\r\n }\r\n this._chainLengths[i] = len;\r\n }\r\n\r\n this._buildBetaSheets();\r\n\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n self._buildAlphaHelices(this._complex._chains[i].getResidues(), this._chainLengths[i], false);\r\n }\r\n }\r\n\r\n _buildAlphaHelices(inResidues, chainLength, inPreferPiHelices) {\r\n // Helix and Turn\r\n for (let stride = 3; stride <= 5; ++stride) {\r\n if (inResidues.length < stride) {\r\n break;\r\n }\r\n\r\n for (let i = 0; i + stride < chainLength; ++i) {\r\n if (this._hbonds.isBond(inResidues[i + stride]._index, inResidues[i]._index)\r\n /* && NoChainBreak(res[i], res[i + stride]) */) {\r\n this._helixFlags[stride][inResidues[i + stride]._index] = HelixFlag.END;\r\n for (let j = i + 1; j < i + stride; ++j) {\r\n if (typeof this._helixFlags[stride][inResidues[j]._index] === 'undefined') {\r\n this._helixFlags[stride][inResidues[j]._index] = HelixFlag.MIDDLE;\r\n }\r\n }\r\n\r\n if (this._helixFlags[stride][inResidues[i]._index] === HelixFlag.END) {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START_AND_END;\r\n } else {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 2; i < chainLength - 2; ++i) {\r\n const kappa = this._kappa(inResidues[i - 2], inResidues[i], inResidues[i + 2]);\r\n this._bend[inResidues[i]._index] = (kappa !== 360 && kappa > 70);\r\n }\r\n\r\n for (let i = 1; i + 4 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 4) && this._isHelixStart(inResidues[i - 1]._index, 4)) {\r\n for (let j = i; j <= i + 3; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_ALPHA;\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 3 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 3) && this._isHelixStart(inResidues[i - 1]._index, 3)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 2; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_310;\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 2; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_310;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 5 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 5) && this._isHelixStart(inResidues[i - 1]._index, 5)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 4; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_PI\r\n || (inPreferPiHelices && this._ss[inResidues[j]._index] === StructureType.HELIX_ALPHA);\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 4; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_PI;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 1 < chainLength; ++i) {\r\n if (typeof this._ss[inResidues[i]._index] === 'undefined') {\r\n let isTurn = false;\r\n for (let stride = 3; stride <= 5 && !isTurn; ++stride) {\r\n for (let k = 1; k < stride && !isTurn; ++k) {\r\n isTurn = (i >= k) && this._isHelixStart(inResidues[i - k]._index, stride);\r\n }\r\n }\r\n\r\n if (isTurn) {\r\n this._ss[inResidues[i]._index] = StructureType.TURN;\r\n } else if (this._bend[inResidues[i]._index]) {\r\n this._ss[inResidues[i]._index] = StructureType.BEND;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _cosinusAngle(p1, p2, p3, p4) {\r\n const v12 = p1.clone().sub(p2);\r\n const v34 = p3.clone().sub(p4);\r\n\r\n let result = 0;\r\n\r\n const x = v12.dot(v12) * v34.dot(v34);\r\n if (x > 0) {\r\n result = v12.dot(v34) / Math.sqrt(x);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _kappa(prevPrev, res, nextNext) {\r\n const curCA = this._residueGetCAlpha(res);\r\n const ppCA = this._residueGetCAlpha(prevPrev);\r\n const nnCA = this._residueGetCAlpha(nextNext);\r\n if (curCA === null || ppCA === null || nnCA === null) {\r\n return 180;\r\n }\r\n\r\n const ckap = this._cosinusAngle(curCA, ppCA, nnCA, curCA);\r\n const skap = Math.sqrt(1 - ckap * ckap);\r\n return Math.atan2(skap, ckap) * 180 / Math.PI;\r\n }\r\n\r\n _isHelixStart(res, stride) {\r\n return (this._helixFlags[stride][res] === HelixFlag.START\r\n || this._helixFlags[stride][res] === HelixFlag.START_AND_END);\r\n }\r\n\r\n _buildBetaSheets() {\r\n // find bridges\r\n // check each chain against each other chain, and against itself\r\n const bridges = [];\r\n for (let a = 0; a < this._complex._chains.length; ++a) {\r\n const lenA = this._chainLengths[a];\r\n if (lenA <= 4) {\r\n continue;\r\n }\r\n\r\n const chainA = this._complex._chains[a].getResidues();\r\n\r\n for (let b = a; b < this._complex._chains.length; ++b) {\r\n const lenB = this._chainLengths[b];\r\n if (lenB <= 4) {\r\n continue;\r\n }\r\n\r\n const chainB = this._complex._chains[b].getResidues();\r\n\r\n for (let i = 1; i + 1 < lenA; ++i) {\r\n const ri = chainA[i];\r\n\r\n let j = 1;\r\n if (b === a) {\r\n j = i + 3; // check for self-bridges forward down the chain\r\n }\r\n\r\n for (; j + 1 < lenB; ++j) {\r\n const rj = chainB[j];\r\n\r\n const type = this._testBridge(chainA, i, chainB, j);\r\n if (type === BridgeType.NO_BRIDGE) {\r\n continue;\r\n }\r\n\r\n // there is a bridge, try to attach it to previously found sequence\r\n let found = false;\r\n for (const bridge of bridges) {\r\n if (type !== bridge.type || ri._index !== bridge.i[bridge.i.length - 1] + 1) {\r\n continue;\r\n }\r\n\r\n if (type === BridgeType.PARALLEL && bridge.j[bridge.j.length - 1] + 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.push(rj._index);\r\n found = true;\r\n break;\r\n }\r\n\r\n if (type === BridgeType.ANTI_PARALLEL && bridge.j[0] - 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.unshift(rj._index);\r\n found = true;\r\n break;\r\n }\r\n }\r\n\r\n // this bridge cannot be attached anywhere, start a new sequence\r\n if (!found) {\r\n bridges.push({\r\n type,\r\n i: [ri._index],\r\n chainI: ri.getChain()._index,\r\n j: [rj._index],\r\n chainJ: rj.getChain()._index,\r\n });\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // extend ladders\r\n bridges.sort((a, b) => {\r\n if (a.chainI < b.chainI || (a.chainI === b.chainI && a.i[0] < b.i[0])) {\r\n return -1;\r\n }\r\n return 1;\r\n });\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n for (let j = i + 1; j < bridges.length; ++j) {\r\n const ibi = bridges[i].i[0];\r\n const iei = bridges[i].i[bridges[i].i.length - 1];\r\n const jbi = bridges[i].j[0];\r\n const jei = bridges[i].j[bridges[i].j.length - 1];\r\n const ibj = bridges[j].i[0];\r\n const iej = bridges[j].i[bridges[j].i.length - 1];\r\n const jbj = bridges[j].j[0];\r\n const jej = bridges[j].j[bridges[j].j.length - 1];\r\n\r\n if (bridges[i].type !== bridges[j].type\r\n || this._hasChainBreak(Math.min(ibi, ibj), Math.max(iei, iej))\r\n || this._hasChainBreak(Math.min(jbi, jbj), Math.max(jei, jej))\r\n || ibj - iei >= 6 || (iei >= ibj && ibi <= iej)) {\r\n continue;\r\n }\r\n\r\n let bulge = false;\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bulge = ((jbj - jei < 6 && ibj - iei < 3) || (jbj - jei < 3));\r\n } else {\r\n bulge = ((jbi - jej < 6 && ibj - iei < 3) || (jbi - jej < 3));\r\n }\r\n\r\n if (bulge) {\r\n bridges[i].i = bridges[i].i.concat(bridges[j].i);\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bridges[i].j = bridges[i].j.concat(bridges[j].j);\r\n } else {\r\n bridges[i].j = bridges[j].j.concat(bridges[i].j);\r\n }\r\n bridges.splice(j--, 1);\r\n }\r\n }\r\n }\r\n\r\n // Sheet\r\n const ladderset = new Set();\r\n for (let i = 0; i < bridges.length; ++i) {\r\n ladderset.add(bridges[i]);\r\n }\r\n\r\n let sheet = 1;\r\n let ladder = 0;\r\n while (ladderset.size > 0) {\r\n let bridge = ladderset.values().next().value;\r\n ladderset.delete(bridge);\r\n\r\n const sheetset = new Set();\r\n sheetset.add(bridge);\r\n\r\n let toMove;\r\n do {\r\n toMove = new Set();\r\n for (const a of sheetset.values()) {\r\n for (const b of ladderset.values()) {\r\n if (this._areBridgesLinked(a, b)) {\r\n toMove.add(b);\r\n }\r\n }\r\n }\r\n for (bridge of toMove.values()) {\r\n sheetset.add(bridge);\r\n ladderset.delete(bridge);\r\n }\r\n } while (toMove.size > 0);\r\n\r\n for (bridge of sheetset.values()) {\r\n bridge.ladder = ladder;\r\n bridge.sheet = sheet;\r\n bridge.link = sheetset;\r\n ++ladder;\r\n }\r\n\r\n ++sheet;\r\n }\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n const bridge = bridges[i];\r\n\r\n // find out if any of the i and j set members already have\r\n // a bridge assigned, if so, we're assigning bridge 2\r\n\r\n let betai = 0;\r\n let betaj = 0;\r\n\r\n for (let l = 0; l < bridge.i.length; ++l) {\r\n if (this._betaPartners[bridge.i[l]][0]) {\r\n betai = 1;\r\n break;\r\n }\r\n }\r\n\r\n for (let l = 0; l < bridge.j.length; ++l) {\r\n if (this._betaPartners[bridge.j[l]][0]) {\r\n betaj = 1;\r\n break;\r\n }\r\n }\r\n\r\n let ss = StructureType.BRIDGE;\r\n if (bridge.i.length > 1) {\r\n ss = StructureType.STRAND;\r\n }\r\n\r\n if (bridge.type === BridgeType.PARALLEL) {\r\n let j = 0;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n\r\n j = 0;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n } else {\r\n let j = bridge.j.length - 1;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n\r\n j = bridge.i.length - 1;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n }\r\n\r\n for (let k = bridge.i[0]; k <= bridge.i[bridge.i.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n\r\n for (let k = bridge.j[0]; k <= bridge.j[bridge.j.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _testBridge(chainA, from, chainB, to) {\r\n let result = BridgeType.NO_BRIDGE;\r\n\r\n const a = chainA[from - 1]._index;\r\n const b = chainA[from]._index;\r\n const c = chainA[from + 1]._index;\r\n const d = chainB[to - 1]._index;\r\n const e = chainB[to]._index;\r\n const f = chainB[to + 1]._index;\r\n\r\n const isBond = this._hbonds.isBond.bind(this._hbonds);\r\n if ((isBond(c, e) && isBond(e, a)) || (isBond(f, b) && isBond(b, d))) {\r\n result = BridgeType.PARALLEL;\r\n } else if ((isBond(c, d) && isBond(f, a)) || (isBond(e, b) && isBond(b, e))) {\r\n result = BridgeType.ANTI_PARALLEL;\r\n }\r\n return result;\r\n }\r\n\r\n // return true if any of the residues in bridge a is identical to any of the residues in bridge b\r\n _areBridgesLinked(a, b) {\r\n const ai = new Set(a.i);\r\n const aj = new Set(a.j);\r\n\r\n for (const i of b.i) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n for (const i of b.j) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n }\r\n\r\n _hasChainBreak(from, to) {\r\n for (let i = from + 1; i <= to; ++i) {\r\n if (this._complex._residues[i]._sequence !== this._complex._residues[i - 1]._sequence + 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\nSecondaryStructureMap.StructureType = StructureType;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport Atom from './Atom';\r\nimport Chain from './Chain';\r\nimport Helix from './Helix';\r\nimport Strand from './Strand';\r\nimport Sheet from './Sheet';\r\nimport Component from './Component';\r\nimport ResidueType from './ResidueType';\r\nimport Bond from './Bond';\r\nimport AutoBond from './AutoBond';\r\nimport AromaticLoopsMarker from './AromaticLoopsMarker';\r\nimport BiologicalUnit from './BiologicalUnit';\r\nimport selectors from './selectors';\r\nimport VoxelWorld from './VoxelWorld';\r\nimport SecondaryStructureMap from './SecondaryStructureMap';\r\nimport StructuralElement from './StructuralElement';\r\n\r\nconst VOXEL_SIZE = 5.0;\r\n\r\nconst { StructureType } = SecondaryStructureMap;\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX\r\nconst helixClassMap = {\r\n [StructureType.HELIX_ALPHA]: 1,\r\n [StructureType.HELIX_PI]: 3,\r\n [StructureType.HELIX_310]: 5,\r\n};\r\n\r\nconst loopMap = {\r\n [StructureType.BRIDGE]: StructuralElementType.BRIDGE,\r\n [StructureType.TURN]: StructuralElementType.TURN,\r\n [StructureType.BEND]: StructuralElementType.BEND,\r\n [StructureType.LOOP]: StructuralElementType.COIL,\r\n};\r\n\r\n/**\r\n * The entire complex of the molecules under study.\r\n *\r\n * @exports Complex\r\n * @constructor\r\n */\r\nclass Complex {\r\n constructor() {\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n\r\n this._residueTypes = Object.create(ResidueType.StandardTypes);\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n this._molecules = [];\r\n this._maskNeedsUpdate = false;\r\n\r\n this.metadata = {};\r\n\r\n this.symmetry = [];\r\n this.units = [new BiologicalUnit(this)];\r\n this._currentUnit = 0; // default biological unit is the asymmetric unit\r\n }\r\n\r\n addAtom(atom) {\r\n const index = this._atoms.length;\r\n this._atoms.push(atom);\r\n return index;\r\n }\r\n\r\n addSheet(sheet) {\r\n const index = this._sheets.length;\r\n this._sheets.push(sheet);\r\n return index;\r\n }\r\n\r\n addHelix(helix) {\r\n const index = this._helices.length;\r\n this._helices.push(helix);\r\n return index;\r\n }\r\n\r\n getAtoms() {\r\n return this._atoms;\r\n }\r\n\r\n getBonds() {\r\n return this._bonds;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n addResidue(residue) {\r\n const index = this._residues.length;\r\n this._residues.push(residue);\r\n return index;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n this.forEachChain((chain) => {\r\n chain.updateToFrame(frameData);\r\n });\r\n }\r\n\r\n addResidueType(resName) {\r\n const rt = this._residueTypes[resName] = new ResidueType(resName, 'Unknown', '');\r\n return rt;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n getSGroupCount() {\r\n return this._sgroups.length;\r\n }\r\n\r\n getSGroups() {\r\n return this._sgroups;\r\n }\r\n\r\n /*\r\n Extract atom by its fullname: #chainName#.#residueId#.#atomName#\r\n */\r\n getAtomByFullname(fullName) {\r\n const parts = fullName.split('.');\r\n if (parts.length !== 3) {\r\n return null;\r\n }\r\n\r\n const chainName = parts[0];\r\n const resId = parseInt(parts[1], 10);\r\n if (Number.isNaN(resId)) {\r\n return null;\r\n }\r\n const atomName = parts[2].toUpperCase();\r\n\r\n let currAtom = null;\r\n this.forEachChain((chain) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (chain._name.localeCompare(chainName) === 0) {\r\n chain.forEachResidue((residue) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (residue._sequence === resId) {\r\n residue.forEachAtom((atom) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (atomName.localeCompare(atom.name) === 0) {\r\n currAtom = atom;\r\n }\r\n });\r\n }\r\n });\r\n }\r\n });\r\n\r\n return currAtom;\r\n }\r\n\r\n /**\r\n * Create a new chain.\r\n *\r\n * @param {string} name - Chain name.\r\n * @returns {Chain} - Newly created chain.\r\n */\r\n addChain(name) {\r\n const result = new Chain(this, name);\r\n this._chains.push(result);\r\n return result;\r\n }\r\n\r\n getChain(name) {\r\n for (let i = 0, n = this._chains.length; i < n; ++i) {\r\n const chain = this._chains[i];\r\n if (chain.getName() === name) {\r\n return chain;\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n getChainCount() {\r\n return this._chains.length;\r\n }\r\n\r\n getMolecules() {\r\n return this._molecules;\r\n }\r\n\r\n getMoleculeCount() {\r\n return this._molecules.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n process(atoms[i]);\r\n }\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._bonds;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n forEachChain(process) {\r\n const chains = this._chains;\r\n for (let i = 0, n = chains.length; i < n; ++i) {\r\n process(chains[i]);\r\n }\r\n }\r\n\r\n forEachMolecule(process) {\r\n const molecules = this._molecules;\r\n const n = molecules.length;\r\n for (let i = 0; i < n; ++i) {\r\n process(molecules[i]);\r\n }\r\n }\r\n\r\n forEachSGroup(process) {\r\n const groups = this._sgroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n process(groups[i]);\r\n }\r\n }\r\n\r\n forEachComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n forEachVisibleComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n addBond(left, right, order, type, fixed) {\r\n const bond = new Bond(left, right, order, type, fixed);\r\n this._bonds.push(bond);\r\n return bond;\r\n }\r\n\r\n getBondCount() {\r\n return this._bonds.length;\r\n }\r\n\r\n getResidueType(name) {\r\n return this._residueTypes[name] || null;\r\n }\r\n\r\n getUnifiedSerial(chain, serial, iCode) {\r\n /* eslint-disable no-magic-numbers */\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n /* eslint-enable no-magic-numbers */\r\n return serial + iCode * maxSerial + chain * chainShift;\r\n }\r\n\r\n splitUnifiedSerial(uniSerial) {\r\n /* eslint-disable no-magic-numbers */\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n /* eslint-enable no-magic-numbers */\r\n const chainId = Math.floor(uniSerial / chainShift);\r\n const remnant = uniSerial - chainId * chainShift;\r\n const insCode = Math.floor(remnant / maxSerial);\r\n const ser = remnant - insCode * maxSerial;\r\n return { chain: chainId, serial: ser, iCode: insCode };\r\n }\r\n\r\n _fillCmpEdit() {\r\n const self = this;\r\n const components = this._components;\r\n\r\n function addComp() {\r\n const comp = new Component(self);\r\n comp._index = components.length;\r\n components[comp._index] = comp;\r\n return comp;\r\n }\r\n\r\n this.forEachChain((chain) => {\r\n const residues = chain._residues;\r\n const resCount = residues.length;\r\n if (resCount < 1) {\r\n return;\r\n }\r\n let comp = addComp();\r\n let currStart = residues[0]._index;\r\n\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)\r\n || currRes._index !== nextRes._index - 1) {\r\n // the last condition is broken and incorrect\r\n // the refactoring of the Component is required in order to fix this issue\r\n comp.setSubDivs([{\r\n start: currStart,\r\n end: currRes._index,\r\n }]);\r\n if (nextRes) {\r\n currStart = nextRes._index;\r\n comp = addComp();\r\n }\r\n }\r\n }\r\n });\r\n }\r\n\r\n // This function was added in the moment of despair\r\n // It was the dark times for miew\r\n _fillCmpNoedit() {\r\n const comp = new Component(this);\r\n comp._index = 0;\r\n\r\n const residues = this._residues;\r\n const resCount = residues.length;\r\n if (resCount === 0) {\r\n return;\r\n }\r\n\r\n const currSubDivs = [];\r\n let currStart = 0;\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)) {\r\n // wrap up this interval\r\n currSubDivs[currSubDivs.length] = {\r\n start: currStart,\r\n end: i,\r\n };\r\n if (nextRes) {\r\n currStart = i + 1;\r\n }\r\n }\r\n }\r\n\r\n comp.setSubDivs(currSubDivs);\r\n this._components[comp._index] = comp;\r\n }\r\n\r\n /**\r\n * Fill components information.\r\n * @param {boolean} enableEditing - Restructure Complex to enable per-component editing.\r\n */\r\n _fillComponents(enableEditing) {\r\n if (enableEditing) {\r\n this._fillCmpEdit();\r\n } else {\r\n this._fillCmpNoedit();\r\n }\r\n }\r\n\r\n getCurrentUnit() {\r\n return this._currentUnit;\r\n }\r\n\r\n getDefaultBoundaries() {\r\n return this.units[0].getBoundaries();\r\n }\r\n\r\n getBoundaries() {\r\n return this.units[this._currentUnit].getBoundaries();\r\n }\r\n\r\n getTransforms() {\r\n return this.units[this._currentUnit].getTransforms();\r\n }\r\n\r\n getSelector() {\r\n return this.units[this._currentUnit].getSelector();\r\n }\r\n\r\n resetCurrentUnit() {\r\n this._currentUnit = 0;\r\n this.setCurrentUnit(1);\r\n }\r\n\r\n setCurrentUnit(newUnit) {\r\n if (newUnit !== null && newUnit !== undefined\r\n && newUnit !== this._currentUnit\r\n && newUnit >= 0\r\n && newUnit < this.units.length) {\r\n this._currentUnit = newUnit;\r\n return true;\r\n }\r\n return false;\r\n }\r\n\r\n _computeBounds() {\r\n const { units } = this;\r\n for (let i = 0, n = units.length; i < n; ++i) {\r\n units[i].computeBoundaries();\r\n }\r\n }\r\n\r\n onAtomPositionChanged() {\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n this.forEachComponent((c) => {\r\n c.update();\r\n });\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n this._finalizeBonds();\r\n this.forEachSGroup((s) => {\r\n s._rebuildSGroupOnAtomChange();\r\n });\r\n }\r\n\r\n update() {\r\n if (this._maskNeedsUpdate) {\r\n this.updateStructuresMask();\r\n this._maskNeedsUpdate = false;\r\n }\r\n }\r\n\r\n _finalizeBonds() {\r\n const bonds = this.getBonds();\r\n const n = bonds.length;\r\n for (let i = 0; i < n; ++i) {\r\n bonds[i]._index = i;\r\n }\r\n }\r\n\r\n /**\r\n * Finalizes complex's inner data(i.e. after parsing).\r\n * @param {objects} opts - Build bonds automatically.\r\n * @param {boolean} opts.needAutoBonding - Build bonds automatically.\r\n * @param {boolean} opts.detectAromaticLoops - Find/mark aromatic loops.\r\n * @param {boolean} opts.enableEditing - Restructure Complex to enable per-component editing.\r\n * @param {Array} [opts.serialAtomMap] - Array of atoms ordered by their serials.\r\n */\r\n finalize(opts) {\r\n opts = opts || {};\r\n // Put bonds into atoms\r\n const bonds = this._bonds;\r\n let i;\r\n let n;\r\n // remove invalid bonds\r\n for (i = bonds.length - 1; i >= 0; i--) {\r\n const bond = bonds[i];\r\n if (bond._left === null || bond._right === null) {\r\n bonds.splice(i, 1);\r\n } else {\r\n bond._left.bonds.push(bond);\r\n bond._right.bonds.push(bond);\r\n }\r\n }\r\n\r\n const residues = this._residues;\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._finalize();\r\n }\r\n\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n\r\n // WARNING! this MUST be done BEFORE computeBounds is called\r\n const { units } = this;\r\n for (i = 0, n = units.length; i < n; ++i) {\r\n units[i].finalize();\r\n }\r\n // try setting first biomolecule by defaults\r\n this.setCurrentUnit(1);\r\n\r\n const residueHash = {};\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n // This code is extremely dangerous for non-PDB formats\r\n residueHash[this.getUnifiedSerial(\r\n res.getChain().getName().charCodeAt(0),\r\n res.getSequence(),\r\n res.getICode().charCodeAt(0),\r\n )] = res;\r\n }\r\n\r\n const { structures } = this;\r\n for (i = 0, n = structures.length; i < n; ++i) {\r\n structures[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const helices = this._helices;\r\n for (i = 0, n = helices.length; i < n; ++i) {\r\n helices[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const sheets = this._sheets;\r\n for (i = 0, n = sheets.length; i < n; ++i) {\r\n sheets[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n\r\n const atoms = this._atoms;\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const currAtom = atoms[i];\r\n currAtom.index = i;\r\n }\r\n\r\n if (opts.needAutoBonding) {\r\n // Ignore errors during autobonding\r\n try {\r\n const autoConnector = new AutoBond(this);\r\n autoConnector.build();\r\n autoConnector.destroy();\r\n } catch (e) {\r\n console.warn('Autobonding failed:', e);\r\n }\r\n }\r\n\r\n const chains = this._chains;\r\n for (i = 0, n = chains.length; i < n; ++i) {\r\n chains[i]._index = i;\r\n }\r\n\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._index = i;\r\n }\r\n\r\n // mark non-polar hydrogens\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n if (atom.flags & Atom.Flags.HYDROGEN && atom.bonds.length === 1) {\r\n const bond = atom.bonds[0];\r\n const other = (bond._left !== atom && bond._left) || bond._right;\r\n if (other.flags & Atom.Flags.CARBON) {\r\n atom.flags |= Atom.Flags.NONPOLARH;\r\n }\r\n }\r\n }\r\n\r\n this._finalizeBonds();\r\n this._fillComponents(opts.enableEditing);\r\n\r\n const marker = new AromaticLoopsMarker(this);\r\n marker.markCycles();\r\n if (opts.detectAromaticLoops) { // TODO remove this condition clause, it is for debug purposes only!\r\n marker.detectCycles(); // TODO add conditional detection\r\n }\r\n\r\n this._finalizeMolecules();\r\n }\r\n\r\n _finalizeMolecules() {\r\n // add reference to molecule into residue\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const molecule = this._molecules[i];\r\n const count = molecule.residues.length;\r\n for (let j = 0; j < count; j++) {\r\n const residue = molecule.residues[j];\r\n residue._molecule = molecule;\r\n }\r\n }\r\n }\r\n\r\n updateStructuresMask() {\r\n const updater = (structure) => structure.collectMask();\r\n this.forEachResidue(updater);\r\n this.forEachChain(updater);\r\n this.forEachMolecule(updater);\r\n }\r\n\r\n countAtomsByMask(mask) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n getNumAtomsBySelector(selector) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n resetAtomMask(mask) {\r\n this.forEachAtom((atom) => {\r\n atom.mask = mask;\r\n });\r\n }\r\n\r\n markAtoms(selector, mask) {\r\n const setMask = mask;\r\n const clearMask = ~setMask;\r\n let count = 0;\r\n const totalSelector = selectors.keyword('And')(selector, this.getSelector());\r\n\r\n this.forEachAtom((atom) => {\r\n if (totalSelector.includesAtom(atom)) {\r\n atom.mask |= setMask;\r\n count++;\r\n } else {\r\n atom.mask &= clearMask;\r\n }\r\n });\r\n this._maskNeedsUpdate = true;\r\n\r\n return count;\r\n }\r\n\r\n markAtomsAdditionally(selector, mask) {\r\n const setMask = mask;\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom) && (atom.mask & mask) !== mask) {\r\n atom.mask |= setMask;\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n clearAtomBits(mask) {\r\n const clearMask = ~mask;\r\n this.forEachAtom((atom) => {\r\n atom.mask &= clearMask;\r\n });\r\n const reseter = (a) => {\r\n a._mask &= clearMask;\r\n };\r\n this.forEachAtom(reseter);\r\n this.forEachResidue(reseter);\r\n this.forEachChain(reseter);\r\n this.forEachMolecule(reseter);\r\n }\r\n\r\n getAtomNames() {\r\n if (this.hasOwnProperty('_atomNames')) {\r\n return this._atomNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.name] = 1;\r\n });\r\n this._atomNames = Object.keys(dict);\r\n\r\n return this._atomNames;\r\n }\r\n\r\n getElements() {\r\n if (this.hasOwnProperty('_elements')) {\r\n return this._elements;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.element.name] = 1;\r\n });\r\n this._elements = Object.keys(dict);\r\n\r\n return this._elements;\r\n }\r\n\r\n getResidueNames() {\r\n if (this.hasOwnProperty('_residueNames')) {\r\n return this._residueNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachResidue((res) => {\r\n dict[res._type._name] = 1;\r\n });\r\n this._residueNames = Object.keys(dict);\r\n\r\n return this._residueNames;\r\n }\r\n\r\n getChainNames() {\r\n if (this.hasOwnProperty('_chainNames')) {\r\n return this._chainNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachChain((chain) => {\r\n dict[chain._name] = 1;\r\n });\r\n this._chainNames = Object.keys(dict);\r\n\r\n return this._chainNames;\r\n }\r\n\r\n getAltLocNames() {\r\n if (this.hasOwnProperty('_altlocNames')) {\r\n return this._altlocNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[String.fromCharCode(atom.location)] = 1;\r\n });\r\n this._altlocNames = Object.keys(dict);\r\n\r\n return this._altlocNames;\r\n }\r\n\r\n getVoxelWorld() {\r\n if (!this.hasOwnProperty('_voxelWorld')) {\r\n try {\r\n this._voxelWorld = new VoxelWorld(\r\n this.getDefaultBoundaries().boundingBox,\r\n new THREE.Vector3(VOXEL_SIZE, VOXEL_SIZE, VOXEL_SIZE),\r\n );\r\n this._voxelWorld.addAtoms(this);\r\n } catch (e) {\r\n logger.warn('Unable to create voxel world');\r\n this._voxelWorld = null;\r\n }\r\n }\r\n\r\n return this._voxelWorld;\r\n }\r\n\r\n /**\r\n * Simple function to make unified routine procedure without code duplication.\r\n * @param {Array} srcArray - Source chemical structure array (will be part of resulting chemical structure array).\r\n * @param {Array} dstArray - Resulting chemical structure array.\r\n * @param {number} param - Parameter for processor.\r\n * @param {function} functor - Processor for every element in array.\r\n */\r\n addElement(srcArray, dstArray, param, functor) {\r\n const { length } = srcArray;\r\n for (let i = 0; i < length; ++i) {\r\n const elem = srcArray[i];\r\n functor(elem, param);\r\n dstArray.push(elem);\r\n }\r\n }\r\n\r\n // this function joins multiple complexes into one (this)\r\n // atom, bond, ... objects are reused -- so input complexes are no longer valid\r\n joinComplexes(complexes) {\r\n // clear target complex\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n\r\n const self = this;\r\n let atomBias = 0;\r\n let bondBias = 0;\r\n let residueBias = 0;\r\n let chainBias = 0;\r\n let componentBias = 0;\r\n\r\n function processAtom(atom, bias) {\r\n atom.serial += bias;\r\n atom.index += bias;\r\n }\r\n\r\n function processBond(bond, bias) {\r\n bond._index += bias;\r\n }\r\n\r\n function processResidue(residue, bias) {\r\n residue._index += bias;\r\n }\r\n\r\n function processChain(chain, bias) {\r\n chain._complex = self;\r\n chain._index += bias;\r\n }\r\n\r\n function processComponent(component, bias) {\r\n component._complex = self;\r\n component._index += bias;\r\n }\r\n\r\n /**\r\n * Simple function to do nothing.\r\n */\r\n function doNothing() {\r\n }\r\n\r\n for (let i = 0; i < complexes.length; ++i) {\r\n const c = complexes[i];\r\n this.addElement(c._atoms, this._atoms, atomBias, processAtom);\r\n this.addElement(c._bonds, this._bonds, bondBias, processBond);\r\n this.addElement(c._residues, this._residues, residueBias, processResidue);\r\n this.addElement(c._chains, this._chains, chainBias, processChain);\r\n this.addElement(c._sheets, this._sheets, 0, doNothing);\r\n this.addElement(c._helices, this._helices, 0, doNothing);\r\n this.addElement(c._sgroups, this._sgroups, 0, doNothing);\r\n this.addElement(c._components, this._components, componentBias, processComponent);\r\n this.addElement(c.structures, this.structures, 0, doNothing);\r\n // merge residue types\r\n for (const rt in c._residueTypes) {\r\n if (c._residueTypes.hasOwnProperty(rt)) {\r\n this._residueTypes[rt] = c._residueTypes[rt];\r\n }\r\n }\r\n\r\n atomBias += c._atoms.length;\r\n bondBias += c._bonds.length;\r\n residueBias += c._residues.length;\r\n chainBias += c._chains.length;\r\n componentBias += c._components.length;\r\n }\r\n\r\n this._computeBounds();\r\n }\r\n\r\n /**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n */\r\n dssp() {\r\n const ssMap = new SecondaryStructureMap(this);\r\n\r\n const structures = this.structures = [];\r\n const helices = this._helices = [];\r\n const sheets = this._sheets = [];\r\n\r\n const getSheet = (index) => {\r\n let item = sheets[index];\r\n if (!item) {\r\n item = sheets[index] = new Sheet(String(index), 0);\r\n }\r\n return item;\r\n };\r\n\r\n let lastCode;\r\n let lastSheetIndex;\r\n let lastHelixIndex = 0;\r\n let curStructure = null;\r\n for (let i = 0, n = this._residues.length; i < n; ++i) {\r\n const curCode = ssMap._ss[i];\r\n const curResidue = this._residues[i];\r\n const curSheetIndex = ssMap._sheet[i];\r\n\r\n // expand the last structure\r\n if (curCode === lastCode && curSheetIndex === lastSheetIndex) {\r\n curResidue._secondary = curStructure;\r\n if (curStructure) {\r\n curStructure.term = curResidue;\r\n }\r\n if (curStructure instanceof Helix) {\r\n curStructure.length++;\r\n }\r\n continue;\r\n }\r\n\r\n // create a new structure\r\n const helixClass = helixClassMap[curCode];\r\n const loopType = loopMap[curCode];\r\n if (curCode === StructureType.STRAND) {\r\n const curSheet = getSheet(curSheetIndex);\r\n curStructure = new Strand(curSheet, curResidue, curResidue, 0, null, null);\r\n curSheet.addStrand(curStructure);\r\n } else if (helixClass !== undefined) {\r\n lastHelixIndex++;\r\n curStructure = new Helix(helixClass, curResidue, curResidue, lastHelixIndex, String(lastHelixIndex), '', 1);\r\n helices.push(curStructure);\r\n } else if (loopType !== undefined) {\r\n curStructure = new StructuralElement(loopType, curResidue, curResidue);\r\n } else {\r\n curStructure = null;\r\n }\r\n\r\n if (curStructure) {\r\n structures.push(curStructure);\r\n }\r\n\r\n curResidue._secondary = curStructure;\r\n\r\n lastCode = curCode;\r\n lastSheetIndex = curSheetIndex;\r\n }\r\n\r\n this._sheets = sheets.filter((_sheet) => true); // squeeze sheets array\r\n }\r\n}\r\n\r\nComplex.prototype.id = 'Complex';\r\nComplex.prototype.name = '';\r\n\r\nexport default Complex;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\nfunction pow2ceil(v) {\r\n let p = 2;\r\n v = (v - 1) >> 1;\r\n while (v) {\r\n p <<= 1;\r\n v >>= 1;\r\n }\r\n return p;\r\n}\r\n\r\n/**\r\n * Volume constructor\r\n *\r\n * @param {Object} type - Float32Array, Int8Array, etc...\r\n * @param {Object|Array} dimensions - number of data points on each axis (x, y, z)\r\n * @param {Box3} box - bounding box defining data place in metric space,\r\n * it's corners correspond to extreme data points\r\n * @param {Number} vecSize - dimension of the field data point (1 = scalar, 3 = 3D vector)\r\n * @param {Object} data - typed array of the same type as specified by the 1st parameter,\r\n * layout: point by point along X,\r\n * row by row along Y,\r\n * plane by plane along Z\r\n * @param {Number} volumeInfo - volume info values to define threshold to filter the noise\r\n */\r\n\r\nclass Volume {\r\n constructor(type, dimensions, box, vecSize, data, volumeInfo) {\r\n this._box = box.clone();\r\n this._dimVec = Math.max(Math.floor(vecSize || 1), 1);\r\n this._volumeInfo = volumeInfo;\r\n\r\n if (dimensions instanceof Array) {\r\n [this._dimX, this._dimY, this._dimZ] = dimensions;\r\n } else {\r\n this._dimX = dimensions.x;\r\n this._dimY = dimensions.y;\r\n this._dimZ = dimensions.z;\r\n }\r\n this._dimX = Math.max(Math.floor(this._dimX), 1);\r\n this._dimY = Math.max(Math.floor(this._dimY), 1);\r\n this._dimZ = Math.max(Math.floor(this._dimZ), 1);\r\n\r\n this._rowElements = this._dimVec * this._dimX;\r\n this._planeElements = this._rowElements * this._dimY;\r\n this._totalElements = this._planeElements * this._dimZ;\r\n\r\n this._data = data || utils.allocateTyped(type, this._totalElements);\r\n\r\n // override getter/setter for vector fields\r\n switch (this._dimVec) {\r\n case 1:\r\n break;\r\n\r\n case 2:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n };\r\n break;\r\n\r\n case 3:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1], this._data[idx + 2]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n this._data[idx + 2] = c;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n this._data[idx + 2] += c;\r\n };\r\n break;\r\n\r\n default:\r\n throw new Error('Volume: invalid vector dimension');\r\n }\r\n }\r\n\r\n // default getter assumes it's a scalar field\r\n getValue(x, y, z) {\r\n return this._data[x + y * this._rowElements + z * this._planeElements];\r\n }\r\n\r\n // default setter assumes it's a scalar field\r\n setValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] = val;\r\n }\r\n\r\n // default adder assumes it's a scalar field\r\n addValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] += val;\r\n }\r\n\r\n getDimensions() {\r\n return [this._dimX, this._dimY, this._dimZ];\r\n }\r\n\r\n getBox() {\r\n return this._box;\r\n }\r\n\r\n getVolumeInfo() {\r\n return this._volumeInfo;\r\n }\r\n\r\n getCellSize() {\r\n const boxSize = new THREE.Vector3();\r\n this._box.getSize(boxSize);\r\n const res = new THREE.Vector3();\r\n res.x = this._dimX > 1 ? boxSize.x / (this._dimX - 1) : 0;\r\n res.y = this._dimY > 1 ? boxSize.y / (this._dimY - 1) : 0;\r\n res.z = this._dimZ > 1 ? boxSize.z / (this._dimZ - 1) : 0;\r\n return res;\r\n }\r\n\r\n computeGradient() {\r\n if (this._dimVec !== 1) {\r\n // gradient can only be computed for scalar fields\r\n return null;\r\n }\r\n\r\n // create a 3D vector field of gradients\r\n const gradient = new Volume(Float32Array, [this._dimX, this._dimY, this._dimZ], this._box, 3);\r\n\r\n // calculate cell side lengths\r\n const vl = this.getCellSize();\r\n\r\n // gradient axis scaling values and averaging factors, to correctly\r\n // calculate the gradient for volumes with irregular cell spacing\r\n const vs = new THREE.Vector3(-0.5 / vl.x, -0.5 / vl.y, -0.5 / vl.z);\r\n\r\n // TODO Check for intended bug in VMD (min is zero)\r\n function clamp(val, min, max) {\r\n return Math.min(max, Math.max(min, val));\r\n }\r\n\r\n const xSize = this._dimX;\r\n const ySize = this._dimY;\r\n const zSize = this._dimZ;\r\n const volMap = this._data;\r\n\r\n function _voxelValue(x, y, z) {\r\n return volMap[z * xSize * ySize + y * xSize + x];\r\n }\r\n\r\n for (let zi = 0; zi < zSize; ++zi) {\r\n const zm = clamp(zi - 1, 0, zSize - 1);\r\n const zp = clamp(zi + 1, 0, zSize - 1);\r\n\r\n for (let yi = 0; yi < ySize; ++yi) {\r\n const ym = clamp(yi - 1, 0, ySize - 1);\r\n const yp = clamp(yi + 1, 0, ySize - 1);\r\n\r\n for (let xi = 0; xi < xSize; ++xi) {\r\n const xm = clamp(xi - 1, 0, xSize - 1);\r\n const xp = clamp(xi + 1, 0, xSize - 1);\r\n\r\n // Calculate the volume gradient at each grid cell.\r\n // Gradients are now stored unnormalized, since we need them in pure\r\n // form in order to draw field lines etc. Shading code will now have\r\n // to do renormalization for itself on-the-fly.\r\n\r\n // XXX this gradient is only correct for orthogonal grids, since\r\n // we're using the array index offsets rather to calculate the gradient\r\n // rather than voxel coordinate offsets. This will have to be\r\n // re-worked for non-orthogonal datasets.\r\n\r\n gradient.setValue(\r\n xi,\r\n yi,\r\n zi,\r\n (_voxelValue(xp, yi, zi) - _voxelValue(xm, yi, zi)) * vs.x,\r\n (_voxelValue(xi, yp, zi) - _voxelValue(xi, ym, zi)) * vs.y,\r\n (_voxelValue(xi, yi, zp) - _voxelValue(xi, yi, zm)) * vs.z,\r\n );\r\n }\r\n }\r\n }\r\n\r\n return gradient;\r\n }\r\n\r\n normalize() {\r\n const data = this._data;\r\n\r\n // get min/max\r\n let min = data[0];\r\n let max = data[0];\r\n for (let i = 1; i < data.length; ++i) {\r\n min = Math.min(min, data[i]);\r\n max = Math.max(max, data[i]);\r\n }\r\n\r\n const d = 1.0 / (max - min);\r\n if (d === 0) {\r\n return;\r\n }\r\n\r\n // normalize\r\n for (let i = 0; i < data.length; ++i) {\r\n data[i] = d * (data[i] - min);\r\n }\r\n }\r\n\r\n getTiledTextureStride() {\r\n return [this._dimX + 2, this._dimY + 2];\r\n }\r\n\r\n buildTiledTexture() {\r\n let tilesX = Math.ceil(Math.sqrt(this._dimZ * this._dimY / this._dimX));\r\n\r\n let width = tilesX * (this._dimX + 2) - 1;\r\n width = pow2ceil(width);\r\n tilesX = Math.floor(width / (this._dimX + 2));\r\n\r\n const tilesY = Math.ceil(this._dimZ / tilesX);\r\n let height = tilesY * (this._dimY + 2) - 1;\r\n height = pow2ceil(height);\r\n\r\n const data = new Uint8Array(width * height);\r\n\r\n let src;\r\n let dst;\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // process each pixel row of this tile row\r\n for (let row = 0; row < this._dimY; ++row) {\r\n src = tileRow * tilesX * this._planeElements + row * this._rowElements;\r\n dst = width * (tileRow * (this._dimY + 2) + row);\r\n // copy a series of rows through several XY planes\r\n for (let t = 0; t < tilesX; ++t) {\r\n // copy one row of one XY plane\r\n for (let x = 0; x < this._dimX; ++x) {\r\n data[dst++] = 255.0 * this._data[src++];\r\n }\r\n\r\n // repeat last pixel of previous tile\r\n data[dst++] = 255.0 * this._data[src - 1];\r\n\r\n if (t < tilesX - 1) {\r\n // skip to the same row of next XY plane\r\n src += this._planeElements - this._rowElements;\r\n // repeat first pixel of next tile\r\n data[dst++] = 255.0 * this._data[src];\r\n }\r\n }\r\n }\r\n }\r\n\r\n // fill pixels between tile rows with copy of edge pixels\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // copy last pixel row of this tile row to the following pixel row of the texture\r\n src = width * (tileRow * (this._dimY + 2) + this._dimY - 1);\r\n dst = src + width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n if (tileRow < tilesY - 1) {\r\n // copy first pixel row of next tile row to the preceding pixel row of the texture\r\n src = width * (tileRow + 1) * (this._dimY + 2);\r\n dst = src - width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n }\r\n }\r\n\r\n const texture = new THREE.DataTexture(\r\n data,\r\n width,\r\n height,\r\n THREE.LuminanceFormat,\r\n THREE.UnsignedByteType,\r\n THREE.UVMapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.LinearFilter,\r\n THREE.LinearFilter,\r\n );\r\n texture.needsUpdate = true;\r\n return texture;\r\n }\r\n\r\n /* ********************************************************************************\r\n *\r\n * Methods that provide direct access to internal array (for better performance)\r\n *\r\n ******************************************************************************** */\r\n\r\n getData() {\r\n return this._data;\r\n }\r\n\r\n getDirectIdx(x, y, z) {\r\n return x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n }\r\n\r\n getStrideX() {\r\n return this._dimVec;\r\n }\r\n\r\n getStrideY() {\r\n return this._rowElements;\r\n }\r\n\r\n getStrideZ() {\r\n return this._planeElements;\r\n }\r\n}\r\n\r\nVolume.prototype.id = 'Volume';\r\n\r\nexport default Volume;\r\n","/**\r\n * Residue Molecule.\r\n *\r\n * @param {Complex} complex - Molecular complex this Molecule belongs to.\r\n * @param {String} name - Molecule's name.\r\n * @param {Integer} index - Molecule's index in file.\r\n *\r\n * @exports Molecule\r\n * @constructor\r\n */\r\nclass Molecule {\r\n constructor(complex, name, index) {\r\n this.complex = complex;\r\n this.name = name || '';\r\n this.residues = [];\r\n this.mask = 1 | 0;\r\n this.index = index || -1; // start with 1\r\n }\r\n\r\n forEachResidue(process) {\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this.mask = mask;\r\n }\r\n}\r\n\r\nexport default Molecule;\r\n","import Atom from './chem/Atom';\r\nimport Element from './chem/Element';\r\nimport Bond from './chem/Bond';\r\nimport Residue from './chem/Residue';\r\nimport ResidueType from './chem/ResidueType';\r\nimport Chain from './chem/Chain';\r\nimport Helix from './chem/Helix';\r\nimport Strand from './chem/Strand';\r\nimport Sheet from './chem/Sheet';\r\nimport SGroup from './chem/SGroup';\r\nimport Assembly from './chem/Assembly';\r\nimport Complex from './chem/Complex';\r\nimport Volume from './chem/Volume';\r\nimport VoxelWorld from './chem/VoxelWorld';\r\nimport selectors from './chem/selectors';\r\nimport Molecule from './chem/Molecule';\r\n\r\nexport default {\r\n Atom,\r\n Element,\r\n Bond,\r\n Residue,\r\n ResidueType,\r\n Chain,\r\n Helix,\r\n Strand,\r\n Sheet,\r\n SGroup,\r\n Assembly,\r\n Complex,\r\n Volume,\r\n VoxelWorld,\r\n selectors,\r\n Molecule,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\n\r\nclass CSS2DObject extends THREE.Object3D {\r\n constructor(element) {\r\n super();\r\n const self = this;\r\n this._element = element;\r\n this._element.style.position = 'absolute';\r\n this.addEventListener('removed', () => {\r\n if (self._element.parentNode !== null) {\r\n self._element.parentNode.removeChild(self._element);\r\n }\r\n });\r\n }\r\n\r\n getElement() {\r\n return this._element;\r\n }\r\n\r\n /**\r\n * Sets label transparency.\r\n *\r\n * @param {number} transp - in [0; 1] 1 means fully transparent\r\n */\r\n setTransparency(transp) {\r\n const el = this.getElement();\r\n if (el === null) {\r\n return;\r\n }\r\n if (transp === 1.0) {\r\n el.style.display = 'none';\r\n return;\r\n }\r\n el.style.display = 'inline';\r\n const op = 1.0 - transp;\r\n const top = op.toString();\r\n const op100 = op * 100;\r\n el.style.opacity = top;\r\n el.style.filter = `alpha(opacity=${op100})`; // IE fallback\r\n }\r\n\r\n clone() {\r\n const obj = new CSS2DObject(this._element);\r\n obj.copy(this);\r\n return obj;\r\n }\r\n}\r\n\r\nexport default CSS2DObject;\r\n","import * as THREE from 'three';\r\n\r\nclass RCGroup extends THREE.Group {\r\n raycast(raycaster, intersects) {\r\n if (!this.visible) {\r\n return;\r\n }\r\n\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n children[i].raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].enableSubset) {\r\n children[i].enableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].disableSubset) {\r\n children[i].disableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n isEmpty() {\r\n return this.children.length === 0;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].updateToFrame) {\r\n children[i].updateToFrame(frameData);\r\n }\r\n }\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n Array.prototype.push.apply(totalSubset, children[i].getSubset(mask, innerOnly));\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default RCGroup;\r\n","/* eslint-disable no-magic-numbers */\r\nimport * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport CSS2DObject from './CSS2DObject';\r\nimport RCGroup from './RCGroup';\r\nimport vertexScreenQuadShader from './shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromTex from './shaders/ScreenQuadFromTex.frag';\r\nimport fragmentScreenQuadFromTexWithDistortion from './shaders/ScreenQuadFromTexWithDistortion.frag';\r\n\r\nconst LAYERS = {\r\n DEFAULT: 0, VOLUME: 1, TRANSPARENT: 2, PREPASS_TRANSPARENT: 3, VOLUME_BFPLANE: 4, COLOR_FROM_POSITION: 5, SHADOWMAP: 6,\r\n};\r\n\r\nconst SELECTION_LAYERS = [ // These layers, that are used in the selection by ray casting\r\n LAYERS.DEFAULT, LAYERS.TRANSPARENT,\r\n];\r\n\r\nTHREE.Object3D.prototype.resetTransform = function () {\r\n this.position.set(0, 0, 0);\r\n this.quaternion.set(0, 0, 0, 1);\r\n this.scale.set(1, 1, 1);\r\n};\r\n\r\n// update world matrix of this object and all its ancestors\r\nTHREE.Object3D.prototype.updateMatrixWorldRecursive = function () {\r\n if (this.parent != null) {\r\n this.parent.updateMatrixWorldRecursive();\r\n }\r\n this.updateMatrixWorld();\r\n};\r\n// add object to parent, saving objects' world transform\r\nTHREE.Object3D.prototype.addSavingWorldTransform = (function () {\r\n const _worldMatrixInverse = new THREE.Matrix4();\r\n\r\n return function (object) {\r\n if (object instanceof THREE.Object3D) {\r\n _worldMatrixInverse.copy(this.matrixWorld).invert();\r\n _worldMatrixInverse.multiply(object.matrixWorld);\r\n object.matrix.copy(_worldMatrixInverse);\r\n object.matrix.decompose(object.position, object.quaternion, object.scale);\r\n this.add(object);\r\n }\r\n };\r\n}());\r\n\r\n// render a tiny transparent quad in the center of the screen\r\nTHREE.WebGLRenderer.prototype.renderDummyQuad = (function () {\r\n const _material = new THREE.MeshBasicMaterial({ transparent: true, opacity: 0.0, depthWrite: false });\r\n\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(0.01, 0.01), _material);\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function () {\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuad = (function () {\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(1.0, 1.0));\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function (material) {\r\n _quad.material = material;\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.isIdentity = (function () {\r\n const identity = new THREE.Matrix4();\r\n return function () {\r\n return identity.equals(this);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.applyToPointsArray = function (array, stride, w) {\r\n if (!array || !stride || stride < 3) {\r\n return array;\r\n }\r\n w = w || 0; // use point as normal by default\r\n const e = this.elements;\r\n for (let i = 0; i < array.length; i += stride) {\r\n const x = array[i];\r\n const y = array[i + 1];\r\n const z = array[i + 2];\r\n\r\n const persp = 1 / (e[3] * x + e[7] * y + e[11] * z + e[15]);\r\n\r\n array[i] = (e[0] * x + e[4] * y + e[8] * z + e[12] * w) * persp;\r\n array[i + 1] = (e[1] * x + e[5] * y + e[9] * z + e[13] * w) * persp;\r\n array[i + 2] = (e[2] * x + e[6] * y + e[10] * z + e[14] * w) * persp;\r\n }\r\n return array;\r\n};\r\n\r\nclass ScreenQuadMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n if (params.uniforms === undefined) {\r\n params.uniforms = {};\r\n }\r\n params.uniforms.srcTex = { type: 't', value: null };\r\n params.vertexShader = vertexScreenQuadShader;\r\n params.transparent = false;\r\n params.depthTest = false;\r\n params.depthWrite = false;\r\n super(params);\r\n }\r\n}\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTex = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { opacity: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTex,\r\n transparent: true,\r\n });\r\n\r\n return function (srcTex, opacity) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.transparent = (opacity < 1.0);\r\n _material.uniforms.opacity.value = opacity;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTexWithDistortion = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { coef: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTexWithDistortion,\r\n });\r\n\r\n return function (srcTex, coef) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.uniforms.coef.value = coef;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\n/**\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setMinimalFov = function (angle) {\r\n if (this.aspect >= 1.0) {\r\n this.fov = angle;\r\n } else {\r\n this.fov = THREE.MathUtils.radToDeg(2 * Math.atan(Math.tan(THREE.MathUtils.degToRad(angle) * 0.5) / this.aspect));\r\n }\r\n};\r\n\r\n/**\r\n * @param {THREE.PerspectiveCamera} camera - Base camera for this stereo camera.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.StereoCamera.prototype.updateHalfSized = function (camera, angle) {\r\n const originalAspect = camera.aspect;\r\n const originalFov = camera.fov;\r\n\r\n camera.aspect = originalAspect / 2.0;\r\n camera.setMinimalFov(angle);\r\n camera.updateProjectionMatrix();\r\n\r\n this.update(camera);\r\n\r\n camera.aspect = originalAspect;\r\n camera.fov = originalFov;\r\n camera.updateProjectionMatrix();\r\n};\r\n\r\n/**\r\n * @param {number} radius - Radius of bounding sphere in angstroms to fit on screen.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setDistanceToFit = function (radius, angle) {\r\n this.position.z = radius / Math.sin(0.5 * THREE.MathUtils.degToRad(angle));\r\n};\r\n\r\n/**\r\n * @param {RCGroup} gfxObj - All objects on scene.\r\n * @param {THREE.PerspectiveCamera} camera - Camera used for rendering.\r\n * @param {number} clipPlane - Distance to clip plane.\r\n * @param {number} fogFarPlane - Distance to fog far plane.\r\n */\r\nTHREE.Raycaster.prototype.intersectVisibleObject = function (gfxObj, camera, clipPlane, fogFarPlane) {\r\n const intersects = this.intersectObject(gfxObj, false);\r\n if (intersects.length === 0) {\r\n return null;\r\n }\r\n\r\n // find point closest to camera that doesn't get clipped by camera near plane or clipPlane (if it exists)\r\n const nearPlane = Math.min(camera.near, clipPlane);\r\n let i;\r\n let p = intersects[0];\r\n const v = new THREE.Vector3();\r\n for (i = 0; i < intersects.length; ++i) {\r\n p = intersects[i];\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -nearPlane) {\r\n break;\r\n }\r\n }\r\n if (i === intersects.length) {\r\n return null;\r\n }\r\n\r\n // check that selected intersection point is not clipped by camera far plane or occluded by fog (if it exists)\r\n const farPlane = Math.min(camera.far, fogFarPlane);\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -farPlane) {\r\n return null;\r\n }\r\n return p;\r\n};\r\n\r\nTHREE.Matrix4.prototype.extractScale = (function () {\r\n const _v = new THREE.Vector3();\r\n\r\n return function (scale) {\r\n if (scale === undefined) {\r\n logger.debug('extractScale(): new is too expensive operation to do it on-the-fly');\r\n scale = _v.clone();\r\n }\r\n\r\n const te = this.elements;\r\n scale.x = _v.set(te[0], te[1], te[2]).length();\r\n scale.y = _v.set(te[4], te[5], te[6]).length();\r\n scale.z = _v.set(te[8], te[9], te[10]).length();\r\n\r\n // if determine is negative, we need to invert one scale\r\n const det = this.determinant();\r\n if (det < 0) {\r\n scale.x = -scale.x;\r\n }\r\n return scale;\r\n };\r\n}());\r\n\r\nfunction _calcCylinderMatrix(posBegin, posEnd, radius) {\r\n const posCenter = posBegin.clone().lerp(posEnd, 0.5);\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(radius, posBegin.distanceTo(posEnd), radius);\r\n\r\n const matRotHalf = new THREE.Matrix4();\r\n matRotHalf.makeRotationX(Math.PI / 2);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n const vUp = new THREE.Vector3(0, 1, 0);\r\n matRotLook.lookAt(posCenter, posEnd, vUp);\r\n\r\n matRotLook.multiply(matRotHalf);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(posCenter);\r\n return matRotLook;\r\n}\r\n\r\nfunction _calcChunkMatrix(eye, target, up, rad) {\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(rad.x, rad.y, 0);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n matRotLook.lookAt(eye, target, up);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(eye);\r\n\r\n return matRotLook;\r\n}\r\n\r\nfunction _groupHasGeometryToRender(group) {\r\n let hasGeoms = false;\r\n group.traverse((node) => {\r\n if (node.hasOwnProperty('geometry') || node instanceof CSS2DObject) {\r\n hasGeoms = true;\r\n }\r\n });\r\n return hasGeoms;\r\n}\r\n\r\nfunction _buildDistorionMesh(widthSegments, heightSegements, coef) {\r\n // solve equation r_u = r_d * (1 + k * r_d^2)\r\n // for r_d using iterations\r\n // takes: r_u^2\r\n // returns: r_d / r_u factor that can be used to distort point coords\r\n function calcInverseBarrel(r2) {\r\n const epsilon = 1e-5;\r\n let prevR2 = 0.0;\r\n let curR2 = r2;\r\n let dr = 1.0;\r\n while (Math.abs(curR2 - prevR2) > epsilon) {\r\n dr = 1.0 + coef * curR2;\r\n prevR2 = curR2;\r\n curR2 = r2 / (dr * dr);\r\n }\r\n\r\n return 1.0 / dr;\r\n }\r\n\r\n const geo = new THREE.PlaneGeometry(2.0, 2.0, widthSegments, heightSegements);\r\n\r\n const pos = geo.getAttribute('position');\r\n for (let i = 0; i < pos.count; ++i) {\r\n const x = pos.array[3 * i];\r\n const y = pos.array[3 * i + 1];\r\n const c = calcInverseBarrel(x * x + y * y);\r\n pos.setXY(i, c * x, c * y);\r\n }\r\n\r\n return geo;\r\n}\r\n\r\nTHREE.BufferAttribute.prototype.copyAtList = function (attribute, indexList) {\r\n console.assert(\r\n this.itemSize === attribute.itemSize,\r\n 'DEBUG: BufferAttribute.copyAtList buffers have different item size.',\r\n );\r\n const { itemSize } = this;\r\n for (let i = 0, n = indexList.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n this.array[i * itemSize + j] = attribute.array[indexList[i] * itemSize + j];\r\n }\r\n }\r\n return this;\r\n};\r\n\r\nfunction fillArray(array, value, startIndex, endIndex) {\r\n startIndex = (typeof startIndex !== 'undefined') ? startIndex : 0;\r\n endIndex = (typeof endIndex !== 'undefined') ? endIndex : array.length;\r\n for (let i = startIndex; i < endIndex; ++i) {\r\n array[i] = value;\r\n }\r\n}\r\n\r\n/** @param {THREE.Object3D} object - Parent object. */\r\nfunction removeChildren(object) {\r\n const { children } = object;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n child.parent = null;\r\n child.dispatchEvent({ type: 'removed' });\r\n }\r\n object.children = [];\r\n}\r\n\r\nfunction clearTree(object) {\r\n object.traverse((obj) => {\r\n if (obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line) {\r\n obj.geometry.dispose();\r\n }\r\n });\r\n removeChildren(object);\r\n}\r\n\r\nfunction destroyObject(object) {\r\n clearTree(object);\r\n if (object.parent) {\r\n object.parent.remove(object);\r\n } else {\r\n object.dispatchEvent({ type: 'removed' });\r\n }\r\n}\r\n\r\nfunction belongToSelectLayers(object) {\r\n for (let i = 0; i < SELECTION_LAYERS.length; i++) {\r\n if (((object.layers.mask >> SELECTION_LAYERS[i]) & 1) === 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n}\r\n\r\nfunction processObjRenderOrder(root, idMaterial) {\r\n // set renderOrder to 0 for Backdrop and to 1 in other cases to render Backdrop earlier all other materials\r\n const renderOrder = +(idMaterial !== 'BA');\r\n root.traverse((object) => {\r\n if (object.isGroup) {\r\n object.renderOrder = renderOrder;\r\n }\r\n });\r\n}\r\n\r\nfunction applySelectionMaterial(geo) {\r\n geo.traverse((node) => {\r\n if ('material' in node) {\r\n node.material = node.material.clone(true);\r\n // using z-offset to magically fix selection rendering artifact (on z-sprites)\r\n node.material.setValues({\r\n depthFunc: THREE.LessEqualDepth,\r\n overrideColor: true,\r\n fog: false,\r\n lights: false,\r\n shadowmap: false,\r\n });\r\n node.material.setUberOptions({ fixedColor: new THREE.Color(0xFFFF00), zOffset: -1e-6 });\r\n }\r\n });\r\n}\r\n\r\nfunction getMiddlePoint(point1, point2, optionalTarget) {\r\n const result = optionalTarget || new THREE.Vector3();\r\n\r\n result.set(0, 0, 0);\r\n result.addScaledVector(point1, 0.5);\r\n result.addScaledVector(point2, 0.5);\r\n\r\n return result;\r\n}\r\n\r\n// Monkey-patch for \"InstancedBufferGeometry.instanceCount becomes undefined after copy()\"\r\n// https://github.com/mrdoob/three.js/issues/22151\r\nconst _oldInstancedBufferGeometryCopy = THREE.InstancedBufferGeometry.prototype.copy;\r\n\r\nTHREE.InstancedBufferGeometry.prototype.copy = function (source) {\r\n _oldInstancedBufferGeometryCopy.call(this, source);\r\n if (this.instanceCount === undefined) {\r\n this.instanceCount = Infinity;\r\n }\r\n};\r\n\r\nexport default {\r\n calcCylinderMatrix: _calcCylinderMatrix,\r\n calcChunkMatrix: _calcChunkMatrix,\r\n groupHasGeometryToRender: _groupHasGeometryToRender,\r\n buildDistorionMesh: _buildDistorionMesh,\r\n RCGroup,\r\n fillArray,\r\n clearTree,\r\n destroyObject,\r\n belongToSelectLayers,\r\n processObjRenderOrder,\r\n applySelectionMaterial,\r\n getMiddlePoint,\r\n LAYERS,\r\n};\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfx/gfxutils';\r\n\r\nconst _defaultBoundaries = {\r\n boundingBox: new THREE.Box3(new THREE.Vector3(-1, -1, -1), new THREE.Vector3(1, 1, 1)),\r\n boundingSphere: new THREE.Sphere(new THREE.Vector3(0, 0, 0), 1),\r\n};\r\n\r\nclass Visual extends gfxutils.RCGroup {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this.name = name;\r\n this._dataSource = dataSource;\r\n }\r\n\r\n release() {\r\n if (this.parent) {\r\n this.parent.remove(this);\r\n }\r\n }\r\n\r\n getDataSource() {\r\n return this._dataSource;\r\n }\r\n\r\n getBoundaries() {\r\n return _defaultBoundaries;\r\n }\r\n}\r\n\r\nexport default Visual;\r\n","function _ensureArray(x) {\r\n if (x === null || x === undefined || Array.isArray(x)) {\r\n return x;\r\n }\r\n return [x];\r\n}\r\n\r\n/** An indexed list of objects or classes. */\r\nclass EntityList {\r\n /**\r\n * Create a list of objects.\r\n * The objects can be indexed by one or more properties for the later retrieval.\r\n *\r\n * @param {!Array=} entities A list of objects to automatically register at creation time.\r\n * @param {!Array=} indices A list of property names to use for case-insensitive indexing.\r\n * By default, a single `.id` property is used.\r\n * @see EntityList#register\r\n */\r\n constructor(entities = [], indices = ['id']) {\r\n this._list = [];\r\n this._dict = {};\r\n this._indices = [...indices];\r\n this._indices.forEach((index) => {\r\n this._dict[index] = {};\r\n });\r\n\r\n entities.forEach((entity) => this.register(entity));\r\n }\r\n\r\n /**\r\n * Add a value to the end of a list.\r\n * The list will contain only one copy of the value.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromList\r\n * @see EntityList.registerInDict\r\n */\r\n static registerInList(list, value) {\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n }\r\n\r\n /**\r\n * Remove a value from a list if it is there.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to remove.\r\n * @see EntityList.registerInList\r\n */\r\n static unregisterFromList(list, value) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n }\r\n\r\n /**\r\n * Add a value to a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromDict\r\n * @see EntityList.registerInList\r\n */\r\n static registerInDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key] = dict[key] || [];\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Remove a value from a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.registerInDict\r\n */\r\n static unregisterFromDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key];\r\n if (list) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n if (list.length === 0) {\r\n delete dict[key];\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Add an entity to this list.\r\n *\r\n * @param {!Object} entity An object or a class to register. The object must include all\r\n * properties specified as indices on construction.\r\n * @see EntityList#unregister\r\n */\r\n register(entity) {\r\n EntityList.registerInList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.registerInDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * Remove an entity from this list.\r\n *\r\n * @param {!Object} entity An object or a class to unregister. The object may be\r\n * missing from the list but it must include all properties specified as indices\r\n * on construction.\r\n * @see EntityList#register\r\n */\r\n unregister(entity) {\r\n EntityList.unregisterFromList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.unregisterFromDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * An ordered list of all registered entities.\r\n * It is a read-only copy, use {@link EntityList#register} and {@link EntityList#unregister}\r\n * to modify it.\r\n *\r\n * @type {!Array}\r\n */\r\n get all() {\r\n return [...this._list];\r\n }\r\n\r\n /**\r\n * The first registered entity.\r\n * Use it if you do not care which entity you are referring to.\r\n *\r\n * @type {Object=}\r\n */\r\n get first() {\r\n return this._list[0];\r\n }\r\n\r\n /**\r\n * Retrieve a list of keys for the index.\r\n *\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {!Array} An unordered list of keys in the index, i.e. particular property\r\n * values for all registered entities.\r\n */\r\n keys(index) {\r\n return Object.keys(this._dict[index || this._indices[0]]);\r\n }\r\n\r\n /**\r\n * Retrieve an entity by its key.\r\n *\r\n * @param {string} key A case-insensitive property value to look-up.\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {Object=} An object registered in the index under the key. If there are multiple\r\n * objects under the same key, the first one is returned.\r\n */\r\n get(key, index) {\r\n const dict = this._dict[index || this._indices[0]];\r\n if (dict) {\r\n const values = dict[key && key.toLowerCase()];\r\n return values && values.length > 0 ? values[0] : undefined;\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nexport default EntityList;\r\n","import settings from '../settings';\r\nimport logger from './logger';\r\n\r\nfunction makeContextDependent(prototype) {\r\n Object.defineProperties(prototype, {\r\n logger: {\r\n get() {\r\n return this.context && this.context.logger ? this.context.logger : logger;\r\n },\r\n },\r\n settings: {\r\n get() {\r\n return this.context && this.context.settings ? this.context.settings : settings;\r\n },\r\n },\r\n });\r\n}\r\n\r\nexport default makeContextDependent;\r\n","import * as THREE from 'three';\r\n\r\nclass CollisionSphere {\r\n constructor(position, radius) {\r\n this._position = position;\r\n this._radius = radius;\r\n }\r\n\r\n static _sphere = new THREE.Sphere();\r\n\r\n raycast(raycaster) {\r\n const sphere = CollisionSphere._sphere;\r\n sphere.set(this._position, this._radius);\r\n\r\n const p = new THREE.Vector3();\r\n if (raycaster.ray.intersectSphere(sphere, p)) {\r\n return {\r\n distance: raycaster.ray.origin.distanceTo(p),\r\n point: p,\r\n };\r\n }\r\n return null;\r\n }\r\n}\r\n\r\nconst SphereCollisionGeo = (base) => class extends base {\r\n constructor(count, ...args) {\r\n super(...args);\r\n this._objects = new Array(count);\r\n this.boundingSphere = null;\r\n this.boundingBox = null;\r\n }\r\n\r\n setSphere(idx, position, radius) {\r\n this._objects[idx] = new CollisionSphere(position, radius);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n // TODO raycast with bounding sphere? How to deal with updates?\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const inters = this._objects[i].raycast(raycaster);\r\n if (inters) {\r\n inters.chunkIdx = i;\r\n intersects.push(inters);\r\n }\r\n }\r\n }\r\n\r\n computeBoundingBox() {\r\n const objects = this._objects;\r\n let { boundingBox } = this;\r\n if (boundingBox === null) {\r\n this.boundingBox = boundingBox = new THREE.Box3();\r\n }\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n boundingBox.expandByPoint(objects[i]._position);\r\n }\r\n }\r\n\r\n computeBoundingSphere() {\r\n this.computeBoundingBox();\r\n const objects = this._objects;\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n const pos = objects[i]._position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n if (this.boundingSphere === null) {\r\n this.boundingSphere = new THREE.Sphere();\r\n }\r\n this.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n};\r\nexport default SphereCollisionGeo;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst tmpColor = new THREE.Color();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\nclass InstancedSpheresGeometry extends SphereCollisionGeo(THREE.InstancedBufferGeometry) {\r\n constructor(spheresCount, sphereComplexity, useZSprites) {\r\n super(spheresCount);\r\n this._sphGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new THREE.SphereBufferGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI);\r\n this._init(spheresCount, this._sphGeometry);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n setArrayXYZW(this._offsets, itemIdx * OFFSET_SIZE, itemPos.x, itemPos.y, itemPos.z, itemRad);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n\r\n setColor(itemIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n setArrayXYZ(this._colors, itemIdx * COLOR_SIZE, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('offset').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[chunkIndices[i]] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._sphGeometry);\r\n\r\n copySubArrays(this._offsets, geom._offsets, chunkIndices, OFFSET_SIZE);\r\n copySubArrays(this._colors, geom._colors, chunkIndices, COLOR_SIZE);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(spheresCount, sphereGeo) {\r\n this.copy(sphereGeo);\r\n\r\n this._offsets = utils.allocateTyped(Float32Array, spheresCount * OFFSET_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, spheresCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('offset', new THREE.InstancedBufferAttribute(this._offsets, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._colors, COLOR_SIZE, false, 1));\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(alpha, 1, false, 1));\r\n }\r\n}\r\nexport default InstancedSpheresGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VEC_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n */\r\n\r\nclass ChunkedObjectsGeometry extends THREE.BufferGeometry {\r\n constructor(chunkGeo, chunksCount) {\r\n super();\r\n\r\n if (this.constructor === ChunkedObjectsGeometry) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n\r\n this._chunkGeo = chunkGeo;\r\n\r\n this._init(chunkGeo, chunksCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('normal').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n const idx = i * VEC_SIZE;\r\n colors[idx] = tmpColor.r;\r\n colors[idx + 1] = tmpColor.g;\r\n colors[idx + 2] = tmpColor.b;\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n _.fill(alphaArr, value, left, left + chunkSize);\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n // use THREE.Mesh raycasting interface for the Geometry. The Mesh is\r\n // created with existed geometry and default material, so it doesn't slowdown.\r\n const mesh = new THREE.Mesh();\r\n mesh.geometry = this;\r\n mesh.raycast(raycaster, inters);\r\n\r\n const facesPerChunk = this._chunkGeo.index.count / 3;\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('faceIndex')) {\r\n continue;\r\n }\r\n inters[i].chunkIdx = Math.floor(inters[i].faceIndex / facesPerChunk);\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.BufferGeometry();\r\n this._init.call(geom, this._chunkGeo, instanceCount);\r\n\r\n const srcPos = this._positions;\r\n const srcNorm = this._normals;\r\n const srcColor = this._colors;\r\n\r\n const dstPos = geom._positions;\r\n const dstNorm = geom._normals;\r\n const dstColor = geom._colors;\r\n\r\n const chunkSize = this._chunkSize * VEC_SIZE;\r\n\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const ptIdxBegin = chunkIndices[i] * chunkSize;\r\n const ptIdxEnd = ptIdxBegin + chunkSize;\r\n dstPos.set(srcPos.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstNorm.set(srcNorm.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstColor.set(srcColor.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n }\r\n\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(chunkGeo, chunksCount) {\r\n const chunkSize = this._chunkSize = chunkGeo.attributes.position.count;\r\n const chunkIndex = chunkGeo.index.array;\r\n const chunkIndexSize = chunkIndex.length;\r\n const pointsCount = this._chunkSize * chunksCount;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n const indexSize = chunkIndexSize * chunksCount;\r\n const index = this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, indexSize);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._normals = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n for (let i = 0; i < chunksCount; ++i) {\r\n const offset = i * chunkIndexSize;\r\n const posOffset = i * chunkSize;\r\n index.set(chunkIndex, offset);\r\n for (let j = 0; j < chunkIndexSize; ++j) {\r\n index[offset + j] += posOffset;\r\n }\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, VEC_SIZE));\r\n this.setAttribute('normal', new THREE.BufferAttribute(this._normals, VEC_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, VEC_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n }\r\n}\r\nexport default ChunkedObjectsGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst VEC_SIZE = 3;\r\n\r\nclass SimpleSpheresGeometry extends SphereCollisionGeo(ChunkedObjectsGeometry) {\r\n constructor(spheresCount, sphereComplexity) {\r\n const sphGeometry = new THREE.SphereBufferGeometry(\r\n 1,\r\n sphereComplexity * 2,\r\n sphereComplexity,\r\n 0,\r\n Math.PI * 2,\r\n 0,\r\n Math.PI,\r\n );\r\n super(spheresCount, sphGeometry, spheresCount);\r\n\r\n const normals = this._normals;\r\n const geoNormals = sphGeometry.attributes.normal.array;\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._tmpPositions = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n for (let i = 0; i < spheresCount; ++i) {\r\n normals.set(geoNormals, chunkSize * VEC_SIZE * i);\r\n }\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n const tmpPos = this._tmpPositions;\r\n const chunkSize = this._chunkSize;\r\n const geoPos = this._chunkPos;\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n const idx = i * 3;\r\n tmpPos[idx] = itemPos.x + geoPos[idx] * itemRad;\r\n tmpPos[idx + 1] = itemPos.y + geoPos[idx + 1] * itemRad;\r\n tmpPos[idx + 2] = itemPos.z + geoPos[idx + 2] * itemRad;\r\n }\r\n\r\n this._positions.set(tmpPos, chunkSize * itemIdx * VEC_SIZE);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n}\r\nexport default SimpleSpheresGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst centerPos = new THREE.Vector3();\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass Simple2CCylindersGeometry extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, 2 * instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const firstOffset = chunkSize * 2 * itemIdx * VEC_SIZE;\r\n const secondOffset = firstOffset + chunkSize * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n centerPos.lerpVectors(botPos, topPos, 0.5);\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, centerPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, firstOffset);\r\n\r\n // now shift center to get another part of the cylinder\r\n centerPos.sub(botPos);\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpArray[idx] += centerPos.x;\r\n tmpArray[idx + 1] += centerPos.y;\r\n tmpArray[idx + 2] += centerPos.z;\r\n }\r\n this._positions.set(tmpArray, secondOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, firstOffset);\r\n this._normals.set(tmpArray, secondOffset);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const first = 2 * itemIdx;\r\n super.setColor(first, colorVal1);\r\n\r\n const second = first + 1;\r\n super.setColor(second, colorVal2);\r\n }\r\n}\r\n\r\nexport default Simple2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_POINTS_COUNT_16BIT = 65536;\r\nconst PTS_PER_TRIANGLE = 3;\r\n\r\nclass CylinderBufferGeometry extends THREE.BufferGeometry {\r\n constructor(\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n ) {\r\n super();\r\n\r\n const thetaStart = 0;\r\n const thetaLength = 2 * Math.PI;\r\n\r\n this.type = 'CylinderBufferGeometry';\r\n\r\n this.parameters = {\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n };\r\n\r\n const hasTop = openEnded === false && radiusTop > 0;\r\n const hasBottom = openEnded === false && radiusBottom > 0;\r\n const vertexCount = (heightSegments + 1) * radialSegments\r\n + hasTop * (radialSegments + 1)\r\n + hasBottom * (radialSegments + 1);\r\n const facesCount = (2 * heightSegments + hasTop + hasBottom) * radialSegments;\r\n\r\n const heightHalf = height / 2;\r\n\r\n /* eslint-disable no-magic-numbers */\r\n const positions = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const normals = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const indices = new THREE.Uint16BufferAttribute(utils.allocateTyped(Uint16Array, facesCount * PTS_PER_TRIANGLE), 1);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n const uvs = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 2), 2);\r\n console.assert(vertexCount < MAX_POINTS_COUNT_16BIT, 'DEBUG: Cylinder Geometry has too many vertices (65536 max).');\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n const tanTheta = -(radiusBottom - radiusTop) / height;\r\n\r\n // setup cylinder data\r\n for (let y = 0; y <= heightSegments; y++) {\r\n // faces\r\n if (y !== heightSegments) {\r\n for (let i = 0; i < radialSegments; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + radialSegments + i;\r\n const v3 = currVtxIdx + radialSegments + ((i + 1) % radialSegments);\r\n const v4 = currVtxIdx + ((i + 1) % radialSegments);\r\n\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n // vertices\r\n const v = y / heightSegments;\r\n const radius = v * (radiusBottom - radiusTop) + radiusTop;\r\n\r\n for (let x = 0; x < radialSegments; x++) {\r\n const u = x / radialSegments;\r\n\r\n const vx = radius * Math.sin(u * thetaLength + thetaStart);\r\n const vy = v * height - heightHalf;\r\n const vz = radius * Math.cos(u * thetaLength + thetaStart);\r\n\r\n const normal = new THREE.Vector3(\r\n vx,\r\n Math.sqrt(vx * vx + vz * vz) * tanTheta,\r\n vz,\r\n ).normalize();\r\n\r\n positions.setXYZ(currVtxIdx, vx, vy, vz);\r\n normals.setXYZ(currVtxIdx, normal.x, normal.y, normal.z);\r\n uvs.setXY(currVtxIdx, u, v);\r\n ++currVtxIdx;\r\n }\r\n }\r\n\r\n // top cap\r\n if (hasTop) {\r\n const startTIdx = currVtxIdx;\r\n const lastIdx = currVtxIdx + radialSegments;\r\n for (let fTIdx = 0; fTIdx < radialSegments; ++fTIdx) {\r\n const currSrcIdx = currVtxIdx - radialSegments;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcIdx),\r\n positions.getY(currSrcIdx),\r\n positions.getZ(currSrcIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n\r\n const nextTVtx = startTIdx + ((fTIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, currVtxIdx, nextTVtx, lastIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n ++currVtxIdx;\r\n }\r\n\r\n // bottom cap\r\n if (hasBottom) {\r\n const startBIdx = currVtxIdx;\r\n const lastBIdx = currVtxIdx + radialSegments;\r\n for (let fBIdx = 0; fBIdx < radialSegments; ++fBIdx) {\r\n const currSrcBIdx = fBIdx;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcBIdx),\r\n positions.getY(currSrcBIdx),\r\n positions.getZ(currSrcBIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n\r\n const nextBVtx = startBIdx + ((fBIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, nextBVtx, currVtxIdx, lastBIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, -heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n }\r\n\r\n this.setIndex(indices);\r\n this.setAttribute('position', positions);\r\n this.setAttribute('normal', normals);\r\n this.setAttribute('uv', uvs);\r\n }\r\n\r\n clone() {\r\n const { parameters } = this;\r\n\r\n return new CylinderBufferGeometry(\r\n parameters.radiusTop,\r\n parameters.radiusBottom,\r\n parameters.height,\r\n parameters.radialSegments,\r\n parameters.heightSegments,\r\n parameters.openEnded,\r\n );\r\n }\r\n}\r\n\r\nexport default CylinderBufferGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport CylinderBufferGeometry from './CylinderBufferGeometry';\r\n\r\nconst tmpColor = new THREE.Color();\r\nconst invMatrix = new THREE.Matrix4();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction sortNumber(a, b) {\r\n return a - b;\r\n}\r\n\r\nfunction _prepareCylinderInfo(chunkIndices) {\r\n chunkIndices.sort(sortNumber);\r\n const chunksIdx = [];\r\n const cylinderInfo = [];\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const val = chunkIndices[i];\r\n const even = (val | 0) % 2 === 0;\r\n const newPar = {\r\n first: false,\r\n second: false,\r\n };\r\n if (even) {\r\n newPar.first = true;\r\n newPar.second = i + 1 < n && chunkIndices[i + 1] === chunkIndices[i] + 1;\r\n if (newPar.second) {\r\n ++i;\r\n }\r\n } else {\r\n newPar.second = true;\r\n }\r\n chunksIdx.push(Math.floor(val / 2));\r\n cylinderInfo.push(newPar);\r\n }\r\n return { indices: chunksIdx, cylinderInfo };\r\n}\r\n\r\nfunction _assignOpacity(cylinderInfo, color1, color2) {\r\n for (let i = 0, n = cylinderInfo.length; i < n; ++i) {\r\n const info = cylinderInfo[i];\r\n if (!info.first) {\r\n color1[COLOR_SIZE * i] = -0.5;\r\n }\r\n if (!info.second) {\r\n color2[COLOR_SIZE * i] = -0.5;\r\n }\r\n }\r\n}\r\nclass Instanced2CCylindersGeometry extends THREE.InstancedBufferGeometry {\r\n constructor(instanceCount, polyComplexity, useZSprites, openEnded) {\r\n super();\r\n this._useZSprites = useZSprites;\r\n this._cylGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new CylinderBufferGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, openEnded);\r\n this._init(instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n this._collisionGeo = new Simple2CCylindersGeometry(instanceCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const matrix = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n let me = matrix.elements;\r\n const mtxOffset = itemIdx * OFFSET_SIZE;\r\n\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, itemRad);\r\n setArrayXYZW(this._matVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._matVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._matVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n\r\n if (this._useZSprites) {\r\n invMatrix.copy(matrix).invert();\r\n me = invMatrix.elements;\r\n setArrayXYZW(this._invmatVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._invmatVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._invmatVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n }\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const colorIdx = itemIdx * COLOR_SIZE;\r\n tmpColor.set(colorVal1);\r\n setArrayXYZ(this._color1, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n tmpColor.set(colorVal2);\r\n setArrayXYZ(this._color2, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n computeBoundingSphere() {\r\n this._collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = this._collisionGeo.boundingSphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n this._collisionGeo.computeBoundingBox();\r\n this.boundingBox = this._collisionGeo.boundingBox;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('matVector1').needsUpdate = true;\r\n this.getAttribute('matVector2').needsUpdate = true;\r\n this.getAttribute('matVector3').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('color2').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n if (this._useZSprites) {\r\n this.getAttribute('invmatVector1').needsUpdate = true;\r\n this.getAttribute('invmatVector2').needsUpdate = true;\r\n this.getAttribute('invmatVector3').needsUpdate = true;\r\n }\r\n\r\n this._collisionGeo.finishUpdate();\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[Math.floor(chunkIndices[i] / 2)] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const info = _prepareCylinderInfo(chunkIndices);\r\n const cylinderIndices = info.indices;\r\n const instanceCount = cylinderIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n copySubArrays(this._matVector1, geom._matVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector2, geom._matVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector3, geom._matVector3, cylinderIndices, OFFSET_SIZE);\r\n\r\n if (this._useZSprites) {\r\n copySubArrays(this._invmatVector1, geom._invmatVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector2, geom._invmatVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector3, geom._invmatVector3, cylinderIndices, OFFSET_SIZE);\r\n }\r\n\r\n copySubArrays(this._color1, geom._color1, cylinderIndices, COLOR_SIZE);\r\n copySubArrays(this._color2, geom._color2, cylinderIndices, COLOR_SIZE);\r\n _assignOpacity(info.cylinderInfo, geom._color1, geom._color2);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n getGeoParams() {\r\n return this._cylGeometry.parameters;\r\n }\r\n\r\n _init(instanceCount, cylinderGeo, useZSprites) {\r\n this.copy(cylinderGeo);\r\n this._matVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._color1 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n this._color2 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, instanceCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('matVector1', new THREE.InstancedBufferAttribute(this._matVector1, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector2', new THREE.InstancedBufferAttribute(this._matVector2, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector3', new THREE.InstancedBufferAttribute(this._matVector3, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._color1, COLOR_SIZE, false, 1));\r\n this.setAttribute('color2', new THREE.InstancedBufferAttribute(this._color2, COLOR_SIZE, false, 1));\r\n\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(this._alpha, 1, false, 1));\r\n\r\n if (useZSprites) {\r\n this._invmatVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n\r\n this.setAttribute(\r\n 'invmatVector1',\r\n new THREE.InstancedBufferAttribute(this._invmatVector1, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector2',\r\n new THREE.InstancedBufferAttribute(this._invmatVector2, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector3',\r\n new THREE.InstancedBufferAttribute(this._invmatVector3, OFFSET_SIZE, false, 1),\r\n );\r\n }\r\n }\r\n}\r\n\r\nexport default Instanced2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst TRI_SIZE = 3;\r\nconst tmpPrev = new THREE.Vector3();\r\nconst tmpNext = new THREE.Vector3();\r\nconst tmpRes = new THREE.Vector3();\r\nconst simpleNormal = new THREE.Vector3(1.0, 0.0, 0.0);\r\nconst normalOnCut = new THREE.Vector3();\r\nconst nearRingPt = new THREE.Vector3();\r\n\r\nfunction _createExtrudedChunkGeometry(shape, ringsCount) {\r\n const geo = new THREE.BufferGeometry();\r\n const ptsCount = shape.length;\r\n const totalPts = ptsCount * ringsCount;\r\n const type = totalPts <= 65536 ? Uint16Array : Uint32Array;\r\n const facesPerChunk = (ringsCount - 1) * ptsCount * 2;\r\n const indices = new THREE.BufferAttribute(utils.allocateTyped(type, facesPerChunk * TRI_SIZE), 1);\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n for (let y = 0; y < ringsCount; y++) {\r\n // faces\r\n if (y !== ringsCount - 1) {\r\n for (let i = 0; i < ptsCount; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + ptsCount + i;\r\n const v3 = currVtxIdx + ptsCount + ((i + 1) % ptsCount);\r\n const v4 = currVtxIdx + ((i + 1) % ptsCount);\r\n\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n currVtxIdx += ptsCount;\r\n }\r\n\r\n geo.setIndex(indices);\r\n const pos = utils.allocateTyped(Float32Array, totalPts * VEC_SIZE);\r\n geo.setAttribute('position', new THREE.BufferAttribute(pos, VEC_SIZE));\r\n\r\n geo._positions = shape;\r\n\r\n return geo;\r\n}\r\n\r\nclass ExtrudedObjectsGeometry extends ChunkedObjectsGeometry {\r\n constructor(shape, ringsCount, chunksCount) {\r\n const chunkGeo = _createExtrudedChunkGeometry(shape, ringsCount);\r\n super(chunkGeo, chunksCount);\r\n this._ringsCount = ringsCount;\r\n\r\n const tmpShape = this._tmpShape = [];\r\n for (let i = 0; i < shape.length; ++i) {\r\n tmpShape[i] = new THREE.Vector3();\r\n }\r\n }\r\n\r\n setItem(itemIdx, matrices, hasSlope = false, hasCut = false) {\r\n const ptsCount = this._chunkGeo._positions.length;\r\n const ringsCount = this._ringsCount;\r\n const chunkStartIdx = ptsCount * this._ringsCount * itemIdx * VEC_SIZE;\r\n\r\n this._setPoints(matrices, ptsCount, ringsCount, chunkStartIdx);\r\n\r\n if (hasSlope) {\r\n this._setSlopeNormals(ptsCount, ringsCount, chunkStartIdx);\r\n } else {\r\n this._setBaseNormals(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n\r\n if (hasCut) {\r\n this._addCut(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n }\r\n\r\n _setPoints(matrices, ptsCount, ringsCount, chunkStartIdx) {\r\n const tmpShape = this._tmpShape;\r\n const positions = this._positions;\r\n const shape = this._chunkGeo._positions;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i) {\r\n const mtx = matrices[i];\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpShape[j].copy(shape[j]).applyMatrix4(mtx).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _setBaseNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, false);\r\n }\r\n }\r\n\r\n _setSlopeNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const normals = this._normals;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First ring\r\n // In all cases, besides cut, second ring is coincident to first. So values of first ring's normals doesn't\r\n // matter (In the cut case special handler will be applied later and will set them to correct values)\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n simpleNormal.toArray(normals, vtxIdx);\r\n }\r\n // second ring\r\n // If it isn't first Item we take normals' values from the last ring of the previous item (these rings are coincident)\r\n // else we count normals' values based on next ring information\r\n if (vtxIdx - 2 * nPtsInRing > 0) {\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(normals, vtxIdx - 2 * nPtsInRing).toArray(normals, vtxIdx);\r\n }\r\n } else {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, +nPtsInRing);\r\n vtxIdx += nPtsInRing;\r\n }\r\n // other rings\r\n // we count normals' values based on previous ring information\r\n for (let i = 2; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, -nPtsInRing);\r\n }\r\n }\r\n\r\n // Counting normals:\r\n // - Slope\r\n // Radius changes throught part => normals aren't parallel with the plane contains section points\r\n // normal = vTangentInSectionPlane x vToSuchPointInPrevSection (all vectors are scaled for being 1 in length)\r\n // - No slope\r\n // Radius doesn't change throught part => normals are parallel with the plane contains section points\r\n // normal = vToPrevPointInSection + vToNextPointInSection (all vectors are scaled for being 1 in length)\r\n _countNormalsInRing(ptsCount, vtxIdx, isSlope, shiftToExtraPt) {\r\n const tmpShape = this._tmpShape;\r\n const normals = this._normals;\r\n\r\n tmpShape[0].fromArray(this._positions, vtxIdx);\r\n tmpShape[ptsCount - 1].fromArray(this._positions, vtxIdx + (ptsCount - 1) * VEC_SIZE);\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n if (j < ptsCount - 1) {\r\n tmpShape[j + 1].fromArray(this._positions, vtxIdx + VEC_SIZE);\r\n }\r\n\r\n if (isSlope) {\r\n nearRingPt.fromArray(this._positions, vtxIdx + shiftToExtraPt);\r\n\r\n tmpPrev.subVectors(tmpShape[(j + ptsCount - 1) % ptsCount], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], nearRingPt).normalize();\r\n tmpRes.crossVectors(tmpNext, tmpPrev).normalize().toArray(normals, vtxIdx);\r\n } else {\r\n tmpPrev.subVectors(tmpShape[j], tmpShape[(j + ptsCount - 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpRes.addVectors(tmpPrev, tmpNext).normalize().toArray(normals, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _addCut(ptsCount, ringsCount, chunkStartIdx) {\r\n // Nothing to do if item is flat or only line\r\n if (ptsCount < 3 || ringsCount < 2) {\r\n return;\r\n }\r\n const positions = this._positions;\r\n const normals = this._normals;\r\n const tmpShape = this._tmpShape;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n // Normal to the cut plane is equal to cross product of two vectors which are lying in it\r\n tmpShape[0].fromArray(positions, chunkStartIdx);\r\n tmpShape[1].fromArray(positions, chunkStartIdx + VEC_SIZE);\r\n tmpShape[2].fromArray(positions, chunkStartIdx + 2 * VEC_SIZE);\r\n\r\n tmpPrev.subVectors(tmpShape[1], tmpShape[0]).normalize();\r\n tmpNext.subVectors(tmpShape[1], tmpShape[2]).normalize();\r\n normalOnCut.crossVectors(tmpPrev, tmpNext).normalize();\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First and second rings normals' values are equal to value of normal to the cutting plane\r\n for (let j = 0; j < ptsCount * 2; ++j, vtxIdx += VEC_SIZE) {\r\n normalOnCut.toArray(normals, vtxIdx);\r\n }\r\n if (ringsCount > 2) {\r\n // Third ring points are coincident to first ring points, but have different normals. It makes sharp angle near cut\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(positions, vtxIdx - nPtsInRing).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default ExtrudedObjectsGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VERTEX_PER_SEGMENT = 4;\r\nconst POS_SIZE = 4;\r\nconst DIR_SIZE = 3;\r\nconst COL_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\nconst direction = new THREE.Vector3();\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction getSubset(arr, startSegmentIdx, segmentsCount, elemSize) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT;\r\n const end = start + segmentsCount * VERTEX_PER_SEGMENT;\r\n return arr.subarray(start * elemSize, end * elemSize);\r\n}\r\n\r\n/**\r\n * This class represents lines geometry which consists of screen-aligned narrow quad of variable width.\r\n *\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * collision geometry.\r\n */\r\n\r\nclass ThickLinesGeometry extends THREE.BufferGeometry {\r\n constructor(segmentsCount) {\r\n super();\r\n this._initVertices(segmentsCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n this.getAttribute('direction').needsUpdate = true;\r\n }\r\n\r\n setColor(segmentIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n setSegment(segmentIdx, pos1, pos2) {\r\n direction.subVectors(pos1, pos2);\r\n direction.normalize();\r\n const positions = this._positions;\r\n const directions = this._directions;\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n let dirIdx = segmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n }\r\n\r\n setOpacity(startSegIdx, endSegIdx, value) {\r\n const start = startSegIdx * VERTEX_PER_SEGMENT;\r\n const end = endSegIdx * VERTEX_PER_SEGMENT;\r\n _.fill(this.alpha, value, end, start);\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubsetSegments(startSegmentIdx, segmentsCount) {\r\n return [\r\n getSubset(this._positions, startSegmentIdx, segmentsCount, POS_SIZE),\r\n getSubset(this._directions, startSegmentIdx, segmentsCount, DIR_SIZE),\r\n ];\r\n }\r\n\r\n getSubsetColors(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._colors, startSegmentIdx, segmentsCount, COL_SIZE);\r\n }\r\n\r\n getSubsetOpacities(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._alpha, startSegmentIdx, segmentsCount, 1);\r\n }\r\n\r\n getNumVertexPerSegment() {\r\n return VERTEX_PER_SEGMENT;\r\n }\r\n\r\n getPositionSize() {\r\n return POS_SIZE;\r\n }\r\n\r\n setSegments(startSegmentIdx, positions) {\r\n const startPos = startSegmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n if (positions instanceof Array && positions.length === 2) {\r\n this._positions.set(positions[0], startPos);\r\n const startDir = startSegmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n this._directions.set(positions[1], startDir); // dirs are geo part of vertex\r\n } else {\r\n this._positions.set(positions, startPos);\r\n }\r\n }\r\n\r\n setColors(startSegmentIdx, colors) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n this._colors.set(colors, start);\r\n }\r\n\r\n _initVertices(segmentsCount) {\r\n this._buffersSize = segmentsCount * VERTEX_PER_SEGMENT;\r\n const pointsCount = this._buffersSize;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, segmentsCount * 6);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * POS_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * COL_SIZE);\r\n this._directions = utils.allocateTyped(Float32Array, pointsCount * DIR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n const index = this._index;\r\n let indexOffset = 0;\r\n let pointOffset = 0;\r\n for (let j = 0; j < segmentsCount; j++, indexOffset += 6, pointOffset += VERTEX_PER_SEGMENT) {\r\n index[indexOffset] = pointOffset;\r\n index[indexOffset + 1] = pointOffset + 1;\r\n index[indexOffset + 2] = pointOffset + 3;\r\n index[indexOffset + 3] = pointOffset;\r\n index[indexOffset + 4] = pointOffset + 2;\r\n index[indexOffset + 5] = pointOffset + 3;\r\n }\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, POS_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, COL_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n this.setAttribute('direction', new THREE.BufferAttribute(this._directions, DIR_SIZE));\r\n }\r\n}\r\n\r\nexport default ThickLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport BaseLinesGeometry from './ThickLinesGeometry';\r\n\r\n/**\r\n * This class represents geometry which consists lines. This can build bounding volumes\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n */\r\nclass LinesGeometry extends BaseLinesGeometry {\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n if (boundingBox) {\r\n boundingBox.getCenter(center);\r\n }\r\n const positions = this._positions;\r\n const sphere = this.boundingSphere || new THREE.Sphere();\r\n const size = this._positions.length;\r\n const pos = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n pos.set(positions[i], positions[i + 1], positions[i + 2]);\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n sphere.set(center, Math.sqrt(radiusSquared));\r\n this.boundingSphere = sphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n const positions = this._positions;\r\n const box = new THREE.Box3();\r\n const size = this._positions.length;\r\n const tmpVec = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n tmpVec.set(positions[i], positions[i + 1], positions[i + 2]);\r\n box.expandByPoint(tmpVec);\r\n }\r\n this.boundingBox = box;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n}\r\n\r\nexport default LinesGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass CylinderCollisionGeo extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const itemOffset = chunkSize * itemIdx * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, itemOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, itemOffset);\r\n }\r\n}\r\nexport default CylinderCollisionGeo;\r\n","import LinesGeometry from './LinesGeometry';\r\nimport CylinderCollisionGeo from './CylinderCollisionGeo';\r\n\r\nconst COLLISION_RAD = 0.1;\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n *\r\n * @param {number} chunksCount Total chunks count.\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * @param {boolean} enableCollision Enable or disable collision where each segment is\r\n * a collidable cylinder.\r\n * collision geometry.\r\n */\r\nclass ChunkedLinesGeometry extends LinesGeometry {\r\n constructor(chunksCount, segmentsCount, enableCollision) {\r\n super(chunksCount * segmentsCount);\r\n this._init(segmentsCount);\r\n this._collisionGeo = enableCollision ? new CylinderCollisionGeo(chunksCount * segmentsCount, 3) : null;\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = collisionGeo.boundingSphere;\r\n return;\r\n }\r\n super.computeBoundingSphere();\r\n }\r\n\r\n computeBoundingBox() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingBox();\r\n this.boundingBox = collisionGeo.boundingBox;\r\n return;\r\n }\r\n super.computeBoundingBox();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const collisionGeo = this._collisionGeo;\r\n if (!collisionGeo) {\r\n return;\r\n }\r\n const segCount = this._chunkSize;\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n for (let i = 0, n = intersects.length; i < n; ++i) {\r\n let { chunkIdx } = intersects[i];\r\n if (chunkIdx === undefined) {\r\n continue;\r\n }\r\n chunkIdx = (chunkIdx / segCount) | 0;\r\n intersects[i].chunkIdx = chunkIdx;\r\n }\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n super.setColor(i, colorVal);\r\n }\r\n }\r\n\r\n setSegment(chunkIdx, segIdx, pos1, pos2) {\r\n const chunkSize = this._chunkSize;\r\n const idx = chunkIdx * chunkSize + segIdx;\r\n super.setSegment(idx, pos1, pos2);\r\n if (this._collisionGeo) {\r\n this._collisionGeo.setItem(chunkIdx * chunkSize + segIdx, pos1, pos2, COLLISION_RAD);\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n super.setOpacity(left, left + chunkSize - 1, value);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const chunkSize = this._chunkSize;\r\n const subset = new ChunkedLinesGeometry(instanceCount, chunkSize, false);\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const startSegIdx = chunkIndices[i] * chunkSize;\r\n subset.setSegments(dstPtOffset, this.getSubsetSegments(startSegIdx, chunkSize));\r\n subset.setColors(dstPtOffset, this.getSubsetColors(startSegIdx, chunkSize));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(chunkSize) {\r\n this._chunkSize = chunkSize;\r\n }\r\n}\r\n\r\nexport default ChunkedLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport LinesGeometry from './LinesGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\n\r\nconst COLLISION_RAD = 0.3;\r\nconst tmpVector = new THREE.Vector3();\r\n\r\nclass TwoColorLinesGeometry extends LinesGeometry {\r\n constructor(segmentsCount) {\r\n super(segmentsCount * 2);\r\n this._init(segmentsCount);\r\n this._collisionGeo = new Simple2CCylindersGeometry(segmentsCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos) {\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, COLLISION_RAD);\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n tmpVector.lerpVectors(botPos, topPos, 0.5);\r\n super.setSegment(offset, botPos, tmpVector);\r\n super.setSegment(offset + 1, tmpVector, topPos);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n super.setColor(offset, colorVal1);\r\n super.setColor(offset + 1, colorVal2);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n if (this._collisionGeo) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n getSubset(segmentIndices) {\r\n const instanceCount = segmentIndices.length;\r\n const subset = new TwoColorLinesGeometry(instanceCount, false);\r\n for (let i = 0, n = instanceCount; i < n; ++i) {\r\n const startSegIdx = segmentIndices[i];\r\n subset.setSegments(i, this.getSubsetSegments(startSegIdx, 1));\r\n subset.setColors(i, this.getSubsetColors(startSegIdx, 1));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(segmentsCount) {\r\n this._segCounts = segmentsCount * 2;\r\n }\r\n}\r\n// (???)parent = LinesGeometry.prototype;\r\n\r\nexport default TwoColorLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst vectors = [\r\n new THREE.Vector3(1, 0, 0),\r\n new THREE.Vector3(-1, 0, 0),\r\n new THREE.Vector3(0, 1, 0),\r\n new THREE.Vector3(0, -1, 0),\r\n new THREE.Vector3(0, 0, 1),\r\n new THREE.Vector3(0, 0, -1),\r\n];\r\nconst vecCount = vectors.length;\r\nconst tempPos1 = new THREE.Vector3();\r\nconst tempPos2 = new THREE.Vector3();\r\n\r\nclass CrossGeometry extends SphereCollisionGeo(ChunkedLinesGeometry) {\r\n constructor(chunksCount) {\r\n super(chunksCount, chunksCount, (vecCount / 2) | 0, false);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n\r\n for (let i = 0; i < vecCount / 2; ++i) {\r\n const first = i * 2;\r\n tempPos1.x = itemPos.x + vectors[first].x * itemRad;\r\n tempPos1.y = itemPos.y + vectors[first].y * itemRad;\r\n tempPos1.z = itemPos.z + vectors[first].z * itemRad;\r\n const second = first + 1;\r\n tempPos2.x = itemPos.x + vectors[second].x * itemRad;\r\n tempPos2.y = itemPos.y + vectors[second].y * itemRad;\r\n tempPos2.z = itemPos.z + vectors[second].z * itemRad;\r\n this.setSegment(itemIdx, i, tempPos1, tempPos2);\r\n }\r\n }\r\n}\r\nexport default CrossGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst POS_RAD_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This is a base class for isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\nclass IsoSurfaceGeometry extends THREE.BufferGeometry {\r\n constructor(spheresCount, opts) {\r\n super();\r\n\r\n this._opts = opts;\r\n this.zClip = this._opts.zClip;\r\n this._posRad = utils.allocateTyped(Float32Array, spheresCount * POS_RAD_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n }\r\n\r\n setItem(chunkIdx, pos, radius) {\r\n const posRad = this._posRad;\r\n let idx = POS_RAD_SIZE * chunkIdx;\r\n posRad[idx++] = pos.x;\r\n posRad[idx++] = pos.y;\r\n posRad[idx++] = pos.z;\r\n posRad[idx] = radius;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n let idx = COLOR_SIZE * chunkIdx;\r\n colors[idx++] = tmpColor.r;\r\n colors[idx++] = tmpColor.g;\r\n colors[idx] = tmpColor.b;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n finishUpdate() {\r\n this._build();\r\n }\r\n\r\n setOpacity() {\r\n // not implemented\r\n }\r\n\r\n raycast() {\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\nexport default IsoSurfaceGeometry;\r\n","import utils from '../../utils';\r\n\r\n/**\r\n * Class for marching cube\r\n * Stores 8 points and 8 float values are stored together in linear array\r\n * Int values for has intersection or not - in integer32 linear array\r\n * Int values for bits flags - in integer32 linear array\r\n *\r\n */\r\nclass IsoSurfaceMarchCube {\r\n constructor() {\r\n this.pointsValuesLinear = null;\r\n this.hasIntersection = null;\r\n this.bitsInside = null;\r\n }\r\n\r\n create(numCellsPerSide) {\r\n const vx7000000 = 0x7000000;\r\n const n3 = numCellsPerSide * numCellsPerSide * numCellsPerSide;\r\n if (n3 > vx7000000) {\r\n throw new Error('Too large cube dimension: lead to memory huge uasge');\r\n }\r\n this.pointsValuesLinear = utils.allocateTyped(Float32Array, (2 << (2 + 2)) * n3);\r\n this.hasIntersection = utils.allocateTyped(Int32Array, n3);\r\n this.bitsInside = utils.allocateTyped(Int32Array, n3);\r\n return 0;\r\n }\r\n\r\n destroy() {\r\n this.bitsInside = null;\r\n this.hasIntersection = null;\r\n this.pointsValuesLinear = null;\r\n }\r\n}\r\n\r\n/* eslint-disable no-magic-numbers */\r\nIsoSurfaceMarchCube.prototype.striIndicesMarchCube = [\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 0, 2, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 8, 3, 2, 10, 8, 10, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 8, 11, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 2, 1, 9, 11, 9, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 1, 11, 10, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 10, 1, 0, 8, 10, 8, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 9, 0, 3, 11, 9, 11, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 7, 3, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 1, 9, 4, 7, 1, 7, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 4, 7, 3, 0, 4, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 9, 0, 2, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 8, 4, 7, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 4, 7, 11, 2, 4, 2, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 8, 4, 7, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1, -1, -1, -1, -1,\r\n 3, 10, 1, 3, 11, 10, 7, 8, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4, -1, -1, -1, -1,\r\n 4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 4, 7, 11, 4, 11, 9, 9, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 1, 5, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 5, 4, 8, 3, 5, 3, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 10, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 2, 10, 5, 4, 2, 4, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8, -1, -1, -1, -1,\r\n 9, 5, 4, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 0, 8, 11, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 0, 1, 5, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5, -1, -1, -1, -1,\r\n 10, 3, 11, 10, 1, 3, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10, -1, -1, -1, -1,\r\n 5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 5, 4, 8, 5, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 5, 7, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 3, 0, 9, 5, 3, 5, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 8, 0, 1, 7, 1, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 9, 5, 7, 10, 1, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3, -1, -1, -1, -1,\r\n 8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2, -1, -1, -1, -1,\r\n 2, 10, 5, 2, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 9, 5, 7, 8, 9, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7, -1, -1, -1, -1,\r\n 11, 2, 1, 11, 1, 7, 7, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11, -1, -1, -1, -1,\r\n 5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0, -1,\r\n 11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0, -1,\r\n 11, 10, 5, 7, 11, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 1, 9, 8, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 2, 6, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 1, 2, 6, 3, 0, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 6, 5, 9, 0, 6, 0, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 0, 8, 11, 2, 0, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11, -1, -1, -1, -1,\r\n 6, 3, 11, 6, 5, 3, 5, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9, -1, -1, -1, -1,\r\n 6, 5, 9, 6, 9, 11, 11, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 4, 7, 3, 6, 5, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 5, 10, 6, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 6, 1, 2, 6, 5, 1, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7, -1, -1, -1, -1,\r\n 8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6, -1, -1, -1, -1,\r\n 7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9, -1,\r\n 3, 11, 2, 7, 8, 4, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1,\r\n 9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6, -1,\r\n 8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11, -1,\r\n 0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7, -1,\r\n 6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9, -1, -1, -1, -1,\r\n 10, 4, 9, 6, 4, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 10, 6, 4, 9, 10, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 0, 1, 10, 6, 0, 6, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 1, 4, 9, 1, 2, 4, 2, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4, -1, -1, -1, -1,\r\n 0, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 2, 8, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 4, 9, 10, 6, 4, 11, 2, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6, -1, -1, -1, -1,\r\n 3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1, -1,\r\n 9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3, -1, -1, -1, -1,\r\n 8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1, -1,\r\n 3, 11, 6, 3, 6, 0, 0, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 4, 8, 11, 6, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 10, 6, 7, 8, 10, 8, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10, -1, -1, -1, -1,\r\n 10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0, -1, -1, -1, -1,\r\n 10, 6, 7, 10, 7, 1, 1, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9, -1,\r\n 7, 8, 0, 7, 0, 6, 6, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 3, 2, 6, 7, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7, -1,\r\n 1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11, -1,\r\n 11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1, -1, -1, -1, -1,\r\n 8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6, -1,\r\n 0, 9, 1, 11, 6, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0, -1, -1, -1, -1,\r\n 7, 11, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 9, 8, 3, 1, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 8, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 9, 0, 2, 10, 9, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8, -1, -1, -1, -1,\r\n 7, 2, 3, 6, 2, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 0, 8, 7, 6, 0, 6, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 7, 6, 2, 3, 7, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6, -1, -1, -1, -1,\r\n 10, 7, 6, 10, 1, 7, 1, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8, -1, -1, -1, -1,\r\n 0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7, -1, -1, -1, -1,\r\n 7, 6, 10, 7, 10, 8, 8, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 8, 4, 11, 8, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 3, 0, 6, 0, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 6, 11, 8, 4, 6, 9, 0, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6, -1, -1, -1, -1,\r\n 6, 8, 4, 6, 11, 8, 2, 10, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6, -1, -1, -1, -1,\r\n 4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9, -1, -1, -1, -1,\r\n 10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3, -1,\r\n 8, 2, 3, 8, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8, -1, -1, -1, -1,\r\n 1, 9, 4, 1, 4, 2, 2, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1, -1, -1, -1, -1,\r\n 10, 1, 0, 10, 0, 6, 6, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3, -1,\r\n 10, 9, 4, 6, 10, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 5, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 1, 5, 4, 0, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5, -1, -1, -1, -1,\r\n 9, 5, 4, 10, 1, 2, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5, -1, -1, -1, -1,\r\n 7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2, -1, -1, -1, -1,\r\n 3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6, -1,\r\n 7, 2, 3, 7, 6, 2, 5, 4, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7, -1, -1, -1, -1,\r\n 3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0, -1, -1, -1, -1,\r\n 6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8, -1,\r\n 9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7, -1, -1, -1, -1,\r\n 1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4, -1,\r\n 4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10, -1,\r\n 7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10, -1, -1, -1, -1,\r\n 6, 9, 5, 6, 11, 9, 11, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5, -1, -1, -1, -1,\r\n 0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11, -1, -1, -1, -1,\r\n 6, 11, 3, 6, 3, 5, 5, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6, -1, -1, -1, -1,\r\n 0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10, -1,\r\n 11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5, -1,\r\n 6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3, -1, -1, -1, -1,\r\n 5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2, -1, -1, -1, -1,\r\n 9, 5, 6, 9, 6, 0, 0, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8, -1,\r\n 1, 5, 6, 2, 1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6, -1,\r\n 10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0, -1, -1, -1, -1,\r\n 0, 3, 8, 5, 6, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 5, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 7, 5, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 11, 7, 5, 8, 3, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 11, 7, 5, 10, 11, 1, 9, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1, -1, -1, -1, -1,\r\n 11, 1, 2, 11, 7, 1, 7, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11, -1, -1, -1, -1,\r\n 9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7, -1, -1, -1, -1,\r\n 7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2, -1,\r\n 2, 5, 10, 2, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2, -1, -1, -1, -1,\r\n 9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2, -1,\r\n 1, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 7, 0, 7, 1, 1, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 3, 9, 3, 5, 5, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 7, 5, 9, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 8, 4, 5, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5, -1, -1, -1, -1,\r\n 10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4, -1,\r\n 2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8, -1, -1, -1, -1,\r\n 0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11, -1,\r\n 0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5, -1,\r\n 9, 4, 5, 2, 11, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4, -1, -1, -1, -1,\r\n 5, 10, 2, 5, 2, 4, 4, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9, -1,\r\n 5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 3, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 5, 1, 0, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5, -1, -1, -1, -1,\r\n 9, 4, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 11, 7, 4, 9, 11, 9, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11, -1, -1, -1, -1,\r\n 1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11, -1, -1, -1, -1,\r\n 3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4, -1,\r\n 4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2, -1, -1, -1, -1,\r\n 9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3, -1,\r\n 11, 7, 4, 11, 4, 2, 2, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4, -1, -1, -1, -1,\r\n 2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9, -1, -1, -1, -1,\r\n 9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7, -1,\r\n 3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10, -1,\r\n 1, 10, 2, 8, 7, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 7, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1, -1, -1, -1, -1,\r\n 4, 0, 3, 7, 4, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 8, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1,\r\n 0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1,\r\n 1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n];\r\n/* eslint-enable no-magic-numbers */\r\n\r\nexport default IsoSurfaceMarchCube;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport utils from '../../utils';\r\n\r\nconst edgeTable = [\r\n 0x0, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c,\r\n 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00,\r\n 0x190, 0x99, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c,\r\n 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90,\r\n 0x230, 0x339, 0x33, 0x13a, 0x636, 0x73f, 0x435, 0x53c,\r\n 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30,\r\n 0x3a0, 0x2a9, 0x1a3, 0xaa, 0x7a6, 0x6af, 0x5a5, 0x4ac,\r\n 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0,\r\n 0x460, 0x569, 0x663, 0x76a, 0x66, 0x16f, 0x265, 0x36c,\r\n 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60,\r\n 0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0xff, 0x3f5, 0x2fc,\r\n 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0,\r\n 0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x55, 0x15c,\r\n 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950,\r\n 0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0xcc,\r\n 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0,\r\n 0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc,\r\n 0xcc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0,\r\n 0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c,\r\n 0x15c, 0x55, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650,\r\n 0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc,\r\n 0x2fc, 0x3f5, 0xff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0,\r\n 0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c,\r\n 0x36c, 0x265, 0x16f, 0x66, 0x76a, 0x663, 0x569, 0x460,\r\n 0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac,\r\n 0x4ac, 0x5a5, 0x6af, 0x7a6, 0xaa, 0x1a3, 0x2a9, 0x3a0,\r\n 0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c,\r\n 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x33, 0x339, 0x230,\r\n 0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c,\r\n 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x99, 0x190,\r\n 0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c,\r\n 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x0];\r\n\r\nfunction _voxelGradientFast(v, point, grad) {\r\n const g = v.getValue(point.x, point.y, point.z);\r\n grad.set(g[0], g[1], g[2]);\r\n}\r\n\r\n// Helper class GridCell\r\nclass GridCell {\r\n constructor() {\r\n this._arrSize = 8;\r\n this.p = new Array(this._arrSize);\r\n this.g = new Array(this._arrSize);\r\n this.val = new Array(this._arrSize);\r\n for (let i = 0; i < this._arrSize; ++i) {\r\n this.p[i] = new THREE.Vector3();\r\n this.g[i] = new THREE.Vector3();\r\n }\r\n this.cubeIndex = 0;\r\n }\r\n}\r\n\r\n// Helper class Triangle\r\nclass Triangle {\r\n constructor() {\r\n this.a = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.b = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.c = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n }\r\n}\r\n\r\nfunction createArray(arrSize) {\r\n const arr = new Array(arrSize);\r\n for (let i = 0; i < arrSize; ++i) {\r\n arr[i] = new THREE.Vector3();\r\n }\r\n\r\n return arr;\r\n}\r\n\r\nclass IsoSurface {\r\n constructor() {\r\n this._numTriangles = 0;\r\n this._numVertices = 0;\r\n this._position = [];\r\n this._normals = [];\r\n this._colors = null;\r\n this._indices = [];\r\n this._volumetricData = null;\r\n this._xAxis = new THREE.Vector3();\r\n this._yAxis = new THREE.Vector3();\r\n this._zAxis = new THREE.Vector3();\r\n this._xDir = new THREE.Vector3();\r\n this._yDir = new THREE.Vector3();\r\n this._zDir = new THREE.Vector3();\r\n }\r\n\r\n _prepareAxesAndDirs() {\r\n const volData = this._volumetricData;\r\n\r\n const cellSize = volData.getCellSize();\r\n\r\n // calculate cell axes\r\n const xAxis = this._xAxis;\r\n const yAxis = this._yAxis;\r\n const zAxis = this._zAxis;\r\n const xDir = this._xDir;\r\n const yDir = this._yDir;\r\n const zDir = this._zDir;\r\n\r\n xAxis.set(cellSize.x, 0, 0);\r\n yAxis.set(0, cellSize.y, 0);\r\n zAxis.set(0, 0, cellSize.z);\r\n\r\n xDir.set(1, 0, 0);\r\n yDir.set(0, 1, 0);\r\n zDir.set(0, 0, 1);\r\n\r\n // flip normals if coordinate system is in the wrong handedness\r\n const tmp = new THREE.Vector3();\r\n tmp.crossVectors(xDir, yDir);\r\n if (tmp.dot(zDir) < 0) {\r\n xDir.negate();\r\n yDir.negate();\r\n zDir.negate();\r\n }\r\n\r\n // check that the grid is in the all-positive octant of the coordinate system\r\n if (xDir.x < 0 || xDir.y < 0 || xDir.z < 0\r\n || yDir.x < 0 || yDir.y < 0 || yDir.z < 0\r\n || zDir.x < 0 || zDir.y < 0 || zDir.z < 0) {\r\n return false;\r\n }\r\n\r\n // check that the grid is axis-aligned\r\n const notZero = (axe) => Math.abs(axe) > Number.EPSILON;\r\n return !(notZero(xAxis.y) || notZero(xAxis.z)\r\n || notZero(yAxis.x) || notZero(yAxis.z)\r\n || notZero(zAxis.x) || notZero(zAxis.y));\r\n }\r\n\r\n _vertexInterp(isoLevel, grid, ind1, ind2, vertex, normal) {\r\n const p1 = grid.p[ind1];\r\n const p2 = grid.p[ind2];\r\n const n1 = grid.g[ind1];\r\n const n2 = grid.g[ind2];\r\n const valP1 = grid.val[ind1];\r\n const valP2 = grid.val[ind2];\r\n const isoDiffP1 = isoLevel - valP1;\r\n const diffValP2P1 = valP2 - valP1;\r\n\r\n let mu = 0.0;\r\n\r\n if (Math.abs(diffValP2P1) > 0.0) {\r\n mu = isoDiffP1 / diffValP2P1;\r\n }\r\n mu = mu > 1.0 ? 1.0 : mu;\r\n vertex.lerpVectors(p1, p2, mu);\r\n normal.lerpVectors(n1, n2, mu);\r\n }\r\n\r\n static _triTable = IsoSurfaceMarchCube.prototype.striIndicesMarchCube;\r\n\r\n static _arrSize = 12;\r\n\r\n static _firstIndices = [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3];\r\n\r\n static _secondIndices = [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7];\r\n\r\n static _vertexList = createArray(IsoSurface._arrSize);\r\n\r\n static _normalList = createArray(IsoSurface._arrSize);\r\n\r\n _polygonize(grid, isoLevel, triangles) {\r\n const { cubeIndex } = grid;\r\n let i = 0;\r\n const arrSize = IsoSurface._arrSize;\r\n const firstIndices = IsoSurface._firstIndices;\r\n const secondIndices = IsoSurface._secondIndices;\r\n const vertexList = IsoSurface._vertexList;\r\n const normalList = IsoSurface._normalList;\r\n\r\n for (; i < arrSize; ++i) {\r\n if (edgeTable[cubeIndex] & (1 << i)) {\r\n this._vertexInterp(\r\n isoLevel,\r\n grid,\r\n firstIndices[i],\r\n secondIndices[i],\r\n vertexList[i],\r\n normalList[i],\r\n );\r\n }\r\n }\r\n\r\n let triCount = 0;\r\n const triTblIdx = cubeIndex * 16;\r\n const triTable = IsoSurface._triTable;\r\n\r\n for (i = 0; triTable[triTblIdx + i] !== -1; i += 3) {\r\n triangles[triCount].a.p.copy(vertexList[triTable[triTblIdx + i]]);\r\n triangles[triCount].a.n.copy(normalList[triTable[triTblIdx + i]]);\r\n\r\n triangles[triCount].b.p.copy(vertexList[triTable[triTblIdx + i + 1]]);\r\n triangles[triCount].b.n.copy(normalList[triTable[triTblIdx + i + 1]]);\r\n\r\n triangles[triCount].c.p.copy(vertexList[triTable[triTblIdx + i + 2]]);\r\n triangles[triCount].c.n.copy(normalList[triTable[triTblIdx + i + 2]]);\r\n ++triCount;\r\n }\r\n\r\n return triCount;\r\n }\r\n\r\n _doGridPosNorms(isoValue, step, appendSimple) {\r\n const vol = this._volumetricData;\r\n const volData = this._volumetricData.getData();\r\n const dim = vol.getDimensions();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n const zSize = dim[2];\r\n const stepX = step * vol.getStrideX();\r\n const stepY = step * vol.getStrideY();\r\n const stepZ = step * vol.getStrideZ();\r\n\r\n const gc = new GridCell();\r\n const gcVal = gc.val;\r\n const gcValSize = gc.val.length;\r\n const additions = [\r\n new THREE.Vector3(0, 0, 0), // 0\r\n new THREE.Vector3(step, 0, 0), // 1\r\n new THREE.Vector3(step, step, 0), // 2\r\n new THREE.Vector3(0, step, 0), // 3\r\n new THREE.Vector3(0, 0, step), // 4\r\n new THREE.Vector3(step, 0, step), // 5\r\n new THREE.Vector3(step, step, step), // 6\r\n new THREE.Vector3(0, step, step), // 7\r\n ];\r\n\r\n const tmpTriCount = 5;\r\n const triangles = new Array(tmpTriCount);\r\n for (let j = 0; j < tmpTriCount; ++j) {\r\n triangles[j] = new Triangle();\r\n }\r\n\r\n let appendVertex;\r\n const self = this;\r\n const positions = this._position;\r\n const normals = this._normals;\r\n if (appendSimple) {\r\n // Special case for axis-aligned grid with positive unit vector normals\r\n appendVertex = (function () {\r\n const axis = new THREE.Vector3(self._xAxis.x, self._yAxis.y, self._zAxis.z);\r\n return function (triVertex) {\r\n const vertex = triVertex.p.clone();\r\n vertex.multiply(axis);\r\n positions.push(vertex.add(self._origin));\r\n normals.push(triVertex.n.clone());\r\n };\r\n }());\r\n } else {\r\n appendVertex = (function () {\r\n const posMtx = new THREE.Matrix3();\r\n posMtx.set(\r\n self._xAxis.x,\r\n self._yAxis.x,\r\n self._zAxis.x,\r\n self._xAxis.y,\r\n self._yAxis.y,\r\n self._zAxis.y,\r\n self._xAxis.z,\r\n self._yAxis.z,\r\n self._zAxis.z,\r\n );\r\n const normMtx = new THREE.Matrix3();\r\n normMtx.set(\r\n self._xDir.x,\r\n self._yDir.x,\r\n self._zDir.x,\r\n self._xDir.y,\r\n self._yDir.y,\r\n self._zDir.y,\r\n self._xDir.z,\r\n self._yDir.z,\r\n self._zDir.z,\r\n );\r\n\r\n return function (triVertex) {\r\n positions.push(triVertex.p.clone().applyMatrix3(posMtx).add(self._origin));\r\n normals.push(triVertex.n.clone().applyMatrix3(normMtx));\r\n };\r\n }());\r\n }\r\n const indices = this._indices;\r\n\r\n let globTriCount = 0;\r\n\r\n for (let z = 0; z < (zSize - step); z += step) {\r\n for (let y = 0; y < (ySize - step); y += step) {\r\n let idx = vol.getDirectIdx(0, y, z);\r\n for (let x = 0; x < (xSize - step); x += step, idx += stepX) {\r\n /* eslint-disable no-multi-spaces */\r\n /* eslint-disable computed-property-spacing */\r\n gcVal[0] = volData[idx];\r\n gcVal[1] = volData[idx + stepX];\r\n gcVal[3] = volData[idx + stepY];\r\n gcVal[2] = volData[idx + stepX + stepY];\r\n gcVal[4] = volData[idx + stepZ];\r\n gcVal[5] = volData[idx + stepX + stepZ];\r\n gcVal[7] = volData[idx + stepY + stepZ];\r\n gcVal[6] = volData[idx + stepX + stepY + stepZ];\r\n /* eslint-enable no-multi-spaces */\r\n /* eslint-enable computed-property-spacing */\r\n\r\n // Determine the index into the edge table which\r\n // tells us which vertices are inside of the surface\r\n let cubeIndex = 0;\r\n let i = 0;\r\n for (; i < gcValSize; ++i) {\r\n if (gcVal[i] < isoValue) {\r\n cubeIndex |= (1 << i);\r\n }\r\n }\r\n\r\n if (edgeTable[cubeIndex] === 0) {\r\n continue;\r\n }\r\n\r\n gc.cubeIndex = cubeIndex;\r\n for (i = 0; i < gcValSize; ++i) {\r\n gc.p[i].set(x + additions[i].x, y + additions[i].y, z + additions[i].z);\r\n _voxelGradientFast(this._gradient, gc.p[i], gc.g[i]);\r\n }\r\n\r\n // calculate vertices and facets for this cube,\r\n // calculate normals by interpolating between the negated\r\n // normalized volume gradients for the 8 reference voxels\r\n const triCount = this._polygonize(gc, isoValue, triangles);\r\n globTriCount += triCount;\r\n\r\n // append triangles using different techniques\r\n for (i = 0; i < triCount; ++i) {\r\n indices.push(this._numTriangles * 3);\r\n indices.push(this._numTriangles * 3 + 1);\r\n indices.push(this._numTriangles * 3 + 2);\r\n ++this._numTriangles;\r\n\r\n appendVertex(triangles[i].a);\r\n appendVertex(triangles[i].b);\r\n appendVertex(triangles[i].c);\r\n }\r\n }\r\n }\r\n }\r\n\r\n return globTriCount;\r\n }\r\n\r\n compute(volData, origin, isoValue, step) {\r\n this._volumetricData = volData;\r\n this._origin = origin;\r\n\r\n this._gradient = volData.computeGradient();\r\n\r\n this._doGridPosNorms(isoValue, step, this._prepareAxesAndDirs());\r\n }\r\n\r\n _remapIndices(vertexMap, idcCount) {\r\n const indices = this._indices;\r\n const newIndices = utils.allocateTyped(Uint32Array, idcCount);\r\n for (let i = 0; i < idcCount; ++i) {\r\n indices[i] = vertexMap[indices[i]];\r\n newIndices[i] = indices[i];\r\n }\r\n this._indices = newIndices;\r\n }\r\n\r\n _remapVertices(vertices, normals, count) {\r\n const newPositions = utils.allocateTyped(Float32Array, count * 3);\r\n const newNormals = utils.allocateTyped(Float32Array, count * 3);\r\n for (let i = 0; i < count; ++i) {\r\n const pos = vertices[i];\r\n newPositions[i * 3] = pos.x;\r\n newPositions[i * 3 + 1] = pos.y;\r\n newPositions[i * 3 + 2] = pos.z;\r\n const norm = normals[i].normalize();\r\n newNormals[i * 3] = norm.x;\r\n newNormals[i * 3 + 1] = norm.y;\r\n newNormals[i * 3 + 2] = norm.z;\r\n }\r\n this._position = newPositions;\r\n this._normals = newNormals;\r\n }\r\n\r\n vertexFusion(offset, len) {\r\n const faceVer = this._indices.length;\r\n const vertices = this._position;\r\n const normals = this._normals;\r\n const oldVerCount = vertices.length | 0;\r\n if (faceVer === 0 || oldVerCount === 0) {\r\n return;\r\n }\r\n const vMap = utils.allocateTyped(Uint32Array, oldVerCount);\r\n vMap[0] = 0;\r\n let newVer = 1;\r\n\r\n let i = 1;\r\n for (; i < oldVerCount; ++i) {\r\n const start = newVer - offset < 0 ? 0 : newVer - offset;\r\n const end = start + len > newVer ? newVer : start + len;\r\n let matchedIndex = -1;\r\n\r\n for (let j = start; j < end; ++j) {\r\n if (Math.abs(vertices[i] - vertices[j]) < Number.EPSILON) {\r\n matchedIndex = j;\r\n break;\r\n }\r\n }\r\n\r\n if (matchedIndex !== -1) {\r\n vMap[i] = matchedIndex;\r\n } else {\r\n vertices[newVer].copy(vertices[i]);\r\n normals[newVer].copy(normals[i]);\r\n vMap[i] = newVer;\r\n ++newVer;\r\n }\r\n }\r\n\r\n this._remapIndices(vMap, faceVer);\r\n this._remapVertices(vertices, normals, newVer);\r\n }\r\n\r\n // Assign per-vertex colors from a volumetric texture map (same dimensions as the original volumetric data).\r\n // Along with color dominating atom is determined for each vertex\r\n // and vertices with atom out of \"visible\" subset get filtered out.\r\n // XXX only handles orthogonal volumes currently\r\n setColorVolTex(colorMap, atomMap, atomWeightMap, visibilitySelector) {\r\n let i;\r\n let idx;\r\n const numVerts = this._position.length / 3;\r\n const vertices = this._position;\r\n const origin = this._origin;\r\n const dim = this._volumetricData.getDimensions();\r\n const xs = dim[0] - 1;\r\n const ys = dim[1] - 1;\r\n const zs = dim[2] - 1;\r\n\r\n const colorData = colorMap.getData();\r\n const strideX = colorMap.getStrideX();\r\n const strideY = colorMap.getStrideY();\r\n const strideZ = colorMap.getStrideZ();\r\n\r\n let atomWeightData;\r\n let atomStrideX;\r\n let atomStrideY;\r\n let atomStrideZ;\r\n\r\n if (visibilitySelector !== null) {\r\n atomWeightData = atomWeightMap.getData();\r\n atomStrideX = atomWeightMap.getStrideX();\r\n atomStrideY = atomWeightMap.getStrideY();\r\n atomStrideZ = atomWeightMap.getStrideZ();\r\n }\r\n\r\n const xInv = 1.0 / this._xAxis.x;\r\n const yInv = 1.0 / this._yAxis.y;\r\n const zInv = 1.0 / this._zAxis.z;\r\n\r\n let atomLookup = [];\r\n let atomWeights = [];\r\n const colors = utils.allocateTyped(Float32Array, numVerts * 3);\r\n\r\n function interp(mu, idx1, idx2, c) {\r\n c[0] = (1 - mu) * colorData[idx1] + mu * colorData[idx2];\r\n c[1] = (1 - mu) * colorData[idx1 + 1] + mu * colorData[idx2 + 1];\r\n c[2] = (1 - mu) * colorData[idx1 + 2] + mu * colorData[idx2 + 2];\r\n }\r\n\r\n function collectWeight(ai, coefX, coefY, coefZ) {\r\n const a = atomMap[ai]; // atomWeightMap is a scalar field, so index into atom map should be the same\r\n if (a != null) {\r\n atomLookup[a.index] = a;\r\n const w = coefX * coefY * coefZ * atomWeightData[ai];\r\n if (typeof atomWeights[a.index] === 'undefined') {\r\n atomWeights[a.index] = w;\r\n } else {\r\n atomWeights[a.index] += w;\r\n }\r\n }\r\n }\r\n\r\n const vMap = utils.allocateTyped(Int32Array, numVerts);\r\n let newVerCount = 0;\r\n\r\n for (i = 0; i < numVerts; i++) {\r\n const ind = i * 3;\r\n const vx = (vertices[ind] - origin.x) * xInv;\r\n const vy = (vertices[ind + 1] - origin.y) * yInv;\r\n const vz = (vertices[ind + 2] - origin.z) * zInv;\r\n const x = Math.min(Math.max(vx, 0), xs) | 0;\r\n const y = Math.min(Math.max(vy, 0), ys) | 0;\r\n const z = Math.min(Math.max(vz, 0), zs) | 0;\r\n\r\n const mux = (vx - x);\r\n const muy = (vy - y);\r\n const muz = (vz - z);\r\n\r\n if (visibilitySelector != null) {\r\n // collect atom weights\r\n atomLookup = [];\r\n atomWeights = [];\r\n idx = atomWeightMap.getDirectIdx(x, y, z);\r\n collectWeight(idx, 1 - mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideX, mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideY, 1 - mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideX + atomStrideY, mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideZ, 1 - mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideZ, mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideY + atomStrideZ, 1 - mux, muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideY + atomStrideZ, mux, muy, muz);\r\n\r\n // find dominant atom\r\n let maxWeight = 0.0;\r\n let dominantIdx = -1;\r\n for (const atomIdx in atomWeights) {\r\n if (atomWeights[atomIdx] > maxWeight) {\r\n dominantIdx = atomIdx;\r\n maxWeight = atomWeights[atomIdx];\r\n }\r\n }\r\n\r\n if (dominantIdx < 0 || !visibilitySelector.includesAtom(atomLookup[dominantIdx])) {\r\n // this vertex doesn't belong to visible subset and will be skipped\r\n vMap[i] = -1;\r\n continue;\r\n }\r\n }\r\n\r\n vMap[i] = newVerCount++;\r\n\r\n // color tri-linear interpolation\r\n const dx = (x < xs) ? strideX : 0;\r\n const dy = (y < ys) ? strideY : 0;\r\n const dz = (z < zs) ? strideZ : 0;\r\n\r\n const c0 = [0, 0, 0];\r\n const c1 = [0, 0, 0];\r\n const c2 = [0, 0, 0];\r\n const c3 = [0, 0, 0];\r\n\r\n idx = colorMap.getDirectIdx(x, y, z);\r\n interp(mux, idx, idx + dx, c0);\r\n interp(mux, idx + dy, idx + dx + dy, c1);\r\n interp(mux, idx + dz, idx + dx + dz, c2);\r\n interp(mux, idx + dy + dz, idx + dx + dy + dz, c3);\r\n\r\n const cz0 = [0, 0, 0];\r\n cz0[0] = (1 - muy) * c0[0] + muy * c1[0];\r\n cz0[1] = (1 - muy) * c0[1] + muy * c1[1];\r\n cz0[2] = (1 - muy) * c0[2] + muy * c1[2];\r\n\r\n const cz1 = [0, 0, 0];\r\n cz1[0] = (1 - muy) * c2[0] + muy * c3[0];\r\n cz1[1] = (1 - muy) * c2[1] + muy * c3[1];\r\n cz1[2] = (1 - muy) * c2[2] + muy * c3[2];\r\n\r\n colors[ind] = (1 - muz) * cz0[0] + muz * cz1[0];\r\n colors[ind + 1] = (1 - muz) * cz0[1] + muz * cz1[1];\r\n colors[ind + 2] = (1 - muz) * cz0[2] + muz * cz1[2];\r\n }\r\n this._colors = colors;\r\n\r\n if (visibilitySelector != null) {\r\n // shift visible vertices towards beginning of array\r\n for (i = 0; i < numVerts; ++i) {\r\n const j = vMap[i];\r\n if (j < 0) {\r\n continue;\r\n }\r\n\r\n // assert: j <= i\r\n this._position[j * 3] = this._position[i * 3];\r\n this._position[j * 3 + 1] = this._position[i * 3 + 1];\r\n this._position[j * 3 + 2] = this._position[i * 3 + 2];\r\n this._normals[j * 3] = this._normals[i * 3];\r\n this._normals[j * 3 + 1] = this._normals[i * 3 + 1];\r\n this._normals[j * 3 + 2] = this._normals[i * 3 + 2];\r\n this._colors[j * 3] = this._colors[i * 3];\r\n this._colors[j * 3 + 1] = this._colors[i * 3 + 1];\r\n this._colors[j * 3 + 2] = this._colors[i * 3 + 2];\r\n }\r\n\r\n // rebuild index list\r\n const numTriangles = this._indices.length / 3;\r\n let newTriCount = 0;\r\n for (i = 0; i < numTriangles; ++i) {\r\n const i0 = vMap[this._indices[3 * i]];\r\n const i1 = vMap[this._indices[3 * i + 1]];\r\n const i2 = vMap[this._indices[3 * i + 2]];\r\n if (i0 >= 0 && i1 >= 0 && i2 >= 0) {\r\n this._indices[3 * newTriCount] = i0;\r\n this._indices[3 * newTriCount + 1] = i1;\r\n this._indices[3 * newTriCount + 2] = i2;\r\n ++newTriCount;\r\n }\r\n }\r\n\r\n // shrink arrays to data size\r\n this._position = new Float32Array(this._position.buffer.slice(0, newVerCount * 3 * 4));\r\n this._normals = new Float32Array(this._normals.buffer.slice(0, newVerCount * 3 * 4));\r\n this._colors = new Float32Array(this._colors.buffer.slice(0, newVerCount * 3 * 4));\r\n this._indices = new Uint32Array(this._indices.buffer.slice(0, newTriCount * 3 * 4));\r\n }\r\n }\r\n\r\n toMesh() {\r\n const geo = new THREE.BufferGeometry();\r\n geo.setIndex(new THREE.BufferAttribute(this._indices, 1));\r\n geo.setAttribute('position', new THREE.BufferAttribute(this._position, 3));\r\n geo.setAttribute('normal', new THREE.BufferAttribute(this._normals, 3));\r\n geo.setAttribute('color', new THREE.BufferAttribute(this._colors, 3));\r\n geo.computeBoundingSphere();\r\n return geo;\r\n }\r\n}\r\nexport default IsoSurface;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurface from './IsoSurface';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * This is a base class for volumetric maps based isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass VolumeSurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n const params = this._opts;\r\n this.numVoxels = [128, 128, 128];\r\n this.xAxis = new THREE.Vector3(1.0, 0.0, 0.0);\r\n this.yAxis = new THREE.Vector3(0.0, 1.0, 0.0);\r\n this.zAxis = new THREE.Vector3(0.0, 0.0, 1.0);\r\n\r\n this.origin = new THREE.Vector3(0.0, 0.0, 0.0);\r\n this._visibilitySelector = params.visibilitySelector;\r\n\r\n this._calcSurface(params);\r\n }\r\n\r\n _findMinMax(posRadArray) {\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n const maxPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n const minPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n for (let i = 1; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n for (let itemIdx = 0; itemIdx < itemSize; ++itemIdx) {\r\n const tmpVal = posRadArray[ind + itemIdx];\r\n maxPosRad[itemIdx] = Math.max(tmpVal, maxPosRad[itemIdx]);\r\n minPosRad[itemIdx] = Math.min(tmpVal, minPosRad[itemIdx]);\r\n }\r\n }\r\n return { maxPosRad, minPosRad };\r\n }\r\n\r\n _findNumVoxels(posRadArray, params) {\r\n const { numVoxels } = this;\r\n const minMaxValues = this._findMinMax(posRadArray);\r\n const minCoordRad = minMaxValues.minPosRad;\r\n const maxCoordRad = minMaxValues.maxPosRad;\r\n\r\n // minrad\r\n if (minCoordRad[3] > 4.0) {\r\n params.gridSpacing *= minCoordRad[3];\r\n }\r\n\r\n let gridPadding = params.radScale * maxCoordRad[3] * 1.7;\r\n let padRad = gridPadding;\r\n padRad = 0.65 * Math.sqrt(4.0 / 3.0 * Math.PI * padRad * padRad * padRad);\r\n gridPadding = Math.max(gridPadding, padRad);\r\n\r\n let i = 0;\r\n for (; i < 3; ++i) {\r\n minCoordRad[i] -= gridPadding;\r\n maxCoordRad[i] += gridPadding;\r\n }\r\n\r\n for (i = 0; i < 3; ++i) {\r\n numVoxels[i] = Math.ceil((maxCoordRad[i] - minCoordRad[i]) / params.gridSpacing);\r\n }\r\n this.xAxis.x = (numVoxels[0] - 1) * params.gridSpacing;\r\n this.yAxis.y = (numVoxels[1] - 1) * params.gridSpacing;\r\n this.zAxis.z = (numVoxels[2] - 1) * params.gridSpacing;\r\n\r\n [this.origin.x, this.origin.y, this.origin.z] = minCoordRad;\r\n\r\n return { bbox: minMaxValues, dim: numVoxels };\r\n }\r\n\r\n _makeSurface(surface, params) {\r\n const isoSurf = new IsoSurface();\r\n isoSurf.compute(surface.volMap, this.origin, params.isoValue, 1);\r\n isoSurf.vertexFusion(9, 9);// normalization is included\r\n\r\n if (isoSurf._numTriangles > 0) {\r\n isoSurf.setColorVolTex(surface.volTexMap, surface.atomMap, surface.atomWeightMap, this._visibilitySelector);\r\n this.setIndex(new THREE.BufferAttribute(isoSurf._indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(isoSurf._position, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(isoSurf._normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(isoSurf._colors, 3));\r\n } else { // geometry should have at least empty position attributes to be processed in wireframe mode by three.js\r\n this.setAttribute('position', new THREE.BufferAttribute(utils.allocateTyped(Float32Array, 0), 3));\r\n }\r\n }\r\n\r\n _calcSurface(params) {\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n\r\n if (packedArrays.posRad.length === 0) {\r\n return;\r\n }\r\n const boundaries = this._findNumVoxels(packedArrays.posRad, params);\r\n\r\n const box = new THREE.Box3(\r\n this.origin,\r\n new THREE.Vector3(this.xAxis.x, this.yAxis.y, this.zAxis.z).add(this.origin),\r\n );\r\n const surface = this._computeSurface(packedArrays, box, boundaries, params);\r\n\r\n this._makeSurface(surface, params);\r\n }\r\n}\r\n\r\nexport default VolumeSurfaceGeometry;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass QuickSurfGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n // beware of shifting this multiple times!\r\n this._shiftByOrigin(packedArrays.posRad);\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3),\r\n };\r\n\r\n if (this._visibilitySelector != null) {\r\n surface.atomMap = [];\r\n surface.atomWeightMap = new Volume(Float32Array, this.numVoxels, box);\r\n }\r\n\r\n this.gaussdensity(surface, packedArrays, null, params);\r\n return surface;\r\n }\r\n\r\n gaussdensity(surface, packedArrays, atomicNum, params) {\r\n const numAtoms = packedArrays.posRad.length / 4;\r\n const { posRad, colors } = packedArrays;\r\n const { numVoxels } = this;\r\n const { radScale, gaussLim, gridSpacing } = params;\r\n const invIsoValue = 1.0 / params.isoValue;\r\n const invGridSpacing = 1.0 / gridSpacing;\r\n const maxVoxelX = numVoxels[0] - 1;\r\n const maxVoxelY = numVoxels[1] - 1;\r\n const maxVoxelZ = numVoxels[2] - 1;\r\n // TODO is densityMap and volTexMap initialized?\r\n\r\n const { volMap, volTexMap } = surface;\r\n const volData = volMap.getData();\r\n const strideX = volMap.getStrideX();\r\n\r\n const volTexData = volTexMap.getData();\r\n const texStrideX = volTexMap.getStrideX();\r\n\r\n let atomWeightData;\r\n if (this._visibilitySelector != null) {\r\n atomWeightData = surface.atomWeightMap.getData();\r\n }\r\n\r\n const { atomMap } = surface;\r\n\r\n for (let i = 0; i < numAtoms; ++i) {\r\n const ind = i * 4;\r\n const scaledRad = posRad[ind + 3] * radScale;\r\n const atomicNumFactor = atomicNum === null ? 1.0 : atomicNum[i];\r\n const radInv = 1 / (2 * scaledRad * scaledRad);\r\n let radLim = gaussLim * scaledRad;\r\n const radLim2 = radLim * radLim;\r\n radLim *= invGridSpacing;\r\n\r\n let tmp = posRad[ind] * invGridSpacing;\r\n const xMin = Math.max((tmp - radLim) | 0, 0);\r\n const xMax = Math.min((tmp + radLim) | 0, maxVoxelX);\r\n tmp = posRad[ind + 1] * invGridSpacing;\r\n const yMin = Math.max((tmp - radLim) | 0, 0);\r\n const yMax = Math.min((tmp + radLim) | 0, maxVoxelY);\r\n tmp = posRad[ind + 2] * invGridSpacing;\r\n const zMin = Math.max((tmp - radLim) | 0, 0);\r\n const zMax = Math.min((tmp + radLim) | 0, maxVoxelZ);\r\n\r\n let dz = zMin * gridSpacing - posRad[ind + 2];\r\n for (let z = zMin; z <= zMax; ++z, dz += gridSpacing) {\r\n let dy = yMin * gridSpacing - posRad[ind + 1];\r\n for (let y = yMin; y <= yMax; ++y, dy += gridSpacing) {\r\n const dy2dz2 = dy * dy + dz * dz;\r\n\r\n if (dy2dz2 >= radLim2) {\r\n continue;\r\n }\r\n\r\n let addr = volMap.getDirectIdx(xMin, y, z);\r\n let texAddr = volTexMap.getDirectIdx(xMin, y, z);\r\n let dx = xMin * gridSpacing - posRad[ind];\r\n for (let x = xMin; x <= xMax; ++x, dx += gridSpacing, addr += strideX, texAddr += texStrideX) {\r\n const r2 = dx * dx + dy2dz2;\r\n const expVal = -r2 * radInv;\r\n\r\n let density = Math.exp(expVal) * atomicNumFactor;\r\n\r\n // store most relevant atom (with highest density)\r\n if (this._visibilitySelector != null\r\n && density > atomWeightData[addr]) { // NOSONAR\r\n atomWeightData[addr] = density;\r\n // we use same index into atom map and atomWeightMap\r\n atomMap[addr] = packedArrays.atoms[i];\r\n }\r\n\r\n volData[addr] += density;\r\n\r\n // TODO check for volTexMap routine?\r\n density *= invIsoValue;\r\n const colInd = i * 3;\r\n volTexData[texAddr] += density * colors[colInd];\r\n volTexData[texAddr + 1] += density * colors[colInd + 1];\r\n volTexData[texAddr + 2] += density * colors[colInd + 2];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n _shiftByOrigin(posRadArray) {\r\n const originX = this.origin.x;\r\n const originY = this.origin.y;\r\n const originZ = this.origin.z;\r\n\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n for (let i = 0; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n posRadArray[ind] -= originX;\r\n posRadArray[ind + 1] -= originY;\r\n posRadArray[ind + 2] -= originZ;\r\n }\r\n }\r\n}\r\n\r\nexport default QuickSurfGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * Modifed from SpatialHash\r\n *\r\n * Main differences are:\r\n * - Optimized grid size to ensure we only ever need to look +/-1 cell\r\n * - Aware of atomic radii and will only output atoms within rAtom + rExtra\r\n * (see withinRadii method)\r\n *\r\n * (Uses rounding rather than bitshifting as consequence of arbitrary grid size)\r\n * @class\r\n * @param {Float32Array} posRad - x, y, z coordinates and radiuses\r\n * @param {Float32Array} min - xyz min coordinates\r\n * @param {Float32Array} max - xyz max coordinates\r\n * @param {number} maxDistance - max distance\r\n */\r\nfunction AVHash(posRad, min, max, maxDistance) {\r\n const itemSize = 4;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const minX = min[0];\r\n const minY = min[1];\r\n const minZ = min[2];\r\n\r\n const maxX = max[0];\r\n const maxY = max[1];\r\n const maxZ = max[2];\r\n\r\n function hashFunc(w, minW) {\r\n return Math.floor((w - minW) / maxDistance);\r\n }\r\n\r\n const iDim = hashFunc(maxX, minX) + 1;\r\n const jDim = hashFunc(maxY, minY) + 1;\r\n const kDim = hashFunc(maxZ, minZ) + 1;\r\n\r\n const nCells = iDim * jDim * kDim;\r\n\r\n const jkDim = jDim * kDim;\r\n\r\n /* Get cellID for cartesian x,y,z */\r\n const cellID = function (x, y, z) {\r\n return (((hashFunc(x, minX) * jDim) + hashFunc(y, minY)) * kDim) + hashFunc(z, minZ);\r\n };\r\n\r\n /* Initial building, could probably be optimized further */\r\n const preHash = [];\r\n let i;\r\n let cid;\r\n for (i = 0; i < nAtoms; i++) {\r\n const iIdx = itemSize * i;\r\n cid = cellID(posRad[iIdx], posRad[iIdx + 1], posRad[iIdx + 2]);\r\n\r\n if (preHash[cid] === undefined) {\r\n preHash[cid] = [i];\r\n } else {\r\n preHash[cid].push(i);\r\n }\r\n }\r\n\r\n const cellOffsets = utils.allocateTyped(Uint32Array, nCells);\r\n const cellLengths = utils.allocateTyped(Uint16Array, nCells);\r\n const data = utils.allocateTyped(Uint32Array, nAtoms);\r\n\r\n let offset = 0;\r\n let maxCellLength = 0;\r\n let j;\r\n for (i = 0; i < nCells; i++) {\r\n const start = cellOffsets[i] = offset;\r\n\r\n const subArray = preHash[i];\r\n\r\n if (subArray !== undefined) {\r\n for (j = 0; j < subArray.length; j++) {\r\n data[offset] = subArray[j];\r\n offset++;\r\n }\r\n }\r\n\r\n const cellLength = offset - start;\r\n cellLengths[i] = cellLength;\r\n\r\n if (cellLength > maxCellLength) {\r\n maxCellLength = cellLength;\r\n }\r\n }\r\n\r\n // Maximum number of neighbours we could ever produce (27 adjacent cells of equal population)\r\n this.neighbourListLength = (27 * maxCellLength) + 1;\r\n\r\n /**\r\n * Populate the supplied out array with atom indices that are within rAtom + rExtra\r\n * of x,y,z\r\n *\r\n * -1 in out array indicates the end of the list\r\n *\r\n * @param {number} x - x coordinate\r\n * @param {number} y - y coordinate\r\n * @param {number} z - z coordinate\r\n * @param {number} rExtra - additional radius\r\n * @param {Float32Array} out - pre-allocated output array\r\n * @return {undefined}\r\n */\r\n this.withinRadii = function (x, y, z, rExtra, out) {\r\n let outIdx = 0;\r\n\r\n const nearI = hashFunc(x, minX);\r\n const nearJ = hashFunc(y, minY);\r\n const nearK = hashFunc(z, minZ);\r\n\r\n const loI = Math.max(0, nearI - 1);\r\n const loJ = Math.max(0, nearJ - 1);\r\n const loK = Math.max(0, nearK - 1);\r\n\r\n const hiI = Math.min(iDim - 1, nearI + 1);\r\n const hiJ = Math.min(jDim - 1, nearJ + 1);\r\n const hiK = Math.min(kDim - 1, nearK + 1);\r\n\r\n for (i = loI; i <= hiI; ++i) {\r\n const iOffset = i * jkDim;\r\n\r\n for (j = loJ; j <= hiJ; ++j) {\r\n const jOffset = j * kDim;\r\n\r\n for (let k = loK; k <= hiK; ++k) {\r\n cid = iOffset + jOffset + k;\r\n\r\n const cellStart = cellOffsets[cid];\r\n const cellEnd = cellStart + cellLengths[cid];\r\n\r\n for (let dataIndex = cellStart; dataIndex < cellEnd; dataIndex++) {\r\n const atomIndex = data[dataIndex];\r\n const baseIndex = itemSize * atomIndex;\r\n const dx = posRad[baseIndex] - x;\r\n const dy = posRad[baseIndex + 1] - y;\r\n const dz = posRad[baseIndex + 2] - z;\r\n const rSum = posRad[baseIndex + 3] + rExtra;\r\n\r\n if ((dx * dx + dy * dy + dz * dz) <= (rSum * rSum)) {\r\n out[outIdx++] = data[dataIndex];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n // Add terminator\r\n out[outIdx] = -1;\r\n };\r\n}\r\nfunction ContactSurface(packedArrays, boundaries, params, _indexList) {\r\n // Field generation method adapted from AstexViewer (Mike Hartshorn)\r\n // by Fred Ludlow.\r\n // Other parts based heavily on NGL (Alexander Rose) EDT Surface class\r\n //\r\n // Should work as a drop-in alternative to EDTSurface (though some of\r\n // the EDT paramters are not relevant in this method).\r\n\r\n const itemSize = 4;\r\n const { posRad, colors, atoms } = packedArrays;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const { bbox } = boundaries;\r\n\r\n const min = bbox.minPosRad;\r\n const max = bbox.maxPosRad;\r\n\r\n let r2; // Atom positions, expanded radii (squared)\r\n let maxRadius;\r\n\r\n // Parameters\r\n let probeRadius;\r\n let scaleFactor;\r\n let probePositions;\r\n\r\n // Cache last value for obscured test\r\n let lastClip = -1;\r\n\r\n // Grid params\r\n let dim;\r\n let grid;\r\n let volTex;\r\n let weights;\r\n let weightsMap = null;\r\n let atomMap = null;\r\n let visibilitySelector = null;\r\n\r\n // grid indices -> xyz coords\r\n let gridx;\r\n let gridy;\r\n let gridz;\r\n\r\n // Lookup tables:\r\n let sinTable;\r\n let cosTable;\r\n\r\n // Spatial Hash\r\n let hash;\r\n\r\n // Neighbour array to be filled by hash\r\n let neighbours;\r\n\r\n // Vectors for Torus Projection\r\n const mid = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n1 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n2 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n let ngTorus;\r\n\r\n function uniformArray(TypeName, n, a) {\r\n const array = utils.allocateTyped(TypeName, n);\r\n for (let innI = 0; innI < n; ++innI) {\r\n array[innI] = a;\r\n }\r\n\r\n return array;\r\n }\r\n\r\n function fillGridDim(a, start, step) {\r\n for (let innI = 0; innI < a.length; innI++) {\r\n a[innI] = start + (step * innI);\r\n }\r\n }\r\n\r\n function initializeGrid() {\r\n ({ scaleFactor } = params);\r\n ({ dim } = boundaries);\r\n\r\n ngTorus = Math.min(5, 2 + Math.floor(probeRadius * scaleFactor));\r\n\r\n const gridSize = dim[0] * dim[1] * dim[2];\r\n grid = uniformArray(Float32Array, gridSize, -1001.0);\r\n volTex = utils.allocateTyped(Float32Array, gridSize * 3);\r\n weights = utils.allocateTyped(Float32Array, gridSize);\r\n if (visibilitySelector) {\r\n weightsMap = utils.allocateTyped(Float32Array, gridSize);\r\n atomMap = [];\r\n }\r\n\r\n gridx = utils.allocateTyped(Float32Array, dim[0]);\r\n gridy = utils.allocateTyped(Float32Array, dim[1]);\r\n gridz = utils.allocateTyped(Float32Array, dim[2]);\r\n\r\n fillGridDim(gridx, min[0], 1 / scaleFactor);\r\n fillGridDim(gridy, min[1], 1 / scaleFactor);\r\n fillGridDim(gridz, min[2], 1 / scaleFactor);\r\n }\r\n\r\n function initializeAngleTables() {\r\n let theta = 0.0;\r\n const step = 2 * Math.PI / probePositions;\r\n\r\n cosTable = utils.allocateTyped(Float32Array, probePositions);\r\n sinTable = utils.allocateTyped(Float32Array, probePositions);\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n cosTable[innI] = Math.cos(theta);\r\n sinTable[innI] = Math.sin(theta);\r\n theta += step;\r\n }\r\n }\r\n\r\n function initializeHash() {\r\n hash = new AVHash(posRad, min, max, 2.01 * maxRadius);\r\n neighbours = new Int32Array(hash.neighbourListLength);\r\n }\r\n\r\n function init() {\r\n ({\r\n probeRadius,\r\n scaleFactor,\r\n probePositions,\r\n visibilitySelector,\r\n } = params);\r\n r2 = utils.allocateTyped(Float32Array, nAtoms);\r\n maxRadius = 0;\r\n for (let innI = 0; innI < nAtoms; ++innI) {\r\n const rExt = posRad[innI * itemSize + 3] += probeRadius;\r\n if (rExt > maxRadius) {\r\n maxRadius = rExt;\r\n }\r\n r2[innI] = rExt * rExt;\r\n }\r\n\r\n initializeGrid();\r\n initializeAngleTables();\r\n initializeHash();\r\n\r\n lastClip = -1;\r\n }\r\n\r\n function singleAtomObscures(ai, innX, innY, innZ) {\r\n const innCI = itemSize * ai;\r\n const ra2 = r2[ai];\r\n const dx = posRad[innCI] - innX;\r\n const dy = posRad[innCI + 1] - innY;\r\n const dz = posRad[innCI + 2] - innZ;\r\n const d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n return d2 < ra2;\r\n }\r\n\r\n function obscured(innX, innY, innZ, a, b) {\r\n // Is the point at x,y,z obscured by any of the atoms\r\n // specifeid by indices in neighbours. Ignore indices\r\n // a and b (these are the relevant atoms in projectPoints/Torii)\r\n\r\n // Cache the last clipped atom (as very often the same one in\r\n // subsequent calls)\r\n let ai;\r\n\r\n if (lastClip !== -1) {\r\n ai = lastClip;\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n return ai;\r\n }\r\n lastClip = -1;\r\n }\r\n\r\n let ni = 0;\r\n ai = neighbours[ni];\r\n while (ai >= 0) {\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n lastClip = ai;\r\n return ai;\r\n }\r\n ai = neighbours[++ni];\r\n }\r\n\r\n lastClip = -1;\r\n\r\n return -1;\r\n }\r\n\r\n function projectPoints() {\r\n // For each atom:\r\n // Iterate over a subsection of the grid, for each point:\r\n // If current value < 0.0, unvisited, set positive\r\n //\r\n // In any case: Project this point onto surface of the atomic sphere\r\n // If this projected point is not obscured by any other atom\r\n // Calcualte delta distance and set grid value to minimum of\r\n // itself and delta\r\n\r\n // Should we alias frequently accessed closure constiables??\r\n // Assume JS engine capable of optimizing this\r\n // anyway...\r\n const maxRad = 4.0;\r\n const sigma = (maxRad) / 3;\r\n const sigma2Inv = 1 / (2 * sigma * sigma);\r\n\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innCI = itemSize * innI;\r\n const ax = posRad[innCI];\r\n const ay = posRad[innCI + 1];\r\n const az = posRad[innCI + 2];\r\n const ar = posRad[innCI + 3];\r\n const ar2 = r2[innI];\r\n\r\n hash.withinRadii(ax, ay, az, ar, neighbours);\r\n\r\n // Number of grid points, round this up...\r\n const ng = Math.ceil(ar * scaleFactor);\r\n\r\n // Center of the atom, mapped to grid points (take floor)\r\n const iax = Math.floor(scaleFactor * (ax - min[0]));\r\n const iay = Math.floor(scaleFactor * (ay - min[1]));\r\n const iaz = Math.floor(scaleFactor * (az - min[2]));\r\n\r\n // Extents of grid to consider for this atom\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n // Add two to these points:\r\n // - iax are floor'd values so this ensures coverage\r\n // - these are loop limits (exclusive)\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n const colIdx = innI * 3;\r\n const cr = colors[colIdx];\r\n const cg = colors[colIdx + 1];\r\n const cb = colors[colIdx + 2];\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n const dz = gridz[iz] - az;\r\n const zOffset = dim[1] * dim[0] * iz;\r\n\r\n for (let iy = miny; iy < maxy; iy++) {\r\n const dy = gridy[iy] - ay;\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n\r\n for (let ix = minx; ix < maxx; ix++) {\r\n const idx = ix + zyOffset;\r\n const dx = gridx[ix] - ax;\r\n const d2 = dzy2 + dx * dx;\r\n\r\n if (d2 < ar2) {\r\n const w = Math.exp(-d2 * sigma2Inv);\r\n const cIdx = idx * 3;\r\n volTex[cIdx] += cr * w;\r\n volTex[cIdx + 1] += cg * w;\r\n volTex[cIdx + 2] += cb * w;\r\n weights[idx] += w;\r\n if (visibilitySelector !== null && w > weightsMap[idx]) {\r\n weightsMap[idx] = w;\r\n atomMap[idx] = atoms[innI];\r\n }\r\n\r\n if (grid[idx] < 0.0) {\r\n // Unvisited, make positive\r\n grid[idx] = -grid[idx];\r\n }\r\n // Project on to the surface of the sphere\r\n // sp is the projected point ( dx, dy, dz ) * ( ra / d )\r\n const d = Math.sqrt(d2);\r\n const ap = ar / d;\r\n let spx = dx * ap;\r\n let spy = dy * ap;\r\n let spz = dz * ap;\r\n\r\n spx += ax;\r\n spy += ay;\r\n spz += az;\r\n\r\n if (obscured(spx, spy, spz, innI, -1) === -1) {\r\n const dd = ar - d;\r\n if (dd < grid[idx]) {\r\n grid[idx] = dd;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function normalToLine(out, p) {\r\n out.x = out.y = out.z = 1.0;\r\n if (p.x !== 0) {\r\n out.x = (p.y + p.z) / -p.x;\r\n } else if (p.y !== 0) {\r\n out.y = (p.x + p.z) / -p.y;\r\n } else if (p.z !== 0) {\r\n out.z = (p.x + p.y) / -p.z;\r\n }\r\n return out;\r\n }\r\n\r\n function projectTorus(a, b) {\r\n const aIdx = itemSize * a;\r\n const bIdx = itemSize * b;\r\n const xa = posRad[aIdx];\r\n const ya = posRad[aIdx + 1];\r\n const za = posRad[aIdx + 2];\r\n const r1 = posRad[aIdx + 3];\r\n let dx = mid.x = posRad[bIdx] - xa;\r\n let dy = mid.y = posRad[bIdx + 1] - ya;\r\n let dz = mid.z = posRad[bIdx + 2] - za;\r\n const innR2 = posRad[bIdx + 3];\r\n let d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n // This check now redundant as already done in AVHash.withinRadii\r\n // if( d2 > (( r1 + r2 ) * ( r1 + r2 )) ){ return; }\r\n\r\n const d = Math.sqrt(d2);\r\n\r\n // Find angle between a->b vector and the circle\r\n // of their intersection by cosine rule\r\n const cosA = (r1 * r1 + d * d - innR2 * innR2) / (2.0 * r1 * d);\r\n\r\n // distance along a->b at intersection\r\n const dmp = r1 * cosA;\r\n\r\n mid.normalize();\r\n\r\n // Create normal to line\r\n normalToLine(n1, mid);\r\n n1.normalize();\r\n\r\n // Cross together for second normal vector\r\n n2.crossVectors(mid, n1);\r\n n2.normalize();\r\n\r\n // r is radius of circle of intersection\r\n const rInt = Math.sqrt(r1 * r1 - dmp * dmp);\r\n\r\n n1.multiplyScalar(rInt);\r\n n2.multiplyScalar(rInt);\r\n mid.multiplyScalar(dmp);\r\n\r\n mid.x += xa;\r\n mid.y += ya;\r\n mid.z += za;\r\n\r\n lastClip = -1;\r\n\r\n const ng = ngTorus;\r\n\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n const cost = cosTable[innI];\r\n const sint = sinTable[innI];\r\n\r\n const px = mid.x + cost * n1.x + sint * n2.x;\r\n const py = mid.y + cost * n1.y + sint * n2.y;\r\n const pz = mid.z + cost * n1.z + sint * n2.z;\r\n\r\n if (obscured(px, py, pz, a, b) === -1) {\r\n // As above, iterate over our grid...\r\n // px, py, pz in grid coords\r\n const iax = Math.floor(scaleFactor * (px - min[0]));\r\n const iay = Math.floor(scaleFactor * (py - min[1]));\r\n const iaz = Math.floor(scaleFactor * (pz - min[2]));\r\n\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n dz = pz - gridz[iz];\r\n const zOffset = dim[1] * dim[0] * iz;\r\n for (let iy = miny; iy < maxy; iy++) {\r\n dy = py - gridy[iy];\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n for (let ix = minx; ix < maxx; ix++) {\r\n dx = px - gridx[ix];\r\n d2 = dzy2 + dx * dx;\r\n const idx = ix + zyOffset;\r\n const current = grid[idx];\r\n\r\n if (current > 0.0 && d2 < (current * current)) {\r\n grid[idx] = Math.sqrt(d2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function projectTorii() {\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innIdx = itemSize * innI;\r\n hash.withinRadii(\r\n posRad[innIdx],\r\n posRad[innIdx + 1],\r\n posRad[innIdx + 2],\r\n posRad[innIdx + 3],\r\n neighbours,\r\n );\r\n let ia = 0;\r\n let ni = neighbours[ia];\r\n while (ni >= 0) {\r\n if (innI < ni) {\r\n projectTorus(innI, ni);\r\n }\r\n ni = neighbours[++ia];\r\n }\r\n }\r\n }\r\n\r\n function fixNegatives() {\r\n for (let innI = 0, n = grid.length; innI < n; innI++) {\r\n if (grid[innI] < 0) grid[innI] = 0;\r\n let w = weights[innI];\r\n if (w > 0) {\r\n w = 1 / w;\r\n const innInnI = innI * 3;\r\n volTex[innInnI] *= w;\r\n volTex[innInnI + 1] *= w;\r\n volTex[innInnI + 2] *= w;\r\n }\r\n }\r\n }\r\n\r\n function getVolume() {\r\n // Basic steps are:\r\n // 1) Initialize\r\n // 2) Project points\r\n // 3) Project torii\r\n console.time('ContactSurface.getVolume');\r\n\r\n console.time('ContactSurface.init');\r\n init();\r\n console.timeEnd('ContactSurface.init');\r\n\r\n console.time('ContactSurface.projectPoints');\r\n projectPoints();\r\n console.timeEnd('ContactSurface.projectPoints');\r\n\r\n console.time('ContactSurface.projectTorii');\r\n projectTorii();\r\n console.timeEnd('ContactSurface.projectTorii');\r\n fixNegatives();\r\n console.timeEnd('ContactSurface.getVolume');\r\n }\r\n\r\n this.build = function () {\r\n // type and cutoff left in for compatibility with EDTSurface.getSurface\r\n // function signature\r\n getVolume();\r\n this.volTexMap = volTex;\r\n this.weightsMap = weightsMap;\r\n this.atomMap = atomMap;\r\n this.volMap = grid;\r\n };\r\n}\r\nexport default ContactSurface;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport ContactSurface from './ContactSurface';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'contact' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass ContactSurfaceGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n const contactSurface = new ContactSurface(packedArrays, boundaries, params);\r\n contactSurface.build();\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.volMap),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3, contactSurface.volTexMap),\r\n atomMap: contactSurface.atomMap,\r\n atomWeightMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.weightsMap),\r\n };\r\n return surface;\r\n }\r\n}\r\n\r\nexport default ContactSurfaceGeometry;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for colored atom. Need for atom structure clusterization\r\n *\r\n * @param {Vector3} vCenter Center of atom\r\n * @param {number} radiusAt Radius of atom\r\n */\r\nclass IsoSurfaceAtomColored {\r\n constructor(vCenter, radiusAt) {\r\n this.coord = new THREE.Vector3();\r\n this.coord.copy(vCenter);\r\n this.radius = radiusAt;\r\n this.colorX = 0.99999;\r\n this.colorY = 0.0;\r\n this.colorZ = 0.0;\r\n this.atomType = 0;\r\n this.srcAtom = null;\r\n }\r\n}\r\nexport default IsoSurfaceAtomColored;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n// suppress some JSHint warnings\r\n/* jshint bitwise: false */\r\n\r\n/**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numAtoms - Number of atoms in molecule\r\n * @param {Element} atoms - Array of atoms\r\n * @param {Vector3} vBoxMin - Bounding box min\r\n * @param {Vector3} vBoxMax - Bounding box max\r\n * @param {number} probeRadius - Normals for output\r\n *\r\n */\r\nclass IsosurfaceBuildNormals {\r\n constructor(numAtoms, atoms, vBoxMin, vBoxMax, probeRadius) {\r\n this._numAtoms = numAtoms;\r\n this._atoms = atoms;\r\n this._vBoxMin = new THREE.Vector3();\r\n this._vBoxMax = new THREE.Vector3();\r\n this._vBoxMin.copy(vBoxMin);\r\n this._vBoxMax.copy(vBoxMax);\r\n this._probeRadius = probeRadius;\r\n\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n }\r\n\r\n createVoxels() {\r\n let numAtomsRefs;\r\n let rad;\r\n const ATOM_VOXEL_REF_SCALE = 4.5;\r\n\r\n const numAtoms = this._numAtoms | 0;\r\n const atoms = this._atoms;\r\n const dx = this._vBoxMax.x - this._vBoxMin.x;\r\n const dy = this._vBoxMax.y - this._vBoxMin.y;\r\n const dz = this._vBoxMax.z - this._vBoxMin.z;\r\n let w = (dx < dy) ? dx : dy;\r\n w = (dz < w) ? dz : w;\r\n let maxRad = 0.0;\r\n let aveRad = 0.0;\r\n\r\n let i;\r\n for (i = 0; i < numAtoms; i++) {\r\n rad = (atoms[i].radius + this._probeRadius) * 2.0;\r\n maxRad = (rad > maxRad) ? rad : maxRad;\r\n aveRad += rad;\r\n }\r\n let numCells = Math.floor(w / maxRad);\r\n if (numCells < 2) {\r\n numCells = 2;\r\n }\r\n aveRad /= numAtoms;\r\n\r\n this._numCells = numCells;\r\n this._aveRad = aveRad;\r\n this._maxRad = maxRad;\r\n\r\n const side = numCells;\r\n const side2 = numCells * numCells;\r\n const side3 = numCells * numCells * numCells;\r\n\r\n const xScale = this._xScale = 1.0 / (this._vBoxMax.x - this._vBoxMin.x);\r\n const yScale = this._yScale = 1.0 / (this._vBoxMax.y - this._vBoxMin.y);\r\n const zScale = this._zScale = 1.0 / (this._vBoxMax.z - this._vBoxMin.z);\r\n\r\n // estimate number of individual atom refs in each voxel list\r\n let maxAtomsRefs = 0;\r\n\r\n const xNumVoxMult = xScale * numCells;\r\n const yNumVoxMult = yScale * numCells;\r\n const zNumVoxMult = zScale * numCells;\r\n\r\n for (i = 0; i < numAtoms; i++) {\r\n const radAffect = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n const diaAffect = radAffect * 2.0;\r\n let numVoxX = Math.floor(xNumVoxMult * diaAffect + 0.8);\r\n let numVoxY = Math.floor(yNumVoxMult * diaAffect + 0.8);\r\n let numVoxZ = Math.floor(zNumVoxMult * diaAffect + 0.8);\r\n // avoid case numVox? == 0\r\n // also use loop i <=\r\n numVoxX++;\r\n numVoxY++;\r\n numVoxZ++;\r\n maxAtomsRefs += numVoxX * numVoxY * numVoxZ;\r\n } // for (i)\r\n // maxAtomsRefs = numAtoms * MAX_ATOMS_IN_SINGLE_VOXEL;\r\n\r\n this._voxelList = utils.allocateTyped(Int32Array, side3);\r\n const atomsList = [];\r\n atomsList.length = maxAtomsRefs;\r\n if ((this._voxelList === null) || (atomsList === null)) {\r\n return 0 - 1;\r\n }\r\n // init voxel list\r\n for (i = 0; i < side3; i++) {\r\n this._voxelList[i] = -1;\r\n }\r\n numAtomsRefs = 0;\r\n\r\n // create voxel lists\r\n for (i = 0; i < numAtoms; i++) {\r\n // use multiplier 4 to locate this atom in different voxels\r\n rad = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n let xIndMin = Math.floor((atoms[i].coord.x - this._vBoxMin.x - rad) * numCells * xScale);\r\n let yIndMin = Math.floor((atoms[i].coord.y - this._vBoxMin.y - rad) * numCells * yScale);\r\n let zIndMin = Math.floor((atoms[i].coord.z - this._vBoxMin.z - rad) * numCells * zScale);\r\n let xIndMax = Math.floor((atoms[i].coord.x - this._vBoxMin.x + rad) * numCells * xScale);\r\n let yIndMax = Math.floor((atoms[i].coord.y - this._vBoxMin.y + rad) * numCells * yScale);\r\n let zIndMax = Math.floor((atoms[i].coord.z - this._vBoxMin.z + rad) * numCells * zScale);\r\n\r\n xIndMin = (xIndMin >= 0) ? xIndMin : 0;\r\n yIndMin = (yIndMin >= 0) ? yIndMin : 0;\r\n zIndMin = (zIndMin >= 0) ? zIndMin : 0;\r\n\r\n xIndMax = (xIndMax < numCells) ? xIndMax : (numCells - 1);\r\n yIndMax = (yIndMax < numCells) ? yIndMax : (numCells - 1);\r\n zIndMax = (zIndMax < numCells) ? zIndMax : (numCells - 1);\r\n\r\n for (let z = zIndMin; z <= zIndMax; z++) {\r\n for (let y = yIndMin; y <= yIndMax; y++) {\r\n for (let x = xIndMin; x <= xIndMax; x++) {\r\n // add atom with index \"i\" to this voxel list\r\n const indVoxel = x + y * side + z * side2;\r\n // assert indVoxel >= 0\r\n // assert indVoxel < side3\r\n\r\n // add first\r\n if (this._voxelList[indVoxel] < 0) {\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = 0 - 1;\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n numAtomsRefs++;\r\n // assert numAtomsRefs < maxAtomsRefs - 1\r\n continue;\r\n }\r\n // insert into head of list\r\n const indexNext = this._voxelList[indVoxel];\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = indexNext;\r\n numAtomsRefs++;\r\n } // for (x)\r\n } // for (y)\r\n } // for (z)\r\n } // for (i)\r\n\r\n // convert Array to Int32Array\r\n this._atomsList = Int32Array.from(atomsList);\r\n\r\n return 0;\r\n }\r\n\r\n destroyVoxels() {\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n\r\n this._atoms = null;\r\n this._vertices = null;\r\n this._vBoxMin = null;\r\n this._vBoxMax = null;\r\n }\r\n\r\n /**\r\n * Enumerate all atoms affecting specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n * @param {func(atom)} process - function to call for each atom\r\n */\r\n forEachRelatedAtom(point, process) {\r\n // find corresponding voxel\r\n const xInd = Math.floor((point.x - this._vBoxMin.x) * this._numCells * this._xScale);\r\n const yInd = Math.floor((point.y - this._vBoxMin.y) * this._numCells * this._yScale);\r\n const zInd = Math.floor((point.z - this._vBoxMin.z) * this._numCells * this._zScale);\r\n const indVoxel = xInd + yInd * this._numCells + zInd * this._numCells * this._numCells;\r\n\r\n // run through atoms affecting this voxel\r\n const atoms = this._atoms;\r\n for (let ref = this._voxelList[indVoxel]; ref >= 0; ref = this._atomsList[ref * 2 + 1]) {\r\n const indexAtom = this._atomsList[ref * 2];\r\n process(atoms[indexAtom]);\r\n }\r\n }\r\n\r\n /**\r\n * Get atom closest to specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n *\r\n * @returns {IsoSurfaceAtomColored} atom, or null if not found\r\n */\r\n getClosestAtom(point) {\r\n let closest = null;\r\n let minDist2 = Number.MAX_VALUE;\r\n\r\n this.forEachRelatedAtom(point, (atom) => {\r\n const dist2 = point.distanceToSquared(atom.coord);\r\n if (dist2 < minDist2) {\r\n minDist2 = dist2;\r\n closest = atom;\r\n }\r\n });\r\n\r\n return closest;\r\n }\r\n\r\n /**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} normals - Normals for output\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildNormals(numVertices, vertices, normals) {\r\n const self = this;\r\n let numCloseAtoms = 0;\r\n let vx = 0;\r\n let vy = 0;\r\n let vz = 0;\r\n let dist2;\r\n let vNormalX = 0;\r\n let vNormalY = 0;\r\n let vNormalZ = 0;\r\n let koef = 0;\r\n let w = 0;\r\n const r25 = 2.5;\r\n const r01 = 0.1;\r\n\r\n const maxRadAffect = this._aveRad * r25;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n const expScale = -this._aveRad * r01;\r\n\r\n // some stats\r\n // numSlowAtoms = 0;\r\n\r\n const gatherNormals = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = Math.exp(expScale * koef);\r\n\r\n vNormalX += dx * w;\r\n vNormalY += dy * w;\r\n vNormalZ += dz * w;\r\n numCloseAtoms++;\r\n };\r\n\r\n let maxClosedAtoms = 0;\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n numCloseAtoms = 0;\r\n vNormalX = vNormalY = vNormalZ = 0.0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherNormals);\r\n\r\n maxClosedAtoms = (numCloseAtoms > maxClosedAtoms) ? numCloseAtoms : maxClosedAtoms;\r\n\r\n // normalize vNormal\r\n dist2 = vNormalX * vNormalX + vNormalY * vNormalY + vNormalZ * vNormalZ;\r\n if (numCloseAtoms > 0) {\r\n koef = 1.0 / Math.sqrt(dist2);\r\n vNormalX *= koef;\r\n vNormalY *= koef;\r\n vNormalZ *= koef;\r\n }\r\n normals[i].x = vNormalX;\r\n normals[i].y = vNormalY;\r\n normals[i].z = vNormalZ;\r\n } // for (i) all vertices\r\n\r\n return 0;\r\n }\r\n\r\n /**\r\n * Build vertex colors for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} colors - Colors for output\r\n * @param {number} radiusColorSmoothness - Radius of smoothness sphere\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildColors(numVertices, vertices, colors, radiusColorSmoothness) {\r\n const self = this;\r\n let vx = 0.0;\r\n let vy = 0.0;\r\n let vz = 0.0;\r\n let koef = 0.0;\r\n let w = 0.0;\r\n const KOEF_ADD = 0.8;\r\n\r\n const maxRadAffect = radiusColorSmoothness;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n\r\n let colorsClose = [];\r\n let weights = [];\r\n let weightsSum = 0;\r\n\r\n const gatherColors = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = 1.0 / (KOEF_ADD + koef);\r\n\r\n colorsClose.push([atom.colorX, atom.colorY, atom.colorZ]);\r\n weights.push(w); // save weights for use\r\n weightsSum += w; // calc sum of weights fo further normalization\r\n };\r\n\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n colorsClose = [];\r\n weights = [];\r\n weightsSum = 0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherColors);\r\n\r\n // normalized weighted sum of colors\r\n for (let j = 0; j < colorsClose.length; ++j) {\r\n const weightNormalized = weights[j] / weightsSum;\r\n colors[i].x += colorsClose[j][0] * weightNormalized;\r\n colors[i].y += colorsClose[j][1] * weightNormalized;\r\n colors[i].z += colorsClose[j][2] * weightNormalized;\r\n }\r\n } // for (i) all vertices\r\n return 0;\r\n }\r\n}\r\nexport default IsosurfaceBuildNormals;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for geometry (triangle mesh) representation\r\n *\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices in mesh\r\n * @param {number} maxNumTriangles Maximum possible number of triangles in mesh\r\n * @param {boolean} needVertexColors Obvious\r\n */\r\nclass IsoSurfaceGeo {\r\n constructor(maxNumVertices, maxNumTriangles, needVertexColors) {\r\n this._maxNumVertices = maxNumVertices;\r\n this._maxNumTriangles = maxNumTriangles;\r\n this._vertices = new Array(maxNumVertices);\r\n this._normals = new Array(maxNumVertices);\r\n this._colors = null;\r\n if (needVertexColors) {\r\n this._colors = new Array(maxNumVertices);\r\n }\r\n this._indices = new Array(maxNumTriangles * (1 + 2));\r\n this._numVertices = 0;\r\n this._numTriangles = 0;\r\n\r\n let i;\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._vertices[i] = new THREE.Vector3();\r\n this._normals[i] = new THREE.Vector3();\r\n }\r\n for (i = 0; i < maxNumTriangles * (1 + 2); i++) {\r\n this._indices[i] = -1;\r\n }\r\n if (needVertexColors) {\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._colors[i] = new THREE.Vector3();\r\n }\r\n }\r\n }\r\n\r\n destroy() {\r\n this._vertices = null;\r\n this._normals = null;\r\n this._indices = null;\r\n }\r\n}\r\nexport default IsoSurfaceGeo;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurfaceAtomColored from './IsoSurfaceAtomColored';\r\nimport IsosurfaceBuildNormals from './IsosurfaceBuildNormals';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport IsoSurfaceGeo from './IsoSurfaceGeo';\r\nimport chem from '../../chem';\r\nimport utils from '../../utils';\r\n\r\nconst COLOR_SIZE = 3;\r\nconst HASH_SIZE = 32768;\r\nconst { Element } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass SSIsosurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n // convert geoOut into arrays of positions, indices, normals\r\n this._innerBuild();\r\n const geoOut = this.getGeo();\r\n this.destroy();\r\n this._fromGeo(geoOut);\r\n }\r\n\r\n _fromGeo(geoOut) {\r\n let colors = null;\r\n const positions = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n const normals = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n if (geoOut._colors !== null) {\r\n colors = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n }\r\n const indices = utils.allocateTyped(Uint32Array, (1 + 2) * geoOut._numTriangles);\r\n\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++) {\r\n positions[j + 0] = (geoOut._vertices[i].x);\r\n positions[j + 1] = (geoOut._vertices[i].y);\r\n positions[j + 2] = (geoOut._vertices[i].z);\r\n normals[j + 0] = geoOut._normals[i].x;\r\n normals[j + 1] = geoOut._normals[i].y;\r\n normals[j + 2] = geoOut._normals[i].z;\r\n j += 3;\r\n }\r\n if (colors !== null) {\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++, j += 3) {\r\n colors[j + 0] = geoOut._colors[i].x;\r\n colors[j + 1] = geoOut._colors[i].y;\r\n colors[j + 2] = geoOut._colors[i].z;\r\n }\r\n }\r\n\r\n const numTri3 = geoOut._numTriangles * (1 + 2);\r\n for (let i = 0; i < numTri3; i++) {\r\n indices[i] = geoOut._indices[i];\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(positions, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(colors, 3));\r\n this.computeBoundingBox();\r\n this.computeBoundingSphere();\r\n\r\n geoOut.destroy();\r\n }\r\n\r\n convertToAtomsColored(packedArrays, atomsColored) {\r\n const { atoms, colors } = packedArrays;\r\n for (let i = 0, numAtoms = atoms.length; i < numAtoms; i++) {\r\n const vCenter = atoms[i].position;\r\n const { radius } = atoms[i].element;\r\n atomsColored[i] = new IsoSurfaceAtomColored(vCenter, radius);\r\n const nm = atoms[i].element.number;\r\n atomsColored[i].atomType = this.getType(nm);\r\n let cIdx = COLOR_SIZE * i;\r\n atomsColored[i].colorX = colors[cIdx++];\r\n atomsColored[i].colorY = colors[cIdx++];\r\n atomsColored[i].colorZ = colors[cIdx];\r\n atomsColored[i].srcAtom = atoms[i];\r\n }\r\n }\r\n\r\n getGeo() {\r\n return this.geoOut;\r\n }\r\n\r\n destroy() {\r\n this.atoms = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n }\r\n\r\n /**\r\n * Calculates bounding box for array with spheres (atoms)\r\n *\r\n * @param {Object} atoms Atoms array\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n */\r\n getBoundingBox(atoms, vBoxMin, vBoxMax) {\r\n const bigNum = 10000000.0;\r\n\r\n vBoxMin.x = vBoxMin.y = vBoxMin.z = bigNum;\r\n vBoxMax.x = vBoxMax.y = vBoxMax.z = 0 - bigNum;\r\n\r\n const probeRadius2 = this.probeRadius * this.atomRadiusScale;\r\n let radMax = 0.0;\r\n for (let i = 0, num = atoms.length; i < num; i++) {\r\n const vCenter = atoms[i].coord;\r\n const rad = atoms[i].radius + probeRadius2;\r\n radMax = (rad > radMax) ? rad : radMax;\r\n if (vCenter.x - rad < vBoxMin.x) {\r\n vBoxMin.x = vCenter.x - rad;\r\n }\r\n if (vCenter.y - rad < vBoxMin.y) {\r\n vBoxMin.y = vCenter.y - rad;\r\n }\r\n if (vCenter.z - rad < vBoxMin.z) {\r\n vBoxMin.z = vCenter.z - rad;\r\n }\r\n if (vCenter.x + rad > vBoxMax.x) {\r\n vBoxMax.x = vCenter.x + rad;\r\n }\r\n if (vCenter.y + rad > vBoxMax.y) {\r\n vBoxMax.y = vCenter.y + rad;\r\n }\r\n if (vCenter.z + rad > vBoxMax.z) {\r\n vBoxMax.z = vCenter.z + rad;\r\n }\r\n }\r\n vBoxMin.x -= radMax;\r\n vBoxMin.y -= radMax;\r\n vBoxMin.z -= radMax;\r\n vBoxMax.x += radMax;\r\n vBoxMax.y += radMax;\r\n vBoxMax.z += radMax;\r\n }\r\n\r\n /**\r\n * Calculate (x,y,z) cordinate of the cell corner point\r\n *\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {number} x Cell integer x coordinate\r\n * @param {number} y Cell integer y coordinate\r\n * @param {number} z Cell integer z coordinate\r\n * @param {number} numPoints NUm points in cell on side\r\n * @param {Vector3} vOut Output vector\r\n */\r\n getCornerCoord(vBoxMin, vBoxMax, x, y, z, numPoints, vOut) {\r\n const invNP = 1.0 / (numPoints - 1.0);\r\n const tx = x * invNP;\r\n const ty = y * invNP;\r\n const tz = z * invNP;\r\n\r\n vOut.x = vBoxMin.x * (1.0 - tx) + vBoxMax.x * tx;\r\n vOut.y = vBoxMin.y * (1.0 - ty) + vBoxMax.y * ty;\r\n vOut.z = vBoxMin.z * (1.0 - tz) + vBoxMax.z * tz;\r\n }\r\n\r\n /**\r\n * Calculate point of intersection of sphere surface\r\n * and cell edge, given by [indexA, indexB] line\r\n *\r\n * @param {number} indexA Cell vertex index in [0..11]\r\n * @param {number} indexB Cell vertex index in [0..11]\r\n * @param {array} sign Sign array for all 8 vertices\r\n * @param {object} cube Cube\r\n * @param {number} indexPointValue for value placement\r\n * @param {Vector3} vOut Point of intersection\r\n */\r\n buildEdgePoint(indexA, indexB, sign, cube, indexPointValue, vOut) {\r\n if (sign[indexA] ^ sign[indexB]) {\r\n const cTwentyFour = 24;\r\n const t = (0 - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA])\r\n / (cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexB]\r\n - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA]);\r\n const xa = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 0];\r\n const ya = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 1];\r\n const za = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 2];\r\n const xb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 0];\r\n const yb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 1];\r\n const zb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 2];\r\n\r\n vOut.x = xa * (1.0 - t) + xb * t;\r\n vOut.y = ya * (1.0 - t) + yb * t;\r\n vOut.z = za * (1.0 - t) + zb * t;\r\n }\r\n }\r\n\r\n /**\r\n * Check if triangle is visible (vertices are close to atoms included in visibility set)\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} true if triangle is visible\r\n */\r\n isTriangleVisible(v0, v1, v2) {\r\n const a0 = this.voxelWorld.getClosestAtom(v0);\r\n const a1 = this.voxelWorld.getClosestAtom(v1);\r\n const a2 = this.voxelWorld.getClosestAtom(v2);\r\n if (a0 === null || a1 === null || a2 === null\r\n || a0.srcAtom === null || a1.srcAtom === null || a2.srcAtom === null) {\r\n return false;\r\n }\r\n\r\n return this.visibilitySelector.includesAtom(a0.srcAtom)\r\n && this.visibilitySelector.includesAtom(a1.srcAtom)\r\n && this.visibilitySelector.includesAtom(a2.srcAtom);\r\n }\r\n\r\n /**\r\n * Add triangle to result geometry\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} false if no more triangles can be added\r\n */\r\n addTriangle(v0, v1, v2) {\r\n if (this.visibilitySelector && !this.isTriangleVisible(v0, v1, v2)) {\r\n return true;\r\n }\r\n\r\n const geo = this.geoOut;\r\n\r\n if (geo._numTriangles >= this.maxNumTriangles) {\r\n return false;\r\n }\r\n\r\n // Add vertex with optimize\r\n const indInGeo0 = this.addVertexToGeo(geo, v0);\r\n const indInGeo1 = this.addVertexToGeo(geo, v1);\r\n const indInGeo2 = this.addVertexToGeo(geo, v2);\r\n if ((indInGeo0 | indInGeo1 | indInGeo2) < 0) {\r\n return false;\r\n }\r\n\r\n const itr = 3 * geo._numTriangles;\r\n geo._indices[itr + 0] = indInGeo0;\r\n geo._indices[itr + 1] = indInGeo1;\r\n geo._indices[itr + 2] = indInGeo2;\r\n geo._numTriangles++;\r\n return true;\r\n }\r\n\r\n /**\r\n * Build result geometry (triangle mesh) from marching cube cells\r\n *\r\n * @param {number} meshRes Marchnig cube vertex count on each side\r\n * @param {Vector3} vBoxMin Bounding box point min\r\n * @param {Vector3} vBoxMax Bounding box point max\r\n * @param {number} corners float values array for each cube point\r\n * @param {Vector3} vCellStep vector to next cube cell diagonal point\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} 0, if success (<0) is error\r\n */\r\n buildGeoFromCorners(meshRes, vBoxMin, vBoxMax, corners, vCellStep, cube) {\r\n const arrSize = 12;\r\n const cNumVerts = 8;\r\n const numCells = meshRes - 1;\r\n const side = meshRes;\r\n const side2 = meshRes * meshRes;\r\n\r\n const vaEdges = new Array(arrSize);\r\n for (let i = 0; i < arrSize; i++) {\r\n vaEdges[i] = new THREE.Vector3();\r\n }\r\n const sign = [];\r\n for (let i = 0; i < cNumVerts; i++) {\r\n sign[i] = 1.0;\r\n }\r\n const vCorner = new THREE.Vector3();\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n if (!cube.hasIntersection[indCell]) {\r\n // next cell\r\n indCell++;\r\n continue;\r\n }\r\n const bitsInside = cube.bitsInside[indCell];\r\n\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, meshRes, vCorner);\r\n\r\n const indPointValues = indCell * (2 << (2 + 2));\r\n for (let i = 0, j = 0; i < cNumVerts; i++) {\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.x;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.y;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.z;\r\n }\r\n\r\n cube.pointsValuesLinear[indPointValues + 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 2 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3] += vCellStep.x;\r\n\r\n cube.pointsValuesLinear[indPointValues + 2 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 3 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 2] += vCellStep.z;\r\n\r\n cube.pointsValuesLinear[indPointValues + 4 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 1] += vCellStep.y;\r\n\r\n // now current cell has intersections (from -x to +x) on some cube edges\r\n const indValues = indPointValues + 24;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n sign[i] = (cube.pointsValuesLinear[indValues + i] < 0.0) ? 1 : 0;\r\n }\r\n\r\n this.buildEdgePoint(0, 1, sign, cube, indPointValues, vaEdges[0]);\r\n this.buildEdgePoint(1, 2, sign, cube, indPointValues, vaEdges[1]);\r\n this.buildEdgePoint(2, 3, sign, cube, indPointValues, vaEdges[2]);\r\n this.buildEdgePoint(3, 0, sign, cube, indPointValues, vaEdges[3]);\r\n\r\n this.buildEdgePoint(4, 5, sign, cube, indPointValues, vaEdges[4]);\r\n this.buildEdgePoint(5, 6, sign, cube, indPointValues, vaEdges[5]);\r\n this.buildEdgePoint(6, 7, sign, cube, indPointValues, vaEdges[6]);\r\n this.buildEdgePoint(7, 4, sign, cube, indPointValues, vaEdges[7]);\r\n\r\n this.buildEdgePoint(0, 4, sign, cube, indPointValues, vaEdges[8]);\r\n this.buildEdgePoint(1, 5, sign, cube, indPointValues, vaEdges[9]);\r\n this.buildEdgePoint(2, 6, sign, cube, indPointValues, vaEdges[10]);\r\n this.buildEdgePoint(3, 7, sign, cube, indPointValues, vaEdges[11]);\r\n\r\n const offs = bitsInside * (2 << (1 + 2));\r\n for (let numTri = 0, indTri = 0; numTri < (2 + 2 + 2); numTri++, indTri += 3) {\r\n // s_triIndicesMarchCube is external array, defined in mold_ind.js\r\n const i0 = cube.striIndicesMarchCube[offs + indTri];\r\n if (i0 < 0) {\r\n break;\r\n }\r\n const i1 = cube.striIndicesMarchCube[offs + indTri + 1];\r\n const i2 = cube.striIndicesMarchCube[offs + indTri + 2];\r\n\r\n if (!this.addTriangle(vaEdges[i0], vaEdges[i1], vaEdges[i2])) {\r\n return 0 - 2;\r\n }\r\n } // for numTri\r\n\r\n // next cell (cube)\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return 0;\r\n }\r\n\r\n /**\r\n * Returns number of cell with intersection with at least one sphere.\r\n * Using this number, we can estimate required number of vertices\r\n * and triangles to build result mesh.\r\n *\r\n * @param {number} side Number of points in cube voxels\r\n * @param {number} numCells Number of cells in cube voxels (per direction)\r\n * @param {array} corners Array of float values for cube corner points\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} numIntersectedCells\r\n */\r\n getNumIntersectedCells(side, numCells, corners, cube) {\r\n const side2 = side * side;\r\n const cNumVerts = 8;\r\n let numIntersectedCells = 0;\r\n\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n const cubeValuesIndex = indCell * (2 << (2 + 2)) + 24;\r\n const indCorner = x + indZ + indY;\r\n\r\n cube.pointsValuesLinear[cubeValuesIndex] = corners[indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 1] = corners[indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 2] = corners[indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 3] = corners[indCorner + side];\r\n cube.pointsValuesLinear[cubeValuesIndex + 4] = corners[side2 + indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 5] = corners[side2 + indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 6] = corners[side2 + indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 7] = corners[side2 + indCorner + side];\r\n\r\n // check read exception\r\n // assert(side2 + indCorner + side + 1 < side3);\r\n\r\n // get bit flags inside\r\n let bitsInside = 0;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n if (cube.pointsValuesLinear[cubeValuesIndex + i] < 0.0) {\r\n bitsInside |= (1 << i);\r\n }\r\n }\r\n\r\n if ((bitsInside === 0) || (bitsInside === ((1 << cNumVerts) - 1))) {\r\n cube.hasIntersection[indCell] = false;\r\n } else {\r\n cube.hasIntersection[indCell] = true;\r\n numIntersectedCells++;\r\n }\r\n cube.bitsInside[indCell] = bitsInside;\r\n // next cell\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return numIntersectedCells;\r\n }\r\n\r\n getType(letter) {\r\n /* eslint-disable no-magic-numbers */\r\n const atomT = [0, 0, 1, 1, 2, 6, 3, 6, 4, 6, 5, 6, 6, 0, 7, 3, 8, 2, 9, 6, 10, 6, 11, 6, 12, 6, 13, 6, 14, 6, 15, 4,\r\n 16, 5, 17, 6, 18, 6, 19, 6, 20, 6, 21, 6, 22, 6, 23, 6, 24, 6, 25, 6, 26, 6, 27, 6, 28, 6, 29, 6, 30, 6, 31, 6,\r\n 32, 6, 33, 6, 34, 6, 35, 6, 36, 6, 37, 6, 38, 6, 39, 6, 40, 6, 41, 6, 42, 6, 43, 6, 44, 6, 45, 6, 46, 6, 47, 6,\r\n 48, 6, 49, 6, 50, 6, 51, 6, 52, 6, 53, 6, 54, 6, 55, 6, 56, 6, 57, 6, 58, 6, 59, 6, 60, 6, 61, 6, 62, 6, 63, 6,\r\n 64, 6, 65, 6, 66, 6, 67, 6, 68, 6, 69, 6, 70, 6, 71, 6, 72, 6, 73, 6, 74, 6, 75, 6, 76, 6, 77, 6, 78, 6, 79, 6,\r\n 80, 6, 81, 6, 82, 6, 83, 6, 84, 6, 85, 6, 86, 6, 87, 6, 88, 6, 89, 6, 90, 6, 91, 6, 92, 6, 93, 6, 94, 6, 95, 6,\r\n 96, 6, 97, 6, 98, 6, 99, 6, 100, 6, 101, 6, 102, 6, 103, 6, 104, 6, 105, 6, 106, 6, 107, 6, 108, 6, 109, 6];\r\n /* eslint-enable no-magic-numbers */\r\n\r\n if (letter < 1 || letter > atomT.length / 2\r\n || (Object.keys(Element.ByAtomicNumber).length * 2) !== atomT.length) {\r\n throw new Error('atomT.length should be equal Element.ByAtomicNumber.length * 2');\r\n }\r\n return atomT[letter * 2];\r\n }\r\n\r\n /**\r\n * Calculate values for marching cube grid points\r\n * positive values are outside sphere, negative - is inside\r\n *\r\n * @param {array} corners array of float values\r\n * @param {number} side Number of point in cube in 1 dimennsion\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {array} atoms Array of input atoms\r\n * @param {number} probeRad radius for atom probing\r\n */\r\n calculateGridCorners(corners, side, vBoxMin, vBoxMax, atoms, probeRad) {\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const vCorner = new THREE.Vector3();\r\n const vDif = new THREE.Vector3();\r\n /* eslint-disable no-magic-numbers */\r\n const aLot = +1.0e12;\r\n /* eslint-enable no-magic-numbers */\r\n\r\n for (let i = 0; i < side3; i++) {\r\n corners[i] = aLot; // to large value\r\n }\r\n\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n for (let s = 0, numAtoms = atoms.length; s < numAtoms; s++) {\r\n const atom = atoms[s];\r\n const radius = atom.radius + probeRad;\r\n\r\n const fx = ((atom.coord.x - radius) - vBoxMin.x) * xScale;\r\n const fy = ((atom.coord.y - radius) - vBoxMin.y) * yScale;\r\n const fz = ((atom.coord.z - radius) - vBoxMin.z) * zScale;\r\n\r\n const indXMin = Math.floor(fx);\r\n const indYMin = Math.floor(fy);\r\n const indZMin = Math.floor(fz);\r\n\r\n let indXMax = Math.floor(((atom.coord.x + radius) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((atom.coord.y + radius) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((atom.coord.z + radius) - vBoxMin.z) * zScale);\r\n\r\n indXMax++;\r\n indYMax++;\r\n indZMax++;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let y = indYMin; y <= indYMax; y++) {\r\n const indY = y * side2;\r\n for (let z = indZMin; z <= indZMax; z++) {\r\n const indZ = z * side;\r\n for (let x = indXMin; x <= indXMax; x++) {\r\n const ind = indY + indZ + x;\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, side, vCorner);\r\n vDif.x = vCorner.x - atom.coord.x;\r\n vDif.y = vCorner.y - atom.coord.y;\r\n vDif.z = vCorner.z - atom.coord.z;\r\n const distToSphere = Math.sqrt(vDif.x * vDif.x + vDif.y * vDif.y + vDif.z * vDif.z);\r\n // val: < 0, if inside sphere\r\n // val: > 0, if outside sphere\r\n const val = distToSphere - radius;\r\n if (val < corners[ind]) {\r\n corners[ind] = val;\r\n }\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n } // for (s)\r\n }\r\n\r\n /**\r\n * Create memory pool for vertex hash management\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices (that will be build)\r\n * @param {number} maxNumTriangles Maximum possible number of triangles (that will be build)\r\n * @returns {number} 0, if success. (<0) is non memory\r\n */\r\n createVertexHash(maxNumVertices, maxNumTriangles) {\r\n this.hashLines = utils.allocateTyped(Int32Array, HASH_SIZE * 2);\r\n if (this.hashLines === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < HASH_SIZE; i++) {\r\n this.hashLines[j++] = 0; // num vertices in this hash line\r\n this.hashLines[j++] = 0 - 1; // index of the first entry\r\n }\r\n\r\n this.maxNumVertices = maxNumVertices;\r\n this.maxNumTriangles = maxNumTriangles;\r\n\r\n this.numHashEtriesAllocated = maxNumVertices;\r\n this.hashEntries = utils.allocateTyped(Int32Array, 2 * this.numHashEtriesAllocated);\r\n if (this.hashEntries === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < this.numHashEtriesAllocated; i++) {\r\n this.hashEntries[j++] = 0 - 1; // index of vertex\r\n this.hashEntries[j++] = 0 - 1; // next hash entry index\r\n }\r\n this.numHashEntryIndex = 0;\r\n return 0;\r\n }\r\n\r\n /**\r\n * Allocate and return new hash entry. Just check possible amount.\r\n *\r\n * @returns {number} index of hash entry, that can be used for geometry add vertex functionality\r\n */\r\n getNewHashEntry() {\r\n if (this.numHashEntryIndex < this.numHashEtriesAllocated) {\r\n const i = this.numHashEntryIndex;\r\n this.numHashEntryIndex++;\r\n return i;\r\n }\r\n return 0 - 1;\r\n }\r\n\r\n /**\r\n * Add vertex to geometry structure\r\n * using vertex hash table to quickly check, is this vertex already exist in geometry\r\n *\r\n * @param {object} geoOut Geometry to build\r\n * @param {Vector3} vAdd Vertex to add\r\n * @returns {number} index of added (or existing) vertex in geometry.\r\n */\r\n addVertexToGeo(geoOut, vAdd) {\r\n let entry;\r\n const oneHynberes = 0.01;\r\n const n815851 = 815851;\r\n const n37633 = 37633;\r\n const n2453543 = 2453543;\r\n const r106 = 1.0e-6;\r\n\r\n const hashResolution = this.marCubeResoultion << 2;\r\n const v = new THREE.Vector3();\r\n const ix = Math.floor(hashResolution * (vAdd.x - this.vBoxMin.x) / (this.vBoxMax.x + oneHynberes - this.vBoxMin.x));\r\n const iy = Math.floor(hashResolution * (vAdd.y - this.vBoxMin.y) / (this.vBoxMax.y + oneHynberes - this.vBoxMin.y));\r\n const iz = Math.floor(hashResolution * (vAdd.z - this.vBoxMin.z) / (this.vBoxMax.z + oneHynberes - this.vBoxMin.z));\r\n let iHash = ix * n815851 + iz * n37633 + iy * n2453543;\r\n iHash &= (HASH_SIZE - 1);\r\n const hLineIndex = iHash + iHash;\r\n\r\n // search vertex via hash\r\n // search in hash list\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n for (entry = this.hashLines[hLineIndex + 1]; entry >= 0; entry = this.hashEntries[entry * 2 + 1]) {\r\n const ind = this.hashEntries[entry * 2 + 0]; // vertex index\r\n v.copy(geoOut._vertices[ind]);\r\n v.x -= vAdd.x;\r\n v.y -= vAdd.y;\r\n v.z -= vAdd.z;\r\n const dot2 = v.x * v.x + v.y * v.y + v.z * v.z;\r\n if (dot2 < r106) {\r\n return ind;\r\n } // if (found)\r\n } // for (entry)\r\n } // search\r\n\r\n // add new vertex to geometry\r\n if (geoOut._numVertices >= this.maxNumVertices) {\r\n return 0 - 1;\r\n }\r\n\r\n const iVertAdd = geoOut._numVertices;\r\n geoOut._vertices[iVertAdd].copy(vAdd);\r\n\r\n // add to hash\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n entry = this.getNewHashEntry();\r\n if (entry < 0) {\r\n return 0 - 1;\r\n }\r\n const entryFirst = this.hashLines[hLineIndex + 1];\r\n this.hashLines[hLineIndex + 1] = entry;\r\n this.hashEntries[entry * 2 + 0] = iVertAdd;\r\n this.hashEntries[entry * 2 + 1] = entryFirst;\r\n\r\n this.hashLines[hLineIndex + 0]++; // num vertices in line ++\r\n }\r\n geoOut._numVertices++;\r\n return iVertAdd;\r\n }\r\n\r\n /**\r\n *\r\n * @param {number} side some placeholder description\r\n * @param {number} probeSphereRadius some placeholder description\r\n * @param {object} vBoxMin some placeholder description\r\n * @param {object} vBoxMax some placeholder description\r\n * @param {object} geoOut some placeholder description\r\n * @param {object} corners some placeholder description\r\n * @returns {number} always 0\r\n */\r\n modifyExcludedFromGeo(\r\n side,\r\n probeSphereRadius,\r\n vBoxMin,\r\n vBoxMax,\r\n geoOut,\r\n corners,\r\n ) {\r\n let ind;\r\n let distToSphere;\r\n let distToBorder;\r\n const r11 = 1.1;\r\n\r\n function innerBlockWorkAround() {\r\n if (distToBorder > 0.0) {\r\n // point is inside probe sphere\r\n if (corners[ind] < 0.0) {\r\n corners[ind] = distToBorder; // was inside surface, now is oustide ( > 0)\r\n }\r\n if (distToBorder > corners[ind]) {\r\n corners[ind] = distToBorder; // find positive maximum\r\n }\r\n } else if (distToBorder > corners[ind]) { // point is outside sphere\r\n corners[ind] = distToBorder; // find negative maximum\r\n }\r\n }\r\n\r\n const side2 = side * side;\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n const probeSpRad2 = (probeSphereRadius * 2) * (probeSphereRadius * 2);\r\n const sideInv = 1.0 / (side - 1);\r\n\r\n for (let i = 0; i < geoOut._numVertices; i++) {\r\n const vCenter = geoOut._vertices[i];\r\n\r\n const radEst = probeSphereRadius * r11;\r\n\r\n let indXMin = Math.floor(((vCenter.x - radEst) - vBoxMin.x) * xScale);\r\n let indYMin = Math.floor(((vCenter.y - radEst) - vBoxMin.y) * yScale);\r\n let indZMin = Math.floor(((vCenter.z - radEst) - vBoxMin.z) * zScale);\r\n\r\n let indXMax = Math.floor(((vCenter.x + radEst) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((vCenter.y + radEst) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((vCenter.z + radEst) - vBoxMin.z) * zScale);\r\n\r\n indXMin = (indXMin >= 0) ? indXMin : 0;\r\n indYMin = (indYMin >= 0) ? indYMin : 0;\r\n indZMin = (indZMin >= 0) ? indZMin : 0;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let iy = indYMin; iy <= indYMax; iy++) {\r\n const indY = iy * side2;\r\n for (let iz = indZMin; iz <= indZMax; iz++) {\r\n const indZ = iz * side;\r\n for (let ix = indXMin; ix <= indXMax; ix++) {\r\n ind = indY + indZ + ix;\r\n // getCornerCoord(vBoxMin, vBoxMax, ix, iy, iz, side, &vCorner);\r\n let t = ix * sideInv;\r\n const xCorner = vBoxMin.x * (1.0 - t) + vBoxMax.x * t;\r\n t = iy * sideInv;\r\n const yCorner = vBoxMin.y * (1.0 - t) + vBoxMax.y * t;\r\n t = iz * sideInv;\r\n const zCorner = vBoxMin.z * (1.0 - t) + vBoxMax.z * t;\r\n\r\n const dx = xCorner - vCenter.x;\r\n const dy = yCorner - vCenter.y;\r\n const dz = zCorner - vCenter.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 < probeSpRad2) {\r\n distToSphere = Math.sqrt(dist2);\r\n distToBorder = -(distToSphere - probeSphereRadius);\r\n innerBlockWorkAround();\r\n } // if (dist from corner point to sphere center more 2 radiuses)\r\n } // for (ix)\r\n } // for (iz)\r\n } // for (iy)\r\n } // for (i) all geo vertices\r\n return 0;\r\n }\r\n\r\n _innerBuild() {\r\n let ok;\r\n const expandFactor = 1.2;\r\n\r\n // performance test\r\n // this.performanceTest();\r\n\r\n // Create temporary atoms (but colored)\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n this.complex = this._opts.parent;\r\n this.atoms = packedArrays.atoms;\r\n this.meshResolution = this._opts.gridSpacing;\r\n this.atomRadiusScale = this._opts.radScale;\r\n this.colorMode = this._opts.colorMode;\r\n this.probeRadius = this._opts.probeRadius;\r\n this.useVertexColors = true;\r\n this.excludeProbe = this._opts.excludeProbe;\r\n this.visibilitySelector = this._opts.visibilitySelector;\r\n\r\n this.geoOut = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n this.numHashEtriesAllocated = 0;\r\n this.numHashEntryIndex = 0;\r\n this.maxNumVertices = 0;\r\n this.maxNumTriangles = 0;\r\n\r\n const atomsColored = new Array(this.atoms.length);\r\n this.convertToAtomsColored(packedArrays, atomsColored);\r\n\r\n // find bbox for spheres scene\r\n const vBoxMin = this.vBoxMin = new THREE.Vector3();\r\n const vBoxMax = this.vBoxMax = new THREE.Vector3();\r\n this.getBoundingBox(atomsColored, vBoxMin, vBoxMax);\r\n\r\n const marCubeResoultion = this.marCubeResoultion = this.meshResolution * (2 + 2);\r\n\r\n // build grid corners for Marching cube algorithm\r\n const side = marCubeResoultion;\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const corners = utils.allocateTyped(Float32Array, side3);\r\n const rProbeRadius = this.probeRadius * this.atomRadiusScale;\r\n\r\n this.calculateGridCorners(corners, side, vBoxMin, vBoxMax, atomsColored, rProbeRadius);\r\n\r\n const numCells = marCubeResoultion - 1;\r\n const cube = new IsoSurfaceMarchCube();\r\n ok = cube.create(numCells);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // copy corners to cells\r\n const vCellStep = new THREE.Vector3();\r\n vCellStep.x = (vBoxMax.x - vBoxMin.x) / numCells;\r\n vCellStep.y = (vBoxMax.y - vBoxMin.y) / numCells;\r\n vCellStep.z = (vBoxMax.z - vBoxMin.z) / numCells;\r\n\r\n let numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n let maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n let maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n\r\n // build voxel world (used to check triangle-to-atom tie and to calculate normals and colors)\r\n let probeRadForNormalsColors = rProbeRadius;\r\n if (this.excludeProbe) {\r\n probeRadForNormalsColors = 0.01;\r\n }\r\n this.voxelWorld = new IsosurfaceBuildNormals(\r\n atomsColored.length,\r\n atomsColored,\r\n vBoxMin,\r\n vBoxMax,\r\n probeRadForNormalsColors,\r\n );\r\n this.voxelWorld.createVoxels();\r\n\r\n ok = this.buildGeoFromCorners(marCubeResoultion, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n if (this.excludeProbe) {\r\n // using 3d mesh (geoOut) as a surface points\r\n // move probe sphere and try to minimuze corners values\r\n this.modifyExcludedFromGeo(side, rProbeRadius, vBoxMin, vBoxMax, this.geoOut, corners);\r\n\r\n // delete old builded geo\r\n this.geoOut._vertices = null;\r\n this.geoOut._colors = null;\r\n this.geoOut._indices = null;\r\n this.geoOut._normals = null;\r\n this.geoOut._numVertices = 0;\r\n this.geoOut._numTriangles = 0;\r\n this.geoOut = null;\r\n\r\n // estimage geo vertices budget again\r\n numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n // creates empty new geometry\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // build vertices and triangles from corners values\r\n ok = this.buildGeoFromCorners(side, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n }\r\n\r\n // build vertex normals\r\n this.voxelWorld.buildNormals(this.geoOut._vertices.length, this.geoOut._vertices, this.geoOut._normals);\r\n // More value : more smooth color mixing\r\n // value about 0.7: very rough colors borders\r\n let radiusColorSmoothness = 6.5;\r\n if (this.excludeProbe) {\r\n radiusColorSmoothness -= 1.5;\r\n }\r\n if (this.useVertexColors) {\r\n this.voxelWorld.buildColors(\r\n this.geoOut._vertices.length,\r\n this.geoOut._vertices,\r\n this.geoOut._colors,\r\n radiusColorSmoothness,\r\n );\r\n }\r\n this.voxelWorld.destroyVoxels();\r\n this.voxelWorld = null;\r\n\r\n // remove objects\r\n cube.destroy();\r\n\r\n return ok;\r\n }\r\n}\r\n\r\n// All code below must be erased from every device and each developer's memory\r\n\r\nexport default SSIsosurfaceGeometry;\r\n","import * as THREE from 'three';\r\nimport EventDispatcher from '../../utils/EventDispatcher';\r\n\r\nfunction createLabel(fieldTxt, className) {\r\n const text = document.createElement('div');\r\n text.className = className;\r\n\r\n if (typeof fieldTxt === 'string') {\r\n const spanText = document.createElement('span');\r\n spanText.style.fontSize = '150%';\r\n const strings = fieldTxt.split('\\n');\r\n\r\n for (let i = 0, n = strings.length; i < n; ++i) {\r\n const spanNodeP = document.createElement('span');\r\n const spanNodeText = document.createTextNode(strings[i]);\r\n spanNodeP.appendChild(spanNodeText);\r\n spanText.appendChild(spanNodeP);\r\n if (i < n - 1) {\r\n spanText.appendChild(document.createElement('br'));\r\n }\r\n }\r\n\r\n text.appendChild(spanText);\r\n } else {\r\n text.appendChild(fieldTxt);\r\n }\r\n text.worldPos = new THREE.Vector3();\r\n return text;\r\n}\r\nclass LabelsGeometry extends EventDispatcher {\r\n constructor(instanceCount, opts) {\r\n super();\r\n this._opts = opts;\r\n this.items = [];\r\n this.needsUpdate = false;\r\n\r\n let xTranslation = -50;\r\n let yTranslation = -50;\r\n switch (opts.horizontalAlign) {\r\n case 'left':\r\n xTranslation = 0;\r\n break;\r\n case 'right':\r\n xTranslation = -100;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n switch (opts.verticalAlign) {\r\n case 'top':\r\n yTranslation = -100;\r\n break;\r\n case 'bottom':\r\n yTranslation = 0;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n const deltaPos = new THREE.Vector3(opts.dx || 0, opts.dy || 0, opts.dz || 0);\r\n this.userData = {\r\n translation: `translate(${xTranslation}%, ${yTranslation}%)`,\r\n offset: deltaPos,\r\n };\r\n }\r\n\r\n setItem(itemIdx, itemPos, fieldTxt) {\r\n const opts = this._opts;\r\n const text = this.items[itemIdx] || createLabel(fieldTxt, 'label');\r\n\r\n text.worldPos.copy(itemPos);\r\n text.style.textAlign = opts.horizontalAlign;\r\n text.style.verticalAlign = opts.verticalAlign;\r\n this.items[itemIdx] = text;\r\n }\r\n\r\n setColor(itemIdx, fColor, bColor) {\r\n const text = this.items[itemIdx];\r\n text.opts = {\r\n color: fColor,\r\n background: bColor,\r\n };\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.needsUpdate = true;\r\n this.dispatchEvent({ type: 'update' });\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n }\r\n\r\n // unimplemented functions\r\n raycast() {\r\n }\r\n\r\n setOpacity() {\r\n\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\n\r\nexport default LabelsGeometry;\r\n","import InstancedSpheresGeometry from './InstancedSpheresGeometry';\r\nimport SimpleSpheresGeometry from './SimpleSpheresGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport Instanced2CCylindersGeometry from './Instanced2CCylindersGeometry';\r\nimport ExtrudedObjectsGeometry from './ExtrudedObjectsGeometry';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport TwoColorLinesGeometry from './TwoColorLinesGeometry';\r\nimport CrossGeometry from './CrossGeometry';\r\nimport QuickSurfGeometry from './QuickSurfGeometry';\r\nimport ContactSurfaceGeometry from './ContactSurfaceGeometry';\r\nimport SSIsosurfaceGeometry from './SSIsosurfaceGeometry';\r\nimport LabelsGeometry from './LabelsGeometry';\r\n\r\nexport default {\r\n InstancedSpheresGeometry,\r\n SimpleSpheresGeometry,\r\n Simple2CCylindersGeometry,\r\n Instanced2CCylindersGeometry,\r\n ExtrudedObjectsGeometry,\r\n ChunkedLinesGeometry,\r\n TwoColorLinesGeometry,\r\n CrossGeometry,\r\n QuickSurfGeometry,\r\n ContactSurfaceGeometry,\r\n SSIsosurfaceGeometry,\r\n LabelsGeometry,\r\n};\r\n","export default {\r\n\r\n precision: 'mediump',\r\n\r\n /**\r\n *\r\n * @param {THREE.WebGLRenderer} renderer\r\n */\r\n init(renderer) {\r\n this.precision = renderer.capabilities.getMaxPrecision('highp');\r\n },\r\n};\r\n","import * as THREE from 'three';\r\n\r\nconst noiseWidth = 4;\r\nconst noiseHeight = 4;\r\nconst _noiseData = new Uint8Array([\r\n 24, 52, 0, 255, 254, 145, 0, 255, 122, 0, 0, 255, 7, 170, 0, 255,\r\n 34, 214, 0, 255, 173, 8, 0, 255, 86, 249, 0, 255, 160, 4, 0, 255,\r\n 226, 46, 0, 255, 224, 211, 0, 255, 3, 157, 0, 255, 174, 247, 0, 255,\r\n 12, 182, 0, 255, 220, 216, 0, 255, 1, 109, 0, 255, 253, 154, 0, 255,\r\n]);\r\nconst _noiseWrapS = THREE.RepeatWrapping;\r\nconst _noiseWrapT = THREE.RepeatWrapping;\r\nconst _noiseMinFilter = THREE.NearestFilter;\r\nconst _noiseMagFilter = THREE.NearestFilter;\r\nconst _noiseMapping = THREE.UVMapping;\r\nconst noiseTexture = new THREE.DataTexture(\r\n _noiseData,\r\n noiseWidth,\r\n noiseHeight,\r\n THREE.RGBAFormat,\r\n THREE.UnsignedByteType,\r\n _noiseMapping,\r\n _noiseWrapS,\r\n _noiseWrapT,\r\n _noiseMagFilter,\r\n _noiseMinFilter,\r\n 1,\r\n);\r\nnoiseTexture.needsUpdate = true;\r\n\r\nexport default {\r\n noiseWidth,\r\n noiseHeight,\r\n noiseTexture,\r\n};\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './Uber.vert';\r\nimport fragmentShader from './Uber.frag';\r\nimport capabilities from '../capabilities';\r\nimport noise from '../noiseTexture';\r\n\r\n// Length of _samplesKernel is used in Uber.frag\r\n// If you want to change length of _samplesKernel, please, remember change it in Uber.frag too.\r\n// You can easy find places for replace using word:_samplesKernel\r\nconst _samplesKernel = [\r\n new THREE.Vector2(-0.541978, 0.840393),\r\n new THREE.Vector2(0.125533, -0.992089),\r\n new THREE.Vector2(0.374329, 0.927296),\r\n new THREE.Vector2(-0.105475, 0.994422),\r\n];\r\n\r\nconst defaultUniforms = THREE.UniformsUtils.merge([\r\n\r\n THREE.UniformsLib.fog,\r\n THREE.UniformsLib.lights,\r\n\r\n {\r\n // are updated automatically by three.js (see THREE.ShaderLib.common)\r\n diffuse: { value: new THREE.Color(0xeeeeee) },\r\n opacity: { value: 1.0 },\r\n\r\n specular: { type: 'c', value: new THREE.Color(0x111111) },\r\n shininess: { type: 'f', value: 30 },\r\n fixedColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n zOffset: { type: 'f', value: 0.0 },\r\n zClipValue: { type: 'f', value: 0.0 },\r\n clipPlaneValue: { type: 'f', value: 0.0 },\r\n nearPlaneValue: { type: 'f', value: -0.5 },\r\n invModelViewMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n world2colorMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n dashedLineSize: { type: 'f', value: 0.1 },\r\n dashedLinePeriod: { type: 'f', value: 0.2 },\r\n projMatrixInv: { type: '4fv', value: new THREE.Matrix4() },\r\n viewport: { type: 'v2', value: new THREE.Vector2() },\r\n lineWidth: { type: 'f', value: 2.0 },\r\n // default value must be the same as settings\r\n fogAlpha: { type: 'f', value: 1.0 },\r\n samplesKernel: { type: 'v2v', value: null },\r\n noiseTex: { type: 't', value: null },\r\n noiseTexelSize: { type: 'v2', value: null },\r\n srcTexelSize: { type: 'v2', value: null },\r\n },\r\n\r\n]);\r\n\r\nconst uberOptionNames = [\r\n 'shininess',\r\n 'opacity',\r\n 'zOffset',\r\n 'diffuse',\r\n 'specular',\r\n 'fixedColor',\r\n 'zClipCoef',\r\n 'zClipValue',\r\n 'clipPlaneValue',\r\n 'world2colorMatrix',\r\n 'dashedLineSize',\r\n 'dashedLinePeriod',\r\n 'projMatrixInv',\r\n 'viewport',\r\n 'lineWidth',\r\n 'fogAlpha',\r\n 'samplesKernel',\r\n 'noiseTex',\r\n 'noiseTexelSize',\r\n 'srcTexelSize',\r\n];\r\n\r\n// properties that convert to uniforms\r\nconst uberOptions = {\r\n diffuse: new THREE.Color(0xffffff), // used in phong lighting\r\n specular: new THREE.Color(0x111111), // used in phong lighting\r\n shininess: 30, // used in phong lighting\r\n opacity: 1, // set mesh opacity\r\n fixedColor: new THREE.Color(0xffffff), // color to override (see OVERRIDE_COLOR)\r\n zOffset: 0.0, // used fo zsprites (see SPHERE_SPRITE CYLINDER_SPRITE)\r\n zClipCoef: 2.0, // use for Surfs clipping (mesh param, isn't used in shader) FIXME move to representation param\r\n zClipValue: 0.0, // value to clip Surfs in shader (see ZCLIP)\r\n clipPlaneValue: 0.0, // value to clip scene globally (see CLIPPLANE)\r\n world2colorMatrix: new THREE.Matrix4(),\r\n dashedLineSize: 0.1,\r\n dashedLinePeriod: 0.3,\r\n projMatrixInv: new THREE.Matrix4(),\r\n viewport: new THREE.Vector2(800, 600),\r\n lineWidth: 2.0,\r\n fogAlpha: 1.0,\r\n samplesKernel: _samplesKernel,\r\n noiseTex: noise.noiseTexture,\r\n noiseTexelSize: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight),\r\n srcTexelSize: new THREE.Vector2(1.0 / 800.0, 1.0 / 600.0),\r\n copy(source) {\r\n this.diffuse.copy(source.diffuse);\r\n this.specular.copy(source.specular);\r\n this.shininess = source.shininess;\r\n this.opacity = source.opacity;\r\n this.fixedColor.copy(source.fixedColor);\r\n this.zOffset = source.zOffset;\r\n this.zClipCoef = source.zClipCoef;\r\n this.zClipValue = source.zClipValue;\r\n this.clipPlaneValue = source.clipPlaneValue;\r\n this.world2colorMatrix.copy(source.world2colorMatrix);\r\n this.dashedLineSize = source.dashedLineSize;\r\n this.dashedLinePeriod = source.dashedLinePeriod;\r\n this.projMatrixInv = source.projMatrixInv;\r\n this.viewport = source.viewport;\r\n this.lineWidth = source.lineWidth; // used for thick lines only\r\n this.toonShading = source.toonShading;\r\n this.fogAlpha = source.fogAlpha;\r\n this.samplesKernel = source.samplesKernel;\r\n this.noiseTex = source.noiseTex;\r\n this.noiseTexelSize = source.noiseTexelSize;\r\n this.srcTexelSize = source.srcTexelSize;\r\n },\r\n};\r\n\r\nclass UberMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // add fog\r\n this.fog = true;\r\n // used for instanced geometry\r\n this.instancedPos = false;\r\n this.instancedMatrix = false;\r\n // atoms and links color\r\n this.attrColor = false;\r\n // second link color for cylinders\r\n this.attrColor2 = false;\r\n //\r\n this.attrAlphaColor = false;\r\n // overrides color for all vertices (used in selection)\r\n this.overrideColor = false;\r\n // zsrpites\r\n this.sphereSprite = false;\r\n this.cylinderSprite = false;\r\n // clip Surfs individually\r\n this.zClip = false;\r\n // clip scene with global clip plane\r\n this.clipPlane = false;\r\n // enable fake (chess-like) opacity\r\n this.fakeOpacity = false;\r\n // render only depth, don't take care about the pixel color (used for transparency depth prepass)\r\n this.prepassTransparancy = false;\r\n // used to render pixel positions\r\n this.colorFromPos = false;\r\n // used to render shadowmap\r\n this.shadowmap = false;\r\n // used to describe shadowmap type\r\n this.shadowmapType = 'random';\r\n // used to render pixel view deph\r\n this.colorFromDepth = false;\r\n // mark that rendering is for orthographic camera\r\n this.orthoCam = false;\r\n // used to render dashed line\r\n this.dashedLine = false;\r\n // mark as transparent\r\n this.transparent = true;\r\n // mark as thick lines\r\n this.thickLine = false;\r\n // makes fog begin transparency (required for transparent background)\r\n this.fogTransparent = false;\r\n // used to render surface normals to G buffer for ssao effect\r\n this.normalsToGBuffer = false;\r\n // used for toon material\r\n this.toonShading = false;\r\n\r\n // uber options of \"root\" materials are inherited from single uber-options object that resides in prototype\r\n this.uberOptions = Object.create(UberMaterial.prototype.uberOptions);\r\n\r\n // set default values\r\n super.setValues({\r\n uniforms: THREE.UniformsUtils.clone(defaultUniforms),\r\n vertexShader: this.precisionString() + vertexShader,\r\n fragmentShader: this.precisionString() + fragmentShader,\r\n lights: true,\r\n fog: true,\r\n side: THREE.DoubleSide,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n precisionString() {\r\n const { precision } = capabilities;\r\n const str = `precision ${precision} float;\\n`\r\n + `precision ${precision} int;\\n\\n`;\r\n return str;\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n\r\n this.fragmentShader = source.fragmentShader;\r\n this.vertexShader = source.vertexShader;\r\n\r\n this.uniforms = THREE.UniformsUtils.clone(source.uniforms);\r\n this.defines = { ...source.defines };\r\n this.extensions = source.extensions;\r\n\r\n this.fog = source.fog;\r\n this.instancedPos = source.instancedPos;\r\n this.instancedMatrix = source.instancedMatrix;\r\n this.attrColor = source.attrColor;\r\n this.attrColor2 = source.attrColor2;\r\n this.attrAlphaColor = source.attrAlphaColor;\r\n this.overrideColor = source.overrideColor;\r\n this.sphereSprite = source.sphereSprite;\r\n this.cylinderSprite = source.cylinderSprite;\r\n this.zClip = source.zClip;\r\n this.clipPlane = source.clipPlane;\r\n this.fakeOpacity = source.fakeOpacity;\r\n this.colorFromPos = source.colorFromPos;\r\n this.shadowmap = source.shadowmap;\r\n this.shadowmapType = source.shadowmapType;\r\n this.colorFromDepth = source.colorFromDepth;\r\n this.orthoCam = source.orthoCam;\r\n this.prepassTransparancy = source.prepassTransparancy;\r\n this.dashedLine = source.dashedLine;\r\n this.thickLine = source.thickLine;\r\n this.fogTransparent = source.fogTransparent;\r\n this.normalsToGBuffer = source.normalsToGBuffer;\r\n this.toonShading = source.toonShading;\r\n\r\n this.uberOptions.copy(source.uberOptions);\r\n\r\n return this;\r\n }\r\n\r\n // create copy of this material\r\n // its options are prototyped after this material's options\r\n createInstance() {\r\n const inst = new UberMaterial();\r\n inst.copy(this);\r\n inst.uberOptions = Object.create(this.uberOptions);\r\n return inst;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n const extensions = {};\r\n\r\n if (this.fog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.instancedPos) {\r\n defines.INSTANCED_POS = 1;\r\n }\r\n if (this.instancedMatrix) {\r\n defines.INSTANCED_MATRIX = 1;\r\n }\r\n if (this.attrColor) {\r\n defines.ATTR_COLOR = 1;\r\n }\r\n if (this.attrColor2) {\r\n defines.ATTR_COLOR2 = 1;\r\n }\r\n if (this.attrAlphaColor) {\r\n defines.ATTR_ALPHA_COLOR = 1;\r\n }\r\n if (this.overrideColor) {\r\n defines.OVERRIDE_COLOR = 1;\r\n }\r\n if (this.sphereSprite) {\r\n defines.SPHERE_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.cylinderSprite) {\r\n defines.CYLINDER_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.zClip) {\r\n defines.ZCLIP = 1;\r\n }\r\n if (this.clipPlane) {\r\n defines.CLIP_PLANE = 1;\r\n }\r\n if (this.fakeOpacity) {\r\n defines.FAKE_OPACITY = 1;\r\n }\r\n if (this.lights) {\r\n defines.USE_LIGHTS = 1;\r\n }\r\n if (this.colorFromPos) {\r\n defines.COLOR_FROM_POS = 1;\r\n }\r\n if (this.shadowmap) {\r\n defines.SHADOWMAP = 1;\r\n if (this.shadowmapType === 'pcf') {\r\n defines.SHADOWMAP_PCF_SHARP = 1;\r\n } else if (this.shadowmapType === 'random') {\r\n defines.SHADOWMAP_PCF_RAND = 1;\r\n } else {\r\n defines.SHADOWMAP_BASIC = 1;\r\n }\r\n }\r\n if (this.colorFromDepth) {\r\n defines.COLOR_FROM_DEPTH = 1;\r\n }\r\n if (this.orthoCam) {\r\n defines.ORTHOGRAPHIC_CAMERA = 1;\r\n }\r\n if (this.prepassTransparancy) {\r\n defines.PREPASS_TRANSP = 1;\r\n }\r\n if (this.dashedLine) {\r\n defines.DASHED_LINE = 1;\r\n }\r\n if (this.thickLine) {\r\n defines.THICK_LINE = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n if (this.normalsToGBuffer) {\r\n extensions.drawBuffers = true;\r\n defines.NORMALS_TO_G_BUFFER = 1;\r\n }\r\n if (this.toonShading) {\r\n defines.TOON_SHADING = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n this.extensions = extensions;\r\n }\r\n\r\n setUberOptions(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n for (const key in values) {\r\n if (!values.hasOwnProperty(key)) {\r\n continue;\r\n }\r\n\r\n if (this.uberOptions[key] instanceof THREE.Color) {\r\n this.uberOptions[key] = values[key].clone();\r\n } else {\r\n this.uberOptions[key] = values[key];\r\n }\r\n }\r\n }\r\n\r\n clone(shallow) {\r\n if (!shallow) {\r\n return super.clone();\r\n }\r\n return this.createInstance();\r\n }\r\n\r\n updateUniforms() {\r\n const self = this;\r\n\r\n uberOptionNames.forEach((p) => {\r\n if (self.uniforms.hasOwnProperty(p)) {\r\n if (self.uberOptions[p] instanceof THREE.Color\r\n || self.uberOptions[p] instanceof THREE.Matrix4) {\r\n self.uniforms[p].value = self.uberOptions[p].clone();\r\n } else {\r\n self.uniforms[p].value = self.uberOptions[p];\r\n }\r\n }\r\n });\r\n }\r\n}\r\n\r\nUberMaterial.prototype.uberOptions = uberOptions;\r\n\r\nexport default UberMaterial;\r\n","import UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default function (SuperClass) {\r\n class NewObjectType extends SuperClass {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.onBeforeRender = NewObjectType.prototype.onBeforeRender;\r\n }\r\n\r\n onBeforeRender(renderer, scene, camera, geometry, material, group) {\r\n this._onBeforeRender(renderer, scene, camera, geometry, material, group);\r\n this._update();\r\n }\r\n\r\n _onBeforeRender() {\r\n }\r\n\r\n _update() {\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material instanceof UberMaterial) {\r\n material.updateUniforms();\r\n }\r\n }\r\n }\r\n\r\n return NewObjectType;\r\n}\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZSpriteMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material.uniforms.invModelViewMatrix) {\r\n // NOTE: update of modelViewMatrix inside threejs is done after onBeforeRender call,\r\n // so we have to do it manually in that place\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n // get inverse matrix\r\n material.uniforms.invModelViewMatrix.value.copy(this.modelViewMatrix).invert();\r\n material.uniforms.nearPlaneValue.value = camera.near;\r\n material.uniformsNeedUpdate = true;\r\n }\r\n }\r\n}\r\n\r\nexport default ZSpriteMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZClippedMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n static _mvLength = new THREE.Vector3();\r\n\r\n static _center = new THREE.Vector3();\r\n\r\n static _modelView = new THREE.Matrix4();\r\n\r\n _onBeforeRender(renderer, scene, camera) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n\r\n const geo = this.geometry;\r\n const { material } = this;\r\n if (!geo.zClip || !material.uberOptions) {\r\n return;\r\n }\r\n\r\n const zClipCoef = 0.5;\r\n\r\n const modelView = ZClippedMesh._modelView;\r\n const mvLength = ZClippedMesh._mvLength;\r\n const center = ZClippedMesh._center;\r\n\r\n modelView.multiplyMatrices(this.matrixWorld, camera.matrixWorldInverse);\r\n const s = mvLength.setFromMatrixColumn(modelView, 0).length();\r\n center.copy(geo.boundingSphere.center);\r\n\r\n this.localToWorld(center);\r\n material.uberOptions.zClipValue = camera.position.z - center.z\r\n - s * (zClipCoef * geo.boundingSphere.radius);\r\n }\r\n}\r\n\r\nexport default ZClippedMesh;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from '../CSS2DObject';\r\nimport utils from '../../utils';\r\n\r\nclass TextMesh extends THREE.Group {\r\n constructor(geometry, _material) {\r\n super();\r\n this.geometry = geometry;\r\n\r\n const self = this;\r\n self.initialized = false;\r\n this.geometry.addEventListener('update', () => {\r\n self.update();\r\n });\r\n }\r\n\r\n init() {\r\n const { children } = this;\r\n for (let i = children.length - 1; i >= 0; --i) {\r\n this.remove(children[i]);\r\n }\r\n\r\n const { items, userData } = this.geometry;\r\n for (let i = 0, n = items.length; i < n; ++i) {\r\n const srcItem = items[i];\r\n if (!srcItem) {\r\n continue;\r\n }\r\n const item = utils.shallowCloneNode(srcItem);\r\n const label = new CSS2DObject(item);\r\n label.userData = _.clone(userData);\r\n const el = label.getElement();\r\n el.style.visibility = 'visible';\r\n label.source = srcItem;\r\n this.add(label);\r\n }\r\n this.initialized = true;\r\n }\r\n\r\n update() {\r\n const geo = this.geometry;\r\n if (!geo.needsUpdate) {\r\n return;\r\n }\r\n const { children } = this;\r\n if (!this.initialized) {\r\n this.init();\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n const item = child.source;\r\n child.position.copy(item.worldPos);\r\n child.userData.color = item.opts.color;\r\n child.userData.background = item.opts.background;\r\n }\r\n }\r\n}\r\n\r\nexport default TextMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass SimpleMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default SimpleMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\nconst _viewport = new THREE.Vector2();\r\n\r\nclass ThickLineMesh extends Mesh {\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!material.uberOptions) {\r\n return;\r\n }\r\n\r\n material.uberOptions.projMatrixInv.copy(camera.projectionMatrix).invert();\r\n renderer.getSize(_viewport);\r\n material.uberOptions.viewport.set(_viewport.width, _viewport.height);\r\n }\r\n}\r\n\r\nexport default ThickLineMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass InstancedMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default InstancedMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\nimport ZSpriteMesh from './ZSpriteMesh';\r\nimport ZClippedMesh from './ZClippedMesh';\r\nimport TextMesh from './TextMesh';\r\nimport SimpleMesh from './SimpleMesh';\r\nimport ThickLineMesh from './ThickLineMesh';\r\nimport InstancedMesh from './InstancedMesh';\r\n\r\nexport default {\r\n ZClipped: ZClippedMesh,\r\n ZSprite: ZSpriteMesh,\r\n Text: TextMesh,\r\n Line: UberObject(THREE.Line),\r\n LineSegments: UberObject(THREE.LineSegments),\r\n Mesh: SimpleMesh,\r\n ThickLineMesh,\r\n Instanced: InstancedMesh,\r\n};\r\n","import geometries from '../geometries/geometries';\r\nimport meshes from './meshes';\r\nimport ThickLinesGeometry from '../geometries/ThickLinesGeometry';\r\n\r\nfunction setMatParams(params, uniforms) {\r\n return function (material) {\r\n material.setValues(params);\r\n material.setUberOptions(uniforms);\r\n };\r\n}\r\n\r\nfunction _createInstancedCylinders(useZSprites, openEnded) {\r\n function Geometry(a, b) {\r\n return new geometries.Instanced2CCylindersGeometry(a, b, useZSprites, openEnded);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedMatrix: true,\r\n attrColor: true,\r\n attrColor2: true,\r\n attrAlphaColor: true,\r\n cylinderSprite: useZSprites,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createLineSegmentsGeoTriplet(geo, renderParams) {\r\n const thickLines = geo.prototype instanceof ThickLinesGeometry;\r\n const lineWidth = renderParams.lineWidth || 0;\r\n return {\r\n Geometry: geo,\r\n Object: thickLines ? meshes.ThickLineMesh : meshes.LineSegments,\r\n initMaterial: setMatParams({\r\n lights: false,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n thickLine: thickLines,\r\n }, {\r\n lineWidth,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createSimpleGeoTriplet(geoClass) {\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.Mesh,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createIsoSurfaceGeoTriplet(geoClass, caps, settings, renderParams) {\r\n const surfaceOpts = {\r\n wireframe: !!renderParams.wireframe,\r\n fakeOpacity: settings.now.isoSurfaceFakeOpacity,\r\n zClip: renderParams.zClip,\r\n };\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.ZClipped,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: false,\r\n wireframe: surfaceOpts.wireframe,\r\n fakeOpacity: surfaceOpts.fakeOpacity,\r\n zClip: surfaceOpts.zClip,\r\n }),\r\n };\r\n}\r\n\r\nclass MeshCreator {\r\n static createSpheres(caps, settings) {\r\n const useZSprites = settings.now.zSprites;\r\n function Geometry(a, b) {\r\n return new geometries.InstancedSpheresGeometry(a, b, useZSprites);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedPos: true,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n sphereSprite: useZSprites,\r\n }),\r\n };\r\n }\r\n\r\n static create2CClosedCylinders(_caps, _settings) {\r\n return _createInstancedCylinders(false, false);\r\n }\r\n\r\n static create2CCylinders(caps, settings) {\r\n return _createInstancedCylinders(settings.now.zSprites, true);\r\n }\r\n\r\n static create2CLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.TwoColorLinesGeometry, renderParams);\r\n }\r\n\r\n static createCrosses(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.CrossGeometry, renderParams);\r\n }\r\n\r\n static createExtrudedChains(_caps, _settings) {\r\n return _createSimpleGeoTriplet(geometries.ExtrudedObjectsGeometry);\r\n }\r\n\r\n static createChunkedLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.ChunkedLinesGeometry, renderParams);\r\n }\r\n\r\n static createQuickSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.QuickSurfGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createContactSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.ContactSurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createSASSES(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.SSIsosurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createLabels(_caps, _settings) {\r\n return {\r\n Geometry: geometries.LabelsGeometry,\r\n Object: meshes.Text,\r\n initMaterial() {\r\n },\r\n };\r\n }\r\n}\r\n\r\nexport default MeshCreator;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../gfxutils';\r\n\r\nclass TransformGroup extends THREE.Object3D {\r\n static _inverseMatrix = new THREE.Matrix4();\r\n\r\n static _ray = new THREE.Ray();\r\n\r\n constructor(geometry, geoParams, material, transforms) {\r\n super();\r\n this._geometry = geometry;\r\n this._geoParams = geoParams;\r\n const mat = material.createInstance();\r\n geoParams.initMaterial(mat);\r\n this._material = mat;\r\n this._transforms = transforms.length > 0 ? transforms : [new THREE.Matrix4()];\r\n const meshes = this._createMeshes(geometry);\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n this.add(meshes[i]);\r\n }\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const ray = TransformGroup._ray;\r\n const inverseMatrix = TransformGroup._inverseMatrix;\r\n const { children } = this;\r\n ray.copy(raycaster.ray);\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n\r\n if (!gfxutils.belongToSelectLayers(child)) {\r\n continue;\r\n }\r\n\r\n child.updateMatrixWorld();\r\n const mtx = child.matrixWorld;\r\n inverseMatrix.copy(mtx).invert();\r\n raycaster.ray.copy(ray).applyMatrix4(inverseMatrix);\r\n const childIntersects = [];\r\n this._geometry.raycast(raycaster, childIntersects);\r\n\r\n for (let j = 0, ciCount = childIntersects.length; j < ciCount; ++j) {\r\n const inters = childIntersects[j];\r\n if (inters.point) {\r\n inters.point.applyMatrix4(mtx);\r\n inters.distance = ray.origin.distanceTo(inters.point);\r\n }\r\n inters.object = child;\r\n intersects[intersects.length] = inters;\r\n }\r\n }\r\n raycaster.ray.copy(ray);\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const geos = this._geometry.getSubset(chunkIndices);\r\n const subset = [];\r\n let subIdx = 0;\r\n\r\n for (let i = 0, n = geos.length; i < n; ++i) {\r\n const meshes = this._createMeshes(geos[i]);\r\n for (let j = 0, meshCnt = meshes.length; j < meshCnt; ++j) {\r\n subset[subIdx++] = meshes[j];\r\n }\r\n }\r\n\r\n return subset;\r\n }\r\n\r\n _createMeshes(geometry) {\r\n const transforms = this._transforms;\r\n const Mesh = this._geoParams.Object;\r\n const material = this._material;\r\n const meshes = [];\r\n for (let i = 0, n = transforms.length; i < n; ++i) {\r\n const mesh = new Mesh(geometry, material);\r\n mesh.applyMatrix4(transforms[i]);\r\n meshes[i] = mesh;\r\n }\r\n\r\n return meshes;\r\n }\r\n}\r\n\r\nexport default TransformGroup;\r\n","import RCGroup from '../../RCGroup';\r\nimport TransformGroup from '../../meshes/TransformGroup';\r\n\r\nfunction wrapper(Name, args) {\r\n const params = [Name].concat(args);\r\n return Name.bind(...params);\r\n}\r\n\r\nclass ChemGroup extends RCGroup {\r\n constructor(geoParams, selection, colorer, mode, transforms, polyComplexity, material) {\r\n super();\r\n if (this.constructor === ChemGroup) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n this._selection = selection;\r\n this._mode = mode;\r\n this._colorer = colorer;\r\n this._chunksIdc = selection.chunks;\r\n this._polyComplexity = polyComplexity;\r\n this._geo = new (wrapper(geoParams.Geometry, this._makeGeoArgs()))();\r\n this._mesh = new TransformGroup(this._geo, geoParams, material, transforms);\r\n this.add(this._mesh);\r\n this._build();\r\n }\r\n\r\n _makeGeoArgs() {\r\n throw new Error('ChemGroup subclass must override _makeGeoArgs() method');\r\n }\r\n\r\n /**\r\n * Builds subset geometry by ATOMS index list\r\n *\r\n * @param {Number} mask - Representation mask\r\n * @param {Boolean} innerOnly - if true returns inner bonds only - without halves\r\n * @returns {Array} Subset geometry\r\n */\r\n getSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : false;\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return [];\r\n }\r\n return this._mesh.getSubset(chunksList);\r\n }\r\n\r\n _changeSubsetOpacity(mask, value, innerOnly) {\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return;\r\n }\r\n this._geo.setOpacity(chunksList, value);\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 1.0, innerOnly);\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 0.0, innerOnly);\r\n }\r\n}\r\n\r\nexport default ChemGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass AtomsGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { atoms } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const atomsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const atomIdx = atomsIdc[inters[i].chunkIdx];\r\n if (atomIdx < atoms.length) {\r\n inters[i].atom = atoms[atomIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { atoms } = this._selection;\r\n const atomsIdc = this._chunksIdc;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n if ((atom.mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default AtomsGroup;\r\n","import AtomsGroup from './AtomsGroup';\r\n\r\nclass AtomsSphereGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, atom.position, mode.calcAtomRadius(atom));\r\n geo.setColor(i, colorer.getAtomColor(atom, parent));\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), mode.calcAtomRadius(atom));\r\n if (updateColor) {\r\n geo.setColor(i, frameData.getAtomColor(colorer, atom));\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsSphereGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSurfaceGroup extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n return [n, opts];\r\n }\r\n}\r\nexport default AtomsSurfaceGroup;\r\n","/* This is a stub class keep it until SAS/SES is refactored */\r\n\r\nimport AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSASSESGroupStub extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n opts.selection = this._selection;\r\n opts.colorMode = this._colorer;\r\n return [n, opts];\r\n }\r\n}\r\n\r\nexport default AtomsSASSESGroupStub;\r\n","import AtomsGroup from './AtomsGroup';\r\nimport utils from '../../../utils';\r\n\r\nfunction adjustColor(color) {\r\n let r = (color >> 16) & 255;\r\n let g = (color >> 8) & 255;\r\n let b = color & 255;\r\n\r\n if (0.2126 * r + 0.7152 * g + 0.0722 * b > 127) {\r\n r = r * 3 / 10;\r\n g = g * 3 / 10;\r\n b = b * 3 / 10;\r\n } else {\r\n r = 255 - ((255 - r) * 3 / 10);\r\n g = 255 - ((255 - g) * 3 / 10);\r\n b = 255 - ((255 - b) * 3 / 10);\r\n }\r\n\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nfunction inverseColor(color) {\r\n const r = (color >> 16) & 255;\r\n const g = (color >> 8) & 255;\r\n const b = color & 255;\r\n\r\n return ((255 - r) << 16) | ((255 - g) << 8) | (255 - b);\r\n}\r\n\r\nfunction getAtomText(atom) {\r\n if (atom.name.getNode() !== null) {\r\n return atom.name.getNode();\r\n }\r\n\r\n return atom.getVisualName();\r\n}\r\n\r\nconst colorMappings = {\r\n none(c) {\r\n return c;\r\n },\r\n adjust: adjustColor,\r\n inverse: inverseColor,\r\n};\r\n\r\nfunction propagateColor(color, rule) {\r\n let result;\r\n if (colorMappings.hasOwnProperty(rule)) {\r\n result = utils.hexColor(colorMappings[rule](color));\r\n } else {\r\n const val = parseInt(rule, 16);\r\n if (!Number.isNaN(val) && rule.toLowerCase().startsWith('0x')) {\r\n result = utils.hexColor(val);\r\n } else {\r\n result = '#000000';\r\n }\r\n }\r\n return result;\r\n}\r\n\r\nconst templateMappings = {\r\n serial(a) {\r\n return a.serial;\r\n },\r\n name(a) {\r\n return a.getVisualName();\r\n },\r\n elem(a) {\r\n return a.element.name;\r\n },\r\n residue(a) {\r\n return a.residue.getType().getName();\r\n },\r\n sequence(a) {\r\n return a.residue.getSequence();\r\n },\r\n chain(a) {\r\n return a.residue.getChain().getName();\r\n },\r\n hetatm(a) {\r\n return a.isHet();\r\n },\r\n water(a) {\r\n return a.residue.getType().getName() === 'HOH' || a.residue.getType().getName() === 'WAT';\r\n },\r\n};\r\n\r\nconst parseTemplate = function (atom, str) {\r\n return str.replace(/\\{\\{(\\s*\\w+\\s*)\\}\\}/g, (m) => {\r\n let key = m.replace(/\\s+/g, '');\r\n key = key.substring(2, key.length - 2).toLowerCase();\r\n\r\n if (templateMappings.hasOwnProperty(key)) {\r\n return templateMappings[key](atom);\r\n }\r\n return 'null';\r\n });\r\n};\r\n\r\nclass AtomsTextGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n const opts = this._mode.getLabelOpts();\r\n return [this._selection.chunks.length, opts];\r\n }\r\n\r\n _build() {\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = colorer.getAtomColor(atom, parent);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, atom.position, text);\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = frameData.getAtomColor(colorer, atom);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), text);\r\n if (updateColor) {\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsTextGroup;\r\n","import * as THREE from 'three';\r\nimport AtomsGroup from './AtomsGroup';\r\n\r\nfunction _slerp(omega, v1, v2, t) {\r\n const oSin = Math.sin(omega);\r\n return v1.clone().multiplyScalar(Math.sin((1 - t) * omega) / oSin).addScaledVector(v2, Math.sin(t * omega) / oSin);\r\n}\r\n\r\nclass AromaticGroup extends AtomsGroup {\r\n _buildInner(radOffset, addChunk) {\r\n const chunksToIdx = this._selection.chunks;\r\n\r\n const prevVector = new THREE.Vector3();\r\n const currVector = new THREE.Vector3();\r\n const segmentsHeight = this._segmentsHeight;\r\n const leprStep = 1.0 / segmentsHeight;\r\n const colorer = this._colorer;\r\n\r\n const { cycles, parent } = this._selection;\r\n let chunkIdx = 0;\r\n let currAtomIdx = chunksToIdx[chunkIdx];\r\n\r\n for (let cIdx = 0, cCount = cycles.length; cIdx < cCount; ++cIdx) {\r\n const cycle = cycles[cIdx];\r\n const cycAtoms = cycle.atoms;\r\n const chunkPoints = [];\r\n const tmpDir = [];\r\n const { center } = cycle;\r\n const cycleRad = cycle.radius - radOffset;\r\n const n = cycAtoms.length;\r\n let i = 0;\r\n const prevPos = cycAtoms[n - 1].position;\r\n let currPos = cycAtoms[i].position;\r\n prevVector.subVectors(prevPos, center);\r\n currVector.subVectors(currPos, center);\r\n const upDir = currVector.clone().cross(prevVector).normalize();\r\n\r\n for (; i < n; ++i) {\r\n const omega = prevVector.angleTo(currVector);\r\n tmpDir[i] = _slerp(omega, prevVector, currVector, 0.5).normalize();\r\n currPos = cycAtoms[(i + 1) % n].position;\r\n prevVector.copy(currVector);\r\n currVector.subVectors(currPos, center);\r\n }\r\n\r\n for (i = 0; i < n; ++i) {\r\n if (cycAtoms[i].index !== currAtomIdx) {\r\n continue;\r\n }\r\n const start = tmpDir[i];\r\n const end = tmpDir[(i + 1) % n];\r\n const color = colorer.getAtomColor(cycAtoms[i], parent);\r\n const currAngle = start.angleTo(end);\r\n\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n chunkPoints[j] = _slerp(currAngle, start, end, j * leprStep).multiplyScalar(cycleRad).add(center);\r\n }\r\n\r\n addChunk(chunkIdx++, color, chunkPoints, center, upDir);\r\n currAtomIdx = chunksToIdx[chunkIdx];\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default AromaticGroup;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../../gfxutils';\r\nimport AromaticGroup from './AromaticGroup';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n for (let i = 0; i < parts; ++i) {\r\n const a = -2 * i / parts * Math.PI;\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\nconst { calcChunkMatrix } = gfxutils;\r\n\r\nclass AromaticTorusGroup extends AromaticGroup {\r\n _build() {\r\n const segmentsHeight = this._segmentsHeight;\r\n const torusRad = this._mode.getAromRadius();\r\n const radiusV = new THREE.Vector2(torusRad, torusRad);\r\n const radOffset = this._mode.calcStickRadius() + 2 * torusRad;\r\n const lookAtVector = new THREE.Vector3();\r\n const mtc = [];\r\n const geo = this._geo;\r\n this._buildInner(radOffset, (chunkIdx, color, points, center, upDir) => {\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n const currDir = currPoint.clone().sub(center).cross(upDir);\r\n lookAtVector.addVectors(currPoint, currDir);\r\n mtc[j] = calcChunkMatrix(currPoint, lookAtVector, upDir, radiusV);\r\n }\r\n geo.setItem(chunkIdx, mtc);\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._polyComplexity;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length];\r\n }\r\n}\r\n\r\nexport default AromaticTorusGroup;\r\n","import AromaticGroup from './AromaticGroup';\r\n\r\nclass AromaticLinesGroup extends AromaticGroup {\r\n _build() {\r\n const geo = this._geo;\r\n const radOffset = this._mode.getAromaticOffset();\r\n this._buildInner(radOffset, (chunkIdx, color, points) => {\r\n let prevPt = points[0];// do not replace with start\r\n for (let j = 1; j <= this._segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n geo.setSegment(chunkIdx, j - 1, prevPt, currPoint);\r\n prevPt = currPoint;\r\n }\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._mode.getAromaticArcChunks();\r\n return [this._selection.chunks.length, this._segmentsHeight, true];\r\n }\r\n}\r\n\r\nexport default AromaticLinesGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[inters[i].chunkIdx];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesGroup;\r\n","import ResiduesGroup from './ResiduesGroup';\r\n\r\nclass NucleicItemGroup extends ResiduesGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[Math.floor(inters[i].chunkIdx / 2)];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n let chunkIdx = 0;\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList[chunkIdx++] = 2 * i;\r\n chunksList[chunkIdx++] = 2 * i + 1;\r\n }\r\n }\r\n return chunksList;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finishUpdate();\r\n }\r\n}\r\n\r\nexport default NucleicItemGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicCylindersGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n geo.setItem(chunkIdx, cyl1, cyl2, stickRad);\r\n geo.setColor(chunkIdx, color, color);\r\n }\r\n}\r\n\r\nexport default NucleicCylindersGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicSpheresGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length * 2, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n let idx = chunkIdx * 2;\r\n geo.setItem(idx, cyl1, stickRad);\r\n geo.setColor(idx, color);\r\n idx++;\r\n geo.setItem(idx, cyl2, stickRad);\r\n geo.setColor(idx, color);\r\n }\r\n}\r\n\r\nexport default NucleicSpheresGroup;\r\n","import * as THREE from 'three';\r\nimport { Smooth } from '../../../../vendor/js/Smooth';\r\nimport gfxutils from '../../gfxutils';\r\nimport chem from '../../../chem';\r\n\r\nconst { ResidueType } = chem;\r\n\r\nconst calcMatrix = gfxutils.calcChunkMatrix;\r\n\r\nfunction _buildStructureInterpolator(points, tension) {\r\n const path = Smooth(points, {\r\n method: Smooth.METHOD_CUBIC,\r\n clip: Smooth.CLIP_CLAMP,\r\n cubicTension: tension,\r\n scaleTo: 1,\r\n });\r\n\r\n return function (t, argTrans) {\r\n let transformT = argTrans;\r\n if (transformT === null) {\r\n // map our range to the [second .. last but one]\r\n transformT = function (tt) {\r\n return (tt * ((points.length - 1) - 2) + 1) / (points.length - 1);\r\n };\r\n }\r\n const newt = transformT(t);\r\n const ans = path(newt);\r\n return new THREE.Vector3(ans[0], ans[1], ans[2]);\r\n };\r\n}\r\n\r\nfunction _addPoints(centerPoints, topPoints, idx, residue) {\r\n if (!residue._isValid) {\r\n centerPoints[idx] = centerPoints[idx - 1];\r\n topPoints[idx] = topPoints[idx - 1];\r\n return;\r\n }\r\n const cp = residue._controlPoint;\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n const tp = cp.clone().add(residue._wingVector);\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n}\r\n\r\nfunction _addPointsForLoneResidue(centerPoints, topPoints, idx, residue) {\r\n const nucleic = (residue._type.flags & ResidueType.Flags.NUCLEIC) !== 0;\r\n const nameFrom = nucleic ? 'C5\\'' : 'N';\r\n const nameTo = nucleic ? 'C3\\'' : 'C';\r\n\r\n let posFrom;\r\n let posTo;\r\n residue.forEachAtom((atom) => {\r\n const name = atom.getVisualName();\r\n if (!posFrom && name === nameFrom) {\r\n posFrom = atom.position;\r\n } else if (!posTo && name === nameTo) {\r\n posTo = atom.position;\r\n }\r\n });\r\n\r\n // provide a fallback for unknown residues\r\n if (!(posFrom && posTo)) {\r\n posFrom = residue._firstAtom.position;\r\n posTo = residue._lastAtom.position;\r\n }\r\n\r\n if (posFrom && posTo) {\r\n const shift = posTo.clone().sub(posFrom);\r\n\r\n const wing = residue._wingVector;\r\n const cp = residue._controlPoint;\r\n const tp = cp.clone().add(wing);\r\n\r\n const cpPrev = cp.clone().sub(shift);\r\n const tpPrev = cpPrev.clone().add(wing);\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n ++idx;\r\n\r\n const cpNext = cp.clone().add(shift);\r\n const tpNext = cpNext.clone().add(wing);\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n ++idx;\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n }\r\n}\r\n\r\nfunction _calcPoints(residues, firstIdx, lastIdx, boundaries) {\r\n const left = boundaries.start;\r\n const right = boundaries.end;\r\n function _prevIdx(idx) {\r\n return idx > left && residues[idx - 1]._isValid ? idx - 1 : idx;\r\n }\r\n function _nextIdx(idx) {\r\n return idx < right && residues[idx + 1]._isValid ? idx + 1 : idx;\r\n }\r\n\r\n const topPoints = [];\r\n const centerPoints = [];\r\n let arrIdx = 0;\r\n function _extrapolate2(currIdx, otherIdx) {\r\n const cp = residues[currIdx]._controlPoint.clone().lerp(residues[otherIdx]._controlPoint, -0.25);\r\n const tp = cp.clone().add(residues[currIdx]._wingVector);\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n }\r\n\r\n // a single disconnected residue\r\n const prevIdx = _prevIdx(firstIdx);\r\n const nextIdx = _nextIdx(lastIdx);\r\n if (prevIdx === nextIdx) {\r\n _addPointsForLoneResidue(centerPoints, topPoints, arrIdx, residues[firstIdx]);\r\n return { centerPoints, topPoints };\r\n }\r\n\r\n // Two points (prev-prev and next-next) are added to support edge conditions for cubic splines, they are ignored\r\n // Another two (prev and next) were added to support the outside of the sub chain\r\n\r\n // prev and prev-prev\r\n if (firstIdx === prevIdx) {\r\n // do the extrapolation\r\n _extrapolate2(firstIdx, _nextIdx(firstIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[_prevIdx(prevIdx)]);\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[prevIdx]);\r\n }\r\n\r\n // main loop\r\n for (let idx = firstIdx; idx <= lastIdx; ++idx) {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[idx]);\r\n }\r\n\r\n // next and next-next\r\n if (nextIdx === _nextIdx(nextIdx)) {\r\n // do the extrapolation\r\n _extrapolate2(lastIdx, _prevIdx(lastIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[nextIdx]);\r\n _addPoints(centerPoints, topPoints, arrIdx, residues[_nextIdx(nextIdx)]);\r\n }\r\n return { centerPoints, topPoints };\r\n}\r\n\r\nclass CartoonHelper {\r\n constructor(residues, startIdx, endIdx, segmentsCount, tension, boundaries) {\r\n const pointsArrays = _calcPoints(residues, startIdx, endIdx, boundaries);\r\n this._topInterp = _buildStructureInterpolator(pointsArrays.topPoints, tension);\r\n this._centerInterp = _buildStructureInterpolator(pointsArrays.centerPoints, tension);\r\n\r\n this._shift = 0.5 / (endIdx - startIdx + 2);\r\n this._valueStep = (1.0 - 2 * this._shift) / (2 * (endIdx - startIdx + 1) * (segmentsCount - 1));\r\n this._segmentsCount = segmentsCount;\r\n }\r\n\r\n prepareMatrices(idx, firstRad, secondRad) {\r\n const mtcCount = this._segmentsCount;\r\n const outMtc = new Array(mtcCount);\r\n const currRad = new THREE.Vector2(0, 0);\r\n\r\n const topInterp = this._topInterp;\r\n const cenInterp = this._centerInterp;\r\n\r\n let currentValue = this._shift + this._valueStep * (mtcCount - 1) * idx;\r\n\r\n for (let mtxIdx = 0; mtxIdx < mtcCount; ++mtxIdx) {\r\n const lerpVal = Math.min(1.0, mtxIdx / (mtcCount - 1));\r\n currRad.lerpVectors(firstRad, secondRad, lerpVal);\r\n\r\n const currTop = topInterp(currentValue, null);\r\n const currCenter = cenInterp(currentValue, null);\r\n currentValue += this._valueStep;\r\n const nextCenter = cenInterp(currentValue, null);\r\n\r\n outMtc[mtxIdx] = calcMatrix(currCenter.clone(), nextCenter.clone(), currTop.clone().sub(currCenter), currRad);\r\n }\r\n\r\n return outMtc;\r\n }\r\n}\r\n\r\nexport default CartoonHelper;\r\n","import * as THREE from 'three';\r\nimport ResiduesGroup from './ResiduesGroup';\r\nimport CartoonHelper from './CartoonHelper';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n\r\n for (let i = 0; i < parts; ++i) {\r\n // starts from pi/2 because it's important that points are lied on the angles of arrows (visual issues if not)\r\n const a = Math.PI / 2.0 - 2 * Math.PI * i / parts;\r\n\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\n\r\nfunction _loopThrough(subDiv, residues, segmentsHeight, tension, mode, callback) {\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n const { boundaries } = subDiv[subDivI];\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const idc = [subs[i].start, subs[i].end];\r\n const matrixHelper = new CartoonHelper(residues, idc[0], idc[1], segmentsHeight, tension, boundaries);\r\n let prevLast = null;\r\n const startIdx = subs[i].start * 2;\r\n const endIdx = subs[i].end * 2 + 1;\r\n let prevSecondRad = mode.getResidueRadius(residues[0], 0);\r\n for (let idx = startIdx; idx <= endIdx; ++idx) {\r\n const resIdx = (idx / 2 | 0);\r\n const currRes = residues[resIdx];\r\n const firstRad = mode.getResidueRadius(currRes, idx % 2);\r\n const secondRad = mode.getResidueRadius(currRes, 1 + (idx % 2));\r\n\r\n const mtc = matrixHelper.prepareMatrices(idx - idc[0] * 2, firstRad, secondRad);\r\n mtc.unshift(prevLast === null ? mtc[0] : prevLast);\r\n\r\n // Slope - radius is changed along this residue part\r\n const hasSlope = (firstRad.x !== secondRad.x) || (firstRad.y !== secondRad.y);\r\n // Cut - end radius of previous part not equal to start radius of this part. First section of this part lies in the orthogonal plane\r\n const hasCut = (firstRad.x !== prevSecondRad.x) || (firstRad.y !== prevSecondRad.y);\r\n\r\n callback(currRes, mtc, hasSlope, hasCut);\r\n\r\n prevLast = mtc[segmentsHeight];\r\n prevSecondRad = secondRad;\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ResiduesSubseqGroup extends ResiduesGroup {\r\n _makeGeoArgs() {\r\n const cmpMultiplier = this._mode.getHeightSegmentsRatio();\r\n this._segmentsHeight = this._polyComplexity * cmpMultiplier | 0;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length * 2];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, (currRes, mtc, hasSlope = false, hasCut = false) => {\r\n const color = colorer.getResidueColor(currRes, parent);\r\n chunkIdc[chunkIdx] = currRes._index;\r\n geo.setItem(chunkIdx, mtc, hasSlope, hasCut);\r\n geo.setColor(chunkIdx++, color);\r\n });\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n const frameRes = frameData.getResidues();\r\n let chunkIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n _loopThrough(this._selection.subdivs, frameRes, this._segmentsHeight, tension, mode, (currRes, mtc) => {\r\n geo.setItem(chunkIdx, mtc);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n });\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default ResiduesSubseqGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesTraceGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const subDiv = this._selection.subdivs;\r\n let chunksCount = 0;\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n chunksCount += subs[i].end - subs[i].start;\r\n }\r\n }\r\n return [chunksCount, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n chunkIdc[chunkIdx] = { first: prevRes._index, second: currRes._index };\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n geo.finalize();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n const { residues } = this._selection;\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksToIdx = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const chunk = chunksToIdx[Math.floor(chunkIdx / 2)];\r\n const resIdx = chunkIdx % 2 === 0 ? chunk.first : chunk.second;\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const chunksToIdx = this._chunksIdc;\r\n const { residues } = this._selection;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const chunk = chunksToIdx[i];\r\n if (residues[chunk.first]._mask & mask) {\r\n chunksList.push(i * 2);\r\n }\r\n if (residues[chunk.second]._mask & mask) {\r\n chunksList.push(i * 2 + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesTraceGroup;\r\n","import ChemGroup from './ChemGroup';\r\nimport Bond from '../../../chem/Bond';\r\n\r\nfunction getCylinderCount(bondOrder) {\r\n return bondOrder < 2 ? 1 : bondOrder;\r\n}\r\n\r\nclass BondsGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const drawMultiple = this._mode.drawMultiorderBonds();\r\n const showAromatic = this._mode.showAromaticLoops();\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n let bondsCount = 0;\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n bondsCount += this.getBondOrder(bonds[bondsIdc[i]], drawMultiple, showAromatic);\r\n }\r\n return [bondsCount, this._polyComplexity];\r\n }\r\n\r\n getBondOrder(bond, drawMultiple, showAromatic) {\r\n let bondOrder = 1;\r\n if (drawMultiple && (!showAromatic || bond._type !== Bond.BondType.AROMATIC)) {\r\n bondOrder = getCylinderCount(bond._order);\r\n }\r\n return bondOrder;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const { bonds } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const bondsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const bondIdx = bondsIdc[Math.floor(chunkIdx / 2)];\r\n if (bondIdx < bonds.length) {\r\n const bond = bonds[bondIdx];\r\n inters[i].atom = chunkIdx % 2 === 0 ? bond._left : bond._right;\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask, innerOnly) {\r\n const chunksList = [];\r\n const { bonds } = this._selection;\r\n const chunksToIdx = this._chunksIdc;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const bond = bonds[chunksToIdx[i]];\r\n if ((bond._left.mask & mask) && (!innerOnly || (bond._right.mask & mask))) {\r\n chunksList.push(2 * i);\r\n }\r\n if ((bond._right.mask & mask) && (!innerOnly || (bond._left.mask & mask))) {\r\n chunksList.push(2 * i + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default BondsGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nclass BondsCylinderGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsCylinderGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nconst STEP_SIZE = 0.15;\r\n\r\nclass BondsLinesGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsLinesGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\nimport AtomsSurfaceGroup from './AtomsSurfaceGroup';\r\nimport AtomsSASSESGroupStub from './AtomsSASSESGroupStub';\r\nimport AtomsTextGroup from './AtomsTextGroup';\r\nimport AromaticTorusGroup from './AromaticTorusGroup';\r\nimport AromaticLinesGroup from './AromaticLinesGroup';\r\nimport NucleicCylindersGroup from './NucleicCylindersGroup';\r\nimport NucleicSpheresGroup from './NucleicSpheresGroup';\r\nimport ResiduesSubseqGroup from './ResiduesSubseqGroup';\r\nimport ResiduesTraceGroup from './ResiduesTraceGroup';\r\nimport BondsCylinderGroup from './BondsCylinderGroup';\r\nimport BondsLinesGroup from './BondsLinesGroup';\r\n\r\nexport default {\r\n AtomsSphereGroup,\r\n AtomsSurfaceGroup,\r\n AtomsSASSESGroupStub,\r\n AtomsTextGroup,\r\n AromaticTorusGroup,\r\n AromaticLinesGroup,\r\n NucleicCylindersGroup,\r\n NucleicSpheresGroup,\r\n ResiduesSubseqGroup,\r\n ResiduesTraceGroup,\r\n BondsCylinderGroup,\r\n BondsLinesGroup,\r\n};\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AtomsProcessor extends RCGroup {\r\n constructor(AtomsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n this._mode = mode;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let atomCount = 0;\r\n component.forEachAtom((atom) => {\r\n if (!self._checkAtom(atom, mask)) {\r\n return;\r\n }\r\n atomsIdc[atomCount++] = atom.index;\r\n });\r\n if (atomCount === 0) {\r\n return;\r\n }\r\n const atomsGroup = new AtomsGroup(geoParams, {\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n _checkAtom(atom, mask) {\r\n return atom.mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AtomsProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\n\r\nclass OrphanAtomsProcessor extends AtomsProcessor {\r\n _checkAtom(atom, mask) {\r\n if (!(atom.mask & mask)) {\r\n return false;\r\n }\r\n\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n if ((bonds[i]._left.mask & mask) && (bonds[i]._right.mask & mask)) {\r\n return false;\r\n }\r\n }\r\n return true;\r\n }\r\n}\r\n\r\nexport default OrphanAtomsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass ResiduesProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n component.forEachResidue((residue) => {\r\n if (self._checkResidue(residue, mask)) {\r\n resIdc[chunksCount++] = residue._index;\r\n }\r\n });\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n checkResidue(residue, mask) {\r\n return residue._mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default ResiduesProcessor;\r\n","import ResidueProcessor from './ResiduesProcessor';\r\n\r\nclass NucleicProcessor extends ResidueProcessor {\r\n _checkResidue(residue, mask) {\r\n return mask & residue._mask && residue._cylinders !== null;\r\n }\r\n}\r\nexport default NucleicProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass SubseqsProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const subDivs = component.getMaskedSubdivSequences(mask);\r\n\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n for (let subDivI = 0, subDivN = subDivs.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDivs[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let j = subs[i].start, jEnd = subs[i].end; j <= jEnd; ++j) {\r\n resIdc[chunksCount++] = residues[j]._index;\r\n }\r\n }\r\n }\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n subdivs: subDivs,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default SubseqsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass BondsProcessor extends RCGroup {\r\n constructor(BondsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const bonds = complex.getBonds();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const bondsIdc = [];\r\n let bondsCount = 0;\r\n component.forEachBond((bond) => {\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n if (!(atom1.mask & mask) || !(atom2.mask & mask)) {\r\n return;\r\n }\r\n bondsIdc[bondsCount++] = bond._index;\r\n });\r\n if (bondsCount === 0) {\r\n return;\r\n }\r\n const bondsGroup = new BondsGroup(geoParams, {\r\n bonds,\r\n chunks: bondsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n bondsGroup._component = component;\r\n self.add(bondsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default BondsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AromaticProcessor extends RCGroup {\r\n constructor(AromaticGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n if (!mode.showAromaticLoops()) {\r\n return;\r\n }\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let chunksCount = 0;\r\n const cycles = [];\r\n let cycleIdx = 0;\r\n component.forEachCycle((cycle) => {\r\n const cycAtoms = cycle.atoms;\r\n let perCycle = 0;\r\n for (let i = 0, n = cycAtoms.length; i < n; ++i) {\r\n if ((cycAtoms[i].mask & mask) !== 0) {\r\n ++perCycle;\r\n atomsIdc[chunksCount++] = cycAtoms[i].index;\r\n }\r\n }\r\n if (perCycle > 0) {\r\n cycles[cycleIdx++] = cycle;\r\n }\r\n });\r\n\r\n const atomsGroup = new AromaticGroup(geoParams, {\r\n cycles,\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AromaticProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\nimport OrphanAtomsProcessor from './OrphanAtomsProcessor';\r\nimport ResiduesProcessor from './ResiduesProcessor';\r\nimport NucleicProcessor from './NucleicProcessor';\r\nimport SubseqsProcessor from './SubseqsProcessor';\r\nimport BondsProcessor from './BondsProcessor';\r\nimport AromaticProcessor from './AromaticProcessor';\r\n\r\nexport default {\r\n Atoms: AtomsProcessor,\r\n OrphanAtoms: OrphanAtomsProcessor,\r\n Residues: ResiduesProcessor,\r\n Nucleic: NucleicProcessor,\r\n Subseqs: SubseqsProcessor,\r\n Bonds: BondsProcessor,\r\n Aromatic: AromaticProcessor,\r\n};\r\n","import MeshCreator from '../../meshes/MeshCreator';\r\nimport groups from './groups';\r\nimport processors from '../processors/processors';\r\n\r\nfunction _bakeGroup(triplet, Processor, Group) {\r\n return function (complex, colorer, mode, polyComplexity, mask, material) {\r\n return new Processor(Group, triplet, complex, colorer, mode, polyComplexity, mask, material);\r\n };\r\n}\r\n\r\nclass GroupsFactory {\r\n static AtomsSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static OrphanedAtomsCrosses(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createCrosses(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.OrphanAtoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static BondsCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsCylinderGroup);\r\n }\r\n\r\n static BondsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.create2CLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsLinesGroup);\r\n }\r\n\r\n static CartoonChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesSubseqGroup);\r\n }\r\n\r\n static TraceChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CClosedCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesTraceGroup);\r\n }\r\n\r\n static NucleicSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicSpheresGroup);\r\n }\r\n\r\n static NucleicCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicCylindersGroup);\r\n }\r\n\r\n static ALoopsTorus(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticTorusGroup);\r\n }\r\n\r\n static ALoopsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createChunkedLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticLinesGroup);\r\n }\r\n\r\n static QuickSurfGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createQuickSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static ContactSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createContactSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static SASSESSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createSASSES(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSASSESGroupStub);\r\n }\r\n\r\n static TextLabelsGeo(caps, settings) {\r\n const gfxTriplet = MeshCreator.createLabels(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsTextGroup);\r\n }\r\n}\r\n\r\nexport default GroupsFactory;\r\n","import _ from 'lodash';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport factory from './groups/GroupsFactory';\r\n\r\n/**\r\n * Create new mode.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the mode after its creation.\r\n *\r\n * @exports Mode\r\n * @this Mode\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available modes used for building and displaying molecule geometry.\r\n */\r\nclass Mode {\r\n constructor(opts) {\r\n if (this.constructor === Mode) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Mode options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts);\r\n }\r\n\r\n /**\r\n * Get mode identification, probably with options.\r\n * @returns {string|Array} Mode identifier string ({@link Mode#id}) or two-element array containing both mode\r\n * identifier and options ({@link Mode#opts}).\r\n * Options are returned if they were changed during or after the mode creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, this.settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const polyComplexity = this.opts.polyComplexity ? this.opts.polyComplexity[this.settings.now.resolution] : 0;\r\n const groupList = this.depGroups;\r\n const groupCount = groupList.length;\r\n const group = new gfxutils.RCGroup();\r\n const self = this;\r\n for (let i = 0; i < groupCount; ++i) {\r\n let currGroup = groupList[i];\r\n let renderParams = {};\r\n if (_.isArray(currGroup)) {\r\n renderParams = currGroup[1].call(this);\r\n [currGroup] = currGroup;\r\n }\r\n const Group = factory[currGroup](null, this.settings, renderParams);\r\n const newGroup = new Group(complex, colorer, self, polyComplexity, mask, material);\r\n if (newGroup.children.length > 0) {\r\n group.add(newGroup);\r\n }\r\n }\r\n return group;\r\n }\r\n}\r\n\r\nmakeContextDependent(Mode.prototype);\r\n\r\n/**\r\n* Mode identifier.\r\n* @type {string}\r\n*/\r\nMode.prototype.id = '__';\r\n\r\n/**\r\n * Mode geo groups.\r\n * @type {Array}\r\n */\r\nMode.prototype.depGroups = [];\r\n\r\nexport default Mode;\r\n","import Mode from './Mode';\r\n\r\nfunction getRenderParams() {\r\n return {\r\n lineWidth: this.opts.lineWidth,\r\n };\r\n}\r\n\r\nclass LinesMode extends Mode {\r\n static id = 'LN';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const groups = this.depGroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n groups[i] = [groups[i], getRenderParams];\r\n }\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n\r\n calcAtomRadius() {\r\n return this.opts.atom;\r\n }\r\n\r\n getAromaticOffset() {\r\n return this.opts.offsarom;\r\n }\r\n\r\n getAromaticArcChunks() {\r\n return this.opts.chunkarom;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n}\r\n\r\nLinesMode.prototype.id = 'LN';\r\nLinesMode.prototype.name = 'Lines';\r\nLinesMode.prototype.shortName = 'Lines';\r\nLinesMode.prototype.depGroups = [\r\n 'ALoopsLines',\r\n 'BondsLines',\r\n 'OrphanedAtomsCrosses',\r\n];\r\n\r\nexport default LinesMode;\r\n","/* eslint-disable no-magic-numbers */\r\nimport Mode from './Mode';\r\n\r\nclass LicoriceMode extends Mode {\r\n static id = 'LC';\r\n\r\n calcAtomRadius(_atom) {\r\n return this.opts.bond;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nLicoriceMode.prototype.id = 'LC';\r\nLicoriceMode.prototype.name = 'Licorice';\r\nLicoriceMode.prototype.shortName = 'Licorice';\r\nLicoriceMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default LicoriceMode;\r\n","/* eslint-disable no-magic-numbers */\r\nimport Mode from './Mode';\r\n\r\nclass BallsAndSticksMode extends Mode {\r\n static id = 'BS';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius * this.opts.atom;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nBallsAndSticksMode.prototype.id = 'BS';\r\nBallsAndSticksMode.prototype.name = 'Balls and Sticks';\r\nBallsAndSticksMode.prototype.shortName = 'Balls';\r\nBallsAndSticksMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default BallsAndSticksMode;\r\n","import Mode from './Mode';\r\n\r\nclass VanDerWaalsMode extends Mode {\r\n static id = 'VW';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n}\r\n\r\nVanDerWaalsMode.prototype.id = 'VW';\r\nVanDerWaalsMode.prototype.name = 'Van der Waals';\r\nVanDerWaalsMode.prototype.shortName = 'VDW';\r\nVanDerWaalsMode.prototype.depGroups = ['AtomsSpheres'];\r\n\r\nexport default VanDerWaalsMode;\r\n","import Mode from './Mode';\r\n\r\nclass TraceMode extends Mode {\r\n static id = 'TR';\r\n\r\n calcStickRadius() {\r\n return this.opts.radius;\r\n }\r\n}\r\n\r\nTraceMode.prototype.id = 'TR';\r\nTraceMode.prototype.name = 'Trace';\r\nTraceMode.prototype.shortName = 'Trace';\r\nTraceMode.prototype.depGroups = ['TraceChains'];\r\n\r\nexport default TraceMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass TubeMode extends Mode {\r\n static id = 'TU';\r\n\r\n getResidueRadius(_residue) {\r\n return this.TUBE_RADIUS;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const rad = this.opts.radius;\r\n this.TUBE_RADIUS = new THREE.Vector2(rad, rad);\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nTubeMode.prototype.id = 'TU';\r\nTubeMode.prototype.name = 'Tube';\r\nTubeMode.prototype.shortName = 'Tube';\r\nTubeMode.prototype.depGroups = ['CartoonChains'];\r\n\r\nexport default TubeMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass CartoonMode extends Mode {\r\n static id = 'CA';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n // cache for secondary structure options\r\n this.secCache = {};\r\n }\r\n\r\n getResidueStartRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (!second || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return secOpts.start;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueEndRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (second === null || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return this.ARROW_END;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueRadius(residue, val) {\r\n const startRad = this.getResidueStartRadius(residue);\r\n if (val === 0) {\r\n return startRad;\r\n }\r\n\r\n const endRad = this.getResidueEndRadius(residue);\r\n if (val === 2) {\r\n return endRad;\r\n }\r\n\r\n return startRad.clone().lerp(endRad, val / 2.0);\r\n }\r\n\r\n calcStickRadius(_res) {\r\n return this.opts.radius;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const tubeRad = this.opts.radius;\r\n const secHeight = this.opts.depth;\r\n\r\n this.TUBE_RADIUS = new THREE.Vector2(tubeRad, tubeRad);\r\n this.ARROW_END = new THREE.Vector2(secHeight, tubeRad);\r\n const secCache = {};\r\n const secData = this.opts.ss;\r\n /* eslint-disable guard-for-in */\r\n for (const prop in secData) {\r\n secCache[prop] = {\r\n center: new THREE.Vector2(secHeight, secData[prop].width),\r\n start: new THREE.Vector2(secHeight, secData[prop].arrow),\r\n };\r\n }\r\n this.secCache = secCache;\r\n /* eslint-enable guard-for-in */\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nCartoonMode.prototype.id = 'CA';\r\nCartoonMode.prototype.name = 'Cartoon';\r\nCartoonMode.prototype.shortName = 'Cartoon';\r\nCartoonMode.prototype.depGroups = [\r\n 'CartoonChains',\r\n 'NucleicSpheres',\r\n 'NucleicCylinders',\r\n];\r\n\r\nexport default CartoonMode;\r\n","import chem from '../../chem';\r\nimport Mode from './Mode';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction getRenderParams() {\r\n return {\r\n wireframe: this.opts.wireframe,\r\n zClip: this.opts.zClip,\r\n };\r\n}\r\n\r\nclass SurfaceMode extends Mode {\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const surfaces = this.surfaceNames;\r\n const groups = this.depGroups;\r\n for (let i = 0, n = surfaces.length; i < n; ++i) {\r\n groups[groups.length] = [surfaces[i], getRenderParams];\r\n }\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getVisibilitySelector() {\r\n let visibilitySelector = null;\r\n if (this.opts.subset !== '') {\r\n const res = selectors.parse(this.opts.subset);\r\n if (!res.error) {\r\n visibilitySelector = res.selector;\r\n }\r\n }\r\n return visibilitySelector;\r\n }\r\n}\r\n\r\nSurfaceMode.prototype.isSurface = true;\r\nSurfaceMode.prototype.surfaceNames = [];\r\n\r\nexport default SurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass QuickSurfaceMode extends SurfaceMode {\r\n static id = 'QS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n useBeads: false,\r\n isoValue: this.opts.isoValue,\r\n gaussLim: this.opts.gaussLim[this.settings.now.resolution],\r\n radScale: this.opts.scale,\r\n gridSpacing: this.opts.gridSpacing[this.settings.now.resolution],\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nQuickSurfaceMode.prototype.id = 'QS';\r\nQuickSurfaceMode.prototype.name = 'Quick Surface';\r\nQuickSurfaceMode.prototype.shortName = 'Quick Surf';\r\nQuickSurfaceMode.prototype.surfaceNames = ['QuickSurfGeo'];\r\n\r\nexport default QuickSurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass IsoSurfaceMode extends SurfaceMode {\r\n constructor(excludeProbe, opts) {\r\n super(opts);\r\n this._excludeProbe = excludeProbe;\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getSurfaceOpts() {\r\n return {\r\n gridSpacing: this.opts.polyComplexity[this.settings.now.resolution],\r\n radScale: this._radScale,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n probeRadius: this.opts.probeRadius,\r\n excludeProbe: this._excludeProbe,\r\n };\r\n }\r\n}\r\n\r\nIsoSurfaceMode.prototype.id = 'SU';\r\nIsoSurfaceMode.prototype.name = 'Surface';\r\nIsoSurfaceMode.prototype.shortName = 'Surface';\r\nIsoSurfaceMode.prototype.surfaceNames = ['SASSESSurfaceGeo'];\r\n\r\nIsoSurfaceMode.prototype._radScale = 1;\r\nIsoSurfaceMode.prototype._excludeProbe = false;\r\n\r\nexport default IsoSurfaceMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSASMode extends IsoSurfaceMode {\r\n static id = 'SA';\r\n\r\n constructor(opts) {\r\n super(false, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSASMode.prototype.id = 'SA';\r\nIsoSurfaceSASMode.prototype.name = 'Solvent Accessible Surface';\r\nIsoSurfaceSASMode.prototype.shortName = 'SAS';\r\n\r\nexport default IsoSurfaceSASMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSESMode extends IsoSurfaceMode {\r\n static id = 'SE';\r\n\r\n constructor(opts) {\r\n super(true, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSESMode.prototype.id = 'SE';\r\nIsoSurfaceSESMode.prototype.name = 'Solvent Excluded Surface';\r\nIsoSurfaceSESMode.prototype.shortName = 'SES';\r\n\r\nexport default IsoSurfaceSESMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass ContactSurfaceMode extends SurfaceMode {\r\n static id = 'CS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n probeRadius: this.opts.probeRadius,\r\n radScale: this.opts.polyComplexity[this.settings.now.resolution],\r\n scaleFactor: this.opts.polyComplexity[this.settings.now.resolution],\r\n gridSpacing: 1.0 / this.opts.polyComplexity[this.settings.now.resolution],\r\n isoValue: this.opts.isoValue,\r\n probePositions: this.opts.probePositions,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nContactSurfaceMode.prototype.id = 'CS';\r\nContactSurfaceMode.prototype.name = 'Contact Surface';\r\nContactSurfaceMode.prototype.shortName = 'Contact Surf';\r\nContactSurfaceMode.prototype.isSurface = true;\r\nContactSurfaceMode.prototype.surfaceNames = ['ContactSurfaceGeo'];\r\n\r\nexport default ContactSurfaceMode;\r\n","import _ from 'lodash';\r\nimport Mode from './Mode';\r\n\r\nclass TextMode extends Mode {\r\n static id = 'TX';\r\n\r\n getTemplateOptions() {\r\n return this.opts.template;\r\n }\r\n\r\n getLabelOpts() {\r\n return _.merge(this.opts, {\r\n colors: true,\r\n adjustColor: true,\r\n transparent: true,\r\n });\r\n }\r\n}\r\n\r\nTextMode.prototype.id = 'TX';\r\nTextMode.prototype.name = 'Text mode';\r\nTextMode.prototype.shortName = 'Text';\r\nTextMode.prototype.depGroups = ['TextLabelsGeo'];\r\n\r\nexport default TextMode;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport LinesMode from './modes/LinesMode';\r\nimport LicoriceMode from './modes/LicoriceMode';\r\nimport BallsAndSticksMode from './modes/BallsAndSticksMode';\r\nimport VanDerWaalsMode from './modes/VanDerWaalsMode';\r\nimport TraceMode from './modes/TraceMode';\r\nimport TubeMode from './modes/TubeMode';\r\nimport CartoonMode from './modes/CartoonMode';\r\nimport QuickSurfaceMode from './modes/QuickSurfaceMode';\r\nimport IsoSurfaceSASMode from './modes/IsoSurfaceSASMode';\r\nimport IsoSurfaceSESMode from './modes/IsoSurfaceSESMode';\r\nimport ContactSurfaceMode from './modes/ContactSurfaceMode';\r\nimport TextMode from './modes/TextMode';\r\n\r\nconst modes = new EntityList([\r\n LinesMode,\r\n LicoriceMode,\r\n BallsAndSticksMode,\r\n VanDerWaalsMode,\r\n TraceMode,\r\n TubeMode,\r\n CartoonMode,\r\n QuickSurfaceMode,\r\n IsoSurfaceSASMode,\r\n IsoSurfaceSESMode,\r\n ContactSurfaceMode,\r\n TextMode,\r\n]);\r\n\r\nexport default modes;\r\n","import _ from 'lodash';\r\n\r\nfunction clamp(x, a, b) {\r\n return x <= b ? x < 0 ? 0 : x : b;\r\n}\r\n\r\nfunction lerpColor(c1, c2, alpha) {\r\n const beta = 1 - alpha;\r\n const r1 = (c1 >> 16) & 0xff;\r\n const g1 = (c1 >> 8) & 0xff;\r\n const b1 = c1 & 0xff;\r\n const r2 = (c2 >> 16) & 0xff;\r\n const g2 = (c2 >> 8) & 0xff;\r\n const b2 = c2 & 0xff;\r\n const r = beta * r1 + alpha * r2;\r\n const g = beta * g1 + alpha * g2;\r\n const b = beta * b1 + alpha * b2;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nclass Palette {\r\n constructor(name, id) {\r\n this.name = name || 'Custom';\r\n this.id = id || 'CP';\r\n }\r\n\r\n getElementColor(name, asIs = false) {\r\n const color = this.elementColors[name];\r\n return color === undefined && !asIs ? this.defaultElementColor : color;\r\n }\r\n\r\n getResidueColor(name, asIs = false) {\r\n const color = this.residueColors[name];\r\n return color === undefined && !asIs ? this.defaultResidueColor : color;\r\n }\r\n\r\n getChainColor(name) {\r\n let chain = name.charCodeAt(0);\r\n chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F)\r\n % this.chainColors.length;\r\n return this.chainColors[chain];\r\n }\r\n\r\n getSecondaryColor(type, asIs = false) {\r\n const color = this.secondaryColors[type];\r\n return color === undefined && !asIs ? this.defaultSecondaryColor : color;\r\n }\r\n\r\n getSequentialColor(index) {\r\n const { colors } = this;\r\n const len = colors.length;\r\n return index < 0 ? colors[(index % len) + len] : colors[index % len];\r\n }\r\n\r\n getGradientColor(value, gradientName) {\r\n const gradient = this.gradients[gradientName];\r\n if (!gradient) {\r\n return this.defaultNamedColor;\r\n }\r\n const count = gradient.length;\r\n const index = value * (count - 1);\r\n let left = Math.floor(index);\r\n const right = clamp(left + 1, 0, count - 1);\r\n left = clamp(left, 0, count - 1);\r\n return lerpColor(gradient[left], gradient[right], index - left);\r\n }\r\n\r\n getNamedColor(name, asIs = false) {\r\n const color = this.namedColors[name];\r\n return color === undefined && !asIs ? this.defaultNamedColor : color;\r\n }\r\n}\r\n\r\n_.assign(Palette.prototype, {\r\n colors: [0xFFFFFF, 0xFF0000, 0x00FF00, 0x0000FF, 0x808080],\r\n\r\n minRangeColor: 0x000000,\r\n midRangeColor: 0x7F7F7F,\r\n maxRangeColor: 0xFFFFFF,\r\n\r\n defaultElementColor: 0xFFFFFF,\r\n elementColors: {},\r\n\r\n defaultResidueColor: 0xFFFFFF,\r\n residueColors: {},\r\n\r\n chainColors: [0xFFFFFF],\r\n\r\n defaultSecondaryColor: 0xFFFFFF,\r\n secondaryColors: {},\r\n\r\n defaultGradientColor: 0x000000,\r\n\r\n defaultNamedColor: 0xFFFFFF,\r\n namedColorsArray: [\r\n /* eslint-disable no-multi-spaces */\r\n ['indianred', 0xcd5c5c],\r\n ['lightcoral', 0xf08080],\r\n ['salmon', 0xfa8072],\r\n ['darksalmon', 0xe9967a],\r\n ['lightsalmon', 0xffa07a],\r\n ['crimson', 0xdc143c],\r\n ['red', 0xff0000],\r\n ['firebrick', 0xb22222],\r\n ['darkred', 0x8b0000],\r\n ['pink', 0xffc0cb],\r\n ['lightpink', 0xffb6c1],\r\n ['hotpink', 0xff69b4],\r\n ['deeppink', 0xff1493],\r\n ['mediumvioletred', 0xc71585],\r\n ['palevioletred', 0xdb7093],\r\n ['coral', 0xff7f50],\r\n ['tomato', 0xff6347],\r\n ['orangered', 0xff4500],\r\n ['darkorange', 0xff8c00],\r\n ['orange', 0xffa500],\r\n ['gold', 0xffd700],\r\n ['yellow', 0xffff00],\r\n ['lightyellow', 0xffffe0],\r\n ['lemonchiffon', 0xfffacd],\r\n ['lightgoldenrodyellow', 0xfafad2],\r\n ['papayawhip', 0xffefd5],\r\n ['moccasin', 0xffe4b5],\r\n ['peachpuff', 0xffdab9],\r\n ['palegoldenrod', 0xeee8aa],\r\n ['khaki', 0xf0e68c],\r\n ['darkkhaki', 0xbdb76b],\r\n ['lavender', 0xe6e6fa],\r\n ['thistle', 0xd8bfd8],\r\n ['plum', 0xdda0dd],\r\n ['violet', 0xee82ee],\r\n ['orchid', 0xda70d6],\r\n ['fuchsia', 0xff00ff],\r\n ['magenta', 0xff00ff],\r\n ['mediumorchid', 0xba55d3],\r\n ['mediumpurple', 0x9370db],\r\n ['rebeccapurple', 0x663399],\r\n ['blueviolet', 0x8a2be2],\r\n ['darkviolet', 0x9400d3],\r\n ['darkorchid', 0x9932cc],\r\n ['darkmagenta', 0x8b008b],\r\n ['purple', 0x800080],\r\n ['indigo', 0x4b0082],\r\n ['slateblue', 0x6a5acd],\r\n ['mediumslateblue', 0x7b68ee],\r\n ['darkslateblue', 0x483d8b],\r\n ['greenyellow', 0xadff2f],\r\n ['chartreuse', 0x7fff00],\r\n ['lawngreen', 0x7cfc00],\r\n ['lime', 0x00ff00],\r\n ['limegreen', 0x32cd32],\r\n ['palegreen', 0x98fb98],\r\n ['lightgreen', 0x90ee90],\r\n ['mediumspringgreen', 0x00fa9a],\r\n ['springgreen', 0x00ff7f],\r\n ['mediumseagreen', 0x3cb371],\r\n ['seagreen', 0x2e8b57],\r\n ['forestgreen', 0x228b22],\r\n ['green', 0x008000],\r\n ['darkgreen', 0x006400],\r\n ['yellowgreen', 0x9acd32],\r\n ['olivedrab', 0x6b8e23],\r\n ['olive', 0x808000],\r\n ['darkolivegreen', 0x556b2f],\r\n ['mediumaquamarine', 0x66cdaa],\r\n ['darkseagreen', 0x8fbc8f],\r\n ['lightseagreen', 0x20b2aa],\r\n ['darkcyan', 0x008b8b],\r\n ['teal', 0x008080],\r\n ['aqua', 0x00ffff],\r\n ['cyan', 0x00ffff],\r\n ['lightcyan', 0xe0ffff],\r\n ['paleturquoise', 0xafeeee],\r\n ['aquamarine', 0x7fffd4],\r\n ['turquoise', 0x40e0d0],\r\n ['mediumturquoise', 0x48d1cc],\r\n ['darkturquoise', 0x00ced1],\r\n ['cadetblue', 0x5f9ea0],\r\n ['steelblue', 0x4682b4],\r\n ['lightsteelblue', 0xb0c4de],\r\n ['powderblue', 0xb0e0e6],\r\n ['lightblue', 0xadd8e6],\r\n ['skyblue', 0x87ceeb],\r\n ['lightskyblue', 0x87cefa],\r\n ['deepskyblue', 0x00bfff],\r\n ['dodgerblue', 0x1e90ff],\r\n ['cornflowerblue', 0x6495ed],\r\n ['royalblue', 0x4169e1],\r\n ['blue', 0x0000ff],\r\n ['mediumblue', 0x0000cd],\r\n ['darkblue', 0x00008b],\r\n ['navy', 0x000080],\r\n ['midnightblue', 0x191970],\r\n ['cornsilk', 0xfff8dc],\r\n ['blanchedalmond', 0xffebcd],\r\n ['bisque', 0xffe4c4],\r\n ['navajowhite', 0xffdead],\r\n ['wheat', 0xf5deb3],\r\n ['burlywood', 0xdeb887],\r\n ['tan', 0xd2b48c],\r\n ['rosybrown', 0xbc8f8f],\r\n ['sandybrown', 0xf4a460],\r\n ['goldenrod', 0xdaa520],\r\n ['darkgoldenrod', 0xb8860b],\r\n ['peru', 0xcd853f],\r\n ['chocolate', 0xd2691e],\r\n ['saddlebrown', 0x8b4513],\r\n ['sienna', 0xa0522d],\r\n ['brown', 0xa52a2a],\r\n ['maroon', 0x800000],\r\n ['white', 0xffffff],\r\n ['snow', 0xfffafa],\r\n ['honeydew', 0xf0fff0],\r\n ['mintcream', 0xf5fffa],\r\n ['azure', 0xf0ffff],\r\n ['aliceblue', 0xf0f8ff],\r\n ['ghostwhite', 0xf8f8ff],\r\n ['whitesmoke', 0xf5f5f5],\r\n ['seashell', 0xfff5ee],\r\n ['beige', 0xf5f5dc],\r\n ['oldlace', 0xfdf5e6],\r\n ['floralwhite', 0xfffaf0],\r\n ['ivory', 0xfffff0],\r\n ['antiquewhite', 0xfaebd7],\r\n ['linen', 0xfaf0e6],\r\n ['lavenderblush', 0xfff0f5],\r\n ['mistyrose', 0xffe4e1],\r\n ['gainsboro', 0xdcdcdc],\r\n ['lightgray', 0xd3d3d3],\r\n ['silver', 0xc0c0c0],\r\n ['darkgray', 0xa9a9a9],\r\n ['gray', 0x808080],\r\n ['dimgray', 0x696969],\r\n ['lightslategray', 0x778899],\r\n ['slategray', 0x708090],\r\n ['darkslategray', 0x2f4f4f],\r\n ['black', 0x000000],\r\n /* eslint-enable no-multi-spaces */\r\n ],\r\n\r\n namedColors: {},\r\n /* eslint-enable no-magic-numbers */\r\n\r\n gradients: {\r\n rainbow: [\r\n 0x0000ff, // blue\r\n 0x00ffff, // cyan\r\n 0x00ff00, // green\r\n 0xffff00, // yellow\r\n 0xff0000, // red\r\n ],\r\n temp: [\r\n 0x0000ff, // blue\r\n 0x007fff, // light-blue\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n hot: [\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n cold: [\r\n 0xffffff, // white\r\n 0x007fff, // light-blue\r\n 0x0000ff, // blue\r\n ],\r\n 'blue-red': [\r\n 0x0000ff, // blue\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n reds: [\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n blues: [\r\n 0xffffff, // white\r\n 0x0000ff, // blue\r\n ],\r\n },\r\n});\r\n\r\nconst { namedColorsArray, namedColors } = Palette.prototype;\r\n\r\nfor (let i = 0, { length } = namedColorsArray; i < length; ++i) {\r\n const [name, value] = namedColorsArray[i];\r\n namedColors[name] = value;\r\n}\r\n\r\nexport default Palette;\r\n","import Palette from './Palette';\r\n\r\nconst palette = new Palette('CPK', 'CP');\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n C: 0x202020,\r\n N: 0x2060FF,\r\n O: 0xEE2010,\r\n F: 0x00FF00,\r\n P: 0x8020FF,\r\n S: 0xFFFF00,\r\n CL: 0x00BB00,\r\n FE: 0xD0D0D0,\r\n CO: 0xD0D0D0,\r\n NI: 0xD0D0D0,\r\n CU: 0xD0D0D0,\r\n BR: 0x008800,\r\n I: 0x005500,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('Jmol', 'JM');\r\n\r\npalette.colors = [\r\n /* eslint-disable no-magic-numbers */\r\n 0x0000FF, // blue\r\n 0x0055FF, //\r\n 0x00ABFF, //\r\n 0x00FFFF, // cyan\r\n 0x00FFAB, //\r\n 0x00FF55, //\r\n 0x00FF00, // green\r\n 0x55FF00, //\r\n 0xABFF00, //\r\n 0xFFFF00, // yellow\r\n 0xFFAB00, //\r\n 0xFF5500, //\r\n 0xFF0000, // red\r\n 0xFF0055, //\r\n 0xFF00AB, //\r\n 0xFF00FF, // magenta\r\n 0xAB00FF, //\r\n 0x5500FF, //\r\n /* eslint-enable no-magic-numbers */\r\n];\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n D: 0xFFFFC0,\r\n T: 0xFFFFA0,\r\n HE: 0xD9FFFF,\r\n LI: 0xCC80FF,\r\n BE: 0xC2FF00,\r\n B: 0xFFB5B5,\r\n C: 0x909090,\r\n N: 0x3050F8,\r\n O: 0xFF0D0D,\r\n F: 0x90E050,\r\n NE: 0xB3E3F5,\r\n NA: 0xAB5CF2,\r\n MG: 0x8AFF00,\r\n AL: 0xBFA6A6,\r\n SI: 0xF0C8A0,\r\n P: 0xFF8000,\r\n S: 0xFFFF30,\r\n CL: 0x1FF01F,\r\n AR: 0x80D1E3,\r\n K: 0x8F40D4,\r\n CA: 0x3DFF00,\r\n SC: 0xE6E6E6,\r\n TI: 0xBFC2C7,\r\n V: 0xA6A6AB,\r\n CR: 0x8A99C7,\r\n MN: 0x9C7AC7,\r\n FE: 0xE06633,\r\n CO: 0xF090A0,\r\n NI: 0x50D050,\r\n CU: 0xC88033,\r\n ZN: 0x7D80B0,\r\n GA: 0xC28F8F,\r\n GE: 0x668F8F,\r\n AS: 0xBD80E3,\r\n SE: 0xFFA100,\r\n BR: 0xA62929,\r\n KR: 0x5CB8D1,\r\n RB: 0x702EB0,\r\n SR: 0x00FF00,\r\n Y: 0x94FFFF,\r\n ZR: 0x94E0E0,\r\n NB: 0x73C2C9,\r\n MO: 0x54B5B5,\r\n TC: 0x3B9E9E,\r\n RU: 0x248F8F,\r\n RH: 0x0A7D8C,\r\n PD: 0x006985,\r\n AG: 0xC0C0C0,\r\n CD: 0xFFD98F,\r\n IN: 0xA67573,\r\n SN: 0x668080,\r\n SB: 0x9E63B5,\r\n TE: 0xD47A00,\r\n I: 0x940094,\r\n XE: 0x429EB0,\r\n CS: 0x57178F,\r\n BA: 0x00C900,\r\n LA: 0x70D4FF,\r\n CE: 0xFFFFC7,\r\n PR: 0xD9FFC7,\r\n ND: 0xC7FFC7,\r\n PM: 0xA3FFC7,\r\n SM: 0x8FFFC7,\r\n EU: 0x61FFC7,\r\n GD: 0x45FFC7,\r\n TB: 0x30FFC7,\r\n DY: 0x1FFFC7,\r\n HO: 0x00FF9C,\r\n ER: 0x00E675,\r\n TM: 0x00D452,\r\n YB: 0x00BF38,\r\n LU: 0x00AB24,\r\n HF: 0x4DC2FF,\r\n TA: 0x4DA6FF,\r\n W: 0x2194D6,\r\n RE: 0x267DAB,\r\n OS: 0x266696,\r\n IR: 0x175487,\r\n PT: 0xD0D0E0,\r\n AU: 0xFFD123,\r\n HG: 0xB8B8D0,\r\n TL: 0xA6544D,\r\n PB: 0x575961,\r\n BI: 0x9E4FB5,\r\n PO: 0xAB5C00,\r\n AT: 0x754F45,\r\n RN: 0x428296,\r\n FR: 0x420066,\r\n RA: 0x007D00,\r\n AC: 0x70ABFA,\r\n TH: 0x00BAFF,\r\n PA: 0x00A1FF,\r\n U: 0x008FFF,\r\n NP: 0x0080FF,\r\n PU: 0x006BFF,\r\n AM: 0x545CF2,\r\n CM: 0x785CE3,\r\n BK: 0x8A4FE3,\r\n CF: 0xA136D4,\r\n ES: 0xB31FD4,\r\n FM: 0xB31FBA,\r\n MD: 0xB30DA6,\r\n NO: 0xBD0D87,\r\n LR: 0xC70066,\r\n RF: 0xCC0059,\r\n DB: 0xD1004F,\r\n SG: 0xD90045,\r\n BH: 0xE00038,\r\n HS: 0xE6002E,\r\n MT: 0xEB0026,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.defaultResidueColor = 0xBEA06E;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: 0xC8C8C8,\r\n ARG: 0x145AFF,\r\n ASN: 0x00DCDC,\r\n ASP: 0xE60A0A,\r\n CYS: 0xE6E600,\r\n GLN: 0x00DCDC,\r\n GLU: 0xE60A0A,\r\n GLY: 0xEBEBEB,\r\n HIS: 0x8282D2,\r\n ILE: 0x0F820F,\r\n LEU: 0x0F820F,\r\n LYS: 0x145AFF,\r\n MET: 0xE6E600,\r\n PHE: 0x3232AA,\r\n PRO: 0xDC9682,\r\n SER: 0xFA9600,\r\n THR: 0xFA9600,\r\n TRP: 0xB45AB4,\r\n TYR: 0x3232AA,\r\n VAL: 0x0F820F,\r\n A: 0xA0A0FF,\r\n C: 0xFF8C4B,\r\n G: 0xFF7070,\r\n I: 0x80FFFF,\r\n T: 0xA0FFA0,\r\n U: 0xFF8080,\r\n DA: 0xA0A0FF,\r\n DC: 0xFF8C4B,\r\n DG: 0xFF7070,\r\n DI: 0x80FFFF,\r\n DT: 0xA0FFA0,\r\n DU: 0xFF8080,\r\n '+A': 0xA0A0FF,\r\n '+C': 0xFF8C4B,\r\n '+G': 0xFF7070,\r\n '+I': 0x80FFFF,\r\n '+T': 0xA0FFA0,\r\n '+U': 0xFF8080,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.chainColors = [\r\n // ' '->0 'A'->1, 'B'->2\r\n 0xFFffffff, // ' ' & '0' white\r\n //\r\n 0xFFC0D0FF, // skyblue\r\n 0xFFB0FFB0, // pastel green\r\n 0xFFFFC0C8, // pink\r\n 0xFFFFFF80, // pastel yellow\r\n 0xFFFFC0FF, // pastel magenta\r\n 0xFFB0F0F0, // pastel cyan\r\n 0xFFFFD070, // pastel gold\r\n 0xFFF08080, // lightcoral\r\n\r\n 0xFFF5DEB3, // wheat\r\n 0xFF00BFFF, // deepskyblue\r\n 0xFFCD5C5C, // indianred\r\n 0xFF66CDAA, // mediumaquamarine\r\n 0xFF9ACD32, // yellowgreen\r\n 0xFFEE82EE, // violet\r\n 0xFF00CED1, // darkturquoise\r\n 0xFF00FF7F, // springgreen\r\n 0xFF3CB371, // mediumseagreen\r\n\r\n 0xFF00008B, // darkblue\r\n 0xFFBDB76B, // darkkhaki\r\n 0xFF006400, // darkgreen\r\n 0xFF800000, // maroon\r\n 0xFF808000, // olive\r\n 0xFF800080, // purple\r\n 0xFF008080, // teal\r\n 0xFFB8860B, // darkgoldenrod\r\n 0xFFB22222, // firebrick\r\n];\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xFF0080,\r\n [StructuralElementType.HELIX_PI]: 0x600080,\r\n [StructuralElementType.HELIX_310]: 0xA00080,\r\n [StructuralElementType.STRAND]: 0xFFC800,\r\n [StructuralElementType.TURN]: 0x6080FF,\r\n dna: 0xAE00FE,\r\n rna: 0xFD0162,\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('VMD', 'VM');\r\n\r\npalette.colors = [\r\n /* eslint-disable no-magic-numbers */\r\n 0x0000FF, // blue\r\n 0xFF0000, // red\r\n 0x606060, // gray\r\n 0xFF8000, // orange\r\n 0xFFFF00, // yellow\r\n 0x808033, // tan\r\n 0x999999, // silver\r\n 0x00FF00, // green\r\n 0xFFFFFF, // white\r\n 0xFF9999, // pink\r\n 0x40C0C0, // cyan\r\n 0xA600A6, // purple\r\n 0x80E666, // lime\r\n 0xE666B3, // mauve\r\n 0x804D00, // ochre\r\n 0x8080C0, // ice blue\r\n /* eslint-enable no-magic-numbers */\r\n];\r\n\r\npalette.defaultElementColor = 0x804D00;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n C: 0x40BFBF,\r\n N: 0x0000FF,\r\n O: 0xFF0000,\r\n P: 0x808033,\r\n S: 0xFFFF00,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.defaultResidueColor = 0x40C0C0;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: 0x0000FF,\r\n ARG: 0xFFFFFF,\r\n ASN: 0x808033,\r\n ASP: 0xFF0000,\r\n CYS: 0xFFFF00,\r\n GLN: 0xFF8000,\r\n GLU: 0xFF9999,\r\n GLY: 0xFFFFFF,\r\n HIS: 0x40C0C0,\r\n ILE: 0x00FF00,\r\n LEU: 0xFF9999,\r\n LYS: 0x40C0C0,\r\n MET: 0xFFFF00,\r\n PHE: 0xA600A6,\r\n PRO: 0x804C00,\r\n SER: 0xFFFF00,\r\n THR: 0xE666B3,\r\n TRP: 0x999999,\r\n TYR: 0x00FF00,\r\n VAL: 0x808033,\r\n A: 0x0000FF,\r\n C: 0xFF8000,\r\n G: 0xFFFF00,\r\n T: 0xA600A6,\r\n U: 0x00FF00,\r\n DA: 0x0000FF,\r\n DC: 0xFF8000,\r\n DG: 0xFFFF00,\r\n DT: 0xA600A6,\r\n DU: 0x00FF00,\r\n '+A': 0x0000FF,\r\n '+C': 0xFF8000,\r\n '+G': 0xFFFF00,\r\n '+T': 0xA600A6,\r\n '+U': 0x00FF00,\r\n WAT: 0x40C0C0,\r\n H2O: 0x40C0C0,\r\n HOH: 0x40C0C0,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.chainColors = [0xFFFFFF].concat(palette.colors);\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xA600A6,\r\n [StructuralElementType.HELIX_310]: 0x0000FF,\r\n [StructuralElementType.HELIX_PI]: 0xFF0000,\r\n [StructuralElementType.STRAND]: 0xFFFF00,\r\n [StructuralElementType.BRIDGE]: 0x808033,\r\n [StructuralElementType.TURN]: 0x40C0C0,\r\n};\r\n\r\nexport default palette;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport cpkPalette from './palettes/cpkPalette';\r\nimport jmolPalette from './palettes/jmolPalette';\r\nimport vmdPalette from './palettes/vmdPalette';\r\n\r\nconst palettes = new EntityList([\r\n cpkPalette,\r\n jmolPalette,\r\n vmdPalette,\r\n]);\r\n\r\nexport default palettes;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport palettes from '../palettes';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports Colorer\r\n * @this Colorer\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available coloring algorithms used for building and displaying molecule geometry.\r\n */\r\nclass Colorer {\r\n constructor(opts) {\r\n if (this.constructor === Colorer) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Colorer options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(settings.now.colorers[this.id], true), opts);\r\n /**\r\n * Palette in use.\r\n * @type {Palette}\r\n */\r\n this.palette = palettes.first;\r\n }\r\n\r\n /**\r\n * Get Colorer identification, probably with options.\r\n * @returns {string|Array} Colorer identifier string ({@link Colorer#id}) or two-element array containing both colorer\r\n * identifier and options ({@link Colorer#opts}).\r\n * Options are returned if they were changed during or after colorer creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, settings.now.colorers[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n}\r\n\r\n/**\r\n * Colorer identifier.\r\n * @type {string}\r\n */\r\n\r\nColorer.prototype.id = '__';\r\n\r\nexport default Colorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Element\r\n *\r\n * @exports ElementColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on chemical element.\r\n */\r\nclass ElementColorer extends Colorer {\r\n static id = 'EL';\r\n\r\n getAtomColor(atom, _complex) {\r\n const type = atom.element.name;\r\n if (type === 'C' && this.opts.carbon >= 0) {\r\n return this.opts.carbon;\r\n }\r\n return this.palette.getElementColor(type);\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nElementColorer.prototype.id = 'EL';\r\nElementColorer.prototype.name = 'Element';\r\nElementColorer.prototype.shortName = 'Element';\r\n\r\nexport default ElementColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Coloring algorithm based on residue type.\r\n *\r\n * @see ResidueType\r\n *\r\n * @exports ResidueTypeColorer\r\n * @constructor\r\n */\r\nclass ResidueTypeColorer extends Colorer {\r\n static id = 'RT';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getResidueColor(residue._type._name);\r\n }\r\n}\r\n\r\nResidueTypeColorer.prototype.id = 'RT';\r\nResidueTypeColorer.prototype.name = 'Residue Type';\r\nResidueTypeColorer.prototype.shortName = 'Residue';\r\n\r\nexport default ResidueTypeColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass SequenceColorer extends Colorer {\r\n static id = 'SQ';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const chain = residue._chain;\r\n if (chain.minSequence === Number.POSITIVE_INFINITY && chain.maxSequence === Number.NEGATIVE_INFINITY) {\r\n return this.palette.defaultNamedColor;\r\n }\r\n const min = chain.minSequence;\r\n const max = chain.maxSequence > min ? chain.maxSequence : min + 1;\r\n return this.palette.getGradientColor((residue._sequence - min) / (max - min), this.opts.gradient);\r\n }\r\n}\r\n\r\nSequenceColorer.prototype.id = 'SQ';\r\nSequenceColorer.prototype.name = 'Sequence';\r\nSequenceColorer.prototype.shortName = 'Sequence';\r\n\r\nexport default SequenceColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ChainColorer extends Colorer {\r\n static id = 'CH';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getChainColor(residue.getChain()._name);\r\n }\r\n}\r\n\r\nChainColorer.prototype.id = 'CH';\r\nChainColorer.prototype.name = 'Chain';\r\nChainColorer.prototype.shortName = 'Chain';\r\n\r\nexport default ChainColorer;\r\n","import Colorer from './Colorer';\r\nimport ResidueType from '../../chem/ResidueType';\r\n\r\nclass SecondaryStructureColorer extends Colorer {\r\n static id = 'SS';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n if (residue._type.flags & ResidueType.Flags.DNA) {\r\n return this.palette.getSecondaryColor('dna');\r\n }\r\n if (residue._type.flags & ResidueType.Flags.RNA) {\r\n return this.palette.getSecondaryColor('rna');\r\n }\r\n const secondary = residue.getSecondary();\r\n if (secondary) {\r\n let color = this.palette.getSecondaryColor(secondary.type, true);\r\n if (color === undefined) {\r\n color = this.palette.getSecondaryColor(secondary.generic);\r\n }\r\n return color;\r\n }\r\n return this.palette.defaultSecondaryColor;\r\n }\r\n}\r\n\r\nSecondaryStructureColorer.prototype.id = 'SS';\r\nSecondaryStructureColorer.prototype.name = 'Secondary Structure';\r\nSecondaryStructureColorer.prototype.shortName = 'Structure';\r\n\r\nexport default SecondaryStructureColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass UniformColorer extends Colorer {\r\n static id = 'UN';\r\n\r\n getAtomColor(_atom, _complex) {\r\n return this.opts.color;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nUniformColorer.prototype.id = 'UN';\r\nUniformColorer.prototype.name = 'Uniform';\r\nUniformColorer.prototype.shortName = 'Uniform';\r\n\r\nexport default UniformColorer;\r\n","import Colorer from './Colorer';\r\nimport selectors from '../../chem/selectors';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports ConditionalColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on a selector string used as a condition.\r\n */\r\nclass ConditionalColorer extends Colorer {\r\n static id = 'CO';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n const parsed = selectors.parse(this.opts.subset);\r\n this._subsetCached = parsed.error ? selectors.none() : parsed.selector;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n return this._subsetCached.includesAtom(atom) ? this.opts.color : this.opts.baseColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const subset = this._subsetCached;\r\n const atoms = residue._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (!subset.includesAtom(atoms[i])) {\r\n return this.opts.baseColor;\r\n }\r\n }\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nConditionalColorer.prototype.id = 'CO';\r\nConditionalColorer.prototype.name = 'Conditional';\r\nConditionalColorer.prototype.shortName = 'Conditional';\r\n\r\nexport default ConditionalColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ConformationColorer extends Colorer {\r\n static id = 'CF';\r\n\r\n getAtomColor(atom, _complex) {\r\n return this.palette.getChainColor(String.fromCharCode(atom.location));\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nConformationColorer.prototype.id = 'CF';\r\nConformationColorer.prototype.name = 'Conformation';\r\nConformationColorer.prototype.shortName = 'Conformation';\r\n\r\nexport default ConformationColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Temperature\r\n *\r\n * @exports TemperatureColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on temperature of chemical element.\r\n */\r\nclass TemperatureColorer extends Colorer {\r\n static id = 'TM';\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n let factor = 1;\r\n if (atom.temperature && opts) {\r\n if (opts.min === opts.max) {\r\n factor = atom.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (atom.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n if (!opts) {\r\n return this.palette.defaultGradientColor;\r\n }\r\n if (residue.temperature) {\r\n let factor = 0;\r\n if (opts.min === opts.max) {\r\n factor = residue.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (residue.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n}\r\n\r\nTemperatureColorer.prototype.id = 'TM'; // [T]e[M]perature\r\nTemperatureColorer.prototype.name = 'Temperature';\r\nTemperatureColorer.prototype.shortName = 'Temperature';\r\n\r\nexport default TemperatureColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Occupancy\r\n *\r\n * @exports OccupancyColorer\r\n * @augments Occupancy\r\n * @constructor\r\n * @classdesc Coloring algorithm based on occupancy of chemical element.\r\n */\r\nclass OccupancyColorer extends Colorer {\r\n static id = 'OC';\r\n\r\n _getColorByOccupancy(occupancy, opts) {\r\n if (occupancy !== undefined) {\r\n const factor = 1 - occupancy;\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(atom.occupancy, opts);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(residue.occupancy, opts);\r\n }\r\n}\r\n\r\nOccupancyColorer.prototype.id = 'OC'; // [OC]cupancy\r\nOccupancyColorer.prototype.name = 'Occupancy';\r\nOccupancyColorer.prototype.shortName = 'Occupancy';\r\n\r\nexport default OccupancyColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass HydrophobicityColorer extends Colorer {\r\n static id = 'HY';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n let color = this.palette.defaultResidueColor;\r\n if (residue._type.hydrophobicity !== undefined) {\r\n // Kyte Doolitle hydro [-4.5,4.5]->[0.1]\r\n const min = -4.5;\r\n const max = 4.5;\r\n color = this.palette.getGradientColor((residue._type.hydrophobicity - min) / (max - min), this.opts.gradient);\r\n }\r\n return color;\r\n }\r\n}\r\n\r\nHydrophobicityColorer.prototype.id = 'HY';\r\nHydrophobicityColorer.prototype.name = 'Hydrophobicity';\r\nHydrophobicityColorer.prototype.shortName = 'Hydrophobicity';\r\n\r\nexport default HydrophobicityColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass MoleculeColorer extends Colorer {\r\n static id = 'MO';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const molecule = residue._molecule;\r\n const count = _complex.getMoleculeCount();\r\n if (count > 1) {\r\n return this.palette.getGradientColor((molecule.index - 1) / (count - 1), this.opts.gradient);\r\n }\r\n return this.palette.getGradientColor(0, this.opts.gradient);\r\n }\r\n}\r\n\r\nMoleculeColorer.prototype.id = 'MO';\r\nMoleculeColorer.prototype.name = 'Molecule';\r\nMoleculeColorer.prototype.shortName = 'Molecule';\r\n\r\nexport default MoleculeColorer;\r\n","import Colorer from './Colorer';\r\nimport Atom from '../../chem/Atom';\r\n\r\nfunction scaleColor(c, factor) {\r\n const r1 = (c >> 16) & 0xff;\r\n const g1 = (c >> 8) & 0xff;\r\n const b1 = c & 0xff;\r\n const r = factor * r1;\r\n const g = factor * g1;\r\n const b = factor * b1;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports CarbonColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on selection carbon atoms.\r\n */\r\nclass CarbonColorer extends Colorer {\r\n static id = 'CB';\r\n\r\n getAtomColor(atom, _complex) {\r\n const colorCarbon = this.opts.color;\r\n const colorNotCarbon = scaleColor(colorCarbon, this.opts.factor);\r\n return (atom.flags & Atom.Flags.CARBON) ? colorCarbon : colorNotCarbon;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nCarbonColorer.prototype.id = 'CB';\r\nCarbonColorer.prototype.name = 'Carbon';\r\nCarbonColorer.prototype.shortName = 'Carbon';\r\n\r\nexport default CarbonColorer;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport ElementColorer from './colorers/ElementColorer';\r\nimport ResidueTypeColorer from './colorers/ResidueTypeColorer';\r\nimport SequenceColorer from './colorers/SequenceColorer';\r\nimport ChainColorer from './colorers/ChainColorer';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\nimport UniformColorer from './colorers/UniformColorer';\r\nimport ConditionalColorer from './colorers/ConditionalColorer';\r\nimport ConformationColorer from './colorers/ConformationColorer';\r\nimport TemperatureColorer from './colorers/TemperatureColorer';\r\nimport OccupancyColorer from './colorers/OccupancyColorer';\r\nimport HydrophobicityColorer from './colorers/HydrophobicityColorer';\r\nimport MoleculeColorer from './colorers/MoleculeColorer';\r\nimport CarbonColorer from './colorers/CarbonColorer';\r\n\r\nconst colorers = new EntityList([\r\n ElementColorer,\r\n ResidueTypeColorer,\r\n SequenceColorer,\r\n ChainColorer,\r\n SecondaryStructureColorer,\r\n UniformColorer,\r\n ConditionalColorer,\r\n ConformationColorer,\r\n TemperatureColorer,\r\n OccupancyColorer,\r\n HydrophobicityColorer,\r\n MoleculeColorer,\r\n CarbonColorer,\r\n]);\r\n\r\nexport default colorers;\r\n","import * as THREE from 'three';\r\nimport EntityList from '../utils/EntityList';\r\n\r\nfunction neutralColor(intensity) {\r\n return new THREE.Color(intensity, intensity, intensity);\r\n}\r\n\r\nconst materialList = [\r\n {\r\n id: 'DF',\r\n name: 'Diffuse',\r\n shortName: 'Diffuse',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'SF',\r\n name: 'Soft Plastic',\r\n shortName: 'Soft',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.1),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'PL',\r\n name: 'Glossy Plastic',\r\n shortName: 'Glossy',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.28),\r\n shininess: 100,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'ME',\r\n name: 'Metal',\r\n shortName: 'Metal',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.55),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TR',\r\n name: 'Transparent',\r\n shortName: 'Transparent',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'GL',\r\n name: 'Glass',\r\n shortName: 'Glass',\r\n uberOptions: {\r\n diffuse: neutralColor(0.50),\r\n specular: neutralColor(0.65),\r\n shininess: 100,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'BA',\r\n name: 'Backdrop',\r\n shortName: 'Backdrop',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: false,\r\n depthWrite: false,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TN',\r\n name: 'Toon',\r\n shortName: 'Toon',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: true,\r\n },\r\n }, {\r\n id: 'FL',\r\n name: 'Flat',\r\n shortName: 'Flat',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 0,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n },\r\n },\r\n];\r\n\r\nconst materials = new EntityList(materialList);\r\n\r\nexport default materials;\r\n","/**\r\n * Utils functions which is worked with meshes\r\n *\r\n * functions for doing something with all/specified meshes\r\n * functions for traversihg tree and create auxiliary meshes for transparency/shadowmaps...\r\n * functions for calculating data connected with meshes\r\n */\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _gatherObjects(root, meshTypes) {\r\n const meshes = [];\r\n root.traverse((object) => {\r\n for (let i = 0; i < meshTypes.length; i++) {\r\n if (object instanceof meshTypes[i]) {\r\n meshes[meshes.length] = object;\r\n break;\r\n }\r\n }\r\n });\r\n return meshes;\r\n}\r\n\r\n// new mesh with the same geometry and specified material values and layer\r\nfunction createDerivativeMesh(mesh, values, layer) {\r\n const material = mesh.material.createInstance();\r\n material.setValues(values);\r\n\r\n const newMesh = new mesh.constructor(mesh.geometry, material);\r\n newMesh.material.needsUpdate = true;\r\n newMesh.applyMatrix4(mesh.matrix);\r\n newMesh.layers.set(layer);\r\n return newMesh;\r\n}\r\n\r\nfunction traverseMeshes(root, meshTypes, func) {\r\n const meshes = _gatherObjects(root, meshTypes);\r\n\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n const mesh = meshes[i];\r\n if (!mesh.parent) {\r\n continue;\r\n }\r\n func(mesh);\r\n }\r\n}\r\n\r\nfunction applyTransformsToMeshes(root, mtc) {\r\n const mtcCount = mtc.length;\r\n if (mtcCount < 1) {\r\n return;\r\n }\r\n\r\n const meshTypes = [THREE.Mesh, THREE.LineSegments, THREE.Line];\r\n traverseMeshes(root, meshTypes, (mesh) => {\r\n mesh.applyMatrix4(mtc[0]);\r\n for (let j = 1; j < mtcCount; ++j) {\r\n const newMesh = new mesh.constructor(mesh.geometry, mesh.material);\r\n mesh.parent.add(newMesh);\r\n newMesh.applyMatrix4(mtc[j]);\r\n }\r\n });\r\n}\r\n\r\nconst processTransparentMaterial = (function () {\r\n const matValues = {\r\n prepassTransparancy: true,\r\n fakeOpacity: false,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n mesh.material.setValues({ prepassTransparancy: false, fakeOpacity: false });\r\n mesh.material.needsUpdate = true;\r\n mesh.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n\r\n const prepassTranspMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n mesh.parent.add(prepassTranspMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst processColFromPosMaterial = (function () {\r\n const matValues = {\r\n colorFromPos: true,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n overrideColor: false,\r\n fogTransparent: false,\r\n attrColor: false,\r\n attrColor2: false,\r\n attrAlphaColor: false,\r\n fakeOpacity: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n const colFromPosMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n mesh.parent.add(colFromPosMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst createShadowmapMaterial = (function () {\r\n const matValues = {\r\n colorFromDepth: true,\r\n orthoCam: true,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (!mesh.receiveShadow && mesh.material.shadowmap) { // remove shadow from non-receivers\r\n mesh.material.setValues({ shadowmap: false });\r\n }\r\n if (!mesh.material.lights) { // skip creating shadowmap meshes for materials without lighting\r\n return;\r\n }\r\n if (!mesh.castShadow) { // skip creating shadowmap meshes for non-casters\r\n return;\r\n }\r\n if (!gfxutils.belongToSelectLayers(mesh)) { // skip creating shadowmap meshes for selection layer\r\n return;\r\n }\r\n\r\n const shadowmapMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.SHADOWMAP);\r\n shadowmapMesh.isShadowmapMesh = true;\r\n mesh.parent.add(shadowmapMesh);\r\n });\r\n };\r\n}());\r\n\r\nfunction removeShadowmapMaterial(root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (mesh.isShadowmapMesh) {\r\n mesh.parent.remove(mesh);\r\n }\r\n });\r\n}\r\n\r\nfunction forEachMeshInGroup(group, process) {\r\n function processObj(object) {\r\n if (object instanceof THREE.Mesh) {\r\n process(object);\r\n }\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n processObj(object.children[i]);\r\n }\r\n }\r\n processObj(group);\r\n}\r\n\r\nfunction _countMeshTriangles(mesh) {\r\n const geom = mesh.geometry;\r\n if (geom instanceof THREE.InstancedBufferGeometry) {\r\n const attribs = geom.attributes;\r\n for (const property in attribs) {\r\n if (attribs.hasOwnProperty(property) && attribs[property] instanceof THREE.InstancedBufferAttribute) {\r\n const currAttr = attribs[property];\r\n const indexSize = geom.index ? geom.index.array.length / 3 : 0;\r\n return indexSize * currAttr.array.length / currAttr.itemSize;\r\n }\r\n }\r\n return 0;\r\n }\r\n if (geom instanceof THREE.BufferGeometry) {\r\n return geom.index ? geom.index.array.length / 3 : 0;\r\n }\r\n return geom.faces ? geom.faces.length : 0;\r\n}\r\n\r\nfunction countTriangles(group) {\r\n let totalCount = 0;\r\n forEachMeshInGroup(group, (mesh) => {\r\n totalCount += _countMeshTriangles(mesh);\r\n });\r\n return totalCount;\r\n}\r\n\r\nexport default {\r\n applyTransformsToMeshes,\r\n processTransparentMaterial,\r\n processColFromPosMaterial,\r\n createShadowmapMaterial,\r\n removeShadowmapMaterial,\r\n forEachMeshInGroup,\r\n countTriangles,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\nimport meshutils from './meshutils';\r\nimport settings from '../settings';\r\nimport materials from './materials';\r\nimport chem from '../chem';\r\n\r\nconst { selectors } = chem;\r\n\r\nclass Representation {\r\n constructor(index, mode, colorer, selector) {\r\n const startMaterialValues = {\r\n clipPlane: settings.now.draft.clipPlane,\r\n fogTransparent: settings.now.bg.transparent,\r\n shadowmap: settings.now.shadow.on,\r\n shadowmapType: settings.now.shadow.type,\r\n };\r\n this.index = index;\r\n this.mode = mode;\r\n this.colorer = colorer;\r\n this.selector = selector;\r\n this.selectorString = '';\r\n this.count = 0;\r\n this.material = new UberMaterial();\r\n this.material.setValues(startMaterialValues);\r\n this.material.setUberOptions({ fogAlpha: settings.now.fogAlpha });\r\n this.materialPreset = materials.first;\r\n this.needsRebuild = true;\r\n this.visible = true;\r\n\r\n // apply mode params & preset\r\n this.setMode(mode);\r\n }\r\n\r\n markAtoms(complex) {\r\n this.count = complex.markAtoms(this.selector, 1 << this.index);\r\n this.needsRebuild = true;\r\n return this.count;\r\n }\r\n\r\n unmarkAtoms(complex) {\r\n complex.clearAtomBits(1 << this.index);\r\n this.count = 0;\r\n }\r\n\r\n setMode(mode) {\r\n this.mode = mode;\r\n }\r\n\r\n setMaterialPreset(preset) {\r\n this.materialPreset = preset;\r\n this.material.setUberOptions(preset.uberOptions);\r\n this.material.setValues(preset.values);\r\n }\r\n\r\n reset() {\r\n this.geo = null;\r\n this.selectionGeo = null;\r\n }\r\n\r\n buildGeometry(complex) {\r\n this.reset();\r\n this.needsRebuild = false;\r\n\r\n if (settings.now.ao) {\r\n this.material.setValues({ normalsToGBuffer: settings.now.ao });\r\n }\r\n\r\n this.geo = this.mode.buildGeometry(complex, this.colorer, 1 << this.index, this.material);\r\n\r\n if (this.material.uberOptions.opacity < 0.99 && settings.now.transparency === 'prepass') {\r\n meshutils.processTransparentMaterial(this.geo, this.material);\r\n }\r\n this.geo.visible = this.visible;\r\n\r\n gfxutils.processObjRenderOrder(this.geo, this.materialPreset.id);\r\n meshutils.processColFromPosMaterial(this.geo, this.material);\r\n\r\n if (settings.now.shadow.on) {\r\n meshutils.createShadowmapMaterial(this.geo, this.material);\r\n }\r\n\r\n return this.geo;\r\n }\r\n\r\n buildSelectionGeometry(mask) {\r\n let sg = null;\r\n\r\n if (this.geo && ('getSubset' in this.geo)) {\r\n const meshes = this.geo.getSubset(mask);\r\n if (meshes && meshes.length > 0) {\r\n sg = new THREE.Group();\r\n sg.matrixAutoUpdate = false;\r\n sg.matrix = this.geo.matrix;\r\n\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n sg.add(m);\r\n }\r\n }\r\n }\r\n\r\n if (sg) {\r\n sg.visible = this.visible;\r\n }\r\n\r\n this.selectionGeo = sg;\r\n return this.selectionGeo;\r\n }\r\n\r\n /**\r\n * Create object that represents difference between current and another rep\r\n * anotherRep could be undefined. In this case everything is reported.\r\n */\r\n compare(repSettings) {\r\n const diff = {};\r\n\r\n const selStr = String(this.selector);\r\n if (!repSettings || selStr.valueOf() !== String(repSettings.selector).valueOf()) {\r\n diff.selector = selStr;\r\n }\r\n\r\n const modeDiff = this.mode.identify();\r\n if (!repSettings || Array.isArray(modeDiff) || modeDiff !== repSettings.mode) {\r\n diff.mode = modeDiff;\r\n }\r\n\r\n const colorerDiff = this.colorer.identify();\r\n if (!repSettings || Array.isArray(colorerDiff) || colorerDiff !== repSettings.colorer) {\r\n diff.colorer = colorerDiff;\r\n }\r\n\r\n if (!repSettings || this.materialPreset.id !== repSettings.material) {\r\n diff.material = this.materialPreset.id;\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n /**\r\n * Change representation. Write fields what was changed into new object, return it.\r\n */\r\n change(repSettings, complex, mode, color) {\r\n const diff = {};\r\n\r\n // modify selector\r\n if (repSettings.selector) {\r\n const newSelectorObject = selectors.parse(repSettings.selector).selector;\r\n const newSelector = String(newSelectorObject);\r\n if (this.selectorString !== newSelector) {\r\n diff.selector = newSelector;\r\n this.selectorString = newSelector;\r\n this.selector = newSelectorObject;\r\n this.markAtoms(complex);\r\n }\r\n }\r\n\r\n // modify mode\r\n if (repSettings.mode) {\r\n const newMode = repSettings.mode;\r\n if (!_.isEqual(this.mode.identify(), newMode)) {\r\n diff.mode = newMode;\r\n this.setMode(mode);\r\n }\r\n }\r\n\r\n // modify colorer\r\n if (repSettings.colorer) {\r\n const newColorer = repSettings.colorer;\r\n if (!_.isEqual(this.colorer.identify(), newColorer)) {\r\n diff.colorer = newColorer;\r\n this.colorer = color;\r\n }\r\n }\r\n\r\n // modify material\r\n if (repSettings.material) {\r\n const newMaterial = repSettings.material;\r\n if (!_.isEqual(this.materialPreset.id, newMaterial)) {\r\n diff.material = newMaterial;\r\n this.setMaterialPreset(materials.get(repSettings.material));\r\n }\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n show(visible) {\r\n this.visible = visible;\r\n if (this.geo) {\r\n this.geo.visible = visible;\r\n }\r\n if (this.selectionGeo) {\r\n this.selectionGeo.visible = visible;\r\n }\r\n }\r\n}\r\n\r\nexport default Representation;\r\n","import * as THREE from 'three';\r\nimport logger from './utils/logger';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport './gfx/modes';\r\n\r\nfunction _traverseComponentGroups(root, component, callback) {\r\n const { children } = root;\r\n if (!children) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n if (child._component === component) {\r\n callback(child);\r\n }\r\n if (child instanceof gfxutils.RCGroup) {\r\n _traverseComponentGroups(child, component, callback);\r\n }\r\n }\r\n}\r\n\r\nfunction ComplexEditor() {\r\n}\r\n\r\nclass ComplexComponentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n // init component matrices\r\n this._componentTransforms = [];\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n const component = complex._components[i];\r\n this._componentTransforms[component._index] = new THREE.Object3D();\r\n }\r\n\r\n this._inProgress = true;\r\n\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const complex = this._complexVisual.getComplex();\r\n\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n this._bakeComponentTransform(complex._components[i]);\r\n }\r\n\r\n complex.onAtomPositionChanged();\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n const visual = this._complexVisual;\r\n const component = visual.getSelectedComponent();\r\n\r\n if (component === null) {\r\n return res;\r\n }\r\n\r\n const selection = this._complexVisual.getSelectionGeo();\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n // find all geo nodes for this component\r\n _traverseComponentGroups(visual, component, (child) => {\r\n res.objects.push(child);\r\n });\r\n\r\n // find all selection nodes for this component\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component') && geo._component === component) {\r\n res.objects.push(geo);\r\n }\r\n }\r\n }\r\n\r\n // add dummy object that stores component transformation\r\n res.objects.push(this._componentTransforms[component._index]);\r\n\r\n const bbmin = new THREE.Vector3(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE);\r\n const bbmax = new THREE.Vector3(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE);\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (j = 0; j < atoms.length; ++j) {\r\n if (atoms[j].mask & selectionMask) {\r\n bbmin.min(atoms[j].position);\r\n bbmax.max(atoms[j].position);\r\n }\r\n }\r\n });\r\n\r\n res.pivot.lerpVectors(bbmin, bbmax, 0.5);\r\n return res;\r\n }\r\n\r\n _bakeComponentTransform(component) {\r\n const t = this._componentTransforms[component._index];\r\n if (t && (!(t.position.x === 0 && t.position.y === 0 && t.position.z === 0)\r\n || !(t.quaternion.x === 0 && t.quaternion.y === 0 && t.quaternion.z === 0 && t.quaternion.w === 1))) {\r\n t.updateMatrix();\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (let j = 0; j < atoms.length; ++j) {\r\n atoms[j].position.applyMatrix4(t.matrix);\r\n }\r\n });\r\n }\r\n }\r\n\r\n _resetComponentTransform() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n for (i = 0; i < this._componentTransforms.length; ++i) {\r\n geo = this._componentTransforms[i];\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n\r\n // reset all geo nodes\r\n for (i = 0; i < visual.children.length; ++i) {\r\n reprNode = visual.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n // reset all selection nodes\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ComplexFragmentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n const atoms = this._getSelectionBorderAtoms();\r\n if (atoms.length < 1 || atoms.length > 2) {\r\n logger.error('Can only edit fragments with one or two bound atoms.');\r\n return false;\r\n }\r\n\r\n this._fragmentBoundAtoms = atoms;\r\n\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n\r\n // hide selected fragment in main model\r\n visual.disableSubset(selectionMask, true);\r\n\r\n // hide selection geo in main model\r\n for (let k = 0; k < selection.children.length; ++k) {\r\n selection.children[k].visible = false;\r\n }\r\n\r\n // create visible fragment representation to rotate\r\n const pivotPos = atoms[0].position.clone();\r\n\r\n if (atoms.length === 2) {\r\n pivotPos.lerp(atoms[1].position, 0.5);\r\n }\r\n\r\n this._fragmentGeo = new THREE.Group();\r\n visual.add(this._fragmentGeo);\r\n this._fragmentGeo.position.copy(pivotPos);\r\n\r\n this._fragmentSelectionGeo = new THREE.Group();\r\n selection.add(this._fragmentSelectionGeo);\r\n this._fragmentSelectionGeo.position.copy(pivotPos);\r\n\r\n const offset = pivotPos.clone();\r\n offset.negate();\r\n\r\n for (let i = 0; i < visual.children.length; ++i) {\r\n const g = visual.children[i];\r\n if (!('getSubset' in g)) {\r\n continue;\r\n }\r\n\r\n const vg = new THREE.Group();\r\n this._fragmentGeo.add(vg);\r\n\r\n const sg = new THREE.Group();\r\n this._fragmentSelectionGeo.add(sg);\r\n\r\n const meshes = g.getSubset(selectionMask, true);\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n vg.add(m);\r\n m.position.copy(offset);\r\n }\r\n\r\n const smeshes = g.getSubset(selectionMask, true);\r\n for (let h = 0; h < smeshes.length; h++) {\r\n const sm = smeshes[h];\r\n sg.add(sm);\r\n sm.position.copy(offset);\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(this._fragmentSelectionGeo);\r\n\r\n this._inProgress = true;\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selectionBit = visual.getSelectionBit();\r\n\r\n const p = this._fragmentGeo.position;\r\n const m = this._fragmentGeo.matrix.clone();\r\n m.multiply(new THREE.Matrix4().makeTranslation(-p.x, -p.y, -p.z));\r\n\r\n this._bakeAtomTransform(m, 1 << selectionBit);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << selectionBit, true);\r\n\r\n visual.getComplex().onAtomPositionChanged();\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n this._fragmentGeo.parent.remove(this._fragmentGeo);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << visual.getSelectionBit(), true);\r\n\r\n // show selection geo in main model (+ remove fragment selection geo)\r\n for (let i = 0; i < selection.children.length; ++i) {\r\n const node = selection.children[i];\r\n if (node.visible) {\r\n selection.remove(node);\r\n } else {\r\n node.visible = true;\r\n }\r\n }\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n isFreeRotationAllowed() {\r\n return (this._fragmentBoundAtoms.length < 2);\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n res.objects.push(this._fragmentGeo, this._fragmentSelectionGeo);\r\n\r\n const boundAtoms = this._fragmentBoundAtoms;\r\n if (boundAtoms.length === 1) {\r\n if (boundAtoms[0].bonds.length === 1) {\r\n // single external bond allows rotation about bond axis\r\n const bond = boundAtoms[0].bonds[0];\r\n res.axis = new THREE.Vector3().subVectors(bond._right.position, bond._left.position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n } else if (boundAtoms.length === 2) {\r\n // two bound atoms allow rotation only about axis running through their centers\r\n res.axis = new THREE.Vector3().subVectors(boundAtoms[1].position, boundAtoms[0].position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _getSelectionBorderAtoms() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n const selectionMask = 1 << this._complexVisual.getSelectionBit();\r\n const atomHash = {};\r\n\r\n complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n atomHash[bond._left.index] = 1;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n atomHash[bond._right.index] = 1;\r\n }\r\n });\r\n\r\n const atoms = [];\r\n const keys = Object.keys(atomHash);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const idx = keys[i];\r\n atoms.push(complex._atoms[idx]);\r\n }\r\n\r\n return atoms;\r\n }\r\n\r\n _bakeAtomTransform(matrix, mask) {\r\n this._complexVisual.getComplex().forEachAtom((atom) => {\r\n if (atom.mask & mask) {\r\n atom.position.applyMatrix4(matrix);\r\n }\r\n });\r\n }\r\n}\r\n\r\nexport default {\r\n ComponentEditor: ComplexComponentEditor,\r\n FragmentEditor: ComplexFragmentEditor,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\nimport chem from './chem';\r\nimport settings from './settings';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport Visual from './Visual';\r\nimport ComplexVisualEdit from './ComplexVisualEdit';\r\nimport meshutils from './gfx/meshutils';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction lookupAndCreate(entityList, specs) {\r\n if (!Array.isArray(specs)) {\r\n specs = [specs];\r\n }\r\n const [id, opts] = specs;\r\n const Entity = entityList.get(id) || entityList.first;\r\n return new Entity(opts);\r\n}\r\n\r\nclass ComplexVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._complex = dataSource;\r\n\r\n /** @type {Representation[]} */\r\n this._reprList = [];\r\n /** @type {?Representation} */\r\n this._repr = null;\r\n this._reprListChanged = true;\r\n\r\n this._selectionBit = 0;\r\n this._reprUsedBits = 0;\r\n this._selectionCount = 0;\r\n\r\n this._selectionGeometry = new THREE.Group();\r\n }\r\n\r\n getBoundaries() {\r\n return this._complex.getBoundaries();\r\n }\r\n\r\n release() {\r\n if (this._selectionGeometry.parent) {\r\n this._selectionGeometry.remove(this._selectionGeometry);\r\n }\r\n Visual.prototype.release.call(this);\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getSelectionCount() {\r\n return this._selectionCount;\r\n }\r\n\r\n getSelectionGeo() {\r\n return this._selectionGeometry;\r\n }\r\n\r\n getSelectionBit() {\r\n return this._selectionBit;\r\n }\r\n\r\n getEditor() {\r\n return this._editor;\r\n }\r\n\r\n resetReps(reps) {\r\n // Create all necessary representations\r\n if (this._complex) {\r\n this._complex.clearAtomBits(~0);\r\n }\r\n this._reprListChanged = true;\r\n this._reprUsedBits = 0;\r\n this._reprList.length = reps.length;\r\n for (let i = 0, n = reps.length; i < n; ++i) {\r\n const rep = reps[i];\r\n\r\n let selector;\r\n let selectorString;\r\n if (typeof rep.selector === 'string') {\r\n selectorString = rep.selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else if (typeof rep.selector === 'undefined') {\r\n selectorString = settings.now.presets.default[0].selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else {\r\n ({ selector } = rep);\r\n selectorString = selector.toString();\r\n }\r\n const mode = lookupAndCreate(modes, rep.mode);\r\n const colorer = lookupAndCreate(colorers, rep.colorer);\r\n const material = materials.get(rep.material) || materials.first;\r\n\r\n this._reprList[i] = new Representation(i, mode, colorer, selector);\r\n this._reprList[i].setMaterialPreset(material);\r\n this._reprList[i].selectorString = selectorString;\r\n\r\n if (this._complex) {\r\n this._complex.markAtoms(selector, 1 << i);\r\n }\r\n\r\n this._reprUsedBits |= 1 << i;\r\n }\r\n this._repr = reps.length > 0 ? this._reprList[0] : null;\r\n\r\n this._selectionBit = reps.length;\r\n this._reprUsedBits |= 1 << this._selectionBit; // selection uses one bit\r\n this._selectionCount = 0;\r\n\r\n if (this._complex) {\r\n this._complex.update();\r\n }\r\n }\r\n\r\n /**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\n repCount() {\r\n return this._reprList.length;\r\n }\r\n\r\n /**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\n repCurrent(index) {\r\n if (index >= 0 && index < this._reprList.length) {\r\n this._repr = this._reprList[index];\r\n } else {\r\n index = this._reprList.indexOf(this._repr);\r\n }\r\n return index;\r\n }\r\n\r\n /**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {Object} {desc, index, status} field desc contains rep description, index - index of correspondent rep,\r\n * status - one of three strings: 'created', 'changed', ''. 'created' means new rep was created during this function,\r\n * 'changed' - rep was changed during this function. '' - something else.\r\n */\r\n rep(index, rep) {\r\n // if index is missing then it is the current\r\n if (!rep && (index === undefined || index instanceof Object)) {\r\n rep = index;\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index > this._reprList.length) {\r\n logger.error(`Rep ${index} does not exist!`);\r\n return null;\r\n }\r\n\r\n // a special case of adding just after the end\r\n if (index === this._reprList.length) {\r\n const res = this.repAdd(rep);\r\n logger.warn(`Rep ${index} does not exist! New representation was created.`);\r\n return { desc: res.desc, index, status: 'created' };\r\n }\r\n\r\n // gather description\r\n const target = this._reprList[index];\r\n const desc = {\r\n selector: target.selectorString,\r\n mode: target.mode.identify(),\r\n colorer: target.colorer.identify(),\r\n material: target.materialPreset.id,\r\n };\r\n\r\n // modification is requested\r\n if (rep) {\r\n // modify\r\n const diff = target.change(\r\n rep,\r\n this._complex,\r\n lookupAndCreate(modes, rep.mode),\r\n lookupAndCreate(colorers, rep.colorer),\r\n );\r\n\r\n // something was changed\r\n if (!_.isEmpty(diff)) {\r\n target.needsRebuild = true;\r\n for (const key in diff) {\r\n if (diff.hasOwnProperty(key)) {\r\n desc[key] = diff[key];\r\n logger.debug(`rep[${index}].${key} changed to ${diff[key]}`);\r\n }\r\n }\r\n\r\n // safety trick: lower resolution for surface modes\r\n if (diff.mode && target.mode.isSurface\r\n && (settings.now.resolution === 'ultra' || settings.now.resolution === 'high')) {\r\n logger.report('Surface resolution was changed to \"medium\" to avoid hang-ups.');\r\n settings.set('resolution', 'medium');\r\n }\r\n return { desc, index, status: 'changed' };\r\n }\r\n }\r\n return { desc, index, status: '' };\r\n }\r\n\r\n /**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\n repGet(index) {\r\n // if index is missing then it is the current\r\n if (index === undefined || index instanceof Object) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return null;\r\n }\r\n\r\n return this._reprList[index];\r\n }\r\n\r\n _getFreeReprIdx() {\r\n let bits = this._reprUsedBits;\r\n for (let i = 0; i <= ComplexVisual.NUM_REPRESENTATION_BITS; ++i, bits >>= 1) {\r\n if ((bits & 1) === 0) {\r\n return i;\r\n }\r\n }\r\n return -1;\r\n }\r\n\r\n /**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {Object} {desc, index} field desc contains added rep description, index - index of this rep.\r\n */\r\n repAdd(rep) {\r\n if (this._reprList.length >= ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n return null;\r\n }\r\n\r\n const newSelectionBit = this._getFreeReprIdx();\r\n if (newSelectionBit < 0) {\r\n return null; // no more slots for representations\r\n }\r\n\r\n const originalSelection = this.buildSelectorFromMask(1 << this._selectionBit);\r\n\r\n // Fill in default values\r\n const def = settings.now.presets.default[0];\r\n const desc = _.merge({\r\n selector: def.selector,\r\n mode: def.mode,\r\n colorer: def.colorer,\r\n material: def.material,\r\n }, rep);\r\n\r\n const selector = (typeof desc.selector === 'string') ? selectors.parse(desc.selector).selector : desc.selector;\r\n const target = new Representation(\r\n this._selectionBit,\r\n lookupAndCreate(modes, desc.mode),\r\n lookupAndCreate(colorers, desc.colorer),\r\n selector,\r\n );\r\n target.selectorString = selector.toString();\r\n target.setMaterialPreset(materials.get(desc.material));\r\n target.markAtoms(this._complex);\r\n this._reprList.push(target);\r\n\r\n // change selection bit\r\n this._selectionBit = newSelectionBit;\r\n this._reprUsedBits |= 1 << this._selectionBit;\r\n\r\n // restore selection using new selection bit\r\n this._complex.markAtoms(originalSelection, 1 << this._selectionBit);\r\n\r\n return { desc, index: this._reprList.length - 1 };\r\n }\r\n\r\n /**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\n repRemove(index) {\r\n if (index === undefined) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // catch out of bounds case\r\n let count = this._reprList.length;\r\n if (index < 0 || index >= count || count <= 1) { // do not allow to remove the single rep\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.unmarkAtoms(this._complex);\r\n this._reprUsedBits &= ~(1 << target.index);\r\n\r\n this._reprList.splice(index, 1);\r\n\r\n // update current rep\r\n if (target === this._repr) {\r\n --count;\r\n index = index < count ? index : count - 1;\r\n this._repr = this._reprList[index];\r\n }\r\n this._reprListChanged = true;\r\n }\r\n\r\n /**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\n repHide(index, hide) {\r\n if (hide === undefined) {\r\n hide = true;\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.show(!hide);\r\n }\r\n\r\n /**\r\n * Select atoms with selector\r\n * @param {Selector} selector - selector\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\n select(selector, append) {\r\n if (append) {\r\n this._selectionCount += this._complex.markAtomsAdditionally(selector, 1 << this._selectionBit);\r\n } else {\r\n this._selectionCount = this._complex.markAtoms(selector, 1 << this._selectionBit);\r\n }\r\n this._complex.updateStructuresMask();\r\n this.rebuildSelectionGeometry();\r\n }\r\n\r\n resetSelectionMask() {\r\n if (this._selectionCount !== 0) {\r\n this._selectionCount = 0;\r\n if (this._complex) {\r\n this._complex.clearAtomBits(1 << this._selectionBit);\r\n }\r\n }\r\n }\r\n\r\n updateSelectionMask(pickedObj) {\r\n const self = this;\r\n const { atom } = pickedObj;\r\n let { residue, chain, molecule } = pickedObj;\r\n const setMask = 1 << this._selectionBit;\r\n const clearMask = ~setMask;\r\n\r\n if (atom) {\r\n residue = atom.residue;\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (atom.mask & setMask) {\r\n atom.mask &= clearMask;\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n if (molecule) {\r\n molecule.mask &= clearMask;\r\n }\r\n this._selectionCount--;\r\n } else {\r\n atom.mask |= setMask;\r\n this._selectionCount++;\r\n\r\n // select residue if all atoms in it are selected\r\n residue.collectMask();\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (residue) {\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (residue._mask & setMask) {\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n residue.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n } else {\r\n residue._mask |= setMask;\r\n residue.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (chain || molecule) {\r\n const obj = chain || molecule;\r\n if (obj._mask & setMask) {\r\n obj._mask &= clearMask;\r\n obj.forEachResidue((r) => {\r\n if (r._mask & setMask) {\r\n r._mask &= clearMask;\r\n r.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n r._mask &= clearMask;\r\n }\r\n });\r\n } else {\r\n obj._mask |= setMask;\r\n obj.forEachResidue((r) => {\r\n if (!(r._mask & setMask)) {\r\n r._mask |= setMask;\r\n r.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n const otherObj = chain ? r.getMolecule() : r.getChain();\r\n if (otherObj) {\r\n otherObj.collectMask();\r\n }\r\n }\r\n });\r\n }\r\n } else {\r\n this.resetSelectionMask();\r\n }\r\n }\r\n\r\n expandSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms to add\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // select marked atoms\r\n const deselectionMask = ~tmpMask;\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask = (atom.mask & deselectionMask) | selectionMask;\r\n ++self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n shrinkSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms neighbouring to unselected ones\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // mark hanging atoms\r\n this._complex.forEachAtom((atom) => {\r\n if ((atom.mask & selectionMask) && (atom.bonds.length === 1)) {\r\n atom.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // deselect marked atoms\r\n const deselectionMask = ~(selectionMask | tmpMask);\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask &= deselectionMask;\r\n --self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n getSelectedComponent() {\r\n const selectionMask = 1 << this._selectionBit;\r\n\r\n let component = null;\r\n let multiple = false;\r\n\r\n // find which component is selected (exclusively)\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & selectionMask) {\r\n if (component === null) {\r\n component = atom.residue._component;\r\n } else if (component !== atom.residue._component) {\r\n multiple = true;\r\n }\r\n }\r\n });\r\n\r\n return multiple ? null : component;\r\n }\r\n\r\n getSelectionCenter(center, includesAtom, selRule) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._complex.forEachAtom((atom) => {\r\n if (includesAtom(atom, selRule)) {\r\n center.add(atom.position);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.applyMatrix4(this.matrix);\r\n return true;\r\n }\r\n\r\n needsRebuild() {\r\n if (this._reprListChanged) {\r\n return true;\r\n }\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n if (repr.needsRebuild) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n /**\r\n * Rebuild molecule geometry asynchronously.\r\n */\r\n rebuild() {\r\n const self = this;\r\n\r\n // Destroy current geometry\r\n gfxutils.clearTree(this);\r\n\r\n return new Promise(((resolve) => {\r\n // Nothing to do?\r\n const complex = self._complex;\r\n if (!complex) {\r\n resolve();\r\n return;\r\n }\r\n\r\n let errorOccured = false;\r\n setTimeout(() => {\r\n console.time('build');\r\n const reprList = self._reprList;\r\n const palette = palettes.get(settings.now.palette) || palettes.first;\r\n let hasGeometry = false;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n repr.colorer.palette = palette;\r\n\r\n if (repr.needsRebuild) {\r\n repr.reset();\r\n\r\n try {\r\n repr.buildGeometry(complex);\r\n } catch (e) {\r\n if (e instanceof utils.OutOfMemoryError) {\r\n repr.needsRebuild = false;\r\n repr.reset();\r\n logger.error(`Not enough memory to build geometry for representation ${repr.index + 1}`);\r\n errorOccured = true;\r\n } else {\r\n throw e;\r\n }\r\n }\r\n\r\n if (DEBUG && !errorOccured) {\r\n logger.debug(`Triangles count: ${meshutils.countTriangles(repr.geo)}`);\r\n }\r\n }\r\n\r\n hasGeometry = errorOccured || hasGeometry || gfxutils.groupHasGeometryToRender(repr.geo);\r\n\r\n if (repr.geo) {\r\n self.add(repr.geo);\r\n }\r\n }\r\n\r\n self._reprListChanged = false;\r\n\r\n console.timeEnd('build');\r\n resolve();\r\n }, 10);\r\n }));\r\n }\r\n\r\n setNeedsRebuild() {\r\n // invalidate all representations\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n reprList[i].needsRebuild = true;\r\n }\r\n }\r\n\r\n rebuildSelectionGeometry() {\r\n const mask = 1 << this._selectionBit;\r\n\r\n gfxutils.clearTree(this._selectionGeometry);\r\n\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const repr = this._reprList[i];\r\n const sg = repr.buildSelectionGeometry(mask);\r\n if (!sg) {\r\n continue;\r\n }\r\n\r\n this._selectionGeometry.add(sg);\r\n for (let j = 0; j < sg.children.length; j++) {\r\n const m = sg.children[j];\r\n\r\n // copy component transform (that's not applied yet)\r\n // TODO make this code obsolete, accessing editor is bad\r\n if (this._editor && this._editor._componentTransforms) {\r\n const t = this._editor._componentTransforms[m._component._index];\r\n if (t) {\r\n m.position.copy(t.position);\r\n m.quaternion.copy(t.quaternion);\r\n }\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(sg);\r\n }\r\n }\r\n\r\n _buildSelectorFromSortedLists(atoms, residues, chains) {\r\n const complex = this._complex;\r\n\r\n function optimizeList(list) {\r\n const result = [];\r\n let k = 0;\r\n let first = NaN;\r\n let last = NaN;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const value = list[i];\r\n if (value === last + 1) {\r\n last = value;\r\n } else {\r\n if (!Number.isNaN(first)) {\r\n result[k++] = new selectors.Range(first, last);\r\n }\r\n first = last = value;\r\n }\r\n }\r\n if (!Number.isNaN(first)) {\r\n result[k] = new selectors.Range(first, last);\r\n }\r\n return result;\r\n }\r\n\r\n let expression = null;\r\n if (chains.length === complex._chains.length) {\r\n expression = selectors.all();\r\n } else {\r\n let selector;\r\n if (chains.length > 0) {\r\n selector = selectors.chain(chains);\r\n expression = expression ? selectors.or(expression, selector) : selector;// NOSONAR\r\n }\r\n if (Object.keys(residues).length > 0) {\r\n for (const ch in residues) {\r\n if (residues.hasOwnProperty(ch)) {\r\n selector = selectors.and(\r\n selectors.chain(ch),\r\n selectors.residx(optimizeList(residues[ch])),\r\n );\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n }\r\n }\r\n if (atoms.length > 0) {\r\n selector = selectors.serial(optimizeList(atoms));\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n\r\n if (!expression) {\r\n expression = selectors.none();\r\n }\r\n }\r\n\r\n return expression;\r\n }\r\n\r\n buildSelectorFromMask(mask) {\r\n const complex = this._complex;\r\n const chains = [];\r\n const residues = {};\r\n const atoms = [];\r\n\r\n complex.forEachChain((chain) => {\r\n if (chain._mask & mask) {\r\n chains.push(chain._name);\r\n }\r\n });\r\n\r\n complex.forEachResidue((residue) => {\r\n if (residue._mask & mask && !(residue._chain._mask & mask)) {\r\n const c = residue._chain._name;\r\n if (!(c in residues)) {\r\n residues[c] = [residue._index];\r\n } else {\r\n residues[c].push(residue._index);\r\n }\r\n }\r\n });\r\n\r\n complex.forEachAtom((atom) => {\r\n if (atom.mask & mask && !(atom.residue._mask & mask)) {\r\n atoms.push(atom.serial);\r\n }\r\n });\r\n\r\n return this._buildSelectorFromSortedLists(atoms, residues, chains);\r\n }\r\n\r\n forSelectedResidues(process) {\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.forEachResidue((residue) => {\r\n if (residue._mask & selectionMask) {\r\n process(residue);\r\n }\r\n });\r\n }\r\n\r\n beginComponentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.ComponentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n beginFragmentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.FragmentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n // should only be called by editors\r\n finalizeEdit() {\r\n this._editor = null;\r\n }\r\n\r\n setMaterialValues(values, needTraverse = false, process = undefined) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setValues(values);\r\n if (needTraverse) {\r\n rep.geo.traverse((object) => {\r\n if (object instanceof THREE.Mesh) {\r\n object.material.setValues(values);\r\n\r\n if (process !== undefined) {\r\n process(object);\r\n }\r\n\r\n object.material.needsUpdate = true;\r\n }\r\n });\r\n }\r\n }\r\n }\r\n\r\n setUberOptions(values) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setUberOptions(values);\r\n }\r\n }\r\n\r\n /**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\n within(selector, radius) {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return false;\r\n }\r\n\r\n // mark atoms of the group as selected\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.markAtoms(selector, selectionMask);\r\n\r\n // mark all atoms within distance as selected\r\n if (vw) {\r\n vw.forEachAtomWithinDistFromMasked(this._complex, selectionMask, Number(radius), (atom) => {\r\n atom.mask |= selectionMask;\r\n });\r\n }\r\n\r\n // update selection count\r\n this._selectionCount = this._complex.countAtomsByMask(selectionMask);\r\n\r\n // update secondary structure mask\r\n this._complex.updateStructuresMask();\r\n\r\n return this.buildSelectorFromMask(selectionMask);\r\n }\r\n}\r\n// 32 bits = 30 bits for reps + 1 for selection + 1 for selection expansion\r\nComplexVisual.NUM_REPRESENTATION_BITS = 30;\r\n\r\nexport default ComplexVisual;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexVolumeFaces from './VolumeFaces.vert';\r\nimport fragmentVolumeFaces from './VolumeFaces.frag';\r\nimport vertexVolume from './Volume.vert';\r\nimport fragmentVolume from './Volume.frag';\r\nimport vertexFarPlane from './VolumeFarPlane.vert';\r\nimport fragmentFarPlane from './VolumeFarPlane.frag';\r\nimport settings from '../../settings';\r\n\r\nconst volumeUniforms = THREE.UniformsUtils.merge([\r\n {\r\n volumeDim: { type: 'v3', value: new THREE.Vector3(512, 512, 512) },\r\n tileTex: { type: 't', value: null },\r\n tileTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n tileStride: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n\r\n boxAngles: { type: 'v3', value: new THREE.Vector3(1, 1, 1) },\r\n delta: { type: 'v3', value: new THREE.Vector3(0, 0, 0) },\r\n\r\n _isoLevel0: { type: 'v2', value: new THREE.Vector3(0.5, 0.75, 1.0) },\r\n _flipV: { type: 'f', value: 0.0 },\r\n _BFLeft: { type: 't', value: null },\r\n _BFRight: { type: 't', value: null },\r\n _FFLeft: { type: 't', value: null },\r\n _FFRight: { type: 't', value: null },\r\n _WFFLeft: { type: 't', value: null },\r\n _WFFRight: { type: 't', value: null },\r\n },\r\n]);\r\n\r\nfunction overrideUniforms(params, defUniforms) {\r\n const uniforms = THREE.UniformsUtils.clone(defUniforms);\r\n for (const p in params) {\r\n if (uniforms.hasOwnProperty(p)) {\r\n uniforms[p].value = params[p];\r\n }\r\n }\r\n return uniforms;\r\n}\r\n\r\nfunction facesPosMaterialParams(params, sideType) {\r\n return {\r\n uniforms: overrideUniforms(params, {}),\r\n vertexShader: vertexVolumeFaces,\r\n fragmentShader: fragmentVolumeFaces,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n side: sideType,\r\n };\r\n}\r\n\r\nclass BackFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const backFaceParams = facesPosMaterialParams(params, THREE.BackSide);\r\n super(backFaceParams);\r\n }\r\n}\r\n\r\nclass ShaderParams {\r\n constructor(params, uniforms, vertexShader, fragmentShader) {\r\n this.uniforms = overrideUniforms(params, uniforms);\r\n this.vertexShader = vertexShader;\r\n this.fragmentShader = fragmentShader;\r\n this.transparent = false;\r\n this.depthTest = false;\r\n this.depthWrite = false;\r\n this.side = THREE.FrontSide;\r\n }\r\n}\r\n\r\nclass BackFacePosMaterialFarPlane extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const matUniforms = THREE.UniformsUtils.merge([\r\n {\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n farZ: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n matWorld2Volume: { type: '4fv', value: new THREE.Matrix4() },\r\n },\r\n ]);\r\n\r\n const shaderParams = new ShaderParams(params, matUniforms, vertexFarPlane, fragmentFarPlane);\r\n super(shaderParams);\r\n }\r\n}\r\n\r\nclass FrontFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const frontFaceParams = facesPosMaterialParams(params, THREE.FrontSide);\r\n super(frontFaceParams);\r\n }\r\n}\r\n\r\nclass VolumeMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const shaderParams = new ShaderParams(params, volumeUniforms, vertexVolume, fragmentVolume);\r\n shaderParams.transparent = true;\r\n shaderParams.depthTest = true;\r\n\r\n super(shaderParams);\r\n this.updateDefines();\r\n }\r\n\r\n updateDefines() {\r\n this.defines = {\r\n ISO_MODE: settings.now.modes.VD.isoMode,\r\n STEPS_COUNT: settings.now.modes.VD.polyComplexity[settings.now.resolution] * 100,\r\n };\r\n this.needsUpdate = true;\r\n }\r\n}\r\n\r\nexport default {\r\n BackFacePosMaterial,\r\n BackFacePosMaterialFarPlane,\r\n FrontFacePosMaterial,\r\n VolumeMaterial,\r\n};\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport settings from '../settings';\r\n\r\nclass VolumeMesh extends THREE.Mesh {\r\n volumeInfo = {}; // data for noise filter\r\n\r\n constructor() {\r\n const geo = new THREE.BufferGeometry();\r\n super(geo);\r\n this.clipPlane = new THREE.Plane();\r\n const size = new THREE.Vector3(0.5, 0.5, 0.5);\r\n this.size = size;\r\n\r\n this.cullFlag = [\r\n true, true, true, true,\r\n true, true, true, true,\r\n false, false, false, false, false, false,\r\n ];\r\n\r\n this.faces = [\r\n { indices: [], norm: new THREE.Vector3(0, 0, -1) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 1) },\r\n { indices: [], norm: new THREE.Vector3(0, -1, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 1, 0) },\r\n { indices: [], norm: new THREE.Vector3(-1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 0) },\r\n ];\r\n\r\n this.vertices = [\r\n new THREE.Vector3(-size.x, -size.y, -size.z),\r\n new THREE.Vector3(-size.x, size.y, -size.z),\r\n new THREE.Vector3(size.x, -size.y, -size.z),\r\n new THREE.Vector3(size.x, size.y, -size.z),\r\n new THREE.Vector3(-size.x, -size.y, size.z),\r\n new THREE.Vector3(-size.x, size.y, size.z),\r\n new THREE.Vector3(size.x, -size.y, size.z),\r\n new THREE.Vector3(size.x, size.y, size.z),\r\n new THREE.Vector3(0.0, 0.0, 0.0), // Placeholder for section\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n ];\r\n\r\n geo.setAttribute('position', new THREE.BufferAttribute(new Float32Array(this.vertices.length * 3), 3));\r\n\r\n this.name = 'VolumeMesh';\r\n }\r\n\r\n static _corners = [\r\n // x, y, z, edge1, edge2, edge3\r\n [-1, -1, -1, 0, 4, 8],\r\n [1, -1, -1, 0, 5, 9],\r\n [1, 1, -1, 1, 5, 10],\r\n [-1, 1, -1, 1, 4, 11],\r\n [-1, -1, 1, 2, 6, 8],\r\n [1, -1, 1, 2, 7, 9],\r\n [1, 1, 1, 3, 7, 10],\r\n [-1, 1, 1, 3, 6, 11],\r\n ];\r\n\r\n static _edges = [\r\n // corner1, corner2, center_x, center_y, center_z\r\n [0, 1, 0, -1, -1],\r\n [2, 3, 0, 1, -1],\r\n [4, 5, 0, -1, 1],\r\n [6, 7, 0, 1, 1],\r\n [0, 3, -1, 0, -1],\r\n [1, 2, 1, 0, -1],\r\n [4, 7, -1, 0, 1],\r\n [5, 6, 1, 0, 1],\r\n [0, 4, -1, -1, 0],\r\n [1, 5, 1, -1, 0],\r\n [2, 6, -1, 1, 0],\r\n [3, 7, 1, 1, 0],\r\n ];\r\n\r\n static _edgeIntersections = (function () {\r\n const edgeIntersections = [];\r\n for (let j = 0; j < 12; ++j) {\r\n edgeIntersections.push(new THREE.Vector3());\r\n }\r\n return edgeIntersections;\r\n }());\r\n\r\n _updateVertices() {\r\n // Algorithm:\r\n // 1. Get plane parameters\r\n // 2. Compute culling flags for all vertices\r\n // 3. If intersection occurs => compute from 3 to 6 intersection points\r\n const corners = VolumeMesh._corners;\r\n const edges = VolumeMesh._edges;\r\n const edgeIntersections = VolumeMesh._edgeIntersections;\r\n\r\n let i;\r\n\r\n const norm = this.clipPlane.normal;\r\n const D = this.clipPlane.constant;\r\n\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n const cornerMark = [0, 0, 0, 0, 0, 0, 0, 0];\r\n const edgeMark = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1];\r\n\r\n const curEdge = new THREE.Vector3();\r\n let curEdgeInter = null;\r\n\r\n function CheckX() {\r\n if (norm.x === 0) return 0;\r\n const x = -(norm.dot(curEdge) + D) / norm.x;\r\n if (-size.x <= x && x <= size.x) {\r\n curEdgeInter.set(x, curEdge.y, curEdge.z);\r\n if (x === size.x) return 2;\r\n if (x === -size.x) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckY() {\r\n if (norm.y === 0) return 0;\r\n const y = -(norm.dot(curEdge) + D) / norm.y;\r\n if (-size.y <= y && y <= size.y) {\r\n curEdgeInter.set(curEdge.x, y, curEdge.z);\r\n if (y === size.y) return 2;\r\n if (y === -size.y) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckZ() {\r\n if (norm.z === 0) return 0;\r\n const z = -(norm.dot(curEdge) + D) / norm.z;\r\n if (-size.z <= z && z <= size.z) {\r\n curEdgeInter.set(curEdge.x, curEdge.y, z);\r\n if (z === size.z) return 2;\r\n if (z === -size.z) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n // for each edge\r\n for (let curEdgeIdx = 0; curEdgeIdx < 12; ++curEdgeIdx) {\r\n const curEdgeSource = edges[curEdgeIdx];\r\n curEdgeInter = edgeIntersections[curEdgeIdx];\r\n\r\n curEdge.set(curEdgeSource[2], curEdgeSource[3], curEdgeSource[4]);\r\n curEdge.multiply(size);\r\n\r\n // calculate intersection point\r\n let flag = 0;\r\n if (curEdgeSource[2] === 0) flag = CheckX();\r\n if (curEdgeSource[3] === 0) flag = CheckY();\r\n if (curEdgeSource[4] === 0) flag = CheckZ();\r\n\r\n // mark corresponding corner (if plane cuts through one)\r\n if (flag === -2) {\r\n cornerMark[curEdgeSource[0]] = 1;\r\n } else if (flag === 2) {\r\n cornerMark[curEdgeSource[1]] = 1;\r\n } else if (flag === 0) {\r\n // edge is not intersected by the plane (doesn't produce a vertex)\r\n edgeMark[curEdgeIdx] = 0;\r\n }\r\n }\r\n\r\n const face = {\r\n indices: [],\r\n norm: norm.clone().negate(),\r\n };\r\n\r\n let nextVertex = 8;\r\n\r\n // for each marked corner\r\n for (i = 0; i < 8; ++i) {\r\n if (cornerMark[i] === 1) {\r\n // add corner as vertex to the face\r\n vert[nextVertex].set(corners[i][0], corners[i][1], corners[i][2]).multiply(size);\r\n face.indices.push(nextVertex++);\r\n // skip adjacent edges\r\n edgeMark[corners[i][3]] = 0;\r\n edgeMark[corners[i][4]] = 0;\r\n edgeMark[corners[i][5]] = 0;\r\n }\r\n }\r\n\r\n // for each edge that has internal intersection\r\n for (i = 0; i < 12; ++i) {\r\n if (edgeMark[i] === 1) {\r\n // add intersection point as vertex to the face\r\n vert[nextVertex].copy(edgeIntersections[i]);\r\n face.indices.push(nextVertex++);\r\n }\r\n }\r\n\r\n this.faces[6] = face;\r\n\r\n const diff = new THREE.Vector3();\r\n const coplanarPoint = new THREE.Vector3();\r\n this.clipPlane.coplanarPoint(coplanarPoint);\r\n for (i = 0; i < vert.length; ++i) {\r\n this.cullFlag[i] = false;\r\n if (i < 8) {\r\n // corners should be culled by clipping plane\r\n diff.subVectors(vert[i], coplanarPoint);\r\n this.cullFlag[i] = (norm.dot(diff) >= 0.0);\r\n } else if (i < 8 + face.indices.length) {\r\n // cross section vertices don't get culled\r\n this.cullFlag[i] = true;\r\n }\r\n }\r\n\r\n // write data to vertex buffer\r\n const positions = this.geometry.getAttribute('position');\r\n let idx = 0;\r\n for (i = 0; i < vert.length; ++i) {\r\n positions.array[idx++] = vert[i].x;\r\n positions.array[idx++] = vert[i].y;\r\n positions.array[idx++] = vert[i].z;\r\n }\r\n positions.needsUpdate = true;\r\n }\r\n\r\n _collectVertices(face, filter) {\r\n let i;\r\n const vert = this.vertices;\r\n face.indices = [];\r\n for (i = 0; i < vert.length; ++i) {\r\n if (this.cullFlag[i] && filter(vert[i])) {\r\n face.indices.push(i);\r\n }\r\n }\r\n }\r\n\r\n _sortIndices(face, right) {\r\n let i;\r\n let j;\r\n const vert = this.vertices;\r\n const angle = [];\r\n\r\n const dir = new THREE.Vector3();\r\n for (i = 1; i < face.indices.length; ++i) {\r\n dir.subVectors(vert[face.indices[i]], vert[face.indices[0]]);\r\n dir.normalize();\r\n dir.cross(right);\r\n dir.negate();\r\n angle[i] = face.norm.dot(dir);\r\n }\r\n\r\n // Exchange sort\r\n for (i = 1; i < face.indices.length - 1; ++i) {\r\n for (j = i + 1; j < face.indices.length; ++j) {\r\n if (angle[j] < angle[i]) {\r\n // swap\r\n let t = angle[i];\r\n angle[i] = angle[j];\r\n angle[j] = t;\r\n\r\n t = face.indices[i];\r\n face.indices[i] = face.indices[j];\r\n face.indices[j] = t;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _updateIndices() {\r\n // Algorithm:\r\n // 1. Get plane vertices (from 3 to 6 vertices)\r\n // 2. Get \"right\" vector in plane\r\n // 3. Sort vertices using Graham-like method\r\n // 4. Create indices\r\n\r\n let i;\r\n let faceIdx;\r\n let face;\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n this._collectVertices(this.faces[0], (vertex) => vertex.z === -size.z);\r\n this._collectVertices(this.faces[1], (vertex) => vertex.z === size.z);\r\n this._collectVertices(this.faces[2], (vertex) => vertex.y === -size.y);\r\n this._collectVertices(this.faces[3], (vertex) => vertex.y === size.y);\r\n this._collectVertices(this.faces[4], (vertex) => vertex.x === -size.x);\r\n this._collectVertices(this.faces[5], (vertex) => vertex.x === size.x);\r\n\r\n const vCenter = new THREE.Vector3();\r\n const vRight = new THREE.Vector3();\r\n const vDir = new THREE.Vector3();\r\n\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n\r\n if (face.indices.length === 0) continue;\r\n\r\n vCenter.set(0, 0, 0);\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vCenter.add(vert[face.indices[i]]);\r\n }\r\n vCenter.multiplyScalar(1.0 / face.indices.length);\r\n vRight.subVectors(vert[face.indices[0]], vCenter);\r\n vRight.normalize();\r\n\r\n const rightProj = [];\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vDir.subVectors(vert[face.indices[i]], vCenter);\r\n rightProj[i] = vDir.dot(vRight);\r\n }\r\n for (i = 1; i < face.indices.length; ++i) {\r\n if (rightProj[i] < rightProj[0]) {\r\n // swap\r\n let t = rightProj[0];\r\n rightProj[0] = rightProj[i];\r\n rightProj[i] = t;\r\n\r\n [t] = face.indices;\r\n face.indices[0] = face.indices[i];\r\n face.indices[i] = t;\r\n }\r\n }\r\n\r\n this._sortIndices(face, vRight);\r\n }\r\n\r\n let numIndices = 0;\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n if (face.indices.length >= 3) {\r\n numIndices += 3 * (face.indices.length - 2);\r\n }\r\n }\r\n let offset = 0;\r\n const indices = new Uint16Array(numIndices);\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n for (i = 0; i < face.indices.length - 2; ++i) {\r\n indices[offset] = face.indices[0]; // eslint-disable-line prefer-destructuring\r\n indices[offset + 1] = face.indices[i + 1];\r\n indices[offset + 2] = face.indices[i + 2];\r\n offset += 3;\r\n }\r\n }\r\n\r\n this.geometry.setIndex(new THREE.BufferAttribute(indices, 1));\r\n }\r\n\r\n setDataSource(dataSource) {\r\n const vm = new VolumeMaterial.VolumeMaterial();\r\n const dim = dataSource.getDimensions();\r\n const stride = dataSource.getTiledTextureStride();\r\n const texture = dataSource.buildTiledTexture();\r\n const bbox = dataSource.getBox();\r\n vm.uniforms.volumeDim.value.set(dim[0], dim[1], dim[2]);\r\n vm.uniforms.tileTex.value = texture;\r\n vm.uniforms.tileTexSize.value.set(texture.image.width, texture.image.height);\r\n vm.uniforms.tileStride.value.set(stride[0], stride[1]);\r\n Object.assign(this.volumeInfo, dataSource.getVolumeInfo());\r\n\r\n const volInfo = this.volumeInfo;\r\n vm.uniforms.delta.value.copy(volInfo.delta);\r\n vm.uniforms.boxAngles.value.set(volInfo.obtuseAngle[0], volInfo.obtuseAngle[1], volInfo.obtuseAngle[2]);\r\n\r\n this.material = vm;\r\n\r\n bbox.getSize(this.scale);\r\n bbox.getCenter(this.position);\r\n }\r\n\r\n _updateIsoLevel() {\r\n const { kSigma, kSigmaMed, kSigmaMax } = settings.now.modes.VD;\r\n const volInfo = this.volumeInfo;\r\n const mean = volInfo.dmean - volInfo.dmin;\r\n const span = volInfo.dmax - volInfo.dmin;\r\n const level = (k) => (mean + k * volInfo.sd) / span;\r\n this.material.uniforms._isoLevel0.value.set(level(kSigma), level(kSigmaMed), level(kSigmaMax));\r\n }\r\n\r\n static _nearClipPlaneOffset = 0.2;\r\n\r\n static _pos = new THREE.Vector3();\r\n\r\n static _norm = new THREE.Vector3();\r\n\r\n static _norm4D = new THREE.Vector4();\r\n\r\n static _matrixWorldToLocal = new THREE.Matrix4();\r\n\r\n static _clipPlane = new THREE.Plane();\r\n\r\n rebuild(camera) {\r\n const nearClipPlaneOffset = VolumeMesh._nearClipPlaneOffset;\r\n const pos = VolumeMesh._pos;\r\n const norm = VolumeMesh._norm;\r\n const norm4D = VolumeMesh._norm4D;\r\n const matrixWorldToLocal = VolumeMesh._matrixWorldToLocal;\r\n const clipPlane = VolumeMesh._clipPlane;\r\n\r\n this._updateIsoLevel();\r\n\r\n // get clip plane in local space\r\n camera.getWorldDirection(norm);\r\n camera.getWorldPosition(pos);\r\n pos.addScaledVector(norm, camera.near + nearClipPlaneOffset);\r\n\r\n // transform pos to local CS\r\n matrixWorldToLocal.copy(this.matrixWorld).invert();\r\n pos.applyMatrix4(matrixWorldToLocal);\r\n\r\n // transform norm to local CS\r\n norm4D.set(norm.x, norm.y, norm.z, 0.0); // NOTE: use homogeneous norm for proper transformation\r\n norm4D.applyMatrix4(matrixWorldToLocal);\r\n norm.copy(norm4D);\r\n norm.normalize();\r\n\r\n clipPlane.setFromNormalAndCoplanarPoint(norm, pos);\r\n\r\n if (!this.clipPlane.equals(clipPlane)) {\r\n this.clipPlane = clipPlane.clone();\r\n this._updateVertices();\r\n this._updateIndices();\r\n }\r\n }\r\n}\r\n\r\nexport default VolumeMesh;\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _flattenArray(input) {\r\n const n = input.length;\r\n const output = new Float32Array(n * 3);\r\n for (let i = 0; i < n; ++i) {\r\n const j = 3 * i;\r\n const v = input[i];\r\n output[j] = v.x;\r\n output[j + 1] = v.y;\r\n output[j + 2] = v.z;\r\n }\r\n return output;\r\n}\r\n\r\nclass VolumeBounds {\r\n static _projectionTable = { // corresponds between (origin axes and angles between them) and between saving vector coordinates\r\n XY: ['x', 2],\r\n XZ: ['y', 1],\r\n YZ: ['z', 0],\r\n };\r\n\r\n constructor(bBox, volInfo) {\r\n const { delta } = volInfo; // {x: XY, y : XZ, z: YZ}\r\n const { obtuseAngle } = volInfo; // 1 - obtuse, 0 - acute\r\n\r\n const bSize = new THREE.Vector3();\r\n bBox.getSize(bSize);\r\n bSize.multiplyScalar(0.5);\r\n\r\n const offsetVert = this._getBaseVertices(delta, obtuseAngle);\r\n\r\n const geometry = new THREE.BufferGeometry();\r\n const vertices = [];\r\n\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(offsetVert[i].clone().multiply(bSize));\r\n vertices.push(offsetVert[(i + 1) % 4].clone().multiply(bSize));\r\n }\r\n const translation = new THREE.Vector3(2 * bSize.x * (1 - delta.x - delta.y), 0, 0);\r\n for (let i = 0; i < 8; i++) {\r\n vertices.push(vertices[i].clone().add(translation));\r\n }\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(vertices[i * 2].clone());\r\n vertices.push(vertices[i * 2 + 8].clone());\r\n }\r\n const center = new THREE.Vector3();\r\n bBox.getCenter(center);\r\n vertices.forEach((vertex) => vertex.add(center)); // pivot shift\r\n\r\n const flatVertices = _flattenArray(vertices);\r\n geometry.setAttribute('position', new THREE.BufferAttribute(flatVertices, 3));\r\n\r\n this._lines = new THREE.LineSegments(geometry, new THREE.LineBasicMaterial({ color: 0xFFFFFF }));\r\n this._lines.layers.set(gfxutils.LAYERS.VOLUME);\r\n }\r\n\r\n // Set one edge (4 points) of frame, from which with parallel transfer the rest of the frame points can be obtained\r\n _getBaseVertices(delta, obtuseAngle) {\r\n const projTable = VolumeBounds._projectionTable;\r\n\r\n const proj = ((index, inv) => { // tricky function to take account of projections: their position(related to box) and sign\r\n const currDelta = delta[projTable[index][0]];\r\n const angleValue = -0.5 * (inv - 1) + inv * obtuseAngle[projTable[index][1]];// inv = 1: alpha; inv = -1: 1 - alpha\r\n return angleValue * currDelta;\r\n });\r\n\r\n const offsetVert = [\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', 1)), -1 + 2 * proj('YZ', 1), -1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', 1)), -1 + 2 * proj('YZ', -1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', -1)), 1 - 2 * proj('YZ', 1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', -1)), 1 - 2 * proj('YZ', -1), -1),\r\n ];\r\n\r\n return offsetVert;\r\n }\r\n\r\n getMesh() {\r\n return this._lines;\r\n }\r\n}\r\n\r\nexport default VolumeBounds;\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport meshes from './meshes/meshes';\r\nimport gfxutils from './gfxutils';\r\n\r\n// Thes geometric far plane is required for correct filling in the BFTexture in case, when far plane cuts the volume\r\n// cube. In cut place of cube there is no correct data in BFTexture and volume rendering integral is calculated\r\n// with errors.\r\n// Far plane cuts the cube in case of large volume scale (zoom), because farplane doesn't change\r\nclass VolumeFarPlane {\r\n // create plane with unit corners coords (for future rescale in vshader according to camera properties)\r\n constructor(volume, width, height) {\r\n const planeGeo = this._initPlaneGeo(width, height);\r\n\r\n const mat = new VolumeMaterial.BackFacePosMaterialFarPlane();\r\n this._plane = new meshes.Mesh(planeGeo, mat);\r\n this._plane.frustumCulled = false;\r\n this._plane.doubleSided = true;\r\n const matWorldToVolume = new THREE.Matrix4();\r\n\r\n this._plane._onBeforeRender = function (_renderer, _scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!volume || !material) {\r\n return;\r\n }\r\n\r\n // count point in world at farplane place\r\n const planeCamPos = new THREE.Vector4(0, 0, -(camera.far - 0.1), 1);\r\n planeCamPos.applyMatrix4(camera.matrixWorld);\r\n\r\n // recalc matrices to make plane be placed as farplane in the World relative to camera\r\n this.matrix.identity();\r\n this.matrix.makeTranslation(planeCamPos.x, planeCamPos.y, planeCamPos.z);\r\n this.matrixWorld.copy(this.matrix);\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n this.normalMatrix.getNormalMatrix(this.modelViewMatrix);\r\n\r\n // build worldToVolume matrix to transform plane into volumeCS (volumeCS coords are written to BackFaceTexture)\r\n const volumeMatrix = volume.matrixWorld;\r\n matWorldToVolume.copy(volumeMatrix).invert();\r\n\r\n // update material props\r\n material.uniforms.aspectRatio.value = camera.aspect;\r\n material.uniforms.farZ.value = camera.far;\r\n material.uniforms.tanHalfFOV.value = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * camera.fov);\r\n material.uniforms.matWorld2Volume.value = matWorldToVolume;\r\n };\r\n\r\n // set it to special layer to draw only into BFTexture\r\n this._plane.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n }\r\n\r\n _initPlaneGeo(width, height) {\r\n const planeGeo = new THREE.BufferGeometry();\r\n\r\n width = width || 1;\r\n height = height || 1;\r\n\r\n const vertices = new Float32Array([\r\n -0.5 * width, 0.5 * height, 0,\r\n 0.5 * width, 0.5 * height, 0,\r\n -0.5 * width, -0.5 * height, 0,\r\n 0.5 * width, -0.5 * height, 0,\r\n ]);\r\n\r\n planeGeo.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n planeGeo.setIndex([0, 2, 1, 2, 3, 1]);\r\n\r\n return planeGeo;\r\n }\r\n\r\n getMesh() {\r\n return this._plane;\r\n }\r\n}\r\n\r\nexport default VolumeFarPlane;\r\n","import * as THREE from 'three';\r\nimport VolumeMesh from './gfx/VolumeMesh';\r\nimport VolumeBounds from './gfx/VolumeBounds';\r\nimport VolumeFarPlane from './gfx/VolumeFarPlane';\r\nimport Visual from './Visual';\r\nimport settings from './settings';\r\n\r\nclass VolumeVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._mesh = new VolumeMesh();\r\n this._mesh.setDataSource(dataSource);\r\n this.add(this._mesh);\r\n\r\n this._frame = new VolumeBounds(this.getBoundaries().boundingBox, this._mesh.volumeInfo);\r\n this.add(this._frame.getMesh());\r\n this.showFrame(settings.now.modes.VD.frame);\r\n\r\n this._farPlane = new VolumeFarPlane(this._mesh, 2, 2);\r\n this.add(this._farPlane.getMesh());\r\n }\r\n\r\n getBoundaries() {\r\n const box = this._dataSource.getBox();\r\n const sphere = new THREE.Sphere();\r\n box.getBoundingSphere(sphere);\r\n\r\n return {\r\n boundingBox: box,\r\n boundingSphere: sphere,\r\n };\r\n }\r\n\r\n getMesh() {\r\n return this._mesh;\r\n }\r\n\r\n showFrame(needShow) {\r\n this._frame.getMesh().material.visible = needShow;\r\n }\r\n}\r\n\r\nexport default VolumeVisual;\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available loaders.\r\n * @extends EntityList\r\n */\r\nclass LoaderList extends EntityList {\r\n /**\r\n * Create a list of loaders.\r\n * The loaders are indexed by supported source types (`.types` property of a Loader\r\n * subclass).\r\n * The loaders can be retrieved later by matching against specs (see {@link LoaderList#find}).\r\n *\r\n * @param {!Array=} someLoaders A list of {@link Loader} subclasses to\r\n * automatically register at creation time.\r\n * @see LoaderList#register\r\n */\r\n constructor(someLoaders = []) {\r\n super(someLoaders, ['types']);\r\n }\r\n\r\n /**\r\n * Find a suitable loader for a source type.\r\n *\r\n * @param {Object} specs Loader specifications.\r\n * @param {string=} specs.type Supported source type.\r\n * @param {*=} specs.source Source to load from.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.type) {\r\n list = this._dict.types[specs.type.toLowerCase()] || [];\r\n } else if (specs.source) {\r\n return this._list.filter((SomeLoader) => SomeLoader.canProbablyLoad && SomeLoader.canProbablyLoad(specs.source));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default LoaderList;\r\n","import EventDispatcher from '../../utils/EventDispatcher';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Loader extends EventDispatcher {\r\n constructor(source, options) {\r\n super();\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n this._agent = null;\r\n }\r\n\r\n load() {\r\n return Promise.reject(new Error('Loading from this source is not implemented'));\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n if (this._agent) {\r\n this._agent.abort();\r\n }\r\n }\r\n\r\n static extractName(_source) {\r\n return undefined;\r\n }\r\n}\r\n\r\nmakeContextDependent(Loader.prototype);\r\n","import Loader from './Loader';\r\n\r\nexport default class FileLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = options.binary === true;\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const blob = this._source;\r\n const reader = this._agent = new FileReader();\r\n\r\n reader.addEventListener('load', () => {\r\n resolve(reader.result);\r\n });\r\n reader.addEventListener('error', () => {\r\n reject(reader.error);\r\n });\r\n reader.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n reader.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n if (this._binary) {\r\n reader.readAsArrayBuffer(blob);\r\n } else {\r\n reader.readAsText(blob);\r\n }\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return (File && source instanceof File) || (Blob && source instanceof Blob);\r\n }\r\n\r\n static extractName(source) {\r\n return source && source.name;\r\n }\r\n}\r\n\r\nFileLoader.types = ['file', 'blob'];\r\n","import _ from 'lodash';\r\nimport Loader from './Loader';\r\n\r\n// we don't need to detect all kinds of URLs, just the evident ones\r\nconst urlStartRegexp = /^(https?|ftp):\\/\\//i;\r\n\r\nexport default class XHRLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = (options.binary === true);\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const url = this._source;\r\n const request = this._agent = new XMLHttpRequest();\r\n\r\n request.addEventListener('load', () => {\r\n if (request.status === 200) {\r\n resolve(request.response);\r\n } else {\r\n reject(new Error(`HTTP ${request.status} while fetching ${url}`));\r\n }\r\n });\r\n request.addEventListener('error', () => {\r\n reject(new Error('HTTP request failed'));\r\n });\r\n request.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n request.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n request.open('GET', url);\r\n if (this._binary) {\r\n request.responseType = 'arraybuffer';\r\n } else {\r\n request.responseType = 'text';\r\n }\r\n request.send();\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return _.isString(source) && urlStartRegexp.test(source);\r\n }\r\n\r\n static extractName(source) {\r\n if (source) {\r\n const last = (source.indexOf('?') + 1 || source.lastIndexOf('#') + 1 || source.length + 1) - 1;\r\n return source.slice(source.lastIndexOf('/', last) + 1, last);\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nXHRLoader.types = ['url'];\r\n","import Loader from './Loader';\r\n\r\nexport default class ImmediateLoader extends Loader {\r\n load() {\r\n return new Promise((resolve) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n resolve(this._source);\r\n });\r\n }\r\n\r\n static canProbablyLoad(_source) {\r\n return false;\r\n }\r\n}\r\n\r\nImmediateLoader.types = ['immediate'];\r\n","import LoaderList from './loaders/LoaderList';\r\n\r\nimport FileLoader from './loaders/FileLoader';\r\nimport XHRLoader from './loaders/XHRLoader';\r\nimport ImmediateLoader from './loaders/ImmediateLoader';\r\n\r\nexport default new LoaderList([\r\n // note: order might be important\r\n FileLoader,\r\n XHRLoader,\r\n ImmediateLoader,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available parsers.\r\n * @extends EntityList\r\n */\r\nclass ParserList extends EntityList {\r\n /**\r\n * Create a list of parsers.\r\n * The parsers are indexed by supported data formats and file extensions (`.formats` and\r\n * `.extensions` properties of a Parser subclass).\r\n * The parsers can be retrieved later by matching against specs (see {@link ParsrerList#find}).\r\n *\r\n * @param {!Array=} someParsers A list of {@link Parser} subclasses to\r\n * automatically register at creation time.\r\n * @see ParserList#register\r\n */\r\n constructor(someParsers = []) {\r\n super(someParsers, ['formats', 'extensions']);\r\n }\r\n\r\n /**\r\n * Find a suitable parser for data.\r\n *\r\n * @param {Object} specs Parser specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {string=} specs.ext Supported filename extension.\r\n * @param {*=} specs.data Data to parse.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n } else if (specs.ext) {\r\n list = this._dict.extensions[specs.ext.toLowerCase()] || [];\r\n }\r\n // autodetect only if no format is forced\r\n if (list.length === 0 && !specs.format && specs.data) {\r\n return this._list.filter((SomeParser) => SomeParser.canProbablyParse && SomeParser.canProbablyParse(specs.data));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ParserList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Parser {\r\n constructor(data, options) {\r\n this._data = data;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n parseSync() {\r\n throw new Error('Parsing this type of data is not implemented');\r\n }\r\n\r\n parse() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Parsing aborted'));\r\n }\r\n return resolve(this.parseSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n // only for volume Parsers\r\n getModel() {\r\n this.model._parseHeader(this._data);\r\n return this.model;\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Parser.prototype);\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 290\".\r\n *\r\n * @exports Remark290\r\n * @constructor\r\n */\r\nclass Remark290 {\r\n constructor() {\r\n /** @type {THREE.Matrix4[]} */\r\n this.matrices = [];\r\n\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (stream.readString(12, 18) === ' SMTRY') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === this.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n }\r\n }\r\n}\r\n\r\nRemark290.prototype.id = 290;\r\n\r\nexport default Remark290;\r\n","import * as THREE from 'three';\r\nimport chem from '../../../chem';\r\n\r\nconst { Assembly } = chem;\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 350\".\r\n *\r\n * @exports Remark350\r\n * @constructor\r\n */\r\nclass Remark350 {\r\n constructor(complex) {\r\n /** @type {Complex} */\r\n this._complex = complex;\r\n /** @type {Assembly[]} */\r\n this.assemblies = [];\r\n\r\n /** @type {?Assembly} */\r\n this._assembly = null;\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?Assembly} */\r\n let assembly = this._assembly;\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (assembly && stream.readString(12, 18) === ' BIOMT') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === assembly.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n } else if (assembly && stream.readString(35, 41) === 'CHAINS:') {\r\n const entries = stream.readString(42, 80).split(',');\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const chain = entries[i].trim();\r\n if (chain.length > 0) {\r\n assembly.addChain(chain);\r\n }\r\n }\r\n } else if (stream.readString(12, 23) === 'BIOMOLECULE:') {\r\n // assert molIndex === this.assemblies.length + 1\r\n this._matrix = null;\r\n this._matrixIndex = -1;\r\n this._assembly = assembly = new Assembly(this._complex);\r\n this.assemblies.push(assembly);\r\n }\r\n }\r\n}\r\n\r\nRemark350.prototype.id = 350;\r\n\r\nexport default Remark350;\r\n","/** Helper class for stream-like reading input files. */\r\nclass PDBStream {\r\n /**\r\n * Create a stream\r\n * @param {String} data Input data\r\n */\r\n constructor(data) {\r\n /** @type String */\r\n this._data = data; // Input file\r\n /** @type Number */\r\n this._start = 0; // Starting position of line\r\n /** @type Number */\r\n this._nextCR = -1; // Position of next CR (0x0D)\r\n /** @type Number */\r\n this._nextLF = -1; // Position of next LF (0x0A)\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n /** @type Number */\r\n this._end = data.length; // End of data\r\n\r\n this.next();\r\n }\r\n\r\n /**\r\n * Reading next line.\r\n * @returns {String} Next line in data (ending with LF or CR)\r\n */\r\n readLine() {\r\n return this._data.slice(this._start, this._next);\r\n }\r\n\r\n /**\r\n * Reading character from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {String} Character from position\r\n */\r\n readChar(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data[pos] : ' ';\r\n }\r\n\r\n /**\r\n * Reading character code from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {Number} Character code from position\r\n */\r\n readCharCode(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data.charCodeAt(pos) : 32;\r\n }\r\n\r\n /**\r\n * Reading string from begin to end points.\r\n * For a reason unknown, numbering assumed not to start from 0, but from 1.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {String} String from begin to end\r\n */\r\n readString(begin, end) {\r\n const from = this._start + begin - 1;\r\n const to = this._start + end;\r\n return this._data.slice(from, to < this._next ? to : this._next);\r\n }\r\n\r\n /**\r\n * Reading integer from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Integer from begin to end\r\n */\r\n readInt(begin, end) {\r\n return parseInt(this.readString(begin, end), 10);\r\n }\r\n\r\n /**\r\n * Reading float from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Float from begin to end\r\n */\r\n readFloat(begin, end) {\r\n return parseFloat(this.readString(begin, end));\r\n }\r\n\r\n /**\r\n * Checking for end of data.\r\n * @returns {boolean} True if data is ended, false otherwise\r\n */\r\n end() {\r\n return this._start >= this._end;\r\n }\r\n\r\n /**\r\n * Procedure to re-arrange current pointers in data.\r\n */\r\n next() {\r\n const start = this._next + 1;\r\n this._start = start < this._end ? start : this._end;\r\n\r\n // support CR, LF, CR+LF line endings\r\n // do not support LF+CR, CR+CR+LF, and other strange combinations\r\n\r\n if (this._start > this._nextCR) {\r\n this._nextCR = (this._data.indexOf('\\r', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n if (this._start > this._nextLF) {\r\n this._nextLF = (this._data.indexOf('\\n', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n this._next = this._nextCR + 1 < this._nextLF ? this._nextCR : this._nextLF;\r\n }\r\n}\r\n\r\nexport default PDBStream;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport Remark290 from './pdb/Remark290';\r\nimport Remark350 from './pdb/Remark350';\r\nimport PDBStream from './PDBStream';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst TAG_LENGTH = 6;\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\n// the most frequently used beginnings; although HEADER is mandatory, it is often missing in handmade files\r\nconst pdbStartRegexp = /^(HEADER\\s|COMPND\\s|REMARK\\s|ATOM {2}|HETATM|MODEL )/i;\r\n\r\nconst remarkParsers = {\r\n // NOTE: please forget the idea to build the method name in runtime, it can be obfuscated.\r\n 290: Remark290,\r\n 350: Remark350,\r\n};\r\n\r\nclass PDBParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._sheet = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._compaundFound = false;\r\n this._biomoleculeFound = false;\r\n this._allowedChainsIDs = null;\r\n this._lastMolId = -1;\r\n\r\n this._remarks = {};\r\n this._remark = null;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n this._compndCurrToken = '';\r\n\r\n this._options.fileType = 'pdb';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && pdbStartRegexp.test(data);\r\n }\r\n\r\n _finalize() {\r\n this._fixBondsArray();\r\n this._fixChains();\r\n\r\n // keep crystallographic symmetry transformations\r\n const remark290 = this._remarks[290];\r\n this._complex.symmetry = _.isUndefined(remark290) ? [] : remark290.matrices;\r\n\r\n // add loaded biological assemblies\r\n const remark350 = this._remarks[350];\r\n this._complex.units = this._complex.units.concat(_.isUndefined(remark350) ? [] : remark350.assemblies);\r\n\r\n // add loaded macromolecules\r\n this._finalizeMolecules();\r\n\r\n // create secondary structure etc.\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _finalizeMolecules() {\r\n // get chains from complex\r\n const chainDict = {};\r\n let i;\r\n const chains = this._complex._chains;\r\n for (i = 0; i < chains.length; ++i) {\r\n const chainObj = chains[i];\r\n const chainName = chainObj._name;\r\n chainDict[chainName] = chainObj;\r\n }\r\n\r\n // aggregate residues from chains\r\n for (i = 0; i < this._molecules.length; i++) {\r\n const m = this._molecules[i];\r\n let residues = [];\r\n for (let j = 0; j < m._chains.length; j++) {\r\n const name = m._chains[j];\r\n const chain = chainDict[name];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, m._name, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _fixChains() {\r\n const idChainMap = {};\r\n const complex = this._complex;\r\n\r\n // prepare\r\n for (let i = 0; i < complex._chains.length; i++) {\r\n const chain = complex._chains[i];\r\n idChainMap[chain._name.charCodeAt(0)] = chain;\r\n }\r\n }\r\n\r\n // FIXME: This function is redundant, CONECT records always follow ATOM and HETATM. Build the map online.\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseATOM(stream) {\r\n if (this._modelId !== 1) {\r\n return;\r\n }\r\n\r\n /* eslint-disable no-magic-numbers */\r\n const het = stream.readCharCode(1) === 0x48;\r\n\r\n // field names according to wwPDB Format\r\n // NOTE: Chimera allows (nonstandard) use of columns 6-11 for the integer atom serial number in ATOM records.\r\n const serial = het ? stream.readInt(7, 11) : stream.readInt(6, 11);\r\n let name = stream.readString(13, 16);\r\n const altLoc = stream.readChar(17);\r\n const resName = stream.readString(18, 20).trim();\r\n const chainID = stream.readChar(22);\r\n const resSeq = stream.readInt(23, 26);\r\n const iCode = stream.readChar(27);\r\n const x = stream.readFloat(31, 38);\r\n const y = stream.readFloat(39, 46);\r\n const z = stream.readFloat(47, 54);\r\n const occupancy = stream.readFloat(55, 60);\r\n const tempFactor = stream.readFloat(61, 66);\r\n const element = stream.readString(77, 78).trim() || nameToElement(name);\r\n const charge = stream.readInt(79, 80) || 0;\r\n /* eslint-enable no-magic-numbers */\r\n // skip waters (there may be lots of them)\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n // PDB uses positional system for atom names. It helps derive element type from the name\r\n // but names may include extra spaces. From this point on we don't need those spaces anymore.\r\n name = name.trim();\r\n\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name]; // FIXME: Maybe should use type as additional index (\" CA \" vs. \"CA \")\r\n\r\n // NOTE: Residues of a particular chain are not required to be listed next to each other.\r\n // https://github.com/biasmv/pv/commit/7319b898b7473ba380c26699e3b028b2b1a7e1a1\r\n let chain = this._chain;\r\n if (!chain || chain.getName() !== chainID) {\r\n this._chain = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n _parseENDMDL() {\r\n this._modelId += 1;\r\n }\r\n\r\n _parseCONECT(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const serial0 = stream.readInt(7, 11);\r\n const serial1 = stream.readInt(12, 16);\r\n const serial2 = stream.readInt(17, 21);\r\n const serial3 = stream.readInt(22, 26);\r\n const serial4 = stream.readInt(27, 31);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n const complex = this._complex;\r\n\r\n // Keep bonds ordered by atom serial\r\n if (serial1 && serial1 > serial0) {\r\n complex.addBond(serial0, serial1, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial2 && serial2 > serial0) {\r\n complex.addBond(serial0, serial2, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial3 && serial3 > serial0) {\r\n complex.addBond(serial0, serial3, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial4 && serial4 > serial0) {\r\n complex.addBond(serial0, serial4, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n }\r\n\r\n _parseCOMPND(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const str = stream.readString(11, 80);\r\n const tokenIdx = str.indexOf(':');\r\n this._compndCurrToken = tokenIdx > 0 ? str.substring(0, tokenIdx).trim() : this._compndCurrToken;\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // start reading new molecule\r\n if (this._compndCurrToken === 'MOL_ID') {\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = parseInt(str.substring(tokenIdx + 1, str.indexOf(';')), 10);\r\n this._molecules.push(this._molecule);\r\n // parse molecule name\r\n } else if (this._compndCurrToken === 'MOLECULE' && this._molecule != null) {\r\n this._molecule._name = str.substring(tokenIdx + 1, str.indexOf(';')).trim();\r\n // parse molecule chains\r\n } else if (this._compndCurrToken === 'CHAIN' && this._molecule != null) {\r\n let chainStr = str.substring(tokenIdx + 1, 80).trim();\r\n const lastChar = chainStr[chainStr.length - 1];\r\n if (lastChar === ';' || lastChar === ',') {\r\n chainStr = chainStr.slice(0, -1);\r\n }\r\n chainStr = chainStr.replace(/\\s+/g, '');\r\n const chains = chainStr.split(',');\r\n this._molecule._chains = this._molecule._chains.concat(chains);\r\n }\r\n }\r\n\r\n _parseREMARK(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const remarkNum = stream.readInt(8, 10);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // create remark parser if needed\r\n let remark = this._remarks[remarkNum];\r\n if (_.isUndefined(remark)) {\r\n const RemarkParser = remarkParsers[remarkNum];\r\n if (_.isFunction(RemarkParser)) {\r\n this._remarks[remarkNum] = remark = new RemarkParser(this._complex);\r\n }\r\n }\r\n\r\n // delegate parsing\r\n if (!_.isUndefined(remark)) {\r\n remark.parse(stream);\r\n }\r\n }\r\n\r\n _parseHELIX(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const fields = [20, 22, 32, 34];\r\n /* eslint-enable no-magic-numbers */\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addHelix(obj);\r\n this._complex.structures.push(obj);\r\n });\r\n }\r\n\r\n _parseSHEET(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const fields = [22, 23, 33, 34];\r\n /* eslint-enable no-magic-numbers */\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addSheet(obj);\r\n });\r\n }\r\n\r\n _parseSTRUCTURE(stream, pars, adder) {\r\n const startId = 0;\r\n const startIndex = 1;\r\n const endId = 2;\r\n const endIndex = 3;\r\n\r\n // identify fields: debugging and stuff\r\n /* eslint-disable no-magic-numbers */\r\n const codeOfS = 0x53;\r\n const serialNumber = stream.readInt(8, 10);\r\n const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim()\r\n const comment = stream.readString(41, 70).trim();\r\n const helLength = stream.readInt(72, 76);\r\n const helixClass = stream.readInt(39, 40);\r\n const shWidth = stream.readInt(15, 16);\r\n const shCur = stream.readInt(42, 45);\r\n const shPrev = stream.readInt(57, 60);\r\n /* eslint-enable no-magic-numbers */\r\n // file fields\r\n const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0);\r\n const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0);\r\n const startSequenceNumber = stream.readInt(pars[startIndex], pars[startIndex] + 3);\r\n let iCodeStr = stream.readString(pars[startIndex] + 4, pars[startIndex] + 4);\r\n let startICode = 0;\r\n\r\n if (iCodeStr.length > 0) {\r\n startICode = iCodeStr.charCodeAt(0);\r\n }\r\n const endSequenceNumber = stream.readInt(pars[endIndex], pars[endIndex] + 3);\r\n iCodeStr = stream.readString(pars[endIndex] + 4, pars[endIndex] + 4);\r\n let endICode = 0;\r\n if (iCodeStr.length > 0) {\r\n endICode = iCodeStr.charCodeAt(0);\r\n }\r\n\r\n let obj;\r\n let cs = this._sheet;\r\n if (stream.readCharCode(1) === codeOfS) {\r\n if (cs !== null && cs.getName() !== structureName) {\r\n cs = null;\r\n this._sheet = null;\r\n }\r\n if (cs === null) {\r\n this._sheet = obj = new Sheet(structureName, shWidth);\r\n adder(obj);\r\n } else {\r\n obj = cs;\r\n }\r\n const strand = new Strand(\r\n obj,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n helixClass,\r\n shCur,\r\n shPrev,\r\n );\r\n obj.addStrand(strand);\r\n this._complex.structures.push(strand);\r\n } else {\r\n obj = new Helix(\r\n helixClass,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n serialNumber,\r\n structureName,\r\n comment,\r\n helLength,\r\n );\r\n adder(obj);\r\n }\r\n }\r\n\r\n _parseHEADER(stream) {\r\n const { metadata } = this._complex;\r\n metadata.classification = stream.readString(11, 50).trim();\r\n metadata.date = stream.readString(51, 59).trim();\r\n\r\n const id = stream.readString(63, 66).trim();\r\n metadata.id = id;\r\n if (id) {\r\n this._complex.name = id;\r\n }\r\n metadata.format = 'pdb';\r\n }\r\n\r\n _parseTITLE(stream) {\r\n const { metadata } = this._complex;\r\n metadata.title = metadata.title || [];\r\n\r\n const line = stream.readInt(9, 10) || 1;\r\n metadata.title[line - 1] = stream.readString(11, 80).trim();\r\n }\r\n\r\n static tagParsers = {\r\n HEADER: PDBParser.prototype._parseHEADER,\r\n 'TITLE ': PDBParser.prototype._parseTITLE,\r\n 'ATOM ': PDBParser.prototype._parseATOM,\r\n HETATM: PDBParser.prototype._parseATOM,\r\n ENDMDL: PDBParser.prototype._parseENDMDL,\r\n CONECT: PDBParser.prototype._parseCONECT,\r\n COMPND: PDBParser.prototype._parseCOMPND,\r\n REMARK: PDBParser.prototype._parseREMARK,\r\n // 'SOURCE': PDBParser.prototype._parseSOURCE,\r\n 'HELIX ': PDBParser.prototype._parseHELIX,\r\n 'SHEET ': PDBParser.prototype._parseSHEET,\r\n\r\n // nonstandard extension to allow range 100,000 - 999,999\r\n 'ATOM 1': PDBParser.prototype._parseATOM,\r\n 'ATOM 2': PDBParser.prototype._parseATOM,\r\n 'ATOM 3': PDBParser.prototype._parseATOM,\r\n 'ATOM 4': PDBParser.prototype._parseATOM,\r\n 'ATOM 5': PDBParser.prototype._parseATOM,\r\n 'ATOM 6': PDBParser.prototype._parseATOM,\r\n 'ATOM 7': PDBParser.prototype._parseATOM,\r\n 'ATOM 8': PDBParser.prototype._parseATOM,\r\n 'ATOM 9': PDBParser.prototype._parseATOM,\r\n };\r\n\r\n parseSync() {\r\n const stream = new PDBStream(this._data);\r\n const result = this._complex = new Complex();\r\n\r\n // parse PDB line by line\r\n while (!stream.end()) {\r\n const tag = stream.readString(1, TAG_LENGTH);\r\n const func = PDBParser.tagParsers[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, stream);\r\n }\r\n stream.next();\r\n }\r\n\r\n // Resolve indices and serials to objects\r\n this._finalize();\r\n\r\n // cleanup\r\n this._serialAtomMap = null;\r\n this._sheet = null;\r\n this._residue = null;\r\n this._chain = null;\r\n this._complex = null;\r\n\r\n if (result.getAtomCount() === 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n\r\nPDBParser.formats = ['pdb'];\r\nPDBParser.extensions = ['.pdb', '.ent'];\r\n\r\nexport default PDBParser;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n SGroup,\r\n Bond,\r\n} = chem;\r\n\r\nconst cOrderCharCodes = {\r\n A: 0,\r\n S: 1,\r\n D: 2,\r\n T: 3,\r\n};\r\n\r\nconst cmlStartRegexp = /\\s*<\\?xml\\b[^?>]*\\?>\\s*<(?:cml|molecule)\\b/i;\r\n\r\nclass CMLParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._complex = null;\r\n this._residue = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._lastMolId = -1;\r\n this._readOnlyOneMolecule = false;\r\n this._options.fileType = 'cml';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && cmlStartRegexp.test(data);\r\n }\r\n\r\n _rebuidBondIndexes(atoms, bonds) {\r\n const count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n\r\n const countBonds = bonds.length;\r\n for (let j = 0; j < countBonds; j++) {\r\n const idxs = bonds[j].atomRefs2.split(' ');\r\n if (idxs[0] === atomId) {\r\n bonds[j].start = i;\r\n }\r\n\r\n if (idxs[1] === atomId) {\r\n bonds[j].end = i;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _createSGroup(molecule, moleculeArr) {\r\n const newGroup = new SGroup(\r\n molecule.id,\r\n molecule.fieldData,\r\n new THREE.Vector3(parseFloat(molecule.x), parseFloat(molecule.y), 0),\r\n molecule.atomRefs,\r\n molecule,\r\n );\r\n if (molecule.placement === 'Relative') {\r\n newGroup._center = new THREE.Vector3(0, 0, 0);\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_CHARGE') {\r\n newGroup._charge = parseInt(molecule.fieldData, 10) || 0;\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_COEFFICIENT') {\r\n newGroup._repeat = parseInt(molecule.fieldData, 10) || 1;\r\n }\r\n moleculeArr.push(newGroup);\r\n }\r\n\r\n _extractSGroup(molecule, moleculeArr) {\r\n if (!Array.isArray(moleculeArr)) {\r\n moleculeArr = [];\r\n }\r\n\r\n if (molecule) {\r\n if (Array.isArray(molecule)) {\r\n const count = molecule.length;\r\n for (let i = 0; i < count; i++) {\r\n if (molecule[i].molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule[i].molecule));\r\n }\r\n this._createSGroup(molecule[i], moleculeArr);\r\n }\r\n } else {\r\n if (molecule.molecule) {\r\n if (molecule.molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule.molecule));\r\n }\r\n }\r\n this._createSGroup(molecule, moleculeArr);\r\n }\r\n }\r\n\r\n return moleculeArr;\r\n }\r\n\r\n _extractSGroups(molecule, atoms) {\r\n const moleculeArr = this._extractSGroup(molecule);\r\n\r\n const count = atoms.length;\r\n let i;\r\n let j;\r\n\r\n for (i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n const firstAtomRef = moleculeArr[j]._atoms.split(' ')[0];\r\n if (firstAtomRef === atomId) {\r\n if (!atoms[i].sgroupRef) {\r\n atoms[i].sgroupRef = [];\r\n }\r\n atoms[i].sgroupRef.push(moleculeArr[j]);\r\n }\r\n }\r\n }\r\n // build sGroups centers\r\n let atomMap = {}; // sgrpmap cache\r\n let mapEntry = null;\r\n const nLimon = 100000000;\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n\r\n function cycleFuncInner(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n moleculeArr[j]._atoms.push(mapEntry.a);\r\n }\r\n }\r\n\r\n function cycleFunc(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n bLow.set(Math.min(bLow.x, mapEntry.x), Math.min(bLow.y, mapEntry.y), Math.min(bLow.z, mapEntry.z));\r\n bHight.set(Math.max(bHight.x, mapEntry.x), Math.max(bHight.y, mapEntry.y), Math.max(bHight.z, mapEntry.z));\r\n cycleFuncInner(e);\r\n }\r\n }\r\n\r\n for (i = 0; i < atoms.length; i++) {\r\n atomMap[atoms[i].id] = {};\r\n atomMap[atoms[i].id].x = atoms[i].x2;\r\n if (atoms[i].x3) {\r\n atomMap[atoms[i].id].x = atoms[i].x3;\r\n }\r\n atomMap[atoms[i].id].x = parseFloat(atomMap[atoms[i].id].x);\r\n atomMap[atoms[i].id].y = atoms[i].y2;\r\n if (atoms[i].y3) {\r\n atomMap[atoms[i].id].y = atoms[i].y3;\r\n }\r\n atomMap[atoms[i].id].y = parseFloat(atomMap[atoms[i].id].y);\r\n atomMap[atoms[i].id].z = '0.0';\r\n if (atoms[i].z3) {\r\n atomMap[atoms[i].id].z = atoms[i].z3;\r\n }\r\n atomMap[atoms[i].id].z = parseFloat(atomMap[atoms[i].id].z);\r\n atomMap[atoms[i].id].a = atoms[i];\r\n }\r\n\r\n let atomsRef;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n if (moleculeArr[j]._center !== null) {\r\n bLow.set(nLimon, nLimon, nLimon);\r\n bHight.set(-nLimon, -nLimon, -nLimon);\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFunc);\r\n\r\n moleculeArr[j]._center.addVectors(bLow, bHight);\r\n moleculeArr[j]._center.multiplyScalar(0.5);\r\n } else {\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFuncInner);\r\n }\r\n }\r\n atomMap = null;\r\n }\r\n\r\n _traverseData(dom) {\r\n function isArray(o) {\r\n return Object.prototype.toString.apply(o) === '[object Array]';\r\n }\r\n\r\n function parseNode(xmlNode, result) {\r\n if (xmlNode.nodeName === '#text' && xmlNode.nodeValue.trim() === '') {\r\n return;\r\n }\r\n\r\n const jsonNode = {};\r\n jsonNode.xmlNode = xmlNode;\r\n const existing = result[xmlNode.nodeName];\r\n if (existing) {\r\n if (!isArray(existing)) {\r\n result[xmlNode.nodeName] = [existing, jsonNode];\r\n } else {\r\n result[xmlNode.nodeName].push(jsonNode);\r\n }\r\n } else {\r\n result[xmlNode.nodeName] = jsonNode;\r\n }\r\n\r\n let length;\r\n let i;\r\n if (xmlNode.attributes) {\r\n ({ length } = xmlNode.attributes);\r\n for (i = 0; i < length; i++) {\r\n const attribute = xmlNode.attributes[i];\r\n jsonNode[attribute.nodeName] = attribute.nodeValue;\r\n }\r\n }\r\n\r\n ({ length } = xmlNode.childNodes);\r\n for (i = 0; i < length; i++) {\r\n parseNode(xmlNode.childNodes[i], jsonNode);\r\n }\r\n }\r\n\r\n const result = {};\r\n if (dom.childNodes.length) {\r\n parseNode(dom.childNodes[0], result);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _findSuitableMolecule(data, molSet) {\r\n for (const key in data) {\r\n if (key === 'xmlNode') {\r\n continue;\r\n } else if (key === 'molecule') {\r\n if (data.molecule) {\r\n if (data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n molSet.push(data);\r\n }\r\n if (Array.isArray(data.molecule)) {\r\n for (let i = 0; i < data.molecule.length; i++) {\r\n if (data.molecule[i].atomArray && data.molecule[i].atomArray.atom) {\r\n molSet.push({ molecule: data.molecule[i] });\r\n }\r\n }\r\n }\r\n }\r\n } else if (data[key] && data[key] !== null && typeof (data[key]) === 'object') {\r\n this._findSuitableMolecule(data[key], molSet);\r\n }\r\n }\r\n }\r\n\r\n _selectComponents(text) {\r\n const parser = new DOMParser();\r\n const doc = parser.parseFromString(text, 'application/xml');\r\n const traversedData = this._traverseData(doc);\r\n let rawData;\r\n const self = this;\r\n\r\n function prepareComponentCompound(data) {\r\n let atoms = [];\r\n if (data.molecule && data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n if (!Array.isArray(data.molecule.atomArray.atom)) {\r\n atoms.push(data.molecule.atomArray.atom);\r\n } else {\r\n atoms = data.molecule.atomArray.atom;\r\n }\r\n } else if (!data.molecule) {\r\n const ret = {};\r\n ret.atomLabels = null;\r\n ret.labelsCount = 1;\r\n return ret;\r\n }\r\n\r\n if (data.molecule.molecule) {\r\n self._extractSGroups(data.molecule.molecule, atoms);\r\n }\r\n\r\n let atom;\r\n let count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges = [];\r\n }\r\n\r\n let localBond = [];\r\n if (data.molecule.bondArray && data.molecule.bondArray.bond) {\r\n if (!Array.isArray(data.molecule.bondArray.bond)) {\r\n localBond.push(data.molecule.bondArray.bond);\r\n } else {\r\n localBond = data.molecule.bondArray.bond;\r\n }\r\n }\r\n let bond;\r\n count = localBond.length;\r\n self._rebuidBondIndexes(atoms, localBond);\r\n\r\n function addCurrBond(index) {\r\n bond = localBond[index];\r\n atom = atoms[bond.start];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.end);\r\n atom = atoms[bond.end];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.start);\r\n return true;\r\n }\r\n\r\n for (let i = 0; i < count; i++) {\r\n if (!addCurrBond(i)) {\r\n // ignore invalid bond\r\n continue;\r\n }\r\n const orderAttr = bond.xmlNode.getAttribute('order');\r\n const tc = parseInt(orderAttr, 10);\r\n // the default bond order is unknown\r\n localBond[i].order = 0;\r\n localBond[i].type = Bond.BondType.UNKNOWN;\r\n if (tc > 1) {\r\n localBond[i].order = tc;\r\n } else {\r\n // another option - bond order is a string\r\n const order = cOrderCharCodes[orderAttr];\r\n if (order !== undefined) {\r\n localBond[i].order = order;\r\n if (orderAttr === 'A') {\r\n localBond[i].type = Bond.BondType.AROMATIC;\r\n }\r\n }\r\n }\r\n }\r\n\r\n count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges.sort();\r\n }\r\n\r\n const labels = self._breadWidthSearch(atoms, 0); // for now\r\n\r\n const retStruct = {};\r\n retStruct.atoms = atoms;\r\n retStruct.bonds = localBond;\r\n retStruct.labels = labels.atomLabels;\r\n retStruct.count = Math.min(1, labels.labelsCount); // for now\r\n retStruct.curr = -1;\r\n retStruct.originalCML = doc;\r\n\r\n return retStruct;\r\n }\r\n\r\n if (traversedData.cml) {\r\n rawData = traversedData.cml;\r\n } else {\r\n rawData = traversedData;\r\n }\r\n const retData = [];\r\n const filteredData = [];\r\n this._findSuitableMolecule(rawData, filteredData);\r\n if (this._readOnlyOneMolecule && filteredData.length > 1) {\r\n filteredData.splice(1, filteredData.length - 1);\r\n }\r\n filteredData.forEach((d) => {\r\n const rd = prepareComponentCompound(d);\r\n if (rd.atoms.length > 0) {\r\n retData.push(rd);\r\n }\r\n });\r\n return retData;\r\n }\r\n\r\n _packLabel(compId, molId) {\r\n const shift = 16;\r\n return (molId << shift) + compId;\r\n }\r\n\r\n _unpackLabel(l) {\r\n const shift = 16;\r\n const mask = (1 << shift) - 1;\r\n return { molId: l >>> shift, compId: l & mask };\r\n }\r\n\r\n _breadWidthSearch(atoms, molID) {\r\n const atomLabels = new Array(atoms.length);\r\n\r\n let id;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n atomLabels[id] = this._packLabel(0, molID);\r\n }\r\n\r\n const breadthQueue = [];\r\n let componentID = 0;\r\n let labeledAtoms = atoms.length;\r\n\r\n while (labeledAtoms > 0) {\r\n componentID++;\r\n\r\n let startID = -1;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n if (this._unpackLabel(atomLabels[id]).compId === 0) {\r\n startID = id;\r\n break;\r\n }\r\n }\r\n\r\n if (startID < 0) {\r\n break;\r\n }\r\n\r\n // Bread first search\r\n breadthQueue.push(atoms[startID]);\r\n atomLabels[startID] = this._packLabel(componentID, molID);\r\n labeledAtoms--;\r\n\r\n while (breadthQueue.length > 0) {\r\n const curr = breadthQueue.shift();\r\n if (!curr) {\r\n continue;\r\n }\r\n\r\n for (let i = 0; i < curr.edges.length; i++) {\r\n if (atomLabels[curr.edges[i]] !== componentID) {\r\n breadthQueue.push(atoms[curr.edges[i]]);\r\n atomLabels[curr.edges[i]] = componentID;\r\n labeledAtoms--;\r\n }\r\n }\r\n }\r\n }\r\n const ret = {};\r\n ret.atomLabels = atomLabels;\r\n ret.labelsCount = componentID;\r\n return ret;\r\n }\r\n\r\n _parseBond(eAtom, mainAtom, order, type) {\r\n if (eAtom >= 0) {\r\n const h = [Math.min(eAtom, mainAtom), Math.max(eAtom, mainAtom)];\r\n this._complex.addBond(h[0], h[1], order, type, true);\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseSet(varData) {\r\n const complex = this._complex = new Complex();\r\n const data = varData;\r\n const currentLabel = data.curr;\r\n const { atoms, labels } = data;\r\n let atom = null;\r\n let i;\r\n let j;\r\n const count = atoms.length;\r\n\r\n function addFunc(a) {\r\n a.xmlNodeRef = atom;\r\n if (atom.x2) {\r\n atom.x3 = atom.x2;\r\n delete atom.x2;\r\n }\r\n if (atom.y2) {\r\n atom.y3 = atom.y2;\r\n delete atom.y2;\r\n }\r\n if (!(atom.z3)) {\r\n atom.z3 = '0.0';\r\n }\r\n atom.complexAtom = a;\r\n }\r\n\r\n let chains = {};\r\n // parse atoms in label order\r\n const reorder = [];\r\n for (i = 0; i < count; i++) {\r\n reorder.push(i);\r\n }\r\n reorder.sort((a, b) => labels[a] - labels[b]);\r\n for (i = 0; i < count; i++) {\r\n const atomCharge = 0;\r\n const lLabel = labels[reorder[i]];\r\n if (this._unpackLabel(lLabel).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[reorder[i]];\r\n const atomFullNameStruct = atom.elementType;\r\n\r\n if (atom.sgroupRef) {\r\n const countRef = atom.sgroupRef.length;\r\n for (let k = 0; k < countRef; ++k) {\r\n complex._sgroups.push(atom.sgroupRef[k]);\r\n }\r\n }\r\n\r\n if (atom.x3 || atom.x2) {\r\n const currAtomComp = this._unpackLabel(lLabel).compId;\r\n // use ' ' by default instead of synthetic creation of chain names\r\n const chainID = ' '; //= String.fromCharCode('A'.charCodeAt(0) + currAtomComp);\r\n const resSeq = currAtomComp;\r\n const iCode = ' ';\r\n let strLabel = currAtomComp.toString();\r\n if (strLabel.length === 1) {\r\n strLabel = `0${strLabel}`;\r\n }\r\n const resName = `N${strLabel}`;\r\n let chain = chains[chainID];\r\n if (!chain || chain.getName() !== chainID) {\r\n chains[chainID] = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n // _x, _y, _z, mname, mindex, atomNameFull, atomName, chainID, serial, isHet, atlLocInd, atomNameToTypeF\r\n let xyz = null;\r\n if (atom.x3) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x3), parseFloat(atom.y3), parseFloat(atom.z3));\r\n } else if (atom.x2) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x2), parseFloat(atom.y2), 0);\r\n }\r\n let element = Element.ByName[atom.elementType.toUpperCase()];\r\n if (!element) {\r\n element = (JSON.parse(JSON.stringify(Element.ByName[\r\n Object.keys(Element.ByName)[Object.keys(Element.ByName).length - 1]])));\r\n element.number += 1;\r\n element.name = atom.elementType.toUpperCase();\r\n element.fullName = 'Unknown';\r\n Element.ByName[atom.elementType.toUpperCase()] = element;\r\n }\r\n const atomSerial = parseInt(atom.id.replace(/[^0-9]/, ''), 10);\r\n const added = residue.addAtom(\r\n atomFullNameStruct,\r\n element,\r\n xyz,\r\n Element.Role.SG,\r\n true,\r\n atomSerial,\r\n ' ',\r\n 1.0,\r\n 0.0,\r\n atomCharge,\r\n );\r\n if (atom.hydrogenCount) {\r\n added.hydrogenCount = parseInt(atom.hydrogenCount, 10);\r\n }\r\n if (atom.mrvValence) {\r\n added.valence = parseInt(atom.mrvValence, 10);\r\n }\r\n addFunc(added);\r\n }\r\n }\r\n }\r\n chains = null;// NOSONAR\r\n for (i = 0; i < data.bonds.length; i++) {\r\n const cb = data.bonds[i];\r\n if (this._unpackLabel(labels[cb.start]).molId === this._unpackLabel(currentLabel).molId\r\n && this._unpackLabel(labels[cb.end]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[cb.start];\r\n if (!atom || !(atoms[cb.end])) {\r\n continue; // skip invalid\r\n }\r\n this._parseBond(\r\n parseInt(atom.id.replace(/[^0-9]/, ''), 10),\r\n parseInt(atoms[cb.end].id.replace(/[^0-9]/, ''), 10),\r\n cb.order,\r\n cb.type,\r\n );\r\n }\r\n }\r\n\r\n for (i = 0; i < this._complex.getSGroupCount(); i++) {\r\n const sGrp = this._complex.getSGroups()[i];\r\n for (j = 0; j < sGrp._atoms.length; j++) {\r\n sGrp._atoms[j] = sGrp._atoms[j].complexAtom;\r\n }\r\n }\r\n for (i = 0; i < count; i++) {\r\n if (this._unpackLabel(labels[i]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[i];\r\n atom.complexAtom = null;\r\n delete atom.complexAtom;\r\n }\r\n }\r\n this._complex.originalCML = data.originalCML;\r\n this._fixBondsArray();\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n this._serialAtomMap = null;\r\n this._complex = null;\r\n return complex;\r\n }\r\n\r\n parseSync() {\r\n const complexes = [];\r\n const self = this;\r\n const moleculaSet = this._selectComponents(this._data);\r\n moleculaSet.forEach((molSet) => {\r\n molSet.curr = 2;\r\n if (molSet.count === 0) {\r\n molSet.count = 1;\r\n }\r\n for (let i = 0; i < molSet.count; i++) {\r\n molSet.curr = (i + 1);\r\n complexes.push(self._parseSet(molSet, false));\r\n }\r\n });\r\n\r\n let totalAtomsParsed = 0;\r\n complexes.forEach((c) => {\r\n totalAtomsParsed += c.getAtomCount();\r\n });\r\n if (totalAtomsParsed <= 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n if (complexes.length > 1) {\r\n const joinedComplex = new Complex();\r\n joinedComplex.joinComplexes(complexes);\r\n joinedComplex.originalCML = complexes[0].originalCML;\r\n return joinedComplex;\r\n }\r\n if (complexes.length === 1) {\r\n return complexes[0];\r\n }\r\n return new Complex();\r\n }\r\n}\r\n\r\nCMLParser.formats = ['cml'];\r\nCMLParser.extensions = ['.cml'];\r\n\r\nexport default CMLParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport MMTF from '../../../vendor/js/mmtf';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst {\r\n Complex,\r\n Chain,\r\n Atom,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nclass ArrayComparator {\r\n constructor(original) {\r\n this._original = Array.from(original);\r\n this._original.sort();\r\n\r\n this._sum = 0;\r\n for (let i = 0; i < this._original.length; ++i) {\r\n this._sum += this._original[i];\r\n }\r\n }\r\n\r\n compare(candidate) {\r\n const len = candidate.length;\r\n if (len !== this._original.length) {\r\n return false;\r\n }\r\n\r\n let sum = 0;\r\n let i;\r\n for (i = 0; i < len; ++i) {\r\n sum += candidate[i];\r\n }\r\n\r\n if (sum !== this._sum) {\r\n return false;\r\n }\r\n\r\n const sorted = Array.from(candidate);\r\n sorted.sort();\r\n\r\n for (i = 0; i < len; ++i) {\r\n if (sorted[i] !== this._original[i]) {\r\n return false;\r\n }\r\n }\r\n\r\n return true;\r\n }\r\n}\r\n\r\nArrayComparator.prototype.constructor = ArrayComparator;\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see https://github.com/rcsb/mmtf-javascript/blob/master/src/mmtf-traverse.js\r\nconst secStructToType = [\r\n StructuralElementType.HELIX_PI, // 0\r\n StructuralElementType.BEND, // 1\r\n StructuralElementType.HELIX_ALPHA, // 2\r\n StructuralElementType.STRAND, // 3\r\n StructuralElementType.HELIX_310, // 4\r\n StructuralElementType.BRIDGE, // 5\r\n StructuralElementType.TURN, // 6\r\n StructuralElementType.COIL, // 7\r\n];\r\n\r\nfunction getFirstByte(buf) {\r\n const bytes = new Uint8Array(buf, 0, 1);\r\n return bytes[0];\r\n}\r\n\r\nclass MMTFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'mmtf';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n // check if it's binary MessagePack format containing a map (dictionary)\r\n // see https://github.com/msgpack/msgpack/blob/master/spec.md\r\n return _.isArrayBuffer(data) && ((getFirstByte(data) | 1) === 0xDF);\r\n }\r\n\r\n _onModel(_modelData) {\r\n }\r\n\r\n _onChain(chainData) {\r\n if (chainData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const chain = new Chain(this._complex, chainData.chainName);\r\n this._complex._chains[chainData.chainIndex] = chain;\r\n chain._index = chainData.chainIndex;\r\n }\r\n\r\n _onGroup(groupData) {\r\n if (groupData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n if (this.settings.now.nowater) {\r\n // skip water\r\n if (groupData.groupName === 'HOH' || groupData.groupName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n const chain = this._complex._chains[groupData.chainIndex];\r\n const icode = !groupData.insCode.charCodeAt(0) ? '' : groupData.insCode;\r\n const residue = chain.addResidue(groupData.groupName, groupData.groupId, icode);\r\n residue._index = groupData.groupIndex;\r\n\r\n this._updateSecStructure(this._complex, residue, groupData);\r\n }\r\n\r\n _onAtom(atomData) {\r\n if (atomData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const altLoc = !atomData.altLoc.charCodeAt(0) ? '' : atomData.altLoc;\r\n const atom = new Atom(\r\n atomData.groupIndex, // we store residue index here to replace it later with actual reference\r\n atomData.atomName,\r\n Element.getByName(atomData.element.toUpperCase()),\r\n new THREE.Vector3(atomData.xCoord, atomData.yCoord, atomData.zCoord),\r\n Element.Role[atomData.atomName],\r\n false, // hetero atoms will be marked later\r\n atomData.atomId,\r\n altLoc,\r\n atomData.occupancy,\r\n atomData.bFactor,\r\n atomData.formalCharge,\r\n );\r\n\r\n this._complex._atoms[atomData.atomIndex] = atom;\r\n atom.index = atomData.atomIndex;\r\n\r\n this._serialAtomMap[atomData.atomId] = atom;\r\n }\r\n\r\n _onBond(bondData) {\r\n const right = Math.max(bondData.atomIndex1, bondData.atomIndex2);\r\n if (right >= this._complex._atoms.length) {\r\n return;\r\n }\r\n const left = Math.min(bondData.atomIndex1, bondData.atomIndex2);\r\n this._complex.addBond(\r\n this._complex._atoms[left],\r\n this._complex._atoms[right],\r\n bondData.bondOrder,\r\n Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n\r\n _updateSecStructure(complex, residue, groupData) {\r\n const helixClasses = [3, -1, 1, -1, 5];\r\n\r\n if (!_.isUndefined(groupData) && groupData.secStruct === this._ssType) {\r\n residue._secondary = this._ssStruct;\r\n if (this._ssStruct) {\r\n this._ssStruct.term = residue;\r\n }\r\n return;\r\n }\r\n\r\n if (!_.isUndefined(groupData)) {\r\n // start new secondary structure\r\n const type = secStructToType[groupData.secStruct];\r\n this._ssType = groupData.secStruct;\r\n this._ssStart = residue;\r\n\r\n let struct = null;\r\n switch (this._ssType) {\r\n case -1: // undefined\r\n case 7: // coil\r\n break;\r\n case 0: // pi helix\r\n case 2: // alpha helix\r\n case 4: // 3-10 helix\r\n struct = new Helix(helixClasses[this._ssType], residue, residue, 0, '', '', 0);\r\n complex._helices.push(struct);\r\n break;\r\n case 3: { // extended\r\n const sheet = new Sheet('', 0);\r\n complex._sheets.push(sheet);\r\n struct = new Strand(sheet, residue, residue, 0, null, null);\r\n break;\r\n }\r\n default:\r\n if (type !== undefined) {\r\n struct = new StructuralElement(type, residue, residue);\r\n }\r\n break;\r\n }\r\n\r\n this._ssStruct = struct;\r\n residue._secondary = struct;\r\n if (struct) {\r\n complex.structures.push(struct);\r\n }\r\n }\r\n }\r\n\r\n _updateMolecules(mmtfData) {\r\n const entities = mmtfData.entityList;\r\n if (!entities) {\r\n return;\r\n }\r\n\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < entities.length; i++) {\r\n const entity = entities[i];\r\n const chains = entity.chainIndexList;\r\n let residues = [];\r\n for (let j = 0; j < chains.length; j++) {\r\n const chainIndex = chains[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, entity.description, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n // populate complex with chains, residues and atoms\r\n _traverse(mmtfData) {\r\n const self = this;\r\n\r\n // get metadata\r\n const { metadata } = this._complex;\r\n metadata.id = mmtfData.structureId;\r\n metadata.title = [];\r\n metadata.title[0] = mmtfData.title;\r\n metadata.date = mmtfData.releaseDate;\r\n metadata.format = 'mmtf';\r\n\r\n // create event callback functions\r\n const eventCallbacks = {\r\n onModel(modelData) {\r\n self._onModel(modelData);\r\n },\r\n onChain(chainData) {\r\n self._onChain(chainData);\r\n },\r\n onGroup(groupData) {\r\n self._onGroup(groupData);\r\n },\r\n onAtom(atomData) {\r\n self._onAtom(atomData);\r\n },\r\n onBond(bondData) {\r\n self._onBond(bondData);\r\n },\r\n };\r\n\r\n // temporary variables used during traversal to track secondary structures\r\n this._ssType = -1;\r\n this._ssStruct = null;\r\n this._ssStart = null;\r\n\r\n // traverse the structure and listen to the events\r\n MMTF.traverse(mmtfData, eventCallbacks);\r\n\r\n this._updateSecStructure(this._complex);\r\n this._updateMolecules(mmtfData);\r\n }\r\n\r\n // During traversal atoms and residues don't come sequentially\r\n // so a residue for certain atom can be unavailable. Thus we\r\n // store residue index in atom.\r\n // This function being called after traversal replaces the index\r\n // with actual reference, and also populates atom lists in residues.\r\n _linkAtomsToResidues() {\r\n for (let i = 0; i < this._complex._atoms.length; ++i) {\r\n const atom = this._complex._atoms[i];\r\n const residue = this._complex._residues[atom.residue];\r\n atom.residue = residue;\r\n residue._atoms.push(atom);\r\n }\r\n }\r\n\r\n _findSynonymousChains() {\r\n const named = {};\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!named.hasOwnProperty(name)) {\r\n named[name] = [];\r\n }\r\n\r\n named[name].push(chain._index);\r\n }\r\n\r\n return named;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _parseAssemblyInfo(mmtfData) {\r\n let i;\r\n let j;\r\n let k;\r\n const assemblies = [];\r\n const { logger } = this;\r\n\r\n for (i = 0; i < mmtfData.bioAssemblyList.length; ++i) {\r\n const baInfo = mmtfData.bioAssemblyList[i];\r\n if (baInfo.transformList.length === 0) {\r\n continue;\r\n }\r\n\r\n const chains = baInfo.transformList[0].chainIndexList;\r\n const chainListCheck = new ArrayComparator(chains);\r\n\r\n // build list of chain names\r\n const chainNames = {};\r\n for (j = 0; j < chains.length; ++j) {\r\n chainNames[this._complex._chains[chains[j]].getName()] = 1;\r\n }\r\n\r\n // all chains with the same name should belong to assembly if one of them belongs\r\n const allChains = [];\r\n let name;\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n // just concat arrays -- there should be no duplicates\r\n Array.prototype.push.apply(allChains, this._chainsByName[name]);\r\n }\r\n }\r\n if (!chainListCheck.compare(allChains)) {\r\n // assembly is missing some of the chains\r\n logger.debug('MMTF: Assembly is missing some of the synonymous chains. Skipping...');\r\n }\r\n\r\n const a = new Assembly(this._complex);\r\n\r\n // add chains to assembly\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n a.addChain(name);\r\n }\r\n }\r\n\r\n // add unique matrices to assembly\r\n a.addMatrix(new THREE.Matrix4().fromArray(baInfo.transformList[0].matrix).transpose());\r\n for (j = 1; j < baInfo.transformList.length; ++j) {\r\n const transform = baInfo.transformList[j];\r\n\r\n if (!chainListCheck.compare(transform.chainIndexList)) {\r\n // list of chains for this transform doesn't match that for other transforms\r\n // this is illegal in our structure\r\n logger.debug('MMTF: Chain lists differ for different transforms in one assembly. Skipping...');\r\n continue;\r\n }\r\n\r\n const m = new THREE.Matrix4().fromArray(transform.matrix).transpose();\r\n\r\n // check if matrix is already in the list\r\n for (k = 0; k < a.matrices.length; ++k) {\r\n if (a.matrices[k].equals(m)) {\r\n break;\r\n }\r\n }\r\n\r\n if (k === a.matrices.length) {\r\n a.addMatrix(m);\r\n }\r\n }\r\n\r\n a.finalize();\r\n assemblies.push(a);\r\n }\r\n\r\n return assemblies;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _markHeteroAtoms(mmtfData) {\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < mmtfData.entityList.length; ++i) {\r\n const entity = mmtfData.entityList[i];\r\n if (entity.type !== 'polymer') {\r\n for (let j = 0; j < entity.chainIndexList.length; ++j) {\r\n const chainIndex = entity.chainIndexList[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n for (let k = 0; k < chain._residues.length; ++k) {\r\n const res = chain._residues[k];\r\n for (let m = 0; m < res._atoms.length; ++m) {\r\n res._atoms[m].het = true;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // joins chains with the same name into single chain\r\n _joinSynonymousChains() {\r\n let i;\r\n let j;\r\n\r\n const primaryChainsArray = [];\r\n const primaryChainsHash = {};\r\n\r\n // join chains\r\n for (i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!primaryChainsHash.hasOwnProperty(name)) {\r\n // new name -- this is a primary chain\r\n primaryChainsHash[name] = chain;\r\n chain._index = primaryChainsArray.length; // update index as this array will later replace original chain list\r\n primaryChainsArray.push(chain);\r\n continue;\r\n }\r\n\r\n // this chain should be joined with the primary chain of the same name\r\n const primary = primaryChainsHash[name];\r\n for (j = 0; j < chain._residues.length; ++j) {\r\n const residue = chain._residues[j];\r\n primary._residues.push(residue);\r\n residue._chain = primary;\r\n }\r\n }\r\n\r\n // replace chains list with one containing only primary chains\r\n // dropping references to all chains but primary\r\n this._complex._chains = primaryChainsArray;\r\n }\r\n\r\n parseSync() {\r\n const mmtfData = MMTF.decode(this._data);\r\n\r\n this._complex = new Complex();\r\n this._serialAtomMap = {}; // filled during traversal\r\n\r\n this._traverse(mmtfData);\r\n this._linkAtomsToResidues();\r\n this._markHeteroAtoms(mmtfData);\r\n this._chainsByName = this._findSynonymousChains();\r\n Array.prototype.push.apply(this._complex.units, this._parseAssemblyInfo(mmtfData));\r\n this._joinSynonymousChains();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n return this._complex;\r\n }\r\n}\r\n\r\nMMTFParser.formats = ['mmtf'];\r\nMMTFParser.extensions = ['.mmtf'];\r\nMMTFParser.binary = true;\r\n\r\nexport default MMTFParser;\r\n","class ParsingError extends Error {\r\n constructor(message, line, column) {\r\n super(`data:${line}:${column}: ${message}`);\r\n\r\n if (Error.captureStackTrace) {\r\n Error.captureStackTrace(this, ParsingError);\r\n }\r\n\r\n this.name = 'ParsingError';\r\n this.parseLine = line;\r\n this.parseColumn = column;\r\n }\r\n}\r\n\r\nexport default ParsingError;\r\n","import _ from 'lodash';\r\nimport ParsingError from './ParsingError';\r\n\r\n// Implemented and being tested against: https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax\r\n\r\nfunction _isWhitespace(ch) {\r\n return ch === 32 || ch === 10 || ch === 13 || ch === 9;\r\n}\r\n\r\nfunction _inlineIndexOf(ch0, str, idx) {\r\n const len = str.length;\r\n let ch = -1;\r\n while (idx < len) {\r\n ch = str.charCodeAt(idx);\r\n if (ch === ch0 || ch === 10) {\r\n break;\r\n }\r\n ++idx;\r\n }\r\n return ch === ch0 ? idx : -1;\r\n}\r\n\r\nexport default function readCIF(source) {\r\n let i = 0;\r\n let j = 0;\r\n const n = source.length;\r\n let code = NaN;\r\n let newline = true;\r\n let line = 1;\r\n let column = 1;\r\n let begin;\r\n let state = 0; // 0 - start, 1 - block, 2 - item, 3 - loop, 4 - values, 5 - value\r\n const result = {};\r\n let block = {};\r\n let keys = [];\r\n let keysCount = 0;\r\n let key = '';\r\n let values = [];\r\n let valuesCount = 0;\r\n let value;\r\n\r\n function _parseValue() {\r\n let val;\r\n if ((code === 46 || code === 63) && (i + 1 >= n || _isWhitespace(source.charCodeAt(i + 1)))) { // '.' or '?' .....\r\n // it's a missing value\r\n ++column;\r\n ++i;\r\n return undefined;\r\n }\r\n if (newline && code === 59) { // ';' ......................................................................\r\n // parse multi-line string\r\n j = i;\r\n let lines = 0;\r\n do {\r\n j = _inlineIndexOf(10, source, j + 1); // '\\n'\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated text block found', line, column);\r\n }\r\n ++lines;\r\n } while ((j + 1 < n && source.charCodeAt(j + 1) !== code) || j + 1 >= n);\r\n val = source.substring(i + 1, j).replace(/\\r/g, '');\r\n i = j + 2;\r\n line += lines;\r\n column = 1;\r\n newline = false;\r\n return val;\r\n }\r\n if (code === 39 || code === 34) { // ''' or '\"' ...........................................................\r\n // parse quoted string\r\n j = i;\r\n do {\r\n j = _inlineIndexOf(code, source, j + 1);\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated quoted string found', line, column);\r\n }\r\n } while (j + 1 < n && !_isWhitespace(source.charCodeAt(j + 1)));\r\n val = source.substring(i + 1, j);\r\n column += j - i + 1;\r\n i = j + 1;\r\n return val;\r\n } // ......................................................................................................\r\n // parse until the first whitespace\r\n j = i;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n val = source.substring(i, j);\r\n column += j - i;\r\n i = j;\r\n // try to convert to a number\r\n const num = Number(val);\r\n if (!Number.isNaN(num)) {\r\n return num;\r\n }\r\n // or leave as an unquoted string\r\n return val;\r\n }\r\n\r\n function _storeKey(tag) {\r\n keys[keysCount++] = tag;\r\n }\r\n\r\n function _storeValue(val) {\r\n const keyIndex = valuesCount % keysCount;\r\n values[keyIndex].push(val);\r\n ++valuesCount;\r\n return val;\r\n }\r\n\r\n while (i <= n) {\r\n code = source.charCodeAt(i); // 'NaN' in place of ''\r\n if (code === 13) { // '\\r' .......................................................................................\r\n // just ignore\r\n } else if (code === 10) { // '\\n' ................................................................................\r\n // take note of new lines\r\n newline = true;\r\n ++line;\r\n column = 1;\r\n } else {\r\n // process inline characters\r\n if (code === 32 || code === 9) { // ' ' or '\\t' ................................................................\r\n // just ignore\r\n } else if (code === 35) { // '#' ...............................................................................\r\n // skip the comment until before the end of the line\r\n i = _inlineIndexOf(10, source, i + 1); // '\\n'\r\n if (i === -1) {\r\n break;\r\n } else {\r\n continue; // don't forget to process the new line\r\n }\r\n } else if (state === 0) { // start =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n j = i + 5;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new data block\r\n result[source.substring(begin, i)] = block = {};\r\n state = 1; // block\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Data block name missing', line, column);\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 1) { // block =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n continue; // parse again in a different state\r\n } else if (code === 95) { // '_' .............................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // start new item\r\n key = source.substring(begin, i);\r\n state = 2; // item\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n i += 5;\r\n column += 5;\r\n if (i < n && !_isWhitespace(source.charCodeAt(i))) {\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n } else {\r\n // start new loop\r\n keys = [];\r\n keysCount = 0;\r\n values = [];\r\n valuesCount = 0;\r\n state = 3; // loop\r\n continue; // don't forget to process the whitespace\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 2) { // item ==============================================================================\r\n if (Number.isNaN(code)) {\r\n break;\r\n }\r\n value = _parseValue();\r\n _.set(block, key, value);\r\n state = 1; // block\r\n continue;\r\n } else if (state === 3) { // loop ==============================================================================\r\n if (code === 95) { // '_' ....................................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new key\r\n _storeKey(source.substring(begin, i));\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else { // ..................................................................................................\r\n if (keysCount > 0) {\r\n for (let keyIndex = 0; keyIndex < keysCount; ++keyIndex) {\r\n value = [];\r\n values[keyIndex] = value;\r\n _.set(block, keys[keyIndex], value);\r\n }\r\n state = 4;\r\n continue; // parse again in a different state\r\n }\r\n throw new ParsingError('Data tags are missing inside a loop', line, column);\r\n }\r\n } else if (state === 4) { // values ============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n } else if (code === 95) { // '_' .............................................................................\r\n state = 1; // block\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n state = 1; // block\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n state = 0;\r\n } else { // ..................................................................................................\r\n _storeValue(_parseValue());\r\n }\r\n continue; // parse again in a different state\r\n } else { // ====================================================================================================\r\n throw new ParsingError(`Unexpected internal state ${state}`, line, column);\r\n }\r\n\r\n newline = false;\r\n ++column;\r\n }\r\n ++i;\r\n }\r\n\r\n if (state === 2) { // item\r\n throw new ParsingError(`Unexpected end of file in state ${state}`, line, column);\r\n }\r\n\r\n return result;\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\nimport readCIF from './readCIF';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nconst cRequiredAtomFields = [\r\n 'auth_seq_id',\r\n 'Cartn_x',\r\n 'Cartn_y',\r\n 'Cartn_z',\r\n 'label_atom_id',\r\n];\r\n\r\nconst cSecondaryCoding = {\r\n helx: 'helix',\r\n turn: 'turn',\r\n strn: 'strand',\r\n};\r\n\r\nfunction getTypeFromId(string) {\r\n const typeId = /[A-Za-z]+/.exec(string);\r\n if (!typeId) {\r\n return null;\r\n }\r\n\r\n return cSecondaryCoding[typeId[0].toLowerCase()];\r\n}\r\n\r\n/**\r\n * Make valid object an array\r\n * @param arrayLikeObject\r\n * @return {array, object} array or object\r\n */\r\nfunction arrize(arrayLikeObject) {\r\n if (arrayLikeObject === null || arrayLikeObject === undefined || _.isArray(arrayLikeObject)) {\r\n return arrayLikeObject;\r\n }\r\n return [arrayLikeObject];\r\n}\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\nclass AtomDataError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'AtomDataError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction _getOperations(operList) {\r\n if (!operList) {\r\n return null;\r\n }\r\n const idc = arrize(operList.id);\r\n const { matrix, vector } = operList;\r\n if (!idc || !matrix || !vector) {\r\n return null;\r\n }\r\n\r\n const ops = [];\r\n for (let i = 0, n = idc.length; i < n; ++i) {\r\n const mtx = new THREE.Matrix4();\r\n const { elements } = mtx;\r\n\r\n for (let row = 0; row < 3; ++row) {\r\n const matrixData = matrix[row + 1];\r\n elements[row] = arrize(matrixData[1])[i];\r\n elements[row + 4] = arrize(matrixData[2])[i];\r\n elements[row + 8] = arrize(matrixData[3])[i];\r\n elements[row + 12] = arrize(vector[row + 1])[i];\r\n }\r\n ops[idc[i]] = mtx;\r\n }\r\n return ops;\r\n}\r\n\r\nfunction _extractOperations(assemblyGen, opsDict) {\r\n assemblyGen = _.isString(assemblyGen) ? assemblyGen : `${assemblyGen}`;\r\n const l = assemblyGen.replace(/\\)\\s*\\(/g, '!').replace(/[()']/g, '');\r\n const groupStr = l.split('!');\r\n const gps = [];\r\n\r\n for (let grIdx = 0, grCount = groupStr.length; grIdx < grCount; ++grIdx) {\r\n const gr = groupStr[grIdx].split(',');\r\n const gp = [];\r\n let idx = 0;\r\n for (let i = 0, n = gr.length; i < n; ++i) {\r\n const s = gr[i];\r\n if (s.includes('-')) {\r\n const es = s.split('-');\r\n let j = parseInt(es[0], 10);\r\n const m = parseInt(es[1], 10);\r\n for (; j <= m; ++j) {\r\n gp[idx++] = opsDict[j];\r\n }\r\n } else {\r\n gp[idx++] = opsDict[s];\r\n }\r\n }\r\n gps.push(gp);\r\n }\r\n\r\n // traverse all groups from the end of array and make all mults\r\n const matrices = [];\r\n let cnt = 0;\r\n function traverse(level, mtx) {\r\n for (let ii = 0, nn = gps[level].length; ii < nn; ++ii) {\r\n const newMtx = mtx ? mtx.clone() : new THREE.Matrix4();\r\n newMtx.multiplyMatrices(gps[level][ii], newMtx);\r\n if (level === 0) {\r\n matrices[cnt++] = newMtx;\r\n } else {\r\n traverse(level - 1, newMtx);\r\n }\r\n }\r\n }\r\n traverse(gps.length - 1);\r\n return matrices;\r\n}\r\n\r\nclass CIFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this.asymDict = {};\r\n this.molecules = [];\r\n this._options.fileType = 'cif';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*data_/i.test(data);\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing CIF file..');\r\n const data = readCIF(this._data);\r\n return this._toComplex(data);\r\n }\r\n\r\n /**\r\n * Convert intermediate structure into our valid Complex object\r\n * @param cifData intermediate CIF object\r\n * @returns {Complex} complex\r\n * @private\r\n */\r\n _toComplex(cifData) {\r\n const complex = new Complex();\r\n const complexData = cifData[Object.keys(cifData)[0]];\r\n this._extractAtoms(complex, complexData);\r\n this._extractSecondary(complex, complexData);\r\n this._extractAssemblies(complex, complexData);\r\n this._extractMolecules(complex, complexData);\r\n this._extractMetadata(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n\r\n return complex;\r\n }\r\n\r\n /**\r\n * Extract metadata\r\n * @param complex structure to fill\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n\r\n _extractMetadata(complex, complexData) {\r\n const { metadata } = complex;\r\n metadata.id = complexData.entry.id;\r\n metadata.classification = complexData.struct_keywords.pdbx_keywords;\r\n const databaserev = complexData.database_PDB_rev;\r\n metadata.date = (databaserev && databaserev.date_original) ? databaserev.date_original : '';\r\n metadata.format = 'cif';\r\n metadata.title = [];\r\n metadata.title[0] = complexData.struct.title;\r\n }\r\n\r\n /**\r\n * Extract molecules information from CIF structure (should be called strictly after _extractAtoms)\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractMolecules(complex, complexData) {\r\n const molData = complexData.entity;\r\n const names = arrize(molData.pdbx_description);\r\n const count = names.length;\r\n let i;\r\n\r\n // molecules names from cif\r\n for (i = 0; i < count; i++) {\r\n if (this.molecules[i]) { // molecule was created during atoms processing\r\n this.molecules[i].name = names[i];\r\n } else { // molecule wasn't created, because there is no atom which is contained\r\n this.molecules[i] = { name: names[i], residues: [] };\r\n }\r\n }\r\n\r\n // reorganize molecules for complex and check chains\r\n const molecules = complex.getMolecules();\r\n for (i = 0; i < count; i++) {\r\n const molecule = this.molecules[i];\r\n molecules[i] = new Molecule(complex, molecule.name, i + 1);\r\n molecules[i].residues = molecule.residues;\r\n }\r\n }\r\n\r\n /**\r\n * Extract atom information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAtoms(complex, complexData) {\r\n const atomData = complexData.atom_site;\r\n if (!atomData) {\r\n throw new AtomDataError('CIF parsing error: atom_site is not specified!');\r\n }\r\n\r\n for (let f = 0, n = cRequiredAtomFields.length; f < n; ++f) {\r\n if (!atomData[cRequiredAtomFields[f]]) {\r\n throw new AtomDataError(`CIF parsing error: requires field ${cRequiredAtomFields[f]} not found!`);\r\n }\r\n }\r\n\r\n const { asymDict } = this;\r\n // required fields\r\n const resIdc = arrize(atomData.auth_seq_id);\r\n const x = arrize(atomData.Cartn_x);\r\n const y = arrize(atomData.Cartn_y);\r\n const z = arrize(atomData.Cartn_z);\r\n const names = arrize(atomData.label_atom_id);\r\n const count = names.length;\r\n // optional fields\r\n const group = arrize(atomData.group_PDB) || [];\r\n const chainIdc = arrize(atomData.auth_asym_id) || [];\r\n const chainLabelIdc = arrize(atomData.label_asym_id) || [];\r\n const serials = arrize(atomData.id) || [];\r\n const iCodes = arrize(atomData.pdbx_PDB_ins_code) || [];\r\n const resNames = arrize(atomData.label_comp_id) || [];\r\n const elements = arrize(atomData.type_symbol) || [];\r\n const tempFactors = arrize(atomData.B_iso_or_equiv) || [];\r\n const occupancies = arrize(atomData.occupancy) || [];\r\n const charges = arrize(atomData.pdbx_formal_charge) || [];\r\n const altLocs = arrize(atomData.label_alt_id) || [];\r\n const models = arrize(atomData.pdbx_PDB_model_num) || [];\r\n const molecules = arrize(atomData.label_entity_id) || [];\r\n\r\n let chain = null;\r\n let residue = null;\r\n for (let i = 0; i < count; ++i) {\r\n const model = models[i] || 1;\r\n if (model !== 1) {\r\n continue;\r\n }\r\n const chainID = String(chainIdc[i] || ' ');\r\n\r\n if (!chain || chain.getName() !== chainID) {\r\n chain = complex.getChain(chainID) || complex.addChain(chainID);\r\n }\r\n asymDict[String(chainLabelIdc[i] || ' ')] = chainID;\r\n const resSeq = resIdc[i];\r\n const iCode = String(iCodes[i] || ' ');\r\n const resName = String(resNames[i] || '');\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n residue = chain.addResidue(resName, resSeq, iCode);\r\n\r\n // store residue in appropriate molecule\r\n const moleculeIdx = molecules[i] - 1;\r\n let entity = this.molecules[moleculeIdx];\r\n if (!entity) { // create new molecule if it hasn't been created\r\n this.molecules[moleculeIdx] = { name: '', residues: [] };\r\n entity = this.molecules[moleculeIdx];\r\n }\r\n entity.residues.push(residue);\r\n }\r\n\r\n const name = names[i];\r\n const element = elements[i] || nameToElement(name);\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name.trim()];\r\n const xyz = new THREE.Vector3(x[i], y[i], z[i]);\r\n const het = group[i] === 'HETATM' || false;\r\n const serial = serials[i] || i;\r\n const tempFactor = tempFactors[i] || 0.0;\r\n const occupancy = occupancies[i] || 0.0;\r\n const altLoc = String(altLocs[i] || '');\r\n const charge = charges[i] || 0;\r\n\r\n residue.addAtom(\r\n name,\r\n type,\r\n xyz,\r\n role,\r\n het,\r\n serial,\r\n altLoc,\r\n occupancy,\r\n tempFactor,\r\n charge,\r\n );\r\n }\r\n }\r\n\r\n /**\r\n * Extracts secondary structure information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex - complex to fill\r\n * @param complexData - CIF complex data\r\n * @private\r\n */\r\n _extractSecondary(complex, complexData) {\r\n if (complexData.struct_conf) {\r\n this._extractConfs(complex, complexData.struct_conf);\r\n }\r\n if (complexData.struct_sheet_range) {\r\n this._extractSheets(complex, complexData.struct_sheet_range);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts sheets information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param sheetData\r\n * @private\r\n */\r\n _extractSheets(complex, sheetData) {\r\n const { asymDict } = this;\r\n if (!sheetData.sheet_id || !sheetData.id || !sheetData.beg_label_seq_id || !sheetData.end_label_seq_id\r\n || !sheetData.beg_label_asym_id) {\r\n return;\r\n }\r\n // Strand(sheet, start, end, sense, cur, prev)\r\n const sheets = complex._sheets;\r\n\r\n function getSheet(name) {\r\n const n = sheets.length;\r\n for (let i = 0; i < n; ++i) {\r\n if (sheets[i]._name === name) {\r\n return sheets[i];\r\n }\r\n }\r\n sheets[n] = new Sheet(name, 0);\r\n return sheets[n];\r\n }\r\n\r\n const sheetNames = arrize(sheetData.sheet_id);\r\n const strandNames = arrize(sheetData.id);\r\n const starts = arrize(sheetData.beg_auth_seq_id);\r\n const ends = arrize(sheetData.end_auth_seq_id);\r\n const chains = arrize(sheetData.beg_label_asym_id);\r\n const stICodes = arrize(sheetData.pdbx_beg_PDB_ins_code) || [];\r\n const endICodes = arrize(sheetData.pdbx_end_PDB_ins_code) || [];\r\n\r\n for (let i = 0, n = strandNames.length; i < n; ++i) {\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n const sheet = getSheet(sheetNames[i]);\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n\r\n const strand = new Strand(sheet, start[0], end[0], 0, null, null);\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = strand;\r\n }\r\n sheet.addStrand(strand);\r\n complex.structures.push(strand);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts helix/turn/strand(?) information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param helicesData\r\n * @private\r\n */\r\n _extractConfs(complex, helicesData) {\r\n const { asymDict } = this;\r\n if (!helicesData.conf_type_id || !helicesData.beg_label_seq_id || !helicesData.end_label_seq_id\r\n || !helicesData.beg_label_asym_id) {\r\n return;\r\n }\r\n\r\n const types = arrize(helicesData.conf_type_id);\r\n const starts = arrize(helicesData.beg_auth_seq_id);\r\n const stICodes = arrize(helicesData.pdbx_beg_PDB_ins_code) || [];\r\n const ends = arrize(helicesData.end_auth_seq_id);\r\n const endICodes = arrize(helicesData.pdbx_end_PDB_ins_code) || [];\r\n const comments = arrize(helicesData.details) || [];\r\n const lengths = arrize(helicesData.pdbx_PDB_helix_length) || [];\r\n const helixClasses = arrize(helicesData.pdbx_PDB_helix_class) || [];\r\n const names = arrize(helicesData.id) || [];\r\n const chains = arrize(helicesData.beg_label_asym_id);\r\n\r\n for (let i = 0, n = types.length; i < n; ++i) {\r\n const type = getTypeFromId(types[i]);\r\n if (!type) {\r\n continue;\r\n }\r\n const name = names[i] || types[i];\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n const comment = comments[i] || '';\r\n const length = lengths[i] || 0;\r\n const helixClass = helixClasses[i] || ' ';\r\n let struct;\r\n if (type === 'helix') {\r\n const idx = complex._helices.length;\r\n struct = new Helix(helixClass, start[0], end[0], idx, name, comment, length);\r\n complex.addHelix(struct);\r\n complex.structures.push(struct);\r\n } else if (type === 'turn') {\r\n struct = new StructuralElement(StructuralElement.Type.TURN, start[0], end[0]);\r\n complex.structures.push(struct);\r\n } else {\r\n struct = null;\r\n }\r\n if (!struct) {\r\n continue;\r\n }\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = struct;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Extract biological assemblies information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAssemblies(complex, complexData) {\r\n const { asymDict } = this;\r\n const asmGen = complexData.pdbx_struct_assembly_gen;\r\n if (!asmGen) {\r\n return;\r\n }\r\n\r\n const asmIdx = arrize(asmGen.assembly_id);\r\n const asmOper = arrize(asmGen.oper_expression);\r\n const asmList = arrize(asmGen.asym_id_list);\r\n if (!asmIdx || !asmOper || !asmList) {\r\n return;\r\n }\r\n\r\n const operList = _getOperations(complexData.pdbx_struct_oper_list);\r\n if (!operList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = asmIdx.length; i < n; ++i) {\r\n const asm = new Assembly(complex);\r\n const assemblyOps = _extractOperations(asmOper[i], operList);\r\n const entries = asmList[i].split(',');\r\n for (let ii = 0, nn = entries.length; ii < nn; ++ii) {\r\n const chain = entries[ii].trim();\r\n if (chain.length > 0) {\r\n asm.addChain(asymDict[chain]);\r\n }\r\n }\r\n asm.matrices = assemblyOps;\r\n complex.units.push(asm);\r\n }\r\n }\r\n}\r\n\r\nCIFParser.formats = ['cif', 'mmcif'];\r\nCIFParser.extensions = ['.cif', '.mmcif'];\r\n\r\nexport default CIFParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Volume from '../../chem/Volume';\r\n\r\nexport const valueType = {\r\n singular: 0,\r\n vector: 1,\r\n array: 2,\r\n buffer: 3,\r\n};\r\n\r\nclass VolumeModel {\r\n _xyz2crs = [];\r\n\r\n _origin = new THREE.Vector3(0, 0, 0);\r\n\r\n constructor() {\r\n this._header = {};\r\n this._boxSize = new THREE.Vector3();\r\n this._boxStart = new THREE.Vector3();\r\n this._header.delta = {};\r\n this._header.extent = [];\r\n this._header.nstart = [];\r\n this._header.grid = [];\r\n this._header.crs2xyz = [];\r\n this._header.cellDims = new THREE.Vector3();\r\n this._header.angles = [];\r\n this._header.origin = new THREE.Vector3(0, 0, 0);\r\n this._header.dmin = 0;\r\n this._header.dmean = 0;\r\n this._header.dmax = 0;\r\n }\r\n\r\n _typedCheck() {\r\n if (_.isTypedArray(this._buff)) {\r\n this._buff = this._buff.buffer;\r\n } else if (!_.isArrayBuffer(this._buff)) {\r\n throw new TypeError('Expected ArrayBuffer or TypedArray');\r\n }\r\n }\r\n\r\n _fillHeader(headerFormat, arrays) {\r\n for (const key in headerFormat) {\r\n if (headerFormat.hasOwnProperty(key)) {\r\n switch (headerFormat[key][0]) {\r\n case valueType.singular:\r\n this._header[key] = arrays[headerFormat[key][1]][headerFormat[key][2]];\r\n break;\r\n\r\n case valueType.array:\r\n this._parseArray(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.vector:\r\n this._parseVector(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.buffer:\r\n this._header[key] = new Uint8Array(\r\n arrays[headerFormat[key][1]],\r\n [headerFormat[key][2]] * 4,\r\n [headerFormat[key][3]] * 4,\r\n );\r\n break;\r\n\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _parseVector(vector, arr, pos) {\r\n [vector.x, vector.y, vector.z] = [arr[pos], arr[pos + 1], arr[pos + 2]];\r\n }\r\n\r\n _parseArray(vector, arr, pos) {\r\n vector[0] = arr[pos];\r\n vector[1] = arr[pos + 1];\r\n vector[2] = arr[pos + 2];\r\n }\r\n\r\n _parseHeader(_buffer) {}\r\n\r\n _setAxisIndices() {}\r\n\r\n _setOrigins() {}\r\n\r\n _getAxis() {\r\n const header = this._header;\r\n\r\n const xScale = header.cellDims.x / header.grid[0];\r\n const yScale = header.cellDims.y / header.grid[1];\r\n const zScale = header.cellDims.z / header.grid[2];\r\n\r\n const [alpha, beta, gamma] = header.angles;\r\n\r\n const z1 = Math.cos(beta);\r\n const z2 = (Math.cos(alpha) - Math.cos(beta)\r\n * Math.cos(gamma)) / Math.sin(gamma);\r\n const z3 = Math.sqrt(1.0 - z1 * z1 - z2 * z2);\r\n\r\n const xaxis = new THREE.Vector3(xScale, 0, 0);\r\n const yaxis = new THREE.Vector3(Math.cos(gamma) * yScale, Math.sin(gamma) * yScale, 0);\r\n const zaxis = new THREE.Vector3(z1 * zScale, z2 * zScale, z3 * zScale);\r\n\r\n return [xaxis, yaxis, zaxis];\r\n }\r\n\r\n _getXYZdim() {\r\n return [this._header.extent[this._xyz2crs[0]],\r\n this._header.extent[this._xyz2crs[1]],\r\n this._header.extent[this._xyz2crs[2]]];\r\n }\r\n\r\n _getVolumeInfo() {\r\n const volInfo = _.pick(this._header, ['dmean', 'dmin', 'dmax', 'sd', 'delta']);\r\n volInfo.obtuseAngle = this._header.angles.map((angle) => Number(angle >= (Math.PI / 2)));\r\n return volInfo;\r\n }\r\n\r\n _setBoxParams(xaxis, yaxis, zaxis) {\r\n // if axes are not orthogonal, the origins might not match with box coordinates - need to make shift\r\n let shiftX = 0;\r\n let shiftY = 0;\r\n const [alpha, beta, gamma] = this._header.angles;\r\n\r\n if (gamma >= Math.PI / 2) {\r\n shiftX += Math.abs(yaxis.x);\r\n }\r\n if (beta >= Math.PI / 2) {\r\n shiftX += Math.abs(zaxis.x);\r\n }\r\n if (alpha >= Math.PI / 2) {\r\n shiftY += Math.abs(zaxis.y);\r\n }\r\n\r\n this._boxStart = new THREE.Vector3(this._origin.x - shiftX, this._origin.y - shiftY, this._origin.z);\r\n this._boxSize = new THREE.Vector3(\r\n Math.abs(xaxis.x) + Math.abs(yaxis.x) + Math.abs(zaxis.x),\r\n Math.abs(yaxis.y) + Math.abs(zaxis.y),\r\n Math.abs(zaxis.z),\r\n );\r\n\r\n const delta = (axe, proj) => (Math.abs(axe[proj]) / this._boxSize[proj]);\r\n this._header.delta.x = delta(yaxis, 'x');\r\n this._header.delta.y = delta(zaxis, 'x');\r\n this._header.delta.z = delta(zaxis, 'y');\r\n }\r\n\r\n _getXYZbox() {\r\n return new THREE.Box3(this._boxStart.clone(), this._boxStart.clone().add(this._boxSize));\r\n }\r\n\r\n _toXYZData() {}\r\n\r\n parse(data) {\r\n this._parseHeader(data);\r\n this._setOrigins();\r\n return new Volume(Float32Array, this._getXYZdim(), this._getXYZbox(), 1, this._toXYZData(), this._getVolumeInfo());\r\n }\r\n}\r\n\r\nexport default VolumeModel;\r\n","import Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\nconst CCP4Header = {\r\n extent: [valueType.array, 'u32', 0],\r\n type: [valueType.singular, 'u32', 3],\r\n nstart: [valueType.array, 'i32', 4],\r\n grid: [valueType.array, 'u32', 7],\r\n cellDims: [valueType.vector, 'f32', 10],\r\n angles: [valueType.array, 'f32', 13],\r\n crs2xyz: [valueType.array, 'i32', 16],\r\n dmin: [valueType.singular, 'f32', 19],\r\n dmax: [valueType.singular, 'f32', 20],\r\n dmean: [valueType.singular, 'f32', 21],\r\n ispg: [valueType.singular, 'u32', 22],\r\n nsymbt: [valueType.singular, 'u32', 23],\r\n lksflg: [valueType.singular, 'u32', 24],\r\n customData: [valueType.buffer, 'buffer', 25, 9],\r\n origin: [valueType.vector, 'f32', 34],\r\n map: [valueType.buffer, 'buffer', 52, 1],\r\n machine: [valueType.singular, 'u32', 53],\r\n sd: [valueType.singular, 'f32', 54],\r\n nlabel: [valueType.singular, 'f32', 55],\r\n label: [valueType.buffer, 'buffer', 56, 200],\r\n};\r\n\r\nclass Ccp4Model extends VolumeModel {\r\n // read header (http://www.ccp4.ac.uk/html/maplib.html)\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n const arrays = {};\r\n arrays.u32 = new Uint32Array(this._buff, 0, 56);\r\n arrays.i32 = new Int32Array(this._buff, 0, 56);\r\n arrays.f32 = new Float32Array(this._buff, 0, 56);\r\n arrays.buffer = this._buff;\r\n const header = this._header;\r\n\r\n this._fillHeader(CCP4Header, arrays);\r\n\r\n // calculate non-orthogonal unit cell coordinates\r\n header.angles.forEach((angle, i, a) => { a[i] *= Math.PI / 180.0; });\r\n }\r\n\r\n _setAxisIndices() {\r\n const header = this._header;\r\n\r\n if (header.cellDims.x === 0.0 && header.cellDims.y === 0.0 && header.cellDims.z === 0.0) {\r\n header.cellDims.set(1.0, 1.0, 1.0);\r\n }\r\n // Apply header conversion\r\n // Mapping between CCP4 column, row, section and VMD x, y, z.\r\n const { crs2xyz } = this._header;\r\n if (crs2xyz[0] === 0 && crs2xyz[1] === 0 && crs2xyz[2] === 0) {\r\n crs2xyz[0] = 1;\r\n crs2xyz[1] = 2;\r\n crs2xyz[2] = 3;\r\n }\r\n\r\n const xyz2crs = this._xyz2crs;\r\n xyz2crs[crs2xyz[0] - 1] = 0; // column\r\n xyz2crs[crs2xyz[1] - 1] = 1; // row\r\n xyz2crs[crs2xyz[2] - 1] = 2; // section\r\n }\r\n\r\n _setOrigins() {\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n const header = this._header;\r\n const xyz2crs = this._xyz2crs;\r\n // Handle both MRC-2000 and older format maps\r\n if (header.origin.x === 0.0 && header.origin.y === 0.0 && header.origin.z === 0.0) {\r\n this._origin.addScaledVector(xaxis, header.nstart[xyz2crs[0]]);\r\n this._origin.addScaledVector(yaxis, header.nstart[xyz2crs[1]]);\r\n this._origin.addScaledVector(zaxis, header.nstart[xyz2crs[2]]);\r\n } else {\r\n this._origin = header.origin;\r\n // Use ORIGIN records rather than old n[xyz]start records\r\n // http://www2.mrc-lmb.cam.ac.uk/image2000.html\r\n // XXX the ORIGIN field is only used by the EM community, and\r\n // has undefined meaning for non-orthogonal maps and/or non-cubic voxels, etc.\r\n }\r\n xaxis.multiplyScalar(header.extent[xyz2crs[0]] - 1);\r\n yaxis.multiplyScalar(header.extent[xyz2crs[1]] - 1);\r\n zaxis.multiplyScalar(header.extent[xyz2crs[2]] - 1);\r\n\r\n if (header.type === 2) {\r\n this._data = new Float32Array(\r\n this._buff,\r\n 1024 + header.nsymbt,\r\n header.extent[0] * header.extent[1] * header.extent[2],\r\n );\r\n } else {\r\n throw new Error(`CCP4: Unsupported format ${header.type}`);\r\n }\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const data = this._data;\r\n const xyz2crs = this._xyz2crs;\r\n const xyzData = new Float32Array(data.length);\r\n\r\n const dim = this._getXYZdim();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n\r\n let crsIdx = 0;\r\n const coord = [];\r\n let x;\r\n let y;\r\n let z;\r\n for (coord[2] = 0; coord[2] < header.extent[2]; coord[2]++) { // Site\r\n for (coord[1] = 0; coord[1] < header.extent[1]; coord[1]++) { // Row\r\n for (coord[0] = 0; coord[0] < header.extent[0]; coord[0]++, crsIdx++) { // Column\r\n x = coord[xyz2crs[0]];\r\n y = coord[xyz2crs[1]];\r\n z = coord[xyz2crs[2]];\r\n xyzData[x + xSize * (y + ySize * z)] = data[crsIdx];\r\n }\r\n }\r\n }\r\n\r\n return xyzData;\r\n }\r\n}\r\n\r\nclass CCP4Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'ccp4';\r\n this.model = new Ccp4Model();\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false; // Autodetection is not implemented yet\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nCCP4Parser.formats = ['ccp4'];\r\nCCP4Parser.extensions = ['.ccp4', '.map', '.mrc'];\r\nCCP4Parser.binary = true;\r\n\r\nexport default CCP4Parser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element, Molecule } = chem;\r\n\r\nclass XYZParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n this._options.fileType = 'xyz';\r\n this._fileName = options.name;\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*\\d+ *\\n[^\\n]*\\n\\s*\\w{1,3}\\s+-?\\d/.test(data);\r\n }\r\n\r\n _parseToAtomsInf(source) {\r\n const endnAtoms = source.indexOf('\\n');\r\n const nAtoms = parseInt(source.substring(0, endnAtoms), 10);\r\n const endComment = source.indexOf('\\n', endnAtoms + 1);\r\n let comment = source.slice(endnAtoms + 1, endComment).trim();\r\n if (comment.length === 0) {\r\n comment = this._fileName;\r\n }\r\n\r\n const startAtomsInf = endComment + source.substring(endComment).search(/\\S/);\r\n this._atomsInf = source.substring(startAtomsInf).split(/[\\s,]*\\n[\\s,]*/);\r\n if (!Number.isNaN(nAtoms) && (this._atomsInf.length - 1 !== nAtoms)) {\r\n this._complex.error = {\r\n message: 'wrong number of atoms',\r\n };\r\n return;\r\n }\r\n\r\n this._complex.metadata.format = 'xyz';\r\n this._complex.name = comment;\r\n }\r\n\r\n _parseAtomsInf() {\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n\r\n const chain = this._complex.addChain('A');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0; i < this._atomsInf.length - 1; i++) {\r\n const words = this._atomsInf[i].split(/[\\s,]+/);\r\n\r\n if (words.length !== 4) {\r\n this._complex.error = {\r\n message: 'missed parameters',\r\n };\r\n break;\r\n }\r\n\r\n const serial = i + 1;\r\n const name = words[0];\r\n const xyz = new THREE.Vector3(parseFloat(words[1]), parseFloat(words[2]), parseFloat(words[3]));\r\n const type = Element.getByName(name);\r\n const role = undefined;\r\n\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n const molecule = new Molecule(this._complex, this._complex.name, 1);\r\n molecule.residues = residue;\r\n this._complex._molecules[0] = molecule;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n\r\n this._parseToAtomsInf(this._data);\r\n this._parseAtomsInf();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n return result;\r\n }\r\n\r\n static formats = ['xyz'];\r\n\r\n static extensions = ['.xyz'];\r\n}\r\n\r\nexport default XYZParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element } = chem;\r\n\r\nclass PubChemParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'pubchem+json';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && data[0] === '{';\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing PubChem JSON file...');\r\n return this._toComplex(JSON.parse(this._data));\r\n }\r\n\r\n _toComplex(jsonData) {\r\n const complex = new Complex();\r\n const complexData = jsonData.PC_Compounds && jsonData.PC_Compounds[0];\r\n if (complexData) {\r\n this._extractAtoms(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n }\r\n return complex;\r\n }\r\n\r\n _extractAtoms(complex, complexData) {\r\n let aids = complexData.atoms && complexData.atoms.aid;\r\n let elements = aids && complexData.atoms.element;\r\n if (!elements || aids.length !== elements.length) {\r\n throw new Error('Unable to parse atom elements');\r\n }\r\n elements = _.fromPairs(_.zip(aids, elements));\r\n const atoms = {};\r\n\r\n const coords = complexData.coords && complexData.coords[0];\r\n const model = coords && coords.conformers && coords.conformers[0];\r\n const xs = model && model.x;\r\n const ys = model && model.y;\r\n const zs = (model && model.z) || [];\r\n aids = coords && coords.aid;\r\n if (!aids || !xs || !ys) {\r\n throw new Error('Coordinates are not found in the file');\r\n }\r\n\r\n const chain = complex.addChain(' ');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0, n = aids.length; i < n; ++i) {\r\n const aid = aids[i];\r\n const element = Element.ByAtomicNumber[elements[aid]];\r\n const xyz = new THREE.Vector3(xs[i], ys[i], zs[i] || 0.0);\r\n atoms[aid] = residue.addAtom(element.name, element, xyz, undefined, true, aid, ' ', 1.0, 0.0, 0);\r\n }\r\n\r\n const aids1 = complexData.bonds && complexData.bonds.aid1;\r\n const aids2 = complexData.bonds && complexData.bonds.aid2;\r\n const orders = (complexData.bonds && complexData.bonds.order) || [];\r\n if (!aids1 || !aids2 || aids1.length !== aids2.length) {\r\n return;\r\n }\r\n\r\n for (let j = 0, m = aids1.length; j < m; ++j) {\r\n complex.addBond(atoms[aids1[j]], atoms[aids2[j]], orders[j] || 1, 0, true);\r\n }\r\n }\r\n}\r\n\r\nPubChemParser.formats = ['pubchem', 'pubchem+json', 'pc'];\r\nPubChemParser.extensions = ['.json'];\r\n\r\nexport default PubChemParser;\r\n","import _ from 'lodash';\r\n\r\nexport default class SDFStream {\r\n constructor(data) {\r\n this._strings = data.split(/\\r?\\n|\\r/);\r\n this._currentStart = 0;\r\n this._currentStringIndx = 0;\r\n }\r\n\r\n setStart(start) {\r\n if (start >= this._strings.length) {\r\n this._currentStart = this._strings.length - 1;\r\n this._currentStringIndx = this._strings.length - 1;\r\n } else {\r\n this._currentStart = start;\r\n this._currentStringIndx = start;\r\n }\r\n }\r\n\r\n getNextString() {\r\n return this._strings[++this._currentStringIndx];\r\n }\r\n\r\n getCurrentString() {\r\n return this._strings[this._currentStringIndx];\r\n }\r\n\r\n getStringFromStart(numb) {\r\n this._currentStringIndx = this._currentStart + numb;\r\n return this._strings[this._currentStart + numb];\r\n }\r\n\r\n findNextDataItem() {\r\n let curStr = this.getNextString();\r\n let res = false;\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n if (curStr.match(/>\\s+<(.*)>/)) {\r\n res = true;\r\n break;\r\n }\r\n curStr = this.getNextString();\r\n }\r\n\r\n return res;\r\n }\r\n\r\n findNextCompoundStart() {\r\n let curStr = this.getCurrentString();\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n curStr = this.getNextString();\r\n }\r\n this.setStart(++this._currentStringIndx);\r\n return this.probablyHaveDataToParse();\r\n }\r\n\r\n probablyHaveDataToParse() {\r\n return this._currentStringIndx < this._strings.length - 2;\r\n }\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport SDFStream from './SDFStream';\r\nimport Assembly from '../../chem/Assembly';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst chargeMap = [0, 3, 2, 1, 0, -1, -2, -3];\r\nconst orderMap = [0, 1, 2, 3, 1, 1, 1, 2];\r\nconst typeMap = [\r\n Bond.BondType.UNKNOWN, // 0 - error\r\n Bond.BondType.COVALENT, // 1 - single\r\n Bond.BondType.COVALENT, // 2 - double\r\n Bond.BondType.COVALENT, // 3 - triple\r\n Bond.BondType.AROMATIC, // 4 - aromatic\r\n Bond.BondType.UNKNOWN, // 5 - single or double\r\n Bond.BondType.AROMATIC, // 6 - single or aromatic\r\n Bond.BondType.AROMATIC, // 7 - double or aromatic\r\n // 8 - any\r\n // 9 - coordination\r\n // 10 - hydrogen\r\n];\r\n\r\nconst sdfAndMolRegexp = /.*(M\\s\\sEND).*|.*(^$$$$).*|.*>\\s+<(.+)>.*/;\r\nconst sdfRegExp = /.*($$$$).*|.*>\\s+<(.+)>.*/;\r\n\r\nconst fileFormat = { SDF: 'sdf', MOL: 'mol' };\r\n\r\nconst possibleNameTags = ['PUBCHEM_IUPAC_TRADITIONAL_NAME', /PUBCHEM_(.+)_NAME/, /(.+)name/, /(.+)NAME/];\r\nconst possibleIDTags = ['PUBCHEM_COMPOUND_CID', 'id', 'ID', /.*CID/, /.*ID/, /.*id/];\r\nconst possibleTitleTags = ['msg', 'MSG', 'message', 'title', 'description', 'desc'];\r\nconst tagsNames = ['name', 'id', 'title'];\r\nconst tags = { name: possibleNameTags, id: possibleIDTags, title: possibleTitleTags };\r\n\r\nfunction buildChainID(index) {\r\n if (!index) {\r\n return 'A';\r\n }\r\n\r\n const codes = [];\r\n while (index) {\r\n codes.push(65 + (index % 26));\r\n index = Math.trunc(index / 26);\r\n }\r\n if (codes.length > 1) {\r\n codes.reverse();\r\n codes[0] -= 1;\r\n }\r\n\r\n return String.fromCharCode(...codes);\r\n}\r\n\r\nexport default class SDFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._format = 'sdf';\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._molecules = null;\r\n this._metadata = {};\r\n this._metadata.molecules = [];\r\n this._currentMolProps = {};\r\n this._compoundIndx = -1;\r\n this._assemblies = [];\r\n this._atomsParsed = 0;\r\n this._atomsIndexes = [];\r\n }\r\n\r\n canProbablyParse(data) {\r\n return _.isString(data) && sdfAndMolRegexp.test(data);\r\n }\r\n\r\n _parseHeader(stream) {\r\n const molecule = {};\r\n molecule.name = stream.getStringFromStart(0);\r\n const date = parseInt(stream.getStringFromStart(1).substr(10, 6).trim(), 10);\r\n molecule.date = date.toString() || '';\r\n molecule.title = stream.getStringFromStart(2);\r\n this._metadata.molecules.push(molecule);\r\n }\r\n\r\n _parseAtoms(stream, atomsNum) {\r\n let curStr;\r\n let serial = this._atomsParsed;\r\n\r\n // each molecule = chain\\residue\r\n const chainID = buildChainID(this._compoundIndx);\r\n const resName = 'UNK';\r\n const resSeq = 1;\r\n\r\n this._chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = this._chain.addResidue(resName, resSeq, ' ');\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n curStr = stream.getNextString();\r\n serial++;\r\n const x = parseFloat(curStr.substr(0, 10));\r\n const y = parseFloat(curStr.substr(10, 10));\r\n const z = parseFloat(curStr.substr(20, 10));\r\n const charge = chargeMap[parseInt(curStr.substr(36, 3), 10)];\r\n const xyz = new THREE.Vector3(x, y, z);\r\n let name = curStr.substr(31, 3).trim().toUpperCase();\r\n const type = Element.getByName(name);\r\n if (!this._atomsIndexes[name]) {\r\n this._atomsIndexes[name] = 0;\r\n }\r\n this._atomsIndexes[name] += 1;\r\n name += this._atomsIndexes[name]; // every atom need to have unique name.\r\n\r\n this._residue.addAtom(name, type, xyz, undefined, true, serial, ' ', 1.0, 0.0, charge);\r\n }\r\n }\r\n\r\n _parseBonds(stream, bondsNum) {\r\n let curStr;\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n curStr = stream.getNextString();\r\n let atom1 = parseInt(curStr.substr(0, 3), 10) + this._atomsParsed;\r\n let atom2 = parseInt(curStr.substr(3, 3), 10) + this._atomsParsed;\r\n const bondType = parseInt(curStr.substr(6, 3), 10);\r\n\r\n if (atom1 > atom2) {\r\n [atom1, atom2] = [atom2, atom1];\r\n }\r\n this._complex.addBond(\r\n atom1,\r\n atom2,\r\n orderMap[bondType] || 1,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _parseMOL(stream) {\r\n this._compoundIndx++;\r\n\r\n this._parseHeader(stream);\r\n const countsLine = stream.getStringFromStart(3);\r\n const atomsNum = parseInt(countsLine.substr(0, 3), 10);\r\n const bondsNum = parseInt(countsLine.substr(3, 3), 10);\r\n this._parseAtoms(stream, atomsNum);\r\n this._parseBonds(stream, bondsNum);\r\n\r\n this._atomsParsed += atomsNum;\r\n\r\n this._metadata.molecules[this._compoundIndx]._residues = [];\r\n this._metadata.molecules[this._compoundIndx]._residues.push(this._residue);\r\n }\r\n\r\n _parseDataItem(stream) {\r\n const tag = stream.getCurrentString();\r\n\r\n let data = [];\r\n let curStr = stream.getNextString();\r\n\r\n // read data\r\n while (curStr.trim() !== '') {\r\n data.push(curStr);\r\n curStr = stream.getNextString();\r\n }\r\n if (data.length === 1) {\r\n [data] = data;\r\n }\r\n this._currentMolProps[tag.replace(/[<>]/g, '').trim()] = data;\r\n }\r\n\r\n _parseCompound(stream) {\r\n this._parseMOL(stream);\r\n\r\n // parse data items block\r\n if (this._format === fileFormat.SDF) {\r\n this._currentMolProps = {};\r\n while (stream.findNextDataItem()) {\r\n this._parseDataItem(stream);\r\n }\r\n if (Object.keys(this._currentMolProps).length !== 0) {\r\n const molecule = this._metadata.molecules[this._compoundIndx];\r\n molecule.props = this._currentMolProps;\r\n this._tryToUpdateMoleculeData(molecule);\r\n }\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n console.log('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _buildAssemblies() {\r\n const chains = this._complex._chains;\r\n\r\n if (chains.length === 1) {\r\n return this._assemblies;\r\n }\r\n\r\n for (let i = 0; i < chains.length; i++) {\r\n const assembly = new Assembly(this._complex);\r\n const matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n assembly.addChain(chains[i]._name);\r\n this._assemblies.push(assembly);\r\n }\r\n\r\n return this._assemblies;\r\n }\r\n\r\n _buildMolecules() {\r\n this._complex._molecules = [];\r\n const { molecules } = this._metadata;\r\n for (let i = 0; i < molecules.length; i++) {\r\n const molecule = new Molecule(this._complex, molecules[i].name, i + 1);\r\n molecule.residues = molecules[i]._residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n\r\n return this._complex._molecules;\r\n }\r\n\r\n _searchTag(tag, props) {\r\n for (let i = 0; i < props.length; i++) {\r\n if ((tag instanceof RegExp && tag.test(props[i].tag)) || tag === props[i].tag) {\r\n return props[i].data;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToFind(tagsList, props) {\r\n for (let j = 0; j < tagsList.length; j++) {\r\n const res = this._searchTag(tagsList[j], props);\r\n if (res) {\r\n return res;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToUpdateMoleculeData(molecule) {\r\n let res = false;\r\n for (let i = 0; i < tagsNames.length; i++) {\r\n const tagPossibleNames = tags[tagsNames[i]];\r\n const data = this._tryToFind(tagPossibleNames, molecule.props);\r\n if (data) {\r\n molecule[tagsNames[i]] = data;\r\n res = true;\r\n }\r\n }\r\n\r\n molecule.name = molecule.name || molecule.id;\r\n if (molecule.name.match(/^\\d+$/)) {\r\n molecule.name = `CID: ${molecule.name}`;\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _finalizeMetadata() {\r\n const { molecules } = this._metadata;\r\n const { metadata } = this._complex;\r\n const complex = this._complex;\r\n\r\n if (molecules.length === 1) {\r\n complex.name = molecules[0].name;\r\n metadata.title = molecules[0].title;\r\n metadata.date = molecules[0].date;\r\n metadata.properties = molecules[0].props;\r\n } else if (molecules.length > 1) {\r\n metadata.molecules = [];\r\n for (let i = 0; i < molecules.length; i++) {\r\n metadata.molecules.push({\r\n name: molecules[i].name, date: molecules[i].date, title: molecules[i].title, properties: molecules[i].props,\r\n });\r\n }\r\n }\r\n }\r\n\r\n _finalize() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n this._complex._finalizeBonds();\r\n this._fixBondsArray();\r\n this._finalizeMetadata();\r\n this._buildAssemblies();\r\n this._complex.units = this._complex.units.concat(this._assemblies);\r\n this._buildMolecules();\r\n this._complex.finalize({\r\n needAutoBonding: false, detectAromaticLoops: false, enableEditing: false, serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n defineFormat(data) {\r\n let format;\r\n if (sdfRegExp.test(data)) {\r\n format = fileFormat.SDF;\r\n } else {\r\n format = fileFormat.MOL;\r\n }\r\n\r\n return format;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const stream = new SDFStream(this._data);\r\n\r\n this._format = this.defineFormat(this._data);\r\n result.metadata.format = this._format;\r\n\r\n do {\r\n this._parseCompound(stream);\r\n } while (stream.findNextCompoundStart());\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nSDFParser.formats = ['mol', 'sdf'];\r\nSDFParser.extensions = ['.mol', '.sdf'];\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\n// http://www.uoxray.uoregon.edu/tnt/manual/node104.html\r\nconst DSN6Header = {\r\n nstart: [valueType.array, 'i16', 0],\r\n extent: [valueType.array, 'i16', 3],\r\n grid: [valueType.array, 'i16', 6],\r\n cellDims: [valueType.vector, 'i16', 9],\r\n angles: [valueType.array, 'i16', 12],\r\n div: [valueType.singular, 'i16', 15],\r\n adder: [valueType.singular, 'i16', 16],\r\n scaleFactor: [valueType.singular, 'i16', 17],\r\n};\r\n\r\nclass DSN6Model extends VolumeModel {\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n\r\n const arrays = {};\r\n arrays.i16 = new Int16Array(this._buff);\r\n\r\n // check and reverse if big endian\r\n if (arrays.i16[18] !== 100) {\r\n for (let i = 0, n = arrays.i16.length; i < n; ++i) {\r\n const val = arrays.i16[i];\r\n arrays.i16[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff);\r\n }\r\n }\r\n if (arrays.i16[18] !== 100) {\r\n throw new Error('DSN6: Incorrect format ');\r\n }\r\n\r\n const header = this._header;\r\n\r\n this._fillHeader(DSN6Header, arrays);\r\n header.cellDims.multiplyScalar(1.0 / header.scaleFactor);\r\n header.angles.forEach((angle, i, a) => { a[i] *= (Math.PI / 180.0) / header.scaleFactor; });\r\n header.div /= 100;\r\n }\r\n\r\n _setAxisIndices() {\r\n this._xyz2crs[0] = 0;\r\n this._xyz2crs[1] = 1;\r\n this._xyz2crs[2] = 2;\r\n }\r\n\r\n _setOrigins() {\r\n const header = this._header;\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n this._origin.addScaledVector(xaxis, header.nstart[0]);\r\n this._origin.addScaledVector(yaxis, header.nstart[1]);\r\n this._origin.addScaledVector(zaxis, header.nstart[2]);\r\n\r\n xaxis.multiplyScalar(header.extent[0]);\r\n yaxis.multiplyScalar(header.extent[1]);\r\n zaxis.multiplyScalar(header.extent[2]);\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _pointCalculate(xyzData, byteBuffer, z, y, x, pos, i) {\r\n const header = this._header;\r\n\r\n if (x < header.extent[0] && y < header.extent[1] && z < header.extent[2]) {\r\n const idx = x + header.extent[0] * (y + header.extent[1] * z);\r\n xyzData[idx] = (byteBuffer[pos.counter] - header.adder) / header.div;\r\n ++pos.counter;\r\n } else {\r\n pos.counter += 8 - i;\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n _blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos) {\r\n for (let k = 0; k < 8; ++k) {\r\n const z = 8 * zBlock + k;\r\n for (let j = 0; j < 8; ++j) {\r\n const y = 8 * yBlock + j;\r\n let inRange = true;\r\n let i = 0;\r\n while (inRange && i < 8) {\r\n const x = 8 * xBlock + i;\r\n inRange = this._pointCalculate(xyzData, byteBuffer, z, y, x, pos, i);\r\n i++;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const byteBuffer = new Uint8Array(this._buff);\r\n const xyzData = new Float32Array(header.extent[0] * header.extent[1] * header.extent[2]);\r\n\r\n const blocks = new THREE.Vector3(header.extent[0] / 8, header.extent[1] / 8, header.extent[2] / 8);\r\n\r\n const pos = {};\r\n pos.counter = 512;\r\n\r\n for (let zBlock = 0; zBlock < blocks.z; ++zBlock) {\r\n for (let yBlock = 0; yBlock < blocks.y; ++yBlock) {\r\n for (let xBlock = 0; xBlock < blocks.x; ++xBlock) {\r\n this._blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos);\r\n }\r\n }\r\n }\r\n this._calculateInfoParams(xyzData);\r\n return xyzData;\r\n }\r\n\r\n _calculateInfoParams(xyzData) {\r\n this._header.dmean /= xyzData.length;\r\n let dispersion = 0;\r\n let minDensity = xyzData[0];\r\n let maxDensity = xyzData[0];\r\n for (let j = 0; j < xyzData.length; j++) {\r\n dispersion += (this._header.dmean - xyzData[j]) ** 2;\r\n\r\n if (xyzData[j] < minDensity) {\r\n minDensity = xyzData[j];\r\n }\r\n if (xyzData[j] > maxDensity) {\r\n maxDensity = xyzData[j];\r\n }\r\n }\r\n this._header.sd = Math.sqrt(dispersion / xyzData.length);\r\n this._header.dmax = maxDensity;\r\n this._header.dmin = minDensity;\r\n }\r\n}\r\n\r\nclass DSN6Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'dsn6';\r\n this.model = new DSN6Model();\r\n }\r\n\r\n static canParse(data, options) {\r\n if (!data) {\r\n return false;\r\n }\r\n return data instanceof ArrayBuffer && Parser.checkDataTypeOptions(options, 'dsn6');\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false;\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nDSN6Parser.formats = ['dsn6'];\r\nDSN6Parser.extensions = ['.dsn6', '.omap'];\r\nDSN6Parser.binary = true;\r\n\r\nexport default DSN6Parser;\r\n","import PDBStream from './PDBStream';\r\n\r\n/**\r\n * Little helper class for GRO Parser usage.\r\n * @extends PDBStream\r\n */\r\nclass GROReader extends PDBStream {\r\n constructor(data) {\r\n super(data);\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n this.next();\r\n }\r\n\r\n /**\r\n * Getting end of string.\r\n * @returns {Number} Pointer to end of string\r\n */\r\n getNext() {\r\n return this._next;\r\n }\r\n}\r\n\r\nexport default GROReader;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport GROReader from './GROReader';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Molecule,\r\n} = chem;\r\n\r\n/**\r\n * Gromos87 file format parser.\r\n * @extends Parser\r\n */\r\nclass GROParser extends Parser {\r\n /**\r\n * Create parser for .gro file format\r\n *\r\n * @param {String} data Input file\r\n * @param {String} options Input options (optional field)\r\n */\r\n constructor(data, options) {\r\n super(data, options);\r\n /** @type Date */\r\n this._time = null; // Time in ps, optional field for animations\r\n /** @type Number */\r\n this._numAtoms = null; // Number of atoms in complex\r\n /** @type Number */\r\n this._residueNumber = null; // Number of exact residue\r\n /** @type String */\r\n this._residueName = ''; // Scientific name of exact residue\r\n /** @type String */\r\n this._atomName = ''; // Scientific name of exact atom\r\n /** @type Number */\r\n this._atomNumber = null; // Sorted number of exact atom\r\n /** @type Array */\r\n this._atomPosition = []; // Array which contains x, y, z position of exact atom\r\n /** @type Array */\r\n this._atomVelocity = []; // Array which contains x, y, z velocity of exact atom (optional)\r\n /** @type Complex */\r\n this._complex = null; // Complex structure for unified molecule representation\r\n /** @type Vector3 */\r\n this._molecules = []; // Molecules array\r\n /** @type Molecule */\r\n this._molecule = null; // Single molecule\r\n /** @type String */\r\n this._options.filetype = 'gro'; // Extension of data file.\r\n }\r\n\r\n /**\r\n * General check for possibility of parsing.\r\n * @param {String} data - Input file\r\n * @returns {boolean} true if this file is in ascii, false otherwise\r\n */\r\n canProbablyParse(data) {\r\n return _.isString(this._data) && /^\\s*[^\\n]*\\n\\s*\\d+ *\\n\\s*\\d+[^\\n\\d]{3}\\s*\\w+\\s*\\d+\\s*-?\\d/.test(data);\r\n }\r\n\r\n /**\r\n * Parsing title of molecule complex.\r\n * NOTE: that names are ESTIMATES, there is no strict rules in Gromos87 standard for first line in input file.\r\n * @param {GROReader} line - Line containing title and time.\r\n */\r\n _parseTitle(line) {\r\n const { metadata } = this._complex;\r\n metadata.id = line.readLine().trim();\r\n metadata.name = metadata.id.slice(metadata.id.lastIndexOf('\\\\') + 1, metadata.id.lastIndexOf('.'));\r\n metadata.format = 'gro';\r\n }\r\n\r\n /**\r\n * Parsing line containing number of atoms information.\r\n * @param {GROReader} line - Line containing number of atoms.\r\n */\r\n _parseNumberOfAtoms(line) {\r\n this._numAtoms = line.readInt(0, line.getNext());\r\n if (Number.isNaN(this._numAtoms)) {\r\n throw new Error('Line 2 is not representing atom number. Consider checking input file');\r\n }\r\n }\r\n\r\n /**\r\n * Parsing line containing information about residues, atoms etc. Also information about box vectors.\r\n * Format of atoms MUST (by Gromos87 standard) be this: (note that numbering starts not from 0, but from 1!)\r\n * ResidueNumber[1 - 5] ResidueName[6 - 10] AtomName[11 - 15] AtomNumber[16 - 20] Position[21 - 45] Velocity[46 - 69]\r\n * @param {GROReader} line - Line containing information about atom.\r\n */\r\n _parseAtom(line) {\r\n this._residueNumber = line.readInt(1, 5);\r\n this._residueName = line.readString(6, 10).trim();\r\n this._atomName = line.readString(11, 15).trim();\r\n this._atomNumber = line.readInt(16, 20);\r\n const positionX = line.readFloat(21, 28) * 10;\r\n const positionY = line.readFloat(29, 36) * 10;\r\n const positionZ = line.readFloat(37, 45) * 10;\r\n if (Number.isNaN(positionX) || Number.isNaN(positionY) || Number.isNaN(positionZ)) {\r\n this._complex.error = {\r\n message: `Atom position is invalid in \"${line.readLine()}\"`,\r\n };\r\n return;\r\n }\r\n /* const velocityX = line.readFloat(46, 53);\r\n const velocityY = line.readFloat(54, 61);\r\n const velocityZ = line.readFloat(62, 69); */\r\n /* Adding residue and atom to complex structure */\r\n const type = Element.getByName(this._atomName[0]); /* MAGIC 0. REASONS: This name is something like \"CA\", where\r\n C - is an element an A is something else. But what about Calcium? */\r\n if (type.fullName === 'Unknown') {\r\n this._complex.error = {\r\n message: `${this._atomName[0]} hasn't been recognised as an atom name.`,\r\n };\r\n return;\r\n }\r\n const role = Element.Role[this._atomName];\r\n /* Firstly, create a dummy chain */\r\n let chain = this._chain;\r\n if (!chain) {\r\n this._chain = chain = this._complex.addChain('A');\r\n }\r\n /* Secondly, add residue to that chain */\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== this._residueNumber) {\r\n this._residue = residue = chain.addResidue(this._residueName, this._residueNumber, ' ');\r\n }\r\n /* Lastly, add atom to that residue */\r\n this._atomPosition = new THREE.Vector3(positionX, positionY, positionZ);\r\n /* Adding default constants to correct atom addition process */\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n residue.addAtom(this._atomName, type, this._atomPosition, role, het, this._atomNumber, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n /**\r\n * Some finalizing procedures. In '.gro' file format there is only 1 chain and 1 molecule.\r\n */\r\n _finalize() {\r\n const molecule = new Molecule(this._complex, this._complex.metadata.name, 1);\r\n // aggregate residues from chain\r\n molecule.residues = this._chain._residues;\r\n molecule._chains = this._chain;\r\n this._complex._molecules[0] = molecule;\r\n this._molecules.push(molecule);\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n /**\r\n * Main parsing procedure.\r\n * @returns {Complex} Complex structure for visualizing.\r\n */\r\n parseSync() {\r\n /* Create \"Complex\" variable */\r\n const result = this._complex = new Complex();\r\n /* Parse input file line-by-line */\r\n const reader = new GROReader(this._data);\r\n let counter = 0; /* Simple counter regarding to format of .gro file */\r\n /* First two lines - technical information, other lines - Atoms */\r\n this._parseTitle(reader);\r\n reader.next();\r\n this._parseNumberOfAtoms(reader);\r\n reader.next();\r\n for (counter = 0; counter < this._numAtoms; ++counter) {\r\n if (!reader.end()) {\r\n this._parseAtom(reader);\r\n reader.next();\r\n } else break;\r\n }\r\n /* If number of atoms in second line is less then actual atoms in file */\r\n if (counter < this._numAtoms) {\r\n this._complex.error = {\r\n message: 'File ended unexpectedly.',\r\n };\r\n }\r\n /* Catch errors occurred in parsing process */\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n\r\n /* Finalizing data */\r\n this._finalize();\r\n\r\n /* Cleaning up */\r\n this._atomPosition = null;\r\n this._complex = null;\r\n this._molecules = null;\r\n this._molecule = null;\r\n\r\n /* Return resulting Complex variable */\r\n return result;\r\n }\r\n}\r\n\r\nGROParser.formats = ['gro'];\r\nGROParser.extensions = ['.gro'];\r\n\r\nexport default GROParser;\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst orderMap = {\r\n un: 0,\r\n 1: 1,\r\n 2: 2,\r\n 3: 3,\r\n ar: 1,\r\n am: 1,\r\n nc: 0,\r\n du: 1,\r\n};\r\nconst typeMap = {\r\n un: Bond.BondType.UNKNOWN, // unknown (cannot be determined from the parameter tables)\r\n 1: Bond.BondType.COVALENT, // single\r\n 2: Bond.BondType.COVALENT, // double\r\n 3: Bond.BondType.COVALENT, // triple\r\n ar: Bond.BondType.AROMATIC, // aromatic\r\n am: Bond.BondType.COVALENT, // amide\r\n nc: Bond.BondType.UNKNOWN, // not connected\r\n du: Bond.BondType.COVALENT, // dummy\r\n};\r\n\r\nconst resNumberRegex = /\\d+$/;\r\nconst spacesRegex = /\\s+/;\r\n\r\nfunction splitToFields(str) {\r\n return str.trim().split(spacesRegex);\r\n}\r\n/* There is no jsdoc documentation because of eslint corrections:\r\n * not all Parser methods are implemented\r\n */\r\n\r\nclass MOL2Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._compoundIndx = -1;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n\r\n this._currPosIdx = 0;\r\n this._currStartIdx = 0;\r\n\r\n this._serialAtomMap = {};\r\n\r\n this._options.fileType = 'mol2';\r\n }\r\n\r\n _parseRawStrings(data) {\r\n return data.split(/\\r?\\n|\\r/);\r\n }\r\n\r\n _toStringFromStart(numb, MOL2Data) {\r\n const newPosIdx = this._currStartIdx + numb;\r\n this._currPosIdx = (newPosIdx < MOL2Data.length) ? newPosIdx : this._currStartIdx;\r\n }\r\n\r\n _toHeaderString(header, MOL2Data) {\r\n this._toStringFromStart(0, MOL2Data);\r\n while (this._currPosIdx < MOL2Data.length) {\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`)) {\r\n return;\r\n }\r\n this._currPosIdx++;\r\n }\r\n this._toStringFromStart(0, MOL2Data);\r\n }\r\n\r\n _toStringFromHeader(header, numb, MOL2Data) {\r\n this._toHeaderString(header, MOL2Data);\r\n const newPosIdx = this._currPosIdx + numb;\r\n\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`) && newPosIdx < MOL2Data.length) {\r\n this._currPosIdx = newPosIdx;\r\n }\r\n }\r\n\r\n _setStart(startPos, MOL2Data) {\r\n if (startPos >= MOL2Data.length) {\r\n this._currStartIdx = this._currPosIdx = MOL2Data.length - 1;\r\n } else {\r\n this._currStartIdx = this._currPosIdx = startPos;\r\n }\r\n }\r\n\r\n _probablyHaveDataToParse(MOL2Data) {\r\n return this._currPosIdx < MOL2Data.length - 2;\r\n }\r\n\r\n _findNextCompoundStart(MOL2Data) {\r\n while (this._currPosIdx < MOL2Data.length && MOL2Data[this._currPosIdx].trim() !== '@MOLECULE>') {\r\n this._currPosIdx++;\r\n }\r\n this._setStart(++this._currPosIdx, MOL2Data);\r\n return this._probablyHaveDataToParse(MOL2Data);\r\n }\r\n\r\n _parseMolecule(MOL2Data) {\r\n this._toHeaderString('MOLECULE', MOL2Data);\r\n\r\n const { metadata } = this._complex;\r\n metadata.name = MOL2Data[++this._currPosIdx];\r\n metadata.format = 'mol2';\r\n\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = this._compoundIndx + 1;\r\n this._molecules.push(this._molecule);\r\n }\r\n\r\n /* Atom format description:\r\n * atomId atomName x y z element [resSeq [resName [charge [statusBit]]]]\r\n * statusBits is the internal SYBYL status bits associated with the atom.\r\n * These should never be set by the user.\r\n * Source: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf\r\n */\r\n _parseAtoms(atomsNum, MOL2Data) {\r\n this._toHeaderString('ATOM', MOL2Data);\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 6) {\r\n throw new Error('MOL2 parsing error: Not enough information to create atom!');\r\n }\r\n const atomId = parseInt(parsedStr[0], 10);\r\n const atomName = parsedStr[1];\r\n\r\n const x = parseFloat(parsedStr[2]);\r\n const y = parseFloat(parsedStr[3]);\r\n const z = parseFloat(parsedStr[4]);\r\n\r\n const element = parsedStr[5].split('.')[0].toUpperCase();\r\n\r\n let charge = 0;\r\n if (parsedStr.length >= 9) {\r\n charge = parseFloat(parsedStr[8]) || 0.0;\r\n }\r\n\r\n let chain = this._chain;\r\n if (!chain) {\r\n // .mol2 may contain information about multiple molecules, but they can't be visualized\r\n // at the same time now. There is no need to create different chain IDs then.\r\n this._chain = chain = this._complex.getChain('A') || this._complex.addChain('A');\r\n this._residue = null;\r\n }\r\n if (!this._setResidue(parsedStr)) {\r\n continue;\r\n }\r\n\r\n // These fields are not listed in mol2 format. Set them default.\r\n // Atoms and het atoms doesn't differ in .mol2,\r\n // but het atoms have special residues. It can be used in next updates\r\n const het = false;\r\n const altLoc = ' ';\r\n const occupancy = 1.0;\r\n const tempFactor = 0.0;\r\n const type = Element.getByName(element);\r\n const role = Element.Role[atomName];\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n this._residue.addAtom(atomName, type, xyz, role, het, atomId, altLoc, occupancy, tempFactor, charge);\r\n }\r\n }\r\n\r\n _setResidue(parsedStr) {\r\n let resSeq = 1;\r\n let resName = 'UNK'; // The same meaning has '<0>' in some mol2 files\r\n\r\n if (parsedStr.length >= 7) {\r\n resSeq = parseInt(parsedStr[6], 10);\r\n }\r\n if (parsedStr.length >= 8 && parsedStr[7] !== '<0>') {\r\n resName = parsedStr[7].replace(resNumberRegex, '');\r\n }\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return false;\r\n }\r\n }\r\n const residue = this._residue;\r\n const chain = this._chain;\r\n if (!residue || residue.getSequence() !== resSeq) {\r\n this._residue = chain.addResidue(resName, resSeq, 'A');\r\n }\r\n return true;\r\n }\r\n\r\n /* Bond format description\r\n * bondId originAtomId targetAtomId bondType [statusBits]\r\n */\r\n _parseBonds(bondsNum, MOL2Data) {\r\n this._toHeaderString('BOND', MOL2Data);\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 3) {\r\n throw new Error('MOL2 parsing error: Missing information about bonds!');\r\n }\r\n\r\n let originAtomId = parseInt(parsedStr[1], 10);\r\n let targetAtomId = parseInt(parsedStr[2], 10);\r\n const bondType = parsedStr[3];\r\n\r\n if (originAtomId > targetAtomId) {\r\n [originAtomId, targetAtomId] = [targetAtomId, originAtomId];\r\n }\r\n this._complex.addBond(\r\n originAtomId,\r\n targetAtomId,\r\n orderMap[bondType] || 0,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _fixSerialAtoms() {\r\n const atoms = this._complex._atoms;\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n this._serialAtomMap[atom.serial] = atom;\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n if (Object.keys(serialAtomMap).length === 0) {\r\n throw new Error('MOL2 parsing error: Missing atom information!');\r\n }\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _finalizeMolecules() {\r\n // Get chain from complex\r\n const chain = this._complex._chains[0];\r\n this._complex._molecules = [];\r\n\r\n // Aggregate residues from chains\r\n // (to be precise from the chain 'A')\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const currMolecule = this._molecules[i];\r\n const molResidues = chain._residues;\r\n const molecule = new Molecule(this._complex, currMolecule._name, i + 1);\r\n molecule.residues = molResidues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _finalize() {\r\n this._complex._finalizeBonds();\r\n this._fixSerialAtoms();\r\n this._fixBondsArray();\r\n this._finalizeMolecules();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _parseCompound(MOL2Data) {\r\n this._compoundIndx++;\r\n this._parseMolecule(MOL2Data);\r\n\r\n // Ignoring comments and everything before @MOLECULE block\r\n this._toStringFromHeader('MOLECULE', 2, MOL2Data);\r\n\r\n const parsedStr = MOL2Data[this._currPosIdx].trim().split(spacesRegex);\r\n const atomsNum = parsedStr[0];\r\n const bondsNum = parsedStr[1];\r\n\r\n this._parseAtoms(atomsNum, MOL2Data);\r\n this._parseBonds(bondsNum, MOL2Data);\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const MOL2Data = this._parseRawStrings(this._data);\r\n do {\r\n this._parseCompound(MOL2Data);\r\n } while (this._findNextCompoundStart(MOL2Data));\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nMOL2Parser.formats = ['mol2'];\r\nMOL2Parser.extensions = ['.mol2', '.ml2', '.sy2'];\r\n\r\nexport default MOL2Parser;\r\n","import ParserList from './parsers/ParserList';\r\n\r\nimport PDBParser from './parsers/PDBParser';\r\nimport CMLParser from './parsers/CMLParser';\r\nimport MMTFParser from './parsers/MMTFParser';\r\nimport CIFParser from './parsers/CIFParser';\r\nimport CCP4Parser from './parsers/CCP4Parser';\r\nimport XYZParser from './parsers/XYZParser';\r\nimport PubChemParser from './parsers/PubChemParser';\r\nimport SDFParser from './parsers/SDFParser';\r\nimport DSN6Parser from './parsers/DSN6Parser';\r\nimport GROParser from './parsers/GROParser';\r\nimport MOL2Parser from './parsers/MOL2Parser';\r\n\r\nexport default new ParserList([\r\n // note: order might be important\r\n PDBParser,\r\n CIFParser,\r\n MMTFParser,\r\n XYZParser,\r\n CMLParser,\r\n PubChemParser,\r\n SDFParser,\r\n CCP4Parser,\r\n DSN6Parser,\r\n GROParser,\r\n MOL2Parser,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available exporters.\r\n * @extends EntityList\r\n */\r\nclass ExporterList extends EntityList {\r\n /**\r\n * Create a list of exporters.\r\n * The exporters are indexed by supported data formats (`.formats` and\r\n * `.extensions` properties of a Exporter subclass).\r\n * The Exporters can be retrieved later by matching against specs (see {@link ExporterList#find}).\r\n *\r\n * @param {!Array=} someExporters A list of {@link Exporter} subclasses to\r\n * automatically register at creation time.\r\n * @see ExporterList#register\r\n */\r\n constructor(someExporters = []) {\r\n super(someExporters, ['formats']);\r\n }\r\n\r\n /**\r\n * Find a suitable exporter for data.\r\n *\r\n * @param {Object} specs Exporter specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {*=} specs.data Data to export.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ExporterList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Exporter {\r\n constructor(source, options) {\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n exportSync() {\r\n throw new Error('Exporting to this source is not implemented');\r\n }\r\n\r\n export() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Export aborted'));\r\n }\r\n return resolve(this.exportSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Exporter.prototype);\r\n","import _ from 'lodash';\r\nimport { Matrix4 } from 'three';\r\n\r\nexport default class PDBResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._currentStr = -1;\r\n this._tag = null;\r\n this._fixedNumeration = false;\r\n this._numeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n\r\n getResult() {\r\n this.writeString('\\n', 81, 81);\r\n return this._resultArray.join('');\r\n }\r\n\r\n _currentStrLength() {\r\n const curStr = this._resultArray[this._currentStr];\r\n return curStr ? curStr.length : 0;\r\n }\r\n\r\n // numeration can be number or boolean\r\n // if numeration is number then just put this number to 8-10 pos in string\r\n // if numeration is boolean then increase number for all new strings\r\n newTag(tag, numeration) {\r\n if (!tag) {\r\n this._tag = null;\r\n } else {\r\n this._tag = tag;\r\n }\r\n if (!_.isUndefined(numeration)) {\r\n if (_.isNumber(numeration)) {\r\n this._tagStrNum = numeration;\r\n this._numeration = true;\r\n this._fixedNumeration = true;\r\n } else if (_.isBoolean(numeration)) {\r\n this._tagStrNum = 0;\r\n this._numeration = numeration;\r\n this._fixedNumeration = false;\r\n }\r\n } else {\r\n this._numeration = false;\r\n this._fixedNumeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n }\r\n\r\n newString(tag) {\r\n this.writeString('\\n', 81, 81);\r\n this._currentStr++;\r\n this._resultArray.push('');\r\n\r\n if (tag) {\r\n this.writeString(tag, 1, 6);\r\n } else if (this._tag) {\r\n this.writeString(this._tag, 1, 6);\r\n }\r\n\r\n if (this._numeration) {\r\n if (!this._fixedNumeration) {\r\n this._tagStrNum++;\r\n }\r\n if (this._tagStrNum !== 1) {\r\n this.writeString(this._tagStrNum.toString(), 10, 8);\r\n }\r\n }\r\n }\r\n\r\n writeEntireString(string, maxStrPos, concat) {\r\n if (!maxStrPos) {\r\n maxStrPos = 81;\r\n }\r\n for (let j = 0; j < string.length; j++) {\r\n if (this._currentStrLength() === maxStrPos && j !== string.length - 1) {\r\n this.newString();\r\n if (concat) { // pretty hardcoddy\r\n this.writeString(concat.tag, concat.begin, concat.end);\r\n }\r\n }\r\n if (string[j] === '\\n') {\r\n this.newString();\r\n } else {\r\n this.writeString(string[j]);\r\n }\r\n }\r\n }\r\n\r\n writeString(string, begin, end) {\r\n let curStr = this._resultArray[this._currentStr];\r\n let str;\r\n\r\n const curStrLength = curStr ? curStr.length : 0;\r\n\r\n if (_.isUndefined(string)) {\r\n return;\r\n }\r\n\r\n if (!_.isNumber(begin)) {\r\n begin = curStrLength + 1;\r\n }\r\n\r\n if (!_.isNumber(end)) {\r\n end = curStrLength + string.length;\r\n }\r\n\r\n if (!_.isString(string)) {\r\n str = string.toString();\r\n } else {\r\n str = string;\r\n }\r\n\r\n const finish = begin < end ? end : begin;\r\n const start = begin < end ? begin : end;\r\n\r\n if (str.length > Math.abs(begin - end) + 1) {\r\n str = str.substr(0, Math.abs(begin - end + 1));\r\n }\r\n\r\n // spaces before start of new data\r\n if (start > curStrLength + 1) {\r\n this._resultArray[this._currentStr] += ' '.repeat(start - curStrLength - 1);\r\n } else if (start <= curStrLength) {\r\n const cStr = this._resultArray[this._currentStr];\r\n this._resultArray[this._currentStr] = cStr.slice(0, start - 1);\r\n }\r\n\r\n // if reverse order\r\n // reverse order of end and begin means that user wants to align text right\r\n if (end < begin) {\r\n const len = begin - end + 1;\r\n str = ' '.repeat(len - str.length) + str;\r\n }\r\n\r\n // some hardcode fix for space between string numeration and data\r\n // (see pdb file format description)\r\n if (start === 11 && this._numeration && this._tagStrNum !== 1) {\r\n str = ` ${str}`;\r\n }\r\n\r\n // append new data to string\r\n this._resultArray[this._currentStr] += str;\r\n curStr = this._resultArray[this._currentStr];\r\n\r\n if (finish > curStr.length) {\r\n this._resultArray[this._currentStr] += ' '.repeat(finish - curStr.length);\r\n }\r\n }\r\n\r\n writeBondsArray(bonds, atom) {\r\n const bondsArrays = this._getSubArrays(bonds, 4);\r\n\r\n for (let k = 0; k < bondsArrays.length; k++) {\r\n this.newString();\r\n this.writeString(atom.serial, 11, 7);\r\n\r\n for (let j = 0; j < bondsArrays[k].length; j++) {\r\n const serial = (bondsArrays[k][j]._left.serial === atom.serial)\r\n ? bondsArrays[k][j]._right.serial : bondsArrays[k][j]._left.serial;\r\n\r\n this.writeString(serial, 16 + 5 * j, 12 + 5 * j);\r\n }\r\n }\r\n }\r\n\r\n _getSubArrays(arr, subArraySize) {\r\n const subArrays = [];\r\n for (let i = 0; i < arr.length; i += subArraySize) {\r\n subArrays.push(arr.slice(i, i + subArraySize));\r\n }\r\n return subArrays;\r\n }\r\n\r\n // function for writing matrix in Remark290 and Remark350 tags\r\n // (see pdb file description)\r\n writeMatrix(matrix, matrixIndx, tag) {\r\n for (let j = 0; j < 3; j++) {\r\n this.newString();\r\n this.writeString(tag, 14, 18);\r\n this.writeString((j + 1).toString(), 19, 19);\r\n this.writeString(matrixIndx.toString(), 23, 20);\r\n for (let k = 0; k < 3; k++) {\r\n const numb = parseFloat(matrix.elements[j * 4 + k]).toFixed(6);\r\n this.writeString(numb.toString(), 33 + k * 10, 24 + k * 10);\r\n }\r\n\r\n const numb = parseFloat(matrix.elements[j * 4 + 3]).toFixed(5);\r\n this.writeString(numb.toString(), 68, 55);\r\n }\r\n }\r\n\r\n writeMatrices(matrices, string) {\r\n if (!matrices) {\r\n return;\r\n }\r\n const matrix = new Matrix4();\r\n for (let j = 0; j < matrices.length; j++) {\r\n matrix.copy(matrices[j]).transpose();\r\n this.writeMatrix(matrix, j + 1, string);\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport Complex from '../../chem/Complex';\r\nimport Exporter from './Exporter';\r\nimport PDBResult from './PDBResult';\r\nimport Assembly from '../../chem/Assembly';\r\nimport { typeByPDBHelixClass } from '../../chem/Helix';\r\n\r\nexport default class PDBExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n this._tags = ['HEADER', 'TITLE', 'COMPND', 'REMARK', 'HELIX', 'SHEET', 'ATOM and HETATM', 'CONECT'];\r\n this._result = null;\r\n this._tagExtractors = {\r\n HEADER: this._extractHEADER,\r\n TITLE: this._extractTITLE,\r\n 'ATOM and HETATM': this._extractATOM,\r\n CONECT: this._extractCONECT,\r\n COMPND: this._extractCOMPND,\r\n REMARK: this._extractREMARK,\r\n HELIX: this._extractHELIX,\r\n SHEET: this._extractSHEET,\r\n };\r\n this._stringForRemark350 = 'COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN\\n'\r\n + 'BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE\\n'\r\n + 'MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS\\n'\r\n + 'GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND\\n'\r\n + 'CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.';\r\n\r\n this._stringForRemark290 = 'CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS\\n'\r\n + 'THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM\\n'\r\n + 'RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY\\n'\r\n + 'RELATED MOLECULES.';\r\n }\r\n\r\n exportSync() {\r\n const result = new PDBResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n for (let i = 0; i < this._tags.length; i++) {\r\n const tag = this._tags[i];\r\n const func = this._tagExtractors[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, result);\r\n }\r\n }\r\n\r\n this._result = result.getResult();\r\n\r\n return this._result;\r\n }\r\n\r\n _extractHEADER(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n result.newTag('HEADER');\r\n result.newString();\r\n if (metadata.classification) {\r\n result.writeString(metadata.classification, 11, 50);\r\n }\r\n if (metadata.date) {\r\n result.writeString(metadata.date, 51, 59);\r\n }\r\n if (metadata.id) {\r\n result.writeString(metadata.id, 63, 66);\r\n }\r\n }\r\n\r\n _extractTITLE(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n if (!metadata.title) {\r\n return;\r\n }\r\n result.newTag('TITLE', true);\r\n for (let i = 0; i < metadata.title.length; i++) {\r\n result.newString();\r\n result.writeString(metadata.title[i], 11, 80);\r\n }\r\n }\r\n\r\n _extractCONECT(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n\r\n const atoms = this._source._atoms;\r\n result.newTag('CONECT');\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const fixedBonds = atoms[i].bonds.filter((bond) => bond._fixed);\r\n if (fixedBonds.length !== 0) {\r\n result.writeBondsArray(fixedBonds.reverse(), atoms[i]);\r\n }\r\n }\r\n }\r\n\r\n _extractSHEET(result) {\r\n if (!this._source._sheets) {\r\n return;\r\n }\r\n\r\n result.newTag('SHEET');\r\n\r\n const sheets = this._source._sheets;\r\n for (let i = 0; i < sheets.length; i++) {\r\n if (sheets[i]._strands) {\r\n const strands = sheets[i]._strands;\r\n for (let j = 0; j < strands.length; j++) {\r\n result.newString();\r\n result.writeString(j + 1, 10, 8);\r\n result.writeString(sheets[i]._name, 14, 12);\r\n result.writeString(strands.length, 16, 15);\r\n result.writeString(strands[j].init._type._name, 18, 20);\r\n result.writeString(strands[j].init._chain._name, 22, 22);\r\n result.writeString(strands[j].init._sequence, 26, 23);\r\n result.writeString(strands[j].init._icode, 27, 27);\r\n result.writeString(strands[j].term._type._name, 29, 31);\r\n result.writeString(strands[j].init._chain._name, 33, 33);\r\n result.writeString(strands[j].term._sequence, 37, 34);\r\n result.writeString(strands[j].term._icode, 38, 38);\r\n result.writeString(strands[j].sense, 40, 39);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _extractHELIX(result) {\r\n if (!this._source._helices) {\r\n return;\r\n }\r\n\r\n result.newTag('HELIX');\r\n const helices = this._source._helices;\r\n for (let i = 0; i < helices.length; i++) {\r\n const helix = helices[i];\r\n const helixClass = _.invert(typeByPDBHelixClass);\r\n result.newString();\r\n result.writeString(helix.serial, 10, 8);\r\n result.writeString(helix.name, 14, 12);\r\n result.writeString(helix.init._type._name, 16, 18);\r\n result.writeString(helix.init._chain._name, 20, 20);\r\n result.writeString(helix.init._sequence, 25, 22);\r\n result.writeString(helix.init._icode, 26, 26);\r\n result.writeString(helix.term._type._name, 28, 30);\r\n result.writeString(helix.term._chain._name, 32, 32);\r\n result.writeString(helix.term._sequence, 37, 34);\r\n result.writeString(helix.term._icode, 38, 38);\r\n result.writeString(helixClass[helix.type], 40, 39);\r\n result.writeString(helix.comment, 41, 70);\r\n result.writeString(helix.length, 76, 72);\r\n }\r\n }\r\n\r\n _extractATOM(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n const atoms = this._source._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const tag = atoms[i].het ? 'HETATM' : 'ATOM';\r\n result.newString(tag);\r\n const startIndx = (atoms[i].element.name.length > 1 || atoms[i].name.length > 3) ? 13 : 14;\r\n result.writeString(atoms[i].serial, 11, 7);\r\n result.writeString(atoms[i].name, startIndx, 16);\r\n result.writeString(String.fromCharCode(atoms[i].location), 17, 17);\r\n result.writeString(atoms[i].residue._type._name, 20, 18);\r\n result.writeString(atoms[i].residue._chain._name, 22, 22);\r\n result.writeString(atoms[i].residue._sequence, 26, 23);\r\n result.writeString(atoms[i].residue._icode, 27, 27);\r\n result.writeString(atoms[i].position.x.toFixed(3), 38, 31);\r\n result.writeString(atoms[i].position.y.toFixed(3), 46, 39);\r\n result.writeString(atoms[i].position.z.toFixed(3), 54, 47);\r\n result.writeString(atoms[i].occupancy.toFixed(2), 60, 55);\r\n result.writeString(atoms[i].temperature.toFixed(2), 66, 61);\r\n result.writeString(atoms[i].element.name, 78, 77);\r\n if (atoms[i].charge) {\r\n result.writeString(atoms[i].charge, 79, 80);\r\n }\r\n }\r\n }\r\n\r\n _extractCOMPND(result) {\r\n if (!this._source._molecules) {\r\n return;\r\n }\r\n const molecules = this._source._molecules;\r\n result.newTag('COMPND', true);\r\n\r\n for (let i = 0; i < molecules.length; i++) {\r\n const chains = this._getMoleculeChains(molecules[i]);\r\n result.newString();\r\n result.writeString(`MOL_ID: ${molecules[i].index};`, 11, 80);\r\n result.newString();\r\n result.writeString(`MOLECULE: ${molecules[i].name};`, 11, 80);\r\n result.newString();\r\n result.writeString('CHAIN: ', 11, 18);\r\n const chainsString = `${chains.join(', ')};`;\r\n result.writeEntireString(chainsString, 81);\r\n }\r\n }\r\n\r\n _extractREMARK(result) {\r\n this._Remark290(result);\r\n this._Remark350(result);\r\n }\r\n\r\n _Remark290(result) {\r\n if (!this._source.symmetry) {\r\n return;\r\n }\r\n\r\n if (this._source.symmetry.length !== 0) {\r\n const matrices = this._source.symmetry;\r\n result.newTag('REMARK', 290);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark290);\r\n result.writeMatrices(matrices, 'SMTRY');\r\n result.newString();\r\n result.newString();\r\n result.writeString('REMARK: NULL', 11, 80);\r\n }\r\n }\r\n\r\n _Remark350(result) {\r\n if (!this._source.units) {\r\n return;\r\n }\r\n const { units } = this._source;\r\n let biomolIndx = 0;\r\n\r\n result.newTag('REMARK', 350);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark350);\r\n\r\n const assemblies = units.filter((unit) => unit instanceof Assembly);\r\n\r\n for (let i = 0; i < assemblies.length; i++) {\r\n result.newString();\r\n result.newString();\r\n biomolIndx++;\r\n result.writeString(`BIOMOLECULE: ${biomolIndx}`, 11, 80);\r\n const chains = assemblies[i].chains.join(', ');\r\n result.newString();\r\n result.writeString('APPLY THE FOLLOWING TO CHAINS: ');\r\n result.writeEntireString(chains, 69, { tag: 'AND CHAINS: ', begin: 31, end: 42 });\r\n\r\n const { matrices } = assemblies[i];\r\n result.writeMatrices(matrices, 'BIOMT');\r\n }\r\n }\r\n\r\n _getMoleculeChains(molecule) {\r\n function getChainName(residue) {\r\n return residue._chain._name;\r\n }\r\n const chainNames = molecule.residues.map(getChainName);\r\n return chainNames.filter((item, pos) => chainNames.indexOf(item) === pos);\r\n }\r\n}\r\n\r\nPDBExporter.formats = ['pdb'];\r\nPDBExporter.SourceClass = Complex;\r\n","import * as THREE from 'three';\r\n\r\nconst FBX_POS_SIZE = 3;\r\nconst FBX_NORM_SIZE = 3;\r\nconst FBX_COL_SIZE = 4;\r\n\r\nfunction copyFbxPoint3(src, srcIdx, dst, dstIdx) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n}\r\n\r\nfunction copyFbxPoint4(src, srcIdx, dst, dstIdx, value) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n dst[dstIdx + 3] = value;\r\n}\r\n\r\nconst vector4 = new THREE.Vector4();\r\nfunction copyTransformedPoint3(src, srcIdx, dst, dstIdx, opts) {\r\n vector4.set(src[srcIdx], src[srcIdx + 1], src[srcIdx + 2], opts.w);\r\n vector4.applyMatrix4(opts.matrix);\r\n dst[dstIdx] = vector4.x;\r\n dst[dstIdx + 1] = vector4.y;\r\n dst[dstIdx + 2] = vector4.z;\r\n}\r\n\r\nfunction setSubArray(src, dst, count, copyFunctor, functorOpts) {\r\n if ((dst.array.length - dst.start) / dst.stride < count\r\n || (src.array.length - src.start) / src.stride < count) {\r\n return; // we've got no space\r\n }\r\n if (src.stride === dst.stride) { // stride is the same\r\n dst.array.set(src.array, dst.start);\r\n } else {\r\n let idx = dst.start;\r\n let arridx = src.start;\r\n for (let i = 0; i < count; ++i, idx += dst.stride, arridx += src.stride) {\r\n copyFunctor(src.array, arridx, dst.array, idx, functorOpts);\r\n }\r\n }\r\n}\r\n\r\nexport default class FBXModel {\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.lastPos = 0;\r\n this.lastNorm = 0;\r\n this.lastCol = 0;\r\n this.lastIdx = 0;\r\n }\r\n\r\n init(vertsCount, indsCount) {\r\n this.positions = new Float32Array(vertsCount * FBX_POS_SIZE);\r\n this.normals = new Float32Array(vertsCount * FBX_NORM_SIZE);\r\n this.colors = new Float32Array(vertsCount * FBX_COL_SIZE);\r\n this.indices = new Int32Array(indsCount);\r\n }\r\n\r\n setPositions(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.positions,\r\n start: this.lastPos,\r\n stride: FBX_POS_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setTransformedPositions(array, start, count, stride, matrix) {\r\n let idx = this.lastPos;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 1 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_POS_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.positions, idx, opts);\r\n }\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setNormals(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.normals,\r\n start: this.lastNorm,\r\n stride: FBX_NORM_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setTransformedNormals(array, start, count, stride, matrix) {\r\n let idx = this.lastNorm;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 0 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_NORM_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.normals, idx, opts);\r\n }\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setColors(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.colors,\r\n start: this.lastCol,\r\n stride: FBX_COL_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint4, 1);\r\n this.lastCol += count * FBX_COL_SIZE;\r\n }\r\n\r\n setIndices(array, start, count) {\r\n this.indices.set(array, this.lastIdx);\r\n this.lastIdx += count;\r\n }\r\n\r\n setShiftedIndices(array, count, shift) {\r\n const shifted = array.map((x) => x + shift);\r\n this.setIndices(shifted, 0, count);\r\n }\r\n\r\n getVerticesNumber() {\r\n return this.lastPos / FBX_POS_SIZE;\r\n }\r\n\r\n addInstance(matrix, geo) {\r\n // add indices at first to take old number of vertices for shift\r\n const currentCount = this.getVerticesNumber();\r\n this.setShiftedIndices(geo.indices, geo.indices.length, currentCount);\r\n // simply write vertices at empty space\r\n const size = geo.itemSize;\r\n this.setTransformedPositions(geo.positions, 0, geo.vertsCount, size.position, matrix);\r\n this.setTransformedNormals(geo.normals, 0, geo.vertsCount, size.normal, matrix);\r\n this.setColors(geo.colors, 0, geo.vertsCount, size.color);\r\n }\r\n}\r\n","/** Base class for fbx geometry contains simply organized attributes: positions+normals+colors, indices. */\r\nexport default class FBXGeometry {\r\n /**\r\n * Create a base geo with necessary members.\r\n */\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.vertsCount = 0;\r\n this.itemSize = null;\r\n }\r\n\r\n /**\r\n * Initialize base geo storing items info from attributes.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n const { attributes } = geo;\r\n // save item size\r\n this.itemSize = {\r\n position: attributes.position.itemSize,\r\n normal: attributes.normal.itemSize,\r\n color: attributes.color.itemSize,\r\n };\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes and creates colors filled with defined value.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX1CGeometry extends FBXGeometry {\r\n /**\r\n * Initialize geo storing positions, normals, indices and create colors.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n super.init(geo, _info);\r\n const {\r\n attributes: {\r\n position,\r\n normal,\r\n },\r\n index,\r\n } = geo;\r\n // copy vertices attributes\r\n this.vertsCount = position.count;\r\n this.positions = position.array;\r\n this.normals = normal.array;\r\n // create color array\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n // indices\r\n this.indices = index.array;\r\n }\r\n\r\n /**\r\n * Set defined color for all items in color attribute\r\n * @param {Object} color - THREE.Color.\r\n */\r\n setColors(color) {\r\n let offset = 0;\r\n for (let i = 0, l = this.colors.length, cl = this.itemSize.color; i < l; i += cl) {\r\n this.colors[offset++] = color.r;\r\n this.colors[offset++] = color.g;\r\n this.colors[offset++] = color.b;\r\n }\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes from cylinder geometry and creates colors filled with two\r\n * defined values.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX2CCylinder extends FBXGeometry {\r\n constructor() {\r\n super();\r\n this._cutRawStart = 0;\r\n this._cutRawEnd = 0;\r\n this._facesPerSlice = 0;\r\n }\r\n\r\n /**\r\n * Initialize geo by creating new attributes, because we extend number of vertices to make cylinder two-colored.\r\n * Indices remain the same. We process open- end close-ended cylinders and consider cylinders od 2 segments\r\n * in height ONLY.\r\n * NOTE: cylinder consists of 2 height segments and stores parts in the order: tube, topCap, bottomCap\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n * @param {Object} info - information needed for geo extend\r\n */\r\n init(geo, info) {\r\n super.init(geo, info);\r\n const {\r\n attributes: {\r\n position,\r\n },\r\n index,\r\n } = geo;\r\n // extend vertices arrays\r\n this.vertsCount = position.count + info.addPerCylinder;\r\n this._facesPerSlice = info.addPerCylinder;\r\n this.positions = new Float32Array(this.vertsCount * position.itemSize);\r\n this.normals = new Float32Array(this.vertsCount * this.itemSize.normal);\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n this._extendVertices(geo, info);\r\n // number of indices stays the same\r\n this.indices = new Uint32Array(index.count);\r\n this._extendIndices(geo, info);\r\n }\r\n\r\n /** Extend vertex attributes to have one more slice to make sharp middle startColor-endColor line. */\r\n _extendVertices(geo, info) {\r\n const { position } = geo.attributes;\r\n const { normal } = geo.attributes;\r\n const geoParams = geo.getGeoParams();\r\n const cutRaw = 1; // we expect cylinders of 2 segments in height => so half segment = 1\r\n this._cutRawStart = cutRaw * geoParams.radialSegments;\r\n this._cutRawEnd = this._cutRawStart + info.addPerCylinder;\r\n { // write first half of cylinder\r\n let temp = position.array.slice(0, this._cutRawEnd * position.itemSize);\r\n this.positions.set(temp, 0);\r\n temp = normal.array.slice(0, this._cutRawEnd * normal.itemSize);\r\n this.normals.set(temp, 0);\r\n }\r\n { // write second part of cylinder\r\n let temp = position.array.slice(this._cutRawStart * position.itemSize, position.array.length);\r\n this.positions.set(temp, this._cutRawEnd * position.itemSize);\r\n temp = normal.array.slice(this._cutRawStart * normal.itemSize, normal.array.length);\r\n this.normals.set(temp, this._cutRawEnd * normal.itemSize);\r\n }\r\n }\r\n\r\n /** Shift values of second part (+caps) indices by newly added vertices count. Number of faces remains the same. */\r\n _extendIndices(geo, info) {\r\n const { index } = geo;\r\n const indicesPerQuad = 6; // quad = 2 triangles => 6 indices\r\n const startToShift = info.addPerCylinder * indicesPerQuad;\r\n const shift = info.addPerCylinder;\r\n let shifted = index.array.slice(startToShift, index.count);\r\n shifted = shifted.map((x) => x + shift); // shift only the endings\r\n this.indices.set(index.array, 0);\r\n this.indices.set(shifted, startToShift);\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {number} start - start color index\r\n * @param {number} end - start color index\r\n * @param {array} array - array of colors\r\n * @param {array} color - color value components\r\n */\r\n _setColorRange(start, end, array, color) {\r\n const colorSize = color.length;\r\n for (let i = start; i < end; i += colorSize) {\r\n array.set(color, i);\r\n }\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {Object} color1 - THREE.Color.\r\n * @param {Object} color2 - THREE.Color.\r\n */\r\n setColors(color1, color2) {\r\n const colorSize = this.itemSize.color;\r\n const part1End = this._cutRawEnd * colorSize;\r\n const part2End = part1End * 2;\r\n this._setColorRange(0, part1End, this.colors, color1.toArray());\r\n this._setColorRange(part1End, part2End, this.colors, color2.toArray());\r\n if (part2End < this.colors.length) { // cylinder has caps, lets paint them\r\n const capSize = (this._facesPerSlice + 1) * colorSize;\r\n const cap1End = part2End + capSize;\r\n this._setColorRange(part2End, cap1End, this.colors, color2.toArray());\r\n const cap2End = cap1End + capSize; // should be equal to this.colors.length;\r\n this._setColorRange(cap1End, cap2End, this.colors, color1.toArray());\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\n\r\nimport utils from '../../../utils';\r\nimport gfxutils from '../../../gfx/gfxutils';\r\nimport logger from '../../../utils/logger';\r\n\r\nimport FBXModel from './FBXModel';\r\nimport ThickLineMesh from '../../../gfx/meshes/ThickLineMesh';\r\nimport ZSpriteMesh from '../../../gfx/meshes/ZSpriteMesh';\r\nimport InstancedSpheresGeometry from '../../../gfx/geometries/InstancedSpheresGeometry';\r\nimport Instanced2CCylindersGeometry from '../../../gfx/geometries/Instanced2CCylindersGeometry';\r\nimport FBX1CGeometry from './FBX1CGeometry';\r\nimport FBX2CCylinder from './FBX2CCylinder';\r\n\r\nexport default class FBXInfoExtractor {\r\n constructor() {\r\n this._materials = [];\r\n this._models = [];\r\n }\r\n\r\n process(data) {\r\n this._extractModelsAndMaterials(data);\r\n const models = this._flattenModels();\r\n\r\n return {\r\n name: data.name,\r\n models,\r\n materials: this._materials,\r\n };\r\n }\r\n\r\n /**\r\n * Extract fbx object information from ComplexVisual\r\n * @param {object} data - complexVisual to get geometry info from\r\n */\r\n _extractModelsAndMaterials(data) {\r\n const layersOfInterest = new THREE.Layers();\r\n layersOfInterest.set(gfxutils.LAYERS.DEFAULT);\r\n layersOfInterest.enable(gfxutils.LAYERS.TRANSPARENT);\r\n data.traverse((object) => {\r\n if (object instanceof THREE.Mesh && object.layers.test(layersOfInterest) && this.checkExportAbility(object)) {\r\n if (object.geometry.type === 'InstancedBufferGeometry') {\r\n this._collectInstancedGeoInfo(object);\r\n } else {\r\n this._collectGeoInfo(object);\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Reworking indices buffer, see https://banexdevblog.wordpress.com/2014/06/23/a-quick-tutorial-about-the-fbx-ascii-format/\r\n * basically, every triangle in Miew has been represented hat way (e.g.) : 0,1,7, but we must (for FBX) rework that\r\n * into: 0,1,-8.\r\n * @param {array} indices - belongs to [0, maxVertIndex]\r\n */\r\n _reworkIndices(indices) {\r\n const faceSize = 3;\r\n for (let i = faceSize - 1; i < indices.length; i += faceSize) {\r\n indices[i] *= -1;\r\n indices[i]--;\r\n }\r\n }\r\n\r\n /**\r\n * Combine geometry from several models having the same material into one Model and finally prepare indices\r\n * @returns {array} models, combined by material id\r\n */\r\n _flattenModels() {\r\n let overallVertsCount = 0;\r\n function shift(x) {\r\n return x + overallVertsCount;\r\n }\r\n const combined = [];\r\n // flatten models geometry\r\n for (let i = 0, n = this._models.length; i < n; i++) {\r\n const models = this._models[i];\r\n let indices = [];\r\n let positions = [];\r\n let normals = [];\r\n let colors = [];\r\n // reorganize every attributes as array of arrays\r\n overallVertsCount = 0;\r\n for (let j = 0; j < models.length; j++) {\r\n const m = models[j];\r\n indices.push(m.indices.map(shift));\r\n overallVertsCount += m.getVerticesNumber();\r\n positions.push(m.positions);\r\n normals.push(m.normals);\r\n colors.push(m.colors);\r\n }\r\n // join all subarrays into one\r\n indices = utils.mergeTypedArraysUnsafe(indices);\r\n this._reworkIndices(indices);\r\n positions = utils.mergeTypedArraysUnsafe(positions);\r\n normals = utils.mergeTypedArraysUnsafe(normals);\r\n colors = utils.mergeTypedArraysUnsafe(colors);\r\n combined.push({\r\n indices,\r\n positions,\r\n normals,\r\n colors,\r\n verticesCount: overallVertsCount,\r\n });\r\n }\r\n return combined;\r\n }\r\n\r\n /**\r\n * Check ability to export the kind of mesh.\r\n * @param {object} mesh - given mesh to check\r\n * @returns {boolean} result of check\r\n */\r\n checkExportAbility(mesh) {\r\n // check mesh on not being empty\r\n if (mesh.geometry.attributes.position.count === 0) {\r\n return false;\r\n }\r\n // check type of mesh\r\n // if (mesh.geometry.isInstancedBufferGeometry && settings.now.zSprites) {\r\n if (mesh instanceof ZSpriteMesh) {\r\n logger.warn('Currently we cannot export \\'sprites\\' modes, like BS, WV, LC. Please turn of settings \\'zSprites\\' and try again');\r\n return false;\r\n }\r\n if (mesh instanceof ThickLineMesh) {\r\n logger.warn('Currently we cannot export Lines mode');\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n /**\r\n * Save geometry info from common mesh, like Surface or Cartoon\r\n */\r\n _collectGeoInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n normal,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const vertCount = position.count;\r\n model.init(vertCount, index.count);\r\n if (matrix.isIdentity()) {\r\n model.setPositions(position.array, 0, vertCount, position.itemSize);\r\n model.setNormals(normal.array, 0, vertCount, normal.itemSize);\r\n } else {\r\n model.setTransformedPositions(position.array, 0, vertCount, position.itemSize, matrix);\r\n model.setTransformedNormals(normal.array, 0, vertCount, normal.itemSize, matrix);\r\n }\r\n model.setColors(color.array, 0, vertCount, color.itemSize);\r\n model.setIndices(index.array, 0, index.count);\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Collect instanced spheres geometry and materials.\r\n * @param {object} mesh - mesh with instanced spheres info\r\n */\r\n _collectSpheresInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount, instCount * indsCount);\r\n const geo = new FBX1CGeometry();\r\n geo.init(mesh.geometry);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const sphereColor = new THREE.Color();\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n sphereColor.fromArray(color.array, colorIdx);\r\n geo.setColors(sphereColor);\r\n // add instance to the model\r\n this._getSphereInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Getting all instanced cylinders from given mesh.\r\n * Divide cylinder (add additional vertexes) for prettiness therefore algorithm is a bit complicated\r\n * @param {object} mesh - given mesh with instanced cylinders\r\n */\r\n _collectCylindersInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n color2,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const oneCCylinder = new FBX1CGeometry();\r\n oneCCylinder.init(mesh.geometry);\r\n const splittingInfo = this._gatherCylindersColoringInfo(mesh.geometry);\r\n let twoCCylinder = null;\r\n if (splittingInfo.needToSplit > 0) {\r\n twoCCylinder = new FBX2CCylinder();\r\n twoCCylinder.init(mesh.geometry, splittingInfo);\r\n }\r\n const additionalVertsCount = splittingInfo.addPerCylinder * splittingInfo.needToSplit;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount + additionalVertsCount, instCount * indsCount);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const colorStart = new THREE.Color();\r\n const colorEnd = new THREE.Color();\r\n let geo = {};\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n if (splittingInfo.is2Colored[instanceIndex]) {\r\n // .color2 contains starting color, and .color contains starting color (see uber.frag ATTR_COLOR2)\r\n colorStart.fromArray(color2.array, colorIdx);\r\n colorEnd.fromArray(color.array, colorIdx);\r\n if (twoCCylinder) {\r\n twoCCylinder.setColors(colorStart, colorEnd);\r\n geo = twoCCylinder;\r\n }\r\n } else {\r\n // has one color per cylinder\r\n colorStart.fromArray(color.array, colorIdx);\r\n oneCCylinder.setColors(colorStart);\r\n geo = oneCCylinder;\r\n }\r\n // add instance to the model\r\n this._getCylinderInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Adding model to pool of models or extend existing ones\r\n * @param {object} model - model to add\r\n * @param {object} material - material to add\r\n */\r\n _addToPool(model, material) {\r\n const materialIdx = this._checkExistingMaterial(material);\r\n if (materialIdx < 0) { // new model-material pair\r\n this._models.push([model]);\r\n this._materials.push(material);\r\n } else { // add model to existing model-material pair\r\n const models = this._models[materialIdx];\r\n models.push(model);\r\n }\r\n }\r\n\r\n /**\r\n * Checking if given material already was registered in materials pool (no need to create new one)\r\n * @param {object} material - given material\r\n * @returns {number} number of model-material pair\r\n */\r\n _checkExistingMaterial(material) {\r\n return _.findIndex(this._materials, (m) => _.isEqual(m, material));\r\n }\r\n\r\n _gatherCylindersColoringInfo(geo) {\r\n const instCount = geo.instanceCount;\r\n const color1 = geo.attributes.color.array;\r\n const color2 = geo.attributes.color2.array;\r\n const stride = geo.attributes.color.itemSize;\r\n const is2Colored = new Array(instCount);\r\n // analyze color instance attributes\r\n let needToSplit = 0;\r\n let colIdx = 0;\r\n for (let i = 0; i < instCount; i++, colIdx += stride) {\r\n const differs = (Math.abs(color1[colIdx] - color2[colIdx]) > 0.0000001) // compare ending colors\r\n || (Math.abs(color1[colIdx + 1] - color2[colIdx + 1]) > 0.0000001)\r\n || (Math.abs(color1[colIdx + 2] - color2[colIdx + 2]) > 0.0000001);\r\n is2Colored[i] = differs;\r\n needToSplit += differs; // count number of 2-colored cylinders\r\n }\r\n // calc number of vertices to add into 2-colored\r\n const geoParams = geo.getGeoParams();\r\n const addPerCylinder = geoParams.radialSegments;\r\n return { is2Colored, needToSplit, addPerCylinder };\r\n }\r\n\r\n /**\r\n * Collect instanced models and materials.\r\n * @param {object} mesh - given mesh with instanced something (spheres or cylinders)\r\n */\r\n _collectInstancedGeoInfo(mesh) {\r\n if (mesh.geometry instanceof InstancedSpheresGeometry) {\r\n this._collectSpheresInfo(mesh);\r\n } else if (mesh.geometry instanceof Instanced2CCylindersGeometry) {\r\n this._collectCylindersInfo(mesh);\r\n }\r\n }\r\n\r\n /**\r\n * Collect Material info from given mesh.\r\n * @param {object} mesh - given mesh with material info\r\n * @returns {object} material\r\n */\r\n _collectMaterialInfo(mesh) {\r\n const { uberOptions } = mesh.material;\r\n return ({\r\n diffuse: uberOptions.diffuse.toArray(),\r\n opacity: uberOptions.opacity,\r\n shininess: uberOptions.shininess,\r\n specular: uberOptions.specular.toArray(),\r\n });\r\n }\r\n\r\n _getCylinderInstanceMatrix(geo, instIdx, matrix) {\r\n const matVector1 = geo.attributes.matVector1.array;\r\n const matVector2 = geo.attributes.matVector2.array;\r\n const matVector3 = geo.attributes.matVector3.array;\r\n const idxOffset = instIdx * 4; // used 4 because offset arrays are stored in quads\r\n matrix.set(\r\n matVector1[idxOffset],\r\n matVector1[idxOffset + 1],\r\n matVector1[idxOffset + 2],\r\n matVector1[idxOffset + 3],\r\n matVector2[idxOffset],\r\n matVector2[idxOffset + 1],\r\n matVector2[idxOffset + 2],\r\n matVector2[idxOffset + 3],\r\n matVector3[idxOffset],\r\n matVector3[idxOffset + 1],\r\n matVector3[idxOffset + 2],\r\n matVector3[idxOffset + 3],\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n\r\n _getSphereInstanceMatrix(geo, instIdx, matrix) {\r\n const { offset } = geo.attributes;\r\n const idx = instIdx * offset.itemSize;\r\n const x = offset.array[idx];\r\n const y = offset.array[idx + 1];\r\n const z = offset.array[idx + 2];\r\n const scale = offset.array[idx + 3];\r\n matrix.set(\r\n scale,\r\n 0,\r\n 0,\r\n x,\r\n 0,\r\n scale,\r\n 0,\r\n y,\r\n 0,\r\n 0,\r\n scale,\r\n z,\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n}\r\n","// Forming default definitions block\r\nconst defaultDefinitions = `\r\nDefinitions: {\r\n Version: 100\r\n Count: 3\r\n ObjectType: \"Model\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Geometry\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Material\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Pose\" {\r\n Count: 1\r\n }\r\n ObjectType: \"GlobalSettings\" {\r\n Count: 1\r\n }\r\n} `;\r\n\r\n// Default model properties\r\nconst defaultProperties = `Properties60: {\r\n Property: \"QuaternionInterpolate\", \"bool\", \"\",0\r\n Property: \"Visibility\", \"Visibility\", \"A\",1\r\n Property: \"Lcl Translation\", \"Lcl Translation\", \"A\",0.000000000000000,0.000000000000000,-1789.238037109375000\r\n Property: \"Lcl Rotation\", \"Lcl Rotation\", \"A\",0.000009334667643,-0.000000000000000,0.000000000000000\r\n Property: \"Lcl Scaling\", \"Lcl Scaling\", \"A\",1.000000000000000,1.000000000000000,1.000000000000000\r\n Property: \"RotationOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationActive\", \"bool\", \"\",0\r\n Property: \"TranslationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMinX\", \"bool\", \"\",0\r\n Property: \"TranslationMinY\", \"bool\", \"\",0\r\n Property: \"TranslationMinZ\", \"bool\", \"\",0\r\n Property: \"TranslationMaxX\", \"bool\", \"\",0\r\n Property: \"TranslationMaxY\", \"bool\", \"\",0\r\n Property: \"TranslationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationOrder\", \"enum\", \"\",0\r\n Property: \"RotationSpaceForLimitOnly\", \"bool\", \"\",0\r\n Property: \"AxisLen\", \"double\", \"\",10\r\n Property: \"PreRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"PostRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationActive\", \"bool\", \"\",0\r\n Property: \"RotationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMinX\", \"bool\", \"\",0\r\n Property: \"RotationMinY\", \"bool\", \"\",0\r\n Property: \"RotationMinZ\", \"bool\", \"\",0\r\n Property: \"RotationMaxX\", \"bool\", \"\",0\r\n Property: \"RotationMaxY\", \"bool\", \"\",0\r\n Property: \"RotationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationStiffnessX\", \"double\", \"\",0\r\n Property: \"RotationStiffnessY\", \"double\", \"\",0\r\n Property: \"RotationStiffnessZ\", \"double\", \"\",0\r\n Property: \"MinDampRangeX\", \"double\", \"\",0\r\n Property: \"MinDampRangeY\", \"double\", \"\",0\r\n Property: \"MinDampRangeZ\", \"double\", \"\",0\r\n Property: \"MaxDampRangeX\", \"double\", \"\",0\r\n Property: \"MaxDampRangeY\", \"double\", \"\",0\r\n Property: \"MaxDampRangeZ\", \"double\", \"\",0\r\n Property: \"MinDampStrengthX\", \"double\", \"\",0\r\n Property: \"MinDampStrengthY\", \"double\", \"\",0\r\n Property: \"MinDampStrengthZ\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthX\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthY\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthZ\", \"double\", \"\",0\r\n Property: \"PreferedAngleX\", \"double\", \"\",0\r\n Property: \"PreferedAngleY\", \"double\", \"\",0\r\n Property: \"PreferedAngleZ\", \"double\", \"\",0\r\n Property: \"InheritType\", \"enum\", \"\",0\r\n Property: \"ScalingActive\", \"bool\", \"\",0\r\n Property: \"ScalingMin\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMax\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMinX\", \"bool\", \"\",0\r\n Property: \"ScalingMinY\", \"bool\", \"\",0\r\n Property: \"ScalingMinZ\", \"bool\", \"\",0\r\n Property: \"ScalingMaxX\", \"bool\", \"\",0\r\n Property: \"ScalingMaxY\", \"bool\", \"\",0\r\n Property: \"ScalingMaxZ\", \"bool\", \"\",0\r\n Property: \"GeometricTranslation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricScaling\", \"Vector3D\", \"\",1,1,1\r\n Property: \"LookAtProperty\", \"object\", \"\"\r\n Property: \"UpVectorProperty\", \"object\", \"\"\r\n Property: \"Show\", \"bool\", \"\",1\r\n Property: \"NegativePercentShapeSupport\", \"bool\", \"\",1\r\n Property: \"DefaultAttributeIndex\", \"int\", \"\",0\r\n Property: \"Color\", \"Color\", \"A+\",0,0,0\r\n Property: \"Size\", \"double\", \"\",100\r\n Property: \"Look\", \"enum\", \"\",1\r\n }`;\r\n\r\n// Default materials layer\r\nconst defaultMaterialLayer = `\r\n LayerElementMaterial: 0 {\r\n Version: 101\r\n Name: \"\"\r\n MappingInformationType: \"AllSame\"\r\n ReferenceInformationType: \"Direct\"\r\n Materials: 0\r\n }`;\r\n\r\n// Default layers block\r\nconst defaultLayerBlock = `\r\n Layer: 0 {\r\n Version: 100\r\n LayerElement: {\r\n Type: \"LayerElementNormal\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementColor\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementMaterial\"\r\n TypedIndex: 0\r\n }\r\n }`;\r\n\r\n/**\r\n * globalSettings info in output file.\r\n */\r\nconst globalSettings = `GlobalSettings: {\r\n Version: 1000\r\n Properties60: {\r\n Property: \"UpAxis\", \"int\", \"\",1\r\n Property: \"UpAxisSign\", \"int\", \"\",1\r\n Property: \"FrontAxis\", \"int\", \"\",2\r\n Property: \"FrontAxisSign\", \"int\", \"\",1\r\n Property: \"CoordAxis\", \"int\", \"\",0\r\n Property: \"CoordAxisSign\", \"int\", \"\",1\r\n Property: \"UnitScaleFactor\", \"double\", \"\",1\r\n }\r\n }`;\r\n\r\nexport default class FBXResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._info = null;\r\n }\r\n\r\n getResult(info) {\r\n this._info = info;\r\n this._resultArray.push(this._writeHeader());\r\n this._resultArray.push(this._writeDefinitions());\r\n this._resultArray.push(this._writeObjects(info.models, info.materials));\r\n this._resultArray.push(this._writeRelations());\r\n this._resultArray.push(this._writeConnections()); // connections between models and materials)\r\n this._info = null;\r\n return this._resultArray.join('');\r\n }\r\n\r\n /**\r\n * Add FBXHeader info to output file.\r\n * Some fields are really confusing, but it seems that all listed fields are very informative\r\n */\r\n _writeHeader() {\r\n const FBXHeaderVersion = 1003; // 1003 is some number which appears to present in many 6.1 ASCII files\r\n const FBXVersion = 6100; // Mandatory and only supported version\r\n const date = new Date();\r\n const timeStampVersion = 1000;\r\n const creator = `Miew FBX Exporter v${this._info.version}`; // Supposed to be an engine\r\n\r\n return `; FBX 6.1.0 project file\r\n; Created by ${creator} Copyright (c) 2015-2024 EPAM Systems, Inc.\r\n; For support please contact miew@epam.com\r\n; ----------------------------------------------------\r\n\r\nFBXHeaderExtension: {\r\n FBXHeaderVersion: ${FBXHeaderVersion}\r\n FBXVersion: ${FBXVersion}\r\n CreationTimeStamp: {\r\n Version: ${timeStampVersion}\r\n Year: ${date.getFullYear()}\r\n Month: ${date.getMonth() + 1}\r\n Day: ${date.getDate()}\r\n Hour: ${date.getHours()}\r\n Minute: ${date.getMinutes()}\r\n Second: ${date.getSeconds()}\r\n Millisecond: ${date.getMilliseconds()}\r\n }\r\n Creator: \"${creator}\"\r\n OtherFlags: {\r\n FlagPLE: 0\r\n }\r\n}\r\nCreationTime: \"${date}\"\r\nCreator: \"${creator}\"\r\n`;\r\n }\r\n\r\n /**\r\n * Add Definitions info to output file.\r\n * Not exactly sure if this section is template section (as it is in 7.4+) or it should every time be like this\r\n */\r\n _writeDefinitions() {\r\n return `\r\n; Object definitions\r\n;------------------------------------------------------------------\r\n\r\n${defaultDefinitions}\r\n`;\r\n }\r\n\r\n /**\r\n * Adding gathered information about Models to resulting string.\r\n * Reminder - there may be more then 1 model in scene, but we must place materials after ALL models.\r\n * @returns {string} string containing all models (vertices, indices, colors, normals etc)\r\n */\r\n _models() {\r\n const modelVersion = 232;\r\n let allModels = '';\r\n const { models } = this._info;\r\n for (let i = 0; i < models.length; ++i) {\r\n const model = models[i];\r\n const vertCount = model.verticesCount;\r\n allModels += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n Version: ${modelVersion}\r\n ${defaultProperties}\r\n ${this._verticesIndices(model.positions, model.indices)}\r\n ${this._normalLayer(model.normals)}\r\n ${this._colorLayer(model.colors, vertCount)}\r\n ${defaultMaterialLayer}\r\n ${defaultLayerBlock}\r\n }`;\r\n }\r\n return allModels;\r\n }\r\n\r\n /**\r\n * Add Material info to result\r\n */\r\n _materials() {\r\n const materialVersion = 102;\r\n let allMaterials = '';\r\n const { materials } = this._info;\r\n for (let i = 0; i < materials.length; ++i) {\r\n const material = materials[i];\r\n allMaterials += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n Version: ${materialVersion}\r\n ShadingModel: \"lambert\"\r\n MultiLayer: 0\r\n ${this._materialProperties(material)}\r\n }`;\r\n }\r\n return allMaterials;\r\n }\r\n\r\n /**\r\n * Add Objects info to output file.\r\n */\r\n _writeObjects() {\r\n return `\r\n; Object properties\r\n;------------------------------------------------------------------\r\n\r\nObjects: {\r\n ${this._models()}\r\n ${this._materials()}\r\n ${globalSettings}\r\n}\r\n`;\r\n }\r\n\r\n /**\r\n * Add Relations info to output file.\r\n */\r\n _writeRelations() {\r\n let modelsList = '';\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n }`;\r\n }\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n }`;\r\n }\r\n\r\n return `\r\n; Object relations\r\n;------------------------------------------------------------------\r\n\r\nRelations: {\r\n ${modelsList}\r\n Model: \"Model::Producer Perspective\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Top\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Bottom\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Front\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Back\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Right\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Left\", \"Camera\" {\r\n }\r\n Model: \"Model::Camera Switcher\", \"CameraSwitcher\" {\r\n }\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Add Connections info to output file.\r\n */\r\n _writeConnections() {\r\n let modelsList = '';\r\n const { name } = this._info;\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Connect: \"OO\", \"Model::${name}_${i}\", \"Model::Scene\"`;\r\n }\r\n\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Connect: \"OO\", \"Material::${name}_${i}_default\", \"Model::${name}_${i}\"`;\r\n }\r\n\r\n return `\r\n; Object connections\r\n;------------------------------------------------------------------\r\n\r\nConnections: {\r\n ${modelsList}\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Write float array to string with limited precision\r\n * @param {Float32Array} array - array to be fixed\r\n * @returns {String} String with fixed floats\r\n */\r\n _floatArrayToString(array) {\r\n const str = [];\r\n for (let i = 0; i < array.length; ++i) {\r\n str[i] = array[i].toFixed(6);\r\n }\r\n return str.join(',');\r\n }\r\n\r\n /**\r\n * Adding color layer to resulting file\r\n * @param {Float32Array} colorArray attribute\r\n * @param {number} vertCount - number of vertices in the model\r\n * @returns {string} color layer info\r\n */\r\n _colorLayer(colorArray, vertCount) {\r\n const layerElementColorNumber = 0;\r\n const layerElementColorVersion = 101;\r\n const layerElementColorName = '';\r\n const colorsStr = this._floatArrayToString(colorArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n // As said [..Array(...)] - fastest and easiest way to produce [0, 1, .....] array\r\n const colorIndices = [...Array(vertCount).keys()];\r\n return `\r\n LayerElementColor: ${layerElementColorNumber} {\r\n Version: ${layerElementColorVersion}\r\n Name: \"${layerElementColorName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Colors: ${colorsStr}\r\n ColorIndex: ${colorIndices}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding normal layer to resulting file\r\n * @param {Float32Array} normalArray attribute\r\n * @returns {string} normal layer info\r\n */\r\n _normalLayer(normalArray) {\r\n const layerElementNormalNumber = 0;\r\n const layerElementNormalVersion = 101;\r\n const layerElementNormalName = '';\r\n const normalsStr = this._floatArrayToString(normalArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n return `\r\n LayerElementNormal: ${layerElementNormalNumber} {\r\n Version: ${layerElementNormalVersion}\r\n Name: \"${layerElementNormalName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Normals: ${normalsStr}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding vertices and indices to resulting string\r\n * @return {string} resulting string in FBX notation\r\n */\r\n _verticesIndices(positions, indices) {\r\n const multiLayer = 0;\r\n const multiTake = 1;\r\n const shading = 'Y';\r\n const culling = 'CullingOff';\r\n const geometryVersion = 124;\r\n const vertStr = this._floatArrayToString(positions);\r\n /* About _correctArrayNotation: Float32Arrays will contains only Float32 numbers, which implies that it will be floating points with 17 numbers after point.\r\n * We cannot (and it's logically incorrect) save all this information, so we convert this Float32Array into Array-like object with numbers with only 6 numbers after point\r\n * Reminder - this is big memory loss (as we must save at one moment two arrays with similar information) */\r\n return `MultiLayer: ${multiLayer}\r\n MultiTake: ${multiTake}\r\n Shading: ${shading}\r\n Culling: \"${culling}\"\r\n Vertices: ${vertStr}\r\n PolygonVertexIndex: ${indices}\r\n GeometryVersion: ${geometryVersion}`;\r\n }\r\n\r\n /**\r\n * Forming material properties block.\r\n * @param {Object} material - given material of model\r\n * @returns {String} material properties string\r\n */\r\n _materialProperties(material) {\r\n return `Properties60: {\r\n Property: \"ShadingModel\", \"KString\", \"\", \"Lambert\"\r\n Property: \"MultiLayer\", \"bool\", \"\",0\r\n Property: \"EmissiveColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"EmissiveFactor\", \"double\", \"\",0.0000\r\n Property: \"AmbientColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"AmbientFactor\", \"double\", \"\",0.0000\r\n Property: \"DiffuseColor\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"DiffuseFactor\", \"double\", \"\",1.0000\r\n Property: \"Bump\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TransparentColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"TransparencyFactor\", \"double\", \"\",0.0000\r\n Property: \"SpecularColor\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"SpecularFactor\", \"double\", \"\",1.0000\r\n Property: \"ShininessExponent\", \"double\", \"\",${material.shininess}\r\n Property: \"ReflectionColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"ReflectionFactor\", \"double\", \"\",1\r\n Property: \"Ambient\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"Diffuse\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"Specular\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"Shininess\", \"double\", \"\",${material.shininess}\r\n Property: \"Opacity\", \"double\", \"\",${material.opacity}\r\n Property: \"Reflectivity\", \"double\", \"\",0\r\n }`;\r\n }\r\n}\r\n","import Exporter from './Exporter';\r\nimport FBXInfoExtractor from './fbx/FBXInfoExtractor';\r\nimport FBXResult from './fbx/FBXResult';\r\nimport ComplexVisual from '../../ComplexVisual';\r\n\r\nexport default class FBXExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n // Data\r\n this._data = source;\r\n this._version = options.miewVersion || '0.0-UNSPECIFIED';\r\n this._extractor = new FBXInfoExtractor();\r\n }\r\n\r\n /**\r\n * Entry point to exporter.\r\n */\r\n exportSync() {\r\n // Creating mandatory blocks\r\n const result = new FBXResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n const info = this._extractor.process(this._data);\r\n info.version = this._version;\r\n this._result = result.getResult(info);\r\n return this._result;\r\n }\r\n}\r\n\r\nFBXExporter.formats = ['fbx'];\r\nFBXExporter.SourceClass = ComplexVisual;\r\n","import ExporterList from './exporters/ExporterList';\r\n\r\nimport PDBExporter from './exporters/PDBExporter';\r\nimport FBXExporter from './exporters/FBXExporter';\r\n\r\nexport default new ExporterList([\r\n PDBExporter,\r\n FBXExporter,\r\n]);\r\n","import loaders from './loaders';\r\nimport parsers from './parsers';\r\nimport exporters from './exporters';\r\n\r\nexport default {\r\n loaders,\r\n parsers,\r\n exporters,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from './CSS2DObject';\r\n\r\nconst tempColor = new THREE.Color();\r\n\r\nclass CSS2DRenderer {\r\n constructor() {\r\n this._width = 0;\r\n this._height = 0;\r\n this._widthHalf = 0;\r\n this._heightHalf = 0;\r\n\r\n this._vector = new THREE.Vector3();\r\n this._viewMatrix = new THREE.Matrix4();\r\n this._projectionMatrix = new THREE.Matrix4();\r\n\r\n this._domElement = document.createElement('div');\r\n this._domElement.style.overflow = 'hidden';\r\n this._domElement.style.position = 'absolute';\r\n this._domElement.style.top = '0';\r\n this._domElement.style.zIndex = '0'; // start a new Stacking Context to enclose all z-ordered children\r\n this._domElement.style.pointerEvents = 'none';\r\n }\r\n\r\n getElement() {\r\n return this._domElement;\r\n }\r\n\r\n reset() {\r\n const myNode = this.getElement();\r\n while (myNode.firstChild) {\r\n myNode.removeChild(myNode.firstChild);\r\n }\r\n }\r\n\r\n setSize(width, height) {\r\n this._width = width;\r\n this._height = height;\r\n\r\n this._widthHalf = this._width / 2;\r\n this._heightHalf = this._height / 2;\r\n\r\n this._domElement.style.width = `${width}px`;\r\n this._domElement.style.height = `${height}px`;\r\n }\r\n\r\n _renderObject(object, camera, scene) {\r\n function lerpColorAsHex(a, b, t) {\r\n tempColor.setHex(a);\r\n tempColor.lerp(b, t);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n function colorAsHex(a) {\r\n tempColor.setHex(a);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n if (object instanceof CSS2DObject) {\r\n this._vector.setFromMatrixPosition(object.matrixWorld);\r\n\r\n if (object.userData !== undefined && object.userData.offset !== undefined) {\r\n const localOffset = new THREE.Vector3(object.userData.offset.x, object.userData.offset.y, 0);\r\n this._vector.add(localOffset.multiplyScalar(object.matrixWorld.getMaxScaleOnAxis()));\r\n }\r\n\r\n this._vector.applyMatrix4(this._viewMatrix);\r\n\r\n const visibility = this._vector.z > -camera.near ? 'hidden' : 'visible';\r\n const zIndex = 10000 * (camera.far - (-this._vector.z)) / (camera.far - camera.near);\r\n\r\n const element = object.getElement();\r\n if (typeof scene.fog === 'undefined') {\r\n element.style.color = colorAsHex(object.userData.color);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = colorAsHex(object.userData.background);\r\n }\r\n } else {\r\n const fogFactor = THREE.MathUtils.smoothstep(-this._vector.z, scene.fog.near, scene.fog.far);\r\n element.style.color = lerpColorAsHex(object.userData.color, scene.fog.color, fogFactor);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = lerpColorAsHex(object.userData.background, scene.fog.color, fogFactor);\r\n }\r\n }\r\n\r\n this._vector.applyMatrix4(this._projectionMatrix);\r\n\r\n const style = `${object.userData !== {} ? object.userData.translation : 'translate(-50%, -50%) '\r\n }translate(${this._vector.x * this._widthHalf + this._widthHalf}px,${\r\n -this._vector.y * this._heightHalf + this._heightHalf}px)`;\r\n element.style.visibility = visibility;\r\n element.style.WebkitTransform = style;\r\n element.style.MozTransform = style;\r\n element.style.oTransform = style;\r\n element.style.transform = style;\r\n element.style.zIndex = Number(zIndex).toFixed(0);\r\n\r\n if (element.parentNode !== this._domElement) {\r\n this._domElement.appendChild(element);\r\n }\r\n }\r\n\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n this._renderObject(object.children[i], camera, scene);\r\n }\r\n }\r\n\r\n render(scene, camera) {\r\n scene.updateMatrixWorld();\r\n\r\n if (camera.parent === null) {\r\n camera.updateMatrixWorld();\r\n }\r\n\r\n camera.matrixWorldInverse.copy(camera.matrixWorld).invert();\r\n\r\n this._viewMatrix.copy(camera.matrixWorldInverse);\r\n this._projectionMatrix.copy(camera.projectionMatrix);\r\n\r\n this._renderObject(scene, camera, scene);\r\n }\r\n}\r\nexport default CSS2DRenderer;\r\n","export default function getTopWindow() {\r\n // intercept the exception if we have cross-origin iframe\r\n try {\r\n if (window.top.location.href !== undefined) {\r\n return window.top;\r\n }\r\n } catch (e) {\r\n // provide fallback\r\n }\r\n return window;\r\n}\r\n","import * as THREE from 'three';\r\nimport Timer from '../Timer';\r\nimport settings from '../settings';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\nimport getTopWindow from '../utils/getTopWindow';\r\n\r\nconst VK_LEFT = 37;\r\nconst VK_UP = 38;\r\nconst VK_RIGHT = 39;\r\nconst VK_DOWN = 40;\r\n\r\nconst STATE = {\r\n NONE: -1, ROTATE: 0, TRANSLATE: 1, SCALE: 2, TRANSLATE_PIVOT: 3,\r\n};\r\n\r\n// pausing for this amount of time before releasing mouse button prevents inertial rotation (seconds)\r\nconst FULL_STOP_THRESHOLD = 0.1;\r\n\r\nconst quaternion = new THREE.Quaternion();\r\nconst matrix4 = new THREE.Matrix4();\r\n\r\n// pivot -- local offset of the rotation pivot point\r\nfunction ObjectHandler(objects, camera, pivot, options) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n this.camera = camera;\r\n this.pivot = pivot;\r\n this.axis = new THREE.Vector3(0, 0, 1);\r\n this.options = options;\r\n\r\n this.lastRotation = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n}\r\n\r\nObjectHandler.prototype._rotate = (function () {\r\n const p = new THREE.Vector3();\r\n const q = new THREE.Quaternion();\r\n const s = new THREE.Vector3();\r\n\r\n const m = new THREE.Matrix4();\r\n\r\n return function (quat) {\r\n const zeroPivot = (this.pivot.x === 0.0 && this.pivot.y === 0.0 && this.pivot.z === 0.0);\r\n\r\n m.copy(this.object.matrix);\r\n\r\n if (zeroPivot) {\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n } else {\r\n m.multiply(matrix4.makeTranslation(this.pivot.x, this.pivot.y, this.pivot.z));\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n m.multiply(matrix4.makeTranslation(-this.pivot.x, -this.pivot.y, -this.pivot.z));\r\n }\r\n\r\n m.decompose(p, q, s);\r\n\r\n // update objects\r\n if (!zeroPivot) {\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].position.copy(p);\r\n }\r\n }\r\n\r\n for (let j = 0; j < this.objects.length; ++j) {\r\n this.objects[j].quaternion.copy(q);\r\n this.objects[j].updateMatrix();\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.setObjects = function (objects) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n};\r\n\r\nObjectHandler.prototype.rotate = (function () {\r\n const rot = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n\r\n return function (quat, mousePrevPos, mouseCurPos, aboutAxis) {\r\n this.mouse2rotation(rot, mousePrevPos, mouseCurPos, aboutAxis);\r\n quat.setFromAxisAngle(rot.axis, rot.angle);\r\n\r\n if (rot.angle) {\r\n this._rotate(quat);\r\n }\r\n\r\n this.lastRotation = rot;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.translate = (function () {\r\n const dir = new THREE.Vector3();\r\n const pivot = new THREE.Vector3();\r\n\r\n return function (delta) {\r\n // reverse-project viewport movement to view coords (compensate for screen aspect ratio)\r\n dir.set(\r\n delta.x / this.camera.projectionMatrix.elements[0],\r\n delta.y / this.camera.projectionMatrix.elements[5],\r\n 0,\r\n );\r\n let dist = dir.length();\r\n dir.normalize();\r\n\r\n // transform movement direction to object local coords\r\n dir.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // visible translate distance shouldn't depend on camera-to-object distance\r\n pivot.copy(this.pivot);\r\n this.object.localToWorld(pivot);\r\n dist *= Math.abs(pivot.z - this.camera.position.z);\r\n\r\n // visible translate distance shouldn't depend on object scale\r\n dist /= this.object.matrixWorld.getMaxScaleOnAxis();\r\n\r\n // all objects are translated similar to principal object\r\n // (we assume they all have identical pivot and scale)\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].translateOnAxis(dir, dist);\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.update = (function () {\r\n const axis = new THREE.Vector3();\r\n\r\n return function (timeSinceLastUpdate, timeSinceMove) {\r\n if (settings.now.autoRotation !== 0.0) {\r\n // auto-rotation with constant speed\r\n\r\n // if rotation axis is fixed or hasn't been defined yet\r\n if (settings.now.autoRotationAxisFixed || this.lastRotation.axis.length() === 0.0) {\r\n // use Y-axis (transformed to local object coords)\r\n axis.set(0, 1, 0).transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n } else {\r\n // use axis defined by last user rotation\r\n axis.copy(this.lastRotation.axis);\r\n }\r\n\r\n this._rotate(quaternion.setFromAxisAngle(axis, settings.now.autoRotation * timeSinceLastUpdate));\r\n return true;\r\n }\r\n\r\n if (this.options.intertia && this.lastRotation.angle) {\r\n // inertial object rotation\r\n const angle = this.lastRotation.angle * ((1.0 - this.options.dynamicDampingFactor) ** (40.0 * timeSinceMove));\r\n\r\n if (Math.abs(angle) <= this.options.intertiaThreshold) {\r\n this.lastRotation.angle = 0.0;\r\n } else {\r\n this._rotate(quaternion.setFromAxisAngle(this.lastRotation.axis, angle));\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.stop = function () {\r\n this.lastRotation.angle = 0.0;\r\n};\r\n\r\n// calculate (axis, angle) pair from mouse/touch movement\r\nObjectHandler.prototype.mouse2rotation = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n const eye = new THREE.Vector3();\r\n const eyeDirection = new THREE.Vector3();\r\n\r\n const cameraUpDirection = new THREE.Vector3();\r\n const cameraSidewaysDirection = new THREE.Vector3();\r\n\r\n const moveDirection = new THREE.Vector3();\r\n\r\n const mouseDelta = new THREE.Vector2();\r\n\r\n return function (rot, mousePrev, mouseCur, aboutAxis) {\r\n if (aboutAxis) {\r\n rot.axis.copy(this.axis);\r\n rot.angle = this.options.axisRotateFactor * (mouseCur.y - mousePrev.y);\r\n\r\n /* cool method that allows rotation around Z axis to be \"tied\" to mouse cursor\r\n\r\n res.axis.copy(this.axis);\r\n\r\n var pivot = this.pivot.clone();\r\n this.object.localToWorld(pivot);\r\n pivot.project(this.camera);\r\n\r\n var v1 = new THREE.Vector3(mousePrev.x, mousePrev.y, this.camera.position.z);\r\n v1.sub(pivot);\r\n var v2 = new THREE.Vector3(mouseCur.x, mouseCur.y, this.camera.position.z);\r\n v2.sub(pivot);\r\n\r\n v1.sub(res.axis.clone().multiplyScalar(v1.dot(res.axis)));\r\n v2.sub(res.axis.clone().multiplyScalar(v2.dot(res.axis)));\r\n\r\n var abs = v1.length() * v2.length();\r\n if (abs > 0) {\r\n res.angle = res.axis.dot(v1.cross(v2)) / abs;\r\n }\r\n */\r\n } else {\r\n mouseDelta.subVectors(mouseCur, mousePrev);\r\n const angle = mouseDelta.length();\r\n if (angle === 0.0) {\r\n return;\r\n }\r\n\r\n center.copy(this.pivot);\r\n this.object.localToWorld(center);\r\n eye.subVectors(this.camera.position, center);\r\n eyeDirection.copy(eye).normalize();\r\n\r\n cameraUpDirection.copy(this.camera.up).normalize();\r\n cameraSidewaysDirection.crossVectors(cameraUpDirection, eyeDirection).normalize();\r\n\r\n cameraUpDirection.setLength(mouseDelta.y);\r\n cameraSidewaysDirection.setLength(mouseDelta.x);\r\n\r\n moveDirection.copy(cameraUpDirection.add(cameraSidewaysDirection));\r\n\r\n rot.axis.crossVectors(moveDirection, eye);\r\n\r\n rot.angle = -angle * this.options.rotateFactor;\r\n }\r\n\r\n rot.axis.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // make sure angle is always positive (thus 'axis' defines both axis and direction of rotation)\r\n if (rot.angle < 0.0) {\r\n rot.axis.negate();\r\n rot.angle = -rot.angle;\r\n }\r\n };\r\n}());\r\n\r\nfunction ObjectControls(object, objectPivot, camera, domElement, getAltObj) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.object = object;\r\n this.objectPivot = objectPivot;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.getAltObj = getAltObj;\r\n\r\n // API\r\n\r\n this.enabled = true;\r\n this.hotkeysEnabled = true;\r\n\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n\r\n this.options = {\r\n rotateFactor: Math.PI, // full screen slide (along short side) would roughly mean 180 deg. rotation\r\n axisRotateFactor: 4 * Math.PI, // full screen slide (along short side) would roughly mean 720 deg. rotation\r\n intertia: true,\r\n dynamicDampingFactor: 0.1,\r\n intertiaThreshold: 1e-3,\r\n };\r\n\r\n // internals\r\n\r\n this._state = STATE.NONE;\r\n\r\n this._mousePrevPos = new THREE.Vector2();\r\n this._mouseCurPos = new THREE.Vector2();\r\n\r\n this._mainObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._altObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._affectedObj = this._mainObj;\r\n this._isAltObjFreeRotationAllowed = true;\r\n this._isTranslationAllowed = true;\r\n this._isKeysTranslatingObj = false;\r\n\r\n this._pressedKeys = [];\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n this._lastUpdateTime = this._clock.getElapsedTime();\r\n\r\n // events\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousewheel',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'DOMMouseScroll',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseout',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchmove',\r\n handler(e) {\r\n self.touchmove(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keydown',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keyup',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'blur',\r\n handler() {\r\n self.resetKeys();\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'contextmenu',\r\n handler(e) {\r\n self.contextmenu(e);\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n\r\n this.resetKeys();\r\n\r\n // force an update at start\r\n this.update();\r\n}\r\n\r\n// methods\r\n\r\nObjectControls.prototype = Object.create(EventDispatcher.prototype);\r\nObjectControls.prototype.constructor = ObjectControls;\r\n\r\nObjectControls.prototype.resetKeys = function () {\r\n this._pressedKeys[VK_LEFT] = false;\r\n this._pressedKeys[VK_UP] = false;\r\n this._pressedKeys[VK_RIGHT] = false;\r\n this._pressedKeys[VK_DOWN] = false;\r\n};\r\n\r\nObjectControls.prototype.contextmenu = function (e) {\r\n e.stopPropagation();\r\n e.preventDefault();\r\n};\r\n\r\nObjectControls.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nObjectControls.prototype.enable = function (enable) {\r\n this.enabled = enable;\r\n};\r\n\r\nObjectControls.prototype.enableHotkeys = function (enable) {\r\n this.hotkeysEnabled = enable;\r\n};\r\n\r\nObjectControls.prototype.allowTranslation = function (allow) {\r\n this._isTranslationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.allowAltObjFreeRotation = function (allow) {\r\n this._isAltObjFreeRotationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.keysTranslateObj = function (on) {\r\n this._isKeysTranslatingObj = on;\r\n};\r\n\r\nObjectControls.prototype.isEditingAltObj = function () {\r\n return ((this._state === STATE.ROTATE) || (this._state === STATE.TRANSLATE))\r\n && (this._affectedObj === this._altObj);\r\n};\r\n\r\n// convert page coords of mouse/touch to uniform coords with smaller side being [-0.5, 0.5]\r\n// (uniform coords keep direct proportion with screen distance travelled by mouse regardless of screen aspect ratio)\r\nObjectControls.prototype.convertMouseToOnCircle = function (coords, pageX, pageY) {\r\n const screenSize = Math.min(this.screen.width, this.screen.height);\r\n\r\n if (screenSize === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n ((pageX - this.screen.width * 0.5 - this.screen.left) / screenSize),\r\n ((0.5 * this.screen.height + this.screen.top - pageY) / screenSize),\r\n );\r\n};\r\n\r\n// convert page coords of mouse/touch to viewport coords with both sides being [-1, 1]\r\n// (those are non-uniform coords affected by screen aspect ratio)\r\nObjectControls.prototype.convertMouseToViewport = function (coords, pageX, pageY) {\r\n if (this.screen.width === 0 || this.screen.height === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n (2.0 * (pageX - this.screen.width * 0.5 - this.screen.left) / this.screen.width),\r\n (2.0 * (0.5 * this.screen.height + this.screen.top - pageY) / this.screen.height),\r\n );\r\n};\r\n\r\nObjectControls.prototype.stop = function () {\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n};\r\n\r\n// rotate object based on latest mouse/touch movement\r\nObjectControls.prototype.rotateByMouse = (function () {\r\n const quat = new THREE.Quaternion();\r\n\r\n return function (aboutZAxis) {\r\n this._affectedObj.rotate(quat, this._mousePrevPos, this._mouseCurPos, aboutZAxis);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n };\r\n}());\r\n\r\n// rotate object by specified quaternion\r\nObjectControls.prototype.rotate = function (quat) {\r\n this.object.quaternion.multiply(quat);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n};\r\n\r\n// get object's orientation\r\nObjectControls.prototype.getOrientation = function () {\r\n return this.object.quaternion;\r\n};\r\n\r\n// set object's orientation\r\nObjectControls.prototype.setOrientation = function (quat) {\r\n this.object.quaternion.copy(quat);\r\n};\r\n\r\n// translate object based on latest mouse/touch movement\r\nObjectControls.prototype.translate = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this._affectedObj.translate(delta);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n };\r\n}());\r\n\r\n// get object scale\r\nObjectControls.prototype.getScale = function () {\r\n return this.object.scale.x;\r\n};\r\n\r\n// set uniform object scale\r\nObjectControls.prototype.setScale = function (scale) {\r\n this.object.scale.set(scale, scale, scale);\r\n};\r\n\r\n// scale object by factor (factor should be greater than zero)\r\nObjectControls.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n return;\r\n }\r\n this.setScale(this.object.scale.x * factor);\r\n this.dispatchEvent({ type: 'change', action: 'zoom', factor });\r\n};\r\n\r\nObjectControls.prototype.update = (function () {\r\n const shift = new THREE.Vector2();\r\n\r\n return function () {\r\n const curTime = this._clock.getElapsedTime();\r\n const timeSinceLastUpdate = curTime - this._lastUpdateTime;\r\n\r\n // update object handler\r\n if (this._state === STATE.NONE) {\r\n const timeSinceMove = curTime - this._lastMouseMoveTime;\r\n if (this._mainObj.update(timeSinceLastUpdate, timeSinceMove)\r\n || this._altObj.update(timeSinceLastUpdate, timeSinceMove)) {\r\n this.dispatchEvent({ type: 'change', action: 'auto' });\r\n }\r\n }\r\n\r\n // apply arrow keys\r\n if (this._isKeysTranslatingObj) {\r\n const speedX = Number(this._pressedKeys[VK_RIGHT]) - Number(this._pressedKeys[VK_LEFT]);\r\n const speedY = Number(this._pressedKeys[VK_UP]) - Number(this._pressedKeys[VK_DOWN]);\r\n if (speedX !== 0.0 || speedY !== 0.0) {\r\n const delta = timeSinceLastUpdate;\r\n\r\n // update object translation\r\n const altObj = this.getAltObj();\r\n if (altObj.objects.length > 0) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n\r\n shift.set(delta * speedX, delta * speedY);\r\n this._altObj.translate(shift);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n }\r\n }\r\n }\r\n\r\n this._lastUpdateTime = curTime;\r\n };\r\n}());\r\n\r\nObjectControls.prototype.reset = function () {\r\n this._state = STATE.NONE;\r\n\r\n this.object.quaternion.copy(quaternion.set(0, 0, 0, 1));\r\n};\r\n\r\n// listeners\r\n\r\nObjectControls.prototype.mousedown = function (event) {\r\n if (this.enabled === false || this._state !== STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (this._state === STATE.NONE) {\r\n if (event.button === 0) {\r\n this._affectedObj.stop(); // can edit only one object at a time\r\n\r\n let workWithAltObj = false;\r\n\r\n if (event.altKey) {\r\n const altObj = this.getAltObj();\r\n workWithAltObj = (altObj.objects.length > 0);\r\n if (workWithAltObj) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n this._affectedObj = workWithAltObj ? this._altObj : this._mainObj;\r\n\r\n this._state = (workWithAltObj && event.ctrlKey && this._isTranslationAllowed) ? STATE.TRANSLATE : STATE.ROTATE;\r\n } else if (event.button === 2) {\r\n this._state = STATE.TRANSLATE_PIVOT;\r\n }\r\n }\r\n\r\n if (this._state === STATE.ROTATE) {\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n\r\n if (this._state === STATE.TRANSLATE || this._state === STATE.TRANSLATE_PIVOT) {\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousemove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this.rotateByMouse((event.altKey && !this._isAltObjFreeRotationAllowed) || event.shiftKey);\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.TRANSLATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translate();\r\n break;\r\n\r\n case STATE.TRANSLATE_PIVOT:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translatePivotByMouse();\r\n break;\r\n\r\n default: break;\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousewheel = function (event) {\r\n if (this.enabled === false || !settings.now.zooming || this._state !== STATE.NONE || event.shiftKey) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n\r\n let delta = 0;\r\n\r\n if (event.wheelDelta) {\r\n // WebKit / Opera / Explorer 9\r\n delta = event.wheelDelta / 40;\r\n } else if (event.detail) {\r\n // Firefox\r\n delta = -event.detail / 3;\r\n }\r\n\r\n let factor = 1.0 + delta * 0.05;\r\n factor = Math.max(factor, 0.01);\r\n this.scale(factor);\r\n};\r\n\r\nObjectControls.prototype.mouseup = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n this._state = STATE.NONE;\r\n\r\n if (this._clock.getElapsedTime() - this._lastMouseMoveTime > FULL_STOP_THRESHOLD) {\r\n this._affectedObj.stop();\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchstartend = function (event) {\r\n if (this.enabled === false) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (event.touches.length) {\r\n case 1:\r\n this._state = STATE.ROTATE;\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n break;\r\n\r\n case 2: {\r\n // prevent inertial rotation\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n\r\n this._state = STATE.SCALE;\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = this._touchDistanceStart = Math.sqrt(dx * dx + dy * dy);\r\n this._scaleStart = this.object.scale.x;\r\n break;\r\n }\r\n\r\n default:\r\n this._state = STATE.NONE;\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchmove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this.rotateByMouse(false);\r\n\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.SCALE:\r\n if (settings.now.zooming) {\r\n // update scale\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = Math.sqrt(dx * dx + dy * dy);\r\n const newScale = this._scaleStart * this._touchDistanceCur / this._touchDistanceStart;\r\n const factor = newScale / this.object.scale.x;\r\n this.scale(factor);\r\n }\r\n break;\r\n\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.keydownup = function (event) {\r\n if (this.enabled === false || this.hotkeysEnabled === false) {\r\n return;\r\n }\r\n\r\n switch (event.keyCode) {\r\n case VK_LEFT:\r\n case VK_UP:\r\n case VK_RIGHT:\r\n case VK_DOWN:\r\n this._pressedKeys[event.keyCode] = (event.type === 'keydown');\r\n event.preventDefault();\r\n event.stopPropagation();\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.getKeyBindObject = function () {\r\n return getTopWindow();\r\n};\r\n\r\nObjectControls.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nObjectControls.prototype.translatePivotByMouse = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this.translatePivotInWorld(settings.now.translationSpeed * delta.x, settings.now.translationSpeed * delta.y, 0);\r\n };\r\n}());\r\n\r\n// Translate in WorldCS, translation is scaled with root scale matrix\r\nObjectControls.prototype.translatePivotInWorld = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.applyMatrix4(this.object.matrixWorld);\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n pos.applyMatrix4(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Translate in ModelCS, x, y, z are Ang\r\nObjectControls.prototype.translatePivot = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Set pivot\r\nObjectControls.prototype.setPivot = function (newPivot) {\r\n this.objectPivot.position.copy(newPivot);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\nexport default ObjectControls;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\nimport Timer from '../Timer';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\n\r\nfunction Picker(gfxObj, camera, domElement) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.gfxObj = gfxObj;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n this._lastMousePos = new THREE.Vector2(0, 0);\r\n this._mouseTotalDist = 0.0;\r\n this._lastClickBeginTime = -1000.0;\r\n this._lastClickPos = new THREE.Vector2(0, 0);\r\n this._clickBeginTime = 0.0;\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstart(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchend(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n}\r\n\r\nPicker.prototype = Object.create(EventDispatcher.prototype);\r\nPicker.prototype.constructor = Picker;\r\n\r\nPicker.prototype.reset = function () {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n};\r\n\r\nPicker.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nPicker.prototype.pickObject = function (screenPos) {\r\n if (!this.gfxObj) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n const { gfxObj } = this;\r\n const rayCaster = new THREE.Raycaster();\r\n rayCaster.ray.origin.setFromMatrixPosition(this.camera.matrixWorld);\r\n rayCaster.ray.direction.set(screenPos.x, screenPos.y, 0.5).unproject(this.camera).sub(rayCaster.ray.origin).normalize();\r\n\r\n const clipPlane = (settings.now.draft.clipPlane && this.clipPlaneValue) ? this.clipPlaneValue : Infinity;\r\n const fogFarPlane = (settings.now.fog && this.fogFarValue) ? this.fogFarValue : Infinity;\r\n const point = rayCaster.intersectVisibleObject(gfxObj, this.camera, clipPlane, fogFarPlane);\r\n if (!point) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n let picked = {};\r\n if (point.residue || point.atom) {\r\n const residue = point.residue || point.atom.residue;\r\n if (settings.now.pick === 'chain') {\r\n picked = { chain: residue.getChain() };\r\n } else if (settings.now.pick === 'molecule') {\r\n picked = { molecule: residue.getMolecule() };\r\n } else if (point.residue || settings.now.pick === 'residue') {\r\n picked = { residue };\r\n } else if (point.atom) {\r\n picked = { atom: point.atom };\r\n }\r\n }\r\n this.picked = picked;\r\n this.dispatchEvent({ type: 'newpick', obj: picked });\r\n};\r\n\r\nPicker.prototype.getMouseInViewport = function (pageX, pageY) {\r\n return new THREE.Vector2(\r\n (pageX - this.screen.left) / this.screen.width * 2 - 1,\r\n -(pageY - this.screen.top) / this.screen.height * 2 + 1,\r\n );\r\n};\r\n\r\nPicker.prototype.mousedown = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n this._lastMousePos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist = 0.0;\r\n this._clickBeginTime = this._clock.getElapsedTime();\r\n }\r\n};\r\n\r\nPicker.prototype.mousemove = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n const pos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist += pos.sub(this._lastMousePos).length();\r\n};\r\n\r\nPicker.prototype.mouseup = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n if (this._mouseTotalDist < 0.01) {\r\n const curTime = this._clock.getElapsedTime();\r\n const curPos = this.getMouseInViewport(event.pageX, event.pageY);\r\n\r\n const timeSinceLastClickBegin = curTime - this._lastClickBeginTime;\r\n if (timeSinceLastClickBegin < 0.7) {\r\n const clickDist = new THREE.Vector2().subVectors(curPos, this._lastClickPos);\r\n if (clickDist.length() < 0.01) {\r\n // it's a double click\r\n this.dispatchEvent({ type: 'dblclick', obj: this.picked });\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = -1000; // this click cannot serve as first click in double-click\r\n return;\r\n }\r\n }\r\n\r\n setTimeout(() => {\r\n self.pickObject(curPos);\r\n }, 0);\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = this._clickBeginTime;\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.touchstart = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 1) {\r\n this._lastTouchdownPos = this.getMouseInViewport(event.touches[0].pageX, event.touches[0].pageY);\r\n }\r\n};\r\n\r\nPicker.prototype.touchend = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 0\r\n && event.changedTouches.length === 1) {\r\n const pos = this.getMouseInViewport(event.changedTouches[0].pageX, event.changedTouches[0].pageY);\r\n const dist = pos.sub(this._lastTouchdownPos).length();\r\n if (dist < 0.01) {\r\n setTimeout(() => {\r\n self.pickObject(self._lastTouchdownPos);\r\n }, 0);\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nexport default Picker;\r\n","import * as THREE from 'three';\r\n\r\nclass Axes {\r\n constructor(target, targetCamera) {\r\n this._target = target;\r\n this._targetCamera = targetCamera;\r\n this._camera = new THREE.PerspectiveCamera(targetCamera.fov, targetCamera.aspect, 1, 100);\r\n this._object = new THREE.AxesHelper(1);\r\n this._scene = new THREE.Scene();\r\n this._scene.add(this._object);\r\n this._full = new THREE.Vector2();\r\n\r\n this._update();\r\n }\r\n\r\n _update() {\r\n const { fov } = this._targetCamera;\r\n const camera = this._camera;\r\n camera.aspect = this._targetCamera.aspect;\r\n camera.setMinimalFov(fov);\r\n camera.setDistanceToFit(1.0, fov);\r\n camera.updateProjectionMatrix();\r\n\r\n this._object.quaternion.copy(this._target.quaternion);\r\n }\r\n\r\n render(renderer) {\r\n this._update();\r\n\r\n renderer.getSize(this._full);\r\n const width = this._full.width * 0.25;\r\n const height = this._full.height * 0.25;\r\n\r\n const { autoClear } = renderer;\r\n renderer.autoClear = false;\r\n renderer.setViewport(0.0, 0.0, width, height);\r\n renderer.clear(false, true, false);\r\n renderer.render(this._scene, this._camera);\r\n renderer.setViewport(0, 0, this._full.width, this._full.height);\r\n renderer.autoClear = autoClear;\r\n }\r\n}\r\nexport default Axes;\r\n","import * as THREE from 'three';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\n\r\nconst cDataOffset = 12;\r\nconst cFirstMask = 0x0FFFFF00;\r\nconst cFirstShift = 8;\r\nconst cSecMask1 = 0x000000FF;\r\nconst cSecShift1 = 12;\r\nconst cSecMask2 = 0xFFF00000;\r\nconst cSecShift2 = 20;\r\nconst cThirdMask = 0x000FFFFF;\r\nconst cStrMask = 0xF0000000;\r\nconst cStrShift = 28;\r\nconst c219 = 1 << 19;\r\nconst c220 = 1 << 20;\r\n\r\nconst cHelixIdx = 1;\r\nconst cSheetIdx = 2;\r\nconst secTypes = ['helix', 'strand'];\r\nconst cSecNames = ['fs', 'ps', 'ns', 'us'];\r\n\r\nfunction _createSecondary(strArray, complex) {\r\n const residues = complex._residues;\r\n const nRes = residues.length;\r\n const resid = new Uint8Array(nRes);\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, n = strArray.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n resid[atom.residue._index] = strArray[i];\r\n }\r\n\r\n const secondary = [];\r\n let rIdx = 0;\r\n while (rIdx < nRes) {\r\n if (resid[rIdx] !== 0) {\r\n const start = rIdx;\r\n const val = resid[rIdx];\r\n while (rIdx < nRes - 1 && resid[rIdx + 1] === val\r\n && residues[rIdx].isConnected(residues[rIdx + 1])) {\r\n ++rIdx;\r\n }\r\n secondary.push({ start, end: rIdx, type: secTypes[val - 1] });\r\n }\r\n ++rIdx;\r\n }\r\n return secondary;\r\n}\r\n\r\nfunction fromUInt20ToInt20(uint20) {\r\n return uint20 >= c219 ? uint20 - c220 : uint20;\r\n}\r\n\r\nclass FrameInfo {\r\n constructor(complex, payload, callbacks) {\r\n this._complex = complex;\r\n this._secondary = null;\r\n this.isLoading = false;\r\n this._framesRange = {\r\n start: 0,\r\n end: -1,\r\n };\r\n this.frameIsReady = false;\r\n this._buffer = null;\r\n this._frameRequest = null;\r\n this._callbacks = callbacks;\r\n if (typeof payload === 'function') {\r\n this._framesRequestLength = 1;\r\n this._downloadDataFn = payload;\r\n } else {\r\n this.parseBinaryData(payload, true);\r\n }\r\n this.reset();\r\n this.setFrame(0);\r\n }\r\n\r\n _prepareBuffer(framesStart, framesEnd) {\r\n if (framesStart === undefined || framesStart === null) {\r\n framesStart = 0;\r\n }\r\n if (framesEnd === undefined || framesEnd === null) {\r\n framesEnd = framesStart + this._framesRequestLength;\r\n }\r\n if (this._framesCount !== undefined) {\r\n framesEnd = Math.min(this._framesCount - 1, framesEnd);\r\n }\r\n if (this._downloadDataFn) {\r\n const self = this;\r\n const onDone = function (data) {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n self._buffer = {\r\n data,\r\n state: 'ready',\r\n start: framesStart,\r\n end: framesEnd,\r\n };\r\n if (self._frameRequest !== null) {\r\n const idx = self._frameRequest;\r\n self._frameRequest = null;\r\n self.setFrame(idx);\r\n }\r\n };\r\n const onFail = function () {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onError === 'function') {\r\n self._callbacks.onError('Streaming failed');\r\n }\r\n };\r\n if (!this._buffer) {\r\n this._buffer = {};\r\n }\r\n this._buffer.state = 'downloading';\r\n this.isLoading = true;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n this._downloadDataFn({ start: framesStart, end: framesEnd + 1 }, onDone, onFail);\r\n }\r\n }\r\n\r\n _parseBuffer() {\r\n if (this._buffer && this._buffer.state === 'ready') {\r\n this._framesRange = {\r\n start: this._buffer.start,\r\n end: this._buffer.end,\r\n };\r\n this.parseBinaryData(this._buffer.data, false);\r\n let _bufferRequestStart = (this._buffer.end + 1) % this._framesCount;\r\n if (_bufferRequestStart >= this._framesCount) {\r\n _bufferRequestStart = 0;\r\n }\r\n this._buffer = {\r\n state: 'none',\r\n };\r\n this._prepareBuffer(_bufferRequestStart, _bufferRequestStart + this._framesRequestLength);\r\n if (this._frameRequest !== null) {\r\n const idx = this._frameRequest;\r\n this._frameRequest = null;\r\n this.setFrame(idx);\r\n }\r\n }\r\n }\r\n\r\n parseBinaryData(arrayBuffer) {\r\n const dataView = new DataView(arrayBuffer);\r\n let offset = 0;\r\n const atomsCount = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const framesCount = dataView.getUint32(offset, true);\r\n this._framesCount = framesCount;\r\n this._framesRange.end = this._framesRange.end > 0\r\n ? Math.min(this._framesRange.end, framesCount - 1) : framesCount - 1;\r\n offset += 4;\r\n this._atomsCount = atomsCount;\r\n const maxSize = 1024 * 1024; // 1 MB\r\n this._framesRequestLength = Math.ceil(maxSize / (atomsCount * 8));\r\n const chunkedFramesCount = this._framesRange.end - this._framesRange.start + 1;\r\n if (atomsCount !== this._complex._atoms.length\r\n || arrayBuffer.byteLength !== cDataOffset + chunkedFramesCount * atomsCount * 8) {\r\n throw new Error();\r\n }\r\n const complex = this._complex;\r\n let timeStep = dataView.getUint32(offset, true);\r\n let iName = 0;\r\n while (timeStep > 1000 && iName < cSecNames.length - 1) {\r\n timeStep /= 1000;\r\n ++iName;\r\n }\r\n\r\n this._timeStep = `${timeStep.toString()} ${cSecNames[iName]}`;\r\n offset += 4;\r\n const secondary = [];\r\n const posData = new Float32Array(chunkedFramesCount * atomsCount * 3);\r\n let coordIdx = 0;\r\n const secondaryArr = new Int8Array(atomsCount);\r\n for (let j = 0; j < chunkedFramesCount; ++j) {\r\n for (let i = 0; i < atomsCount; ++i) {\r\n const hiWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const loWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const str = (loWord & cStrMask) >>> cStrShift;\r\n const x = fromUInt20ToInt20(((loWord & cFirstMask) >>> cFirstShift) >> 0);\r\n const y = fromUInt20ToInt20((((loWord & cSecMask1) << cSecShift1)\r\n | ((hiWord & cSecMask2) >>> cSecShift2)) >> 0);\r\n const z = fromUInt20ToInt20((hiWord & cThirdMask) >> 0);\r\n secondaryArr[i] = 0;\r\n if (str > 0 && str < 4) {\r\n secondaryArr[i] = cHelixIdx;\r\n } else if (str === 4) {\r\n secondaryArr[i] = cSheetIdx;\r\n }\r\n posData[coordIdx++] = x / 100;\r\n posData[coordIdx++] = y / 100;\r\n posData[coordIdx++] = z / 100;\r\n }\r\n secondary.push(_createSecondary(secondaryArr, complex));\r\n }\r\n this._secondaryData = secondary;\r\n this._data = posData;\r\n }\r\n\r\n nextFrame() {\r\n this.setFrame((this._currFrame + 1) % this._framesCount);\r\n }\r\n\r\n needsColorUpdate(colorer) {\r\n return colorer instanceof SecondaryStructureColorer;\r\n }\r\n\r\n getAtomColor(colorer, atom) {\r\n return colorer.getResidueColor(this._residues[atom.residue._index], this._complex);\r\n }\r\n\r\n getResidueColor(colorer, residue) {\r\n return colorer.getResidueColor(this._residues[residue._index], this._complex);\r\n }\r\n\r\n _updateSecondary() {\r\n let i;\r\n const myResidues = this._residues;\r\n let n = myResidues.length;\r\n for (i = 0; i < n; ++i) {\r\n myResidues[i]._secondary = null;\r\n }\r\n const sec = this._secondaryData[this._currFrame - this._framesRange.start];\r\n for (i = 0, n = sec.length; i < n; ++i) {\r\n const oldSec = sec[i];\r\n const { start, end } = oldSec;\r\n const nSec = {\r\n _start: myResidues[start],\r\n _end: myResidues[end],\r\n type: oldSec.type,\r\n generic: oldSec.generic,\r\n };\r\n for (let j = start; j <= end; ++j) {\r\n myResidues[j]._secondary = nSec;\r\n }\r\n }\r\n }\r\n\r\n reset() {\r\n const compRes = this._complex._residues;\r\n const n = compRes.length;\r\n this._residues = new Array(n);\r\n const myResidues = this._residues;\r\n const getSec = function () {\r\n return this._secondary;\r\n };\r\n for (let i = 0; i < n; ++i) {\r\n myResidues[i] = {\r\n _type: compRes[i]._type,\r\n _isValid: compRes[i]._isValid,\r\n _controlPoint: null,\r\n _wingVector: null,\r\n _secondary: null,\r\n getSecondary: getSec,\r\n };\r\n }\r\n }\r\n\r\n setFrame(frameIdx) {\r\n this.frameIsReady = false;\r\n if (frameIdx >= this._framesRange.start && frameIdx <= this._framesRange.end) {\r\n this._currFrame = frameIdx;\r\n this._cachedResidues = false;\r\n this._updateSecondary();\r\n this.frameIsReady = true;\r\n } else {\r\n this._frameRequest = frameIdx;\r\n if (!this._buffer) {\r\n this._prepareBuffer(frameIdx);\r\n } else {\r\n const self = this;\r\n switch (this._buffer.state) {\r\n case 'none':\r\n this._prepareBuffer(frameIdx);\r\n break;\r\n case 'ready':\r\n self._parseBuffer();\r\n break;\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n disableEvents() {\r\n this._callbacks = null;\r\n }\r\n\r\n /**\r\n * Returns link to atom pos vector, clone it if needed\r\n */\r\n\r\n static _vec = new THREE.Vector3();\r\n\r\n getAtomPos(atomIdx) {\r\n const vec = FrameInfo._vec;\r\n const self = this;\r\n const data = self._data;\r\n const idx = (self._atomsCount * (self._currFrame - self._framesRange.start) + atomIdx) * 3;\r\n vec.set(data[idx], data[idx + 1], data[idx + 2]);\r\n return vec;\r\n }\r\n\r\n getResidues() {\r\n if (this._cachedResidues) {\r\n return this._residues;\r\n }\r\n this._complex.updateToFrame(this);\r\n return this._residues;\r\n }\r\n}\r\nexport default FrameInfo;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\n\r\n/**\r\n * Create new scene object.\r\n *\r\n * @param {array=} params - Object required params.\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports SceneObject\r\n * @this SceneObject\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all scene objects that are not reps.\r\n */\r\nclass SceneObject {\r\n constructor(params, opts) {\r\n if (this.constructor === SceneObject) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Object's options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.params = params;\r\n this.opts = _.merge(utils.deriveDeep(settings.now.objects[this.type], true), opts);\r\n this.needsRebuild = false;\r\n this._mesh = null;\r\n this.id = null;\r\n }\r\n\r\n /**\r\n * Get object identification, probably with options.\r\n * @returns {Object} field type contains type information, params - object's formal parameters,\r\n * opts - changed options\r\n * Options are returned if they were changed during or after object creation.\r\n */\r\n identify() {\r\n const result = {\r\n type: this.type,\r\n params: this.params,\r\n };\r\n const diff = utils.objectsDiff(this.opts, settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n result.opts = diff;\r\n }\r\n return result;\r\n }\r\n\r\n toString() {\r\n const paramsStr = `o=${this.type},${this.params.join(',')}`;\r\n const optsStr = utils.compareOptionsWithDefaults(this.opts, settings.defaults.objects[this.type]);\r\n return paramsStr + optsStr;\r\n }\r\n\r\n getGeometry() {\r\n return this._mesh;\r\n }\r\n\r\n destroy() {\r\n if (this._mesh) {\r\n gfxutils.destroyObject(this._mesh);\r\n }\r\n }\r\n}\r\n\r\n/**\r\n * Scene object identifier.\r\n * @type {string}\r\n */\r\nSceneObject.prototype.type = '__';\r\n\r\nexport default SceneObject;\r\n","import * as THREE from 'three';\r\nimport SceneObject from './SceneObject';\r\nimport meshutils from '../meshutils';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\nimport meshes from '../meshes/meshes';\r\nimport settings from '../../settings';\r\n\r\nclass LinesObj extends SceneObject {\r\n constructor(params, opts) {\r\n super(params, opts);\r\n if (params.length < 2) {\r\n throw new Error('Wrong number of argumets on line object creation!');\r\n }\r\n [this._id1, this._id2] = params;\r\n }\r\n\r\n _getAtomFromName(complex, atomId) {\r\n const err = ' - Wrong atom format it must be \\'#CHAIN_NAME.#RESIDUE_NUMBER.#ATOM_NAME\\' (e.g. \\'A.38.CO1\\')';\r\n const atom1 = complex.getAtomByFullname(atomId);\r\n if (!atom1) {\r\n throw new Error(atomId + err);\r\n }\r\n return atom1;\r\n }\r\n\r\n build(complex) {\r\n const geom = new THREE.BufferGeometry();\r\n this._atom1 = this._getAtomFromName(complex, this._id1);\r\n this._atom2 = this._getAtomFromName(complex, this._id2);\r\n\r\n const p1 = this._atom1.position;\r\n const p2 = this._atom2.position;\r\n const vertices = new Float32Array([\r\n p1.x, p1.y, p1.z,\r\n p2.x, p2.y, p2.z,\r\n ]);\r\n\r\n geom.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n geom.computeBoundingBox();\r\n\r\n this._line = new meshes.Line(geom, new UberMaterial({\r\n lights: false,\r\n overrideColor: true,\r\n dashedLine: true,\r\n fogTransparent: settings.now.bg.transparent,\r\n }));\r\n this._line.computeLineDistances();\r\n this._line.material.setUberOptions({\r\n fixedColor: new THREE.Color(this.opts.color),\r\n dashedLineSize: this.opts.dashSize,\r\n dashedLinePeriod: this.opts.dashSize + this.opts.gapSize,\r\n });\r\n this._line.material.updateUniforms();\r\n\r\n this._line.raycast = function (_raycaster, _intersects) {};\r\n this._mesh = this._line;\r\n const transforms = complex.getTransforms();\r\n if (transforms.length > 0) {\r\n this._mesh = new THREE.Group();\r\n this._mesh.add(this._line);\r\n meshutils.applyTransformsToMeshes(this._mesh, transforms);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n if (!this._atom1 || !this._atom2 || !this._line) {\r\n return;\r\n }\r\n\r\n const geo = this._line.geometry;\r\n geo.vertices[0].copy(frameData.getAtomPos(this._atom1.index));\r\n geo.vertices[1].copy(frameData.getAtomPos(this._atom2.index));\r\n this._line.computeLineDistances();\r\n geo.computeBoundingSphere();\r\n\r\n geo.verticesNeedUpdate = true;\r\n }\r\n}\r\n\r\nLinesObj.prototype.constructor = LinesObj;\r\nLinesObj.prototype.type = 'line';\r\n\r\nexport default LinesObj;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Outline.frag';\r\n\r\nclass OutlineMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n // add depth outline\r\n super(params);\r\n\r\n const settings = {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcDepthTex: { type: 't', value: null },\r\n srcTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n color: { type: 'v3', value: null },\r\n threshold: { type: 'f', value: null },\r\n opacity: { type: 'f', value: 1.0 },\r\n thickness: { type: 'v2', value: new THREE.Vector2(1, 1) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: true,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n\r\n this.setValues(settings);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n const defines = {};\r\n\r\n if (this.depth) {\r\n defines.DEPTH_OUTLINE = 1;\r\n }\r\n\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nOutlineMaterial.prototype.depth = false;\r\n\r\nexport default OutlineMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './FXAA.frag';\r\n\r\nclass FXAAMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n bgColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.bgTransparent) {\r\n defines.BG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nFXAAMaterial.prototype.bgTransparent = false;\r\n\r\nexport default FXAAMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AO.frag';\r\nimport noise from '../noiseTexture';\r\n\r\nconst _samplesKernel = [\r\n // hemisphere samples adopted to sphere\r\n new THREE.Vector3(0.295184, 0.077723, 0.068429),\r\n new THREE.Vector3(-0.271976, -0.365221, 0.838363),\r\n new THREE.Vector3(0.547713, 0.467576, 0.488515),\r\n new THREE.Vector3(0.662808, -0.031733, 0.584758),\r\n new THREE.Vector3(-0.025717, 0.218955, 0.657094),\r\n new THREE.Vector3(-0.310153, -0.365223, 0.370701),\r\n new THREE.Vector3(-0.101407, -0.006313, 0.747665),\r\n new THREE.Vector3(-0.769138, 0.360399, 0.086847),\r\n new THREE.Vector3(-0.271988, -0.275140, 0.905353),\r\n new THREE.Vector3(0.096740, -0.566901, 0.700151),\r\n new THREE.Vector3(0.562872, -0.735136, 0.094647),\r\n new THREE.Vector3(0.379877, 0.359278, 0.190061),\r\n new THREE.Vector3(0.519064, -0.023055, 0.405068),\r\n new THREE.Vector3(-0.301036, 0.114696, 0.088885),\r\n new THREE.Vector3(-0.282922, 0.598305, 0.487214),\r\n new THREE.Vector3(-0.181859, 0.251670, 0.679702),\r\n new THREE.Vector3(-0.191463, -0.635818, 0.512919),\r\n new THREE.Vector3(-0.293655, 0.427423, 0.078921),\r\n new THREE.Vector3(-0.267983, 0.680534, 0.132880),\r\n new THREE.Vector3(0.139611, 0.319637, 0.477439),\r\n new THREE.Vector3(-0.352086, 0.311040, 0.653913),\r\n new THREE.Vector3(0.321032, 0.805279, 0.487345),\r\n new THREE.Vector3(0.073516, 0.820734, 0.414183),\r\n new THREE.Vector3(-0.155324, 0.589983, 0.411460),\r\n new THREE.Vector3(0.335976, 0.170782, 0.527627),\r\n new THREE.Vector3(0.463460, -0.355658, 0.167689),\r\n new THREE.Vector3(0.222654, 0.596550, 0.769406),\r\n new THREE.Vector3(0.922138, -0.042070, 0.147555),\r\n new THREE.Vector3(-0.727050, -0.329192, 0.369826),\r\n new THREE.Vector3(-0.090731, 0.533820, 0.463767),\r\n new THREE.Vector3(-0.323457, -0.876559, 0.238524),\r\n new THREE.Vector3(-0.663277, -0.372384, 0.342856),\r\n];\r\n\r\nclass AOMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n noiseTexture: { type: 't', value: noise.noiseTexture },\r\n noiseTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight) },\r\n diffuseTexture: { type: 't', value: null },\r\n normalTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n camNearFar: { type: 'v2', value: new THREE.Vector2(1.0, 10.0) },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n samplesKernel: { type: 'v3v', value: _samplesKernel },\r\n kernelRadius: { type: 'f', value: 1.0 },\r\n depthThreshold: { type: 'f', value: 1.0 },\r\n factor: { type: 'f', value: 1.0 },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOHorBlur.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOHorBlurMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOHorBlurMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOVertBlurWithBlend.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOVertBlurWithBlendMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n diffuseTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n fogNearFar: { type: 'v2', value: new THREE.Vector2(100.0, 100.0) },\r\n fogColor: { type: 'v4', value: new THREE.Vector4(0.0, 0.5, 0.0, 1.0) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.useFog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nAOVertBlurWithBlendMaterial.prototype.useFog = true;\r\nAOVertBlurWithBlendMaterial.prototype.fogTransparent = false;\r\n\r\nexport default AOVertBlurWithBlendMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Anaglyph.frag';\r\n\r\nclass AnaglyphMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n const settings = {\r\n uniforms: {\r\n srcL: { type: 't', value: null },\r\n srcR: { type: 't', value: null },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n this.setValues(settings);\r\n }\r\n}\r\n\r\nexport default AnaglyphMaterial;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\n\r\nclass View {\r\n constructor() {\r\n this.position = new THREE.Vector3(0, 0, 0);\r\n this.scale = 1;\r\n this.orientation = new THREE.Quaternion(0, 0, 0, 1);\r\n }\r\n\r\n set(position, scale, orientation) {\r\n this.position = position;\r\n this.scale = scale;\r\n this.orientation = orientation;\r\n }\r\n}\r\n\r\nconst _transitionTime = 1.5; // in seconds\r\n\r\nexport default class ViewInterpolator {\r\n setup(startView, endView) {\r\n this._startTime = undefined;\r\n this._endTime = undefined;\r\n this._isPaused = false;\r\n\r\n this._srcView = startView;\r\n this._dstView = endView;\r\n this._isMoving = false;\r\n }\r\n\r\n isMoving() {\r\n return this._isMoving;\r\n }\r\n\r\n wasStarted() {\r\n return typeof this._startTime !== 'undefined' && typeof this._endTime !== 'undefined';\r\n }\r\n\r\n start() {\r\n this._startTime = Date.now();\r\n const transTime = settings.now.interpolateViews ? _transitionTime * 1000 : 0;\r\n this._endTime = this._startTime + transTime;\r\n this._isMoving = true;\r\n }\r\n\r\n getCurrentView() {\r\n if (typeof this._srcView === 'undefined' || typeof this._dstView === 'undefined'\r\n || !this._isMoving || !this.wasStarted()) {\r\n return { success: false };\r\n }\r\n\r\n let view = this.createView();\r\n const time = Date.now();\r\n if (time > this._endTime) {\r\n view = this._dstView;\r\n this.reset();\r\n return { success: true, view };\r\n }\r\n\r\n const factor = (time - this._startTime) / (this._endTime - this._startTime);\r\n view.position.copy(this._srcView.position);\r\n view.position.lerp(this._dstView.position, factor);\r\n view.scale = (1 - factor) * this._srcView.scale + factor * this._dstView.scale;\r\n view.orientation.copy(this._srcView.orientation);\r\n view.orientation.slerp(this._dstView.orientation, factor);\r\n return { success: true, view };\r\n }\r\n\r\n reset() {\r\n this._startTime = this._endTime = 0;\r\n this._isMoving = false;\r\n }\r\n\r\n pause() {\r\n if (!this._isPaused) {\r\n this.setup(this.getCurrentView().view, this._dstView);\r\n this._isPaused = true;\r\n }\r\n }\r\n\r\n resume() {\r\n this._isPaused = false;\r\n }\r\n\r\n createView() {\r\n return new View();\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport makeContextDependent from './makeContextDependent';\r\n\r\nconst MAX_COOKIE_LEN = 4000;\r\nconst COUNT_SUFFIX = 'Cnt';\r\n\r\nfunction _chunkString(string, chunkLen) {\r\n const l = string.length;\r\n const chunks = [];\r\n for (let c = 0, lc = 0; lc < l; c++, lc += chunkLen) {\r\n chunks[c] = string.slice(lc, lc + chunkLen);\r\n }\r\n return chunks;\r\n}\r\n\r\n/**\r\n * Create new context dependent Cookie holder object.\r\n * @param context\r\n * @param {Object} opts - options\r\n * @param {string} opts.path - cookie path\r\n * @constructor\r\n */\r\nfunction Cookies(context, opts) {\r\n this.context = context;\r\n this._opts = _.merge({\r\n path: '/',\r\n }, opts);\r\n}\r\n\r\nmakeContextDependent(Cookies.prototype);\r\n\r\n/**\r\n * Remove cookie by the name.\r\n * @param key\r\n */\r\nCookies.prototype.removeCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n this._removeSimpleCookie(key);\r\n return;\r\n }\r\n this._removeSimpleCookie(cntKey);\r\n cntVal = parseInt(cntVal, 10);\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._removeSimpleCookie(key + i);\r\n }\r\n};\r\n\r\n/**\r\n * Set new cookie value. Automatically splits\r\n * values that are too large into multiple cookies.\r\n * @param key\r\n * @param value\r\n */\r\nCookies.prototype.setCookie = function (key, value) {\r\n this.removeCookie(key);\r\n value = encodeURIComponent(value);\r\n const values = _chunkString(value, MAX_COOKIE_LEN - key.length - 1);\r\n const cntVal = values.length;\r\n if (cntVal === 1) {\r\n this._setSimpleCookie(key, value);\r\n return;\r\n }\r\n const cntKey = this._toCount(key);\r\n this._setSimpleCookie(cntKey, cntVal.toString());\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._setSimpleCookie(key + i, values[i]);\r\n }\r\n};\r\n\r\n/**\r\n * Obtain the value of a compound cookie.\r\n * @param key\r\n */\r\nCookies.prototype.getCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n return this._getSimpleCookie(key);\r\n }\r\n cntVal = parseInt(cntVal, 10);\r\n const value = [];\r\n for (let i = 0; i < cntVal; ++i) {\r\n value[i] = this._getSimpleCookie(key + i);\r\n }\r\n return value.join('');\r\n};\r\n\r\nCookies.prototype._toCount = function (key) {\r\n return key + COUNT_SUFFIX;\r\n};\r\n\r\nCookies.prototype._removeSimpleCookie = function (key) {\r\n document.cookie = `${key}=; expires=Thu, 01 Jan 1970 00:00:01 GMT;`;\r\n};\r\n\r\nCookies.prototype._getExpirationDate = function () {\r\n const today = new Date();\r\n const EXP_PERIOD_YEARS = 10;\r\n today.setFullYear(today.getFullYear() + EXP_PERIOD_YEARS);\r\n return today;\r\n};\r\n\r\nCookies.prototype._setSimpleCookie = function (key, value) {\r\n document.cookie = `${key}=${value\r\n };expires=${this._getExpirationDate().toUTCString()\r\n };path=${this._opts.path}`;\r\n};\r\n\r\nCookies.prototype._getSimpleCookie = function (key) {\r\n const matches = document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n return matches ? decodeURIComponent(matches[1]) : '';\r\n};\r\n\r\nCookies.prototype._exists = function (key) {\r\n return document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n};\r\n\r\nexport default Cookies;\r\n","/*\r\n * Toggling WebVR is done through button.click because of limitations on calling requestPresent in webVR:\r\n * VRDisplay::requestPresent should be called from user gesture:\r\n * https://developer.mozilla.org/en-US/docs/Web/API/VRDisplay/requestPresent\r\n */\r\nexport default function (webVRPoC) {\r\n function showEnterVR(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'pointer';\r\n button.style.left = 'calc(50% - 50px)';\r\n button.style.width = '100px';\r\n\r\n button.textContent = 'ENTER VR';\r\n\r\n let currentSession = null;\r\n\r\n function onSessionEnded(/* event */) {\r\n currentSession.removeEventListener('end', onSessionEnded);\r\n button.textContent = 'ENTER VR';\r\n currentSession = null;\r\n }\r\n\r\n function onSessionStarted(session) {\r\n session.addEventListener('end', onSessionEnded);\r\n webVRPoC._gfx.renderer.xr.setReferenceSpaceType('local');\r\n webVRPoC._gfx.renderer.xr.setSession(session);\r\n button.textContent = 'EXIT VR';\r\n currentSession = session;\r\n }\r\n\r\n button.onmouseenter = function () { button.style.opacity = '1.0'; };\r\n button.onmouseleave = function () { button.style.opacity = '0.5'; };\r\n\r\n button.onclick = function () {\r\n if (currentSession === null) {\r\n // WebXR's requestReferenceSpace only works if the corresponding feature\r\n // was requested at session creation time. For simplicity, just ask for\r\n // the interesting ones as optional features, but be aware that the\r\n // requestReferenceSpace call will fail if it turns out to be unavailable.\r\n // ('local' is always available for immersive sessions and doesn't need to\r\n // be requested separately.)\r\n\r\n const sessionInit = { optionalFeatures: ['local-floor', 'bounded-floor'] };\r\n navigator.xr.requestSession('immersive-vr', sessionInit).then(onSessionStarted);\r\n webVRPoC.moveSceneBehindHeadset();\r\n } else {\r\n currentSession.end();\r\n }\r\n };\r\n }\r\n\r\n function showWebXRNotFound(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'auto';\r\n button.style.left = 'calc(50% - 75px)';\r\n button.style.width = '150px';\r\n button.textContent = 'VR NOT FOUND';\r\n button.onmouseenter = null;\r\n button.onmouseleave = null;\r\n button.onclick = null;\r\n }\r\n\r\n function stylizeElement(element) {\r\n element.style.position = 'absolute';\r\n element.style.bottom = '20px';\r\n element.style.padding = '12px 6px';\r\n element.style.border = '1px solid #fff';\r\n element.style.borderRadius = '4px';\r\n element.style.background = 'transparent';\r\n element.style.color = '#fff';\r\n element.style.font = 'normal 13px sans-serif';\r\n element.style.textAlign = 'center';\r\n element.style.opacity = '0.5';\r\n element.style.outline = 'none';\r\n element.style.zIndex = '999';\r\n }\r\n\r\n if ('xr' in navigator) {\r\n const button = document.createElement('button');\r\n button.style.display = 'none';\r\n stylizeElement(button);\r\n navigator.xr.isSessionSupported('immersive-vr').then((supported) => (\r\n supported ? showEnterVR(button) : showWebXRNotFound(button)\r\n ));\r\n return button;\r\n }\r\n const message = document.createElement('a');\r\n message.href = 'https://webvr.info';\r\n message.innerHTML = 'WEBXR NOT SUPPORTED';\r\n message.style.left = 'calc(50% - 90px)';\r\n message.style.width = '180px';\r\n message.style.textDecoration = 'none';\r\n stylizeElement(message);\r\n return message;\r\n}\r\n","import * as THREE from 'three';\r\nimport createWebVRButton from './createWebVRButton';\r\nimport gfxutils from '../gfxutils';\r\nimport logger from '../../utils/logger';\r\nimport settings from '../../settings';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default class WebVRPoC {\r\n constructor(onToggle) {\r\n this._mainCamera = new THREE.PerspectiveCamera();\r\n this._button = null;\r\n this._onToggle = onToggle;\r\n\r\n this._molContainer = new gfxutils.RCGroup();\r\n this._user = new gfxutils.RCGroup();\r\n this._scalingPivot = new THREE.Object3D();\r\n this._user.add(this._scalingPivot);\r\n\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n this._pressedGripsCounter = 0;\r\n this._distance = 0;\r\n\r\n this._gfx = null;\r\n }\r\n\r\n startScalingByControllers() {\r\n // reset scale\r\n this._distance = this._controller1.position.distanceTo(this._controller2.position);\r\n gfxutils.getMiddlePoint(this._controller1.position, this._controller2.position, this._scalingPivot.position);\r\n this._scalingPivot.scale.set(1, 1, 1);\r\n this._scalingPivot.updateMatrix();\r\n this._scalingPivot.updateMatrixWorld();\r\n // link molecule to pivot\r\n this._scalingPivot.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n stopScalingByControllers() {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n handleGripsDown(event) {\r\n this._pressedGripsCounter++;\r\n if (this._pressedGripsCounter === 2) {\r\n this.startScalingByControllers();\r\n } else if (this._pressedGripsCounter === 1) {\r\n event.target.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n handleGripsUp(event) {\r\n this._pressedGripsCounter--;\r\n if (this._pressedGripsCounter === 1) {\r\n this.stopScalingByControllers();\r\n // reattach molecule to other controller\r\n const anotherController = event.target === this._controller1 ? this._controller2 : this._controller1;\r\n anotherController.addSavingWorldTransform(this._molContainer);\r\n } else if (this._pressedGripsCounter === 0) {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n enable(gfx) {\r\n if (!gfx) {\r\n logger.warn('WebVR couldn\\'t be enabled, because gfx is not defined');\r\n return;\r\n }\r\n this._gfx = gfx;\r\n const { renderer, camera } = gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n if (!camera) {\r\n throw new Error('No camera is available to toggle WebVR');\r\n }\r\n\r\n // enable xr in renderer\r\n renderer.xr.enabled = true;\r\n // add button for turning vr mode\r\n if (!this._button) {\r\n this._button = createWebVRButton(this);\r\n document.body.appendChild(this._button);\r\n } else {\r\n this._button.style.display = 'block';\r\n }\r\n // store fog setting\r\n this._mainFog = settings.now.fog;\r\n settings.set('fog', false);\r\n\r\n this._plugVRNodesIntoScene(gfx, renderer);\r\n this._setControllersListeners();\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n _plugVRNodesIntoScene(gfx, renderer) {\r\n // store common scene camera\r\n this._mainCamera.copy(gfx.camera);\r\n // add hierarchical structure for webVR into scene\r\n gfx.scene.add(this._user);\r\n // turn on webvr transformation\r\n gfx.scene.add(this._molContainer);\r\n this._molContainer.add(gfx.root);\r\n\r\n this._controller1 = renderer.xr.getController(0);\r\n this._controller2 = renderer.xr.getController(1);\r\n const mesh = this._createControllerMesh();\r\n this._controller1.add(mesh);\r\n this._controller2.add(mesh.clone());\r\n this._user.add(this._controller1);\r\n this._user.add(this._controller2);\r\n }\r\n\r\n _setControllersListeners() {\r\n this._controller1.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n\r\n this._controller1.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n }\r\n\r\n disable() {\r\n if (!this._gfx) {\r\n return;\r\n }\r\n const { renderer, camera } = this._gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n\r\n // nullify webxr callback for animation frame\r\n renderer.setAnimationLoop(null);\r\n const session = renderer.xr.getSession();\r\n if (session) {\r\n session.end();\r\n }\r\n renderer.xr.enabled = false;\r\n // remove button of VR entering\r\n if (this._button) {\r\n this._button.style.display = 'none';\r\n }\r\n // restore fog param\r\n settings.set('fog', this._mainFog);\r\n\r\n this._unplugVRNodesFromScene(camera);\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(false);\r\n }\r\n }\r\n\r\n _unplugVRNodesFromScene(camera) {\r\n // restore common camera\r\n if (this._mainCamera && camera) {\r\n camera.copy(this._mainCamera);\r\n }\r\n // turn off webvr transformation\r\n const root = this._molContainer.children[0];\r\n if (root) {\r\n this._gfx.scene.add(root);\r\n }\r\n this._molContainer.parent.remove(this._molContainer);\r\n if (this._user) {\r\n this._gfx.scene.remove(this._user);\r\n }\r\n // free scene nodes\r\n this._molContainer = null;\r\n this._user = null;\r\n this._scalingPivot = null;\r\n this._user = null;\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n }\r\n\r\n _createControllerMesh() {\r\n // visualize controllers with cylinders\r\n const geometry = new THREE.CylinderGeometry(0.04, 0.04, 0.3);\r\n const material = new UberMaterial({ lights: false, overrideColor: true });\r\n material.setUberOptions({ fixedColor: new THREE.Color(0x4444ff) });\r\n material.updateUniforms();\r\n const cylinder = new THREE.Mesh(geometry, material);\r\n cylinder.rotateX(-Math.PI / 2);\r\n return cylinder;\r\n }\r\n\r\n updateMoleculeScale() {\r\n if (!this._controller1 || !this._controller2) {\r\n return;\r\n }\r\n\r\n const self = this;\r\n // update molecule scaling by controllers\r\n if (self._pressedGripsCounter === 2) {\r\n // recalc scaling pivot\r\n gfxutils.getMiddlePoint(self._controller1.position, self._controller2.position, self._scalingPivot.position);\r\n // recalc scaler\r\n const dist = self._controller1.position.distanceTo(self._controller2.position);\r\n const scaler = dist / self._distance;\r\n self._scalingPivot.scale.multiplyScalar(scaler);\r\n // save cur distance for next frame\r\n self._distance = dist;\r\n }\r\n }\r\n\r\n /**\r\n * Reposition molecule right before the camera.\r\n * @note The proper way is to initiate headset in the place of common Miew's camera.\r\n * But threejs limitations on setting new XRReferenceSpace enforce the molecule repositioning\r\n * Hope, something will change.\r\n */\r\n moveSceneBehindHeadset() {\r\n const gfx = this._gfx;\r\n const { camera } = gfx;\r\n\r\n // set container position in camera space\r\n const container = this._molContainer;\r\n container.matrix.identity();\r\n container.position.set(0, 0, -4.0);\r\n container.updateMatrix();\r\n\r\n // update container world matrix\r\n container.matrixWorld.multiplyMatrices(camera.matrixWorld, container.matrix);\r\n // readd to scene\r\n gfx.scene.addSavingWorldTransform(container);\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n getCanvas() {\r\n const gfx = this._gfx;\r\n return (gfx && gfx.renderer) ? gfx.renderer.domElement : null;\r\n }\r\n}\r\n","/* global PACKAGE_VERSION:false */\r\nimport _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport { Spinner } from 'spin.js';\r\nimport Stats from './gfx/Stats';\r\nimport utils from './utils';\r\nimport JobHandle from './utils/JobHandle';\r\nimport options from './options';\r\nimport settings from './settings';\r\nimport chem from './chem';\r\nimport Visual from './Visual';\r\nimport ComplexVisual from './ComplexVisual';\r\nimport Complex from './chem/Complex';\r\nimport VolumeVisual from './VolumeVisual';\r\nimport io from './io/io';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport CSS2DRenderer from './gfx/CSS2DRenderer';\r\nimport ObjectControls from './ui/ObjectControls';\r\nimport Picker from './ui/Picker';\r\nimport Axes from './gfx/Axes';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport meshutils from './gfx/meshutils';\r\nimport FrameInfo from './gfx/FrameInfo';\r\nimport meshes from './gfx/meshes/meshes';\r\nimport LinesObject from './gfx/objects/LinesObj';\r\nimport UberMaterial from './gfx/shaders/UberMaterial';\r\nimport OutlineMaterial from './gfx/shaders/OutlineMaterial';\r\nimport FXAAMaterial from './gfx/shaders/FXAAMaterial';\r\nimport AOMaterial from './gfx/shaders/AOMaterial';\r\nimport AOHorBlurMaterial from './gfx/shaders/AOHorBlurMaterial';\r\nimport AOVertBlurWithBlendMaterial from './gfx/shaders/AOVertBlurWithBlendMaterial';\r\nimport AnaglyphMaterial from './gfx/shaders/AnaglyphMaterial';\r\nimport VolumeMaterial from './gfx/shaders/VolumeMaterial';\r\nimport ViewInterpolator from './gfx/ViewInterpolator';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\nimport logger from './utils/logger';\r\nimport Cookies from './utils/Cookies';\r\nimport capabilities from './gfx/capabilities';\r\nimport WebVRPoC from './gfx/vr/WebVRPoC';\r\nimport vertexScreenQuadShader from './gfx/shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromDistTex from './gfx/shaders/ScreenQuadFromDistortionTex.frag';\r\nimport getTopWindow from './utils/getTopWindow';\r\n\r\nconst {\r\n selectors,\r\n Atom,\r\n Residue,\r\n Chain,\r\n Molecule,\r\n} = chem;\r\n\r\nconst EDIT_MODE = { COMPLEX: 0, COMPONENT: 1, FRAGMENT: 2 };\r\n\r\nconst LOADER_NOT_FOUND = 'Could not find suitable loader for this source';\r\nconst PARSER_NOT_FOUND = 'Could not find suitable parser for this source';\r\n\r\n// Color management changed a lot in threejs 152+ version.\r\n// To keep miew colors we disable the new color management system\r\nTHREE.ColorManagement.enabled = false;\r\n\r\nconst { createElement } = utils;\r\n\r\nfunction updateFogRange(fog, center, radius) {\r\n fog.near = center - radius * settings.now.fogNearFactor;\r\n fog.far = center + radius * settings.now.fogFarFactor;\r\n}\r\n\r\nfunction removeExtension(fileName) {\r\n const dot = fileName.lastIndexOf('.');\r\n if (dot >= 0) {\r\n fileName = fileName.substr(0, dot);\r\n }\r\n return fileName;\r\n}\r\n\r\nfunction hasValidResidues(complex) {\r\n let hasValidRes = false;\r\n complex.forEachComponent((component) => {\r\n component.forEachResidue((residue) => {\r\n if (residue._isValid) {\r\n hasValidRes = true;\r\n }\r\n });\r\n });\r\n return hasValidRes;\r\n}\r\n\r\nfunction reportProgress(log, action, percent) {\r\n const TOTAL_PERCENT = 100;\r\n if (percent !== undefined) {\r\n log.debug(`${action}... ${Math.floor(percent * TOTAL_PERCENT)}%`);\r\n } else {\r\n log.debug(`${action}...`);\r\n }\r\n}\r\n\r\nfunction chooseFogColor() {\r\n return settings.now.fogColorEnable ? settings.now.fogColor : settings.now.bg.color;\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\n/**\r\n * Main 3D Molecular Viewer class.\r\n *\r\n * @param {object} opts - Viewer options.\r\n * @param {HTMLElement=} opts.container - DOM element that serves as a viewer container.\r\n * @param {object=} opts.settings - An object with properties to override default settings.\r\n * @param {string=} opts.settingsCookie='settings' - The name of the cookie to save current settings to.\r\n * @param {string=} opts.cookiePath='/' - The path option for cookies. Defaults to root.\r\n *\r\n * @exports Miew\r\n * @constructor\r\n */\r\nfunction Miew(opts) {\r\n EventDispatcher.call(this);\r\n this._opts = _.merge({\r\n settingsCookie: 'settings',\r\n cookiePath: '/',\r\n }, opts);\r\n /** @type {?object} */\r\n this._gfx = null;\r\n /** @type {ViewInterpolator} */\r\n this._interpolator = new ViewInterpolator();\r\n /** @type {HTMLElement} */\r\n this._container = (opts && opts.container)\r\n || document.getElementById('miew-container')\r\n || _.head(document.getElementsByClassName('miew-container'))\r\n || document.body;\r\n /** @type {HTMLElement} */\r\n this._containerRoot = this._container;\r\n\r\n /** @type {boolean} */\r\n this._running = false;\r\n /** @type {boolean} */\r\n this._halting = false;\r\n /** @type {boolean} */\r\n this._building = false;\r\n /** @type {boolean} */\r\n this._needRender = true;\r\n /** @type {boolean} */\r\n this._hotKeysEnabled = true;\r\n\r\n /** @type {Settings} */\r\n this.settings = settings;\r\n const log = logger;\r\n log.console = DEBUG;\r\n log.level = DEBUG ? 'debug' : 'info';\r\n /**\r\n * @type {Logger}\r\n * @example\r\n * miew.logger.addEventListener('message', function _onLogMessage(evt) {\r\n * console.log(evt.message);\r\n * });\r\n */\r\n this.logger = log;\r\n\r\n this._cookies = new Cookies(this);\r\n this.restoreSettings();\r\n if (opts && opts.settings) {\r\n this.settings.set(opts.settings);\r\n }\r\n\r\n /** @type {?Spinner} */\r\n this._spinner = null;\r\n /** @type {JobHandle[]} */\r\n this._loading = [];\r\n /** @type {?number}\r\n * @deprecated until Animation system refactoring\r\n */\r\n this._animInterval = null;\r\n\r\n /** @type {object} */\r\n this._visuals = {};\r\n /** @type {?string} */\r\n this._curVisualName = null;\r\n\r\n /** @type {array} */\r\n this._objects = [];\r\n\r\n /** @type {object} */\r\n this._sourceWindow = null;\r\n\r\n this.reset();\r\n\r\n if (this._repr) {\r\n log.debug(`Selected ${this._repr.mode.name} mode with ${this._repr.colorer.name} colorer.`);\r\n }\r\n\r\n const self = this;\r\n Miew.registeredPlugins.forEach((plugin) => {\r\n plugin.call(self);\r\n });\r\n\r\n this._initOnSettingsChanged();\r\n}\r\n\r\nMiew.prototype = Object.create(EventDispatcher.prototype);\r\nMiew.prototype.constructor = Miew;\r\n\r\nMiew.prototype.getMaxRepresentationCount = function () {\r\n return ComplexVisual.NUM_REPRESENTATION_BITS;\r\n};\r\n\r\n/**\r\n * Replace viewer container contents with a DOM element.\r\n * @param {HTMLElement} container - parent container.\r\n * @param {HTMLElement} element - DOM element to show.\r\n * @private\r\n */\r\nfunction _setContainerContents(container, element) {\r\n const parent = container;\r\n while (parent.firstChild) {\r\n parent.removeChild(parent.firstChild);\r\n }\r\n parent.appendChild(element);\r\n}\r\n\r\n/**\r\n * Update Shadow Camera target position and frustum.\r\n * @private\r\n */\r\nMiew.prototype._updateShadowCamera = (function () {\r\n const shadowMatrix = new THREE.Matrix4();\r\n const direction = new THREE.Vector3();\r\n const OBB = { center: new THREE.Vector3(), halfSize: new THREE.Vector3() };\r\n\r\n return function () {\r\n this._gfx.scene.updateMatrixWorld();\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = this._gfx.scene.children[i];\r\n shadowMatrix.copy(light.shadow.camera.matrixWorldInverse);\r\n this.getOBB(shadowMatrix, OBB);\r\n\r\n direction.subVectors(light.target.position, light.position);\r\n light.position.subVectors(OBB.center, direction);\r\n light.target.position.copy(OBB.center);\r\n\r\n light.shadow.bias = 0.09;\r\n light.shadow.camera.bottom = -OBB.halfSize.y;\r\n light.shadow.camera.top = OBB.halfSize.y;\r\n light.shadow.camera.right = OBB.halfSize.x;\r\n light.shadow.camera.left = -OBB.halfSize.x;\r\n light.shadow.camera.near = direction.length() - OBB.halfSize.z;\r\n light.shadow.camera.far = direction.length() + OBB.halfSize.z;\r\n\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Initialize the viewer.\r\n * @returns {boolean} true on success.\r\n * @throws Forwards exception raised during initialization.\r\n * @see Miew#term\r\n */\r\nMiew.prototype.init = function () {\r\n const container = this._container;\r\n const elem = utils.createElement('div', { class: 'miew-canvas' });\r\n _setContainerContents(container, elem);\r\n this._container = elem;\r\n\r\n const frag = document.createDocumentFragment();\r\n frag.appendChild(this._msgMode = createElement(\r\n 'div',\r\n { class: 'mode-message overlay' },\r\n createElement('p', {}, 'COMPONENT EDIT MODE'),\r\n ));\r\n frag.appendChild(this._msgAtomInfo = createElement(\r\n 'div',\r\n { class: 'atom-info overlay' },\r\n createElement('p', {}, ''),\r\n ));\r\n container.appendChild(frag);\r\n\r\n if (this._gfx !== null) { // block double init\r\n return true;\r\n }\r\n\r\n const self = this;\r\n this._showMessage('Viewer is being initialized...');\r\n try {\r\n this._initGfx();\r\n\r\n this._initListeners();\r\n this._spinner = new Spinner({\r\n lines: 13,\r\n length: 28,\r\n width: 14,\r\n radius: 42,\r\n color: '#fff',\r\n zIndex: 700,\r\n });\r\n\r\n const target = getTopWindow();\r\n target.addEventListener('keydown', (event) => {\r\n self._onKeyDown(event);\r\n });\r\n\r\n target.addEventListener('keyup', (event) => {\r\n self._onKeyUp(event);\r\n });\r\n\r\n this._objectControls = new ObjectControls(\r\n this._gfx.root,\r\n this._gfx.pivot,\r\n this._gfx.camera,\r\n this._gfx.renderer.domElement,\r\n () => self._getAltObj(),\r\n );\r\n this._objectControls.addEventListener('change', (e) => {\r\n if (settings.now.shadow.on) {\r\n self._updateShadowCamera();\r\n }\r\n // route rotate, zoom, translate and translatePivot events to the external API\r\n switch (e.action) {\r\n case 'rotate':\r\n self.dispatchEvent({ type: 'rotate', quaternion: e.quaternion });\r\n break;\r\n case 'zoom':\r\n self.dispatchEvent({ type: 'zoom', factor: e.factor });\r\n break;\r\n default:\r\n self.dispatchEvent({ type: e.action });\r\n }\r\n self.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n });\r\n\r\n const gfx = this._gfx;\r\n this._picker = new Picker(gfx.root, gfx.camera, gfx.renderer.domElement);\r\n this._picker.addEventListener('newpick', (event) => {\r\n self._onPick(event);\r\n });\r\n this._picker.addEventListener('dblclick', (event) => {\r\n self.center(event);\r\n });\r\n } catch (error) {\r\n if (error.name === 'TypeError' && error.message === 'Cannot read property \\'getExtension\\' of null') {\r\n this._showMessage('Could not create WebGL context.');\r\n } else if (error.message.search(/webgl/i) > 1) {\r\n this._showMessage(error.message);\r\n } else {\r\n this._showMessage('Viewer initialization failed.');\r\n throw error;\r\n }\r\n return false;\r\n }\r\n\r\n // automatically load default file\r\n const file = this._opts && this._opts.load;\r\n if (file) {\r\n const type = this._opts && this._opts.type;\r\n this.load(file, { fileType: type, keepRepsInfo: true });\r\n }\r\n\r\n return true;\r\n};\r\n\r\n/**\r\n * Terminate the viewer completely.\r\n * @see Miew#init\r\n */\r\nMiew.prototype.term = function () {\r\n this._showMessage('Viewer has been terminated.');\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n this.halt();\r\n this._gfx = null;\r\n};\r\n\r\n/**\r\n * Display message inside the viewer container, hiding WebGL canvas.\r\n * @param {string} msg - Message to show.\r\n * @private\r\n */\r\nMiew.prototype._showMessage = function (msg) {\r\n const element = document.createElement('div');\r\n element.setAttribute('class', 'miew-message');\r\n element.appendChild(document.createElement('p')).appendChild(document.createTextNode(msg));\r\n _setContainerContents(this._container, element);\r\n};\r\n\r\n/**\r\n * Display WebGL canvas inside the viewer container, hiding any message shown.\r\n * @private\r\n */\r\nMiew.prototype._showCanvas = function () {\r\n _setContainerContents(this._container, this._gfx.renderer.domElement);\r\n};\r\n\r\nMiew.prototype._requestAnimationFrame = function (callback) {\r\n const { xr } = this._gfx.renderer;\r\n if (xr && xr.enabled) {\r\n this._gfx.renderer.setAnimationLoop(callback);\r\n return;\r\n }\r\n requestAnimationFrame(callback);\r\n};\r\n\r\nfunction arezSpritesSupported(context) {\r\n return context.getExtension('EXT_frag_depth');\r\n}\r\n\r\nfunction isAOSupported(context) {\r\n return (context.getExtension('WEBGL_depth_texture')\r\n && context.getExtension('WEBGL_draw_buffers'));\r\n}\r\n\r\n/**\r\n * Initialize WebGL and set 3D scene up.\r\n * @private\r\n */\r\nMiew.prototype._initGfx = function () {\r\n const gfx = {\r\n width: this._container.clientWidth,\r\n height: this._container.clientHeight,\r\n };\r\n\r\n const webGLOptions = { preserveDrawingBuffer: true, alpha: true, premultipliedAlpha: false };\r\n if (settings.now.antialias) {\r\n webGLOptions.antialias = true;\r\n }\r\n\r\n gfx.renderer2d = new CSS2DRenderer();\r\n\r\n gfx.renderer = new THREE.WebGL1Renderer(webGLOptions);\r\n gfx.renderer.shadowMap.enabled = settings.now.shadow.on;\r\n gfx.renderer.shadowMap.autoUpdate = false;\r\n gfx.renderer.shadowMap.type = THREE.PCFShadowMap;\r\n capabilities.init(gfx.renderer);\r\n\r\n // z-sprites and ambient occlusion possibility\r\n if (!arezSpritesSupported(gfx.renderer.getContext())) {\r\n settings.set('zSprites', false);\r\n }\r\n if (!isAOSupported(gfx.renderer.getContext())) {\r\n settings.set('ao', false);\r\n }\r\n\r\n gfx.renderer.autoClear = false;\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n gfx.camera = new THREE.PerspectiveCamera(\r\n settings.now.camFov,\r\n gfx.width / gfx.height,\r\n settings.now.camNear,\r\n settings.now.camFar,\r\n );\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.position.z = settings.now.camDistance;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n\r\n gfx.stereoCam = new THREE.StereoCamera();\r\n\r\n gfx.scene = new THREE.Scene();\r\n\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color, settings.now.camNear, settings.now.camFar);\r\n\r\n gfx.root = new gfxutils.RCGroup();\r\n gfx.scene.add(gfx.root);\r\n\r\n gfx.pivot = new gfxutils.RCGroup();\r\n gfx.root.add(gfx.pivot);\r\n\r\n gfx.selectionScene = new THREE.Scene();\r\n gfx.selectionRoot = new THREE.Group();\r\n gfx.selectionRoot.matrixAutoUpdate = false;\r\n gfx.selectionScene.add(gfx.selectionRoot);\r\n\r\n gfx.selectionPivot = new THREE.Group();\r\n gfx.selectionPivot.matrixAutoUpdate = false;\r\n gfx.selectionRoot.add(gfx.selectionPivot);\r\n\r\n const light12 = new THREE.DirectionalLight(0xffffff, 0.45);\r\n light12.position.set(0, 0.414, 1);\r\n light12.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n light12.castShadow = true;\r\n light12.shadow.bias = 0.09;\r\n light12.shadow.radius = settings.now.shadow.radius;\r\n light12.shadow.camera.layers.set(gfxutils.LAYERS.SHADOWMAP);\r\n\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n const shadowMapSize = Math.max(gfx.width, gfx.height) * pixelRatio;\r\n light12.shadow.mapSize.width = shadowMapSize;\r\n light12.shadow.mapSize.height = shadowMapSize;\r\n light12.target.position.set(0.0, 0.0, 0.0);\r\n gfx.scene.add(light12);\r\n gfx.scene.add(light12.target);\r\n\r\n const light3 = new THREE.AmbientLight(0x666666);\r\n light3.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.scene.add(light3);\r\n\r\n // add axes\r\n gfx.axes = new Axes(gfx.root, gfx.camera);\r\n const deviceWidth = gfx.width * pixelRatio;\r\n const deviceHeight = gfx.height * pixelRatio;\r\n\r\n gfx.offscreenBuf = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat, depthBuffer: true,\r\n },\r\n );\r\n\r\n if (gfx.renderer.getContext().getExtension('WEBGL_depth_texture')) {\r\n gfx.offscreenBuf.depthTexture = new THREE.DepthTexture();\r\n gfx.offscreenBuf.depthTexture.type = THREE.UnsignedShortType;\r\n }\r\n\r\n gfx.offscreenBuf2 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf3 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf4 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf3;\r\n gfx.volFFTex = gfx.offscreenBuf4;\r\n gfx.volWFFTex = gfx.offscreenBuf;\r\n\r\n // use float textures for volume rendering if possible\r\n if (gfx.renderer.getContext().getExtension('OES_texture_float')) {\r\n gfx.offscreenBuf5 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf6 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf7 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf5;\r\n gfx.volFFTex = gfx.offscreenBuf6;\r\n gfx.volWFFTex = gfx.offscreenBuf7;\r\n } else {\r\n this.logger.warn('Device doesn\\'t support OES_texture_float extension');\r\n }\r\n\r\n gfx.stereoBufL = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.stereoBufR = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n this._gfx = gfx;\r\n this._showCanvas();\r\n\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n\r\n this._container.appendChild(gfx.renderer2d.getElement());\r\n\r\n // add FPS counter\r\n const stats = new Stats();\r\n stats.domElement.style.position = 'absolute';\r\n stats.domElement.style.right = '0';\r\n stats.domElement.style.bottom = '0';\r\n this._container.appendChild(stats.domElement);\r\n this._fps = stats;\r\n this._fps.show(settings.now.fps);\r\n};\r\n\r\n/**\r\n * Setup event listeners.\r\n * @private\r\n */\r\nMiew.prototype._initListeners = function () {\r\n const self = this;\r\n window.addEventListener('resize', () => {\r\n self._onResize();\r\n });\r\n};\r\n\r\n/**\r\n * Try to add numbers to the base name to make it unique among visuals\r\n * @private\r\n */\r\nMiew.prototype._makeUniqueVisualName = function (baseName) {\r\n if (!baseName) {\r\n return Math.random().toString();\r\n }\r\n\r\n let name = baseName;\r\n let suffix = 1;\r\n while (this._visuals.hasOwnProperty(name)) {\r\n name = `${baseName} (${suffix.toString()})`;\r\n suffix++;\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Add visual to the viewer\r\n * @private\r\n */\r\nMiew.prototype._addVisual = function (visual) {\r\n if (!visual) {\r\n return null;\r\n }\r\n\r\n // change visual name in order to make it unique\r\n const name = this._makeUniqueVisualName(visual.name);\r\n visual.name = name;\r\n\r\n this._visuals[name] = visual;\r\n this._gfx.pivot.add(visual);\r\n if (visual.getSelectionGeo) {\r\n this._gfx.selectionPivot.add(visual.getSelectionGeo());\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Remove visual from the viewer\r\n * @private\r\n */\r\nMiew.prototype._removeVisual = function (visual) {\r\n let name = '';\r\n let obj = null;\r\n if (visual instanceof Visual) {\r\n ({ name } = visual);\r\n obj = visual;\r\n } else if (typeof visual === 'string') {\r\n name = visual;\r\n obj = this._visuals[name];\r\n }\r\n\r\n if (!obj || !this._visuals.hasOwnProperty(name) || this._visuals[name] !== obj) {\r\n return;\r\n }\r\n\r\n if (name === this._curVisualName) {\r\n this._curVisualName = undefined;\r\n }\r\n\r\n delete this._visuals[name];\r\n obj.release(); // removes nodes from scene\r\n\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Call specified function for each Visual\r\n * @private\r\n */\r\nMiew.prototype._forEachVisual = function (callback) {\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Release (destroy) all visuals in the scene\r\n * @private\r\n */\r\nMiew.prototype._releaseAllVisuals = function () {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n this._visuals[name].release();\r\n }\r\n }\r\n\r\n this._visuals = {};\r\n};\r\n\r\n/**\r\n * Call specified function for each ComplexVisual\r\n * @private\r\n */\r\nMiew.prototype._forEachComplexVisual = function (callback) {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)\r\n && this._visuals[name] instanceof ComplexVisual) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual with specified name, or current (if not found), or any, or null\r\n * @private\r\n */\r\nMiew.prototype._getComplexVisual = function (name) {\r\n name = name || this._curVisualName;\r\n let any = null;\r\n let named = null;\r\n this._forEachComplexVisual((visual) => {\r\n any = visual;\r\n if (visual.name === name) {\r\n named = visual;\r\n }\r\n });\r\n return named || any;\r\n};\r\n\r\n/**\r\n * Returns first found VolumeVisual (no more than one should be present actually)\r\n * @private\r\n */\r\nMiew.prototype._getVolumeVisual = function () {\r\n let any = null;\r\n this._forEachVisual((visual) => {\r\n if (visual instanceof VolumeVisual) {\r\n any = visual;\r\n }\r\n });\r\n return any;\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual corresponding to specified complex\r\n * @private\r\n */\r\nMiew.prototype._getVisualForComplex = function (complex) {\r\n if (!complex) {\r\n return null;\r\n }\r\n\r\n let found = null;\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getComplex() === complex) {\r\n found = visual;\r\n }\r\n });\r\n return found;\r\n};\r\n\r\n/*\r\n * Get a list of names of visuals currently shown by the viewer\r\n */\r\nMiew.prototype.getVisuals = function () {\r\n return Object.keys(this._visuals);\r\n};\r\n\r\n/*\r\n * Get complex visuals count\r\n */\r\nMiew.prototype.getComplexVisualsCount = function () {\r\n let count = 0;\r\n this._forEachComplexVisual(() => count++);\r\n return count;\r\n};\r\n\r\n/*\r\n * Get current visual\r\n */\r\nMiew.prototype.getCurrentVisual = function () {\r\n return this._curVisualName;\r\n};\r\n\r\n/*\r\n * Set current visual.\r\n * All further operations will be performed on this visual (complex) if not stated otherwise.\r\n */\r\nMiew.prototype.setCurrentVisual = function (name) {\r\n if (!this._visuals[name]) {\r\n return;\r\n }\r\n\r\n this._curVisualName = name;\r\n};\r\n\r\n/**\r\n * Run the viewer, start processing update/render frames periodically.\r\n * Has no effect if already running.\r\n * @see Miew#halt\r\n */\r\nMiew.prototype.run = function () {\r\n if (!this._running) {\r\n this._running = true;\r\n if (this._halting) {\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._objectControls.enable(true);\r\n this._interpolator.resume();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to stop.\r\n * Will be processed during the next frame.\r\n * @see Miew#run\r\n */\r\nMiew.prototype.halt = function () {\r\n if (this._running) {\r\n this._discardComponentEdit();\r\n this._discardFragmentEdit();\r\n this._objectControls.enable(false);\r\n this._interpolator.pause();\r\n this._halting = true;\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to start / stop responsing\r\n * on hot keys.\r\n * @param enabled - start (true) or stop (false) response on hot keys.\r\n */\r\nMiew.prototype.enableHotKeys = function (enabled) {\r\n this._hotKeysEnabled = enabled;\r\n this._objectControls.enableHotkeys(enabled);\r\n};\r\n\r\n/**\r\n * Callback which processes window resize.\r\n * @private\r\n */\r\nMiew.prototype._onResize = function () {\r\n const gfx = this._gfx;\r\n if (!gfx) {\r\n return;\r\n }\r\n\r\n this._needRender = true;\r\n\r\n gfx.width = this._container.clientWidth;\r\n gfx.height = this._container.clientHeight;\r\n\r\n gfx.camera.aspect = gfx.width / gfx.height;\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n this.dispatchEvent({ type: 'resize' });\r\n};\r\n\r\nMiew.prototype._resizeOffscreenBuffers = function (width, height, stereo) {\r\n const gfx = this._gfx;\r\n stereo = stereo || 'NONE';\r\n const isAnaglyph = (stereo === 'NONE' || stereo === 'ANAGLYPH');\r\n const multi = isAnaglyph ? 1 : 0.5;\r\n gfx.offscreenBuf.setSize(multi * width, height);\r\n gfx.offscreenBuf2.setSize(multi * width, height);\r\n gfx.offscreenBuf3.setSize(multi * width, height);\r\n gfx.offscreenBuf4.setSize(multi * width, height);\r\n if (gfx.offscreenBuf5) {\r\n gfx.offscreenBuf5.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf6) {\r\n gfx.offscreenBuf6.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf7) {\r\n gfx.offscreenBuf7.setSize(multi * width, height);\r\n }\r\n if (isAnaglyph) {\r\n gfx.stereoBufL.setSize(width, height);\r\n gfx.stereoBufR.setSize(width, height);\r\n }\r\n};\r\n\r\n/**\r\n * Callback which processes update/render frames.\r\n * @private\r\n */\r\nMiew.prototype._onTick = function () {\r\n if (this._halting) {\r\n this._running = false;\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._fps.update();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n\r\n this._onUpdate();\r\n if (this._needRender) {\r\n this._onRender();\r\n this._needRender = !settings.now.suspendRender || settings.now.stereo === 'WEBVR';\r\n }\r\n};\r\n\r\nMiew.prototype._getBSphereRadius = function () {\r\n // calculate radius that would include all visuals\r\n let radius = 0;\r\n this._forEachVisual((visual) => {\r\n radius = Math.max(radius, visual.getBoundaries().boundingSphere.radius);\r\n });\r\n return radius * this._objectControls.getScale();\r\n};\r\n\r\n/**\r\n * Calculate bounding box that would include all visuals and being axis aligned in world defined by\r\n * transformation matrix: matrix\r\n * @param {Matrix4} matrix - transformation matrix.\r\n * @param {object} OBB - calculating bounding box.\r\n * @param {Vector3} OBB.center - OBB center.\r\n * @param {Vector3} OBB.halfSize - half magnitude of OBB sizes.\r\n */\r\nMiew.prototype.getOBB = (function () {\r\n const _bSphereForOneVisual = new THREE.Sphere();\r\n const _bBoxForOneVisual = new THREE.Box3();\r\n const _bBox = new THREE.Box3();\r\n\r\n const _invMatrix = new THREE.Matrix4();\r\n\r\n const _points = [\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n ];\r\n\r\n return function (matrix, OBB) {\r\n _bBox.makeEmpty();\r\n\r\n this._forEachVisual((visual) => {\r\n _bSphereForOneVisual.copy(visual.getBoundaries().boundingSphere);\r\n _bSphereForOneVisual.applyMatrix4(visual.matrixWorld).applyMatrix4(matrix);\r\n _bSphereForOneVisual.getBoundingBox(_bBoxForOneVisual);\r\n _bBox.union(_bBoxForOneVisual);\r\n });\r\n _bBox.getCenter(OBB.center);\r\n\r\n _invMatrix.copy(matrix).invert();\r\n OBB.center.applyMatrix4(_invMatrix);\r\n\r\n const { min } = _bBox;\r\n const { max } = _bBox;\r\n _points[0].set(min.x, min.y, min.z); // 000\r\n _points[1].set(max.x, min.y, min.z); // 100\r\n _points[2].set(min.x, max.y, min.z); // 010\r\n _points[3].set(min.x, min.y, max.z); // 001\r\n for (let i = 0, l = _points.length; i < l; i++) {\r\n _points[i].applyMatrix4(_invMatrix);\r\n }\r\n\r\n OBB.halfSize.set(\r\n Math.abs(_points[0].x - _points[1].x),\r\n Math.abs(_points[0].y - _points[2].y),\r\n Math.abs(_points[0].z - _points[3].z),\r\n ).multiplyScalar(0.5);\r\n };\r\n}());\r\n\r\nMiew.prototype._updateFog = function () {\r\n const gfx = this._gfx;\r\n\r\n if (settings.now.fog) {\r\n if (typeof gfx.scene.fog === 'undefined' || gfx.scene.fog === null) {\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color);\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n updateFogRange(gfx.scene.fog, gfx.camera.position.z, this._getBSphereRadius());\r\n } else if (gfx.scene.fog) {\r\n gfx.scene.fog = undefined;\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n};\r\n\r\nMiew.prototype._onUpdate = function () {\r\n if (this.isScriptingCommandAvailable !== undefined && this.isScriptingCommandAvailable() && !this._building) {\r\n this.callNextCmd();\r\n }\r\n\r\n this._objectControls.update();\r\n\r\n this._forEachComplexVisual((visual) => {\r\n visual.getComplex().update();\r\n });\r\n\r\n if (settings.now.autobuild && !this._loading.length && !this._building && this._needRebuild()) {\r\n this.rebuild();\r\n }\r\n\r\n if (!this._loading.length && !this._building && !this._needRebuild()) {\r\n this._updateView();\r\n }\r\n\r\n this._updateFog();\r\n\r\n if (this._gfx.renderer.xr.enabled) {\r\n this.webVR.updateMoleculeScale();\r\n }\r\n};\r\n\r\nMiew.prototype._onRender = function () {\r\n const gfx = this._gfx;\r\n\r\n // update all matrices\r\n gfx.scene.updateMatrixWorld();\r\n gfx.camera.updateMatrixWorld();\r\n\r\n this._clipPlaneUpdateValue(this._getBSphereRadius());\r\n this._fogFarUpdateValue();\r\n\r\n gfx.renderer.setRenderTarget(null);\r\n gfx.renderer.clear();\r\n\r\n this._renderFrame(settings.now.stereo);\r\n};\r\n\r\nMiew.prototype._renderFrame = (function () {\r\n const _anaglyphMat = new AnaglyphMaterial();\r\n const _size = new THREE.Vector2();\r\n\r\n return function (stereo) {\r\n const gfx = this._gfx;\r\n const { renderer } = gfx;\r\n\r\n renderer.getSize(_size);\r\n\r\n if (stereo !== 'NONE') {\r\n gfx.camera.focus = gfx.camera.position.z; // set focus to the center of the object\r\n gfx.stereoCam.aspect = 1.0;\r\n\r\n // in anaglyph mode we render full-size image for each eye\r\n // while in other stereo modes only half-size (two images on the screen)\r\n if (stereo === 'ANAGLYPH') {\r\n gfx.stereoCam.update(gfx.camera);\r\n } else {\r\n gfx.stereoCam.updateHalfSized(gfx.camera, settings.now.camFov);\r\n }\r\n }\r\n\r\n // resize offscreen buffers to match the target\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n this._resizeOffscreenBuffers(_size.width * pixelRatio, _size.height * pixelRatio, stereo);\r\n\r\n this._renderShadowMap();\r\n\r\n switch (stereo) {\r\n case 'WEBVR':\r\n case 'NONE':\r\n this._renderScene(gfx.camera, false);\r\n break;\r\n case 'SIMPLE':\r\n case 'DISTORTED':\r\n renderer.setScissorTest(true);\r\n\r\n renderer.setScissor(0, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(0, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraL, stereo === 'DISTORTED');\r\n\r\n renderer.setScissor(_size.width / 2, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(_size.width / 2, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraR, stereo === 'DISTORTED');\r\n\r\n renderer.setScissorTest(false);\r\n break;\r\n case 'ANAGLYPH':\r\n this._renderScene(this._gfx.stereoCam.cameraL, false, gfx.stereoBufL);\r\n this._renderScene(this._gfx.stereoCam.cameraR, false, gfx.stereoBufR);\r\n renderer.setRenderTarget(null);\r\n _anaglyphMat.uniforms.srcL.value = gfx.stereoBufL.texture;\r\n _anaglyphMat.uniforms.srcR.value = gfx.stereoBufR.texture;\r\n gfx.renderer.renderScreenQuad(_anaglyphMat);\r\n break;\r\n default:\r\n }\r\n\r\n gfx.renderer2d.render(gfx.scene, gfx.camera);\r\n\r\n if (settings.now.axes && gfx.axes && !gfx.renderer.xr.enabled) {\r\n gfx.axes.render(renderer);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._onBgColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx) {\r\n if (gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onFogColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx && gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._setUberMaterialValues = function (values) {\r\n this._gfx.root.traverse((obj) => {\r\n if ((obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line)\r\n && obj.material instanceof UberMaterial) {\r\n obj.material.setValues(values);\r\n obj.material.needsUpdate = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) {\r\n const gfx = this._gfx;\r\n const gl = gfx.renderer.getContext();\r\n const ext = gl.getExtension('WEBGL_draw_buffers');\r\n const { properties } = gfx.renderer;\r\n\r\n if (!on) {\r\n ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, null]);\r\n return;\r\n }\r\n\r\n // take extra texture from Texture Buffer\r\n gfx.renderer.setRenderTarget(textureBuffer);\r\n const tx8 = properties.get(textureBuffer.texture).__webglTexture;\r\n gl.bindTexture(gl.TEXTURE_2D, tx8);\r\n\r\n // take texture and framebuffer from renderbuffer\r\n gfx.renderer.setRenderTarget(renderBuffer);\r\n const fb = properties.get(renderBuffer).__webglFramebuffer;\r\n const tx = properties.get(renderBuffer.texture).__webglTexture;\r\n\r\n // set framebuffer\r\n gl.bindFramebuffer(gl.FRAMEBUFFER, fb);\r\n fb.width = renderBuffer.width;\r\n fb.height = renderBuffer.height;\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT0, gl.TEXTURE_2D, tx, 0);\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, ext.COLOR_ATTACHMENT1_WEBGL, gl.TEXTURE_2D, tx8, 0);\r\n\r\n // mapping textures\r\n ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, ext.COLOR_ATTACHMENT1_WEBGL]);\r\n};\r\n\r\nMiew.prototype._renderScene = (function () {\r\n return function (camera, distortion, target) {\r\n distortion = distortion || false;\r\n target = target || null;\r\n\r\n const gfx = this._gfx;\r\n\r\n // render to offscreen buffer\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.clear();\r\n if (gfx.renderer.xr.enabled) {\r\n gfx.renderer.render(gfx.scene, camera);\r\n return;\r\n }\r\n\r\n // clean buffer for normals texture\r\n gfx.renderer.setClearColor(0x000000, 0.0);\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf4);\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.clear();\r\n\r\n const bHaveComplexes = (this._getComplexVisual() !== null);\r\n const volumeVisual = this._getVolumeVisual();\r\n const ssao = bHaveComplexes && settings.now.ao;\r\n\r\n if (ssao) {\r\n this._enableMRT(true, gfx.offscreenBuf, gfx.offscreenBuf4);\r\n }\r\n\r\n if (settings.now.transparency === 'prepass') {\r\n this._renderWithPrepassTransparency(camera, gfx.offscreenBuf);\r\n } else if (settings.now.transparency === 'standard') {\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n }\r\n\r\n if (ssao) {\r\n this._enableMRT(false, null, null);\r\n }\r\n\r\n // when fxaa we should get resulting image in temp off-screen buff2 for further postprocessing with fxaa filter\r\n // otherwise we render to canvas\r\n const outline = bHaveComplexes && settings.now.outline.on;\r\n const fxaa = bHaveComplexes && settings.now.fxaa;\r\n const volume = (volumeVisual !== null) && (volumeVisual.getMesh().material != null);\r\n let dstBuffer = (ssao || outline || volume || fxaa || distortion) ? gfx.offscreenBuf2 : target;\r\n let srcBuffer = gfx.offscreenBuf;\r\n\r\n if (ssao) {\r\n this._performAO(\r\n srcBuffer,\r\n gfx.offscreenBuf4,\r\n gfx.offscreenBuf.depthTexture,\r\n dstBuffer,\r\n gfx.offscreenBuf3,\r\n gfx.offscreenBuf2,\r\n );\r\n if (!fxaa && !distortion && !volume && !outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = target;\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n } else {\r\n // just copy color buffer to dst buffer\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n\r\n // outline\r\n if (outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = (volume || fxaa || distortion) ? gfx.offscreenBuf3 : target;\r\n if (srcBuffer != null) {\r\n this._renderOutline(camera, gfx.offscreenBuf, srcBuffer, dstBuffer);\r\n }\r\n }\r\n\r\n // render selected part with outline material\r\n this._renderSelection(camera, gfx.offscreenBuf, dstBuffer);\r\n\r\n if (volume) {\r\n // copy current picture to the buffer that retains depth-data of the original molecule render\r\n // so that volume renderer could use depth-test\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n dstBuffer = gfx.offscreenBuf;\r\n this._renderVolume(volumeVisual, camera, dstBuffer, gfx.volBFTex, gfx.volFFTex, gfx.volWFFTex);\r\n\r\n // if this is the last stage -- copy image to target\r\n if (!fxaa && !distortion) {\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n }\r\n }\r\n\r\n srcBuffer = dstBuffer;\r\n\r\n if (fxaa) {\r\n dstBuffer = distortion ? gfx.offscreenBuf4 : target;\r\n this._performFXAA(srcBuffer, dstBuffer);\r\n srcBuffer = dstBuffer;\r\n }\r\n\r\n if (distortion) {\r\n dstBuffer = target;\r\n this._performDistortion(srcBuffer, dstBuffer, true);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._performDistortion = (function () {\r\n const _scene = new THREE.Scene();\r\n const _camera = new THREE.OrthographicCamera(-1.0, 1.0, 1.0, -1.0, -500, 1000);\r\n\r\n const _material = new THREE.RawShaderMaterial({\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n aberration: { type: 'fv3', value: new THREE.Vector3(1.0) },\r\n },\r\n vertexShader: vertexScreenQuadShader,\r\n fragmentShader: fragmentScreenQuadFromDistTex,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n const _geo = gfxutils.buildDistorionMesh(10, 10, settings.now.debug.stereoBarrel);\r\n _scene.add(new meshes.Mesh(_geo, _material));\r\n\r\n return function (srcBuffer, targetBuffer, mesh) {\r\n this._gfx.renderer.setRenderTarget(targetBuffer);\r\n this._gfx.renderer.clear();\r\n\r\n if (mesh) {\r\n _material.uniforms.srcTex.value = srcBuffer.texture;\r\n _material.uniforms.aberration.value.set(0.995, 1.0, 1.01);\r\n this._gfx.renderer.render(_scene, _camera);\r\n } else {\r\n this._gfx.renderer.renderScreenQuadFromTexWithDistortion(srcBuffer, settings.now.debug.stereoBarrel);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._renderOutline = (function () {\r\n const _outlineMaterial = new OutlineMaterial({ depth: true });\r\n\r\n return function (camera, srcDepthBuffer, srcColorBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcColorBuffer.texture;\r\n _outlineMaterial.uniforms.srcDepthTex.value = srcDepthBuffer.depthTexture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcDepthBuffer.width, srcDepthBuffer.height);\r\n _outlineMaterial.uniforms.color.value = new THREE.Color(settings.now.outline.color);\r\n _outlineMaterial.uniforms.threshold.value = settings.now.outline.threshold;\r\n _outlineMaterial.uniforms.thickness.value = new THREE.Vector2(\r\n settings.now.outline.thickness,\r\n settings.now.outline.thickness,\r\n );\r\n\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._renderShadowMap = (function () {\r\n const pars = { minFilter: THREE.NearestFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat };\r\n\r\n return function () {\r\n if (!settings.now.shadow.on) {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n const currentRenderTarget = gfx.renderer.getRenderTarget();\r\n const activeCubeFace = gfx.renderer.getActiveCubeFace();\r\n const activeMipmapLevel = gfx.renderer.getActiveMipmapLevel();\r\n\r\n const _state = gfx.renderer.state;\r\n\r\n // Set GL state for depth map.\r\n _state.setBlending(THREE.NoBlending);\r\n _state.buffers.color.setClear(1, 1, 1, 1);\r\n _state.buffers.depth.setTest(true);\r\n _state.setScissorTest(false);\r\n\r\n for (let i = 0; i < gfx.scene.children.length; i++) {\r\n if (gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = gfx.scene.children[i];\r\n\r\n if (light.shadow.map == null) {\r\n light.shadow.map = new THREE.WebGLRenderTarget(light.shadow.mapSize.width, light.shadow.mapSize.height, pars);\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n light.shadow.updateMatrices(light);\r\n\r\n gfx.renderer.setRenderTarget(light.shadow.map);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.render(gfx.scene, light.shadow.camera);\r\n }\r\n }\r\n gfx.renderer.setRenderTarget(currentRenderTarget, activeCubeFace, activeMipmapLevel);\r\n };\r\n}());\r\n\r\n/**\r\n * Check if there is selection which must be rendered or not.\r\n * @private\r\n * @returns {boolean} true on existing selection to render\r\n */\r\nMiew.prototype._hasSelectionToRender = function () {\r\n const selPivot = this._gfx.selectionPivot;\r\n\r\n for (let i = 0; i < selPivot.children.length; i++) {\r\n const selPivotChild = selPivot.children[i];\r\n if (selPivotChild.children.length > 0) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n};\r\n\r\nMiew.prototype._renderSelection = (function () {\r\n const _outlineMaterial = new OutlineMaterial();\r\n\r\n return function (camera, srcBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // clear offscreen buffer (leave z-buffer intact)\r\n gfx.renderer.setClearColor('black', 0);\r\n\r\n // render selection to offscreen buffer\r\n gfx.renderer.setRenderTarget(srcBuffer);\r\n gfx.renderer.clear(true, false, false);\r\n if (self._hasSelectionToRender()) {\r\n gfx.selectionRoot.matrix = gfx.root.matrix;\r\n gfx.selectionPivot.matrix = gfx.pivot.matrix;\r\n gfx.renderer.render(gfx.selectionScene, camera);\r\n } else {\r\n // just render something to force \"target clear\" operation to finish\r\n gfx.renderer.renderDummyQuad();\r\n }\r\n\r\n // overlay to screen\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 0.6);\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcBuffer.width, srcBuffer.height);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._checkVolumeRenderingSupport = function (renderTarget) {\r\n if (!renderTarget) {\r\n return false;\r\n }\r\n const gfx = this._gfx;\r\n const oldRT = gfx.renderer.getRenderTarget();\r\n\r\n gfx.renderer.setRenderTarget(renderTarget);\r\n const context = gfx.renderer.getContext();\r\n const result = context.checkFramebufferStatus(context.FRAMEBUFFER);\r\n gfx.renderer.setRenderTarget(oldRT);\r\n if (result !== context.FRAMEBUFFER_COMPLETE) {\r\n // floatFrameBufferWarning = ;\r\n this.logger.warn('Device doesn\\'t support electron density rendering');\r\n return false;\r\n }\r\n return true;\r\n};\r\n\r\nMiew.prototype._renderVolume = (function () {\r\n const volumeBFMat = new VolumeMaterial.BackFacePosMaterial();\r\n const volumeFFMat = new VolumeMaterial.FrontFacePosMaterial();\r\n const cubeOffsetMat = new THREE.Matrix4().makeTranslation(0.5, 0.5, 0.5);\r\n const world2colorMat = new THREE.Matrix4();\r\n\r\n let volumeRenderingSupported;\r\n\r\n return function (volumeVisual, camera, dstBuf, tmpBuf1, tmpBuf2, tmpBuf3) {\r\n const gfx = this._gfx;\r\n\r\n if (typeof volumeRenderingSupported === 'undefined') {\r\n volumeRenderingSupported = this._checkVolumeRenderingSupport(tmpBuf1);\r\n }\r\n\r\n if (!volumeRenderingSupported) {\r\n return;\r\n }\r\n\r\n const mesh = volumeVisual.getMesh();\r\n\r\n mesh.rebuild(gfx.camera);\r\n\r\n // use main camera to prepare special textures to be used by volumetric rendering\r\n // these textures have the size of the window and are stored in offscreen buffers\r\n gfx.renderer.setClearColor('black', 0);\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n // draw plane with its own material, because it differs slightly from volumeBFMat\r\n camera.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeBFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeFFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.scene.overrideMaterial = null;\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n\r\n // prepare texture that contains molecule positions\r\n world2colorMat.copy(mesh.matrixWorld).invert();\r\n UberMaterial.prototype.uberOptions.world2colorMatrix.multiplyMatrices(cubeOffsetMat, world2colorMat);\r\n camera.layers.set(gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // render volume\r\n const vm = mesh.material;\r\n vm.uniforms._BFRight.value = tmpBuf1.texture;\r\n vm.uniforms._FFRight.value = tmpBuf2.texture;\r\n vm.uniforms._WFFRight.value = tmpBuf3.texture;\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.renderer.setRenderTarget(dstBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\n/* Render scene with 'ZPrepass transparency Effect'\r\n * Idea: transparent objects are rendered in two passes. The first one writes result only into depth buffer.\r\n * The second pass reads depth buffer and writes only to color buffer. The method results in\r\n * correct image of front part of the semi-transparent objects, but we can see only front transparent objects\r\n * and opaque objects inside, there is no transparent objects inside.\r\n * Notes: 1. Opaque objects should be rendered strictly before semi-transparent ones.\r\n * 2. Realization doesn't use camera layers because scene traversing is used for material changes and\r\n * we can use it to select needed meshes and don't complicate meshes builders with layers\r\n */\r\nMiew.prototype._renderWithPrepassTransparency = (function () {\r\n return function (camera, targetBuffer) {\r\n const gfx = this._gfx;\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n\r\n // opaque objects\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // transparent objects z prepass\r\n camera.layers.set(gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n gfx.renderer.getContext().colorMask(false, false, false, false); // don't update color buffer\r\n gfx.renderer.render(gfx.scene, camera);\r\n gfx.renderer.getContext().colorMask(true, true, true, true); // update color buffer\r\n\r\n // transparent objects color pass\r\n camera.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // restore default layer\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\nMiew.prototype._performFXAA = (function () {\r\n const _fxaaMaterial = new FXAAMaterial();\r\n\r\n return function (srcBuffer, targetBuffer) {\r\n if (typeof srcBuffer === 'undefined' || typeof targetBuffer === 'undefined') {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n\r\n // clear canvas\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.clear();\r\n\r\n // do fxaa processing of offscreen buff2\r\n _fxaaMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _fxaaMaterial.uniforms.srcTexelSize.value.set(1.0 / srcBuffer.width, 1.0 / srcBuffer.height);\r\n _fxaaMaterial.uniforms.bgColor.value.set(settings.now.bg.color);\r\n\r\n if (_fxaaMaterial.bgTransparent !== settings.now.bg.transparent) {\r\n _fxaaMaterial.setValues({ bgTransparent: settings.now.bg.transparent });\r\n _fxaaMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.renderScreenQuad(_fxaaMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._performAO = (function () {\r\n const _aoMaterial = new AOMaterial();\r\n const _horBlurMaterial = new AOHorBlurMaterial();\r\n const _vertBlurMaterial = new AOVertBlurWithBlendMaterial();\r\n\r\n const _scale = new THREE.Vector3();\r\n return function (srcColorBuffer, normalBuffer, srcDepthTexture, targetBuffer, tempBuffer, tempBuffer1) {\r\n if (!srcColorBuffer || !normalBuffer || !srcDepthTexture || !targetBuffer || !tempBuffer || !tempBuffer1) {\r\n return;\r\n }\r\n const gfx = this._gfx;\r\n const tanHalfFOV = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * gfx.camera.fov);\r\n\r\n _aoMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _aoMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _aoMaterial.uniforms.normalTexture.value = normalBuffer.texture;\r\n _aoMaterial.uniforms.srcTexelSize.value.set(1.0 / srcColorBuffer.width, 1.0 / srcColorBuffer.height);\r\n _aoMaterial.uniforms.camNearFar.value.set(gfx.camera.near, gfx.camera.far);\r\n _aoMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _aoMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _aoMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n gfx.root.matrix.extractScale(_scale);\r\n _aoMaterial.uniforms.kernelRadius.value = settings.now.debug.ssaoKernelRadius * _scale.x;\r\n _aoMaterial.uniforms.depthThreshold.value = 2.0 * this._getBSphereRadius(); // diameter\r\n _aoMaterial.uniforms.factor.value = settings.now.debug.ssaoFactor;\r\n // N: should be tempBuffer1 for proper use of buffers (see buffers using outside the function)\r\n gfx.renderer.setRenderTarget(tempBuffer1);\r\n gfx.renderer.renderScreenQuad(_aoMaterial);\r\n\r\n _horBlurMaterial.uniforms.aoMap.value = tempBuffer1.texture;\r\n _horBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer1.width, 1.0 / tempBuffer1.height);\r\n _horBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n gfx.renderer.setRenderTarget(tempBuffer);\r\n gfx.renderer.renderScreenQuad(_horBlurMaterial);\r\n\r\n _vertBlurMaterial.uniforms.aoMap.value = tempBuffer.texture;\r\n _vertBlurMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _vertBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer.width, 1.0 / tempBuffer.height);\r\n _vertBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _vertBlurMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _vertBlurMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _vertBlurMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n const { fog } = gfx.scene;\r\n if (fog) {\r\n _vertBlurMaterial.uniforms.fogNearFar.value.set(fog.near, fog.far);\r\n _vertBlurMaterial.uniforms.fogColor.value.set(fog.color.r, fog.color.g, fog.color.b, settings.now.fogAlpha);\r\n }\r\n if ((_vertBlurMaterial.useFog !== settings.now.fog)\r\n || (_vertBlurMaterial.fogTransparent !== settings.now.bg.transparent)) {\r\n _vertBlurMaterial.setValues({ useFog: settings.now.fog, fogTransparent: settings.now.bg.transparent });\r\n _vertBlurMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_vertBlurMaterial);\r\n };\r\n}());\r\n\r\n/**\r\n * Reset the viewer, unload molecules.\r\n * @param {boolean=} keepReps - Keep representations while resetting viewer state.\r\n */\r\nMiew.prototype.reset = function (/* keepReps */) {\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._lastPick = null;\r\n\r\n this._releaseAllVisuals();\r\n\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._resetObjects();\r\n\r\n if (this._gfx) {\r\n gfxutils.clearTree(this._gfx.pivot);\r\n this._gfx.renderer2d.reset();\r\n }\r\n\r\n this.setNeedRender();\r\n};\r\n\r\nMiew.prototype._resetScene = function () {\r\n this._objectControls.reset();\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n this.resetReps();\r\n this.resetPivot();\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype.resetView = function () {\r\n // reset controls\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._resetScene();\r\n\r\n // reset selection\r\n this._forEachComplexVisual((visual) => {\r\n visual.updateSelectionMask({});\r\n visual.rebuildSelectionGeometry();\r\n });\r\n};\r\n\r\nMiew.prototype._export = function (format) {\r\n const TheExporter = _.head(io.exporters.find({ format }));\r\n if (!TheExporter) {\r\n this.logger.error('Could not find suitable exporter for this source');\r\n return Promise.reject(new Error('Could not find suitable exporter for this source'));\r\n }\r\n this.dispatchEvent({ type: 'exporting' });\r\n\r\n if (this._visuals[this._curVisualName] instanceof ComplexVisual) {\r\n let dataSource = null;\r\n if (TheExporter.SourceClass === ComplexVisual) {\r\n dataSource = this._visuals[this._curVisualName];\r\n } else if (TheExporter.SourceClass === Complex) {\r\n dataSource = this._visuals[this._curVisualName]._complex;\r\n }\r\n const exporter = new TheExporter(dataSource, { miewVersion: Miew.VERSION });\r\n return exporter.export().then((data) => data);\r\n }\r\n if (this._visuals[this._curVisualName] instanceof VolumeVisual) {\r\n return Promise.reject(new Error('Sorry, exporter for volume data not implemented yet'));\r\n }\r\n return Promise.reject(new Error('Unexpected format of data'));\r\n};\r\n\r\nconst rePdbId = /^(?:(pdb|cif|ccp4|dsn6):\\s*)?(\\d[a-z\\d]{3})$/i;\r\nconst rePubchem = /^(?:pc|pubchem):\\s*([a-z]+)$/i;\r\nconst reUrlScheme = /^([a-z][a-z\\d\\-+.]*):/i;\r\n\r\nfunction resolveSourceShortcut(source, opts) {\r\n if (!_.isString(source)) {\r\n return source;\r\n }\r\n\r\n // e.g. \"cif:1CRN\"\r\n const matchesPdbId = rePdbId.exec(source);\r\n if (matchesPdbId) {\r\n let [, format = 'pdb', id] = matchesPdbId;\r\n\r\n format = format.toLowerCase();\r\n id = id.toUpperCase();\r\n\r\n switch (format) {\r\n case 'pdb':\r\n source = `https://files.rcsb.org/download/${id}.pdb`;\r\n break;\r\n case 'cif':\r\n source = `https://files.rcsb.org/download/${id}.cif`;\r\n break;\r\n case 'ccp4':\r\n source = `https://www.ebi.ac.uk/pdbe/coordinates/files/${id.toLowerCase()}.ccp4`;\r\n break;\r\n case 'dsn6':\r\n source = `https://edmaps.rcsb.org/maps/${id.toLowerCase()}_2fofc.dsn6`;\r\n break;\r\n default:\r\n throw new Error('Unexpected data format shortcut');\r\n }\r\n\r\n opts.fileType = format;\r\n opts.fileName = `${id}.${format}`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // e.g. \"pc:aspirin\"\r\n const matchesPubchem = rePubchem.exec(source);\r\n if (matchesPubchem) {\r\n const compound = matchesPubchem[1].toLowerCase();\r\n source = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${compound}/JSON?record_type=3d`;\r\n opts.fileType = 'pubchem';\r\n opts.fileName = `${compound}.json`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // otherwise is should be an URL\r\n if (opts.sourceType === 'url' || opts.sourceType === undefined) {\r\n opts.sourceType = 'url';\r\n\r\n // e.g. \"./data/1CRN.pdb\"\r\n if (!reUrlScheme.test(source)) {\r\n source = utils.resolveURL(source);\r\n }\r\n }\r\n\r\n return source;\r\n}\r\n\r\nfunction updateBinaryMode(opts) {\r\n let { binary } = opts;\r\n\r\n // detect by format\r\n if (opts.fileType !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n } else {\r\n throw new Error('Could not find suitable parser for this format');\r\n }\r\n }\r\n\r\n // detect by file extension\r\n if (binary === undefined && opts.fileExt !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ ext: opts.fileExt }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n }\r\n }\r\n\r\n // temporary workaround for animation\r\n if (opts.fileExt !== undefined && opts.fileExt.toLowerCase() === '.man') {\r\n opts.binary = true;\r\n opts.animation = true; // who cares?\r\n }\r\n\r\n // update if detected\r\n if (binary !== undefined) {\r\n if (opts.binary !== undefined && opts.binary !== binary) {\r\n opts.context.logger.warn('Overriding incorrect binary mode');\r\n }\r\n }\r\n\r\n opts.binary = binary || false;\r\n}\r\n\r\nfunction _fetchData(source, opts, job) {\r\n return new Promise(((resolve) => {\r\n if (job.shouldCancel()) {\r\n throw new Error('Operation cancelled');\r\n }\r\n job.notify({ type: 'fetching' });\r\n\r\n // allow for source shortcuts\r\n source = resolveSourceShortcut(source, opts);\r\n\r\n // detect a proper loader\r\n const TheLoader = _.head(io.loaders.find({ type: opts.sourceType, source }));\r\n if (!TheLoader) {\r\n throw new Error(LOADER_NOT_FOUND);\r\n }\r\n\r\n // split file name\r\n const fileName = opts.fileName || TheLoader.extractName(source);\r\n if (fileName) {\r\n const [name, fileExt] = utils.splitFileName(fileName);\r\n _.defaults(opts, { name, fileExt, fileName });\r\n }\r\n\r\n // should it be text or binary?\r\n updateBinaryMode(opts);\r\n\r\n // FIXME: All new settings retrieved from server are applied after the loading is complete. However, we need some\r\n // flags to alter the loading process itself. Here we apply them in advance. Dirty hack. Kill the server, remove\r\n // all hacks and everybody's happy.\r\n let newOptions = _.get(opts, 'preset.expression');\r\n if (!_.isUndefined(newOptions)) {\r\n newOptions = JSON.parse(newOptions);\r\n if (newOptions && newOptions.settings) {\r\n const keys = ['singleUnit'];\r\n for (let keyIndex = 0, keyCount = keys.length; keyIndex < keyCount; ++keyIndex) {\r\n const key = keys[keyIndex];\r\n const value = _.get(newOptions.settings, key);\r\n if (!_.isUndefined(value)) {\r\n settings.set(key, value);\r\n }\r\n }\r\n }\r\n }\r\n\r\n // create a loader\r\n const loader = new TheLoader(source, opts);\r\n loader.context = opts.context;\r\n job.addEventListener('cancel', () => loader.abort());\r\n\r\n loader.addEventListener('progress', (event) => {\r\n if (event.lengthComputable && event.total > 0) {\r\n reportProgress(loader.logger, 'Fetching', event.loaded / event.total);\r\n } else {\r\n reportProgress(loader.logger, 'Fetching');\r\n }\r\n });\r\n\r\n console.time('fetch');\r\n const promise = loader.load()\r\n .then((data) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.info('Fetching finished');\r\n job.notify({ type: 'fetchingDone', data });\r\n return data;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Fetching failed');\r\n job.notify({ type: 'fetchingDone', error });\r\n throw error;\r\n });\r\n resolve(promise);\r\n }));\r\n}\r\n\r\nfunction _parseData(data, opts, job) {\r\n if (job.shouldCancel()) {\r\n return Promise.reject(new Error('Operation cancelled'));\r\n }\r\n\r\n job.notify({ type: 'parsing' });\r\n\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType, ext: opts.fileExt, data }));\r\n if (!TheParser) {\r\n return Promise.reject(new Error('Could not find suitable parser'));\r\n }\r\n\r\n const parser = new TheParser(data, opts);\r\n parser.context = opts.context;\r\n job.addEventListener('cancel', () => parser.abort());\r\n\r\n console.time('parse');\r\n return parser.parse()\r\n .then((dataSet) => {\r\n console.timeEnd('parse');\r\n job.notify({ type: 'parsingDone', data: dataSet });\r\n return dataSet;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('parse');\r\n opts.error = error;\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Parsing failed');\r\n job.notify({ type: 'parsingDone', error });\r\n throw error;\r\n });\r\n}\r\n\r\n/**\r\n * Load molecule asynchronously.\r\n * @param {string|File} source - Molecule source to load (e.g. PDB ID, URL or File object).\r\n * @param {object=} opts - Options.\r\n * @param {string=} opts.sourceType - Data source type (e.g. 'url', 'file').\r\n * @param {string=} opts.fileType - Data contents type (e.g. 'pdb', 'cml').\r\n * @param {string=} opts.mdFile - .nc file path.\r\n * @param {boolean=} opts.keepRepsInfo - prevent reset of object and reps information.\r\n * @returns {Promise} name of the visual that was added to the viewer\r\n */\r\nMiew.prototype.load = function (source, opts) {\r\n opts = _.merge({}, opts, {\r\n context: this,\r\n });\r\n\r\n // for a single-file scenario\r\n if (!this.settings.now.use.multiFile) {\r\n // abort all loaders in progress\r\n if (this._loading.length) {\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n }\r\n\r\n // reset\r\n if (!opts.animation) { // FIXME: sometimes it is set AFTERWARDS!\r\n this.reset(true);\r\n }\r\n }\r\n\r\n this._interpolator.reset();\r\n\r\n this.dispatchEvent({ type: 'loading', options: opts, source });\r\n\r\n const job = new JobHandle();\r\n this._loading.push(job);\r\n job.addEventListener('notification', (e) => {\r\n this.dispatchEvent(e.slaveEvent);\r\n });\r\n\r\n this._spinner.spin(this._container);\r\n\r\n const onLoadEnd = (anything) => {\r\n const jobIndex = this._loading.indexOf(job);\r\n if (jobIndex !== -1) {\r\n this._loading.splice(jobIndex, 1);\r\n }\r\n this._spinner.stop();\r\n this._refreshTitle();\r\n job.notify({ type: 'loadingDone', anything });\r\n return anything;\r\n };\r\n\r\n return _fetchData(source, opts, job)\r\n .then((data) => _parseData(data, opts, job))\r\n .then((object) => {\r\n const name = this._onLoad(object, opts);\r\n return onLoadEnd(name);\r\n })\r\n .catch((err) => {\r\n this.logger.error('Could not load data');\r\n this.logger.debug(err);\r\n throw onLoadEnd(err);\r\n });\r\n};\r\n\r\n/**\r\n * Unload molecule (delete corresponding visual).\r\n * @param {string=} name - name of the visual\r\n */\r\nMiew.prototype.unload = function (name) {\r\n this._removeVisual(name || this.getCurrentVisual());\r\n this.resetPivot();\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n};\r\n\r\n/**\r\n * Start new animation. Now is broken.\r\n * @param fileData - new data to animate\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._startAnimation = function (fileData) {\r\n this._stopAnimation();\r\n const self = this;\r\n const visual = this._getComplexVisual();\r\n if (visual === null) {\r\n this.logger.error('Unable to start animation - no molecule is loaded.');\r\n return;\r\n }\r\n try {\r\n this._frameInfo = new FrameInfo(\r\n visual.getComplex(),\r\n fileData,\r\n {\r\n onLoadStatusChanged() {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo ? self._frameInfo.isLoading : true,\r\n },\r\n });\r\n },\r\n onError(message) {\r\n self._stopAnimation();\r\n self.logger.error(message);\r\n },\r\n },\r\n );\r\n } catch (e) {\r\n this.logger.error('Animation file does not fit to current complex!');\r\n return;\r\n }\r\n this._continueAnimation();\r\n};\r\n\r\n/**\r\n * Pause current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._pauseAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n this._isAnimating = false;\r\n clearInterval(this._animInterval);\r\n this._animInterval = null;\r\n if (this._frameInfo) {\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: this._isAnimating,\r\n isLoading: this._frameInfo.isLoading,\r\n },\r\n });\r\n }\r\n};\r\n\r\n/**\r\n * Continue current animation after pausing. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._continueAnimation = function () {\r\n this._isAnimating = true;\r\n let minFrameTime = 1000 / settings.now.maxfps;\r\n minFrameTime = Number.isNaN(minFrameTime) ? 0 : minFrameTime;\r\n const self = this;\r\n const { pivot } = self._gfx;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.resetSelectionMask();\r\n visual.rebuildSelectionGeometry();\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n }\r\n this._animInterval = setInterval(() => {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo.isLoading,\r\n },\r\n });\r\n if (self._frameInfo.frameIsReady) {\r\n pivot.updateToFrame(self._frameInfo);\r\n self._updateObjsToFrame(self._frameInfo);\r\n self._refreshTitle(` Frame ${self._frameInfo._currFrame} of ${self._frameInfo._framesCount\r\n } time interval - ${self._frameInfo._timeStep}`);\r\n try {\r\n self._frameInfo.nextFrame();\r\n } catch (e) {\r\n self.logger.error('Error during animation');\r\n self._stopAnimation();\r\n return;\r\n }\r\n self._needRender = true;\r\n }\r\n }, minFrameTime);\r\n};\r\n\r\n/**\r\n * Stop current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._stopAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n clearInterval(this._animInterval);\r\n this._frameInfo.disableEvents();\r\n this._frameInfo = null;\r\n this._animInterval = null;\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: null,\r\n });\r\n};\r\n\r\n/**\r\n * Invoked upon successful loading of some data source\r\n * @param {DataSource} dataSource - Data source for visualization (molecular complex or other)\r\n * @param {object} opts - Options.\r\n * @private\r\n */\r\nMiew.prototype._onLoad = function (dataSource, opts) {\r\n const gfx = this._gfx;\r\n let visualName = null;\r\n\r\n if (opts.animation) {\r\n this._refreshTitle();\r\n this._startAnimation(dataSource);\r\n return null;\r\n }\r\n this._stopAnimation();\r\n if (!opts || !opts.keepRepsInfo) {\r\n this._opts.reps = null;\r\n this._opts._objects = null;\r\n }\r\n\r\n if (dataSource.id === 'Complex') {\r\n const complex = dataSource;\r\n\r\n // update title\r\n if (opts.fileName) {\r\n complex.name = complex.name || removeExtension(opts.fileName).toUpperCase();\r\n } else if (opts.amberFileName) {\r\n complex.name = complex.name || removeExtension(opts.amberFileName).toUpperCase();\r\n } else {\r\n complex.name = `Dynamic ${opts.fileType} molecule`;\r\n }\r\n\r\n visualName = this._addVisual(new ComplexVisual(complex.name, complex));\r\n this._curVisualName = visualName;\r\n\r\n const desc = this.info();\r\n this.logger.info(`Parsed ${opts.fileName} (${\r\n desc.atoms} atoms, ${\r\n desc.bonds} bonds, ${\r\n desc.residues} residues, ${\r\n desc.chains} chains).`);\r\n\r\n if (_.isNumber(this._opts.unit)) {\r\n complex.setCurrentUnit(this._opts.unit);\r\n }\r\n\r\n if (opts.preset) {\r\n // ...removed server access...\r\n } else if (settings.now.autoPreset) {\r\n switch (opts.fileType) {\r\n case 'cml':\r\n this.resetReps('small');\r\n break;\r\n case 'pdb':\r\n case 'mmtf':\r\n case 'cif':\r\n if (hasValidResidues(complex)) {\r\n this.resetReps('macro');\r\n } else {\r\n this.resetReps('small');\r\n }\r\n break;\r\n default:\r\n this.resetReps('default');\r\n break;\r\n }\r\n } else {\r\n this.resetReps('default');\r\n }\r\n } else if (dataSource.id === 'Volume') {\r\n this.resetEd();\r\n visualName = this._onLoadEd(dataSource);\r\n }\r\n\r\n gfx.camera.updateProjectionMatrix();\r\n this._updateFog();\r\n\r\n // reset global transform\r\n gfx.root.resetTransform();\r\n this.resetPivot();\r\n\r\n // set scale to fit everything on the screen\r\n this._objectControls.setScale(settings.now.radiusToFit / this._getBSphereRadius());\r\n\r\n this._resetObjects();\r\n\r\n if (settings.now.autoResolution) {\r\n this._tweakResolution();\r\n }\r\n\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n this._refreshTitle();\r\n\r\n return visualName;\r\n};\r\n\r\nMiew.prototype.resetEd = function () {\r\n if (this._edLoader) {\r\n this._edLoader.abort();\r\n this._edLoader = null;\r\n }\r\n\r\n // free all resources\r\n this._removeVisual(this._getVolumeVisual());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype.loadEd = function (source) {\r\n this.resetEd();\r\n\r\n const TheLoader = _.head(io.loaders.find({ source }));\r\n if (!TheLoader) {\r\n this.logger.error(LOADER_NOT_FOUND);\r\n return Promise.reject(new Error(LOADER_NOT_FOUND));\r\n }\r\n\r\n const loader = this._edLoader = new TheLoader(source, { binary: true });\r\n loader.context = this;\r\n return loader.load().then((data) => {\r\n const TheParser = _.head(io.parsers.find({ format: 'ccp4' }));\r\n if (!TheParser) {\r\n throw new Error(PARSER_NOT_FOUND);\r\n }\r\n const parser = new TheParser(data);\r\n parser.context = this;\r\n return parser.parse().then((dataSource) => {\r\n this._onLoadEd(dataSource);\r\n });\r\n }).catch((error) => {\r\n this.logger.error('Could not load ED data');\r\n this.logger.debug(error);\r\n });\r\n};\r\n\r\nMiew.prototype._onLoadEd = function (dataSource) {\r\n dataSource.normalize();\r\n\r\n const volumeVisual = new VolumeVisual('volume', dataSource);\r\n volumeVisual.getMesh().layers.set(gfxutils.LAYERS.VOLUME); // volume mesh is not visible to common render\r\n const visualName = this._addVisual(volumeVisual);\r\n\r\n this._needRender = true;\r\n return visualName;\r\n};\r\n\r\nMiew.prototype._needRebuild = function () {\r\n let needsRebuild = false;\r\n this._forEachComplexVisual((visual) => {\r\n needsRebuild = needsRebuild || visual.needsRebuild();\r\n });\r\n return needsRebuild;\r\n};\r\n\r\nMiew.prototype._rebuildObjects = function () {\r\n const self = this;\r\n const gfx = this._gfx;\r\n let i;\r\n let n;\r\n\r\n // remove old object geometry\r\n const toRemove = [];\r\n for (i = 0; i < gfx.pivot.children.length; ++i) {\r\n const child = gfx.pivot.children[i];\r\n if (!(child instanceof Visual)) {\r\n toRemove.push(child);\r\n }\r\n }\r\n for (i = 0; i < toRemove.length; ++i) {\r\n toRemove[i].parent.remove(toRemove[i]);\r\n }\r\n\r\n setTimeout(() => {\r\n const objList = self._objects;\r\n for (i = 0, n = objList.length; i < n; ++i) {\r\n const obj = objList[i];\r\n if (obj.needsRebuild) {\r\n obj.build();\r\n }\r\n if (obj.getGeometry()) {\r\n gfx.pivot.add(obj.getGeometry());\r\n }\r\n }\r\n }, 10);\r\n};\r\n\r\nMiew.prototype.changeUnit = function (unitIdx, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n throw new Error('There is no complex to change!');\r\n }\r\n\r\n function currentUnitInfo() {\r\n const unit = visual ? visual.getComplex().getCurrentUnit() : 0;\r\n const type = unit > 0 ? (`Bio molecule ${unit}`) : 'Asymmetric unit';\r\n return `Current unit: ${unit} (${type})`;\r\n }\r\n\r\n if (unitIdx === undefined) {\r\n return currentUnitInfo();\r\n }\r\n if (_.isString(unitIdx)) {\r\n unitIdx = Math.max(parseInt(unitIdx, 10), 0);\r\n }\r\n if (visual.getComplex().setCurrentUnit(unitIdx)) {\r\n this._resetScene();\r\n this._updateInfoPanel();\r\n }\r\n return currentUnitInfo();\r\n};\r\n\r\n/**\r\n * Start to rebuild geometry asynchronously.\r\n */\r\nMiew.prototype.rebuild = function () {\r\n if (this._building) {\r\n this.logger.warn('Miew.rebuild(): already building!');\r\n return;\r\n }\r\n this._building = true;\r\n\r\n this.dispatchEvent({ type: 'rebuilding' });\r\n\r\n this._rebuildObjects();\r\n\r\n this._gfx.renderer2d.reset();\r\n\r\n const rebuildActions = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.needsRebuild()) {\r\n rebuildActions.push(visual.rebuild().then(() => new Promise(((resolve) => {\r\n visual.rebuildSelectionGeometry();\r\n resolve();\r\n }))));\r\n }\r\n });\r\n\r\n // Start asynchronous rebuild\r\n const self = this;\r\n this._spinner.spin(this._container);\r\n Promise.all(rebuildActions).then(() => {\r\n self._spinner.stop();\r\n\r\n self._needRender = true;\r\n\r\n self._refreshTitle();\r\n this.dispatchEvent({ type: 'buildingDone' });\r\n self._building = false;\r\n });\r\n};\r\n\r\n/** Mark all representations for rebuilding */\r\nMiew.prototype.rebuildAll = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setNeedsRebuild();\r\n });\r\n};\r\n\r\nMiew.prototype._refreshTitle = function (appendix) {\r\n let title;\r\n appendix = appendix === undefined ? '' : appendix;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n title = visual.getComplex().name;\r\n const rep = visual.repGet(visual.repCurrent());\r\n title += (rep ? ` – ${rep.mode.name} Mode` : '');\r\n } else {\r\n title = Object.keys(this._visuals).length > 0 ? 'Unknown' : 'No Data';\r\n }\r\n title += appendix;\r\n\r\n this.dispatchEvent({ type: 'titleChanged', data: title });\r\n};\r\n\r\nMiew.prototype.setNeedRender = function () {\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._extractRepresentation = function () {\r\n const changed = [];\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCount() === 0) {\r\n return;\r\n }\r\n\r\n const selector = visual.buildSelectorFromMask(1 << visual.getSelectionBit());\r\n const defPreset = settings.now.presets.default;\r\n const res = visual.repAdd({\r\n selector,\r\n mode: defPreset[0].mode.id,\r\n colorer: defPreset[0].colorer.id,\r\n material: defPreset[0].material.id,\r\n });\r\n if (!res) {\r\n if (visual.repCount() === ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n this.logger.warn(`Number of representations is limited to ${ComplexVisual.NUM_REPRESENTATION_BITS}`);\r\n }\r\n return;\r\n }\r\n\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n visual.repCurrent(res.index);\r\n\r\n changed.push(visual.name);\r\n });\r\n\r\n if (changed.length > 0) {\r\n this.logger.report(`New representation from selection for complexes: ${changed.join(', ')}`);\r\n }\r\n};\r\n\r\n/**\r\n * Change current representation list.\r\n * @param {array} reps - Representation list.\r\n */\r\nMiew.prototype._setReps = function (reps) {\r\n reps = reps || (this._opts && this._opts.reps) || [];\r\n this._forEachComplexVisual((visual) => visual.resetReps(reps));\r\n};\r\n\r\n/**\r\n * Apply existing preset to current scene.\r\n * @param preset\r\n */\r\nMiew.prototype.applyPreset = function (preset) {\r\n const { presets } = settings.now;\r\n const presList = [\r\n preset || settings.defaults.preset,\r\n settings.defaults.preset,\r\n Object.keys(presets)[0],\r\n ];\r\n let reps = null;\r\n for (let i = 0; !reps && i < presList.length; ++i) {\r\n settings.set('preset', presList[i]);\r\n reps = presets[settings.now.preset];\r\n if (!reps) {\r\n this.logger.warn(`Unknown preset \"${settings.now.preset}\"`);\r\n }\r\n }\r\n this._setReps(reps);\r\n};\r\n\r\n/**\r\n * Reset current representation list to initial values.\r\n * @param {string} [preset] - The source preset in case of uninitialized representation list.\r\n */\r\nMiew.prototype.resetReps = function (preset) {\r\n const reps = this._opts && this._opts.reps;\r\n if (reps) {\r\n this._setReps(reps);\r\n } else {\r\n this.applyPreset(preset);\r\n }\r\n};\r\n\r\n/**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\nMiew.prototype.repCount = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repCount() : 0;\r\n};\r\n\r\n/**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {string=} [name] - Complex name. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\nMiew.prototype.repCurrent = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n const newIdx = visual ? visual.repCurrent(index) : -1;\r\n if (index && newIdx !== index) {\r\n this.logger.warn(`Representation ${index} was not found. Current rep remains unchanged.`);\r\n }\r\n return newIdx;\r\n};\r\n\r\n/**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {?object} Representation description.\r\n */\r\nMiew.prototype.rep = function (index, rep) {\r\n const visual = this._getComplexVisual('');\r\n if (!visual) {\r\n return null;\r\n }\r\n const res = visual.rep(index, rep);\r\n if (res.status === 'created') {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n } else if (res.status === 'changed') {\r\n this.dispatchEvent({ type: 'repChanged', index: res.index, name: visual.name });\r\n }\r\n return res.desc;\r\n};\r\n\r\n/**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\nMiew.prototype.repGet = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repGet(index) : null;\r\n};\r\n\r\n/**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {number} Index of the new representation.\r\n */\r\nMiew.prototype.repAdd = function (rep, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return -1;\r\n }\r\n\r\n const res = visual.repAdd(rep);\r\n if (res) {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name });\r\n return res.index;\r\n }\r\n return -1;\r\n};\r\n\r\n/**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\nMiew.prototype.repRemove = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n visual.repRemove(index);\r\n this.dispatchEvent({ type: 'repRemoved', index, name });\r\n};\r\n\r\n/**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\nMiew.prototype.repHide = function (index, hide, name) {\r\n this._needRender = true;\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repHide(index, hide) : null;\r\n};\r\n\r\nMiew.prototype._setEditMode = function (mode) {\r\n this._editMode = mode;\r\n\r\n const elem = this._msgMode;\r\n if (elem) {\r\n elem.style.opacity = (mode === EDIT_MODE.COMPLEX) ? 0.0 : 1.0;\r\n\r\n if (mode !== EDIT_MODE.COMPLEX) {\r\n const t = elem.getElementsByTagName('p')[0];\r\n t.innerHTML = (mode === EDIT_MODE.COMPONENT) ? 'COMPONENT EDIT MODE' : 'FRAGMENT EDIT MODE';\r\n }\r\n }\r\n\r\n this.dispatchEvent({ type: 'editModeChanged', data: mode === EDIT_MODE.COMPLEX });\r\n};\r\n\r\nMiew.prototype._enterComponentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const editors = [];\r\n this._forEachComplexVisual((visual) => {\r\n const editor = visual.beginComponentEdit();\r\n if (editor) {\r\n editors.push(editor);\r\n }\r\n });\r\n\r\n if (editors === []) {\r\n return;\r\n }\r\n\r\n this._editors = editors;\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- ON');\r\n this._setEditMode(EDIT_MODE.COMPONENT);\r\n this._objectControls.keysTranslateObj(true);\r\n};\r\n\r\nMiew.prototype._applyComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._needRender = true;\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._enterFragmentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const selectedVisuals = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual instanceof ComplexVisual\r\n && visual.getSelectionCount() > 0) {\r\n selectedVisuals.push(visual);\r\n }\r\n });\r\n\r\n if (selectedVisuals.length !== 1) {\r\n // either we have no selection or\r\n // we have selected atoms in two or more visuals -- not supported\r\n return;\r\n }\r\n\r\n const editor = selectedVisuals[0].beginFragmentEdit();\r\n if (!editor) {\r\n return;\r\n }\r\n this._editors = [editor];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- ON (single bond)');\r\n this._setEditMode(EDIT_MODE.FRAGMENT);\r\n this._objectControls.allowTranslation(false);\r\n this._objectControls.allowAltObjFreeRotation(editor.isFreeRotationAllowed());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._applyFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onPick = function (event) {\r\n if (!settings.now.picking) {\r\n // picking is disabled\r\n return;\r\n }\r\n\r\n if (this._animInterval !== null) {\r\n // animation playback is on\r\n return;\r\n }\r\n\r\n if (this._editMode === EDIT_MODE.FRAGMENT) {\r\n // prevent picking in fragment edit mode\r\n return;\r\n }\r\n\r\n if (this._objectControls.isEditingAltObj()) {\r\n // prevent picking during component rotation\r\n return;\r\n }\r\n\r\n // update last pick & find complex\r\n let complex = null;\r\n if (event.obj.atom) {\r\n complex = event.obj.atom.residue.getChain().getComplex();\r\n this._lastPick = event.obj.atom;\r\n } else if (event.obj.residue) {\r\n complex = event.obj.residue.getChain().getComplex();\r\n this._lastPick = event.obj.residue;\r\n } else if (event.obj.chain) {\r\n complex = event.obj.chain.getComplex();\r\n this._lastPick = event.obj.chain;\r\n } else if (event.obj.molecule) {\r\n complex = event.obj.molecule.complex;\r\n this._lastPick = event.obj.molecule;\r\n } else {\r\n this._lastPick = null;\r\n }\r\n\r\n function _updateSelection(visual) {\r\n visual.updateSelectionMask(event.obj);\r\n visual.rebuildSelectionGeometry();\r\n }\r\n\r\n // update visual\r\n if (complex) {\r\n const visual = this._getVisualForComplex(complex);\r\n if (visual) {\r\n _updateSelection(visual);\r\n this._needRender = true;\r\n }\r\n } else {\r\n this._forEachComplexVisual(_updateSelection);\r\n this._needRender = true;\r\n }\r\n\r\n this._updateInfoPanel();\r\n this.dispatchEvent(event);\r\n};\r\n\r\nMiew.prototype._onKeyDown = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n // editing keys\r\n if (settings.now.editing) {\r\n switch (event.code) {\r\n case 'KeyC':\r\n this._enterComponentEditMode();\r\n break;\r\n case 'KeyF':\r\n this._enterFragmentEditMode();\r\n break;\r\n case 'KeyA':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._applyComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._applyFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n case 'KeyD':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._discardComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._discardFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n default:\r\n }\r\n }\r\n\r\n // other keys\r\n switch (event.code) {\r\n case 'NumpadAdd':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.expandSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n case 'NumpadSubtract':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.shrinkSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nMiew.prototype._onKeyUp = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n if (event.code === 'KeyX') {\r\n this._extractRepresentation();\r\n }\r\n};\r\n\r\nMiew.prototype._updateInfoPanel = function () {\r\n const info = this._msgAtomInfo.getElementsByTagName('p')[0];\r\n let atom;\r\n let residue;\r\n\r\n let count = 0;\r\n this._forEachComplexVisual((visual) => {\r\n count += visual.getSelectionCount();\r\n });\r\n\r\n while (info.firstChild) {\r\n info.removeChild(info.firstChild);\r\n }\r\n\r\n if (count === 0) {\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n return;\r\n }\r\n\r\n let firstLine = `${String(count)} atom${count !== 1 ? 's' : ''} selected`;\r\n if (this._lastPick !== null) {\r\n firstLine += ', the last pick:';\r\n }\r\n let secondLine = '';\r\n let aName = '';\r\n let coordLine = '';\r\n\r\n if (this._lastPick instanceof Atom) {\r\n atom = this._lastPick;\r\n residue = atom.residue;\r\n\r\n aName = atom.name;\r\n const location = (atom.location !== 32) ? String.fromCharCode(atom.location) : ''; // 32 is code of white-space\r\n secondLine = `${atom.element.fullName} #${atom.serial}${location}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}.`;\r\n secondLine += aName;\r\n\r\n coordLine = `Coord: (${atom.position.x.toFixed(2).toString()},\\\r\n ${atom.position.y.toFixed(2).toString()},\\\r\n ${atom.position.z.toFixed(2).toString()})`;\r\n } else if (this._lastPick instanceof Residue) {\r\n residue = this._lastPick;\r\n\r\n secondLine = `${residue._type._fullName}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}`;\r\n } else if (this._lastPick instanceof Chain) {\r\n secondLine = `chain ${this._lastPick._name}`;\r\n } else if (this._lastPick instanceof Molecule) {\r\n secondLine = `molecule ${this._lastPick._name}`;\r\n }\r\n\r\n info.appendChild(document.createTextNode(firstLine));\r\n\r\n if (secondLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(secondLine));\r\n }\r\n\r\n if (coordLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(coordLine));\r\n }\r\n\r\n this._msgAtomInfo.style.opacity = 1.0;\r\n};\r\n\r\nMiew.prototype._getAltObj = function () {\r\n if (this._editors) {\r\n let altObj = null;\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n const nextAltObj = this._editors[i].getAltObj();\r\n if (nextAltObj.objects.length > 0) {\r\n if (altObj) {\r\n // we have selected atoms in two or more visuals -- not supported\r\n altObj = null;\r\n break;\r\n }\r\n altObj = nextAltObj;\r\n }\r\n }\r\n if (altObj) {\r\n return altObj;\r\n }\r\n }\r\n\r\n return {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n};\r\n\r\nMiew.prototype.resetPivot = (function () {\r\n const boundingBox = new THREE.Box3();\r\n const center = new THREE.Vector3();\r\n\r\n return function () {\r\n boundingBox.makeEmpty();\r\n this._forEachVisual((visual) => {\r\n boundingBox.union(visual.getBoundaries().boundingBox);\r\n });\r\n\r\n boundingBox.getCenter(center);\r\n this._objectControls.setPivot(center.negate());\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotResidue = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (residue) {\r\n const visual = this._getVisualForComplex(residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n if (residue._controlPoint) {\r\n center.copy(residue._controlPoint);\r\n } else {\r\n let x = 0;\r\n let y = 0;\r\n let z = 0;\r\n const amount = residue._atoms.length;\r\n for (let i = 0; i < amount; ++i) {\r\n const p = residue._atoms[i].position;\r\n x += p.x / amount;\r\n y += p.y / amount;\r\n z += p.z / amount;\r\n }\r\n center.set(x, y, z);\r\n }\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotAtom = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (atom) {\r\n const visual = this._getVisualForComplex(atom.residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n center.copy(atom.position);\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.getSelectionCenter = (function () {\r\n const _centerInVisual = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n return function (center, includesAtom, selector) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCenter(_centerInVisual, includesAtom, selector || visual.getSelectionBit())) {\r\n center.add(_centerInVisual);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.negate();\r\n return true;\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotSubset = (function () {\r\n const _center = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n function _includesInCurSelection(atom, selectionBit) {\r\n return atom.mask & (1 << selectionBit);\r\n }\r\n\r\n function _includesInSelector(atom, selector) {\r\n return selector.selector.includesAtom(atom);\r\n }\r\n\r\n return function (selector) {\r\n const includesAtom = (selector) ? _includesInSelector : _includesInCurSelection;\r\n\r\n if (this.getSelectionCenter(_center, includesAtom, selector)) {\r\n this._objectControls.setPivot(_center);\r\n this.dispatchEvent({ type: 'transform' });\r\n } else {\r\n this.logger.warn('selection is empty. Center operation not performed');\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Makes a screenshot.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n * @returns {string} Data URL representing the image contents.\r\n */\r\nMiew.prototype.screenshot = function (width, height) {\r\n const gfx = this._gfx;\r\n const deviceWidth = gfx.renderer.domElement.width;\r\n const deviceHeight = gfx.renderer.domElement.height;\r\n\r\n function fov2Tan(fov) {\r\n return Math.tan(THREE.MathUtils.degToRad(0.5 * fov));\r\n }\r\n\r\n function tan2Fov(tan) {\r\n return THREE.MathUtils.radToDeg(Math.atan(tan)) * 2.0;\r\n }\r\n\r\n function getDataURL() {\r\n let dataURL;\r\n const currBrowser = utils.getBrowser();\r\n\r\n if (currBrowser === utils.browserType.SAFARI) {\r\n const canvas = document.createElement('canvas');\r\n const canvasContext = canvas.getContext('2d');\r\n\r\n canvas.width = width === undefined ? deviceWidth : width;\r\n canvas.height = height === undefined ? deviceHeight : height;\r\n\r\n canvasContext.drawImage(gfx.renderer.domElement, 0, 0, canvas.width, canvas.height);\r\n dataURL = canvas.toDataURL('image/png');\r\n } else {\r\n // Copy current canvas to screenshot\r\n dataURL = gfx.renderer.domElement.toDataURL('image/png');\r\n }\r\n return dataURL;\r\n }\r\n height = height || width;\r\n\r\n let screenshotURI;\r\n if ((width === undefined && height === undefined)\r\n || (width === deviceWidth && height === deviceHeight)) {\r\n // renderer.domElement.toDataURL('image/png') returns flipped image in Safari\r\n // It hasn't been resolved yet, but getScreenshotSafari()\r\n // fixes it using an extra canvas.\r\n screenshotURI = getDataURL();\r\n } else {\r\n const originalAspect = gfx.camera.aspect;\r\n const originalFov = gfx.camera.fov;\r\n const originalTanFov2 = fov2Tan(gfx.camera.fov);\r\n\r\n // screenshot should contain the principal area of interest (a centered square touching screen sides)\r\n const areaOfInterestSize = Math.min(gfx.width, gfx.height);\r\n const areaOfInterestTanFov2 = originalTanFov2 * areaOfInterestSize / gfx.height;\r\n\r\n // set appropriate camera aspect & FOV\r\n const shotAspect = width / height;\r\n gfx.renderer.setPixelRatio(1);\r\n gfx.camera.aspect = shotAspect;\r\n gfx.camera.fov = tan2Fov(areaOfInterestTanFov2 / Math.min(shotAspect, 1.0));\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n // resize canvas to the required size of screenshot\r\n gfx.renderer.setDrawingBufferSize(width, height, 1);\r\n\r\n // make screenshot\r\n this._renderFrame(settings.now.stereo);\r\n screenshotURI = getDataURL();\r\n\r\n // restore original camera & canvas proportions\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.camera.aspect = originalAspect;\r\n gfx.camera.fov = originalFov;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.renderer.setDrawingBufferSize(gfx.width, gfx.height, window.devicePixelRatio);\r\n this._needRender = true;\r\n }\r\n\r\n return screenshotURI;\r\n};\r\n\r\n/**\r\n * Makes screenshot and initiates a download.\r\n * @param {string} [filename] - Name of a file. Default to a 'screenshot-XXXXX.png', where XXXXX is a current\r\n * date/time in seconds.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n */\r\nMiew.prototype.screenshotSave = function (filename, width, height) {\r\n const uri = this.screenshot(width, height);\r\n utils.shotDownload(uri, filename);\r\n};\r\n\r\nMiew.prototype.save = function (opts) {\r\n this._export(opts.fileType).then((dataString) => {\r\n const filename = this._visuals[this._curVisualName]._complex.name;\r\n utils.download(dataString, filename, opts.fileType);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone' });\r\n }).catch((error) => {\r\n this.logger.error('Could not export data');\r\n this.logger.debug(error);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone', error });\r\n });\r\n};\r\n\r\nMiew.prototype._tweakResolution = function () {\r\n const maxPerf = [\r\n ['poor', 100],\r\n ['low', 500],\r\n ['medium', 1000],\r\n ['high', 5000],\r\n ['ultra', Number.MAX_VALUE],\r\n ];\r\n\r\n let atomCount = 0;\r\n this._forEachComplexVisual((visual) => {\r\n atomCount += visual.getComplex().getAtomCount();\r\n });\r\n\r\n if (atomCount > 0) {\r\n const performance = this._gfxScore * 10e5 / atomCount;\r\n // set resolution based on estimated performance\r\n for (let i = 0; i < maxPerf.length; ++i) {\r\n if (performance < maxPerf[i][1]) {\r\n this._autoChangeResolution(maxPerf[i][0]);\r\n break;\r\n }\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._autoChangeResolution = function (resolution) {\r\n if (resolution !== settings.now.resolution) {\r\n this.logger.report(`Your rendering resolution was changed to \"${resolution}\" for best performance.`);\r\n }\r\n settings.now.resolution = resolution;\r\n};\r\n\r\n/**\r\n * Save current settings to cookies.\r\n */\r\nMiew.prototype.saveSettings = function () {\r\n this._cookies.setCookie(this._opts.settingsCookie, JSON.stringify(this.settings.getDiffs(true)));\r\n};\r\n\r\n/**\r\n * Load settings from cookies.\r\n */\r\nMiew.prototype.restoreSettings = function () {\r\n try {\r\n const cookie = this._cookies.getCookie(this._opts.settingsCookie);\r\n const diffs = cookie ? JSON.parse(cookie) : {};\r\n this.settings.applyDiffs(diffs, true);\r\n } catch (e) {\r\n this.logger.error(`Cookies parse error: ${e.message}`);\r\n }\r\n};\r\n\r\n/**\r\n * Reset current settings to the defaults.\r\n */\r\nMiew.prototype.resetSettings = function () {\r\n this.settings.reset();\r\n};\r\n\r\n/*\r\n * DANGEROUS and TEMPORARY. The method should change or disappear in future versions.\r\n * @param {string|object} opts - See {@link Miew} constructor.\r\n * @see {@link Miew#set}, {@link Miew#repAdd}, {@link Miew#rep}.\r\n */\r\nMiew.prototype.setOptions = function (opts) {\r\n if (typeof opts === 'string') {\r\n opts = Miew.options.fromAttr(opts);\r\n }\r\n if (opts.reps) {\r\n this._opts.reps = null;\r\n }\r\n _.merge(this._opts, opts);\r\n if (opts.settings) {\r\n this.set(opts.settings);\r\n }\r\n\r\n this._opts._objects = opts._objects;\r\n this._resetObjects();\r\n\r\n if (opts.load) {\r\n this.load(opts.load, { fileType: opts.type });\r\n }\r\n\r\n if (opts.preset) {\r\n settings.now.preset = opts.preset;\r\n }\r\n\r\n if (opts.reps) {\r\n this.resetReps(opts.preset);\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.getComplex().resetCurrentUnit();\r\n if (_.isNumber(opts.unit)) {\r\n visual.getComplex().setCurrentUnit(opts.unit);\r\n }\r\n this.resetView();\r\n this.rebuildAll();\r\n }\r\n};\r\n\r\nMiew.prototype.info = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return {};\r\n }\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n return {\r\n id: metadata.id || complex.name || 'UNKNOWN',\r\n title: (metadata.title && metadata.title.join(' ')) || 'UNKNOWN DATA',\r\n atoms: complex.getAtomCount(),\r\n bonds: complex.getBondCount(),\r\n residues: complex.getResidueCount(),\r\n chains: complex.getChainCount(),\r\n };\r\n};\r\n\r\n/*\r\n * OBJECTS SEGMENT\r\n */\r\n\r\nMiew.prototype.addObject = function (objData, bThrow) {\r\n let Ctor = null;\r\n\r\n if (objData.type === LinesObject.prototype.type) {\r\n Ctor = LinesObject;\r\n }\r\n\r\n if (Ctor === null) {\r\n throw new Error(`Unknown scene object type - ${objData.type}`);\r\n }\r\n\r\n try {\r\n const newObj = new Ctor(objData.params, objData.opts);\r\n this._addSceneObject(newObj);\r\n } catch (error) {\r\n if (!bThrow) {\r\n this.logger.debug(`Error during scene object creation: ${error.message}`);\r\n } else {\r\n throw error;\r\n }\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._addSceneObject = function (sceneObject) {\r\n const visual = this._getComplexVisual();\r\n if (sceneObject.build && visual) {\r\n sceneObject.build(visual.getComplex());\r\n this._gfx.pivot.add(sceneObject.getGeometry());\r\n }\r\n const objects = this._objects;\r\n objects[objects.length] = sceneObject;\r\n};\r\n\r\nMiew.prototype._updateObjsToFrame = function (frameData) {\r\n const objs = this._objects;\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n if (objs[i].updateToFrame) {\r\n objs[i].updateToFrame(frameData);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._resetObjects = function () {\r\n const objs = this._opts._objects;\r\n\r\n this._objects = [];\r\n if (objs) {\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n this.addObject(objs[i], false);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype.removeObject = function (index) {\r\n const obj = this._objects[index];\r\n if (!obj) {\r\n throw new Error(`Scene object with index ${index} does not exist`);\r\n }\r\n obj.destroy();\r\n this._objects.splice(index, 1);\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Get a string with a URL to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {string} URL\r\n */\r\nMiew.prototype.getURL = function (opts) {\r\n return options.toURL(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n })));\r\n};\r\n\r\n/**\r\n * Get a string with a script to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=true] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=true] - when this flag is true, a view information is included\r\n * @returns {string} script\r\n */\r\nMiew.prototype.getScript = function (opts) {\r\n return options.toScript(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: true,\r\n view: true,\r\n })));\r\n};\r\n\r\n/*\r\n * Generates object that represents the current state of representations list\r\n * @param {boolean} compareWithDefaults - when this flag is true, reps list is compared (if possible)\r\n * to preset's defaults and only diffs are generated\r\n */\r\nMiew.prototype._compareReps = function (complexVisual, compareWithDefaults) {\r\n const ans = {};\r\n let repCount = 0;\r\n\r\n if (complexVisual) {\r\n repCount = complexVisual.repCount();\r\n }\r\n\r\n const currPreset = settings.defaults.presets[settings.now.preset];\r\n let compare = compareWithDefaults;\r\n if (currPreset === undefined || currPreset.length > repCount) {\r\n compare = false;\r\n ans.preset = 'empty';\r\n } else if (settings.now.preset !== settings.defaults.preset) {\r\n ans.preset = settings.now.preset;\r\n }\r\n\r\n const repsDiff = [];\r\n let emptyReps = true;\r\n for (let i = 0, n = repCount; i < n; ++i) {\r\n repsDiff[i] = complexVisual.repGet(i).compare(compare ? currPreset[i] : null);\r\n if (!_.isEmpty(repsDiff[i])) {\r\n emptyReps = false;\r\n }\r\n }\r\n if (!emptyReps) {\r\n ans.reps = repsDiff;\r\n }\r\n return ans;\r\n};\r\n\r\n/*\r\n * Obtain object that represents current state of miew (might be used as options in constructor).\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {Object} State object.\r\n */\r\nMiew.prototype.getState = function (opts) {\r\n const state = {};\r\n\r\n opts = _.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n });\r\n\r\n // load\r\n const visual = this._getComplexVisual();\r\n if (visual !== null) {\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n if (metadata.id) {\r\n const format = metadata.format ? `${metadata.format}:` : '';\r\n state.load = format + metadata.id;\r\n }\r\n const unit = complex.getCurrentUnit();\r\n if (unit !== 1) {\r\n state.unit = unit;\r\n }\r\n }\r\n\r\n // representations\r\n const repsInfo = this._compareReps(visual, opts.compact);\r\n if (repsInfo.preset) {\r\n state.preset = repsInfo.preset;\r\n }\r\n\r\n if (repsInfo.reps) {\r\n state.reps = repsInfo.reps;\r\n }\r\n\r\n // objects\r\n const objects = this._objects;\r\n const objectsState = [];\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n objectsState[i] = objects[i].identify();\r\n }\r\n if (objects.length > 0) {\r\n state._objects = objectsState;\r\n }\r\n\r\n // view\r\n if (opts.view) {\r\n state.view = this.view();\r\n }\r\n\r\n // settings\r\n if (opts.settings) {\r\n const diff = this.settings.getDiffs(false);\r\n if (!_.isEmpty(diff)) {\r\n state.settings = diff;\r\n }\r\n }\r\n\r\n return state;\r\n};\r\n\r\n/**\r\n * Get parameter value.\r\n * @param {string} param - Parameter name or path (e.g. 'modes.BS.atom').\r\n * @param {*=} value - Default value.\r\n * @returns {*} Parameter value.\r\n */\r\nMiew.prototype.get = function (param, value) {\r\n return settings.get(param, value);\r\n};\r\n\r\nMiew.prototype._clipPlaneUpdateValue = function (radius) {\r\n const clipPlaneValue = Math.max(\r\n this._gfx.camera.position.z - radius * settings.now.draft.clipPlaneFactor,\r\n settings.now.camNear,\r\n );\r\n\r\n const opts = { clipPlaneValue };\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions(opts);\r\n });\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setUberOptions(opts);\r\n }\r\n }\r\n if (this._picker !== null) {\r\n this._picker.clipPlaneValue = clipPlaneValue;\r\n }\r\n};\r\n\r\nMiew.prototype._fogFarUpdateValue = function () {\r\n if (this._picker !== null) {\r\n if (this._gfx.scene.fog) {\r\n this._picker.fogFarValue = this._gfx.scene.fog.far;\r\n } else {\r\n this._picker.fogFarValue = undefined;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._updateShadowmapMeshes = function (process) {\r\n this._forEachComplexVisual((visual) => {\r\n const reprList = visual._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n process(repr.geo, repr.material);\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._updateMaterials = function (values, needTraverse = false, process = undefined) {\r\n this._forEachComplexVisual((visual) => visual.setMaterialValues(values, needTraverse, process));\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setValues(values);\r\n obj._line.material.needsUpdate = true;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._fogAlphaChanged = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions({\r\n fogAlpha: settings.now.fogAlpha,\r\n });\r\n });\r\n};\r\n\r\nMiew.prototype._embedWebXR = function () {\r\n // switch off\r\n if (settings.now.stereo !== 'WEBVR') {\r\n if (this.webVR) {\r\n this.webVR.disable();\r\n }\r\n this.webVR = null;\r\n return;\r\n }\r\n // switch on\r\n if (!this.webVR) {\r\n this.webVR = new WebVRPoC(() => {\r\n this._requestAnimationFrame(() => this._onTick());\r\n this._needRender = true;\r\n this._onResize();\r\n });\r\n }\r\n this.webVR.enable(this._gfx);\r\n};\r\n\r\nMiew.prototype._initOnSettingsChanged = function () {\r\n const on = (props, func) => {\r\n props = _.isArray(props) ? props : [props];\r\n props.forEach((prop) => {\r\n this.settings.addEventListener(`change:${prop}`, func);\r\n });\r\n };\r\n\r\n on('modes.VD.frame', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.showFrame(settings.now.modes.VD.frame);\r\n this._needRender = true;\r\n });\r\n\r\n on('modes.VD.isoMode', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n });\r\n\r\n on('bg.color', () => {\r\n this._onBgColorChanged();\r\n });\r\n\r\n on('ao', () => {\r\n if (settings.now.ao && !isAOSupported(this._gfx.renderer.getContext())) {\r\n this.logger.warn('Your device or browser does not support ao');\r\n settings.set('ao', false);\r\n } else {\r\n const values = { normalsToGBuffer: settings.now.ao };\r\n this._setUberMaterialValues(values);\r\n }\r\n });\r\n\r\n on('zSprites', () => {\r\n if (settings.now.zSprites && !arezSpritesSupported(this._gfx.renderer.getContext())) {\r\n this.logger.warn('Your device or browser does not support zSprites');\r\n settings.set('zSprites', false);\r\n }\r\n this.rebuildAll();\r\n });\r\n\r\n on('fogColor', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('fogColorEnable', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('bg.transparent', (evt) => {\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n // update materials\r\n this._updateMaterials({ fogTransparent: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('draft.clipPlane', (evt) => {\r\n // update materials\r\n this._updateMaterials({ clipPlane: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('shadow.on', (evt) => {\r\n // update materials\r\n const values = { shadowmap: evt.value, shadowmapType: settings.now.shadow.type };\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.shadowMap.enabled = Boolean(values.shadowmap);\r\n }\r\n this._updateMaterials(values, true);\r\n if (values.shadowmap) {\r\n this._updateShadowCamera();\r\n this._updateShadowmapMeshes(meshutils.createShadowmapMaterial);\r\n } else {\r\n this._updateShadowmapMeshes(meshutils.removeShadowmapMaterial);\r\n }\r\n this._needRender = true;\r\n });\r\n\r\n on('shadow.type', (evt) => {\r\n // update materials if shadowmap is enable\r\n if (settings.now.shadow.on) {\r\n this._updateMaterials({ shadowmapType: evt.value }, true);\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on('shadow.radius', (evt) => {\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].shadow !== undefined) {\r\n const light = this._gfx.scene.children[i];\r\n light.shadow.radius = evt.value;\r\n this._needRender = true;\r\n }\r\n }\r\n });\r\n\r\n on('fps', () => {\r\n this._fps.show(settings.now.fps);\r\n });\r\n\r\n on(['fog', 'fogNearFactor', 'fogFarFactor'], () => {\r\n this._updateFog();\r\n this._needRender = true;\r\n });\r\n\r\n on('fogAlpha', () => {\r\n const { fogAlpha } = settings.now;\r\n if (fogAlpha < 0 || fogAlpha > 1) {\r\n this.logger.warn('fogAlpha must belong range [0,1]');\r\n }\r\n this._fogAlphaChanged();\r\n this._needRender = true;\r\n });\r\n\r\n on('autoResolution', (evt) => {\r\n if (evt.value && !this._gfxScore) {\r\n this.logger.warn('Benchmarks are missed, autoresolution will not work! '\r\n + 'Autoresolution should be set during miew startup.');\r\n }\r\n });\r\n\r\n on('stereo', () => {\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n this._needRender = true;\r\n });\r\n\r\n on(['transparency', 'palette'], () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('resolution', () => {\r\n // update complex visuals\r\n this.rebuildAll();\r\n\r\n // update volume visual\r\n const volume = this._getVolumeVisual();\r\n if (volume) {\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on(['axes', 'fxaa', 'ao',\r\n 'outline.on', 'outline.color', 'outline.threshold', 'outline.thickness'], () => {\r\n this._needRender = true;\r\n });\r\n};\r\n\r\n/**\r\n * Set parameter value.\r\n * @param {string|object} params - Parameter name or path (e.g. 'modes.BS.atom') or even settings object.\r\n * @param {*=} value - Value.\r\n */\r\nMiew.prototype.set = function (params, value) {\r\n settings.set(params, value);\r\n};\r\n\r\n/**\r\n * Select atoms with selection string.\r\n * @param {string} expression - string expression of selection\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\nMiew.prototype.select = function (expression, append) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n let sel = expression;\r\n if (_.isString(expression)) {\r\n sel = selectors.parse(expression).selector;\r\n }\r\n\r\n visual.select(sel, append);\r\n this._lastPick = null;\r\n\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n};\r\n\r\nconst VIEW_VERSION = '1';\r\n\r\n/**\r\n * Get or set view info packed into string.\r\n *\r\n * **Note:** view is stored for *left-handed* cs, euler angles are stored in radians and *ZXY-order*,\r\n *\r\n * @param {string=} expression - Optional string encoded the view\r\n */\r\nMiew.prototype.view = function (expression) {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n let transform = [];\r\n const eulerOrder = 'ZXY';\r\n\r\n function encode() {\r\n const pos = pivot.position;\r\n const scale = self._objectControls.getScale() / settings.now.radiusToFit;\r\n const euler = new THREE.Euler();\r\n euler.setFromQuaternion(self._objectControls.getOrientation(), eulerOrder);\r\n transform = [\r\n pos.x, pos.y, pos.z,\r\n scale,\r\n euler.x, euler.y, euler.z,\r\n ];\r\n return VIEW_VERSION + utils.arrayToBase64(transform, Float32Array);\r\n }\r\n\r\n function decode() {\r\n // backwards compatible: old non-versioned view is the 0th version\r\n if (expression.length === 40) {\r\n expression = `0${expression}`;\r\n }\r\n\r\n const version = expression[0];\r\n transform = utils.arrayFromBase64(expression.substr(1), Float32Array);\r\n\r\n // apply adapter for old versions\r\n if (version !== VIEW_VERSION) {\r\n if (version === '0') {\r\n // cancel radiusToFit included in old views\r\n transform[3] /= 8.0;\r\n } else {\r\n // do nothing\r\n self.logger.warn(`Encoded view version mismatch, stored as ${version} vs ${VIEW_VERSION} expected`);\r\n return;\r\n }\r\n }\r\n\r\n const interpolator = self._interpolator;\r\n const srcView = interpolator.createView();\r\n srcView.position.copy(pivot.position);\r\n srcView.scale = self._objectControls.getScale();\r\n srcView.orientation.copy(self._objectControls.getOrientation());\r\n\r\n const dstView = interpolator.createView();\r\n dstView.position.set(transform[0], transform[1], transform[2]);\r\n\r\n // hack to make preset views work after we moved centering offset to visual nodes\r\n // FIXME should only store main pivot offset in preset\r\n if (self._getComplexVisual()) {\r\n dstView.position.sub(self._getComplexVisual().position);\r\n }\r\n\r\n dstView.scale = transform[3]; // eslint-disable-line prefer-destructuring\r\n dstView.orientation.setFromEuler(new THREE.Euler(transform[4], transform[5], transform[6], eulerOrder));\r\n\r\n interpolator.setup(srcView, dstView);\r\n }\r\n\r\n if (typeof expression === 'undefined') {\r\n return encode();\r\n }\r\n decode();\r\n\r\n return expression;\r\n};\r\n\r\n/*\r\n * Update current view due to viewinterpolator state\r\n */\r\nMiew.prototype._updateView = function () {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n\r\n const interpolator = this._interpolator;\r\n if (!interpolator.wasStarted()) {\r\n interpolator.start();\r\n }\r\n\r\n if (!interpolator.isMoving()) {\r\n return;\r\n }\r\n\r\n const res = interpolator.getCurrentView();\r\n if (res.success) {\r\n const curr = res.view;\r\n pivot.position.copy(curr.position);\r\n self._objectControls.setScale(curr.scale * settings.now.radiusToFit);\r\n self._objectControls.setOrientation(curr.orientation);\r\n this.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n }\r\n};\r\n\r\n/**\r\n * Translate object by vector\r\n * @param {number} x - translation value (Ang) along model's X axis\r\n * @param {number} y - translation value (Ang) along model's Y axis\r\n * @param {number} z - translation value (Ang) along model's Z axis\r\n */\r\nMiew.prototype.translate = function (x, y, z) {\r\n this._objectControls.translatePivot(x, y, z);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Rotate object by Euler angles\r\n * @param {number} x - rotation angle around X axis in radians\r\n * @param {number} y - rotation angle around Y axis in radians\r\n * @param {number} z - rotation angle around Z axis in radians\r\n */\r\nMiew.prototype.rotate = function (x, y, z) {\r\n this._objectControls.rotate(new THREE.Quaternion().setFromEuler(new THREE.Euler(x, y, z, 'XYZ')));\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Scale object by factor\r\n * @param {number} factor - scale multiplier, should greater than zero\r\n */\r\nMiew.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n throw new RangeError('Scale should be greater than zero');\r\n }\r\n this._objectControls.scale(factor);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Center view on selection\r\n * @param {empty | subset | string} selector - defines part of molecule which must be centered (\r\n * empty - center on current selection;\r\n * subset - center on picked atom/residue/molecule;\r\n * string - center on atoms correspond to selection string)\r\n */\r\nMiew.prototype.center = function (selector) {\r\n // no arguments - center on current selection;\r\n if (selector === undefined) {\r\n this.setPivotSubset();\r\n this._needRender = true;\r\n return;\r\n }\r\n // subset with atom or residue - center on picked atom/residue;\r\n if (selector.obj !== undefined && ('atom' in selector.obj || 'residue' in selector.obj)) { // from event with selection\r\n if ('atom' in selector.obj) {\r\n this.setPivotAtom(selector.obj.atom);\r\n } else {\r\n this.setPivotResidue(selector.obj.residue);\r\n }\r\n this._needRender = true;\r\n return;\r\n }\r\n // string - center on atoms correspond to selection string\r\n if (selector.obj === undefined && selector !== '') {\r\n const sel = selectors.parse(selector);\r\n if (sel.error === undefined) {\r\n this.setPivotSubset(sel);\r\n this._needRender = true;\r\n return;\r\n }\r\n }\r\n // empty subset or incorrect/empty string - center on all molecule;\r\n this.resetPivot();\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\nMiew.prototype.within = function (selector, radius) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return selectors.None();\r\n }\r\n\r\n if (selector instanceof String) {\r\n selector = selectors.parse(selector);\r\n }\r\n\r\n const res = visual.within(selector, radius);\r\n if (res) {\r\n visual.rebuildSelectionGeometry();\r\n this._needRender = true;\r\n }\r\n return res;\r\n};\r\n\r\n/**\r\n * Get atom position in 2D canvas coords\r\n * @param {string} fullAtomName - full atom name, like A.38.CG\r\n * @returns {Object} {x, y} or false if atom not found\r\n */\r\nMiew.prototype.projected = function (fullAtomName, complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return false;\r\n }\r\n\r\n const atom = visual.getComplex().getAtomByFullname(fullAtomName);\r\n if (atom === null) {\r\n return false;\r\n }\r\n\r\n const pos = atom.position.clone();\r\n // we consider atom position to be affected only by common complex transform\r\n // ignoring any transformations that may add during editing\r\n this._gfx.pivot.updateMatrixWorldRecursive();\r\n this._gfx.camera.updateMatrixWorldRecursive();\r\n this._gfx.pivot.localToWorld(pos);\r\n pos.project(this._gfx.camera);\r\n\r\n return {\r\n x: (pos.x + 1.0) * 0.5 * this._gfx.width,\r\n y: (1.0 - pos.y) * 0.5 * this._gfx.height,\r\n };\r\n};\r\n\r\n/**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n *\r\n * @param {string=} complexName - complex name\r\n */\r\nMiew.prototype.dssp = function (complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return;\r\n }\r\n visual.getComplex().dssp();\r\n\r\n // rebuild dependent representations (cartoon or ss-colored)\r\n visual._reprList.forEach((rep) => {\r\n if (rep.mode.id === 'CA' || rep.colorer.id === 'SS') {\r\n rep.needsRebuild = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype.exportCML = function () {\r\n const self = this;\r\n\r\n function extractRotation(m) {\r\n const xAxis = new THREE.Vector3();\r\n const yAxis = new THREE.Vector3();\r\n const zAxis = new THREE.Vector3();\r\n m.extractBasis(xAxis, yAxis, zAxis);\r\n xAxis.normalize();\r\n yAxis.normalize();\r\n zAxis.normalize();\r\n const retMat = new THREE.Matrix4();\r\n retMat.identity();\r\n retMat.makeBasis(xAxis, yAxis, zAxis);\r\n return retMat;\r\n }\r\n\r\n function updateCMLData(complex) {\r\n const { root } = self._gfx;\r\n const mat = extractRotation(root.matrixWorld);\r\n const v4 = new THREE.Vector4(0, 0, 0, 0);\r\n const vCenter = new THREE.Vector4(0, 0, 0, 0);\r\n let xml = null;\r\n let ap = null;\r\n\r\n // update atoms in cml\r\n complex.forEachAtom((atom) => {\r\n if (atom.xmlNodeRef && atom.xmlNodeRef.xmlNode) {\r\n xml = atom.xmlNodeRef.xmlNode;\r\n ap = atom.position;\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n v4.applyMatrix4(mat);\r\n xml.setAttribute('x3', v4.x.toString());\r\n xml.setAttribute('y3', v4.y.toString());\r\n xml.setAttribute('z3', v4.z.toString());\r\n xml.removeAttribute('x2');\r\n xml.removeAttribute('y2');\r\n }\r\n });\r\n // update stereo groups in cml\r\n complex.forEachSGroup((sGroup) => {\r\n if (sGroup.xmlNodeRef && sGroup.xmlNodeRef.xmlNode) {\r\n xml = sGroup.xmlNodeRef.xmlNode;\r\n ap = sGroup.getPosition();\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n const cp = sGroup.getCentralPoint();\r\n if (cp === null) {\r\n v4.applyMatrix4(mat);\r\n } else {\r\n vCenter.set(cp.x, cp.y, cp.z, 0.0);\r\n v4.add(vCenter);\r\n v4.applyMatrix4(mat); // pos in global space\r\n vCenter.set(cp.x, cp.y, cp.z, 1.0);\r\n vCenter.applyMatrix4(mat);\r\n v4.sub(vCenter);\r\n }\r\n xml.setAttribute('x', v4.x.toString());\r\n xml.setAttribute('y', v4.y.toString());\r\n xml.setAttribute('z', v4.z.toString());\r\n }\r\n });\r\n }\r\n\r\n const visual = self._getComplexVisual();\r\n const complex = visual ? visual.getComplex() : null;\r\n if (complex && complex.originalCML) {\r\n updateCMLData(complex);\r\n\r\n // serialize xml structure to string\r\n const oSerializer = new XMLSerializer();\r\n return oSerializer.serializeToString(complex.originalCML);\r\n }\r\n\r\n return null;\r\n};\r\n\r\n/**\r\n * Reproduce the RCSB PDB Molecule of the Month style by David S. Goodsell\r\n *\r\n * @see http://pdb101.rcsb.org/motm/motm-about\r\n */\r\nMiew.prototype.motm = function () {\r\n settings.set({\r\n fogColorEnable: true,\r\n fogColor: 0x000000,\r\n outline: { on: true, threshold: 0.01 },\r\n bg: { color: 0xffffff },\r\n });\r\n\r\n this._forEachComplexVisual((visual) => {\r\n const rep = [];\r\n const complex = visual.getComplex();\r\n const palette = palettes.get(settings.now.palette);\r\n for (let i = 0; i < complex.getChainCount(); i++) {\r\n const curChainName = complex._chains[i]._name;\r\n const curChainColor = palette.getChainColor(curChainName);\r\n rep[i] = {\r\n selector: `chain ${curChainName}`,\r\n mode: 'VW',\r\n colorer: ['CB', { color: curChainColor, factor: 0.9 }],\r\n material: 'FL',\r\n };\r\n }\r\n visual.resetReps(rep);\r\n });\r\n};\r\n\r\nMiew.prototype.VERSION = (typeof PACKAGE_VERSION !== 'undefined' && PACKAGE_VERSION) || '0.0.0-dev';\r\n\r\n// Uncomment this to get debug trace:\r\n// Miew.prototype.debugTracer = new utils.DebugTracer(Miew.prototype);\r\n\r\n_.assign(Miew, /** @lends Miew */ {\r\n VERSION: Miew.prototype.VERSION,\r\n\r\n registeredPlugins: [],\r\n\r\n // export namespaces // TODO: WIP: refactoring external interface\r\n chem,\r\n io,\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n utils,\r\n gfx: {\r\n Representation,\r\n },\r\n\r\n /**\r\n * Third-party libraries packaged together with Miew.\r\n *\r\n * @property {object} lodash - [Lodash](https://lodash.com/), a modern JavaScript utility library delivering\r\n * modularity, performance & extras.\r\n * @property {object} three - [three.js](https://threejs.org/), JavaScript 3D library.\r\n *\r\n * @example\r\n * var _ = Miew.thirdParty.lodash;\r\n * var opts = _.merge({ ... }, Miew.options.fromURL(window.location.search));\r\n * var miew = new Miew(opts);\r\n */\r\n thirdParty: {\r\n lodash: _,\r\n three: THREE,\r\n },\r\n});\r\n\r\nexport default Miew;\r\n","import palettes from '../gfx/palettes';\r\nimport settings from '../settings';\r\n\r\nconst modeIdDesc = {\r\n $help: [\r\n 'Rendering mode shortcut',\r\n ' BS - balls and sticks mode',\r\n ' LN - lines mode',\r\n ' LC - licorice mode',\r\n ' VW - van der waals mode',\r\n ' TR - trace mode',\r\n ' TU - tube mode',\r\n ' CA - cartoon mode',\r\n ' SA - isosurface mode',\r\n ' QS - quick surface mode',\r\n ' SE - solvent excluded mode',\r\n ' TX - text mode',\r\n ],\r\n BS: {\r\n $help: [\r\n ' Balls and sticks',\r\n ' aromrad = #aromatic radius',\r\n ' atom = #atom radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n CA: {\r\n $help: [\r\n ' Cartoon',\r\n ' arrow = #arrow size',\r\n ' depth = #depth of surface',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = #',\r\n ' width = #secondary width\\n',\r\n ],\r\n },\r\n LN: {\r\n $help: [\r\n ' Lines',\r\n ' atom = #atom radius',\r\n ' chunkarom = ',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' offsarom = \\n',\r\n ],\r\n },\r\n LC: {\r\n $help: [\r\n ' Licorice',\r\n ' aromrad = #aromatic radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n VW: {\r\n $help: [\r\n ' Van der Waals',\r\n ' nothing\\n',\r\n ],\r\n },\r\n TR: {\r\n $help: [\r\n ' Trace',\r\n ' radius = #tube radius\\n',\r\n ],\r\n },\r\n TU: {\r\n $help: [\r\n ' Tube',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = \\n',\r\n ],\r\n },\r\n SA: {\r\n $help: [\r\n ' Surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n QS: {\r\n $help: [\r\n ' Quick surface',\r\n ' isoValue = ',\r\n ' scale = ',\r\n ' wireframe = ',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n SE: {\r\n $help: [\r\n ' Solvent excluded surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n TX: {\r\n $help: [\r\n ' Text mode',\r\n ' template = string that can include \"{{ id }}\"',\r\n ' it will be replaced by value, id can be one of next:',\r\n ' serial, name, type, sequence, residue, chain, hetatm, water\\n',\r\n ' horizontalAlign = {\"left\", \"right\", \"center\"}',\r\n ' verticalAlign = {\"top\", \"bottom\", \"middle\"}',\r\n ' dx = #offset along x',\r\n ' dy = #offset along y',\r\n ' dz = #offset along z',\r\n ' fg = #text color modificator',\r\n ' could be keyword, named color or hex',\r\n ' fg = #back color modificator',\r\n ' could be keyword, named color or hex',\r\n ' showBg = #if set show background',\r\n ' plate under text',\r\n ],\r\n },\r\n};\r\n\r\nconst colorDesc = {\r\n $help: [\r\n 'Coloring mode shortcut',\r\n ' EL - color by element',\r\n ' CH - color by chain',\r\n ' SQ - color by sequence',\r\n ' RT - color by residue type',\r\n ' SS - color by secondary structure',\r\n ' UN - uniform',\r\n ],\r\n UN: {\r\n $help: [\r\n 'Parameters of coloring modes customization',\r\n ' Uniform',\r\n ' color = #RGB->HEX->dec\\n',\r\n ],\r\n color: {\r\n $help: Object.keys(palettes.get(settings.now.palette).namedColors).sort().join('\\n'),\r\n },\r\n },\r\n};\r\n\r\nconst materialDesc = {\r\n $help: [\r\n 'Material shortcut',\r\n ' DF - diffuse',\r\n ' TR - transparent',\r\n ' SF - soft plastic',\r\n ' PL - glossy plastic',\r\n ' ME - metal',\r\n ' GL - glass',\r\n ],\r\n};\r\n\r\nconst addRepDesc = {\r\n $help: [\r\n 'Short (packed) representation description as a set of variables',\r\n ' s=',\r\n ' selector property',\r\n ' m=[!:[,...]]',\r\n ' render mode property',\r\n ' c=[!:[,...]]',\r\n ' color mode property',\r\n ' mt=',\r\n ' material property',\r\n ],\r\n s: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n m: modeIdDesc,\r\n c: colorDesc,\r\n mt: materialDesc,\r\n};\r\n\r\nconst setGetParameterDesc = {\r\n $help: [\r\n 'Parameters of rendering modes customization: modes',\r\n 'Parameters of colorer customization: colorers',\r\n 'Autobuild: autobuild = (|)',\r\n ],\r\n modes: modeIdDesc,\r\n colorers: colorDesc,\r\n};\r\n\r\nconst help = {\r\n $help: [\r\n 'help (| )',\r\n 'You can get detailed information about command options',\r\n ' using \"help cmd.opt.opt.[...]\"\\n',\r\n ' you can use one line comments',\r\n ' everything started from (#|//) will be skipped',\r\n ' Example: >build //some comment\\n',\r\n 'List of available commands:',\r\n ],\r\n reset: {\r\n $help: [\r\n 'Reload current object, delete all representations',\r\n ' Nothing will work until load new object',\r\n ],\r\n },\r\n load: {\r\n $help: [\r\n 'load (||-f [<*.NC FILE URL STRING>])',\r\n ' Load new pdb object from selected source',\r\n ],\r\n PDBID: {\r\n $help: 'pdb id in remote molecule database',\r\n },\r\n URL: {\r\n $help: 'url to source file',\r\n },\r\n f: {\r\n $help: [\r\n 'open file system dialog to fetch local file',\r\n 'optionally you can determine trajectory file',\r\n 'via URL for *.top model',\r\n ],\r\n },\r\n },\r\n clear: {\r\n $help: 'No args. Clear terminal',\r\n },\r\n add: {\r\n $help: [\r\n 'add [] []',\r\n ' Add new item to representation set with',\r\n ' default or params',\r\n ],\r\n REP_NAME: {\r\n $help: 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n rep: {\r\n $help: [\r\n 'rep [|] []',\r\n ' set current representation by name or index',\r\n ' edit current representation by ',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n remove: {\r\n $help: [\r\n 'remove (|)',\r\n 'Remove representation by name or index',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n },\r\n selector: {\r\n $help: [\r\n 'selector ',\r\n ' set selector from EXPRESSION to current representation',\r\n ],\r\n EXPRESSION: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n },\r\n mode: {\r\n $help: [\r\n 'mode [=...]',\r\n ' set rendering mode and apply parameters to current representation',\r\n ],\r\n MODE_ID: modeIdDesc,\r\n },\r\n color: {\r\n $help: [\r\n 'color [=...]',\r\n ' set colorer and apply parameters to current representation',\r\n ],\r\n COLORER_ID: colorDesc,\r\n },\r\n material: {\r\n $help: [\r\n 'material ',\r\n ' set material to current representation',\r\n ],\r\n MATERIAL_ID: materialDesc,\r\n },\r\n build: {\r\n $help: 'build help str',\r\n add: {\r\n $help: 'build.add',\r\n new: {\r\n $help: [\r\n 'add.new',\r\n 'add.new new line 1',\r\n 'add.new new line 2',\r\n 'add.new new line 3',\r\n ],\r\n },\r\n },\r\n del: {\r\n $help: 'build.del',\r\n },\r\n },\r\n list: {\r\n $help: [\r\n 'list [-e|-s||]',\r\n 'Print representations if no args print list of representations',\r\n ' -e expand list and show all representations',\r\n ' -s show all user-registered selectors',\r\n ' | show only current representation',\r\n ],\r\n },\r\n hide: {\r\n $help: [\r\n 'hide (|)',\r\n 'Hide representation referenced in args',\r\n ],\r\n },\r\n show: {\r\n $help: [\r\n 'show (|)',\r\n 'Show representation referenced in args',\r\n ],\r\n },\r\n get: {\r\n $help: [\r\n 'get ',\r\n 'Print value',\r\n ' - path to option use get.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set: {\r\n $help: [\r\n 'set ',\r\n 'Set with ',\r\n ' - path to option use set.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set_save: {\r\n $help: [\r\n 'set_save',\r\n 'Save current settings to cookie',\r\n ],\r\n },\r\n set_restore: {\r\n $help: [\r\n 'set_restore',\r\n 'Load and apply settings from cookie',\r\n ],\r\n },\r\n set_reset: {\r\n $help: [\r\n 'set_reset',\r\n 'Reset current settings to the defaults',\r\n ],\r\n },\r\n preset: {\r\n $help: [\r\n 'preset []',\r\n 'Reset current representation or set preset to ',\r\n ],\r\n PRESET: {\r\n $help: [\r\n 'default',\r\n 'wire',\r\n 'small',\r\n 'macro',\r\n ],\r\n },\r\n },\r\n unit: {\r\n $help: [\r\n 'unit []',\r\n 'Change current biological structure view. Zero value means asymmetric unit,',\r\n 'positive values set an assembly with corresponding number.',\r\n 'Being called with no parameters command prints current unit information.',\r\n ],\r\n },\r\n view: {\r\n $help: [\r\n 'view []',\r\n 'Get current encoded view or set if ENCODED_VIEW placed as argument',\r\n ],\r\n ENCODED_VIEW: {\r\n $help: [\r\n 'encoded view matrix string (binary code)',\r\n ],\r\n },\r\n },\r\n rotate: {\r\n $help: [\r\n 'rotate (x|y|z) [] [(x|y|z) []]...',\r\n 'Rotate scene',\r\n ],\r\n },\r\n scale: {\r\n $help: [\r\n 'scale ',\r\n 'Scale scene',\r\n ],\r\n },\r\n select: {\r\n $help: [\r\n 'select [as ]',\r\n 'Select atoms using selector defined in SELECTOR_STRING',\r\n ' and if SELECTOR_NAME is defined register it in viewer',\r\n ' you can use it later as a complex selector',\r\n ],\r\n },\r\n within: {\r\n $help: [\r\n 'within of as ',\r\n 'Build within named selector',\r\n ' DISTANCE ',\r\n ' SELECTOR_STRING ',\r\n ' SELECTOR_NAME ',\r\n ],\r\n },\r\n url: {\r\n $help: [\r\n 'url [-s] [-v]',\r\n 'Report URL encoded scene',\r\n ' if -s set that include settings in the URL',\r\n ' if -v set that include view in the URL',\r\n ],\r\n },\r\n screenshot: {\r\n $help: [\r\n 'screenshot [ []]',\r\n 'Make a screenshot of the scene',\r\n ' WIDTH in pixels',\r\n ' HEIGHT in pixels, equal to WIDTH by default',\r\n ],\r\n },\r\n line: {\r\n $help: [\r\n 'line [=]',\r\n 'Draw dashed line between two specified atoms',\r\n ],\r\n },\r\n removeobj: {\r\n $help: [\r\n 'removeobj ',\r\n 'Remove scene object by its index. Indices could be obtained by command',\r\n ],\r\n },\r\n listobj: {\r\n $help: [\r\n 'listobj',\r\n 'Display the list of all existing scene objects',\r\n ],\r\n },\r\n};\r\n\r\nexport default help;\r\n","import _ from 'lodash';\r\nimport Miew from './Miew';\r\nimport { parser as parsercli } from './utils/MiewCLIParser';\r\nimport clihelp from './utils/MiewCLIHelp';\r\nimport logger from './utils/logger';\r\nimport utils from './utils';\r\n\r\nconst {\r\n chem: { selectors },\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n} = Miew;\r\n\r\nfunction None() {\r\n}\r\n\r\nconst NULL = (function () {\r\n const obj = new None();\r\n return function () {\r\n return obj;\r\n };\r\n}());\r\n\r\nclass RepresentationMap {\r\n constructor() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n\r\n get(strId) {\r\n return this.representationMap[strId] || this.representationID[strId] || '';\r\n }\r\n\r\n add(strId, index) {\r\n if (strId === -1) {\r\n return 'Can not create representation: there is no data';\r\n }\r\n\r\n if (index !== undefined) {\r\n if (!this.representationMap.hasOwnProperty(strId)) {\r\n this.representationMap[strId.toString()] = index;\r\n this.representationID[index] = strId.toString();\r\n } else {\r\n return 'This name has already existed, registered without name';\r\n }\r\n }\r\n return `Representation ${strId} successfully added`;\r\n }\r\n\r\n remove(index) {\r\n if (index && this.representationID.hasOwnProperty(index)) {\r\n delete this.representationMap[this.representationID[index]];\r\n delete this.representationID[index];\r\n }\r\n\r\n const sortedKeys = Object.keys(this.representationID).sort();\r\n for (const i in sortedKeys) {\r\n if (sortedKeys.hasOwnProperty(i)) {\r\n const id = sortedKeys[i];\r\n if (id > index) {\r\n this.representationID[id - 1] = this.representationID[id];\r\n this.representationMap[this.representationID[id]] -= 1;\r\n delete this.representationID[id];\r\n }\r\n }\r\n }\r\n }\r\n\r\n clear() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n}\r\n\r\nconst representationsStorage = new RepresentationMap();\r\n\r\nfunction keyRemap(key) {\r\n const keys = {\r\n s: 'selector',\r\n m: 'mode',\r\n c: 'colorer',\r\n mt: 'material',\r\n mode: 'modes',\r\n color: 'colorers',\r\n colorer: 'colorers',\r\n select: 'selector',\r\n material: 'materials',\r\n selector: 'selector',\r\n };\r\n const ans = keys[key];\r\n return ans === undefined ? key : ans;\r\n}\r\n\r\nclass CLIUtils {\r\n list(miew, repMap, key) {\r\n let ret = '';\r\n if (miew && repMap !== undefined) {\r\n if (key === undefined || key === '-e') {\r\n const count = miew.repCount();\r\n\r\n for (let i = 0; i < count; i++) {\r\n ret += this.listRep(miew, repMap, i, key);\r\n }\r\n }\r\n }\r\n return ret;\r\n }\r\n\r\n listRep(miew, repMap, repIndex, key) {\r\n let ret = '';\r\n const rep = miew.repGet(repIndex);\r\n if (!rep) {\r\n logger.warn(`Rep ${repIndex} does not exist!`);\r\n return ret;\r\n }\r\n const index = repIndex;\r\n const repName = repMap.get(index);\r\n\r\n const { mode, colorer } = rep;\r\n const selectionStr = rep.selectorString;\r\n const material = rep.materialPreset;\r\n\r\n ret += `#${index} : ${mode.name}${repName === '' ? '' : `, ${repName}`}\\n`;\r\n\r\n if (key !== undefined) {\r\n ret += ` selection : \"${selectionStr}\"\\n`;\r\n ret += ` mode : (${mode.id}), ${mode.name}\\n`;\r\n ret += ` colorer : (${colorer.id}), ${colorer.name}\\n`;\r\n ret += ` material : (${material.id}), ${material.name}\\n`;\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listSelector(miew, context) {\r\n let ret = '';\r\n\r\n for (const k in context) {\r\n if (context.hasOwnProperty(k)) {\r\n ret += `${k} : \"${context[k]}\"\\n`;\r\n }\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listObjs(miew) {\r\n const objs = miew._objects;\r\n\r\n if (!objs || !Array.isArray(objs) || objs.length === 0) {\r\n return 'There are no objects on the scene';\r\n }\r\n\r\n const strList = [];\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n strList[i] = `${i}: ${objs[i].toString()}`;\r\n }\r\n\r\n return strList.join('\\n');\r\n }\r\n\r\n joinHelpStr(helpData) {\r\n if (helpData instanceof Array) {\r\n return helpData.join('\\n');\r\n }\r\n return helpData;\r\n }\r\n\r\n help(path) {\r\n if (_.isUndefined(path)) {\r\n return `${this.joinHelpStr(clihelp.$help)}\\n${_.slice(_.sortBy(_.keys(clihelp)), 1).join(', ')}\\n`;\r\n }\r\n\r\n const helpItem = _.get(clihelp, path);\r\n return _.isUndefined(helpItem) ? this.help() : `${this.joinHelpStr(helpItem.$help)}\\n`;\r\n }\r\n\r\n load(miew, arg) {\r\n if (miew === undefined || arg === undefined || arg === '-f') {\r\n return;\r\n }\r\n miew.awaitWhileCMDisInProcess();\r\n const finish = () => miew.finishAwaitingCMDInProcess();\r\n miew.load(arg).then(finish, finish);\r\n }\r\n\r\n checkArg(key, arg, modificate) {\r\n if (key !== undefined && arg !== undefined) {\r\n if (keyRemap(key) === 'selector') {\r\n const res = selectors.parse(arg);\r\n\r\n if (res.error !== undefined) {\r\n const selExc = { message: res.error };\r\n throw selExc;\r\n }\r\n\r\n if (modificate !== undefined && modificate) {\r\n return res.selector;\r\n }\r\n return arg;\r\n }\r\n\r\n const modificators = {\r\n colorers,\r\n modes,\r\n materials,\r\n };\r\n\r\n let modificator = key;\r\n let temp;\r\n while (modificator !== temp) {\r\n temp = modificator;\r\n modificator = keyRemap(temp);\r\n }\r\n\r\n if (modificators[modificator].get(arg) === undefined) {\r\n const exc = { message: `${arg} is not existed in ${modificator}` };\r\n throw exc;\r\n }\r\n return arg;\r\n }\r\n return NULL;\r\n }\r\n\r\n propagateProp(path, arg) {\r\n if (path !== undefined) {\r\n let argExc = {};\r\n const adapter = options.adapters[typeof _.get(settings.defaults, path)];\r\n if (adapter === undefined) {\r\n const pathExc = { message: `${path} is not existed` };\r\n throw pathExc;\r\n }\r\n\r\n if ((path.endsWith('.color') || path.endsWith('.baseColor')\r\n || path.endsWith('.EL.carbon')) && typeof arg !== 'number') {\r\n arg = palettes.get(settings.now.palette).getNamedColor(arg);\r\n }\r\n\r\n if (path.endsWith('.fg') || path.endsWith('.bg')) {\r\n if (typeof arg !== 'number') {\r\n const val = palettes.get(settings.now.palette).getNamedColor(arg, true);\r\n if (val !== undefined) {\r\n arg = `0x${val.toString(16)}`;\r\n }\r\n } else {\r\n arg = `0x${arg.toString(16)}`;\r\n }\r\n }\r\n\r\n if (path.endsWith('.template')) {\r\n arg = arg.replace(/\\\\n/g, '\\n');// NOSONAR\r\n }\r\n\r\n if (arg !== undefined && adapter(arg) !== arg && adapter(arg) !== (arg > 0)) {\r\n argExc = { message: `${path} must be a \"${typeof _.get(settings.defaults, path)}\"` };\r\n throw argExc;\r\n }\r\n }\r\n return arg;\r\n }\r\n\r\n unquoteString(value) {\r\n return utils.unquoteString(value);\r\n }\r\n}\r\n// repIndexOrRepMap could be RepresentationMap or index\r\n\r\nconst utilFunctions = new CLIUtils();\r\n\r\nfunction CreateObjectPair(a, b) {\r\n const obj = {};\r\n obj[a] = b;\r\n return obj;\r\n}\r\n\r\nfunction ArgList(arg) {\r\n if (arg instanceof this.constructor) {\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n}\r\n\r\nArgList.prototype.append = function (value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n};\r\n\r\nArgList.prototype.remove = function (value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n};\r\n\r\nArgList.prototype.toJSO = function (cliUtils, cmd, arg) {\r\n const res = {};\r\n\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n _.set(res, list[i].id, cliUtils.propagateProp(`${keyRemap(cmd)}.${arg}.${list[i].id}`, list[i].val));\r\n }\r\n\r\n return res;\r\n};\r\n\r\nfunction Arg(_id, _val) {\r\n this.id = _id;\r\n this.val = _val;\r\n}\r\n\r\nconst cliutils = Object.create({});\r\n\r\ncliutils.Arg = Arg;\r\ncliutils.ArgList = ArgList;\r\n\r\ncliutils.miew = null;\r\ncliutils.echo = null;\r\ncliutils.representations = representationsStorage;\r\ncliutils.utils = utilFunctions;\r\n\r\ncliutils._ = _;\r\ncliutils.CreateObjectPair = CreateObjectPair;\r\ncliutils.keyRemap = keyRemap;\r\ncliutils.Context = selectors.Context;\r\ncliutils.ClearContext = selectors.ClearContext;\r\n\r\ncliutils.NULL = NULL;\r\n\r\ncliutils.notimplemented = function () {\r\n return this.NULL;\r\n};\r\n\r\nMiew.prototype.script = function (script, _printCallback, _errorCallback) {\r\n parsercli.yy.miew = this;\r\n parsercli.yy.echo = _printCallback;\r\n parsercli.yy.error = _errorCallback;\r\n if (this.cmdQueue === undefined) {\r\n this.cmdQueue = [];\r\n }\r\n\r\n if (this.commandInAction === undefined) {\r\n this.commandInAction = false;\r\n }\r\n\r\n this.cmdQueue = this.cmdQueue.concat(script.split('\\n'));\r\n};\r\n\r\nMiew.prototype.awaitWhileCMDisInProcess = function () {\r\n this.commandInAction = true;\r\n};\r\n\r\nMiew.prototype.finishAwaitingCMDInProcess = function () {\r\n this.commandInAction = false;\r\n};\r\n\r\nMiew.prototype.isScriptingCommandAvailable = function () {\r\n return this.commandInAction !== undefined\r\n && !this.commandInAction\r\n && this.cmdQueue !== undefined\r\n && this.cmdQueue.length > 0;\r\n};\r\n\r\nMiew.prototype.callNextCmd = function () {\r\n if (this.isScriptingCommandAvailable()) {\r\n const cmd = this.cmdQueue.shift();\r\n\r\n const res = {};\r\n res.success = false;\r\n try {\r\n parsercli.parse(cmd);\r\n res.success = true;\r\n } catch (e) {\r\n res.error = e.message;\r\n parsercli.yy.error(res.error);\r\n this.finishAwaitingCMDInProcess();\r\n }\r\n return res;\r\n }\r\n return '';\r\n};\r\n\r\nparsercli.yy = cliutils;\r\n// workaround for incorrect JISON parser generator for AMD module\r\nparsercli.yy.parseError = parsercli.parseError;\r\n","import Miew from './Miew';\r\nimport './Miew-cli';\r\n\r\nexport default 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function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.miew.reset(false); yy.ClearContext(); yy.miew.resetReps(\"empty\");\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.miew.rebuild();\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.miew.rebuildAll(); yy.miew.rebuild();\r\nbreak;\r\ncase 6:\r\nthis.$ = yy.echo(yy.utils.help().toString());\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.echo(yy.utils.help($$[$0]).toString());\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.miew.motm();\r\nbreak;\r\ncase 10: case 11:\r\nthis.$ = yy.utils.propagateProp($$[$0]); yy.echo(yy.miew.get($$[$0]).toString());\r\nbreak;\r\ncase 12: case 13:\r\nthis.$ = yy.miew.set($$[$0-1], yy.utils.propagateProp($$[$0-1], $$[$0]));;\r\nbreak;\r\ncase 14:\r\nthis.$ = yy.miew.saveSettings();;\r\nbreak;\r\ncase 15:\r\nthis.$ = yy.miew.restoreSettings();;\r\nbreak;\r\ncase 16:\r\nthis.$ = yy.miew.resetSettings();;\r\nbreak;\r\ncase 17:\r\nthis.$ = yy.miew.resetReps();\r\nbreak;\r\ncase 18:\r\nthis.$ = yy.miew.applyPreset($$[$0]);\r\nbreak;\r\ncase 21:\r\nthis.$ = yy.miew.repRemove($$[$0]); yy.representations.remove($$[$0]);\r\nbreak;\r\ncase 22:\r\nthis.$ = yy.miew.repHide($$[$0]);\r\nbreak;\r\ncase 23:\r\nthis.$ = yy.miew.repHide($$[$0], false);\r\nbreak;\r\ncase 24:\r\nthis.$ = yy.echo(yy.utils.listRep(yy.miew, yy.representations, $$[$0], '-e'));\r\nbreak;\r\ncase 25:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations));\r\nbreak;\r\ncase 26:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations, $$[$0]));\r\nbreak;\r\ncase 27:\r\nthis.$ = yy.echo(yy.utils.listSelector(yy.miew, yy.Context));\r\nbreak;\r\ncase 28:\r\nthis.$ = yy.miew.select(yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0], true));\r\nbreak;\r\ncase 29:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.utils.checkArg($$[$0-3].toLowerCase(), $$[$0-2], true); yy.miew.select(yy.Context[$$[$0].toLowerCase()]);\r\nbreak;\r\ncase 30:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {selector : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0])});\r\nbreak;\r\ncase 31:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.miew.within(yy.utils.checkArg(\"select\", $$[$0-2], true), Number($$[$0-4]));\r\nbreak;\r\ncase 32:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {material : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 35:\r\nthis.$ = yy.echo(yy.miew.view());\r\nbreak;\r\ncase 36: case 37:\r\nthis.$ = yy.miew.view($$[$0]);\r\nbreak;\r\ncase 38:\r\nthis.$ = yy.echo(yy.miew.changeUnit());\r\nbreak;\r\ncase 39:\r\nthis.$ = yy.echo(yy.miew.changeUnit($$[$0]));\r\nbreak;\r\ncase 40:\r\nthis.$ = yy.miew.dssp();\r\nbreak;\r\ncase 41:\r\nthis.$ = yy.miew.scale($$[$0]);\r\nbreak;\r\ncase 42:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.rotate($$[$0][i]['x'] * Math.PI / 180.0, $$[$0][i]['y'] * Math.PI / 180.0, $$[$0][i]['z'] * Math.PI / 180.0)} \r\nbreak;\r\ncase 43:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.translate($$[$0][i]['x'] || 0, $$[$0][i]['y'] || 0, $$[$0][i]['z'] || 0)} \r\nbreak;\r\ncase 44:\r\nthis.$ = yy.miew.center();\r\nbreak;\r\ncase 45:\r\nthis.$ = yy.miew.center($$[$0]);\r\nbreak;\r\ncase 48: case 49:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-1], $$[$0]]}, true);\r\nbreak;\r\ncase 50: case 51:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-2], $$[$0-1]], opts:$$[$0].toJSO(yy.utils, 'objects', 'line')}, true);\r\nbreak;\r\ncase 52:\r\nthis.$ = yy.echo(yy.utils.listObjs(yy.miew));\r\nbreak;\r\ncase 53:\r\nthis.$ = yy.miew.removeObject($$[$0]);\r\nbreak;\r\ncase 54:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: false}));\r\nbreak;\r\ncase 55:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: true}));\r\nbreak;\r\ncase 56:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: false}));\r\nbreak;\r\ncase 57: case 58:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: true}));\r\nbreak;\r\ncase 59:\r\nthis.$ = yy.miew.screenshotSave();\r\nbreak;\r\ncase 60:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0]));\r\nbreak;\r\ncase 61:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0-1]), Number($$[$0]));\r\nbreak;\r\ncase 62: case 63: case 64:\r\nthis.$ = yy.utils.load(yy.miew, $$[$0]); yy.representations.clear();\r\nbreak;\r\ncase 65:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd()));\r\nbreak;\r\ncase 66:\r\nthis.$ = yy.echo(yy.representations.add($$[$0], yy.miew.repAdd()));\r\nbreak;\r\ncase 67:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 68:\r\nthis.$ = yy.echo(yy.representations.add($$[$0-1], yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 69:\r\nthis.$ = yy.miew.rep($$[$0]); yy.miew.repCurrent($$[$0]);\r\nbreak;\r\ncase 70:\r\nthis.$ = yy.miew.rep($$[$0-1], $$[$0]); yy.miew.repCurrent($$[$0-1]);\r\nbreak;\r\ncase 71:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 72:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 73:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 74:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 75:\r\nthis.$ = Number(yy.representations.get($$[$0]));\r\nbreak;\r\ncase 76: case 92:\r\nthis.$ = Number($$[$0]);\r\nbreak;\r\ncase 77:\r\nthis.$ = $$[$0];\r\nbreak;\r\ncase 78:\r\nthis.$ = yy._.assign($$[$0-1], $$[$0]);\r\nbreak;\r\ncase 79:\r\nthis.$ = yy._.assign($$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 80:\r\nthis.$ = yy._.assign($$[$0-3], $$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 81: case 82:\r\nthis.$ = yy.CreateObjectPair($$[$0].key, $$[$0].val);\r\nbreak;\r\ncase 83:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].key, new Array($$[$0-1].val, $$[$0].toJSO(yy.utils, $$[$0-1].key, $$[$0-1].val)));\r\nbreak;\r\ncase 84: case 85:\r\nthis.$ = Object.create({'key': yy.keyRemap($$[$0-2]), 'val': yy.utils.checkArg($$[$0-2], $$[$0])});\r\nbreak;\r\ncase 86:\r\nthis.$ = [$$[$0]];\r\nbreak;\r\ncase 87:\r\nthis.$ = $$[$0-1].concat($$[$0]);\r\nbreak;\r\ncase 88:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].toLowerCase(), Number($$[$0]));\r\nbreak;\r\ncase 89:\r\nthis.$ = new yy.ArgList($$[$0]);\r\nbreak;\r\ncase 90:\r\nthis.$ = $$[$0-1].append($$[$0]);\r\nbreak;\r\ncase 91:\r\nthis.$ = new yy.Arg($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 93:\r\nthis.$ = parseInt($$[$0]);\r\nbreak;\r\ncase 94:\r\nthis.$ = JSON.parse($$[$0]);\r\nbreak;\r\ncase 95: case 96:\r\nthis.$ = String($$[$0]);\r\nbreak;\r\ncase 157: case 158: case 161: case 162: case 163:\r\nthis.$ = $$[$0-2] + $$[$0-1] + $$[$0] //cause of could be color word in path;\r\nbreak;\r\ncase 166:\r\nthis.$ = $$[$0-2] = $$[$0-2] + $$[$0-1] + $$[$0];\r\nbreak;\r\n}\r\n},\r\ntable: 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,[2,90]),{14:$VS,16:197,35:$VT,38:$VU,77:$VV,78:$VW},{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,33:$Ve,34:$Vf,35:[1,199],37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,79:198,80:52,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN},o($V41,[2,84]),o($V31,[2,85]),{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,32:200,33:$Ve,34:$Vf,37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,70:$Vx,72:$Vy,74:$Vz,79:184,80:52,81:185,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN,96:$VO,97:$VP,98:$VQ,99:$VR},{5:[2,80]},o($V31,[2,91]),o($V61,[2,157]),o($V61,[2,158]),{5:[2,31]}],\r\ndefaultActions: {3:[2,2],4:[2,3],7:[2,8],8:[2,9],11:[2,14],12:[2,15],13:[2,16],15:[2,19],16:[2,20],25:[2,33],26:[2,34],29:[2,40],34:[2,46],35:[2,47],37:[2,52],46:[2,1],47:[2,5],107:[2,11],110:[2,18],116:[2,21],119:[2,22],120:[2,23],121:[2,24],122:[2,26],123:[2,27],125:[2,30],127:[2,32],128:[2,36],129:[2,37],130:[2,39],131:[2,41],136:[2,45],139:[2,53],140:[2,62],141:[2,63],142:[2,64],143:[2,164],145:[2,67],158:[2,12],159:[2,13],166:[2,68],174:[2,70],177:[2,57],178:[2,58],179:[2,61],183:[2,29],184:[2,99],185:[2,100],196:[2,80],200:[2,31]},\r\nparseError: function parseError (str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function(match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex () {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin (condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState () {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules () {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState (n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState (condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* ignore whitespace */\r\nbreak;\r\ncase 1:return '';\r\nbreak;\r\ncase 2:return '';\r\nbreak;\r\ncase 3:return 42;\r\nbreak;\r\ncase 4:return 35;\r\nbreak;\r\ncase 5:return 77;\r\nbreak;\r\ncase 6:return 78;\r\nbreak;\r\ncase 7:return 78;\r\nbreak;\r\ncase 8:return 8;\r\nbreak;\r\ncase 9:return 6;\r\nbreak;\r\ncase 10:return 82;\r\nbreak;\r\ncase 11:return 7;\r\nbreak;\r\ncase 12:return 9;\r\nbreak;\r\ncase 13:return 59;\r\nbreak;\r\ncase 14:return 13\r\nbreak;\r\ncase 15:return 15\r\nbreak;\r\ncase 16:return 17\r\nbreak;\r\ncase 17:return 18\r\nbreak;\r\ncase 18:return 19\r\nbreak;\r\ncase 19:return 20\r\nbreak;\r\ncase 20:return 11\r\nbreak;\r\ncase 21:return 62\r\nbreak;\r\ncase 22:return 64\r\nbreak;\r\ncase 23:return 23\r\nbreak;\r\ncase 24:return 25\r\nbreak;\r\ncase 25:return 26\r\nbreak;\r\ncase 26:return 27\r\nbreak;\r\ncase 27:return 30\r\nbreak;\r\ncase 28:return 34\r\nbreak;\r\ncase 29:return 33\r\nbreak;\r\ncase 30:return 65\r\nbreak;\r\ncase 31:return 66\r\nbreak;\r\ncase 32:return 37\r\nbreak;\r\ncase 33:return 41\r\nbreak;\r\ncase 34:return 43\r\nbreak;\r\ncase 35:return 52\r\nbreak;\r\ncase 36:return 54\r\nbreak;\r\ncase 37:return 55\r\nbreak;\r\ncase 38:return 46\r\nbreak;\r\ncase 39:return 48\r\nbreak;\r\ncase 40:return 45\r\nbreak;\r\ncase 41:return 49\r\nbreak;\r\ncase 42:return 56\r\nbreak;\r\ncase 43:return 58;\r\nbreak;\r\ncase 44:return 44\r\nbreak;\r\ncase 45:return 83\r\nbreak;\r\ncase 46:return 84\r\nbreak;\r\ncase 47:return 85\r\nbreak;\r\ncase 48:return 86\r\nbreak;\r\ncase 49:return 87\r\nbreak;\r\ncase 50:return 88\r\nbreak;\r\ncase 51:return 89\r\nbreak;\r\ncase 52:return 90\r\nbreak;\r\ncase 53:return 91\r\nbreak;\r\ncase 54:return 92\r\nbreak;\r\ncase 55:return 93\r\nbreak;\r\ncase 56:return 94\r\nbreak;\r\ncase 57:return 95\r\nbreak;\r\ncase 58:return 70\r\nbreak;\r\ncase 59:return 70\r\nbreak;\r\ncase 60:return 72\r\nbreak;\r\ncase 61:return 72\r\nbreak;\r\ncase 62:return 74\r\nbreak;\r\ncase 63:return 74\r\nbreak;\r\ncase 64:return 74\r\nbreak;\r\ncase 65:return 31\r\nbreak;\r\ncase 66:return 36\r\nbreak;\r\ncase 67:return 96\r\nbreak;\r\ncase 68:return 97\r\nbreak;\r\ncase 69:return 98\r\nbreak;\r\ncase 70:return 99\r\nbreak;\r\ncase 71:yy_.yytext = yy.utils.unquoteString(yy_.yytext); return 14;\r\nbreak;\r\ncase 72:return 38;\r\nbreak;\r\ncase 73:return 5;\r\nbreak;\r\ncase 74:return 101;\r\nbreak;\r\ncase 75:return 103;\r\nbreak;\r\ncase 76:return '\\\\';\r\nbreak;\r\ncase 77:return 28\r\nbreak;\r\ncase 78:return 61\r\nbreak;\r\ncase 79:return 29\r\nbreak;\r\ncase 80:return 57\r\nbreak;\r\ncase 81:return 71\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:[#].*)/i,/^(?:\\/\\/.*)/i,/^(?:([_A-Z0-9\\/\\+]+==))/i,/^(?:-?[0-9]+(\\.[0-9]+)?\\b)/i,/^(?:0[xX][0-9A-F]+\\b)/i,/^(?:false\\b)/i,/^(?:true\\b)/i,/^(?:all\\b)/i,/^(?:reset\\b)/i,/^(?:clear\\b)/i,/^(?:build\\b)/i,/^(?:help\\b)/i,/^(?:load\\b)/i,/^(?:get\\b)/i,/^(?:set\\b)/i,/^(?:set_save\\b)/i,/^(?:set_restore\\b)/i,/^(?:set_reset\\b)/i,/^(?:preset\\b)/i,/^(?:motm\\b)/i,/^(?:add\\b)/i,/^(?:rep\\b)/i,/^(?:remove\\b)/i,/^(?:hide\\b)/i,/^(?:show\\b)/i,/^(?:list\\b)/i,/^(?:select\\b)/i,/^(?:within\\b)/i,/^(?:selector\\b)/i,/^(?:mode\\b)/i,/^(?:color\\b)/i,/^(?:material\\b)/i,/^(?:view\\b)/i,/^(?:unit\\b)/i,/^(?:line\\b)/i,/^(?:listobj\\b)/i,/^(?:removeobj\\b)/i,/^(?:rotate\\b)/i,/^(?:translate\\b)/i,/^(?:scale\\b)/i,/^(?:center\\b)/i,/^(?:url\\b)/i,/^(?:screenshot\\b)/i,/^(?:dssp\\b)/i,/^(?:file_list\\b)/i,/^(?:file_register\\b)/i,/^(?:file_delete\\b)/i,/^(?:preset_add\\b)/i,/^(?:preset_delete\\b)/i,/^(?:preset_update\\b)/i,/^(?:preset_rename\\b)/i,/^(?:preset_open\\b)/i,/^(?:create_scenario\\b)/i,/^(?:reset_scenario\\b)/i,/^(?:delete_scenario\\b)/i,/^(?:add_scenario_item\\b)/i,/^(?:list_scenario\\b)/i,/^(?:s\\b)/i,/^(?:mt\\b)/i,/^(?:m\\b)/i,/^(?:c\\b)/i,/^(?:x\\b)/i,/^(?:y\\b)/i,/^(?:z\\b)/i,/^(?:as\\b)/i,/^(?:of\\b)/i,/^(?:pdb\\b)/i,/^(?:delay\\b)/i,/^(?:prst\\b)/i,/^(?:desc\\b)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:\\.)/i,/^(?:\\/)/i,/^(?:\\\\)/i,/^(?:-e\\b)/i,/^(?:-f\\b)/i,/^(?:-s\\b)/i,/^(?:-v\\b)/i,/^(?:=)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","/* eslint-disable */\r\n// DO NOT EDIT! Automatically generated from .jison\r\n/* parser generated by jison 0.4.18 */\r\n/*\r\n Returns a Parser object of the following structure:\r\n\r\n Parser: {\r\n yy: {}\r\n }\r\n\r\n Parser.prototype: {\r\n yy: {},\r\n trace: function(),\r\n symbols_: {associative list: name ==> number},\r\n terminals_: {associative list: number ==> name},\r\n productions_: [...],\r\n performAction: function anonymous(yytext, yyleng, yylineno, yy, yystate, $$, _$),\r\n table: [...],\r\n defaultActions: {...},\r\n parseError: function(str, hash),\r\n parse: function(input),\r\n\r\n lexer: {\r\n EOF: 1,\r\n parseError: function(str, hash),\r\n setInput: function(input),\r\n input: function(),\r\n unput: function(str),\r\n more: function(),\r\n less: function(n),\r\n pastInput: function(),\r\n upcomingInput: function(),\r\n showPosition: function(),\r\n test_match: function(regex_match_array, rule_index),\r\n next: function(),\r\n lex: function(),\r\n begin: function(condition),\r\n popState: function(),\r\n _currentRules: function(),\r\n topState: function(),\r\n pushState: function(condition),\r\n\r\n options: {\r\n ranges: boolean (optional: true ==> token location info will include a .range[] member)\r\n flex: boolean (optional: true ==> flex-like lexing behaviour where the rules are tested exhaustively to find the longest match)\r\n backtrack_lexer: boolean (optional: true ==> lexer regexes are tested in order and for each matching regex the action code is invoked; the lexer terminates the scan when a token is returned by the action code)\r\n },\r\n\r\n performAction: function(yy, yy_, $avoiding_name_collisions, YY_START),\r\n rules: [...],\r\n conditions: {associative list: name ==> set},\r\n }\r\n }\r\n\r\n\r\n token location info (@$, _$, etc.): {\r\n first_line: n,\r\n last_line: n,\r\n first_column: n,\r\n last_column: n,\r\n range: [start_number, end_number] (where the numbers are indexes into the input string, regular zero-based)\r\n }\r\n\r\n\r\n the parseError function receives a 'hash' object with these members for lexer and parser errors: {\r\n text: (matched text)\r\n token: (the produced terminal token, if any)\r\n line: (yylineno)\r\n }\r\n while parser (grammar) errors will also provide these members, i.e. parser errors deliver a superset of attributes: {\r\n loc: (yylloc)\r\n expected: (string describing the set of expected tokens)\r\n recoverable: (boolean: TRUE when the parser has a error recovery rule available for this particular error)\r\n }\r\n*/\r\nvar parser = (function(){\r\nvar o=function(k,v,o,l){for(o=o||{},l=k.length;l--;o[k[l]]=v);return o},$V0=[1,4],$V1=[1,5],$V2=[1,6],$V3=[1,7],$V4=[1,8],$V5=[1,9],$V6=[1,11],$V7=[1,12],$V8=[5,7,8,11],$V9=[1,17],$Va=[1,22],$Vb=[1,20],$Vc=[1,21],$Vd=[5,7,8,11,19];\r\nvar parser = {trace: function trace() { },\r\nyy: {},\r\nsymbols_: {\"error\":2,\"Program\":3,\"Expression\":4,\"EOF\":5,\"Selector\":6,\"OR\":7,\"AND\":8,\"NOT\":9,\"(\":10,\")\":11,\"SELECTOR\":12,\"NAMED_SELECTOR\":13,\"SELECTOR_RANGED\":14,\"RangeList\":15,\"SELECTOR_NAMED\":16,\"NameList\":17,\"Range\":18,\",\":19,\"NUMBER\":20,\":\":21,\"Name\":22,\"IDENTIFIER\":23,\"STRING\":24,\"$accept\":0,\"$end\":1},\r\nterminals_: {2:\"error\",5:\"EOF\",7:\"OR\",8:\"AND\",9:\"NOT\",10:\"(\",11:\")\",12:\"SELECTOR\",13:\"NAMED_SELECTOR\",14:\"SELECTOR_RANGED\",16:\"SELECTOR_NAMED\",19:\",\",20:\"NUMBER\",21:\":\",23:\"IDENTIFIER\",24:\"STRING\"},\r\nproductions_: [0,[3,2],[4,1],[4,3],[4,3],[4,2],[4,3],[6,1],[6,1],[6,2],[6,2],[15,1],[15,3],[18,1],[18,3],[17,1],[17,3],[22,1],[22,1],[22,1]],\r\nperformAction: function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.keyword('or')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.keyword('and')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.keyword('not')($$[$0]);\r\nbreak;\r\ncase 6:\r\nthis.$ = $$[$0-1];\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.keyword($$[$0])();\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.GetSelector($$[$0].toLowerCase().slice(1, $$[$0].length));\r\nbreak;\r\ncase 9: case 10:\r\nthis.$ = yy.keyword($$[$0-1])($$[$0]);\r\nbreak;\r\ncase 11:\r\nthis.$ = new yy.RangeList($$[$0]);\r\nbreak;\r\ncase 12: case 16:\r\nthis.$ = $$[$0-2].append($$[$0]);\r\nbreak;\r\ncase 13:\r\nthis.$ = new yy.Range(Number($$[$0]));\r\nbreak;\r\ncase 14:\r\nthis.$ = new yy.Range(Number($$[$0-2]), Number($$[$0]));\r\nbreak;\r\ncase 15:\r\nthis.$ = new yy.ValueList($$[$0]);\r\nbreak;\r\n}\r\n},\r\ntable: [{3:1,4:2,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{1:[3]},{5:[1,10],7:$V6,8:$V7},o($V8,[2,2]),{4:13,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:14,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,7]),o($V8,[2,8]),{15:15,18:16,20:$V9},{17:18,20:$Va,22:19,23:$Vb,24:$Vc},{1:[2,1]},{4:23,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:24,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,5]),{7:$V6,8:$V7,11:[1,25]},o($V8,[2,9],{19:[1,26]}),o($Vd,[2,11]),o($Vd,[2,13],{21:[1,27]}),o($V8,[2,10],{19:[1,28]}),o($Vd,[2,15]),o($Vd,[2,17]),o($Vd,[2,18]),o($Vd,[2,19]),o([5,7,11],[2,3],{8:$V7}),o($V8,[2,4]),o($V8,[2,6]),{18:29,20:$V9},{20:[1,30]},{20:$Va,22:31,23:$Vb,24:$Vc},o($Vd,[2,12]),o($Vd,[2,14]),o($Vd,[2,16])],\r\ndefaultActions: {10:[2,1]},\r\nparseError: function parseError(str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function (match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex() {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin(condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState() {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules() {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState(n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState(condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* skip whitespace */\r\nbreak;\r\ncase 1:return 20;\r\nbreak;\r\ncase 2:return 7;\r\nbreak;\r\ncase 3:return 8;\r\nbreak;\r\ncase 4:return 9;\r\nbreak;\r\ncase 5:return 12;\r\nbreak;\r\ncase 6:return 16;\r\nbreak;\r\ncase 7:return 14;\r\nbreak;\r\ncase 8:return 10;\r\nbreak;\r\ncase 9:return 11;\r\nbreak;\r\ncase 10:return 19;\r\nbreak;\r\ncase 11:return 21;\r\nbreak;\r\ncase 12:return '<=';\r\nbreak;\r\ncase 13:return '>=';\r\nbreak;\r\ncase 14:return '<';\r\nbreak;\r\ncase 15:return '>';\r\nbreak;\r\ncase 16:yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2); return 24;\r\nbreak;\r\ncase 17:return 13;\r\nbreak;\r\ncase 18:return 23;\r\nbreak;\r\ncase 19:return 5;\r\nbreak;\r\ncase 20:return 'INVALID';\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:(-?(?:[1-9][0-9]+|[0-9]))\\b)/i,/^(?:OR\\b)/i,/^(?:AND\\b)/i,/^(?:NOT\\b)/i,/^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\\b)/i,/^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\\b)/i,/^(?:((SERIAL|SEQUENCE|RESIDX))\\b)/i,/^(?:\\()/i,/^(?:\\))/i,/^(?:,)/i,/^(?::)/i,/^(?:<=)/i,/^(?:>=)/i,/^(?:<)/i,/^(?:>)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:(@[_A-Z0-9]+))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:.)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","\r\n/*\r\nSmooth.js version 0.1.7\r\n\r\nTurn arrays into smooth functions.\r\n\r\nCopyright 2012 Spencer Cohen\r\nLicensed under MIT license (see \"Smooth.js MIT license.txt\")\r\n*/\r\n\r\n/*Constants (these are accessible by Smooth.WHATEVER in user space)\r\n*/\r\n\r\n(function() {\r\n var AbstractInterpolator, CubicInterpolator, Enum, LinearInterpolator, NearestInterpolator, PI, SincFilterInterpolator, Smooth, clipClamp, clipMirror, clipPeriodic, defaultConfig, getColumn, getType, isValidNumber, k, makeLanczosWindow, makeScaledFunction, makeSincKernel, normalizeScaleTo, shallowCopy, sin, sinc, v, validateNumber, validateVector,\r\n __hasProp = Object.prototype.hasOwnProperty,\r\n __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor; child.__super__ = parent.prototype; return child; };\r\n\r\n Enum = {\r\n /*Interpolation methods\r\n */\r\n METHOD_NEAREST: 'nearest',\r\n METHOD_LINEAR: 'linear',\r\n METHOD_CUBIC: 'cubic',\r\n METHOD_LANCZOS: 'lanczos',\r\n METHOD_SINC: 'sinc',\r\n /*Input clipping modes\r\n */\r\n CLIP_CLAMP: 'clamp',\r\n CLIP_ZERO: 'zero',\r\n CLIP_PERIODIC: 'periodic',\r\n CLIP_MIRROR: 'mirror',\r\n /* Constants for control over the cubic interpolation tension\r\n */\r\n CUBIC_TENSION_DEFAULT: 0,\r\n CUBIC_TENSION_CATMULL_ROM: 0\r\n };\r\n\r\n defaultConfig = {\r\n method: Enum.METHOD_CUBIC,\r\n cubicTension: Enum.CUBIC_TENSION_DEFAULT,\r\n clip: Enum.CLIP_CLAMP,\r\n scaleTo: 0,\r\n sincFilterSize: 2,\r\n sincWindow: void 0\r\n };\r\n\r\n /*Index clipping functions\r\n */\r\n\r\n clipClamp = function(i, n) {\r\n return Math.max(0, Math.min(i, n - 1));\r\n };\r\n\r\n clipPeriodic = function(i, n) {\r\n i = i % n;\r\n if (i < 0) i += n;\r\n return i;\r\n };\r\n\r\n clipMirror = function(i, n) {\r\n var period;\r\n period = 2 * (n - 1);\r\n i = clipPeriodic(i, period);\r\n if (i > n - 1) i = period - i;\r\n return i;\r\n };\r\n\r\n /*\r\n Abstract scalar interpolation class which provides common functionality for all interpolators\r\n \r\n Subclasses must override interpolate().\r\n */\r\n\r\n AbstractInterpolator = (function() {\r\n\r\n function AbstractInterpolator(array, config) {\r\n this.array = array.slice(0);\r\n this.length = this.array.length;\r\n if (!(this.clipHelper = {\r\n clamp: this.clipHelperClamp,\r\n zero: this.clipHelperZero,\r\n periodic: this.clipHelperPeriodic,\r\n mirror: this.clipHelperMirror\r\n }[config.clip])) {\r\n throw \"Invalid clip: \" + config.clip;\r\n }\r\n }\r\n\r\n AbstractInterpolator.prototype.getClippedInput = function(i) {\r\n if ((0 <= i && i < this.length)) {\r\n return this.array[i];\r\n } else {\r\n return this.clipHelper(i);\r\n }\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperClamp = function(i) {\r\n return this.array[clipClamp(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperZero = function(i) {\r\n return 0;\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperPeriodic = function(i) {\r\n return this.array[clipPeriodic(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperMirror = function(i) {\r\n return this.array[clipMirror(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.interpolate = function(t) {\r\n throw 'Subclasses of AbstractInterpolator must override the interpolate() method.';\r\n };\r\n\r\n return AbstractInterpolator;\r\n\r\n })();\r\n\r\n NearestInterpolator = (function(_super) {\r\n\r\n __extends(NearestInterpolator, _super);\r\n\r\n function NearestInterpolator() {\r\n NearestInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n NearestInterpolator.prototype.interpolate = function(t) {\r\n return this.getClippedInput(Math.round(t));\r\n };\r\n\r\n return NearestInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n LinearInterpolator = (function(_super) {\r\n\r\n __extends(LinearInterpolator, _super);\r\n\r\n function LinearInterpolator() {\r\n LinearInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n LinearInterpolator.prototype.interpolate = function(t) {\r\n var k;\r\n k = Math.floor(t);\r\n t -= k;\r\n return (1 - t) * this.getClippedInput(k) + t * this.getClippedInput(k + 1);\r\n };\r\n\r\n return LinearInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n CubicInterpolator = (function(_super) {\r\n\r\n __extends(CubicInterpolator, _super);\r\n\r\n function CubicInterpolator(array, config) {\r\n this.tangentFactor = 1 - Math.max(-1, Math.min(1, config.cubicTension));\r\n CubicInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n CubicInterpolator.prototype.getTangent = function(k) {\r\n return this.tangentFactor * (this.getClippedInput(k + 1) - this.getClippedInput(k - 1)) / 2;\r\n };\r\n\r\n CubicInterpolator.prototype.interpolate = function(t) {\r\n var k, m, p, t2, t3;\r\n k = Math.floor(t);\r\n m = [this.getTangent(k), this.getTangent(k + 1)];\r\n p = [this.getClippedInput(k), this.getClippedInput(k + 1)];\r\n t -= k;\r\n t2 = t * t;\r\n t3 = t * t2;\r\n return (2 * t3 - 3 * t2 + 1) * p[0] + (t3 - 2 * t2 + t) * m[0] + (-2 * t3 + 3 * t2) * p[1] + (t3 - t2) * m[1];\r\n };\r\n\r\n return CubicInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n sin = Math.sin, PI = Math.PI;\r\n\r\n sinc = function(x) {\r\n if (x === 0) {\r\n return 1;\r\n } else {\r\n return sin(PI * x) / (PI * x);\r\n }\r\n };\r\n\r\n makeLanczosWindow = function(a) {\r\n return function(x) {\r\n return sinc(x / a);\r\n };\r\n };\r\n\r\n makeSincKernel = function(window) {\r\n return function(x) {\r\n return sinc(x) * window(x);\r\n };\r\n };\r\n\r\n SincFilterInterpolator = (function(_super) {\r\n\r\n __extends(SincFilterInterpolator, _super);\r\n\r\n function SincFilterInterpolator(array, config) {\r\n SincFilterInterpolator.__super__.constructor.apply(this, arguments);\r\n this.a = config.sincFilterSize;\r\n if (!config.sincWindow) throw 'No sincWindow provided';\r\n this.kernel = makeSincKernel(config.sincWindow);\r\n }\r\n\r\n SincFilterInterpolator.prototype.interpolate = function(t) {\r\n var k, n, sum, _ref, _ref2;\r\n k = Math.floor(t);\r\n sum = 0;\r\n for (n = _ref = k - this.a + 1, _ref2 = k + this.a; _ref <= _ref2 ? n <= _ref2 : n >= _ref2; _ref <= _ref2 ? n++ : n--) {\r\n sum += this.kernel(t - n) * this.getClippedInput(n);\r\n }\r\n return sum;\r\n };\r\n\r\n return SincFilterInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n getColumn = function(arr, i) {\r\n var row, _i, _len, _results;\r\n _results = [];\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n row = arr[_i];\r\n _results.push(row[i]);\r\n }\r\n return _results;\r\n };\r\n\r\n makeScaledFunction = function(f, baseScale, scaleRange) {\r\n var scaleFactor, translation;\r\n if (scaleRange.join === '0,1') {\r\n return f;\r\n } else {\r\n scaleFactor = baseScale / (scaleRange[1] - scaleRange[0]);\r\n translation = scaleRange[0];\r\n return function(t) {\r\n return f(scaleFactor * (t - translation));\r\n };\r\n }\r\n };\r\n\r\n getType = function(x) {\r\n return Object.prototype.toString.call(x).slice('[object '.length, -1);\r\n };\r\n\r\n validateNumber = function(n) {\r\n if (isNaN(n)) throw 'NaN in Smooth() input';\r\n if (getType(n) !== 'Number') throw 'Non-number in Smooth() input';\r\n if (!isFinite(n)) throw 'Infinity in Smooth() input';\r\n };\r\n\r\n validateVector = function(v, dimension) {\r\n var n, _i, _len;\r\n if (getType(v) !== 'Array') throw 'Non-vector in Smooth() input';\r\n if (v.length !== dimension) throw 'Inconsistent dimension in Smooth() input';\r\n for (_i = 0, _len = v.length; _i < _len; _i++) {\r\n n = v[_i];\r\n validateNumber(n);\r\n }\r\n };\r\n\r\n isValidNumber = function(n) {\r\n return (getType(n) === 'Number') && isFinite(n) && !isNaN(n);\r\n };\r\n\r\n normalizeScaleTo = function(s) {\r\n var invalidErr;\r\n invalidErr = \"scaleTo param must be number or array of two numbers\";\r\n switch (getType(s)) {\r\n case 'Number':\r\n if (!isValidNumber(s)) throw invalidErr;\r\n s = [0, s];\r\n break;\r\n case 'Array':\r\n if (s.length !== 2) throw invalidErr;\r\n if (!(isValidNumber(s[0]) && isValidNumber(s[1]))) throw invalidErr;\r\n break;\r\n default:\r\n throw invalidErr;\r\n }\r\n return s;\r\n };\r\n\r\n shallowCopy = function(obj) {\r\n var copy, k, v;\r\n copy = {};\r\n for (k in obj) {\r\n if (!__hasProp.call(obj, k)) continue;\r\n v = obj[k];\r\n copy[k] = v;\r\n }\r\n return copy;\r\n };\r\n\r\n Smooth = function(arr, config) {\r\n var baseDomainEnd, dimension, i, interpolator, interpolatorClass, interpolators, k, n, properties, smoothFunc, v;\r\n if (config == null) config = {};\r\n properties = {};\r\n config = shallowCopy(config);\r\n properties.config = shallowCopy(config);\r\n if (config.scaleTo == null) config.scaleTo = config.period;\r\n if (config.sincFilterSize == null) {\r\n config.sincFilterSize = config.lanczosFilterSize;\r\n }\r\n for (k in defaultConfig) {\r\n if (!__hasProp.call(defaultConfig, k)) continue;\r\n v = defaultConfig[k];\r\n if (config[k] == null) config[k] = v;\r\n }\r\n if (!(interpolatorClass = {\r\n nearest: NearestInterpolator,\r\n linear: LinearInterpolator,\r\n cubic: CubicInterpolator,\r\n lanczos: SincFilterInterpolator,\r\n sinc: SincFilterInterpolator\r\n }[config.method])) {\r\n throw \"Invalid method: \" + config.method;\r\n }\r\n if (config.method === 'lanczos') {\r\n config.sincWindow = makeLanczosWindow(config.sincFilterSize);\r\n }\r\n if (arr.length < 2) throw 'Array must have at least two elements';\r\n properties.count = arr.length;\r\n smoothFunc = (function() {\r\n var _i, _j, _len, _len2;\r\n switch (getType(arr[0])) {\r\n case 'Number':\r\n properties.dimension = 'scalar';\r\n if (Smooth.deepValidation) {\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n n = arr[_i];\r\n validateNumber(n);\r\n }\r\n }\r\n interpolator = new interpolatorClass(arr, config);\r\n return function(t) {\r\n return interpolator.interpolate(t);\r\n };\r\n case 'Array':\r\n properties.dimension = dimension = arr[0].length;\r\n if (!dimension) throw 'Vectors must be non-empty';\r\n if (Smooth.deepValidation) {\r\n for (_j = 0, _len2 = arr.length; _j < _len2; _j++) {\r\n v = arr[_j];\r\n validateVector(v, dimension);\r\n }\r\n }\r\n interpolators = (function() {\r\n var _results;\r\n _results = [];\r\n for (i = 0; 0 <= dimension ? i < dimension : i > dimension; 0 <= dimension ? i++ : i--) {\r\n _results.push(new interpolatorClass(getColumn(arr, i), config));\r\n }\r\n return _results;\r\n })();\r\n return function(t) {\r\n var interpolator, _k, _len3, _results;\r\n _results = [];\r\n for (_k = 0, _len3 = interpolators.length; _k < _len3; _k++) {\r\n interpolator = interpolators[_k];\r\n _results.push(interpolator.interpolate(t));\r\n }\r\n return _results;\r\n };\r\n default:\r\n throw \"Invalid element type: \" + (getType(arr[0]));\r\n }\r\n })();\r\n if (config.clip === 'periodic') {\r\n baseDomainEnd = arr.length;\r\n } else {\r\n baseDomainEnd = arr.length - 1;\r\n }\r\n config.scaleTo || (config.scaleTo = baseDomainEnd);\r\n properties.domain = normalizeScaleTo(config.scaleTo);\r\n smoothFunc = makeScaledFunction(smoothFunc, baseDomainEnd, properties.domain);\r\n properties.domain.sort();\r\n /*copy properties\r\n */\r\n for (k in properties) {\r\n if (!__hasProp.call(properties, k)) continue;\r\n v = properties[k];\r\n smoothFunc[k] = v;\r\n }\r\n return smoothFunc;\r\n };\r\n\r\n for (k in Enum) {\r\n if (!__hasProp.call(Enum, k)) continue;\r\n v = Enum[k];\r\n Smooth[k] = v;\r\n }\r\n\r\n Smooth.deepValidation = true;\r\n\r\n (typeof exports !== \"undefined\" && exports !== null ? exports : window).Smooth = Smooth;\r\n\r\n}).call(this);\r\n","!function(r,t){if(\"function\"==typeof define&&define.amd)define([\"exports\"],t);else if(\"object\"==typeof exports&&\"undefined\"!=typeof module)t(exports);else t(r.MMTF=r.MMTF||{})}(this,function(r){\"use strict\";function t(r,t,n){for(var e=(r.byteLength,0),i=n.length;i>e;e++){var o=n.charCodeAt(e);if(128>o)r.setUint8(t++,o>>>0&127|0);else if(2048>o)r.setUint8(t++,o>>>6&31|192),r.setUint8(t++,o>>>0&63|128);else if(65536>o)r.setUint8(t++,o>>>12&15|224),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128);else{if(!(1114112>o))throw new Error(\"bad codepoint \"+o);r.setUint8(t++,o>>>18&7|240),r.setUint8(t++,o>>>12&63|128),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128)}}}function n(r){for(var t=0,n=0,e=r.length;e>n;n++){var i=r.charCodeAt(n);if(128>i)t+=1;else if(2048>i)t+=2;else if(65536>i)t+=3;else{if(!(1114112>i))throw new Error(\"bad codepoint \"+i);t+=4}}return t}function e(r,i,o){var a=typeof r;if(\"string\"===a){var u=n(r);if(32>u)return i.setUint8(o,160|u),t(i,o+1,r),1+u;if(256>u)return i.setUint8(o,217),i.setUint8(o+1,u),t(i,o+2,r),2+u;if(65536>u)return 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zIndex: 2e9,\n className: 'spinner',\n top: '50%',\n left: '50%',\n shadow: '0 0 1px transparent', // prevent aliased lines\n position: 'absolute',\n};\nvar Spinner = /** @class */ (function () {\n function Spinner(opts) {\n if (opts === void 0) { opts = {}; }\n this.opts = __assign(__assign({}, defaults), opts);\n }\n /**\n * Adds the spinner to the given target element. If this instance is already\n * spinning, it is automatically removed from its previous target by calling\n * stop() internally.\n */\n Spinner.prototype.spin = function (target) {\n this.stop();\n this.el = document.createElement('div');\n this.el.className = this.opts.className;\n this.el.setAttribute('role', 'progressbar');\n this.el.style.position = this.opts.position;\n this.el.style.width = \"0\";\n this.el.style.zIndex = this.opts.zIndex.toString();\n this.el.style.left = this.opts.left;\n this.el.style.top = this.opts.top;\n this.el.style.transform = \"scale(\".concat(this.opts.scale, \")\");\n if (target) {\n target.insertBefore(this.el, target.firstChild || null);\n }\n drawLines(this.el, this.opts);\n return this;\n };\n /**\n * Stops and removes the Spinner.\n * Stopped spinners may be reused by calling spin() again.\n */\n Spinner.prototype.stop = function () {\n if (this.el) {\n if (this.el.parentNode) {\n this.el.parentNode.removeChild(this.el);\n }\n this.el = undefined;\n }\n return this;\n };\n return Spinner;\n}());\nexport { Spinner };\n/**\n * Returns the line color from the given string or array.\n */\nfunction getColor(color, idx) {\n return typeof color == 'string' ? color : color[idx % color.length];\n}\n/**\n * Internal method that draws the individual lines.\n */\nfunction drawLines(el, opts) {\n var borderRadius = (Math.round(opts.corners * opts.width * 500) / 1000) + 'px';\n var shadow = 'none';\n if (opts.shadow === true) {\n shadow = '0 2px 4px #000'; // default shadow\n }\n else if (typeof opts.shadow === 'string') {\n shadow = opts.shadow;\n }\n var shadows = parseBoxShadow(shadow);\n for (var i = 0; i < opts.lines; i++) {\n var degrees = ~~(360 / opts.lines * i + opts.rotate);\n var backgroundLine = document.createElement('div');\n backgroundLine.style.position = 'absolute';\n backgroundLine.style.top = \"\".concat(-opts.width / 2, \"px\");\n backgroundLine.style.width = (opts.length + opts.width) + 'px';\n backgroundLine.style.height = opts.width + 'px';\n backgroundLine.style.background = getColor(opts.fadeColor, i);\n backgroundLine.style.borderRadius = borderRadius;\n backgroundLine.style.transformOrigin = 'left';\n backgroundLine.style.transform = \"rotate(\".concat(degrees, \"deg) translateX(\").concat(opts.radius, \"px)\");\n var delay = i * opts.direction / opts.lines / opts.speed;\n delay -= 1 / opts.speed; // so initial animation state will include trail\n var line = document.createElement('div');\n line.style.width = '100%';\n line.style.height = '100%';\n line.style.background = getColor(opts.color, i);\n line.style.borderRadius = borderRadius;\n line.style.boxShadow = normalizeShadow(shadows, degrees);\n line.style.animation = \"\".concat(1 / opts.speed, \"s linear \").concat(delay, \"s infinite \").concat(opts.animation);\n backgroundLine.appendChild(line);\n el.appendChild(backgroundLine);\n }\n}\nfunction parseBoxShadow(boxShadow) {\n var regex = /^\\s*([a-zA-Z]+\\s+)?(-?\\d+(\\.\\d+)?)([a-zA-Z]*)\\s+(-?\\d+(\\.\\d+)?)([a-zA-Z]*)(.*)$/;\n var shadows = [];\n for (var _i = 0, _a = boxShadow.split(','); _i < _a.length; _i++) {\n var shadow = _a[_i];\n var matches = shadow.match(regex);\n if (matches === null) {\n continue; // invalid syntax\n }\n var x = +matches[2];\n var y = +matches[5];\n var xUnits = matches[4];\n var yUnits = matches[7];\n if (x === 0 && !xUnits) {\n xUnits = yUnits;\n }\n if (y === 0 && !yUnits) {\n yUnits = xUnits;\n }\n if (xUnits !== yUnits) {\n continue; // units must match to use as coordinates\n }\n shadows.push({\n prefix: matches[1] || '', // could have value of 'inset' or undefined\n x: x,\n y: y,\n xUnits: xUnits,\n yUnits: yUnits,\n end: matches[8],\n });\n }\n return shadows;\n}\n/**\n * Modify box-shadow x/y offsets to counteract rotation\n */\nfunction normalizeShadow(shadows, degrees) {\n var normalized = [];\n for (var _i = 0, shadows_1 = shadows; _i < shadows_1.length; _i++) {\n var shadow = shadows_1[_i];\n var xy = convertOffset(shadow.x, shadow.y, degrees);\n normalized.push(shadow.prefix + xy[0] + shadow.xUnits + ' ' + xy[1] + shadow.yUnits + shadow.end);\n }\n return normalized.join(', ');\n}\nfunction convertOffset(x, y, degrees) {\n var radians = degrees * Math.PI / 180;\n var sin = Math.sin(radians);\n var cos = Math.cos(radians);\n return [\n Math.round((x * cos + y * sin) * 1000) / 1000,\n Math.round((-x * sin + y * cos) * 1000) / 1000,\n ];\n}\n","//----------------------------------------------------------------------------\r\n// Timer\r\n\r\nexport default class Timer {\r\n constructor() {\r\n this.startTime = 0;\r\n this.oldTime = 0;\r\n this.elapsedTime = 0;\r\n this.running = false;\r\n }\r\n\r\n start() {\r\n this.startTime = Timer.now();\r\n this.oldTime = this.startTime;\r\n this.running = true;\r\n }\r\n\r\n stop() {\r\n this.getElapsedTime();\r\n this.running = false;\r\n }\r\n\r\n getElapsedTime() {\r\n this.update();\r\n return this.elapsedTime;\r\n }\r\n\r\n update() {\r\n let delta = 0;\r\n if (this.running) {\r\n const newTime = Timer.now();\r\n delta = 0.001 * (newTime - this.oldTime);\r\n this.oldTime = newTime;\r\n this.elapsedTime += delta;\r\n }\r\n\r\n return delta;\r\n }\r\n}\r\n\r\nTimer.now = (function () {\r\n const p = typeof window !== 'undefined' && window.performance;\r\n return (p && p.now) ? p.now.bind(p) : Date.now;\r\n}());\r\n","import Timer from '../Timer';\r\n\r\nconst { now } = Timer;\r\n\r\nfunction createElement(tag, id, css) {\r\n const element = document.createElement(tag);\r\n element.id = id;\r\n element.style.cssText = css;\r\n return element;\r\n}\r\n\r\nclass Stats {\r\n constructor() {\r\n this.domElement = createElement('div', 'stats', 'padding:8px');\r\n this._text = createElement('p', 'fps', 'margin:0;color:silver;font-size:large');\r\n this.domElement.appendChild(this._text);\r\n\r\n this._startTime = now();\r\n this._prevTime = this._startTime;\r\n\r\n this._deltas = new Array(20);\r\n this._index = 0;\r\n this._total = 0.0;\r\n this._count = 0;\r\n }\r\n\r\n end() {\r\n const time = now();\r\n const delta = time - this._startTime;\r\n\r\n if (this._count < this._deltas.length) {\r\n this._count++;\r\n } else {\r\n this._total -= this._deltas[this._index];\r\n }\r\n this._total += delta;\r\n this._deltas[this._index] = delta;\r\n this._index = (this._index + 1) % this._deltas.length;\r\n\r\n this.ms = this._total / this._count;\r\n this.fps = 1000 / this.ms;\r\n\r\n if (time > this._prevTime + 1000) {\r\n this._text.textContent = this.fps.toPrecision(2);\r\n this._prevTime = time;\r\n }\r\n\r\n return time;\r\n }\r\n\r\n update() {\r\n this._startTime = this.end();\r\n }\r\n\r\n show(on) {\r\n if (on === undefined) {\r\n on = true;\r\n }\r\n this.domElement.style.display = on ? 'block' : 'none';\r\n }\r\n}\r\n\r\nexport default Stats;\r\n","/**\r\n * This class introduces the simplest event system.\r\n */\r\n\r\nimport _ from 'lodash';\r\n\r\nfunction isUndefOrEqual(param, value) {\r\n return !param || param === value;\r\n}\r\n\r\n/**\r\n * Creates empty dispatcher.\r\n *\r\n * @exports EventDispatcher\r\n * @constructor\r\n */\r\nfunction EventDispatcher() {\r\n this._handlers = {};\r\n}\r\n\r\n/**\r\n * Binds callback on specific event type. Optional `context` parameter\r\n * could be used as 'this' for the `callback`.\r\n * @param {string} type Event name.\r\n * @param {function} callback Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.addEventListener = function (type, callback, context) {\r\n let handlers = this._handlers[type];\r\n\r\n if (!handlers) {\r\n this._handlers[type] = [];\r\n handlers = this._handlers[type];\r\n }\r\n\r\n const params = [callback, context];\r\n function _checkPar(par) {\r\n return par[0] === params[0] && par[1] === params[1];\r\n }\r\n\r\n if (_.find(handlers, _checkPar) === undefined) {\r\n handlers.push(params);\r\n }\r\n};\r\n\r\n/**\r\n * Removes a previously-bound callback function from an object.\r\n * If no `context` is specified, all versions of the `callback` with different\r\n * contexts will be removed.\r\n * If no `callback` is specified, all callbacks of the `type` will be removed.\r\n * If no `type` is specified, callbacks for all events will be removed.\r\n * @param {?string} [type] Event type.\r\n * @param {function} [callback] Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.removeEventListener = function (type, callback, context) {\r\n const self = this;\r\n _.forEach(self._handlers, (handler, ev) => {\r\n _.remove(handler, (values) => isUndefOrEqual(type, ev)\r\n && isUndefOrEqual(callback, values[0])\r\n && isUndefOrEqual(context, values[1] || self));\r\n });\r\n\r\n this._handlers = _.omitBy(self._handlers, (handler) => handler.length === 0);\r\n};\r\n\r\n/**\r\n * Makes all the callbacks for the specific `event` to trigger.\r\n * @param {Object} event Event.\r\n * @param {string} event.type Type of the event.\r\n */\r\nEventDispatcher.prototype.dispatchEvent = function (event) {\r\n const self = this;\r\n\r\n _.forEach(this._handlers[event.type], (callback) => {\r\n const context = callback[1] || self;\r\n callback[0].apply(context, [event]);\r\n });\r\n};\r\n\r\nexport default EventDispatcher;\r\n","/**\r\n * This module contains class for logging.\r\n * Returns an instance of a logger that have already been created.\r\n * Allows users to log messages for five different levels,\r\n * enable console output and catch signal on each message.\r\n */\r\nimport _ from 'lodash';\r\nimport EventDispatcher from './EventDispatcher';\r\n\r\nconst priorities = {\r\n debug: 0,\r\n info: 1,\r\n report: 2,\r\n warn: 3,\r\n error: 4,\r\n};\r\n\r\n/**\r\n * Create new Logger.\r\n *\r\n * @exports Logger\r\n * @extends EventDispatcher\r\n * @constructor\r\n */\r\nfunction Logger() {\r\n EventDispatcher.call(this);\r\n /** Boolean flag that toggles output to browser console.\r\n * @type {boolean}\r\n */\r\n this.console = false;\r\n this._priority = priorities.warn;\r\n}\r\n\r\nLogger.prototype = Object.create(EventDispatcher.prototype);\r\nLogger.prototype.constructor = Logger;\r\n\r\n/**\r\n * Create new clean instance of the logger.\r\n * @returns {Logger}\r\n */\r\nLogger.prototype.instantiate = function () {\r\n return new Logger();\r\n};\r\n\r\nfunction verify(number) {\r\n if (!_.isNumber(number)) {\r\n throw new Error('Wrong log level specified!');\r\n }\r\n return number;\r\n}\r\n\r\n/**\r\n * @property {string} current threshold for signals and console output.\r\n * @name Logger#level\r\n */\r\nObject.defineProperty(Logger.prototype, 'level', {\r\n get() {\r\n return _.findKey(priorities, (value) => value === this._priority);\r\n },\r\n set(level) {\r\n this._priority = verify(priorities[level]);\r\n },\r\n});\r\n\r\n/**\r\n * Returns the list of all possible level values.\r\n * @returns {Array}\r\n */\r\nLogger.prototype.levels = function () {\r\n return Object.keys(priorities);\r\n};\r\n\r\n/**\r\n * Add new message with specified level.\r\n * @param {string} level - level of the message, must be one of the\r\n * {'debug' | 'info' | 'report' | 'warn' | 'error'}\r\n * @param {string} message\r\n */\r\nLogger.prototype.message = function (level, message) {\r\n const priority = verify(priorities[level]);\r\n this._message(priority, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('debug', ...);\r\n * @param message\r\n */\r\nLogger.prototype.debug = function (message) {\r\n this._message(priorities.debug, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('info', ...);\r\n * @param message\r\n */\r\nLogger.prototype.info = function (message) {\r\n this._message(priorities.info, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('report', ...);\r\n * @param message\r\n */\r\nLogger.prototype.report = function (message) {\r\n this._message(priorities.report, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('warn', ...);\r\n * @param message\r\n */\r\nLogger.prototype.warn = function (message) {\r\n this._message(priorities.warn, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('error', ...);\r\n * @param message\r\n */\r\nLogger.prototype.error = function (message) {\r\n this._message(priorities.error, message);\r\n};\r\n\r\n/**\r\n * Add new message with specified priority.\r\n * @param {number} priority - priority of the message\r\n * @param {string} message\r\n * @private\r\n */\r\nLogger.prototype._message = function (priority, message) {\r\n if (priority < this._priority) {\r\n return;\r\n }\r\n const level = _.findKey(priorities, (value) => value === priority);\r\n message = String(message);\r\n if (this.console) {\r\n const output = `miew:${level}: ${message}`;\r\n if (level === 'error') {\r\n console.error(output); // NOSONAR\r\n } else if (level === 'warn') {\r\n console.warn(output); // NOSONAR\r\n } else {\r\n console.log(output); // NOSONAR\r\n }\r\n }\r\n this.dispatchEvent({ type: 'message', level, message });\r\n};\r\n\r\nexport default new Logger();\r\n","import _ from 'lodash';\r\nimport logger from './utils/logger';\r\n\r\nconst browserType = {\r\n DEFAULT: 0,\r\n SAFARI: 1,\r\n};\r\n//----------------------------------------------------------------------------\r\n// Query string\r\n\r\n/**\r\n * Escape only dangerous chars in a query string component, use a plus instead of a space.\r\n *\r\n * [RFC 3986](https://tools.ietf.org/html/rfc3986) allows the following chars in the query (see 3.4):\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! $ & ' ( ) * + , ; = : @ / ?\r\n *\r\n * For query string elements we need to escape ampersand, equal sign, and plus,\r\n * but encodeURIComponent() function encodes anything except for the following:\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! ' ( ) *\r\n *\r\n * @param {string} text - key or value to encode\r\n * @param {string} excludeExp - regexp for symbols to exclude from encoding\r\n * @returns {string} encoded string\r\n */\r\nfunction encodeQueryComponent(text, excludeExp) {\r\n const encode = (code) => String.fromCharCode(parseInt(code.substr(1), 16));\r\n return encodeURIComponent(text).replace(excludeExp, encode).replace(/%20/g, '+');\r\n}\r\n\r\n/**\r\n * Unescape dangerous chars in a query string component.\r\n *\r\n * @param {string} text - encoded key or value\r\n * @returns {string} decoded string\r\n * @see {@link encodeQueryComponent}\r\n */\r\nfunction decodeQueryComponent(text) {\r\n return decodeURIComponent(text.replace(/\\+/g, ' '));\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Array} array of (key, value) pairs.\r\n */\r\nfunction getUrlParameters(url) {\r\n url = url || window.location.search;\r\n\r\n const query = url.substring(url.indexOf('?') + 1);\r\n const search = /([^&=]+)=?([^&]*)/g;\r\n const result = [];\r\n let match;\r\n\r\n while ((match = search.exec(query)) !== null) { // eslint-disable-line no-cond-assign\r\n result.push([decodeQueryComponent(match[1]), decodeQueryComponent(match[2])]);\r\n }\r\n\r\n return result;\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters as a hash.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Object}\r\n */\r\nfunction getUrlParametersAsDict(url) {\r\n const result = {};\r\n const a = getUrlParameters(url);\r\n for (let i = 0; i < a.length; ++i) {\r\n const [key, value] = a[i];\r\n result[key] = value;\r\n }\r\n return result;\r\n}\r\n\r\nfunction resolveURL(str) {\r\n if (typeof URL !== 'undefined') {\r\n try {\r\n if (typeof window !== 'undefined') {\r\n return new URL(str, window.location).href;\r\n }\r\n return new URL(str).href;\r\n } catch {\r\n // IE 11 has a URL object with no constructor available so just try a different approach instead\r\n }\r\n }\r\n if (typeof document !== 'undefined') {\r\n const anchor = document.createElement('a');\r\n anchor.href = str;\r\n return anchor.href;\r\n }\r\n return str;\r\n}\r\n\r\n/**\r\n * Generates regular expression object that includes all symbols\r\n * listed in the argument\r\n * @param symbolStr {string} - String containing characters list.\r\n * @returns {RegExp} - Regular expression.\r\n */\r\nfunction generateRegExp(symbolStr) {\r\n const symbolList = [];\r\n\r\n for (let i = 0, n = symbolStr.length; i < n; ++i) {\r\n symbolList[symbolList.length] = symbolStr[i].charCodeAt(0).toString(16);\r\n }\r\n\r\n const listStr = symbolList.join('|');\r\n\r\n return new RegExp(`%(?:${listStr})`, 'gi');\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Create HTML element\r\n\r\nfunction createElement(tag, attrs, content) {\r\n const element = document.createElement(tag);\r\n let i;\r\n let n;\r\n if (attrs) {\r\n const keys = Object.keys(attrs);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n element.setAttribute(key, attrs[key]);\r\n }\r\n }\r\n if (content) {\r\n if (!(content instanceof Array)) {\r\n content = [content];\r\n }\r\n for (i = 0, n = content.length; i < n; ++i) {\r\n const child = content[i];\r\n if (typeof child === 'string') {\r\n element.appendChild(document.createTextNode(child));\r\n } else if (child instanceof HTMLElement) {\r\n element.appendChild(child);\r\n }\r\n }\r\n }\r\n return element;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Easy inheritance\r\n\r\n/**\r\n * Derive the class from the base.\r\n * @param cls {function} - Class (constructor) to derive.\r\n * @param base {function} - Class (constructor) to derive from.\r\n * @param members {object=} - Optional instance members to add.\r\n * @param statics {object=} - Optional static class members to add.\r\n * @returns {function} Original class.\r\n */\r\nfunction deriveClass(cls, base, members, statics) {\r\n cls.prototype = _.assign(Object.create(base.prototype), { constructor: cls }, members);\r\n if (statics) {\r\n _.assign(cls, statics);\r\n }\r\n return cls;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Deep prototyping\r\n\r\nfunction deriveDeep(obj, needZeroOwnProperties) {\r\n let res = obj;\r\n let i;\r\n let n;\r\n if (obj instanceof Array) {\r\n res = new Array(obj.length);\r\n for (i = 0, n = obj.length; i < n; ++i) {\r\n res[i] = deriveDeep(obj[i]);\r\n }\r\n } else if (obj instanceof Object) {\r\n res = Object.create(obj);\r\n const keys = Object.keys(obj);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = obj[key];\r\n const copy = deriveDeep(value);\r\n if (copy !== value) {\r\n res[key] = copy;\r\n }\r\n }\r\n if (needZeroOwnProperties && Object.keys(res).length > 0) {\r\n res = Object.create(res);\r\n }\r\n }\r\n return res;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Colors\r\n\r\nfunction hexColor(color) {\r\n const hex = (`0000000${color.toString(16)}`).substr(-6);\r\n return `#${hex}`;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Debug tracing\r\n\r\nfunction DebugTracer(namespace) {\r\n let enabled = false;\r\n\r\n this.enable = function (on) {\r\n enabled = on;\r\n };\r\n\r\n let indent = 0;\r\n const methods = Object.keys(namespace);\r\n\r\n function wrap(method_, name_) {\r\n return function (...args) {\r\n const spaces = DebugTracer.spaces.substr(0, indent * 2);\r\n if (enabled) {\r\n logger.debug(`${spaces + name_} {`);\r\n }\r\n indent++;\r\n const result = method_.apply(this, args);\r\n indent--;\r\n if (enabled) {\r\n logger.debug(`${spaces}} // ${name_}`);\r\n }\r\n return result;\r\n };\r\n }\r\n\r\n for (let i = 0, n = methods.length; i < n; ++i) {\r\n const name = methods[i];\r\n const method = namespace[name];\r\n if (method instanceof Function && name !== 'constructor') {\r\n namespace[name] = wrap(method, name);\r\n }\r\n }\r\n}\r\n\r\nDebugTracer.spaces = ' ';\r\n\r\nclass OutOfMemoryError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'OutOfMemoryError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction allocateTyped(TypedArrayName, size) {\r\n let result = null;\r\n try {\r\n result = new TypedArrayName(size);\r\n } catch (e) {\r\n if (e instanceof RangeError) {\r\n throw new OutOfMemoryError(e.message);\r\n } else {\r\n throw e;\r\n }\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Float array conversion\r\n\r\nfunction bytesToBase64(/** ArrayBuffer */ buffer) {\r\n const bytes = new Uint8Array(buffer);\r\n let binary = '';\r\n for (let i = 0; i < bytes.byteLength; i++) {\r\n binary += String.fromCharCode(bytes[i]);\r\n }\r\n return window.btoa(binary);\r\n}\r\n\r\nfunction bytesFromBase64(/** string */ str) {\r\n const binary = window.atob(str);\r\n const bytes = new Uint8Array(binary.length);\r\n for (let i = 0; i < bytes.length; ++i) {\r\n bytes[i] = binary[i].charCodeAt(0);\r\n }\r\n return bytes.buffer;\r\n}\r\n\r\nfunction arrayToBase64(/** number[] */ array, /** function */ TypedArrayClass) {\r\n return bytesToBase64(new TypedArrayClass(array).buffer);\r\n}\r\n\r\nfunction arrayFromBase64(/** string */ str, /** function */ TypedArrayClass) {\r\n return Array.prototype.slice.call(new TypedArrayClass(bytesFromBase64(str)));\r\n}\r\n\r\n// NOTE: this is 1-level comparison\r\nfunction compareOptionsWithDefaults(opts, defOpts) {\r\n const optsStr = [];\r\n if (defOpts && opts) {\r\n const keys = Object.keys(opts);\r\n for (let p = 0; p < keys.length; ++p) {\r\n const key = keys[p];\r\n const value = opts[key];\r\n // TODO add processing for tree structure\r\n if (!(value instanceof Object) && typeof defOpts[key] !== 'undefined' && defOpts[key] !== value) {\r\n optsStr.push(`${key}:${value}`);\r\n }\r\n }\r\n if (optsStr.length > 0) {\r\n return `!${optsStr.join()}`;\r\n }\r\n }\r\n return '';\r\n}\r\n\r\nfunction isAlmostPlainObject(o) {\r\n if (_.isPlainObject(o)) {\r\n return true;\r\n }\r\n const proto = o && Object.getPrototypeOf(o);\r\n return !!proto && !proto.hasOwnProperty('constructor') && isAlmostPlainObject(proto);\r\n}\r\n\r\n/**\r\n * Build an object that contains properties (and subproperties) of `src` different from those\r\n * in `dst`. Objects are parsed recursively, other values (including arrays) are compared for\r\n * equality using `_.isEqual()`.\r\n * @param {!object} src - a new object to compare, may contain changed or new properties\r\n * @param {!object} dst - an old reference object\r\n */\r\nfunction objectsDiff(src, dst) {\r\n const diff = {};\r\n _.forIn(src, (srcValue, key) => {\r\n const dstValue = dst[key];\r\n if (isAlmostPlainObject(srcValue) && isAlmostPlainObject(dstValue)) {\r\n const deepDiff = objectsDiff(srcValue, dstValue);\r\n if (!_.isEmpty(deepDiff)) {\r\n diff[key] = deepDiff;\r\n }\r\n } else if (!_.isEqual(srcValue, dstValue)) {\r\n diff[key] = srcValue;\r\n }\r\n });\r\n return diff;\r\n}\r\n\r\nfunction forInRecursive(object, callback) {\r\n function iterateThrough(obj, prefix) {\r\n _.forIn(obj, (value, key) => {\r\n const newPref = prefix + (prefix.length > 0 ? '.' : '');\r\n if (value instanceof Object) {\r\n iterateThrough(value, newPref + key);\r\n } else if (value !== undefined) {\r\n callback(value, newPref + key);\r\n }\r\n });\r\n }\r\n iterateThrough(object, '');\r\n}\r\n\r\nfunction enquoteString(value) {\r\n if (_.isString(value)) {\r\n return `\"${value.replace(/\"/g, '\\\\\"')}\"`;\r\n }\r\n return value;\r\n}\r\n\r\nfunction unquoteString(value) {\r\n if (!_.isString(value)) {\r\n return value;\r\n }\r\n if (value[0] === '\"' && value[value.length - 1] === '\"') {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\\"/g, '\"');\r\n }\r\n if (value[0] === \"'\" && value[value.length - 1] === \"'\") {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\'/g, \"'\");\r\n }\r\n throw new SyntaxError('Incorrect string format, can\\'t unqute it');\r\n}\r\n\r\nfunction getFileExtension(fileName) {\r\n return fileName.slice((Math.max(0, fileName.lastIndexOf('.')) || Infinity));\r\n}\r\n\r\nfunction splitFileName(fileName) {\r\n const ext = getFileExtension(fileName);\r\n const name = fileName.slice(0, fileName.length - ext.length);\r\n return [name, ext];\r\n}\r\n\r\nfunction dataUrlToBlob(url) {\r\n const parts = url.split(/[:;,]/);\r\n const partsCount = parts.length;\r\n if (partsCount >= 3 && parts[partsCount - 2] === 'base64') {\r\n return new Blob([bytesFromBase64(parts[partsCount - 1])]);\r\n }\r\n return null;\r\n}\r\n\r\nfunction getBrowser() {\r\n if (navigator.vendor && navigator.vendor.indexOf('Apple') > -1\r\n && navigator.userAgent\r\n && navigator.userAgent.indexOf('CriOS') === -1\r\n && navigator.userAgent.indexOf('FxiOS') === -1) {\r\n return browserType.SAFARI;\r\n }\r\n return browserType.DEFAULT;\r\n}\r\n\r\nfunction shotOpen(url) {\r\n if (typeof window !== 'undefined') {\r\n window.open().document.write(``);\r\n }\r\n}\r\n\r\nfunction shotDownload(dataUrl, filename) {\r\n if (!dataUrl || dataUrl.substr(0, 5) !== 'data:') {\r\n return;\r\n }\r\n if (!filename) {\r\n filename = ['screenshot-', +new Date(), '.png'].join('');\r\n }\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(dataUrlToBlob(dataUrl), filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(dataUrlToBlob(dataUrl));\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction download(data, filename, type) {\r\n const blobData = new Blob([data]);\r\n\r\n if (!filename) {\r\n filename = ['data', +new Date()].join('');\r\n }\r\n\r\n if (!type) {\r\n filename += blobData.type || '.bin';\r\n } else {\r\n filename += `.${type}`;\r\n }\r\n\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(blobData, filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(blobData);\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction copySubArrays(src, dst, indices, itemSize) {\r\n for (let i = 0, n = indices.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n dst[i * itemSize + j] = src[indices[i] * itemSize + j];\r\n }\r\n }\r\n}\r\n\r\nfunction shallowCloneNode(node) {\r\n const newNode = node.cloneNode(true);\r\n newNode.worldPos = node.worldPos;\r\n // .style property is readonly, so \"newNode.style = node.style;\" won't work (and we don't need it, right?)\r\n return newNode;\r\n}\r\n\r\nconst unquotedStringRE = /^[a-zA-Z0-9_]*$/;\r\nconst enquoteHelper = ['\"', '', '\"'];\r\n\r\n// verify and correct if needed selctor identifier\r\nfunction correctSelectorIdentifier(value) {\r\n if (unquotedStringRE.test(value)) {\r\n return value;\r\n }\r\n // quote incorrect identifier\r\n enquoteHelper[1] = value;\r\n return enquoteHelper.join('');\r\n}\r\n\r\n/**\r\n * Concatenates two TypedArray. Doesn't check null refs o type equality\r\n * Attention! It must be use very rarely because requires memory reallocation every time. Use MergeTypedArraysUnsafe to\r\n * unite array of subarrays.\r\n * @param{TypedArray} first - destination array\r\n * @param{TypedArray} second - source array\r\n * @returns{TypedArray} resulting concatenated array\r\n */\r\nfunction concatTypedArraysUnsafe(first, second) {\r\n const result = new first.constructor(first.length + second.length);\r\n result.set(first);\r\n result.set(second, first.length);\r\n return result;\r\n}\r\n\r\n/**\r\n * Merges array of TypedArray into TypedArray. Doesn't check null refs o type equality\r\n * @param{array} array - source array of subarrays\r\n * @returns{TypedArray} resulting merged array\r\n */\r\nfunction mergeTypedArraysUnsafe(array) {\r\n if (array.length <= 0) {\r\n return null;\r\n }\r\n // count the size\r\n const size = array.reduce((acc, cur) => acc + cur.length, 0);\r\n // create combined array\r\n const result = new array[0].constructor(size);\r\n for (let i = 0, start = 0; i < array.length; i++) {\r\n const count = array[i].length;\r\n result.set(array[i], start);\r\n start += count;\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Exports\r\n\r\nexport default {\r\n browserType,\r\n encodeQueryComponent,\r\n decodeQueryComponent,\r\n getUrlParameters,\r\n getUrlParametersAsDict,\r\n resolveURL,\r\n generateRegExp,\r\n createElement,\r\n deriveClass,\r\n deriveDeep,\r\n hexColor,\r\n DebugTracer,\r\n OutOfMemoryError,\r\n allocateTyped,\r\n bytesFromBase64,\r\n bytesToBase64,\r\n arrayFromBase64,\r\n arrayToBase64,\r\n compareOptionsWithDefaults,\r\n objectsDiff,\r\n forInRecursive,\r\n enquoteString,\r\n unquoteString,\r\n getBrowser,\r\n shotOpen,\r\n shotDownload,\r\n copySubArrays,\r\n shallowCloneNode,\r\n correctSelectorIdentifier,\r\n getFileExtension,\r\n splitFileName,\r\n download,\r\n concatTypedArraysUnsafe,\r\n mergeTypedArraysUnsafe,\r\n};\r\n","import EventDispatcher from './EventDispatcher';\r\n\r\nexport default class JobHandle extends EventDispatcher {\r\n constructor() {\r\n super();\r\n this._shouldCancel = false;\r\n }\r\n\r\n cancel() {\r\n this._shouldCancel = true;\r\n this.dispatchEvent({ type: 'cancel' });\r\n }\r\n\r\n shouldCancel() {\r\n return this._shouldCancel;\r\n }\r\n\r\n // slaves use this to notify master about their events\r\n // master routes these notifications to a single event slot\r\n notify(event) {\r\n this.dispatchEvent({ type: 'notification', slaveEvent: event });\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport utils from './utils';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\n\r\nconst VERSION = 0;\r\n\r\n//----------------------------------------------------------------------------\r\n// DEFAULT SETTINGS\r\n//----------------------------------------------------------------------------\r\n\r\n/**\r\n * Polygonal complexity settings.\r\n *\r\n * @typedef PolyComplexity\r\n * @property {number} poor\r\n * @property {number} low\r\n * @property {number} medium\r\n * @property {number} high\r\n * @property {number} ultra\r\n */\r\n\r\n/**\r\n * @alias SettingsObject\r\n * @namespace\r\n */\r\nconst defaults = {\r\n /**\r\n * Default options for all available modes.\r\n * Use {@link Mode.id} as a dictionary key to access mode options.\r\n *\r\n * Usually you don't need to override these settings. You may specify mode options as a parameter during\r\n * {@link Mode} construction.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {LinesModeOptions} LN - Lines mode options.\r\n * @property {LicoriceModeOptions} LC - Licorice mode options.\r\n * @property {BallsAndSticksModeOptions} BS - Balls and Sticks mode options.\r\n * @property {VanDerWaalsModeOptions} VW - Van der Waals mode options.\r\n * @property {TraceModeOptions} TR - Trace mode options.\r\n * @property {TubeModeOptions} TU - Tube mode options.\r\n * @property {CartoonModeOptions} CA - Cartoon mode options.\r\n * @property {QuickSurfaceModeOptions} QS - Contact Surface mode options.\r\n * @property {IsoSurfaceSASModeOptions} SA - Solvent Accessible Surface mode options.\r\n * @property {IsoSurfaceSESModeOptions} SE - Solvent Excluded Surface mode options.\r\n * @property {ContactSurfaceModeOptions} CS - Contact Surface mode options.\r\n * @property {TextModeOptions} TX - Text mode options.\r\n * @property {VolumeDensityModeOptions} VD - Volume Density mode options.\r\n */\r\n modes: {\r\n //----------------------------------------------------------------------------\r\n // BALLS AND STICKS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Balls and Sticks mode options.\r\n *\r\n * @typedef BallsAndSticksModeOptions\r\n *\r\n * @property {number} atom - Sphere radius as a fraction of Van der Waals atom radius.\r\n * @property {number} bond - Cylinder radius in angstroms.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n BS: {\r\n atom: 0.23,\r\n bond: 0.15,\r\n space: 0.5,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VAN DER WAALS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Van der Waals mode options.\r\n *\r\n * @typedef VanDerWaalsModeOptions\r\n *\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VW: {\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 8,\r\n high: 16,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LINES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Lines mode options.\r\n *\r\n * @typedef LinesModeOptions\r\n *\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {number} offsarom - Offset between bonds and aromatic cycle.\r\n * @property {number} chunkarom - Number of pieces in a-loop arc, corresponding to atom.\r\n * @property {number} atom - Collision radius for atoms picking.\r\n * @property {number} lineWidth - Line width in pixels (not used in thin lines).\r\n */\r\n LN: {\r\n multibond: true,\r\n showarom: true,\r\n offsarom: 0.2,\r\n chunkarom: 10,\r\n atom: 0.23,\r\n lineWidth: 2,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LICORICE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Licorice mode options.\r\n *\r\n * @typedef LicoriceModeOptions\r\n *\r\n * @property {number} bond - Bond cylinder radius.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Poly complexity values for render modes.\r\n */\r\n LC: {\r\n bond: 0.20,\r\n space: 0.0,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SAS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Accessible Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSASModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SA: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Excluded Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSESModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SE: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // QUICK SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Quick Surface mode options.\r\n *\r\n * @typedef QuickSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} scale - Radius scale for the surface being built.\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} gaussLim - Gauss lim for coloring the bigger the value, the smoother our colors are.\r\n * @property {PolyComplexity} gridSpacing - Poly complexity values for render modes. In this case the value\r\n * corresponds to the grid density.\r\n */\r\n QS: {\r\n isoValue: 0.5,\r\n gaussLim: {\r\n poor: 1.5,\r\n low: 2.0,\r\n medium: 2.5,\r\n high: 3.0,\r\n ultra: 4.0,\r\n },\r\n scale: 1.0,\r\n wireframe: false,\r\n gridSpacing: {\r\n poor: 2,\r\n low: 1.5,\r\n medium: 1,\r\n high: 0.5,\r\n ultra: 0.25,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CONTACT SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Contact Surface mode options.\r\n *\r\n * @typedef ContactSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} probeRadius - Probe radius.\r\n * @property {number} probePositions\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Radius scale for the surface being built.\r\n * Poly complexity values for render modes. In this case the value corresponds to the grid density.\r\n */\r\n CS: {\r\n probeRadius: 1.4,\r\n isoValue: 1.5,\r\n wireframe: false,\r\n probePositions: 30,\r\n polyComplexity: {\r\n poor: 0.5,\r\n low: 1.0,\r\n medium: 1.5,\r\n high: 1.75,\r\n ultra: 2.0,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TRACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Trace mode options.\r\n *\r\n * @typedef TraceModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n TR: {\r\n radius: 0.30,\r\n polyComplexity: {\r\n poor: 12,\r\n low: 16,\r\n medium: 32,\r\n high: 64,\r\n ultra: 64,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TUBE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Tube mode options.\r\n *\r\n * @typedef TubeModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {number} tension - Tension for interpolation.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n TU: {\r\n radius: 0.30,\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CARTOON\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Cartoon mode options.\r\n *\r\n * @typedef CartoonModeOptions\r\n *\r\n * @property {number} radius - Standard tube radius.\r\n * @property {number} depth - Height of the secondary structure ribbon.\r\n * @property {number} tension - Tension for interpolation.\r\n * @proprety {object} ss - Secondary structure parameters.\r\n * @proprety {object} ss.helix - Options for helices render.\r\n * @proprety {number} ss.helix.width - Width of the secondary structure ribbon.\r\n * @proprety {number} ss.helix.arrow - Secondary structure's arrow width.\r\n * @proprety {object} ss.strand - Options for strands render.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * polyComplexity must be even for producing symmetric arrows.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n CA: {\r\n radius: 0.30,\r\n depth: 0.25,\r\n ss: {\r\n helix: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n strand: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n },\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TEXT\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Text mode options.\r\n *\r\n * @typedef TextModeOptions\r\n *\r\n * @property {string} template - Format string for building output text.\r\n * @property {string} horizontalAlign - Text alignment ('left', 'right', 'center').\r\n * @property {string} verticalAlign - Vertical text box alignment ('top', 'bottom', 'middle').\r\n * @property {number} dx - Text offset x in angstroms.\r\n * @property {number} dy - Text offset y in angstroms.\r\n * @property {number} dz - Text offset z in angstroms.\r\n * @property {string} fg - Color rule for foreground.\r\n * @property {string} bg - Color rule for background.\r\n * @property {boolean} showBg - Flag, that toggles background rendering.\r\n *\r\n */\r\n TX: {\r\n template: '{{Chain}}.{{Residue}}{{Sequence}}.{{Name}}',\r\n horizontalAlign: 'center',\r\n verticalAlign: 'middle',\r\n dx: 0,\r\n dy: 0,\r\n dz: 1,\r\n fg: 'none',\r\n bg: '0x202020',\r\n showBg: true,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VOLUME DENSITY\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Volume density mode options.\r\n *\r\n * @typedef VolumeDensityModeOptions\r\n *\r\n * @property {number} kSigma - Noise threshold coefficient.\r\n * @property {boolean} frame - flag, that turns on box frame painting.\r\n * @property {boolean} isoMode - flag, that turns on IsoSurface mode instead of Volume Rendering.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VD: {\r\n kSigma: 1.0,\r\n kSigmaMed: 2.0,\r\n kSigmaMax: 4.0,\r\n frame: true,\r\n isoMode: false,\r\n polyComplexity: {\r\n poor: 2,\r\n low: 3,\r\n medium: 4,\r\n high: 8,\r\n ultra: 10,\r\n },\r\n },\r\n },\r\n\r\n /**\r\n * Default options for all available colorers.\r\n * Use {@link Colorer.id} as a dictionary key to access colorer options.\r\n *\r\n * Usually you don't need to override these settings. You may specify colorer options as a parameter during\r\n * {@link Colorer} construction.\r\n *\r\n * Not all colorers have options.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {ElementColorerOptions} EL - Element colorer options.\r\n * @property {SequenceColorerOptions} SQ - Sequence colorer options.\r\n * @property {MoleculeColorerOptions} MO - Molecule colorer options.\r\n * @property {UniformColorerOptions} UN - Uniform colorer options.\r\n * @property {ConditionalColorerOptions} CO - Conditional colorer options.\r\n * @property {TemperatureColorerOptions} TM - Temperature colorer options.\r\n * @property {OccupancyColorerOptions} OC - Occupancy colorer options.\r\n * @property {HydrophobicityColorerOptions} HY - Hydrophobicity colorer options.\r\n */\r\n colorers: {\r\n /**\r\n * Element colorer options.\r\n *\r\n * @typedef ElementColorerOptions\r\n *\r\n * @property {number} carbon - Carbon color or -1 to use default.\r\n */\r\n EL: {\r\n carbon: -1,\r\n },\r\n\r\n /**\r\n * Uniform colorer options.\r\n *\r\n * @typedef UniformColorerOptions\r\n *\r\n * @property {number} color - Single color to paint with.\r\n */\r\n UN: {\r\n color: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Conditional colorer options.\r\n *\r\n * @typedef ConditionalColorerOptions\r\n *\r\n * @property {string} subset - Selector string.\r\n * @property {number} color - Color of selected atoms.\r\n * @property {number} baseColor - Color of other atoms.\r\n */\r\n CO: {\r\n subset: 'charged',\r\n color: 0xFF0000,\r\n baseColor: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Carbon colorer options.\r\n *\r\n * @typedef CarbonColorerOptions\r\n *\r\n * @property {number} color - Single color to paint carbons\r\n * @property {number} factor - Color factor for not carbon atoms.\r\n */\r\n CB: {\r\n color: 0x909090,\r\n factor: 0.6,\r\n },\r\n\r\n /**\r\n * Sequence colorer options.\r\n *\r\n * @typedef SequenceColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n SQ: {\r\n gradient: 'rainbow',\r\n },\r\n\r\n /**\r\n * Temperature colorer options.\r\n *\r\n * @typedef TemperatureColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n * @property {number} min - Minimal temperature.\r\n * @property {number} max - Maximal temperature.\r\n */\r\n TM: {\r\n gradient: 'temp',\r\n min: 5,\r\n max: 40,\r\n },\r\n\r\n /**\r\n * Occupancy colorer options.\r\n *\r\n * @typedef OccupancyColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n OC: {\r\n gradient: 'reds',\r\n },\r\n\r\n /**\r\n * Hydrophobicity colorer options.\r\n *\r\n * @typedef HydrophobicityColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n HY: {\r\n gradient: 'blue-red',\r\n },\r\n\r\n /**\r\n * Molecule colorer options.\r\n *\r\n * @typedef MoleculeColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n MO: {\r\n gradient: 'rainbow',\r\n },\r\n },\r\n\r\n /*\r\n * Use antialiasing in WebGL.\r\n * @type {boolean}\r\n */\r\n antialias: true,\r\n\r\n /*\r\n * Camera field of view in degrees.\r\n * @type {number}\r\n */\r\n camFov: 45.0,\r\n\r\n /*\r\n * Camera near plane distance.\r\n * @type {number}\r\n */\r\n camNear: 0.5,\r\n\r\n /*\r\n * Camera far plane distance.\r\n * @type {number}\r\n */\r\n camFar: 100.0,\r\n\r\n camDistance: 2.5,\r\n\r\n radiusToFit: 1.0,\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogNearFactor: 0.5, // [0, 1]\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogFarFactor: 1, // [0, 1]\r\n fogAlpha: 1.0,\r\n fogColor: 0x000000,\r\n fogColorEnable: false,\r\n\r\n /**\r\n * Palette used for molecule coloring.\r\n * @type {string}\r\n */\r\n palette: 'JM',\r\n\r\n /*\r\n * Geometry resolution.\r\n * @type {string}\r\n */\r\n resolution: 'medium',\r\n\r\n autoResolution: false/* true */,\r\n\r\n autoPreset: true,\r\n\r\n preset: 'default', // TODO: remove 'preset' from settings, implement autodetection\r\n\r\n presets: {\r\n // Default\r\n default: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n empty: [],\r\n\r\n // Wireframe\r\n wire: [{\r\n mode: 'LN',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Small molecules\r\n small: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Proteins, nucleic acids etc.\r\n macro: [{\r\n mode: 'CA',\r\n colorer: 'SS',\r\n selector: 'not hetatm',\r\n material: 'SF',\r\n }, {\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'hetatm and not water',\r\n material: 'SF',\r\n }],\r\n },\r\n\r\n objects: {\r\n line: {\r\n color: 0xFFFFFFFF,\r\n dashSize: 0.3,\r\n gapSize: 0.05,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n\r\n bg: {\r\n color: 0x202020,\r\n transparent: false,\r\n },\r\n\r\n draft: {\r\n clipPlane: false,\r\n clipPlaneFactor: 0.5,\r\n clipPlaneSpeed: 0.00003,\r\n },\r\n\r\n /*\r\n * Separate group for plugins.\r\n * Each plugin handles its field by itself.\r\n */\r\n plugins: {\r\n\r\n },\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n axes: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fog: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fps: true,\r\n\r\n /**\r\n * Switch using of z-sprites for sphere and cylinder geometry\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zSprites: true,\r\n\r\n isoSurfaceFakeOpacity: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n suspendRender: true,\r\n\r\n nowater: false,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autobuild: true,\r\n\r\n /**\r\n * Anti-aliasing.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fxaa: true,\r\n /**\r\n * Outline depths\r\n * @type {boolean}\r\n * @instance\r\n */\r\n outline: {\r\n on: false,\r\n color: 0x000000,\r\n threshold: 0.1,\r\n thickness: 1,\r\n },\r\n\r\n /**\r\n * Ambient Occlusion special effect.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n ao: false,\r\n\r\n /**\r\n * Shadows options.\r\n *\r\n * @property {boolean} shadowMap - enable/disable.\r\n * @property {string} basic/percentage-closer filtering/non-uniform randomizing pcf.\r\n * @property {number} radius for percentage-closer filtering.\r\n */\r\n shadow: {\r\n on: false,\r\n type: 'random'/* basic, pcf, random */,\r\n radius: 1.0,\r\n },\r\n\r\n /**\r\n * Auto-rotation with constant speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n autoRotation: 0.0,\r\n\r\n /**\r\n * Set maximum fps for animation.\r\n * @type {number}\r\n * @instance\r\n */\r\n maxfps: 30,\r\n\r\n /**\r\n * Set fbx output precision.\r\n * @type {number}\r\n * @instance\r\n */\r\n fbxprec: 4,\r\n\r\n /**\r\n * Auto-rotation axis.\r\n *\r\n * - true: complex auto-rotation is about vertical axis\r\n * - false: rotation axis is defined by last user rotation\r\n *\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autoRotationAxisFixed: true,\r\n\r\n /**\r\n * Enable zooming with mouse wheel or pinch gesture.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zooming: true,\r\n\r\n /**\r\n * Enable picking atoms & residues with left mouse button or touch.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n picking: true,\r\n\r\n /**\r\n * Set picking mode ('atom', 'residue', 'chain', 'molecule').\r\n * @type {string}\r\n * @instance\r\n */\r\n pick: 'atom',\r\n\r\n /**\r\n * Make \"component\" and \"fragment\" editing modes available.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n editing: false,\r\n\r\n /**\r\n * Detect aromatic loops.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n aromatic: false,\r\n\r\n /**\r\n * Load only one biological unit from all those described in PDB file.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n singleUnit: true,\r\n\r\n /**\r\n * Set stereo mode ('NONE', 'SIMPLE', 'DISTORTED', 'ANAGLYPH', 'WEBVR').\r\n * @type {string}\r\n * @instance\r\n */\r\n stereo: 'NONE',\r\n\r\n /**\r\n * Enable smooth transition between views\r\n * @type {boolean}\r\n * @instance\r\n */\r\n interpolateViews: true,\r\n\r\n /**\r\n * Set transparency mode ('standard', 'prepass').\r\n * @type {string}\r\n * @instance\r\n */\r\n transparency: 'prepass',\r\n\r\n /**\r\n * Mouse translation speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n translationSpeed: 2,\r\n\r\n debug: {\r\n example: 3.5,\r\n text: 'hello!',\r\n good: true,\r\n ssaoKernelRadius: 0.7,\r\n ssaoFactor: 0.7,\r\n stereoBarrel: 0.25,\r\n },\r\n use: {\r\n multiFile: false,\r\n },\r\n};\r\n\r\n//----------------------------------------------------------------------------\r\n// SETTINGS CLASS\r\n//----------------------------------------------------------------------------\r\n\r\nfunction Settings() {\r\n EventDispatcher.call(this);\r\n\r\n this.old = null;\r\n this.now = {};\r\n this._changed = {};\r\n\r\n this.reset();\r\n}\r\n\r\nutils.deriveClass(Settings, EventDispatcher, {\r\n defaults,\r\n\r\n set(path, value) {\r\n if (_.isString(path)) {\r\n const oldValue = _.get(this.now, path);\r\n if (oldValue !== value) {\r\n _.set(this.now, path, value);\r\n this._notifyChange(path, value);\r\n }\r\n } else {\r\n const diff = utils.objectsDiff(path, this.now);\r\n if (!_.isEmpty(diff)) {\r\n _.merge(this.now, diff);\r\n this._notifyChanges(diff);\r\n }\r\n }\r\n },\r\n\r\n get(path, defaultValue) {\r\n return _.get(this.now, path, defaultValue);\r\n },\r\n\r\n reset() {\r\n const diff = utils.objectsDiff(defaults, this.now);\r\n this.now = _.cloneDeep(defaults);\r\n this.old = null;\r\n this._notifyChanges(diff);\r\n this._changed = {};\r\n },\r\n\r\n checkpoint() {\r\n this.old = _.cloneDeep(this.now);\r\n this._changed = {};\r\n },\r\n\r\n _notifyChange(path, value) {\r\n this._changed[path] = true;\r\n this.dispatchEvent({ type: `change:${path}`, value });\r\n },\r\n\r\n _notifyChanges(diff) {\r\n utils.forInRecursive(diff, (deepValue, deepPath) => {\r\n this._notifyChange(deepPath, deepValue);\r\n });\r\n },\r\n\r\n changed() {\r\n if (!this.old) {\r\n return [];\r\n }\r\n const { old, now } = this;\r\n const keys = _.filter(Object.keys(this._changed), (key) => _.get(old, key) !== _.get(now, key));\r\n return keys;\r\n },\r\n\r\n applyDiffs(diffs) {\r\n if (diffs.hasOwnProperty('VERSION') && diffs.VERSION !== VERSION) {\r\n throw new Error('Settings version does not match!');\r\n }\r\n // VERSION shouldn't be presented inside settings structure\r\n delete diffs.VERSION;\r\n this.reset();\r\n this.set(diffs);\r\n },\r\n\r\n getDiffs(versioned) {\r\n const diffs = utils.objectsDiff(this.now, defaults);\r\n if (versioned) {\r\n diffs.VERSION = VERSION;\r\n }\r\n return diffs;\r\n },\r\n\r\n setPluginOpts(plugin, opts) {\r\n defaults.plugins[plugin] = _.cloneDeep(opts);\r\n this.now.plugins[plugin] = _.cloneDeep(opts);\r\n },\r\n});\r\n\r\nexport default new Settings();\r\n","import _ from 'lodash';\r\nimport settings from './settings';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\n\r\nlet repIndex = 0;\r\n\r\nfunction asBoolean(value) {\r\n return !(!value || value === '0' || (_.isString(value) && value.toLowerCase() === 'false'));\r\n}\r\n\r\nconst adapters = {\r\n string: String,\r\n number: Number,\r\n boolean: asBoolean,\r\n};\r\n\r\n// Level 1 assignment symbol\r\nconst cL1Ass = '=';\r\n\r\nconst cOptsSep = '!';\r\n// Level 2 (options) assignment symbol\r\nconst cL2Ass = ':';\r\n// Level 2 (options) separator symbol\r\nconst cLSep = ',';\r\n\r\nconst cCommonIgnoreSymbols = '$;@/?';\r\n/**\r\n * We may (and should) leave as is for better readability:\r\n *\r\n * $ , ; : @ / ?\r\n */\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n */\r\nfunction getLevel1ExcludedExpr() {\r\n const cLevel1Ignores = ':,';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel1Ignores);\r\n}\r\n\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n * (options, etc, ..)\r\n */\r\nfunction getLevel2ExcludedExpr() {\r\n const cLevel2Ignores = ' ';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel2Ignores);\r\n}\r\n\r\nconst cL1ExclExpr = getLevel1ExcludedExpr();\r\nfunction encodeQueryComponentL1(value) {\r\n return utils.encodeQueryComponent(value, cL1ExclExpr);\r\n}\r\n\r\nconst cL2ExclExpr = getLevel2ExcludedExpr();\r\nfunction encodeQueryComponentL2(value) {\r\n return utils.encodeQueryComponent(value, cL2ExclExpr);\r\n}\r\n\r\nfunction ensureRepList(opts) {\r\n let { reps } = opts;\r\n if (!reps) {\r\n const { presets } = settings.now;\r\n let preset = opts.preset || settings.now.preset;\r\n reps = presets[preset];\r\n if (!reps) {\r\n logger.warn(`Unknown preset \"${preset}\"`);\r\n [preset] = Object.keys(presets);\r\n reps = presets[preset]; // fall back to any preset\r\n }\r\n opts.preset = preset;\r\n opts.reps = utils.deriveDeep(reps, true);\r\n }\r\n}\r\n\r\nfunction ensureRepAssign(opts, prop, value) {\r\n ensureRepList(opts);\r\n const rep = opts.reps[repIndex];\r\n // prop specified twice therefore start new rep by cloning the current\r\n if (rep.hasOwnProperty(prop)) {\r\n repIndex = opts.reps.length;\r\n opts.reps[repIndex] = utils.deriveDeep(rep, true);\r\n }\r\n if (value !== undefined) {\r\n opts.reps[repIndex][prop] = value;\r\n }\r\n}\r\n\r\nfunction addObject(opts, params, options) {\r\n if (opts._objects === undefined) {\r\n opts._objects = [];\r\n }\r\n\r\n const [type, newOpts] = options;\r\n const newObj = {\r\n type,\r\n params,\r\n };\r\n\r\n if (newOpts !== undefined) {\r\n newObj.opts = newOpts;\r\n }\r\n\r\n opts._objects[opts._objects.length] = newObj;\r\n}\r\n\r\nfunction parseParams(str, params) {\r\n const sep = str.indexOf(',');\r\n if (sep >= 0) {\r\n params.push(str.substr(sep + 1).split(','));\r\n return str.substr(0, sep);\r\n }\r\n // keep this untouched if no params were extracted\r\n return str;\r\n}\r\n\r\nfunction extractArgs(input, defaultsDict, params) {\r\n if (input) {\r\n const bang = input.indexOf(cOptsSep);\r\n const inputVal = parseParams(input.substr(0, bang >= 0 ? bang : undefined), params);\r\n if (bang >= 0) {\r\n const args = input.substr(bang + 1).split(cLSep);\r\n input = inputVal;\r\n if (defaultsDict) {\r\n const defaults = defaultsDict[input];\r\n const opts = utils.deriveDeep(defaults, true);\r\n args.forEach((arg) => {\r\n const pair = arg.split(cL2Ass, 2);\r\n const key = decodeURIComponent(pair[0]);\r\n const value = decodeURIComponent(pair[1]);\r\n const adapter = adapters[typeof _.get(defaults, key)];\r\n if (adapter) {\r\n _.set(opts, key, adapter(value));\r\n } else {\r\n logger.warn(`Unknown argument \"${key}\" for option \"${input}\"`);\r\n }\r\n });\r\n if (Object.keys(opts).length > 0) {\r\n input = [input, opts];\r\n }\r\n }\r\n } else {\r\n input = inputVal;\r\n }\r\n }\r\n return input;\r\n}\r\n\r\nconst actions = {\r\n\r\n l: 'load',\r\n load: String,\r\n t: 'type',\r\n type: String,\r\n v: 'view',\r\n view: String,\r\n u: 'unit',\r\n unit: Number,\r\n menu: asBoolean,\r\n\r\n // Commands\r\n\r\n o: 'object',\r\n object(value, opts) {\r\n const params = [];\r\n let options = extractArgs(value, settings.defaults.objects, params);\r\n if (!Array.isArray(options)) {\r\n options = [options];\r\n }\r\n addObject(opts, params[0], options);\r\n },\r\n\r\n p: 'preset',\r\n preset(value, opts) {\r\n opts.preset = value;\r\n opts.reps = null;\r\n ensureRepList(opts);\r\n },\r\n\r\n r: 'rep',\r\n rep(value, opts) {\r\n ensureRepList(opts);\r\n repIndex = Number(value);\r\n // clamp the index to one greater than the last\r\n repIndex = repIndex <= opts.reps.length ? (repIndex < 0 ? 0 : repIndex) : opts.reps.length;\r\n // create a new rep if it is adjacent to the existing ones\r\n if (repIndex === opts.reps.length) {\r\n // if there is no rep to derive from, derive from the first rep of the default\r\n opts.reps[repIndex] = repIndex > 0 ? utils.deriveDeep(opts.reps[repIndex - 1], true)\r\n : utils.deriveDeep(settings.defaults.presets.default[0], true);\r\n }\r\n },\r\n\r\n s: 'select',\r\n select(value, opts) {\r\n ensureRepAssign(opts, 'selector', value);\r\n },\r\n\r\n m: 'mode',\r\n mode(value, opts) {\r\n ensureRepAssign(opts, 'mode', extractArgs(value, settings.defaults.modes));\r\n },\r\n\r\n c: 'color',\r\n color(value, opts) {\r\n ensureRepAssign(opts, 'colorer', extractArgs(value, settings.defaults.colorers));\r\n },\r\n\r\n mt: 'material',\r\n material(value, opts) {\r\n ensureRepAssign(opts, 'material', extractArgs(value, settings.defaults.materials));\r\n },\r\n\r\n dup(value, opts) {\r\n ensureRepList(opts);\r\n const { reps } = opts;\r\n const rep = reps[repIndex];\r\n repIndex = reps.length;\r\n reps[repIndex] = utils.deriveDeep(rep, true);\r\n },\r\n\r\n // Settings shortcuts\r\n\r\n ar: 'autoResolution',\r\n};\r\n\r\nfunction _fromArray(entries) {\r\n repIndex = 0;\r\n\r\n const opts = {};\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const /** string[] */ entry = entries[i];\r\n let /** string? */ key = entry[0];\r\n const /** string? */ value = entry[1];\r\n let /** function|string? */ action = actions[key];\r\n\r\n // unwind shortcuts and aliases\r\n while (_.isString(action)) {\r\n key = action;\r\n action = actions[key];\r\n }\r\n\r\n // either set a property or use specialized parser\r\n if (!action) {\r\n const adapter = adapters[typeof _.get(settings.defaults, key)];\r\n if (adapter) {\r\n _.set(opts, `settings.${key}`, adapter(value));\r\n } else {\r\n logger.warn(`Unknown option \"${key}\"`);\r\n }\r\n } else if (_.isFunction(action)) {\r\n const result = action(value, opts);\r\n if (result !== undefined) {\r\n opts[key] = result;\r\n }\r\n }\r\n }\r\n\r\n return opts;\r\n}\r\n\r\nfunction fromAttr(attr) {\r\n return _fromArray(utils.getUrlParameters(`?${attr || ''}`));\r\n}\r\n\r\nfunction fromURL(url) {\r\n return _fromArray(utils.getUrlParameters(url));\r\n}\r\n\r\nfunction _processOptsForURL(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = encodeQueryComponentL2(key) + cL2Ass + encodeQueryComponentL2(value);\r\n });\r\n return str.join(cLSep);\r\n}\r\n\r\nfunction _processArgsForURL(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]}${cOptsSep}${_processOptsForURL(args[1])}`;\r\n}\r\n\r\nfunction _processObjForURL(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += `,${objOpts.params.join(',')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += cOptsSep + _processOptsForURL(objOpts.opts);\r\n }\r\n return res;\r\n}\r\n\r\nfunction toURL(opts) {\r\n const stringList = [];\r\n let idx = 0;\r\n\r\n function checkAndAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n stringList[idx++] = encodeQueryComponentL1(prefix)\r\n + cL1Ass + encodeQueryComponentL1(value);\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n if (_.isEmpty(repList[i])) {\r\n continue;\r\n }\r\n checkAndAdd('r', i);\r\n checkAndAdd('s', repList[i].selector);\r\n checkAndAdd('m', _processArgsForURL(repList[i].mode));\r\n checkAndAdd('c', _processArgsForURL(repList[i].colorer));\r\n checkAndAdd('mt', _processArgsForURL(repList[i].material));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('o', _processObjForURL(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('l', opts.load);\r\n checkAndAdd('u', opts.unit);\r\n checkAndAdd('p', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n checkAndAdd('v', opts.view);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(key, value);\r\n });\r\n\r\n let url = '';\r\n if (typeof window !== 'undefined') {\r\n const { location } = window;\r\n url = `${location.protocol}//${location.host}${location.pathname}`;\r\n }\r\n if (stringList.length > 0) {\r\n url += `?${stringList.join('&')}`;\r\n }\r\n\r\n return url;\r\n}\r\n\r\nfunction _processOptsForScript(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = `${key}=${utils.enquoteString(value)}`;\r\n });\r\n return str.join(' ');\r\n}\r\n\r\nfunction _processArgsForScript(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]} ${_processOptsForScript(args[1])}`;\r\n}\r\n\r\nfunction _processObjForScript(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += ` ${objOpts.params.map(utils.enquoteString).join(' ')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += ` ${_processOptsForScript(objOpts.opts)}`;\r\n }\r\n return res;\r\n}\r\n\r\nfunction _processRepsForScript(rep, index) {\r\n const repString = [];\r\n let strIdx = 0;\r\n function localAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n repString[strIdx++] = prefix + value;\r\n }\r\n }\r\n if (_.isEmpty(rep)) {\r\n return null;\r\n }\r\n localAdd('', index);\r\n localAdd('s=', utils.enquoteString(rep.selector));\r\n localAdd('m=', _processArgsForScript(rep.mode));\r\n localAdd('c=', _processArgsForScript(rep.colorer));\r\n localAdd('mt=', _processArgsForScript(rep.material));\r\n return repString.join(' ');\r\n}\r\n\r\nfunction toScript(opts) {\r\n const commandsList = [];\r\n let idx = 0;\r\n function checkAndAdd(command, value, saveQuotes) {\r\n if (value !== null && value !== undefined) {\r\n const quote = (typeof value === 'string' && saveQuotes) ? '\"' : '';\r\n commandsList[idx++] = `${command} ${quote}${value}${quote}`.trim();\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n checkAndAdd('rep', _processRepsForScript(repList[i], i));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('', _processObjForScript(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('set', 'autobuild false');\r\n checkAndAdd('load', opts.load, true);\r\n checkAndAdd('unit', opts.unit);\r\n checkAndAdd('preset', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(`set ${key}`, value, true);\r\n });\r\n checkAndAdd('view', opts.view);\r\n checkAndAdd('set', 'autobuild true');\r\n return commandsList.join('\\n');\r\n}\r\n\r\nexport default {\r\n fromURL,\r\n fromAttr,\r\n adapters,\r\n toURL,\r\n toScript,\r\n};\r\n","/**\r\n * Atom measurements.\r\n *\r\n * @param {Residue} residue - (required) Residue containing the atom\r\n * @param {string} name - (required) Name, unique in the residue\r\n * @param {Element} type - (required) Chemical element reference\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n *\r\n * @param {number} role - Role of atom inside monomer: Lead and wing are particularity interesting\r\n * @param {boolean} het - Non-standard residue indicator\r\n *\r\n * @param {number} serial - Serial number, unique in the model\r\n * @param {string} location - Alternative location indicator (usually space or A-Z)\r\n * @param {number} occupancy - Occupancy percentage, from 0 to 1\r\n * @param {number} temperature - Temperature\r\n * @param {number} charge - Charge\r\n *\r\n * @exports Atom\r\n * @constructor\r\n */\r\n\r\nclass Atom {\r\n constructor(residue, name, type, position, role, het, serial, location, occupancy, temperature, charge) {\r\n this.index = -1;\r\n this.residue = residue;\r\n this.name = name;\r\n this.element = type;\r\n this.position = position;\r\n this.role = role;\r\n this.mask = 1 | 0;\r\n\r\n this.het = het;\r\n\r\n this.serial = serial;\r\n this.location = (location || ' ').charCodeAt(0);\r\n this.occupancy = occupancy || 1;\r\n this.temperature = temperature;\r\n this.charge = charge;\r\n this.hydrogenCount = -1; // explicitly invalid\r\n this.radicalCount = 0;\r\n this.valence = -1; // explicitly invalid\r\n\r\n this.bonds = [];\r\n\r\n this.flags = 0x0000;\r\n if (type.name === 'H') {\r\n this.flags |= Atom.Flags.HYDROGEN;\r\n } else if (type.name === 'C') {\r\n this.flags |= Atom.Flags.CARBON;\r\n }\r\n }\r\n\r\n isHet() {\r\n return this.het;\r\n }\r\n\r\n isHydrogen() {\r\n return this.element.number === 1;\r\n }\r\n\r\n getVisualName() {\r\n const { name } = this;\r\n if (name.length > 0) {\r\n return name;\r\n }\r\n return this.element.name.trim();\r\n }\r\n\r\n forEachBond(process) {\r\n const { bonds } = this;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n getFullName() {\r\n let name = '';\r\n if (this.residue !== null) {\r\n if (this.residue._chain !== null) {\r\n name += `${this.residue._chain.getName()}.`;\r\n }\r\n name += `${this.residue._sequence}.`;\r\n }\r\n name += this.name;\r\n return name;\r\n }\r\n\r\n /**\r\n * Enumeration of atom flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n CARBON: 0x0001,\r\n // OXYGEN: 0x0002,\r\n // NITROGEN: 0x0004,\r\n HYDROGEN: 0x0008,\r\n /** Non-polar hydrogen (it is also a HYDROGEN) */\r\n NONPOLARH: 0x1008,\r\n };\r\n}\r\n\r\nexport default Atom;\r\n","class Element {\r\n constructor(number, name, fullName, weight, radius, radiusBonding, hValency) {\r\n this.number = number;\r\n this.name = name;\r\n this.fullName = fullName;\r\n this.weight = weight;\r\n this.radius = radius;\r\n this.radiusBonding = radiusBonding;\r\n this.hydrogenValency = hValency;\r\n }\r\n\r\n static Constants = {\r\n\r\n U1: 1,\r\n Lead: 2,\r\n U2: 3,\r\n Wing: 4,\r\n U18: 18,\r\n\r\n };\r\n\r\n static Role = {\r\n\r\n N: Element.Constants.U1,\r\n CA: Element.Constants.Lead,\r\n C: Element.Constants.U2,\r\n O: Element.Constants.Wing,\r\n SG: Element.Constants.U18,\r\n\r\n };\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByAtomicNumber = [\r\n\r\n null,\r\n new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]),\r\n new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]),\r\n new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]),\r\n new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]),\r\n new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]),\r\n new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]),\r\n new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]),\r\n new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]),\r\n new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]),\r\n new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]),\r\n new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]),\r\n new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]),\r\n new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]),\r\n new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]),\r\n new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]),\r\n new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]),\r\n new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]),\r\n new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]),\r\n new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]),\r\n new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]),\r\n new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]),\r\n new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]),\r\n new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]),\r\n new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]),\r\n new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]),\r\n new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]),\r\n new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]),\r\n new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]),\r\n new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]),\r\n new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]),\r\n new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]),\r\n new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]),\r\n new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]),\r\n new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]),\r\n new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]),\r\n new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]),\r\n new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]),\r\n new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]),\r\n new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]),\r\n new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]),\r\n new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]),\r\n new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]),\r\n new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]),\r\n new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]),\r\n new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]),\r\n new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]),\r\n new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]),\r\n new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]),\r\n new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]),\r\n new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]),\r\n new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]),\r\n new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]),\r\n new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]),\r\n new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]),\r\n new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]),\r\n new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]),\r\n new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]),\r\n new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]),\r\n new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]),\r\n new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]),\r\n new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]),\r\n new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]),\r\n new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]),\r\n new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]),\r\n new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]),\r\n new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]),\r\n new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]),\r\n new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]),\r\n new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]),\r\n new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]),\r\n new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]),\r\n new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]),\r\n new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]),\r\n new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]),\r\n new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]),\r\n new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]),\r\n new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]),\r\n new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]),\r\n new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]),\r\n new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]),\r\n new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]),\r\n new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]),\r\n new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]),\r\n new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]),\r\n new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]),\r\n new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]),\r\n new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]),\r\n new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]),\r\n new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]),\r\n new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]),\r\n new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]),\r\n new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]),\r\n new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]),\r\n new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]),\r\n new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]),\r\n new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]),\r\n new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]),\r\n new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]),\r\n new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]),\r\n new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]),\r\n new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]),\r\n new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]),\r\n new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]),\r\n new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]),\r\n new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]),\r\n new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]),\r\n new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]),\r\n new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]),\r\n new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0]),\r\n\r\n ];\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByName = {\r\n // Duplicate atomic numbers (isotopes)\r\n\r\n D: new Element(1, 'D', 'Deuterium', 2.014, 1.2, 0.23, [1]),\r\n T: new Element(1, 'T', 'Tritium', 3.016, 1.2, 0.23, [1]),\r\n\r\n // All regular elements will be added later, automatically\r\n };\r\n}\r\n\r\n(function () {\r\n const byAtomicNumber = Element.ByAtomicNumber;\r\n const byName = Element.ByName;\r\n for (let i = 0, n = byAtomicNumber.length; i < n; ++i) {\r\n const element = byAtomicNumber[i];\r\n if (element) {\r\n byName[element.name] = element;\r\n }\r\n }\r\n}());\r\n\r\n// find atom type by chemical element (or create if missing)\r\nElement.getByName = function (element) {\r\n let type = Element.ByName[element];\r\n if (!type) {\r\n type = Element.ByName[element] = new Element(0, element, 'Unknown', 0, 1.0, 0.01, [0]);\r\n }\r\n return type;\r\n};\r\n\r\nexport default Element;\r\n","const cBondTypes = {\r\n /** Was generated manually */\r\n UNKNOWN: 0,\r\n /** Simple covalent bond */\r\n COVALENT: 1,\r\n /** Aromatic bond */\r\n AROMATIC: 2,\r\n};\r\n\r\nfunction getAtomPos(atom) {\r\n return atom.position;\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Atom} left - The first atom.\r\n * @param {Atom} right - The second atom.\r\n * @param {number} order - Order of current bond.\r\n * @param {number} type - Bond type.\r\n * @param {boolean} fixed - Indicator of a pre-specified connection (in contrast with guessed one).\r\n *\r\n * @exports Bond\r\n * @constructor\r\n */\r\nclass Bond {\r\n constructor(left, right, order, type, fixed) {\r\n this._left = left;\r\n this._right = right;\r\n this._fixed = fixed;\r\n this._index = -1;\r\n if (left > right) {\r\n throw new Error('In a bond atom indices must be in increasing order');\r\n }\r\n this._order = order;\r\n this._type = type;\r\n }\r\n\r\n getLeft() {\r\n return this._left;\r\n }\r\n\r\n getRight() {\r\n return this._right;\r\n }\r\n\r\n getOrder() {\r\n return this._order;\r\n }\r\n\r\n calcLength() {\r\n return this._left.position.distanceTo(this._right.position);\r\n }\r\n\r\n _forEachNeighbour(currAtom, process) {\r\n const { bonds } = currAtom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]._left !== currAtom ? bonds[i]._left : bonds[i]._right);\r\n }\r\n }\r\n\r\n forEachLevelOne(process) {\r\n const left = this._left;\r\n const right = this._right;\r\n this._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n this._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n }\r\n\r\n forEachLevelTwo(process) {\r\n // TODO refactor this piece of an art?\r\n const left = this._left;\r\n const right = this._right;\r\n const self = this;\r\n self._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === left) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n self._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === right) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n }\r\n\r\n _fixDir(refPoint, currDir, posGetter) {\r\n // count atoms to the right and to the left of the current plane\r\n let rightCount = 0;\r\n let leftCount = 0;\r\n const tmpVec = refPoint.clone();\r\n function checkDir(atom) {\r\n tmpVec.copy(posGetter(atom));\r\n tmpVec.sub(refPoint);\r\n const dotProd = currDir.dot(tmpVec);\r\n if (dotProd > 0) {\r\n ++rightCount;\r\n } else {\r\n ++leftCount;\r\n }\r\n }\r\n function checkCarbon(atom) {\r\n if (atom.element.name === 'C') {\r\n checkDir(atom);\r\n }\r\n }\r\n // count all atoms to the left and right of our plane, start from level 1 and carbons\r\n const stages = [\r\n [this.forEachLevelOne, checkCarbon],\r\n [this.forEachLevelOne, checkDir],\r\n [this.forEachLevelTwo, checkCarbon],\r\n [this.forEachLevelTwo, checkDir],\r\n ];\r\n\r\n for (let stageId = 0; stageId < stages.length; ++stageId) {\r\n stages[stageId][0].call(this, stages[stageId][1]);\r\n if (leftCount > rightCount) {\r\n return currDir.multiplyScalar(-1);\r\n }\r\n if (leftCount < rightCount) {\r\n return currDir;\r\n }\r\n }\r\n return currDir;\r\n }\r\n\r\n calcNormalDir(posGetter) {\r\n const left = this._left;\r\n const right = this._right;\r\n let first = left;\r\n let second = right;\r\n posGetter = posGetter === undefined ? getAtomPos : posGetter;\r\n if (left.bonds.length > right.bonds.length) {\r\n first = right;\r\n second = left;\r\n }\r\n let third = first;\r\n let maxNeibs = 0;\r\n const { bonds } = second;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n let another = bonds[i]._left;\r\n if (bonds[i]._left === second) {\r\n another = bonds[i]._right;\r\n }\r\n if (another.bonds.length > maxNeibs && another !== first) {\r\n third = another;\r\n maxNeibs = another.bonds.length;\r\n }\r\n }\r\n const secondPos = posGetter(second);\r\n const firstV = posGetter(first).clone().sub(secondPos);\r\n const secondV = posGetter(third).clone().sub(secondPos);\r\n secondV.crossVectors(firstV, secondV);\r\n if (secondV.lengthSq() < 0.0001) {\r\n secondV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n secondV.normalize();\r\n firstV.crossVectors(secondV, firstV);\r\n if (firstV.lengthSq() < 0.0001) {\r\n firstV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n return this._fixDir(secondPos, firstV, posGetter);\r\n }\r\n\r\n static BondType = cBondTypes;\r\n}\r\n\r\nBond.prototype.BondType = cBondTypes;\r\n\r\nexport default Bond;\r\n","import * as THREE from 'three';\r\nimport Atom from './Atom';\r\nimport Element from './Element';\r\n\r\nconst cNucleicControlNames = ['C3\\'', 'C3*', 'P', 'H5T', 'H3T'];\r\nconst cNucleicWing1Names = ['OP1', 'O1P'];\r\nconst cNucleicWing2Names = ['OP2', 'O2P'];\r\n\r\nconst cCylinderSource = ['C3\\'', 'C3*', 'C1', 'C1\\'', 'C1*', 'P'];\r\nconst cCylinderTarget = [{\r\n types: ['A', 'DA', 'G', 'DG'],\r\n atoms: ['N1'],\r\n}, {\r\n types: ['C', 'DC'],\r\n atoms: ['N3'],\r\n}, {\r\n types: ['T', 'DT', 'U', 'DU'],\r\n atoms: ['O4'],\r\n}];\r\n\r\n/**\r\n * Residue instance.\r\n *\r\n * @param {Chain} chain - Chain this residue belongs to.\r\n * @param {ResidueType} type - Generic residue instance type.\r\n * @param {number} sequence - Sequence ID.\r\n * @param {string} icode - One character insertion code (usually space or A-Z).\r\n *\r\n * @exports Residue\r\n * @constructor\r\n */\r\nclass Residue {\r\n constructor(chain, type, sequence, icode) {\r\n this._chain = chain;\r\n this._component = null;\r\n this._type = type;\r\n this._sequence = sequence;\r\n this._icode = icode;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n\r\n this._atoms = [];\r\n this._secondary = null;\r\n this._firstAtom = null;\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n this._lastAtom = null;\r\n this._controlPoint = null;\r\n this._midPoint = null;\r\n this._wingVector = null;\r\n this._cylinders = null;\r\n this._isValid = true;\r\n this._het = false;\r\n this._molecule = null;\r\n this.temperature = null;\r\n this.occupancy = null;\r\n }\r\n\r\n // Getters and setters\r\n getChain() {\r\n return this._chain;\r\n }\r\n\r\n getMolecule() {\r\n return this._molecule;\r\n }\r\n\r\n getType() {\r\n return this._type;\r\n }\r\n\r\n getSequence() {\r\n return this._sequence;\r\n }\r\n\r\n getSecondary() {\r\n return this._secondary;\r\n }\r\n\r\n getICode() {\r\n return this._icode;\r\n }\r\n\r\n // Other methods\r\n\r\n addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge) {\r\n const atom = new Atom(this, name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n const complex = this._chain.getComplex();\r\n complex.addAtom(atom);\r\n this._atoms.push(atom);\r\n this._het = this._het || het;\r\n return atom;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (process(atoms[i])) {\r\n break;\r\n }\r\n }\r\n }\r\n\r\n _findAtomByName(name) {\r\n let res = null;\r\n this.forEachAtom((atom) => {\r\n if (atom.name === name) {\r\n res = atom;\r\n return true;\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _findFirstAtomInList(names) {\r\n let res = null;\r\n for (let i = 0; i < names.length; ++i) {\r\n res = this._findAtomByName(names[i]);\r\n if (res !== null) {\r\n return res;\r\n }\r\n }\r\n return res;\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n mask &= atoms[i].mask;\r\n }\r\n this._mask = mask;\r\n }\r\n\r\n getCylinderTargetList() {\r\n const type = this._type._name;\r\n for (let i = 0, n = cCylinderTarget.length; i < n; ++i) {\r\n for (let j = 0, m = cCylinderTarget[i].types.length; j < m; ++j) {\r\n if (type === cCylinderTarget[i].types[j]) {\r\n return cCylinderTarget[i].atoms;\r\n }\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n _detectLeadWing(dst, next, getAtomPosition) {\r\n const leadAtom = this._findFirstAtomInList(cNucleicControlNames);\r\n let wingStart = this._findFirstAtomInList(cNucleicWing1Names);\r\n let wingEnd = this._findFirstAtomInList(cNucleicWing2Names);\r\n\r\n if (wingStart === null && next !== null) {\r\n wingStart = next._findFirstAtomInList(cNucleicWing1Names);\r\n }\r\n\r\n if (wingEnd === null && next !== null) {\r\n wingEnd = next._findFirstAtomInList(cNucleicWing2Names);\r\n }\r\n\r\n if (leadAtom === null || wingStart === null || wingEnd === null) {\r\n return;\r\n }\r\n\r\n dst._leadAtom = leadAtom;\r\n dst._controlPoint = getAtomPosition(leadAtom);\r\n dst._wingVector = getAtomPosition(wingEnd).clone().sub(getAtomPosition(wingStart));\r\n dst._isValid = true;\r\n\r\n const cylSource = this._findFirstAtomInList(cCylinderSource);\r\n const targetList = this.getCylinderTargetList();\r\n const cylTarget = targetList !== null ? this._findFirstAtomInList(targetList) : null;\r\n if (cylSource === null || cylTarget === null) {\r\n return;\r\n }\r\n dst._cylinders = [getAtomPosition(cylSource), getAtomPosition(cylTarget)];\r\n }\r\n\r\n calcWing(prevLeadPos, currLeadPos, prevWingPos, prevWing) {\r\n const vectorA = currLeadPos.clone().sub(prevLeadPos);\r\n const vectorB = prevLeadPos.clone().sub(prevWingPos);\r\n vectorB.crossVectors(vectorA, vectorB);\r\n vectorB.crossVectors(vectorA, vectorB).normalize();\r\n if (prevWing !== null && prevWing.length() > 0.0001) {\r\n const needToNegate = vectorB.length() > 0.0001 && Math.abs(prevWing.angleTo(vectorB)) > Math.PI / 2;\r\n if (needToNegate) {\r\n vectorB.negate();\r\n }\r\n }\r\n return vectorB;\r\n }\r\n\r\n _innerFinalize(prevRes, prev, nextRes, dst, chainAsNucleic, getAtomPosition) {\r\n const bFirstInChain = prev === null;\r\n\r\n const lp = getAtomPosition(this._leadAtom);\r\n const currLeadPos = new THREE.Vector3(lp.x, lp.y, lp.z);\r\n if (chainAsNucleic) {\r\n this._detectLeadWing(dst, nextRes, getAtomPosition);\r\n return;\r\n }\r\n\r\n if (bFirstInChain) { // for first one in chain\r\n dst._midPoint = getAtomPosition(this._firstAtom).clone();\r\n } else {\r\n const prevLeadPos = prev._controlPoint; // lead point of previous monomer\r\n dst._midPoint = prevLeadPos.clone().lerp(currLeadPos, 0.5);\r\n dst._wingVector = this.calcWing(prevLeadPos, currLeadPos, getAtomPosition(prevRes._wingAtom), prev._wingVector);\r\n }\r\n dst._controlPoint = currLeadPos;\r\n }\r\n\r\n _finalize2(prev, next, asNucleic) {\r\n // Should be called AFTER first finalize\r\n this._innerFinalize(prev, prev, next, this, asNucleic, (atom) => atom.position);\r\n }\r\n\r\n isConnected(anotherResidue) {\r\n if (this._chain !== anotherResidue._chain) {\r\n return false;\r\n }\r\n if (this === anotherResidue) {\r\n return true;\r\n }\r\n let res = false;\r\n this.forEachAtom((atom) => {\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue === anotherResidue || bond._right.residue === anotherResidue) {\r\n res = true;\r\n return true;\r\n }\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _finalize() {\r\n const self = this;\r\n [this._firstAtom] = this._atoms;\r\n this._lastAtom = this._atoms[this._atoms.length - 1];\r\n\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n\r\n let tempCount = 0;\r\n let temperature = 0; // average temperature\r\n let occupCount = 0;\r\n let occupancy = 0; // average occupancy\r\n this.forEachAtom((a) => {\r\n if (self._leadAtom === null) {\r\n if (a.role === Element.Constants.Lead) {\r\n self._leadAtom = a;\r\n }\r\n }\r\n if (self._wingAtom === null) {\r\n if (a.role === Element.Constants.Wing) {\r\n self._wingAtom = a;\r\n }\r\n }\r\n if (a.temperature) {\r\n temperature += a.temperature;\r\n tempCount++;\r\n }\r\n if (a.occupancy) {\r\n occupancy += a.occupancy;\r\n occupCount++;\r\n }\r\n return (self._leadAtom !== null && self._wingAtom !== null);\r\n });\r\n\r\n if (tempCount > 0) {\r\n this.temperature = temperature / tempCount;\r\n }\r\n if (occupCount > 0) {\r\n this.occupancy = occupancy / occupCount;\r\n }\r\n\r\n // Still try to make monomer look valid\r\n if (this._leadAtom === null || this._wingAtom === null) {\r\n this._isValid = false;\r\n }\r\n if (this._leadAtom === null) {\r\n this._leadAtom = this._firstAtom;\r\n }\r\n if (this._wingAtom === null) {\r\n this._wingAtom = this._lastAtom;\r\n }\r\n }\r\n}\r\n\r\nexport default Residue;\r\n","/**\r\n * Residue type.\r\n *\r\n * Predefined acid or created with HET, HETNAM, etc.\r\n *\r\n * @param {string} name - Short name, either standard (ALA, MET, etc.) or non-standard one.\r\n * @param {string} fullName - Full residue name.\r\n * @param {string} letterCode - 1-letter symbol.\r\n *\r\n * @exports ResidueType\r\n * @constructor\r\n */\r\nclass ResidueType {\r\n constructor(name, fullName, letterCode) {\r\n this._name = name;\r\n this._fullName = fullName;\r\n this.letterCode = letterCode;\r\n this.flags = 0x0000;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\n static StandardTypes = {\r\n\r\n ALA: new ResidueType('ALA', 'Alanine', 'A'),\r\n ARG: new ResidueType('ARG', 'Arginine', 'R'),\r\n ASN: new ResidueType('ASN', 'Asparagine', 'N'),\r\n ASP: new ResidueType('ASP', 'Aspartic Acid', 'D'),\r\n CYS: new ResidueType('CYS', 'Cysteine', 'C'),\r\n GLN: new ResidueType('GLN', 'Glutamine', 'Q'),\r\n GLU: new ResidueType('GLU', 'Glutamic Acid', 'E'),\r\n GLY: new ResidueType('GLY', 'Glycine', 'G'),\r\n HIS: new ResidueType('HIS', 'Histidine', 'H'),\r\n ILE: new ResidueType('ILE', 'Isoleucine', 'I'),\r\n LEU: new ResidueType('LEU', 'Leucine', 'L'),\r\n LYS: new ResidueType('LYS', 'Lysine', 'K'),\r\n MET: new ResidueType('MET', 'Methionine', 'M'),\r\n PHE: new ResidueType('PHE', 'Phenylalanine', 'F'),\r\n PRO: new ResidueType('PRO', 'Proline', 'P'),\r\n PYL: new ResidueType('PYL', 'Pyrrolysine', 'O'),\r\n SEC: new ResidueType('SEC', 'Selenocysteine', 'U'),\r\n SER: new ResidueType('SER', 'Serine', 'S'),\r\n THR: new ResidueType('THR', 'Threonine', 'T'),\r\n TRP: new ResidueType('TRP', 'Tryptophan', 'W'),\r\n TYR: new ResidueType('TYR', 'Tyrosine', 'Y'),\r\n VAL: new ResidueType('VAL', 'Valine', 'V'),\r\n A: new ResidueType('A', 'Adenine', 'A'),\r\n C: new ResidueType('C', 'Cytosine', 'C'),\r\n G: new ResidueType('G', 'Guanine', 'G'),\r\n I: new ResidueType('I', 'Inosine', 'I'),\r\n T: new ResidueType('T', 'Thymine', 'T'),\r\n U: new ResidueType('U', 'Uracil', 'U'),\r\n DA: new ResidueType('DA', 'Adenine', 'A'),\r\n DC: new ResidueType('DC', 'Cytosine', 'C'),\r\n DG: new ResidueType('DG', 'Guanine', 'G'),\r\n DI: new ResidueType('DI', 'Inosine', 'I'),\r\n DT: new ResidueType('DT', 'Thymine', 'T'),\r\n DU: new ResidueType('DU', 'Uracil', 'U'),\r\n '+A': new ResidueType('+A', 'Adenine', 'A'),\r\n '+C': new ResidueType('+C', 'Cytosine', 'C'),\r\n '+G': new ResidueType('+G', 'Guanine', 'G'),\r\n '+I': new ResidueType('+I', 'Inosine', 'I'),\r\n '+T': new ResidueType('+T', 'Thymine', 'T'),\r\n '+U': new ResidueType('+U', 'Uracil', 'U'),\r\n WAT: new ResidueType('WAT', 'Water', ''),\r\n H2O: new ResidueType('H2O', 'Water', ''),\r\n HOH: new ResidueType('HOH', 'Water', ''),\r\n DOD: new ResidueType('DOD', 'Water', ''),\r\n UNK: new ResidueType('UNK', 'Unknown', ''),\r\n UNL: new ResidueType('UNL', 'Unknown Ligand', ''),\r\n\r\n };\r\n\r\n /**\r\n * Enumeration of residue flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n // Amino acids\r\n /** Amino acid residue */\r\n PROTEIN: 0x0001,\r\n /** Basic amino acid residue */\r\n BASIC: 0x0002,\r\n /** Acidic amino acid residue */\r\n ACIDIC: 0x0004,\r\n /** Polar uncharged side chain amino acid residue */\r\n POLAR: 0x0008,\r\n /** Non-polar hydrophobic side chain amino acid residue */\r\n NONPOLAR: 0x0010,\r\n /** Aromatic amino acid residue */\r\n AROMATIC: 0x0020,\r\n\r\n // Nucleic acids\r\n\r\n /** Nucleic residue */\r\n NUCLEIC: 0x0100,\r\n /** Purine nucleic residue */\r\n PURINE: 0x0200,\r\n /** Pyrimidine nucleic residue */\r\n PYRIMIDINE: 0x0400,\r\n /** DNA */\r\n DNA: 0x0800,\r\n /** RNA */\r\n RNA: 0x1000,\r\n\r\n /** Water */\r\n WATER: 0x10000,\r\n };\r\n}\r\n\r\n// Flag combinations\r\nfunction _addFlag(flag, list) {\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const res = ResidueType.StandardTypes[list[i]];\r\n if (res) {\r\n res.flags |= flag;\r\n }\r\n }\r\n}\r\n\r\nconst { Flags } = ResidueType;\r\n_addFlag(Flags.WATER, ['WAT', 'H2O', 'HOH', 'DOD']);\r\n\r\n_addFlag(Flags.PROTEIN, [\r\n 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLY', 'GLU', 'GLN', 'HIS', 'ILE',\r\n 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'PYL', 'SEC', 'SER', 'THR', 'TRP',\r\n 'TYR', 'VAL',\r\n]);\r\n_addFlag(Flags.BASIC, ['ARG', 'HIS', 'LYS']);\r\n_addFlag(Flags.ACIDIC, ['ASP', 'GLU']);\r\n_addFlag(Flags.POLAR, ['ASN', 'CYS', 'GLN', 'SER', 'THR', 'TYR']);\r\n_addFlag(Flags.NONPOLAR, ['ALA', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'VAL', 'GLY']);\r\n_addFlag(Flags.AROMATIC, ['PHE', 'TRP', 'TYR']);\r\n\r\n_addFlag(Flags.NUCLEIC, [\r\n 'A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I',\r\n 'C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U',\r\n]);\r\n_addFlag(Flags.PURINE, ['A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I']);\r\n_addFlag(Flags.PYRIMIDINE, ['C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U']);\r\n_addFlag(Flags.DNA, ['DA', 'DG', 'DI', 'DC', 'DT', 'DU']);\r\n_addFlag(Flags.RNA, ['A', 'G', 'I', 'C', 'T', 'U']);\r\n// Table of kdHydrophobicity\r\nconst hydro = {\r\n ILE: 4.5,\r\n VAL: 4.2,\r\n LEU: 3.8,\r\n PHE: 2.8,\r\n CYS: 2.5,\r\n MET: 1.9,\r\n ALA: 1.8,\r\n GLY: -0.4,\r\n THR: -0.7,\r\n SER: -0.8,\r\n TRP: -0.9,\r\n TYR: -1.3,\r\n PRO: -1.6,\r\n HIS: -3.2,\r\n GLU: -3.5,\r\n GLN: -3.5,\r\n ASP: -3.5,\r\n ASN: -3.5,\r\n LYS: -3.9,\r\n ARG: -4.5,\r\n};\r\n\r\nfunction _addParam(param, list) {\r\n const keys = Object.keys(list);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = list[key];\r\n ResidueType.StandardTypes[key][param] = value;\r\n }\r\n}\r\n\r\n_addParam('hydrophobicity', hydro);\r\n\r\nexport default ResidueType;\r\n","import * as THREE from 'three';\r\nimport Residue from './Residue';\r\nimport ResidueType from './ResidueType';\r\n\r\n/**\r\n * Residues in chain are either amino acid either nucleic acid (and water)\r\n * There might be some modified/mutated residues, which type could not be determined by their name (nucleic or amino); In this\r\n * case firstly program definites the chain type (by well-known residues) and then definites modified/mutated residues\r\n */\r\nconst ChainType = {\r\n UNKNOWN: 0,\r\n PROTEIN: 1,\r\n NUCLEIC: 2,\r\n};\r\n\r\n/**\r\n * Residue chain.\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n * @param {string} name - One character identifier (usually space, A-Z, 0-9, or a-z).\r\n *\r\n * @exports Chain\r\n * @constructor\r\n */\r\nclass Chain {\r\n constructor(complex, name) {\r\n this._complex = complex;\r\n this._name = name;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n this._residues = [];\r\n\r\n this.minSequence = Number.POSITIVE_INFINITY;\r\n this.maxSequence = Number.NEGATIVE_INFINITY;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n _determineType() {\r\n const residues = this._residues;\r\n\r\n const { PROTEIN, NUCLEIC } = ResidueType.Flags;\r\n\r\n this.type = ChainType.UNKNOWN;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const { flags } = residues[i]._type;\r\n\r\n if ((flags & NUCLEIC) !== 0) {\r\n this.type = ChainType.NUCLEIC;\r\n break;\r\n } else if ((flags & PROTEIN) !== 0) {\r\n this.type = ChainType.PROTEIN;\r\n break;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Finds thre residue with specified sequence number and inserion code\r\n * @param {Number} seqNum sequence number\r\n * @param {string} iCode insertion code\r\n * @returns {*} Residue or null if not found\r\n */\r\n findResidue(seqNum, iCode) {\r\n const residues = this._residues;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n if (res._sequence === seqNum && res._icode === iCode) {\r\n return [res, i];\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _finalize() {\r\n this._determineType();\r\n\r\n const residues = this._residues;\r\n\r\n let prev = null;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const next = (i + 1 < n) ? residues[i + 1] : null;\r\n const curr = residues[i];\r\n // TODO: skip invalid residues\r\n if (1 /* curr._isValid */) { // eslint-disable-line no-constant-condition\r\n curr._finalize2(prev, next, this.type === ChainType.NUCLEIC);\r\n prev = curr;\r\n }\r\n }\r\n\r\n // fix very first wing\r\n if (residues.length > 1 && residues[1]._wingVector) {\r\n const p = residues[1]._wingVector;\r\n residues[0]._wingVector = new THREE.Vector3(p.x, p.y, p.z);\r\n } else if (residues.length > 0) {\r\n residues[0]._wingVector = new THREE.Vector3(1, 0, 0);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const residues = this._residues;\r\n let prev = null;\r\n let prevData = null;\r\n const frameRes = frameData._residues;\r\n const n = residues.length;\r\n function getAtomPos(atom) {\r\n return frameData.getAtomPos(atom.index);\r\n }\r\n\r\n for (let i = 0; i < n; ++i) {\r\n const curr = residues[i];\r\n const currData = frameRes[curr._index];\r\n const nextRes = (i + 1 < n) ? residues[i + 1] : null;\r\n curr._innerFinalize(prev, prevData, nextRes, currData, this.type === ChainType.NUCLEIC, getAtomPos);\r\n prev = curr;\r\n prevData = currData;\r\n }\r\n\r\n frameRes[residues[0]._index]._wingVector = n > 1\r\n ? frameRes[residues[1]._index]._wingVector\r\n : new THREE.Vector3(1, 0, 0);\r\n }\r\n\r\n /**\r\n * Create a new residue.\r\n *\r\n * @param {string} name - Residue name.\r\n * @param {number} sequence - Residue sequence number.\r\n * @param {string} iCode - Insertion code.\r\n * @returns {Residue} - Newly created residue instance.\r\n */\r\n addResidue(name, sequence, iCode) {\r\n let type = this._complex.getResidueType(name);\r\n if (type === null) {\r\n type = this._complex.addResidueType(name);\r\n }\r\n const residue = new Residue(this, type, sequence, iCode);\r\n this._complex.addResidue(residue);\r\n this._residues.push(residue);\r\n\r\n if (type.flags & (ResidueType.Flags.NUCLEIC | ResidueType.Flags.PROTEIN)) {\r\n if (this.maxSequence < sequence) {\r\n this.maxSequence = sequence;\r\n }\r\n if (this.minSequence > sequence) {\r\n this.minSequence = sequence;\r\n }\r\n }\r\n\r\n return residue;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this._mask = mask;\r\n }\r\n}\r\n\r\nexport default Chain;\r\n","import Residue from './Residue';\r\n\r\n/** An element of protein secondary structure. */\r\nclass StructuralElement {\r\n /**\r\n * Create a secondary structural element of the specified type.\r\n *\r\n * @param {StructuralElement.Type} type Secondary structure type.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n */\r\n constructor(type, init, term) {\r\n /**\r\n * Secondary structure type.\r\n * @type {StructuralElement.Type}\r\n */\r\n this.type = type;\r\n /**\r\n * Generic secondary structure type.\r\n * @type {StructuralElement.Generic}\r\n */\r\n this.generic = StructuralElement.genericByType[this.type] || 'loop';\r\n /**\r\n * Initial residue.\r\n * @type Residue\r\n */\r\n this.init = init;\r\n /**\r\n * Terminal residue.\r\n * @type Residue\r\n */\r\n this.term = term;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n if (this.init instanceof Residue && this.term instanceof Residue) {\r\n return;\r\n }\r\n\r\n // Link all intermediate residues to this structural element\r\n const start = complex.splitUnifiedSerial(this.init);\r\n const end = complex.splitUnifiedSerial(this.term);\r\n for (let chainId = start.chain; chainId <= end.chain; chainId++) {\r\n for (let serialId = start.serial; serialId <= end.serial; serialId++) {\r\n for (let { iCode } = start; iCode <= end.iCode; iCode++) {\r\n const hashCode = complex.getUnifiedSerial(chainId, serialId, iCode);\r\n if (residueHash[hashCode]) {\r\n residueHash[hashCode]._secondary = this;\r\n }\r\n }\r\n }\r\n }\r\n\r\n // Replace unfined serials by objects\r\n this.init = residueHash[this.init];\r\n this.term = residueHash[this.term];\r\n }\r\n}\r\n\r\n/**\r\n * Specific type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Generic\r\n */\r\nStructuralElement.Type = {\r\n /** A strand of a [beta-sheet](https://en.wikipedia.org/wiki/Beta_sheet). */\r\n STRAND: 'E',\r\n /** An isolated beta-bridge (too small for a beta-sheet). */\r\n BRIDGE: 'B',\r\n\r\n /** A [3/10 helix](https://en.wikipedia.org/wiki/310_helix) (hydrogen bonding is 3 residues apart). */\r\n HELIX_310: 'G',\r\n /** An [alpha-helix](https://en.wikipedia.org/wiki/Alpha_helix) (hydrogen bonding is 4 residues apart). */\r\n HELIX_ALPHA: 'H',\r\n /** A [pi-helix](https://en.wikipedia.org/wiki/Pi_helix) (hydrogen bonding is 5 residues apart). */\r\n HELIX_PI: 'I',\r\n /** A generic helix of unspecified bonding distance. */\r\n HELIX: 'X',\r\n\r\n /** An isolated 3/10-like helical turn. */\r\n TURN_310: '3',\r\n /** An isolated alpha-like helical turn. */\r\n TURN_ALPHA: '4',\r\n /** An isolated pi-like helical turn. */\r\n TURN_PI: '5',\r\n /** An isolated helical [turn](https://en.wikipedia.org/wiki/Turn_(biochemistry)) of unspecified bonding distance. */\r\n TURN: 'T',\r\n\r\n /** A bend (a region of high curvature). */\r\n BEND: 'S',\r\n /** Just a protein section with no particular conformation. */\r\n COIL: 'C',\r\n};\r\n\r\n/**\r\n * Generic type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Type\r\n */\r\nStructuralElement.Generic = {\r\n /** A strand of a sheet. */\r\n STRAND: 'strand',\r\n /** A helix. */\r\n HELIX: 'helix',\r\n /** Just a protein section with no particular conformation. */\r\n LOOP: 'loop',\r\n};\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\nconst StructuralElementGeneric = StructuralElement.Generic;\r\n\r\n/**\r\n * A mapping from specific types to generic ones.\r\n * @type {Object}\r\n */\r\nStructuralElement.genericByType = {\r\n [StructuralElementType.STRAND]: StructuralElementGeneric.STRAND,\r\n [StructuralElementType.HELIX_310]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_ALPHA]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_PI]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX]: StructuralElementGeneric.HELIX,\r\n};\r\n\r\nexport default StructuralElement;\r\n","import StructuralElement from './StructuralElement';\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\nexport const typeByPDBHelixClass = {\r\n 1: StructuralElementType.HELIX_ALPHA,\r\n 3: StructuralElementType.HELIX_PI,\r\n 5: StructuralElementType.HELIX_310,\r\n};\r\n\r\n/**\r\n * Helical secondary structure of a protein.\r\n * @extends StructuralElement\r\n */\r\nclass Helix extends StructuralElement {\r\n /**\r\n * Create a helix.\r\n *\r\n * @param {number} helixClass A helix class according to the\r\n * [PDB Format](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX).\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} serial Serial number of the helix (see PDB Format).\r\n * @param {string} name Helix identifier (see PDB Format).\r\n * @param {string} comment Comment about this helix (see PDB Format).\r\n * @param {number} length Length of this helix, in residues (see PDB Format).\r\n */\r\n constructor(helixClass, init, term, serial, name, comment, length) {\r\n super(typeByPDBHelixClass[helixClass] || StructuralElement.Type.HELIX, init, term);\r\n\r\n /**\r\n * Serial number of the helix (see PDB Format).\r\n * @type {number}\r\n */\r\n this.serial = serial;\r\n /**\r\n * Helix identifier (see PDB Format).\r\n * @type {string}\r\n */\r\n this.name = name;\r\n /**\r\n * Comment about this helix (see PDB Format).\r\n * @type {string}\r\n */\r\n this.comment = comment;\r\n /**\r\n * Length of this helix, in residues (see PDB Format).\r\n * @type {number}\r\n */\r\n this.length = length;\r\n }\r\n}\r\n\r\nexport default Helix;\r\n","import StructuralElement from './StructuralElement';\r\n\r\n/**\r\n * A single strand of a sheet in a protein secondary structure.\r\n * @extends StructuralElement\r\n */\r\nclass Strand extends StructuralElement {\r\n /**\r\n * Create a strand.\r\n *\r\n * @param {Sheet} sheet Parent sheet this strand belongs to.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} sense Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @param {Atom} atomCur Atom in current strand (see PDB Format).\r\n * @param {Atom} atomPrev Atom in previous strand (see PDB Format).\r\n */\r\n constructor(sheet, init, term, sense, atomCur, atomPrev) {\r\n super(StructuralElement.Type.STRAND, init, term);\r\n\r\n /**\r\n * Parent sheet this strand belongs to.\r\n * @type {Sheet}\r\n */\r\n this.sheet = sheet;\r\n /**\r\n * Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @type {number}\r\n */\r\n this.sense = sense;\r\n /**\r\n * Atom in current strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomCur = atomCur;\r\n /**\r\n * Atom in previous strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomPrev = atomPrev;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n *\r\n * @override\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n super._finalize(serialAtomMap, residueHash, complex);\r\n\r\n let as = this.atomCur;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomCur = serialAtomMap[as];\r\n }\r\n as = this.atomPrev;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomPrev = serialAtomMap[as];\r\n }\r\n }\r\n}\r\n\r\nexport default Strand;\r\n","import Strand from './Strand';\r\n\r\n/**\r\n * Sheet secondary structure of a protein.\r\n *\r\n * @param {string} name -\r\n * @param {number} width -\r\n *\r\n * @exports Sheet\r\n * @constructor\r\n */\r\nclass Sheet {\r\n constructor(name, width) {\r\n this._name = name;\r\n this._width = width;\r\n\r\n this._strands = [];\r\n }\r\n\r\n // Getters and setters\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getWidth() {\r\n return this._width;\r\n }\r\n\r\n addStrand(strand) {\r\n this._strands.push(strand);\r\n this._width = this._strands.length;\r\n }\r\n\r\n addEmptyStrand() {\r\n this._strands.push(new Strand(null, null, null, null, null, null));\r\n }\r\n\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n const s = this._strands;\r\n for (let i = 0, n = s.length; i < n; ++i) {\r\n s[i]._finalize(serialAtomMap, residueHash, complex);\r\n }\r\n if (!this._width) {\r\n this._width = s.length;\r\n }\r\n if (s.length !== this._width) {\r\n throw new Error(`Sheet ${this._name} is inconsistent.`);\r\n }\r\n }\r\n}\r\n\r\nexport default Sheet;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Atom measurements.\r\n *\r\n * @param {string} id - SGroup id\r\n * @param {string} name - Name of the group\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n * @param {array} atoms - Atoms group consists of\r\n * @param {object} saveNode - XML node from file for saving\r\n *\r\n * @exports SGroup\r\n * @constructor\r\n */\r\nclass SGroup {\r\n constructor(id, name, position, atoms, saveNode) {\r\n this._id = id;\r\n this._name = name;\r\n this._position = position || new THREE.Vector3();\r\n this._atoms = atoms || [];\r\n this._charge = 0; // default group charge\r\n this._repeat = 1; // how many times group repeated: always > 0\r\n this._center = null;\r\n this.xmlNodeRef = saveNode || null;\r\n }\r\n\r\n /**\r\n * Get atom full name.\r\n * @returns {string} Atom full name.\r\n */\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getPosition() {\r\n return this._position;\r\n }\r\n\r\n getCentralPoint() {\r\n return this._center;\r\n }\r\n\r\n _rebuildSGroupOnAtomChange() {\r\n const nLimon = 100000000;\r\n if (this._center === null) {\r\n return; // nothing to do if we are not relative\r\n }\r\n\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n for (let j = 0, n = this._atoms.length; j < n; j++) {\r\n const aPos = this._atoms[j].position;\r\n bLow.set(Math.min(bLow.x, aPos.x), Math.min(bLow.y, aPos.y), Math.min(bLow.z, aPos.z));\r\n bHight.set(Math.max(bHight.x, aPos.x), Math.max(bHight.y, aPos.y), Math.max(bHight.z, aPos.z));\r\n }\r\n this._center.addVectors(bLow, bHight);\r\n this._center.multiplyScalar(0.5);\r\n }\r\n}\r\n\r\nexport default SGroup;\r\n","import utils from '../../utils';\r\n\r\n//----------------------------------------------------------------------------\r\nclass Range {\r\n constructor(min, max) {\r\n this.min = min;\r\n this.max = typeof max === 'undefined' ? min : max;\r\n }\r\n\r\n includes(value) {\r\n return this.min <= value && value <= this.max;\r\n }\r\n\r\n toString() {\r\n const { min, max } = this;\r\n return min === max ? String(min) : [min, max].join(':');\r\n }\r\n\r\n toJSON() {\r\n return [this.min, this.max];\r\n }\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\nclass List {\r\n constructor(arg) {\r\n if (arg instanceof this.constructor) {\r\n // delegate construction to a different class\r\n // eslint-disable-next-line no-constructor-return\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n }\r\n\r\n append(value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n }\r\n\r\n toString() {\r\n return this._values.join(',');\r\n }\r\n\r\n toJSON() {\r\n const values = this._values;\r\n const result = [];\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n result[i] = value.toJSON ? value.toJSON() : value;\r\n }\r\n return result;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nclass RangeList extends List {\r\n includes(value) {\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n if (list[i].includes(value)) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nconst valuesArray = [];\r\n\r\nclass ValueList extends List {\r\n constructor(arg, upperOnly) {\r\n const list = super(arg);\r\n if (upperOnly) {\r\n this.upperOnly = true;\r\n const values = list._values;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n if (typeof value === 'string') {\r\n values[i] = value.toUpperCase();\r\n }\r\n }\r\n } else {\r\n this.upperOnly = false;\r\n }\r\n // return constructed object\r\n // eslint-disable-next-line no-constructor-return\r\n return list;\r\n }\r\n\r\n includes(value) {\r\n // we do not convert to upper case here for perfomance reasons\r\n // if list is upper case only, value must be converted before it is sent up to here\r\n return this._values.indexOf(value) !== -1;\r\n }\r\n\r\n toString() {\r\n // Quote values that are not correct identifiers\r\n const values = this._values;\r\n valuesArray.length = 0;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n valuesArray[i] = utils.correctSelectorIdentifier(String(values[i]));\r\n }\r\n return valuesArray.join(',');\r\n }\r\n\r\n _validate(value) {\r\n return (this.upperOnly && typeof value === 'string') ? value.toUpperCase() : value;\r\n }\r\n\r\n append(value) {\r\n super.append(this._validate(value));\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n super.remove(this._validate(value));\r\n return this;\r\n }\r\n}\r\n\r\nexport {\r\n Range,\r\n List,\r\n RangeList,\r\n ValueList,\r\n};\r\n","import { RangeList, ValueList } from './selectArgs';\r\n\r\n/** Base class for atom selectors. */\r\nclass Selector {\r\n toString() {\r\n return this.keyword;\r\n }\r\n\r\n toJSON() {\r\n return [this.name];\r\n }\r\n}\r\n\r\nSelector.prototype.name = 'Error';\r\nSelector.prototype.keyword = 'error';\r\n\r\n/** Base class for list-based atom selectors. */\r\nclass ListSelector extends Selector {\r\n constructor(list) {\r\n super();\r\n this.list = list;\r\n }\r\n\r\n toString() {\r\n return `${this.keyword} ${this.list}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.list.toJSON()];\r\n }\r\n}\r\n\r\nclass RangeListSelector extends ListSelector {\r\n constructor(arg) {\r\n super(new RangeList(arg));\r\n }\r\n}\r\n\r\nclass ValueListSelector extends ListSelector {\r\n constructor(arg, caseSensitive) {\r\n super(new ValueList(arg, !caseSensitive));\r\n }\r\n}\r\n\r\nclass NoneSelector extends Selector {\r\n includesAtom(_atom) {\r\n return false;\r\n }\r\n}\r\n\r\nNoneSelector.prototype.name = 'None';\r\nNoneSelector.prototype.keyword = 'none';\r\n\r\nclass AllSelector extends Selector {\r\n includesAtom(_atom) {\r\n return true;\r\n }\r\n}\r\n\r\nAllSelector.prototype.name = 'All';\r\nAllSelector.prototype.keyword = 'all';\r\n\r\nexport {\r\n Selector,\r\n ListSelector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n};\r\n","import { Selector, NoneSelector } from './selectorsBase';\r\n\r\n//----------------------------------------------------------------------------\r\n// Operators\r\n//----------------------------------------------------------------------------\r\nconst none = new NoneSelector();\r\n\r\nclass PrefixOperator extends Selector {\r\n constructor(rhs) {\r\n super();\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nPrefixOperator.prototype.priority = 1;\r\n\r\nclass InfixOperator extends Selector {\r\n constructor(lhs, rhs) {\r\n super();\r\n this.lhs = lhs || none;\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const lhs = this.lhs.priority && this.lhs.priority > this.priority ? `(${this.lhs})` : this.lhs;\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${lhs} ${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.lhs.toJSON(), this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nInfixOperator.prototype.priority = 1000;\r\n\r\nexport { PrefixOperator, InfixOperator };\r\n","import Atom from './Atom';\r\nimport ResidueType from './ResidueType';\r\nimport { parser } from '../utils/SelectionParser';\r\nimport { Range, RangeList, ValueList } from './selectors/selectArgs';\r\nimport { PrefixOperator, InfixOperator } from './selectors/selectOps';\r\nimport {\r\n Selector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n} from './selectors/selectorsBase';\r\n\r\nconst keywords = {};\r\n\r\n//----------------------------------------------------------------------------\r\n// Named selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineSelector(name, SelectorClass) {\r\n const keyword = name.toLowerCase();\r\n SelectorClass.prototype.keyword = keyword;\r\n SelectorClass.prototype.name = name;\r\n\r\n const factory = ((...args) => new SelectorClass(...args));\r\n factory.SelectorClass = SelectorClass;\r\n keywords[keyword] = factory;\r\n\r\n return SelectorClass;\r\n}\r\n\r\ndefineSelector('Serial', class SerialSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.serial);\r\n }\r\n});\r\n\r\ndefineSelector('Name', class NameSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.name);\r\n }\r\n});\r\n\r\ndefineSelector('AltLoc', class AltLocSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(String.fromCharCode(atom.location));\r\n }\r\n});\r\n\r\ndefineSelector('Elem', class ElemSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.element.name);\r\n }\r\n});\r\n\r\ndefineSelector('Residue', class ResidueSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._type._name);\r\n }\r\n});\r\n\r\ndefineSelector('Sequence', class SequenceSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._sequence);\r\n }\r\n});\r\n\r\ndefineSelector('ICode', class ICodeSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._icode);\r\n }\r\n});\r\n\r\ndefineSelector('ResIdx', class ResIdxSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._index);\r\n }\r\n});\r\n\r\ndefineSelector('Chain', class ChainSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._chain._name);\r\n }\r\n});\r\n\r\ndefineSelector('Hetatm', class HetatmSelector extends Selector {\r\n includesAtom(atom) {\r\n return atom.het;\r\n }\r\n});\r\n\r\ndefineSelector('PolarH', class PolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.HYDROGEN;\r\n }\r\n});\r\n\r\ndefineSelector('NonPolarH', class NonPolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.NONPOLARH;\r\n }\r\n});\r\n\r\ndefineSelector('All', AllSelector);\r\n\r\ndefineSelector('None', NoneSelector);\r\n\r\nconst NULL_SELECTOR = keywords.none();\r\n\r\n//----------------------------------------------------------------------------\r\n// Named operators\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineOperator(name, priority, OperatorClass) {\r\n OperatorClass.prototype.priority = priority;\r\n return defineSelector(name, OperatorClass);\r\n}\r\ndefineOperator('Not', 1, class NotOperator extends PrefixOperator {\r\n includesAtom(atom) {\r\n return !this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('And', 2, class AndOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) && this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('Or', 3, class OrOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) || this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\n//----------------------------------------------------------------------------\r\n// Flag selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction byResidueTypeFlag(flag, name) {\r\n return defineSelector(name, class extends Selector {\r\n includesAtom(atom) {\r\n return (atom.residue._type.flags & flag) !== 0;\r\n }\r\n });\r\n}\r\n\r\nbyResidueTypeFlag(ResidueType.Flags.PROTEIN, 'Protein');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC, 'Basic');\r\nbyResidueTypeFlag(ResidueType.Flags.ACIDIC, 'Acidic');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC | ResidueType.Flags.ACIDIC, 'Charged');\r\nbyResidueTypeFlag(ResidueType.Flags.POLAR, 'Polar');\r\nbyResidueTypeFlag(ResidueType.Flags.NONPOLAR, 'NonPolar');\r\nbyResidueTypeFlag(ResidueType.Flags.AROMATIC, 'Aromatic');\r\nbyResidueTypeFlag(ResidueType.Flags.NUCLEIC, 'Nucleic');\r\nbyResidueTypeFlag(ResidueType.Flags.PURINE, 'Purine');\r\nbyResidueTypeFlag(ResidueType.Flags.PYRIMIDINE, 'Pyrimidine');\r\nbyResidueTypeFlag(ResidueType.Flags.WATER, 'Water');\r\n\r\n//----------------------------------------------------------------------------\r\nconst selectors = Object.create(keywords);\r\n\r\nselectors.Selector = Selector;\r\nselectors.RangeListSelector = RangeListSelector;\r\nselectors.ValueListSelector = ValueListSelector;\r\nselectors.Range = Range;\r\nselectors.RangeList = RangeList;\r\nselectors.ValueList = ValueList;\r\nselectors.PrefixOperator = PrefixOperator;\r\nselectors.InfixOperator = InfixOperator;\r\nselectors.Context = Object.create({});\r\n\r\nselectors.GetSelector = function (key) {\r\n if (!selectors.Context.hasOwnProperty(key)) {\r\n const exc = { message: `selector ${key} is not registered` };\r\n throw exc;\r\n }\r\n return selectors.Context[key] || NULL_SELECTOR;\r\n};\r\n\r\nselectors.ClearContext = function () {\r\n Object.keys(selectors.Context).forEach((k) => { delete selectors.Context[k]; });\r\n};\r\n\r\nselectors.keyword = function (key) {\r\n return keywords[key.toLowerCase()] || keywords.none;\r\n};\r\n\r\nselectors.parse = function (str) {\r\n const res = {};\r\n try {\r\n res.selector = parser.parse(str);\r\n } catch (e) {\r\n res.selector = NULL_SELECTOR;\r\n res.error = e.message;\r\n }\r\n return res;\r\n};\r\n\r\nparser.yy = selectors;\r\nparser.yy.parseError = parser.parseError; // workaround for incorrect JISON parser generator for AMD module\r\n\r\nexport default selectors;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\n\r\n/**\r\n * Basic biological unit class.\r\n *\r\n * @exports BiologicalUnit\r\n * @constructor\r\n */\r\nclass BiologicalUnit {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._selector = selectors.keyword('All')();\r\n this._boundaries = {\r\n boundingBox: new THREE.Box3(),\r\n boundingSphere: new THREE.Sphere(),\r\n };\r\n }\r\n\r\n computeBoundaries() {\r\n const atoms = this._complex._atoms;\r\n const n = atoms.length;\r\n const selector = this._selector;\r\n\r\n const { boundingBox } = this._boundaries;\r\n boundingBox.makeEmpty();\r\n if (n === 1) {\r\n boundingBox.expandByPoint(atoms[0].position);\r\n const bbc = new THREE.Vector3();\r\n boundingBox.getCenter(bbc);\r\n const s = 2 * atoms[0].element.radius;\r\n boundingBox.setFromCenterAndSize(bbc, new THREE.Vector3(s, s, s));\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (selector.includesAtom(atoms[i])) {\r\n boundingBox.expandByPoint(atoms[i].position);\r\n }\r\n }\r\n }\r\n\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n if (n === 1) {\r\n this._boundaries.boundingSphere.set(center, atoms[0].element.radius);\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (!selector.includesAtom(atoms[i])) {\r\n continue;\r\n }\r\n const pos = atoms[i].position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n this._boundaries.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n }\r\n\r\n getTransforms() {\r\n return [];\r\n }\r\n\r\n getSelector() {\r\n return this._selector;\r\n }\r\n\r\n getBoundaries() {\r\n return this._boundaries;\r\n }\r\n\r\n finalize() {\r\n }\r\n}\r\n\r\nexport default BiologicalUnit;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\nimport BiologicalUnit from './BiologicalUnit';\r\n\r\n/**\r\n * Biological assembly.\r\n *\r\n * @exports Assembly\r\n * @constructor\r\n */\r\n\r\nclass Assembly extends BiologicalUnit {\r\n constructor(complex) {\r\n super(complex);\r\n this.chains = [];\r\n this.matrices = [];\r\n }\r\n\r\n computeBoundaries() {\r\n super.computeBoundaries();\r\n // fix up the boundaries\r\n const { matrices } = this;\r\n const oldCenter = this._boundaries.boundingSphere.center;\r\n const oldRad = this._boundaries.boundingSphere.radius;\r\n const boundingBox = this._boundaries.boundingBox = new THREE.Box3();\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = matrices.length; i < n; ++i) {\r\n boundingBox.expandByPoint(oldCenter.clone().applyMatrix4(matrices[i]));\r\n }\r\n\r\n const newRad = boundingBox.max.distanceTo(boundingBox.min) / 2 + oldRad;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n this._boundaries.boundingSphere = new THREE.Sphere().set(center, newRad);\r\n boundingBox.max.addScalar(oldRad);\r\n boundingBox.min.subScalar(oldRad);\r\n }\r\n\r\n /**\r\n * Mark a chain as belonging to this biological assembly.\r\n * @param {string} chain - chain identifier, usually a single letter\r\n */\r\n addChain(chain) {\r\n this.chains[this.chains.length] = chain;\r\n }\r\n\r\n /**\r\n * Add a transformation matrix.\r\n * @param {THREE.Matrix4} matrix - transformation matrix\r\n */\r\n addMatrix(matrix) {\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n getTransforms() {\r\n return this.matrices;\r\n }\r\n\r\n finalize() {\r\n if (this.chains.length > 0) {\r\n this._selector = selectors.keyword('Chain')(this.chains);\r\n } else {\r\n this._selector = selectors.keyword('None')();\r\n }\r\n }\r\n}\r\n\r\nexport default Assembly;\r\n","/**\r\n * This class represents connected component as a part of a complex.\r\n * WARNING! The whole component entity is build under the assumption that residues\r\n * are placed in the chains and complex in ascending order of indices\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n *\r\n * @exports Component\r\n * @constructor\r\n */\r\nclass Component {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._index = -1;\r\n this._residueIndices = [];\r\n this._cycles = [];\r\n this._subDivs = [];\r\n this._residueCount = 0;\r\n }\r\n\r\n getResidues() {\r\n return this._complex._residues;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residueCount;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._complex._residues;\r\n const resIdc = this._residueIndices;\r\n for (let idIdc = 0, idCount = resIdc.length; idIdc < idCount; ++idIdc) {\r\n for (let idx = resIdc[idIdc].start, last = resIdc[idIdc].end; idx <= last; ++idx) {\r\n process(residues[idx]);\r\n }\r\n }\r\n }\r\n\r\n setSubDivs(subDivs) {\r\n this._subDivs = subDivs;\r\n let curr = 0;\r\n const resIdc = [];\r\n let resCnt = 0;\r\n for (let i = 0, n = subDivs.length; i < n; ++i) {\r\n if (i === n - 1 || subDivs[i].end + 1 !== subDivs[i + 1].start) {\r\n const { start } = subDivs[curr];\r\n const { end } = subDivs[i];\r\n resIdc[resIdc.length] = {\r\n start,\r\n end,\r\n };\r\n resCnt += end - start + 1;\r\n curr = i + 1;\r\n }\r\n }\r\n\r\n this._residueIndices = resIdc;\r\n this._residueCount = resCnt;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._complex._bonds;\r\n\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue._component === this) {\r\n process(bond);\r\n }\r\n }\r\n }\r\n\r\n update() {\r\n this.forEachCycle((cycle) => {\r\n cycle.update();\r\n });\r\n }\r\n\r\n forEachAtom(process) {\r\n this.forEachResidue((residue) => {\r\n residue.forEachAtom(process);\r\n });\r\n }\r\n\r\n addCycle(cycle) {\r\n this._cycles.push(cycle);\r\n }\r\n\r\n forEachCycle(process) {\r\n const cycles = this._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n process(cycles[i]);\r\n }\r\n }\r\n\r\n markResidues() {\r\n const self = this;\r\n self.forEachResidue((residue) => {\r\n residue._component = self;\r\n });\r\n }\r\n\r\n _forEachSubChain(mask, process) {\r\n const residues = this._complex._residues;\r\n const subs = this._subDivs;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let idx = subs[i].start, last = subs[i].end; idx <= last; ++idx) {\r\n const currRes = residues[idx];\r\n if (mask & currRes._mask && currRes._isValid) {\r\n let end = idx + 1;\r\n for (; end <= last; ++end) {\r\n const endRes = residues[end];\r\n if (!(mask & endRes._mask && endRes._isValid)) {\r\n break;\r\n }\r\n }\r\n process(i, idx, end - 1);\r\n idx = end;\r\n }\r\n }\r\n }\r\n }\r\n\r\n getMaskedSequences(mask) {\r\n const subs = [];\r\n let idx = 0;\r\n this._forEachSubChain(mask, (_subIdx, start, end) => {\r\n subs[idx++] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n\r\n getMaskedSubdivSequences(mask) {\r\n const subs = [];\r\n let currIdx = -1;\r\n let lastSubIdx = -1;\r\n const subDivs = this._subDivs;\r\n\r\n this._forEachSubChain(mask, (subIdx, start, end) => {\r\n if (lastSubIdx !== subIdx) {\r\n ++currIdx;\r\n subs[currIdx] = {\r\n arr: [],\r\n boundaries: subDivs[subIdx],\r\n };\r\n lastSubIdx = subIdx;\r\n }\r\n subs[currIdx].arr[subs[currIdx].arr.length] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n}\r\n\r\nexport default Component;\r\n","import utils from '../utils';\r\n\r\nconst cMaxPairsForHashCode = 32;\r\nconst cHashTableSize = 1024 * 1024;\r\nconst cNumbersPerPair = 4;\r\nconst cMaxNeighbours = 14;\r\nconst cInvalidVal = -1;\r\n// 89237 is a large simple number, can be used for pseudo random hash code create\r\nconst cBigPrime = 89237;\r\n\r\nclass AtomPairs {\r\n constructor(maxPairsEstimate) {\r\n this.numPairs = 0;\r\n this.numMaxPairs = maxPairsEstimate;\r\n this.intBuffer = utils.allocateTyped(Int32Array, maxPairsEstimate * cNumbersPerPair);\r\n for (let i = 0; i < maxPairsEstimate * cNumbersPerPair; i++) {\r\n this.intBuffer[i] = cInvalidVal;\r\n }\r\n this.hashBuffer = utils.allocateTyped(Int32Array, cHashTableSize * cMaxPairsForHashCode);\r\n for (let i = 0; i < cHashTableSize * cMaxPairsForHashCode; i++) {\r\n this.hashBuffer[i] = cInvalidVal;\r\n }\r\n }\r\n\r\n /**\r\n * Destroy all pairs memory\r\n */\r\n destroy() {\r\n this.intBuffer = null;\r\n this.hashBuffer = null;\r\n }\r\n\r\n /**\r\n * Add pair of atoms to collection\r\n * @param {number} indexA - Index of the 1st vertex.\r\n * @param {number} indexB - Index of the 2nd vertex.\r\n */\r\n addPair(indexA, indexB) {\r\n const ia = (indexA < indexB) ? indexA : indexB;\r\n const ib = (indexA > indexB) ? indexA : indexB;\r\n const codeToAdd = ia + (ib << cMaxNeighbours);\r\n\r\n const hashCode = (ia + (ib * cBigPrime)) & (cHashTableSize - 1);\r\n let j = hashCode * cMaxPairsForHashCode;\r\n let apI = 0;\r\n for (; apI < cMaxPairsForHashCode; apI++) {\r\n const code = this.hashBuffer[j + apI];\r\n if (code === cInvalidVal) {\r\n break;\r\n }\r\n if (code === codeToAdd) {\r\n return false;\r\n }\r\n }\r\n // add this new hash code\r\n if (apI >= cMaxPairsForHashCode) {\r\n throw new Error('addPair: increase cMaxPairsForHashCode');\r\n }\r\n this.hashBuffer[j + apI] = codeToAdd;\r\n\r\n // actually add\r\n if (this.numPairs >= this.numMaxPairs) {\r\n throw new Error('addPair: increase num pairs');\r\n }\r\n j = this.numPairs * cNumbersPerPair;\r\n this.intBuffer[j] = ia;\r\n this.intBuffer[j + 1] = ib;\r\n this.intBuffer[j + 2] = codeToAdd;\r\n this.numPairs++;\r\n return true;\r\n }\r\n}\r\n\r\nexport default AtomPairs;\r\n","import AtomPairs from './AtomPairs';\r\nimport Bond from './Bond';\r\n\r\nconst cProfileBondBuilder = false;\r\nconst cEstBondsMultiplier = 4;\r\nconst cSpaceCode = 32;\r\nconst cBondTolerance = 0.45;\r\nconst cVMDTolerance = 0.6;\r\nconst cBondRadInJMOL = true;\r\nconst cEpsilon = 0.001;\r\n\r\n/**\r\n * Get radius used for building bonds.\r\n *\r\n * @param {Atom} atom - Atom object.\r\n * @returns {number} special value for bonding radius for this atom\r\n */\r\nfunction _getBondingRadius(atom) {\r\n const { element } = atom;\r\n if (element) {\r\n return element.radiusBonding;\r\n }\r\n throw new Error('_getBondingRadius: Logic error.');\r\n}\r\n\r\nfunction _isAtomEligible(atom) {\r\n // build for all non-hetatm and for hetatm without bonds\r\n return !atom.isHet() || (atom.bonds && atom.bonds.length === 0);\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Complex} complex molecular complex\r\n\r\n * @exports AutoBond\r\n * @constructor\r\n */\r\nclass AutoBond {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._maxRad = 1.8;\r\n const bBox = this._complex.getDefaultBoundaries().boundingBox;\r\n this._vBoxMin = bBox.min.clone();\r\n this._vBoxMax = bBox.max.clone();\r\n\r\n this._pairCollection = null;\r\n }\r\n\r\n /**\r\n * Add existing pairs of connectors (from pdb file after its reading)\r\n * @returns {number} 0\r\n */\r\n _addExistingPairs() {\r\n const atoms = this._complex.getAtoms();\r\n const numAtoms = atoms.length;\r\n let aInd = 0;\r\n const collection = this._pairCollection;\r\n\r\n for (; aInd < numAtoms; aInd++) {\r\n const { bonds } = atoms[aInd];\r\n const numBondsForAtom = bonds.length;\r\n for (let bInd = 0; bInd < numBondsForAtom; bInd++) {\r\n const bond = bonds[bInd];\r\n const indTo = bond._left.index;\r\n if (indTo === aInd) {\r\n collection.addPair(aInd, bond._right.index);\r\n }\r\n } // for (b) all bonds in atom\r\n } // for (a)\r\n return 0;\r\n }\r\n\r\n _findPairs() {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const atoms = this._complex._atoms;\r\n const atomsNum = atoms.length;\r\n const self = this;\r\n\r\n let rA;\r\n let isHydrogenA;\r\n let posA;\r\n let locationA;\r\n let atomA;\r\n\r\n const processAtom = function (atomB) {\r\n if (isHydrogenA && atomB.isHydrogen()) {\r\n return;\r\n }\r\n\r\n const locationB = atomB.location;\r\n if ((locationA !== cSpaceCode)\r\n && (locationB !== cSpaceCode)\r\n && (locationA !== locationB)) {\r\n return;\r\n }\r\n\r\n const dist2 = posA.distanceToSquared(atomB.position);\r\n const rB = atomB.element.radiusBonding;\r\n const maxAcceptable = cBondRadInJMOL ? rA + rB + cBondTolerance : cVMDTolerance * (rA + rB);\r\n\r\n if (dist2 > (maxAcceptable * maxAcceptable)) {\r\n return;\r\n }\r\n\r\n if (dist2 < cEpsilon) {\r\n return;\r\n }\r\n\r\n self._pairCollection.addPair(atomA.index, atomB.index);\r\n };\r\n\r\n for (let i = 0; i < atomsNum; ++i) {\r\n atomA = atoms[i];\r\n if (!_isAtomEligible(atomA)) {\r\n continue;\r\n }\r\n\r\n rA = atomA.element.radiusBonding;\r\n isHydrogenA = atomA.isHydrogen();\r\n posA = atomA.position;\r\n locationA = atomA.location;\r\n\r\n vw.forEachAtomWithinRadius(posA, 2 * this._maxRad + cBondTolerance, processAtom);\r\n }\r\n }\r\n\r\n _addPairs() {\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0, k = 0; i < this._pairCollection.numPairs; i++, k += 4) {\r\n const iA = this._pairCollection.intBuffer[k];\r\n const iB = this._pairCollection.intBuffer[k + 1];\r\n this._addPair(atoms[iA], atoms[iB]);\r\n }\r\n }\r\n\r\n _addPair(atomA, atomB) {\r\n const bondsA = atomA.bonds;\r\n const indexA = atomA.index;\r\n const indexB = atomB.index;\r\n for (let j = 0, numBonds = bondsA.length; j < numBonds; ++j) {\r\n const bond = bondsA[j];\r\n if (bond._left.index === indexB || bond._right.index === indexB) {\r\n return;\r\n }\r\n }\r\n const left = indexA < indexB ? atomA : atomB;\r\n const right = indexA < indexB ? atomB : atomA;\r\n const newBond = this._complex.addBond(left, right, 0, Bond.BondType.UNKNOWN, false);\r\n bondsA.push(newBond);\r\n atomB.bonds.push(newBond);\r\n }\r\n\r\n build() {\r\n if (cProfileBondBuilder) {\r\n console.time('Bonds Builder');\r\n }\r\n this._buildInner();\r\n\r\n if (cProfileBondBuilder) {\r\n console.timeEnd('Bonds Builder');\r\n }\r\n }\r\n\r\n _buildInner() {\r\n const atoms = this._complex._atoms;\r\n if (atoms.length < 2) {\r\n return;\r\n }\r\n if (atoms[0].index < 0) {\r\n throw new Error('AutoBond: Atoms in complex were not indexed.');\r\n }\r\n\r\n this._calcBoundingBox();\r\n this._pairCollection = new AtomPairs(atoms.length * cEstBondsMultiplier);\r\n this._addExistingPairs();\r\n this._findPairs();\r\n this._addPairs();\r\n }\r\n\r\n _calcBoundingBox() {\r\n const atoms = this._complex._atoms;\r\n const nAtoms = atoms.length;\r\n let maxRad = _getBondingRadius(atoms[0]);\r\n for (let i = 1; i < nAtoms; ++i) {\r\n maxRad = Math.max(maxRad, _getBondingRadius(atoms[i]));\r\n }\r\n this._vBoxMax.addScalar(maxRad);\r\n this._vBoxMin.addScalar(-maxRad);\r\n this._maxRad = maxRad * 1.2;\r\n }\r\n\r\n destroy() {\r\n if (this._pairCollection) {\r\n this._pairCollection.destroy();\r\n }\r\n }\r\n}\r\n\r\nexport default AutoBond;\r\n","import * as THREE from 'three';\r\nimport Bond from './Bond';\r\nimport Element from './Element';\r\n\r\nconst cCrossThresh = 0.1;\r\nconst cAromaticType = Bond.BondType.AROMATIC;\r\nconst cAromaticAtoms = [\r\n Element.ByName.C.number,\r\n Element.ByName.N.number,\r\n // Element.ByName.O.number,\r\n // Element.ByName.S.number,\r\n];\r\n\r\n/** Conditions for bonds:\r\n * - Cross product with each subsequent bond to add is collinear and point to the same direction\r\n * - Each pair of a adjacent bonds belong to not more than one cycle\r\n * - If there is more than one candidates we try them in ascending order of angle values\r\n */\r\n\r\nconst _coDirVectors = (function () {\r\n const v1Tmp = new THREE.Vector3();\r\n const v2Tmp = new THREE.Vector3();\r\n const cp = new THREE.Vector3();\r\n return function (v1, v2) {\r\n v1Tmp.copy(v1).normalize();\r\n v2Tmp.copy(v2).normalize();\r\n cp.crossVectors(v1Tmp, v2Tmp);\r\n if (cp.length() > cCrossThresh) {\r\n return false;\r\n }\r\n // zero vector in out terms must be collinear to any\r\n return v1Tmp.dot(v2Tmp) >= 0;\r\n };\r\n}());\r\n\r\nfunction _insertAscending(arr, val) {\r\n let idx = 0;\r\n while (idx < arr.length && arr[idx] < val) {\r\n ++idx;\r\n }\r\n arr.splice(idx, 0, val);\r\n}\r\n\r\nfunction _anotherAtom(bond, currAtom) {\r\n return bond._left === currAtom ? bond._right : bond._left;\r\n}\r\n\r\nfunction _cosBetween(v1, v2) {\r\n const theta = v1.dot(v2) / (Math.sqrt(v1.lengthSq() * v2.lengthSq()));\r\n return THREE.MathUtils.clamp(theta, -1, 1);\r\n}\r\n\r\nfunction _markAromatic(bond) {\r\n bond._type = cAromaticType;\r\n}\r\n\r\nclass Cycle {\r\n constructor(atomsList) {\r\n this.atoms = atomsList;\r\n this.update();\r\n }\r\n\r\n update() {\r\n const { atoms } = this;\r\n const center = new THREE.Vector3();\r\n const nA = atoms.length;\r\n for (let j = 0; j < nA; ++j) {\r\n center.add(atoms[j].position);\r\n }\r\n center.multiplyScalar(1.0 / nA);\r\n this.center = center;\r\n this.radius = center.distanceTo(atoms[0].position.clone().lerp(atoms[1].position, 0.5));\r\n }\r\n\r\n forEachBond(process) {\r\n const { atoms } = this;\r\n const nA = atoms.length;\r\n let currAtom = atoms[0];\r\n let nextAtom;\r\n\r\n function checkBond(bond) {\r\n if (bond._left === nextAtom || bond._right === nextAtom) {\r\n process(bond);\r\n }\r\n }\r\n\r\n for (let i = 0; i < nA; ++i) {\r\n nextAtom = atoms[(i + 1) % nA];\r\n currAtom.forEachBond(checkBond);\r\n currAtom = nextAtom;\r\n }\r\n }\r\n}\r\n\r\nfunction _isAromatic(bond) {\r\n return bond._type === cAromaticType;\r\n}\r\n\r\nfunction _isPossibleAromatic(bond) {\r\n if (bond.type === cAromaticType) {\r\n return true;\r\n }\r\n const rightIdx = cAromaticAtoms.indexOf(bond._right.element.number);\r\n const leftIdx = cAromaticAtoms.indexOf(bond._left.element.number);\r\n return rightIdx !== -1 && leftIdx !== -1;\r\n}\r\n\r\nfunction _checkCycleSimple(cycle) {\r\n return cycle.length > 3;\r\n}\r\n\r\nfunction _checkCycleComplex(cycle) {\r\n console.assert(cycle.length > 2);\r\n return true;\r\n}\r\n\r\nclass AromaticLoopsMarker {\r\n constructor(complex) {\r\n this._complex = complex;\r\n const bondsData = new Array(complex._bonds.length);\r\n const bondMarks = new Array(complex._bonds.length);\r\n for (let i = 0, n = bondsData.length; i < n; ++i) {\r\n bondsData[i] = [];\r\n bondMarks[i] = false;\r\n }\r\n this._bondsData = bondsData;\r\n this._bondMarks = bondMarks;\r\n this._resetCycles();\r\n }\r\n\r\n _resetCycles() {\r\n this._cycles = [];\r\n this._currIdx = -1;\r\n }\r\n\r\n _haveSameCycle(bondsData, bond1, bond2) {\r\n const arr1 = bondsData[bond1._index];\r\n const arr2 = bondsData[bond2._index];\r\n const n1 = arr1.length;\r\n const n2 = arr2.length;\r\n let i1 = 0;\r\n let i2 = 0;\r\n while (i1 < n1 && i2 < n2) {\r\n if (arr1[i1] === arr2[i2]) {\r\n return true;\r\n }\r\n if (arr1[i1] > arr2[i2]) {\r\n ++i2;\r\n } else {\r\n ++i1;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _tryBond(prevBond, currRight, currDir) {\r\n const bondsOrder = [];\r\n const bondsData = this._bondsData;\r\n const currLeft = _anotherAtom(prevBond, currRight);\r\n const currVec = currRight.position.clone().sub(currLeft.position);\r\n const startAtomRef = this._currStart;\r\n const self = this;\r\n const bondMarks = this._bondMarks;\r\n let checkAromatic = this._checkBond;\r\n bondMarks[prevBond._index] = true;\r\n checkAromatic = checkAromatic === undefined ? _isAromatic : checkAromatic;\r\n currRight.forEachBond((newBond) => {\r\n if (!checkAromatic(newBond)\r\n || newBond === prevBond\r\n || bondMarks[newBond._index]\r\n || self._haveSameCycle(bondsData, prevBond, newBond)) {\r\n return;\r\n }\r\n const anotherAtom = _anotherAtom(newBond, currRight);\r\n const anotherVec = anotherAtom.position.clone().sub(currRight.position);\r\n const val = anotherAtom === startAtomRef ? -2.0 : 1 - _cosBetween(currVec, anotherVec);\r\n const newDir = anotherVec.cross(currVec);\r\n if (!_coDirVectors(newDir, currDir)) {\r\n return;\r\n }\r\n let idx = 0;\r\n while (idx < bondsOrder.length && bondsOrder[idx].val < val) {\r\n ++idx;\r\n }\r\n bondsOrder.splice(idx, 0, { bond: newBond, val, dir: newDir });\r\n });\r\n\r\n for (let i = 0, n = bondsOrder.length; i < n; ++i) {\r\n const { bond } = bondsOrder[i];\r\n const newRight = bond._left === currRight ? bond._right : bond._left;\r\n if (newRight === startAtomRef) {\r\n ++this._currIdx;\r\n this._cycles.push([currRight]);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n if (this._tryBond(bond, newRight, bondsOrder[i].dir)) {\r\n _insertAscending(bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(currRight);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n }\r\n bondMarks[prevBond._index] = false;\r\n return false;\r\n }\r\n\r\n _startCycle(bond) {\r\n // start from left to right\r\n this._currStart = bond._left;\r\n if (this._tryBond(bond, bond._right, new THREE.Vector3())) {\r\n _insertAscending(this._bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(bond._left);\r\n }\r\n }\r\n\r\n _findLoops(checkBond, checkCycle) {\r\n this._checkBond = checkBond;\r\n const complex = this._complex;\r\n const self = this;\r\n\r\n complex.forEachComponent((component) => {\r\n self._resetCycles();\r\n component.forEachBond((bond) => {\r\n if (checkBond(bond)) {\r\n self._startCycle(bond);\r\n }\r\n });\r\n const cycles = self._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n const cycle = cycles[i];\r\n if (!checkCycle(cycle)) {\r\n continue;\r\n }\r\n const newCycle = new Cycle(cycle);\r\n newCycle.forEachBond(_markAromatic);\r\n component.addCycle(newCycle);\r\n }\r\n });\r\n }\r\n\r\n markCycles() {\r\n this._findLoops(_isAromatic, _checkCycleSimple);\r\n }\r\n\r\n detectCycles() {\r\n this._findLoops(_isPossibleAromatic, _checkCycleComplex);\r\n }\r\n}\r\n\r\nexport default AromaticLoopsMarker;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\n/**\r\n * Calculate min & max radius of a sphere slice between zMin & zMax\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {number} zMin - lower bound of the slice\r\n * @param {number} zMax - upper bound of the slice\r\n */\r\nfunction _getSphereSliceRadiusRange(center, radius, zMin, zMax) {\r\n const dzMin = zMin - center.z;\r\n const dzMax = zMax - center.z;\r\n const rzMin = Math.sqrt(Math.max(radius * radius - dzMin * dzMin, 0.0));\r\n const rzMax = Math.sqrt(Math.max(radius * radius - dzMax * dzMax, 0.0));\r\n\r\n const rMin = Math.min(rzMin, rzMax);\r\n let rMax;\r\n\r\n if (zMin <= center.z && zMax >= center.z) {\r\n // sphere's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(rzMin, rzMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * Calculate min & max radius of a circle slice between yMin & yMax.\r\n *\r\n * To maintain analogy with _getSphereSliceRadiusRange we call radius what in fact is\r\n * half-width (along X axis) of the slice, i.e. 1D-sphere radius.\r\n *\r\n * @param {Vector3} center - center of the circle (z can be ignored)\r\n * @param {number} radius - circle radius\r\n * @param {number} yMin - lower bound of the slice\r\n * @param {number} yMax - upper bound of the slice\r\n * @returns {Array} - array of two numbers (min & max radius, or half-width)\r\n */\r\nfunction _getCircleSliceRadiusRange(center, radius, yMin, yMax) {\r\n const dyMin = yMin - center.y;\r\n const dyMax = yMax - center.y;\r\n const ryMin = Math.sqrt(Math.max(radius * radius - dyMin * dyMin, 0.0));\r\n const ryMax = Math.sqrt(Math.max(radius * radius - dyMax * dyMax, 0.0));\r\n\r\n const rMin = Math.min(ryMin, ryMax);\r\n let rMax;\r\n\r\n if (yMin <= center.y && yMax >= center.y) {\r\n // slice's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(ryMin, ryMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * VoxelWorld constructor\r\n *\r\n * @param {Box3} box - bounding box of the volume to be partitioned\r\n * @param {Vector3} vCellSizeHint - target voxel size (actual voxel size may differ from this)\r\n */\r\nclass VoxelWorld {\r\n constructor(box, vCellSizeHint) {\r\n this._box = box.clone();\r\n const size = new THREE.Vector3();\r\n box.getSize(size);\r\n this._count = size.clone().divide(vCellSizeHint).floor().max(new THREE.Vector3(1, 1, 1));\r\n this._last = this._count.clone().subScalar(1);\r\n this._cellSize = size.clone().divide(this._count);\r\n this._cellInnerR = 0.5 * Math.min(Math.min(this._cellSize.x, this._cellSize.y), this._cellSize.z);\r\n this._cellOuterR = 0.5 * Math.sqrt(this._cellSize.dot(this._cellSize));\r\n\r\n // array of voxels, each element contains index of first atom in voxel\r\n const numVoxels = this._count.x * this._count.y * this._count.z;\r\n this._voxels = utils.allocateTyped(Int32Array, numVoxels);\r\n for (let i = 0; i < numVoxels; ++i) {\r\n this._voxels[i] = -1;\r\n }\r\n\r\n // array of atoms that stores multiple single-linked lists\r\n // two elements for each atom: Atom ref, index of next atom (in this array\r\n this._atoms = [];\r\n }\r\n\r\n /**\r\n * Add all atoms from a complex to voxel world\r\n *\r\n * @param {Complex} complex - complex\r\n */\r\n addAtoms(complex) {\r\n const self = this;\r\n\r\n let idx = this._atoms.length;\r\n\r\n // resize array of atoms\r\n this._atoms.length += 2 * complex.getAtomCount();\r\n\r\n complex.forEachAtom((atom) => {\r\n // find which voxel contains this atom\r\n const voxelIdx = self._findVoxel(atom.position);\r\n\r\n // push current atom to the head of voxel's atom list\r\n self._atoms[idx] = atom;\r\n self._atoms[idx + 1] = self._voxels[voxelIdx];\r\n self._voxels[voxelIdx] = idx;\r\n\r\n idx += 2;\r\n });\r\n }\r\n\r\n /**\r\n * Get voxel that contains specified 3D point (we use clamp at the edges)\r\n *\r\n * @param {Vector3} point - a point in 3D\r\n * @returns {number} - index of voxel\r\n */\r\n static _zero = new THREE.Vector3(0, 0, 0);\r\n\r\n static _voxel = new THREE.Vector3();\r\n\r\n _findVoxel(point) {\r\n const zero = VoxelWorld._zero;\r\n const voxel = VoxelWorld._voxel;\r\n voxel.copy(point)\r\n .sub(this._box.min)\r\n .divide(this._cellSize)\r\n .floor()\r\n .clamp(zero, this._last);\r\n return voxel.x + this._count.x * (voxel.y + this._count.y * voxel.z);\r\n }\r\n\r\n /**\r\n * Call a function for each atom in voxel\r\n *\r\n * @param {number} voxel - index of voxel\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomInVoxel(voxel, process) {\r\n for (let i = this._voxels[voxel]; i >= 0; i = this._atoms[i + 1]) {\r\n process(this._atoms[i]);\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _xRange = new THREE.Vector2();\r\n\r\n static _yRange = new THREE.Vector2();\r\n\r\n static _zRange = new THREE.Vector2();\r\n\r\n _forEachVoxelWithinRadius(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n\r\n // switch to a faster method unless cell size is much smaller than sphere radius\r\n if (radius / this._cellInnerR < 10) {\r\n this._forEachVoxelWithinRadiusSimple(center, radius, process);\r\n return;\r\n }\r\n\r\n let rRangeXY;\r\n let rRangeX;\r\n let xVal;\r\n let yVal;\r\n let zVal;\r\n let isInsideX;\r\n let isInsideY;\r\n let isInsideZ;\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor()\r\n .clampScalar(0, this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n\r\n isInsideZ = (center.z - radius <= zVal[0]) && (zVal[1] <= center.z + radius);\r\n\r\n rRangeXY = _getSphereSliceRadiusRange(center, radius, zVal[0], zVal[1]);\r\n\r\n yRange.set(center.y - rRangeXY[1], center.y + rRangeXY[1]);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor()\r\n .clampScalar(0, this._count.y - 1);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n\r\n isInsideY = (center.y - rRangeXY[0] <= yVal[0]) && (yVal[1] <= center.y + rRangeXY[0]);\r\n\r\n rRangeX = _getCircleSliceRadiusRange(center, rRangeXY[1], yVal[0], yVal[1]);\r\n\r\n xRange.set(center.x - rRangeX[1], center.x + rRangeX[1]);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor()\r\n .clampScalar(0, this._count.x - 1);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n isInsideX = (center.x - rRangeX[0] <= xVal[0]) && (xVal[1] <= center.x + rRangeX[0]);\r\n\r\n process(x + this._count.x * (y + this._count.y * z), isInsideX && isInsideY && isInsideZ);\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n * This is a version of method that doesn't try to \"calculate\" what voxels fall inside radius\r\n * but instead just checks all voxels inside sphere's bounding box. This should be faster\r\n * unless cell size is much smaller than sphere radius.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _vCenter = new THREE.Vector3();\r\n\r\n _forEachVoxelWithinRadiusSimple(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n const vCenter = VoxelWorld._vCenter;\r\n\r\n const distTouch2 = (radius + this._cellOuterR) * (radius + this._cellOuterR);\r\n let distInside2 = -1.0;\r\n if (radius > this._cellOuterR) {\r\n distInside2 = (radius - this._cellOuterR) * (radius - this._cellOuterR);\r\n }\r\n\r\n // calculate bounding box for the sphere\r\n xRange.set(center.x - radius, center.x + radius);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor();\r\n xRange.x = Math.min(Math.max(xRange.x, 0), this._count.x - 1);\r\n xRange.y = Math.min(Math.max(xRange.y, 0), this._count.x - 1);\r\n\r\n yRange.set(center.y - radius, center.y + radius);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor();\r\n yRange.x = Math.min(Math.max(yRange.x, 0), this._count.y - 1);\r\n yRange.y = Math.min(Math.max(yRange.y, 0), this._count.y - 1);\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor();\r\n zRange.x = Math.min(Math.max(zRange.x, 0), this._count.z - 1);\r\n zRange.y = Math.min(Math.max(zRange.y, 0), this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n const zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n vCenter.z = 0.5 * (zVal[0] + zVal[1]);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n const yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n vCenter.y = 0.5 * (yVal[0] + yVal[1]);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n const xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n vCenter.x = 0.5 * (xVal[0] + xVal[1]);\r\n\r\n const d2 = center.distanceToSquared(vCenter);\r\n if (d2 <= distTouch2) {\r\n process(x + this._count.x * (y + this._count.y * z), d2 <= distInside2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each atom within given sphere\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinRadius(center, radius, process) {\r\n const self = this;\r\n const r2 = radius * radius;\r\n\r\n self._forEachVoxelWithinRadius(center, radius, (voxel, isInside) => {\r\n if (isInside) {\r\n self._forEachAtomInVoxel(voxel, process);\r\n } else {\r\n self._forEachAtomInVoxel(voxel, (atom) => {\r\n if (center.distanceToSquared(atom.position) <= r2) {\r\n process(atom);\r\n }\r\n });\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by mask\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} mask - bit mask\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromMasked(complex, mask, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by selector\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} selector - selector\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromSelected(complex, selector, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms\r\n *\r\n * @param {function} forEachAtom - enumerator of atoms in the group\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomWithinDistFromGroup(forEachAtom, dist, process) {\r\n const self = this;\r\n const r2 = dist * dist;\r\n\r\n const voxels = [];\r\n const atoms = [];\r\n let idx = 0;\r\n\r\n // build \"within radius\" atom list for each voxel\r\n forEachAtom((atom) => {\r\n self._forEachVoxelWithinRadius(atom.position, dist, (voxel, isInside) => {\r\n if (isInside) {\r\n // this voxel is inside circle -- no check will be required\r\n voxels[voxel] = -1;\r\n } else if (typeof voxels[voxel] === 'undefined') {\r\n // this voxel isn't covered yet -- start building list of atoms\r\n atoms.push(atom);\r\n atoms.push(-1);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n } else if (voxels[voxel] !== -1) {\r\n // this voxel has a list of atoms required for distance check -- add atom to the list\r\n atoms.push(atom);\r\n atoms.push(voxels[voxel]);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n }\r\n });\r\n });\r\n\r\n let voxel;\r\n\r\n const processIfWithin = function (atom) {\r\n if (typeof voxels[voxel] === 'undefined') {\r\n return;\r\n }\r\n\r\n idx = voxels[voxel];\r\n if (idx === -1) {\r\n // this voxel is fully covered\r\n process(atom);\r\n return;\r\n }\r\n\r\n // check distance to each atom within radius from this voxel\r\n for (; idx >= 0; idx = atoms[idx + 1]) {\r\n if (atom.position.distanceToSquared(atoms[idx].position) < r2) {\r\n process(atom);\r\n break;\r\n }\r\n }\r\n };\r\n\r\n // for each marked voxel\r\n for (voxel in voxels) {\r\n if (voxels.hasOwnProperty(voxel)) {\r\n self._forEachAtomInVoxel(voxel, processIfWithin);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default VoxelWorld;\r\n","import ResidueType from './ResidueType';\r\nimport PairCollection from './AtomPairs';\r\n\r\nconst MINIMAL_DISTANCE = 0.5;\r\nconst MIN_HBOND_ENERGY = -9.9;\r\nconst MAX_HBOND_ENERGY = -0.5;\r\nconst COUPLING_CONSTANT = -27.888; // = -332 * 0.42 * 0.2\r\nconst MAX_COUPLING_DISTANCE = 5.0; // how far is the closest atom of a potential partner residue from CA atom\r\nconst MAX_RESIDUES_THRESHOLD = 1000;\r\n\r\nexport default class HBondInfo {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._hbonds = []; // array of bond info for each residue\r\n if (this._complex._residues.length > MAX_RESIDUES_THRESHOLD) {\r\n this._buildVW(); // optimized version using voxel grid\r\n } else {\r\n this._build(); // test all pairs of residues\r\n }\r\n }\r\n\r\n isBond(from, to) {\r\n if (this._hbonds[from]) {\r\n const [acc0, acc1] = this._hbonds[from].acceptor;\r\n if (acc0 && acc0.residue === to && acc0.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n if (acc1 && acc1.residue === to && acc1.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n\r\n for (let i = 0; i < this._complex._residues.length - 1; ++i) {\r\n const ri = this._complex._residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let preri = null;\r\n if (i > 0 && (this._complex._residues[i - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && ri._sequence === this._complex._residues[i - 1]._sequence + 1) {\r\n preri = this._complex._residues[i - 1];\r\n }\r\n\r\n for (let j = i + 1; j < this._complex._residues.length; ++j) {\r\n const rj = this._complex._residues[j];\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = null;\r\n if ((this._complex._residues[j - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && rj._sequence === this._complex._residues[j - 1]._sequence + 1) {\r\n prerj = this._complex._residues[j - 1];\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (j !== i + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _buildVW() {\r\n const self = this;\r\n const residues = this._complex._residues;\r\n let ri;\r\n let preri;\r\n\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const pairs = new PairCollection(this._complex._residues.length * this._complex._residues.length / 2);\r\n\r\n function processAtom(atom) {\r\n const rj = atom.residue;\r\n\r\n if (rj._index === ri._index) {\r\n return;\r\n }\r\n\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n return;\r\n }\r\n\r\n if (!pairs.addPair(ri._index, rj._index)) {\r\n // we've seen this pair\r\n return;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = rj._index > 0 ? residues[rj._index - 1] : null;\r\n if (prerj\r\n && ((prerj.getType().flags & ResidueType.Flags.PROTEIN) === 0 || rj._sequence !== prerj._sequence + 1)) {\r\n prerj = null;\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (rj._index !== ri._index + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n\r\n for (let i = 0; i < residues.length - 1; ++i) {\r\n ri = residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n preri = i > 0 ? residues[i - 1] : null;\r\n if (preri\r\n && ((preri.getType().flags & ResidueType.Flags.PROTEIN) === 0 || ri._sequence !== preri._sequence + 1)) {\r\n preri = null;\r\n }\r\n\r\n vw.forEachAtomWithinRadius(this._residueGetCAlpha(ri), MAX_COUPLING_DISTANCE, processAtom);\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _residueGetCO(res) {\r\n let c = null;\r\n let o = null;\r\n\r\n res.forEachAtom((a) => {\r\n if (a.name === 'C') {\r\n c = a.position;\r\n } else if (a.name === 'O') {\r\n o = a.position;\r\n }\r\n });\r\n\r\n return [c, o];\r\n }\r\n\r\n // TODO Support hydrogen defined in complex\r\n _residueGetNH(prev, res) {\r\n const [c, o] = this._residueGetCO(prev);\r\n\r\n let n;\r\n res.forEachAtom((a) => {\r\n if (a.name === 'N') {\r\n n = a.position;\r\n }\r\n });\r\n\r\n if (c && o && n) {\r\n // calculate hydrogen position\r\n const h = c.clone();\r\n h.sub(o);\r\n h.multiplyScalar(1.0 / h.length());\r\n h.add(n);\r\n\r\n return [n, h];\r\n }\r\n\r\n return [null, null];\r\n }\r\n\r\n _calcHBondEnergy(predonor, donor, acceptor) {\r\n let result = 0;\r\n\r\n if (predonor === null) {\r\n return result;\r\n }\r\n\r\n if (donor.getType().getName() !== 'PRO') {\r\n const [n, h] = this._residueGetNH(predonor, donor);\r\n const [c, o] = this._residueGetCO(acceptor);\r\n\r\n if (n === null || h === null || c === null || o === null) {\r\n return result;\r\n }\r\n\r\n const distanceHO = h.distanceTo(o);\r\n const distanceHC = h.distanceTo(c);\r\n const distanceNC = n.distanceTo(c);\r\n const distanceNO = n.distanceTo(o);\r\n\r\n if (distanceHO < MINIMAL_DISTANCE || distanceHC < MINIMAL_DISTANCE\r\n || distanceNC < MINIMAL_DISTANCE || distanceNO < MINIMAL_DISTANCE) {\r\n result = MIN_HBOND_ENERGY;\r\n } else {\r\n result = COUPLING_CONSTANT / distanceHO - COUPLING_CONSTANT / distanceHC\r\n + COUPLING_CONSTANT / distanceNC - COUPLING_CONSTANT / distanceNO;\r\n }\r\n\r\n // DSSP compatibility mode:\r\n result = Math.round(result * 1000) / 1000;\r\n\r\n if (result < MIN_HBOND_ENERGY) {\r\n result = MIN_HBOND_ENERGY;\r\n }\r\n }\r\n\r\n // update donor\r\n if (typeof this._hbonds[donor._index] === 'undefined') {\r\n this._hbonds[donor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const donorInfo = this._hbonds[donor._index];\r\n\r\n if (donorInfo.acceptor.length < 2) {\r\n donorInfo.acceptor.push({\r\n residue: acceptor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (donorInfo.acceptor.length > 1) {\r\n if (result < donorInfo.acceptor[0].energy) {\r\n donorInfo.acceptor[1].residue = donorInfo.acceptor[0].residue;\r\n donorInfo.acceptor[1].energy = donorInfo.acceptor[0].energy;\r\n donorInfo.acceptor[0].residue = acceptor._index;\r\n donorInfo.acceptor[0].energy = result;\r\n } else if (result < donorInfo.acceptor[1].energy) {\r\n donorInfo.acceptor[1].residue = acceptor._index;\r\n donorInfo.acceptor[1].energy = result;\r\n }\r\n }\r\n\r\n // update acceptor\r\n if (typeof this._hbonds[acceptor._index] === 'undefined') {\r\n this._hbonds[acceptor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const accInfo = this._hbonds[acceptor._index];\r\n\r\n if (accInfo.donor.length < 2) {\r\n accInfo.donor.push({\r\n residue: donor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (accInfo.donor.length > 1) {\r\n if (result < accInfo.donor[0].energy) {\r\n accInfo.donor[1].residue = accInfo.donor[0].residue;\r\n accInfo.donor[1].energy = accInfo.donor[0].energy;\r\n accInfo.donor[0].residue = donor._index;\r\n accInfo.donor[0].energy = result;\r\n } else if (result < accInfo.donor[1].energy) {\r\n accInfo.donor[1].residue = donor._index;\r\n accInfo.donor[1].energy = result;\r\n }\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n","import HBondInfo from './HBondInfo';\r\nimport ResidueType from './ResidueType';\r\n\r\nconst BridgeType = Object.freeze({\r\n NO_BRIDGE: 0,\r\n PARALLEL: 1,\r\n ANTI_PARALLEL: 2,\r\n});\r\n\r\nconst HelixFlag = Object.freeze({\r\n START: 1,\r\n MIDDLE: 2,\r\n END: 3,\r\n START_AND_END: 4,\r\n});\r\n\r\nconst StructureType = Object.freeze({\r\n STRAND: 'E',\r\n BRIDGE: 'B',\r\n HELIX_310: 'G',\r\n HELIX_ALPHA: 'H',\r\n HELIX_PI: 'I',\r\n TURN: 'T',\r\n BEND: 'S',\r\n LOOP: ' ',\r\n});\r\n\r\nexport default class SecondaryStructureMap {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._build();\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n this._hbonds = new HBondInfo(this._complex);\r\n this._ss = []; // DSSP map by residue\r\n\r\n // auxilliary data\r\n this._sheet = [];\r\n this._betaPartners = [];\r\n this._bend = [];\r\n for (let i = 0; i < this._complex.getResidues().length; ++i) {\r\n this._betaPartners[i] = [];\r\n }\r\n this._helixFlags = [];\r\n this._helixFlags[3] = [];\r\n this._helixFlags[4] = [];\r\n this._helixFlags[5] = [];\r\n\r\n // calculate peptide chain lengths\r\n this._chainLengths = [];\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i].getResidues();\r\n let len = 0;\r\n for (; len < chain.length; ++len) {\r\n if ((chain[len].getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n break;\r\n }\r\n }\r\n this._chainLengths[i] = len;\r\n }\r\n\r\n this._buildBetaSheets();\r\n\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n self._buildAlphaHelices(this._complex._chains[i].getResidues(), this._chainLengths[i], false);\r\n }\r\n }\r\n\r\n _buildAlphaHelices(inResidues, chainLength, inPreferPiHelices) {\r\n // Helix and Turn\r\n for (let stride = 3; stride <= 5; ++stride) {\r\n if (inResidues.length < stride) {\r\n break;\r\n }\r\n\r\n for (let i = 0; i + stride < chainLength; ++i) {\r\n if (this._hbonds.isBond(inResidues[i + stride]._index, inResidues[i]._index)\r\n /* && NoChainBreak(res[i], res[i + stride]) */) {\r\n this._helixFlags[stride][inResidues[i + stride]._index] = HelixFlag.END;\r\n for (let j = i + 1; j < i + stride; ++j) {\r\n if (typeof this._helixFlags[stride][inResidues[j]._index] === 'undefined') {\r\n this._helixFlags[stride][inResidues[j]._index] = HelixFlag.MIDDLE;\r\n }\r\n }\r\n\r\n if (this._helixFlags[stride][inResidues[i]._index] === HelixFlag.END) {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START_AND_END;\r\n } else {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 2; i < chainLength - 2; ++i) {\r\n const kappa = this._kappa(inResidues[i - 2], inResidues[i], inResidues[i + 2]);\r\n this._bend[inResidues[i]._index] = (kappa !== 360 && kappa > 70);\r\n }\r\n\r\n for (let i = 1; i + 4 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 4) && this._isHelixStart(inResidues[i - 1]._index, 4)) {\r\n for (let j = i; j <= i + 3; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_ALPHA;\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 3 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 3) && this._isHelixStart(inResidues[i - 1]._index, 3)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 2; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_310;\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 2; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_310;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 5 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 5) && this._isHelixStart(inResidues[i - 1]._index, 5)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 4; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_PI\r\n || (inPreferPiHelices && this._ss[inResidues[j]._index] === StructureType.HELIX_ALPHA);\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 4; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_PI;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 1 < chainLength; ++i) {\r\n if (typeof this._ss[inResidues[i]._index] === 'undefined') {\r\n let isTurn = false;\r\n for (let stride = 3; stride <= 5 && !isTurn; ++stride) {\r\n for (let k = 1; k < stride && !isTurn; ++k) {\r\n isTurn = (i >= k) && this._isHelixStart(inResidues[i - k]._index, stride);\r\n }\r\n }\r\n\r\n if (isTurn) {\r\n this._ss[inResidues[i]._index] = StructureType.TURN;\r\n } else if (this._bend[inResidues[i]._index]) {\r\n this._ss[inResidues[i]._index] = StructureType.BEND;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _cosinusAngle(p1, p2, p3, p4) {\r\n const v12 = p1.clone().sub(p2);\r\n const v34 = p3.clone().sub(p4);\r\n\r\n let result = 0;\r\n\r\n const x = v12.dot(v12) * v34.dot(v34);\r\n if (x > 0) {\r\n result = v12.dot(v34) / Math.sqrt(x);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _kappa(prevPrev, res, nextNext) {\r\n const curCA = this._residueGetCAlpha(res);\r\n const ppCA = this._residueGetCAlpha(prevPrev);\r\n const nnCA = this._residueGetCAlpha(nextNext);\r\n if (curCA === null || ppCA === null || nnCA === null) {\r\n return 180;\r\n }\r\n\r\n const ckap = this._cosinusAngle(curCA, ppCA, nnCA, curCA);\r\n const skap = Math.sqrt(1 - ckap * ckap);\r\n return Math.atan2(skap, ckap) * 180 / Math.PI;\r\n }\r\n\r\n _isHelixStart(res, stride) {\r\n return (this._helixFlags[stride][res] === HelixFlag.START\r\n || this._helixFlags[stride][res] === HelixFlag.START_AND_END);\r\n }\r\n\r\n _buildBetaSheets() {\r\n // find bridges\r\n // check each chain against each other chain, and against itself\r\n const bridges = [];\r\n for (let a = 0; a < this._complex._chains.length; ++a) {\r\n const lenA = this._chainLengths[a];\r\n if (lenA <= 4) {\r\n continue;\r\n }\r\n\r\n const chainA = this._complex._chains[a].getResidues();\r\n\r\n for (let b = a; b < this._complex._chains.length; ++b) {\r\n const lenB = this._chainLengths[b];\r\n if (lenB <= 4) {\r\n continue;\r\n }\r\n\r\n const chainB = this._complex._chains[b].getResidues();\r\n\r\n for (let i = 1; i + 1 < lenA; ++i) {\r\n const ri = chainA[i];\r\n\r\n let j = 1;\r\n if (b === a) {\r\n j = i + 3; // check for self-bridges forward down the chain\r\n }\r\n\r\n for (; j + 1 < lenB; ++j) {\r\n const rj = chainB[j];\r\n\r\n const type = this._testBridge(chainA, i, chainB, j);\r\n if (type === BridgeType.NO_BRIDGE) {\r\n continue;\r\n }\r\n\r\n // there is a bridge, try to attach it to previously found sequence\r\n let found = false;\r\n for (const bridge of bridges) {\r\n if (type !== bridge.type || ri._index !== bridge.i[bridge.i.length - 1] + 1) {\r\n continue;\r\n }\r\n\r\n if (type === BridgeType.PARALLEL && bridge.j[bridge.j.length - 1] + 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.push(rj._index);\r\n found = true;\r\n break;\r\n }\r\n\r\n if (type === BridgeType.ANTI_PARALLEL && bridge.j[0] - 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.unshift(rj._index);\r\n found = true;\r\n break;\r\n }\r\n }\r\n\r\n // this bridge cannot be attached anywhere, start a new sequence\r\n if (!found) {\r\n bridges.push({\r\n type,\r\n i: [ri._index],\r\n chainI: ri.getChain()._index,\r\n j: [rj._index],\r\n chainJ: rj.getChain()._index,\r\n });\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // extend ladders\r\n bridges.sort((a, b) => {\r\n if (a.chainI < b.chainI || (a.chainI === b.chainI && a.i[0] < b.i[0])) {\r\n return -1;\r\n }\r\n return 1;\r\n });\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n for (let j = i + 1; j < bridges.length; ++j) {\r\n const ibi = bridges[i].i[0];\r\n const iei = bridges[i].i[bridges[i].i.length - 1];\r\n const jbi = bridges[i].j[0];\r\n const jei = bridges[i].j[bridges[i].j.length - 1];\r\n const ibj = bridges[j].i[0];\r\n const iej = bridges[j].i[bridges[j].i.length - 1];\r\n const jbj = bridges[j].j[0];\r\n const jej = bridges[j].j[bridges[j].j.length - 1];\r\n\r\n if (bridges[i].type !== bridges[j].type\r\n || this._hasChainBreak(Math.min(ibi, ibj), Math.max(iei, iej))\r\n || this._hasChainBreak(Math.min(jbi, jbj), Math.max(jei, jej))\r\n || ibj - iei >= 6 || (iei >= ibj && ibi <= iej)) {\r\n continue;\r\n }\r\n\r\n let bulge = false;\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bulge = ((jbj - jei < 6 && ibj - iei < 3) || (jbj - jei < 3));\r\n } else {\r\n bulge = ((jbi - jej < 6 && ibj - iei < 3) || (jbi - jej < 3));\r\n }\r\n\r\n if (bulge) {\r\n bridges[i].i = bridges[i].i.concat(bridges[j].i);\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bridges[i].j = bridges[i].j.concat(bridges[j].j);\r\n } else {\r\n bridges[i].j = bridges[j].j.concat(bridges[i].j);\r\n }\r\n bridges.splice(j--, 1);\r\n }\r\n }\r\n }\r\n\r\n // Sheet\r\n const ladderset = new Set();\r\n for (let i = 0; i < bridges.length; ++i) {\r\n ladderset.add(bridges[i]);\r\n }\r\n\r\n let sheet = 1;\r\n let ladder = 0;\r\n while (ladderset.size > 0) {\r\n let bridge = ladderset.values().next().value;\r\n ladderset.delete(bridge);\r\n\r\n const sheetset = new Set();\r\n sheetset.add(bridge);\r\n\r\n let toMove;\r\n do {\r\n toMove = new Set();\r\n for (const a of sheetset.values()) {\r\n for (const b of ladderset.values()) {\r\n if (this._areBridgesLinked(a, b)) {\r\n toMove.add(b);\r\n }\r\n }\r\n }\r\n for (bridge of toMove.values()) {\r\n sheetset.add(bridge);\r\n ladderset.delete(bridge);\r\n }\r\n } while (toMove.size > 0);\r\n\r\n for (bridge of sheetset.values()) {\r\n bridge.ladder = ladder;\r\n bridge.sheet = sheet;\r\n bridge.link = sheetset;\r\n ++ladder;\r\n }\r\n\r\n ++sheet;\r\n }\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n const bridge = bridges[i];\r\n\r\n // find out if any of the i and j set members already have\r\n // a bridge assigned, if so, we're assigning bridge 2\r\n\r\n let betai = 0;\r\n let betaj = 0;\r\n\r\n for (let l = 0; l < bridge.i.length; ++l) {\r\n if (this._betaPartners[bridge.i[l]][0]) {\r\n betai = 1;\r\n break;\r\n }\r\n }\r\n\r\n for (let l = 0; l < bridge.j.length; ++l) {\r\n if (this._betaPartners[bridge.j[l]][0]) {\r\n betaj = 1;\r\n break;\r\n }\r\n }\r\n\r\n let ss = StructureType.BRIDGE;\r\n if (bridge.i.length > 1) {\r\n ss = StructureType.STRAND;\r\n }\r\n\r\n if (bridge.type === BridgeType.PARALLEL) {\r\n let j = 0;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n\r\n j = 0;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n } else {\r\n let j = bridge.j.length - 1;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n\r\n j = bridge.i.length - 1;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n }\r\n\r\n for (let k = bridge.i[0]; k <= bridge.i[bridge.i.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n\r\n for (let k = bridge.j[0]; k <= bridge.j[bridge.j.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _testBridge(chainA, from, chainB, to) {\r\n let result = BridgeType.NO_BRIDGE;\r\n\r\n const a = chainA[from - 1]._index;\r\n const b = chainA[from]._index;\r\n const c = chainA[from + 1]._index;\r\n const d = chainB[to - 1]._index;\r\n const e = chainB[to]._index;\r\n const f = chainB[to + 1]._index;\r\n\r\n const isBond = this._hbonds.isBond.bind(this._hbonds);\r\n if ((isBond(c, e) && isBond(e, a)) || (isBond(f, b) && isBond(b, d))) {\r\n result = BridgeType.PARALLEL;\r\n } else if ((isBond(c, d) && isBond(f, a)) || (isBond(e, b) && isBond(b, e))) {\r\n result = BridgeType.ANTI_PARALLEL;\r\n }\r\n return result;\r\n }\r\n\r\n // return true if any of the residues in bridge a is identical to any of the residues in bridge b\r\n _areBridgesLinked(a, b) {\r\n const ai = new Set(a.i);\r\n const aj = new Set(a.j);\r\n\r\n for (const i of b.i) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n for (const i of b.j) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n }\r\n\r\n _hasChainBreak(from, to) {\r\n for (let i = from + 1; i <= to; ++i) {\r\n if (this._complex._residues[i]._sequence !== this._complex._residues[i - 1]._sequence + 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\nSecondaryStructureMap.StructureType = StructureType;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport Atom from './Atom';\r\nimport Chain from './Chain';\r\nimport Helix from './Helix';\r\nimport Strand from './Strand';\r\nimport Sheet from './Sheet';\r\nimport Component from './Component';\r\nimport ResidueType from './ResidueType';\r\nimport Bond from './Bond';\r\nimport AutoBond from './AutoBond';\r\nimport AromaticLoopsMarker from './AromaticLoopsMarker';\r\nimport BiologicalUnit from './BiologicalUnit';\r\nimport selectors from './selectors';\r\nimport VoxelWorld from './VoxelWorld';\r\nimport SecondaryStructureMap from './SecondaryStructureMap';\r\nimport StructuralElement from './StructuralElement';\r\n\r\nconst VOXEL_SIZE = 5.0;\r\n\r\nconst { StructureType } = SecondaryStructureMap;\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX\r\nconst helixClassMap = {\r\n [StructureType.HELIX_ALPHA]: 1,\r\n [StructureType.HELIX_PI]: 3,\r\n [StructureType.HELIX_310]: 5,\r\n};\r\n\r\nconst loopMap = {\r\n [StructureType.BRIDGE]: StructuralElementType.BRIDGE,\r\n [StructureType.TURN]: StructuralElementType.TURN,\r\n [StructureType.BEND]: StructuralElementType.BEND,\r\n [StructureType.LOOP]: StructuralElementType.COIL,\r\n};\r\n\r\n/**\r\n * The entire complex of the molecules under study.\r\n *\r\n * @exports Complex\r\n * @constructor\r\n */\r\nclass Complex {\r\n constructor() {\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n\r\n this._residueTypes = Object.create(ResidueType.StandardTypes);\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n this._molecules = [];\r\n this._maskNeedsUpdate = false;\r\n\r\n this.metadata = {};\r\n\r\n this.symmetry = [];\r\n this.units = [new BiologicalUnit(this)];\r\n this._currentUnit = 0; // default biological unit is the asymmetric unit\r\n }\r\n\r\n addAtom(atom) {\r\n const index = this._atoms.length;\r\n this._atoms.push(atom);\r\n return index;\r\n }\r\n\r\n addSheet(sheet) {\r\n const index = this._sheets.length;\r\n this._sheets.push(sheet);\r\n return index;\r\n }\r\n\r\n addHelix(helix) {\r\n const index = this._helices.length;\r\n this._helices.push(helix);\r\n return index;\r\n }\r\n\r\n getAtoms() {\r\n return this._atoms;\r\n }\r\n\r\n getBonds() {\r\n return this._bonds;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n addResidue(residue) {\r\n const index = this._residues.length;\r\n this._residues.push(residue);\r\n return index;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n this.forEachChain((chain) => {\r\n chain.updateToFrame(frameData);\r\n });\r\n }\r\n\r\n addResidueType(resName) {\r\n const rt = this._residueTypes[resName] = new ResidueType(resName, 'Unknown', '');\r\n return rt;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n getSGroupCount() {\r\n return this._sgroups.length;\r\n }\r\n\r\n getSGroups() {\r\n return this._sgroups;\r\n }\r\n\r\n /*\r\n Extract atom by its fullname: #chainName#.#residueId#.#atomName#\r\n */\r\n getAtomByFullname(fullName) {\r\n const parts = fullName.split('.');\r\n if (parts.length !== 3) {\r\n return null;\r\n }\r\n\r\n const chainName = parts[0];\r\n const resId = parseInt(parts[1], 10);\r\n if (Number.isNaN(resId)) {\r\n return null;\r\n }\r\n const atomName = parts[2].toUpperCase();\r\n\r\n let currAtom = null;\r\n this.forEachChain((chain) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (chain._name.localeCompare(chainName) === 0) {\r\n chain.forEachResidue((residue) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (residue._sequence === resId) {\r\n residue.forEachAtom((atom) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (atomName.localeCompare(atom.name) === 0) {\r\n currAtom = atom;\r\n }\r\n });\r\n }\r\n });\r\n }\r\n });\r\n\r\n return currAtom;\r\n }\r\n\r\n /**\r\n * Create a new chain.\r\n *\r\n * @param {string} name - Chain name.\r\n * @returns {Chain} - Newly created chain.\r\n */\r\n addChain(name) {\r\n const result = new Chain(this, name);\r\n this._chains.push(result);\r\n return result;\r\n }\r\n\r\n getChain(name) {\r\n for (let i = 0, n = this._chains.length; i < n; ++i) {\r\n const chain = this._chains[i];\r\n if (chain.getName() === name) {\r\n return chain;\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n getChainCount() {\r\n return this._chains.length;\r\n }\r\n\r\n getMolecules() {\r\n return this._molecules;\r\n }\r\n\r\n getMoleculeCount() {\r\n return this._molecules.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n process(atoms[i]);\r\n }\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._bonds;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n forEachChain(process) {\r\n const chains = this._chains;\r\n for (let i = 0, n = chains.length; i < n; ++i) {\r\n process(chains[i]);\r\n }\r\n }\r\n\r\n forEachMolecule(process) {\r\n const molecules = this._molecules;\r\n const n = molecules.length;\r\n for (let i = 0; i < n; ++i) {\r\n process(molecules[i]);\r\n }\r\n }\r\n\r\n forEachSGroup(process) {\r\n const groups = this._sgroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n process(groups[i]);\r\n }\r\n }\r\n\r\n forEachComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n forEachVisibleComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n addBond(left, right, order, type, fixed) {\r\n const bond = new Bond(left, right, order, type, fixed);\r\n this._bonds.push(bond);\r\n return bond;\r\n }\r\n\r\n getBondCount() {\r\n return this._bonds.length;\r\n }\r\n\r\n getResidueType(name) {\r\n return this._residueTypes[name] || null;\r\n }\r\n\r\n getUnifiedSerial(chain, serial, iCode) {\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n return serial + iCode * maxSerial + chain * chainShift;\r\n }\r\n\r\n splitUnifiedSerial(uniSerial) {\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n const chainId = Math.floor(uniSerial / chainShift);\r\n const remnant = uniSerial - chainId * chainShift;\r\n const insCode = Math.floor(remnant / maxSerial);\r\n const ser = remnant - insCode * maxSerial;\r\n return { chain: chainId, serial: ser, iCode: insCode };\r\n }\r\n\r\n _fillCmpEdit() {\r\n const self = this;\r\n const components = this._components;\r\n\r\n function addComp() {\r\n const comp = new Component(self);\r\n comp._index = components.length;\r\n components[comp._index] = comp;\r\n return comp;\r\n }\r\n\r\n this.forEachChain((chain) => {\r\n const residues = chain._residues;\r\n const resCount = residues.length;\r\n if (resCount < 1) {\r\n return;\r\n }\r\n let comp = addComp();\r\n let currStart = residues[0]._index;\r\n\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)\r\n || currRes._index !== nextRes._index - 1) {\r\n // the last condition is broken and incorrect\r\n // the refactoring of the Component is required in order to fix this issue\r\n comp.setSubDivs([{\r\n start: currStart,\r\n end: currRes._index,\r\n }]);\r\n if (nextRes) {\r\n currStart = nextRes._index;\r\n comp = addComp();\r\n }\r\n }\r\n }\r\n });\r\n }\r\n\r\n // This function was added in the moment of despair\r\n // It was the dark times for miew\r\n _fillCmpNoedit() {\r\n const comp = new Component(this);\r\n comp._index = 0;\r\n\r\n const residues = this._residues;\r\n const resCount = residues.length;\r\n if (resCount === 0) {\r\n return;\r\n }\r\n\r\n const currSubDivs = [];\r\n let currStart = 0;\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)) {\r\n // wrap up this interval\r\n currSubDivs[currSubDivs.length] = {\r\n start: currStart,\r\n end: i,\r\n };\r\n if (nextRes) {\r\n currStart = i + 1;\r\n }\r\n }\r\n }\r\n\r\n comp.setSubDivs(currSubDivs);\r\n this._components[comp._index] = comp;\r\n }\r\n\r\n /**\r\n * Fill components information.\r\n * @param {boolean} enableEditing - Restructure Complex to enable per-component editing.\r\n */\r\n _fillComponents(enableEditing) {\r\n if (enableEditing) {\r\n this._fillCmpEdit();\r\n } else {\r\n this._fillCmpNoedit();\r\n }\r\n }\r\n\r\n getCurrentUnit() {\r\n return this._currentUnit;\r\n }\r\n\r\n getDefaultBoundaries() {\r\n return this.units[0].getBoundaries();\r\n }\r\n\r\n getBoundaries() {\r\n return this.units[this._currentUnit].getBoundaries();\r\n }\r\n\r\n getTransforms() {\r\n return this.units[this._currentUnit].getTransforms();\r\n }\r\n\r\n getSelector() {\r\n return this.units[this._currentUnit].getSelector();\r\n }\r\n\r\n resetCurrentUnit() {\r\n this._currentUnit = 0;\r\n this.setCurrentUnit(1);\r\n }\r\n\r\n setCurrentUnit(newUnit) {\r\n if (newUnit !== null && newUnit !== undefined\r\n && newUnit !== this._currentUnit\r\n && newUnit >= 0\r\n && newUnit < this.units.length) {\r\n this._currentUnit = newUnit;\r\n return true;\r\n }\r\n return false;\r\n }\r\n\r\n _computeBounds() {\r\n const { units } = this;\r\n for (let i = 0, n = units.length; i < n; ++i) {\r\n units[i].computeBoundaries();\r\n }\r\n }\r\n\r\n onAtomPositionChanged() {\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n this.forEachComponent((c) => {\r\n c.update();\r\n });\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n this._finalizeBonds();\r\n this.forEachSGroup((s) => {\r\n s._rebuildSGroupOnAtomChange();\r\n });\r\n }\r\n\r\n update() {\r\n if (this._maskNeedsUpdate) {\r\n this.updateStructuresMask();\r\n this._maskNeedsUpdate = false;\r\n }\r\n }\r\n\r\n _finalizeBonds() {\r\n const bonds = this.getBonds();\r\n const n = bonds.length;\r\n for (let i = 0; i < n; ++i) {\r\n bonds[i]._index = i;\r\n }\r\n }\r\n\r\n /**\r\n * Finalizes complex's inner data(i.e. after parsing).\r\n * @param {objects} opts - Build bonds automatically.\r\n * @param {boolean} opts.needAutoBonding - Build bonds automatically.\r\n * @param {boolean} opts.detectAromaticLoops - Find/mark aromatic loops.\r\n * @param {boolean} opts.enableEditing - Restructure Complex to enable per-component editing.\r\n * @param {Array} [opts.serialAtomMap] - Array of atoms ordered by their serials.\r\n */\r\n finalize(opts) {\r\n opts = opts || {};\r\n // Put bonds into atoms\r\n const bonds = this._bonds;\r\n let i;\r\n let n;\r\n // remove invalid bonds\r\n for (i = bonds.length - 1; i >= 0; i--) {\r\n const bond = bonds[i];\r\n if (bond._left === null || bond._right === null) {\r\n bonds.splice(i, 1);\r\n } else {\r\n bond._left.bonds.push(bond);\r\n bond._right.bonds.push(bond);\r\n }\r\n }\r\n\r\n const residues = this._residues;\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._finalize();\r\n }\r\n\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n\r\n // WARNING! this MUST be done BEFORE computeBounds is called\r\n const { units } = this;\r\n for (i = 0, n = units.length; i < n; ++i) {\r\n units[i].finalize();\r\n }\r\n // try setting first biomolecule by defaults\r\n this.setCurrentUnit(1);\r\n\r\n const residueHash = {};\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n // This code is extremely dangerous for non-PDB formats\r\n residueHash[this.getUnifiedSerial(\r\n res.getChain().getName().charCodeAt(0),\r\n res.getSequence(),\r\n res.getICode().charCodeAt(0),\r\n )] = res;\r\n }\r\n\r\n const { structures } = this;\r\n for (i = 0, n = structures.length; i < n; ++i) {\r\n structures[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const helices = this._helices;\r\n for (i = 0, n = helices.length; i < n; ++i) {\r\n helices[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const sheets = this._sheets;\r\n for (i = 0, n = sheets.length; i < n; ++i) {\r\n sheets[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n\r\n const atoms = this._atoms;\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const currAtom = atoms[i];\r\n currAtom.index = i;\r\n }\r\n\r\n if (opts.needAutoBonding) {\r\n // Ignore errors during autobonding\r\n try {\r\n const autoConnector = new AutoBond(this);\r\n autoConnector.build();\r\n autoConnector.destroy();\r\n } catch (e) {\r\n console.warn('Autobonding failed:', e);\r\n }\r\n }\r\n\r\n const chains = this._chains;\r\n for (i = 0, n = chains.length; i < n; ++i) {\r\n chains[i]._index = i;\r\n }\r\n\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._index = i;\r\n }\r\n\r\n // mark non-polar hydrogens\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n if (atom.flags & Atom.Flags.HYDROGEN && atom.bonds.length === 1) {\r\n const bond = atom.bonds[0];\r\n const other = (bond._left !== atom && bond._left) || bond._right;\r\n if (other.flags & Atom.Flags.CARBON) {\r\n atom.flags |= Atom.Flags.NONPOLARH;\r\n }\r\n }\r\n }\r\n\r\n this._finalizeBonds();\r\n this._fillComponents(opts.enableEditing);\r\n\r\n const marker = new AromaticLoopsMarker(this);\r\n marker.markCycles();\r\n if (opts.detectAromaticLoops) { // TODO remove this condition clause, it is for debug purposes only!\r\n marker.detectCycles(); // TODO add conditional detection\r\n }\r\n\r\n this._finalizeMolecules();\r\n }\r\n\r\n _finalizeMolecules() {\r\n // add reference to molecule into residue\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const molecule = this._molecules[i];\r\n const count = molecule.residues.length;\r\n for (let j = 0; j < count; j++) {\r\n const residue = molecule.residues[j];\r\n residue._molecule = molecule;\r\n }\r\n }\r\n }\r\n\r\n updateStructuresMask() {\r\n const updater = (structure) => structure.collectMask();\r\n this.forEachResidue(updater);\r\n this.forEachChain(updater);\r\n this.forEachMolecule(updater);\r\n }\r\n\r\n countAtomsByMask(mask) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n getNumAtomsBySelector(selector) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n resetAtomMask(mask) {\r\n this.forEachAtom((atom) => {\r\n atom.mask = mask;\r\n });\r\n }\r\n\r\n markAtoms(selector, mask) {\r\n const setMask = mask;\r\n const clearMask = ~setMask;\r\n let count = 0;\r\n const totalSelector = selectors.keyword('And')(selector, this.getSelector());\r\n\r\n this.forEachAtom((atom) => {\r\n if (totalSelector.includesAtom(atom)) {\r\n atom.mask |= setMask;\r\n count++;\r\n } else {\r\n atom.mask &= clearMask;\r\n }\r\n });\r\n this._maskNeedsUpdate = true;\r\n\r\n return count;\r\n }\r\n\r\n markAtomsAdditionally(selector, mask) {\r\n const setMask = mask;\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom) && (atom.mask & mask) !== mask) {\r\n atom.mask |= setMask;\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n clearAtomBits(mask) {\r\n const clearMask = ~mask;\r\n this.forEachAtom((atom) => {\r\n atom.mask &= clearMask;\r\n });\r\n const reseter = (a) => {\r\n a._mask &= clearMask;\r\n };\r\n this.forEachAtom(reseter);\r\n this.forEachResidue(reseter);\r\n this.forEachChain(reseter);\r\n this.forEachMolecule(reseter);\r\n }\r\n\r\n getAtomNames() {\r\n if (this.hasOwnProperty('_atomNames')) {\r\n return this._atomNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.name] = 1;\r\n });\r\n this._atomNames = Object.keys(dict);\r\n\r\n return this._atomNames;\r\n }\r\n\r\n getElements() {\r\n if (this.hasOwnProperty('_elements')) {\r\n return this._elements;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.element.name] = 1;\r\n });\r\n this._elements = Object.keys(dict);\r\n\r\n return this._elements;\r\n }\r\n\r\n getResidueNames() {\r\n if (this.hasOwnProperty('_residueNames')) {\r\n return this._residueNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachResidue((res) => {\r\n dict[res._type._name] = 1;\r\n });\r\n this._residueNames = Object.keys(dict);\r\n\r\n return this._residueNames;\r\n }\r\n\r\n getChainNames() {\r\n if (this.hasOwnProperty('_chainNames')) {\r\n return this._chainNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachChain((chain) => {\r\n dict[chain._name] = 1;\r\n });\r\n this._chainNames = Object.keys(dict);\r\n\r\n return this._chainNames;\r\n }\r\n\r\n getAltLocNames() {\r\n if (this.hasOwnProperty('_altlocNames')) {\r\n return this._altlocNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[String.fromCharCode(atom.location)] = 1;\r\n });\r\n this._altlocNames = Object.keys(dict);\r\n\r\n return this._altlocNames;\r\n }\r\n\r\n getVoxelWorld() {\r\n if (!this.hasOwnProperty('_voxelWorld')) {\r\n try {\r\n this._voxelWorld = new VoxelWorld(\r\n this.getDefaultBoundaries().boundingBox,\r\n new THREE.Vector3(VOXEL_SIZE, VOXEL_SIZE, VOXEL_SIZE),\r\n );\r\n this._voxelWorld.addAtoms(this);\r\n } catch {\r\n logger.warn('Unable to create voxel world');\r\n this._voxelWorld = null;\r\n }\r\n }\r\n\r\n return this._voxelWorld;\r\n }\r\n\r\n /**\r\n * Simple function to make unified routine procedure without code duplication.\r\n * @param {Array} srcArray - Source chemical structure array (will be part of resulting chemical structure array).\r\n * @param {Array} dstArray - Resulting chemical structure array.\r\n * @param {number} param - Parameter for processor.\r\n * @param {function} functor - Processor for every element in array.\r\n */\r\n addElement(srcArray, dstArray, param, functor) {\r\n const { length } = srcArray;\r\n for (let i = 0; i < length; ++i) {\r\n const elem = srcArray[i];\r\n functor(elem, param);\r\n dstArray.push(elem);\r\n }\r\n }\r\n\r\n // this function joins multiple complexes into one (this)\r\n // atom, bond, ... objects are reused -- so input complexes are no longer valid\r\n joinComplexes(complexes) {\r\n // clear target complex\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n\r\n const self = this;\r\n let atomBias = 0;\r\n let bondBias = 0;\r\n let residueBias = 0;\r\n let chainBias = 0;\r\n let componentBias = 0;\r\n\r\n function processAtom(atom, bias) {\r\n atom.serial += bias;\r\n atom.index += bias;\r\n }\r\n\r\n function processBond(bond, bias) {\r\n bond._index += bias;\r\n }\r\n\r\n function processResidue(residue, bias) {\r\n residue._index += bias;\r\n }\r\n\r\n function processChain(chain, bias) {\r\n chain._complex = self;\r\n chain._index += bias;\r\n }\r\n\r\n function processComponent(component, bias) {\r\n component._complex = self;\r\n component._index += bias;\r\n }\r\n\r\n /**\r\n * Simple function to do nothing.\r\n */\r\n function doNothing() {\r\n }\r\n\r\n for (let i = 0; i < complexes.length; ++i) {\r\n const c = complexes[i];\r\n this.addElement(c._atoms, this._atoms, atomBias, processAtom);\r\n this.addElement(c._bonds, this._bonds, bondBias, processBond);\r\n this.addElement(c._residues, this._residues, residueBias, processResidue);\r\n this.addElement(c._chains, this._chains, chainBias, processChain);\r\n this.addElement(c._sheets, this._sheets, 0, doNothing);\r\n this.addElement(c._helices, this._helices, 0, doNothing);\r\n this.addElement(c._sgroups, this._sgroups, 0, doNothing);\r\n this.addElement(c._components, this._components, componentBias, processComponent);\r\n this.addElement(c.structures, this.structures, 0, doNothing);\r\n // merge residue types\r\n for (const rt in c._residueTypes) {\r\n if (c._residueTypes.hasOwnProperty(rt)) {\r\n this._residueTypes[rt] = c._residueTypes[rt];\r\n }\r\n }\r\n\r\n atomBias += c._atoms.length;\r\n bondBias += c._bonds.length;\r\n residueBias += c._residues.length;\r\n chainBias += c._chains.length;\r\n componentBias += c._components.length;\r\n }\r\n\r\n this._computeBounds();\r\n }\r\n\r\n /**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n */\r\n dssp() {\r\n const ssMap = new SecondaryStructureMap(this);\r\n\r\n const structures = this.structures = [];\r\n const helices = this._helices = [];\r\n const sheets = this._sheets = [];\r\n\r\n const getSheet = (index) => {\r\n let item = sheets[index];\r\n if (!item) {\r\n item = sheets[index] = new Sheet(String(index), 0);\r\n }\r\n return item;\r\n };\r\n\r\n let lastCode;\r\n let lastSheetIndex;\r\n let lastHelixIndex = 0;\r\n let curStructure = null;\r\n for (let i = 0, n = this._residues.length; i < n; ++i) {\r\n const curCode = ssMap._ss[i];\r\n const curResidue = this._residues[i];\r\n const curSheetIndex = ssMap._sheet[i];\r\n\r\n // expand the last structure\r\n if (curCode === lastCode && curSheetIndex === lastSheetIndex) {\r\n curResidue._secondary = curStructure;\r\n if (curStructure) {\r\n curStructure.term = curResidue;\r\n }\r\n if (curStructure instanceof Helix) {\r\n curStructure.length++;\r\n }\r\n continue;\r\n }\r\n\r\n // create a new structure\r\n const helixClass = helixClassMap[curCode];\r\n const loopType = loopMap[curCode];\r\n if (curCode === StructureType.STRAND) {\r\n const curSheet = getSheet(curSheetIndex);\r\n curStructure = new Strand(curSheet, curResidue, curResidue, 0, null, null);\r\n curSheet.addStrand(curStructure);\r\n } else if (helixClass !== undefined) {\r\n lastHelixIndex++;\r\n curStructure = new Helix(helixClass, curResidue, curResidue, lastHelixIndex, String(lastHelixIndex), '', 1);\r\n helices.push(curStructure);\r\n } else if (loopType !== undefined) {\r\n curStructure = new StructuralElement(loopType, curResidue, curResidue);\r\n } else {\r\n curStructure = null;\r\n }\r\n\r\n if (curStructure) {\r\n structures.push(curStructure);\r\n }\r\n\r\n curResidue._secondary = curStructure;\r\n\r\n lastCode = curCode;\r\n lastSheetIndex = curSheetIndex;\r\n }\r\n\r\n this._sheets = sheets.filter((_sheet) => true); // squeeze sheets array\r\n }\r\n}\r\n\r\nComplex.prototype.id = 'Complex';\r\nComplex.prototype.name = '';\r\n\r\nexport default Complex;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\nfunction pow2ceil(v) {\r\n let p = 2;\r\n v = (v - 1) >> 1;\r\n while (v) {\r\n p <<= 1;\r\n v >>= 1;\r\n }\r\n return p;\r\n}\r\n\r\n/**\r\n * Volume constructor\r\n *\r\n * @param {Object} type - Float32Array, Int8Array, etc...\r\n * @param {Object|Array} dimensions - number of data points on each axis (x, y, z)\r\n * @param {Box3} box - bounding box defining data place in metric space,\r\n * it's corners correspond to extreme data points\r\n * @param {Number} vecSize - dimension of the field data point (1 = scalar, 3 = 3D vector)\r\n * @param {Object} data - typed array of the same type as specified by the 1st parameter,\r\n * layout: point by point along X,\r\n * row by row along Y,\r\n * plane by plane along Z\r\n * @param {Number} volumeInfo - volume info values to define threshold to filter the noise\r\n */\r\n\r\nclass Volume {\r\n constructor(type, dimensions, box, vecSize, data, volumeInfo) {\r\n this._box = box.clone();\r\n this._dimVec = Math.max(Math.floor(vecSize || 1), 1);\r\n this._volumeInfo = volumeInfo;\r\n\r\n if (dimensions instanceof Array) {\r\n [this._dimX, this._dimY, this._dimZ] = dimensions;\r\n } else {\r\n this._dimX = dimensions.x;\r\n this._dimY = dimensions.y;\r\n this._dimZ = dimensions.z;\r\n }\r\n this._dimX = Math.max(Math.floor(this._dimX), 1);\r\n this._dimY = Math.max(Math.floor(this._dimY), 1);\r\n this._dimZ = Math.max(Math.floor(this._dimZ), 1);\r\n\r\n this._rowElements = this._dimVec * this._dimX;\r\n this._planeElements = this._rowElements * this._dimY;\r\n this._totalElements = this._planeElements * this._dimZ;\r\n\r\n this._data = data || utils.allocateTyped(type, this._totalElements);\r\n\r\n // override getter/setter for vector fields\r\n switch (this._dimVec) {\r\n case 1:\r\n break;\r\n\r\n case 2:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n };\r\n break;\r\n\r\n case 3:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1], this._data[idx + 2]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n this._data[idx + 2] = c;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n this._data[idx + 2] += c;\r\n };\r\n break;\r\n\r\n default:\r\n throw new Error('Volume: invalid vector dimension');\r\n }\r\n }\r\n\r\n // default getter assumes it's a scalar field\r\n getValue(x, y, z) {\r\n return this._data[x + y * this._rowElements + z * this._planeElements];\r\n }\r\n\r\n // default setter assumes it's a scalar field\r\n setValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] = val;\r\n }\r\n\r\n // default adder assumes it's a scalar field\r\n addValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] += val;\r\n }\r\n\r\n getDimensions() {\r\n return [this._dimX, this._dimY, this._dimZ];\r\n }\r\n\r\n getBox() {\r\n return this._box;\r\n }\r\n\r\n getVolumeInfo() {\r\n return this._volumeInfo;\r\n }\r\n\r\n getCellSize() {\r\n const boxSize = new THREE.Vector3();\r\n this._box.getSize(boxSize);\r\n const res = new THREE.Vector3();\r\n res.x = this._dimX > 1 ? boxSize.x / (this._dimX - 1) : 0;\r\n res.y = this._dimY > 1 ? boxSize.y / (this._dimY - 1) : 0;\r\n res.z = this._dimZ > 1 ? boxSize.z / (this._dimZ - 1) : 0;\r\n return res;\r\n }\r\n\r\n computeGradient() {\r\n if (this._dimVec !== 1) {\r\n // gradient can only be computed for scalar fields\r\n return null;\r\n }\r\n\r\n // create a 3D vector field of gradients\r\n const gradient = new Volume(Float32Array, [this._dimX, this._dimY, this._dimZ], this._box, 3);\r\n\r\n // calculate cell side lengths\r\n const vl = this.getCellSize();\r\n\r\n // gradient axis scaling values and averaging factors, to correctly\r\n // calculate the gradient for volumes with irregular cell spacing\r\n const vs = new THREE.Vector3(-0.5 / vl.x, -0.5 / vl.y, -0.5 / vl.z);\r\n\r\n // TODO Check for intended bug in VMD (min is zero)\r\n function clamp(val, min, max) {\r\n return Math.min(max, Math.max(min, val));\r\n }\r\n\r\n const xSize = this._dimX;\r\n const ySize = this._dimY;\r\n const zSize = this._dimZ;\r\n const volMap = this._data;\r\n\r\n function _voxelValue(x, y, z) {\r\n return volMap[z * xSize * ySize + y * xSize + x];\r\n }\r\n\r\n for (let zi = 0; zi < zSize; ++zi) {\r\n const zm = clamp(zi - 1, 0, zSize - 1);\r\n const zp = clamp(zi + 1, 0, zSize - 1);\r\n\r\n for (let yi = 0; yi < ySize; ++yi) {\r\n const ym = clamp(yi - 1, 0, ySize - 1);\r\n const yp = clamp(yi + 1, 0, ySize - 1);\r\n\r\n for (let xi = 0; xi < xSize; ++xi) {\r\n const xm = clamp(xi - 1, 0, xSize - 1);\r\n const xp = clamp(xi + 1, 0, xSize - 1);\r\n\r\n // Calculate the volume gradient at each grid cell.\r\n // Gradients are now stored unnormalized, since we need them in pure\r\n // form in order to draw field lines etc. Shading code will now have\r\n // to do renormalization for itself on-the-fly.\r\n\r\n // XXX this gradient is only correct for orthogonal grids, since\r\n // we're using the array index offsets rather to calculate the gradient\r\n // rather than voxel coordinate offsets. This will have to be\r\n // re-worked for non-orthogonal datasets.\r\n\r\n gradient.setValue(\r\n xi,\r\n yi,\r\n zi,\r\n (_voxelValue(xp, yi, zi) - _voxelValue(xm, yi, zi)) * vs.x,\r\n (_voxelValue(xi, yp, zi) - _voxelValue(xi, ym, zi)) * vs.y,\r\n (_voxelValue(xi, yi, zp) - _voxelValue(xi, yi, zm)) * vs.z,\r\n );\r\n }\r\n }\r\n }\r\n\r\n return gradient;\r\n }\r\n\r\n normalize() {\r\n const data = this._data;\r\n\r\n // get min/max\r\n let min = data[0];\r\n let max = data[0];\r\n for (let i = 1; i < data.length; ++i) {\r\n min = Math.min(min, data[i]);\r\n max = Math.max(max, data[i]);\r\n }\r\n\r\n const d = 1.0 / (max - min);\r\n if (d === 0) {\r\n return;\r\n }\r\n\r\n // normalize\r\n for (let i = 0; i < data.length; ++i) {\r\n data[i] = d * (data[i] - min);\r\n }\r\n }\r\n\r\n getTiledTextureStride() {\r\n return [this._dimX + 2, this._dimY + 2];\r\n }\r\n\r\n buildTiledTexture() {\r\n let tilesX = Math.ceil(Math.sqrt(this._dimZ * this._dimY / this._dimX));\r\n\r\n let width = tilesX * (this._dimX + 2) - 1;\r\n width = pow2ceil(width);\r\n tilesX = Math.floor(width / (this._dimX + 2));\r\n\r\n const tilesY = Math.ceil(this._dimZ / tilesX);\r\n let height = tilesY * (this._dimY + 2) - 1;\r\n height = pow2ceil(height);\r\n\r\n const data = new Uint8Array(width * height);\r\n\r\n let src;\r\n let dst;\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // process each pixel row of this tile row\r\n for (let row = 0; row < this._dimY; ++row) {\r\n src = tileRow * tilesX * this._planeElements + row * this._rowElements;\r\n dst = width * (tileRow * (this._dimY + 2) + row);\r\n // copy a series of rows through several XY planes\r\n for (let t = 0; t < tilesX; ++t) {\r\n // copy one row of one XY plane\r\n for (let x = 0; x < this._dimX; ++x) {\r\n data[dst++] = 255.0 * this._data[src++];\r\n }\r\n\r\n // repeat last pixel of previous tile\r\n data[dst++] = 255.0 * this._data[src - 1];\r\n\r\n if (t < tilesX - 1) {\r\n // skip to the same row of next XY plane\r\n src += this._planeElements - this._rowElements;\r\n // repeat first pixel of next tile\r\n data[dst++] = 255.0 * this._data[src];\r\n }\r\n }\r\n }\r\n }\r\n\r\n // fill pixels between tile rows with copy of edge pixels\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // copy last pixel row of this tile row to the following pixel row of the texture\r\n src = width * (tileRow * (this._dimY + 2) + this._dimY - 1);\r\n dst = src + width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n if (tileRow < tilesY - 1) {\r\n // copy first pixel row of next tile row to the preceding pixel row of the texture\r\n src = width * (tileRow + 1) * (this._dimY + 2);\r\n dst = src - width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n }\r\n }\r\n\r\n const texture = new THREE.DataTexture(\r\n data,\r\n width,\r\n height,\r\n THREE.RedFormat,\r\n THREE.UnsignedByteType,\r\n THREE.UVMapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.LinearFilter,\r\n THREE.LinearFilter,\r\n );\r\n texture.needsUpdate = true;\r\n return texture;\r\n }\r\n\r\n /* ********************************************************************************\r\n *\r\n * Methods that provide direct access to internal array (for better performance)\r\n *\r\n ******************************************************************************** */\r\n\r\n getData() {\r\n return this._data;\r\n }\r\n\r\n getDirectIdx(x, y, z) {\r\n return x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n }\r\n\r\n getStrideX() {\r\n return this._dimVec;\r\n }\r\n\r\n getStrideY() {\r\n return this._rowElements;\r\n }\r\n\r\n getStrideZ() {\r\n return this._planeElements;\r\n }\r\n}\r\n\r\nVolume.prototype.id = 'Volume';\r\n\r\nexport default Volume;\r\n","/**\r\n * Residue Molecule.\r\n *\r\n * @param {Complex} complex - Molecular complex this Molecule belongs to.\r\n * @param {String} name - Molecule's name.\r\n * @param {Integer} index - Molecule's index in file.\r\n *\r\n * @exports Molecule\r\n * @constructor\r\n */\r\nclass Molecule {\r\n constructor(complex, name, index) {\r\n this.complex = complex;\r\n this.name = name || '';\r\n this.residues = [];\r\n this.mask = 1 | 0;\r\n this.index = index || -1; // start with 1\r\n }\r\n\r\n forEachResidue(process) {\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this.mask = mask;\r\n }\r\n}\r\n\r\nexport default Molecule;\r\n","import Atom from './chem/Atom';\r\nimport Element from './chem/Element';\r\nimport Bond from './chem/Bond';\r\nimport Residue from './chem/Residue';\r\nimport ResidueType from './chem/ResidueType';\r\nimport Chain from './chem/Chain';\r\nimport Helix from './chem/Helix';\r\nimport Strand from './chem/Strand';\r\nimport Sheet from './chem/Sheet';\r\nimport SGroup from './chem/SGroup';\r\nimport Assembly from './chem/Assembly';\r\nimport Complex from './chem/Complex';\r\nimport Volume from './chem/Volume';\r\nimport VoxelWorld from './chem/VoxelWorld';\r\nimport selectors from './chem/selectors';\r\nimport Molecule from './chem/Molecule';\r\n\r\nexport default {\r\n Atom,\r\n Element,\r\n Bond,\r\n Residue,\r\n ResidueType,\r\n Chain,\r\n Helix,\r\n Strand,\r\n Sheet,\r\n SGroup,\r\n Assembly,\r\n Complex,\r\n Volume,\r\n VoxelWorld,\r\n selectors,\r\n Molecule,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\n\r\nclass CSS2DObject extends THREE.Object3D {\r\n constructor(element) {\r\n super();\r\n const self = this;\r\n this._element = element;\r\n this._element.style.position = 'absolute';\r\n this.addEventListener('removed', () => {\r\n if (self._element.parentNode !== null) {\r\n self._element.parentNode.removeChild(self._element);\r\n }\r\n });\r\n }\r\n\r\n getElement() {\r\n return this._element;\r\n }\r\n\r\n /**\r\n * Sets label transparency.\r\n *\r\n * @param {number} transp - in [0; 1] 1 means fully transparent\r\n */\r\n setTransparency(transp) {\r\n const el = this.getElement();\r\n if (el === null) {\r\n return;\r\n }\r\n if (transp === 1.0) {\r\n el.style.display = 'none';\r\n return;\r\n }\r\n el.style.display = 'inline';\r\n const op = 1.0 - transp;\r\n const top = op.toString();\r\n const op100 = op * 100;\r\n el.style.opacity = top;\r\n el.style.filter = `alpha(opacity=${op100})`; // IE fallback\r\n }\r\n\r\n clone() {\r\n const obj = new CSS2DObject(this._element);\r\n obj.copy(this);\r\n return obj;\r\n }\r\n}\r\n\r\nexport default CSS2DObject;\r\n","import * as THREE from 'three';\r\n\r\nclass RCGroup extends THREE.Group {\r\n raycast(raycaster, intersects) {\r\n if (!this.visible) {\r\n return;\r\n }\r\n\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n children[i].raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].enableSubset) {\r\n children[i].enableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].disableSubset) {\r\n children[i].disableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n isEmpty() {\r\n return this.children.length === 0;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].updateToFrame) {\r\n children[i].updateToFrame(frameData);\r\n }\r\n }\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n Array.prototype.push.apply(totalSubset, children[i].getSubset(mask, innerOnly));\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default RCGroup;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport CSS2DObject from './CSS2DObject';\r\nimport RCGroup from './RCGroup';\r\nimport vertexScreenQuadShader from './shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromTex from './shaders/ScreenQuadFromTex.frag';\r\nimport fragmentScreenQuadFromTexWithDistortion from './shaders/ScreenQuadFromTexWithDistortion.frag';\r\n\r\nconst LAYERS = {\r\n DEFAULT: 0, VOLUME: 1, TRANSPARENT: 2, PREPASS_TRANSPARENT: 3, VOLUME_BFPLANE: 4, COLOR_FROM_POSITION: 5, SHADOWMAP: 6,\r\n};\r\n\r\nconst SELECTION_LAYERS = [ // These layers, that are used in the selection by ray casting\r\n LAYERS.DEFAULT, LAYERS.TRANSPARENT,\r\n];\r\n\r\nTHREE.Object3D.prototype.resetTransform = function () {\r\n this.position.set(0, 0, 0);\r\n this.quaternion.set(0, 0, 0, 1);\r\n this.scale.set(1, 1, 1);\r\n};\r\n\r\n// update world matrix of this object and all its ancestors\r\nTHREE.Object3D.prototype.updateMatrixWorldRecursive = function () {\r\n if (this.parent != null) {\r\n this.parent.updateMatrixWorldRecursive();\r\n }\r\n this.updateMatrixWorld();\r\n};\r\n// add object to parent, saving objects' world transform\r\nTHREE.Object3D.prototype.addSavingWorldTransform = (function () {\r\n const _worldMatrixInverse = new THREE.Matrix4();\r\n\r\n return function (object) {\r\n if (object instanceof THREE.Object3D) {\r\n _worldMatrixInverse.copy(this.matrixWorld).invert();\r\n _worldMatrixInverse.multiply(object.matrixWorld);\r\n object.matrix.copy(_worldMatrixInverse);\r\n object.matrix.decompose(object.position, object.quaternion, object.scale);\r\n this.add(object);\r\n }\r\n };\r\n}());\r\n\r\n// render a tiny transparent quad in the center of the screen\r\nTHREE.WebGLRenderer.prototype.renderDummyQuad = (function () {\r\n const _material = new THREE.MeshBasicMaterial({ transparent: true, opacity: 0.0, depthWrite: false });\r\n\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(0.01, 0.01), _material);\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function () {\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuad = (function () {\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(1.0, 1.0));\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function (material) {\r\n _quad.material = material;\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.isIdentity = (function () {\r\n const identity = new THREE.Matrix4();\r\n return function () {\r\n return identity.equals(this);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.applyToPointsArray = function (array, stride, w) {\r\n if (!array || !stride || stride < 3) {\r\n return array;\r\n }\r\n w = w || 0; // use point as normal by default\r\n const e = this.elements;\r\n for (let i = 0; i < array.length; i += stride) {\r\n const x = array[i];\r\n const y = array[i + 1];\r\n const z = array[i + 2];\r\n\r\n const persp = 1 / (e[3] * x + e[7] * y + e[11] * z + e[15]);\r\n\r\n array[i] = (e[0] * x + e[4] * y + e[8] * z + e[12] * w) * persp;\r\n array[i + 1] = (e[1] * x + e[5] * y + e[9] * z + e[13] * w) * persp;\r\n array[i + 2] = (e[2] * x + e[6] * y + e[10] * z + e[14] * w) * persp;\r\n }\r\n return array;\r\n};\r\n\r\nclass ScreenQuadMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n if (params.uniforms === undefined) {\r\n params.uniforms = {};\r\n }\r\n params.uniforms.srcTex = { type: 't', value: null };\r\n params.vertexShader = vertexScreenQuadShader;\r\n params.transparent = false;\r\n params.depthTest = false;\r\n params.depthWrite = false;\r\n super(params);\r\n }\r\n}\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTex = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { opacity: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTex,\r\n transparent: true,\r\n });\r\n\r\n return function (srcTex, opacity) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.transparent = (opacity < 1.0);\r\n _material.uniforms.opacity.value = opacity;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTexWithDistortion = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { coef: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTexWithDistortion,\r\n });\r\n\r\n return function (srcTex, coef) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.uniforms.coef.value = coef;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\n/**\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setMinimalFov = function (angle) {\r\n if (this.aspect >= 1.0) {\r\n this.fov = angle;\r\n } else {\r\n this.fov = THREE.MathUtils.radToDeg(2 * Math.atan(Math.tan(THREE.MathUtils.degToRad(angle) * 0.5) / this.aspect));\r\n }\r\n};\r\n\r\n/**\r\n * @param {THREE.PerspectiveCamera} camera - Base camera for this stereo camera.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.StereoCamera.prototype.updateHalfSized = function (camera, angle) {\r\n const originalAspect = camera.aspect;\r\n const originalFov = camera.fov;\r\n\r\n camera.aspect = originalAspect / 2.0;\r\n camera.setMinimalFov(angle);\r\n camera.updateProjectionMatrix();\r\n\r\n this.update(camera);\r\n\r\n camera.aspect = originalAspect;\r\n camera.fov = originalFov;\r\n camera.updateProjectionMatrix();\r\n};\r\n\r\n/**\r\n * @param {number} radius - Radius of bounding sphere in angstroms to fit on screen.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setDistanceToFit = function (radius, angle) {\r\n this.position.z = radius / Math.sin(0.5 * THREE.MathUtils.degToRad(angle));\r\n};\r\n\r\n/**\r\n * @param {RCGroup} gfxObj - All objects on scene.\r\n * @param {THREE.PerspectiveCamera} camera - Camera used for rendering.\r\n * @param {number} clipPlane - Distance to clip plane.\r\n * @param {number} fogFarPlane - Distance to fog far plane.\r\n */\r\nTHREE.Raycaster.prototype.intersectVisibleObject = function (gfxObj, camera, clipPlane, fogFarPlane) {\r\n const intersects = this.intersectObject(gfxObj, false);\r\n if (intersects.length === 0) {\r\n return null;\r\n }\r\n\r\n // find point closest to camera that doesn't get clipped by camera near plane or clipPlane (if it exists)\r\n const nearPlane = Math.min(camera.near, clipPlane);\r\n let i;\r\n let p = intersects[0];\r\n const v = new THREE.Vector3();\r\n for (i = 0; i < intersects.length; ++i) {\r\n p = intersects[i];\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -nearPlane) {\r\n break;\r\n }\r\n }\r\n if (i === intersects.length) {\r\n return null;\r\n }\r\n\r\n // check that selected intersection point is not clipped by camera far plane or occluded by fog (if it exists)\r\n const farPlane = Math.min(camera.far, fogFarPlane);\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -farPlane) {\r\n return null;\r\n }\r\n return p;\r\n};\r\n\r\nTHREE.Matrix4.prototype.extractScale = (function () {\r\n const _v = new THREE.Vector3();\r\n\r\n return function (scale) {\r\n if (scale === undefined) {\r\n logger.debug('extractScale(): new is too expensive operation to do it on-the-fly');\r\n scale = _v.clone();\r\n }\r\n\r\n const te = this.elements;\r\n scale.x = _v.set(te[0], te[1], te[2]).length();\r\n scale.y = _v.set(te[4], te[5], te[6]).length();\r\n scale.z = _v.set(te[8], te[9], te[10]).length();\r\n\r\n // if determine is negative, we need to invert one scale\r\n const det = this.determinant();\r\n if (det < 0) {\r\n scale.x = -scale.x;\r\n }\r\n return scale;\r\n };\r\n}());\r\n\r\nfunction _calcCylinderMatrix(posBegin, posEnd, radius) {\r\n const posCenter = posBegin.clone().lerp(posEnd, 0.5);\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(radius, posBegin.distanceTo(posEnd), radius);\r\n\r\n const matRotHalf = new THREE.Matrix4();\r\n matRotHalf.makeRotationX(Math.PI / 2);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n const vUp = new THREE.Vector3(0, 1, 0);\r\n matRotLook.lookAt(posCenter, posEnd, vUp);\r\n\r\n matRotLook.multiply(matRotHalf);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(posCenter);\r\n return matRotLook;\r\n}\r\n\r\nfunction _calcChunkMatrix(eye, target, up, rad) {\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(rad.x, rad.y, 0);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n matRotLook.lookAt(eye, target, up);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(eye);\r\n\r\n return matRotLook;\r\n}\r\n\r\nfunction _groupHasGeometryToRender(group) {\r\n let hasGeoms = false;\r\n group.traverse((node) => {\r\n if (node.hasOwnProperty('geometry') || node instanceof CSS2DObject) {\r\n hasGeoms = true;\r\n }\r\n });\r\n return hasGeoms;\r\n}\r\n\r\nfunction _buildDistorionMesh(widthSegments, heightSegements, coef) {\r\n // solve equation r_u = r_d * (1 + k * r_d^2)\r\n // for r_d using iterations\r\n // takes: r_u^2\r\n // returns: r_d / r_u factor that can be used to distort point coords\r\n function calcInverseBarrel(r2) {\r\n const epsilon = 1e-5;\r\n let prevR2 = 0.0;\r\n let curR2 = r2;\r\n let dr = 1.0;\r\n while (Math.abs(curR2 - prevR2) > epsilon) {\r\n dr = 1.0 + coef * curR2;\r\n prevR2 = curR2;\r\n curR2 = r2 / (dr * dr);\r\n }\r\n\r\n return 1.0 / dr;\r\n }\r\n\r\n const geo = new THREE.PlaneGeometry(2.0, 2.0, widthSegments, heightSegements);\r\n\r\n const pos = geo.getAttribute('position');\r\n for (let i = 0; i < pos.count; ++i) {\r\n const x = pos.array[3 * i];\r\n const y = pos.array[3 * i + 1];\r\n const c = calcInverseBarrel(x * x + y * y);\r\n pos.setXY(i, c * x, c * y);\r\n }\r\n\r\n return geo;\r\n}\r\n\r\nTHREE.BufferAttribute.prototype.copyAtList = function (attribute, indexList) {\r\n console.assert(\r\n this.itemSize === attribute.itemSize,\r\n 'DEBUG: BufferAttribute.copyAtList buffers have different item size.',\r\n );\r\n const { itemSize } = this;\r\n for (let i = 0, n = indexList.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n this.array[i * itemSize + j] = attribute.array[indexList[i] * itemSize + j];\r\n }\r\n }\r\n return this;\r\n};\r\n\r\nfunction fillArray(array, value, startIndex, endIndex) {\r\n startIndex = (typeof startIndex !== 'undefined') ? startIndex : 0;\r\n endIndex = (typeof endIndex !== 'undefined') ? endIndex : array.length;\r\n for (let i = startIndex; i < endIndex; ++i) {\r\n array[i] = value;\r\n }\r\n}\r\n\r\n/** @param {THREE.Object3D} object - Parent object. */\r\nfunction removeChildren(object) {\r\n const { children } = object;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n child.parent = null;\r\n child.dispatchEvent({ type: 'removed' });\r\n }\r\n object.children = [];\r\n}\r\n\r\nfunction clearTree(object) {\r\n object.traverse((obj) => {\r\n if (obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line) {\r\n obj.geometry.dispose();\r\n }\r\n });\r\n removeChildren(object);\r\n}\r\n\r\nfunction destroyObject(object) {\r\n clearTree(object);\r\n if (object.parent) {\r\n object.parent.remove(object);\r\n } else {\r\n object.dispatchEvent({ type: 'removed' });\r\n }\r\n}\r\n\r\nfunction belongToSelectLayers(object) {\r\n for (let i = 0; i < SELECTION_LAYERS.length; i++) {\r\n if (((object.layers.mask >> SELECTION_LAYERS[i]) & 1) === 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n}\r\n\r\nfunction processObjRenderOrder(root, idMaterial) {\r\n // set renderOrder to 0 for Backdrop and to 1 in other cases to render Backdrop earlier all other materials\r\n const renderOrder = +(idMaterial !== 'BA');\r\n root.traverse((object) => {\r\n if (object.isGroup) {\r\n object.renderOrder = renderOrder;\r\n }\r\n });\r\n}\r\n\r\nfunction applySelectionMaterial(geo) {\r\n geo.traverse((node) => {\r\n if ('material' in node) {\r\n node.material = node.material.clone(true);\r\n // using z-offset to magically fix selection rendering artifact (on z-sprites)\r\n node.material.setValues({\r\n depthFunc: THREE.LessEqualDepth,\r\n overrideColor: true,\r\n fog: false,\r\n lights: false,\r\n shadowmap: false,\r\n });\r\n node.material.setUberOptions({ fixedColor: new THREE.Color(0xFFFF00), zOffset: -1e-6 });\r\n }\r\n });\r\n}\r\n\r\nfunction getMiddlePoint(point1, point2, optionalTarget) {\r\n const result = optionalTarget || new THREE.Vector3();\r\n\r\n result.set(0, 0, 0);\r\n result.addScaledVector(point1, 0.5);\r\n result.addScaledVector(point2, 0.5);\r\n\r\n return result;\r\n}\r\n\r\n// Monkey-patch for \"InstancedBufferGeometry.instanceCount becomes undefined after copy()\"\r\n// https://github.com/mrdoob/three.js/issues/22151\r\nconst _oldInstancedBufferGeometryCopy = THREE.InstancedBufferGeometry.prototype.copy;\r\n\r\nTHREE.InstancedBufferGeometry.prototype.copy = function (source) {\r\n _oldInstancedBufferGeometryCopy.call(this, source);\r\n if (this.instanceCount === undefined) {\r\n this.instanceCount = Infinity;\r\n }\r\n};\r\n\r\nexport default {\r\n calcCylinderMatrix: _calcCylinderMatrix,\r\n calcChunkMatrix: _calcChunkMatrix,\r\n groupHasGeometryToRender: _groupHasGeometryToRender,\r\n buildDistorionMesh: _buildDistorionMesh,\r\n RCGroup,\r\n fillArray,\r\n clearTree,\r\n destroyObject,\r\n belongToSelectLayers,\r\n processObjRenderOrder,\r\n applySelectionMaterial,\r\n getMiddlePoint,\r\n LAYERS,\r\n};\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfx/gfxutils';\r\n\r\nconst _defaultBoundaries = {\r\n boundingBox: new THREE.Box3(new THREE.Vector3(-1, -1, -1), new THREE.Vector3(1, 1, 1)),\r\n boundingSphere: new THREE.Sphere(new THREE.Vector3(0, 0, 0), 1),\r\n};\r\n\r\nclass Visual extends gfxutils.RCGroup {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this.name = name;\r\n this._dataSource = dataSource;\r\n }\r\n\r\n release() {\r\n if (this.parent) {\r\n this.parent.remove(this);\r\n }\r\n }\r\n\r\n getDataSource() {\r\n return this._dataSource;\r\n }\r\n\r\n getBoundaries() {\r\n return _defaultBoundaries;\r\n }\r\n}\r\n\r\nexport default Visual;\r\n","function _ensureArray(x) {\r\n if (x === null || x === undefined || Array.isArray(x)) {\r\n return x;\r\n }\r\n return [x];\r\n}\r\n\r\n/** An indexed list of objects or classes. */\r\nclass EntityList {\r\n /**\r\n * Create a list of objects.\r\n * The objects can be indexed by one or more properties for the later retrieval.\r\n *\r\n * @param {!Array=} entities A list of objects to automatically register at creation time.\r\n * @param {!Array=} indices A list of property names to use for case-insensitive indexing.\r\n * By default, a single `.id` property is used.\r\n * @see EntityList#register\r\n */\r\n constructor(entities = [], indices = ['id']) {\r\n this._list = [];\r\n this._dict = {};\r\n this._indices = [...indices];\r\n this._indices.forEach((index) => {\r\n this._dict[index] = {};\r\n });\r\n\r\n entities.forEach((entity) => this.register(entity));\r\n }\r\n\r\n /**\r\n * Add a value to the end of a list.\r\n * The list will contain only one copy of the value.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromList\r\n * @see EntityList.registerInDict\r\n */\r\n static registerInList(list, value) {\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n }\r\n\r\n /**\r\n * Remove a value from a list if it is there.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to remove.\r\n * @see EntityList.registerInList\r\n */\r\n static unregisterFromList(list, value) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n }\r\n\r\n /**\r\n * Add a value to a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromDict\r\n * @see EntityList.registerInList\r\n */\r\n static registerInDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key] = dict[key] || [];\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Remove a value from a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.registerInDict\r\n */\r\n static unregisterFromDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key];\r\n if (list) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n if (list.length === 0) {\r\n delete dict[key];\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Add an entity to this list.\r\n *\r\n * @param {!Object} entity An object or a class to register. The object must include all\r\n * properties specified as indices on construction.\r\n * @see EntityList#unregister\r\n */\r\n register(entity) {\r\n EntityList.registerInList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.registerInDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * Remove an entity from this list.\r\n *\r\n * @param {!Object} entity An object or a class to unregister. The object may be\r\n * missing from the list but it must include all properties specified as indices\r\n * on construction.\r\n * @see EntityList#register\r\n */\r\n unregister(entity) {\r\n EntityList.unregisterFromList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.unregisterFromDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * An ordered list of all registered entities.\r\n * It is a read-only copy, use {@link EntityList#register} and {@link EntityList#unregister}\r\n * to modify it.\r\n *\r\n * @type {!Array}\r\n */\r\n get all() {\r\n return [...this._list];\r\n }\r\n\r\n /**\r\n * The first registered entity.\r\n * Use it if you do not care which entity you are referring to.\r\n *\r\n * @type {Object=}\r\n */\r\n get first() {\r\n return this._list[0];\r\n }\r\n\r\n /**\r\n * Retrieve a list of keys for the index.\r\n *\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {!Array} An unordered list of keys in the index, i.e. particular property\r\n * values for all registered entities.\r\n */\r\n keys(index) {\r\n return Object.keys(this._dict[index || this._indices[0]]);\r\n }\r\n\r\n /**\r\n * Retrieve an entity by its key.\r\n *\r\n * @param {string} key A case-insensitive property value to look-up.\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {Object=} An object registered in the index under the key. If there are multiple\r\n * objects under the same key, the first one is returned.\r\n */\r\n get(key, index) {\r\n const dict = this._dict[index || this._indices[0]];\r\n if (dict) {\r\n const values = dict[key && key.toLowerCase()];\r\n return values && values.length > 0 ? values[0] : undefined;\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nexport default EntityList;\r\n","import settings from '../settings';\r\nimport logger from './logger';\r\n\r\nfunction makeContextDependent(prototype) {\r\n Object.defineProperties(prototype, {\r\n logger: {\r\n get() {\r\n return this.context && this.context.logger ? this.context.logger : logger;\r\n },\r\n },\r\n settings: {\r\n get() {\r\n return this.context && this.context.settings ? this.context.settings : settings;\r\n },\r\n },\r\n });\r\n}\r\n\r\nexport default makeContextDependent;\r\n","import * as THREE from 'three';\r\n\r\nclass CollisionSphere {\r\n constructor(position, radius) {\r\n this._position = position;\r\n this._radius = radius;\r\n }\r\n\r\n static _sphere = new THREE.Sphere();\r\n\r\n raycast(raycaster) {\r\n const sphere = CollisionSphere._sphere;\r\n sphere.set(this._position, this._radius);\r\n\r\n const p = new THREE.Vector3();\r\n if (raycaster.ray.intersectSphere(sphere, p)) {\r\n return {\r\n distance: raycaster.ray.origin.distanceTo(p),\r\n point: p,\r\n };\r\n }\r\n return null;\r\n }\r\n}\r\n\r\nconst SphereCollisionGeo = (base) => class extends base {\r\n constructor(count, ...args) {\r\n super(...args);\r\n this._objects = new Array(count);\r\n this.boundingSphere = null;\r\n this.boundingBox = null;\r\n }\r\n\r\n setSphere(idx, position, radius) {\r\n this._objects[idx] = new CollisionSphere(position, radius);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n // TODO raycast with bounding sphere? How to deal with updates?\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const inters = this._objects[i].raycast(raycaster);\r\n if (inters) {\r\n inters.chunkIdx = i;\r\n intersects.push(inters);\r\n }\r\n }\r\n }\r\n\r\n computeBoundingBox() {\r\n const objects = this._objects;\r\n let { boundingBox } = this;\r\n if (boundingBox === null) {\r\n this.boundingBox = boundingBox = new THREE.Box3();\r\n }\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n boundingBox.expandByPoint(objects[i]._position);\r\n }\r\n }\r\n\r\n computeBoundingSphere() {\r\n this.computeBoundingBox();\r\n const objects = this._objects;\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n const pos = objects[i]._position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n if (this.boundingSphere === null) {\r\n this.boundingSphere = new THREE.Sphere();\r\n }\r\n this.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n};\r\nexport default SphereCollisionGeo;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst tmpColor = new THREE.Color();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\nclass InstancedSpheresGeometry extends SphereCollisionGeo(THREE.InstancedBufferGeometry) {\r\n constructor(spheresCount, sphereComplexity, useZSprites) {\r\n super(spheresCount);\r\n this._sphGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new THREE.SphereGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI);\r\n this._init(spheresCount, this._sphGeometry);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n setArrayXYZW(this._offsets, itemIdx * OFFSET_SIZE, itemPos.x, itemPos.y, itemPos.z, itemRad);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n\r\n setColor(itemIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n setArrayXYZ(this._colors, itemIdx * COLOR_SIZE, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('offset').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[chunkIndices[i]] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._sphGeometry);\r\n\r\n copySubArrays(this._offsets, geom._offsets, chunkIndices, OFFSET_SIZE);\r\n copySubArrays(this._colors, geom._colors, chunkIndices, COLOR_SIZE);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(spheresCount, sphereGeo) {\r\n this.copy(sphereGeo);\r\n\r\n this._offsets = utils.allocateTyped(Float32Array, spheresCount * OFFSET_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, spheresCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('offset', new THREE.InstancedBufferAttribute(this._offsets, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._colors, COLOR_SIZE, false, 1));\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(alpha, 1, false, 1));\r\n }\r\n}\r\nexport default InstancedSpheresGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VEC_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n */\r\n\r\nclass ChunkedObjectsGeometry extends THREE.BufferGeometry {\r\n constructor(chunkGeo, chunksCount) {\r\n super();\r\n\r\n if (this.constructor === ChunkedObjectsGeometry) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n\r\n this._chunkGeo = chunkGeo;\r\n\r\n this._init(chunkGeo, chunksCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('normal').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n const idx = i * VEC_SIZE;\r\n colors[idx] = tmpColor.r;\r\n colors[idx + 1] = tmpColor.g;\r\n colors[idx + 2] = tmpColor.b;\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n _.fill(alphaArr, value, left, left + chunkSize);\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n // use THREE.Mesh raycasting interface for the Geometry. The Mesh is\r\n // created with existed geometry and default material, so it doesn't slowdown.\r\n const mesh = new THREE.Mesh();\r\n mesh.geometry = this;\r\n mesh.raycast(raycaster, inters);\r\n\r\n const facesPerChunk = this._chunkGeo.index.count / 3;\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('faceIndex')) {\r\n continue;\r\n }\r\n inters[i].chunkIdx = Math.floor(inters[i].faceIndex / facesPerChunk);\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.BufferGeometry();\r\n this._init.call(geom, this._chunkGeo, instanceCount);\r\n\r\n const srcPos = this._positions;\r\n const srcNorm = this._normals;\r\n const srcColor = this._colors;\r\n\r\n const dstPos = geom._positions;\r\n const dstNorm = geom._normals;\r\n const dstColor = geom._colors;\r\n\r\n const chunkSize = this._chunkSize * VEC_SIZE;\r\n\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const ptIdxBegin = chunkIndices[i] * chunkSize;\r\n const ptIdxEnd = ptIdxBegin + chunkSize;\r\n dstPos.set(srcPos.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstNorm.set(srcNorm.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstColor.set(srcColor.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n }\r\n\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(chunkGeo, chunksCount) {\r\n const chunkSize = this._chunkSize = chunkGeo.attributes.position.count;\r\n const chunkIndex = chunkGeo.index.array;\r\n const chunkIndexSize = chunkIndex.length;\r\n const pointsCount = this._chunkSize * chunksCount;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n const indexSize = chunkIndexSize * chunksCount;\r\n const index = this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, indexSize);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._normals = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n for (let i = 0; i < chunksCount; ++i) {\r\n const offset = i * chunkIndexSize;\r\n const posOffset = i * chunkSize;\r\n index.set(chunkIndex, offset);\r\n for (let j = 0; j < chunkIndexSize; ++j) {\r\n index[offset + j] += posOffset;\r\n }\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, VEC_SIZE));\r\n this.setAttribute('normal', new THREE.BufferAttribute(this._normals, VEC_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, VEC_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n }\r\n}\r\nexport default ChunkedObjectsGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst VEC_SIZE = 3;\r\n\r\nclass SimpleSpheresGeometry extends SphereCollisionGeo(ChunkedObjectsGeometry) {\r\n constructor(spheresCount, sphereComplexity) {\r\n const sphGeometry = new THREE.SphereGeometry(\r\n 1,\r\n sphereComplexity * 2,\r\n sphereComplexity,\r\n 0,\r\n Math.PI * 2,\r\n 0,\r\n Math.PI,\r\n );\r\n super(spheresCount, sphGeometry, spheresCount);\r\n\r\n const normals = this._normals;\r\n const geoNormals = sphGeometry.attributes.normal.array;\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._tmpPositions = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n for (let i = 0; i < spheresCount; ++i) {\r\n normals.set(geoNormals, chunkSize * VEC_SIZE * i);\r\n }\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n const tmpPos = this._tmpPositions;\r\n const chunkSize = this._chunkSize;\r\n const geoPos = this._chunkPos;\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n const idx = i * 3;\r\n tmpPos[idx] = itemPos.x + geoPos[idx] * itemRad;\r\n tmpPos[idx + 1] = itemPos.y + geoPos[idx + 1] * itemRad;\r\n tmpPos[idx + 2] = itemPos.z + geoPos[idx + 2] * itemRad;\r\n }\r\n\r\n this._positions.set(tmpPos, chunkSize * itemIdx * VEC_SIZE);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n}\r\nexport default SimpleSpheresGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst centerPos = new THREE.Vector3();\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass Simple2CCylindersGeometry extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, 2 * instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const firstOffset = chunkSize * 2 * itemIdx * VEC_SIZE;\r\n const secondOffset = firstOffset + chunkSize * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n centerPos.lerpVectors(botPos, topPos, 0.5);\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, centerPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, firstOffset);\r\n\r\n // now shift center to get another part of the cylinder\r\n centerPos.sub(botPos);\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpArray[idx] += centerPos.x;\r\n tmpArray[idx + 1] += centerPos.y;\r\n tmpArray[idx + 2] += centerPos.z;\r\n }\r\n this._positions.set(tmpArray, secondOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, firstOffset);\r\n this._normals.set(tmpArray, secondOffset);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const first = 2 * itemIdx;\r\n super.setColor(first, colorVal1);\r\n\r\n const second = first + 1;\r\n super.setColor(second, colorVal2);\r\n }\r\n}\r\n\r\nexport default Simple2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_POINTS_COUNT_16BIT = 65536;\r\nconst PTS_PER_TRIANGLE = 3;\r\n\r\nclass CylinderBufferGeometry extends THREE.BufferGeometry {\r\n constructor(\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n ) {\r\n super();\r\n\r\n const thetaStart = 0;\r\n const thetaLength = 2 * Math.PI;\r\n\r\n this.type = 'CylinderBufferGeometry';\r\n\r\n this.parameters = {\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n };\r\n\r\n const hasTop = openEnded === false && radiusTop > 0;\r\n const hasBottom = openEnded === false && radiusBottom > 0;\r\n const vertexCount = (heightSegments + 1) * radialSegments\r\n + hasTop * (radialSegments + 1)\r\n + hasBottom * (radialSegments + 1);\r\n const facesCount = (2 * heightSegments + hasTop + hasBottom) * radialSegments;\r\n\r\n const heightHalf = height / 2;\r\n\r\n const positions = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const normals = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const indices = new THREE.Uint16BufferAttribute(utils.allocateTyped(Uint16Array, facesCount * PTS_PER_TRIANGLE), 1);\r\n\r\n const uvs = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 2), 2);\r\n console.assert(vertexCount < MAX_POINTS_COUNT_16BIT, 'DEBUG: Cylinder Geometry has too many vertices (65536 max).');\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n const tanTheta = -(radiusBottom - radiusTop) / height;\r\n\r\n // setup cylinder data\r\n for (let y = 0; y <= heightSegments; y++) {\r\n // faces\r\n if (y !== heightSegments) {\r\n for (let i = 0; i < radialSegments; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + radialSegments + i;\r\n const v3 = currVtxIdx + radialSegments + ((i + 1) % radialSegments);\r\n const v4 = currVtxIdx + ((i + 1) % radialSegments);\r\n\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n // vertices\r\n const v = y / heightSegments;\r\n const radius = v * (radiusBottom - radiusTop) + radiusTop;\r\n\r\n for (let x = 0; x < radialSegments; x++) {\r\n const u = x / radialSegments;\r\n\r\n const vx = radius * Math.sin(u * thetaLength + thetaStart);\r\n const vy = v * height - heightHalf;\r\n const vz = radius * Math.cos(u * thetaLength + thetaStart);\r\n\r\n const normal = new THREE.Vector3(\r\n vx,\r\n Math.sqrt(vx * vx + vz * vz) * tanTheta,\r\n vz,\r\n ).normalize();\r\n\r\n positions.setXYZ(currVtxIdx, vx, vy, vz);\r\n normals.setXYZ(currVtxIdx, normal.x, normal.y, normal.z);\r\n uvs.setXY(currVtxIdx, u, v);\r\n ++currVtxIdx;\r\n }\r\n }\r\n\r\n // top cap\r\n if (hasTop) {\r\n const startTIdx = currVtxIdx;\r\n const lastIdx = currVtxIdx + radialSegments;\r\n for (let fTIdx = 0; fTIdx < radialSegments; ++fTIdx) {\r\n const currSrcIdx = currVtxIdx - radialSegments;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcIdx),\r\n positions.getY(currSrcIdx),\r\n positions.getZ(currSrcIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n\r\n const nextTVtx = startTIdx + ((fTIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, currVtxIdx, nextTVtx, lastIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n ++currVtxIdx;\r\n }\r\n\r\n // bottom cap\r\n if (hasBottom) {\r\n const startBIdx = currVtxIdx;\r\n const lastBIdx = currVtxIdx + radialSegments;\r\n for (let fBIdx = 0; fBIdx < radialSegments; ++fBIdx) {\r\n const currSrcBIdx = fBIdx;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcBIdx),\r\n positions.getY(currSrcBIdx),\r\n positions.getZ(currSrcBIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n\r\n const nextBVtx = startBIdx + ((fBIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, nextBVtx, currVtxIdx, lastBIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, -heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n }\r\n\r\n this.setIndex(indices);\r\n this.setAttribute('position', positions);\r\n this.setAttribute('normal', normals);\r\n this.setAttribute('uv', uvs);\r\n }\r\n\r\n clone() {\r\n const { parameters } = this;\r\n\r\n return new CylinderBufferGeometry(\r\n parameters.radiusTop,\r\n parameters.radiusBottom,\r\n parameters.height,\r\n parameters.radialSegments,\r\n parameters.heightSegments,\r\n parameters.openEnded,\r\n );\r\n }\r\n}\r\n\r\nexport default CylinderBufferGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport CylinderBufferGeometry from './CylinderBufferGeometry';\r\n\r\nconst tmpColor = new THREE.Color();\r\nconst invMatrix = new THREE.Matrix4();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction sortNumber(a, b) {\r\n return a - b;\r\n}\r\n\r\nfunction _prepareCylinderInfo(chunkIndices) {\r\n chunkIndices.sort(sortNumber);\r\n const chunksIdx = [];\r\n const cylinderInfo = [];\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const val = chunkIndices[i];\r\n const even = (val | 0) % 2 === 0;\r\n const newPar = {\r\n first: false,\r\n second: false,\r\n };\r\n if (even) {\r\n newPar.first = true;\r\n newPar.second = i + 1 < n && chunkIndices[i + 1] === chunkIndices[i] + 1;\r\n if (newPar.second) {\r\n ++i;\r\n }\r\n } else {\r\n newPar.second = true;\r\n }\r\n chunksIdx.push(Math.floor(val / 2));\r\n cylinderInfo.push(newPar);\r\n }\r\n return { indices: chunksIdx, cylinderInfo };\r\n}\r\n\r\nfunction _assignOpacity(cylinderInfo, color1, color2) {\r\n for (let i = 0, n = cylinderInfo.length; i < n; ++i) {\r\n const info = cylinderInfo[i];\r\n if (!info.first) {\r\n color1[COLOR_SIZE * i] = -0.5;\r\n }\r\n if (!info.second) {\r\n color2[COLOR_SIZE * i] = -0.5;\r\n }\r\n }\r\n}\r\nclass Instanced2CCylindersGeometry extends THREE.InstancedBufferGeometry {\r\n constructor(instanceCount, polyComplexity, useZSprites, openEnded) {\r\n super();\r\n this._useZSprites = useZSprites;\r\n this._cylGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new CylinderBufferGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, openEnded);\r\n this._init(instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n this._collisionGeo = new Simple2CCylindersGeometry(instanceCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const matrix = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n let me = matrix.elements;\r\n const mtxOffset = itemIdx * OFFSET_SIZE;\r\n\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, itemRad);\r\n setArrayXYZW(this._matVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._matVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._matVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n\r\n if (this._useZSprites) {\r\n invMatrix.copy(matrix).invert();\r\n me = invMatrix.elements;\r\n setArrayXYZW(this._invmatVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._invmatVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._invmatVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n }\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const colorIdx = itemIdx * COLOR_SIZE;\r\n tmpColor.set(colorVal1);\r\n setArrayXYZ(this._color1, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n tmpColor.set(colorVal2);\r\n setArrayXYZ(this._color2, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n computeBoundingSphere() {\r\n this._collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = this._collisionGeo.boundingSphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n this._collisionGeo.computeBoundingBox();\r\n this.boundingBox = this._collisionGeo.boundingBox;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('matVector1').needsUpdate = true;\r\n this.getAttribute('matVector2').needsUpdate = true;\r\n this.getAttribute('matVector3').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('color2').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n if (this._useZSprites) {\r\n this.getAttribute('invmatVector1').needsUpdate = true;\r\n this.getAttribute('invmatVector2').needsUpdate = true;\r\n this.getAttribute('invmatVector3').needsUpdate = true;\r\n }\r\n\r\n this._collisionGeo.finishUpdate();\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[Math.floor(chunkIndices[i] / 2)] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const info = _prepareCylinderInfo(chunkIndices);\r\n const cylinderIndices = info.indices;\r\n const instanceCount = cylinderIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n copySubArrays(this._matVector1, geom._matVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector2, geom._matVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector3, geom._matVector3, cylinderIndices, OFFSET_SIZE);\r\n\r\n if (this._useZSprites) {\r\n copySubArrays(this._invmatVector1, geom._invmatVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector2, geom._invmatVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector3, geom._invmatVector3, cylinderIndices, OFFSET_SIZE);\r\n }\r\n\r\n copySubArrays(this._color1, geom._color1, cylinderIndices, COLOR_SIZE);\r\n copySubArrays(this._color2, geom._color2, cylinderIndices, COLOR_SIZE);\r\n _assignOpacity(info.cylinderInfo, geom._color1, geom._color2);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n getGeoParams() {\r\n return this._cylGeometry.parameters;\r\n }\r\n\r\n _init(instanceCount, cylinderGeo, useZSprites) {\r\n this.copy(cylinderGeo);\r\n this._matVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._color1 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n this._color2 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, instanceCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('matVector1', new THREE.InstancedBufferAttribute(this._matVector1, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector2', new THREE.InstancedBufferAttribute(this._matVector2, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector3', new THREE.InstancedBufferAttribute(this._matVector3, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._color1, COLOR_SIZE, false, 1));\r\n this.setAttribute('color2', new THREE.InstancedBufferAttribute(this._color2, COLOR_SIZE, false, 1));\r\n\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(this._alpha, 1, false, 1));\r\n\r\n if (useZSprites) {\r\n this._invmatVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n\r\n this.setAttribute(\r\n 'invmatVector1',\r\n new THREE.InstancedBufferAttribute(this._invmatVector1, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector2',\r\n new THREE.InstancedBufferAttribute(this._invmatVector2, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector3',\r\n new THREE.InstancedBufferAttribute(this._invmatVector3, OFFSET_SIZE, false, 1),\r\n );\r\n }\r\n }\r\n}\r\n\r\nexport default Instanced2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst TRI_SIZE = 3;\r\nconst tmpPrev = new THREE.Vector3();\r\nconst tmpNext = new THREE.Vector3();\r\nconst tmpRes = new THREE.Vector3();\r\nconst simpleNormal = new THREE.Vector3(1.0, 0.0, 0.0);\r\nconst normalOnCut = new THREE.Vector3();\r\nconst nearRingPt = new THREE.Vector3();\r\n\r\nfunction _createExtrudedChunkGeometry(shape, ringsCount) {\r\n const geo = new THREE.BufferGeometry();\r\n const ptsCount = shape.length;\r\n const totalPts = ptsCount * ringsCount;\r\n const type = totalPts <= 65536 ? Uint16Array : Uint32Array;\r\n const facesPerChunk = (ringsCount - 1) * ptsCount * 2;\r\n const indices = new THREE.BufferAttribute(utils.allocateTyped(type, facesPerChunk * TRI_SIZE), 1);\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n for (let y = 0; y < ringsCount; y++) {\r\n // faces\r\n if (y !== ringsCount - 1) {\r\n for (let i = 0; i < ptsCount; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + ptsCount + i;\r\n const v3 = currVtxIdx + ptsCount + ((i + 1) % ptsCount);\r\n const v4 = currVtxIdx + ((i + 1) % ptsCount);\r\n\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n currVtxIdx += ptsCount;\r\n }\r\n\r\n geo.setIndex(indices);\r\n const pos = utils.allocateTyped(Float32Array, totalPts * VEC_SIZE);\r\n geo.setAttribute('position', new THREE.BufferAttribute(pos, VEC_SIZE));\r\n\r\n geo._positions = shape;\r\n\r\n return geo;\r\n}\r\n\r\nclass ExtrudedObjectsGeometry extends ChunkedObjectsGeometry {\r\n constructor(shape, ringsCount, chunksCount) {\r\n const chunkGeo = _createExtrudedChunkGeometry(shape, ringsCount);\r\n super(chunkGeo, chunksCount);\r\n this._ringsCount = ringsCount;\r\n\r\n const tmpShape = this._tmpShape = [];\r\n for (let i = 0; i < shape.length; ++i) {\r\n tmpShape[i] = new THREE.Vector3();\r\n }\r\n }\r\n\r\n setItem(itemIdx, matrices, hasSlope = false, hasCut = false) {\r\n const ptsCount = this._chunkGeo._positions.length;\r\n const ringsCount = this._ringsCount;\r\n const chunkStartIdx = ptsCount * this._ringsCount * itemIdx * VEC_SIZE;\r\n\r\n this._setPoints(matrices, ptsCount, ringsCount, chunkStartIdx);\r\n\r\n if (hasSlope) {\r\n this._setSlopeNormals(ptsCount, ringsCount, chunkStartIdx);\r\n } else {\r\n this._setBaseNormals(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n\r\n if (hasCut) {\r\n this._addCut(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n }\r\n\r\n _setPoints(matrices, ptsCount, ringsCount, chunkStartIdx) {\r\n const tmpShape = this._tmpShape;\r\n const positions = this._positions;\r\n const shape = this._chunkGeo._positions;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i) {\r\n const mtx = matrices[i];\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpShape[j].copy(shape[j]).applyMatrix4(mtx).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _setBaseNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, false);\r\n }\r\n }\r\n\r\n _setSlopeNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const normals = this._normals;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First ring\r\n // In all cases, besides cut, second ring is coincident to first. So values of first ring's normals doesn't\r\n // matter (In the cut case special handler will be applied later and will set them to correct values)\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n simpleNormal.toArray(normals, vtxIdx);\r\n }\r\n // second ring\r\n // If it isn't first Item we take normals' values from the last ring of the previous item (these rings are coincident)\r\n // else we count normals' values based on next ring information\r\n if (vtxIdx - 2 * nPtsInRing > 0) {\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(normals, vtxIdx - 2 * nPtsInRing).toArray(normals, vtxIdx);\r\n }\r\n } else {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, +nPtsInRing);\r\n vtxIdx += nPtsInRing;\r\n }\r\n // other rings\r\n // we count normals' values based on previous ring information\r\n for (let i = 2; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, -nPtsInRing);\r\n }\r\n }\r\n\r\n // Counting normals:\r\n // - Slope\r\n // Radius changes throught part => normals aren't parallel with the plane contains section points\r\n // normal = vTangentInSectionPlane x vToSuchPointInPrevSection (all vectors are scaled for being 1 in length)\r\n // - No slope\r\n // Radius doesn't change throught part => normals are parallel with the plane contains section points\r\n // normal = vToPrevPointInSection + vToNextPointInSection (all vectors are scaled for being 1 in length)\r\n _countNormalsInRing(ptsCount, vtxIdx, isSlope, shiftToExtraPt) {\r\n const tmpShape = this._tmpShape;\r\n const normals = this._normals;\r\n\r\n tmpShape[0].fromArray(this._positions, vtxIdx);\r\n tmpShape[ptsCount - 1].fromArray(this._positions, vtxIdx + (ptsCount - 1) * VEC_SIZE);\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n if (j < ptsCount - 1) {\r\n tmpShape[j + 1].fromArray(this._positions, vtxIdx + VEC_SIZE);\r\n }\r\n\r\n if (isSlope) {\r\n nearRingPt.fromArray(this._positions, vtxIdx + shiftToExtraPt);\r\n\r\n tmpPrev.subVectors(tmpShape[(j + ptsCount - 1) % ptsCount], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], nearRingPt).normalize();\r\n tmpRes.crossVectors(tmpNext, tmpPrev).normalize().toArray(normals, vtxIdx);\r\n } else {\r\n tmpPrev.subVectors(tmpShape[j], tmpShape[(j + ptsCount - 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpRes.addVectors(tmpPrev, tmpNext).normalize().toArray(normals, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _addCut(ptsCount, ringsCount, chunkStartIdx) {\r\n // Nothing to do if item is flat or only line\r\n if (ptsCount < 3 || ringsCount < 2) {\r\n return;\r\n }\r\n const positions = this._positions;\r\n const normals = this._normals;\r\n const tmpShape = this._tmpShape;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n // Normal to the cut plane is equal to cross product of two vectors which are lying in it\r\n tmpShape[0].fromArray(positions, chunkStartIdx);\r\n tmpShape[1].fromArray(positions, chunkStartIdx + VEC_SIZE);\r\n tmpShape[2].fromArray(positions, chunkStartIdx + 2 * VEC_SIZE);\r\n\r\n tmpPrev.subVectors(tmpShape[1], tmpShape[0]).normalize();\r\n tmpNext.subVectors(tmpShape[1], tmpShape[2]).normalize();\r\n normalOnCut.crossVectors(tmpPrev, tmpNext).normalize();\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First and second rings normals' values are equal to value of normal to the cutting plane\r\n for (let j = 0; j < ptsCount * 2; ++j, vtxIdx += VEC_SIZE) {\r\n normalOnCut.toArray(normals, vtxIdx);\r\n }\r\n if (ringsCount > 2) {\r\n // Third ring points are coincident to first ring points, but have different normals. It makes sharp angle near cut\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(positions, vtxIdx - nPtsInRing).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default ExtrudedObjectsGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VERTEX_PER_SEGMENT = 4;\r\nconst POS_SIZE = 4;\r\nconst DIR_SIZE = 3;\r\nconst COL_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\nconst direction = new THREE.Vector3();\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction getSubset(arr, startSegmentIdx, segmentsCount, elemSize) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT;\r\n const end = start + segmentsCount * VERTEX_PER_SEGMENT;\r\n return arr.subarray(start * elemSize, end * elemSize);\r\n}\r\n\r\n/**\r\n * This class represents lines geometry which consists of screen-aligned narrow quad of variable width.\r\n *\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * collision geometry.\r\n */\r\n\r\nclass ThickLinesGeometry extends THREE.BufferGeometry {\r\n constructor(segmentsCount) {\r\n super();\r\n this._initVertices(segmentsCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n this.getAttribute('direction').needsUpdate = true;\r\n }\r\n\r\n setColor(segmentIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n setSegment(segmentIdx, pos1, pos2) {\r\n direction.subVectors(pos1, pos2);\r\n direction.normalize();\r\n const positions = this._positions;\r\n const directions = this._directions;\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n let dirIdx = segmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n }\r\n\r\n setOpacity(startSegIdx, endSegIdx, value) {\r\n const start = startSegIdx * VERTEX_PER_SEGMENT;\r\n const end = endSegIdx * VERTEX_PER_SEGMENT;\r\n _.fill(this.alpha, value, end, start);\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubsetSegments(startSegmentIdx, segmentsCount) {\r\n return [\r\n getSubset(this._positions, startSegmentIdx, segmentsCount, POS_SIZE),\r\n getSubset(this._directions, startSegmentIdx, segmentsCount, DIR_SIZE),\r\n ];\r\n }\r\n\r\n getSubsetColors(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._colors, startSegmentIdx, segmentsCount, COL_SIZE);\r\n }\r\n\r\n getSubsetOpacities(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._alpha, startSegmentIdx, segmentsCount, 1);\r\n }\r\n\r\n getNumVertexPerSegment() {\r\n return VERTEX_PER_SEGMENT;\r\n }\r\n\r\n getPositionSize() {\r\n return POS_SIZE;\r\n }\r\n\r\n setSegments(startSegmentIdx, positions) {\r\n const startPos = startSegmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n if (positions instanceof Array && positions.length === 2) {\r\n this._positions.set(positions[0], startPos);\r\n const startDir = startSegmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n this._directions.set(positions[1], startDir); // dirs are geo part of vertex\r\n } else {\r\n this._positions.set(positions, startPos);\r\n }\r\n }\r\n\r\n setColors(startSegmentIdx, colors) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n this._colors.set(colors, start);\r\n }\r\n\r\n _initVertices(segmentsCount) {\r\n this._buffersSize = segmentsCount * VERTEX_PER_SEGMENT;\r\n const pointsCount = this._buffersSize;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, segmentsCount * 6);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * POS_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * COL_SIZE);\r\n this._directions = utils.allocateTyped(Float32Array, pointsCount * DIR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n const index = this._index;\r\n let indexOffset = 0;\r\n let pointOffset = 0;\r\n for (let j = 0; j < segmentsCount; j++, indexOffset += 6, pointOffset += VERTEX_PER_SEGMENT) {\r\n index[indexOffset] = pointOffset;\r\n index[indexOffset + 1] = pointOffset + 1;\r\n index[indexOffset + 2] = pointOffset + 3;\r\n index[indexOffset + 3] = pointOffset;\r\n index[indexOffset + 4] = pointOffset + 2;\r\n index[indexOffset + 5] = pointOffset + 3;\r\n }\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, POS_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, COL_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n this.setAttribute('direction', new THREE.BufferAttribute(this._directions, DIR_SIZE));\r\n }\r\n}\r\n\r\nexport default ThickLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport BaseLinesGeometry from './ThickLinesGeometry';\r\n\r\n/**\r\n * This class represents geometry which consists lines. This can build bounding volumes\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n */\r\nclass LinesGeometry extends BaseLinesGeometry {\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n if (boundingBox) {\r\n boundingBox.getCenter(center);\r\n }\r\n const positions = this._positions;\r\n const sphere = this.boundingSphere || new THREE.Sphere();\r\n const size = this._positions.length;\r\n const pos = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n pos.set(positions[i], positions[i + 1], positions[i + 2]);\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n sphere.set(center, Math.sqrt(radiusSquared));\r\n this.boundingSphere = sphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n const positions = this._positions;\r\n const box = new THREE.Box3();\r\n const size = this._positions.length;\r\n const tmpVec = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n tmpVec.set(positions[i], positions[i + 1], positions[i + 2]);\r\n box.expandByPoint(tmpVec);\r\n }\r\n this.boundingBox = box;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n}\r\n\r\nexport default LinesGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass CylinderCollisionGeo extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const itemOffset = chunkSize * itemIdx * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, itemOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, itemOffset);\r\n }\r\n}\r\nexport default CylinderCollisionGeo;\r\n","import LinesGeometry from './LinesGeometry';\r\nimport CylinderCollisionGeo from './CylinderCollisionGeo';\r\n\r\nconst COLLISION_RAD = 0.1;\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n *\r\n * @param {number} chunksCount Total chunks count.\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * @param {boolean} enableCollision Enable or disable collision where each segment is\r\n * a collidable cylinder.\r\n * collision geometry.\r\n */\r\nclass ChunkedLinesGeometry extends LinesGeometry {\r\n constructor(chunksCount, segmentsCount, enableCollision) {\r\n super(chunksCount * segmentsCount);\r\n this._init(segmentsCount);\r\n this._collisionGeo = enableCollision ? new CylinderCollisionGeo(chunksCount * segmentsCount, 3) : null;\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = collisionGeo.boundingSphere;\r\n return;\r\n }\r\n super.computeBoundingSphere();\r\n }\r\n\r\n computeBoundingBox() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingBox();\r\n this.boundingBox = collisionGeo.boundingBox;\r\n return;\r\n }\r\n super.computeBoundingBox();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const collisionGeo = this._collisionGeo;\r\n if (!collisionGeo) {\r\n return;\r\n }\r\n const segCount = this._chunkSize;\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n for (let i = 0, n = intersects.length; i < n; ++i) {\r\n let { chunkIdx } = intersects[i];\r\n if (chunkIdx === undefined) {\r\n continue;\r\n }\r\n chunkIdx = (chunkIdx / segCount) | 0;\r\n intersects[i].chunkIdx = chunkIdx;\r\n }\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n super.setColor(i, colorVal);\r\n }\r\n }\r\n\r\n setSegment(chunkIdx, segIdx, pos1, pos2) {\r\n const chunkSize = this._chunkSize;\r\n const idx = chunkIdx * chunkSize + segIdx;\r\n super.setSegment(idx, pos1, pos2);\r\n if (this._collisionGeo) {\r\n this._collisionGeo.setItem(chunkIdx * chunkSize + segIdx, pos1, pos2, COLLISION_RAD);\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n super.setOpacity(left, left + chunkSize - 1, value);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const chunkSize = this._chunkSize;\r\n const subset = new ChunkedLinesGeometry(instanceCount, chunkSize, false);\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const startSegIdx = chunkIndices[i] * chunkSize;\r\n subset.setSegments(dstPtOffset, this.getSubsetSegments(startSegIdx, chunkSize));\r\n subset.setColors(dstPtOffset, this.getSubsetColors(startSegIdx, chunkSize));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(chunkSize) {\r\n this._chunkSize = chunkSize;\r\n }\r\n}\r\n\r\nexport default ChunkedLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport LinesGeometry from './LinesGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\n\r\nconst COLLISION_RAD = 0.3;\r\nconst tmpVector = new THREE.Vector3();\r\n\r\nclass TwoColorLinesGeometry extends LinesGeometry {\r\n constructor(segmentsCount) {\r\n super(segmentsCount * 2);\r\n this._init(segmentsCount);\r\n this._collisionGeo = new Simple2CCylindersGeometry(segmentsCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos) {\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, COLLISION_RAD);\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n tmpVector.lerpVectors(botPos, topPos, 0.5);\r\n super.setSegment(offset, botPos, tmpVector);\r\n super.setSegment(offset + 1, tmpVector, topPos);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n super.setColor(offset, colorVal1);\r\n super.setColor(offset + 1, colorVal2);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n if (this._collisionGeo) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n getSubset(segmentIndices) {\r\n const instanceCount = segmentIndices.length;\r\n const subset = new TwoColorLinesGeometry(instanceCount, false);\r\n for (let i = 0, n = instanceCount; i < n; ++i) {\r\n const startSegIdx = segmentIndices[i];\r\n subset.setSegments(i, this.getSubsetSegments(startSegIdx, 1));\r\n subset.setColors(i, this.getSubsetColors(startSegIdx, 1));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(segmentsCount) {\r\n this._segCounts = segmentsCount * 2;\r\n }\r\n}\r\n// (???)parent = LinesGeometry.prototype;\r\n\r\nexport default TwoColorLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst vectors = [\r\n new THREE.Vector3(1, 0, 0),\r\n new THREE.Vector3(-1, 0, 0),\r\n new THREE.Vector3(0, 1, 0),\r\n new THREE.Vector3(0, -1, 0),\r\n new THREE.Vector3(0, 0, 1),\r\n new THREE.Vector3(0, 0, -1),\r\n];\r\nconst vecCount = vectors.length;\r\nconst tempPos1 = new THREE.Vector3();\r\nconst tempPos2 = new THREE.Vector3();\r\n\r\nclass CrossGeometry extends SphereCollisionGeo(ChunkedLinesGeometry) {\r\n constructor(chunksCount) {\r\n super(chunksCount, chunksCount, (vecCount / 2) | 0, false);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n\r\n for (let i = 0; i < vecCount / 2; ++i) {\r\n const first = i * 2;\r\n tempPos1.x = itemPos.x + vectors[first].x * itemRad;\r\n tempPos1.y = itemPos.y + vectors[first].y * itemRad;\r\n tempPos1.z = itemPos.z + vectors[first].z * itemRad;\r\n const second = first + 1;\r\n tempPos2.x = itemPos.x + vectors[second].x * itemRad;\r\n tempPos2.y = itemPos.y + vectors[second].y * itemRad;\r\n tempPos2.z = itemPos.z + vectors[second].z * itemRad;\r\n this.setSegment(itemIdx, i, tempPos1, tempPos2);\r\n }\r\n }\r\n}\r\nexport default CrossGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst POS_RAD_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This is a base class for isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\nclass IsoSurfaceGeometry extends THREE.BufferGeometry {\r\n constructor(spheresCount, opts) {\r\n super();\r\n\r\n this._opts = opts;\r\n this.zClip = this._opts.zClip;\r\n this._posRad = utils.allocateTyped(Float32Array, spheresCount * POS_RAD_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n }\r\n\r\n setItem(chunkIdx, pos, radius) {\r\n const posRad = this._posRad;\r\n let idx = POS_RAD_SIZE * chunkIdx;\r\n posRad[idx++] = pos.x;\r\n posRad[idx++] = pos.y;\r\n posRad[idx++] = pos.z;\r\n posRad[idx] = radius;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n let idx = COLOR_SIZE * chunkIdx;\r\n colors[idx++] = tmpColor.r;\r\n colors[idx++] = tmpColor.g;\r\n colors[idx] = tmpColor.b;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n finishUpdate() {\r\n this._build();\r\n }\r\n\r\n setOpacity() {\r\n // not implemented\r\n }\r\n\r\n raycast() {\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\nexport default IsoSurfaceGeometry;\r\n","import utils from '../../utils';\r\n\r\n/**\r\n * Class for marching cube\r\n * Stores 8 points and 8 float values are stored together in linear array\r\n * Int values for has intersection or not - in integer32 linear array\r\n * Int values for bits flags - in integer32 linear array\r\n *\r\n */\r\nclass IsoSurfaceMarchCube {\r\n constructor() {\r\n this.pointsValuesLinear = null;\r\n this.hasIntersection = null;\r\n this.bitsInside = null;\r\n }\r\n\r\n create(numCellsPerSide) {\r\n const vx7000000 = 0x7000000;\r\n const n3 = numCellsPerSide * numCellsPerSide * numCellsPerSide;\r\n if (n3 > vx7000000) {\r\n throw new Error('Too large cube dimension: lead to memory huge uasge');\r\n }\r\n this.pointsValuesLinear = utils.allocateTyped(Float32Array, (2 << (2 + 2)) * n3);\r\n this.hasIntersection = utils.allocateTyped(Int32Array, n3);\r\n this.bitsInside = utils.allocateTyped(Int32Array, n3);\r\n return 0;\r\n }\r\n\r\n destroy() {\r\n this.bitsInside = null;\r\n this.hasIntersection = null;\r\n this.pointsValuesLinear = null;\r\n }\r\n}\r\n\r\nIsoSurfaceMarchCube.prototype.striIndicesMarchCube = [\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 0, 2, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 8, 3, 2, 10, 8, 10, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 8, 11, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 2, 1, 9, 11, 9, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 1, 11, 10, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 10, 1, 0, 8, 10, 8, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 9, 0, 3, 11, 9, 11, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 7, 3, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 1, 9, 4, 7, 1, 7, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 4, 7, 3, 0, 4, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 9, 0, 2, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 8, 4, 7, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 4, 7, 11, 2, 4, 2, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 8, 4, 7, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1, -1, -1, -1, -1,\r\n 3, 10, 1, 3, 11, 10, 7, 8, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4, -1, -1, -1, -1,\r\n 4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 4, 7, 11, 4, 11, 9, 9, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 1, 5, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 5, 4, 8, 3, 5, 3, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 10, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 2, 10, 5, 4, 2, 4, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8, -1, -1, -1, -1,\r\n 9, 5, 4, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 0, 8, 11, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 0, 1, 5, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5, -1, -1, -1, -1,\r\n 10, 3, 11, 10, 1, 3, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10, -1, -1, -1, -1,\r\n 5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 5, 4, 8, 5, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 5, 7, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 3, 0, 9, 5, 3, 5, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 8, 0, 1, 7, 1, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 9, 5, 7, 10, 1, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3, -1, -1, -1, -1,\r\n 8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2, -1, -1, -1, -1,\r\n 2, 10, 5, 2, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 9, 5, 7, 8, 9, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7, -1, -1, -1, -1,\r\n 11, 2, 1, 11, 1, 7, 7, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11, -1, -1, -1, -1,\r\n 5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0, -1,\r\n 11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0, -1,\r\n 11, 10, 5, 7, 11, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 1, 9, 8, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 2, 6, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 1, 2, 6, 3, 0, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 6, 5, 9, 0, 6, 0, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 0, 8, 11, 2, 0, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11, -1, -1, -1, -1,\r\n 6, 3, 11, 6, 5, 3, 5, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9, -1, -1, -1, -1,\r\n 6, 5, 9, 6, 9, 11, 11, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 4, 7, 3, 6, 5, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 5, 10, 6, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 6, 1, 2, 6, 5, 1, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7, -1, -1, -1, -1,\r\n 8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6, -1, -1, -1, -1,\r\n 7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9, -1,\r\n 3, 11, 2, 7, 8, 4, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1,\r\n 9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6, -1,\r\n 8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11, -1,\r\n 0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7, -1,\r\n 6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9, -1, -1, -1, -1,\r\n 10, 4, 9, 6, 4, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 10, 6, 4, 9, 10, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 0, 1, 10, 6, 0, 6, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 1, 4, 9, 1, 2, 4, 2, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4, -1, -1, -1, -1,\r\n 0, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 2, 8, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 4, 9, 10, 6, 4, 11, 2, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6, -1, -1, -1, -1,\r\n 3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1, -1,\r\n 9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3, -1, -1, -1, -1,\r\n 8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1, -1,\r\n 3, 11, 6, 3, 6, 0, 0, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 4, 8, 11, 6, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 10, 6, 7, 8, 10, 8, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10, -1, -1, -1, -1,\r\n 10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0, -1, -1, -1, -1,\r\n 10, 6, 7, 10, 7, 1, 1, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9, -1,\r\n 7, 8, 0, 7, 0, 6, 6, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 3, 2, 6, 7, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7, -1,\r\n 1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11, -1,\r\n 11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1, -1, -1, -1, -1,\r\n 8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6, -1,\r\n 0, 9, 1, 11, 6, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0, -1, -1, -1, -1,\r\n 7, 11, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 9, 8, 3, 1, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 8, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 9, 0, 2, 10, 9, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8, -1, -1, -1, -1,\r\n 7, 2, 3, 6, 2, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 0, 8, 7, 6, 0, 6, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 7, 6, 2, 3, 7, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6, -1, -1, -1, -1,\r\n 10, 7, 6, 10, 1, 7, 1, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8, -1, -1, -1, -1,\r\n 0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7, -1, -1, -1, -1,\r\n 7, 6, 10, 7, 10, 8, 8, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 8, 4, 11, 8, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 3, 0, 6, 0, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 6, 11, 8, 4, 6, 9, 0, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6, -1, -1, -1, -1,\r\n 6, 8, 4, 6, 11, 8, 2, 10, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6, -1, -1, -1, -1,\r\n 4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9, -1, -1, -1, -1,\r\n 10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3, -1,\r\n 8, 2, 3, 8, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8, -1, -1, -1, -1,\r\n 1, 9, 4, 1, 4, 2, 2, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1, -1, -1, -1, -1,\r\n 10, 1, 0, 10, 0, 6, 6, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3, -1,\r\n 10, 9, 4, 6, 10, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 5, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 1, 5, 4, 0, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5, -1, -1, -1, -1,\r\n 9, 5, 4, 10, 1, 2, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5, -1, -1, -1, -1,\r\n 7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2, -1, -1, -1, -1,\r\n 3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6, -1,\r\n 7, 2, 3, 7, 6, 2, 5, 4, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7, -1, -1, -1, -1,\r\n 3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0, -1, -1, -1, -1,\r\n 6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8, -1,\r\n 9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7, -1, -1, -1, -1,\r\n 1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4, -1,\r\n 4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10, -1,\r\n 7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10, -1, -1, -1, -1,\r\n 6, 9, 5, 6, 11, 9, 11, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5, -1, -1, -1, -1,\r\n 0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11, -1, -1, -1, -1,\r\n 6, 11, 3, 6, 3, 5, 5, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6, -1, -1, -1, -1,\r\n 0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10, -1,\r\n 11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5, -1,\r\n 6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3, -1, -1, -1, -1,\r\n 5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2, -1, -1, -1, -1,\r\n 9, 5, 6, 9, 6, 0, 0, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8, -1,\r\n 1, 5, 6, 2, 1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6, -1,\r\n 10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0, -1, -1, -1, -1,\r\n 0, 3, 8, 5, 6, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 5, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 7, 5, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 11, 7, 5, 8, 3, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 11, 7, 5, 10, 11, 1, 9, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1, -1, -1, -1, -1,\r\n 11, 1, 2, 11, 7, 1, 7, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11, -1, -1, -1, -1,\r\n 9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7, -1, -1, -1, -1,\r\n 7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2, -1,\r\n 2, 5, 10, 2, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2, -1, -1, -1, -1,\r\n 9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2, -1,\r\n 1, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 7, 0, 7, 1, 1, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 3, 9, 3, 5, 5, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 7, 5, 9, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 8, 4, 5, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5, -1, -1, -1, -1,\r\n 10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4, -1,\r\n 2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8, -1, -1, -1, -1,\r\n 0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11, -1,\r\n 0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5, -1,\r\n 9, 4, 5, 2, 11, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4, -1, -1, -1, -1,\r\n 5, 10, 2, 5, 2, 4, 4, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9, -1,\r\n 5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 3, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 5, 1, 0, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5, -1, -1, -1, -1,\r\n 9, 4, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 11, 7, 4, 9, 11, 9, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11, -1, -1, -1, -1,\r\n 1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11, -1, -1, -1, -1,\r\n 3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4, -1,\r\n 4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2, -1, -1, -1, -1,\r\n 9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3, -1,\r\n 11, 7, 4, 11, 4, 2, 2, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4, -1, -1, -1, -1,\r\n 2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9, -1, -1, -1, -1,\r\n 9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7, -1,\r\n 3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10, -1,\r\n 1, 10, 2, 8, 7, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 7, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1, -1, -1, -1, -1,\r\n 4, 0, 3, 7, 4, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 8, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1,\r\n 0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1,\r\n 1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n];\r\n\r\nexport default IsoSurfaceMarchCube;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport utils from '../../utils';\r\n\r\nconst edgeTable = [\r\n 0x0, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c,\r\n 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00,\r\n 0x190, 0x99, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c,\r\n 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90,\r\n 0x230, 0x339, 0x33, 0x13a, 0x636, 0x73f, 0x435, 0x53c,\r\n 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30,\r\n 0x3a0, 0x2a9, 0x1a3, 0xaa, 0x7a6, 0x6af, 0x5a5, 0x4ac,\r\n 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0,\r\n 0x460, 0x569, 0x663, 0x76a, 0x66, 0x16f, 0x265, 0x36c,\r\n 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60,\r\n 0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0xff, 0x3f5, 0x2fc,\r\n 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0,\r\n 0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x55, 0x15c,\r\n 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950,\r\n 0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0xcc,\r\n 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0,\r\n 0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc,\r\n 0xcc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0,\r\n 0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c,\r\n 0x15c, 0x55, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650,\r\n 0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc,\r\n 0x2fc, 0x3f5, 0xff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0,\r\n 0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c,\r\n 0x36c, 0x265, 0x16f, 0x66, 0x76a, 0x663, 0x569, 0x460,\r\n 0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac,\r\n 0x4ac, 0x5a5, 0x6af, 0x7a6, 0xaa, 0x1a3, 0x2a9, 0x3a0,\r\n 0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c,\r\n 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x33, 0x339, 0x230,\r\n 0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c,\r\n 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x99, 0x190,\r\n 0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c,\r\n 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x0];\r\n\r\nfunction _voxelGradientFast(v, point, grad) {\r\n const g = v.getValue(point.x, point.y, point.z);\r\n grad.set(g[0], g[1], g[2]);\r\n}\r\n\r\n// Helper class GridCell\r\nclass GridCell {\r\n constructor() {\r\n this._arrSize = 8;\r\n this.p = new Array(this._arrSize);\r\n this.g = new Array(this._arrSize);\r\n this.val = new Array(this._arrSize);\r\n for (let i = 0; i < this._arrSize; ++i) {\r\n this.p[i] = new THREE.Vector3();\r\n this.g[i] = new THREE.Vector3();\r\n }\r\n this.cubeIndex = 0;\r\n }\r\n}\r\n\r\n// Helper class Triangle\r\nclass Triangle {\r\n constructor() {\r\n this.a = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.b = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.c = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n }\r\n}\r\n\r\nfunction createArray(arrSize) {\r\n const arr = new Array(arrSize);\r\n for (let i = 0; i < arrSize; ++i) {\r\n arr[i] = new THREE.Vector3();\r\n }\r\n\r\n return arr;\r\n}\r\n\r\nclass IsoSurface {\r\n constructor() {\r\n this._numTriangles = 0;\r\n this._numVertices = 0;\r\n this._position = [];\r\n this._normals = [];\r\n this._colors = null;\r\n this._indices = [];\r\n this._volumetricData = null;\r\n this._xAxis = new THREE.Vector3();\r\n this._yAxis = new THREE.Vector3();\r\n this._zAxis = new THREE.Vector3();\r\n this._xDir = new THREE.Vector3();\r\n this._yDir = new THREE.Vector3();\r\n this._zDir = new THREE.Vector3();\r\n }\r\n\r\n _prepareAxesAndDirs() {\r\n const volData = this._volumetricData;\r\n\r\n const cellSize = volData.getCellSize();\r\n\r\n // calculate cell axes\r\n const xAxis = this._xAxis;\r\n const yAxis = this._yAxis;\r\n const zAxis = this._zAxis;\r\n const xDir = this._xDir;\r\n const yDir = this._yDir;\r\n const zDir = this._zDir;\r\n\r\n xAxis.set(cellSize.x, 0, 0);\r\n yAxis.set(0, cellSize.y, 0);\r\n zAxis.set(0, 0, cellSize.z);\r\n\r\n xDir.set(1, 0, 0);\r\n yDir.set(0, 1, 0);\r\n zDir.set(0, 0, 1);\r\n\r\n // flip normals if coordinate system is in the wrong handedness\r\n const tmp = new THREE.Vector3();\r\n tmp.crossVectors(xDir, yDir);\r\n if (tmp.dot(zDir) < 0) {\r\n xDir.negate();\r\n yDir.negate();\r\n zDir.negate();\r\n }\r\n\r\n // check that the grid is in the all-positive octant of the coordinate system\r\n if (xDir.x < 0 || xDir.y < 0 || xDir.z < 0\r\n || yDir.x < 0 || yDir.y < 0 || yDir.z < 0\r\n || zDir.x < 0 || zDir.y < 0 || zDir.z < 0) {\r\n return false;\r\n }\r\n\r\n // check that the grid is axis-aligned\r\n const notZero = (axe) => Math.abs(axe) > Number.EPSILON;\r\n return !(notZero(xAxis.y) || notZero(xAxis.z)\r\n || notZero(yAxis.x) || notZero(yAxis.z)\r\n || notZero(zAxis.x) || notZero(zAxis.y));\r\n }\r\n\r\n _vertexInterp(isoLevel, grid, ind1, ind2, vertex, normal) {\r\n const p1 = grid.p[ind1];\r\n const p2 = grid.p[ind2];\r\n const n1 = grid.g[ind1];\r\n const n2 = grid.g[ind2];\r\n const valP1 = grid.val[ind1];\r\n const valP2 = grid.val[ind2];\r\n const isoDiffP1 = isoLevel - valP1;\r\n const diffValP2P1 = valP2 - valP1;\r\n\r\n let mu = 0.0;\r\n\r\n if (Math.abs(diffValP2P1) > 0.0) {\r\n mu = isoDiffP1 / diffValP2P1;\r\n }\r\n mu = mu > 1.0 ? 1.0 : mu;\r\n vertex.lerpVectors(p1, p2, mu);\r\n normal.lerpVectors(n1, n2, mu);\r\n }\r\n\r\n static _triTable = IsoSurfaceMarchCube.prototype.striIndicesMarchCube;\r\n\r\n static _arrSize = 12;\r\n\r\n static _firstIndices = [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3];\r\n\r\n static _secondIndices = [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7];\r\n\r\n static _vertexList = createArray(IsoSurface._arrSize);\r\n\r\n static _normalList = createArray(IsoSurface._arrSize);\r\n\r\n _polygonize(grid, isoLevel, triangles) {\r\n const { cubeIndex } = grid;\r\n let i = 0;\r\n const arrSize = IsoSurface._arrSize;\r\n const firstIndices = IsoSurface._firstIndices;\r\n const secondIndices = IsoSurface._secondIndices;\r\n const vertexList = IsoSurface._vertexList;\r\n const normalList = IsoSurface._normalList;\r\n\r\n for (; i < arrSize; ++i) {\r\n if (edgeTable[cubeIndex] & (1 << i)) {\r\n this._vertexInterp(\r\n isoLevel,\r\n grid,\r\n firstIndices[i],\r\n secondIndices[i],\r\n vertexList[i],\r\n normalList[i],\r\n );\r\n }\r\n }\r\n\r\n let triCount = 0;\r\n const triTblIdx = cubeIndex * 16;\r\n const triTable = IsoSurface._triTable;\r\n\r\n for (i = 0; triTable[triTblIdx + i] !== -1; i += 3) {\r\n triangles[triCount].a.p.copy(vertexList[triTable[triTblIdx + i]]);\r\n triangles[triCount].a.n.copy(normalList[triTable[triTblIdx + i]]);\r\n\r\n triangles[triCount].b.p.copy(vertexList[triTable[triTblIdx + i + 1]]);\r\n triangles[triCount].b.n.copy(normalList[triTable[triTblIdx + i + 1]]);\r\n\r\n triangles[triCount].c.p.copy(vertexList[triTable[triTblIdx + i + 2]]);\r\n triangles[triCount].c.n.copy(normalList[triTable[triTblIdx + i + 2]]);\r\n ++triCount;\r\n }\r\n\r\n return triCount;\r\n }\r\n\r\n _doGridPosNorms(isoValue, step, appendSimple) {\r\n const vol = this._volumetricData;\r\n const volData = this._volumetricData.getData();\r\n const dim = vol.getDimensions();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n const zSize = dim[2];\r\n const stepX = step * vol.getStrideX();\r\n const stepY = step * vol.getStrideY();\r\n const stepZ = step * vol.getStrideZ();\r\n\r\n const gc = new GridCell();\r\n const gcVal = gc.val;\r\n const gcValSize = gc.val.length;\r\n const additions = [\r\n new THREE.Vector3(0, 0, 0), // 0\r\n new THREE.Vector3(step, 0, 0), // 1\r\n new THREE.Vector3(step, step, 0), // 2\r\n new THREE.Vector3(0, step, 0), // 3\r\n new THREE.Vector3(0, 0, step), // 4\r\n new THREE.Vector3(step, 0, step), // 5\r\n new THREE.Vector3(step, step, step), // 6\r\n new THREE.Vector3(0, step, step), // 7\r\n ];\r\n\r\n const tmpTriCount = 5;\r\n const triangles = new Array(tmpTriCount);\r\n for (let j = 0; j < tmpTriCount; ++j) {\r\n triangles[j] = new Triangle();\r\n }\r\n\r\n let appendVertex;\r\n const self = this;\r\n const positions = this._position;\r\n const normals = this._normals;\r\n if (appendSimple) {\r\n // Special case for axis-aligned grid with positive unit vector normals\r\n appendVertex = (function () {\r\n const axis = new THREE.Vector3(self._xAxis.x, self._yAxis.y, self._zAxis.z);\r\n return function (triVertex) {\r\n const vertex = triVertex.p.clone();\r\n vertex.multiply(axis);\r\n positions.push(vertex.add(self._origin));\r\n normals.push(triVertex.n.clone());\r\n };\r\n }());\r\n } else {\r\n appendVertex = (function () {\r\n const posMtx = new THREE.Matrix3();\r\n posMtx.set(\r\n self._xAxis.x,\r\n self._yAxis.x,\r\n self._zAxis.x,\r\n self._xAxis.y,\r\n self._yAxis.y,\r\n self._zAxis.y,\r\n self._xAxis.z,\r\n self._yAxis.z,\r\n self._zAxis.z,\r\n );\r\n const normMtx = new THREE.Matrix3();\r\n normMtx.set(\r\n self._xDir.x,\r\n self._yDir.x,\r\n self._zDir.x,\r\n self._xDir.y,\r\n self._yDir.y,\r\n self._zDir.y,\r\n self._xDir.z,\r\n self._yDir.z,\r\n self._zDir.z,\r\n );\r\n\r\n return function (triVertex) {\r\n positions.push(triVertex.p.clone().applyMatrix3(posMtx).add(self._origin));\r\n normals.push(triVertex.n.clone().applyMatrix3(normMtx));\r\n };\r\n }());\r\n }\r\n const indices = this._indices;\r\n\r\n let globTriCount = 0;\r\n\r\n for (let z = 0; z < (zSize - step); z += step) {\r\n for (let y = 0; y < (ySize - step); y += step) {\r\n let idx = vol.getDirectIdx(0, y, z);\r\n for (let x = 0; x < (xSize - step); x += step, idx += stepX) {\r\n gcVal[0] = volData[idx];\r\n gcVal[1] = volData[idx + stepX];\r\n gcVal[3] = volData[idx + stepY];\r\n gcVal[2] = volData[idx + stepX + stepY];\r\n gcVal[4] = volData[idx + stepZ];\r\n gcVal[5] = volData[idx + stepX + stepZ];\r\n gcVal[7] = volData[idx + stepY + stepZ];\r\n gcVal[6] = volData[idx + stepX + stepY + stepZ];\r\n\r\n // Determine the index into the edge table which\r\n // tells us which vertices are inside of the surface\r\n let cubeIndex = 0;\r\n let i = 0;\r\n for (; i < gcValSize; ++i) {\r\n if (gcVal[i] < isoValue) {\r\n cubeIndex |= (1 << i);\r\n }\r\n }\r\n\r\n if (edgeTable[cubeIndex] === 0) {\r\n continue;\r\n }\r\n\r\n gc.cubeIndex = cubeIndex;\r\n for (i = 0; i < gcValSize; ++i) {\r\n gc.p[i].set(x + additions[i].x, y + additions[i].y, z + additions[i].z);\r\n _voxelGradientFast(this._gradient, gc.p[i], gc.g[i]);\r\n }\r\n\r\n // calculate vertices and facets for this cube,\r\n // calculate normals by interpolating between the negated\r\n // normalized volume gradients for the 8 reference voxels\r\n const triCount = this._polygonize(gc, isoValue, triangles);\r\n globTriCount += triCount;\r\n\r\n // append triangles using different techniques\r\n for (i = 0; i < triCount; ++i) {\r\n indices.push(this._numTriangles * 3);\r\n indices.push(this._numTriangles * 3 + 1);\r\n indices.push(this._numTriangles * 3 + 2);\r\n ++this._numTriangles;\r\n\r\n appendVertex(triangles[i].a);\r\n appendVertex(triangles[i].b);\r\n appendVertex(triangles[i].c);\r\n }\r\n }\r\n }\r\n }\r\n\r\n return globTriCount;\r\n }\r\n\r\n compute(volData, origin, isoValue, step) {\r\n this._volumetricData = volData;\r\n this._origin = origin;\r\n\r\n this._gradient = volData.computeGradient();\r\n\r\n this._doGridPosNorms(isoValue, step, this._prepareAxesAndDirs());\r\n }\r\n\r\n _remapIndices(vertexMap, idcCount) {\r\n const indices = this._indices;\r\n const newIndices = utils.allocateTyped(Uint32Array, idcCount);\r\n for (let i = 0; i < idcCount; ++i) {\r\n indices[i] = vertexMap[indices[i]];\r\n newIndices[i] = indices[i];\r\n }\r\n this._indices = newIndices;\r\n }\r\n\r\n _remapVertices(vertices, normals, count) {\r\n const newPositions = utils.allocateTyped(Float32Array, count * 3);\r\n const newNormals = utils.allocateTyped(Float32Array, count * 3);\r\n for (let i = 0; i < count; ++i) {\r\n const pos = vertices[i];\r\n newPositions[i * 3] = pos.x;\r\n newPositions[i * 3 + 1] = pos.y;\r\n newPositions[i * 3 + 2] = pos.z;\r\n const norm = normals[i].normalize();\r\n newNormals[i * 3] = norm.x;\r\n newNormals[i * 3 + 1] = norm.y;\r\n newNormals[i * 3 + 2] = norm.z;\r\n }\r\n this._position = newPositions;\r\n this._normals = newNormals;\r\n }\r\n\r\n vertexFusion(offset, len) {\r\n const faceVer = this._indices.length;\r\n const vertices = this._position;\r\n const normals = this._normals;\r\n const oldVerCount = vertices.length | 0;\r\n if (faceVer === 0 || oldVerCount === 0) {\r\n return;\r\n }\r\n const vMap = utils.allocateTyped(Uint32Array, oldVerCount);\r\n vMap[0] = 0;\r\n let newVer = 1;\r\n\r\n let i = 1;\r\n for (; i < oldVerCount; ++i) {\r\n const start = newVer - offset < 0 ? 0 : newVer - offset;\r\n const end = start + len > newVer ? newVer : start + len;\r\n let matchedIndex = -1;\r\n\r\n for (let j = start; j < end; ++j) {\r\n if (Math.abs(vertices[i] - vertices[j]) < Number.EPSILON) {\r\n matchedIndex = j;\r\n break;\r\n }\r\n }\r\n\r\n if (matchedIndex !== -1) {\r\n vMap[i] = matchedIndex;\r\n } else {\r\n vertices[newVer].copy(vertices[i]);\r\n normals[newVer].copy(normals[i]);\r\n vMap[i] = newVer;\r\n ++newVer;\r\n }\r\n }\r\n\r\n this._remapIndices(vMap, faceVer);\r\n this._remapVertices(vertices, normals, newVer);\r\n }\r\n\r\n // Assign per-vertex colors from a volumetric texture map (same dimensions as the original volumetric data).\r\n // Along with color dominating atom is determined for each vertex\r\n // and vertices with atom out of \"visible\" subset get filtered out.\r\n // XXX only handles orthogonal volumes currently\r\n setColorVolTex(colorMap, atomMap, atomWeightMap, visibilitySelector) {\r\n let i;\r\n let idx;\r\n const numVerts = this._position.length / 3;\r\n const vertices = this._position;\r\n const origin = this._origin;\r\n const dim = this._volumetricData.getDimensions();\r\n const xs = dim[0] - 1;\r\n const ys = dim[1] - 1;\r\n const zs = dim[2] - 1;\r\n\r\n const colorData = colorMap.getData();\r\n const strideX = colorMap.getStrideX();\r\n const strideY = colorMap.getStrideY();\r\n const strideZ = colorMap.getStrideZ();\r\n\r\n let atomWeightData;\r\n let atomStrideX;\r\n let atomStrideY;\r\n let atomStrideZ;\r\n\r\n if (visibilitySelector !== null) {\r\n atomWeightData = atomWeightMap.getData();\r\n atomStrideX = atomWeightMap.getStrideX();\r\n atomStrideY = atomWeightMap.getStrideY();\r\n atomStrideZ = atomWeightMap.getStrideZ();\r\n }\r\n\r\n const xInv = 1.0 / this._xAxis.x;\r\n const yInv = 1.0 / this._yAxis.y;\r\n const zInv = 1.0 / this._zAxis.z;\r\n\r\n let atomLookup = [];\r\n let atomWeights = [];\r\n const colors = utils.allocateTyped(Float32Array, numVerts * 3);\r\n\r\n function interp(mu, idx1, idx2, c) {\r\n c[0] = (1 - mu) * colorData[idx1] + mu * colorData[idx2];\r\n c[1] = (1 - mu) * colorData[idx1 + 1] + mu * colorData[idx2 + 1];\r\n c[2] = (1 - mu) * colorData[idx1 + 2] + mu * colorData[idx2 + 2];\r\n }\r\n\r\n function collectWeight(ai, coefX, coefY, coefZ) {\r\n const a = atomMap[ai]; // atomWeightMap is a scalar field, so index into atom map should be the same\r\n if (a != null) {\r\n atomLookup[a.index] = a;\r\n const w = coefX * coefY * coefZ * atomWeightData[ai];\r\n if (typeof atomWeights[a.index] === 'undefined') {\r\n atomWeights[a.index] = w;\r\n } else {\r\n atomWeights[a.index] += w;\r\n }\r\n }\r\n }\r\n\r\n const vMap = utils.allocateTyped(Int32Array, numVerts);\r\n let newVerCount = 0;\r\n\r\n for (i = 0; i < numVerts; i++) {\r\n const ind = i * 3;\r\n const vx = (vertices[ind] - origin.x) * xInv;\r\n const vy = (vertices[ind + 1] - origin.y) * yInv;\r\n const vz = (vertices[ind + 2] - origin.z) * zInv;\r\n const x = Math.min(Math.max(vx, 0), xs) | 0;\r\n const y = Math.min(Math.max(vy, 0), ys) | 0;\r\n const z = Math.min(Math.max(vz, 0), zs) | 0;\r\n\r\n const mux = (vx - x);\r\n const muy = (vy - y);\r\n const muz = (vz - z);\r\n\r\n if (visibilitySelector != null) {\r\n // collect atom weights\r\n atomLookup = [];\r\n atomWeights = [];\r\n idx = atomWeightMap.getDirectIdx(x, y, z);\r\n collectWeight(idx, 1 - mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideX, mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideY, 1 - mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideX + atomStrideY, mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideZ, 1 - mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideZ, mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideY + atomStrideZ, 1 - mux, muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideY + atomStrideZ, mux, muy, muz);\r\n\r\n // find dominant atom\r\n let maxWeight = 0.0;\r\n let dominantIdx = -1;\r\n for (const atomIdx in atomWeights) {\r\n if (atomWeights[atomIdx] > maxWeight) {\r\n dominantIdx = atomIdx;\r\n maxWeight = atomWeights[atomIdx];\r\n }\r\n }\r\n\r\n if (dominantIdx < 0 || !visibilitySelector.includesAtom(atomLookup[dominantIdx])) {\r\n // this vertex doesn't belong to visible subset and will be skipped\r\n vMap[i] = -1;\r\n continue;\r\n }\r\n }\r\n\r\n vMap[i] = newVerCount++;\r\n\r\n // color tri-linear interpolation\r\n const dx = (x < xs) ? strideX : 0;\r\n const dy = (y < ys) ? strideY : 0;\r\n const dz = (z < zs) ? strideZ : 0;\r\n\r\n const c0 = [0, 0, 0];\r\n const c1 = [0, 0, 0];\r\n const c2 = [0, 0, 0];\r\n const c3 = [0, 0, 0];\r\n\r\n idx = colorMap.getDirectIdx(x, y, z);\r\n interp(mux, idx, idx + dx, c0);\r\n interp(mux, idx + dy, idx + dx + dy, c1);\r\n interp(mux, idx + dz, idx + dx + dz, c2);\r\n interp(mux, idx + dy + dz, idx + dx + dy + dz, c3);\r\n\r\n const cz0 = [0, 0, 0];\r\n cz0[0] = (1 - muy) * c0[0] + muy * c1[0];\r\n cz0[1] = (1 - muy) * c0[1] + muy * c1[1];\r\n cz0[2] = (1 - muy) * c0[2] + muy * c1[2];\r\n\r\n const cz1 = [0, 0, 0];\r\n cz1[0] = (1 - muy) * c2[0] + muy * c3[0];\r\n cz1[1] = (1 - muy) * c2[1] + muy * c3[1];\r\n cz1[2] = (1 - muy) * c2[2] + muy * c3[2];\r\n\r\n colors[ind] = (1 - muz) * cz0[0] + muz * cz1[0];\r\n colors[ind + 1] = (1 - muz) * cz0[1] + muz * cz1[1];\r\n colors[ind + 2] = (1 - muz) * cz0[2] + muz * cz1[2];\r\n }\r\n this._colors = colors;\r\n\r\n if (visibilitySelector != null) {\r\n // shift visible vertices towards beginning of array\r\n for (i = 0; i < numVerts; ++i) {\r\n const j = vMap[i];\r\n if (j < 0) {\r\n continue;\r\n }\r\n\r\n // assert: j <= i\r\n this._position[j * 3] = this._position[i * 3];\r\n this._position[j * 3 + 1] = this._position[i * 3 + 1];\r\n this._position[j * 3 + 2] = this._position[i * 3 + 2];\r\n this._normals[j * 3] = this._normals[i * 3];\r\n this._normals[j * 3 + 1] = this._normals[i * 3 + 1];\r\n this._normals[j * 3 + 2] = this._normals[i * 3 + 2];\r\n this._colors[j * 3] = this._colors[i * 3];\r\n this._colors[j * 3 + 1] = this._colors[i * 3 + 1];\r\n this._colors[j * 3 + 2] = this._colors[i * 3 + 2];\r\n }\r\n\r\n // rebuild index list\r\n const numTriangles = this._indices.length / 3;\r\n let newTriCount = 0;\r\n for (i = 0; i < numTriangles; ++i) {\r\n const i0 = vMap[this._indices[3 * i]];\r\n const i1 = vMap[this._indices[3 * i + 1]];\r\n const i2 = vMap[this._indices[3 * i + 2]];\r\n if (i0 >= 0 && i1 >= 0 && i2 >= 0) {\r\n this._indices[3 * newTriCount] = i0;\r\n this._indices[3 * newTriCount + 1] = i1;\r\n this._indices[3 * newTriCount + 2] = i2;\r\n ++newTriCount;\r\n }\r\n }\r\n\r\n // shrink arrays to data size\r\n this._position = new Float32Array(this._position.buffer.slice(0, newVerCount * 3 * 4));\r\n this._normals = new Float32Array(this._normals.buffer.slice(0, newVerCount * 3 * 4));\r\n this._colors = new Float32Array(this._colors.buffer.slice(0, newVerCount * 3 * 4));\r\n this._indices = new Uint32Array(this._indices.buffer.slice(0, newTriCount * 3 * 4));\r\n }\r\n }\r\n\r\n toMesh() {\r\n const geo = new THREE.BufferGeometry();\r\n geo.setIndex(new THREE.BufferAttribute(this._indices, 1));\r\n geo.setAttribute('position', new THREE.BufferAttribute(this._position, 3));\r\n geo.setAttribute('normal', new THREE.BufferAttribute(this._normals, 3));\r\n geo.setAttribute('color', new THREE.BufferAttribute(this._colors, 3));\r\n geo.computeBoundingSphere();\r\n return geo;\r\n }\r\n}\r\nexport default IsoSurface;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurface from './IsoSurface';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * This is a base class for volumetric maps based isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass VolumeSurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n const params = this._opts;\r\n this.numVoxels = [128, 128, 128];\r\n this.xAxis = new THREE.Vector3(1.0, 0.0, 0.0);\r\n this.yAxis = new THREE.Vector3(0.0, 1.0, 0.0);\r\n this.zAxis = new THREE.Vector3(0.0, 0.0, 1.0);\r\n\r\n this.origin = new THREE.Vector3(0.0, 0.0, 0.0);\r\n this._visibilitySelector = params.visibilitySelector;\r\n\r\n this._calcSurface(params);\r\n }\r\n\r\n _findMinMax(posRadArray) {\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n const maxPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n const minPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n for (let i = 1; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n for (let itemIdx = 0; itemIdx < itemSize; ++itemIdx) {\r\n const tmpVal = posRadArray[ind + itemIdx];\r\n maxPosRad[itemIdx] = Math.max(tmpVal, maxPosRad[itemIdx]);\r\n minPosRad[itemIdx] = Math.min(tmpVal, minPosRad[itemIdx]);\r\n }\r\n }\r\n return { maxPosRad, minPosRad };\r\n }\r\n\r\n _findNumVoxels(posRadArray, params) {\r\n const { numVoxels } = this;\r\n const minMaxValues = this._findMinMax(posRadArray);\r\n const minCoordRad = minMaxValues.minPosRad;\r\n const maxCoordRad = minMaxValues.maxPosRad;\r\n\r\n // minrad\r\n if (minCoordRad[3] > 4.0) {\r\n params.gridSpacing *= minCoordRad[3];\r\n }\r\n\r\n let gridPadding = params.radScale * maxCoordRad[3] * 1.7;\r\n let padRad = gridPadding;\r\n padRad = 0.65 * Math.sqrt(4.0 / 3.0 * Math.PI * padRad * padRad * padRad);\r\n gridPadding = Math.max(gridPadding, padRad);\r\n\r\n let i = 0;\r\n for (; i < 3; ++i) {\r\n minCoordRad[i] -= gridPadding;\r\n maxCoordRad[i] += gridPadding;\r\n }\r\n\r\n for (i = 0; i < 3; ++i) {\r\n numVoxels[i] = Math.ceil((maxCoordRad[i] - minCoordRad[i]) / params.gridSpacing);\r\n }\r\n this.xAxis.x = (numVoxels[0] - 1) * params.gridSpacing;\r\n this.yAxis.y = (numVoxels[1] - 1) * params.gridSpacing;\r\n this.zAxis.z = (numVoxels[2] - 1) * params.gridSpacing;\r\n\r\n [this.origin.x, this.origin.y, this.origin.z] = minCoordRad;\r\n\r\n return { bbox: minMaxValues, dim: numVoxels };\r\n }\r\n\r\n _makeSurface(surface, params) {\r\n const isoSurf = new IsoSurface();\r\n isoSurf.compute(surface.volMap, this.origin, params.isoValue, 1);\r\n isoSurf.vertexFusion(9, 9);// normalization is included\r\n\r\n if (isoSurf._numTriangles > 0) {\r\n isoSurf.setColorVolTex(surface.volTexMap, surface.atomMap, surface.atomWeightMap, this._visibilitySelector);\r\n this.setIndex(new THREE.BufferAttribute(isoSurf._indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(isoSurf._position, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(isoSurf._normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(isoSurf._colors, 3));\r\n } else { // geometry should have at least empty position attributes to be processed in wireframe mode by three.js\r\n this.setAttribute('position', new THREE.BufferAttribute(utils.allocateTyped(Float32Array, 0), 3));\r\n }\r\n }\r\n\r\n _calcSurface(params) {\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n\r\n if (packedArrays.posRad.length === 0) {\r\n return;\r\n }\r\n const boundaries = this._findNumVoxels(packedArrays.posRad, params);\r\n\r\n const box = new THREE.Box3(\r\n this.origin,\r\n new THREE.Vector3(this.xAxis.x, this.yAxis.y, this.zAxis.z).add(this.origin),\r\n );\r\n const surface = this._computeSurface(packedArrays, box, boundaries, params);\r\n\r\n this._makeSurface(surface, params);\r\n }\r\n}\r\n\r\nexport default VolumeSurfaceGeometry;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass QuickSurfGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n // beware of shifting this multiple times!\r\n this._shiftByOrigin(packedArrays.posRad);\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3),\r\n };\r\n\r\n if (this._visibilitySelector != null) {\r\n surface.atomMap = [];\r\n surface.atomWeightMap = new Volume(Float32Array, this.numVoxels, box);\r\n }\r\n\r\n this.gaussdensity(surface, packedArrays, null, params);\r\n return surface;\r\n }\r\n\r\n gaussdensity(surface, packedArrays, atomicNum, params) {\r\n const numAtoms = packedArrays.posRad.length / 4;\r\n const { posRad, colors } = packedArrays;\r\n const { numVoxels } = this;\r\n const { radScale, gaussLim, gridSpacing } = params;\r\n const invIsoValue = 1.0 / params.isoValue;\r\n const invGridSpacing = 1.0 / gridSpacing;\r\n const maxVoxelX = numVoxels[0] - 1;\r\n const maxVoxelY = numVoxels[1] - 1;\r\n const maxVoxelZ = numVoxels[2] - 1;\r\n // TODO is densityMap and volTexMap initialized?\r\n\r\n const { volMap, volTexMap } = surface;\r\n const volData = volMap.getData();\r\n const strideX = volMap.getStrideX();\r\n\r\n const volTexData = volTexMap.getData();\r\n const texStrideX = volTexMap.getStrideX();\r\n\r\n let atomWeightData;\r\n if (this._visibilitySelector != null) {\r\n atomWeightData = surface.atomWeightMap.getData();\r\n }\r\n\r\n const { atomMap } = surface;\r\n\r\n for (let i = 0; i < numAtoms; ++i) {\r\n const ind = i * 4;\r\n const scaledRad = posRad[ind + 3] * radScale;\r\n const atomicNumFactor = atomicNum === null ? 1.0 : atomicNum[i];\r\n const radInv = 1 / (2 * scaledRad * scaledRad);\r\n let radLim = gaussLim * scaledRad;\r\n const radLim2 = radLim * radLim;\r\n radLim *= invGridSpacing;\r\n\r\n let tmp = posRad[ind] * invGridSpacing;\r\n const xMin = Math.max((tmp - radLim) | 0, 0);\r\n const xMax = Math.min((tmp + radLim) | 0, maxVoxelX);\r\n tmp = posRad[ind + 1] * invGridSpacing;\r\n const yMin = Math.max((tmp - radLim) | 0, 0);\r\n const yMax = Math.min((tmp + radLim) | 0, maxVoxelY);\r\n tmp = posRad[ind + 2] * invGridSpacing;\r\n const zMin = Math.max((tmp - radLim) | 0, 0);\r\n const zMax = Math.min((tmp + radLim) | 0, maxVoxelZ);\r\n\r\n let dz = zMin * gridSpacing - posRad[ind + 2];\r\n for (let z = zMin; z <= zMax; ++z, dz += gridSpacing) {\r\n let dy = yMin * gridSpacing - posRad[ind + 1];\r\n for (let y = yMin; y <= yMax; ++y, dy += gridSpacing) {\r\n const dy2dz2 = dy * dy + dz * dz;\r\n\r\n if (dy2dz2 >= radLim2) {\r\n continue;\r\n }\r\n\r\n let addr = volMap.getDirectIdx(xMin, y, z);\r\n let texAddr = volTexMap.getDirectIdx(xMin, y, z);\r\n let dx = xMin * gridSpacing - posRad[ind];\r\n for (let x = xMin; x <= xMax; ++x, dx += gridSpacing, addr += strideX, texAddr += texStrideX) {\r\n const r2 = dx * dx + dy2dz2;\r\n const expVal = -r2 * radInv;\r\n\r\n let density = Math.exp(expVal) * atomicNumFactor;\r\n\r\n // store most relevant atom (with highest density)\r\n if (this._visibilitySelector != null\r\n && density > atomWeightData[addr]) { // NOSONAR\r\n atomWeightData[addr] = density;\r\n // we use same index into atom map and atomWeightMap\r\n atomMap[addr] = packedArrays.atoms[i];\r\n }\r\n\r\n volData[addr] += density;\r\n\r\n // TODO check for volTexMap routine?\r\n density *= invIsoValue;\r\n const colInd = i * 3;\r\n volTexData[texAddr] += density * colors[colInd];\r\n volTexData[texAddr + 1] += density * colors[colInd + 1];\r\n volTexData[texAddr + 2] += density * colors[colInd + 2];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n _shiftByOrigin(posRadArray) {\r\n const originX = this.origin.x;\r\n const originY = this.origin.y;\r\n const originZ = this.origin.z;\r\n\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n for (let i = 0; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n posRadArray[ind] -= originX;\r\n posRadArray[ind + 1] -= originY;\r\n posRadArray[ind + 2] -= originZ;\r\n }\r\n }\r\n}\r\n\r\nexport default QuickSurfGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * Modifed from SpatialHash\r\n *\r\n * Main differences are:\r\n * - Optimized grid size to ensure we only ever need to look +/-1 cell\r\n * - Aware of atomic radii and will only output atoms within rAtom + rExtra\r\n * (see withinRadii method)\r\n *\r\n * (Uses rounding rather than bitshifting as consequence of arbitrary grid size)\r\n * @class\r\n * @param {Float32Array} posRad - x, y, z coordinates and radiuses\r\n * @param {Float32Array} min - xyz min coordinates\r\n * @param {Float32Array} max - xyz max coordinates\r\n * @param {number} maxDistance - max distance\r\n */\r\nfunction AVHash(posRad, min, max, maxDistance) {\r\n const itemSize = 4;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const minX = min[0];\r\n const minY = min[1];\r\n const minZ = min[2];\r\n\r\n const maxX = max[0];\r\n const maxY = max[1];\r\n const maxZ = max[2];\r\n\r\n function hashFunc(w, minW) {\r\n return Math.floor((w - minW) / maxDistance);\r\n }\r\n\r\n const iDim = hashFunc(maxX, minX) + 1;\r\n const jDim = hashFunc(maxY, minY) + 1;\r\n const kDim = hashFunc(maxZ, minZ) + 1;\r\n\r\n const nCells = iDim * jDim * kDim;\r\n\r\n const jkDim = jDim * kDim;\r\n\r\n /* Get cellID for cartesian x,y,z */\r\n const cellID = function (x, y, z) {\r\n return (((hashFunc(x, minX) * jDim) + hashFunc(y, minY)) * kDim) + hashFunc(z, minZ);\r\n };\r\n\r\n /* Initial building, could probably be optimized further */\r\n const preHash = [];\r\n let i;\r\n let cid;\r\n for (i = 0; i < nAtoms; i++) {\r\n const iIdx = itemSize * i;\r\n cid = cellID(posRad[iIdx], posRad[iIdx + 1], posRad[iIdx + 2]);\r\n\r\n if (preHash[cid] === undefined) {\r\n preHash[cid] = [i];\r\n } else {\r\n preHash[cid].push(i);\r\n }\r\n }\r\n\r\n const cellOffsets = utils.allocateTyped(Uint32Array, nCells);\r\n const cellLengths = utils.allocateTyped(Uint16Array, nCells);\r\n const data = utils.allocateTyped(Uint32Array, nAtoms);\r\n\r\n let offset = 0;\r\n let maxCellLength = 0;\r\n let j;\r\n for (i = 0; i < nCells; i++) {\r\n const start = cellOffsets[i] = offset;\r\n\r\n const subArray = preHash[i];\r\n\r\n if (subArray !== undefined) {\r\n for (j = 0; j < subArray.length; j++) {\r\n data[offset] = subArray[j];\r\n offset++;\r\n }\r\n }\r\n\r\n const cellLength = offset - start;\r\n cellLengths[i] = cellLength;\r\n\r\n if (cellLength > maxCellLength) {\r\n maxCellLength = cellLength;\r\n }\r\n }\r\n\r\n // Maximum number of neighbours we could ever produce (27 adjacent cells of equal population)\r\n this.neighbourListLength = (27 * maxCellLength) + 1;\r\n\r\n /**\r\n * Populate the supplied out array with atom indices that are within rAtom + rExtra\r\n * of x,y,z\r\n *\r\n * -1 in out array indicates the end of the list\r\n *\r\n * @param {number} x - x coordinate\r\n * @param {number} y - y coordinate\r\n * @param {number} z - z coordinate\r\n * @param {number} rExtra - additional radius\r\n * @param {Float32Array} out - pre-allocated output array\r\n * @return {undefined}\r\n */\r\n this.withinRadii = function (x, y, z, rExtra, out) {\r\n let outIdx = 0;\r\n\r\n const nearI = hashFunc(x, minX);\r\n const nearJ = hashFunc(y, minY);\r\n const nearK = hashFunc(z, minZ);\r\n\r\n const loI = Math.max(0, nearI - 1);\r\n const loJ = Math.max(0, nearJ - 1);\r\n const loK = Math.max(0, nearK - 1);\r\n\r\n const hiI = Math.min(iDim - 1, nearI + 1);\r\n const hiJ = Math.min(jDim - 1, nearJ + 1);\r\n const hiK = Math.min(kDim - 1, nearK + 1);\r\n\r\n for (i = loI; i <= hiI; ++i) {\r\n const iOffset = i * jkDim;\r\n\r\n for (j = loJ; j <= hiJ; ++j) {\r\n const jOffset = j * kDim;\r\n\r\n for (let k = loK; k <= hiK; ++k) {\r\n cid = iOffset + jOffset + k;\r\n\r\n const cellStart = cellOffsets[cid];\r\n const cellEnd = cellStart + cellLengths[cid];\r\n\r\n for (let dataIndex = cellStart; dataIndex < cellEnd; dataIndex++) {\r\n const atomIndex = data[dataIndex];\r\n const baseIndex = itemSize * atomIndex;\r\n const dx = posRad[baseIndex] - x;\r\n const dy = posRad[baseIndex + 1] - y;\r\n const dz = posRad[baseIndex + 2] - z;\r\n const rSum = posRad[baseIndex + 3] + rExtra;\r\n\r\n if ((dx * dx + dy * dy + dz * dz) <= (rSum * rSum)) {\r\n out[outIdx++] = data[dataIndex];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n // Add terminator\r\n out[outIdx] = -1;\r\n };\r\n}\r\nfunction ContactSurface(packedArrays, boundaries, params, _indexList) {\r\n // Field generation method adapted from AstexViewer (Mike Hartshorn)\r\n // by Fred Ludlow.\r\n // Other parts based heavily on NGL (Alexander Rose) EDT Surface class\r\n //\r\n // Should work as a drop-in alternative to EDTSurface (though some of\r\n // the EDT paramters are not relevant in this method).\r\n\r\n const itemSize = 4;\r\n const { posRad, colors, atoms } = packedArrays;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const { bbox } = boundaries;\r\n\r\n const min = bbox.minPosRad;\r\n const max = bbox.maxPosRad;\r\n\r\n let r2; // Atom positions, expanded radii (squared)\r\n let maxRadius;\r\n\r\n // Parameters\r\n let probeRadius;\r\n let scaleFactor;\r\n let probePositions;\r\n\r\n // Cache last value for obscured test\r\n let lastClip = -1;\r\n\r\n // Grid params\r\n let dim;\r\n let grid;\r\n let volTex;\r\n let weights;\r\n let weightsMap = null;\r\n let atomMap = null;\r\n let visibilitySelector = null;\r\n\r\n // grid indices -> xyz coords\r\n let gridx;\r\n let gridy;\r\n let gridz;\r\n\r\n // Lookup tables:\r\n let sinTable;\r\n let cosTable;\r\n\r\n // Spatial Hash\r\n let hash;\r\n\r\n // Neighbour array to be filled by hash\r\n let neighbours;\r\n\r\n // Vectors for Torus Projection\r\n const mid = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n1 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n2 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n let ngTorus;\r\n\r\n function uniformArray(TypeName, n, a) {\r\n const array = utils.allocateTyped(TypeName, n);\r\n for (let innI = 0; innI < n; ++innI) {\r\n array[innI] = a;\r\n }\r\n\r\n return array;\r\n }\r\n\r\n function fillGridDim(a, start, step) {\r\n for (let innI = 0; innI < a.length; innI++) {\r\n a[innI] = start + (step * innI);\r\n }\r\n }\r\n\r\n function initializeGrid() {\r\n ({ scaleFactor } = params);\r\n ({ dim } = boundaries);\r\n\r\n ngTorus = Math.min(5, 2 + Math.floor(probeRadius * scaleFactor));\r\n\r\n const gridSize = dim[0] * dim[1] * dim[2];\r\n grid = uniformArray(Float32Array, gridSize, -1001.0);\r\n volTex = utils.allocateTyped(Float32Array, gridSize * 3);\r\n weights = utils.allocateTyped(Float32Array, gridSize);\r\n if (visibilitySelector) {\r\n weightsMap = utils.allocateTyped(Float32Array, gridSize);\r\n atomMap = [];\r\n }\r\n\r\n gridx = utils.allocateTyped(Float32Array, dim[0]);\r\n gridy = utils.allocateTyped(Float32Array, dim[1]);\r\n gridz = utils.allocateTyped(Float32Array, dim[2]);\r\n\r\n fillGridDim(gridx, min[0], 1 / scaleFactor);\r\n fillGridDim(gridy, min[1], 1 / scaleFactor);\r\n fillGridDim(gridz, min[2], 1 / scaleFactor);\r\n }\r\n\r\n function initializeAngleTables() {\r\n let theta = 0.0;\r\n const step = 2 * Math.PI / probePositions;\r\n\r\n cosTable = utils.allocateTyped(Float32Array, probePositions);\r\n sinTable = utils.allocateTyped(Float32Array, probePositions);\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n cosTable[innI] = Math.cos(theta);\r\n sinTable[innI] = Math.sin(theta);\r\n theta += step;\r\n }\r\n }\r\n\r\n function initializeHash() {\r\n hash = new AVHash(posRad, min, max, 2.01 * maxRadius);\r\n neighbours = new Int32Array(hash.neighbourListLength);\r\n }\r\n\r\n function init() {\r\n ({\r\n probeRadius,\r\n scaleFactor,\r\n probePositions,\r\n visibilitySelector,\r\n } = params);\r\n r2 = utils.allocateTyped(Float32Array, nAtoms);\r\n maxRadius = 0;\r\n for (let innI = 0; innI < nAtoms; ++innI) {\r\n const rExt = posRad[innI * itemSize + 3] += probeRadius;\r\n if (rExt > maxRadius) {\r\n maxRadius = rExt;\r\n }\r\n r2[innI] = rExt * rExt;\r\n }\r\n\r\n initializeGrid();\r\n initializeAngleTables();\r\n initializeHash();\r\n\r\n lastClip = -1;\r\n }\r\n\r\n function singleAtomObscures(ai, innX, innY, innZ) {\r\n const innCI = itemSize * ai;\r\n const ra2 = r2[ai];\r\n const dx = posRad[innCI] - innX;\r\n const dy = posRad[innCI + 1] - innY;\r\n const dz = posRad[innCI + 2] - innZ;\r\n const d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n return d2 < ra2;\r\n }\r\n\r\n function obscured(innX, innY, innZ, a, b) {\r\n // Is the point at x,y,z obscured by any of the atoms\r\n // specifeid by indices in neighbours. Ignore indices\r\n // a and b (these are the relevant atoms in projectPoints/Torii)\r\n\r\n // Cache the last clipped atom (as very often the same one in\r\n // subsequent calls)\r\n let ai;\r\n\r\n if (lastClip !== -1) {\r\n ai = lastClip;\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n return ai;\r\n }\r\n lastClip = -1;\r\n }\r\n\r\n let ni = 0;\r\n ai = neighbours[ni];\r\n while (ai >= 0) {\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n lastClip = ai;\r\n return ai;\r\n }\r\n ai = neighbours[++ni];\r\n }\r\n\r\n lastClip = -1;\r\n\r\n return -1;\r\n }\r\n\r\n function projectPoints() {\r\n // For each atom:\r\n // Iterate over a subsection of the grid, for each point:\r\n // If current value < 0.0, unvisited, set positive\r\n //\r\n // In any case: Project this point onto surface of the atomic sphere\r\n // If this projected point is not obscured by any other atom\r\n // Calcualte delta distance and set grid value to minimum of\r\n // itself and delta\r\n\r\n // Should we alias frequently accessed closure constiables??\r\n // Assume JS engine capable of optimizing this\r\n // anyway...\r\n const maxRad = 4.0;\r\n const sigma = (maxRad) / 3;\r\n const sigma2Inv = 1 / (2 * sigma * sigma);\r\n\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innCI = itemSize * innI;\r\n const ax = posRad[innCI];\r\n const ay = posRad[innCI + 1];\r\n const az = posRad[innCI + 2];\r\n const ar = posRad[innCI + 3];\r\n const ar2 = r2[innI];\r\n\r\n hash.withinRadii(ax, ay, az, ar, neighbours);\r\n\r\n // Number of grid points, round this up...\r\n const ng = Math.ceil(ar * scaleFactor);\r\n\r\n // Center of the atom, mapped to grid points (take floor)\r\n const iax = Math.floor(scaleFactor * (ax - min[0]));\r\n const iay = Math.floor(scaleFactor * (ay - min[1]));\r\n const iaz = Math.floor(scaleFactor * (az - min[2]));\r\n\r\n // Extents of grid to consider for this atom\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n // Add two to these points:\r\n // - iax are floor'd values so this ensures coverage\r\n // - these are loop limits (exclusive)\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n const colIdx = innI * 3;\r\n const cr = colors[colIdx];\r\n const cg = colors[colIdx + 1];\r\n const cb = colors[colIdx + 2];\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n const dz = gridz[iz] - az;\r\n const zOffset = dim[1] * dim[0] * iz;\r\n\r\n for (let iy = miny; iy < maxy; iy++) {\r\n const dy = gridy[iy] - ay;\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n\r\n for (let ix = minx; ix < maxx; ix++) {\r\n const idx = ix + zyOffset;\r\n const dx = gridx[ix] - ax;\r\n const d2 = dzy2 + dx * dx;\r\n\r\n if (d2 < ar2) {\r\n const w = Math.exp(-d2 * sigma2Inv);\r\n const cIdx = idx * 3;\r\n volTex[cIdx] += cr * w;\r\n volTex[cIdx + 1] += cg * w;\r\n volTex[cIdx + 2] += cb * w;\r\n weights[idx] += w;\r\n if (visibilitySelector !== null && w > weightsMap[idx]) {\r\n weightsMap[idx] = w;\r\n atomMap[idx] = atoms[innI];\r\n }\r\n\r\n if (grid[idx] < 0.0) {\r\n // Unvisited, make positive\r\n grid[idx] = -grid[idx];\r\n }\r\n // Project on to the surface of the sphere\r\n // sp is the projected point ( dx, dy, dz ) * ( ra / d )\r\n const d = Math.sqrt(d2);\r\n const ap = ar / d;\r\n let spx = dx * ap;\r\n let spy = dy * ap;\r\n let spz = dz * ap;\r\n\r\n spx += ax;\r\n spy += ay;\r\n spz += az;\r\n\r\n if (obscured(spx, spy, spz, innI, -1) === -1) {\r\n const dd = ar - d;\r\n if (dd < grid[idx]) {\r\n grid[idx] = dd;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function normalToLine(out, p) {\r\n out.x = out.y = out.z = 1.0;\r\n if (p.x !== 0) {\r\n out.x = (p.y + p.z) / -p.x;\r\n } else if (p.y !== 0) {\r\n out.y = (p.x + p.z) / -p.y;\r\n } else if (p.z !== 0) {\r\n out.z = (p.x + p.y) / -p.z;\r\n }\r\n return out;\r\n }\r\n\r\n function projectTorus(a, b) {\r\n const aIdx = itemSize * a;\r\n const bIdx = itemSize * b;\r\n const xa = posRad[aIdx];\r\n const ya = posRad[aIdx + 1];\r\n const za = posRad[aIdx + 2];\r\n const r1 = posRad[aIdx + 3];\r\n let dx = mid.x = posRad[bIdx] - xa;\r\n let dy = mid.y = posRad[bIdx + 1] - ya;\r\n let dz = mid.z = posRad[bIdx + 2] - za;\r\n const innR2 = posRad[bIdx + 3];\r\n let d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n // This check now redundant as already done in AVHash.withinRadii\r\n // if( d2 > (( r1 + r2 ) * ( r1 + r2 )) ){ return; }\r\n\r\n const d = Math.sqrt(d2);\r\n\r\n // Find angle between a->b vector and the circle\r\n // of their intersection by cosine rule\r\n const cosA = (r1 * r1 + d * d - innR2 * innR2) / (2.0 * r1 * d);\r\n\r\n // distance along a->b at intersection\r\n const dmp = r1 * cosA;\r\n\r\n mid.normalize();\r\n\r\n // Create normal to line\r\n normalToLine(n1, mid);\r\n n1.normalize();\r\n\r\n // Cross together for second normal vector\r\n n2.crossVectors(mid, n1);\r\n n2.normalize();\r\n\r\n // r is radius of circle of intersection\r\n const rInt = Math.sqrt(r1 * r1 - dmp * dmp);\r\n\r\n n1.multiplyScalar(rInt);\r\n n2.multiplyScalar(rInt);\r\n mid.multiplyScalar(dmp);\r\n\r\n mid.x += xa;\r\n mid.y += ya;\r\n mid.z += za;\r\n\r\n lastClip = -1;\r\n\r\n const ng = ngTorus;\r\n\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n const cost = cosTable[innI];\r\n const sint = sinTable[innI];\r\n\r\n const px = mid.x + cost * n1.x + sint * n2.x;\r\n const py = mid.y + cost * n1.y + sint * n2.y;\r\n const pz = mid.z + cost * n1.z + sint * n2.z;\r\n\r\n if (obscured(px, py, pz, a, b) === -1) {\r\n // As above, iterate over our grid...\r\n // px, py, pz in grid coords\r\n const iax = Math.floor(scaleFactor * (px - min[0]));\r\n const iay = Math.floor(scaleFactor * (py - min[1]));\r\n const iaz = Math.floor(scaleFactor * (pz - min[2]));\r\n\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n dz = pz - gridz[iz];\r\n const zOffset = dim[1] * dim[0] * iz;\r\n for (let iy = miny; iy < maxy; iy++) {\r\n dy = py - gridy[iy];\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n for (let ix = minx; ix < maxx; ix++) {\r\n dx = px - gridx[ix];\r\n d2 = dzy2 + dx * dx;\r\n const idx = ix + zyOffset;\r\n const current = grid[idx];\r\n\r\n if (current > 0.0 && d2 < (current * current)) {\r\n grid[idx] = Math.sqrt(d2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function projectTorii() {\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innIdx = itemSize * innI;\r\n hash.withinRadii(\r\n posRad[innIdx],\r\n posRad[innIdx + 1],\r\n posRad[innIdx + 2],\r\n posRad[innIdx + 3],\r\n neighbours,\r\n );\r\n let ia = 0;\r\n let ni = neighbours[ia];\r\n while (ni >= 0) {\r\n if (innI < ni) {\r\n projectTorus(innI, ni);\r\n }\r\n ni = neighbours[++ia];\r\n }\r\n }\r\n }\r\n\r\n function fixNegatives() {\r\n for (let innI = 0, n = grid.length; innI < n; innI++) {\r\n if (grid[innI] < 0) grid[innI] = 0;\r\n let w = weights[innI];\r\n if (w > 0) {\r\n w = 1 / w;\r\n const innInnI = innI * 3;\r\n volTex[innInnI] *= w;\r\n volTex[innInnI + 1] *= w;\r\n volTex[innInnI + 2] *= w;\r\n }\r\n }\r\n }\r\n\r\n function getVolume() {\r\n // Basic steps are:\r\n // 1) Initialize\r\n // 2) Project points\r\n // 3) Project torii\r\n console.time('ContactSurface.getVolume');\r\n\r\n console.time('ContactSurface.init');\r\n init();\r\n console.timeEnd('ContactSurface.init');\r\n\r\n console.time('ContactSurface.projectPoints');\r\n projectPoints();\r\n console.timeEnd('ContactSurface.projectPoints');\r\n\r\n console.time('ContactSurface.projectTorii');\r\n projectTorii();\r\n console.timeEnd('ContactSurface.projectTorii');\r\n fixNegatives();\r\n console.timeEnd('ContactSurface.getVolume');\r\n }\r\n\r\n this.build = function () {\r\n // type and cutoff left in for compatibility with EDTSurface.getSurface\r\n // function signature\r\n getVolume();\r\n this.volTexMap = volTex;\r\n this.weightsMap = weightsMap;\r\n this.atomMap = atomMap;\r\n this.volMap = grid;\r\n };\r\n}\r\nexport default ContactSurface;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport ContactSurface from './ContactSurface';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'contact' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass ContactSurfaceGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n const contactSurface = new ContactSurface(packedArrays, boundaries, params);\r\n contactSurface.build();\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.volMap),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3, contactSurface.volTexMap),\r\n atomMap: contactSurface.atomMap,\r\n atomWeightMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.weightsMap),\r\n };\r\n return surface;\r\n }\r\n}\r\n\r\nexport default ContactSurfaceGeometry;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for colored atom. Need for atom structure clusterization\r\n *\r\n * @param {Vector3} vCenter Center of atom\r\n * @param {number} radiusAt Radius of atom\r\n */\r\nclass IsoSurfaceAtomColored {\r\n constructor(vCenter, radiusAt) {\r\n this.coord = new THREE.Vector3();\r\n this.coord.copy(vCenter);\r\n this.radius = radiusAt;\r\n this.colorX = 0.99999;\r\n this.colorY = 0.0;\r\n this.colorZ = 0.0;\r\n this.atomType = 0;\r\n this.srcAtom = null;\r\n }\r\n}\r\nexport default IsoSurfaceAtomColored;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n// suppress some JSHint warnings\r\n/* jshint bitwise: false */\r\n\r\n/**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numAtoms - Number of atoms in molecule\r\n * @param {Element} atoms - Array of atoms\r\n * @param {Vector3} vBoxMin - Bounding box min\r\n * @param {Vector3} vBoxMax - Bounding box max\r\n * @param {number} probeRadius - Normals for output\r\n *\r\n */\r\nclass IsosurfaceBuildNormals {\r\n constructor(numAtoms, atoms, vBoxMin, vBoxMax, probeRadius) {\r\n this._numAtoms = numAtoms;\r\n this._atoms = atoms;\r\n this._vBoxMin = new THREE.Vector3();\r\n this._vBoxMax = new THREE.Vector3();\r\n this._vBoxMin.copy(vBoxMin);\r\n this._vBoxMax.copy(vBoxMax);\r\n this._probeRadius = probeRadius;\r\n\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n }\r\n\r\n createVoxels() {\r\n let numAtomsRefs;\r\n let rad;\r\n const ATOM_VOXEL_REF_SCALE = 4.5;\r\n\r\n const numAtoms = this._numAtoms | 0;\r\n const atoms = this._atoms;\r\n const dx = this._vBoxMax.x - this._vBoxMin.x;\r\n const dy = this._vBoxMax.y - this._vBoxMin.y;\r\n const dz = this._vBoxMax.z - this._vBoxMin.z;\r\n let w = (dx < dy) ? dx : dy;\r\n w = (dz < w) ? dz : w;\r\n let maxRad = 0.0;\r\n let aveRad = 0.0;\r\n\r\n let i;\r\n for (i = 0; i < numAtoms; i++) {\r\n rad = (atoms[i].radius + this._probeRadius) * 2.0;\r\n maxRad = (rad > maxRad) ? rad : maxRad;\r\n aveRad += rad;\r\n }\r\n let numCells = Math.floor(w / maxRad);\r\n if (numCells < 2) {\r\n numCells = 2;\r\n }\r\n aveRad /= numAtoms;\r\n\r\n this._numCells = numCells;\r\n this._aveRad = aveRad;\r\n this._maxRad = maxRad;\r\n\r\n const side = numCells;\r\n const side2 = numCells * numCells;\r\n const side3 = numCells * numCells * numCells;\r\n\r\n const xScale = this._xScale = 1.0 / (this._vBoxMax.x - this._vBoxMin.x);\r\n const yScale = this._yScale = 1.0 / (this._vBoxMax.y - this._vBoxMin.y);\r\n const zScale = this._zScale = 1.0 / (this._vBoxMax.z - this._vBoxMin.z);\r\n\r\n // estimate number of individual atom refs in each voxel list\r\n let maxAtomsRefs = 0;\r\n\r\n const xNumVoxMult = xScale * numCells;\r\n const yNumVoxMult = yScale * numCells;\r\n const zNumVoxMult = zScale * numCells;\r\n\r\n for (i = 0; i < numAtoms; i++) {\r\n const radAffect = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n const diaAffect = radAffect * 2.0;\r\n let numVoxX = Math.floor(xNumVoxMult * diaAffect + 0.8);\r\n let numVoxY = Math.floor(yNumVoxMult * diaAffect + 0.8);\r\n let numVoxZ = Math.floor(zNumVoxMult * diaAffect + 0.8);\r\n // avoid case numVox? == 0\r\n // also use loop i <=\r\n numVoxX++;\r\n numVoxY++;\r\n numVoxZ++;\r\n maxAtomsRefs += numVoxX * numVoxY * numVoxZ;\r\n } // for (i)\r\n // maxAtomsRefs = numAtoms * MAX_ATOMS_IN_SINGLE_VOXEL;\r\n\r\n this._voxelList = utils.allocateTyped(Int32Array, side3);\r\n const atomsList = [];\r\n atomsList.length = maxAtomsRefs;\r\n if ((this._voxelList === null) || (atomsList === null)) {\r\n return 0 - 1;\r\n }\r\n // init voxel list\r\n for (i = 0; i < side3; i++) {\r\n this._voxelList[i] = -1;\r\n }\r\n numAtomsRefs = 0;\r\n\r\n // create voxel lists\r\n for (i = 0; i < numAtoms; i++) {\r\n // use multiplier 4 to locate this atom in different voxels\r\n rad = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n let xIndMin = Math.floor((atoms[i].coord.x - this._vBoxMin.x - rad) * numCells * xScale);\r\n let yIndMin = Math.floor((atoms[i].coord.y - this._vBoxMin.y - rad) * numCells * yScale);\r\n let zIndMin = Math.floor((atoms[i].coord.z - this._vBoxMin.z - rad) * numCells * zScale);\r\n let xIndMax = Math.floor((atoms[i].coord.x - this._vBoxMin.x + rad) * numCells * xScale);\r\n let yIndMax = Math.floor((atoms[i].coord.y - this._vBoxMin.y + rad) * numCells * yScale);\r\n let zIndMax = Math.floor((atoms[i].coord.z - this._vBoxMin.z + rad) * numCells * zScale);\r\n\r\n xIndMin = (xIndMin >= 0) ? xIndMin : 0;\r\n yIndMin = (yIndMin >= 0) ? yIndMin : 0;\r\n zIndMin = (zIndMin >= 0) ? zIndMin : 0;\r\n\r\n xIndMax = (xIndMax < numCells) ? xIndMax : (numCells - 1);\r\n yIndMax = (yIndMax < numCells) ? yIndMax : (numCells - 1);\r\n zIndMax = (zIndMax < numCells) ? zIndMax : (numCells - 1);\r\n\r\n for (let z = zIndMin; z <= zIndMax; z++) {\r\n for (let y = yIndMin; y <= yIndMax; y++) {\r\n for (let x = xIndMin; x <= xIndMax; x++) {\r\n // add atom with index \"i\" to this voxel list\r\n const indVoxel = x + y * side + z * side2;\r\n // assert indVoxel >= 0\r\n // assert indVoxel < side3\r\n\r\n // add first\r\n if (this._voxelList[indVoxel] < 0) {\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = 0 - 1;\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n numAtomsRefs++;\r\n // assert numAtomsRefs < maxAtomsRefs - 1\r\n continue;\r\n }\r\n // insert into head of list\r\n const indexNext = this._voxelList[indVoxel];\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = indexNext;\r\n numAtomsRefs++;\r\n } // for (x)\r\n } // for (y)\r\n } // for (z)\r\n } // for (i)\r\n\r\n // convert Array to Int32Array\r\n this._atomsList = Int32Array.from(atomsList);\r\n\r\n return 0;\r\n }\r\n\r\n destroyVoxels() {\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n\r\n this._atoms = null;\r\n this._vertices = null;\r\n this._vBoxMin = null;\r\n this._vBoxMax = null;\r\n }\r\n\r\n /**\r\n * Enumerate all atoms affecting specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n * @param {func(atom)} process - function to call for each atom\r\n */\r\n forEachRelatedAtom(point, process) {\r\n // find corresponding voxel\r\n const xInd = Math.floor((point.x - this._vBoxMin.x) * this._numCells * this._xScale);\r\n const yInd = Math.floor((point.y - this._vBoxMin.y) * this._numCells * this._yScale);\r\n const zInd = Math.floor((point.z - this._vBoxMin.z) * this._numCells * this._zScale);\r\n const indVoxel = xInd + yInd * this._numCells + zInd * this._numCells * this._numCells;\r\n\r\n // run through atoms affecting this voxel\r\n const atoms = this._atoms;\r\n for (let ref = this._voxelList[indVoxel]; ref >= 0; ref = this._atomsList[ref * 2 + 1]) {\r\n const indexAtom = this._atomsList[ref * 2];\r\n process(atoms[indexAtom]);\r\n }\r\n }\r\n\r\n /**\r\n * Get atom closest to specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n *\r\n * @returns {IsoSurfaceAtomColored} atom, or null if not found\r\n */\r\n getClosestAtom(point) {\r\n let closest = null;\r\n let minDist2 = Number.MAX_VALUE;\r\n\r\n this.forEachRelatedAtom(point, (atom) => {\r\n const dist2 = point.distanceToSquared(atom.coord);\r\n if (dist2 < minDist2) {\r\n minDist2 = dist2;\r\n closest = atom;\r\n }\r\n });\r\n\r\n return closest;\r\n }\r\n\r\n /**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} normals - Normals for output\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildNormals(numVertices, vertices, normals) {\r\n const self = this;\r\n let numCloseAtoms = 0;\r\n let vx = 0;\r\n let vy = 0;\r\n let vz = 0;\r\n let dist2;\r\n let vNormalX = 0;\r\n let vNormalY = 0;\r\n let vNormalZ = 0;\r\n let koef = 0;\r\n let w = 0;\r\n const r25 = 2.5;\r\n const r01 = 0.1;\r\n\r\n const maxRadAffect = this._aveRad * r25;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n const expScale = -this._aveRad * r01;\r\n\r\n // some stats\r\n // numSlowAtoms = 0;\r\n\r\n const gatherNormals = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = Math.exp(expScale * koef);\r\n\r\n vNormalX += dx * w;\r\n vNormalY += dy * w;\r\n vNormalZ += dz * w;\r\n numCloseAtoms++;\r\n };\r\n\r\n let maxClosedAtoms = 0;\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n numCloseAtoms = 0;\r\n vNormalX = vNormalY = vNormalZ = 0.0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherNormals);\r\n\r\n maxClosedAtoms = (numCloseAtoms > maxClosedAtoms) ? numCloseAtoms : maxClosedAtoms;\r\n\r\n // normalize vNormal\r\n dist2 = vNormalX * vNormalX + vNormalY * vNormalY + vNormalZ * vNormalZ;\r\n if (numCloseAtoms > 0) {\r\n koef = 1.0 / Math.sqrt(dist2);\r\n vNormalX *= koef;\r\n vNormalY *= koef;\r\n vNormalZ *= koef;\r\n }\r\n normals[i].x = vNormalX;\r\n normals[i].y = vNormalY;\r\n normals[i].z = vNormalZ;\r\n } // for (i) all vertices\r\n\r\n return 0;\r\n }\r\n\r\n /**\r\n * Build vertex colors for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} colors - Colors for output\r\n * @param {number} radiusColorSmoothness - Radius of smoothness sphere\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildColors(numVertices, vertices, colors, radiusColorSmoothness) {\r\n const self = this;\r\n let vx = 0.0;\r\n let vy = 0.0;\r\n let vz = 0.0;\r\n let koef = 0.0;\r\n let w = 0.0;\r\n const KOEF_ADD = 0.8;\r\n\r\n const maxRadAffect = radiusColorSmoothness;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n\r\n let colorsClose = [];\r\n let weights = [];\r\n let weightsSum = 0;\r\n\r\n const gatherColors = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = 1.0 / (KOEF_ADD + koef);\r\n\r\n colorsClose.push([atom.colorX, atom.colorY, atom.colorZ]);\r\n weights.push(w); // save weights for use\r\n weightsSum += w; // calc sum of weights fo further normalization\r\n };\r\n\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n colorsClose = [];\r\n weights = [];\r\n weightsSum = 0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherColors);\r\n\r\n // normalized weighted sum of colors\r\n for (let j = 0; j < colorsClose.length; ++j) {\r\n const weightNormalized = weights[j] / weightsSum;\r\n colors[i].x += colorsClose[j][0] * weightNormalized;\r\n colors[i].y += colorsClose[j][1] * weightNormalized;\r\n colors[i].z += colorsClose[j][2] * weightNormalized;\r\n }\r\n } // for (i) all vertices\r\n return 0;\r\n }\r\n}\r\nexport default IsosurfaceBuildNormals;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for geometry (triangle mesh) representation\r\n *\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices in mesh\r\n * @param {number} maxNumTriangles Maximum possible number of triangles in mesh\r\n * @param {boolean} needVertexColors Obvious\r\n */\r\nclass IsoSurfaceGeo {\r\n constructor(maxNumVertices, maxNumTriangles, needVertexColors) {\r\n this._maxNumVertices = maxNumVertices;\r\n this._maxNumTriangles = maxNumTriangles;\r\n this._vertices = new Array(maxNumVertices);\r\n this._normals = new Array(maxNumVertices);\r\n this._colors = null;\r\n if (needVertexColors) {\r\n this._colors = new Array(maxNumVertices);\r\n }\r\n this._indices = new Array(maxNumTriangles * (1 + 2));\r\n this._numVertices = 0;\r\n this._numTriangles = 0;\r\n\r\n let i;\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._vertices[i] = new THREE.Vector3();\r\n this._normals[i] = new THREE.Vector3();\r\n }\r\n for (i = 0; i < maxNumTriangles * (1 + 2); i++) {\r\n this._indices[i] = -1;\r\n }\r\n if (needVertexColors) {\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._colors[i] = new THREE.Vector3();\r\n }\r\n }\r\n }\r\n\r\n destroy() {\r\n this._vertices = null;\r\n this._normals = null;\r\n this._indices = null;\r\n }\r\n}\r\nexport default IsoSurfaceGeo;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurfaceAtomColored from './IsoSurfaceAtomColored';\r\nimport IsosurfaceBuildNormals from './IsosurfaceBuildNormals';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport IsoSurfaceGeo from './IsoSurfaceGeo';\r\nimport chem from '../../chem';\r\nimport utils from '../../utils';\r\n\r\nconst COLOR_SIZE = 3;\r\nconst HASH_SIZE = 32768;\r\nconst { Element } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass SSIsosurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n // convert geoOut into arrays of positions, indices, normals\r\n this._innerBuild();\r\n const geoOut = this.getGeo();\r\n this.destroy();\r\n this._fromGeo(geoOut);\r\n }\r\n\r\n _fromGeo(geoOut) {\r\n let colors = null;\r\n const positions = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n const normals = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n if (geoOut._colors !== null) {\r\n colors = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n }\r\n const indices = utils.allocateTyped(Uint32Array, (1 + 2) * geoOut._numTriangles);\r\n\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++) {\r\n positions[j + 0] = (geoOut._vertices[i].x);\r\n positions[j + 1] = (geoOut._vertices[i].y);\r\n positions[j + 2] = (geoOut._vertices[i].z);\r\n normals[j + 0] = geoOut._normals[i].x;\r\n normals[j + 1] = geoOut._normals[i].y;\r\n normals[j + 2] = geoOut._normals[i].z;\r\n j += 3;\r\n }\r\n if (colors !== null) {\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++, j += 3) {\r\n colors[j + 0] = geoOut._colors[i].x;\r\n colors[j + 1] = geoOut._colors[i].y;\r\n colors[j + 2] = geoOut._colors[i].z;\r\n }\r\n }\r\n\r\n const numTri3 = geoOut._numTriangles * (1 + 2);\r\n for (let i = 0; i < numTri3; i++) {\r\n indices[i] = geoOut._indices[i];\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(positions, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(colors, 3));\r\n this.computeBoundingBox();\r\n this.computeBoundingSphere();\r\n\r\n geoOut.destroy();\r\n }\r\n\r\n convertToAtomsColored(packedArrays, atomsColored) {\r\n const { atoms, colors } = packedArrays;\r\n for (let i = 0, numAtoms = atoms.length; i < numAtoms; i++) {\r\n const vCenter = atoms[i].position;\r\n const { radius } = atoms[i].element;\r\n atomsColored[i] = new IsoSurfaceAtomColored(vCenter, radius);\r\n const nm = atoms[i].element.number;\r\n atomsColored[i].atomType = this.getType(nm);\r\n let cIdx = COLOR_SIZE * i;\r\n atomsColored[i].colorX = colors[cIdx++];\r\n atomsColored[i].colorY = colors[cIdx++];\r\n atomsColored[i].colorZ = colors[cIdx];\r\n atomsColored[i].srcAtom = atoms[i];\r\n }\r\n }\r\n\r\n getGeo() {\r\n return this.geoOut;\r\n }\r\n\r\n destroy() {\r\n this.atoms = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n }\r\n\r\n /**\r\n * Calculates bounding box for array with spheres (atoms)\r\n *\r\n * @param {Object} atoms Atoms array\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n */\r\n getBoundingBox(atoms, vBoxMin, vBoxMax) {\r\n const bigNum = 10000000.0;\r\n\r\n vBoxMin.x = vBoxMin.y = vBoxMin.z = bigNum;\r\n vBoxMax.x = vBoxMax.y = vBoxMax.z = 0 - bigNum;\r\n\r\n const probeRadius2 = this.probeRadius * this.atomRadiusScale;\r\n let radMax = 0.0;\r\n for (let i = 0, num = atoms.length; i < num; i++) {\r\n const vCenter = atoms[i].coord;\r\n const rad = atoms[i].radius + probeRadius2;\r\n radMax = (rad > radMax) ? rad : radMax;\r\n if (vCenter.x - rad < vBoxMin.x) {\r\n vBoxMin.x = vCenter.x - rad;\r\n }\r\n if (vCenter.y - rad < vBoxMin.y) {\r\n vBoxMin.y = vCenter.y - rad;\r\n }\r\n if (vCenter.z - rad < vBoxMin.z) {\r\n vBoxMin.z = vCenter.z - rad;\r\n }\r\n if (vCenter.x + rad > vBoxMax.x) {\r\n vBoxMax.x = vCenter.x + rad;\r\n }\r\n if (vCenter.y + rad > vBoxMax.y) {\r\n vBoxMax.y = vCenter.y + rad;\r\n }\r\n if (vCenter.z + rad > vBoxMax.z) {\r\n vBoxMax.z = vCenter.z + rad;\r\n }\r\n }\r\n vBoxMin.x -= radMax;\r\n vBoxMin.y -= radMax;\r\n vBoxMin.z -= radMax;\r\n vBoxMax.x += radMax;\r\n vBoxMax.y += radMax;\r\n vBoxMax.z += radMax;\r\n }\r\n\r\n /**\r\n * Calculate (x,y,z) cordinate of the cell corner point\r\n *\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {number} x Cell integer x coordinate\r\n * @param {number} y Cell integer y coordinate\r\n * @param {number} z Cell integer z coordinate\r\n * @param {number} numPoints NUm points in cell on side\r\n * @param {Vector3} vOut Output vector\r\n */\r\n getCornerCoord(vBoxMin, vBoxMax, x, y, z, numPoints, vOut) {\r\n const invNP = 1.0 / (numPoints - 1.0);\r\n const tx = x * invNP;\r\n const ty = y * invNP;\r\n const tz = z * invNP;\r\n\r\n vOut.x = vBoxMin.x * (1.0 - tx) + vBoxMax.x * tx;\r\n vOut.y = vBoxMin.y * (1.0 - ty) + vBoxMax.y * ty;\r\n vOut.z = vBoxMin.z * (1.0 - tz) + vBoxMax.z * tz;\r\n }\r\n\r\n /**\r\n * Calculate point of intersection of sphere surface\r\n * and cell edge, given by [indexA, indexB] line\r\n *\r\n * @param {number} indexA Cell vertex index in [0..11]\r\n * @param {number} indexB Cell vertex index in [0..11]\r\n * @param {array} sign Sign array for all 8 vertices\r\n * @param {object} cube Cube\r\n * @param {number} indexPointValue for value placement\r\n * @param {Vector3} vOut Point of intersection\r\n */\r\n buildEdgePoint(indexA, indexB, sign, cube, indexPointValue, vOut) {\r\n if (sign[indexA] ^ sign[indexB]) {\r\n const cTwentyFour = 24;\r\n const t = (0 - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA])\r\n / (cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexB]\r\n - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA]);\r\n const xa = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 0];\r\n const ya = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 1];\r\n const za = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 2];\r\n const xb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 0];\r\n const yb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 1];\r\n const zb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 2];\r\n\r\n vOut.x = xa * (1.0 - t) + xb * t;\r\n vOut.y = ya * (1.0 - t) + yb * t;\r\n vOut.z = za * (1.0 - t) + zb * t;\r\n }\r\n }\r\n\r\n /**\r\n * Check if triangle is visible (vertices are close to atoms included in visibility set)\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} true if triangle is visible\r\n */\r\n isTriangleVisible(v0, v1, v2) {\r\n const a0 = this.voxelWorld.getClosestAtom(v0);\r\n const a1 = this.voxelWorld.getClosestAtom(v1);\r\n const a2 = this.voxelWorld.getClosestAtom(v2);\r\n if (a0 === null || a1 === null || a2 === null\r\n || a0.srcAtom === null || a1.srcAtom === null || a2.srcAtom === null) {\r\n return false;\r\n }\r\n\r\n return this.visibilitySelector.includesAtom(a0.srcAtom)\r\n && this.visibilitySelector.includesAtom(a1.srcAtom)\r\n && this.visibilitySelector.includesAtom(a2.srcAtom);\r\n }\r\n\r\n /**\r\n * Add triangle to result geometry\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} false if no more triangles can be added\r\n */\r\n addTriangle(v0, v1, v2) {\r\n if (this.visibilitySelector && !this.isTriangleVisible(v0, v1, v2)) {\r\n return true;\r\n }\r\n\r\n const geo = this.geoOut;\r\n\r\n if (geo._numTriangles >= this.maxNumTriangles) {\r\n return false;\r\n }\r\n\r\n // Add vertex with optimize\r\n const indInGeo0 = this.addVertexToGeo(geo, v0);\r\n const indInGeo1 = this.addVertexToGeo(geo, v1);\r\n const indInGeo2 = this.addVertexToGeo(geo, v2);\r\n if ((indInGeo0 | indInGeo1 | indInGeo2) < 0) {\r\n return false;\r\n }\r\n\r\n const itr = 3 * geo._numTriangles;\r\n geo._indices[itr + 0] = indInGeo0;\r\n geo._indices[itr + 1] = indInGeo1;\r\n geo._indices[itr + 2] = indInGeo2;\r\n geo._numTriangles++;\r\n return true;\r\n }\r\n\r\n /**\r\n * Build result geometry (triangle mesh) from marching cube cells\r\n *\r\n * @param {number} meshRes Marchnig cube vertex count on each side\r\n * @param {Vector3} vBoxMin Bounding box point min\r\n * @param {Vector3} vBoxMax Bounding box point max\r\n * @param {number} corners float values array for each cube point\r\n * @param {Vector3} vCellStep vector to next cube cell diagonal point\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} 0, if success (<0) is error\r\n */\r\n buildGeoFromCorners(meshRes, vBoxMin, vBoxMax, corners, vCellStep, cube) {\r\n const arrSize = 12;\r\n const cNumVerts = 8;\r\n const numCells = meshRes - 1;\r\n const side = meshRes;\r\n const side2 = meshRes * meshRes;\r\n\r\n const vaEdges = new Array(arrSize);\r\n for (let i = 0; i < arrSize; i++) {\r\n vaEdges[i] = new THREE.Vector3();\r\n }\r\n const sign = [];\r\n for (let i = 0; i < cNumVerts; i++) {\r\n sign[i] = 1.0;\r\n }\r\n const vCorner = new THREE.Vector3();\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n if (!cube.hasIntersection[indCell]) {\r\n // next cell\r\n indCell++;\r\n continue;\r\n }\r\n const bitsInside = cube.bitsInside[indCell];\r\n\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, meshRes, vCorner);\r\n\r\n const indPointValues = indCell * (2 << (2 + 2));\r\n for (let i = 0, j = 0; i < cNumVerts; i++) {\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.x;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.y;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.z;\r\n }\r\n\r\n cube.pointsValuesLinear[indPointValues + 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 2 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3] += vCellStep.x;\r\n\r\n cube.pointsValuesLinear[indPointValues + 2 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 3 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 2] += vCellStep.z;\r\n\r\n cube.pointsValuesLinear[indPointValues + 4 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 1] += vCellStep.y;\r\n\r\n // now current cell has intersections (from -x to +x) on some cube edges\r\n const indValues = indPointValues + 24;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n sign[i] = (cube.pointsValuesLinear[indValues + i] < 0.0) ? 1 : 0;\r\n }\r\n\r\n this.buildEdgePoint(0, 1, sign, cube, indPointValues, vaEdges[0]);\r\n this.buildEdgePoint(1, 2, sign, cube, indPointValues, vaEdges[1]);\r\n this.buildEdgePoint(2, 3, sign, cube, indPointValues, vaEdges[2]);\r\n this.buildEdgePoint(3, 0, sign, cube, indPointValues, vaEdges[3]);\r\n\r\n this.buildEdgePoint(4, 5, sign, cube, indPointValues, vaEdges[4]);\r\n this.buildEdgePoint(5, 6, sign, cube, indPointValues, vaEdges[5]);\r\n this.buildEdgePoint(6, 7, sign, cube, indPointValues, vaEdges[6]);\r\n this.buildEdgePoint(7, 4, sign, cube, indPointValues, vaEdges[7]);\r\n\r\n this.buildEdgePoint(0, 4, sign, cube, indPointValues, vaEdges[8]);\r\n this.buildEdgePoint(1, 5, sign, cube, indPointValues, vaEdges[9]);\r\n this.buildEdgePoint(2, 6, sign, cube, indPointValues, vaEdges[10]);\r\n this.buildEdgePoint(3, 7, sign, cube, indPointValues, vaEdges[11]);\r\n\r\n const offs = bitsInside * (2 << (1 + 2));\r\n for (let numTri = 0, indTri = 0; numTri < (2 + 2 + 2); numTri++, indTri += 3) {\r\n // s_triIndicesMarchCube is external array, defined in mold_ind.js\r\n const i0 = cube.striIndicesMarchCube[offs + indTri];\r\n if (i0 < 0) {\r\n break;\r\n }\r\n const i1 = cube.striIndicesMarchCube[offs + indTri + 1];\r\n const i2 = cube.striIndicesMarchCube[offs + indTri + 2];\r\n\r\n if (!this.addTriangle(vaEdges[i0], vaEdges[i1], vaEdges[i2])) {\r\n return 0 - 2;\r\n }\r\n } // for numTri\r\n\r\n // next cell (cube)\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return 0;\r\n }\r\n\r\n /**\r\n * Returns number of cell with intersection with at least one sphere.\r\n * Using this number, we can estimate required number of vertices\r\n * and triangles to build result mesh.\r\n *\r\n * @param {number} side Number of points in cube voxels\r\n * @param {number} numCells Number of cells in cube voxels (per direction)\r\n * @param {array} corners Array of float values for cube corner points\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} numIntersectedCells\r\n */\r\n getNumIntersectedCells(side, numCells, corners, cube) {\r\n const side2 = side * side;\r\n const cNumVerts = 8;\r\n let numIntersectedCells = 0;\r\n\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n const cubeValuesIndex = indCell * (2 << (2 + 2)) + 24;\r\n const indCorner = x + indZ + indY;\r\n\r\n cube.pointsValuesLinear[cubeValuesIndex] = corners[indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 1] = corners[indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 2] = corners[indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 3] = corners[indCorner + side];\r\n cube.pointsValuesLinear[cubeValuesIndex + 4] = corners[side2 + indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 5] = corners[side2 + indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 6] = corners[side2 + indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 7] = corners[side2 + indCorner + side];\r\n\r\n // check read exception\r\n // assert(side2 + indCorner + side + 1 < side3);\r\n\r\n // get bit flags inside\r\n let bitsInside = 0;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n if (cube.pointsValuesLinear[cubeValuesIndex + i] < 0.0) {\r\n bitsInside |= (1 << i);\r\n }\r\n }\r\n\r\n if ((bitsInside === 0) || (bitsInside === ((1 << cNumVerts) - 1))) {\r\n cube.hasIntersection[indCell] = false;\r\n } else {\r\n cube.hasIntersection[indCell] = true;\r\n numIntersectedCells++;\r\n }\r\n cube.bitsInside[indCell] = bitsInside;\r\n // next cell\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return numIntersectedCells;\r\n }\r\n\r\n getType(letter) {\r\n const atomT = [0, 0, 1, 1, 2, 6, 3, 6, 4, 6, 5, 6, 6, 0, 7, 3, 8, 2, 9, 6, 10, 6, 11, 6, 12, 6, 13, 6, 14, 6, 15, 4,\r\n 16, 5, 17, 6, 18, 6, 19, 6, 20, 6, 21, 6, 22, 6, 23, 6, 24, 6, 25, 6, 26, 6, 27, 6, 28, 6, 29, 6, 30, 6, 31, 6,\r\n 32, 6, 33, 6, 34, 6, 35, 6, 36, 6, 37, 6, 38, 6, 39, 6, 40, 6, 41, 6, 42, 6, 43, 6, 44, 6, 45, 6, 46, 6, 47, 6,\r\n 48, 6, 49, 6, 50, 6, 51, 6, 52, 6, 53, 6, 54, 6, 55, 6, 56, 6, 57, 6, 58, 6, 59, 6, 60, 6, 61, 6, 62, 6, 63, 6,\r\n 64, 6, 65, 6, 66, 6, 67, 6, 68, 6, 69, 6, 70, 6, 71, 6, 72, 6, 73, 6, 74, 6, 75, 6, 76, 6, 77, 6, 78, 6, 79, 6,\r\n 80, 6, 81, 6, 82, 6, 83, 6, 84, 6, 85, 6, 86, 6, 87, 6, 88, 6, 89, 6, 90, 6, 91, 6, 92, 6, 93, 6, 94, 6, 95, 6,\r\n 96, 6, 97, 6, 98, 6, 99, 6, 100, 6, 101, 6, 102, 6, 103, 6, 104, 6, 105, 6, 106, 6, 107, 6, 108, 6, 109, 6];\r\n\r\n if (letter < 1 || letter > atomT.length / 2\r\n || (Object.keys(Element.ByAtomicNumber).length * 2) !== atomT.length) {\r\n throw new Error('atomT.length should be equal Element.ByAtomicNumber.length * 2');\r\n }\r\n return atomT[letter * 2];\r\n }\r\n\r\n /**\r\n * Calculate values for marching cube grid points\r\n * positive values are outside sphere, negative - is inside\r\n *\r\n * @param {array} corners array of float values\r\n * @param {number} side Number of point in cube in 1 dimennsion\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {array} atoms Array of input atoms\r\n * @param {number} probeRad radius for atom probing\r\n */\r\n calculateGridCorners(corners, side, vBoxMin, vBoxMax, atoms, probeRad) {\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const vCorner = new THREE.Vector3();\r\n const vDif = new THREE.Vector3();\r\n\r\n const aLot = +1.0e12;\r\n\r\n for (let i = 0; i < side3; i++) {\r\n corners[i] = aLot; // to large value\r\n }\r\n\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n for (let s = 0, numAtoms = atoms.length; s < numAtoms; s++) {\r\n const atom = atoms[s];\r\n const radius = atom.radius + probeRad;\r\n\r\n const fx = ((atom.coord.x - radius) - vBoxMin.x) * xScale;\r\n const fy = ((atom.coord.y - radius) - vBoxMin.y) * yScale;\r\n const fz = ((atom.coord.z - radius) - vBoxMin.z) * zScale;\r\n\r\n const indXMin = Math.floor(fx);\r\n const indYMin = Math.floor(fy);\r\n const indZMin = Math.floor(fz);\r\n\r\n let indXMax = Math.floor(((atom.coord.x + radius) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((atom.coord.y + radius) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((atom.coord.z + radius) - vBoxMin.z) * zScale);\r\n\r\n indXMax++;\r\n indYMax++;\r\n indZMax++;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let y = indYMin; y <= indYMax; y++) {\r\n const indY = y * side2;\r\n for (let z = indZMin; z <= indZMax; z++) {\r\n const indZ = z * side;\r\n for (let x = indXMin; x <= indXMax; x++) {\r\n const ind = indY + indZ + x;\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, side, vCorner);\r\n vDif.x = vCorner.x - atom.coord.x;\r\n vDif.y = vCorner.y - atom.coord.y;\r\n vDif.z = vCorner.z - atom.coord.z;\r\n const distToSphere = Math.sqrt(vDif.x * vDif.x + vDif.y * vDif.y + vDif.z * vDif.z);\r\n // val: < 0, if inside sphere\r\n // val: > 0, if outside sphere\r\n const val = distToSphere - radius;\r\n if (val < corners[ind]) {\r\n corners[ind] = val;\r\n }\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n } // for (s)\r\n }\r\n\r\n /**\r\n * Create memory pool for vertex hash management\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices (that will be build)\r\n * @param {number} maxNumTriangles Maximum possible number of triangles (that will be build)\r\n * @returns {number} 0, if success. (<0) is non memory\r\n */\r\n createVertexHash(maxNumVertices, maxNumTriangles) {\r\n this.hashLines = utils.allocateTyped(Int32Array, HASH_SIZE * 2);\r\n if (this.hashLines === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < HASH_SIZE; i++) {\r\n this.hashLines[j++] = 0; // num vertices in this hash line\r\n this.hashLines[j++] = 0 - 1; // index of the first entry\r\n }\r\n\r\n this.maxNumVertices = maxNumVertices;\r\n this.maxNumTriangles = maxNumTriangles;\r\n\r\n this.numHashEtriesAllocated = maxNumVertices;\r\n this.hashEntries = utils.allocateTyped(Int32Array, 2 * this.numHashEtriesAllocated);\r\n if (this.hashEntries === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < this.numHashEtriesAllocated; i++) {\r\n this.hashEntries[j++] = 0 - 1; // index of vertex\r\n this.hashEntries[j++] = 0 - 1; // next hash entry index\r\n }\r\n this.numHashEntryIndex = 0;\r\n return 0;\r\n }\r\n\r\n /**\r\n * Allocate and return new hash entry. Just check possible amount.\r\n *\r\n * @returns {number} index of hash entry, that can be used for geometry add vertex functionality\r\n */\r\n getNewHashEntry() {\r\n if (this.numHashEntryIndex < this.numHashEtriesAllocated) {\r\n const i = this.numHashEntryIndex;\r\n this.numHashEntryIndex++;\r\n return i;\r\n }\r\n return 0 - 1;\r\n }\r\n\r\n /**\r\n * Add vertex to geometry structure\r\n * using vertex hash table to quickly check, is this vertex already exist in geometry\r\n *\r\n * @param {object} geoOut Geometry to build\r\n * @param {Vector3} vAdd Vertex to add\r\n * @returns {number} index of added (or existing) vertex in geometry.\r\n */\r\n addVertexToGeo(geoOut, vAdd) {\r\n let entry;\r\n const oneHynberes = 0.01;\r\n const n815851 = 815851;\r\n const n37633 = 37633;\r\n const n2453543 = 2453543;\r\n const r106 = 1.0e-6;\r\n\r\n const hashResolution = this.marCubeResoultion << 2;\r\n const v = new THREE.Vector3();\r\n const ix = Math.floor(hashResolution * (vAdd.x - this.vBoxMin.x) / (this.vBoxMax.x + oneHynberes - this.vBoxMin.x));\r\n const iy = Math.floor(hashResolution * (vAdd.y - this.vBoxMin.y) / (this.vBoxMax.y + oneHynberes - this.vBoxMin.y));\r\n const iz = Math.floor(hashResolution * (vAdd.z - this.vBoxMin.z) / (this.vBoxMax.z + oneHynberes - this.vBoxMin.z));\r\n let iHash = ix * n815851 + iz * n37633 + iy * n2453543;\r\n iHash &= (HASH_SIZE - 1);\r\n const hLineIndex = iHash + iHash;\r\n\r\n // search vertex via hash\r\n // search in hash list\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n for (entry = this.hashLines[hLineIndex + 1]; entry >= 0; entry = this.hashEntries[entry * 2 + 1]) {\r\n const ind = this.hashEntries[entry * 2 + 0]; // vertex index\r\n v.copy(geoOut._vertices[ind]);\r\n v.x -= vAdd.x;\r\n v.y -= vAdd.y;\r\n v.z -= vAdd.z;\r\n const dot2 = v.x * v.x + v.y * v.y + v.z * v.z;\r\n if (dot2 < r106) {\r\n return ind;\r\n } // if (found)\r\n } // for (entry)\r\n } // search\r\n\r\n // add new vertex to geometry\r\n if (geoOut._numVertices >= this.maxNumVertices) {\r\n return 0 - 1;\r\n }\r\n\r\n const iVertAdd = geoOut._numVertices;\r\n geoOut._vertices[iVertAdd].copy(vAdd);\r\n\r\n // add to hash\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n entry = this.getNewHashEntry();\r\n if (entry < 0) {\r\n return 0 - 1;\r\n }\r\n const entryFirst = this.hashLines[hLineIndex + 1];\r\n this.hashLines[hLineIndex + 1] = entry;\r\n this.hashEntries[entry * 2 + 0] = iVertAdd;\r\n this.hashEntries[entry * 2 + 1] = entryFirst;\r\n\r\n this.hashLines[hLineIndex + 0]++; // num vertices in line ++\r\n }\r\n geoOut._numVertices++;\r\n return iVertAdd;\r\n }\r\n\r\n /**\r\n *\r\n * @param {number} side some placeholder description\r\n * @param {number} probeSphereRadius some placeholder description\r\n * @param {object} vBoxMin some placeholder description\r\n * @param {object} vBoxMax some placeholder description\r\n * @param {object} geoOut some placeholder description\r\n * @param {object} corners some placeholder description\r\n * @returns {number} always 0\r\n */\r\n modifyExcludedFromGeo(\r\n side,\r\n probeSphereRadius,\r\n vBoxMin,\r\n vBoxMax,\r\n geoOut,\r\n corners,\r\n ) {\r\n let ind;\r\n let distToSphere;\r\n let distToBorder;\r\n const r11 = 1.1;\r\n\r\n function innerBlockWorkAround() {\r\n if (distToBorder > 0.0) {\r\n // point is inside probe sphere\r\n if (corners[ind] < 0.0) {\r\n corners[ind] = distToBorder; // was inside surface, now is oustide ( > 0)\r\n }\r\n if (distToBorder > corners[ind]) {\r\n corners[ind] = distToBorder; // find positive maximum\r\n }\r\n } else if (distToBorder > corners[ind]) { // point is outside sphere\r\n corners[ind] = distToBorder; // find negative maximum\r\n }\r\n }\r\n\r\n const side2 = side * side;\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n const probeSpRad2 = (probeSphereRadius * 2) * (probeSphereRadius * 2);\r\n const sideInv = 1.0 / (side - 1);\r\n\r\n for (let i = 0; i < geoOut._numVertices; i++) {\r\n const vCenter = geoOut._vertices[i];\r\n\r\n const radEst = probeSphereRadius * r11;\r\n\r\n let indXMin = Math.floor(((vCenter.x - radEst) - vBoxMin.x) * xScale);\r\n let indYMin = Math.floor(((vCenter.y - radEst) - vBoxMin.y) * yScale);\r\n let indZMin = Math.floor(((vCenter.z - radEst) - vBoxMin.z) * zScale);\r\n\r\n let indXMax = Math.floor(((vCenter.x + radEst) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((vCenter.y + radEst) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((vCenter.z + radEst) - vBoxMin.z) * zScale);\r\n\r\n indXMin = (indXMin >= 0) ? indXMin : 0;\r\n indYMin = (indYMin >= 0) ? indYMin : 0;\r\n indZMin = (indZMin >= 0) ? indZMin : 0;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let iy = indYMin; iy <= indYMax; iy++) {\r\n const indY = iy * side2;\r\n for (let iz = indZMin; iz <= indZMax; iz++) {\r\n const indZ = iz * side;\r\n for (let ix = indXMin; ix <= indXMax; ix++) {\r\n ind = indY + indZ + ix;\r\n // getCornerCoord(vBoxMin, vBoxMax, ix, iy, iz, side, &vCorner);\r\n let t = ix * sideInv;\r\n const xCorner = vBoxMin.x * (1.0 - t) + vBoxMax.x * t;\r\n t = iy * sideInv;\r\n const yCorner = vBoxMin.y * (1.0 - t) + vBoxMax.y * t;\r\n t = iz * sideInv;\r\n const zCorner = vBoxMin.z * (1.0 - t) + vBoxMax.z * t;\r\n\r\n const dx = xCorner - vCenter.x;\r\n const dy = yCorner - vCenter.y;\r\n const dz = zCorner - vCenter.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 < probeSpRad2) {\r\n distToSphere = Math.sqrt(dist2);\r\n distToBorder = -(distToSphere - probeSphereRadius);\r\n innerBlockWorkAround();\r\n } // if (dist from corner point to sphere center more 2 radiuses)\r\n } // for (ix)\r\n } // for (iz)\r\n } // for (iy)\r\n } // for (i) all geo vertices\r\n return 0;\r\n }\r\n\r\n _innerBuild() {\r\n let ok;\r\n const expandFactor = 1.2;\r\n\r\n // performance test\r\n // this.performanceTest();\r\n\r\n // Create temporary atoms (but colored)\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n this.complex = this._opts.parent;\r\n this.atoms = packedArrays.atoms;\r\n this.meshResolution = this._opts.gridSpacing;\r\n this.atomRadiusScale = this._opts.radScale;\r\n this.colorMode = this._opts.colorMode;\r\n this.probeRadius = this._opts.probeRadius;\r\n this.useVertexColors = true;\r\n this.excludeProbe = this._opts.excludeProbe;\r\n this.visibilitySelector = this._opts.visibilitySelector;\r\n\r\n this.geoOut = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n this.numHashEtriesAllocated = 0;\r\n this.numHashEntryIndex = 0;\r\n this.maxNumVertices = 0;\r\n this.maxNumTriangles = 0;\r\n\r\n const atomsColored = new Array(this.atoms.length);\r\n this.convertToAtomsColored(packedArrays, atomsColored);\r\n\r\n // find bbox for spheres scene\r\n const vBoxMin = this.vBoxMin = new THREE.Vector3();\r\n const vBoxMax = this.vBoxMax = new THREE.Vector3();\r\n this.getBoundingBox(atomsColored, vBoxMin, vBoxMax);\r\n\r\n const marCubeResoultion = this.marCubeResoultion = this.meshResolution * (2 + 2);\r\n\r\n // build grid corners for Marching cube algorithm\r\n const side = marCubeResoultion;\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const corners = utils.allocateTyped(Float32Array, side3);\r\n const rProbeRadius = this.probeRadius * this.atomRadiusScale;\r\n\r\n this.calculateGridCorners(corners, side, vBoxMin, vBoxMax, atomsColored, rProbeRadius);\r\n\r\n const numCells = marCubeResoultion - 1;\r\n const cube = new IsoSurfaceMarchCube();\r\n ok = cube.create(numCells);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // copy corners to cells\r\n const vCellStep = new THREE.Vector3();\r\n vCellStep.x = (vBoxMax.x - vBoxMin.x) / numCells;\r\n vCellStep.y = (vBoxMax.y - vBoxMin.y) / numCells;\r\n vCellStep.z = (vBoxMax.z - vBoxMin.z) / numCells;\r\n\r\n let numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n let maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n let maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n\r\n // build voxel world (used to check triangle-to-atom tie and to calculate normals and colors)\r\n let probeRadForNormalsColors = rProbeRadius;\r\n if (this.excludeProbe) {\r\n probeRadForNormalsColors = 0.01;\r\n }\r\n this.voxelWorld = new IsosurfaceBuildNormals(\r\n atomsColored.length,\r\n atomsColored,\r\n vBoxMin,\r\n vBoxMax,\r\n probeRadForNormalsColors,\r\n );\r\n this.voxelWorld.createVoxels();\r\n\r\n ok = this.buildGeoFromCorners(marCubeResoultion, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n if (this.excludeProbe) {\r\n // using 3d mesh (geoOut) as a surface points\r\n // move probe sphere and try to minimuze corners values\r\n this.modifyExcludedFromGeo(side, rProbeRadius, vBoxMin, vBoxMax, this.geoOut, corners);\r\n\r\n // delete old builded geo\r\n this.geoOut._vertices = null;\r\n this.geoOut._colors = null;\r\n this.geoOut._indices = null;\r\n this.geoOut._normals = null;\r\n this.geoOut._numVertices = 0;\r\n this.geoOut._numTriangles = 0;\r\n this.geoOut = null;\r\n\r\n // estimage geo vertices budget again\r\n numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n // creates empty new geometry\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // build vertices and triangles from corners values\r\n ok = this.buildGeoFromCorners(side, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n }\r\n\r\n // build vertex normals\r\n this.voxelWorld.buildNormals(this.geoOut._vertices.length, this.geoOut._vertices, this.geoOut._normals);\r\n // More value : more smooth color mixing\r\n // value about 0.7: very rough colors borders\r\n let radiusColorSmoothness = 6.5;\r\n if (this.excludeProbe) {\r\n radiusColorSmoothness -= 1.5;\r\n }\r\n if (this.useVertexColors) {\r\n this.voxelWorld.buildColors(\r\n this.geoOut._vertices.length,\r\n this.geoOut._vertices,\r\n this.geoOut._colors,\r\n radiusColorSmoothness,\r\n );\r\n }\r\n this.voxelWorld.destroyVoxels();\r\n this.voxelWorld = null;\r\n\r\n // remove objects\r\n cube.destroy();\r\n\r\n return ok;\r\n }\r\n}\r\n\r\n// All code below must be erased from every device and each developer's memory\r\n\r\nexport default SSIsosurfaceGeometry;\r\n","import * as THREE from 'three';\r\nimport EventDispatcher from '../../utils/EventDispatcher';\r\n\r\nfunction createLabel(fieldTxt, className) {\r\n const text = document.createElement('div');\r\n text.className = className;\r\n\r\n if (typeof fieldTxt === 'string') {\r\n const spanText = document.createElement('span');\r\n spanText.style.fontSize = '150%';\r\n const strings = fieldTxt.split('\\n');\r\n\r\n for (let i = 0, n = strings.length; i < n; ++i) {\r\n const spanNodeP = document.createElement('span');\r\n const spanNodeText = document.createTextNode(strings[i]);\r\n spanNodeP.appendChild(spanNodeText);\r\n spanText.appendChild(spanNodeP);\r\n if (i < n - 1) {\r\n spanText.appendChild(document.createElement('br'));\r\n }\r\n }\r\n\r\n text.appendChild(spanText);\r\n } else {\r\n text.appendChild(fieldTxt);\r\n }\r\n text.worldPos = new THREE.Vector3();\r\n return text;\r\n}\r\nclass LabelsGeometry extends EventDispatcher {\r\n constructor(instanceCount, opts) {\r\n super();\r\n this._opts = opts;\r\n this.items = [];\r\n this.needsUpdate = false;\r\n\r\n let xTranslation = -50;\r\n let yTranslation = -50;\r\n switch (opts.horizontalAlign) {\r\n case 'left':\r\n xTranslation = 0;\r\n break;\r\n case 'right':\r\n xTranslation = -100;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n switch (opts.verticalAlign) {\r\n case 'top':\r\n yTranslation = -100;\r\n break;\r\n case 'bottom':\r\n yTranslation = 0;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n const deltaPos = new THREE.Vector3(opts.dx || 0, opts.dy || 0, opts.dz || 0);\r\n this.userData = {\r\n translation: `translate(${xTranslation}%, ${yTranslation}%)`,\r\n offset: deltaPos,\r\n };\r\n }\r\n\r\n setItem(itemIdx, itemPos, fieldTxt) {\r\n const opts = this._opts;\r\n const text = this.items[itemIdx] || createLabel(fieldTxt, 'label');\r\n\r\n text.worldPos.copy(itemPos);\r\n text.style.textAlign = opts.horizontalAlign;\r\n text.style.verticalAlign = opts.verticalAlign;\r\n this.items[itemIdx] = text;\r\n }\r\n\r\n setColor(itemIdx, fColor, bColor) {\r\n const text = this.items[itemIdx];\r\n text.opts = {\r\n color: fColor,\r\n background: bColor,\r\n };\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.needsUpdate = true;\r\n this.dispatchEvent({ type: 'update' });\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n }\r\n\r\n // unimplemented functions\r\n raycast() {\r\n }\r\n\r\n setOpacity() {\r\n\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\n\r\nexport default LabelsGeometry;\r\n","import InstancedSpheresGeometry from './InstancedSpheresGeometry';\r\nimport SimpleSpheresGeometry from './SimpleSpheresGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport Instanced2CCylindersGeometry from './Instanced2CCylindersGeometry';\r\nimport ExtrudedObjectsGeometry from './ExtrudedObjectsGeometry';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport TwoColorLinesGeometry from './TwoColorLinesGeometry';\r\nimport CrossGeometry from './CrossGeometry';\r\nimport QuickSurfGeometry from './QuickSurfGeometry';\r\nimport ContactSurfaceGeometry from './ContactSurfaceGeometry';\r\nimport SSIsosurfaceGeometry from './SSIsosurfaceGeometry';\r\nimport LabelsGeometry from './LabelsGeometry';\r\n\r\nexport default {\r\n InstancedSpheresGeometry,\r\n SimpleSpheresGeometry,\r\n Simple2CCylindersGeometry,\r\n Instanced2CCylindersGeometry,\r\n ExtrudedObjectsGeometry,\r\n ChunkedLinesGeometry,\r\n TwoColorLinesGeometry,\r\n CrossGeometry,\r\n QuickSurfGeometry,\r\n ContactSurfaceGeometry,\r\n SSIsosurfaceGeometry,\r\n LabelsGeometry,\r\n};\r\n","export default {\r\n\r\n precision: 'mediump',\r\n\r\n /**\r\n *\r\n * @param {THREE.WebGLRenderer} renderer\r\n */\r\n init(renderer) {\r\n this.precision = renderer.capabilities.getMaxPrecision('highp');\r\n },\r\n};\r\n","import * as THREE from 'three';\r\n\r\nconst noiseWidth = 4;\r\nconst noiseHeight = 4;\r\nconst _noiseData = new Uint8Array([\r\n 24, 52, 0, 255, 254, 145, 0, 255, 122, 0, 0, 255, 7, 170, 0, 255,\r\n 34, 214, 0, 255, 173, 8, 0, 255, 86, 249, 0, 255, 160, 4, 0, 255,\r\n 226, 46, 0, 255, 224, 211, 0, 255, 3, 157, 0, 255, 174, 247, 0, 255,\r\n 12, 182, 0, 255, 220, 216, 0, 255, 1, 109, 0, 255, 253, 154, 0, 255,\r\n]);\r\nconst _noiseWrapS = THREE.RepeatWrapping;\r\nconst _noiseWrapT = THREE.RepeatWrapping;\r\nconst _noiseMinFilter = THREE.NearestFilter;\r\nconst _noiseMagFilter = THREE.NearestFilter;\r\nconst _noiseMapping = THREE.UVMapping;\r\nconst noiseTexture = new THREE.DataTexture(\r\n _noiseData,\r\n noiseWidth,\r\n noiseHeight,\r\n THREE.RGBAFormat,\r\n THREE.UnsignedByteType,\r\n _noiseMapping,\r\n _noiseWrapS,\r\n _noiseWrapT,\r\n _noiseMagFilter,\r\n _noiseMinFilter,\r\n 1,\r\n);\r\nnoiseTexture.needsUpdate = true;\r\n\r\nexport default {\r\n noiseWidth,\r\n noiseHeight,\r\n noiseTexture,\r\n};\r\n","import * as THREE from 'three';\r\nimport vertexShader from './Uber.vert';\r\nimport fragmentShader from './Uber.frag';\r\nimport capabilities from '../capabilities';\r\nimport noise from '../noiseTexture';\r\n\r\n// Length of _samplesKernel is used in Uber.frag\r\n// If you want to change length of _samplesKernel, please, remember change it in Uber.frag too.\r\n// You can easy find places for replace using word:_samplesKernel\r\nconst _samplesKernel = [\r\n new THREE.Vector2(-0.541978, 0.840393),\r\n new THREE.Vector2(0.125533, -0.992089),\r\n new THREE.Vector2(0.374329, 0.927296),\r\n new THREE.Vector2(-0.105475, 0.994422),\r\n];\r\n\r\nconst defaultUniforms = THREE.UniformsUtils.merge([\r\n\r\n THREE.UniformsLib.fog,\r\n THREE.UniformsLib.lights,\r\n\r\n {\r\n // are updated automatically by three.js (see THREE.ShaderLib.common)\r\n diffuse: { value: new THREE.Color(0xeeeeee) },\r\n opacity: { value: 1.0 },\r\n\r\n specular: { type: 'c', value: new THREE.Color(0x111111) },\r\n shininess: { type: 'f', value: 30 },\r\n fixedColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n zOffset: { type: 'f', value: 0.0 },\r\n zClipValue: { type: 'f', value: 0.0 },\r\n clipPlaneValue: { type: 'f', value: 0.0 },\r\n nearPlaneValue: { type: 'f', value: -0.5 },\r\n invModelViewMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n world2colorMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n dashedLineSize: { type: 'f', value: 0.1 },\r\n dashedLinePeriod: { type: 'f', value: 0.2 },\r\n projMatrixInv: { type: '4fv', value: new THREE.Matrix4() },\r\n viewport: { type: 'v2', value: new THREE.Vector2() },\r\n lineWidth: { type: 'f', value: 2.0 },\r\n // default value must be the same as settings\r\n fogAlpha: { type: 'f', value: 1.0 },\r\n samplesKernel: { type: 'v2v', value: null },\r\n noiseTex: { type: 't', value: null },\r\n noiseTexelSize: { type: 'v2', value: null },\r\n srcTexelSize: { type: 'v2', value: null },\r\n },\r\n\r\n]);\r\n\r\nconst uberOptionNames = [\r\n 'shininess',\r\n 'opacity',\r\n 'zOffset',\r\n 'diffuse',\r\n 'specular',\r\n 'fixedColor',\r\n 'zClipCoef',\r\n 'zClipValue',\r\n 'clipPlaneValue',\r\n 'world2colorMatrix',\r\n 'dashedLineSize',\r\n 'dashedLinePeriod',\r\n 'projMatrixInv',\r\n 'viewport',\r\n 'lineWidth',\r\n 'fogAlpha',\r\n 'samplesKernel',\r\n 'noiseTex',\r\n 'noiseTexelSize',\r\n 'srcTexelSize',\r\n];\r\n\r\n// properties that convert to uniforms\r\nconst uberOptions = {\r\n diffuse: new THREE.Color(0xffffff), // used in phong lighting\r\n specular: new THREE.Color(0x111111), // used in phong lighting\r\n shininess: 30, // used in phong lighting\r\n opacity: 1, // set mesh opacity\r\n fixedColor: new THREE.Color(0xffffff), // color to override (see OVERRIDE_COLOR)\r\n zOffset: 0.0, // used fo zsprites (see SPHERE_SPRITE CYLINDER_SPRITE)\r\n zClipCoef: 2.0, // use for Surfs clipping (mesh param, isn't used in shader) FIXME move to representation param\r\n zClipValue: 0.0, // value to clip Surfs in shader (see ZCLIP)\r\n clipPlaneValue: 0.0, // value to clip scene globally (see CLIPPLANE)\r\n world2colorMatrix: new THREE.Matrix4(),\r\n dashedLineSize: 0.1,\r\n dashedLinePeriod: 0.3,\r\n projMatrixInv: new THREE.Matrix4(),\r\n viewport: new THREE.Vector2(800, 600),\r\n lineWidth: 2.0,\r\n fogAlpha: 1.0,\r\n samplesKernel: _samplesKernel,\r\n noiseTex: noise.noiseTexture,\r\n noiseTexelSize: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight),\r\n srcTexelSize: new THREE.Vector2(1.0 / 800.0, 1.0 / 600.0),\r\n copy(source) {\r\n this.diffuse.copy(source.diffuse);\r\n this.specular.copy(source.specular);\r\n this.shininess = source.shininess;\r\n this.opacity = source.opacity;\r\n this.fixedColor.copy(source.fixedColor);\r\n this.zOffset = source.zOffset;\r\n this.zClipCoef = source.zClipCoef;\r\n this.zClipValue = source.zClipValue;\r\n this.clipPlaneValue = source.clipPlaneValue;\r\n this.world2colorMatrix.copy(source.world2colorMatrix);\r\n this.dashedLineSize = source.dashedLineSize;\r\n this.dashedLinePeriod = source.dashedLinePeriod;\r\n this.projMatrixInv = source.projMatrixInv;\r\n this.viewport = source.viewport;\r\n this.lineWidth = source.lineWidth; // used for thick lines only\r\n this.toonShading = source.toonShading;\r\n this.fogAlpha = source.fogAlpha;\r\n this.samplesKernel = source.samplesKernel;\r\n this.noiseTex = source.noiseTex;\r\n this.noiseTexelSize = source.noiseTexelSize;\r\n this.srcTexelSize = source.srcTexelSize;\r\n },\r\n};\r\n\r\nclass UberMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // add fog\r\n this.fog = true;\r\n // used for instanced geometry\r\n this.instancedPos = false;\r\n this.instancedMatrix = false;\r\n // atoms and links color\r\n this.attrColor = false;\r\n // second link color for cylinders\r\n this.attrColor2 = false;\r\n //\r\n this.attrAlphaColor = false;\r\n // overrides color for all vertices (used in selection)\r\n this.overrideColor = false;\r\n // zsrpites\r\n this.sphereSprite = false;\r\n this.cylinderSprite = false;\r\n // clip Surfs individually\r\n this.zClip = false;\r\n // clip scene with global clip plane\r\n this.clipPlane = false;\r\n // enable fake (chess-like) opacity\r\n this.fakeOpacity = false;\r\n // render only depth, don't take care about the pixel color (used for transparency depth prepass)\r\n this.prepassTransparancy = false;\r\n // used to render pixel positions\r\n this.colorFromPos = false;\r\n // used to render shadowmap\r\n this.shadowmap = false;\r\n // used to describe shadowmap type\r\n this.shadowmapType = 'random';\r\n // used to render pixel view deph\r\n this.colorFromDepth = false;\r\n // mark that rendering is for orthographic camera\r\n this.orthoCam = false;\r\n // used to render dashed line\r\n this.dashedLine = false;\r\n // mark as transparent\r\n this.transparent = true;\r\n // mark as thick lines\r\n this.thickLine = false;\r\n // makes fog begin transparency (required for transparent background)\r\n this.fogTransparent = false;\r\n // used to render surface normals to G buffer for ssao effect\r\n this.normalsToGBuffer = false;\r\n // used for toon material\r\n this.toonShading = false;\r\n\r\n // uber options of \"root\" materials are inherited from single uber-options object that resides in prototype\r\n this.uberOptions = Object.create(UberMaterial.prototype.uberOptions);\r\n\r\n // set default values\r\n super.setValues({\r\n glslVersion: THREE.GLSL3,\r\n vertexShader: this.precisionString() + vertexShader,\r\n fragmentShader: this.precisionString() + fragmentShader,\r\n uniforms: THREE.UniformsUtils.clone(defaultUniforms),\r\n lights: true,\r\n fog: true,\r\n side: THREE.DoubleSide,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n precisionString() {\r\n const { precision } = capabilities;\r\n const str = `precision ${precision} float;\\n`\r\n + `precision ${precision} int;\\n\\n`;\r\n return str;\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n\r\n this.fragmentShader = source.fragmentShader;\r\n this.vertexShader = source.vertexShader;\r\n\r\n this.uniforms = THREE.UniformsUtils.clone(source.uniforms);\r\n this.defines = { ...source.defines };\r\n this.extensions = source.extensions;\r\n\r\n this.fog = source.fog;\r\n this.instancedPos = source.instancedPos;\r\n this.instancedMatrix = source.instancedMatrix;\r\n this.attrColor = source.attrColor;\r\n this.attrColor2 = source.attrColor2;\r\n this.attrAlphaColor = source.attrAlphaColor;\r\n this.overrideColor = source.overrideColor;\r\n this.sphereSprite = source.sphereSprite;\r\n this.cylinderSprite = source.cylinderSprite;\r\n this.zClip = source.zClip;\r\n this.clipPlane = source.clipPlane;\r\n this.fakeOpacity = source.fakeOpacity;\r\n this.colorFromPos = source.colorFromPos;\r\n this.shadowmap = source.shadowmap;\r\n this.shadowmapType = source.shadowmapType;\r\n this.colorFromDepth = source.colorFromDepth;\r\n this.orthoCam = source.orthoCam;\r\n this.prepassTransparancy = source.prepassTransparancy;\r\n this.dashedLine = source.dashedLine;\r\n this.thickLine = source.thickLine;\r\n this.fogTransparent = source.fogTransparent;\r\n this.normalsToGBuffer = source.normalsToGBuffer;\r\n this.toonShading = source.toonShading;\r\n\r\n this.uberOptions.copy(source.uberOptions);\r\n\r\n return this;\r\n }\r\n\r\n // create copy of this material\r\n // its options are prototyped after this material's options\r\n createInstance() {\r\n const inst = new UberMaterial();\r\n inst.copy(this);\r\n inst.uberOptions = Object.create(this.uberOptions);\r\n return inst;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n const extensions = {};\r\n\r\n if (this.fog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.instancedPos) {\r\n defines.INSTANCED_POS = 1;\r\n }\r\n if (this.instancedMatrix) {\r\n defines.INSTANCED_MATRIX = 1;\r\n }\r\n if (this.attrColor) {\r\n defines.ATTR_COLOR = 1;\r\n }\r\n if (this.attrColor2) {\r\n defines.ATTR_COLOR2 = 1;\r\n }\r\n if (this.attrAlphaColor) {\r\n defines.ATTR_ALPHA_COLOR = 1;\r\n }\r\n if (this.overrideColor) {\r\n defines.OVERRIDE_COLOR = 1;\r\n }\r\n if (this.sphereSprite) {\r\n defines.SPHERE_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.cylinderSprite) {\r\n defines.CYLINDER_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.zClip) {\r\n defines.ZCLIP = 1;\r\n }\r\n if (this.clipPlane) {\r\n defines.CLIP_PLANE = 1;\r\n }\r\n if (this.fakeOpacity) {\r\n defines.FAKE_OPACITY = 1;\r\n }\r\n if (this.lights) {\r\n defines.USE_LIGHTS = 1;\r\n }\r\n if (this.colorFromPos) {\r\n defines.COLOR_FROM_POS = 1;\r\n }\r\n if (this.shadowmap) {\r\n defines.SHADOWMAP = 1;\r\n if (this.shadowmapType === 'pcf') {\r\n defines.SHADOWMAP_PCF_SHARP = 1;\r\n } else if (this.shadowmapType === 'random') {\r\n defines.SHADOWMAP_PCF_RAND = 1;\r\n } else {\r\n defines.SHADOWMAP_BASIC = 1;\r\n }\r\n }\r\n if (this.colorFromDepth) {\r\n defines.COLOR_FROM_DEPTH = 1;\r\n }\r\n if (this.orthoCam) {\r\n defines.ORTHOGRAPHIC_CAMERA = 1;\r\n }\r\n if (this.prepassTransparancy) {\r\n defines.PREPASS_TRANSP = 1;\r\n }\r\n if (this.dashedLine) {\r\n defines.DASHED_LINE = 1;\r\n }\r\n if (this.thickLine) {\r\n defines.THICK_LINE = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n if (this.normalsToGBuffer) {\r\n extensions.drawBuffers = true;\r\n defines.NORMALS_TO_G_BUFFER = 1;\r\n }\r\n if (this.toonShading) {\r\n defines.TOON_SHADING = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n this.extensions = extensions;\r\n }\r\n\r\n setUberOptions(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n for (const key in values) {\r\n if (!values.hasOwnProperty(key)) {\r\n continue;\r\n }\r\n\r\n if (this.uberOptions[key] instanceof THREE.Color) {\r\n this.uberOptions[key] = values[key].clone();\r\n } else {\r\n this.uberOptions[key] = values[key];\r\n }\r\n }\r\n }\r\n\r\n clone(shallow) {\r\n if (!shallow) {\r\n return super.clone();\r\n }\r\n return this.createInstance();\r\n }\r\n\r\n updateUniforms() {\r\n const self = this;\r\n\r\n uberOptionNames.forEach((p) => {\r\n if (self.uniforms.hasOwnProperty(p)) {\r\n if (self.uberOptions[p] instanceof THREE.Color\r\n || self.uberOptions[p] instanceof THREE.Matrix4) {\r\n self.uniforms[p].value = self.uberOptions[p].clone();\r\n } else {\r\n self.uniforms[p].value = self.uberOptions[p];\r\n }\r\n }\r\n });\r\n }\r\n}\r\n\r\nUberMaterial.prototype.uberOptions = uberOptions;\r\n\r\nexport default UberMaterial;\r\n","import UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default function (SuperClass) {\r\n class NewObjectType extends SuperClass {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.onBeforeRender = NewObjectType.prototype.onBeforeRender;\r\n }\r\n\r\n onBeforeRender(renderer, scene, camera, geometry, material, group) {\r\n this._onBeforeRender(renderer, scene, camera, geometry, material, group);\r\n this._update();\r\n }\r\n\r\n _onBeforeRender() {\r\n }\r\n\r\n _update() {\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material instanceof UberMaterial) {\r\n material.updateUniforms();\r\n }\r\n }\r\n }\r\n\r\n return NewObjectType;\r\n}\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZSpriteMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material.uniforms.invModelViewMatrix) {\r\n // NOTE: update of modelViewMatrix inside threejs is done after onBeforeRender call,\r\n // so we have to do it manually in that place\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n // get inverse matrix\r\n material.uniforms.invModelViewMatrix.value.copy(this.modelViewMatrix).invert();\r\n material.uniforms.nearPlaneValue.value = camera.near;\r\n material.uniformsNeedUpdate = true;\r\n }\r\n }\r\n}\r\n\r\nexport default ZSpriteMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZClippedMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n static _mvLength = new THREE.Vector3();\r\n\r\n static _center = new THREE.Vector3();\r\n\r\n static _modelView = new THREE.Matrix4();\r\n\r\n _onBeforeRender(renderer, scene, camera) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n\r\n const geo = this.geometry;\r\n const { material } = this;\r\n if (!geo.zClip || !material.uberOptions) {\r\n return;\r\n }\r\n\r\n const zClipCoef = 0.5;\r\n\r\n const modelView = ZClippedMesh._modelView;\r\n const mvLength = ZClippedMesh._mvLength;\r\n const center = ZClippedMesh._center;\r\n\r\n modelView.multiplyMatrices(this.matrixWorld, camera.matrixWorldInverse);\r\n const s = mvLength.setFromMatrixColumn(modelView, 0).length();\r\n center.copy(geo.boundingSphere.center);\r\n\r\n this.localToWorld(center);\r\n material.uberOptions.zClipValue = camera.position.z - center.z\r\n - s * (zClipCoef * geo.boundingSphere.radius);\r\n }\r\n}\r\n\r\nexport default ZClippedMesh;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from '../CSS2DObject';\r\nimport utils from '../../utils';\r\n\r\nclass TextMesh extends THREE.Group {\r\n constructor(geometry, _material) {\r\n super();\r\n this.geometry = geometry;\r\n\r\n const self = this;\r\n self.initialized = false;\r\n this.geometry.addEventListener('update', () => {\r\n self.update();\r\n });\r\n }\r\n\r\n init() {\r\n const { children } = this;\r\n for (let i = children.length - 1; i >= 0; --i) {\r\n this.remove(children[i]);\r\n }\r\n\r\n const { items, userData } = this.geometry;\r\n for (let i = 0, n = items.length; i < n; ++i) {\r\n const srcItem = items[i];\r\n if (!srcItem) {\r\n continue;\r\n }\r\n const item = utils.shallowCloneNode(srcItem);\r\n const label = new CSS2DObject(item);\r\n label.userData = _.clone(userData);\r\n const el = label.getElement();\r\n el.style.visibility = 'visible';\r\n label.source = srcItem;\r\n this.add(label);\r\n }\r\n this.initialized = true;\r\n }\r\n\r\n update() {\r\n const geo = this.geometry;\r\n if (!geo.needsUpdate) {\r\n return;\r\n }\r\n const { children } = this;\r\n if (!this.initialized) {\r\n this.init();\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n const item = child.source;\r\n child.position.copy(item.worldPos);\r\n child.userData.color = item.opts.color;\r\n child.userData.background = item.opts.background;\r\n }\r\n }\r\n}\r\n\r\nexport default TextMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass SimpleMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default SimpleMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\nconst _viewport = new THREE.Vector2();\r\n\r\nclass ThickLineMesh extends Mesh {\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!material.uberOptions) {\r\n return;\r\n }\r\n\r\n material.uberOptions.projMatrixInv.copy(camera.projectionMatrix).invert();\r\n renderer.getSize(_viewport);\r\n material.uberOptions.viewport.set(_viewport.width, _viewport.height);\r\n }\r\n}\r\n\r\nexport default ThickLineMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass InstancedMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default InstancedMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\nimport ZSpriteMesh from './ZSpriteMesh';\r\nimport ZClippedMesh from './ZClippedMesh';\r\nimport TextMesh from './TextMesh';\r\nimport SimpleMesh from './SimpleMesh';\r\nimport ThickLineMesh from './ThickLineMesh';\r\nimport InstancedMesh from './InstancedMesh';\r\n\r\nexport default {\r\n ZClipped: ZClippedMesh,\r\n ZSprite: ZSpriteMesh,\r\n Text: TextMesh,\r\n Line: UberObject(THREE.Line),\r\n LineSegments: UberObject(THREE.LineSegments),\r\n Mesh: SimpleMesh,\r\n ThickLineMesh,\r\n Instanced: InstancedMesh,\r\n};\r\n","import geometries from '../geometries/geometries';\r\nimport meshes from './meshes';\r\nimport ThickLinesGeometry from '../geometries/ThickLinesGeometry';\r\n\r\nfunction setMatParams(params, uniforms) {\r\n return function (material) {\r\n material.setValues(params);\r\n material.setUberOptions(uniforms);\r\n };\r\n}\r\n\r\nfunction _createInstancedCylinders(useZSprites, openEnded) {\r\n function Geometry(a, b) {\r\n return new geometries.Instanced2CCylindersGeometry(a, b, useZSprites, openEnded);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedMatrix: true,\r\n attrColor: true,\r\n attrColor2: true,\r\n attrAlphaColor: true,\r\n cylinderSprite: useZSprites,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createLineSegmentsGeoTriplet(geo, renderParams) {\r\n const thickLines = geo.prototype instanceof ThickLinesGeometry;\r\n const lineWidth = renderParams.lineWidth || 0;\r\n return {\r\n Geometry: geo,\r\n Object: thickLines ? meshes.ThickLineMesh : meshes.LineSegments,\r\n initMaterial: setMatParams({\r\n lights: false,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n thickLine: thickLines,\r\n }, {\r\n lineWidth,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createSimpleGeoTriplet(geoClass) {\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.Mesh,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createIsoSurfaceGeoTriplet(geoClass, caps, settings, renderParams) {\r\n const surfaceOpts = {\r\n wireframe: !!renderParams.wireframe,\r\n fakeOpacity: settings.now.isoSurfaceFakeOpacity,\r\n zClip: renderParams.zClip,\r\n };\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.ZClipped,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: false,\r\n wireframe: surfaceOpts.wireframe,\r\n fakeOpacity: surfaceOpts.fakeOpacity,\r\n zClip: surfaceOpts.zClip,\r\n }),\r\n };\r\n}\r\n\r\nclass MeshCreator {\r\n static createSpheres(caps, settings) {\r\n const useZSprites = settings.now.zSprites;\r\n function Geometry(a, b) {\r\n return new geometries.InstancedSpheresGeometry(a, b, useZSprites);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedPos: true,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n sphereSprite: useZSprites,\r\n }),\r\n };\r\n }\r\n\r\n static create2CClosedCylinders(_caps, _settings) {\r\n return _createInstancedCylinders(false, false);\r\n }\r\n\r\n static create2CCylinders(caps, settings) {\r\n return _createInstancedCylinders(settings.now.zSprites, true);\r\n }\r\n\r\n static create2CLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.TwoColorLinesGeometry, renderParams);\r\n }\r\n\r\n static createCrosses(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.CrossGeometry, renderParams);\r\n }\r\n\r\n static createExtrudedChains(_caps, _settings) {\r\n return _createSimpleGeoTriplet(geometries.ExtrudedObjectsGeometry);\r\n }\r\n\r\n static createChunkedLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.ChunkedLinesGeometry, renderParams);\r\n }\r\n\r\n static createQuickSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.QuickSurfGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createContactSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.ContactSurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createSASSES(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.SSIsosurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createLabels(_caps, _settings) {\r\n return {\r\n Geometry: geometries.LabelsGeometry,\r\n Object: meshes.Text,\r\n initMaterial() {\r\n },\r\n };\r\n }\r\n}\r\n\r\nexport default MeshCreator;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../gfxutils';\r\n\r\nclass TransformGroup extends THREE.Object3D {\r\n static _inverseMatrix = new THREE.Matrix4();\r\n\r\n static _ray = new THREE.Ray();\r\n\r\n constructor(geometry, geoParams, material, transforms) {\r\n super();\r\n this._geometry = geometry;\r\n this._geoParams = geoParams;\r\n const mat = material.createInstance();\r\n geoParams.initMaterial(mat);\r\n this._material = mat;\r\n this._transforms = transforms.length > 0 ? transforms : [new THREE.Matrix4()];\r\n const meshes = this._createMeshes(geometry);\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n this.add(meshes[i]);\r\n }\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const ray = TransformGroup._ray;\r\n const inverseMatrix = TransformGroup._inverseMatrix;\r\n const { children } = this;\r\n ray.copy(raycaster.ray);\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n\r\n if (!gfxutils.belongToSelectLayers(child)) {\r\n continue;\r\n }\r\n\r\n child.updateMatrixWorld();\r\n const mtx = child.matrixWorld;\r\n inverseMatrix.copy(mtx).invert();\r\n raycaster.ray.copy(ray).applyMatrix4(inverseMatrix);\r\n const childIntersects = [];\r\n this._geometry.raycast(raycaster, childIntersects);\r\n\r\n for (let j = 0, ciCount = childIntersects.length; j < ciCount; ++j) {\r\n const inters = childIntersects[j];\r\n if (inters.point) {\r\n inters.point.applyMatrix4(mtx);\r\n inters.distance = ray.origin.distanceTo(inters.point);\r\n }\r\n inters.object = child;\r\n intersects[intersects.length] = inters;\r\n }\r\n }\r\n raycaster.ray.copy(ray);\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const geos = this._geometry.getSubset(chunkIndices);\r\n const subset = [];\r\n let subIdx = 0;\r\n\r\n for (let i = 0, n = geos.length; i < n; ++i) {\r\n const meshes = this._createMeshes(geos[i]);\r\n for (let j = 0, meshCnt = meshes.length; j < meshCnt; ++j) {\r\n subset[subIdx++] = meshes[j];\r\n }\r\n }\r\n\r\n return subset;\r\n }\r\n\r\n _createMeshes(geometry) {\r\n const transforms = this._transforms;\r\n const Mesh = this._geoParams.Object;\r\n const material = this._material;\r\n const meshes = [];\r\n for (let i = 0, n = transforms.length; i < n; ++i) {\r\n const mesh = new Mesh(geometry, material);\r\n mesh.applyMatrix4(transforms[i]);\r\n meshes[i] = mesh;\r\n }\r\n\r\n return meshes;\r\n }\r\n}\r\n\r\nexport default TransformGroup;\r\n","import RCGroup from '../../RCGroup';\r\nimport TransformGroup from '../../meshes/TransformGroup';\r\n\r\nfunction wrapper(Name, args) {\r\n const params = [Name].concat(args);\r\n return Name.bind(...params);\r\n}\r\n\r\nclass ChemGroup extends RCGroup {\r\n constructor(geoParams, selection, colorer, mode, transforms, polyComplexity, material) {\r\n super();\r\n if (this.constructor === ChemGroup) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n this._selection = selection;\r\n this._mode = mode;\r\n this._colorer = colorer;\r\n this._chunksIdc = selection.chunks;\r\n this._polyComplexity = polyComplexity;\r\n this._geo = new (wrapper(geoParams.Geometry, this._makeGeoArgs()))();\r\n this._mesh = new TransformGroup(this._geo, geoParams, material, transforms);\r\n this.add(this._mesh);\r\n this._build();\r\n }\r\n\r\n _makeGeoArgs() {\r\n throw new Error('ChemGroup subclass must override _makeGeoArgs() method');\r\n }\r\n\r\n /**\r\n * Builds subset geometry by ATOMS index list\r\n *\r\n * @param {Number} mask - Representation mask\r\n * @param {Boolean} innerOnly - if true returns inner bonds only - without halves\r\n * @returns {Array} Subset geometry\r\n */\r\n getSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : false;\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return [];\r\n }\r\n return this._mesh.getSubset(chunksList);\r\n }\r\n\r\n _changeSubsetOpacity(mask, value, innerOnly) {\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return;\r\n }\r\n this._geo.setOpacity(chunksList, value);\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 1.0, innerOnly);\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 0.0, innerOnly);\r\n }\r\n}\r\n\r\nexport default ChemGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass AtomsGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { atoms } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const atomsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const atomIdx = atomsIdc[inters[i].chunkIdx];\r\n if (atomIdx < atoms.length) {\r\n inters[i].atom = atoms[atomIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { atoms } = this._selection;\r\n const atomsIdc = this._chunksIdc;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n if ((atom.mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default AtomsGroup;\r\n","import AtomsGroup from './AtomsGroup';\r\n\r\nclass AtomsSphereGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, atom.position, mode.calcAtomRadius(atom));\r\n geo.setColor(i, colorer.getAtomColor(atom, parent));\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), mode.calcAtomRadius(atom));\r\n if (updateColor) {\r\n geo.setColor(i, frameData.getAtomColor(colorer, atom));\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsSphereGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSurfaceGroup extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n return [n, opts];\r\n }\r\n}\r\nexport default AtomsSurfaceGroup;\r\n","/* This is a stub class keep it until SAS/SES is refactored */\r\n\r\nimport AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSASSESGroupStub extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n opts.selection = this._selection;\r\n opts.colorMode = this._colorer;\r\n return [n, opts];\r\n }\r\n}\r\n\r\nexport default AtomsSASSESGroupStub;\r\n","import AtomsGroup from './AtomsGroup';\r\nimport utils from '../../../utils';\r\n\r\nfunction adjustColor(color) {\r\n let r = (color >> 16) & 255;\r\n let g = (color >> 8) & 255;\r\n let b = color & 255;\r\n\r\n if (0.2126 * r + 0.7152 * g + 0.0722 * b > 127) {\r\n r = r * 3 / 10;\r\n g = g * 3 / 10;\r\n b = b * 3 / 10;\r\n } else {\r\n r = 255 - ((255 - r) * 3 / 10);\r\n g = 255 - ((255 - g) * 3 / 10);\r\n b = 255 - ((255 - b) * 3 / 10);\r\n }\r\n\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nfunction inverseColor(color) {\r\n const r = (color >> 16) & 255;\r\n const g = (color >> 8) & 255;\r\n const b = color & 255;\r\n\r\n return ((255 - r) << 16) | ((255 - g) << 8) | (255 - b);\r\n}\r\n\r\nfunction getAtomText(atom) {\r\n if (atom.name.getNode() !== null) {\r\n return atom.name.getNode();\r\n }\r\n\r\n return atom.getVisualName();\r\n}\r\n\r\nconst colorMappings = {\r\n none(c) {\r\n return c;\r\n },\r\n adjust: adjustColor,\r\n inverse: inverseColor,\r\n};\r\n\r\nfunction propagateColor(color, rule) {\r\n let result;\r\n if (colorMappings.hasOwnProperty(rule)) {\r\n result = utils.hexColor(colorMappings[rule](color));\r\n } else {\r\n const val = parseInt(rule, 16);\r\n if (!Number.isNaN(val) && rule.toLowerCase().startsWith('0x')) {\r\n result = utils.hexColor(val);\r\n } else {\r\n result = '#000000';\r\n }\r\n }\r\n return result;\r\n}\r\n\r\nconst templateMappings = {\r\n serial(a) {\r\n return a.serial;\r\n },\r\n name(a) {\r\n return a.getVisualName();\r\n },\r\n elem(a) {\r\n return a.element.name;\r\n },\r\n residue(a) {\r\n return a.residue.getType().getName();\r\n },\r\n sequence(a) {\r\n return a.residue.getSequence();\r\n },\r\n chain(a) {\r\n return a.residue.getChain().getName();\r\n },\r\n hetatm(a) {\r\n return a.isHet();\r\n },\r\n water(a) {\r\n return a.residue.getType().getName() === 'HOH' || a.residue.getType().getName() === 'WAT';\r\n },\r\n};\r\n\r\nconst parseTemplate = function (atom, str) {\r\n return str.replace(/\\{\\{(\\s*\\w+\\s*)\\}\\}/g, (m) => {\r\n let key = m.replace(/\\s+/g, '');\r\n key = key.substring(2, key.length - 2).toLowerCase();\r\n\r\n if (templateMappings.hasOwnProperty(key)) {\r\n return templateMappings[key](atom);\r\n }\r\n return 'null';\r\n });\r\n};\r\n\r\nclass AtomsTextGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n const opts = this._mode.getLabelOpts();\r\n return [this._selection.chunks.length, opts];\r\n }\r\n\r\n _build() {\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = colorer.getAtomColor(atom, parent);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, atom.position, text);\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = frameData.getAtomColor(colorer, atom);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), text);\r\n if (updateColor) {\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsTextGroup;\r\n","import * as THREE from 'three';\r\nimport AtomsGroup from './AtomsGroup';\r\n\r\nfunction _slerp(omega, v1, v2, t) {\r\n const oSin = Math.sin(omega);\r\n return v1.clone().multiplyScalar(Math.sin((1 - t) * omega) / oSin).addScaledVector(v2, Math.sin(t * omega) / oSin);\r\n}\r\n\r\nclass AromaticGroup extends AtomsGroup {\r\n _buildInner(radOffset, addChunk) {\r\n const chunksToIdx = this._selection.chunks;\r\n\r\n const prevVector = new THREE.Vector3();\r\n const currVector = new THREE.Vector3();\r\n const segmentsHeight = this._segmentsHeight;\r\n const leprStep = 1.0 / segmentsHeight;\r\n const colorer = this._colorer;\r\n\r\n const { cycles, parent } = this._selection;\r\n let chunkIdx = 0;\r\n let currAtomIdx = chunksToIdx[chunkIdx];\r\n\r\n for (let cIdx = 0, cCount = cycles.length; cIdx < cCount; ++cIdx) {\r\n const cycle = cycles[cIdx];\r\n const cycAtoms = cycle.atoms;\r\n const chunkPoints = [];\r\n const tmpDir = [];\r\n const { center } = cycle;\r\n const cycleRad = cycle.radius - radOffset;\r\n const n = cycAtoms.length;\r\n let i = 0;\r\n const prevPos = cycAtoms[n - 1].position;\r\n let currPos = cycAtoms[i].position;\r\n prevVector.subVectors(prevPos, center);\r\n currVector.subVectors(currPos, center);\r\n const upDir = currVector.clone().cross(prevVector).normalize();\r\n\r\n for (; i < n; ++i) {\r\n const omega = prevVector.angleTo(currVector);\r\n tmpDir[i] = _slerp(omega, prevVector, currVector, 0.5).normalize();\r\n currPos = cycAtoms[(i + 1) % n].position;\r\n prevVector.copy(currVector);\r\n currVector.subVectors(currPos, center);\r\n }\r\n\r\n for (i = 0; i < n; ++i) {\r\n if (cycAtoms[i].index !== currAtomIdx) {\r\n continue;\r\n }\r\n const start = tmpDir[i];\r\n const end = tmpDir[(i + 1) % n];\r\n const color = colorer.getAtomColor(cycAtoms[i], parent);\r\n const currAngle = start.angleTo(end);\r\n\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n chunkPoints[j] = _slerp(currAngle, start, end, j * leprStep).multiplyScalar(cycleRad).add(center);\r\n }\r\n\r\n addChunk(chunkIdx++, color, chunkPoints, center, upDir);\r\n currAtomIdx = chunksToIdx[chunkIdx];\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default AromaticGroup;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../../gfxutils';\r\nimport AromaticGroup from './AromaticGroup';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n for (let i = 0; i < parts; ++i) {\r\n const a = -2 * i / parts * Math.PI;\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\nconst { calcChunkMatrix } = gfxutils;\r\n\r\nclass AromaticTorusGroup extends AromaticGroup {\r\n _build() {\r\n const segmentsHeight = this._segmentsHeight;\r\n const torusRad = this._mode.getAromRadius();\r\n const radiusV = new THREE.Vector2(torusRad, torusRad);\r\n const radOffset = this._mode.calcStickRadius() + 2 * torusRad;\r\n const lookAtVector = new THREE.Vector3();\r\n const mtc = [];\r\n const geo = this._geo;\r\n this._buildInner(radOffset, (chunkIdx, color, points, center, upDir) => {\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n const currDir = currPoint.clone().sub(center).cross(upDir);\r\n lookAtVector.addVectors(currPoint, currDir);\r\n mtc[j] = calcChunkMatrix(currPoint, lookAtVector, upDir, radiusV);\r\n }\r\n geo.setItem(chunkIdx, mtc);\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._polyComplexity;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length];\r\n }\r\n}\r\n\r\nexport default AromaticTorusGroup;\r\n","import AromaticGroup from './AromaticGroup';\r\n\r\nclass AromaticLinesGroup extends AromaticGroup {\r\n _build() {\r\n const geo = this._geo;\r\n const radOffset = this._mode.getAromaticOffset();\r\n this._buildInner(radOffset, (chunkIdx, color, points) => {\r\n let prevPt = points[0];// do not replace with start\r\n for (let j = 1; j <= this._segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n geo.setSegment(chunkIdx, j - 1, prevPt, currPoint);\r\n prevPt = currPoint;\r\n }\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._mode.getAromaticArcChunks();\r\n return [this._selection.chunks.length, this._segmentsHeight, true];\r\n }\r\n}\r\n\r\nexport default AromaticLinesGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[inters[i].chunkIdx];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesGroup;\r\n","import ResiduesGroup from './ResiduesGroup';\r\n\r\nclass NucleicItemGroup extends ResiduesGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[Math.floor(inters[i].chunkIdx / 2)];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n let chunkIdx = 0;\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList[chunkIdx++] = 2 * i;\r\n chunksList[chunkIdx++] = 2 * i + 1;\r\n }\r\n }\r\n return chunksList;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finishUpdate();\r\n }\r\n}\r\n\r\nexport default NucleicItemGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicCylindersGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n geo.setItem(chunkIdx, cyl1, cyl2, stickRad);\r\n geo.setColor(chunkIdx, color, color);\r\n }\r\n}\r\n\r\nexport default NucleicCylindersGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicSpheresGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length * 2, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n let idx = chunkIdx * 2;\r\n geo.setItem(idx, cyl1, stickRad);\r\n geo.setColor(idx, color);\r\n idx++;\r\n geo.setItem(idx, cyl2, stickRad);\r\n geo.setColor(idx, color);\r\n }\r\n}\r\n\r\nexport default NucleicSpheresGroup;\r\n","import * as THREE from 'three';\r\nimport { Smooth } from '../../../../vendor/js/Smooth';\r\nimport gfxutils from '../../gfxutils';\r\nimport chem from '../../../chem';\r\n\r\nconst { ResidueType } = chem;\r\n\r\nconst calcMatrix = gfxutils.calcChunkMatrix;\r\n\r\nfunction _buildStructureInterpolator(points, tension) {\r\n const path = Smooth(points, {\r\n method: Smooth.METHOD_CUBIC,\r\n clip: Smooth.CLIP_CLAMP,\r\n cubicTension: tension,\r\n scaleTo: 1,\r\n });\r\n\r\n return function (t, argTrans) {\r\n let transformT = argTrans;\r\n if (transformT === null) {\r\n // map our range to the [second .. last but one]\r\n transformT = function (tt) {\r\n return (tt * ((points.length - 1) - 2) + 1) / (points.length - 1);\r\n };\r\n }\r\n const newt = transformT(t);\r\n const ans = path(newt);\r\n return new THREE.Vector3(ans[0], ans[1], ans[2]);\r\n };\r\n}\r\n\r\nfunction _addPoints(centerPoints, topPoints, idx, residue) {\r\n if (!residue._isValid) {\r\n centerPoints[idx] = centerPoints[idx - 1];\r\n topPoints[idx] = topPoints[idx - 1];\r\n return;\r\n }\r\n const cp = residue._controlPoint;\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n const tp = cp.clone().add(residue._wingVector);\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n}\r\n\r\nfunction _addPointsForLoneResidue(centerPoints, topPoints, idx, residue) {\r\n const nucleic = (residue._type.flags & ResidueType.Flags.NUCLEIC) !== 0;\r\n const nameFrom = nucleic ? 'C5\\'' : 'N';\r\n const nameTo = nucleic ? 'C3\\'' : 'C';\r\n\r\n let posFrom;\r\n let posTo;\r\n residue.forEachAtom((atom) => {\r\n const name = atom.getVisualName();\r\n if (!posFrom && name === nameFrom) {\r\n posFrom = atom.position;\r\n } else if (!posTo && name === nameTo) {\r\n posTo = atom.position;\r\n }\r\n });\r\n\r\n // provide a fallback for unknown residues\r\n if (!(posFrom && posTo)) {\r\n posFrom = residue._firstAtom.position;\r\n posTo = residue._lastAtom.position;\r\n }\r\n\r\n if (posFrom && posTo) {\r\n const shift = posTo.clone().sub(posFrom);\r\n\r\n const wing = residue._wingVector;\r\n const cp = residue._controlPoint;\r\n const tp = cp.clone().add(wing);\r\n\r\n const cpPrev = cp.clone().sub(shift);\r\n const tpPrev = cpPrev.clone().add(wing);\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n ++idx;\r\n\r\n const cpNext = cp.clone().add(shift);\r\n const tpNext = cpNext.clone().add(wing);\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n ++idx;\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n }\r\n}\r\n\r\nfunction _calcPoints(residues, firstIdx, lastIdx, boundaries) {\r\n const left = boundaries.start;\r\n const right = boundaries.end;\r\n function _prevIdx(idx) {\r\n return idx > left && residues[idx - 1]._isValid ? idx - 1 : idx;\r\n }\r\n function _nextIdx(idx) {\r\n return idx < right && residues[idx + 1]._isValid ? idx + 1 : idx;\r\n }\r\n\r\n const topPoints = [];\r\n const centerPoints = [];\r\n let arrIdx = 0;\r\n function _extrapolate2(currIdx, otherIdx) {\r\n const cp = residues[currIdx]._controlPoint.clone().lerp(residues[otherIdx]._controlPoint, -0.25);\r\n const tp = cp.clone().add(residues[currIdx]._wingVector);\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n }\r\n\r\n // a single disconnected residue\r\n const prevIdx = _prevIdx(firstIdx);\r\n const nextIdx = _nextIdx(lastIdx);\r\n if (prevIdx === nextIdx) {\r\n _addPointsForLoneResidue(centerPoints, topPoints, arrIdx, residues[firstIdx]);\r\n return { centerPoints, topPoints };\r\n }\r\n\r\n // Two points (prev-prev and next-next) are added to support edge conditions for cubic splines, they are ignored\r\n // Another two (prev and next) were added to support the outside of the sub chain\r\n\r\n // prev and prev-prev\r\n if (firstIdx === prevIdx) {\r\n // do the extrapolation\r\n _extrapolate2(firstIdx, _nextIdx(firstIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[_prevIdx(prevIdx)]);\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[prevIdx]);\r\n }\r\n\r\n // main loop\r\n for (let idx = firstIdx; idx <= lastIdx; ++idx) {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[idx]);\r\n }\r\n\r\n // next and next-next\r\n if (nextIdx === _nextIdx(nextIdx)) {\r\n // do the extrapolation\r\n _extrapolate2(lastIdx, _prevIdx(lastIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[nextIdx]);\r\n _addPoints(centerPoints, topPoints, arrIdx, residues[_nextIdx(nextIdx)]);\r\n }\r\n return { centerPoints, topPoints };\r\n}\r\n\r\nclass CartoonHelper {\r\n constructor(residues, startIdx, endIdx, segmentsCount, tension, boundaries) {\r\n const pointsArrays = _calcPoints(residues, startIdx, endIdx, boundaries);\r\n this._topInterp = _buildStructureInterpolator(pointsArrays.topPoints, tension);\r\n this._centerInterp = _buildStructureInterpolator(pointsArrays.centerPoints, tension);\r\n\r\n this._shift = 0.5 / (endIdx - startIdx + 2);\r\n this._valueStep = (1.0 - 2 * this._shift) / (2 * (endIdx - startIdx + 1) * (segmentsCount - 1));\r\n this._segmentsCount = segmentsCount;\r\n }\r\n\r\n prepareMatrices(idx, firstRad, secondRad) {\r\n const mtcCount = this._segmentsCount;\r\n const outMtc = new Array(mtcCount);\r\n const currRad = new THREE.Vector2(0, 0);\r\n\r\n const topInterp = this._topInterp;\r\n const cenInterp = this._centerInterp;\r\n\r\n let currentValue = this._shift + this._valueStep * (mtcCount - 1) * idx;\r\n\r\n for (let mtxIdx = 0; mtxIdx < mtcCount; ++mtxIdx) {\r\n const lerpVal = Math.min(1.0, mtxIdx / (mtcCount - 1));\r\n currRad.lerpVectors(firstRad, secondRad, lerpVal);\r\n\r\n const currTop = topInterp(currentValue, null);\r\n const currCenter = cenInterp(currentValue, null);\r\n currentValue += this._valueStep;\r\n const nextCenter = cenInterp(currentValue, null);\r\n\r\n outMtc[mtxIdx] = calcMatrix(currCenter.clone(), nextCenter.clone(), currTop.clone().sub(currCenter), currRad);\r\n }\r\n\r\n return outMtc;\r\n }\r\n}\r\n\r\nexport default CartoonHelper;\r\n","import * as THREE from 'three';\r\nimport ResiduesGroup from './ResiduesGroup';\r\nimport CartoonHelper from './CartoonHelper';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n\r\n for (let i = 0; i < parts; ++i) {\r\n // starts from pi/2 because it's important that points are lied on the angles of arrows (visual issues if not)\r\n const a = Math.PI / 2.0 - 2 * Math.PI * i / parts;\r\n\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\n\r\nfunction _loopThrough(subDiv, residues, segmentsHeight, tension, mode, callback) {\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n const { boundaries } = subDiv[subDivI];\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const idc = [subs[i].start, subs[i].end];\r\n const matrixHelper = new CartoonHelper(residues, idc[0], idc[1], segmentsHeight, tension, boundaries);\r\n let prevLast = null;\r\n const startIdx = subs[i].start * 2;\r\n const endIdx = subs[i].end * 2 + 1;\r\n let prevSecondRad = mode.getResidueRadius(residues[0], 0);\r\n for (let idx = startIdx; idx <= endIdx; ++idx) {\r\n const resIdx = (idx / 2 | 0);\r\n const currRes = residues[resIdx];\r\n const firstRad = mode.getResidueRadius(currRes, idx % 2);\r\n const secondRad = mode.getResidueRadius(currRes, 1 + (idx % 2));\r\n\r\n const mtc = matrixHelper.prepareMatrices(idx - idc[0] * 2, firstRad, secondRad);\r\n mtc.unshift(prevLast === null ? mtc[0] : prevLast);\r\n\r\n // Slope - radius is changed along this residue part\r\n const hasSlope = (firstRad.x !== secondRad.x) || (firstRad.y !== secondRad.y);\r\n // Cut - end radius of previous part not equal to start radius of this part. First section of this part lies in the orthogonal plane\r\n const hasCut = (firstRad.x !== prevSecondRad.x) || (firstRad.y !== prevSecondRad.y);\r\n\r\n callback(currRes, mtc, hasSlope, hasCut);\r\n\r\n prevLast = mtc[segmentsHeight];\r\n prevSecondRad = secondRad;\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ResiduesSubseqGroup extends ResiduesGroup {\r\n _makeGeoArgs() {\r\n const cmpMultiplier = this._mode.getHeightSegmentsRatio();\r\n this._segmentsHeight = this._polyComplexity * cmpMultiplier | 0;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length * 2];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, (currRes, mtc, hasSlope = false, hasCut = false) => {\r\n const color = colorer.getResidueColor(currRes, parent);\r\n chunkIdc[chunkIdx] = currRes._index;\r\n geo.setItem(chunkIdx, mtc, hasSlope, hasCut);\r\n geo.setColor(chunkIdx++, color);\r\n });\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n const frameRes = frameData.getResidues();\r\n let chunkIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n _loopThrough(this._selection.subdivs, frameRes, this._segmentsHeight, tension, mode, (currRes, mtc) => {\r\n geo.setItem(chunkIdx, mtc);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n });\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default ResiduesSubseqGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesTraceGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const subDiv = this._selection.subdivs;\r\n let chunksCount = 0;\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n chunksCount += subs[i].end - subs[i].start;\r\n }\r\n }\r\n return [chunksCount, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n chunkIdc[chunkIdx] = { first: prevRes._index, second: currRes._index };\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n geo.finalize();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n const { residues } = this._selection;\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksToIdx = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const chunk = chunksToIdx[Math.floor(chunkIdx / 2)];\r\n const resIdx = chunkIdx % 2 === 0 ? chunk.first : chunk.second;\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const chunksToIdx = this._chunksIdc;\r\n const { residues } = this._selection;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const chunk = chunksToIdx[i];\r\n if (residues[chunk.first]._mask & mask) {\r\n chunksList.push(i * 2);\r\n }\r\n if (residues[chunk.second]._mask & mask) {\r\n chunksList.push(i * 2 + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesTraceGroup;\r\n","import ChemGroup from './ChemGroup';\r\nimport Bond from '../../../chem/Bond';\r\n\r\nfunction getCylinderCount(bondOrder) {\r\n return bondOrder < 2 ? 1 : bondOrder;\r\n}\r\n\r\nclass BondsGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const drawMultiple = this._mode.drawMultiorderBonds();\r\n const showAromatic = this._mode.showAromaticLoops();\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n let bondsCount = 0;\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n bondsCount += this.getBondOrder(bonds[bondsIdc[i]], drawMultiple, showAromatic);\r\n }\r\n return [bondsCount, this._polyComplexity];\r\n }\r\n\r\n getBondOrder(bond, drawMultiple, showAromatic) {\r\n let bondOrder = 1;\r\n if (drawMultiple && (!showAromatic || bond._type !== Bond.BondType.AROMATIC)) {\r\n bondOrder = getCylinderCount(bond._order);\r\n }\r\n return bondOrder;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const { bonds } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const bondsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const bondIdx = bondsIdc[Math.floor(chunkIdx / 2)];\r\n if (bondIdx < bonds.length) {\r\n const bond = bonds[bondIdx];\r\n inters[i].atom = chunkIdx % 2 === 0 ? bond._left : bond._right;\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask, innerOnly) {\r\n const chunksList = [];\r\n const { bonds } = this._selection;\r\n const chunksToIdx = this._chunksIdc;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const bond = bonds[chunksToIdx[i]];\r\n if ((bond._left.mask & mask) && (!innerOnly || (bond._right.mask & mask))) {\r\n chunksList.push(2 * i);\r\n }\r\n if ((bond._right.mask & mask) && (!innerOnly || (bond._left.mask & mask))) {\r\n chunksList.push(2 * i + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default BondsGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nclass BondsCylinderGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsCylinderGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nconst STEP_SIZE = 0.15;\r\n\r\nclass BondsLinesGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsLinesGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\nimport AtomsSurfaceGroup from './AtomsSurfaceGroup';\r\nimport AtomsSASSESGroupStub from './AtomsSASSESGroupStub';\r\nimport AtomsTextGroup from './AtomsTextGroup';\r\nimport AromaticTorusGroup from './AromaticTorusGroup';\r\nimport AromaticLinesGroup from './AromaticLinesGroup';\r\nimport NucleicCylindersGroup from './NucleicCylindersGroup';\r\nimport NucleicSpheresGroup from './NucleicSpheresGroup';\r\nimport ResiduesSubseqGroup from './ResiduesSubseqGroup';\r\nimport ResiduesTraceGroup from './ResiduesTraceGroup';\r\nimport BondsCylinderGroup from './BondsCylinderGroup';\r\nimport BondsLinesGroup from './BondsLinesGroup';\r\n\r\nexport default {\r\n AtomsSphereGroup,\r\n AtomsSurfaceGroup,\r\n AtomsSASSESGroupStub,\r\n AtomsTextGroup,\r\n AromaticTorusGroup,\r\n AromaticLinesGroup,\r\n NucleicCylindersGroup,\r\n NucleicSpheresGroup,\r\n ResiduesSubseqGroup,\r\n ResiduesTraceGroup,\r\n BondsCylinderGroup,\r\n BondsLinesGroup,\r\n};\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AtomsProcessor extends RCGroup {\r\n constructor(AtomsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n this._mode = mode;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let atomCount = 0;\r\n component.forEachAtom((atom) => {\r\n if (!self._checkAtom(atom, mask)) {\r\n return;\r\n }\r\n atomsIdc[atomCount++] = atom.index;\r\n });\r\n if (atomCount === 0) {\r\n return;\r\n }\r\n const atomsGroup = new AtomsGroup(geoParams, {\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n _checkAtom(atom, mask) {\r\n return atom.mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AtomsProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\n\r\nclass OrphanAtomsProcessor extends AtomsProcessor {\r\n _checkAtom(atom, mask) {\r\n if (!(atom.mask & mask)) {\r\n return false;\r\n }\r\n\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n if ((bonds[i]._left.mask & mask) && (bonds[i]._right.mask & mask)) {\r\n return false;\r\n }\r\n }\r\n return true;\r\n }\r\n}\r\n\r\nexport default OrphanAtomsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass ResiduesProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n component.forEachResidue((residue) => {\r\n if (self._checkResidue(residue, mask)) {\r\n resIdc[chunksCount++] = residue._index;\r\n }\r\n });\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n checkResidue(residue, mask) {\r\n return residue._mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default ResiduesProcessor;\r\n","import ResidueProcessor from './ResiduesProcessor';\r\n\r\nclass NucleicProcessor extends ResidueProcessor {\r\n _checkResidue(residue, mask) {\r\n return mask & residue._mask && residue._cylinders !== null;\r\n }\r\n}\r\nexport default NucleicProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass SubseqsProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const subDivs = component.getMaskedSubdivSequences(mask);\r\n\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n for (let subDivI = 0, subDivN = subDivs.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDivs[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let j = subs[i].start, jEnd = subs[i].end; j <= jEnd; ++j) {\r\n resIdc[chunksCount++] = residues[j]._index;\r\n }\r\n }\r\n }\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n subdivs: subDivs,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default SubseqsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass BondsProcessor extends RCGroup {\r\n constructor(BondsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const bonds = complex.getBonds();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const bondsIdc = [];\r\n let bondsCount = 0;\r\n component.forEachBond((bond) => {\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n if (!(atom1.mask & mask) || !(atom2.mask & mask)) {\r\n return;\r\n }\r\n bondsIdc[bondsCount++] = bond._index;\r\n });\r\n if (bondsCount === 0) {\r\n return;\r\n }\r\n const bondsGroup = new BondsGroup(geoParams, {\r\n bonds,\r\n chunks: bondsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n bondsGroup._component = component;\r\n self.add(bondsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default BondsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AromaticProcessor extends RCGroup {\r\n constructor(AromaticGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n if (!mode.showAromaticLoops()) {\r\n return;\r\n }\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let chunksCount = 0;\r\n const cycles = [];\r\n let cycleIdx = 0;\r\n component.forEachCycle((cycle) => {\r\n const cycAtoms = cycle.atoms;\r\n let perCycle = 0;\r\n for (let i = 0, n = cycAtoms.length; i < n; ++i) {\r\n if ((cycAtoms[i].mask & mask) !== 0) {\r\n ++perCycle;\r\n atomsIdc[chunksCount++] = cycAtoms[i].index;\r\n }\r\n }\r\n if (perCycle > 0) {\r\n cycles[cycleIdx++] = cycle;\r\n }\r\n });\r\n\r\n const atomsGroup = new AromaticGroup(geoParams, {\r\n cycles,\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AromaticProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\nimport OrphanAtomsProcessor from './OrphanAtomsProcessor';\r\nimport ResiduesProcessor from './ResiduesProcessor';\r\nimport NucleicProcessor from './NucleicProcessor';\r\nimport SubseqsProcessor from './SubseqsProcessor';\r\nimport BondsProcessor from './BondsProcessor';\r\nimport AromaticProcessor from './AromaticProcessor';\r\n\r\nexport default {\r\n Atoms: AtomsProcessor,\r\n OrphanAtoms: OrphanAtomsProcessor,\r\n Residues: ResiduesProcessor,\r\n Nucleic: NucleicProcessor,\r\n Subseqs: SubseqsProcessor,\r\n Bonds: BondsProcessor,\r\n Aromatic: AromaticProcessor,\r\n};\r\n","import MeshCreator from '../../meshes/MeshCreator';\r\nimport groups from './groups';\r\nimport processors from '../processors/processors';\r\n\r\nfunction _bakeGroup(triplet, Processor, Group) {\r\n return function (complex, colorer, mode, polyComplexity, mask, material) {\r\n return new Processor(Group, triplet, complex, colorer, mode, polyComplexity, mask, material);\r\n };\r\n}\r\n\r\nclass GroupsFactory {\r\n static AtomsSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static OrphanedAtomsCrosses(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createCrosses(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.OrphanAtoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static BondsCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsCylinderGroup);\r\n }\r\n\r\n static BondsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.create2CLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsLinesGroup);\r\n }\r\n\r\n static CartoonChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesSubseqGroup);\r\n }\r\n\r\n static TraceChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CClosedCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesTraceGroup);\r\n }\r\n\r\n static NucleicSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicSpheresGroup);\r\n }\r\n\r\n static NucleicCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicCylindersGroup);\r\n }\r\n\r\n static ALoopsTorus(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticTorusGroup);\r\n }\r\n\r\n static ALoopsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createChunkedLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticLinesGroup);\r\n }\r\n\r\n static QuickSurfGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createQuickSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static ContactSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createContactSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static SASSESSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createSASSES(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSASSESGroupStub);\r\n }\r\n\r\n static TextLabelsGeo(caps, settings) {\r\n const gfxTriplet = MeshCreator.createLabels(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsTextGroup);\r\n }\r\n}\r\n\r\nexport default GroupsFactory;\r\n","import _ from 'lodash';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport factory from './groups/GroupsFactory';\r\n\r\n/**\r\n * Create new mode.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the mode after its creation.\r\n *\r\n * @exports Mode\r\n * @this Mode\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available modes used for building and displaying molecule geometry.\r\n */\r\nclass Mode {\r\n constructor(opts) {\r\n if (this.constructor === Mode) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Mode options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts);\r\n }\r\n\r\n /**\r\n * Get mode identification, probably with options.\r\n * @returns {string|Array} Mode identifier string ({@link Mode#id}) or two-element array containing both mode\r\n * identifier and options ({@link Mode#opts}).\r\n * Options are returned if they were changed during or after the mode creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, this.settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const polyComplexity = this.opts.polyComplexity ? this.opts.polyComplexity[this.settings.now.resolution] : 0;\r\n const groupList = this.depGroups;\r\n const groupCount = groupList.length;\r\n const group = new gfxutils.RCGroup();\r\n const self = this;\r\n for (let i = 0; i < groupCount; ++i) {\r\n let currGroup = groupList[i];\r\n let renderParams = {};\r\n if (_.isArray(currGroup)) {\r\n renderParams = currGroup[1].call(this);\r\n [currGroup] = currGroup;\r\n }\r\n const Group = factory[currGroup](null, this.settings, renderParams);\r\n const newGroup = new Group(complex, colorer, self, polyComplexity, mask, material);\r\n if (newGroup.children.length > 0) {\r\n group.add(newGroup);\r\n }\r\n }\r\n return group;\r\n }\r\n}\r\n\r\nmakeContextDependent(Mode.prototype);\r\n\r\n/**\r\n* Mode identifier.\r\n* @type {string}\r\n*/\r\nMode.prototype.id = '__';\r\n\r\n/**\r\n * Mode geo groups.\r\n * @type {Array}\r\n */\r\nMode.prototype.depGroups = [];\r\n\r\nexport default Mode;\r\n","import Mode from './Mode';\r\n\r\nfunction getRenderParams() {\r\n return {\r\n lineWidth: this.opts.lineWidth,\r\n };\r\n}\r\n\r\nclass LinesMode extends Mode {\r\n static id = 'LN';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const groups = this.depGroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n groups[i] = [groups[i], getRenderParams];\r\n }\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n\r\n calcAtomRadius() {\r\n return this.opts.atom;\r\n }\r\n\r\n getAromaticOffset() {\r\n return this.opts.offsarom;\r\n }\r\n\r\n getAromaticArcChunks() {\r\n return this.opts.chunkarom;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n}\r\n\r\nLinesMode.prototype.id = 'LN';\r\nLinesMode.prototype.name = 'Lines';\r\nLinesMode.prototype.shortName = 'Lines';\r\nLinesMode.prototype.depGroups = [\r\n 'ALoopsLines',\r\n 'BondsLines',\r\n 'OrphanedAtomsCrosses',\r\n];\r\n\r\nexport default LinesMode;\r\n","import Mode from './Mode';\r\n\r\nclass LicoriceMode extends Mode {\r\n static id = 'LC';\r\n\r\n calcAtomRadius(_atom) {\r\n return this.opts.bond;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nLicoriceMode.prototype.id = 'LC';\r\nLicoriceMode.prototype.name = 'Licorice';\r\nLicoriceMode.prototype.shortName = 'Licorice';\r\nLicoriceMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default LicoriceMode;\r\n","import Mode from './Mode';\r\n\r\nclass BallsAndSticksMode extends Mode {\r\n static id = 'BS';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius * this.opts.atom;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nBallsAndSticksMode.prototype.id = 'BS';\r\nBallsAndSticksMode.prototype.name = 'Balls and Sticks';\r\nBallsAndSticksMode.prototype.shortName = 'Balls';\r\nBallsAndSticksMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default BallsAndSticksMode;\r\n","import Mode from './Mode';\r\n\r\nclass VanDerWaalsMode extends Mode {\r\n static id = 'VW';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n}\r\n\r\nVanDerWaalsMode.prototype.id = 'VW';\r\nVanDerWaalsMode.prototype.name = 'Van der Waals';\r\nVanDerWaalsMode.prototype.shortName = 'VDW';\r\nVanDerWaalsMode.prototype.depGroups = ['AtomsSpheres'];\r\n\r\nexport default VanDerWaalsMode;\r\n","import Mode from './Mode';\r\n\r\nclass TraceMode extends Mode {\r\n static id = 'TR';\r\n\r\n calcStickRadius() {\r\n return this.opts.radius;\r\n }\r\n}\r\n\r\nTraceMode.prototype.id = 'TR';\r\nTraceMode.prototype.name = 'Trace';\r\nTraceMode.prototype.shortName = 'Trace';\r\nTraceMode.prototype.depGroups = ['TraceChains'];\r\n\r\nexport default TraceMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass TubeMode extends Mode {\r\n static id = 'TU';\r\n\r\n getResidueRadius(_residue) {\r\n return this.TUBE_RADIUS;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const rad = this.opts.radius;\r\n this.TUBE_RADIUS = new THREE.Vector2(rad, rad);\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nTubeMode.prototype.id = 'TU';\r\nTubeMode.prototype.name = 'Tube';\r\nTubeMode.prototype.shortName = 'Tube';\r\nTubeMode.prototype.depGroups = ['CartoonChains'];\r\n\r\nexport default TubeMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass CartoonMode extends Mode {\r\n static id = 'CA';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n // cache for secondary structure options\r\n this.secCache = {};\r\n }\r\n\r\n getResidueStartRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (!second || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return secOpts.start;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueEndRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (second === null || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return this.ARROW_END;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueRadius(residue, val) {\r\n const startRad = this.getResidueStartRadius(residue);\r\n if (val === 0) {\r\n return startRad;\r\n }\r\n\r\n const endRad = this.getResidueEndRadius(residue);\r\n if (val === 2) {\r\n return endRad;\r\n }\r\n\r\n return startRad.clone().lerp(endRad, val / 2.0);\r\n }\r\n\r\n calcStickRadius(_res) {\r\n return this.opts.radius;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const tubeRad = this.opts.radius;\r\n const secHeight = this.opts.depth;\r\n\r\n this.TUBE_RADIUS = new THREE.Vector2(tubeRad, tubeRad);\r\n this.ARROW_END = new THREE.Vector2(secHeight, tubeRad);\r\n const secCache = {};\r\n const secData = this.opts.ss;\r\n /* eslint-disable guard-for-in */\r\n for (const prop in secData) {\r\n secCache[prop] = {\r\n center: new THREE.Vector2(secHeight, secData[prop].width),\r\n start: new THREE.Vector2(secHeight, secData[prop].arrow),\r\n };\r\n }\r\n this.secCache = secCache;\r\n /* eslint-enable guard-for-in */\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nCartoonMode.prototype.id = 'CA';\r\nCartoonMode.prototype.name = 'Cartoon';\r\nCartoonMode.prototype.shortName = 'Cartoon';\r\nCartoonMode.prototype.depGroups = [\r\n 'CartoonChains',\r\n 'NucleicSpheres',\r\n 'NucleicCylinders',\r\n];\r\n\r\nexport default CartoonMode;\r\n","import chem from '../../chem';\r\nimport Mode from './Mode';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction getRenderParams() {\r\n return {\r\n wireframe: this.opts.wireframe,\r\n zClip: this.opts.zClip,\r\n };\r\n}\r\n\r\nclass SurfaceMode extends Mode {\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const surfaces = this.surfaceNames;\r\n const groups = this.depGroups;\r\n for (let i = 0, n = surfaces.length; i < n; ++i) {\r\n groups[groups.length] = [surfaces[i], getRenderParams];\r\n }\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getVisibilitySelector() {\r\n let visibilitySelector = null;\r\n if (this.opts.subset !== '') {\r\n const res = selectors.parse(this.opts.subset);\r\n if (!res.error) {\r\n visibilitySelector = res.selector;\r\n }\r\n }\r\n return visibilitySelector;\r\n }\r\n}\r\n\r\nSurfaceMode.prototype.isSurface = true;\r\nSurfaceMode.prototype.surfaceNames = [];\r\n\r\nexport default SurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass QuickSurfaceMode extends SurfaceMode {\r\n static id = 'QS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n useBeads: false,\r\n isoValue: this.opts.isoValue,\r\n gaussLim: this.opts.gaussLim[this.settings.now.resolution],\r\n radScale: this.opts.scale,\r\n gridSpacing: this.opts.gridSpacing[this.settings.now.resolution],\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nQuickSurfaceMode.prototype.id = 'QS';\r\nQuickSurfaceMode.prototype.name = 'Quick Surface';\r\nQuickSurfaceMode.prototype.shortName = 'Quick Surf';\r\nQuickSurfaceMode.prototype.surfaceNames = ['QuickSurfGeo'];\r\n\r\nexport default QuickSurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass IsoSurfaceMode extends SurfaceMode {\r\n constructor(excludeProbe, opts) {\r\n super(opts);\r\n this._excludeProbe = excludeProbe;\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getSurfaceOpts() {\r\n return {\r\n gridSpacing: this.opts.polyComplexity[this.settings.now.resolution],\r\n radScale: this._radScale,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n probeRadius: this.opts.probeRadius,\r\n excludeProbe: this._excludeProbe,\r\n };\r\n }\r\n}\r\n\r\nIsoSurfaceMode.prototype.id = 'SU';\r\nIsoSurfaceMode.prototype.name = 'Surface';\r\nIsoSurfaceMode.prototype.shortName = 'Surface';\r\nIsoSurfaceMode.prototype.surfaceNames = ['SASSESSurfaceGeo'];\r\n\r\nIsoSurfaceMode.prototype._radScale = 1;\r\nIsoSurfaceMode.prototype._excludeProbe = false;\r\n\r\nexport default IsoSurfaceMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSASMode extends IsoSurfaceMode {\r\n static id = 'SA';\r\n\r\n constructor(opts) {\r\n super(false, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSASMode.prototype.id = 'SA';\r\nIsoSurfaceSASMode.prototype.name = 'Solvent Accessible Surface';\r\nIsoSurfaceSASMode.prototype.shortName = 'SAS';\r\n\r\nexport default IsoSurfaceSASMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSESMode extends IsoSurfaceMode {\r\n static id = 'SE';\r\n\r\n constructor(opts) {\r\n super(true, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSESMode.prototype.id = 'SE';\r\nIsoSurfaceSESMode.prototype.name = 'Solvent Excluded Surface';\r\nIsoSurfaceSESMode.prototype.shortName = 'SES';\r\n\r\nexport default IsoSurfaceSESMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass ContactSurfaceMode extends SurfaceMode {\r\n static id = 'CS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n probeRadius: this.opts.probeRadius,\r\n radScale: this.opts.polyComplexity[this.settings.now.resolution],\r\n scaleFactor: this.opts.polyComplexity[this.settings.now.resolution],\r\n gridSpacing: 1.0 / this.opts.polyComplexity[this.settings.now.resolution],\r\n isoValue: this.opts.isoValue,\r\n probePositions: this.opts.probePositions,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nContactSurfaceMode.prototype.id = 'CS';\r\nContactSurfaceMode.prototype.name = 'Contact Surface';\r\nContactSurfaceMode.prototype.shortName = 'Contact Surf';\r\nContactSurfaceMode.prototype.isSurface = true;\r\nContactSurfaceMode.prototype.surfaceNames = ['ContactSurfaceGeo'];\r\n\r\nexport default ContactSurfaceMode;\r\n","import _ from 'lodash';\r\nimport Mode from './Mode';\r\n\r\nclass TextMode extends Mode {\r\n static id = 'TX';\r\n\r\n getTemplateOptions() {\r\n return this.opts.template;\r\n }\r\n\r\n getLabelOpts() {\r\n return _.merge(this.opts, {\r\n colors: true,\r\n adjustColor: true,\r\n transparent: true,\r\n });\r\n }\r\n}\r\n\r\nTextMode.prototype.id = 'TX';\r\nTextMode.prototype.name = 'Text mode';\r\nTextMode.prototype.shortName = 'Text';\r\nTextMode.prototype.depGroups = ['TextLabelsGeo'];\r\n\r\nexport default TextMode;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport LinesMode from './modes/LinesMode';\r\nimport LicoriceMode from './modes/LicoriceMode';\r\nimport BallsAndSticksMode from './modes/BallsAndSticksMode';\r\nimport VanDerWaalsMode from './modes/VanDerWaalsMode';\r\nimport TraceMode from './modes/TraceMode';\r\nimport TubeMode from './modes/TubeMode';\r\nimport CartoonMode from './modes/CartoonMode';\r\nimport QuickSurfaceMode from './modes/QuickSurfaceMode';\r\nimport IsoSurfaceSASMode from './modes/IsoSurfaceSASMode';\r\nimport IsoSurfaceSESMode from './modes/IsoSurfaceSESMode';\r\nimport ContactSurfaceMode from './modes/ContactSurfaceMode';\r\nimport TextMode from './modes/TextMode';\r\n\r\nconst modes = new EntityList([\r\n LinesMode,\r\n LicoriceMode,\r\n BallsAndSticksMode,\r\n VanDerWaalsMode,\r\n TraceMode,\r\n TubeMode,\r\n CartoonMode,\r\n QuickSurfaceMode,\r\n IsoSurfaceSASMode,\r\n IsoSurfaceSESMode,\r\n ContactSurfaceMode,\r\n TextMode,\r\n]);\r\n\r\nexport default modes;\r\n","import _ from 'lodash';\r\n\r\nfunction clamp(x, a, b) {\r\n return x <= b ? x < 0 ? 0 : x : b;\r\n}\r\n\r\nfunction lerpColor(c1, c2, alpha) {\r\n const beta = 1 - alpha;\r\n const r1 = (c1 >> 16) & 0xff;\r\n const g1 = (c1 >> 8) & 0xff;\r\n const b1 = c1 & 0xff;\r\n const r2 = (c2 >> 16) & 0xff;\r\n const g2 = (c2 >> 8) & 0xff;\r\n const b2 = c2 & 0xff;\r\n const r = beta * r1 + alpha * r2;\r\n const g = beta * g1 + alpha * g2;\r\n const b = beta * b1 + alpha * b2;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nclass Palette {\r\n constructor(name, id) {\r\n this.name = name || 'Custom';\r\n this.id = id || 'CP';\r\n }\r\n\r\n getElementColor(name, asIs = false) {\r\n const color = this.elementColors[name];\r\n return color === undefined && !asIs ? this.defaultElementColor : color;\r\n }\r\n\r\n getResidueColor(name, asIs = false) {\r\n const color = this.residueColors[name];\r\n return color === undefined && !asIs ? this.defaultResidueColor : color;\r\n }\r\n\r\n getChainColor(name) {\r\n let chain = name.charCodeAt(0);\r\n chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F)\r\n % this.chainColors.length;\r\n return this.chainColors[chain];\r\n }\r\n\r\n getSecondaryColor(type, asIs = false) {\r\n const color = this.secondaryColors[type];\r\n return color === undefined && !asIs ? this.defaultSecondaryColor : color;\r\n }\r\n\r\n getSequentialColor(index) {\r\n const { colors } = this;\r\n const len = colors.length;\r\n return index < 0 ? colors[(index % len) + len] : colors[index % len];\r\n }\r\n\r\n getGradientColor(value, gradientName) {\r\n const gradient = this.gradients[gradientName];\r\n if (!gradient) {\r\n return this.defaultNamedColor;\r\n }\r\n const count = gradient.length;\r\n const index = value * (count - 1);\r\n let left = Math.floor(index);\r\n const right = clamp(left + 1, 0, count - 1);\r\n left = clamp(left, 0, count - 1);\r\n return lerpColor(gradient[left], gradient[right], index - left);\r\n }\r\n\r\n getNamedColor(name, asIs = false) {\r\n const color = this.namedColors[name];\r\n return color === undefined && !asIs ? this.defaultNamedColor : color;\r\n }\r\n}\r\n\r\n_.assign(Palette.prototype, {\r\n colors: [0xFFFFFF, 0xFF0000, 0x00FF00, 0x0000FF, 0x808080],\r\n\r\n minRangeColor: 0x000000,\r\n midRangeColor: 0x7F7F7F,\r\n maxRangeColor: 0xFFFFFF,\r\n\r\n defaultElementColor: 0xFFFFFF,\r\n elementColors: {},\r\n\r\n defaultResidueColor: 0xFFFFFF,\r\n residueColors: {},\r\n\r\n chainColors: [0xFFFFFF],\r\n\r\n defaultSecondaryColor: 0xFFFFFF,\r\n secondaryColors: {},\r\n\r\n defaultGradientColor: 0x000000,\r\n\r\n defaultNamedColor: 0xFFFFFF,\r\n namedColorsArray: [\r\n /* eslint-disable no-multi-spaces */\r\n ['indianred', 0xcd5c5c],\r\n ['lightcoral', 0xf08080],\r\n ['salmon', 0xfa8072],\r\n ['darksalmon', 0xe9967a],\r\n ['lightsalmon', 0xffa07a],\r\n ['crimson', 0xdc143c],\r\n ['red', 0xff0000],\r\n ['firebrick', 0xb22222],\r\n ['darkred', 0x8b0000],\r\n ['pink', 0xffc0cb],\r\n ['lightpink', 0xffb6c1],\r\n ['hotpink', 0xff69b4],\r\n ['deeppink', 0xff1493],\r\n ['mediumvioletred', 0xc71585],\r\n ['palevioletred', 0xdb7093],\r\n ['coral', 0xff7f50],\r\n ['tomato', 0xff6347],\r\n ['orangered', 0xff4500],\r\n ['darkorange', 0xff8c00],\r\n ['orange', 0xffa500],\r\n ['gold', 0xffd700],\r\n ['yellow', 0xffff00],\r\n ['lightyellow', 0xffffe0],\r\n ['lemonchiffon', 0xfffacd],\r\n ['lightgoldenrodyellow', 0xfafad2],\r\n ['papayawhip', 0xffefd5],\r\n ['moccasin', 0xffe4b5],\r\n ['peachpuff', 0xffdab9],\r\n ['palegoldenrod', 0xeee8aa],\r\n ['khaki', 0xf0e68c],\r\n ['darkkhaki', 0xbdb76b],\r\n ['lavender', 0xe6e6fa],\r\n ['thistle', 0xd8bfd8],\r\n ['plum', 0xdda0dd],\r\n ['violet', 0xee82ee],\r\n ['orchid', 0xda70d6],\r\n ['fuchsia', 0xff00ff],\r\n ['magenta', 0xff00ff],\r\n ['mediumorchid', 0xba55d3],\r\n ['mediumpurple', 0x9370db],\r\n ['rebeccapurple', 0x663399],\r\n ['blueviolet', 0x8a2be2],\r\n ['darkviolet', 0x9400d3],\r\n ['darkorchid', 0x9932cc],\r\n ['darkmagenta', 0x8b008b],\r\n ['purple', 0x800080],\r\n ['indigo', 0x4b0082],\r\n ['slateblue', 0x6a5acd],\r\n ['mediumslateblue', 0x7b68ee],\r\n ['darkslateblue', 0x483d8b],\r\n ['greenyellow', 0xadff2f],\r\n ['chartreuse', 0x7fff00],\r\n ['lawngreen', 0x7cfc00],\r\n ['lime', 0x00ff00],\r\n ['limegreen', 0x32cd32],\r\n ['palegreen', 0x98fb98],\r\n ['lightgreen', 0x90ee90],\r\n ['mediumspringgreen', 0x00fa9a],\r\n ['springgreen', 0x00ff7f],\r\n ['mediumseagreen', 0x3cb371],\r\n ['seagreen', 0x2e8b57],\r\n ['forestgreen', 0x228b22],\r\n ['green', 0x008000],\r\n ['darkgreen', 0x006400],\r\n ['yellowgreen', 0x9acd32],\r\n ['olivedrab', 0x6b8e23],\r\n ['olive', 0x808000],\r\n ['darkolivegreen', 0x556b2f],\r\n ['mediumaquamarine', 0x66cdaa],\r\n ['darkseagreen', 0x8fbc8f],\r\n ['lightseagreen', 0x20b2aa],\r\n ['darkcyan', 0x008b8b],\r\n ['teal', 0x008080],\r\n ['aqua', 0x00ffff],\r\n ['cyan', 0x00ffff],\r\n ['lightcyan', 0xe0ffff],\r\n ['paleturquoise', 0xafeeee],\r\n ['aquamarine', 0x7fffd4],\r\n ['turquoise', 0x40e0d0],\r\n ['mediumturquoise', 0x48d1cc],\r\n ['darkturquoise', 0x00ced1],\r\n ['cadetblue', 0x5f9ea0],\r\n ['steelblue', 0x4682b4],\r\n ['lightsteelblue', 0xb0c4de],\r\n ['powderblue', 0xb0e0e6],\r\n ['lightblue', 0xadd8e6],\r\n ['skyblue', 0x87ceeb],\r\n ['lightskyblue', 0x87cefa],\r\n ['deepskyblue', 0x00bfff],\r\n ['dodgerblue', 0x1e90ff],\r\n ['cornflowerblue', 0x6495ed],\r\n ['royalblue', 0x4169e1],\r\n ['blue', 0x0000ff],\r\n ['mediumblue', 0x0000cd],\r\n ['darkblue', 0x00008b],\r\n ['navy', 0x000080],\r\n ['midnightblue', 0x191970],\r\n ['cornsilk', 0xfff8dc],\r\n ['blanchedalmond', 0xffebcd],\r\n ['bisque', 0xffe4c4],\r\n ['navajowhite', 0xffdead],\r\n ['wheat', 0xf5deb3],\r\n ['burlywood', 0xdeb887],\r\n ['tan', 0xd2b48c],\r\n ['rosybrown', 0xbc8f8f],\r\n ['sandybrown', 0xf4a460],\r\n ['goldenrod', 0xdaa520],\r\n ['darkgoldenrod', 0xb8860b],\r\n ['peru', 0xcd853f],\r\n ['chocolate', 0xd2691e],\r\n ['saddlebrown', 0x8b4513],\r\n ['sienna', 0xa0522d],\r\n ['brown', 0xa52a2a],\r\n ['maroon', 0x800000],\r\n ['white', 0xffffff],\r\n ['snow', 0xfffafa],\r\n ['honeydew', 0xf0fff0],\r\n ['mintcream', 0xf5fffa],\r\n ['azure', 0xf0ffff],\r\n ['aliceblue', 0xf0f8ff],\r\n ['ghostwhite', 0xf8f8ff],\r\n ['whitesmoke', 0xf5f5f5],\r\n ['seashell', 0xfff5ee],\r\n ['beige', 0xf5f5dc],\r\n ['oldlace', 0xfdf5e6],\r\n ['floralwhite', 0xfffaf0],\r\n ['ivory', 0xfffff0],\r\n ['antiquewhite', 0xfaebd7],\r\n ['linen', 0xfaf0e6],\r\n ['lavenderblush', 0xfff0f5],\r\n ['mistyrose', 0xffe4e1],\r\n ['gainsboro', 0xdcdcdc],\r\n ['lightgray', 0xd3d3d3],\r\n ['silver', 0xc0c0c0],\r\n ['darkgray', 0xa9a9a9],\r\n ['gray', 0x808080],\r\n ['dimgray', 0x696969],\r\n ['lightslategray', 0x778899],\r\n ['slategray', 0x708090],\r\n ['darkslategray', 0x2f4f4f],\r\n ['black', 0x000000],\r\n /* eslint-enable no-multi-spaces */\r\n ],\r\n\r\n namedColors: {},\r\n\r\n gradients: {\r\n rainbow: [\r\n 0x0000ff, // blue\r\n 0x00ffff, // cyan\r\n 0x00ff00, // green\r\n 0xffff00, // yellow\r\n 0xff0000, // red\r\n ],\r\n temp: [\r\n 0x0000ff, // blue\r\n 0x007fff, // light-blue\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n hot: [\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n cold: [\r\n 0xffffff, // white\r\n 0x007fff, // light-blue\r\n 0x0000ff, // blue\r\n ],\r\n 'blue-red': [\r\n 0x0000ff, // blue\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n reds: [\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n blues: [\r\n 0xffffff, // white\r\n 0x0000ff, // blue\r\n ],\r\n },\r\n});\r\n\r\nconst { namedColorsArray, namedColors } = Palette.prototype;\r\n\r\nfor (let i = 0, { length } = namedColorsArray; i < length; ++i) {\r\n const [name, value] = namedColorsArray[i];\r\n namedColors[name] = value;\r\n}\r\n\r\nexport default Palette;\r\n","import Palette from './Palette';\r\n\r\nconst palette = new Palette('CPK', 'CP');\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n C: 0x202020,\r\n N: 0x2060FF,\r\n O: 0xEE2010,\r\n F: 0x00FF00,\r\n P: 0x8020FF,\r\n S: 0xFFFF00,\r\n CL: 0x00BB00,\r\n FE: 0xD0D0D0,\r\n CO: 0xD0D0D0,\r\n NI: 0xD0D0D0,\r\n CU: 0xD0D0D0,\r\n BR: 0x008800,\r\n I: 0x005500,\r\n\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('Jmol', 'JM');\r\n\r\npalette.colors = [\r\n\r\n 0x0000FF, // blue\r\n 0x0055FF, //\r\n 0x00ABFF, //\r\n 0x00FFFF, // cyan\r\n 0x00FFAB, //\r\n 0x00FF55, //\r\n 0x00FF00, // green\r\n 0x55FF00, //\r\n 0xABFF00, //\r\n 0xFFFF00, // yellow\r\n 0xFFAB00, //\r\n 0xFF5500, //\r\n 0xFF0000, // red\r\n 0xFF0055, //\r\n 0xFF00AB, //\r\n 0xFF00FF, // magenta\r\n 0xAB00FF, //\r\n 0x5500FF, //\r\n\r\n];\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n D: 0xFFFFC0,\r\n T: 0xFFFFA0,\r\n HE: 0xD9FFFF,\r\n LI: 0xCC80FF,\r\n BE: 0xC2FF00,\r\n B: 0xFFB5B5,\r\n C: 0x909090,\r\n N: 0x3050F8,\r\n O: 0xFF0D0D,\r\n F: 0x90E050,\r\n NE: 0xB3E3F5,\r\n NA: 0xAB5CF2,\r\n MG: 0x8AFF00,\r\n AL: 0xBFA6A6,\r\n SI: 0xF0C8A0,\r\n P: 0xFF8000,\r\n S: 0xFFFF30,\r\n CL: 0x1FF01F,\r\n AR: 0x80D1E3,\r\n K: 0x8F40D4,\r\n CA: 0x3DFF00,\r\n SC: 0xE6E6E6,\r\n TI: 0xBFC2C7,\r\n V: 0xA6A6AB,\r\n CR: 0x8A99C7,\r\n MN: 0x9C7AC7,\r\n FE: 0xE06633,\r\n CO: 0xF090A0,\r\n NI: 0x50D050,\r\n CU: 0xC88033,\r\n ZN: 0x7D80B0,\r\n GA: 0xC28F8F,\r\n GE: 0x668F8F,\r\n AS: 0xBD80E3,\r\n SE: 0xFFA100,\r\n BR: 0xA62929,\r\n KR: 0x5CB8D1,\r\n RB: 0x702EB0,\r\n SR: 0x00FF00,\r\n Y: 0x94FFFF,\r\n ZR: 0x94E0E0,\r\n NB: 0x73C2C9,\r\n MO: 0x54B5B5,\r\n TC: 0x3B9E9E,\r\n RU: 0x248F8F,\r\n RH: 0x0A7D8C,\r\n PD: 0x006985,\r\n AG: 0xC0C0C0,\r\n CD: 0xFFD98F,\r\n IN: 0xA67573,\r\n SN: 0x668080,\r\n SB: 0x9E63B5,\r\n TE: 0xD47A00,\r\n I: 0x940094,\r\n XE: 0x429EB0,\r\n CS: 0x57178F,\r\n BA: 0x00C900,\r\n LA: 0x70D4FF,\r\n CE: 0xFFFFC7,\r\n PR: 0xD9FFC7,\r\n ND: 0xC7FFC7,\r\n PM: 0xA3FFC7,\r\n SM: 0x8FFFC7,\r\n EU: 0x61FFC7,\r\n GD: 0x45FFC7,\r\n TB: 0x30FFC7,\r\n DY: 0x1FFFC7,\r\n HO: 0x00FF9C,\r\n ER: 0x00E675,\r\n TM: 0x00D452,\r\n YB: 0x00BF38,\r\n LU: 0x00AB24,\r\n HF: 0x4DC2FF,\r\n TA: 0x4DA6FF,\r\n W: 0x2194D6,\r\n RE: 0x267DAB,\r\n OS: 0x266696,\r\n IR: 0x175487,\r\n PT: 0xD0D0E0,\r\n AU: 0xFFD123,\r\n HG: 0xB8B8D0,\r\n TL: 0xA6544D,\r\n PB: 0x575961,\r\n BI: 0x9E4FB5,\r\n PO: 0xAB5C00,\r\n AT: 0x754F45,\r\n RN: 0x428296,\r\n FR: 0x420066,\r\n RA: 0x007D00,\r\n AC: 0x70ABFA,\r\n TH: 0x00BAFF,\r\n PA: 0x00A1FF,\r\n U: 0x008FFF,\r\n NP: 0x0080FF,\r\n PU: 0x006BFF,\r\n AM: 0x545CF2,\r\n CM: 0x785CE3,\r\n BK: 0x8A4FE3,\r\n CF: 0xA136D4,\r\n ES: 0xB31FD4,\r\n FM: 0xB31FBA,\r\n MD: 0xB30DA6,\r\n NO: 0xBD0D87,\r\n LR: 0xC70066,\r\n RF: 0xCC0059,\r\n DB: 0xD1004F,\r\n SG: 0xD90045,\r\n BH: 0xE00038,\r\n HS: 0xE6002E,\r\n MT: 0xEB0026,\r\n\r\n};\r\n\r\npalette.defaultResidueColor = 0xBEA06E;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n\r\n ALA: 0xC8C8C8,\r\n ARG: 0x145AFF,\r\n ASN: 0x00DCDC,\r\n ASP: 0xE60A0A,\r\n CYS: 0xE6E600,\r\n GLN: 0x00DCDC,\r\n GLU: 0xE60A0A,\r\n GLY: 0xEBEBEB,\r\n HIS: 0x8282D2,\r\n ILE: 0x0F820F,\r\n LEU: 0x0F820F,\r\n LYS: 0x145AFF,\r\n MET: 0xE6E600,\r\n PHE: 0x3232AA,\r\n PRO: 0xDC9682,\r\n SER: 0xFA9600,\r\n THR: 0xFA9600,\r\n TRP: 0xB45AB4,\r\n TYR: 0x3232AA,\r\n VAL: 0x0F820F,\r\n A: 0xA0A0FF,\r\n C: 0xFF8C4B,\r\n G: 0xFF7070,\r\n I: 0x80FFFF,\r\n T: 0xA0FFA0,\r\n U: 0xFF8080,\r\n DA: 0xA0A0FF,\r\n DC: 0xFF8C4B,\r\n DG: 0xFF7070,\r\n DI: 0x80FFFF,\r\n DT: 0xA0FFA0,\r\n DU: 0xFF8080,\r\n '+A': 0xA0A0FF,\r\n '+C': 0xFF8C4B,\r\n '+G': 0xFF7070,\r\n '+I': 0x80FFFF,\r\n '+T': 0xA0FFA0,\r\n '+U': 0xFF8080,\r\n\r\n};\r\n\r\npalette.chainColors = [\r\n // ' '->0 'A'->1, 'B'->2\r\n 0xFFffffff, // ' ' & '0' white\r\n //\r\n 0xFFC0D0FF, // skyblue\r\n 0xFFB0FFB0, // pastel green\r\n 0xFFFFC0C8, // pink\r\n 0xFFFFFF80, // pastel yellow\r\n 0xFFFFC0FF, // pastel magenta\r\n 0xFFB0F0F0, // pastel cyan\r\n 0xFFFFD070, // pastel gold\r\n 0xFFF08080, // lightcoral\r\n\r\n 0xFFF5DEB3, // wheat\r\n 0xFF00BFFF, // deepskyblue\r\n 0xFFCD5C5C, // indianred\r\n 0xFF66CDAA, // mediumaquamarine\r\n 0xFF9ACD32, // yellowgreen\r\n 0xFFEE82EE, // violet\r\n 0xFF00CED1, // darkturquoise\r\n 0xFF00FF7F, // springgreen\r\n 0xFF3CB371, // mediumseagreen\r\n\r\n 0xFF00008B, // darkblue\r\n 0xFFBDB76B, // darkkhaki\r\n 0xFF006400, // darkgreen\r\n 0xFF800000, // maroon\r\n 0xFF808000, // olive\r\n 0xFF800080, // purple\r\n 0xFF008080, // teal\r\n 0xFFB8860B, // darkgoldenrod\r\n 0xFFB22222, // firebrick\r\n];\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xFF0080,\r\n [StructuralElementType.HELIX_PI]: 0x600080,\r\n [StructuralElementType.HELIX_310]: 0xA00080,\r\n [StructuralElementType.STRAND]: 0xFFC800,\r\n [StructuralElementType.TURN]: 0x6080FF,\r\n dna: 0xAE00FE,\r\n rna: 0xFD0162,\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('VMD', 'VM');\r\n\r\npalette.colors = [\r\n\r\n 0x0000FF, // blue\r\n 0xFF0000, // red\r\n 0x606060, // gray\r\n 0xFF8000, // orange\r\n 0xFFFF00, // yellow\r\n 0x808033, // tan\r\n 0x999999, // silver\r\n 0x00FF00, // green\r\n 0xFFFFFF, // white\r\n 0xFF9999, // pink\r\n 0x40C0C0, // cyan\r\n 0xA600A6, // purple\r\n 0x80E666, // lime\r\n 0xE666B3, // mauve\r\n 0x804D00, // ochre\r\n 0x8080C0, // ice blue\r\n\r\n];\r\n\r\npalette.defaultElementColor = 0x804D00;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n C: 0x40BFBF,\r\n N: 0x0000FF,\r\n O: 0xFF0000,\r\n P: 0x808033,\r\n S: 0xFFFF00,\r\n\r\n};\r\n\r\npalette.defaultResidueColor = 0x40C0C0;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n\r\n ALA: 0x0000FF,\r\n ARG: 0xFFFFFF,\r\n ASN: 0x808033,\r\n ASP: 0xFF0000,\r\n CYS: 0xFFFF00,\r\n GLN: 0xFF8000,\r\n GLU: 0xFF9999,\r\n GLY: 0xFFFFFF,\r\n HIS: 0x40C0C0,\r\n ILE: 0x00FF00,\r\n LEU: 0xFF9999,\r\n LYS: 0x40C0C0,\r\n MET: 0xFFFF00,\r\n PHE: 0xA600A6,\r\n PRO: 0x804C00,\r\n SER: 0xFFFF00,\r\n THR: 0xE666B3,\r\n TRP: 0x999999,\r\n TYR: 0x00FF00,\r\n VAL: 0x808033,\r\n A: 0x0000FF,\r\n C: 0xFF8000,\r\n G: 0xFFFF00,\r\n T: 0xA600A6,\r\n U: 0x00FF00,\r\n DA: 0x0000FF,\r\n DC: 0xFF8000,\r\n DG: 0xFFFF00,\r\n DT: 0xA600A6,\r\n DU: 0x00FF00,\r\n '+A': 0x0000FF,\r\n '+C': 0xFF8000,\r\n '+G': 0xFFFF00,\r\n '+T': 0xA600A6,\r\n '+U': 0x00FF00,\r\n WAT: 0x40C0C0,\r\n H2O: 0x40C0C0,\r\n HOH: 0x40C0C0,\r\n\r\n};\r\n\r\npalette.chainColors = [0xFFFFFF].concat(palette.colors);\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xA600A6,\r\n [StructuralElementType.HELIX_310]: 0x0000FF,\r\n [StructuralElementType.HELIX_PI]: 0xFF0000,\r\n [StructuralElementType.STRAND]: 0xFFFF00,\r\n [StructuralElementType.BRIDGE]: 0x808033,\r\n [StructuralElementType.TURN]: 0x40C0C0,\r\n};\r\n\r\nexport default palette;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport cpkPalette from './palettes/cpkPalette';\r\nimport jmolPalette from './palettes/jmolPalette';\r\nimport vmdPalette from './palettes/vmdPalette';\r\n\r\nconst palettes = new EntityList([\r\n cpkPalette,\r\n jmolPalette,\r\n vmdPalette,\r\n]);\r\n\r\nexport default palettes;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport palettes from '../palettes';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports Colorer\r\n * @this Colorer\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available coloring algorithms used for building and displaying molecule geometry.\r\n */\r\nclass Colorer {\r\n constructor(opts) {\r\n if (this.constructor === Colorer) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Colorer options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(settings.now.colorers[this.id], true), opts);\r\n /**\r\n * Palette in use.\r\n * @type {Palette}\r\n */\r\n this.palette = palettes.first;\r\n }\r\n\r\n /**\r\n * Get Colorer identification, probably with options.\r\n * @returns {string|Array} Colorer identifier string ({@link Colorer#id}) or two-element array containing both colorer\r\n * identifier and options ({@link Colorer#opts}).\r\n * Options are returned if they were changed during or after colorer creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, settings.now.colorers[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n}\r\n\r\n/**\r\n * Colorer identifier.\r\n * @type {string}\r\n */\r\n\r\nColorer.prototype.id = '__';\r\n\r\nexport default Colorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Element\r\n *\r\n * @exports ElementColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on chemical element.\r\n */\r\nclass ElementColorer extends Colorer {\r\n static id = 'EL';\r\n\r\n getAtomColor(atom, _complex) {\r\n const type = atom.element.name;\r\n if (type === 'C' && this.opts.carbon >= 0) {\r\n return this.opts.carbon;\r\n }\r\n return this.palette.getElementColor(type);\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nElementColorer.prototype.id = 'EL';\r\nElementColorer.prototype.name = 'Element';\r\nElementColorer.prototype.shortName = 'Element';\r\n\r\nexport default ElementColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Coloring algorithm based on residue type.\r\n *\r\n * @see ResidueType\r\n *\r\n * @exports ResidueTypeColorer\r\n * @constructor\r\n */\r\nclass ResidueTypeColorer extends Colorer {\r\n static id = 'RT';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getResidueColor(residue._type._name);\r\n }\r\n}\r\n\r\nResidueTypeColorer.prototype.id = 'RT';\r\nResidueTypeColorer.prototype.name = 'Residue Type';\r\nResidueTypeColorer.prototype.shortName = 'Residue';\r\n\r\nexport default ResidueTypeColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass SequenceColorer extends Colorer {\r\n static id = 'SQ';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const chain = residue._chain;\r\n if (chain.minSequence === Number.POSITIVE_INFINITY && chain.maxSequence === Number.NEGATIVE_INFINITY) {\r\n return this.palette.defaultNamedColor;\r\n }\r\n const min = chain.minSequence;\r\n const max = chain.maxSequence > min ? chain.maxSequence : min + 1;\r\n return this.palette.getGradientColor((residue._sequence - min) / (max - min), this.opts.gradient);\r\n }\r\n}\r\n\r\nSequenceColorer.prototype.id = 'SQ';\r\nSequenceColorer.prototype.name = 'Sequence';\r\nSequenceColorer.prototype.shortName = 'Sequence';\r\n\r\nexport default SequenceColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ChainColorer extends Colorer {\r\n static id = 'CH';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getChainColor(residue.getChain()._name);\r\n }\r\n}\r\n\r\nChainColorer.prototype.id = 'CH';\r\nChainColorer.prototype.name = 'Chain';\r\nChainColorer.prototype.shortName = 'Chain';\r\n\r\nexport default ChainColorer;\r\n","import Colorer from './Colorer';\r\nimport ResidueType from '../../chem/ResidueType';\r\n\r\nclass SecondaryStructureColorer extends Colorer {\r\n static id = 'SS';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n if (residue._type.flags & ResidueType.Flags.DNA) {\r\n return this.palette.getSecondaryColor('dna');\r\n }\r\n if (residue._type.flags & ResidueType.Flags.RNA) {\r\n return this.palette.getSecondaryColor('rna');\r\n }\r\n const secondary = residue.getSecondary();\r\n if (secondary) {\r\n let color = this.palette.getSecondaryColor(secondary.type, true);\r\n if (color === undefined) {\r\n color = this.palette.getSecondaryColor(secondary.generic);\r\n }\r\n return color;\r\n }\r\n return this.palette.defaultSecondaryColor;\r\n }\r\n}\r\n\r\nSecondaryStructureColorer.prototype.id = 'SS';\r\nSecondaryStructureColorer.prototype.name = 'Secondary Structure';\r\nSecondaryStructureColorer.prototype.shortName = 'Structure';\r\n\r\nexport default SecondaryStructureColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass UniformColorer extends Colorer {\r\n static id = 'UN';\r\n\r\n getAtomColor(_atom, _complex) {\r\n return this.opts.color;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nUniformColorer.prototype.id = 'UN';\r\nUniformColorer.prototype.name = 'Uniform';\r\nUniformColorer.prototype.shortName = 'Uniform';\r\n\r\nexport default UniformColorer;\r\n","import Colorer from './Colorer';\r\nimport selectors from '../../chem/selectors';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports ConditionalColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on a selector string used as a condition.\r\n */\r\nclass ConditionalColorer extends Colorer {\r\n static id = 'CO';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n const parsed = selectors.parse(this.opts.subset);\r\n this._subsetCached = parsed.error ? selectors.none() : parsed.selector;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n return this._subsetCached.includesAtom(atom) ? this.opts.color : this.opts.baseColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const subset = this._subsetCached;\r\n const atoms = residue._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (!subset.includesAtom(atoms[i])) {\r\n return this.opts.baseColor;\r\n }\r\n }\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nConditionalColorer.prototype.id = 'CO';\r\nConditionalColorer.prototype.name = 'Conditional';\r\nConditionalColorer.prototype.shortName = 'Conditional';\r\n\r\nexport default ConditionalColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ConformationColorer extends Colorer {\r\n static id = 'CF';\r\n\r\n getAtomColor(atom, _complex) {\r\n return this.palette.getChainColor(String.fromCharCode(atom.location));\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nConformationColorer.prototype.id = 'CF';\r\nConformationColorer.prototype.name = 'Conformation';\r\nConformationColorer.prototype.shortName = 'Conformation';\r\n\r\nexport default ConformationColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Temperature\r\n *\r\n * @exports TemperatureColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on temperature of chemical element.\r\n */\r\nclass TemperatureColorer extends Colorer {\r\n static id = 'TM';\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n let factor = 1;\r\n if (atom.temperature && opts) {\r\n if (opts.min === opts.max) {\r\n factor = atom.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (atom.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n if (!opts) {\r\n return this.palette.defaultGradientColor;\r\n }\r\n if (residue.temperature) {\r\n let factor = 0;\r\n if (opts.min === opts.max) {\r\n factor = residue.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (residue.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n}\r\n\r\nTemperatureColorer.prototype.id = 'TM'; // [T]e[M]perature\r\nTemperatureColorer.prototype.name = 'Temperature';\r\nTemperatureColorer.prototype.shortName = 'Temperature';\r\n\r\nexport default TemperatureColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Occupancy\r\n *\r\n * @exports OccupancyColorer\r\n * @augments Occupancy\r\n * @constructor\r\n * @classdesc Coloring algorithm based on occupancy of chemical element.\r\n */\r\nclass OccupancyColorer extends Colorer {\r\n static id = 'OC';\r\n\r\n _getColorByOccupancy(occupancy, opts) {\r\n if (occupancy !== undefined) {\r\n const factor = 1 - occupancy;\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(atom.occupancy, opts);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(residue.occupancy, opts);\r\n }\r\n}\r\n\r\nOccupancyColorer.prototype.id = 'OC'; // [OC]cupancy\r\nOccupancyColorer.prototype.name = 'Occupancy';\r\nOccupancyColorer.prototype.shortName = 'Occupancy';\r\n\r\nexport default OccupancyColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass HydrophobicityColorer extends Colorer {\r\n static id = 'HY';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n let color = this.palette.defaultResidueColor;\r\n if (residue._type.hydrophobicity !== undefined) {\r\n // Kyte Doolitle hydro [-4.5,4.5]->[0.1]\r\n const min = -4.5;\r\n const max = 4.5;\r\n color = this.palette.getGradientColor((residue._type.hydrophobicity - min) / (max - min), this.opts.gradient);\r\n }\r\n return color;\r\n }\r\n}\r\n\r\nHydrophobicityColorer.prototype.id = 'HY';\r\nHydrophobicityColorer.prototype.name = 'Hydrophobicity';\r\nHydrophobicityColorer.prototype.shortName = 'Hydrophobicity';\r\n\r\nexport default HydrophobicityColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass MoleculeColorer extends Colorer {\r\n static id = 'MO';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const molecule = residue._molecule;\r\n const count = _complex.getMoleculeCount();\r\n if (count > 1) {\r\n return this.palette.getGradientColor((molecule.index - 1) / (count - 1), this.opts.gradient);\r\n }\r\n return this.palette.getGradientColor(0, this.opts.gradient);\r\n }\r\n}\r\n\r\nMoleculeColorer.prototype.id = 'MO';\r\nMoleculeColorer.prototype.name = 'Molecule';\r\nMoleculeColorer.prototype.shortName = 'Molecule';\r\n\r\nexport default MoleculeColorer;\r\n","import Colorer from './Colorer';\r\nimport Atom from '../../chem/Atom';\r\n\r\nfunction scaleColor(c, factor) {\r\n const r1 = (c >> 16) & 0xff;\r\n const g1 = (c >> 8) & 0xff;\r\n const b1 = c & 0xff;\r\n const r = factor * r1;\r\n const g = factor * g1;\r\n const b = factor * b1;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports CarbonColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on selection carbon atoms.\r\n */\r\nclass CarbonColorer extends Colorer {\r\n static id = 'CB';\r\n\r\n getAtomColor(atom, _complex) {\r\n const colorCarbon = this.opts.color;\r\n const colorNotCarbon = scaleColor(colorCarbon, this.opts.factor);\r\n return (atom.flags & Atom.Flags.CARBON) ? colorCarbon : colorNotCarbon;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nCarbonColorer.prototype.id = 'CB';\r\nCarbonColorer.prototype.name = 'Carbon';\r\nCarbonColorer.prototype.shortName = 'Carbon';\r\n\r\nexport default CarbonColorer;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport ElementColorer from './colorers/ElementColorer';\r\nimport ResidueTypeColorer from './colorers/ResidueTypeColorer';\r\nimport SequenceColorer from './colorers/SequenceColorer';\r\nimport ChainColorer from './colorers/ChainColorer';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\nimport UniformColorer from './colorers/UniformColorer';\r\nimport ConditionalColorer from './colorers/ConditionalColorer';\r\nimport ConformationColorer from './colorers/ConformationColorer';\r\nimport TemperatureColorer from './colorers/TemperatureColorer';\r\nimport OccupancyColorer from './colorers/OccupancyColorer';\r\nimport HydrophobicityColorer from './colorers/HydrophobicityColorer';\r\nimport MoleculeColorer from './colorers/MoleculeColorer';\r\nimport CarbonColorer from './colorers/CarbonColorer';\r\n\r\nconst colorers = new EntityList([\r\n ElementColorer,\r\n ResidueTypeColorer,\r\n SequenceColorer,\r\n ChainColorer,\r\n SecondaryStructureColorer,\r\n UniformColorer,\r\n ConditionalColorer,\r\n ConformationColorer,\r\n TemperatureColorer,\r\n OccupancyColorer,\r\n HydrophobicityColorer,\r\n MoleculeColorer,\r\n CarbonColorer,\r\n]);\r\n\r\nexport default colorers;\r\n","import * as THREE from 'three';\r\nimport EntityList from '../utils/EntityList';\r\n\r\nfunction neutralColor(intensity) {\r\n return new THREE.Color(intensity, intensity, intensity);\r\n}\r\n\r\nconst materialList = [\r\n {\r\n id: 'DF',\r\n name: 'Diffuse',\r\n shortName: 'Diffuse',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'SF',\r\n name: 'Soft Plastic',\r\n shortName: 'Soft',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.1),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'PL',\r\n name: 'Glossy Plastic',\r\n shortName: 'Glossy',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.28),\r\n shininess: 100,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'ME',\r\n name: 'Metal',\r\n shortName: 'Metal',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.55),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TR',\r\n name: 'Transparent',\r\n shortName: 'Transparent',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'GL',\r\n name: 'Glass',\r\n shortName: 'Glass',\r\n uberOptions: {\r\n diffuse: neutralColor(0.50),\r\n specular: neutralColor(0.65),\r\n shininess: 100,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'BA',\r\n name: 'Backdrop',\r\n shortName: 'Backdrop',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: false,\r\n depthWrite: false,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TN',\r\n name: 'Toon',\r\n shortName: 'Toon',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: true,\r\n },\r\n }, {\r\n id: 'FL',\r\n name: 'Flat',\r\n shortName: 'Flat',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 0,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n },\r\n },\r\n];\r\n\r\nconst materials = new EntityList(materialList);\r\n\r\nexport default materials;\r\n","/**\r\n * Utils functions which is worked with meshes\r\n *\r\n * functions for doing something with all/specified meshes\r\n * functions for traversihg tree and create auxiliary meshes for transparency/shadowmaps...\r\n * functions for calculating data connected with meshes\r\n */\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _gatherObjects(root, meshTypes) {\r\n const meshes = [];\r\n root.traverse((object) => {\r\n for (let i = 0; i < meshTypes.length; i++) {\r\n if (object instanceof meshTypes[i]) {\r\n meshes[meshes.length] = object;\r\n break;\r\n }\r\n }\r\n });\r\n return meshes;\r\n}\r\n\r\n// new mesh with the same geometry and specified material values and layer\r\nfunction createDerivativeMesh(mesh, values, layer) {\r\n const material = mesh.material.createInstance();\r\n material.setValues(values);\r\n\r\n const newMesh = new mesh.constructor(mesh.geometry, material);\r\n newMesh.material.needsUpdate = true;\r\n newMesh.applyMatrix4(mesh.matrix);\r\n newMesh.layers.set(layer);\r\n return newMesh;\r\n}\r\n\r\nfunction traverseMeshes(root, meshTypes, func) {\r\n const meshes = _gatherObjects(root, meshTypes);\r\n\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n const mesh = meshes[i];\r\n if (!mesh.parent) {\r\n continue;\r\n }\r\n func(mesh);\r\n }\r\n}\r\n\r\nfunction applyTransformsToMeshes(root, mtc) {\r\n const mtcCount = mtc.length;\r\n if (mtcCount < 1) {\r\n return;\r\n }\r\n\r\n const meshTypes = [THREE.Mesh, THREE.LineSegments, THREE.Line];\r\n traverseMeshes(root, meshTypes, (mesh) => {\r\n mesh.applyMatrix4(mtc[0]);\r\n for (let j = 1; j < mtcCount; ++j) {\r\n const newMesh = new mesh.constructor(mesh.geometry, mesh.material);\r\n mesh.parent.add(newMesh);\r\n newMesh.applyMatrix4(mtc[j]);\r\n }\r\n });\r\n}\r\n\r\nconst processTransparentMaterial = (function () {\r\n const matValues = {\r\n prepassTransparancy: true,\r\n fakeOpacity: false,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n mesh.material.setValues({ prepassTransparancy: false, fakeOpacity: false });\r\n mesh.material.needsUpdate = true;\r\n mesh.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n\r\n const prepassTranspMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n mesh.parent.add(prepassTranspMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst processColFromPosMaterial = (function () {\r\n const matValues = {\r\n colorFromPos: true,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n overrideColor: false,\r\n fogTransparent: false,\r\n attrColor: false,\r\n attrColor2: false,\r\n attrAlphaColor: false,\r\n fakeOpacity: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n const colFromPosMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n mesh.parent.add(colFromPosMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst createShadowmapMaterial = (function () {\r\n const matValues = {\r\n colorFromDepth: true,\r\n orthoCam: true,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (!mesh.receiveShadow && mesh.material.shadowmap) { // remove shadow from non-receivers\r\n mesh.material.setValues({ shadowmap: false });\r\n }\r\n if (!mesh.material.lights) { // skip creating shadowmap meshes for materials without lighting\r\n return;\r\n }\r\n if (!mesh.castShadow) { // skip creating shadowmap meshes for non-casters\r\n return;\r\n }\r\n if (!gfxutils.belongToSelectLayers(mesh)) { // skip creating shadowmap meshes for selection layer\r\n return;\r\n }\r\n\r\n const shadowmapMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.SHADOWMAP);\r\n shadowmapMesh.isShadowmapMesh = true;\r\n mesh.parent.add(shadowmapMesh);\r\n });\r\n };\r\n}());\r\n\r\nfunction removeShadowmapMaterial(root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (mesh.isShadowmapMesh) {\r\n mesh.parent.remove(mesh);\r\n }\r\n });\r\n}\r\n\r\nfunction forEachMeshInGroup(group, process) {\r\n function processObj(object) {\r\n if (object instanceof THREE.Mesh) {\r\n process(object);\r\n }\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n processObj(object.children[i]);\r\n }\r\n }\r\n processObj(group);\r\n}\r\n\r\nfunction _countMeshTriangles(mesh) {\r\n const geom = mesh.geometry;\r\n if (geom instanceof THREE.InstancedBufferGeometry) {\r\n const attribs = geom.attributes;\r\n for (const property in attribs) {\r\n if (attribs.hasOwnProperty(property) && attribs[property] instanceof THREE.InstancedBufferAttribute) {\r\n const currAttr = attribs[property];\r\n const indexSize = geom.index ? geom.index.array.length / 3 : 0;\r\n return indexSize * currAttr.array.length / currAttr.itemSize;\r\n }\r\n }\r\n return 0;\r\n }\r\n if (geom instanceof THREE.BufferGeometry) {\r\n return geom.index ? geom.index.array.length / 3 : 0;\r\n }\r\n return geom.faces ? geom.faces.length : 0;\r\n}\r\n\r\nfunction countTriangles(group) {\r\n let totalCount = 0;\r\n forEachMeshInGroup(group, (mesh) => {\r\n totalCount += _countMeshTriangles(mesh);\r\n });\r\n return totalCount;\r\n}\r\n\r\nexport default {\r\n applyTransformsToMeshes,\r\n processTransparentMaterial,\r\n processColFromPosMaterial,\r\n createShadowmapMaterial,\r\n removeShadowmapMaterial,\r\n forEachMeshInGroup,\r\n countTriangles,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\nimport meshutils from './meshutils';\r\nimport settings from '../settings';\r\nimport materials from './materials';\r\nimport chem from '../chem';\r\n\r\nconst { selectors } = chem;\r\n\r\nclass Representation {\r\n constructor(index, mode, colorer, selector) {\r\n const startMaterialValues = {\r\n clipPlane: settings.now.draft.clipPlane,\r\n fogTransparent: settings.now.bg.transparent,\r\n shadowmap: settings.now.shadow.on,\r\n shadowmapType: settings.now.shadow.type,\r\n };\r\n this.index = index;\r\n this.mode = mode;\r\n this.colorer = colorer;\r\n this.selector = selector;\r\n this.selectorString = '';\r\n this.count = 0;\r\n this.material = new UberMaterial();\r\n this.material.setValues(startMaterialValues);\r\n this.material.setUberOptions({ fogAlpha: settings.now.fogAlpha });\r\n this.materialPreset = materials.first;\r\n this.needsRebuild = true;\r\n this.visible = true;\r\n\r\n // apply mode params & preset\r\n this.setMode(mode);\r\n }\r\n\r\n markAtoms(complex) {\r\n this.count = complex.markAtoms(this.selector, 1 << this.index);\r\n this.needsRebuild = true;\r\n return this.count;\r\n }\r\n\r\n unmarkAtoms(complex) {\r\n complex.clearAtomBits(1 << this.index);\r\n this.count = 0;\r\n }\r\n\r\n setMode(mode) {\r\n this.mode = mode;\r\n }\r\n\r\n setMaterialPreset(preset) {\r\n this.materialPreset = preset;\r\n this.material.setUberOptions(preset.uberOptions);\r\n this.material.setValues(preset.values);\r\n }\r\n\r\n reset() {\r\n this.geo = null;\r\n this.selectionGeo = null;\r\n }\r\n\r\n buildGeometry(complex) {\r\n this.reset();\r\n this.needsRebuild = false;\r\n\r\n if (settings.now.ao) {\r\n this.material.setValues({ normalsToGBuffer: settings.now.ao });\r\n }\r\n\r\n this.geo = this.mode.buildGeometry(complex, this.colorer, 1 << this.index, this.material);\r\n\r\n if (this.material.uberOptions.opacity < 0.99 && settings.now.transparency === 'prepass') {\r\n meshutils.processTransparentMaterial(this.geo, this.material);\r\n }\r\n this.geo.visible = this.visible;\r\n\r\n gfxutils.processObjRenderOrder(this.geo, this.materialPreset.id);\r\n meshutils.processColFromPosMaterial(this.geo, this.material);\r\n\r\n if (settings.now.shadow.on) {\r\n meshutils.createShadowmapMaterial(this.geo, this.material);\r\n }\r\n\r\n return this.geo;\r\n }\r\n\r\n buildSelectionGeometry(mask) {\r\n let sg = null;\r\n\r\n if (this.geo && ('getSubset' in this.geo)) {\r\n const meshes = this.geo.getSubset(mask);\r\n if (meshes && meshes.length > 0) {\r\n sg = new THREE.Group();\r\n sg.matrixAutoUpdate = false;\r\n sg.matrix = this.geo.matrix;\r\n\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n sg.add(m);\r\n }\r\n }\r\n }\r\n\r\n if (sg) {\r\n sg.visible = this.visible;\r\n }\r\n\r\n this.selectionGeo = sg;\r\n return this.selectionGeo;\r\n }\r\n\r\n /**\r\n * Create object that represents difference between current and another rep\r\n * anotherRep could be undefined. In this case everything is reported.\r\n */\r\n compare(repSettings) {\r\n const diff = {};\r\n\r\n const selStr = String(this.selector);\r\n if (!repSettings || selStr.valueOf() !== String(repSettings.selector).valueOf()) {\r\n diff.selector = selStr;\r\n }\r\n\r\n const modeDiff = this.mode.identify();\r\n if (!repSettings || Array.isArray(modeDiff) || modeDiff !== repSettings.mode) {\r\n diff.mode = modeDiff;\r\n }\r\n\r\n const colorerDiff = this.colorer.identify();\r\n if (!repSettings || Array.isArray(colorerDiff) || colorerDiff !== repSettings.colorer) {\r\n diff.colorer = colorerDiff;\r\n }\r\n\r\n if (!repSettings || this.materialPreset.id !== repSettings.material) {\r\n diff.material = this.materialPreset.id;\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n /**\r\n * Change representation. Write fields what was changed into new object, return it.\r\n */\r\n change(repSettings, complex, mode, color) {\r\n const diff = {};\r\n\r\n // modify selector\r\n if (repSettings.selector) {\r\n const newSelectorObject = selectors.parse(repSettings.selector).selector;\r\n const newSelector = String(newSelectorObject);\r\n if (this.selectorString !== newSelector) {\r\n diff.selector = newSelector;\r\n this.selectorString = newSelector;\r\n this.selector = newSelectorObject;\r\n this.markAtoms(complex);\r\n }\r\n }\r\n\r\n // modify mode\r\n if (repSettings.mode) {\r\n const newMode = repSettings.mode;\r\n if (!_.isEqual(this.mode.identify(), newMode)) {\r\n diff.mode = newMode;\r\n this.setMode(mode);\r\n }\r\n }\r\n\r\n // modify colorer\r\n if (repSettings.colorer) {\r\n const newColorer = repSettings.colorer;\r\n if (!_.isEqual(this.colorer.identify(), newColorer)) {\r\n diff.colorer = newColorer;\r\n this.colorer = color;\r\n }\r\n }\r\n\r\n // modify material\r\n if (repSettings.material) {\r\n const newMaterial = repSettings.material;\r\n if (!_.isEqual(this.materialPreset.id, newMaterial)) {\r\n diff.material = newMaterial;\r\n this.setMaterialPreset(materials.get(repSettings.material));\r\n }\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n show(visible) {\r\n this.visible = visible;\r\n if (this.geo) {\r\n this.geo.visible = visible;\r\n }\r\n if (this.selectionGeo) {\r\n this.selectionGeo.visible = visible;\r\n }\r\n }\r\n}\r\n\r\nexport default Representation;\r\n","import * as THREE from 'three';\r\nimport logger from './utils/logger';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport './gfx/modes';\r\n\r\nfunction _traverseComponentGroups(root, component, callback) {\r\n const { children } = root;\r\n if (!children) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n if (child._component === component) {\r\n callback(child);\r\n }\r\n if (child instanceof gfxutils.RCGroup) {\r\n _traverseComponentGroups(child, component, callback);\r\n }\r\n }\r\n}\r\n\r\nfunction ComplexEditor() {\r\n}\r\n\r\nclass ComplexComponentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n // init component matrices\r\n this._componentTransforms = [];\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n const component = complex._components[i];\r\n this._componentTransforms[component._index] = new THREE.Object3D();\r\n }\r\n\r\n this._inProgress = true;\r\n\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const complex = this._complexVisual.getComplex();\r\n\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n this._bakeComponentTransform(complex._components[i]);\r\n }\r\n\r\n complex.onAtomPositionChanged();\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n const visual = this._complexVisual;\r\n const component = visual.getSelectedComponent();\r\n\r\n if (component === null) {\r\n return res;\r\n }\r\n\r\n const selection = this._complexVisual.getSelectionGeo();\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n // find all geo nodes for this component\r\n _traverseComponentGroups(visual, component, (child) => {\r\n res.objects.push(child);\r\n });\r\n\r\n // find all selection nodes for this component\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component') && geo._component === component) {\r\n res.objects.push(geo);\r\n }\r\n }\r\n }\r\n\r\n // add dummy object that stores component transformation\r\n res.objects.push(this._componentTransforms[component._index]);\r\n\r\n const bbmin = new THREE.Vector3(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE);\r\n const bbmax = new THREE.Vector3(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE);\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (j = 0; j < atoms.length; ++j) {\r\n if (atoms[j].mask & selectionMask) {\r\n bbmin.min(atoms[j].position);\r\n bbmax.max(atoms[j].position);\r\n }\r\n }\r\n });\r\n\r\n res.pivot.lerpVectors(bbmin, bbmax, 0.5);\r\n return res;\r\n }\r\n\r\n _bakeComponentTransform(component) {\r\n const t = this._componentTransforms[component._index];\r\n if (t && (!(t.position.x === 0 && t.position.y === 0 && t.position.z === 0)\r\n || !(t.quaternion.x === 0 && t.quaternion.y === 0 && t.quaternion.z === 0 && t.quaternion.w === 1))) {\r\n t.updateMatrix();\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (let j = 0; j < atoms.length; ++j) {\r\n atoms[j].position.applyMatrix4(t.matrix);\r\n }\r\n });\r\n }\r\n }\r\n\r\n _resetComponentTransform() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n for (i = 0; i < this._componentTransforms.length; ++i) {\r\n geo = this._componentTransforms[i];\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n\r\n // reset all geo nodes\r\n for (i = 0; i < visual.children.length; ++i) {\r\n reprNode = visual.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n // reset all selection nodes\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ComplexFragmentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n const atoms = this._getSelectionBorderAtoms();\r\n if (atoms.length < 1 || atoms.length > 2) {\r\n logger.error('Can only edit fragments with one or two bound atoms.');\r\n return false;\r\n }\r\n\r\n this._fragmentBoundAtoms = atoms;\r\n\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n\r\n // hide selected fragment in main model\r\n visual.disableSubset(selectionMask, true);\r\n\r\n // hide selection geo in main model\r\n for (let k = 0; k < selection.children.length; ++k) {\r\n selection.children[k].visible = false;\r\n }\r\n\r\n // create visible fragment representation to rotate\r\n const pivotPos = atoms[0].position.clone();\r\n\r\n if (atoms.length === 2) {\r\n pivotPos.lerp(atoms[1].position, 0.5);\r\n }\r\n\r\n this._fragmentGeo = new THREE.Group();\r\n visual.add(this._fragmentGeo);\r\n this._fragmentGeo.position.copy(pivotPos);\r\n\r\n this._fragmentSelectionGeo = new THREE.Group();\r\n selection.add(this._fragmentSelectionGeo);\r\n this._fragmentSelectionGeo.position.copy(pivotPos);\r\n\r\n const offset = pivotPos.clone();\r\n offset.negate();\r\n\r\n for (let i = 0; i < visual.children.length; ++i) {\r\n const g = visual.children[i];\r\n if (!('getSubset' in g)) {\r\n continue;\r\n }\r\n\r\n const vg = new THREE.Group();\r\n this._fragmentGeo.add(vg);\r\n\r\n const sg = new THREE.Group();\r\n this._fragmentSelectionGeo.add(sg);\r\n\r\n const meshes = g.getSubset(selectionMask, true);\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n vg.add(m);\r\n m.position.copy(offset);\r\n }\r\n\r\n const smeshes = g.getSubset(selectionMask, true);\r\n for (let h = 0; h < smeshes.length; h++) {\r\n const sm = smeshes[h];\r\n sg.add(sm);\r\n sm.position.copy(offset);\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(this._fragmentSelectionGeo);\r\n\r\n this._inProgress = true;\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selectionBit = visual.getSelectionBit();\r\n\r\n const p = this._fragmentGeo.position;\r\n const m = this._fragmentGeo.matrix.clone();\r\n m.multiply(new THREE.Matrix4().makeTranslation(-p.x, -p.y, -p.z));\r\n\r\n this._bakeAtomTransform(m, 1 << selectionBit);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << selectionBit, true);\r\n\r\n visual.getComplex().onAtomPositionChanged();\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n this._fragmentGeo.parent.remove(this._fragmentGeo);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << visual.getSelectionBit(), true);\r\n\r\n // show selection geo in main model (+ remove fragment selection geo)\r\n for (let i = 0; i < selection.children.length; ++i) {\r\n const node = selection.children[i];\r\n if (node.visible) {\r\n selection.remove(node);\r\n } else {\r\n node.visible = true;\r\n }\r\n }\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n isFreeRotationAllowed() {\r\n return (this._fragmentBoundAtoms.length < 2);\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n res.objects.push(this._fragmentGeo, this._fragmentSelectionGeo);\r\n\r\n const boundAtoms = this._fragmentBoundAtoms;\r\n if (boundAtoms.length === 1) {\r\n if (boundAtoms[0].bonds.length === 1) {\r\n // single external bond allows rotation about bond axis\r\n const bond = boundAtoms[0].bonds[0];\r\n res.axis = new THREE.Vector3().subVectors(bond._right.position, bond._left.position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n } else if (boundAtoms.length === 2) {\r\n // two bound atoms allow rotation only about axis running through their centers\r\n res.axis = new THREE.Vector3().subVectors(boundAtoms[1].position, boundAtoms[0].position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _getSelectionBorderAtoms() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n const selectionMask = 1 << this._complexVisual.getSelectionBit();\r\n const atomHash = {};\r\n\r\n complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n atomHash[bond._left.index] = 1;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n atomHash[bond._right.index] = 1;\r\n }\r\n });\r\n\r\n const atoms = [];\r\n const keys = Object.keys(atomHash);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const idx = keys[i];\r\n atoms.push(complex._atoms[idx]);\r\n }\r\n\r\n return atoms;\r\n }\r\n\r\n _bakeAtomTransform(matrix, mask) {\r\n this._complexVisual.getComplex().forEachAtom((atom) => {\r\n if (atom.mask & mask) {\r\n atom.position.applyMatrix4(matrix);\r\n }\r\n });\r\n }\r\n}\r\n\r\nexport default {\r\n ComponentEditor: ComplexComponentEditor,\r\n FragmentEditor: ComplexFragmentEditor,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\nimport chem from './chem';\r\nimport settings from './settings';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport Visual from './Visual';\r\nimport ComplexVisualEdit from './ComplexVisualEdit';\r\nimport meshutils from './gfx/meshutils';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction lookupAndCreate(entityList, specs) {\r\n if (!Array.isArray(specs)) {\r\n specs = [specs];\r\n }\r\n const [id, opts] = specs;\r\n const Entity = entityList.get(id) || entityList.first;\r\n return new Entity(opts);\r\n}\r\n\r\nclass ComplexVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._complex = dataSource;\r\n\r\n /** @type {Representation[]} */\r\n this._reprList = [];\r\n /** @type {?Representation} */\r\n this._repr = null;\r\n this._reprListChanged = true;\r\n\r\n this._selectionBit = 0;\r\n this._reprUsedBits = 0;\r\n this._selectionCount = 0;\r\n\r\n this._selectionGeometry = new THREE.Group();\r\n }\r\n\r\n getBoundaries() {\r\n return this._complex.getBoundaries();\r\n }\r\n\r\n release() {\r\n if (this._selectionGeometry.parent) {\r\n this._selectionGeometry.remove(this._selectionGeometry);\r\n }\r\n Visual.prototype.release.call(this);\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getSelectionCount() {\r\n return this._selectionCount;\r\n }\r\n\r\n getSelectionGeo() {\r\n return this._selectionGeometry;\r\n }\r\n\r\n getSelectionBit() {\r\n return this._selectionBit;\r\n }\r\n\r\n getEditor() {\r\n return this._editor;\r\n }\r\n\r\n resetReps(reps) {\r\n // Create all necessary representations\r\n if (this._complex) {\r\n this._complex.clearAtomBits(~0);\r\n }\r\n this._reprListChanged = true;\r\n this._reprUsedBits = 0;\r\n this._reprList.length = reps.length;\r\n for (let i = 0, n = reps.length; i < n; ++i) {\r\n const rep = reps[i];\r\n\r\n let selector;\r\n let selectorString;\r\n if (typeof rep.selector === 'string') {\r\n selectorString = rep.selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else if (typeof rep.selector === 'undefined') {\r\n selectorString = settings.now.presets.default[0].selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else {\r\n ({ selector } = rep);\r\n selectorString = selector.toString();\r\n }\r\n const mode = lookupAndCreate(modes, rep.mode);\r\n const colorer = lookupAndCreate(colorers, rep.colorer);\r\n const material = materials.get(rep.material) || materials.first;\r\n\r\n this._reprList[i] = new Representation(i, mode, colorer, selector);\r\n this._reprList[i].setMaterialPreset(material);\r\n this._reprList[i].selectorString = selectorString;\r\n\r\n if (this._complex) {\r\n this._complex.markAtoms(selector, 1 << i);\r\n }\r\n\r\n this._reprUsedBits |= 1 << i;\r\n }\r\n this._repr = reps.length > 0 ? this._reprList[0] : null;\r\n\r\n this._selectionBit = reps.length;\r\n this._reprUsedBits |= 1 << this._selectionBit; // selection uses one bit\r\n this._selectionCount = 0;\r\n\r\n if (this._complex) {\r\n this._complex.update();\r\n }\r\n }\r\n\r\n /**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\n repCount() {\r\n return this._reprList.length;\r\n }\r\n\r\n /**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\n repCurrent(index) {\r\n if (index >= 0 && index < this._reprList.length) {\r\n this._repr = this._reprList[index];\r\n } else {\r\n index = this._reprList.indexOf(this._repr);\r\n }\r\n return index;\r\n }\r\n\r\n /**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {Object} {desc, index, status} field desc contains rep description, index - index of correspondent rep,\r\n * status - one of three strings: 'created', 'changed', ''. 'created' means new rep was created during this function,\r\n * 'changed' - rep was changed during this function. '' - something else.\r\n */\r\n rep(index, rep) {\r\n // if index is missing then it is the current\r\n if (!rep && (index === undefined || index instanceof Object)) {\r\n rep = index;\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index > this._reprList.length) {\r\n logger.error(`Rep ${index} does not exist!`);\r\n return null;\r\n }\r\n\r\n // a special case of adding just after the end\r\n if (index === this._reprList.length) {\r\n const res = this.repAdd(rep);\r\n logger.warn(`Rep ${index} does not exist! New representation was created.`);\r\n return { desc: res.desc, index, status: 'created' };\r\n }\r\n\r\n // gather description\r\n const target = this._reprList[index];\r\n const desc = {\r\n selector: target.selectorString,\r\n mode: target.mode.identify(),\r\n colorer: target.colorer.identify(),\r\n material: target.materialPreset.id,\r\n };\r\n\r\n // modification is requested\r\n if (rep) {\r\n // modify\r\n const diff = target.change(\r\n rep,\r\n this._complex,\r\n lookupAndCreate(modes, rep.mode),\r\n lookupAndCreate(colorers, rep.colorer),\r\n );\r\n\r\n // something was changed\r\n if (!_.isEmpty(diff)) {\r\n target.needsRebuild = true;\r\n for (const key in diff) {\r\n if (diff.hasOwnProperty(key)) {\r\n desc[key] = diff[key];\r\n logger.debug(`rep[${index}].${key} changed to ${diff[key]}`);\r\n }\r\n }\r\n\r\n // safety trick: lower resolution for surface modes\r\n if (diff.mode && target.mode.isSurface\r\n && (settings.now.resolution === 'ultra' || settings.now.resolution === 'high')) {\r\n logger.report('Surface resolution was changed to \"medium\" to avoid hang-ups.');\r\n settings.set('resolution', 'medium');\r\n }\r\n return { desc, index, status: 'changed' };\r\n }\r\n }\r\n return { desc, index, status: '' };\r\n }\r\n\r\n /**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\n repGet(index) {\r\n // if index is missing then it is the current\r\n if (index === undefined || index instanceof Object) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return null;\r\n }\r\n\r\n return this._reprList[index];\r\n }\r\n\r\n _getFreeReprIdx() {\r\n let bits = this._reprUsedBits;\r\n for (let i = 0; i <= ComplexVisual.NUM_REPRESENTATION_BITS; ++i, bits >>= 1) {\r\n if ((bits & 1) === 0) {\r\n return i;\r\n }\r\n }\r\n return -1;\r\n }\r\n\r\n /**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {Object} {desc, index} field desc contains added rep description, index - index of this rep.\r\n */\r\n repAdd(rep) {\r\n if (this._reprList.length >= ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n return null;\r\n }\r\n\r\n const newSelectionBit = this._getFreeReprIdx();\r\n if (newSelectionBit < 0) {\r\n return null; // no more slots for representations\r\n }\r\n\r\n const originalSelection = this.buildSelectorFromMask(1 << this._selectionBit);\r\n\r\n // Fill in default values\r\n const def = settings.now.presets.default[0];\r\n const desc = _.merge({\r\n selector: def.selector,\r\n mode: def.mode,\r\n colorer: def.colorer,\r\n material: def.material,\r\n }, rep);\r\n\r\n const selector = (typeof desc.selector === 'string') ? selectors.parse(desc.selector).selector : desc.selector;\r\n const target = new Representation(\r\n this._selectionBit,\r\n lookupAndCreate(modes, desc.mode),\r\n lookupAndCreate(colorers, desc.colorer),\r\n selector,\r\n );\r\n target.selectorString = selector.toString();\r\n target.setMaterialPreset(materials.get(desc.material));\r\n target.markAtoms(this._complex);\r\n this._reprList.push(target);\r\n\r\n // change selection bit\r\n this._selectionBit = newSelectionBit;\r\n this._reprUsedBits |= 1 << this._selectionBit;\r\n\r\n // restore selection using new selection bit\r\n this._complex.markAtoms(originalSelection, 1 << this._selectionBit);\r\n\r\n return { desc, index: this._reprList.length - 1 };\r\n }\r\n\r\n /**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\n repRemove(index) {\r\n if (index === undefined) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // catch out of bounds case\r\n let count = this._reprList.length;\r\n if (index < 0 || index >= count || count <= 1) { // do not allow to remove the single rep\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.unmarkAtoms(this._complex);\r\n this._reprUsedBits &= ~(1 << target.index);\r\n\r\n this._reprList.splice(index, 1);\r\n\r\n // update current rep\r\n if (target === this._repr) {\r\n --count;\r\n index = index < count ? index : count - 1;\r\n this._repr = this._reprList[index];\r\n }\r\n this._reprListChanged = true;\r\n }\r\n\r\n /**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\n repHide(index, hide) {\r\n if (hide === undefined) {\r\n hide = true;\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.show(!hide);\r\n }\r\n\r\n /**\r\n * Select atoms with selector\r\n * @param {Selector} selector - selector\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\n select(selector, append) {\r\n if (append) {\r\n this._selectionCount += this._complex.markAtomsAdditionally(selector, 1 << this._selectionBit);\r\n } else {\r\n this._selectionCount = this._complex.markAtoms(selector, 1 << this._selectionBit);\r\n }\r\n this._complex.updateStructuresMask();\r\n this.rebuildSelectionGeometry();\r\n }\r\n\r\n resetSelectionMask() {\r\n if (this._selectionCount !== 0) {\r\n this._selectionCount = 0;\r\n if (this._complex) {\r\n this._complex.clearAtomBits(1 << this._selectionBit);\r\n }\r\n }\r\n }\r\n\r\n updateSelectionMask(pickedObj) {\r\n const self = this;\r\n const { atom } = pickedObj;\r\n let { residue, chain, molecule } = pickedObj;\r\n const setMask = 1 << this._selectionBit;\r\n const clearMask = ~setMask;\r\n\r\n if (atom) {\r\n residue = atom.residue;\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (atom.mask & setMask) {\r\n atom.mask &= clearMask;\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n if (molecule) {\r\n molecule.mask &= clearMask;\r\n }\r\n this._selectionCount--;\r\n } else {\r\n atom.mask |= setMask;\r\n this._selectionCount++;\r\n\r\n // select residue if all atoms in it are selected\r\n residue.collectMask();\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (residue) {\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (residue._mask & setMask) {\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n residue.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n } else {\r\n residue._mask |= setMask;\r\n residue.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (chain || molecule) {\r\n const obj = chain || molecule;\r\n if (obj._mask & setMask) {\r\n obj._mask &= clearMask;\r\n obj.forEachResidue((r) => {\r\n if (r._mask & setMask) {\r\n r._mask &= clearMask;\r\n r.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n r._mask &= clearMask;\r\n }\r\n });\r\n } else {\r\n obj._mask |= setMask;\r\n obj.forEachResidue((r) => {\r\n if (!(r._mask & setMask)) {\r\n r._mask |= setMask;\r\n r.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n const otherObj = chain ? r.getMolecule() : r.getChain();\r\n if (otherObj) {\r\n otherObj.collectMask();\r\n }\r\n }\r\n });\r\n }\r\n } else {\r\n this.resetSelectionMask();\r\n }\r\n }\r\n\r\n expandSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms to add\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // select marked atoms\r\n const deselectionMask = ~tmpMask;\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask = (atom.mask & deselectionMask) | selectionMask;\r\n ++self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n shrinkSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms neighbouring to unselected ones\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // mark hanging atoms\r\n this._complex.forEachAtom((atom) => {\r\n if ((atom.mask & selectionMask) && (atom.bonds.length === 1)) {\r\n atom.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // deselect marked atoms\r\n const deselectionMask = ~(selectionMask | tmpMask);\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask &= deselectionMask;\r\n --self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n getSelectedComponent() {\r\n const selectionMask = 1 << this._selectionBit;\r\n\r\n let component = null;\r\n let multiple = false;\r\n\r\n // find which component is selected (exclusively)\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & selectionMask) {\r\n if (component === null) {\r\n component = atom.residue._component;\r\n } else if (component !== atom.residue._component) {\r\n multiple = true;\r\n }\r\n }\r\n });\r\n\r\n return multiple ? null : component;\r\n }\r\n\r\n getSelectionCenter(center, includesAtom, selRule) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._complex.forEachAtom((atom) => {\r\n if (includesAtom(atom, selRule)) {\r\n center.add(atom.position);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.applyMatrix4(this.matrix);\r\n return true;\r\n }\r\n\r\n needsRebuild() {\r\n if (this._reprListChanged) {\r\n return true;\r\n }\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n if (repr.needsRebuild) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n /**\r\n * Rebuild molecule geometry asynchronously.\r\n */\r\n rebuild() {\r\n const self = this;\r\n\r\n // Destroy current geometry\r\n gfxutils.clearTree(this);\r\n\r\n return new Promise(((resolve) => {\r\n // Nothing to do?\r\n const complex = self._complex;\r\n if (!complex) {\r\n resolve();\r\n return;\r\n }\r\n\r\n let errorOccured = false;\r\n setTimeout(() => {\r\n console.time('build');\r\n const reprList = self._reprList;\r\n const palette = palettes.get(settings.now.palette) || palettes.first;\r\n let hasGeometry = false;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n repr.colorer.palette = palette;\r\n\r\n if (repr.needsRebuild) {\r\n repr.reset();\r\n\r\n try {\r\n repr.buildGeometry(complex);\r\n } catch (e) {\r\n if (e instanceof utils.OutOfMemoryError) {\r\n repr.needsRebuild = false;\r\n repr.reset();\r\n logger.error(`Not enough memory to build geometry for representation ${repr.index + 1}`);\r\n errorOccured = true;\r\n } else {\r\n throw e;\r\n }\r\n }\r\n\r\n if (DEBUG && !errorOccured) {\r\n logger.debug(`Triangles count: ${meshutils.countTriangles(repr.geo)}`);\r\n }\r\n }\r\n\r\n hasGeometry = errorOccured || hasGeometry || gfxutils.groupHasGeometryToRender(repr.geo);\r\n\r\n if (repr.geo) {\r\n self.add(repr.geo);\r\n }\r\n }\r\n\r\n self._reprListChanged = false;\r\n\r\n console.timeEnd('build');\r\n resolve();\r\n }, 10);\r\n }));\r\n }\r\n\r\n setNeedsRebuild() {\r\n // invalidate all representations\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n reprList[i].needsRebuild = true;\r\n }\r\n }\r\n\r\n rebuildSelectionGeometry() {\r\n const mask = 1 << this._selectionBit;\r\n\r\n gfxutils.clearTree(this._selectionGeometry);\r\n\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const repr = this._reprList[i];\r\n const sg = repr.buildSelectionGeometry(mask);\r\n if (!sg) {\r\n continue;\r\n }\r\n\r\n this._selectionGeometry.add(sg);\r\n for (let j = 0; j < sg.children.length; j++) {\r\n const m = sg.children[j];\r\n\r\n // copy component transform (that's not applied yet)\r\n // TODO make this code obsolete, accessing editor is bad\r\n if (this._editor && this._editor._componentTransforms) {\r\n const t = this._editor._componentTransforms[m._component._index];\r\n if (t) {\r\n m.position.copy(t.position);\r\n m.quaternion.copy(t.quaternion);\r\n }\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(sg);\r\n }\r\n }\r\n\r\n _buildSelectorFromSortedLists(atoms, residues, chains) {\r\n const complex = this._complex;\r\n\r\n function optimizeList(list) {\r\n const result = [];\r\n let k = 0;\r\n let first = NaN;\r\n let last = NaN;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const value = list[i];\r\n if (value === last + 1) {\r\n last = value;\r\n } else {\r\n if (!Number.isNaN(first)) {\r\n result[k++] = new selectors.Range(first, last);\r\n }\r\n first = last = value;\r\n }\r\n }\r\n if (!Number.isNaN(first)) {\r\n result[k] = new selectors.Range(first, last);\r\n }\r\n return result;\r\n }\r\n\r\n let expression = null;\r\n if (chains.length === complex._chains.length) {\r\n expression = selectors.all();\r\n } else {\r\n let selector;\r\n if (chains.length > 0) {\r\n selector = selectors.chain(chains);\r\n expression = expression ? selectors.or(expression, selector) : selector;// NOSONAR\r\n }\r\n if (Object.keys(residues).length > 0) {\r\n for (const ch in residues) {\r\n if (residues.hasOwnProperty(ch)) {\r\n selector = selectors.and(\r\n selectors.chain(ch),\r\n selectors.residx(optimizeList(residues[ch])),\r\n );\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n }\r\n }\r\n if (atoms.length > 0) {\r\n selector = selectors.serial(optimizeList(atoms));\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n\r\n if (!expression) {\r\n expression = selectors.none();\r\n }\r\n }\r\n\r\n return expression;\r\n }\r\n\r\n buildSelectorFromMask(mask) {\r\n const complex = this._complex;\r\n const chains = [];\r\n const residues = {};\r\n const atoms = [];\r\n\r\n complex.forEachChain((chain) => {\r\n if (chain._mask & mask) {\r\n chains.push(chain._name);\r\n }\r\n });\r\n\r\n complex.forEachResidue((residue) => {\r\n if (residue._mask & mask && !(residue._chain._mask & mask)) {\r\n const c = residue._chain._name;\r\n if (!(c in residues)) {\r\n residues[c] = [residue._index];\r\n } else {\r\n residues[c].push(residue._index);\r\n }\r\n }\r\n });\r\n\r\n complex.forEachAtom((atom) => {\r\n if (atom.mask & mask && !(atom.residue._mask & mask)) {\r\n atoms.push(atom.serial);\r\n }\r\n });\r\n\r\n return this._buildSelectorFromSortedLists(atoms, residues, chains);\r\n }\r\n\r\n forSelectedResidues(process) {\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.forEachResidue((residue) => {\r\n if (residue._mask & selectionMask) {\r\n process(residue);\r\n }\r\n });\r\n }\r\n\r\n beginComponentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.ComponentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n beginFragmentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.FragmentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n // should only be called by editors\r\n finalizeEdit() {\r\n this._editor = null;\r\n }\r\n\r\n setMaterialValues(values, needTraverse = false, process = undefined) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setValues(values);\r\n if (needTraverse) {\r\n rep.geo.traverse((object) => {\r\n if (object instanceof THREE.Mesh) {\r\n object.material.setValues(values);\r\n\r\n if (process !== undefined) {\r\n process(object);\r\n }\r\n\r\n object.material.needsUpdate = true;\r\n }\r\n });\r\n }\r\n }\r\n }\r\n\r\n setUberOptions(values) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setUberOptions(values);\r\n }\r\n }\r\n\r\n /**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\n within(selector, radius) {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return false;\r\n }\r\n\r\n // mark atoms of the group as selected\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.markAtoms(selector, selectionMask);\r\n\r\n // mark all atoms within distance as selected\r\n if (vw) {\r\n vw.forEachAtomWithinDistFromMasked(this._complex, selectionMask, Number(radius), (atom) => {\r\n atom.mask |= selectionMask;\r\n });\r\n }\r\n\r\n // update selection count\r\n this._selectionCount = this._complex.countAtomsByMask(selectionMask);\r\n\r\n // update secondary structure mask\r\n this._complex.updateStructuresMask();\r\n\r\n return this.buildSelectorFromMask(selectionMask);\r\n }\r\n}\r\n// 32 bits = 30 bits for reps + 1 for selection + 1 for selection expansion\r\nComplexVisual.NUM_REPRESENTATION_BITS = 30;\r\n\r\nexport default ComplexVisual;\r\n","import * as THREE from 'three';\r\nimport vertexVolumeFaces from './VolumeFaces.vert';\r\nimport fragmentVolumeFaces from './VolumeFaces.frag';\r\nimport vertexVolume from './Volume.vert';\r\nimport fragmentVolume from './Volume.frag';\r\nimport vertexFarPlane from './VolumeFarPlane.vert';\r\nimport fragmentFarPlane from './VolumeFarPlane.frag';\r\nimport settings from '../../settings';\r\n\r\nconst volumeUniforms = THREE.UniformsUtils.merge([\r\n {\r\n volumeDim: { type: 'v3', value: new THREE.Vector3(512, 512, 512) },\r\n tileTex: { type: 't', value: null },\r\n tileTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n tileStride: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n\r\n boxAngles: { type: 'v3', value: new THREE.Vector3(1, 1, 1) },\r\n delta: { type: 'v3', value: new THREE.Vector3(0, 0, 0) },\r\n\r\n _isoLevel0: { type: 'v2', value: new THREE.Vector3(0.5, 0.75, 1.0) },\r\n _flipV: { type: 'f', value: 0.0 },\r\n _BFLeft: { type: 't', value: null },\r\n _BFRight: { type: 't', value: null },\r\n _FFLeft: { type: 't', value: null },\r\n _FFRight: { type: 't', value: null },\r\n _WFFLeft: { type: 't', value: null },\r\n _WFFRight: { type: 't', value: null },\r\n },\r\n]);\r\n\r\nfunction overrideUniforms(params, defUniforms) {\r\n const uniforms = THREE.UniformsUtils.clone(defUniforms);\r\n for (const p in params) {\r\n if (uniforms.hasOwnProperty(p)) {\r\n uniforms[p].value = params[p];\r\n }\r\n }\r\n return uniforms;\r\n}\r\n\r\nfunction facesPosMaterialParams(params, sideType) {\r\n return {\r\n uniforms: overrideUniforms(params, {}),\r\n vertexShader: vertexVolumeFaces,\r\n fragmentShader: fragmentVolumeFaces,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n side: sideType,\r\n };\r\n}\r\n\r\nclass BackFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const backFaceParams = facesPosMaterialParams(params, THREE.BackSide);\r\n super(backFaceParams);\r\n }\r\n}\r\n\r\nclass ShaderParams {\r\n constructor(params, uniforms, vertexShader, fragmentShader) {\r\n this.uniforms = overrideUniforms(params, uniforms);\r\n this.vertexShader = vertexShader;\r\n this.fragmentShader = fragmentShader;\r\n this.transparent = false;\r\n this.depthTest = false;\r\n this.depthWrite = false;\r\n this.side = THREE.FrontSide;\r\n }\r\n}\r\n\r\nclass BackFacePosMaterialFarPlane extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const matUniforms = THREE.UniformsUtils.merge([\r\n {\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n farZ: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n matWorld2Volume: { type: '4fv', value: new THREE.Matrix4() },\r\n },\r\n ]);\r\n\r\n const shaderParams = new ShaderParams(params, matUniforms, vertexFarPlane, fragmentFarPlane);\r\n super(shaderParams);\r\n }\r\n}\r\n\r\nclass FrontFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const frontFaceParams = facesPosMaterialParams(params, THREE.FrontSide);\r\n super(frontFaceParams);\r\n }\r\n}\r\n\r\nclass VolumeMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const shaderParams = new ShaderParams(params, volumeUniforms, vertexVolume, fragmentVolume);\r\n shaderParams.transparent = true;\r\n shaderParams.depthTest = true;\r\n\r\n super(shaderParams);\r\n this.updateDefines();\r\n }\r\n\r\n updateDefines() {\r\n this.defines = {\r\n ISO_MODE: settings.now.modes.VD.isoMode,\r\n STEPS_COUNT: settings.now.modes.VD.polyComplexity[settings.now.resolution] * 100,\r\n };\r\n this.needsUpdate = true;\r\n }\r\n}\r\n\r\nexport default {\r\n BackFacePosMaterial,\r\n BackFacePosMaterialFarPlane,\r\n FrontFacePosMaterial,\r\n VolumeMaterial,\r\n};\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport settings from '../settings';\r\n\r\nclass VolumeMesh extends THREE.Mesh {\r\n volumeInfo = {}; // data for noise filter\r\n\r\n constructor() {\r\n const geo = new THREE.BufferGeometry();\r\n super(geo);\r\n this.clipPlane = new THREE.Plane();\r\n const size = new THREE.Vector3(0.5, 0.5, 0.5);\r\n this.size = size;\r\n\r\n this.cullFlag = [\r\n true, true, true, true,\r\n true, true, true, true,\r\n false, false, false, false, false, false,\r\n ];\r\n\r\n this.faces = [\r\n { indices: [], norm: new THREE.Vector3(0, 0, -1) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 1) },\r\n { indices: [], norm: new THREE.Vector3(0, -1, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 1, 0) },\r\n { indices: [], norm: new THREE.Vector3(-1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 0) },\r\n ];\r\n\r\n this.vertices = [\r\n new THREE.Vector3(-size.x, -size.y, -size.z),\r\n new THREE.Vector3(-size.x, size.y, -size.z),\r\n new THREE.Vector3(size.x, -size.y, -size.z),\r\n new THREE.Vector3(size.x, size.y, -size.z),\r\n new THREE.Vector3(-size.x, -size.y, size.z),\r\n new THREE.Vector3(-size.x, size.y, size.z),\r\n new THREE.Vector3(size.x, -size.y, size.z),\r\n new THREE.Vector3(size.x, size.y, size.z),\r\n new THREE.Vector3(0.0, 0.0, 0.0), // Placeholder for section\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n ];\r\n\r\n geo.setAttribute('position', new THREE.BufferAttribute(new Float32Array(this.vertices.length * 3), 3));\r\n\r\n this.name = 'VolumeMesh';\r\n }\r\n\r\n static _corners = [\r\n // x, y, z, edge1, edge2, edge3\r\n [-1, -1, -1, 0, 4, 8],\r\n [1, -1, -1, 0, 5, 9],\r\n [1, 1, -1, 1, 5, 10],\r\n [-1, 1, -1, 1, 4, 11],\r\n [-1, -1, 1, 2, 6, 8],\r\n [1, -1, 1, 2, 7, 9],\r\n [1, 1, 1, 3, 7, 10],\r\n [-1, 1, 1, 3, 6, 11],\r\n ];\r\n\r\n static _edges = [\r\n // corner1, corner2, center_x, center_y, center_z\r\n [0, 1, 0, -1, -1],\r\n [2, 3, 0, 1, -1],\r\n [4, 5, 0, -1, 1],\r\n [6, 7, 0, 1, 1],\r\n [0, 3, -1, 0, -1],\r\n [1, 2, 1, 0, -1],\r\n [4, 7, -1, 0, 1],\r\n [5, 6, 1, 0, 1],\r\n [0, 4, -1, -1, 0],\r\n [1, 5, 1, -1, 0],\r\n [2, 6, -1, 1, 0],\r\n [3, 7, 1, 1, 0],\r\n ];\r\n\r\n static _edgeIntersections = (function () {\r\n const edgeIntersections = [];\r\n for (let j = 0; j < 12; ++j) {\r\n edgeIntersections.push(new THREE.Vector3());\r\n }\r\n return edgeIntersections;\r\n }());\r\n\r\n _updateVertices() {\r\n // Algorithm:\r\n // 1. Get plane parameters\r\n // 2. Compute culling flags for all vertices\r\n // 3. If intersection occurs => compute from 3 to 6 intersection points\r\n const corners = VolumeMesh._corners;\r\n const edges = VolumeMesh._edges;\r\n const edgeIntersections = VolumeMesh._edgeIntersections;\r\n\r\n let i;\r\n\r\n const norm = this.clipPlane.normal;\r\n const D = this.clipPlane.constant;\r\n\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n const cornerMark = [0, 0, 0, 0, 0, 0, 0, 0];\r\n const edgeMark = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1];\r\n\r\n const curEdge = new THREE.Vector3();\r\n let curEdgeInter = null;\r\n\r\n function CheckX() {\r\n if (norm.x === 0) return 0;\r\n const x = -(norm.dot(curEdge) + D) / norm.x;\r\n if (-size.x <= x && x <= size.x) {\r\n curEdgeInter.set(x, curEdge.y, curEdge.z);\r\n if (x === size.x) return 2;\r\n if (x === -size.x) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckY() {\r\n if (norm.y === 0) return 0;\r\n const y = -(norm.dot(curEdge) + D) / norm.y;\r\n if (-size.y <= y && y <= size.y) {\r\n curEdgeInter.set(curEdge.x, y, curEdge.z);\r\n if (y === size.y) return 2;\r\n if (y === -size.y) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckZ() {\r\n if (norm.z === 0) return 0;\r\n const z = -(norm.dot(curEdge) + D) / norm.z;\r\n if (-size.z <= z && z <= size.z) {\r\n curEdgeInter.set(curEdge.x, curEdge.y, z);\r\n if (z === size.z) return 2;\r\n if (z === -size.z) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n // for each edge\r\n for (let curEdgeIdx = 0; curEdgeIdx < 12; ++curEdgeIdx) {\r\n const curEdgeSource = edges[curEdgeIdx];\r\n curEdgeInter = edgeIntersections[curEdgeIdx];\r\n\r\n curEdge.set(curEdgeSource[2], curEdgeSource[3], curEdgeSource[4]);\r\n curEdge.multiply(size);\r\n\r\n // calculate intersection point\r\n let flag = 0;\r\n if (curEdgeSource[2] === 0) flag = CheckX();\r\n if (curEdgeSource[3] === 0) flag = CheckY();\r\n if (curEdgeSource[4] === 0) flag = CheckZ();\r\n\r\n // mark corresponding corner (if plane cuts through one)\r\n if (flag === -2) {\r\n cornerMark[curEdgeSource[0]] = 1;\r\n } else if (flag === 2) {\r\n cornerMark[curEdgeSource[1]] = 1;\r\n } else if (flag === 0) {\r\n // edge is not intersected by the plane (doesn't produce a vertex)\r\n edgeMark[curEdgeIdx] = 0;\r\n }\r\n }\r\n\r\n const face = {\r\n indices: [],\r\n norm: norm.clone().negate(),\r\n };\r\n\r\n let nextVertex = 8;\r\n\r\n // for each marked corner\r\n for (i = 0; i < 8; ++i) {\r\n if (cornerMark[i] === 1) {\r\n // add corner as vertex to the face\r\n vert[nextVertex].set(corners[i][0], corners[i][1], corners[i][2]).multiply(size);\r\n face.indices.push(nextVertex++);\r\n // skip adjacent edges\r\n edgeMark[corners[i][3]] = 0;\r\n edgeMark[corners[i][4]] = 0;\r\n edgeMark[corners[i][5]] = 0;\r\n }\r\n }\r\n\r\n // for each edge that has internal intersection\r\n for (i = 0; i < 12; ++i) {\r\n if (edgeMark[i] === 1) {\r\n // add intersection point as vertex to the face\r\n vert[nextVertex].copy(edgeIntersections[i]);\r\n face.indices.push(nextVertex++);\r\n }\r\n }\r\n\r\n this.faces[6] = face;\r\n\r\n const diff = new THREE.Vector3();\r\n const coplanarPoint = new THREE.Vector3();\r\n this.clipPlane.coplanarPoint(coplanarPoint);\r\n for (i = 0; i < vert.length; ++i) {\r\n this.cullFlag[i] = false;\r\n if (i < 8) {\r\n // corners should be culled by clipping plane\r\n diff.subVectors(vert[i], coplanarPoint);\r\n this.cullFlag[i] = (norm.dot(diff) >= 0.0);\r\n } else if (i < 8 + face.indices.length) {\r\n // cross section vertices don't get culled\r\n this.cullFlag[i] = true;\r\n }\r\n }\r\n\r\n // write data to vertex buffer\r\n const positions = this.geometry.getAttribute('position');\r\n let idx = 0;\r\n for (i = 0; i < vert.length; ++i) {\r\n positions.array[idx++] = vert[i].x;\r\n positions.array[idx++] = vert[i].y;\r\n positions.array[idx++] = vert[i].z;\r\n }\r\n positions.needsUpdate = true;\r\n }\r\n\r\n _collectVertices(face, filter) {\r\n let i;\r\n const vert = this.vertices;\r\n face.indices = [];\r\n for (i = 0; i < vert.length; ++i) {\r\n if (this.cullFlag[i] && filter(vert[i])) {\r\n face.indices.push(i);\r\n }\r\n }\r\n }\r\n\r\n _sortIndices(face, right) {\r\n let i;\r\n let j;\r\n const vert = this.vertices;\r\n const angle = [];\r\n\r\n const dir = new THREE.Vector3();\r\n for (i = 1; i < face.indices.length; ++i) {\r\n dir.subVectors(vert[face.indices[i]], vert[face.indices[0]]);\r\n dir.normalize();\r\n dir.cross(right);\r\n dir.negate();\r\n angle[i] = face.norm.dot(dir);\r\n }\r\n\r\n // Exchange sort\r\n for (i = 1; i < face.indices.length - 1; ++i) {\r\n for (j = i + 1; j < face.indices.length; ++j) {\r\n if (angle[j] < angle[i]) {\r\n // swap\r\n let t = angle[i];\r\n angle[i] = angle[j];\r\n angle[j] = t;\r\n\r\n t = face.indices[i];\r\n face.indices[i] = face.indices[j];\r\n face.indices[j] = t;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _updateIndices() {\r\n // Algorithm:\r\n // 1. Get plane vertices (from 3 to 6 vertices)\r\n // 2. Get \"right\" vector in plane\r\n // 3. Sort vertices using Graham-like method\r\n // 4. Create indices\r\n\r\n let i;\r\n let faceIdx;\r\n let face;\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n this._collectVertices(this.faces[0], (vertex) => vertex.z === -size.z);\r\n this._collectVertices(this.faces[1], (vertex) => vertex.z === size.z);\r\n this._collectVertices(this.faces[2], (vertex) => vertex.y === -size.y);\r\n this._collectVertices(this.faces[3], (vertex) => vertex.y === size.y);\r\n this._collectVertices(this.faces[4], (vertex) => vertex.x === -size.x);\r\n this._collectVertices(this.faces[5], (vertex) => vertex.x === size.x);\r\n\r\n const vCenter = new THREE.Vector3();\r\n const vRight = new THREE.Vector3();\r\n const vDir = new THREE.Vector3();\r\n\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n\r\n if (face.indices.length === 0) continue;\r\n\r\n vCenter.set(0, 0, 0);\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vCenter.add(vert[face.indices[i]]);\r\n }\r\n vCenter.multiplyScalar(1.0 / face.indices.length);\r\n vRight.subVectors(vert[face.indices[0]], vCenter);\r\n vRight.normalize();\r\n\r\n const rightProj = [];\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vDir.subVectors(vert[face.indices[i]], vCenter);\r\n rightProj[i] = vDir.dot(vRight);\r\n }\r\n for (i = 1; i < face.indices.length; ++i) {\r\n if (rightProj[i] < rightProj[0]) {\r\n // swap\r\n let t = rightProj[0];\r\n rightProj[0] = rightProj[i];\r\n rightProj[i] = t;\r\n\r\n [t] = face.indices;\r\n face.indices[0] = face.indices[i];\r\n face.indices[i] = t;\r\n }\r\n }\r\n\r\n this._sortIndices(face, vRight);\r\n }\r\n\r\n let numIndices = 0;\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n if (face.indices.length >= 3) {\r\n numIndices += 3 * (face.indices.length - 2);\r\n }\r\n }\r\n let offset = 0;\r\n const indices = new Uint16Array(numIndices);\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n for (i = 0; i < face.indices.length - 2; ++i) {\r\n indices[offset] = face.indices[0]; // eslint-disable-line prefer-destructuring\r\n indices[offset + 1] = face.indices[i + 1];\r\n indices[offset + 2] = face.indices[i + 2];\r\n offset += 3;\r\n }\r\n }\r\n\r\n this.geometry.setIndex(new THREE.BufferAttribute(indices, 1));\r\n }\r\n\r\n setDataSource(dataSource) {\r\n const vm = new VolumeMaterial.VolumeMaterial();\r\n const dim = dataSource.getDimensions();\r\n const stride = dataSource.getTiledTextureStride();\r\n const texture = dataSource.buildTiledTexture();\r\n const bbox = dataSource.getBox();\r\n vm.uniforms.volumeDim.value.set(dim[0], dim[1], dim[2]);\r\n vm.uniforms.tileTex.value = texture;\r\n vm.uniforms.tileTexSize.value.set(texture.image.width, texture.image.height);\r\n vm.uniforms.tileStride.value.set(stride[0], stride[1]);\r\n Object.assign(this.volumeInfo, dataSource.getVolumeInfo());\r\n\r\n const volInfo = this.volumeInfo;\r\n vm.uniforms.delta.value.copy(volInfo.delta);\r\n vm.uniforms.boxAngles.value.set(volInfo.obtuseAngle[0], volInfo.obtuseAngle[1], volInfo.obtuseAngle[2]);\r\n\r\n this.material = vm;\r\n\r\n bbox.getSize(this.scale);\r\n bbox.getCenter(this.position);\r\n }\r\n\r\n _updateIsoLevel() {\r\n const { kSigma, kSigmaMed, kSigmaMax } = settings.now.modes.VD;\r\n const volInfo = this.volumeInfo;\r\n const mean = volInfo.dmean - volInfo.dmin;\r\n const span = volInfo.dmax - volInfo.dmin;\r\n const level = (k) => (mean + k * volInfo.sd) / span;\r\n this.material.uniforms._isoLevel0.value.set(level(kSigma), level(kSigmaMed), level(kSigmaMax));\r\n }\r\n\r\n static _nearClipPlaneOffset = 0.2;\r\n\r\n static _pos = new THREE.Vector3();\r\n\r\n static _norm = new THREE.Vector3();\r\n\r\n static _norm4D = new THREE.Vector4();\r\n\r\n static _matrixWorldToLocal = new THREE.Matrix4();\r\n\r\n static _clipPlane = new THREE.Plane();\r\n\r\n rebuild(camera) {\r\n const nearClipPlaneOffset = VolumeMesh._nearClipPlaneOffset;\r\n const pos = VolumeMesh._pos;\r\n const norm = VolumeMesh._norm;\r\n const norm4D = VolumeMesh._norm4D;\r\n const matrixWorldToLocal = VolumeMesh._matrixWorldToLocal;\r\n const clipPlane = VolumeMesh._clipPlane;\r\n\r\n this._updateIsoLevel();\r\n\r\n // get clip plane in local space\r\n camera.getWorldDirection(norm);\r\n camera.getWorldPosition(pos);\r\n pos.addScaledVector(norm, camera.near + nearClipPlaneOffset);\r\n\r\n // transform pos to local CS\r\n matrixWorldToLocal.copy(this.matrixWorld).invert();\r\n pos.applyMatrix4(matrixWorldToLocal);\r\n\r\n // transform norm to local CS\r\n norm4D.set(norm.x, norm.y, norm.z, 0.0); // NOTE: use homogeneous norm for proper transformation\r\n norm4D.applyMatrix4(matrixWorldToLocal);\r\n norm.copy(norm4D);\r\n norm.normalize();\r\n\r\n clipPlane.setFromNormalAndCoplanarPoint(norm, pos);\r\n\r\n if (!this.clipPlane.equals(clipPlane)) {\r\n this.clipPlane = clipPlane.clone();\r\n this._updateVertices();\r\n this._updateIndices();\r\n }\r\n }\r\n}\r\n\r\nexport default VolumeMesh;\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _flattenArray(input) {\r\n const n = input.length;\r\n const output = new Float32Array(n * 3);\r\n for (let i = 0; i < n; ++i) {\r\n const j = 3 * i;\r\n const v = input[i];\r\n output[j] = v.x;\r\n output[j + 1] = v.y;\r\n output[j + 2] = v.z;\r\n }\r\n return output;\r\n}\r\n\r\nclass VolumeBounds {\r\n static _projectionTable = { // corresponds between (origin axes and angles between them) and between saving vector coordinates\r\n XY: ['x', 2],\r\n XZ: ['y', 1],\r\n YZ: ['z', 0],\r\n };\r\n\r\n constructor(bBox, volInfo) {\r\n const { delta } = volInfo; // {x: XY, y : XZ, z: YZ}\r\n const { obtuseAngle } = volInfo; // 1 - obtuse, 0 - acute\r\n\r\n const bSize = new THREE.Vector3();\r\n bBox.getSize(bSize);\r\n bSize.multiplyScalar(0.5);\r\n\r\n const offsetVert = this._getBaseVertices(delta, obtuseAngle);\r\n\r\n const geometry = new THREE.BufferGeometry();\r\n const vertices = [];\r\n\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(offsetVert[i].clone().multiply(bSize));\r\n vertices.push(offsetVert[(i + 1) % 4].clone().multiply(bSize));\r\n }\r\n const translation = new THREE.Vector3(2 * bSize.x * (1 - delta.x - delta.y), 0, 0);\r\n for (let i = 0; i < 8; i++) {\r\n vertices.push(vertices[i].clone().add(translation));\r\n }\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(vertices[i * 2].clone());\r\n vertices.push(vertices[i * 2 + 8].clone());\r\n }\r\n const center = new THREE.Vector3();\r\n bBox.getCenter(center);\r\n vertices.forEach((vertex) => vertex.add(center)); // pivot shift\r\n\r\n const flatVertices = _flattenArray(vertices);\r\n geometry.setAttribute('position', new THREE.BufferAttribute(flatVertices, 3));\r\n\r\n this._lines = new THREE.LineSegments(geometry, new THREE.LineBasicMaterial({ color: 0xFFFFFF }));\r\n this._lines.layers.set(gfxutils.LAYERS.VOLUME);\r\n }\r\n\r\n // Set one edge (4 points) of frame, from which with parallel transfer the rest of the frame points can be obtained\r\n _getBaseVertices(delta, obtuseAngle) {\r\n const projTable = VolumeBounds._projectionTable;\r\n\r\n const proj = ((index, inv) => { // tricky function to take account of projections: their position(related to box) and sign\r\n const currDelta = delta[projTable[index][0]];\r\n const angleValue = -0.5 * (inv - 1) + inv * obtuseAngle[projTable[index][1]];// inv = 1: alpha; inv = -1: 1 - alpha\r\n return angleValue * currDelta;\r\n });\r\n\r\n const offsetVert = [\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', 1)), -1 + 2 * proj('YZ', 1), -1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', 1)), -1 + 2 * proj('YZ', -1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', -1)), 1 - 2 * proj('YZ', 1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', -1)), 1 - 2 * proj('YZ', -1), -1),\r\n ];\r\n\r\n return offsetVert;\r\n }\r\n\r\n getMesh() {\r\n return this._lines;\r\n }\r\n}\r\n\r\nexport default VolumeBounds;\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport meshes from './meshes/meshes';\r\nimport gfxutils from './gfxutils';\r\n\r\n// Thes geometric far plane is required for correct filling in the BFTexture in case, when far plane cuts the volume\r\n// cube. In cut place of cube there is no correct data in BFTexture and volume rendering integral is calculated\r\n// with errors.\r\n// Far plane cuts the cube in case of large volume scale (zoom), because farplane doesn't change\r\nclass VolumeFarPlane {\r\n // create plane with unit corners coords (for future rescale in vshader according to camera properties)\r\n constructor(volume, width, height) {\r\n const planeGeo = this._initPlaneGeo(width, height);\r\n\r\n const mat = new VolumeMaterial.BackFacePosMaterialFarPlane();\r\n this._plane = new meshes.Mesh(planeGeo, mat);\r\n this._plane.frustumCulled = false;\r\n this._plane.doubleSided = true;\r\n const matWorldToVolume = new THREE.Matrix4();\r\n\r\n this._plane._onBeforeRender = function (_renderer, _scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!volume || !material) {\r\n return;\r\n }\r\n\r\n // count point in world at farplane place\r\n const planeCamPos = new THREE.Vector4(0, 0, -(camera.far - 0.1), 1);\r\n planeCamPos.applyMatrix4(camera.matrixWorld);\r\n\r\n // recalc matrices to make plane be placed as farplane in the World relative to camera\r\n this.matrix.identity();\r\n this.matrix.makeTranslation(planeCamPos.x, planeCamPos.y, planeCamPos.z);\r\n this.matrixWorld.copy(this.matrix);\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n this.normalMatrix.getNormalMatrix(this.modelViewMatrix);\r\n\r\n // build worldToVolume matrix to transform plane into volumeCS (volumeCS coords are written to BackFaceTexture)\r\n const volumeMatrix = volume.matrixWorld;\r\n matWorldToVolume.copy(volumeMatrix).invert();\r\n\r\n // update material props\r\n material.uniforms.aspectRatio.value = camera.aspect;\r\n material.uniforms.farZ.value = camera.far;\r\n material.uniforms.tanHalfFOV.value = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * camera.fov);\r\n material.uniforms.matWorld2Volume.value = matWorldToVolume;\r\n };\r\n\r\n // set it to special layer to draw only into BFTexture\r\n this._plane.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n }\r\n\r\n _initPlaneGeo(width, height) {\r\n const planeGeo = new THREE.BufferGeometry();\r\n\r\n width = width || 1;\r\n height = height || 1;\r\n\r\n const vertices = new Float32Array([\r\n -0.5 * width, 0.5 * height, 0,\r\n 0.5 * width, 0.5 * height, 0,\r\n -0.5 * width, -0.5 * height, 0,\r\n 0.5 * width, -0.5 * height, 0,\r\n ]);\r\n\r\n planeGeo.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n planeGeo.setIndex([0, 2, 1, 2, 3, 1]);\r\n\r\n return planeGeo;\r\n }\r\n\r\n getMesh() {\r\n return this._plane;\r\n }\r\n}\r\n\r\nexport default VolumeFarPlane;\r\n","import * as THREE from 'three';\r\nimport VolumeMesh from './gfx/VolumeMesh';\r\nimport VolumeBounds from './gfx/VolumeBounds';\r\nimport VolumeFarPlane from './gfx/VolumeFarPlane';\r\nimport Visual from './Visual';\r\nimport settings from './settings';\r\n\r\nclass VolumeVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._mesh = new VolumeMesh();\r\n this._mesh.setDataSource(dataSource);\r\n this.add(this._mesh);\r\n\r\n this._frame = new VolumeBounds(this.getBoundaries().boundingBox, this._mesh.volumeInfo);\r\n this.add(this._frame.getMesh());\r\n this.showFrame(settings.now.modes.VD.frame);\r\n\r\n this._farPlane = new VolumeFarPlane(this._mesh, 2, 2);\r\n this.add(this._farPlane.getMesh());\r\n }\r\n\r\n getBoundaries() {\r\n const box = this._dataSource.getBox();\r\n const sphere = new THREE.Sphere();\r\n box.getBoundingSphere(sphere);\r\n\r\n return {\r\n boundingBox: box,\r\n boundingSphere: sphere,\r\n };\r\n }\r\n\r\n getMesh() {\r\n return this._mesh;\r\n }\r\n\r\n showFrame(needShow) {\r\n this._frame.getMesh().material.visible = needShow;\r\n }\r\n}\r\n\r\nexport default VolumeVisual;\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available loaders.\r\n * @extends EntityList\r\n */\r\nclass LoaderList extends EntityList {\r\n /**\r\n * Create a list of loaders.\r\n * The loaders are indexed by supported source types (`.types` property of a Loader\r\n * subclass).\r\n * The loaders can be retrieved later by matching against specs (see {@link LoaderList#find}).\r\n *\r\n * @param {!Array=} someLoaders A list of {@link Loader} subclasses to\r\n * automatically register at creation time.\r\n * @see LoaderList#register\r\n */\r\n constructor(someLoaders = []) {\r\n super(someLoaders, ['types']);\r\n }\r\n\r\n /**\r\n * Find a suitable loader for a source type.\r\n *\r\n * @param {Object} specs Loader specifications.\r\n * @param {string=} specs.type Supported source type.\r\n * @param {*=} specs.source Source to load from.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.type) {\r\n list = this._dict.types[specs.type.toLowerCase()] || [];\r\n } else if (specs.source) {\r\n return this._list.filter((SomeLoader) => SomeLoader.canProbablyLoad && SomeLoader.canProbablyLoad(specs.source));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default LoaderList;\r\n","import EventDispatcher from '../../utils/EventDispatcher';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Loader extends EventDispatcher {\r\n constructor(source, options) {\r\n super();\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n this._agent = null;\r\n }\r\n\r\n load() {\r\n return Promise.reject(new Error('Loading from this source is not implemented'));\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n if (this._agent) {\r\n this._agent.abort();\r\n }\r\n }\r\n\r\n static extractName(_source) {\r\n return undefined;\r\n }\r\n}\r\n\r\nmakeContextDependent(Loader.prototype);\r\n","import Loader from './Loader';\r\n\r\nexport default class FileLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = options.binary === true;\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const blob = this._source;\r\n const reader = this._agent = new FileReader();\r\n\r\n reader.addEventListener('load', () => {\r\n resolve(reader.result);\r\n });\r\n reader.addEventListener('error', () => {\r\n reject(reader.error);\r\n });\r\n reader.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n reader.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n if (this._binary) {\r\n reader.readAsArrayBuffer(blob);\r\n } else {\r\n reader.readAsText(blob);\r\n }\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return (File && source instanceof File) || (Blob && source instanceof Blob);\r\n }\r\n\r\n static extractName(source) {\r\n return source && source.name;\r\n }\r\n}\r\n\r\nFileLoader.types = ['file', 'blob'];\r\n","import _ from 'lodash';\r\nimport Loader from './Loader';\r\n\r\n// we don't need to detect all kinds of URLs, just the evident ones\r\nconst urlStartRegexp = /^(https?|ftp):\\/\\//i;\r\n\r\nexport default class XHRLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = (options.binary === true);\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const url = this._source;\r\n const request = this._agent = new XMLHttpRequest();\r\n\r\n request.addEventListener('load', () => {\r\n if (request.status === 200) {\r\n resolve(request.response);\r\n } else {\r\n reject(new Error(`HTTP ${request.status} while fetching ${url}`));\r\n }\r\n });\r\n request.addEventListener('error', () => {\r\n reject(new Error('HTTP request failed'));\r\n });\r\n request.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n request.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n request.open('GET', url);\r\n if (this._binary) {\r\n request.responseType = 'arraybuffer';\r\n } else {\r\n request.responseType = 'text';\r\n }\r\n request.send();\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return _.isString(source) && urlStartRegexp.test(source);\r\n }\r\n\r\n static extractName(source) {\r\n if (source) {\r\n const last = (source.indexOf('?') + 1 || source.lastIndexOf('#') + 1 || source.length + 1) - 1;\r\n return source.slice(source.lastIndexOf('/', last) + 1, last);\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nXHRLoader.types = ['url'];\r\n","import Loader from './Loader';\r\n\r\nexport default class ImmediateLoader extends Loader {\r\n load() {\r\n return new Promise((resolve) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n resolve(this._source);\r\n });\r\n }\r\n\r\n static canProbablyLoad(_source) {\r\n return false;\r\n }\r\n}\r\n\r\nImmediateLoader.types = ['immediate'];\r\n","import LoaderList from './loaders/LoaderList';\r\n\r\nimport FileLoader from './loaders/FileLoader';\r\nimport XHRLoader from './loaders/XHRLoader';\r\nimport ImmediateLoader from './loaders/ImmediateLoader';\r\n\r\nexport default new LoaderList([\r\n // note: order might be important\r\n FileLoader,\r\n XHRLoader,\r\n ImmediateLoader,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available parsers.\r\n * @extends EntityList\r\n */\r\nclass ParserList extends EntityList {\r\n /**\r\n * Create a list of parsers.\r\n * The parsers are indexed by supported data formats and file extensions (`.formats` and\r\n * `.extensions` properties of a Parser subclass).\r\n * The parsers can be retrieved later by matching against specs (see {@link ParsrerList#find}).\r\n *\r\n * @param {!Array=} someParsers A list of {@link Parser} subclasses to\r\n * automatically register at creation time.\r\n * @see ParserList#register\r\n */\r\n constructor(someParsers = []) {\r\n super(someParsers, ['formats', 'extensions']);\r\n }\r\n\r\n /**\r\n * Find a suitable parser for data.\r\n *\r\n * @param {Object} specs Parser specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {string=} specs.ext Supported filename extension.\r\n * @param {*=} specs.data Data to parse.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n } else if (specs.ext) {\r\n list = this._dict.extensions[specs.ext.toLowerCase()] || [];\r\n }\r\n // autodetect only if no format is forced\r\n if (list.length === 0 && !specs.format && specs.data) {\r\n return this._list.filter((SomeParser) => SomeParser.canProbablyParse && SomeParser.canProbablyParse(specs.data));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ParserList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Parser {\r\n constructor(data, options) {\r\n this._data = data;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n parseSync() {\r\n throw new Error('Parsing this type of data is not implemented');\r\n }\r\n\r\n parse() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Parsing aborted'));\r\n }\r\n return resolve(this.parseSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n // only for volume Parsers\r\n getModel() {\r\n this.model._parseHeader(this._data);\r\n return this.model;\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Parser.prototype);\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 290\".\r\n *\r\n * @exports Remark290\r\n * @constructor\r\n */\r\nclass Remark290 {\r\n constructor() {\r\n /** @type {THREE.Matrix4[]} */\r\n this.matrices = [];\r\n\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (stream.readString(12, 18) === ' SMTRY') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === this.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n }\r\n }\r\n}\r\n\r\nRemark290.prototype.id = 290;\r\n\r\nexport default Remark290;\r\n","import * as THREE from 'three';\r\nimport chem from '../../../chem';\r\n\r\nconst { Assembly } = chem;\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 350\".\r\n *\r\n * @exports Remark350\r\n * @constructor\r\n */\r\nclass Remark350 {\r\n constructor(complex) {\r\n /** @type {Complex} */\r\n this._complex = complex;\r\n /** @type {Assembly[]} */\r\n this.assemblies = [];\r\n\r\n /** @type {?Assembly} */\r\n this._assembly = null;\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?Assembly} */\r\n let assembly = this._assembly;\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (assembly && stream.readString(12, 18) === ' BIOMT') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === assembly.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n } else if (assembly && stream.readString(35, 41) === 'CHAINS:') {\r\n const entries = stream.readString(42, 80).split(',');\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const chain = entries[i].trim();\r\n if (chain.length > 0) {\r\n assembly.addChain(chain);\r\n }\r\n }\r\n } else if (stream.readString(12, 23) === 'BIOMOLECULE:') {\r\n // assert molIndex === this.assemblies.length + 1\r\n this._matrix = null;\r\n this._matrixIndex = -1;\r\n this._assembly = assembly = new Assembly(this._complex);\r\n this.assemblies.push(assembly);\r\n }\r\n }\r\n}\r\n\r\nRemark350.prototype.id = 350;\r\n\r\nexport default Remark350;\r\n","/** Helper class for stream-like reading input files. */\r\nclass PDBStream {\r\n /**\r\n * Create a stream\r\n * @param {String} data Input data\r\n */\r\n constructor(data) {\r\n /** @type String */\r\n this._data = data; // Input file\r\n /** @type Number */\r\n this._start = 0; // Starting position of line\r\n /** @type Number */\r\n this._nextCR = -1; // Position of next CR (0x0D)\r\n /** @type Number */\r\n this._nextLF = -1; // Position of next LF (0x0A)\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n /** @type Number */\r\n this._end = data.length; // End of data\r\n\r\n this.next();\r\n }\r\n\r\n /**\r\n * Reading next line.\r\n * @returns {String} Next line in data (ending with LF or CR)\r\n */\r\n readLine() {\r\n return this._data.slice(this._start, this._next);\r\n }\r\n\r\n /**\r\n * Reading character from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {String} Character from position\r\n */\r\n readChar(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data[pos] : ' ';\r\n }\r\n\r\n /**\r\n * Reading character code from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {Number} Character code from position\r\n */\r\n readCharCode(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data.charCodeAt(pos) : 32;\r\n }\r\n\r\n /**\r\n * Reading string from begin to end points.\r\n * For a reason unknown, numbering assumed not to start from 0, but from 1.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {String} String from begin to end\r\n */\r\n readString(begin, end) {\r\n const from = this._start + begin - 1;\r\n const to = this._start + end;\r\n return this._data.slice(from, to < this._next ? to : this._next);\r\n }\r\n\r\n /**\r\n * Reading integer from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Integer from begin to end\r\n */\r\n readInt(begin, end) {\r\n return parseInt(this.readString(begin, end), 10);\r\n }\r\n\r\n /**\r\n * Reading float from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Float from begin to end\r\n */\r\n readFloat(begin, end) {\r\n return parseFloat(this.readString(begin, end));\r\n }\r\n\r\n /**\r\n * Checking for end of data.\r\n * @returns {boolean} True if data is ended, false otherwise\r\n */\r\n end() {\r\n return this._start >= this._end;\r\n }\r\n\r\n /**\r\n * Procedure to re-arrange current pointers in data.\r\n */\r\n next() {\r\n const start = this._next + 1;\r\n this._start = start < this._end ? start : this._end;\r\n\r\n // support CR, LF, CR+LF line endings\r\n // do not support LF+CR, CR+CR+LF, and other strange combinations\r\n\r\n if (this._start > this._nextCR) {\r\n this._nextCR = (this._data.indexOf('\\r', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n if (this._start > this._nextLF) {\r\n this._nextLF = (this._data.indexOf('\\n', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n this._next = this._nextCR + 1 < this._nextLF ? this._nextCR : this._nextLF;\r\n }\r\n}\r\n\r\nexport default PDBStream;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport Remark290 from './pdb/Remark290';\r\nimport Remark350 from './pdb/Remark350';\r\nimport PDBStream from './PDBStream';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst TAG_LENGTH = 6;\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\n// the most frequently used beginnings; although HEADER is mandatory, it is often missing in handmade files\r\nconst pdbStartRegexp = /^(HEADER\\s|COMPND\\s|REMARK\\s|ATOM {2}|HETATM|MODEL )/i;\r\n\r\nconst remarkParsers = {\r\n // NOTE: please forget the idea to build the method name in runtime, it can be obfuscated.\r\n 290: Remark290,\r\n 350: Remark350,\r\n};\r\n\r\nclass PDBParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._sheet = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._compaundFound = false;\r\n this._biomoleculeFound = false;\r\n this._allowedChainsIDs = null;\r\n this._lastMolId = -1;\r\n\r\n this._remarks = {};\r\n this._remark = null;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n this._compndCurrToken = '';\r\n\r\n this._options.fileType = 'pdb';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && pdbStartRegexp.test(data);\r\n }\r\n\r\n _finalize() {\r\n this._fixBondsArray();\r\n this._fixChains();\r\n\r\n // keep crystallographic symmetry transformations\r\n const remark290 = this._remarks[290];\r\n this._complex.symmetry = _.isUndefined(remark290) ? [] : remark290.matrices;\r\n\r\n // add loaded biological assemblies\r\n const remark350 = this._remarks[350];\r\n this._complex.units = this._complex.units.concat(_.isUndefined(remark350) ? [] : remark350.assemblies);\r\n\r\n // add loaded macromolecules\r\n this._finalizeMolecules();\r\n\r\n // create secondary structure etc.\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _finalizeMolecules() {\r\n // get chains from complex\r\n const chainDict = {};\r\n let i;\r\n const chains = this._complex._chains;\r\n for (i = 0; i < chains.length; ++i) {\r\n const chainObj = chains[i];\r\n const chainName = chainObj._name;\r\n chainDict[chainName] = chainObj;\r\n }\r\n\r\n // aggregate residues from chains\r\n for (i = 0; i < this._molecules.length; i++) {\r\n const m = this._molecules[i];\r\n let residues = [];\r\n for (let j = 0; j < m._chains.length; j++) {\r\n const name = m._chains[j];\r\n const chain = chainDict[name];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, m._name, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _fixChains() {\r\n const idChainMap = {};\r\n const complex = this._complex;\r\n\r\n // prepare\r\n for (let i = 0; i < complex._chains.length; i++) {\r\n const chain = complex._chains[i];\r\n idChainMap[chain._name.charCodeAt(0)] = chain;\r\n }\r\n }\r\n\r\n // FIXME: This function is redundant, CONECT records always follow ATOM and HETATM. Build the map online.\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseATOM(stream) {\r\n if (this._modelId !== 1) {\r\n return;\r\n }\r\n\r\n const het = stream.readCharCode(1) === 0x48;\r\n\r\n // field names according to wwPDB Format\r\n // NOTE: Chimera allows (nonstandard) use of columns 6-11 for the integer atom serial number in ATOM records.\r\n const serial = het ? stream.readInt(7, 11) : stream.readInt(6, 11);\r\n let name = stream.readString(13, 16);\r\n const altLoc = stream.readChar(17);\r\n const resName = stream.readString(18, 20).trim();\r\n const chainID = stream.readChar(22);\r\n const resSeq = stream.readInt(23, 26);\r\n const iCode = stream.readChar(27);\r\n const x = stream.readFloat(31, 38);\r\n const y = stream.readFloat(39, 46);\r\n const z = stream.readFloat(47, 54);\r\n const occupancy = stream.readFloat(55, 60);\r\n const tempFactor = stream.readFloat(61, 66);\r\n const element = stream.readString(77, 78).trim() || nameToElement(name);\r\n const charge = stream.readInt(79, 80) || 0;\r\n\r\n // skip waters (there may be lots of them)\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n // PDB uses positional system for atom names. It helps derive element type from the name\r\n // but names may include extra spaces. From this point on we don't need those spaces anymore.\r\n name = name.trim();\r\n\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name]; // FIXME: Maybe should use type as additional index (\" CA \" vs. \"CA \")\r\n\r\n // NOTE: Residues of a particular chain are not required to be listed next to each other.\r\n // https://github.com/biasmv/pv/commit/7319b898b7473ba380c26699e3b028b2b1a7e1a1\r\n let chain = this._chain;\r\n if (!chain || chain.getName() !== chainID) {\r\n this._chain = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n _parseENDMDL() {\r\n this._modelId += 1;\r\n }\r\n\r\n _parseCONECT(stream) {\r\n const serial0 = stream.readInt(7, 11);\r\n const serial1 = stream.readInt(12, 16);\r\n const serial2 = stream.readInt(17, 21);\r\n const serial3 = stream.readInt(22, 26);\r\n const serial4 = stream.readInt(27, 31);\r\n\r\n const complex = this._complex;\r\n\r\n // Keep bonds ordered by atom serial\r\n if (serial1 && serial1 > serial0) {\r\n complex.addBond(serial0, serial1, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial2 && serial2 > serial0) {\r\n complex.addBond(serial0, serial2, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial3 && serial3 > serial0) {\r\n complex.addBond(serial0, serial3, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial4 && serial4 > serial0) {\r\n complex.addBond(serial0, serial4, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n }\r\n\r\n _parseCOMPND(stream) {\r\n const str = stream.readString(11, 80);\r\n const tokenIdx = str.indexOf(':');\r\n this._compndCurrToken = tokenIdx > 0 ? str.substring(0, tokenIdx).trim() : this._compndCurrToken;\r\n\r\n // start reading new molecule\r\n if (this._compndCurrToken === 'MOL_ID') {\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = parseInt(str.substring(tokenIdx + 1, str.indexOf(';')), 10);\r\n this._molecules.push(this._molecule);\r\n // parse molecule name\r\n } else if (this._compndCurrToken === 'MOLECULE' && this._molecule != null) {\r\n this._molecule._name = str.substring(tokenIdx + 1, str.indexOf(';')).trim();\r\n // parse molecule chains\r\n } else if (this._compndCurrToken === 'CHAIN' && this._molecule != null) {\r\n let chainStr = str.substring(tokenIdx + 1, 80).trim();\r\n const lastChar = chainStr[chainStr.length - 1];\r\n if (lastChar === ';' || lastChar === ',') {\r\n chainStr = chainStr.slice(0, -1);\r\n }\r\n chainStr = chainStr.replace(/\\s+/g, '');\r\n const chains = chainStr.split(',');\r\n this._molecule._chains = this._molecule._chains.concat(chains);\r\n }\r\n }\r\n\r\n _parseREMARK(stream) {\r\n const remarkNum = stream.readInt(8, 10);\r\n\r\n // create remark parser if needed\r\n let remark = this._remarks[remarkNum];\r\n if (_.isUndefined(remark)) {\r\n const RemarkParser = remarkParsers[remarkNum];\r\n if (_.isFunction(RemarkParser)) {\r\n this._remarks[remarkNum] = remark = new RemarkParser(this._complex);\r\n }\r\n }\r\n\r\n // delegate parsing\r\n if (!_.isUndefined(remark)) {\r\n remark.parse(stream);\r\n }\r\n }\r\n\r\n _parseHELIX(stream) {\r\n const fields = [20, 22, 32, 34];\r\n\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addHelix(obj);\r\n this._complex.structures.push(obj);\r\n });\r\n }\r\n\r\n _parseSHEET(stream) {\r\n const fields = [22, 23, 33, 34];\r\n\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addSheet(obj);\r\n });\r\n }\r\n\r\n _parseSTRUCTURE(stream, pars, adder) {\r\n const startId = 0;\r\n const startIndex = 1;\r\n const endId = 2;\r\n const endIndex = 3;\r\n\r\n // identify fields: debugging and stuff\r\n\r\n const codeOfS = 0x53;\r\n const serialNumber = stream.readInt(8, 10);\r\n const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim()\r\n const comment = stream.readString(41, 70).trim();\r\n const helLength = stream.readInt(72, 76);\r\n const helixClass = stream.readInt(39, 40);\r\n const shWidth = stream.readInt(15, 16);\r\n const shCur = stream.readInt(42, 45);\r\n const shPrev = stream.readInt(57, 60);\r\n\r\n // file fields\r\n const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0);\r\n const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0);\r\n const startSequenceNumber = stream.readInt(pars[startIndex], pars[startIndex] + 3);\r\n let iCodeStr = stream.readString(pars[startIndex] + 4, pars[startIndex] + 4);\r\n let startICode = 0;\r\n\r\n if (iCodeStr.length > 0) {\r\n startICode = iCodeStr.charCodeAt(0);\r\n }\r\n const endSequenceNumber = stream.readInt(pars[endIndex], pars[endIndex] + 3);\r\n iCodeStr = stream.readString(pars[endIndex] + 4, pars[endIndex] + 4);\r\n let endICode = 0;\r\n if (iCodeStr.length > 0) {\r\n endICode = iCodeStr.charCodeAt(0);\r\n }\r\n\r\n let obj;\r\n let cs = this._sheet;\r\n if (stream.readCharCode(1) === codeOfS) {\r\n if (cs !== null && cs.getName() !== structureName) {\r\n cs = null;\r\n this._sheet = null;\r\n }\r\n if (cs === null) {\r\n this._sheet = obj = new Sheet(structureName, shWidth);\r\n adder(obj);\r\n } else {\r\n obj = cs;\r\n }\r\n const strand = new Strand(\r\n obj,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n helixClass,\r\n shCur,\r\n shPrev,\r\n );\r\n obj.addStrand(strand);\r\n this._complex.structures.push(strand);\r\n } else {\r\n obj = new Helix(\r\n helixClass,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n serialNumber,\r\n structureName,\r\n comment,\r\n helLength,\r\n );\r\n adder(obj);\r\n }\r\n }\r\n\r\n _parseHEADER(stream) {\r\n const { metadata } = this._complex;\r\n metadata.classification = stream.readString(11, 50).trim();\r\n metadata.date = stream.readString(51, 59).trim();\r\n\r\n const id = stream.readString(63, 66).trim();\r\n metadata.id = id;\r\n if (id) {\r\n this._complex.name = id;\r\n }\r\n metadata.format = 'pdb';\r\n }\r\n\r\n _parseTITLE(stream) {\r\n const { metadata } = this._complex;\r\n metadata.title = metadata.title || [];\r\n\r\n const line = stream.readInt(9, 10) || 1;\r\n metadata.title[line - 1] = stream.readString(11, 80).trim();\r\n }\r\n\r\n static tagParsers = {\r\n HEADER: PDBParser.prototype._parseHEADER,\r\n 'TITLE ': PDBParser.prototype._parseTITLE,\r\n 'ATOM ': PDBParser.prototype._parseATOM,\r\n HETATM: PDBParser.prototype._parseATOM,\r\n ENDMDL: PDBParser.prototype._parseENDMDL,\r\n CONECT: PDBParser.prototype._parseCONECT,\r\n COMPND: PDBParser.prototype._parseCOMPND,\r\n REMARK: PDBParser.prototype._parseREMARK,\r\n // 'SOURCE': PDBParser.prototype._parseSOURCE,\r\n 'HELIX ': PDBParser.prototype._parseHELIX,\r\n 'SHEET ': PDBParser.prototype._parseSHEET,\r\n\r\n // nonstandard extension to allow range 100,000 - 999,999\r\n 'ATOM 1': PDBParser.prototype._parseATOM,\r\n 'ATOM 2': PDBParser.prototype._parseATOM,\r\n 'ATOM 3': PDBParser.prototype._parseATOM,\r\n 'ATOM 4': PDBParser.prototype._parseATOM,\r\n 'ATOM 5': PDBParser.prototype._parseATOM,\r\n 'ATOM 6': PDBParser.prototype._parseATOM,\r\n 'ATOM 7': PDBParser.prototype._parseATOM,\r\n 'ATOM 8': PDBParser.prototype._parseATOM,\r\n 'ATOM 9': PDBParser.prototype._parseATOM,\r\n };\r\n\r\n parseSync() {\r\n const stream = new PDBStream(this._data);\r\n const result = this._complex = new Complex();\r\n\r\n // parse PDB line by line\r\n while (!stream.end()) {\r\n const tag = stream.readString(1, TAG_LENGTH);\r\n const func = PDBParser.tagParsers[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, stream);\r\n }\r\n stream.next();\r\n }\r\n\r\n // Resolve indices and serials to objects\r\n this._finalize();\r\n\r\n // cleanup\r\n this._serialAtomMap = null;\r\n this._sheet = null;\r\n this._residue = null;\r\n this._chain = null;\r\n this._complex = null;\r\n\r\n if (result.getAtomCount() === 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n\r\nPDBParser.formats = ['pdb'];\r\nPDBParser.extensions = ['.pdb', '.ent'];\r\n\r\nexport default PDBParser;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n SGroup,\r\n Bond,\r\n} = chem;\r\n\r\nconst cOrderCharCodes = {\r\n A: 0,\r\n S: 1,\r\n D: 2,\r\n T: 3,\r\n};\r\n\r\nconst cmlStartRegexp = /\\s*<\\?xml\\b[^?>]*\\?>\\s*<(?:cml|molecule)\\b/i;\r\n\r\nclass CMLParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._complex = null;\r\n this._residue = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._lastMolId = -1;\r\n this._readOnlyOneMolecule = false;\r\n this._options.fileType = 'cml';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && cmlStartRegexp.test(data);\r\n }\r\n\r\n _rebuidBondIndexes(atoms, bonds) {\r\n const count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n\r\n const countBonds = bonds.length;\r\n for (let j = 0; j < countBonds; j++) {\r\n const idxs = bonds[j].atomRefs2.split(' ');\r\n if (idxs[0] === atomId) {\r\n bonds[j].start = i;\r\n }\r\n\r\n if (idxs[1] === atomId) {\r\n bonds[j].end = i;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _createSGroup(molecule, moleculeArr) {\r\n const newGroup = new SGroup(\r\n molecule.id,\r\n molecule.fieldData,\r\n new THREE.Vector3(parseFloat(molecule.x), parseFloat(molecule.y), 0),\r\n molecule.atomRefs,\r\n molecule,\r\n );\r\n if (molecule.placement === 'Relative') {\r\n newGroup._center = new THREE.Vector3(0, 0, 0);\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_CHARGE') {\r\n newGroup._charge = parseInt(molecule.fieldData, 10) || 0;\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_COEFFICIENT') {\r\n newGroup._repeat = parseInt(molecule.fieldData, 10) || 1;\r\n }\r\n moleculeArr.push(newGroup);\r\n }\r\n\r\n _extractSGroup(molecule, moleculeArr) {\r\n if (!Array.isArray(moleculeArr)) {\r\n moleculeArr = [];\r\n }\r\n\r\n if (molecule) {\r\n if (Array.isArray(molecule)) {\r\n const count = molecule.length;\r\n for (let i = 0; i < count; i++) {\r\n if (molecule[i].molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule[i].molecule));\r\n }\r\n this._createSGroup(molecule[i], moleculeArr);\r\n }\r\n } else {\r\n if (molecule.molecule) {\r\n if (molecule.molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule.molecule));\r\n }\r\n }\r\n this._createSGroup(molecule, moleculeArr);\r\n }\r\n }\r\n\r\n return moleculeArr;\r\n }\r\n\r\n _extractSGroups(molecule, atoms) {\r\n const moleculeArr = this._extractSGroup(molecule);\r\n\r\n const count = atoms.length;\r\n let i;\r\n let j;\r\n\r\n for (i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n const firstAtomRef = moleculeArr[j]._atoms.split(' ')[0];\r\n if (firstAtomRef === atomId) {\r\n if (!atoms[i].sgroupRef) {\r\n atoms[i].sgroupRef = [];\r\n }\r\n atoms[i].sgroupRef.push(moleculeArr[j]);\r\n }\r\n }\r\n }\r\n // build sGroups centers\r\n let atomMap = {}; // sgrpmap cache\r\n let mapEntry = null;\r\n const nLimon = 100000000;\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n\r\n function cycleFuncInner(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n moleculeArr[j]._atoms.push(mapEntry.a);\r\n }\r\n }\r\n\r\n function cycleFunc(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n bLow.set(Math.min(bLow.x, mapEntry.x), Math.min(bLow.y, mapEntry.y), Math.min(bLow.z, mapEntry.z));\r\n bHight.set(Math.max(bHight.x, mapEntry.x), Math.max(bHight.y, mapEntry.y), Math.max(bHight.z, mapEntry.z));\r\n cycleFuncInner(e);\r\n }\r\n }\r\n\r\n for (i = 0; i < atoms.length; i++) {\r\n atomMap[atoms[i].id] = {};\r\n atomMap[atoms[i].id].x = atoms[i].x2;\r\n if (atoms[i].x3) {\r\n atomMap[atoms[i].id].x = atoms[i].x3;\r\n }\r\n atomMap[atoms[i].id].x = parseFloat(atomMap[atoms[i].id].x);\r\n atomMap[atoms[i].id].y = atoms[i].y2;\r\n if (atoms[i].y3) {\r\n atomMap[atoms[i].id].y = atoms[i].y3;\r\n }\r\n atomMap[atoms[i].id].y = parseFloat(atomMap[atoms[i].id].y);\r\n atomMap[atoms[i].id].z = '0.0';\r\n if (atoms[i].z3) {\r\n atomMap[atoms[i].id].z = atoms[i].z3;\r\n }\r\n atomMap[atoms[i].id].z = parseFloat(atomMap[atoms[i].id].z);\r\n atomMap[atoms[i].id].a = atoms[i];\r\n }\r\n\r\n let atomsRef;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n if (moleculeArr[j]._center !== null) {\r\n bLow.set(nLimon, nLimon, nLimon);\r\n bHight.set(-nLimon, -nLimon, -nLimon);\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFunc);\r\n\r\n moleculeArr[j]._center.addVectors(bLow, bHight);\r\n moleculeArr[j]._center.multiplyScalar(0.5);\r\n } else {\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFuncInner);\r\n }\r\n }\r\n atomMap = null;\r\n }\r\n\r\n _traverseData(dom) {\r\n function isArray(o) {\r\n return Object.prototype.toString.apply(o) === '[object Array]';\r\n }\r\n\r\n function parseNode(xmlNode, result) {\r\n if (xmlNode.nodeName === '#text' && xmlNode.nodeValue.trim() === '') {\r\n return;\r\n }\r\n\r\n const jsonNode = {};\r\n jsonNode.xmlNode = xmlNode;\r\n const existing = result[xmlNode.nodeName];\r\n if (existing) {\r\n if (!isArray(existing)) {\r\n result[xmlNode.nodeName] = [existing, jsonNode];\r\n } else {\r\n result[xmlNode.nodeName].push(jsonNode);\r\n }\r\n } else {\r\n result[xmlNode.nodeName] = jsonNode;\r\n }\r\n\r\n let length;\r\n let i;\r\n if (xmlNode.attributes) {\r\n ({ length } = xmlNode.attributes);\r\n for (i = 0; i < length; i++) {\r\n const attribute = xmlNode.attributes[i];\r\n jsonNode[attribute.nodeName] = attribute.nodeValue;\r\n }\r\n }\r\n\r\n ({ length } = xmlNode.childNodes);\r\n for (i = 0; i < length; i++) {\r\n parseNode(xmlNode.childNodes[i], jsonNode);\r\n }\r\n }\r\n\r\n const result = {};\r\n if (dom.childNodes.length) {\r\n parseNode(dom.childNodes[0], result);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _findSuitableMolecule(data, molSet) {\r\n for (const key in data) {\r\n if (key === 'xmlNode') {\r\n continue;\r\n } else if (key === 'molecule') {\r\n if (data.molecule) {\r\n if (data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n molSet.push(data);\r\n }\r\n if (Array.isArray(data.molecule)) {\r\n for (let i = 0; i < data.molecule.length; i++) {\r\n if (data.molecule[i].atomArray && data.molecule[i].atomArray.atom) {\r\n molSet.push({ molecule: data.molecule[i] });\r\n }\r\n }\r\n }\r\n }\r\n } else if (data[key] && data[key] !== null && typeof (data[key]) === 'object') {\r\n this._findSuitableMolecule(data[key], molSet);\r\n }\r\n }\r\n }\r\n\r\n _selectComponents(text) {\r\n const parser = new DOMParser();\r\n const doc = parser.parseFromString(text, 'application/xml');\r\n const traversedData = this._traverseData(doc);\r\n let rawData;\r\n const self = this;\r\n\r\n function prepareComponentCompound(data) {\r\n let atoms = [];\r\n if (data.molecule && data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n if (!Array.isArray(data.molecule.atomArray.atom)) {\r\n atoms.push(data.molecule.atomArray.atom);\r\n } else {\r\n atoms = data.molecule.atomArray.atom;\r\n }\r\n } else if (!data.molecule) {\r\n const ret = {};\r\n ret.atomLabels = null;\r\n ret.labelsCount = 1;\r\n return ret;\r\n }\r\n\r\n if (data.molecule.molecule) {\r\n self._extractSGroups(data.molecule.molecule, atoms);\r\n }\r\n\r\n let atom;\r\n let count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges = [];\r\n }\r\n\r\n let localBond = [];\r\n if (data.molecule.bondArray && data.molecule.bondArray.bond) {\r\n if (!Array.isArray(data.molecule.bondArray.bond)) {\r\n localBond.push(data.molecule.bondArray.bond);\r\n } else {\r\n localBond = data.molecule.bondArray.bond;\r\n }\r\n }\r\n let bond;\r\n count = localBond.length;\r\n self._rebuidBondIndexes(atoms, localBond);\r\n\r\n function addCurrBond(index) {\r\n bond = localBond[index];\r\n atom = atoms[bond.start];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.end);\r\n atom = atoms[bond.end];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.start);\r\n return true;\r\n }\r\n\r\n for (let i = 0; i < count; i++) {\r\n if (!addCurrBond(i)) {\r\n // ignore invalid bond\r\n continue;\r\n }\r\n const orderAttr = bond.xmlNode.getAttribute('order');\r\n const tc = parseInt(orderAttr, 10);\r\n // the default bond order is unknown\r\n localBond[i].order = 0;\r\n localBond[i].type = Bond.BondType.UNKNOWN;\r\n if (tc > 1) {\r\n localBond[i].order = tc;\r\n } else {\r\n // another option - bond order is a string\r\n const order = cOrderCharCodes[orderAttr];\r\n if (order !== undefined) {\r\n localBond[i].order = order;\r\n if (orderAttr === 'A') {\r\n localBond[i].type = Bond.BondType.AROMATIC;\r\n }\r\n }\r\n }\r\n }\r\n\r\n count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges.sort();\r\n }\r\n\r\n const labels = self._breadWidthSearch(atoms, 0); // for now\r\n\r\n const retStruct = {};\r\n retStruct.atoms = atoms;\r\n retStruct.bonds = localBond;\r\n retStruct.labels = labels.atomLabels;\r\n retStruct.count = Math.min(1, labels.labelsCount); // for now\r\n retStruct.curr = -1;\r\n retStruct.originalCML = doc;\r\n\r\n return retStruct;\r\n }\r\n\r\n if (traversedData.cml) {\r\n rawData = traversedData.cml;\r\n } else {\r\n rawData = traversedData;\r\n }\r\n const retData = [];\r\n const filteredData = [];\r\n this._findSuitableMolecule(rawData, filteredData);\r\n if (this._readOnlyOneMolecule && filteredData.length > 1) {\r\n filteredData.splice(1, filteredData.length - 1);\r\n }\r\n filteredData.forEach((d) => {\r\n const rd = prepareComponentCompound(d);\r\n if (rd.atoms.length > 0) {\r\n retData.push(rd);\r\n }\r\n });\r\n return retData;\r\n }\r\n\r\n _packLabel(compId, molId) {\r\n const shift = 16;\r\n return (molId << shift) + compId;\r\n }\r\n\r\n _unpackLabel(l) {\r\n const shift = 16;\r\n const mask = (1 << shift) - 1;\r\n return { molId: l >>> shift, compId: l & mask };\r\n }\r\n\r\n _breadWidthSearch(atoms, molID) {\r\n const atomLabels = new Array(atoms.length);\r\n\r\n let id;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n atomLabels[id] = this._packLabel(0, molID);\r\n }\r\n\r\n const breadthQueue = [];\r\n let componentID = 0;\r\n let labeledAtoms = atoms.length;\r\n\r\n while (labeledAtoms > 0) {\r\n componentID++;\r\n\r\n let startID = -1;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n if (this._unpackLabel(atomLabels[id]).compId === 0) {\r\n startID = id;\r\n break;\r\n }\r\n }\r\n\r\n if (startID < 0) {\r\n break;\r\n }\r\n\r\n // Bread first search\r\n breadthQueue.push(atoms[startID]);\r\n atomLabels[startID] = this._packLabel(componentID, molID);\r\n labeledAtoms--;\r\n\r\n while (breadthQueue.length > 0) {\r\n const curr = breadthQueue.shift();\r\n if (!curr) {\r\n continue;\r\n }\r\n\r\n for (let i = 0; i < curr.edges.length; i++) {\r\n if (atomLabels[curr.edges[i]] !== componentID) {\r\n breadthQueue.push(atoms[curr.edges[i]]);\r\n atomLabels[curr.edges[i]] = componentID;\r\n labeledAtoms--;\r\n }\r\n }\r\n }\r\n }\r\n const ret = {};\r\n ret.atomLabels = atomLabels;\r\n ret.labelsCount = componentID;\r\n return ret;\r\n }\r\n\r\n _parseBond(eAtom, mainAtom, order, type) {\r\n if (eAtom >= 0) {\r\n const h = [Math.min(eAtom, mainAtom), Math.max(eAtom, mainAtom)];\r\n this._complex.addBond(h[0], h[1], order, type, true);\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseSet(varData) {\r\n const complex = this._complex = new Complex();\r\n const data = varData;\r\n const currentLabel = data.curr;\r\n const { atoms, labels } = data;\r\n let atom = null;\r\n let i;\r\n let j;\r\n const count = atoms.length;\r\n\r\n function addFunc(a) {\r\n a.xmlNodeRef = atom;\r\n if (atom.x2) {\r\n atom.x3 = atom.x2;\r\n delete atom.x2;\r\n }\r\n if (atom.y2) {\r\n atom.y3 = atom.y2;\r\n delete atom.y2;\r\n }\r\n if (!(atom.z3)) {\r\n atom.z3 = '0.0';\r\n }\r\n atom.complexAtom = a;\r\n }\r\n\r\n let chains = {};\r\n // parse atoms in label order\r\n const reorder = [];\r\n for (i = 0; i < count; i++) {\r\n reorder.push(i);\r\n }\r\n reorder.sort((a, b) => labels[a] - labels[b]);\r\n for (i = 0; i < count; i++) {\r\n const atomCharge = 0;\r\n const lLabel = labels[reorder[i]];\r\n if (this._unpackLabel(lLabel).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[reorder[i]];\r\n const atomFullNameStruct = atom.elementType;\r\n\r\n if (atom.sgroupRef) {\r\n const countRef = atom.sgroupRef.length;\r\n for (let k = 0; k < countRef; ++k) {\r\n complex._sgroups.push(atom.sgroupRef[k]);\r\n }\r\n }\r\n\r\n if (atom.x3 || atom.x2) {\r\n const currAtomComp = this._unpackLabel(lLabel).compId;\r\n // use ' ' by default instead of synthetic creation of chain names\r\n const chainID = ' '; //= String.fromCharCode('A'.charCodeAt(0) + currAtomComp);\r\n const resSeq = currAtomComp;\r\n const iCode = ' ';\r\n let strLabel = currAtomComp.toString();\r\n if (strLabel.length === 1) {\r\n strLabel = `0${strLabel}`;\r\n }\r\n const resName = `N${strLabel}`;\r\n let chain = chains[chainID];\r\n if (!chain || chain.getName() !== chainID) {\r\n chains[chainID] = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n // _x, _y, _z, mname, mindex, atomNameFull, atomName, chainID, serial, isHet, atlLocInd, atomNameToTypeF\r\n let xyz = null;\r\n if (atom.x3) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x3), parseFloat(atom.y3), parseFloat(atom.z3));\r\n } else if (atom.x2) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x2), parseFloat(atom.y2), 0);\r\n }\r\n let element = Element.ByName[atom.elementType.toUpperCase()];\r\n if (!element) {\r\n element = (JSON.parse(JSON.stringify(Element.ByName[\r\n Object.keys(Element.ByName)[Object.keys(Element.ByName).length - 1]])));\r\n element.number += 1;\r\n element.name = atom.elementType.toUpperCase();\r\n element.fullName = 'Unknown';\r\n Element.ByName[atom.elementType.toUpperCase()] = element;\r\n }\r\n const atomSerial = parseInt(atom.id.replace(/[^0-9]/, ''), 10);\r\n const added = residue.addAtom(\r\n atomFullNameStruct,\r\n element,\r\n xyz,\r\n Element.Role.SG,\r\n true,\r\n atomSerial,\r\n ' ',\r\n 1.0,\r\n 0.0,\r\n atomCharge,\r\n );\r\n if (atom.hydrogenCount) {\r\n added.hydrogenCount = parseInt(atom.hydrogenCount, 10);\r\n }\r\n if (atom.mrvValence) {\r\n added.valence = parseInt(atom.mrvValence, 10);\r\n }\r\n addFunc(added);\r\n }\r\n }\r\n }\r\n chains = null;// NOSONAR\r\n for (i = 0; i < data.bonds.length; i++) {\r\n const cb = data.bonds[i];\r\n if (this._unpackLabel(labels[cb.start]).molId === this._unpackLabel(currentLabel).molId\r\n && this._unpackLabel(labels[cb.end]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[cb.start];\r\n if (!atom || !(atoms[cb.end])) {\r\n continue; // skip invalid\r\n }\r\n this._parseBond(\r\n parseInt(atom.id.replace(/[^0-9]/, ''), 10),\r\n parseInt(atoms[cb.end].id.replace(/[^0-9]/, ''), 10),\r\n cb.order,\r\n cb.type,\r\n );\r\n }\r\n }\r\n\r\n for (i = 0; i < this._complex.getSGroupCount(); i++) {\r\n const sGrp = this._complex.getSGroups()[i];\r\n for (j = 0; j < sGrp._atoms.length; j++) {\r\n sGrp._atoms[j] = sGrp._atoms[j].complexAtom;\r\n }\r\n }\r\n for (i = 0; i < count; i++) {\r\n if (this._unpackLabel(labels[i]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[i];\r\n atom.complexAtom = null;\r\n delete atom.complexAtom;\r\n }\r\n }\r\n this._complex.originalCML = data.originalCML;\r\n this._fixBondsArray();\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n this._serialAtomMap = null;\r\n this._complex = null;\r\n return complex;\r\n }\r\n\r\n parseSync() {\r\n const complexes = [];\r\n const self = this;\r\n const moleculaSet = this._selectComponents(this._data);\r\n moleculaSet.forEach((molSet) => {\r\n molSet.curr = 2;\r\n if (molSet.count === 0) {\r\n molSet.count = 1;\r\n }\r\n for (let i = 0; i < molSet.count; i++) {\r\n molSet.curr = (i + 1);\r\n complexes.push(self._parseSet(molSet, false));\r\n }\r\n });\r\n\r\n let totalAtomsParsed = 0;\r\n complexes.forEach((c) => {\r\n totalAtomsParsed += c.getAtomCount();\r\n });\r\n if (totalAtomsParsed <= 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n if (complexes.length > 1) {\r\n const joinedComplex = new Complex();\r\n joinedComplex.joinComplexes(complexes);\r\n joinedComplex.originalCML = complexes[0].originalCML;\r\n return joinedComplex;\r\n }\r\n if (complexes.length === 1) {\r\n return complexes[0];\r\n }\r\n return new Complex();\r\n }\r\n}\r\n\r\nCMLParser.formats = ['cml'];\r\nCMLParser.extensions = ['.cml'];\r\n\r\nexport default CMLParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport MMTF from '../../../vendor/js/mmtf';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst {\r\n Complex,\r\n Chain,\r\n Atom,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nclass ArrayComparator {\r\n constructor(original) {\r\n this._original = Array.from(original);\r\n this._original.sort();\r\n\r\n this._sum = 0;\r\n for (let i = 0; i < this._original.length; ++i) {\r\n this._sum += this._original[i];\r\n }\r\n }\r\n\r\n compare(candidate) {\r\n const len = candidate.length;\r\n if (len !== this._original.length) {\r\n return false;\r\n }\r\n\r\n let sum = 0;\r\n let i;\r\n for (i = 0; i < len; ++i) {\r\n sum += candidate[i];\r\n }\r\n\r\n if (sum !== this._sum) {\r\n return false;\r\n }\r\n\r\n const sorted = Array.from(candidate);\r\n sorted.sort();\r\n\r\n for (i = 0; i < len; ++i) {\r\n if (sorted[i] !== this._original[i]) {\r\n return false;\r\n }\r\n }\r\n\r\n return true;\r\n }\r\n}\r\n\r\nArrayComparator.prototype.constructor = ArrayComparator;\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see https://github.com/rcsb/mmtf-javascript/blob/master/src/mmtf-traverse.js\r\nconst secStructToType = [\r\n StructuralElementType.HELIX_PI, // 0\r\n StructuralElementType.BEND, // 1\r\n StructuralElementType.HELIX_ALPHA, // 2\r\n StructuralElementType.STRAND, // 3\r\n StructuralElementType.HELIX_310, // 4\r\n StructuralElementType.BRIDGE, // 5\r\n StructuralElementType.TURN, // 6\r\n StructuralElementType.COIL, // 7\r\n];\r\n\r\nfunction getFirstByte(buf) {\r\n const bytes = new Uint8Array(buf, 0, 1);\r\n return bytes[0];\r\n}\r\n\r\nclass MMTFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'mmtf';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n // check if it's binary MessagePack format containing a map (dictionary)\r\n // see https://github.com/msgpack/msgpack/blob/master/spec.md\r\n return _.isArrayBuffer(data) && ((getFirstByte(data) | 1) === 0xDF);\r\n }\r\n\r\n _onModel(_modelData) {\r\n }\r\n\r\n _onChain(chainData) {\r\n if (chainData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const chain = new Chain(this._complex, chainData.chainName);\r\n this._complex._chains[chainData.chainIndex] = chain;\r\n chain._index = chainData.chainIndex;\r\n }\r\n\r\n _onGroup(groupData) {\r\n if (groupData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n if (this.settings.now.nowater) {\r\n // skip water\r\n if (groupData.groupName === 'HOH' || groupData.groupName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n const chain = this._complex._chains[groupData.chainIndex];\r\n const icode = !groupData.insCode.charCodeAt(0) ? '' : groupData.insCode;\r\n const residue = chain.addResidue(groupData.groupName, groupData.groupId, icode);\r\n residue._index = groupData.groupIndex;\r\n\r\n this._updateSecStructure(this._complex, residue, groupData);\r\n }\r\n\r\n _onAtom(atomData) {\r\n if (atomData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const altLoc = !atomData.altLoc.charCodeAt(0) ? '' : atomData.altLoc;\r\n const atom = new Atom(\r\n atomData.groupIndex, // we store residue index here to replace it later with actual reference\r\n atomData.atomName,\r\n Element.getByName(atomData.element.toUpperCase()),\r\n new THREE.Vector3(atomData.xCoord, atomData.yCoord, atomData.zCoord),\r\n Element.Role[atomData.atomName],\r\n false, // hetero atoms will be marked later\r\n atomData.atomId,\r\n altLoc,\r\n atomData.occupancy,\r\n atomData.bFactor,\r\n atomData.formalCharge,\r\n );\r\n\r\n this._complex._atoms[atomData.atomIndex] = atom;\r\n atom.index = atomData.atomIndex;\r\n\r\n this._serialAtomMap[atomData.atomId] = atom;\r\n }\r\n\r\n _onBond(bondData) {\r\n const right = Math.max(bondData.atomIndex1, bondData.atomIndex2);\r\n if (right >= this._complex._atoms.length) {\r\n return;\r\n }\r\n const left = Math.min(bondData.atomIndex1, bondData.atomIndex2);\r\n this._complex.addBond(\r\n this._complex._atoms[left],\r\n this._complex._atoms[right],\r\n bondData.bondOrder,\r\n Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n\r\n _updateSecStructure(complex, residue, groupData) {\r\n const helixClasses = [3, -1, 1, -1, 5];\r\n\r\n if (!_.isUndefined(groupData) && groupData.secStruct === this._ssType) {\r\n residue._secondary = this._ssStruct;\r\n if (this._ssStruct) {\r\n this._ssStruct.term = residue;\r\n }\r\n return;\r\n }\r\n\r\n if (!_.isUndefined(groupData)) {\r\n // start new secondary structure\r\n const type = secStructToType[groupData.secStruct];\r\n this._ssType = groupData.secStruct;\r\n this._ssStart = residue;\r\n\r\n let struct = null;\r\n switch (this._ssType) {\r\n case -1: // undefined\r\n case 7: // coil\r\n break;\r\n case 0: // pi helix\r\n case 2: // alpha helix\r\n case 4: // 3-10 helix\r\n struct = new Helix(helixClasses[this._ssType], residue, residue, 0, '', '', 0);\r\n complex._helices.push(struct);\r\n break;\r\n case 3: { // extended\r\n const sheet = new Sheet('', 0);\r\n complex._sheets.push(sheet);\r\n struct = new Strand(sheet, residue, residue, 0, null, null);\r\n break;\r\n }\r\n default:\r\n if (type !== undefined) {\r\n struct = new StructuralElement(type, residue, residue);\r\n }\r\n break;\r\n }\r\n\r\n this._ssStruct = struct;\r\n residue._secondary = struct;\r\n if (struct) {\r\n complex.structures.push(struct);\r\n }\r\n }\r\n }\r\n\r\n _updateMolecules(mmtfData) {\r\n const entities = mmtfData.entityList;\r\n if (!entities) {\r\n return;\r\n }\r\n\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < entities.length; i++) {\r\n const entity = entities[i];\r\n const chains = entity.chainIndexList;\r\n let residues = [];\r\n for (let j = 0; j < chains.length; j++) {\r\n const chainIndex = chains[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, entity.description, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n // populate complex with chains, residues and atoms\r\n _traverse(mmtfData) {\r\n const self = this;\r\n\r\n // get metadata\r\n const { metadata } = this._complex;\r\n metadata.id = mmtfData.structureId;\r\n metadata.title = [];\r\n metadata.title[0] = mmtfData.title;\r\n metadata.date = mmtfData.releaseDate;\r\n metadata.format = 'mmtf';\r\n\r\n // create event callback functions\r\n const eventCallbacks = {\r\n onModel(modelData) {\r\n self._onModel(modelData);\r\n },\r\n onChain(chainData) {\r\n self._onChain(chainData);\r\n },\r\n onGroup(groupData) {\r\n self._onGroup(groupData);\r\n },\r\n onAtom(atomData) {\r\n self._onAtom(atomData);\r\n },\r\n onBond(bondData) {\r\n self._onBond(bondData);\r\n },\r\n };\r\n\r\n // temporary variables used during traversal to track secondary structures\r\n this._ssType = -1;\r\n this._ssStruct = null;\r\n this._ssStart = null;\r\n\r\n // traverse the structure and listen to the events\r\n MMTF.traverse(mmtfData, eventCallbacks);\r\n\r\n this._updateSecStructure(this._complex);\r\n this._updateMolecules(mmtfData);\r\n }\r\n\r\n // During traversal atoms and residues don't come sequentially\r\n // so a residue for certain atom can be unavailable. Thus we\r\n // store residue index in atom.\r\n // This function being called after traversal replaces the index\r\n // with actual reference, and also populates atom lists in residues.\r\n _linkAtomsToResidues() {\r\n for (let i = 0; i < this._complex._atoms.length; ++i) {\r\n const atom = this._complex._atoms[i];\r\n const residue = this._complex._residues[atom.residue];\r\n atom.residue = residue;\r\n residue._atoms.push(atom);\r\n }\r\n }\r\n\r\n _findSynonymousChains() {\r\n const named = {};\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!named.hasOwnProperty(name)) {\r\n named[name] = [];\r\n }\r\n\r\n named[name].push(chain._index);\r\n }\r\n\r\n return named;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _parseAssemblyInfo(mmtfData) {\r\n let i;\r\n let j;\r\n let k;\r\n const assemblies = [];\r\n const { logger } = this;\r\n\r\n for (i = 0; i < mmtfData.bioAssemblyList.length; ++i) {\r\n const baInfo = mmtfData.bioAssemblyList[i];\r\n if (baInfo.transformList.length === 0) {\r\n continue;\r\n }\r\n\r\n const chains = baInfo.transformList[0].chainIndexList;\r\n const chainListCheck = new ArrayComparator(chains);\r\n\r\n // build list of chain names\r\n const chainNames = {};\r\n for (j = 0; j < chains.length; ++j) {\r\n chainNames[this._complex._chains[chains[j]].getName()] = 1;\r\n }\r\n\r\n // all chains with the same name should belong to assembly if one of them belongs\r\n const allChains = [];\r\n let name;\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n // just concat arrays -- there should be no duplicates\r\n Array.prototype.push.apply(allChains, this._chainsByName[name]);\r\n }\r\n }\r\n if (!chainListCheck.compare(allChains)) {\r\n // assembly is missing some of the chains\r\n logger.debug('MMTF: Assembly is missing some of the synonymous chains. Skipping...');\r\n }\r\n\r\n const a = new Assembly(this._complex);\r\n\r\n // add chains to assembly\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n a.addChain(name);\r\n }\r\n }\r\n\r\n // add unique matrices to assembly\r\n a.addMatrix(new THREE.Matrix4().fromArray(baInfo.transformList[0].matrix).transpose());\r\n for (j = 1; j < baInfo.transformList.length; ++j) {\r\n const transform = baInfo.transformList[j];\r\n\r\n if (!chainListCheck.compare(transform.chainIndexList)) {\r\n // list of chains for this transform doesn't match that for other transforms\r\n // this is illegal in our structure\r\n logger.debug('MMTF: Chain lists differ for different transforms in one assembly. Skipping...');\r\n continue;\r\n }\r\n\r\n const m = new THREE.Matrix4().fromArray(transform.matrix).transpose();\r\n\r\n // check if matrix is already in the list\r\n for (k = 0; k < a.matrices.length; ++k) {\r\n if (a.matrices[k].equals(m)) {\r\n break;\r\n }\r\n }\r\n\r\n if (k === a.matrices.length) {\r\n a.addMatrix(m);\r\n }\r\n }\r\n\r\n a.finalize();\r\n assemblies.push(a);\r\n }\r\n\r\n return assemblies;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _markHeteroAtoms(mmtfData) {\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < mmtfData.entityList.length; ++i) {\r\n const entity = mmtfData.entityList[i];\r\n if (entity.type !== 'polymer') {\r\n for (let j = 0; j < entity.chainIndexList.length; ++j) {\r\n const chainIndex = entity.chainIndexList[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n for (let k = 0; k < chain._residues.length; ++k) {\r\n const res = chain._residues[k];\r\n for (let m = 0; m < res._atoms.length; ++m) {\r\n res._atoms[m].het = true;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // joins chains with the same name into single chain\r\n _joinSynonymousChains() {\r\n let i;\r\n let j;\r\n\r\n const primaryChainsArray = [];\r\n const primaryChainsHash = {};\r\n\r\n // join chains\r\n for (i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!primaryChainsHash.hasOwnProperty(name)) {\r\n // new name -- this is a primary chain\r\n primaryChainsHash[name] = chain;\r\n chain._index = primaryChainsArray.length; // update index as this array will later replace original chain list\r\n primaryChainsArray.push(chain);\r\n continue;\r\n }\r\n\r\n // this chain should be joined with the primary chain of the same name\r\n const primary = primaryChainsHash[name];\r\n for (j = 0; j < chain._residues.length; ++j) {\r\n const residue = chain._residues[j];\r\n primary._residues.push(residue);\r\n residue._chain = primary;\r\n }\r\n }\r\n\r\n // replace chains list with one containing only primary chains\r\n // dropping references to all chains but primary\r\n this._complex._chains = primaryChainsArray;\r\n }\r\n\r\n parseSync() {\r\n const mmtfData = MMTF.decode(this._data);\r\n\r\n this._complex = new Complex();\r\n this._serialAtomMap = {}; // filled during traversal\r\n\r\n this._traverse(mmtfData);\r\n this._linkAtomsToResidues();\r\n this._markHeteroAtoms(mmtfData);\r\n this._chainsByName = this._findSynonymousChains();\r\n Array.prototype.push.apply(this._complex.units, this._parseAssemblyInfo(mmtfData));\r\n this._joinSynonymousChains();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n return this._complex;\r\n }\r\n}\r\n\r\nMMTFParser.formats = ['mmtf'];\r\nMMTFParser.extensions = ['.mmtf'];\r\nMMTFParser.binary = true;\r\n\r\nexport default MMTFParser;\r\n","class ParsingError extends Error {\r\n constructor(message, line, column) {\r\n super(`data:${line}:${column}: ${message}`);\r\n\r\n if (Error.captureStackTrace) {\r\n Error.captureStackTrace(this, ParsingError);\r\n }\r\n\r\n this.name = 'ParsingError';\r\n this.parseLine = line;\r\n this.parseColumn = column;\r\n }\r\n}\r\n\r\nexport default ParsingError;\r\n","import _ from 'lodash';\r\nimport ParsingError from './ParsingError';\r\n\r\n// Implemented and being tested against: https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax\r\n\r\nfunction _isWhitespace(ch) {\r\n return ch === 32 || ch === 10 || ch === 13 || ch === 9;\r\n}\r\n\r\nfunction _inlineIndexOf(ch0, str, idx) {\r\n const len = str.length;\r\n let ch = -1;\r\n while (idx < len) {\r\n ch = str.charCodeAt(idx);\r\n if (ch === ch0 || ch === 10) {\r\n break;\r\n }\r\n ++idx;\r\n }\r\n return ch === ch0 ? idx : -1;\r\n}\r\n\r\nexport default function readCIF(source) {\r\n let i = 0;\r\n let j = 0;\r\n const n = source.length;\r\n let code = NaN;\r\n let newline = true;\r\n let line = 1;\r\n let column = 1;\r\n let begin;\r\n let state = 0; // 0 - start, 1 - block, 2 - item, 3 - loop, 4 - values, 5 - value\r\n const result = {};\r\n let block = {};\r\n let keys = [];\r\n let keysCount = 0;\r\n let key = '';\r\n let values = [];\r\n let valuesCount = 0;\r\n let value;\r\n\r\n function _parseValue() {\r\n let val;\r\n if ((code === 46 || code === 63) && (i + 1 >= n || _isWhitespace(source.charCodeAt(i + 1)))) { // '.' or '?' .....\r\n // it's a missing value\r\n ++column;\r\n ++i;\r\n return undefined;\r\n }\r\n if (newline && code === 59) { // ';' ......................................................................\r\n // parse multi-line string\r\n j = i;\r\n let lines = 0;\r\n do {\r\n j = _inlineIndexOf(10, source, j + 1); // '\\n'\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated text block found', line, column);\r\n }\r\n ++lines;\r\n } while ((j + 1 < n && source.charCodeAt(j + 1) !== code) || j + 1 >= n);\r\n val = source.substring(i + 1, j).replace(/\\r/g, '');\r\n i = j + 2;\r\n line += lines;\r\n column = 1;\r\n newline = false;\r\n return val;\r\n }\r\n if (code === 39 || code === 34) { // ''' or '\"' ...........................................................\r\n // parse quoted string\r\n j = i;\r\n do {\r\n j = _inlineIndexOf(code, source, j + 1);\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated quoted string found', line, column);\r\n }\r\n } while (j + 1 < n && !_isWhitespace(source.charCodeAt(j + 1)));\r\n val = source.substring(i + 1, j);\r\n column += j - i + 1;\r\n i = j + 1;\r\n return val;\r\n } // ......................................................................................................\r\n // parse until the first whitespace\r\n j = i;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n val = source.substring(i, j);\r\n column += j - i;\r\n i = j;\r\n // try to convert to a number\r\n const num = Number(val);\r\n if (!Number.isNaN(num)) {\r\n return num;\r\n }\r\n // or leave as an unquoted string\r\n return val;\r\n }\r\n\r\n function _storeKey(tag) {\r\n keys[keysCount++] = tag;\r\n }\r\n\r\n function _storeValue(val) {\r\n const keyIndex = valuesCount % keysCount;\r\n values[keyIndex].push(val);\r\n ++valuesCount;\r\n return val;\r\n }\r\n\r\n while (i <= n) {\r\n code = source.charCodeAt(i); // 'NaN' in place of ''\r\n if (code === 13) { // '\\r' .......................................................................................\r\n // just ignore\r\n } else if (code === 10) { // '\\n' ................................................................................\r\n // take note of new lines\r\n newline = true;\r\n ++line;\r\n column = 1;\r\n } else {\r\n // process inline characters\r\n if (code === 32 || code === 9) { // ' ' or '\\t' ................................................................\r\n // just ignore\r\n } else if (code === 35) { // '#' ...............................................................................\r\n // skip the comment until before the end of the line\r\n i = _inlineIndexOf(10, source, i + 1); // '\\n'\r\n if (i === -1) {\r\n break;\r\n } else {\r\n continue; // don't forget to process the new line\r\n }\r\n } else if (state === 0) { // start =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n j = i + 5;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new data block\r\n result[source.substring(begin, i)] = block = {};\r\n state = 1; // block\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Data block name missing', line, column);\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 1) { // block =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n continue; // parse again in a different state\r\n } else if (code === 95) { // '_' .............................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // start new item\r\n key = source.substring(begin, i);\r\n state = 2; // item\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n i += 5;\r\n column += 5;\r\n if (i < n && !_isWhitespace(source.charCodeAt(i))) {\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n } else {\r\n // start new loop\r\n keys = [];\r\n keysCount = 0;\r\n values = [];\r\n valuesCount = 0;\r\n state = 3; // loop\r\n continue; // don't forget to process the whitespace\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 2) { // item ==============================================================================\r\n if (Number.isNaN(code)) {\r\n break;\r\n }\r\n value = _parseValue();\r\n _.set(block, key, value);\r\n state = 1; // block\r\n continue;\r\n } else if (state === 3) { // loop ==============================================================================\r\n if (code === 95) { // '_' ....................................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new key\r\n _storeKey(source.substring(begin, i));\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else { // ..................................................................................................\r\n if (keysCount > 0) {\r\n for (let keyIndex = 0; keyIndex < keysCount; ++keyIndex) {\r\n value = [];\r\n values[keyIndex] = value;\r\n _.set(block, keys[keyIndex], value);\r\n }\r\n state = 4;\r\n continue; // parse again in a different state\r\n }\r\n throw new ParsingError('Data tags are missing inside a loop', line, column);\r\n }\r\n } else if (state === 4) { // values ============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n } else if (code === 95) { // '_' .............................................................................\r\n state = 1; // block\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n state = 1; // block\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n state = 0;\r\n } else { // ..................................................................................................\r\n _storeValue(_parseValue());\r\n }\r\n continue; // parse again in a different state\r\n } else { // ====================================================================================================\r\n throw new ParsingError(`Unexpected internal state ${state}`, line, column);\r\n }\r\n\r\n newline = false;\r\n ++column;\r\n }\r\n ++i;\r\n }\r\n\r\n if (state === 2) { // item\r\n throw new ParsingError(`Unexpected end of file in state ${state}`, line, column);\r\n }\r\n\r\n return result;\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\nimport readCIF from './readCIF';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nconst cRequiredAtomFields = [\r\n 'auth_seq_id',\r\n 'Cartn_x',\r\n 'Cartn_y',\r\n 'Cartn_z',\r\n 'label_atom_id',\r\n];\r\n\r\nconst cSecondaryCoding = {\r\n helx: 'helix',\r\n turn: 'turn',\r\n strn: 'strand',\r\n};\r\n\r\nfunction getTypeFromId(string) {\r\n const typeId = /[A-Za-z]+/.exec(string);\r\n if (!typeId) {\r\n return null;\r\n }\r\n\r\n return cSecondaryCoding[typeId[0].toLowerCase()];\r\n}\r\n\r\n/**\r\n * Make valid object an array\r\n * @param arrayLikeObject\r\n * @return {array, object} array or object\r\n */\r\nfunction arrize(arrayLikeObject) {\r\n if (arrayLikeObject === null || arrayLikeObject === undefined || _.isArray(arrayLikeObject)) {\r\n return arrayLikeObject;\r\n }\r\n return [arrayLikeObject];\r\n}\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\nclass AtomDataError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'AtomDataError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction _getOperations(operList) {\r\n if (!operList) {\r\n return null;\r\n }\r\n const idc = arrize(operList.id);\r\n const { matrix, vector } = operList;\r\n if (!idc || !matrix || !vector) {\r\n return null;\r\n }\r\n\r\n const ops = [];\r\n for (let i = 0, n = idc.length; i < n; ++i) {\r\n const mtx = new THREE.Matrix4();\r\n const { elements } = mtx;\r\n\r\n for (let row = 0; row < 3; ++row) {\r\n const matrixData = matrix[row + 1];\r\n elements[row] = arrize(matrixData[1])[i];\r\n elements[row + 4] = arrize(matrixData[2])[i];\r\n elements[row + 8] = arrize(matrixData[3])[i];\r\n elements[row + 12] = arrize(vector[row + 1])[i];\r\n }\r\n ops[idc[i]] = mtx;\r\n }\r\n return ops;\r\n}\r\n\r\nfunction _extractOperations(assemblyGen, opsDict) {\r\n assemblyGen = _.isString(assemblyGen) ? assemblyGen : `${assemblyGen}`;\r\n const l = assemblyGen.replace(/\\)\\s*\\(/g, '!').replace(/[()']/g, '');\r\n const groupStr = l.split('!');\r\n const gps = [];\r\n\r\n for (let grIdx = 0, grCount = groupStr.length; grIdx < grCount; ++grIdx) {\r\n const gr = groupStr[grIdx].split(',');\r\n const gp = [];\r\n let idx = 0;\r\n for (let i = 0, n = gr.length; i < n; ++i) {\r\n const s = gr[i];\r\n if (s.includes('-')) {\r\n const es = s.split('-');\r\n let j = parseInt(es[0], 10);\r\n const m = parseInt(es[1], 10);\r\n for (; j <= m; ++j) {\r\n gp[idx++] = opsDict[j];\r\n }\r\n } else {\r\n gp[idx++] = opsDict[s];\r\n }\r\n }\r\n gps.push(gp);\r\n }\r\n\r\n // traverse all groups from the end of array and make all mults\r\n const matrices = [];\r\n let cnt = 0;\r\n function traverse(level, mtx) {\r\n for (let ii = 0, nn = gps[level].length; ii < nn; ++ii) {\r\n const newMtx = mtx ? mtx.clone() : new THREE.Matrix4();\r\n newMtx.multiplyMatrices(gps[level][ii], newMtx);\r\n if (level === 0) {\r\n matrices[cnt++] = newMtx;\r\n } else {\r\n traverse(level - 1, newMtx);\r\n }\r\n }\r\n }\r\n traverse(gps.length - 1);\r\n return matrices;\r\n}\r\n\r\nclass CIFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this.asymDict = {};\r\n this.molecules = [];\r\n this._options.fileType = 'cif';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*data_/i.test(data);\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing CIF file..');\r\n const data = readCIF(this._data);\r\n return this._toComplex(data);\r\n }\r\n\r\n /**\r\n * Convert intermediate structure into our valid Complex object\r\n * @param cifData intermediate CIF object\r\n * @returns {Complex} complex\r\n * @private\r\n */\r\n _toComplex(cifData) {\r\n const complex = new Complex();\r\n const complexData = cifData[Object.keys(cifData)[0]];\r\n this._extractAtoms(complex, complexData);\r\n this._extractSecondary(complex, complexData);\r\n this._extractAssemblies(complex, complexData);\r\n this._extractMolecules(complex, complexData);\r\n this._extractMetadata(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n\r\n return complex;\r\n }\r\n\r\n /**\r\n * Extract metadata\r\n * @param complex structure to fill\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n\r\n _extractMetadata(complex, complexData) {\r\n const { metadata } = complex;\r\n metadata.id = complexData.entry.id;\r\n metadata.classification = complexData.struct_keywords.pdbx_keywords;\r\n const databaserev = complexData.database_PDB_rev;\r\n metadata.date = (databaserev && databaserev.date_original) ? databaserev.date_original : '';\r\n metadata.format = 'cif';\r\n metadata.title = [];\r\n metadata.title[0] = complexData.struct.title;\r\n }\r\n\r\n /**\r\n * Extract molecules information from CIF structure (should be called strictly after _extractAtoms)\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractMolecules(complex, complexData) {\r\n const molData = complexData.entity;\r\n const names = arrize(molData.pdbx_description);\r\n const count = names.length;\r\n let i;\r\n\r\n // molecules names from cif\r\n for (i = 0; i < count; i++) {\r\n if (this.molecules[i]) { // molecule was created during atoms processing\r\n this.molecules[i].name = names[i];\r\n } else { // molecule wasn't created, because there is no atom which is contained\r\n this.molecules[i] = { name: names[i], residues: [] };\r\n }\r\n }\r\n\r\n // reorganize molecules for complex and check chains\r\n const molecules = complex.getMolecules();\r\n for (i = 0; i < count; i++) {\r\n const molecule = this.molecules[i];\r\n molecules[i] = new Molecule(complex, molecule.name, i + 1);\r\n molecules[i].residues = molecule.residues;\r\n }\r\n }\r\n\r\n /**\r\n * Extract atom information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAtoms(complex, complexData) {\r\n const atomData = complexData.atom_site;\r\n if (!atomData) {\r\n throw new AtomDataError('CIF parsing error: atom_site is not specified!');\r\n }\r\n\r\n for (let f = 0, n = cRequiredAtomFields.length; f < n; ++f) {\r\n if (!atomData[cRequiredAtomFields[f]]) {\r\n throw new AtomDataError(`CIF parsing error: requires field ${cRequiredAtomFields[f]} not found!`);\r\n }\r\n }\r\n\r\n const { asymDict } = this;\r\n // required fields\r\n const resIdc = arrize(atomData.auth_seq_id);\r\n const x = arrize(atomData.Cartn_x);\r\n const y = arrize(atomData.Cartn_y);\r\n const z = arrize(atomData.Cartn_z);\r\n const names = arrize(atomData.label_atom_id);\r\n const count = names.length;\r\n // optional fields\r\n const group = arrize(atomData.group_PDB) || [];\r\n const chainIdc = arrize(atomData.auth_asym_id) || [];\r\n const chainLabelIdc = arrize(atomData.label_asym_id) || [];\r\n const serials = arrize(atomData.id) || [];\r\n const iCodes = arrize(atomData.pdbx_PDB_ins_code) || [];\r\n const resNames = arrize(atomData.label_comp_id) || [];\r\n const elements = arrize(atomData.type_symbol) || [];\r\n const tempFactors = arrize(atomData.B_iso_or_equiv) || [];\r\n const occupancies = arrize(atomData.occupancy) || [];\r\n const charges = arrize(atomData.pdbx_formal_charge) || [];\r\n const altLocs = arrize(atomData.label_alt_id) || [];\r\n const models = arrize(atomData.pdbx_PDB_model_num) || [];\r\n const molecules = arrize(atomData.label_entity_id) || [];\r\n\r\n let chain = null;\r\n let residue = null;\r\n for (let i = 0; i < count; ++i) {\r\n const model = models[i] || 1;\r\n if (model !== 1) {\r\n continue;\r\n }\r\n const chainID = String(chainIdc[i] || ' ');\r\n\r\n if (!chain || chain.getName() !== chainID) {\r\n chain = complex.getChain(chainID) || complex.addChain(chainID);\r\n }\r\n asymDict[String(chainLabelIdc[i] || ' ')] = chainID;\r\n const resSeq = resIdc[i];\r\n const iCode = String(iCodes[i] || ' ');\r\n const resName = String(resNames[i] || '');\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n residue = chain.addResidue(resName, resSeq, iCode);\r\n\r\n // store residue in appropriate molecule\r\n const moleculeIdx = molecules[i] - 1;\r\n let entity = this.molecules[moleculeIdx];\r\n if (!entity) { // create new molecule if it hasn't been created\r\n this.molecules[moleculeIdx] = { name: '', residues: [] };\r\n entity = this.molecules[moleculeIdx];\r\n }\r\n entity.residues.push(residue);\r\n }\r\n\r\n const name = names[i];\r\n const element = elements[i] || nameToElement(name);\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name.trim()];\r\n const xyz = new THREE.Vector3(x[i], y[i], z[i]);\r\n const het = group[i] === 'HETATM' || false;\r\n const serial = serials[i] || i;\r\n const tempFactor = tempFactors[i] || 0.0;\r\n const occupancy = occupancies[i] || 0.0;\r\n const altLoc = String(altLocs[i] || '');\r\n const charge = charges[i] || 0;\r\n\r\n residue.addAtom(\r\n name,\r\n type,\r\n xyz,\r\n role,\r\n het,\r\n serial,\r\n altLoc,\r\n occupancy,\r\n tempFactor,\r\n charge,\r\n );\r\n }\r\n }\r\n\r\n /**\r\n * Extracts secondary structure information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex - complex to fill\r\n * @param complexData - CIF complex data\r\n * @private\r\n */\r\n _extractSecondary(complex, complexData) {\r\n if (complexData.struct_conf) {\r\n this._extractConfs(complex, complexData.struct_conf);\r\n }\r\n if (complexData.struct_sheet_range) {\r\n this._extractSheets(complex, complexData.struct_sheet_range);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts sheets information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param sheetData\r\n * @private\r\n */\r\n _extractSheets(complex, sheetData) {\r\n const { asymDict } = this;\r\n if (!sheetData.sheet_id || !sheetData.id || !sheetData.beg_label_seq_id || !sheetData.end_label_seq_id\r\n || !sheetData.beg_label_asym_id) {\r\n return;\r\n }\r\n // Strand(sheet, start, end, sense, cur, prev)\r\n const sheets = complex._sheets;\r\n\r\n function getSheet(name) {\r\n const n = sheets.length;\r\n for (let i = 0; i < n; ++i) {\r\n if (sheets[i]._name === name) {\r\n return sheets[i];\r\n }\r\n }\r\n sheets[n] = new Sheet(name, 0);\r\n return sheets[n];\r\n }\r\n\r\n const sheetNames = arrize(sheetData.sheet_id);\r\n const strandNames = arrize(sheetData.id);\r\n const starts = arrize(sheetData.beg_auth_seq_id);\r\n const ends = arrize(sheetData.end_auth_seq_id);\r\n const chains = arrize(sheetData.beg_label_asym_id);\r\n const stICodes = arrize(sheetData.pdbx_beg_PDB_ins_code) || [];\r\n const endICodes = arrize(sheetData.pdbx_end_PDB_ins_code) || [];\r\n\r\n for (let i = 0, n = strandNames.length; i < n; ++i) {\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n const sheet = getSheet(sheetNames[i]);\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n\r\n const strand = new Strand(sheet, start[0], end[0], 0, null, null);\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = strand;\r\n }\r\n sheet.addStrand(strand);\r\n complex.structures.push(strand);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts helix/turn/strand(?) information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param helicesData\r\n * @private\r\n */\r\n _extractConfs(complex, helicesData) {\r\n const { asymDict } = this;\r\n if (!helicesData.conf_type_id || !helicesData.beg_label_seq_id || !helicesData.end_label_seq_id\r\n || !helicesData.beg_label_asym_id) {\r\n return;\r\n }\r\n\r\n const types = arrize(helicesData.conf_type_id);\r\n const starts = arrize(helicesData.beg_auth_seq_id);\r\n const stICodes = arrize(helicesData.pdbx_beg_PDB_ins_code) || [];\r\n const ends = arrize(helicesData.end_auth_seq_id);\r\n const endICodes = arrize(helicesData.pdbx_end_PDB_ins_code) || [];\r\n const comments = arrize(helicesData.details) || [];\r\n const lengths = arrize(helicesData.pdbx_PDB_helix_length) || [];\r\n const helixClasses = arrize(helicesData.pdbx_PDB_helix_class) || [];\r\n const names = arrize(helicesData.id) || [];\r\n const chains = arrize(helicesData.beg_label_asym_id);\r\n\r\n for (let i = 0, n = types.length; i < n; ++i) {\r\n const type = getTypeFromId(types[i]);\r\n if (!type) {\r\n continue;\r\n }\r\n const name = names[i] || types[i];\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n const comment = comments[i] || '';\r\n const length = lengths[i] || 0;\r\n const helixClass = helixClasses[i] || ' ';\r\n let struct;\r\n if (type === 'helix') {\r\n const idx = complex._helices.length;\r\n struct = new Helix(helixClass, start[0], end[0], idx, name, comment, length);\r\n complex.addHelix(struct);\r\n complex.structures.push(struct);\r\n } else if (type === 'turn') {\r\n struct = new StructuralElement(StructuralElement.Type.TURN, start[0], end[0]);\r\n complex.structures.push(struct);\r\n } else {\r\n struct = null;\r\n }\r\n if (!struct) {\r\n continue;\r\n }\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = struct;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Extract biological assemblies information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAssemblies(complex, complexData) {\r\n const { asymDict } = this;\r\n const asmGen = complexData.pdbx_struct_assembly_gen;\r\n if (!asmGen) {\r\n return;\r\n }\r\n\r\n const asmIdx = arrize(asmGen.assembly_id);\r\n const asmOper = arrize(asmGen.oper_expression);\r\n const asmList = arrize(asmGen.asym_id_list);\r\n if (!asmIdx || !asmOper || !asmList) {\r\n return;\r\n }\r\n\r\n const operList = _getOperations(complexData.pdbx_struct_oper_list);\r\n if (!operList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = asmIdx.length; i < n; ++i) {\r\n const asm = new Assembly(complex);\r\n const assemblyOps = _extractOperations(asmOper[i], operList);\r\n const entries = asmList[i].split(',');\r\n for (let ii = 0, nn = entries.length; ii < nn; ++ii) {\r\n const chain = entries[ii].trim();\r\n if (chain.length > 0) {\r\n asm.addChain(asymDict[chain]);\r\n }\r\n }\r\n asm.matrices = assemblyOps;\r\n complex.units.push(asm);\r\n }\r\n }\r\n}\r\n\r\nCIFParser.formats = ['cif', 'mmcif'];\r\nCIFParser.extensions = ['.cif', '.mmcif'];\r\n\r\nexport default CIFParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Volume from '../../chem/Volume';\r\n\r\nexport const valueType = {\r\n singular: 0,\r\n vector: 1,\r\n array: 2,\r\n buffer: 3,\r\n};\r\n\r\nclass VolumeModel {\r\n _xyz2crs = [];\r\n\r\n _origin = new THREE.Vector3(0, 0, 0);\r\n\r\n constructor() {\r\n this._header = {};\r\n this._boxSize = new THREE.Vector3();\r\n this._boxStart = new THREE.Vector3();\r\n this._header.delta = {};\r\n this._header.extent = [];\r\n this._header.nstart = [];\r\n this._header.grid = [];\r\n this._header.crs2xyz = [];\r\n this._header.cellDims = new THREE.Vector3();\r\n this._header.angles = [];\r\n this._header.origin = new THREE.Vector3(0, 0, 0);\r\n this._header.dmin = 0;\r\n this._header.dmean = 0;\r\n this._header.dmax = 0;\r\n }\r\n\r\n _typedCheck() {\r\n if (_.isTypedArray(this._buff)) {\r\n this._buff = this._buff.buffer;\r\n } else if (!_.isArrayBuffer(this._buff)) {\r\n throw new TypeError('Expected ArrayBuffer or TypedArray');\r\n }\r\n }\r\n\r\n _fillHeader(headerFormat, arrays) {\r\n for (const key in headerFormat) {\r\n if (headerFormat.hasOwnProperty(key)) {\r\n switch (headerFormat[key][0]) {\r\n case valueType.singular:\r\n this._header[key] = arrays[headerFormat[key][1]][headerFormat[key][2]];\r\n break;\r\n\r\n case valueType.array:\r\n this._parseArray(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.vector:\r\n this._parseVector(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.buffer:\r\n this._header[key] = new Uint8Array(\r\n arrays[headerFormat[key][1]],\r\n [headerFormat[key][2]] * 4,\r\n [headerFormat[key][3]] * 4,\r\n );\r\n break;\r\n\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _parseVector(vector, arr, pos) {\r\n [vector.x, vector.y, vector.z] = [arr[pos], arr[pos + 1], arr[pos + 2]];\r\n }\r\n\r\n _parseArray(vector, arr, pos) {\r\n vector[0] = arr[pos];\r\n vector[1] = arr[pos + 1];\r\n vector[2] = arr[pos + 2];\r\n }\r\n\r\n _parseHeader(_buffer) {}\r\n\r\n _setAxisIndices() {}\r\n\r\n _setOrigins() {}\r\n\r\n _getAxis() {\r\n const header = this._header;\r\n\r\n const xScale = header.cellDims.x / header.grid[0];\r\n const yScale = header.cellDims.y / header.grid[1];\r\n const zScale = header.cellDims.z / header.grid[2];\r\n\r\n const [alpha, beta, gamma] = header.angles;\r\n\r\n const z1 = Math.cos(beta);\r\n const z2 = (Math.cos(alpha) - Math.cos(beta)\r\n * Math.cos(gamma)) / Math.sin(gamma);\r\n const z3 = Math.sqrt(1.0 - z1 * z1 - z2 * z2);\r\n\r\n const xaxis = new THREE.Vector3(xScale, 0, 0);\r\n const yaxis = new THREE.Vector3(Math.cos(gamma) * yScale, Math.sin(gamma) * yScale, 0);\r\n const zaxis = new THREE.Vector3(z1 * zScale, z2 * zScale, z3 * zScale);\r\n\r\n return [xaxis, yaxis, zaxis];\r\n }\r\n\r\n _getXYZdim() {\r\n return [this._header.extent[this._xyz2crs[0]],\r\n this._header.extent[this._xyz2crs[1]],\r\n this._header.extent[this._xyz2crs[2]]];\r\n }\r\n\r\n _getVolumeInfo() {\r\n const volInfo = _.pick(this._header, ['dmean', 'dmin', 'dmax', 'sd', 'delta']);\r\n volInfo.obtuseAngle = this._header.angles.map((angle) => Number(angle >= (Math.PI / 2)));\r\n return volInfo;\r\n }\r\n\r\n _setBoxParams(xaxis, yaxis, zaxis) {\r\n // if axes are not orthogonal, the origins might not match with box coordinates - need to make shift\r\n let shiftX = 0;\r\n let shiftY = 0;\r\n const [alpha, beta, gamma] = this._header.angles;\r\n\r\n if (gamma >= Math.PI / 2) {\r\n shiftX += Math.abs(yaxis.x);\r\n }\r\n if (beta >= Math.PI / 2) {\r\n shiftX += Math.abs(zaxis.x);\r\n }\r\n if (alpha >= Math.PI / 2) {\r\n shiftY += Math.abs(zaxis.y);\r\n }\r\n\r\n this._boxStart = new THREE.Vector3(this._origin.x - shiftX, this._origin.y - shiftY, this._origin.z);\r\n this._boxSize = new THREE.Vector3(\r\n Math.abs(xaxis.x) + Math.abs(yaxis.x) + Math.abs(zaxis.x),\r\n Math.abs(yaxis.y) + Math.abs(zaxis.y),\r\n Math.abs(zaxis.z),\r\n );\r\n\r\n const delta = (axe, proj) => (Math.abs(axe[proj]) / this._boxSize[proj]);\r\n this._header.delta.x = delta(yaxis, 'x');\r\n this._header.delta.y = delta(zaxis, 'x');\r\n this._header.delta.z = delta(zaxis, 'y');\r\n }\r\n\r\n _getXYZbox() {\r\n return new THREE.Box3(this._boxStart.clone(), this._boxStart.clone().add(this._boxSize));\r\n }\r\n\r\n _toXYZData() {}\r\n\r\n parse(data) {\r\n this._parseHeader(data);\r\n this._setOrigins();\r\n return new Volume(Float32Array, this._getXYZdim(), this._getXYZbox(), 1, this._toXYZData(), this._getVolumeInfo());\r\n }\r\n}\r\n\r\nexport default VolumeModel;\r\n","import Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\nconst CCP4Header = {\r\n extent: [valueType.array, 'u32', 0],\r\n type: [valueType.singular, 'u32', 3],\r\n nstart: [valueType.array, 'i32', 4],\r\n grid: [valueType.array, 'u32', 7],\r\n cellDims: [valueType.vector, 'f32', 10],\r\n angles: [valueType.array, 'f32', 13],\r\n crs2xyz: [valueType.array, 'i32', 16],\r\n dmin: [valueType.singular, 'f32', 19],\r\n dmax: [valueType.singular, 'f32', 20],\r\n dmean: [valueType.singular, 'f32', 21],\r\n ispg: [valueType.singular, 'u32', 22],\r\n nsymbt: [valueType.singular, 'u32', 23],\r\n lksflg: [valueType.singular, 'u32', 24],\r\n customData: [valueType.buffer, 'buffer', 25, 9],\r\n origin: [valueType.vector, 'f32', 34],\r\n map: [valueType.buffer, 'buffer', 52, 1],\r\n machine: [valueType.singular, 'u32', 53],\r\n sd: [valueType.singular, 'f32', 54],\r\n nlabel: [valueType.singular, 'f32', 55],\r\n label: [valueType.buffer, 'buffer', 56, 200],\r\n};\r\n\r\nclass Ccp4Model extends VolumeModel {\r\n // read header (http://www.ccp4.ac.uk/html/maplib.html)\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n const arrays = {};\r\n arrays.u32 = new Uint32Array(this._buff, 0, 56);\r\n arrays.i32 = new Int32Array(this._buff, 0, 56);\r\n arrays.f32 = new Float32Array(this._buff, 0, 56);\r\n arrays.buffer = this._buff;\r\n const header = this._header;\r\n\r\n this._fillHeader(CCP4Header, arrays);\r\n\r\n // calculate non-orthogonal unit cell coordinates\r\n header.angles.forEach((angle, i, a) => { a[i] *= Math.PI / 180.0; });\r\n }\r\n\r\n _setAxisIndices() {\r\n const header = this._header;\r\n\r\n if (header.cellDims.x === 0.0 && header.cellDims.y === 0.0 && header.cellDims.z === 0.0) {\r\n header.cellDims.set(1.0, 1.0, 1.0);\r\n }\r\n // Apply header conversion\r\n // Mapping between CCP4 column, row, section and VMD x, y, z.\r\n const { crs2xyz } = this._header;\r\n if (crs2xyz[0] === 0 && crs2xyz[1] === 0 && crs2xyz[2] === 0) {\r\n crs2xyz[0] = 1;\r\n crs2xyz[1] = 2;\r\n crs2xyz[2] = 3;\r\n }\r\n\r\n const xyz2crs = this._xyz2crs;\r\n xyz2crs[crs2xyz[0] - 1] = 0; // column\r\n xyz2crs[crs2xyz[1] - 1] = 1; // row\r\n xyz2crs[crs2xyz[2] - 1] = 2; // section\r\n }\r\n\r\n _setOrigins() {\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n const header = this._header;\r\n const xyz2crs = this._xyz2crs;\r\n // Handle both MRC-2000 and older format maps\r\n if (header.origin.x === 0.0 && header.origin.y === 0.0 && header.origin.z === 0.0) {\r\n this._origin.addScaledVector(xaxis, header.nstart[xyz2crs[0]]);\r\n this._origin.addScaledVector(yaxis, header.nstart[xyz2crs[1]]);\r\n this._origin.addScaledVector(zaxis, header.nstart[xyz2crs[2]]);\r\n } else {\r\n this._origin = header.origin;\r\n // Use ORIGIN records rather than old n[xyz]start records\r\n // http://www2.mrc-lmb.cam.ac.uk/image2000.html\r\n // XXX the ORIGIN field is only used by the EM community, and\r\n // has undefined meaning for non-orthogonal maps and/or non-cubic voxels, etc.\r\n }\r\n xaxis.multiplyScalar(header.extent[xyz2crs[0]] - 1);\r\n yaxis.multiplyScalar(header.extent[xyz2crs[1]] - 1);\r\n zaxis.multiplyScalar(header.extent[xyz2crs[2]] - 1);\r\n\r\n if (header.type === 2) {\r\n this._data = new Float32Array(\r\n this._buff,\r\n 1024 + header.nsymbt,\r\n header.extent[0] * header.extent[1] * header.extent[2],\r\n );\r\n } else {\r\n throw new Error(`CCP4: Unsupported format ${header.type}`);\r\n }\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const data = this._data;\r\n const xyz2crs = this._xyz2crs;\r\n const xyzData = new Float32Array(data.length);\r\n\r\n const dim = this._getXYZdim();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n\r\n let crsIdx = 0;\r\n const coord = [];\r\n let x;\r\n let y;\r\n let z;\r\n for (coord[2] = 0; coord[2] < header.extent[2]; coord[2]++) { // Site\r\n for (coord[1] = 0; coord[1] < header.extent[1]; coord[1]++) { // Row\r\n for (coord[0] = 0; coord[0] < header.extent[0]; coord[0]++, crsIdx++) { // Column\r\n x = coord[xyz2crs[0]];\r\n y = coord[xyz2crs[1]];\r\n z = coord[xyz2crs[2]];\r\n xyzData[x + xSize * (y + ySize * z)] = data[crsIdx];\r\n }\r\n }\r\n }\r\n\r\n return xyzData;\r\n }\r\n}\r\n\r\nclass CCP4Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'ccp4';\r\n this.model = new Ccp4Model();\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false; // Autodetection is not implemented yet\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nCCP4Parser.formats = ['ccp4'];\r\nCCP4Parser.extensions = ['.ccp4', '.map', '.mrc'];\r\nCCP4Parser.binary = true;\r\n\r\nexport default CCP4Parser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element, Molecule } = chem;\r\n\r\nclass XYZParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n this._options.fileType = 'xyz';\r\n this._fileName = options.name;\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*\\d+ *\\n[^\\n]*\\n\\s*\\w{1,3}\\s+-?\\d/.test(data);\r\n }\r\n\r\n _parseToAtomsInf(source) {\r\n const endnAtoms = source.indexOf('\\n');\r\n const nAtoms = parseInt(source.substring(0, endnAtoms), 10);\r\n const endComment = source.indexOf('\\n', endnAtoms + 1);\r\n let comment = source.slice(endnAtoms + 1, endComment).trim();\r\n if (comment.length === 0) {\r\n comment = this._fileName;\r\n }\r\n\r\n const startAtomsInf = endComment + source.substring(endComment).search(/\\S/);\r\n this._atomsInf = source.substring(startAtomsInf).split(/[\\s,]*\\n[\\s,]*/);\r\n if (!Number.isNaN(nAtoms) && (this._atomsInf.length - 1 !== nAtoms)) {\r\n this._complex.error = {\r\n message: 'wrong number of atoms',\r\n };\r\n return;\r\n }\r\n\r\n this._complex.metadata.format = 'xyz';\r\n this._complex.name = comment;\r\n }\r\n\r\n _parseAtomsInf() {\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n\r\n const chain = this._complex.addChain('A');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0; i < this._atomsInf.length - 1; i++) {\r\n const words = this._atomsInf[i].split(/[\\s,]+/);\r\n\r\n if (words.length !== 4) {\r\n this._complex.error = {\r\n message: 'missed parameters',\r\n };\r\n break;\r\n }\r\n\r\n const serial = i + 1;\r\n const name = words[0];\r\n const xyz = new THREE.Vector3(parseFloat(words[1]), parseFloat(words[2]), parseFloat(words[3]));\r\n const type = Element.getByName(name);\r\n const role = undefined;\r\n\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n const molecule = new Molecule(this._complex, this._complex.name, 1);\r\n molecule.residues = residue;\r\n this._complex._molecules[0] = molecule;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n\r\n this._parseToAtomsInf(this._data);\r\n this._parseAtomsInf();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n return result;\r\n }\r\n\r\n static formats = ['xyz'];\r\n\r\n static extensions = ['.xyz'];\r\n}\r\n\r\nexport default XYZParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element } = chem;\r\n\r\nclass PubChemParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'pubchem+json';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && data[0] === '{';\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing PubChem JSON file...');\r\n return this._toComplex(JSON.parse(this._data));\r\n }\r\n\r\n _toComplex(jsonData) {\r\n const complex = new Complex();\r\n const complexData = jsonData.PC_Compounds && jsonData.PC_Compounds[0];\r\n if (complexData) {\r\n this._extractAtoms(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n }\r\n return complex;\r\n }\r\n\r\n _extractAtoms(complex, complexData) {\r\n let aids = complexData.atoms && complexData.atoms.aid;\r\n let elements = aids && complexData.atoms.element;\r\n if (!elements || aids.length !== elements.length) {\r\n throw new Error('Unable to parse atom elements');\r\n }\r\n elements = _.fromPairs(_.zip(aids, elements));\r\n const atoms = {};\r\n\r\n const coords = complexData.coords && complexData.coords[0];\r\n const model = coords && coords.conformers && coords.conformers[0];\r\n const xs = model && model.x;\r\n const ys = model && model.y;\r\n const zs = (model && model.z) || [];\r\n aids = coords && coords.aid;\r\n if (!aids || !xs || !ys) {\r\n throw new Error('Coordinates are not found in the file');\r\n }\r\n\r\n const chain = complex.addChain(' ');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0, n = aids.length; i < n; ++i) {\r\n const aid = aids[i];\r\n const element = Element.ByAtomicNumber[elements[aid]];\r\n const xyz = new THREE.Vector3(xs[i], ys[i], zs[i] || 0.0);\r\n atoms[aid] = residue.addAtom(element.name, element, xyz, undefined, true, aid, ' ', 1.0, 0.0, 0);\r\n }\r\n\r\n const aids1 = complexData.bonds && complexData.bonds.aid1;\r\n const aids2 = complexData.bonds && complexData.bonds.aid2;\r\n const orders = (complexData.bonds && complexData.bonds.order) || [];\r\n if (!aids1 || !aids2 || aids1.length !== aids2.length) {\r\n return;\r\n }\r\n\r\n for (let j = 0, m = aids1.length; j < m; ++j) {\r\n complex.addBond(atoms[aids1[j]], atoms[aids2[j]], orders[j] || 1, 0, true);\r\n }\r\n }\r\n}\r\n\r\nPubChemParser.formats = ['pubchem', 'pubchem+json', 'pc'];\r\nPubChemParser.extensions = ['.json'];\r\n\r\nexport default PubChemParser;\r\n","import _ from 'lodash';\r\n\r\nexport default class SDFStream {\r\n constructor(data) {\r\n this._strings = data.split(/\\r?\\n|\\r/);\r\n this._currentStart = 0;\r\n this._currentStringIndx = 0;\r\n }\r\n\r\n setStart(start) {\r\n if (start >= this._strings.length) {\r\n this._currentStart = this._strings.length - 1;\r\n this._currentStringIndx = this._strings.length - 1;\r\n } else {\r\n this._currentStart = start;\r\n this._currentStringIndx = start;\r\n }\r\n }\r\n\r\n getNextString() {\r\n return this._strings[++this._currentStringIndx];\r\n }\r\n\r\n getCurrentString() {\r\n return this._strings[this._currentStringIndx];\r\n }\r\n\r\n getStringFromStart(numb) {\r\n this._currentStringIndx = this._currentStart + numb;\r\n return this._strings[this._currentStart + numb];\r\n }\r\n\r\n findNextDataItem() {\r\n let curStr = this.getNextString();\r\n let res = false;\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n if (curStr.match(/>\\s+<(.*)>/)) {\r\n res = true;\r\n break;\r\n }\r\n curStr = this.getNextString();\r\n }\r\n\r\n return res;\r\n }\r\n\r\n findNextCompoundStart() {\r\n let curStr = this.getCurrentString();\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n curStr = this.getNextString();\r\n }\r\n this.setStart(++this._currentStringIndx);\r\n return this.probablyHaveDataToParse();\r\n }\r\n\r\n probablyHaveDataToParse() {\r\n return this._currentStringIndx < this._strings.length - 2;\r\n }\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport SDFStream from './SDFStream';\r\nimport Assembly from '../../chem/Assembly';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst chargeMap = [0, 3, 2, 1, 0, -1, -2, -3];\r\nconst orderMap = [0, 1, 2, 3, 1, 1, 1, 2];\r\nconst typeMap = [\r\n Bond.BondType.UNKNOWN, // 0 - error\r\n Bond.BondType.COVALENT, // 1 - single\r\n Bond.BondType.COVALENT, // 2 - double\r\n Bond.BondType.COVALENT, // 3 - triple\r\n Bond.BondType.AROMATIC, // 4 - aromatic\r\n Bond.BondType.UNKNOWN, // 5 - single or double\r\n Bond.BondType.AROMATIC, // 6 - single or aromatic\r\n Bond.BondType.AROMATIC, // 7 - double or aromatic\r\n // 8 - any\r\n // 9 - coordination\r\n // 10 - hydrogen\r\n];\r\n\r\nconst sdfAndMolRegexp = /.*(M\\s\\sEND).*|.*(^$$$$).*|.*>\\s+<(.+)>.*/;\r\nconst sdfRegExp = /.*($$$$).*|.*>\\s+<(.+)>.*/;\r\n\r\nconst fileFormat = { SDF: 'sdf', MOL: 'mol' };\r\n\r\nconst possibleNameTags = ['PUBCHEM_IUPAC_TRADITIONAL_NAME', /PUBCHEM_(.+)_NAME/, /(.+)name/, /(.+)NAME/];\r\nconst possibleIDTags = ['PUBCHEM_COMPOUND_CID', 'id', 'ID', /.*CID/, /.*ID/, /.*id/];\r\nconst possibleTitleTags = ['msg', 'MSG', 'message', 'title', 'description', 'desc'];\r\nconst tagsNames = ['name', 'id', 'title'];\r\nconst tags = { name: possibleNameTags, id: possibleIDTags, title: possibleTitleTags };\r\n\r\nfunction buildChainID(index) {\r\n if (!index) {\r\n return 'A';\r\n }\r\n\r\n const codes = [];\r\n while (index) {\r\n codes.push(65 + (index % 26));\r\n index = Math.trunc(index / 26);\r\n }\r\n if (codes.length > 1) {\r\n codes.reverse();\r\n codes[0] -= 1;\r\n }\r\n\r\n return String.fromCharCode(...codes);\r\n}\r\n\r\nexport default class SDFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._format = 'sdf';\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._molecules = null;\r\n this._metadata = {};\r\n this._metadata.molecules = [];\r\n this._currentMolProps = {};\r\n this._compoundIndx = -1;\r\n this._assemblies = [];\r\n this._atomsParsed = 0;\r\n this._atomsIndexes = [];\r\n }\r\n\r\n canProbablyParse(data) {\r\n return _.isString(data) && sdfAndMolRegexp.test(data);\r\n }\r\n\r\n _parseHeader(stream) {\r\n const molecule = {};\r\n molecule.name = stream.getStringFromStart(0);\r\n const date = parseInt(stream.getStringFromStart(1).substr(10, 6).trim(), 10);\r\n molecule.date = date.toString() || '';\r\n molecule.title = stream.getStringFromStart(2);\r\n this._metadata.molecules.push(molecule);\r\n }\r\n\r\n _parseAtoms(stream, atomsNum) {\r\n let curStr;\r\n let serial = this._atomsParsed;\r\n\r\n // each molecule = chain\\residue\r\n const chainID = buildChainID(this._compoundIndx);\r\n const resName = 'UNK';\r\n const resSeq = 1;\r\n\r\n this._chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = this._chain.addResidue(resName, resSeq, ' ');\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n curStr = stream.getNextString();\r\n serial++;\r\n const x = parseFloat(curStr.substr(0, 10));\r\n const y = parseFloat(curStr.substr(10, 10));\r\n const z = parseFloat(curStr.substr(20, 10));\r\n const charge = chargeMap[parseInt(curStr.substr(36, 3), 10)];\r\n const xyz = new THREE.Vector3(x, y, z);\r\n let name = curStr.substr(31, 3).trim().toUpperCase();\r\n const type = Element.getByName(name);\r\n if (!this._atomsIndexes[name]) {\r\n this._atomsIndexes[name] = 0;\r\n }\r\n this._atomsIndexes[name] += 1;\r\n name += this._atomsIndexes[name]; // every atom need to have unique name.\r\n\r\n this._residue.addAtom(name, type, xyz, undefined, true, serial, ' ', 1.0, 0.0, charge);\r\n }\r\n }\r\n\r\n _parseBonds(stream, bondsNum) {\r\n let curStr;\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n curStr = stream.getNextString();\r\n let atom1 = parseInt(curStr.substr(0, 3), 10) + this._atomsParsed;\r\n let atom2 = parseInt(curStr.substr(3, 3), 10) + this._atomsParsed;\r\n const bondType = parseInt(curStr.substr(6, 3), 10);\r\n\r\n if (atom1 > atom2) {\r\n [atom1, atom2] = [atom2, atom1];\r\n }\r\n this._complex.addBond(\r\n atom1,\r\n atom2,\r\n orderMap[bondType] || 1,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _parseMOL(stream) {\r\n this._compoundIndx++;\r\n\r\n this._parseHeader(stream);\r\n const countsLine = stream.getStringFromStart(3);\r\n const atomsNum = parseInt(countsLine.substr(0, 3), 10);\r\n const bondsNum = parseInt(countsLine.substr(3, 3), 10);\r\n this._parseAtoms(stream, atomsNum);\r\n this._parseBonds(stream, bondsNum);\r\n\r\n this._atomsParsed += atomsNum;\r\n\r\n this._metadata.molecules[this._compoundIndx]._residues = [];\r\n this._metadata.molecules[this._compoundIndx]._residues.push(this._residue);\r\n }\r\n\r\n _parseDataItem(stream) {\r\n const tag = stream.getCurrentString();\r\n\r\n let data = [];\r\n let curStr = stream.getNextString();\r\n\r\n // read data\r\n while (curStr.trim() !== '') {\r\n data.push(curStr);\r\n curStr = stream.getNextString();\r\n }\r\n if (data.length === 1) {\r\n [data] = data;\r\n }\r\n this._currentMolProps[tag.replace(/[<>]/g, '').trim()] = data;\r\n }\r\n\r\n _parseCompound(stream) {\r\n this._parseMOL(stream);\r\n\r\n // parse data items block\r\n if (this._format === fileFormat.SDF) {\r\n this._currentMolProps = {};\r\n while (stream.findNextDataItem()) {\r\n this._parseDataItem(stream);\r\n }\r\n if (Object.keys(this._currentMolProps).length !== 0) {\r\n const molecule = this._metadata.molecules[this._compoundIndx];\r\n molecule.props = this._currentMolProps;\r\n this._tryToUpdateMoleculeData(molecule);\r\n }\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n console.log('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _buildAssemblies() {\r\n const chains = this._complex._chains;\r\n\r\n if (chains.length === 1) {\r\n return this._assemblies;\r\n }\r\n\r\n for (let i = 0; i < chains.length; i++) {\r\n const assembly = new Assembly(this._complex);\r\n const matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n assembly.addChain(chains[i]._name);\r\n this._assemblies.push(assembly);\r\n }\r\n\r\n return this._assemblies;\r\n }\r\n\r\n _buildMolecules() {\r\n this._complex._molecules = [];\r\n const { molecules } = this._metadata;\r\n for (let i = 0; i < molecules.length; i++) {\r\n const molecule = new Molecule(this._complex, molecules[i].name, i + 1);\r\n molecule.residues = molecules[i]._residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n\r\n return this._complex._molecules;\r\n }\r\n\r\n _searchTag(tag, props) {\r\n for (let i = 0; i < props.length; i++) {\r\n if ((tag instanceof RegExp && tag.test(props[i].tag)) || tag === props[i].tag) {\r\n return props[i].data;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToFind(tagsList, props) {\r\n for (let j = 0; j < tagsList.length; j++) {\r\n const res = this._searchTag(tagsList[j], props);\r\n if (res) {\r\n return res;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToUpdateMoleculeData(molecule) {\r\n let res = false;\r\n for (let i = 0; i < tagsNames.length; i++) {\r\n const tagPossibleNames = tags[tagsNames[i]];\r\n const data = this._tryToFind(tagPossibleNames, molecule.props);\r\n if (data) {\r\n molecule[tagsNames[i]] = data;\r\n res = true;\r\n }\r\n }\r\n\r\n molecule.name = molecule.name || molecule.id;\r\n if (molecule.name.match(/^\\d+$/)) {\r\n molecule.name = `CID: ${molecule.name}`;\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _finalizeMetadata() {\r\n const { molecules } = this._metadata;\r\n const { metadata } = this._complex;\r\n const complex = this._complex;\r\n\r\n if (molecules.length === 1) {\r\n complex.name = molecules[0].name;\r\n metadata.title = molecules[0].title;\r\n metadata.date = molecules[0].date;\r\n metadata.properties = molecules[0].props;\r\n } else if (molecules.length > 1) {\r\n metadata.molecules = [];\r\n for (let i = 0; i < molecules.length; i++) {\r\n metadata.molecules.push({\r\n name: molecules[i].name, date: molecules[i].date, title: molecules[i].title, properties: molecules[i].props,\r\n });\r\n }\r\n }\r\n }\r\n\r\n _finalize() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n this._complex._finalizeBonds();\r\n this._fixBondsArray();\r\n this._finalizeMetadata();\r\n this._buildAssemblies();\r\n this._complex.units = this._complex.units.concat(this._assemblies);\r\n this._buildMolecules();\r\n this._complex.finalize({\r\n needAutoBonding: false, detectAromaticLoops: false, enableEditing: false, serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n defineFormat(data) {\r\n let format;\r\n if (sdfRegExp.test(data)) {\r\n format = fileFormat.SDF;\r\n } else {\r\n format = fileFormat.MOL;\r\n }\r\n\r\n return format;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const stream = new SDFStream(this._data);\r\n\r\n this._format = this.defineFormat(this._data);\r\n result.metadata.format = this._format;\r\n\r\n do {\r\n this._parseCompound(stream);\r\n } while (stream.findNextCompoundStart());\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nSDFParser.formats = ['mol', 'sdf'];\r\nSDFParser.extensions = ['.mol', '.sdf'];\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\n// http://www.uoxray.uoregon.edu/tnt/manual/node104.html\r\nconst DSN6Header = {\r\n nstart: [valueType.array, 'i16', 0],\r\n extent: [valueType.array, 'i16', 3],\r\n grid: [valueType.array, 'i16', 6],\r\n cellDims: [valueType.vector, 'i16', 9],\r\n angles: [valueType.array, 'i16', 12],\r\n div: [valueType.singular, 'i16', 15],\r\n adder: [valueType.singular, 'i16', 16],\r\n scaleFactor: [valueType.singular, 'i16', 17],\r\n};\r\n\r\nclass DSN6Model extends VolumeModel {\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n\r\n const arrays = {};\r\n arrays.i16 = new Int16Array(this._buff);\r\n\r\n // check and reverse if big endian\r\n if (arrays.i16[18] !== 100) {\r\n for (let i = 0, n = arrays.i16.length; i < n; ++i) {\r\n const val = arrays.i16[i];\r\n arrays.i16[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff);\r\n }\r\n }\r\n if (arrays.i16[18] !== 100) {\r\n throw new Error('DSN6: Incorrect format ');\r\n }\r\n\r\n const header = this._header;\r\n\r\n this._fillHeader(DSN6Header, arrays);\r\n header.cellDims.multiplyScalar(1.0 / header.scaleFactor);\r\n header.angles.forEach((angle, i, a) => { a[i] *= (Math.PI / 180.0) / header.scaleFactor; });\r\n header.div /= 100;\r\n }\r\n\r\n _setAxisIndices() {\r\n this._xyz2crs[0] = 0;\r\n this._xyz2crs[1] = 1;\r\n this._xyz2crs[2] = 2;\r\n }\r\n\r\n _setOrigins() {\r\n const header = this._header;\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n this._origin.addScaledVector(xaxis, header.nstart[0]);\r\n this._origin.addScaledVector(yaxis, header.nstart[1]);\r\n this._origin.addScaledVector(zaxis, header.nstart[2]);\r\n\r\n xaxis.multiplyScalar(header.extent[0]);\r\n yaxis.multiplyScalar(header.extent[1]);\r\n zaxis.multiplyScalar(header.extent[2]);\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _pointCalculate(xyzData, byteBuffer, z, y, x, pos, i) {\r\n const header = this._header;\r\n\r\n if (x < header.extent[0] && y < header.extent[1] && z < header.extent[2]) {\r\n const idx = x + header.extent[0] * (y + header.extent[1] * z);\r\n xyzData[idx] = (byteBuffer[pos.counter] - header.adder) / header.div;\r\n ++pos.counter;\r\n } else {\r\n pos.counter += 8 - i;\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n _blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos) {\r\n for (let k = 0; k < 8; ++k) {\r\n const z = 8 * zBlock + k;\r\n for (let j = 0; j < 8; ++j) {\r\n const y = 8 * yBlock + j;\r\n let inRange = true;\r\n let i = 0;\r\n while (inRange && i < 8) {\r\n const x = 8 * xBlock + i;\r\n inRange = this._pointCalculate(xyzData, byteBuffer, z, y, x, pos, i);\r\n i++;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const byteBuffer = new Uint8Array(this._buff);\r\n const xyzData = new Float32Array(header.extent[0] * header.extent[1] * header.extent[2]);\r\n\r\n const blocks = new THREE.Vector3(header.extent[0] / 8, header.extent[1] / 8, header.extent[2] / 8);\r\n\r\n const pos = {};\r\n pos.counter = 512;\r\n\r\n for (let zBlock = 0; zBlock < blocks.z; ++zBlock) {\r\n for (let yBlock = 0; yBlock < blocks.y; ++yBlock) {\r\n for (let xBlock = 0; xBlock < blocks.x; ++xBlock) {\r\n this._blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos);\r\n }\r\n }\r\n }\r\n this._calculateInfoParams(xyzData);\r\n return xyzData;\r\n }\r\n\r\n _calculateInfoParams(xyzData) {\r\n this._header.dmean /= xyzData.length;\r\n let dispersion = 0;\r\n let minDensity = xyzData[0];\r\n let maxDensity = xyzData[0];\r\n for (let j = 0; j < xyzData.length; j++) {\r\n dispersion += (this._header.dmean - xyzData[j]) ** 2;\r\n\r\n if (xyzData[j] < minDensity) {\r\n minDensity = xyzData[j];\r\n }\r\n if (xyzData[j] > maxDensity) {\r\n maxDensity = xyzData[j];\r\n }\r\n }\r\n this._header.sd = Math.sqrt(dispersion / xyzData.length);\r\n this._header.dmax = maxDensity;\r\n this._header.dmin = minDensity;\r\n }\r\n}\r\n\r\nclass DSN6Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'dsn6';\r\n this.model = new DSN6Model();\r\n }\r\n\r\n static canParse(data, options) {\r\n if (!data) {\r\n return false;\r\n }\r\n return data instanceof ArrayBuffer && Parser.checkDataTypeOptions(options, 'dsn6');\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false;\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nDSN6Parser.formats = ['dsn6'];\r\nDSN6Parser.extensions = ['.dsn6', '.omap'];\r\nDSN6Parser.binary = true;\r\n\r\nexport default DSN6Parser;\r\n","import PDBStream from './PDBStream';\r\n\r\n/**\r\n * Little helper class for GRO Parser usage.\r\n * @extends PDBStream\r\n */\r\nclass GROReader extends PDBStream {\r\n constructor(data) {\r\n super(data);\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n this.next();\r\n }\r\n\r\n /**\r\n * Getting end of string.\r\n * @returns {Number} Pointer to end of string\r\n */\r\n getNext() {\r\n return this._next;\r\n }\r\n}\r\n\r\nexport default GROReader;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport GROReader from './GROReader';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Molecule,\r\n} = chem;\r\n\r\n/**\r\n * Gromos87 file format parser.\r\n * @extends Parser\r\n */\r\nclass GROParser extends Parser {\r\n /**\r\n * Create parser for .gro file format\r\n *\r\n * @param {String} data Input file\r\n * @param {String} options Input options (optional field)\r\n */\r\n constructor(data, options) {\r\n super(data, options);\r\n /** @type Date */\r\n this._time = null; // Time in ps, optional field for animations\r\n /** @type Number */\r\n this._numAtoms = null; // Number of atoms in complex\r\n /** @type Number */\r\n this._residueNumber = null; // Number of exact residue\r\n /** @type String */\r\n this._residueName = ''; // Scientific name of exact residue\r\n /** @type String */\r\n this._atomName = ''; // Scientific name of exact atom\r\n /** @type Number */\r\n this._atomNumber = null; // Sorted number of exact atom\r\n /** @type Array */\r\n this._atomPosition = []; // Array which contains x, y, z position of exact atom\r\n /** @type Array */\r\n this._atomVelocity = []; // Array which contains x, y, z velocity of exact atom (optional)\r\n /** @type Complex */\r\n this._complex = null; // Complex structure for unified molecule representation\r\n /** @type Vector3 */\r\n this._molecules = []; // Molecules array\r\n /** @type Molecule */\r\n this._molecule = null; // Single molecule\r\n /** @type String */\r\n this._options.filetype = 'gro'; // Extension of data file.\r\n }\r\n\r\n /**\r\n * General check for possibility of parsing.\r\n * @param {String} data - Input file\r\n * @returns {boolean} true if this file is in ascii, false otherwise\r\n */\r\n canProbablyParse(data) {\r\n return _.isString(this._data) && /^\\s*[^\\n]*\\n\\s*\\d+ *\\n\\s*\\d+[^\\n\\d]{3}\\s*\\w+\\s*\\d+\\s*-?\\d/.test(data);\r\n }\r\n\r\n /**\r\n * Parsing title of molecule complex.\r\n * NOTE: that names are ESTIMATES, there is no strict rules in Gromos87 standard for first line in input file.\r\n * @param {GROReader} line - Line containing title and time.\r\n */\r\n _parseTitle(line) {\r\n const { metadata } = this._complex;\r\n metadata.id = line.readLine().trim();\r\n metadata.name = metadata.id.slice(metadata.id.lastIndexOf('\\\\') + 1, metadata.id.lastIndexOf('.'));\r\n metadata.format = 'gro';\r\n }\r\n\r\n /**\r\n * Parsing line containing number of atoms information.\r\n * @param {GROReader} line - Line containing number of atoms.\r\n */\r\n _parseNumberOfAtoms(line) {\r\n this._numAtoms = line.readInt(0, line.getNext());\r\n if (Number.isNaN(this._numAtoms)) {\r\n throw new Error('Line 2 is not representing atom number. Consider checking input file');\r\n }\r\n }\r\n\r\n /**\r\n * Parsing line containing information about residues, atoms etc. Also information about box vectors.\r\n * Format of atoms MUST (by Gromos87 standard) be this: (note that numbering starts not from 0, but from 1!)\r\n * ResidueNumber[1 - 5] ResidueName[6 - 10] AtomName[11 - 15] AtomNumber[16 - 20] Position[21 - 45] Velocity[46 - 69]\r\n * @param {GROReader} line - Line containing information about atom.\r\n */\r\n _parseAtom(line) {\r\n this._residueNumber = line.readInt(1, 5);\r\n this._residueName = line.readString(6, 10).trim();\r\n this._atomName = line.readString(11, 15).trim();\r\n this._atomNumber = line.readInt(16, 20);\r\n const positionX = line.readFloat(21, 28) * 10;\r\n const positionY = line.readFloat(29, 36) * 10;\r\n const positionZ = line.readFloat(37, 45) * 10;\r\n if (Number.isNaN(positionX) || Number.isNaN(positionY) || Number.isNaN(positionZ)) {\r\n this._complex.error = {\r\n message: `Atom position is invalid in \"${line.readLine()}\"`,\r\n };\r\n return;\r\n }\r\n /* const velocityX = line.readFloat(46, 53);\r\n const velocityY = line.readFloat(54, 61);\r\n const velocityZ = line.readFloat(62, 69); */\r\n /* Adding residue and atom to complex structure */\r\n const type = Element.getByName(this._atomName[0]); /* MAGIC 0. REASONS: This name is something like \"CA\", where\r\n C - is an element an A is something else. But what about Calcium? */\r\n if (type.fullName === 'Unknown') {\r\n this._complex.error = {\r\n message: `${this._atomName[0]} hasn't been recognised as an atom name.`,\r\n };\r\n return;\r\n }\r\n const role = Element.Role[this._atomName];\r\n /* Firstly, create a dummy chain */\r\n let chain = this._chain;\r\n if (!chain) {\r\n this._chain = chain = this._complex.addChain('A');\r\n }\r\n /* Secondly, add residue to that chain */\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== this._residueNumber) {\r\n this._residue = residue = chain.addResidue(this._residueName, this._residueNumber, ' ');\r\n }\r\n /* Lastly, add atom to that residue */\r\n this._atomPosition = new THREE.Vector3(positionX, positionY, positionZ);\r\n /* Adding default constants to correct atom addition process */\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n residue.addAtom(this._atomName, type, this._atomPosition, role, het, this._atomNumber, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n /**\r\n * Some finalizing procedures. In '.gro' file format there is only 1 chain and 1 molecule.\r\n */\r\n _finalize() {\r\n const molecule = new Molecule(this._complex, this._complex.metadata.name, 1);\r\n // aggregate residues from chain\r\n molecule.residues = this._chain._residues;\r\n molecule._chains = this._chain;\r\n this._complex._molecules[0] = molecule;\r\n this._molecules.push(molecule);\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n /**\r\n * Main parsing procedure.\r\n * @returns {Complex} Complex structure for visualizing.\r\n */\r\n parseSync() {\r\n /* Create \"Complex\" variable */\r\n const result = this._complex = new Complex();\r\n /* Parse input file line-by-line */\r\n const reader = new GROReader(this._data);\r\n let counter = 0; /* Simple counter regarding to format of .gro file */\r\n /* First two lines - technical information, other lines - Atoms */\r\n this._parseTitle(reader);\r\n reader.next();\r\n this._parseNumberOfAtoms(reader);\r\n reader.next();\r\n for (counter = 0; counter < this._numAtoms; ++counter) {\r\n if (!reader.end()) {\r\n this._parseAtom(reader);\r\n reader.next();\r\n } else break;\r\n }\r\n /* If number of atoms in second line is less then actual atoms in file */\r\n if (counter < this._numAtoms) {\r\n this._complex.error = {\r\n message: 'File ended unexpectedly.',\r\n };\r\n }\r\n /* Catch errors occurred in parsing process */\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n\r\n /* Finalizing data */\r\n this._finalize();\r\n\r\n /* Cleaning up */\r\n this._atomPosition = null;\r\n this._complex = null;\r\n this._molecules = null;\r\n this._molecule = null;\r\n\r\n /* Return resulting Complex variable */\r\n return result;\r\n }\r\n}\r\n\r\nGROParser.formats = ['gro'];\r\nGROParser.extensions = ['.gro'];\r\n\r\nexport default GROParser;\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst orderMap = {\r\n un: 0,\r\n 1: 1,\r\n 2: 2,\r\n 3: 3,\r\n ar: 1,\r\n am: 1,\r\n nc: 0,\r\n du: 1,\r\n};\r\nconst typeMap = {\r\n un: Bond.BondType.UNKNOWN, // unknown (cannot be determined from the parameter tables)\r\n 1: Bond.BondType.COVALENT, // single\r\n 2: Bond.BondType.COVALENT, // double\r\n 3: Bond.BondType.COVALENT, // triple\r\n ar: Bond.BondType.AROMATIC, // aromatic\r\n am: Bond.BondType.COVALENT, // amide\r\n nc: Bond.BondType.UNKNOWN, // not connected\r\n du: Bond.BondType.COVALENT, // dummy\r\n};\r\n\r\nconst resNumberRegex = /\\d+$/;\r\nconst spacesRegex = /\\s+/;\r\n\r\nfunction splitToFields(str) {\r\n return str.trim().split(spacesRegex);\r\n}\r\n/* There is no jsdoc documentation because of eslint corrections:\r\n * not all Parser methods are implemented\r\n */\r\n\r\nclass MOL2Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._compoundIndx = -1;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n\r\n this._currPosIdx = 0;\r\n this._currStartIdx = 0;\r\n\r\n this._serialAtomMap = {};\r\n\r\n this._options.fileType = 'mol2';\r\n }\r\n\r\n _parseRawStrings(data) {\r\n return data.split(/\\r?\\n|\\r/);\r\n }\r\n\r\n _toStringFromStart(numb, MOL2Data) {\r\n const newPosIdx = this._currStartIdx + numb;\r\n this._currPosIdx = (newPosIdx < MOL2Data.length) ? newPosIdx : this._currStartIdx;\r\n }\r\n\r\n _toHeaderString(header, MOL2Data) {\r\n this._toStringFromStart(0, MOL2Data);\r\n while (this._currPosIdx < MOL2Data.length) {\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`)) {\r\n return;\r\n }\r\n this._currPosIdx++;\r\n }\r\n this._toStringFromStart(0, MOL2Data);\r\n }\r\n\r\n _toStringFromHeader(header, numb, MOL2Data) {\r\n this._toHeaderString(header, MOL2Data);\r\n const newPosIdx = this._currPosIdx + numb;\r\n\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`) && newPosIdx < MOL2Data.length) {\r\n this._currPosIdx = newPosIdx;\r\n }\r\n }\r\n\r\n _setStart(startPos, MOL2Data) {\r\n if (startPos >= MOL2Data.length) {\r\n this._currStartIdx = this._currPosIdx = MOL2Data.length - 1;\r\n } else {\r\n this._currStartIdx = this._currPosIdx = startPos;\r\n }\r\n }\r\n\r\n _probablyHaveDataToParse(MOL2Data) {\r\n return this._currPosIdx < MOL2Data.length - 2;\r\n }\r\n\r\n _findNextCompoundStart(MOL2Data) {\r\n while (this._currPosIdx < MOL2Data.length && MOL2Data[this._currPosIdx].trim() !== '@MOLECULE>') {\r\n this._currPosIdx++;\r\n }\r\n this._setStart(++this._currPosIdx, MOL2Data);\r\n return this._probablyHaveDataToParse(MOL2Data);\r\n }\r\n\r\n _parseMolecule(MOL2Data) {\r\n this._toHeaderString('MOLECULE', MOL2Data);\r\n\r\n const { metadata } = this._complex;\r\n metadata.name = MOL2Data[++this._currPosIdx];\r\n metadata.format = 'mol2';\r\n\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = this._compoundIndx + 1;\r\n this._molecules.push(this._molecule);\r\n }\r\n\r\n /* Atom format description:\r\n * atomId atomName x y z element [resSeq [resName [charge [statusBit]]]]\r\n * statusBits is the internal SYBYL status bits associated with the atom.\r\n * These should never be set by the user.\r\n * Source: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf\r\n */\r\n _parseAtoms(atomsNum, MOL2Data) {\r\n this._toHeaderString('ATOM', MOL2Data);\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 6) {\r\n throw new Error('MOL2 parsing error: Not enough information to create atom!');\r\n }\r\n const atomId = parseInt(parsedStr[0], 10);\r\n const atomName = parsedStr[1];\r\n\r\n const x = parseFloat(parsedStr[2]);\r\n const y = parseFloat(parsedStr[3]);\r\n const z = parseFloat(parsedStr[4]);\r\n\r\n const element = parsedStr[5].split('.')[0].toUpperCase();\r\n\r\n let charge = 0;\r\n if (parsedStr.length >= 9) {\r\n charge = parseFloat(parsedStr[8]) || 0.0;\r\n }\r\n\r\n let chain = this._chain;\r\n if (!chain) {\r\n // .mol2 may contain information about multiple molecules, but they can't be visualized\r\n // at the same time now. There is no need to create different chain IDs then.\r\n this._chain = chain = this._complex.getChain('A') || this._complex.addChain('A');\r\n this._residue = null;\r\n }\r\n if (!this._setResidue(parsedStr)) {\r\n continue;\r\n }\r\n\r\n // These fields are not listed in mol2 format. Set them default.\r\n // Atoms and het atoms doesn't differ in .mol2,\r\n // but het atoms have special residues. It can be used in next updates\r\n const het = false;\r\n const altLoc = ' ';\r\n const occupancy = 1.0;\r\n const tempFactor = 0.0;\r\n const type = Element.getByName(element);\r\n const role = Element.Role[atomName];\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n this._residue.addAtom(atomName, type, xyz, role, het, atomId, altLoc, occupancy, tempFactor, charge);\r\n }\r\n }\r\n\r\n _setResidue(parsedStr) {\r\n let resSeq = 1;\r\n let resName = 'UNK'; // The same meaning has '<0>' in some mol2 files\r\n\r\n if (parsedStr.length >= 7) {\r\n resSeq = parseInt(parsedStr[6], 10);\r\n }\r\n if (parsedStr.length >= 8 && parsedStr[7] !== '<0>') {\r\n resName = parsedStr[7].replace(resNumberRegex, '');\r\n }\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return false;\r\n }\r\n }\r\n const residue = this._residue;\r\n const chain = this._chain;\r\n if (!residue || residue.getSequence() !== resSeq) {\r\n this._residue = chain.addResidue(resName, resSeq, 'A');\r\n }\r\n return true;\r\n }\r\n\r\n /* Bond format description\r\n * bondId originAtomId targetAtomId bondType [statusBits]\r\n */\r\n _parseBonds(bondsNum, MOL2Data) {\r\n this._toHeaderString('BOND', MOL2Data);\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 3) {\r\n throw new Error('MOL2 parsing error: Missing information about bonds!');\r\n }\r\n\r\n let originAtomId = parseInt(parsedStr[1], 10);\r\n let targetAtomId = parseInt(parsedStr[2], 10);\r\n const bondType = parsedStr[3];\r\n\r\n if (originAtomId > targetAtomId) {\r\n [originAtomId, targetAtomId] = [targetAtomId, originAtomId];\r\n }\r\n this._complex.addBond(\r\n originAtomId,\r\n targetAtomId,\r\n orderMap[bondType] || 0,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _fixSerialAtoms() {\r\n const atoms = this._complex._atoms;\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n this._serialAtomMap[atom.serial] = atom;\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n if (Object.keys(serialAtomMap).length === 0) {\r\n throw new Error('MOL2 parsing error: Missing atom information!');\r\n }\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _finalizeMolecules() {\r\n // Get chain from complex\r\n const chain = this._complex._chains[0];\r\n this._complex._molecules = [];\r\n\r\n // Aggregate residues from chains\r\n // (to be precise from the chain 'A')\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const currMolecule = this._molecules[i];\r\n const molResidues = chain._residues;\r\n const molecule = new Molecule(this._complex, currMolecule._name, i + 1);\r\n molecule.residues = molResidues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _finalize() {\r\n this._complex._finalizeBonds();\r\n this._fixSerialAtoms();\r\n this._fixBondsArray();\r\n this._finalizeMolecules();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _parseCompound(MOL2Data) {\r\n this._compoundIndx++;\r\n this._parseMolecule(MOL2Data);\r\n\r\n // Ignoring comments and everything before @MOLECULE block\r\n this._toStringFromHeader('MOLECULE', 2, MOL2Data);\r\n\r\n const parsedStr = MOL2Data[this._currPosIdx].trim().split(spacesRegex);\r\n const atomsNum = parsedStr[0];\r\n const bondsNum = parsedStr[1];\r\n\r\n this._parseAtoms(atomsNum, MOL2Data);\r\n this._parseBonds(bondsNum, MOL2Data);\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const MOL2Data = this._parseRawStrings(this._data);\r\n do {\r\n this._parseCompound(MOL2Data);\r\n } while (this._findNextCompoundStart(MOL2Data));\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nMOL2Parser.formats = ['mol2'];\r\nMOL2Parser.extensions = ['.mol2', '.ml2', '.sy2'];\r\n\r\nexport default MOL2Parser;\r\n","import ParserList from './parsers/ParserList';\r\n\r\nimport PDBParser from './parsers/PDBParser';\r\nimport CMLParser from './parsers/CMLParser';\r\nimport MMTFParser from './parsers/MMTFParser';\r\nimport CIFParser from './parsers/CIFParser';\r\nimport CCP4Parser from './parsers/CCP4Parser';\r\nimport XYZParser from './parsers/XYZParser';\r\nimport PubChemParser from './parsers/PubChemParser';\r\nimport SDFParser from './parsers/SDFParser';\r\nimport DSN6Parser from './parsers/DSN6Parser';\r\nimport GROParser from './parsers/GROParser';\r\nimport MOL2Parser from './parsers/MOL2Parser';\r\n\r\nexport default new ParserList([\r\n // note: order might be important\r\n PDBParser,\r\n CIFParser,\r\n MMTFParser,\r\n XYZParser,\r\n CMLParser,\r\n PubChemParser,\r\n SDFParser,\r\n CCP4Parser,\r\n DSN6Parser,\r\n GROParser,\r\n MOL2Parser,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available exporters.\r\n * @extends EntityList\r\n */\r\nclass ExporterList extends EntityList {\r\n /**\r\n * Create a list of exporters.\r\n * The exporters are indexed by supported data formats (`.formats` and\r\n * `.extensions` properties of a Exporter subclass).\r\n * The Exporters can be retrieved later by matching against specs (see {@link ExporterList#find}).\r\n *\r\n * @param {!Array=} someExporters A list of {@link Exporter} subclasses to\r\n * automatically register at creation time.\r\n * @see ExporterList#register\r\n */\r\n constructor(someExporters = []) {\r\n super(someExporters, ['formats']);\r\n }\r\n\r\n /**\r\n * Find a suitable exporter for data.\r\n *\r\n * @param {Object} specs Exporter specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {*=} specs.data Data to export.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ExporterList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Exporter {\r\n constructor(source, options) {\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n exportSync() {\r\n throw new Error('Exporting to this source is not implemented');\r\n }\r\n\r\n export() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Export aborted'));\r\n }\r\n return resolve(this.exportSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Exporter.prototype);\r\n","import _ from 'lodash';\r\nimport { Matrix4 } from 'three';\r\n\r\nexport default class PDBResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._currentStr = -1;\r\n this._tag = null;\r\n this._fixedNumeration = false;\r\n this._numeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n\r\n getResult() {\r\n this.writeString('\\n', 81, 81);\r\n return this._resultArray.join('');\r\n }\r\n\r\n _currentStrLength() {\r\n const curStr = this._resultArray[this._currentStr];\r\n return curStr ? curStr.length : 0;\r\n }\r\n\r\n // numeration can be number or boolean\r\n // if numeration is number then just put this number to 8-10 pos in string\r\n // if numeration is boolean then increase number for all new strings\r\n newTag(tag, numeration) {\r\n if (!tag) {\r\n this._tag = null;\r\n } else {\r\n this._tag = tag;\r\n }\r\n if (!_.isUndefined(numeration)) {\r\n if (_.isNumber(numeration)) {\r\n this._tagStrNum = numeration;\r\n this._numeration = true;\r\n this._fixedNumeration = true;\r\n } else if (_.isBoolean(numeration)) {\r\n this._tagStrNum = 0;\r\n this._numeration = numeration;\r\n this._fixedNumeration = false;\r\n }\r\n } else {\r\n this._numeration = false;\r\n this._fixedNumeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n }\r\n\r\n newString(tag) {\r\n this.writeString('\\n', 81, 81);\r\n this._currentStr++;\r\n this._resultArray.push('');\r\n\r\n if (tag) {\r\n this.writeString(tag, 1, 6);\r\n } else if (this._tag) {\r\n this.writeString(this._tag, 1, 6);\r\n }\r\n\r\n if (this._numeration) {\r\n if (!this._fixedNumeration) {\r\n this._tagStrNum++;\r\n }\r\n if (this._tagStrNum !== 1) {\r\n this.writeString(this._tagStrNum.toString(), 10, 8);\r\n }\r\n }\r\n }\r\n\r\n writeEntireString(string, maxStrPos, concat) {\r\n if (!maxStrPos) {\r\n maxStrPos = 81;\r\n }\r\n for (let j = 0; j < string.length; j++) {\r\n if (this._currentStrLength() === maxStrPos && j !== string.length - 1) {\r\n this.newString();\r\n if (concat) { // pretty hardcoddy\r\n this.writeString(concat.tag, concat.begin, concat.end);\r\n }\r\n }\r\n if (string[j] === '\\n') {\r\n this.newString();\r\n } else {\r\n this.writeString(string[j]);\r\n }\r\n }\r\n }\r\n\r\n writeString(string, begin, end) {\r\n let curStr = this._resultArray[this._currentStr];\r\n let str;\r\n\r\n const curStrLength = curStr ? curStr.length : 0;\r\n\r\n if (_.isUndefined(string)) {\r\n return;\r\n }\r\n\r\n if (!_.isNumber(begin)) {\r\n begin = curStrLength + 1;\r\n }\r\n\r\n if (!_.isNumber(end)) {\r\n end = curStrLength + string.length;\r\n }\r\n\r\n if (!_.isString(string)) {\r\n str = string.toString();\r\n } else {\r\n str = string;\r\n }\r\n\r\n const finish = begin < end ? end : begin;\r\n const start = begin < end ? begin : end;\r\n\r\n if (str.length > Math.abs(begin - end) + 1) {\r\n str = str.substr(0, Math.abs(begin - end + 1));\r\n }\r\n\r\n // spaces before start of new data\r\n if (start > curStrLength + 1) {\r\n this._resultArray[this._currentStr] += ' '.repeat(start - curStrLength - 1);\r\n } else if (start <= curStrLength) {\r\n const cStr = this._resultArray[this._currentStr];\r\n this._resultArray[this._currentStr] = cStr.slice(0, start - 1);\r\n }\r\n\r\n // if reverse order\r\n // reverse order of end and begin means that user wants to align text right\r\n if (end < begin) {\r\n const len = begin - end + 1;\r\n str = ' '.repeat(len - str.length) + str;\r\n }\r\n\r\n // some hardcode fix for space between string numeration and data\r\n // (see pdb file format description)\r\n if (start === 11 && this._numeration && this._tagStrNum !== 1) {\r\n str = ` ${str}`;\r\n }\r\n\r\n // append new data to string\r\n this._resultArray[this._currentStr] += str;\r\n curStr = this._resultArray[this._currentStr];\r\n\r\n if (finish > curStr.length) {\r\n this._resultArray[this._currentStr] += ' '.repeat(finish - curStr.length);\r\n }\r\n }\r\n\r\n writeBondsArray(bonds, atom) {\r\n const bondsArrays = this._getSubArrays(bonds, 4);\r\n\r\n for (let k = 0; k < bondsArrays.length; k++) {\r\n this.newString();\r\n this.writeString(atom.serial, 11, 7);\r\n\r\n for (let j = 0; j < bondsArrays[k].length; j++) {\r\n const serial = (bondsArrays[k][j]._left.serial === atom.serial)\r\n ? bondsArrays[k][j]._right.serial : bondsArrays[k][j]._left.serial;\r\n\r\n this.writeString(serial, 16 + 5 * j, 12 + 5 * j);\r\n }\r\n }\r\n }\r\n\r\n _getSubArrays(arr, subArraySize) {\r\n const subArrays = [];\r\n for (let i = 0; i < arr.length; i += subArraySize) {\r\n subArrays.push(arr.slice(i, i + subArraySize));\r\n }\r\n return subArrays;\r\n }\r\n\r\n // function for writing matrix in Remark290 and Remark350 tags\r\n // (see pdb file description)\r\n writeMatrix(matrix, matrixIndx, tag) {\r\n for (let j = 0; j < 3; j++) {\r\n this.newString();\r\n this.writeString(tag, 14, 18);\r\n this.writeString((j + 1).toString(), 19, 19);\r\n this.writeString(matrixIndx.toString(), 23, 20);\r\n for (let k = 0; k < 3; k++) {\r\n const numb = parseFloat(matrix.elements[j * 4 + k]).toFixed(6);\r\n this.writeString(numb.toString(), 33 + k * 10, 24 + k * 10);\r\n }\r\n\r\n const numb = parseFloat(matrix.elements[j * 4 + 3]).toFixed(5);\r\n this.writeString(numb.toString(), 68, 55);\r\n }\r\n }\r\n\r\n writeMatrices(matrices, string) {\r\n if (!matrices) {\r\n return;\r\n }\r\n const matrix = new Matrix4();\r\n for (let j = 0; j < matrices.length; j++) {\r\n matrix.copy(matrices[j]).transpose();\r\n this.writeMatrix(matrix, j + 1, string);\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport Complex from '../../chem/Complex';\r\nimport Exporter from './Exporter';\r\nimport PDBResult from './PDBResult';\r\nimport Assembly from '../../chem/Assembly';\r\nimport { typeByPDBHelixClass } from '../../chem/Helix';\r\n\r\nexport default class PDBExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n this._tags = ['HEADER', 'TITLE', 'COMPND', 'REMARK', 'HELIX', 'SHEET', 'ATOM and HETATM', 'CONECT'];\r\n this._result = null;\r\n this._tagExtractors = {\r\n HEADER: this._extractHEADER,\r\n TITLE: this._extractTITLE,\r\n 'ATOM and HETATM': this._extractATOM,\r\n CONECT: this._extractCONECT,\r\n COMPND: this._extractCOMPND,\r\n REMARK: this._extractREMARK,\r\n HELIX: this._extractHELIX,\r\n SHEET: this._extractSHEET,\r\n };\r\n this._stringForRemark350 = 'COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN\\n'\r\n + 'BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE\\n'\r\n + 'MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS\\n'\r\n + 'GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND\\n'\r\n + 'CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.';\r\n\r\n this._stringForRemark290 = 'CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS\\n'\r\n + 'THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM\\n'\r\n + 'RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY\\n'\r\n + 'RELATED MOLECULES.';\r\n }\r\n\r\n exportSync() {\r\n const result = new PDBResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n for (let i = 0; i < this._tags.length; i++) {\r\n const tag = this._tags[i];\r\n const func = this._tagExtractors[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, result);\r\n }\r\n }\r\n\r\n this._result = result.getResult();\r\n\r\n return this._result;\r\n }\r\n\r\n _extractHEADER(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n result.newTag('HEADER');\r\n result.newString();\r\n if (metadata.classification) {\r\n result.writeString(metadata.classification, 11, 50);\r\n }\r\n if (metadata.date) {\r\n result.writeString(metadata.date, 51, 59);\r\n }\r\n if (metadata.id) {\r\n result.writeString(metadata.id, 63, 66);\r\n }\r\n }\r\n\r\n _extractTITLE(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n if (!metadata.title) {\r\n return;\r\n }\r\n result.newTag('TITLE', true);\r\n for (let i = 0; i < metadata.title.length; i++) {\r\n result.newString();\r\n result.writeString(metadata.title[i], 11, 80);\r\n }\r\n }\r\n\r\n _extractCONECT(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n\r\n const atoms = this._source._atoms;\r\n result.newTag('CONECT');\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const fixedBonds = atoms[i].bonds.filter((bond) => bond._fixed);\r\n if (fixedBonds.length !== 0) {\r\n result.writeBondsArray(fixedBonds.reverse(), atoms[i]);\r\n }\r\n }\r\n }\r\n\r\n _extractSHEET(result) {\r\n if (!this._source._sheets) {\r\n return;\r\n }\r\n\r\n result.newTag('SHEET');\r\n\r\n const sheets = this._source._sheets;\r\n for (let i = 0; i < sheets.length; i++) {\r\n if (sheets[i]._strands) {\r\n const strands = sheets[i]._strands;\r\n for (let j = 0; j < strands.length; j++) {\r\n result.newString();\r\n result.writeString(j + 1, 10, 8);\r\n result.writeString(sheets[i]._name, 14, 12);\r\n result.writeString(strands.length, 16, 15);\r\n result.writeString(strands[j].init._type._name, 18, 20);\r\n result.writeString(strands[j].init._chain._name, 22, 22);\r\n result.writeString(strands[j].init._sequence, 26, 23);\r\n result.writeString(strands[j].init._icode, 27, 27);\r\n result.writeString(strands[j].term._type._name, 29, 31);\r\n result.writeString(strands[j].init._chain._name, 33, 33);\r\n result.writeString(strands[j].term._sequence, 37, 34);\r\n result.writeString(strands[j].term._icode, 38, 38);\r\n result.writeString(strands[j].sense, 40, 39);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _extractHELIX(result) {\r\n if (!this._source._helices) {\r\n return;\r\n }\r\n\r\n result.newTag('HELIX');\r\n const helices = this._source._helices;\r\n for (let i = 0; i < helices.length; i++) {\r\n const helix = helices[i];\r\n const helixClass = _.invert(typeByPDBHelixClass);\r\n result.newString();\r\n result.writeString(helix.serial, 10, 8);\r\n result.writeString(helix.name, 14, 12);\r\n result.writeString(helix.init._type._name, 16, 18);\r\n result.writeString(helix.init._chain._name, 20, 20);\r\n result.writeString(helix.init._sequence, 25, 22);\r\n result.writeString(helix.init._icode, 26, 26);\r\n result.writeString(helix.term._type._name, 28, 30);\r\n result.writeString(helix.term._chain._name, 32, 32);\r\n result.writeString(helix.term._sequence, 37, 34);\r\n result.writeString(helix.term._icode, 38, 38);\r\n result.writeString(helixClass[helix.type], 40, 39);\r\n result.writeString(helix.comment, 41, 70);\r\n result.writeString(helix.length, 76, 72);\r\n }\r\n }\r\n\r\n _extractATOM(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n const atoms = this._source._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const tag = atoms[i].het ? 'HETATM' : 'ATOM';\r\n result.newString(tag);\r\n const startIndx = (atoms[i].element.name.length > 1 || atoms[i].name.length > 3) ? 13 : 14;\r\n result.writeString(atoms[i].serial, 11, 7);\r\n result.writeString(atoms[i].name, startIndx, 16);\r\n result.writeString(String.fromCharCode(atoms[i].location), 17, 17);\r\n result.writeString(atoms[i].residue._type._name, 20, 18);\r\n result.writeString(atoms[i].residue._chain._name, 22, 22);\r\n result.writeString(atoms[i].residue._sequence, 26, 23);\r\n result.writeString(atoms[i].residue._icode, 27, 27);\r\n result.writeString(atoms[i].position.x.toFixed(3), 38, 31);\r\n result.writeString(atoms[i].position.y.toFixed(3), 46, 39);\r\n result.writeString(atoms[i].position.z.toFixed(3), 54, 47);\r\n result.writeString(atoms[i].occupancy.toFixed(2), 60, 55);\r\n result.writeString(atoms[i].temperature.toFixed(2), 66, 61);\r\n result.writeString(atoms[i].element.name, 78, 77);\r\n if (atoms[i].charge) {\r\n result.writeString(atoms[i].charge, 79, 80);\r\n }\r\n }\r\n }\r\n\r\n _extractCOMPND(result) {\r\n if (!this._source._molecules) {\r\n return;\r\n }\r\n const molecules = this._source._molecules;\r\n result.newTag('COMPND', true);\r\n\r\n for (let i = 0; i < molecules.length; i++) {\r\n const chains = this._getMoleculeChains(molecules[i]);\r\n result.newString();\r\n result.writeString(`MOL_ID: ${molecules[i].index};`, 11, 80);\r\n result.newString();\r\n result.writeString(`MOLECULE: ${molecules[i].name};`, 11, 80);\r\n result.newString();\r\n result.writeString('CHAIN: ', 11, 18);\r\n const chainsString = `${chains.join(', ')};`;\r\n result.writeEntireString(chainsString, 81);\r\n }\r\n }\r\n\r\n _extractREMARK(result) {\r\n this._Remark290(result);\r\n this._Remark350(result);\r\n }\r\n\r\n _Remark290(result) {\r\n if (!this._source.symmetry) {\r\n return;\r\n }\r\n\r\n if (this._source.symmetry.length !== 0) {\r\n const matrices = this._source.symmetry;\r\n result.newTag('REMARK', 290);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark290);\r\n result.writeMatrices(matrices, 'SMTRY');\r\n result.newString();\r\n result.newString();\r\n result.writeString('REMARK: NULL', 11, 80);\r\n }\r\n }\r\n\r\n _Remark350(result) {\r\n if (!this._source.units) {\r\n return;\r\n }\r\n const { units } = this._source;\r\n let biomolIndx = 0;\r\n\r\n result.newTag('REMARK', 350);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark350);\r\n\r\n const assemblies = units.filter((unit) => unit instanceof Assembly);\r\n\r\n for (let i = 0; i < assemblies.length; i++) {\r\n result.newString();\r\n result.newString();\r\n biomolIndx++;\r\n result.writeString(`BIOMOLECULE: ${biomolIndx}`, 11, 80);\r\n const chains = assemblies[i].chains.join(', ');\r\n result.newString();\r\n result.writeString('APPLY THE FOLLOWING TO CHAINS: ');\r\n result.writeEntireString(chains, 69, { tag: 'AND CHAINS: ', begin: 31, end: 42 });\r\n\r\n const { matrices } = assemblies[i];\r\n result.writeMatrices(matrices, 'BIOMT');\r\n }\r\n }\r\n\r\n _getMoleculeChains(molecule) {\r\n function getChainName(residue) {\r\n return residue._chain._name;\r\n }\r\n const chainNames = molecule.residues.map(getChainName);\r\n return chainNames.filter((item, pos) => chainNames.indexOf(item) === pos);\r\n }\r\n}\r\n\r\nPDBExporter.formats = ['pdb'];\r\nPDBExporter.SourceClass = Complex;\r\n","import * as THREE from 'three';\r\n\r\nconst FBX_POS_SIZE = 3;\r\nconst FBX_NORM_SIZE = 3;\r\nconst FBX_COL_SIZE = 4;\r\n\r\nfunction copyFbxPoint3(src, srcIdx, dst, dstIdx) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n}\r\n\r\nfunction copyFbxPoint4(src, srcIdx, dst, dstIdx, value) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n dst[dstIdx + 3] = value;\r\n}\r\n\r\nconst vector4 = new THREE.Vector4();\r\nfunction copyTransformedPoint3(src, srcIdx, dst, dstIdx, opts) {\r\n vector4.set(src[srcIdx], src[srcIdx + 1], src[srcIdx + 2], opts.w);\r\n vector4.applyMatrix4(opts.matrix);\r\n dst[dstIdx] = vector4.x;\r\n dst[dstIdx + 1] = vector4.y;\r\n dst[dstIdx + 2] = vector4.z;\r\n}\r\n\r\nfunction setSubArray(src, dst, count, copyFunctor, functorOpts) {\r\n if ((dst.array.length - dst.start) / dst.stride < count\r\n || (src.array.length - src.start) / src.stride < count) {\r\n return; // we've got no space\r\n }\r\n if (src.stride === dst.stride) { // stride is the same\r\n dst.array.set(src.array, dst.start);\r\n } else {\r\n let idx = dst.start;\r\n let arridx = src.start;\r\n for (let i = 0; i < count; ++i, idx += dst.stride, arridx += src.stride) {\r\n copyFunctor(src.array, arridx, dst.array, idx, functorOpts);\r\n }\r\n }\r\n}\r\n\r\nexport default class FBXModel {\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.lastPos = 0;\r\n this.lastNorm = 0;\r\n this.lastCol = 0;\r\n this.lastIdx = 0;\r\n }\r\n\r\n init(vertsCount, indsCount) {\r\n this.positions = new Float32Array(vertsCount * FBX_POS_SIZE);\r\n this.normals = new Float32Array(vertsCount * FBX_NORM_SIZE);\r\n this.colors = new Float32Array(vertsCount * FBX_COL_SIZE);\r\n this.indices = new Int32Array(indsCount);\r\n }\r\n\r\n setPositions(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.positions,\r\n start: this.lastPos,\r\n stride: FBX_POS_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setTransformedPositions(array, start, count, stride, matrix) {\r\n let idx = this.lastPos;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 1 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_POS_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.positions, idx, opts);\r\n }\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setNormals(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.normals,\r\n start: this.lastNorm,\r\n stride: FBX_NORM_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setTransformedNormals(array, start, count, stride, matrix) {\r\n let idx = this.lastNorm;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 0 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_NORM_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.normals, idx, opts);\r\n }\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setColors(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.colors,\r\n start: this.lastCol,\r\n stride: FBX_COL_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint4, 1);\r\n this.lastCol += count * FBX_COL_SIZE;\r\n }\r\n\r\n setIndices(array, start, count) {\r\n this.indices.set(array, this.lastIdx);\r\n this.lastIdx += count;\r\n }\r\n\r\n setShiftedIndices(array, count, shift) {\r\n const shifted = array.map((x) => x + shift);\r\n this.setIndices(shifted, 0, count);\r\n }\r\n\r\n getVerticesNumber() {\r\n return this.lastPos / FBX_POS_SIZE;\r\n }\r\n\r\n addInstance(matrix, geo) {\r\n // add indices at first to take old number of vertices for shift\r\n const currentCount = this.getVerticesNumber();\r\n this.setShiftedIndices(geo.indices, geo.indices.length, currentCount);\r\n // simply write vertices at empty space\r\n const size = geo.itemSize;\r\n this.setTransformedPositions(geo.positions, 0, geo.vertsCount, size.position, matrix);\r\n this.setTransformedNormals(geo.normals, 0, geo.vertsCount, size.normal, matrix);\r\n this.setColors(geo.colors, 0, geo.vertsCount, size.color);\r\n }\r\n}\r\n","/** Base class for fbx geometry contains simply organized attributes: positions+normals+colors, indices. */\r\nexport default class FBXGeometry {\r\n /**\r\n * Create a base geo with necessary members.\r\n */\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.vertsCount = 0;\r\n this.itemSize = null;\r\n }\r\n\r\n /**\r\n * Initialize base geo storing items info from attributes.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n const { attributes } = geo;\r\n // save item size\r\n this.itemSize = {\r\n position: attributes.position.itemSize,\r\n normal: attributes.normal.itemSize,\r\n color: attributes.color.itemSize,\r\n };\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes and creates colors filled with defined value.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX1CGeometry extends FBXGeometry {\r\n /**\r\n * Initialize geo storing positions, normals, indices and create colors.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n super.init(geo, _info);\r\n const {\r\n attributes: {\r\n position,\r\n normal,\r\n },\r\n index,\r\n } = geo;\r\n // copy vertices attributes\r\n this.vertsCount = position.count;\r\n this.positions = position.array;\r\n this.normals = normal.array;\r\n // create color array\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n // indices\r\n this.indices = index.array;\r\n }\r\n\r\n /**\r\n * Set defined color for all items in color attribute\r\n * @param {Object} color - THREE.Color.\r\n */\r\n setColors(color) {\r\n let offset = 0;\r\n for (let i = 0, l = this.colors.length, cl = this.itemSize.color; i < l; i += cl) {\r\n this.colors[offset++] = color.r;\r\n this.colors[offset++] = color.g;\r\n this.colors[offset++] = color.b;\r\n }\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes from cylinder geometry and creates colors filled with two\r\n * defined values.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX2CCylinder extends FBXGeometry {\r\n constructor() {\r\n super();\r\n this._cutRawStart = 0;\r\n this._cutRawEnd = 0;\r\n this._facesPerSlice = 0;\r\n }\r\n\r\n /**\r\n * Initialize geo by creating new attributes, because we extend number of vertices to make cylinder two-colored.\r\n * Indices remain the same. We process open- end close-ended cylinders and consider cylinders od 2 segments\r\n * in height ONLY.\r\n * NOTE: cylinder consists of 2 height segments and stores parts in the order: tube, topCap, bottomCap\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n * @param {Object} info - information needed for geo extend\r\n */\r\n init(geo, info) {\r\n super.init(geo, info);\r\n const {\r\n attributes: {\r\n position,\r\n },\r\n index,\r\n } = geo;\r\n // extend vertices arrays\r\n this.vertsCount = position.count + info.addPerCylinder;\r\n this._facesPerSlice = info.addPerCylinder;\r\n this.positions = new Float32Array(this.vertsCount * position.itemSize);\r\n this.normals = new Float32Array(this.vertsCount * this.itemSize.normal);\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n this._extendVertices(geo, info);\r\n // number of indices stays the same\r\n this.indices = new Uint32Array(index.count);\r\n this._extendIndices(geo, info);\r\n }\r\n\r\n /** Extend vertex attributes to have one more slice to make sharp middle startColor-endColor line. */\r\n _extendVertices(geo, info) {\r\n const { position } = geo.attributes;\r\n const { normal } = geo.attributes;\r\n const geoParams = geo.getGeoParams();\r\n const cutRaw = 1; // we expect cylinders of 2 segments in height => so half segment = 1\r\n this._cutRawStart = cutRaw * geoParams.radialSegments;\r\n this._cutRawEnd = this._cutRawStart + info.addPerCylinder;\r\n { // write first half of cylinder\r\n let temp = position.array.slice(0, this._cutRawEnd * position.itemSize);\r\n this.positions.set(temp, 0);\r\n temp = normal.array.slice(0, this._cutRawEnd * normal.itemSize);\r\n this.normals.set(temp, 0);\r\n }\r\n { // write second part of cylinder\r\n let temp = position.array.slice(this._cutRawStart * position.itemSize, position.array.length);\r\n this.positions.set(temp, this._cutRawEnd * position.itemSize);\r\n temp = normal.array.slice(this._cutRawStart * normal.itemSize, normal.array.length);\r\n this.normals.set(temp, this._cutRawEnd * normal.itemSize);\r\n }\r\n }\r\n\r\n /** Shift values of second part (+caps) indices by newly added vertices count. Number of faces remains the same. */\r\n _extendIndices(geo, info) {\r\n const { index } = geo;\r\n const indicesPerQuad = 6; // quad = 2 triangles => 6 indices\r\n const startToShift = info.addPerCylinder * indicesPerQuad;\r\n const shift = info.addPerCylinder;\r\n let shifted = index.array.slice(startToShift, index.count);\r\n shifted = shifted.map((x) => x + shift); // shift only the endings\r\n this.indices.set(index.array, 0);\r\n this.indices.set(shifted, startToShift);\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {number} start - start color index\r\n * @param {number} end - start color index\r\n * @param {array} array - array of colors\r\n * @param {array} color - color value components\r\n */\r\n _setColorRange(start, end, array, color) {\r\n const colorSize = color.length;\r\n for (let i = start; i < end; i += colorSize) {\r\n array.set(color, i);\r\n }\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {Object} color1 - THREE.Color.\r\n * @param {Object} color2 - THREE.Color.\r\n */\r\n setColors(color1, color2) {\r\n const colorSize = this.itemSize.color;\r\n const part1End = this._cutRawEnd * colorSize;\r\n const part2End = part1End * 2;\r\n this._setColorRange(0, part1End, this.colors, color1.toArray());\r\n this._setColorRange(part1End, part2End, this.colors, color2.toArray());\r\n if (part2End < this.colors.length) { // cylinder has caps, lets paint them\r\n const capSize = (this._facesPerSlice + 1) * colorSize;\r\n const cap1End = part2End + capSize;\r\n this._setColorRange(part2End, cap1End, this.colors, color2.toArray());\r\n const cap2End = cap1End + capSize; // should be equal to this.colors.length;\r\n this._setColorRange(cap1End, cap2End, this.colors, color1.toArray());\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\n\r\nimport utils from '../../../utils';\r\nimport gfxutils from '../../../gfx/gfxutils';\r\nimport logger from '../../../utils/logger';\r\n\r\nimport FBXModel from './FBXModel';\r\nimport ThickLineMesh from '../../../gfx/meshes/ThickLineMesh';\r\nimport ZSpriteMesh from '../../../gfx/meshes/ZSpriteMesh';\r\nimport InstancedSpheresGeometry from '../../../gfx/geometries/InstancedSpheresGeometry';\r\nimport Instanced2CCylindersGeometry from '../../../gfx/geometries/Instanced2CCylindersGeometry';\r\nimport FBX1CGeometry from './FBX1CGeometry';\r\nimport FBX2CCylinder from './FBX2CCylinder';\r\n\r\nexport default class FBXInfoExtractor {\r\n constructor() {\r\n this._materials = [];\r\n this._models = [];\r\n }\r\n\r\n process(data) {\r\n this._extractModelsAndMaterials(data);\r\n const models = this._flattenModels();\r\n\r\n return {\r\n name: data.name,\r\n models,\r\n materials: this._materials,\r\n };\r\n }\r\n\r\n /**\r\n * Extract fbx object information from ComplexVisual\r\n * @param {object} data - complexVisual to get geometry info from\r\n */\r\n _extractModelsAndMaterials(data) {\r\n const layersOfInterest = new THREE.Layers();\r\n layersOfInterest.set(gfxutils.LAYERS.DEFAULT);\r\n layersOfInterest.enable(gfxutils.LAYERS.TRANSPARENT);\r\n data.traverse((object) => {\r\n if (object instanceof THREE.Mesh && object.layers.test(layersOfInterest) && this.checkExportAbility(object)) {\r\n if (object.geometry.type === 'InstancedBufferGeometry') {\r\n this._collectInstancedGeoInfo(object);\r\n } else {\r\n this._collectGeoInfo(object);\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Reworking indices buffer, see https://banexdevblog.wordpress.com/2014/06/23/a-quick-tutorial-about-the-fbx-ascii-format/\r\n * basically, every triangle in Miew has been represented hat way (e.g.) : 0,1,7, but we must (for FBX) rework that\r\n * into: 0,1,-8.\r\n * @param {array} indices - belongs to [0, maxVertIndex]\r\n */\r\n _reworkIndices(indices) {\r\n const faceSize = 3;\r\n for (let i = faceSize - 1; i < indices.length; i += faceSize) {\r\n indices[i] *= -1;\r\n indices[i]--;\r\n }\r\n }\r\n\r\n /**\r\n * Combine geometry from several models having the same material into one Model and finally prepare indices\r\n * @returns {array} models, combined by material id\r\n */\r\n _flattenModels() {\r\n let overallVertsCount = 0;\r\n function shift(x) {\r\n return x + overallVertsCount;\r\n }\r\n const combined = [];\r\n // flatten models geometry\r\n for (let i = 0, n = this._models.length; i < n; i++) {\r\n const models = this._models[i];\r\n let indices = [];\r\n let positions = [];\r\n let normals = [];\r\n let colors = [];\r\n // reorganize every attributes as array of arrays\r\n overallVertsCount = 0;\r\n for (let j = 0; j < models.length; j++) {\r\n const m = models[j];\r\n indices.push(m.indices.map(shift));\r\n overallVertsCount += m.getVerticesNumber();\r\n positions.push(m.positions);\r\n normals.push(m.normals);\r\n colors.push(m.colors);\r\n }\r\n // join all subarrays into one\r\n indices = utils.mergeTypedArraysUnsafe(indices);\r\n this._reworkIndices(indices);\r\n positions = utils.mergeTypedArraysUnsafe(positions);\r\n normals = utils.mergeTypedArraysUnsafe(normals);\r\n colors = utils.mergeTypedArraysUnsafe(colors);\r\n combined.push({\r\n indices,\r\n positions,\r\n normals,\r\n colors,\r\n verticesCount: overallVertsCount,\r\n });\r\n }\r\n return combined;\r\n }\r\n\r\n /**\r\n * Check ability to export the kind of mesh.\r\n * @param {object} mesh - given mesh to check\r\n * @returns {boolean} result of check\r\n */\r\n checkExportAbility(mesh) {\r\n // check mesh on not being empty\r\n if (mesh.geometry.attributes.position.count === 0) {\r\n return false;\r\n }\r\n // check type of mesh\r\n // if (mesh.geometry.isInstancedBufferGeometry && settings.now.zSprites) {\r\n if (mesh instanceof ZSpriteMesh) {\r\n logger.warn('Currently we cannot export \\'sprites\\' modes, like BS, WV, LC. Please turn of settings \\'zSprites\\' and try again');\r\n return false;\r\n }\r\n if (mesh instanceof ThickLineMesh) {\r\n logger.warn('Currently we cannot export Lines mode');\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n /**\r\n * Save geometry info from common mesh, like Surface or Cartoon\r\n */\r\n _collectGeoInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n normal,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const vertCount = position.count;\r\n model.init(vertCount, index.count);\r\n if (matrix.isIdentity()) {\r\n model.setPositions(position.array, 0, vertCount, position.itemSize);\r\n model.setNormals(normal.array, 0, vertCount, normal.itemSize);\r\n } else {\r\n model.setTransformedPositions(position.array, 0, vertCount, position.itemSize, matrix);\r\n model.setTransformedNormals(normal.array, 0, vertCount, normal.itemSize, matrix);\r\n }\r\n model.setColors(color.array, 0, vertCount, color.itemSize);\r\n model.setIndices(index.array, 0, index.count);\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Collect instanced spheres geometry and materials.\r\n * @param {object} mesh - mesh with instanced spheres info\r\n */\r\n _collectSpheresInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount, instCount * indsCount);\r\n const geo = new FBX1CGeometry();\r\n geo.init(mesh.geometry);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const sphereColor = new THREE.Color();\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n sphereColor.fromArray(color.array, colorIdx);\r\n geo.setColors(sphereColor);\r\n // add instance to the model\r\n this._getSphereInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Getting all instanced cylinders from given mesh.\r\n * Divide cylinder (add additional vertexes) for prettiness therefore algorithm is a bit complicated\r\n * @param {object} mesh - given mesh with instanced cylinders\r\n */\r\n _collectCylindersInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n color2,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const oneCCylinder = new FBX1CGeometry();\r\n oneCCylinder.init(mesh.geometry);\r\n const splittingInfo = this._gatherCylindersColoringInfo(mesh.geometry);\r\n let twoCCylinder = null;\r\n if (splittingInfo.needToSplit > 0) {\r\n twoCCylinder = new FBX2CCylinder();\r\n twoCCylinder.init(mesh.geometry, splittingInfo);\r\n }\r\n const additionalVertsCount = splittingInfo.addPerCylinder * splittingInfo.needToSplit;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount + additionalVertsCount, instCount * indsCount);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const colorStart = new THREE.Color();\r\n const colorEnd = new THREE.Color();\r\n let geo = {};\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n if (splittingInfo.is2Colored[instanceIndex]) {\r\n // .color2 contains starting color, and .color contains starting color (see uber.frag ATTR_COLOR2)\r\n colorStart.fromArray(color2.array, colorIdx);\r\n colorEnd.fromArray(color.array, colorIdx);\r\n if (twoCCylinder) {\r\n twoCCylinder.setColors(colorStart, colorEnd);\r\n geo = twoCCylinder;\r\n }\r\n } else {\r\n // has one color per cylinder\r\n colorStart.fromArray(color.array, colorIdx);\r\n oneCCylinder.setColors(colorStart);\r\n geo = oneCCylinder;\r\n }\r\n // add instance to the model\r\n this._getCylinderInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Adding model to pool of models or extend existing ones\r\n * @param {object} model - model to add\r\n * @param {object} material - material to add\r\n */\r\n _addToPool(model, material) {\r\n const materialIdx = this._checkExistingMaterial(material);\r\n if (materialIdx < 0) { // new model-material pair\r\n this._models.push([model]);\r\n this._materials.push(material);\r\n } else { // add model to existing model-material pair\r\n const models = this._models[materialIdx];\r\n models.push(model);\r\n }\r\n }\r\n\r\n /**\r\n * Checking if given material already was registered in materials pool (no need to create new one)\r\n * @param {object} material - given material\r\n * @returns {number} number of model-material pair\r\n */\r\n _checkExistingMaterial(material) {\r\n return _.findIndex(this._materials, (m) => _.isEqual(m, material));\r\n }\r\n\r\n _gatherCylindersColoringInfo(geo) {\r\n const instCount = geo.instanceCount;\r\n const color1 = geo.attributes.color.array;\r\n const color2 = geo.attributes.color2.array;\r\n const stride = geo.attributes.color.itemSize;\r\n const is2Colored = new Array(instCount);\r\n // analyze color instance attributes\r\n let needToSplit = 0;\r\n let colIdx = 0;\r\n for (let i = 0; i < instCount; i++, colIdx += stride) {\r\n const differs = (Math.abs(color1[colIdx] - color2[colIdx]) > 0.0000001) // compare ending colors\r\n || (Math.abs(color1[colIdx + 1] - color2[colIdx + 1]) > 0.0000001)\r\n || (Math.abs(color1[colIdx + 2] - color2[colIdx + 2]) > 0.0000001);\r\n is2Colored[i] = differs;\r\n needToSplit += differs; // count number of 2-colored cylinders\r\n }\r\n // calc number of vertices to add into 2-colored\r\n const geoParams = geo.getGeoParams();\r\n const addPerCylinder = geoParams.radialSegments;\r\n return { is2Colored, needToSplit, addPerCylinder };\r\n }\r\n\r\n /**\r\n * Collect instanced models and materials.\r\n * @param {object} mesh - given mesh with instanced something (spheres or cylinders)\r\n */\r\n _collectInstancedGeoInfo(mesh) {\r\n if (mesh.geometry instanceof InstancedSpheresGeometry) {\r\n this._collectSpheresInfo(mesh);\r\n } else if (mesh.geometry instanceof Instanced2CCylindersGeometry) {\r\n this._collectCylindersInfo(mesh);\r\n }\r\n }\r\n\r\n /**\r\n * Collect Material info from given mesh.\r\n * @param {object} mesh - given mesh with material info\r\n * @returns {object} material\r\n */\r\n _collectMaterialInfo(mesh) {\r\n const { uberOptions } = mesh.material;\r\n return ({\r\n diffuse: uberOptions.diffuse.toArray(),\r\n opacity: uberOptions.opacity,\r\n shininess: uberOptions.shininess,\r\n specular: uberOptions.specular.toArray(),\r\n });\r\n }\r\n\r\n _getCylinderInstanceMatrix(geo, instIdx, matrix) {\r\n const matVector1 = geo.attributes.matVector1.array;\r\n const matVector2 = geo.attributes.matVector2.array;\r\n const matVector3 = geo.attributes.matVector3.array;\r\n const idxOffset = instIdx * 4; // used 4 because offset arrays are stored in quads\r\n matrix.set(\r\n matVector1[idxOffset],\r\n matVector1[idxOffset + 1],\r\n matVector1[idxOffset + 2],\r\n matVector1[idxOffset + 3],\r\n matVector2[idxOffset],\r\n matVector2[idxOffset + 1],\r\n matVector2[idxOffset + 2],\r\n matVector2[idxOffset + 3],\r\n matVector3[idxOffset],\r\n matVector3[idxOffset + 1],\r\n matVector3[idxOffset + 2],\r\n matVector3[idxOffset + 3],\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n\r\n _getSphereInstanceMatrix(geo, instIdx, matrix) {\r\n const { offset } = geo.attributes;\r\n const idx = instIdx * offset.itemSize;\r\n const x = offset.array[idx];\r\n const y = offset.array[idx + 1];\r\n const z = offset.array[idx + 2];\r\n const scale = offset.array[idx + 3];\r\n matrix.set(\r\n scale,\r\n 0,\r\n 0,\r\n x,\r\n 0,\r\n scale,\r\n 0,\r\n y,\r\n 0,\r\n 0,\r\n scale,\r\n z,\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n}\r\n","// Forming default definitions block\r\nconst defaultDefinitions = `\r\nDefinitions: {\r\n Version: 100\r\n Count: 3\r\n ObjectType: \"Model\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Geometry\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Material\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Pose\" {\r\n Count: 1\r\n }\r\n ObjectType: \"GlobalSettings\" {\r\n Count: 1\r\n }\r\n} `;\r\n\r\n// Default model properties\r\nconst defaultProperties = `Properties60: {\r\n Property: \"QuaternionInterpolate\", \"bool\", \"\",0\r\n Property: \"Visibility\", \"Visibility\", \"A\",1\r\n Property: \"Lcl Translation\", \"Lcl Translation\", \"A\",0.000000000000000,0.000000000000000,-1789.238037109375000\r\n Property: \"Lcl Rotation\", \"Lcl Rotation\", \"A\",0.000009334667643,-0.000000000000000,0.000000000000000\r\n Property: \"Lcl Scaling\", \"Lcl Scaling\", \"A\",1.000000000000000,1.000000000000000,1.000000000000000\r\n Property: \"RotationOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationActive\", \"bool\", \"\",0\r\n Property: \"TranslationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMinX\", \"bool\", \"\",0\r\n Property: \"TranslationMinY\", \"bool\", \"\",0\r\n Property: \"TranslationMinZ\", \"bool\", \"\",0\r\n Property: \"TranslationMaxX\", \"bool\", \"\",0\r\n Property: \"TranslationMaxY\", \"bool\", \"\",0\r\n Property: \"TranslationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationOrder\", \"enum\", \"\",0\r\n Property: \"RotationSpaceForLimitOnly\", \"bool\", \"\",0\r\n Property: \"AxisLen\", \"double\", \"\",10\r\n Property: \"PreRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"PostRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationActive\", \"bool\", \"\",0\r\n Property: \"RotationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMinX\", \"bool\", \"\",0\r\n Property: \"RotationMinY\", \"bool\", \"\",0\r\n Property: \"RotationMinZ\", \"bool\", \"\",0\r\n Property: \"RotationMaxX\", \"bool\", \"\",0\r\n Property: \"RotationMaxY\", \"bool\", \"\",0\r\n Property: \"RotationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationStiffnessX\", \"double\", \"\",0\r\n Property: \"RotationStiffnessY\", \"double\", \"\",0\r\n Property: \"RotationStiffnessZ\", \"double\", \"\",0\r\n Property: \"MinDampRangeX\", \"double\", \"\",0\r\n Property: \"MinDampRangeY\", \"double\", \"\",0\r\n Property: \"MinDampRangeZ\", \"double\", \"\",0\r\n Property: \"MaxDampRangeX\", \"double\", \"\",0\r\n Property: \"MaxDampRangeY\", \"double\", \"\",0\r\n Property: \"MaxDampRangeZ\", \"double\", \"\",0\r\n Property: \"MinDampStrengthX\", \"double\", \"\",0\r\n Property: \"MinDampStrengthY\", \"double\", \"\",0\r\n Property: \"MinDampStrengthZ\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthX\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthY\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthZ\", \"double\", \"\",0\r\n Property: \"PreferedAngleX\", \"double\", \"\",0\r\n Property: \"PreferedAngleY\", \"double\", \"\",0\r\n Property: \"PreferedAngleZ\", \"double\", \"\",0\r\n Property: \"InheritType\", \"enum\", \"\",0\r\n Property: \"ScalingActive\", \"bool\", \"\",0\r\n Property: \"ScalingMin\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMax\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMinX\", \"bool\", \"\",0\r\n Property: \"ScalingMinY\", \"bool\", \"\",0\r\n Property: \"ScalingMinZ\", \"bool\", \"\",0\r\n Property: \"ScalingMaxX\", \"bool\", \"\",0\r\n Property: \"ScalingMaxY\", \"bool\", \"\",0\r\n Property: \"ScalingMaxZ\", \"bool\", \"\",0\r\n Property: \"GeometricTranslation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricScaling\", \"Vector3D\", \"\",1,1,1\r\n Property: \"LookAtProperty\", \"object\", \"\"\r\n Property: \"UpVectorProperty\", \"object\", \"\"\r\n Property: \"Show\", \"bool\", \"\",1\r\n Property: \"NegativePercentShapeSupport\", \"bool\", \"\",1\r\n Property: \"DefaultAttributeIndex\", \"int\", \"\",0\r\n Property: \"Color\", \"Color\", \"A+\",0,0,0\r\n Property: \"Size\", \"double\", \"\",100\r\n Property: \"Look\", \"enum\", \"\",1\r\n }`;\r\n\r\n// Default materials layer\r\nconst defaultMaterialLayer = `\r\n LayerElementMaterial: 0 {\r\n Version: 101\r\n Name: \"\"\r\n MappingInformationType: \"AllSame\"\r\n ReferenceInformationType: \"Direct\"\r\n Materials: 0\r\n }`;\r\n\r\n// Default layers block\r\nconst defaultLayerBlock = `\r\n Layer: 0 {\r\n Version: 100\r\n LayerElement: {\r\n Type: \"LayerElementNormal\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementColor\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementMaterial\"\r\n TypedIndex: 0\r\n }\r\n }`;\r\n\r\n/**\r\n * globalSettings info in output file.\r\n */\r\nconst globalSettings = `GlobalSettings: {\r\n Version: 1000\r\n Properties60: {\r\n Property: \"UpAxis\", \"int\", \"\",1\r\n Property: \"UpAxisSign\", \"int\", \"\",1\r\n Property: \"FrontAxis\", \"int\", \"\",2\r\n Property: \"FrontAxisSign\", \"int\", \"\",1\r\n Property: \"CoordAxis\", \"int\", \"\",0\r\n Property: \"CoordAxisSign\", \"int\", \"\",1\r\n Property: \"UnitScaleFactor\", \"double\", \"\",1\r\n }\r\n }`;\r\n\r\nexport default class FBXResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._info = null;\r\n }\r\n\r\n getResult(info) {\r\n this._info = info;\r\n this._resultArray.push(this._writeHeader());\r\n this._resultArray.push(this._writeDefinitions());\r\n this._resultArray.push(this._writeObjects(info.models, info.materials));\r\n this._resultArray.push(this._writeRelations());\r\n this._resultArray.push(this._writeConnections()); // connections between models and materials)\r\n this._info = null;\r\n return this._resultArray.join('');\r\n }\r\n\r\n /**\r\n * Add FBXHeader info to output file.\r\n * Some fields are really confusing, but it seems that all listed fields are very informative\r\n */\r\n _writeHeader() {\r\n const FBXHeaderVersion = 1003; // 1003 is some number which appears to present in many 6.1 ASCII files\r\n const FBXVersion = 6100; // Mandatory and only supported version\r\n const date = new Date();\r\n const timeStampVersion = 1000;\r\n const creator = `Miew FBX Exporter v${this._info.version}`; // Supposed to be an engine\r\n\r\n return `; FBX 6.1.0 project file\r\n; Created by ${creator} Copyright (c) 2015-2026 EPAM Systems, Inc.\r\n; For support please contact miew@epam.com\r\n; ----------------------------------------------------\r\n\r\nFBXHeaderExtension: {\r\n FBXHeaderVersion: ${FBXHeaderVersion}\r\n FBXVersion: ${FBXVersion}\r\n CreationTimeStamp: {\r\n Version: ${timeStampVersion}\r\n Year: ${date.getFullYear()}\r\n Month: ${date.getMonth() + 1}\r\n Day: ${date.getDate()}\r\n Hour: ${date.getHours()}\r\n Minute: ${date.getMinutes()}\r\n Second: ${date.getSeconds()}\r\n Millisecond: ${date.getMilliseconds()}\r\n }\r\n Creator: \"${creator}\"\r\n OtherFlags: {\r\n FlagPLE: 0\r\n }\r\n}\r\nCreationTime: \"${date}\"\r\nCreator: \"${creator}\"\r\n`;\r\n }\r\n\r\n /**\r\n * Add Definitions info to output file.\r\n * Not exactly sure if this section is template section (as it is in 7.4+) or it should every time be like this\r\n */\r\n _writeDefinitions() {\r\n return `\r\n; Object definitions\r\n;------------------------------------------------------------------\r\n\r\n${defaultDefinitions}\r\n`;\r\n }\r\n\r\n /**\r\n * Adding gathered information about Models to resulting string.\r\n * Reminder - there may be more then 1 model in scene, but we must place materials after ALL models.\r\n * @returns {string} string containing all models (vertices, indices, colors, normals etc)\r\n */\r\n _models() {\r\n const modelVersion = 232;\r\n let allModels = '';\r\n const { models } = this._info;\r\n for (let i = 0; i < models.length; ++i) {\r\n const model = models[i];\r\n const vertCount = model.verticesCount;\r\n allModels += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n Version: ${modelVersion}\r\n ${defaultProperties}\r\n ${this._verticesIndices(model.positions, model.indices)}\r\n ${this._normalLayer(model.normals)}\r\n ${this._colorLayer(model.colors, vertCount)}\r\n ${defaultMaterialLayer}\r\n ${defaultLayerBlock}\r\n }`;\r\n }\r\n return allModels;\r\n }\r\n\r\n /**\r\n * Add Material info to result\r\n */\r\n _materials() {\r\n const materialVersion = 102;\r\n let allMaterials = '';\r\n const { materials } = this._info;\r\n for (let i = 0; i < materials.length; ++i) {\r\n const material = materials[i];\r\n allMaterials += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n Version: ${materialVersion}\r\n ShadingModel: \"lambert\"\r\n MultiLayer: 0\r\n ${this._materialProperties(material)}\r\n }`;\r\n }\r\n return allMaterials;\r\n }\r\n\r\n /**\r\n * Add Objects info to output file.\r\n */\r\n _writeObjects() {\r\n return `\r\n; Object properties\r\n;------------------------------------------------------------------\r\n\r\nObjects: {\r\n ${this._models()}\r\n ${this._materials()}\r\n ${globalSettings}\r\n}\r\n`;\r\n }\r\n\r\n /**\r\n * Add Relations info to output file.\r\n */\r\n _writeRelations() {\r\n let modelsList = '';\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n }`;\r\n }\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n }`;\r\n }\r\n\r\n return `\r\n; Object relations\r\n;------------------------------------------------------------------\r\n\r\nRelations: {\r\n ${modelsList}\r\n Model: \"Model::Producer Perspective\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Top\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Bottom\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Front\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Back\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Right\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Left\", \"Camera\" {\r\n }\r\n Model: \"Model::Camera Switcher\", \"CameraSwitcher\" {\r\n }\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Add Connections info to output file.\r\n */\r\n _writeConnections() {\r\n let modelsList = '';\r\n const { name } = this._info;\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Connect: \"OO\", \"Model::${name}_${i}\", \"Model::Scene\"`;\r\n }\r\n\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Connect: \"OO\", \"Material::${name}_${i}_default\", \"Model::${name}_${i}\"`;\r\n }\r\n\r\n return `\r\n; Object connections\r\n;------------------------------------------------------------------\r\n\r\nConnections: {\r\n ${modelsList}\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Write float array to string with limited precision\r\n * @param {Float32Array} array - array to be fixed\r\n * @returns {String} String with fixed floats\r\n */\r\n _floatArrayToString(array) {\r\n const str = [];\r\n for (let i = 0; i < array.length; ++i) {\r\n str[i] = array[i].toFixed(6);\r\n }\r\n return str.join(',');\r\n }\r\n\r\n /**\r\n * Adding color layer to resulting file\r\n * @param {Float32Array} colorArray attribute\r\n * @param {number} vertCount - number of vertices in the model\r\n * @returns {string} color layer info\r\n */\r\n _colorLayer(colorArray, vertCount) {\r\n const layerElementColorNumber = 0;\r\n const layerElementColorVersion = 101;\r\n const layerElementColorName = '';\r\n const colorsStr = this._floatArrayToString(colorArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n // As said [..Array(...)] - fastest and easiest way to produce [0, 1, .....] array\r\n const colorIndices = [...Array(vertCount).keys()];\r\n return `\r\n LayerElementColor: ${layerElementColorNumber} {\r\n Version: ${layerElementColorVersion}\r\n Name: \"${layerElementColorName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Colors: ${colorsStr}\r\n ColorIndex: ${colorIndices}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding normal layer to resulting file\r\n * @param {Float32Array} normalArray attribute\r\n * @returns {string} normal layer info\r\n */\r\n _normalLayer(normalArray) {\r\n const layerElementNormalNumber = 0;\r\n const layerElementNormalVersion = 101;\r\n const layerElementNormalName = '';\r\n const normalsStr = this._floatArrayToString(normalArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n return `\r\n LayerElementNormal: ${layerElementNormalNumber} {\r\n Version: ${layerElementNormalVersion}\r\n Name: \"${layerElementNormalName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Normals: ${normalsStr}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding vertices and indices to resulting string\r\n * @return {string} resulting string in FBX notation\r\n */\r\n _verticesIndices(positions, indices) {\r\n const multiLayer = 0;\r\n const multiTake = 1;\r\n const shading = 'Y';\r\n const culling = 'CullingOff';\r\n const geometryVersion = 124;\r\n const vertStr = this._floatArrayToString(positions);\r\n /* About _correctArrayNotation: Float32Arrays will contains only Float32 numbers, which implies that it will be floating points with 17 numbers after point.\r\n * We cannot (and it's logically incorrect) save all this information, so we convert this Float32Array into Array-like object with numbers with only 6 numbers after point\r\n * Reminder - this is big memory loss (as we must save at one moment two arrays with similar information) */\r\n return `MultiLayer: ${multiLayer}\r\n MultiTake: ${multiTake}\r\n Shading: ${shading}\r\n Culling: \"${culling}\"\r\n Vertices: ${vertStr}\r\n PolygonVertexIndex: ${indices}\r\n GeometryVersion: ${geometryVersion}`;\r\n }\r\n\r\n /**\r\n * Forming material properties block.\r\n * @param {Object} material - given material of model\r\n * @returns {String} material properties string\r\n */\r\n _materialProperties(material) {\r\n return `Properties60: {\r\n Property: \"ShadingModel\", \"KString\", \"\", \"Lambert\"\r\n Property: \"MultiLayer\", \"bool\", \"\",0\r\n Property: \"EmissiveColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"EmissiveFactor\", \"double\", \"\",0.0000\r\n Property: \"AmbientColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"AmbientFactor\", \"double\", \"\",0.0000\r\n Property: \"DiffuseColor\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"DiffuseFactor\", \"double\", \"\",1.0000\r\n Property: \"Bump\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TransparentColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"TransparencyFactor\", \"double\", \"\",0.0000\r\n Property: \"SpecularColor\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"SpecularFactor\", \"double\", \"\",1.0000\r\n Property: \"ShininessExponent\", \"double\", \"\",${material.shininess}\r\n Property: \"ReflectionColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"ReflectionFactor\", \"double\", \"\",1\r\n Property: \"Ambient\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"Diffuse\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"Specular\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"Shininess\", \"double\", \"\",${material.shininess}\r\n Property: \"Opacity\", \"double\", \"\",${material.opacity}\r\n Property: \"Reflectivity\", \"double\", \"\",0\r\n }`;\r\n }\r\n}\r\n","import Exporter from './Exporter';\r\nimport FBXInfoExtractor from './fbx/FBXInfoExtractor';\r\nimport FBXResult from './fbx/FBXResult';\r\nimport ComplexVisual from '../../ComplexVisual';\r\n\r\nexport default class FBXExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n // Data\r\n this._data = source;\r\n this._version = options.miewVersion || '0.0-UNSPECIFIED';\r\n this._extractor = new FBXInfoExtractor();\r\n }\r\n\r\n /**\r\n * Entry point to exporter.\r\n */\r\n exportSync() {\r\n // Creating mandatory blocks\r\n const result = new FBXResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n const info = this._extractor.process(this._data);\r\n info.version = this._version;\r\n this._result = result.getResult(info);\r\n return this._result;\r\n }\r\n}\r\n\r\nFBXExporter.formats = ['fbx'];\r\nFBXExporter.SourceClass = ComplexVisual;\r\n","import ExporterList from './exporters/ExporterList';\r\n\r\nimport PDBExporter from './exporters/PDBExporter';\r\nimport FBXExporter from './exporters/FBXExporter';\r\n\r\nexport default new ExporterList([\r\n PDBExporter,\r\n FBXExporter,\r\n]);\r\n","import loaders from './loaders';\r\nimport parsers from './parsers';\r\nimport exporters from './exporters';\r\n\r\nexport default {\r\n loaders,\r\n parsers,\r\n exporters,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from './CSS2DObject';\r\n\r\nconst tempColor = new THREE.Color();\r\n\r\nclass CSS2DRenderer {\r\n constructor() {\r\n this._width = 0;\r\n this._height = 0;\r\n this._widthHalf = 0;\r\n this._heightHalf = 0;\r\n\r\n this._vector = new THREE.Vector3();\r\n this._viewMatrix = new THREE.Matrix4();\r\n this._projectionMatrix = new THREE.Matrix4();\r\n\r\n this._domElement = document.createElement('div');\r\n this._domElement.style.overflow = 'hidden';\r\n this._domElement.style.position = 'absolute';\r\n this._domElement.style.top = '0';\r\n this._domElement.style.zIndex = '0'; // start a new Stacking Context to enclose all z-ordered children\r\n this._domElement.style.pointerEvents = 'none';\r\n }\r\n\r\n getElement() {\r\n return this._domElement;\r\n }\r\n\r\n reset() {\r\n const myNode = this.getElement();\r\n while (myNode.firstChild) {\r\n myNode.removeChild(myNode.firstChild);\r\n }\r\n }\r\n\r\n setSize(width, height) {\r\n this._width = width;\r\n this._height = height;\r\n\r\n this._widthHalf = this._width / 2;\r\n this._heightHalf = this._height / 2;\r\n\r\n this._domElement.style.width = `${width}px`;\r\n this._domElement.style.height = `${height}px`;\r\n }\r\n\r\n _renderObject(object, camera, scene) {\r\n function lerpColorAsHex(a, b, t) {\r\n tempColor.setHex(a);\r\n tempColor.lerp(b, t);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n function colorAsHex(a) {\r\n tempColor.setHex(a);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n if (object instanceof CSS2DObject) {\r\n this._vector.setFromMatrixPosition(object.matrixWorld);\r\n\r\n if (object.userData !== undefined && object.userData.offset !== undefined) {\r\n const localOffset = new THREE.Vector3(object.userData.offset.x, object.userData.offset.y, 0);\r\n this._vector.add(localOffset.multiplyScalar(object.matrixWorld.getMaxScaleOnAxis()));\r\n }\r\n\r\n this._vector.applyMatrix4(this._viewMatrix);\r\n\r\n const visibility = this._vector.z > -camera.near ? 'hidden' : 'visible';\r\n const zIndex = 10000 * (camera.far - (-this._vector.z)) / (camera.far - camera.near);\r\n\r\n const element = object.getElement();\r\n if (typeof scene.fog === 'undefined') {\r\n element.style.color = colorAsHex(object.userData.color);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = colorAsHex(object.userData.background);\r\n }\r\n } else {\r\n const fogFactor = THREE.MathUtils.smoothstep(-this._vector.z, scene.fog.near, scene.fog.far);\r\n element.style.color = lerpColorAsHex(object.userData.color, scene.fog.color, fogFactor);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = lerpColorAsHex(object.userData.background, scene.fog.color, fogFactor);\r\n }\r\n }\r\n\r\n this._vector.applyMatrix4(this._projectionMatrix);\r\n\r\n const style = `${object.userData !== {} ? object.userData.translation : 'translate(-50%, -50%) '\r\n }translate(${this._vector.x * this._widthHalf + this._widthHalf}px,${\r\n -this._vector.y * this._heightHalf + this._heightHalf}px)`;\r\n element.style.visibility = visibility;\r\n element.style.WebkitTransform = style;\r\n element.style.MozTransform = style;\r\n element.style.oTransform = style;\r\n element.style.transform = style;\r\n element.style.zIndex = Number(zIndex).toFixed(0);\r\n\r\n if (element.parentNode !== this._domElement) {\r\n this._domElement.appendChild(element);\r\n }\r\n }\r\n\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n this._renderObject(object.children[i], camera, scene);\r\n }\r\n }\r\n\r\n render(scene, camera) {\r\n scene.updateMatrixWorld();\r\n\r\n if (camera.parent === null) {\r\n camera.updateMatrixWorld();\r\n }\r\n\r\n camera.matrixWorldInverse.copy(camera.matrixWorld).invert();\r\n\r\n this._viewMatrix.copy(camera.matrixWorldInverse);\r\n this._projectionMatrix.copy(camera.projectionMatrix);\r\n\r\n this._renderObject(scene, camera, scene);\r\n }\r\n}\r\nexport default CSS2DRenderer;\r\n","export default function getTopWindow() {\r\n // intercept the exception if we have cross-origin iframe\r\n try {\r\n if (window.top.location.href !== undefined) {\r\n return window.top;\r\n }\r\n } catch {\r\n // provide fallback\r\n }\r\n return window;\r\n}\r\n","import * as THREE from 'three';\r\nimport Timer from '../Timer';\r\nimport settings from '../settings';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\nimport getTopWindow from '../utils/getTopWindow';\r\n\r\nconst VK_LEFT = 37;\r\nconst VK_UP = 38;\r\nconst VK_RIGHT = 39;\r\nconst VK_DOWN = 40;\r\n\r\nconst STATE = {\r\n NONE: -1, ROTATE: 0, TRANSLATE: 1, SCALE: 2, TRANSLATE_PIVOT: 3,\r\n};\r\n\r\n// pausing for this amount of time before releasing mouse button prevents inertial rotation (seconds)\r\nconst FULL_STOP_THRESHOLD = 0.1;\r\n\r\nconst quaternion = new THREE.Quaternion();\r\nconst matrix4 = new THREE.Matrix4();\r\n\r\n// pivot -- local offset of the rotation pivot point\r\nfunction ObjectHandler(objects, camera, pivot, options) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n this.camera = camera;\r\n this.pivot = pivot;\r\n this.axis = new THREE.Vector3(0, 0, 1);\r\n this.options = options;\r\n\r\n this.lastRotation = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n}\r\n\r\nObjectHandler.prototype._rotate = (function () {\r\n const p = new THREE.Vector3();\r\n const q = new THREE.Quaternion();\r\n const s = new THREE.Vector3();\r\n\r\n const m = new THREE.Matrix4();\r\n\r\n return function (quat) {\r\n const zeroPivot = (this.pivot.x === 0.0 && this.pivot.y === 0.0 && this.pivot.z === 0.0);\r\n\r\n m.copy(this.object.matrix);\r\n\r\n if (zeroPivot) {\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n } else {\r\n m.multiply(matrix4.makeTranslation(this.pivot.x, this.pivot.y, this.pivot.z));\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n m.multiply(matrix4.makeTranslation(-this.pivot.x, -this.pivot.y, -this.pivot.z));\r\n }\r\n\r\n m.decompose(p, q, s);\r\n\r\n // update objects\r\n if (!zeroPivot) {\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].position.copy(p);\r\n }\r\n }\r\n\r\n for (let j = 0; j < this.objects.length; ++j) {\r\n this.objects[j].quaternion.copy(q);\r\n this.objects[j].updateMatrix();\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.setObjects = function (objects) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n};\r\n\r\nObjectHandler.prototype.rotate = (function () {\r\n const rot = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n\r\n return function (quat, mousePrevPos, mouseCurPos, aboutAxis) {\r\n this.mouse2rotation(rot, mousePrevPos, mouseCurPos, aboutAxis);\r\n quat.setFromAxisAngle(rot.axis, rot.angle);\r\n\r\n if (rot.angle) {\r\n this._rotate(quat);\r\n }\r\n\r\n this.lastRotation = rot;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.translate = (function () {\r\n const dir = new THREE.Vector3();\r\n const pivot = new THREE.Vector3();\r\n\r\n return function (delta) {\r\n // reverse-project viewport movement to view coords (compensate for screen aspect ratio)\r\n dir.set(\r\n delta.x / this.camera.projectionMatrix.elements[0],\r\n delta.y / this.camera.projectionMatrix.elements[5],\r\n 0,\r\n );\r\n let dist = dir.length();\r\n dir.normalize();\r\n\r\n // transform movement direction to object local coords\r\n dir.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // visible translate distance shouldn't depend on camera-to-object distance\r\n pivot.copy(this.pivot);\r\n this.object.localToWorld(pivot);\r\n dist *= Math.abs(pivot.z - this.camera.position.z);\r\n\r\n // visible translate distance shouldn't depend on object scale\r\n dist /= this.object.matrixWorld.getMaxScaleOnAxis();\r\n\r\n // all objects are translated similar to principal object\r\n // (we assume they all have identical pivot and scale)\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].translateOnAxis(dir, dist);\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.update = (function () {\r\n const axis = new THREE.Vector3();\r\n\r\n return function (timeSinceLastUpdate, timeSinceMove) {\r\n if (settings.now.autoRotation !== 0.0) {\r\n // auto-rotation with constant speed\r\n\r\n // if rotation axis is fixed or hasn't been defined yet\r\n if (settings.now.autoRotationAxisFixed || this.lastRotation.axis.length() === 0.0) {\r\n // use Y-axis (transformed to local object coords)\r\n axis.set(0, 1, 0).transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n } else {\r\n // use axis defined by last user rotation\r\n axis.copy(this.lastRotation.axis);\r\n }\r\n\r\n this._rotate(quaternion.setFromAxisAngle(axis, settings.now.autoRotation * timeSinceLastUpdate));\r\n return true;\r\n }\r\n\r\n if (this.options.intertia && this.lastRotation.angle) {\r\n // inertial object rotation\r\n const angle = this.lastRotation.angle * ((1.0 - this.options.dynamicDampingFactor) ** (40.0 * timeSinceMove));\r\n\r\n if (Math.abs(angle) <= this.options.intertiaThreshold) {\r\n this.lastRotation.angle = 0.0;\r\n } else {\r\n this._rotate(quaternion.setFromAxisAngle(this.lastRotation.axis, angle));\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.stop = function () {\r\n this.lastRotation.angle = 0.0;\r\n};\r\n\r\n// calculate (axis, angle) pair from mouse/touch movement\r\nObjectHandler.prototype.mouse2rotation = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n const eye = new THREE.Vector3();\r\n const eyeDirection = new THREE.Vector3();\r\n\r\n const cameraUpDirection = new THREE.Vector3();\r\n const cameraSidewaysDirection = new THREE.Vector3();\r\n\r\n const moveDirection = new THREE.Vector3();\r\n\r\n const mouseDelta = new THREE.Vector2();\r\n\r\n return function (rot, mousePrev, mouseCur, aboutAxis) {\r\n if (aboutAxis) {\r\n rot.axis.copy(this.axis);\r\n rot.angle = this.options.axisRotateFactor * (mouseCur.y - mousePrev.y);\r\n\r\n /* cool method that allows rotation around Z axis to be \"tied\" to mouse cursor\r\n\r\n res.axis.copy(this.axis);\r\n\r\n var pivot = this.pivot.clone();\r\n this.object.localToWorld(pivot);\r\n pivot.project(this.camera);\r\n\r\n var v1 = new THREE.Vector3(mousePrev.x, mousePrev.y, this.camera.position.z);\r\n v1.sub(pivot);\r\n var v2 = new THREE.Vector3(mouseCur.x, mouseCur.y, this.camera.position.z);\r\n v2.sub(pivot);\r\n\r\n v1.sub(res.axis.clone().multiplyScalar(v1.dot(res.axis)));\r\n v2.sub(res.axis.clone().multiplyScalar(v2.dot(res.axis)));\r\n\r\n var abs = v1.length() * v2.length();\r\n if (abs > 0) {\r\n res.angle = res.axis.dot(v1.cross(v2)) / abs;\r\n }\r\n */\r\n } else {\r\n mouseDelta.subVectors(mouseCur, mousePrev);\r\n const angle = mouseDelta.length();\r\n if (angle === 0.0) {\r\n return;\r\n }\r\n\r\n center.copy(this.pivot);\r\n this.object.localToWorld(center);\r\n eye.subVectors(this.camera.position, center);\r\n eyeDirection.copy(eye).normalize();\r\n\r\n cameraUpDirection.copy(this.camera.up).normalize();\r\n cameraSidewaysDirection.crossVectors(cameraUpDirection, eyeDirection).normalize();\r\n\r\n cameraUpDirection.setLength(mouseDelta.y);\r\n cameraSidewaysDirection.setLength(mouseDelta.x);\r\n\r\n moveDirection.copy(cameraUpDirection.add(cameraSidewaysDirection));\r\n\r\n rot.axis.crossVectors(moveDirection, eye);\r\n\r\n rot.angle = -angle * this.options.rotateFactor;\r\n }\r\n\r\n rot.axis.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // make sure angle is always positive (thus 'axis' defines both axis and direction of rotation)\r\n if (rot.angle < 0.0) {\r\n rot.axis.negate();\r\n rot.angle = -rot.angle;\r\n }\r\n };\r\n}());\r\n\r\nfunction ObjectControls(object, objectPivot, camera, domElement, getAltObj) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.object = object;\r\n this.objectPivot = objectPivot;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.getAltObj = getAltObj;\r\n\r\n // API\r\n\r\n this.enabled = true;\r\n this.hotkeysEnabled = true;\r\n\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n\r\n this.options = {\r\n rotateFactor: Math.PI, // full screen slide (along short side) would roughly mean 180 deg. rotation\r\n axisRotateFactor: 4 * Math.PI, // full screen slide (along short side) would roughly mean 720 deg. rotation\r\n intertia: true,\r\n dynamicDampingFactor: 0.1,\r\n intertiaThreshold: 1e-3,\r\n };\r\n\r\n // internals\r\n\r\n this._state = STATE.NONE;\r\n\r\n this._mousePrevPos = new THREE.Vector2();\r\n this._mouseCurPos = new THREE.Vector2();\r\n\r\n this._mainObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._altObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._affectedObj = this._mainObj;\r\n this._isAltObjFreeRotationAllowed = true;\r\n this._isTranslationAllowed = true;\r\n this._isKeysTranslatingObj = false;\r\n\r\n this._pressedKeys = [];\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n this._lastUpdateTime = this._clock.getElapsedTime();\r\n\r\n // events\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousewheel',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'DOMMouseScroll',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseout',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchmove',\r\n handler(e) {\r\n self.touchmove(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keydown',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keyup',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'blur',\r\n handler() {\r\n self.resetKeys();\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'contextmenu',\r\n handler(e) {\r\n self.contextmenu(e);\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n\r\n this.resetKeys();\r\n\r\n // force an update at start\r\n this.update();\r\n}\r\n\r\n// methods\r\n\r\nObjectControls.prototype = Object.create(EventDispatcher.prototype);\r\nObjectControls.prototype.constructor = ObjectControls;\r\n\r\nObjectControls.prototype.resetKeys = function () {\r\n this._pressedKeys[VK_LEFT] = false;\r\n this._pressedKeys[VK_UP] = false;\r\n this._pressedKeys[VK_RIGHT] = false;\r\n this._pressedKeys[VK_DOWN] = false;\r\n};\r\n\r\nObjectControls.prototype.contextmenu = function (e) {\r\n e.stopPropagation();\r\n e.preventDefault();\r\n};\r\n\r\nObjectControls.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nObjectControls.prototype.enable = function (enable) {\r\n this.enabled = enable;\r\n};\r\n\r\nObjectControls.prototype.enableHotkeys = function (enable) {\r\n this.hotkeysEnabled = enable;\r\n};\r\n\r\nObjectControls.prototype.allowTranslation = function (allow) {\r\n this._isTranslationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.allowAltObjFreeRotation = function (allow) {\r\n this._isAltObjFreeRotationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.keysTranslateObj = function (on) {\r\n this._isKeysTranslatingObj = on;\r\n};\r\n\r\nObjectControls.prototype.isEditingAltObj = function () {\r\n return ((this._state === STATE.ROTATE) || (this._state === STATE.TRANSLATE))\r\n && (this._affectedObj === this._altObj);\r\n};\r\n\r\n// convert page coords of mouse/touch to uniform coords with smaller side being [-0.5, 0.5]\r\n// (uniform coords keep direct proportion with screen distance travelled by mouse regardless of screen aspect ratio)\r\nObjectControls.prototype.convertMouseToOnCircle = function (coords, pageX, pageY) {\r\n const screenSize = Math.min(this.screen.width, this.screen.height);\r\n\r\n if (screenSize === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n ((pageX - this.screen.width * 0.5 - this.screen.left) / screenSize),\r\n ((0.5 * this.screen.height + this.screen.top - pageY) / screenSize),\r\n );\r\n};\r\n\r\n// convert page coords of mouse/touch to viewport coords with both sides being [-1, 1]\r\n// (those are non-uniform coords affected by screen aspect ratio)\r\nObjectControls.prototype.convertMouseToViewport = function (coords, pageX, pageY) {\r\n if (this.screen.width === 0 || this.screen.height === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n (2.0 * (pageX - this.screen.width * 0.5 - this.screen.left) / this.screen.width),\r\n (2.0 * (0.5 * this.screen.height + this.screen.top - pageY) / this.screen.height),\r\n );\r\n};\r\n\r\nObjectControls.prototype.stop = function () {\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n};\r\n\r\n// rotate object based on latest mouse/touch movement\r\nObjectControls.prototype.rotateByMouse = (function () {\r\n const quat = new THREE.Quaternion();\r\n\r\n return function (aboutZAxis) {\r\n this._affectedObj.rotate(quat, this._mousePrevPos, this._mouseCurPos, aboutZAxis);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n };\r\n}());\r\n\r\n// rotate object by specified quaternion\r\nObjectControls.prototype.rotate = function (quat) {\r\n this.object.quaternion.multiply(quat);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n};\r\n\r\n// get object's orientation\r\nObjectControls.prototype.getOrientation = function () {\r\n return this.object.quaternion;\r\n};\r\n\r\n// set object's orientation\r\nObjectControls.prototype.setOrientation = function (quat) {\r\n this.object.quaternion.copy(quat);\r\n};\r\n\r\n// translate object based on latest mouse/touch movement\r\nObjectControls.prototype.translate = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this._affectedObj.translate(delta);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n };\r\n}());\r\n\r\n// get object scale\r\nObjectControls.prototype.getScale = function () {\r\n return this.object.scale.x;\r\n};\r\n\r\n// set uniform object scale\r\nObjectControls.prototype.setScale = function (scale) {\r\n this.object.scale.set(scale, scale, scale);\r\n};\r\n\r\n// scale object by factor (factor should be greater than zero)\r\nObjectControls.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n return;\r\n }\r\n this.setScale(this.object.scale.x * factor);\r\n this.dispatchEvent({ type: 'change', action: 'zoom', factor });\r\n};\r\n\r\nObjectControls.prototype.update = (function () {\r\n const shift = new THREE.Vector2();\r\n\r\n return function () {\r\n const curTime = this._clock.getElapsedTime();\r\n const timeSinceLastUpdate = curTime - this._lastUpdateTime;\r\n\r\n // update object handler\r\n if (this._state === STATE.NONE) {\r\n const timeSinceMove = curTime - this._lastMouseMoveTime;\r\n if (this._mainObj.update(timeSinceLastUpdate, timeSinceMove)\r\n || this._altObj.update(timeSinceLastUpdate, timeSinceMove)) {\r\n this.dispatchEvent({ type: 'change', action: 'auto' });\r\n }\r\n }\r\n\r\n // apply arrow keys\r\n if (this._isKeysTranslatingObj) {\r\n const speedX = Number(this._pressedKeys[VK_RIGHT]) - Number(this._pressedKeys[VK_LEFT]);\r\n const speedY = Number(this._pressedKeys[VK_UP]) - Number(this._pressedKeys[VK_DOWN]);\r\n if (speedX !== 0.0 || speedY !== 0.0) {\r\n const delta = timeSinceLastUpdate;\r\n\r\n // update object translation\r\n const altObj = this.getAltObj();\r\n if (altObj.objects.length > 0) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n\r\n shift.set(delta * speedX, delta * speedY);\r\n this._altObj.translate(shift);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n }\r\n }\r\n }\r\n\r\n this._lastUpdateTime = curTime;\r\n };\r\n}());\r\n\r\nObjectControls.prototype.reset = function () {\r\n this._state = STATE.NONE;\r\n\r\n this.object.quaternion.copy(quaternion.set(0, 0, 0, 1));\r\n};\r\n\r\n// listeners\r\n\r\nObjectControls.prototype.mousedown = function (event) {\r\n if (this.enabled === false || this._state !== STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (this._state === STATE.NONE) {\r\n if (event.button === 0) {\r\n this._affectedObj.stop(); // can edit only one object at a time\r\n\r\n let workWithAltObj = false;\r\n\r\n if (event.altKey) {\r\n const altObj = this.getAltObj();\r\n workWithAltObj = (altObj.objects.length > 0);\r\n if (workWithAltObj) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n this._affectedObj = workWithAltObj ? this._altObj : this._mainObj;\r\n\r\n this._state = (workWithAltObj && event.ctrlKey && this._isTranslationAllowed) ? STATE.TRANSLATE : STATE.ROTATE;\r\n } else if (event.button === 2) {\r\n this._state = STATE.TRANSLATE_PIVOT;\r\n }\r\n }\r\n\r\n if (this._state === STATE.ROTATE) {\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n\r\n if (this._state === STATE.TRANSLATE || this._state === STATE.TRANSLATE_PIVOT) {\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousemove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this.rotateByMouse((event.altKey && !this._isAltObjFreeRotationAllowed) || event.shiftKey);\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.TRANSLATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translate();\r\n break;\r\n\r\n case STATE.TRANSLATE_PIVOT:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translatePivotByMouse();\r\n break;\r\n\r\n default: break;\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousewheel = function (event) {\r\n if (this.enabled === false || !settings.now.zooming || this._state !== STATE.NONE || event.shiftKey) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n\r\n let delta = 0;\r\n\r\n if (event.wheelDelta) {\r\n // WebKit / Opera / Explorer 9\r\n delta = event.wheelDelta / 40;\r\n } else if (event.detail) {\r\n // Firefox\r\n delta = -event.detail / 3;\r\n }\r\n\r\n let factor = 1.0 + delta * 0.05;\r\n factor = Math.max(factor, 0.01);\r\n this.scale(factor);\r\n};\r\n\r\nObjectControls.prototype.mouseup = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n this._state = STATE.NONE;\r\n\r\n if (this._clock.getElapsedTime() - this._lastMouseMoveTime > FULL_STOP_THRESHOLD) {\r\n this._affectedObj.stop();\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchstartend = function (event) {\r\n if (this.enabled === false) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (event.touches.length) {\r\n case 1:\r\n this._state = STATE.ROTATE;\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n break;\r\n\r\n case 2: {\r\n // prevent inertial rotation\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n\r\n this._state = STATE.SCALE;\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = this._touchDistanceStart = Math.sqrt(dx * dx + dy * dy);\r\n this._scaleStart = this.object.scale.x;\r\n break;\r\n }\r\n\r\n default:\r\n this._state = STATE.NONE;\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchmove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this.rotateByMouse(false);\r\n\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.SCALE:\r\n if (settings.now.zooming) {\r\n // update scale\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = Math.sqrt(dx * dx + dy * dy);\r\n const newScale = this._scaleStart * this._touchDistanceCur / this._touchDistanceStart;\r\n const factor = newScale / this.object.scale.x;\r\n this.scale(factor);\r\n }\r\n break;\r\n\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.keydownup = function (event) {\r\n if (this.enabled === false || this.hotkeysEnabled === false) {\r\n return;\r\n }\r\n\r\n switch (event.keyCode) {\r\n case VK_LEFT:\r\n case VK_UP:\r\n case VK_RIGHT:\r\n case VK_DOWN:\r\n this._pressedKeys[event.keyCode] = (event.type === 'keydown');\r\n event.preventDefault();\r\n event.stopPropagation();\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.getKeyBindObject = function () {\r\n return getTopWindow();\r\n};\r\n\r\nObjectControls.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nObjectControls.prototype.translatePivotByMouse = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this.translatePivotInWorld(settings.now.translationSpeed * delta.x, settings.now.translationSpeed * delta.y, 0);\r\n };\r\n}());\r\n\r\n// Translate in WorldCS, translation is scaled with root scale matrix\r\nObjectControls.prototype.translatePivotInWorld = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.applyMatrix4(this.object.matrixWorld);\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n pos.applyMatrix4(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Translate in ModelCS, x, y, z are Ang\r\nObjectControls.prototype.translatePivot = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Set pivot\r\nObjectControls.prototype.setPivot = function (newPivot) {\r\n this.objectPivot.position.copy(newPivot);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\nexport default ObjectControls;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\nimport Timer from '../Timer';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\n\r\nfunction Picker(gfxObj, camera, domElement) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.gfxObj = gfxObj;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n this._lastMousePos = new THREE.Vector2(0, 0);\r\n this._mouseTotalDist = 0.0;\r\n this._lastClickBeginTime = -1000.0;\r\n this._lastClickPos = new THREE.Vector2(0, 0);\r\n this._clickBeginTime = 0.0;\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstart(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchend(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n}\r\n\r\nPicker.prototype = Object.create(EventDispatcher.prototype);\r\nPicker.prototype.constructor = Picker;\r\n\r\nPicker.prototype.reset = function () {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n};\r\n\r\nPicker.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nPicker.prototype.pickObject = function (screenPos) {\r\n if (!this.gfxObj) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n const { gfxObj } = this;\r\n const rayCaster = new THREE.Raycaster();\r\n rayCaster.ray.origin.setFromMatrixPosition(this.camera.matrixWorld);\r\n rayCaster.ray.direction.set(screenPos.x, screenPos.y, 0.5).unproject(this.camera).sub(rayCaster.ray.origin).normalize();\r\n\r\n const clipPlane = (settings.now.draft.clipPlane && this.clipPlaneValue) ? this.clipPlaneValue : Infinity;\r\n const fogFarPlane = (settings.now.fog && this.fogFarValue) ? this.fogFarValue : Infinity;\r\n const point = rayCaster.intersectVisibleObject(gfxObj, this.camera, clipPlane, fogFarPlane);\r\n if (!point) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n let picked = {};\r\n if (point.residue || point.atom) {\r\n const residue = point.residue || point.atom.residue;\r\n if (settings.now.pick === 'chain') {\r\n picked = { chain: residue.getChain() };\r\n } else if (settings.now.pick === 'molecule') {\r\n picked = { molecule: residue.getMolecule() };\r\n } else if (point.residue || settings.now.pick === 'residue') {\r\n picked = { residue };\r\n } else if (point.atom) {\r\n picked = { atom: point.atom };\r\n }\r\n }\r\n this.picked = picked;\r\n this.dispatchEvent({ type: 'newpick', obj: picked });\r\n};\r\n\r\nPicker.prototype.getMouseInViewport = function (pageX, pageY) {\r\n return new THREE.Vector2(\r\n (pageX - this.screen.left) / this.screen.width * 2 - 1,\r\n -(pageY - this.screen.top) / this.screen.height * 2 + 1,\r\n );\r\n};\r\n\r\nPicker.prototype.mousedown = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n this._lastMousePos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist = 0.0;\r\n this._clickBeginTime = this._clock.getElapsedTime();\r\n }\r\n};\r\n\r\nPicker.prototype.mousemove = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n const pos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist += pos.sub(this._lastMousePos).length();\r\n};\r\n\r\nPicker.prototype.mouseup = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n if (this._mouseTotalDist < 0.01) {\r\n const curTime = this._clock.getElapsedTime();\r\n const curPos = this.getMouseInViewport(event.pageX, event.pageY);\r\n\r\n const timeSinceLastClickBegin = curTime - this._lastClickBeginTime;\r\n if (timeSinceLastClickBegin < 0.7) {\r\n const clickDist = new THREE.Vector2().subVectors(curPos, this._lastClickPos);\r\n if (clickDist.length() < 0.01) {\r\n // it's a double click\r\n this.dispatchEvent({ type: 'dblclick', obj: this.picked });\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = -1000; // this click cannot serve as first click in double-click\r\n return;\r\n }\r\n }\r\n\r\n setTimeout(() => {\r\n self.pickObject(curPos);\r\n }, 0);\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = this._clickBeginTime;\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.touchstart = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 1) {\r\n this._lastTouchdownPos = this.getMouseInViewport(event.touches[0].pageX, event.touches[0].pageY);\r\n }\r\n};\r\n\r\nPicker.prototype.touchend = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 0\r\n && event.changedTouches.length === 1) {\r\n const pos = this.getMouseInViewport(event.changedTouches[0].pageX, event.changedTouches[0].pageY);\r\n const dist = pos.sub(this._lastTouchdownPos).length();\r\n if (dist < 0.01) {\r\n setTimeout(() => {\r\n self.pickObject(self._lastTouchdownPos);\r\n }, 0);\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nexport default Picker;\r\n","import * as THREE from 'three';\r\n\r\nclass Axes {\r\n constructor(target, targetCamera) {\r\n this._target = target;\r\n this._targetCamera = targetCamera;\r\n this._camera = new THREE.PerspectiveCamera(targetCamera.fov, targetCamera.aspect, 1, 100);\r\n this._object = new THREE.AxesHelper(1);\r\n this._scene = new THREE.Scene();\r\n this._scene.add(this._object);\r\n this._full = new THREE.Vector2();\r\n\r\n this._update();\r\n }\r\n\r\n _update() {\r\n const { fov } = this._targetCamera;\r\n const camera = this._camera;\r\n camera.aspect = this._targetCamera.aspect;\r\n camera.setMinimalFov(fov);\r\n camera.setDistanceToFit(1.0, fov);\r\n camera.updateProjectionMatrix();\r\n\r\n this._object.quaternion.copy(this._target.quaternion);\r\n }\r\n\r\n render(renderer) {\r\n this._update();\r\n\r\n renderer.getSize(this._full);\r\n const width = this._full.width * 0.25;\r\n const height = this._full.height * 0.25;\r\n\r\n const { autoClear } = renderer;\r\n renderer.autoClear = false;\r\n renderer.setViewport(0.0, 0.0, width, height);\r\n renderer.clear(false, true, false);\r\n renderer.render(this._scene, this._camera);\r\n renderer.setViewport(0, 0, this._full.width, this._full.height);\r\n renderer.autoClear = autoClear;\r\n }\r\n}\r\nexport default Axes;\r\n","import * as THREE from 'three';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\n\r\nconst cDataOffset = 12;\r\nconst cFirstMask = 0x0FFFFF00;\r\nconst cFirstShift = 8;\r\nconst cSecMask1 = 0x000000FF;\r\nconst cSecShift1 = 12;\r\nconst cSecMask2 = 0xFFF00000;\r\nconst cSecShift2 = 20;\r\nconst cThirdMask = 0x000FFFFF;\r\nconst cStrMask = 0xF0000000;\r\nconst cStrShift = 28;\r\nconst c219 = 1 << 19;\r\nconst c220 = 1 << 20;\r\n\r\nconst cHelixIdx = 1;\r\nconst cSheetIdx = 2;\r\nconst secTypes = ['helix', 'strand'];\r\nconst cSecNames = ['fs', 'ps', 'ns', 'us'];\r\n\r\nfunction _createSecondary(strArray, complex) {\r\n const residues = complex._residues;\r\n const nRes = residues.length;\r\n const resid = new Uint8Array(nRes);\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, n = strArray.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n resid[atom.residue._index] = strArray[i];\r\n }\r\n\r\n const secondary = [];\r\n let rIdx = 0;\r\n while (rIdx < nRes) {\r\n if (resid[rIdx] !== 0) {\r\n const start = rIdx;\r\n const val = resid[rIdx];\r\n while (rIdx < nRes - 1 && resid[rIdx + 1] === val\r\n && residues[rIdx].isConnected(residues[rIdx + 1])) {\r\n ++rIdx;\r\n }\r\n secondary.push({ start, end: rIdx, type: secTypes[val - 1] });\r\n }\r\n ++rIdx;\r\n }\r\n return secondary;\r\n}\r\n\r\nfunction fromUInt20ToInt20(uint20) {\r\n return uint20 >= c219 ? uint20 - c220 : uint20;\r\n}\r\n\r\nclass FrameInfo {\r\n constructor(complex, payload, callbacks) {\r\n this._complex = complex;\r\n this._secondary = null;\r\n this.isLoading = false;\r\n this._framesRange = {\r\n start: 0,\r\n end: -1,\r\n };\r\n this.frameIsReady = false;\r\n this._buffer = null;\r\n this._frameRequest = null;\r\n this._callbacks = callbacks;\r\n if (typeof payload === 'function') {\r\n this._framesRequestLength = 1;\r\n this._downloadDataFn = payload;\r\n } else {\r\n this.parseBinaryData(payload, true);\r\n }\r\n this.reset();\r\n this.setFrame(0);\r\n }\r\n\r\n _prepareBuffer(framesStart, framesEnd) {\r\n if (framesStart === undefined || framesStart === null) {\r\n framesStart = 0;\r\n }\r\n if (framesEnd === undefined || framesEnd === null) {\r\n framesEnd = framesStart + this._framesRequestLength;\r\n }\r\n if (this._framesCount !== undefined) {\r\n framesEnd = Math.min(this._framesCount - 1, framesEnd);\r\n }\r\n if (this._downloadDataFn) {\r\n const self = this;\r\n const onDone = function (data) {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n self._buffer = {\r\n data,\r\n state: 'ready',\r\n start: framesStart,\r\n end: framesEnd,\r\n };\r\n if (self._frameRequest !== null) {\r\n const idx = self._frameRequest;\r\n self._frameRequest = null;\r\n self.setFrame(idx);\r\n }\r\n };\r\n const onFail = function () {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onError === 'function') {\r\n self._callbacks.onError('Streaming failed');\r\n }\r\n };\r\n if (!this._buffer) {\r\n this._buffer = {};\r\n }\r\n this._buffer.state = 'downloading';\r\n this.isLoading = true;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n this._downloadDataFn({ start: framesStart, end: framesEnd + 1 }, onDone, onFail);\r\n }\r\n }\r\n\r\n _parseBuffer() {\r\n if (this._buffer && this._buffer.state === 'ready') {\r\n this._framesRange = {\r\n start: this._buffer.start,\r\n end: this._buffer.end,\r\n };\r\n this.parseBinaryData(this._buffer.data, false);\r\n let _bufferRequestStart = (this._buffer.end + 1) % this._framesCount;\r\n if (_bufferRequestStart >= this._framesCount) {\r\n _bufferRequestStart = 0;\r\n }\r\n this._buffer = {\r\n state: 'none',\r\n };\r\n this._prepareBuffer(_bufferRequestStart, _bufferRequestStart + this._framesRequestLength);\r\n if (this._frameRequest !== null) {\r\n const idx = this._frameRequest;\r\n this._frameRequest = null;\r\n this.setFrame(idx);\r\n }\r\n }\r\n }\r\n\r\n parseBinaryData(arrayBuffer) {\r\n const dataView = new DataView(arrayBuffer);\r\n let offset = 0;\r\n const atomsCount = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const framesCount = dataView.getUint32(offset, true);\r\n this._framesCount = framesCount;\r\n this._framesRange.end = this._framesRange.end > 0\r\n ? Math.min(this._framesRange.end, framesCount - 1) : framesCount - 1;\r\n offset += 4;\r\n this._atomsCount = atomsCount;\r\n const maxSize = 1024 * 1024; // 1 MB\r\n this._framesRequestLength = Math.ceil(maxSize / (atomsCount * 8));\r\n const chunkedFramesCount = this._framesRange.end - this._framesRange.start + 1;\r\n if (atomsCount !== this._complex._atoms.length\r\n || arrayBuffer.byteLength !== cDataOffset + chunkedFramesCount * atomsCount * 8) {\r\n throw new Error();\r\n }\r\n const complex = this._complex;\r\n let timeStep = dataView.getUint32(offset, true);\r\n let iName = 0;\r\n while (timeStep > 1000 && iName < cSecNames.length - 1) {\r\n timeStep /= 1000;\r\n ++iName;\r\n }\r\n\r\n this._timeStep = `${timeStep.toString()} ${cSecNames[iName]}`;\r\n offset += 4;\r\n const secondary = [];\r\n const posData = new Float32Array(chunkedFramesCount * atomsCount * 3);\r\n let coordIdx = 0;\r\n const secondaryArr = new Int8Array(atomsCount);\r\n for (let j = 0; j < chunkedFramesCount; ++j) {\r\n for (let i = 0; i < atomsCount; ++i) {\r\n const hiWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const loWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const str = (loWord & cStrMask) >>> cStrShift;\r\n const x = fromUInt20ToInt20(((loWord & cFirstMask) >>> cFirstShift) >> 0);\r\n const y = fromUInt20ToInt20((((loWord & cSecMask1) << cSecShift1)\r\n | ((hiWord & cSecMask2) >>> cSecShift2)) >> 0);\r\n const z = fromUInt20ToInt20((hiWord & cThirdMask) >> 0);\r\n secondaryArr[i] = 0;\r\n if (str > 0 && str < 4) {\r\n secondaryArr[i] = cHelixIdx;\r\n } else if (str === 4) {\r\n secondaryArr[i] = cSheetIdx;\r\n }\r\n posData[coordIdx++] = x / 100;\r\n posData[coordIdx++] = y / 100;\r\n posData[coordIdx++] = z / 100;\r\n }\r\n secondary.push(_createSecondary(secondaryArr, complex));\r\n }\r\n this._secondaryData = secondary;\r\n this._data = posData;\r\n }\r\n\r\n nextFrame() {\r\n this.setFrame((this._currFrame + 1) % this._framesCount);\r\n }\r\n\r\n needsColorUpdate(colorer) {\r\n return colorer instanceof SecondaryStructureColorer;\r\n }\r\n\r\n getAtomColor(colorer, atom) {\r\n return colorer.getResidueColor(this._residues[atom.residue._index], this._complex);\r\n }\r\n\r\n getResidueColor(colorer, residue) {\r\n return colorer.getResidueColor(this._residues[residue._index], this._complex);\r\n }\r\n\r\n _updateSecondary() {\r\n let i;\r\n const myResidues = this._residues;\r\n let n = myResidues.length;\r\n for (i = 0; i < n; ++i) {\r\n myResidues[i]._secondary = null;\r\n }\r\n const sec = this._secondaryData[this._currFrame - this._framesRange.start];\r\n for (i = 0, n = sec.length; i < n; ++i) {\r\n const oldSec = sec[i];\r\n const { start, end } = oldSec;\r\n const nSec = {\r\n _start: myResidues[start],\r\n _end: myResidues[end],\r\n type: oldSec.type,\r\n generic: oldSec.generic,\r\n };\r\n for (let j = start; j <= end; ++j) {\r\n myResidues[j]._secondary = nSec;\r\n }\r\n }\r\n }\r\n\r\n reset() {\r\n const compRes = this._complex._residues;\r\n const n = compRes.length;\r\n this._residues = new Array(n);\r\n const myResidues = this._residues;\r\n const getSec = function () {\r\n return this._secondary;\r\n };\r\n for (let i = 0; i < n; ++i) {\r\n myResidues[i] = {\r\n _type: compRes[i]._type,\r\n _isValid: compRes[i]._isValid,\r\n _controlPoint: null,\r\n _wingVector: null,\r\n _secondary: null,\r\n getSecondary: getSec,\r\n };\r\n }\r\n }\r\n\r\n setFrame(frameIdx) {\r\n this.frameIsReady = false;\r\n if (frameIdx >= this._framesRange.start && frameIdx <= this._framesRange.end) {\r\n this._currFrame = frameIdx;\r\n this._cachedResidues = false;\r\n this._updateSecondary();\r\n this.frameIsReady = true;\r\n } else {\r\n this._frameRequest = frameIdx;\r\n if (!this._buffer) {\r\n this._prepareBuffer(frameIdx);\r\n } else {\r\n const self = this;\r\n switch (this._buffer.state) {\r\n case 'none':\r\n this._prepareBuffer(frameIdx);\r\n break;\r\n case 'ready':\r\n self._parseBuffer();\r\n break;\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n disableEvents() {\r\n this._callbacks = null;\r\n }\r\n\r\n /**\r\n * Returns link to atom pos vector, clone it if needed\r\n */\r\n\r\n static _vec = new THREE.Vector3();\r\n\r\n getAtomPos(atomIdx) {\r\n const vec = FrameInfo._vec;\r\n const self = this;\r\n const data = self._data;\r\n const idx = (self._atomsCount * (self._currFrame - self._framesRange.start) + atomIdx) * 3;\r\n vec.set(data[idx], data[idx + 1], data[idx + 2]);\r\n return vec;\r\n }\r\n\r\n getResidues() {\r\n if (this._cachedResidues) {\r\n return this._residues;\r\n }\r\n this._complex.updateToFrame(this);\r\n return this._residues;\r\n }\r\n}\r\nexport default FrameInfo;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\n\r\n/**\r\n * Create new scene object.\r\n *\r\n * @param {array=} params - Object required params.\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports SceneObject\r\n * @this SceneObject\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all scene objects that are not reps.\r\n */\r\nclass SceneObject {\r\n constructor(params, opts) {\r\n if (this.constructor === SceneObject) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Object's options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.params = params;\r\n this.opts = _.merge(utils.deriveDeep(settings.now.objects[this.type], true), opts);\r\n this.needsRebuild = false;\r\n this._mesh = null;\r\n this.id = null;\r\n }\r\n\r\n /**\r\n * Get object identification, probably with options.\r\n * @returns {Object} field type contains type information, params - object's formal parameters,\r\n * opts - changed options\r\n * Options are returned if they were changed during or after object creation.\r\n */\r\n identify() {\r\n const result = {\r\n type: this.type,\r\n params: this.params,\r\n };\r\n const diff = utils.objectsDiff(this.opts, settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n result.opts = diff;\r\n }\r\n return result;\r\n }\r\n\r\n toString() {\r\n const paramsStr = `o=${this.type},${this.params.join(',')}`;\r\n const optsStr = utils.compareOptionsWithDefaults(this.opts, settings.defaults.objects[this.type]);\r\n return paramsStr + optsStr;\r\n }\r\n\r\n getGeometry() {\r\n return this._mesh;\r\n }\r\n\r\n destroy() {\r\n if (this._mesh) {\r\n gfxutils.destroyObject(this._mesh);\r\n }\r\n }\r\n}\r\n\r\n/**\r\n * Scene object identifier.\r\n * @type {string}\r\n */\r\nSceneObject.prototype.type = '__';\r\n\r\nexport default SceneObject;\r\n","import * as THREE from 'three';\r\nimport SceneObject from './SceneObject';\r\nimport meshutils from '../meshutils';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\nimport meshes from '../meshes/meshes';\r\nimport settings from '../../settings';\r\n\r\nclass LinesObj extends SceneObject {\r\n constructor(params, opts) {\r\n super(params, opts);\r\n if (params.length < 2) {\r\n throw new Error('Wrong number of argumets on line object creation!');\r\n }\r\n [this._id1, this._id2] = params;\r\n }\r\n\r\n _getAtomFromName(complex, atomId) {\r\n const err = ' - Wrong atom format it must be \\'#CHAIN_NAME.#RESIDUE_NUMBER.#ATOM_NAME\\' (e.g. \\'A.38.CO1\\')';\r\n const atom1 = complex.getAtomByFullname(atomId);\r\n if (!atom1) {\r\n throw new Error(atomId + err);\r\n }\r\n return atom1;\r\n }\r\n\r\n build(complex) {\r\n const geom = new THREE.BufferGeometry();\r\n this._atom1 = this._getAtomFromName(complex, this._id1);\r\n this._atom2 = this._getAtomFromName(complex, this._id2);\r\n\r\n const p1 = this._atom1.position;\r\n const p2 = this._atom2.position;\r\n const vertices = new Float32Array([\r\n p1.x, p1.y, p1.z,\r\n p2.x, p2.y, p2.z,\r\n ]);\r\n\r\n geom.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n geom.computeBoundingBox();\r\n\r\n this._line = new meshes.Line(geom, new UberMaterial({\r\n lights: false,\r\n overrideColor: true,\r\n dashedLine: true,\r\n fogTransparent: settings.now.bg.transparent,\r\n }));\r\n this._line.computeLineDistances();\r\n this._line.material.setUberOptions({\r\n fixedColor: new THREE.Color(this.opts.color),\r\n dashedLineSize: this.opts.dashSize,\r\n dashedLinePeriod: this.opts.dashSize + this.opts.gapSize,\r\n });\r\n this._line.material.updateUniforms();\r\n\r\n this._line.raycast = function (_raycaster, _intersects) {};\r\n this._mesh = this._line;\r\n const transforms = complex.getTransforms();\r\n if (transforms.length > 0) {\r\n this._mesh = new THREE.Group();\r\n this._mesh.add(this._line);\r\n meshutils.applyTransformsToMeshes(this._mesh, transforms);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n if (!this._atom1 || !this._atom2 || !this._line) {\r\n return;\r\n }\r\n\r\n const geo = this._line.geometry;\r\n geo.vertices[0].copy(frameData.getAtomPos(this._atom1.index));\r\n geo.vertices[1].copy(frameData.getAtomPos(this._atom2.index));\r\n this._line.computeLineDistances();\r\n geo.computeBoundingSphere();\r\n\r\n geo.verticesNeedUpdate = true;\r\n }\r\n}\r\n\r\nLinesObj.prototype.constructor = LinesObj;\r\nLinesObj.prototype.type = 'line';\r\n\r\nexport default LinesObj;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Outline.frag';\r\n\r\nclass OutlineMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n // add depth outline\r\n super(params);\r\n\r\n const settings = {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcDepthTex: { type: 't', value: null },\r\n srcTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n color: { type: 'v3', value: null },\r\n threshold: { type: 'f', value: null },\r\n opacity: { type: 'f', value: 1.0 },\r\n thickness: { type: 'v2', value: new THREE.Vector2(1, 1) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: true,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n\r\n this.setValues(settings);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n const defines = {};\r\n\r\n if (this.depth) {\r\n defines.DEPTH_OUTLINE = 1;\r\n }\r\n\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nOutlineMaterial.prototype.depth = false;\r\n\r\nexport default OutlineMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './FXAA.frag';\r\n\r\nclass FXAAMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n bgColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.bgTransparent) {\r\n defines.BG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nFXAAMaterial.prototype.bgTransparent = false;\r\n\r\nexport default FXAAMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AO.frag';\r\nimport noise from '../noiseTexture';\r\n\r\nconst _samplesKernel = [\r\n // hemisphere samples adopted to sphere\r\n new THREE.Vector3(0.295184, 0.077723, 0.068429),\r\n new THREE.Vector3(-0.271976, -0.365221, 0.838363),\r\n new THREE.Vector3(0.547713, 0.467576, 0.488515),\r\n new THREE.Vector3(0.662808, -0.031733, 0.584758),\r\n new THREE.Vector3(-0.025717, 0.218955, 0.657094),\r\n new THREE.Vector3(-0.310153, -0.365223, 0.370701),\r\n new THREE.Vector3(-0.101407, -0.006313, 0.747665),\r\n new THREE.Vector3(-0.769138, 0.360399, 0.086847),\r\n new THREE.Vector3(-0.271988, -0.275140, 0.905353),\r\n new THREE.Vector3(0.096740, -0.566901, 0.700151),\r\n new THREE.Vector3(0.562872, -0.735136, 0.094647),\r\n new THREE.Vector3(0.379877, 0.359278, 0.190061),\r\n new THREE.Vector3(0.519064, -0.023055, 0.405068),\r\n new THREE.Vector3(-0.301036, 0.114696, 0.088885),\r\n new THREE.Vector3(-0.282922, 0.598305, 0.487214),\r\n new THREE.Vector3(-0.181859, 0.251670, 0.679702),\r\n new THREE.Vector3(-0.191463, -0.635818, 0.512919),\r\n new THREE.Vector3(-0.293655, 0.427423, 0.078921),\r\n new THREE.Vector3(-0.267983, 0.680534, 0.132880),\r\n new THREE.Vector3(0.139611, 0.319637, 0.477439),\r\n new THREE.Vector3(-0.352086, 0.311040, 0.653913),\r\n new THREE.Vector3(0.321032, 0.805279, 0.487345),\r\n new THREE.Vector3(0.073516, 0.820734, 0.414183),\r\n new THREE.Vector3(-0.155324, 0.589983, 0.411460),\r\n new THREE.Vector3(0.335976, 0.170782, 0.527627),\r\n new THREE.Vector3(0.463460, -0.355658, 0.167689),\r\n new THREE.Vector3(0.222654, 0.596550, 0.769406),\r\n new THREE.Vector3(0.922138, -0.042070, 0.147555),\r\n new THREE.Vector3(-0.727050, -0.329192, 0.369826),\r\n new THREE.Vector3(-0.090731, 0.533820, 0.463767),\r\n new THREE.Vector3(-0.323457, -0.876559, 0.238524),\r\n new THREE.Vector3(-0.663277, -0.372384, 0.342856),\r\n];\r\n\r\nclass AOMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n noiseTexture: { type: 't', value: noise.noiseTexture },\r\n noiseTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight) },\r\n diffuseTexture: { type: 't', value: null },\r\n normalTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n camNearFar: { type: 'v2', value: new THREE.Vector2(1.0, 10.0) },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n samplesKernel: { type: 'v3v', value: _samplesKernel },\r\n kernelRadius: { type: 'f', value: 1.0 },\r\n depthThreshold: { type: 'f', value: 1.0 },\r\n factor: { type: 'f', value: 1.0 },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOHorBlur.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOHorBlurMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOHorBlurMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOVertBlurWithBlend.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOVertBlurWithBlendMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n diffuseTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n fogNearFar: { type: 'v2', value: new THREE.Vector2(100.0, 100.0) },\r\n fogColor: { type: 'v4', value: new THREE.Vector4(0.0, 0.5, 0.0, 1.0) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.useFog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nAOVertBlurWithBlendMaterial.prototype.useFog = true;\r\nAOVertBlurWithBlendMaterial.prototype.fogTransparent = false;\r\n\r\nexport default AOVertBlurWithBlendMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Anaglyph.frag';\r\n\r\nclass AnaglyphMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n const settings = {\r\n uniforms: {\r\n srcL: { type: 't', value: null },\r\n srcR: { type: 't', value: null },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n this.setValues(settings);\r\n }\r\n}\r\n\r\nexport default AnaglyphMaterial;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\n\r\nclass View {\r\n constructor() {\r\n this.position = new THREE.Vector3(0, 0, 0);\r\n this.scale = 1;\r\n this.orientation = new THREE.Quaternion(0, 0, 0, 1);\r\n }\r\n\r\n set(position, scale, orientation) {\r\n this.position = position;\r\n this.scale = scale;\r\n this.orientation = orientation;\r\n }\r\n}\r\n\r\nconst _transitionTime = 1.5; // in seconds\r\n\r\nexport default class ViewInterpolator {\r\n setup(startView, endView) {\r\n this._startTime = undefined;\r\n this._endTime = undefined;\r\n this._isPaused = false;\r\n\r\n this._srcView = startView;\r\n this._dstView = endView;\r\n this._isMoving = false;\r\n }\r\n\r\n isMoving() {\r\n return this._isMoving;\r\n }\r\n\r\n wasStarted() {\r\n return typeof this._startTime !== 'undefined' && typeof this._endTime !== 'undefined';\r\n }\r\n\r\n start() {\r\n this._startTime = Date.now();\r\n const transTime = settings.now.interpolateViews ? _transitionTime * 1000 : 0;\r\n this._endTime = this._startTime + transTime;\r\n this._isMoving = true;\r\n }\r\n\r\n getCurrentView() {\r\n if (typeof this._srcView === 'undefined' || typeof this._dstView === 'undefined'\r\n || !this._isMoving || !this.wasStarted()) {\r\n return { success: false };\r\n }\r\n\r\n let view = this.createView();\r\n const time = Date.now();\r\n if (time > this._endTime) {\r\n view = this._dstView;\r\n this.reset();\r\n return { success: true, view };\r\n }\r\n\r\n const factor = (time - this._startTime) / (this._endTime - this._startTime);\r\n view.position.copy(this._srcView.position);\r\n view.position.lerp(this._dstView.position, factor);\r\n view.scale = (1 - factor) * this._srcView.scale + factor * this._dstView.scale;\r\n view.orientation.copy(this._srcView.orientation);\r\n view.orientation.slerp(this._dstView.orientation, factor);\r\n return { success: true, view };\r\n }\r\n\r\n reset() {\r\n this._startTime = this._endTime = 0;\r\n this._isMoving = false;\r\n }\r\n\r\n pause() {\r\n if (!this._isPaused) {\r\n this.setup(this.getCurrentView().view, this._dstView);\r\n this._isPaused = true;\r\n }\r\n }\r\n\r\n resume() {\r\n this._isPaused = false;\r\n }\r\n\r\n createView() {\r\n return new View();\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport makeContextDependent from './makeContextDependent';\r\n\r\nconst MAX_COOKIE_LEN = 4000;\r\nconst COUNT_SUFFIX = 'Cnt';\r\n\r\nfunction _chunkString(string, chunkLen) {\r\n const l = string.length;\r\n const chunks = [];\r\n for (let c = 0, lc = 0; lc < l; c++, lc += chunkLen) {\r\n chunks[c] = string.slice(lc, lc + chunkLen);\r\n }\r\n return chunks;\r\n}\r\n\r\n/**\r\n * Create new context dependent Cookie holder object.\r\n * @param context\r\n * @param {Object} opts - options\r\n * @param {string} opts.path - cookie path\r\n * @constructor\r\n */\r\nfunction Cookies(context, opts) {\r\n this.context = context;\r\n this._opts = _.merge({\r\n path: '/',\r\n }, opts);\r\n}\r\n\r\nmakeContextDependent(Cookies.prototype);\r\n\r\n/**\r\n * Remove cookie by the name.\r\n * @param key\r\n */\r\nCookies.prototype.removeCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n this._removeSimpleCookie(key);\r\n return;\r\n }\r\n this._removeSimpleCookie(cntKey);\r\n cntVal = parseInt(cntVal, 10);\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._removeSimpleCookie(key + i);\r\n }\r\n};\r\n\r\n/**\r\n * Set new cookie value. Automatically splits\r\n * values that are too large into multiple cookies.\r\n * @param key\r\n * @param value\r\n */\r\nCookies.prototype.setCookie = function (key, value) {\r\n this.removeCookie(key);\r\n value = encodeURIComponent(value);\r\n const values = _chunkString(value, MAX_COOKIE_LEN - key.length - 1);\r\n const cntVal = values.length;\r\n if (cntVal === 1) {\r\n this._setSimpleCookie(key, value);\r\n return;\r\n }\r\n const cntKey = this._toCount(key);\r\n this._setSimpleCookie(cntKey, cntVal.toString());\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._setSimpleCookie(key + i, values[i]);\r\n }\r\n};\r\n\r\n/**\r\n * Obtain the value of a compound cookie.\r\n * @param key\r\n */\r\nCookies.prototype.getCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n return this._getSimpleCookie(key);\r\n }\r\n cntVal = parseInt(cntVal, 10);\r\n const value = [];\r\n for (let i = 0; i < cntVal; ++i) {\r\n value[i] = this._getSimpleCookie(key + i);\r\n }\r\n return value.join('');\r\n};\r\n\r\nCookies.prototype._toCount = function (key) {\r\n return key + COUNT_SUFFIX;\r\n};\r\n\r\nCookies.prototype._removeSimpleCookie = function (key) {\r\n document.cookie = `${key}=; expires=Thu, 01 Jan 1970 00:00:01 GMT;`;\r\n};\r\n\r\nCookies.prototype._getExpirationDate = function () {\r\n const today = new Date();\r\n const EXP_PERIOD_YEARS = 10;\r\n today.setFullYear(today.getFullYear() + EXP_PERIOD_YEARS);\r\n return today;\r\n};\r\n\r\nCookies.prototype._setSimpleCookie = function (key, value) {\r\n document.cookie = `${key}=${value\r\n };expires=${this._getExpirationDate().toUTCString()\r\n };path=${this._opts.path}`;\r\n};\r\n\r\nCookies.prototype._getSimpleCookie = function (key) {\r\n const matches = document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n return matches ? decodeURIComponent(matches[1]) : '';\r\n};\r\n\r\nCookies.prototype._exists = function (key) {\r\n return document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n};\r\n\r\nexport default Cookies;\r\n","/*\r\n * Toggling WebVR is done through button.click because of limitations on calling requestPresent in webVR:\r\n * VRDisplay::requestPresent should be called from user gesture:\r\n * https://developer.mozilla.org/en-US/docs/Web/API/VRDisplay/requestPresent\r\n */\r\nexport default function (webVRPoC) {\r\n function showEnterVR(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'pointer';\r\n button.style.left = 'calc(50% - 50px)';\r\n button.style.width = '100px';\r\n\r\n button.textContent = 'ENTER VR';\r\n\r\n let currentSession = null;\r\n\r\n function onSessionEnded(/* event */) {\r\n currentSession.removeEventListener('end', onSessionEnded);\r\n button.textContent = 'ENTER VR';\r\n currentSession = null;\r\n }\r\n\r\n function onSessionStarted(session) {\r\n session.addEventListener('end', onSessionEnded);\r\n webVRPoC._gfx.renderer.xr.setReferenceSpaceType('local');\r\n webVRPoC._gfx.renderer.xr.setSession(session);\r\n button.textContent = 'EXIT VR';\r\n currentSession = session;\r\n }\r\n\r\n button.onmouseenter = function () { button.style.opacity = '1.0'; };\r\n button.onmouseleave = function () { button.style.opacity = '0.5'; };\r\n\r\n button.onclick = function () {\r\n if (currentSession === null) {\r\n // WebXR's requestReferenceSpace only works if the corresponding feature\r\n // was requested at session creation time. For simplicity, just ask for\r\n // the interesting ones as optional features, but be aware that the\r\n // requestReferenceSpace call will fail if it turns out to be unavailable.\r\n // ('local' is always available for immersive sessions and doesn't need to\r\n // be requested separately.)\r\n\r\n const sessionInit = { optionalFeatures: ['local-floor', 'bounded-floor'] };\r\n navigator.xr.requestSession('immersive-vr', sessionInit).then(onSessionStarted);\r\n webVRPoC.moveSceneBehindHeadset();\r\n } else {\r\n currentSession.end();\r\n }\r\n };\r\n }\r\n\r\n function showWebXRNotFound(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'auto';\r\n button.style.left = 'calc(50% - 75px)';\r\n button.style.width = '150px';\r\n button.textContent = 'VR NOT FOUND';\r\n button.onmouseenter = null;\r\n button.onmouseleave = null;\r\n button.onclick = null;\r\n }\r\n\r\n function stylizeElement(element) {\r\n element.style.position = 'absolute';\r\n element.style.bottom = '20px';\r\n element.style.padding = '12px 6px';\r\n element.style.border = '1px solid #fff';\r\n element.style.borderRadius = '4px';\r\n element.style.background = 'transparent';\r\n element.style.color = '#fff';\r\n element.style.font = 'normal 13px sans-serif';\r\n element.style.textAlign = 'center';\r\n element.style.opacity = '0.5';\r\n element.style.outline = 'none';\r\n element.style.zIndex = '999';\r\n }\r\n\r\n if ('xr' in navigator) {\r\n const button = document.createElement('button');\r\n button.style.display = 'none';\r\n stylizeElement(button);\r\n navigator.xr.isSessionSupported('immersive-vr').then((supported) => (\r\n supported ? showEnterVR(button) : showWebXRNotFound(button)\r\n ));\r\n return button;\r\n }\r\n const message = document.createElement('a');\r\n message.href = 'https://webvr.info';\r\n message.innerHTML = 'WEBXR NOT SUPPORTED';\r\n message.style.left = 'calc(50% - 90px)';\r\n message.style.width = '180px';\r\n message.style.textDecoration = 'none';\r\n stylizeElement(message);\r\n return message;\r\n}\r\n","import * as THREE from 'three';\r\nimport createWebVRButton from './createWebVRButton';\r\nimport gfxutils from '../gfxutils';\r\nimport logger from '../../utils/logger';\r\nimport settings from '../../settings';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default class WebVRPoC {\r\n constructor(onToggle) {\r\n this._mainCamera = new THREE.PerspectiveCamera();\r\n this._button = null;\r\n this._onToggle = onToggle;\r\n\r\n this._molContainer = new gfxutils.RCGroup();\r\n this._user = new gfxutils.RCGroup();\r\n this._scalingPivot = new THREE.Object3D();\r\n this._user.add(this._scalingPivot);\r\n\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n this._pressedGripsCounter = 0;\r\n this._distance = 0;\r\n\r\n this._gfx = null;\r\n }\r\n\r\n startScalingByControllers() {\r\n // reset scale\r\n this._distance = this._controller1.position.distanceTo(this._controller2.position);\r\n gfxutils.getMiddlePoint(this._controller1.position, this._controller2.position, this._scalingPivot.position);\r\n this._scalingPivot.scale.set(1, 1, 1);\r\n this._scalingPivot.updateMatrix();\r\n this._scalingPivot.updateMatrixWorld();\r\n // link molecule to pivot\r\n this._scalingPivot.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n stopScalingByControllers() {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n handleGripsDown(event) {\r\n this._pressedGripsCounter++;\r\n if (this._pressedGripsCounter === 2) {\r\n this.startScalingByControllers();\r\n } else if (this._pressedGripsCounter === 1) {\r\n event.target.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n handleGripsUp(event) {\r\n this._pressedGripsCounter--;\r\n if (this._pressedGripsCounter === 1) {\r\n this.stopScalingByControllers();\r\n // reattach molecule to other controller\r\n const anotherController = event.target === this._controller1 ? this._controller2 : this._controller1;\r\n anotherController.addSavingWorldTransform(this._molContainer);\r\n } else if (this._pressedGripsCounter === 0) {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n enable(gfx) {\r\n if (!gfx) {\r\n logger.warn('WebVR couldn\\'t be enabled, because gfx is not defined');\r\n return;\r\n }\r\n this._gfx = gfx;\r\n const { renderer, camera } = gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n if (!camera) {\r\n throw new Error('No camera is available to toggle WebVR');\r\n }\r\n\r\n // enable xr in renderer\r\n renderer.xr.enabled = true;\r\n // add button for turning vr mode\r\n if (!this._button) {\r\n this._button = createWebVRButton(this);\r\n document.body.appendChild(this._button);\r\n } else {\r\n this._button.style.display = 'block';\r\n }\r\n // store fog setting\r\n this._mainFog = settings.now.fog;\r\n settings.set('fog', false);\r\n\r\n this._plugVRNodesIntoScene(gfx, renderer);\r\n this._setControllersListeners();\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n _plugVRNodesIntoScene(gfx, renderer) {\r\n // store common scene camera\r\n this._mainCamera.copy(gfx.camera);\r\n // add hierarchical structure for webVR into scene\r\n gfx.scene.add(this._user);\r\n // turn on webvr transformation\r\n gfx.scene.add(this._molContainer);\r\n this._molContainer.add(gfx.root);\r\n\r\n this._controller1 = renderer.xr.getController(0);\r\n this._controller2 = renderer.xr.getController(1);\r\n const mesh = this._createControllerMesh();\r\n this._controller1.add(mesh);\r\n this._controller2.add(mesh.clone());\r\n this._user.add(this._controller1);\r\n this._user.add(this._controller2);\r\n }\r\n\r\n _setControllersListeners() {\r\n this._controller1.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n\r\n this._controller1.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n }\r\n\r\n disable() {\r\n if (!this._gfx) {\r\n return;\r\n }\r\n const { renderer, camera } = this._gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n\r\n // nullify webxr callback for animation frame\r\n renderer.setAnimationLoop(null);\r\n const session = renderer.xr.getSession();\r\n if (session) {\r\n session.end();\r\n }\r\n renderer.xr.enabled = false;\r\n // remove button of VR entering\r\n if (this._button) {\r\n this._button.style.display = 'none';\r\n }\r\n // restore fog param\r\n settings.set('fog', this._mainFog);\r\n\r\n this._unplugVRNodesFromScene(camera);\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(false);\r\n }\r\n }\r\n\r\n _unplugVRNodesFromScene(camera) {\r\n // restore common camera\r\n if (this._mainCamera && camera) {\r\n camera.copy(this._mainCamera);\r\n }\r\n // turn off webvr transformation\r\n const root = this._molContainer.children[0];\r\n if (root) {\r\n this._gfx.scene.add(root);\r\n }\r\n this._molContainer.parent.remove(this._molContainer);\r\n if (this._user) {\r\n this._gfx.scene.remove(this._user);\r\n }\r\n // free scene nodes\r\n this._molContainer = null;\r\n this._user = null;\r\n this._scalingPivot = null;\r\n this._user = null;\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n }\r\n\r\n _createControllerMesh() {\r\n // visualize controllers with cylinders\r\n const geometry = new THREE.CylinderGeometry(0.04, 0.04, 0.3);\r\n const material = new UberMaterial({ lights: false, overrideColor: true });\r\n material.setUberOptions({ fixedColor: new THREE.Color(0x4444ff) });\r\n material.updateUniforms();\r\n const cylinder = new THREE.Mesh(geometry, material);\r\n cylinder.rotateX(-Math.PI / 2);\r\n return cylinder;\r\n }\r\n\r\n updateMoleculeScale() {\r\n if (!this._controller1 || !this._controller2) {\r\n return;\r\n }\r\n\r\n const self = this;\r\n // update molecule scaling by controllers\r\n if (self._pressedGripsCounter === 2) {\r\n // recalc scaling pivot\r\n gfxutils.getMiddlePoint(self._controller1.position, self._controller2.position, self._scalingPivot.position);\r\n // recalc scaler\r\n const dist = self._controller1.position.distanceTo(self._controller2.position);\r\n const scaler = dist / self._distance;\r\n self._scalingPivot.scale.multiplyScalar(scaler);\r\n // save cur distance for next frame\r\n self._distance = dist;\r\n }\r\n }\r\n\r\n /**\r\n * Reposition molecule right before the camera.\r\n * @note The proper way is to initiate headset in the place of common Miew's camera.\r\n * But threejs limitations on setting new XRReferenceSpace enforce the molecule repositioning\r\n * Hope, something will change.\r\n */\r\n moveSceneBehindHeadset() {\r\n const gfx = this._gfx;\r\n const { camera } = gfx;\r\n\r\n // set container position in camera space\r\n const container = this._molContainer;\r\n container.matrix.identity();\r\n container.position.set(0, 0, -4.0);\r\n container.updateMatrix();\r\n\r\n // update container world matrix\r\n container.matrixWorld.multiplyMatrices(camera.matrixWorld, container.matrix);\r\n // readd to scene\r\n gfx.scene.addSavingWorldTransform(container);\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n getCanvas() {\r\n const gfx = this._gfx;\r\n return (gfx && gfx.renderer) ? gfx.renderer.domElement : null;\r\n }\r\n}\r\n","/* global PACKAGE_VERSION:false */\r\nimport _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport { Spinner } from 'spin.js';\r\nimport Stats from './gfx/Stats';\r\nimport utils from './utils';\r\nimport JobHandle from './utils/JobHandle';\r\nimport options from './options';\r\nimport settings from './settings';\r\nimport chem from './chem';\r\nimport Visual from './Visual';\r\nimport ComplexVisual from './ComplexVisual';\r\nimport Complex from './chem/Complex';\r\nimport VolumeVisual from './VolumeVisual';\r\nimport io from './io/io';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport CSS2DRenderer from './gfx/CSS2DRenderer';\r\nimport ObjectControls from './ui/ObjectControls';\r\nimport Picker from './ui/Picker';\r\nimport Axes from './gfx/Axes';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport meshutils from './gfx/meshutils';\r\nimport FrameInfo from './gfx/FrameInfo';\r\nimport meshes from './gfx/meshes/meshes';\r\nimport LinesObject from './gfx/objects/LinesObj';\r\nimport UberMaterial from './gfx/shaders/UberMaterial';\r\nimport OutlineMaterial from './gfx/shaders/OutlineMaterial';\r\nimport FXAAMaterial from './gfx/shaders/FXAAMaterial';\r\nimport AOMaterial from './gfx/shaders/AOMaterial';\r\nimport AOHorBlurMaterial from './gfx/shaders/AOHorBlurMaterial';\r\nimport AOVertBlurWithBlendMaterial from './gfx/shaders/AOVertBlurWithBlendMaterial';\r\nimport AnaglyphMaterial from './gfx/shaders/AnaglyphMaterial';\r\nimport VolumeMaterial from './gfx/shaders/VolumeMaterial';\r\nimport ViewInterpolator from './gfx/ViewInterpolator';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\nimport logger from './utils/logger';\r\nimport Cookies from './utils/Cookies';\r\nimport capabilities from './gfx/capabilities';\r\nimport WebVRPoC from './gfx/vr/WebVRPoC';\r\nimport vertexScreenQuadShader from './gfx/shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromDistTex from './gfx/shaders/ScreenQuadFromDistortionTex.frag';\r\nimport getTopWindow from './utils/getTopWindow';\r\n\r\nconst {\r\n selectors,\r\n Atom,\r\n Residue,\r\n Chain,\r\n Molecule,\r\n} = chem;\r\n\r\nconst EDIT_MODE = { COMPLEX: 0, COMPONENT: 1, FRAGMENT: 2 };\r\n\r\nconst LOADER_NOT_FOUND = 'Could not find suitable loader for this source';\r\nconst PARSER_NOT_FOUND = 'Could not find suitable parser for this source';\r\n\r\n// Color management changed a lot in threejs 152+ version.\r\n// To keep miew colors we disable the new color management system\r\nTHREE.ColorManagement.enabled = false;\r\n\r\nconst { createElement } = utils;\r\n\r\nfunction updateFogRange(fog, center, radius) {\r\n fog.near = center - radius * settings.now.fogNearFactor;\r\n fog.far = center + radius * settings.now.fogFarFactor;\r\n}\r\n\r\nfunction removeExtension(fileName) {\r\n const dot = fileName.lastIndexOf('.');\r\n if (dot >= 0) {\r\n fileName = fileName.substr(0, dot);\r\n }\r\n return fileName;\r\n}\r\n\r\nfunction hasValidResidues(complex) {\r\n let hasValidRes = false;\r\n complex.forEachComponent((component) => {\r\n component.forEachResidue((residue) => {\r\n if (residue._isValid) {\r\n hasValidRes = true;\r\n }\r\n });\r\n });\r\n return hasValidRes;\r\n}\r\n\r\nfunction reportProgress(log, action, percent) {\r\n const TOTAL_PERCENT = 100;\r\n if (percent !== undefined) {\r\n log.debug(`${action}... ${Math.floor(percent * TOTAL_PERCENT)}%`);\r\n } else {\r\n log.debug(`${action}...`);\r\n }\r\n}\r\n\r\nfunction chooseFogColor() {\r\n return settings.now.fogColorEnable ? settings.now.fogColor : settings.now.bg.color;\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\n/**\r\n * Main 3D Molecular Viewer class.\r\n *\r\n * @param {object} opts - Viewer options.\r\n * @param {HTMLElement=} opts.container - DOM element that serves as a viewer container.\r\n * @param {object=} opts.settings - An object with properties to override default settings.\r\n * @param {string=} opts.settingsCookie='settings' - The name of the cookie to save current settings to.\r\n * @param {string=} opts.cookiePath='/' - The path option for cookies. Defaults to root.\r\n *\r\n * @exports Miew\r\n * @constructor\r\n */\r\nfunction Miew(opts) {\r\n EventDispatcher.call(this);\r\n this._opts = _.merge({\r\n settingsCookie: 'settings',\r\n cookiePath: '/',\r\n }, opts);\r\n /** @type {?object} */\r\n this._gfx = null;\r\n /** @type {ViewInterpolator} */\r\n this._interpolator = new ViewInterpolator();\r\n /** @type {HTMLElement} */\r\n this._container = (opts && opts.container)\r\n || document.getElementById('miew-container')\r\n || _.head(document.getElementsByClassName('miew-container'))\r\n || document.body;\r\n /** @type {HTMLElement} */\r\n this._containerRoot = this._container;\r\n\r\n /** @type {boolean} */\r\n this._running = false;\r\n /** @type {boolean} */\r\n this._halting = false;\r\n /** @type {boolean} */\r\n this._building = false;\r\n /** @type {boolean} */\r\n this._needRender = true;\r\n /** @type {boolean} */\r\n this._hotKeysEnabled = true;\r\n\r\n /** @type {Settings} */\r\n this.settings = settings;\r\n const log = logger;\r\n log.console = DEBUG;\r\n log.level = DEBUG ? 'debug' : 'info';\r\n /**\r\n * @type {Logger}\r\n * @example\r\n * miew.logger.addEventListener('message', function _onLogMessage(evt) {\r\n * console.log(evt.message);\r\n * });\r\n */\r\n this.logger = log;\r\n\r\n this._cookies = new Cookies(this);\r\n this.restoreSettings();\r\n if (opts && opts.settings) {\r\n this.settings.set(opts.settings);\r\n }\r\n\r\n /** @type {?Spinner} */\r\n this._spinner = null;\r\n /** @type {JobHandle[]} */\r\n this._loading = [];\r\n /** @type {?number}\r\n * @deprecated until Animation system refactoring\r\n */\r\n this._animInterval = null;\r\n\r\n /** @type {object} */\r\n this._visuals = {};\r\n /** @type {?string} */\r\n this._curVisualName = null;\r\n\r\n /** @type {array} */\r\n this._objects = [];\r\n\r\n /** @type {object} */\r\n this._sourceWindow = null;\r\n\r\n this.reset();\r\n\r\n if (this._repr) {\r\n log.debug(`Selected ${this._repr.mode.name} mode with ${this._repr.colorer.name} colorer.`);\r\n }\r\n\r\n const self = this;\r\n Miew.registeredPlugins.forEach((plugin) => {\r\n plugin.call(self);\r\n });\r\n\r\n this._initOnSettingsChanged();\r\n}\r\n\r\nMiew.prototype = Object.create(EventDispatcher.prototype);\r\nMiew.prototype.constructor = Miew;\r\n\r\nMiew.prototype.getMaxRepresentationCount = function () {\r\n return ComplexVisual.NUM_REPRESENTATION_BITS;\r\n};\r\n\r\n/**\r\n * Replace viewer container contents with a DOM element.\r\n * @param {HTMLElement} container - parent container.\r\n * @param {HTMLElement} element - DOM element to show.\r\n * @private\r\n */\r\nfunction _setContainerContents(container, element) {\r\n const parent = container;\r\n while (parent.firstChild) {\r\n parent.removeChild(parent.firstChild);\r\n }\r\n parent.appendChild(element);\r\n}\r\n\r\n/**\r\n * Update Shadow Camera target position and frustum.\r\n * @private\r\n */\r\nMiew.prototype._updateShadowCamera = (function () {\r\n const shadowMatrix = new THREE.Matrix4();\r\n const direction = new THREE.Vector3();\r\n const OBB = { center: new THREE.Vector3(), halfSize: new THREE.Vector3() };\r\n\r\n return function () {\r\n this._gfx.scene.updateMatrixWorld();\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = this._gfx.scene.children[i];\r\n shadowMatrix.copy(light.shadow.camera.matrixWorldInverse);\r\n this.getOBB(shadowMatrix, OBB);\r\n\r\n direction.subVectors(light.target.position, light.position);\r\n light.position.subVectors(OBB.center, direction);\r\n light.target.position.copy(OBB.center);\r\n\r\n light.shadow.bias = 0.09;\r\n light.shadow.camera.bottom = -OBB.halfSize.y;\r\n light.shadow.camera.top = OBB.halfSize.y;\r\n light.shadow.camera.right = OBB.halfSize.x;\r\n light.shadow.camera.left = -OBB.halfSize.x;\r\n light.shadow.camera.near = direction.length() - OBB.halfSize.z;\r\n light.shadow.camera.far = direction.length() + OBB.halfSize.z;\r\n\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Initialize the viewer.\r\n * @returns {boolean} true on success.\r\n * @throws Forwards exception raised during initialization.\r\n * @see Miew#term\r\n */\r\nMiew.prototype.init = function () {\r\n const container = this._container;\r\n const elem = utils.createElement('div', { class: 'miew-canvas' });\r\n _setContainerContents(container, elem);\r\n this._container = elem;\r\n\r\n const frag = document.createDocumentFragment();\r\n frag.appendChild(this._msgMode = createElement(\r\n 'div',\r\n { class: 'mode-message overlay' },\r\n createElement('p', {}, 'COMPONENT EDIT MODE'),\r\n ));\r\n frag.appendChild(this._msgAtomInfo = createElement(\r\n 'div',\r\n { class: 'atom-info overlay' },\r\n createElement('p', {}, ''),\r\n ));\r\n container.appendChild(frag);\r\n\r\n if (this._gfx !== null) { // block double init\r\n return true;\r\n }\r\n\r\n const self = this;\r\n this._showMessage('Viewer is being initialized...');\r\n try {\r\n this._initGfx();\r\n\r\n this._initListeners();\r\n this._spinner = new Spinner({\r\n lines: 13,\r\n length: 28,\r\n width: 14,\r\n radius: 42,\r\n color: '#fff',\r\n zIndex: 700,\r\n });\r\n\r\n const target = getTopWindow();\r\n target.addEventListener('keydown', (event) => {\r\n self._onKeyDown(event);\r\n });\r\n\r\n target.addEventListener('keyup', (event) => {\r\n self._onKeyUp(event);\r\n });\r\n\r\n this._objectControls = new ObjectControls(\r\n this._gfx.root,\r\n this._gfx.pivot,\r\n this._gfx.camera,\r\n this._gfx.renderer.domElement,\r\n () => self._getAltObj(),\r\n );\r\n this._objectControls.addEventListener('change', (e) => {\r\n if (settings.now.shadow.on) {\r\n self._updateShadowCamera();\r\n }\r\n // route rotate, zoom, translate and translatePivot events to the external API\r\n switch (e.action) {\r\n case 'rotate':\r\n self.dispatchEvent({ type: 'rotate', quaternion: e.quaternion });\r\n break;\r\n case 'zoom':\r\n self.dispatchEvent({ type: 'zoom', factor: e.factor });\r\n break;\r\n default:\r\n self.dispatchEvent({ type: e.action });\r\n }\r\n self.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n });\r\n\r\n const gfx = this._gfx;\r\n this._picker = new Picker(gfx.root, gfx.camera, gfx.renderer.domElement);\r\n this._picker.addEventListener('newpick', (event) => {\r\n self._onPick(event);\r\n });\r\n this._picker.addEventListener('dblclick', (event) => {\r\n self.center(event);\r\n });\r\n } catch (error) {\r\n if (error.name === 'TypeError' && error.message === 'Cannot read property \\'getExtension\\' of null') {\r\n this._showMessage('Could not create WebGL context.');\r\n } else if (error.message.search(/webgl/i) > 1) {\r\n this._showMessage(error.message);\r\n } else {\r\n this._showMessage('Viewer initialization failed.');\r\n throw error;\r\n }\r\n return false;\r\n }\r\n\r\n // automatically load default file\r\n const file = this._opts && this._opts.load;\r\n if (file) {\r\n const type = this._opts && this._opts.type;\r\n this.load(file, { fileType: type, keepRepsInfo: true });\r\n }\r\n\r\n return true;\r\n};\r\n\r\n/**\r\n * Terminate the viewer completely.\r\n * @see Miew#init\r\n */\r\nMiew.prototype.term = function () {\r\n this._showMessage('Viewer has been terminated.');\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n this.halt();\r\n this._gfx = null;\r\n};\r\n\r\n/**\r\n * Display message inside the viewer container, hiding WebGL canvas.\r\n * @param {string} msg - Message to show.\r\n * @private\r\n */\r\nMiew.prototype._showMessage = function (msg) {\r\n const element = document.createElement('div');\r\n element.setAttribute('class', 'miew-message');\r\n element.appendChild(document.createElement('p')).appendChild(document.createTextNode(msg));\r\n _setContainerContents(this._container, element);\r\n};\r\n\r\n/**\r\n * Display WebGL canvas inside the viewer container, hiding any message shown.\r\n * @private\r\n */\r\nMiew.prototype._showCanvas = function () {\r\n _setContainerContents(this._container, this._gfx.renderer.domElement);\r\n};\r\n\r\nMiew.prototype._requestAnimationFrame = function (callback) {\r\n const { xr } = this._gfx.renderer;\r\n if (xr && xr.enabled) {\r\n this._gfx.renderer.setAnimationLoop(callback);\r\n return;\r\n }\r\n requestAnimationFrame(callback);\r\n};\r\n\r\n/**\r\n * Initialize WebGL and set 3D scene up.\r\n * @private\r\n */\r\nMiew.prototype._initGfx = function () {\r\n const gfx = {\r\n width: this._container.clientWidth,\r\n height: this._container.clientHeight,\r\n };\r\n\r\n const webGLOptions = { preserveDrawingBuffer: true, alpha: true, premultipliedAlpha: false };\r\n if (settings.now.antialias) {\r\n webGLOptions.antialias = true;\r\n }\r\n\r\n gfx.renderer2d = new CSS2DRenderer();\r\n\r\n gfx.renderer = new THREE.WebGLRenderer(webGLOptions);\r\n gfx.renderer.shadowMap.enabled = settings.now.shadow.on;\r\n gfx.renderer.shadowMap.autoUpdate = false;\r\n gfx.renderer.shadowMap.type = THREE.PCFShadowMap;\r\n capabilities.init(gfx.renderer);\r\n\r\n gfx.renderer.autoClear = false;\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n gfx.camera = new THREE.PerspectiveCamera(\r\n settings.now.camFov,\r\n gfx.width / gfx.height,\r\n settings.now.camNear,\r\n settings.now.camFar,\r\n );\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.position.z = settings.now.camDistance;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n\r\n gfx.stereoCam = new THREE.StereoCamera();\r\n\r\n gfx.scene = new THREE.Scene();\r\n\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color, settings.now.camNear, settings.now.camFar);\r\n\r\n gfx.root = new gfxutils.RCGroup();\r\n gfx.scene.add(gfx.root);\r\n\r\n gfx.pivot = new gfxutils.RCGroup();\r\n gfx.root.add(gfx.pivot);\r\n\r\n gfx.selectionScene = new THREE.Scene();\r\n gfx.selectionRoot = new THREE.Group();\r\n gfx.selectionRoot.matrixAutoUpdate = false;\r\n gfx.selectionScene.add(gfx.selectionRoot);\r\n\r\n gfx.selectionPivot = new THREE.Group();\r\n gfx.selectionPivot.matrixAutoUpdate = false;\r\n gfx.selectionRoot.add(gfx.selectionPivot);\r\n\r\n const light12 = new THREE.DirectionalLight(0xffffff, 0.45);\r\n light12.position.set(0, 0.414, 1);\r\n light12.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n light12.castShadow = true;\r\n light12.shadow.bias = 0.09;\r\n light12.shadow.radius = settings.now.shadow.radius;\r\n light12.shadow.camera.layers.set(gfxutils.LAYERS.SHADOWMAP);\r\n\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n const shadowMapSize = Math.max(gfx.width, gfx.height) * pixelRatio;\r\n light12.shadow.mapSize.width = shadowMapSize;\r\n light12.shadow.mapSize.height = shadowMapSize;\r\n light12.target.position.set(0.0, 0.0, 0.0);\r\n gfx.scene.add(light12);\r\n gfx.scene.add(light12.target);\r\n\r\n const light3 = new THREE.AmbientLight(0x666666);\r\n light3.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.scene.add(light3);\r\n\r\n // add axes\r\n gfx.axes = new Axes(gfx.root, gfx.camera);\r\n const deviceWidth = gfx.width * pixelRatio;\r\n const deviceHeight = gfx.height * pixelRatio;\r\n\r\n gfx.offscreenBuf = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat, depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf.depthTexture = new THREE.DepthTexture();\r\n gfx.offscreenBuf.depthTexture.type = THREE.UnsignedShortType;\r\n\r\n gfx.offscreenBuf2 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf3 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf4 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf3;\r\n gfx.volFFTex = gfx.offscreenBuf4;\r\n gfx.volWFFTex = gfx.offscreenBuf;\r\n\r\n // use float textures for volume rendering (WebGL2 core feature)\r\n gfx.offscreenBuf5 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf6 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf7 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf5;\r\n gfx.volFFTex = gfx.offscreenBuf6;\r\n gfx.volWFFTex = gfx.offscreenBuf7;\r\n\r\n gfx.stereoBufL = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.stereoBufR = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n this._gfx = gfx;\r\n this._showCanvas();\r\n\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n\r\n this._container.appendChild(gfx.renderer2d.getElement());\r\n\r\n // add FPS counter\r\n const stats = new Stats();\r\n stats.domElement.style.position = 'absolute';\r\n stats.domElement.style.right = '0';\r\n stats.domElement.style.bottom = '0';\r\n this._container.appendChild(stats.domElement);\r\n this._fps = stats;\r\n this._fps.show(settings.now.fps);\r\n};\r\n\r\n/**\r\n * Setup event listeners.\r\n * @private\r\n */\r\nMiew.prototype._initListeners = function () {\r\n const self = this;\r\n window.addEventListener('resize', () => {\r\n self._onResize();\r\n });\r\n};\r\n\r\n/**\r\n * Try to add numbers to the base name to make it unique among visuals\r\n * @private\r\n */\r\nMiew.prototype._makeUniqueVisualName = function (baseName) {\r\n if (!baseName) {\r\n return Math.random().toString();\r\n }\r\n\r\n let name = baseName;\r\n let suffix = 1;\r\n while (this._visuals.hasOwnProperty(name)) {\r\n name = `${baseName} (${suffix.toString()})`;\r\n suffix++;\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Add visual to the viewer\r\n * @private\r\n */\r\nMiew.prototype._addVisual = function (visual) {\r\n if (!visual) {\r\n return null;\r\n }\r\n\r\n // change visual name in order to make it unique\r\n const name = this._makeUniqueVisualName(visual.name);\r\n visual.name = name;\r\n\r\n this._visuals[name] = visual;\r\n this._gfx.pivot.add(visual);\r\n if (visual.getSelectionGeo) {\r\n this._gfx.selectionPivot.add(visual.getSelectionGeo());\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Remove visual from the viewer\r\n * @private\r\n */\r\nMiew.prototype._removeVisual = function (visual) {\r\n let name = '';\r\n let obj = null;\r\n if (visual instanceof Visual) {\r\n ({ name } = visual);\r\n obj = visual;\r\n } else if (typeof visual === 'string') {\r\n name = visual;\r\n obj = this._visuals[name];\r\n }\r\n\r\n if (!obj || !this._visuals.hasOwnProperty(name) || this._visuals[name] !== obj) {\r\n return;\r\n }\r\n\r\n if (name === this._curVisualName) {\r\n this._curVisualName = undefined;\r\n }\r\n\r\n delete this._visuals[name];\r\n obj.release(); // removes nodes from scene\r\n\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Call specified function for each Visual\r\n * @private\r\n */\r\nMiew.prototype._forEachVisual = function (callback) {\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Release (destroy) all visuals in the scene\r\n * @private\r\n */\r\nMiew.prototype._releaseAllVisuals = function () {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n this._visuals[name].release();\r\n }\r\n }\r\n\r\n this._visuals = {};\r\n};\r\n\r\n/**\r\n * Call specified function for each ComplexVisual\r\n * @private\r\n */\r\nMiew.prototype._forEachComplexVisual = function (callback) {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)\r\n && this._visuals[name] instanceof ComplexVisual) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual with specified name, or current (if not found), or any, or null\r\n * @private\r\n */\r\nMiew.prototype._getComplexVisual = function (name) {\r\n name = name || this._curVisualName;\r\n let any = null;\r\n let named = null;\r\n this._forEachComplexVisual((visual) => {\r\n any = visual;\r\n if (visual.name === name) {\r\n named = visual;\r\n }\r\n });\r\n return named || any;\r\n};\r\n\r\n/**\r\n * Returns first found VolumeVisual (no more than one should be present actually)\r\n * @private\r\n */\r\nMiew.prototype._getVolumeVisual = function () {\r\n let any = null;\r\n this._forEachVisual((visual) => {\r\n if (visual instanceof VolumeVisual) {\r\n any = visual;\r\n }\r\n });\r\n return any;\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual corresponding to specified complex\r\n * @private\r\n */\r\nMiew.prototype._getVisualForComplex = function (complex) {\r\n if (!complex) {\r\n return null;\r\n }\r\n\r\n let found = null;\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getComplex() === complex) {\r\n found = visual;\r\n }\r\n });\r\n return found;\r\n};\r\n\r\n/*\r\n * Get a list of names of visuals currently shown by the viewer\r\n */\r\nMiew.prototype.getVisuals = function () {\r\n return Object.keys(this._visuals);\r\n};\r\n\r\n/*\r\n * Get complex visuals count\r\n */\r\nMiew.prototype.getComplexVisualsCount = function () {\r\n let count = 0;\r\n this._forEachComplexVisual(() => count++);\r\n return count;\r\n};\r\n\r\n/*\r\n * Get current visual\r\n */\r\nMiew.prototype.getCurrentVisual = function () {\r\n return this._curVisualName;\r\n};\r\n\r\n/*\r\n * Set current visual.\r\n * All further operations will be performed on this visual (complex) if not stated otherwise.\r\n */\r\nMiew.prototype.setCurrentVisual = function (name) {\r\n if (!this._visuals[name]) {\r\n return;\r\n }\r\n\r\n this._curVisualName = name;\r\n};\r\n\r\n/**\r\n * Run the viewer, start processing update/render frames periodically.\r\n * Has no effect if already running.\r\n * @see Miew#halt\r\n */\r\nMiew.prototype.run = function () {\r\n if (!this._running) {\r\n this._running = true;\r\n if (this._halting) {\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._objectControls.enable(true);\r\n this._interpolator.resume();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to stop.\r\n * Will be processed during the next frame.\r\n * @see Miew#run\r\n */\r\nMiew.prototype.halt = function () {\r\n if (this._running) {\r\n this._discardComponentEdit();\r\n this._discardFragmentEdit();\r\n this._objectControls.enable(false);\r\n this._interpolator.pause();\r\n this._halting = true;\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to start / stop responsing\r\n * on hot keys.\r\n * @param enabled - start (true) or stop (false) response on hot keys.\r\n */\r\nMiew.prototype.enableHotKeys = function (enabled) {\r\n this._hotKeysEnabled = enabled;\r\n this._objectControls.enableHotkeys(enabled);\r\n};\r\n\r\n/**\r\n * Callback which processes window resize.\r\n * @private\r\n */\r\nMiew.prototype._onResize = function () {\r\n const gfx = this._gfx;\r\n if (!gfx) {\r\n return;\r\n }\r\n\r\n this._needRender = true;\r\n\r\n gfx.width = this._container.clientWidth;\r\n gfx.height = this._container.clientHeight;\r\n\r\n gfx.camera.aspect = gfx.width / gfx.height;\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n this.dispatchEvent({ type: 'resize' });\r\n};\r\n\r\nMiew.prototype._resizeOffscreenBuffers = function (width, height, stereo) {\r\n const gfx = this._gfx;\r\n stereo = stereo || 'NONE';\r\n const isAnaglyph = (stereo === 'NONE' || stereo === 'ANAGLYPH');\r\n const multi = isAnaglyph ? 1 : 0.5;\r\n gfx.offscreenBuf.setSize(multi * width, height);\r\n gfx.offscreenBuf2.setSize(multi * width, height);\r\n gfx.offscreenBuf3.setSize(multi * width, height);\r\n gfx.offscreenBuf4.setSize(multi * width, height);\r\n if (gfx.offscreenBuf5) {\r\n gfx.offscreenBuf5.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf6) {\r\n gfx.offscreenBuf6.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf7) {\r\n gfx.offscreenBuf7.setSize(multi * width, height);\r\n }\r\n if (isAnaglyph) {\r\n gfx.stereoBufL.setSize(width, height);\r\n gfx.stereoBufR.setSize(width, height);\r\n }\r\n};\r\n\r\n/**\r\n * Callback which processes update/render frames.\r\n * @private\r\n */\r\nMiew.prototype._onTick = function () {\r\n if (this._halting) {\r\n this._running = false;\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._fps.update();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n\r\n this._onUpdate();\r\n if (this._needRender) {\r\n this._onRender();\r\n this._needRender = !settings.now.suspendRender || settings.now.stereo === 'WEBVR';\r\n }\r\n};\r\n\r\nMiew.prototype._getBSphereRadius = function () {\r\n // calculate radius that would include all visuals\r\n let radius = 0;\r\n this._forEachVisual((visual) => {\r\n radius = Math.max(radius, visual.getBoundaries().boundingSphere.radius);\r\n });\r\n return radius * this._objectControls.getScale();\r\n};\r\n\r\n/**\r\n * Calculate bounding box that would include all visuals and being axis aligned in world defined by\r\n * transformation matrix: matrix\r\n * @param {Matrix4} matrix - transformation matrix.\r\n * @param {object} OBB - calculating bounding box.\r\n * @param {Vector3} OBB.center - OBB center.\r\n * @param {Vector3} OBB.halfSize - half magnitude of OBB sizes.\r\n */\r\nMiew.prototype.getOBB = (function () {\r\n const _bSphereForOneVisual = new THREE.Sphere();\r\n const _bBoxForOneVisual = new THREE.Box3();\r\n const _bBox = new THREE.Box3();\r\n\r\n const _invMatrix = new THREE.Matrix4();\r\n\r\n const _points = [\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n ];\r\n\r\n return function (matrix, OBB) {\r\n _bBox.makeEmpty();\r\n\r\n this._forEachVisual((visual) => {\r\n _bSphereForOneVisual.copy(visual.getBoundaries().boundingSphere);\r\n _bSphereForOneVisual.applyMatrix4(visual.matrixWorld).applyMatrix4(matrix);\r\n _bSphereForOneVisual.getBoundingBox(_bBoxForOneVisual);\r\n _bBox.union(_bBoxForOneVisual);\r\n });\r\n _bBox.getCenter(OBB.center);\r\n\r\n _invMatrix.copy(matrix).invert();\r\n OBB.center.applyMatrix4(_invMatrix);\r\n\r\n const { min } = _bBox;\r\n const { max } = _bBox;\r\n _points[0].set(min.x, min.y, min.z); // 000\r\n _points[1].set(max.x, min.y, min.z); // 100\r\n _points[2].set(min.x, max.y, min.z); // 010\r\n _points[3].set(min.x, min.y, max.z); // 001\r\n for (let i = 0, l = _points.length; i < l; i++) {\r\n _points[i].applyMatrix4(_invMatrix);\r\n }\r\n\r\n OBB.halfSize.set(\r\n Math.abs(_points[0].x - _points[1].x),\r\n Math.abs(_points[0].y - _points[2].y),\r\n Math.abs(_points[0].z - _points[3].z),\r\n ).multiplyScalar(0.5);\r\n };\r\n}());\r\n\r\nMiew.prototype._updateFog = function () {\r\n const gfx = this._gfx;\r\n\r\n if (settings.now.fog) {\r\n if (typeof gfx.scene.fog === 'undefined' || gfx.scene.fog === null) {\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color);\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n updateFogRange(gfx.scene.fog, gfx.camera.position.z, this._getBSphereRadius());\r\n } else if (gfx.scene.fog) {\r\n gfx.scene.fog = undefined;\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n};\r\n\r\nMiew.prototype._onUpdate = function () {\r\n if (this.isScriptingCommandAvailable !== undefined && this.isScriptingCommandAvailable() && !this._building) {\r\n this.callNextCmd();\r\n }\r\n\r\n this._objectControls.update();\r\n\r\n this._forEachComplexVisual((visual) => {\r\n visual.getComplex().update();\r\n });\r\n\r\n if (settings.now.autobuild && !this._loading.length && !this._building && this._needRebuild()) {\r\n this.rebuild();\r\n }\r\n\r\n if (!this._loading.length && !this._building && !this._needRebuild()) {\r\n this._updateView();\r\n }\r\n\r\n this._updateFog();\r\n\r\n if (this._gfx.renderer.xr.enabled) {\r\n this.webVR.updateMoleculeScale();\r\n }\r\n};\r\n\r\nMiew.prototype._onRender = function () {\r\n const gfx = this._gfx;\r\n\r\n // update all matrices\r\n gfx.scene.updateMatrixWorld();\r\n gfx.camera.updateMatrixWorld();\r\n\r\n this._clipPlaneUpdateValue(this._getBSphereRadius());\r\n this._fogFarUpdateValue();\r\n\r\n gfx.renderer.setRenderTarget(null);\r\n gfx.renderer.clear();\r\n\r\n this._renderFrame(settings.now.stereo);\r\n};\r\n\r\nMiew.prototype._renderFrame = (function () {\r\n const _anaglyphMat = new AnaglyphMaterial();\r\n const _size = new THREE.Vector2();\r\n\r\n return function (stereo) {\r\n const gfx = this._gfx;\r\n const { renderer } = gfx;\r\n\r\n renderer.getSize(_size);\r\n\r\n if (stereo !== 'NONE') {\r\n gfx.camera.focus = gfx.camera.position.z; // set focus to the center of the object\r\n gfx.stereoCam.aspect = 1.0;\r\n\r\n // in anaglyph mode we render full-size image for each eye\r\n // while in other stereo modes only half-size (two images on the screen)\r\n if (stereo === 'ANAGLYPH') {\r\n gfx.stereoCam.update(gfx.camera);\r\n } else {\r\n gfx.stereoCam.updateHalfSized(gfx.camera, settings.now.camFov);\r\n }\r\n }\r\n\r\n // resize offscreen buffers to match the target\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n this._resizeOffscreenBuffers(_size.width * pixelRatio, _size.height * pixelRatio, stereo);\r\n\r\n this._renderShadowMap();\r\n\r\n switch (stereo) {\r\n case 'WEBVR':\r\n case 'NONE':\r\n this._renderScene(gfx.camera, false);\r\n break;\r\n case 'SIMPLE':\r\n case 'DISTORTED':\r\n renderer.setScissorTest(true);\r\n\r\n renderer.setScissor(0, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(0, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraL, stereo === 'DISTORTED');\r\n\r\n renderer.setScissor(_size.width / 2, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(_size.width / 2, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraR, stereo === 'DISTORTED');\r\n\r\n renderer.setScissorTest(false);\r\n break;\r\n case 'ANAGLYPH':\r\n this._renderScene(this._gfx.stereoCam.cameraL, false, gfx.stereoBufL);\r\n this._renderScene(this._gfx.stereoCam.cameraR, false, gfx.stereoBufR);\r\n renderer.setRenderTarget(null);\r\n _anaglyphMat.uniforms.srcL.value = gfx.stereoBufL.texture;\r\n _anaglyphMat.uniforms.srcR.value = gfx.stereoBufR.texture;\r\n gfx.renderer.renderScreenQuad(_anaglyphMat);\r\n break;\r\n default:\r\n }\r\n\r\n gfx.renderer2d.render(gfx.scene, gfx.camera);\r\n\r\n if (settings.now.axes && gfx.axes && !gfx.renderer.xr.enabled) {\r\n gfx.axes.render(renderer);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._onBgColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx) {\r\n if (gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onFogColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx && gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._setUberMaterialValues = function (values) {\r\n this._gfx.root.traverse((obj) => {\r\n if ((obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line)\r\n && obj.material instanceof UberMaterial) {\r\n obj.material.setValues(values);\r\n obj.material.needsUpdate = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) {\r\n const gfx = this._gfx;\r\n const gl = gfx.renderer.getContext();\r\n const { properties } = gfx.renderer;\r\n\r\n if (!on) {\r\n gl.drawBuffers([gl.COLOR_ATTACHMENT0, null]);\r\n return;\r\n }\r\n\r\n // take extra texture from Texture Buffer\r\n gfx.renderer.setRenderTarget(textureBuffer);\r\n const tx8 = properties.get(textureBuffer.texture).__webglTexture;\r\n gl.bindTexture(gl.TEXTURE_2D, tx8);\r\n\r\n // take texture and framebuffer from renderbuffer\r\n gfx.renderer.setRenderTarget(renderBuffer);\r\n const fb = properties.get(renderBuffer).__webglFramebuffer;\r\n const tx = properties.get(renderBuffer.texture).__webglTexture;\r\n\r\n // set framebuffer\r\n gl.bindFramebuffer(gl.FRAMEBUFFER, fb);\r\n fb.width = renderBuffer.width;\r\n fb.height = renderBuffer.height;\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT0, gl.TEXTURE_2D, tx, 0);\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT1, gl.TEXTURE_2D, tx8, 0);\r\n\r\n // mapping textures (MRT is core feature in WebGL2)\r\n gl.drawBuffers([gl.COLOR_ATTACHMENT0, gl.COLOR_ATTACHMENT1]);\r\n};\r\n\r\nMiew.prototype._renderScene = (function () {\r\n return function (camera, distortion, target) {\r\n distortion = distortion || false;\r\n target = target || null;\r\n\r\n const gfx = this._gfx;\r\n\r\n // render to offscreen buffer\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.clear();\r\n if (gfx.renderer.xr.enabled) {\r\n gfx.renderer.render(gfx.scene, camera);\r\n return;\r\n }\r\n\r\n // clean buffer for normals texture\r\n gfx.renderer.setClearColor(0x000000, 0.0);\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf4);\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.clear();\r\n\r\n const bHaveComplexes = (this._getComplexVisual() !== null);\r\n const volumeVisual = this._getVolumeVisual();\r\n const ssao = bHaveComplexes && settings.now.ao;\r\n\r\n if (ssao) {\r\n this._enableMRT(true, gfx.offscreenBuf, gfx.offscreenBuf4);\r\n }\r\n\r\n if (settings.now.transparency === 'prepass') {\r\n this._renderWithPrepassTransparency(camera, gfx.offscreenBuf);\r\n } else if (settings.now.transparency === 'standard') {\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n }\r\n\r\n if (ssao) {\r\n this._enableMRT(false, null, null);\r\n }\r\n\r\n // when fxaa we should get resulting image in temp off-screen buff2 for further postprocessing with fxaa filter\r\n // otherwise we render to canvas\r\n const outline = bHaveComplexes && settings.now.outline.on;\r\n const fxaa = bHaveComplexes && settings.now.fxaa;\r\n const volume = (volumeVisual !== null) && (volumeVisual.getMesh().material != null);\r\n let dstBuffer = (ssao || outline || volume || fxaa || distortion) ? gfx.offscreenBuf2 : target;\r\n let srcBuffer = gfx.offscreenBuf;\r\n\r\n if (ssao) {\r\n this._performAO(\r\n srcBuffer,\r\n gfx.offscreenBuf4,\r\n gfx.offscreenBuf.depthTexture,\r\n dstBuffer,\r\n gfx.offscreenBuf3,\r\n gfx.offscreenBuf2,\r\n );\r\n if (!fxaa && !distortion && !volume && !outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = target;\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n } else {\r\n // just copy color buffer to dst buffer\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n\r\n // outline\r\n if (outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = (volume || fxaa || distortion) ? gfx.offscreenBuf3 : target;\r\n if (srcBuffer != null) {\r\n this._renderOutline(camera, gfx.offscreenBuf, srcBuffer, dstBuffer);\r\n }\r\n }\r\n\r\n // render selected part with outline material\r\n this._renderSelection(camera, gfx.offscreenBuf, dstBuffer);\r\n\r\n if (volume) {\r\n // copy current picture to the buffer that retains depth-data of the original molecule render\r\n // so that volume renderer could use depth-test\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n dstBuffer = gfx.offscreenBuf;\r\n this._renderVolume(volumeVisual, camera, dstBuffer, gfx.volBFTex, gfx.volFFTex, gfx.volWFFTex);\r\n\r\n // if this is the last stage -- copy image to target\r\n if (!fxaa && !distortion) {\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n }\r\n }\r\n\r\n srcBuffer = dstBuffer;\r\n\r\n if (fxaa) {\r\n dstBuffer = distortion ? gfx.offscreenBuf4 : target;\r\n this._performFXAA(srcBuffer, dstBuffer);\r\n srcBuffer = dstBuffer;\r\n }\r\n\r\n if (distortion) {\r\n dstBuffer = target;\r\n this._performDistortion(srcBuffer, dstBuffer, true);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._performDistortion = (function () {\r\n const _scene = new THREE.Scene();\r\n const _camera = new THREE.OrthographicCamera(-1.0, 1.0, 1.0, -1.0, -500, 1000);\r\n\r\n const _material = new THREE.RawShaderMaterial({\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n aberration: { type: 'fv3', value: new THREE.Vector3(1.0) },\r\n },\r\n vertexShader: vertexScreenQuadShader,\r\n fragmentShader: fragmentScreenQuadFromDistTex,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n const _geo = gfxutils.buildDistorionMesh(10, 10, settings.now.debug.stereoBarrel);\r\n _scene.add(new meshes.Mesh(_geo, _material));\r\n\r\n return function (srcBuffer, targetBuffer, mesh) {\r\n this._gfx.renderer.setRenderTarget(targetBuffer);\r\n this._gfx.renderer.clear();\r\n\r\n if (mesh) {\r\n _material.uniforms.srcTex.value = srcBuffer.texture;\r\n _material.uniforms.aberration.value.set(0.995, 1.0, 1.01);\r\n this._gfx.renderer.render(_scene, _camera);\r\n } else {\r\n this._gfx.renderer.renderScreenQuadFromTexWithDistortion(srcBuffer, settings.now.debug.stereoBarrel);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._renderOutline = (function () {\r\n const _outlineMaterial = new OutlineMaterial({ depth: true });\r\n\r\n return function (camera, srcDepthBuffer, srcColorBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcColorBuffer.texture;\r\n _outlineMaterial.uniforms.srcDepthTex.value = srcDepthBuffer.depthTexture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcDepthBuffer.width, srcDepthBuffer.height);\r\n _outlineMaterial.uniforms.color.value = new THREE.Color(settings.now.outline.color);\r\n _outlineMaterial.uniforms.threshold.value = settings.now.outline.threshold;\r\n _outlineMaterial.uniforms.thickness.value = new THREE.Vector2(\r\n settings.now.outline.thickness,\r\n settings.now.outline.thickness,\r\n );\r\n\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._renderShadowMap = (function () {\r\n const pars = { minFilter: THREE.NearestFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat };\r\n\r\n return function () {\r\n if (!settings.now.shadow.on) {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n const currentRenderTarget = gfx.renderer.getRenderTarget();\r\n const activeCubeFace = gfx.renderer.getActiveCubeFace();\r\n const activeMipmapLevel = gfx.renderer.getActiveMipmapLevel();\r\n\r\n const _state = gfx.renderer.state;\r\n\r\n // Set GL state for depth map.\r\n _state.setBlending(THREE.NoBlending);\r\n _state.buffers.color.setClear(1, 1, 1, 1);\r\n _state.buffers.depth.setTest(true);\r\n _state.setScissorTest(false);\r\n\r\n for (let i = 0; i < gfx.scene.children.length; i++) {\r\n if (gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = gfx.scene.children[i];\r\n\r\n if (light.shadow.map == null) {\r\n light.shadow.map = new THREE.WebGLRenderTarget(light.shadow.mapSize.width, light.shadow.mapSize.height, pars);\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n light.shadow.updateMatrices(light);\r\n\r\n gfx.renderer.setRenderTarget(light.shadow.map);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.render(gfx.scene, light.shadow.camera);\r\n }\r\n }\r\n gfx.renderer.setRenderTarget(currentRenderTarget, activeCubeFace, activeMipmapLevel);\r\n };\r\n}());\r\n\r\n/**\r\n * Check if there is selection which must be rendered or not.\r\n * @private\r\n * @returns {boolean} true on existing selection to render\r\n */\r\nMiew.prototype._hasSelectionToRender = function () {\r\n const selPivot = this._gfx.selectionPivot;\r\n\r\n for (let i = 0; i < selPivot.children.length; i++) {\r\n const selPivotChild = selPivot.children[i];\r\n if (selPivotChild.children.length > 0) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n};\r\n\r\nMiew.prototype._renderSelection = (function () {\r\n const _outlineMaterial = new OutlineMaterial();\r\n\r\n return function (camera, srcBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // clear offscreen buffer (leave z-buffer intact)\r\n gfx.renderer.setClearColor('black', 0);\r\n\r\n // render selection to offscreen buffer\r\n gfx.renderer.setRenderTarget(srcBuffer);\r\n gfx.renderer.clear(true, false, false);\r\n if (self._hasSelectionToRender()) {\r\n gfx.selectionRoot.matrix = gfx.root.matrix;\r\n gfx.selectionPivot.matrix = gfx.pivot.matrix;\r\n gfx.renderer.render(gfx.selectionScene, camera);\r\n } else {\r\n // just render something to force \"target clear\" operation to finish\r\n gfx.renderer.renderDummyQuad();\r\n }\r\n\r\n // overlay to screen\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 0.6);\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcBuffer.width, srcBuffer.height);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._checkVolumeRenderingSupport = function (renderTarget) {\r\n if (!renderTarget) {\r\n return false;\r\n }\r\n const gfx = this._gfx;\r\n const oldRT = gfx.renderer.getRenderTarget();\r\n\r\n gfx.renderer.setRenderTarget(renderTarget);\r\n const context = gfx.renderer.getContext();\r\n const result = context.checkFramebufferStatus(context.FRAMEBUFFER);\r\n gfx.renderer.setRenderTarget(oldRT);\r\n if (result !== context.FRAMEBUFFER_COMPLETE) {\r\n // floatFrameBufferWarning = ;\r\n this.logger.warn('Device doesn\\'t support electron density rendering');\r\n return false;\r\n }\r\n return true;\r\n};\r\n\r\nMiew.prototype._renderVolume = (function () {\r\n const volumeBFMat = new VolumeMaterial.BackFacePosMaterial();\r\n const volumeFFMat = new VolumeMaterial.FrontFacePosMaterial();\r\n const cubeOffsetMat = new THREE.Matrix4().makeTranslation(0.5, 0.5, 0.5);\r\n const world2colorMat = new THREE.Matrix4();\r\n\r\n let volumeRenderingSupported;\r\n\r\n return function (volumeVisual, camera, dstBuf, tmpBuf1, tmpBuf2, tmpBuf3) {\r\n const gfx = this._gfx;\r\n\r\n if (typeof volumeRenderingSupported === 'undefined') {\r\n volumeRenderingSupported = this._checkVolumeRenderingSupport(tmpBuf1);\r\n }\r\n\r\n if (!volumeRenderingSupported) {\r\n return;\r\n }\r\n\r\n const mesh = volumeVisual.getMesh();\r\n\r\n mesh.rebuild(gfx.camera);\r\n\r\n // use main camera to prepare special textures to be used by volumetric rendering\r\n // these textures have the size of the window and are stored in offscreen buffers\r\n gfx.renderer.setClearColor('black', 0);\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n // draw plane with its own material, because it differs slightly from volumeBFMat\r\n camera.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeBFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeFFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.scene.overrideMaterial = null;\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n\r\n // prepare texture that contains molecule positions\r\n world2colorMat.copy(mesh.matrixWorld).invert();\r\n UberMaterial.prototype.uberOptions.world2colorMatrix.multiplyMatrices(cubeOffsetMat, world2colorMat);\r\n camera.layers.set(gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // render volume\r\n const vm = mesh.material;\r\n vm.uniforms._BFRight.value = tmpBuf1.texture;\r\n vm.uniforms._FFRight.value = tmpBuf2.texture;\r\n vm.uniforms._WFFRight.value = tmpBuf3.texture;\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.renderer.setRenderTarget(dstBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\n/* Render scene with 'ZPrepass transparency Effect'\r\n * Idea: transparent objects are rendered in two passes. The first one writes result only into depth buffer.\r\n * The second pass reads depth buffer and writes only to color buffer. The method results in\r\n * correct image of front part of the semi-transparent objects, but we can see only front transparent objects\r\n * and opaque objects inside, there is no transparent objects inside.\r\n * Notes: 1. Opaque objects should be rendered strictly before semi-transparent ones.\r\n * 2. Realization doesn't use camera layers because scene traversing is used for material changes and\r\n * we can use it to select needed meshes and don't complicate meshes builders with layers\r\n */\r\nMiew.prototype._renderWithPrepassTransparency = (function () {\r\n return function (camera, targetBuffer) {\r\n const gfx = this._gfx;\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n\r\n // opaque objects\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // transparent objects z prepass\r\n camera.layers.set(gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n gfx.renderer.getContext().colorMask(false, false, false, false); // don't update color buffer\r\n gfx.renderer.render(gfx.scene, camera);\r\n gfx.renderer.getContext().colorMask(true, true, true, true); // update color buffer\r\n\r\n // transparent objects color pass\r\n camera.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // restore default layer\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\nMiew.prototype._performFXAA = (function () {\r\n const _fxaaMaterial = new FXAAMaterial();\r\n\r\n return function (srcBuffer, targetBuffer) {\r\n if (typeof srcBuffer === 'undefined' || typeof targetBuffer === 'undefined') {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n\r\n // clear canvas\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.clear();\r\n\r\n // do fxaa processing of offscreen buff2\r\n _fxaaMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _fxaaMaterial.uniforms.srcTexelSize.value.set(1.0 / srcBuffer.width, 1.0 / srcBuffer.height);\r\n _fxaaMaterial.uniforms.bgColor.value.set(settings.now.bg.color);\r\n\r\n if (_fxaaMaterial.bgTransparent !== settings.now.bg.transparent) {\r\n _fxaaMaterial.setValues({ bgTransparent: settings.now.bg.transparent });\r\n _fxaaMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.renderScreenQuad(_fxaaMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._performAO = (function () {\r\n const _aoMaterial = new AOMaterial();\r\n const _horBlurMaterial = new AOHorBlurMaterial();\r\n const _vertBlurMaterial = new AOVertBlurWithBlendMaterial();\r\n\r\n const _scale = new THREE.Vector3();\r\n return function (srcColorBuffer, normalBuffer, srcDepthTexture, targetBuffer, tempBuffer, tempBuffer1) {\r\n if (!srcColorBuffer || !normalBuffer || !srcDepthTexture || !targetBuffer || !tempBuffer || !tempBuffer1) {\r\n return;\r\n }\r\n const gfx = this._gfx;\r\n const tanHalfFOV = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * gfx.camera.fov);\r\n\r\n _aoMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _aoMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _aoMaterial.uniforms.normalTexture.value = normalBuffer.texture;\r\n _aoMaterial.uniforms.srcTexelSize.value.set(1.0 / srcColorBuffer.width, 1.0 / srcColorBuffer.height);\r\n _aoMaterial.uniforms.camNearFar.value.set(gfx.camera.near, gfx.camera.far);\r\n _aoMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _aoMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _aoMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n gfx.root.matrix.extractScale(_scale);\r\n _aoMaterial.uniforms.kernelRadius.value = settings.now.debug.ssaoKernelRadius * _scale.x;\r\n _aoMaterial.uniforms.depthThreshold.value = 2.0 * this._getBSphereRadius(); // diameter\r\n _aoMaterial.uniforms.factor.value = settings.now.debug.ssaoFactor;\r\n // N: should be tempBuffer1 for proper use of buffers (see buffers using outside the function)\r\n gfx.renderer.setRenderTarget(tempBuffer1);\r\n gfx.renderer.renderScreenQuad(_aoMaterial);\r\n\r\n _horBlurMaterial.uniforms.aoMap.value = tempBuffer1.texture;\r\n _horBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer1.width, 1.0 / tempBuffer1.height);\r\n _horBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n gfx.renderer.setRenderTarget(tempBuffer);\r\n gfx.renderer.renderScreenQuad(_horBlurMaterial);\r\n\r\n _vertBlurMaterial.uniforms.aoMap.value = tempBuffer.texture;\r\n _vertBlurMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _vertBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer.width, 1.0 / tempBuffer.height);\r\n _vertBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _vertBlurMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _vertBlurMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _vertBlurMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n const { fog } = gfx.scene;\r\n if (fog) {\r\n _vertBlurMaterial.uniforms.fogNearFar.value.set(fog.near, fog.far);\r\n _vertBlurMaterial.uniforms.fogColor.value.set(fog.color.r, fog.color.g, fog.color.b, settings.now.fogAlpha);\r\n }\r\n if ((_vertBlurMaterial.useFog !== settings.now.fog)\r\n || (_vertBlurMaterial.fogTransparent !== settings.now.bg.transparent)) {\r\n _vertBlurMaterial.setValues({ useFog: settings.now.fog, fogTransparent: settings.now.bg.transparent });\r\n _vertBlurMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_vertBlurMaterial);\r\n };\r\n}());\r\n\r\n/**\r\n * Reset the viewer, unload molecules.\r\n * @param {boolean=} keepReps - Keep representations while resetting viewer state.\r\n */\r\nMiew.prototype.reset = function (/* keepReps */) {\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._lastPick = null;\r\n\r\n this._releaseAllVisuals();\r\n\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._resetObjects();\r\n\r\n if (this._gfx) {\r\n gfxutils.clearTree(this._gfx.pivot);\r\n this._gfx.renderer2d.reset();\r\n }\r\n\r\n this.setNeedRender();\r\n};\r\n\r\nMiew.prototype._resetScene = function () {\r\n this._objectControls.reset();\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n this.resetReps();\r\n this.resetPivot();\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype.resetView = function () {\r\n // reset controls\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._resetScene();\r\n\r\n // reset selection\r\n this._forEachComplexVisual((visual) => {\r\n visual.updateSelectionMask({});\r\n visual.rebuildSelectionGeometry();\r\n });\r\n};\r\n\r\nMiew.prototype._export = function (format) {\r\n const TheExporter = _.head(io.exporters.find({ format }));\r\n if (!TheExporter) {\r\n this.logger.error('Could not find suitable exporter for this source');\r\n return Promise.reject(new Error('Could not find suitable exporter for this source'));\r\n }\r\n this.dispatchEvent({ type: 'exporting' });\r\n\r\n if (this._visuals[this._curVisualName] instanceof ComplexVisual) {\r\n let dataSource = null;\r\n if (TheExporter.SourceClass === ComplexVisual) {\r\n dataSource = this._visuals[this._curVisualName];\r\n } else if (TheExporter.SourceClass === Complex) {\r\n dataSource = this._visuals[this._curVisualName]._complex;\r\n }\r\n const exporter = new TheExporter(dataSource, { miewVersion: Miew.VERSION });\r\n return exporter.export().then((data) => data);\r\n }\r\n if (this._visuals[this._curVisualName] instanceof VolumeVisual) {\r\n return Promise.reject(new Error('Sorry, exporter for volume data not implemented yet'));\r\n }\r\n return Promise.reject(new Error('Unexpected format of data'));\r\n};\r\n\r\nconst rePdbId = /^(?:(pdb|cif|ccp4|dsn6):\\s*)?(\\d[a-z\\d]{3})$/i;\r\nconst rePubchem = /^(?:pc|pubchem):\\s*([a-z]+)$/i;\r\nconst reUrlScheme = /^([a-z][a-z\\d\\-+.]*):/i;\r\n\r\nfunction resolveSourceShortcut(source, opts) {\r\n if (!_.isString(source)) {\r\n return source;\r\n }\r\n\r\n // e.g. \"cif:1CRN\"\r\n const matchesPdbId = rePdbId.exec(source);\r\n if (matchesPdbId) {\r\n let [, format = 'pdb', id] = matchesPdbId;\r\n\r\n format = format.toLowerCase();\r\n id = id.toUpperCase();\r\n\r\n switch (format) {\r\n case 'pdb':\r\n source = `https://files.rcsb.org/download/${id}.pdb`;\r\n break;\r\n case 'cif':\r\n source = `https://files.rcsb.org/download/${id}.cif`;\r\n break;\r\n case 'ccp4':\r\n source = `https://www.ebi.ac.uk/pdbe/coordinates/files/${id.toLowerCase()}.ccp4`;\r\n break;\r\n case 'dsn6':\r\n source = `https://edmaps.rcsb.org/maps/${id.toLowerCase()}_2fofc.dsn6`;\r\n break;\r\n default:\r\n throw new Error('Unexpected data format shortcut');\r\n }\r\n\r\n opts.fileType = format;\r\n opts.fileName = `${id}.${format}`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // e.g. \"pc:aspirin\"\r\n const matchesPubchem = rePubchem.exec(source);\r\n if (matchesPubchem) {\r\n const compound = matchesPubchem[1].toLowerCase();\r\n source = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${compound}/JSON?record_type=3d`;\r\n opts.fileType = 'pubchem';\r\n opts.fileName = `${compound}.json`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // otherwise is should be an URL\r\n if (opts.sourceType === 'url' || opts.sourceType === undefined) {\r\n opts.sourceType = 'url';\r\n\r\n // e.g. \"./data/1CRN.pdb\"\r\n if (!reUrlScheme.test(source)) {\r\n source = utils.resolveURL(source);\r\n }\r\n }\r\n\r\n return source;\r\n}\r\n\r\nfunction updateBinaryMode(opts) {\r\n let { binary } = opts;\r\n\r\n // detect by format\r\n if (opts.fileType !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n } else {\r\n throw new Error('Could not find suitable parser for this format');\r\n }\r\n }\r\n\r\n // detect by file extension\r\n if (binary === undefined && opts.fileExt !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ ext: opts.fileExt }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n }\r\n }\r\n\r\n // temporary workaround for animation\r\n if (opts.fileExt !== undefined && opts.fileExt.toLowerCase() === '.man') {\r\n opts.binary = true;\r\n opts.animation = true; // who cares?\r\n }\r\n\r\n // update if detected\r\n if (binary !== undefined) {\r\n if (opts.binary !== undefined && opts.binary !== binary) {\r\n opts.context.logger.warn('Overriding incorrect binary mode');\r\n }\r\n }\r\n\r\n opts.binary = binary || false;\r\n}\r\n\r\nfunction _fetchData(source, opts, job) {\r\n return new Promise(((resolve) => {\r\n if (job.shouldCancel()) {\r\n throw new Error('Operation cancelled');\r\n }\r\n job.notify({ type: 'fetching' });\r\n\r\n // allow for source shortcuts\r\n source = resolveSourceShortcut(source, opts);\r\n\r\n // detect a proper loader\r\n const TheLoader = _.head(io.loaders.find({ type: opts.sourceType, source }));\r\n if (!TheLoader) {\r\n throw new Error(LOADER_NOT_FOUND);\r\n }\r\n\r\n // split file name\r\n const fileName = opts.fileName || TheLoader.extractName(source);\r\n if (fileName) {\r\n const [name, fileExt] = utils.splitFileName(fileName);\r\n _.defaults(opts, { name, fileExt, fileName });\r\n }\r\n\r\n // should it be text or binary?\r\n updateBinaryMode(opts);\r\n\r\n // FIXME: All new settings retrieved from server are applied after the loading is complete. However, we need some\r\n // flags to alter the loading process itself. Here we apply them in advance. Dirty hack. Kill the server, remove\r\n // all hacks and everybody's happy.\r\n let newOptions = _.get(opts, 'preset.expression');\r\n if (!_.isUndefined(newOptions)) {\r\n newOptions = JSON.parse(newOptions);\r\n if (newOptions && newOptions.settings) {\r\n const keys = ['singleUnit'];\r\n for (let keyIndex = 0, keyCount = keys.length; keyIndex < keyCount; ++keyIndex) {\r\n const key = keys[keyIndex];\r\n const value = _.get(newOptions.settings, key);\r\n if (!_.isUndefined(value)) {\r\n settings.set(key, value);\r\n }\r\n }\r\n }\r\n }\r\n\r\n // create a loader\r\n const loader = new TheLoader(source, opts);\r\n loader.context = opts.context;\r\n job.addEventListener('cancel', () => loader.abort());\r\n\r\n loader.addEventListener('progress', (event) => {\r\n if (event.lengthComputable && event.total > 0) {\r\n reportProgress(loader.logger, 'Fetching', event.loaded / event.total);\r\n } else {\r\n reportProgress(loader.logger, 'Fetching');\r\n }\r\n });\r\n\r\n console.time('fetch');\r\n const promise = loader.load()\r\n .then((data) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.info('Fetching finished');\r\n job.notify({ type: 'fetchingDone', data });\r\n return data;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Fetching failed');\r\n job.notify({ type: 'fetchingDone', error });\r\n throw error;\r\n });\r\n resolve(promise);\r\n }));\r\n}\r\n\r\nfunction _parseData(data, opts, job) {\r\n if (job.shouldCancel()) {\r\n return Promise.reject(new Error('Operation cancelled'));\r\n }\r\n\r\n job.notify({ type: 'parsing' });\r\n\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType, ext: opts.fileExt, data }));\r\n if (!TheParser) {\r\n return Promise.reject(new Error('Could not find suitable parser'));\r\n }\r\n\r\n const parser = new TheParser(data, opts);\r\n parser.context = opts.context;\r\n job.addEventListener('cancel', () => parser.abort());\r\n\r\n console.time('parse');\r\n return parser.parse()\r\n .then((dataSet) => {\r\n console.timeEnd('parse');\r\n job.notify({ type: 'parsingDone', data: dataSet });\r\n return dataSet;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('parse');\r\n opts.error = error;\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Parsing failed');\r\n job.notify({ type: 'parsingDone', error });\r\n throw error;\r\n });\r\n}\r\n\r\n/**\r\n * Load molecule asynchronously.\r\n * @param {string|File} source - Molecule source to load (e.g. PDB ID, URL or File object).\r\n * @param {object=} opts - Options.\r\n * @param {string=} opts.sourceType - Data source type (e.g. 'url', 'file').\r\n * @param {string=} opts.fileType - Data contents type (e.g. 'pdb', 'cml').\r\n * @param {string=} opts.mdFile - .nc file path.\r\n * @param {boolean=} opts.keepRepsInfo - prevent reset of object and reps information.\r\n * @returns {Promise} name of the visual that was added to the viewer\r\n */\r\nMiew.prototype.load = function (source, opts) {\r\n opts = _.merge({}, opts, {\r\n context: this,\r\n });\r\n\r\n // for a single-file scenario\r\n if (!this.settings.now.use.multiFile) {\r\n // abort all loaders in progress\r\n if (this._loading.length) {\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n }\r\n\r\n // reset\r\n if (!opts.animation) { // FIXME: sometimes it is set AFTERWARDS!\r\n this.reset(true);\r\n }\r\n }\r\n\r\n this._interpolator.reset();\r\n\r\n this.dispatchEvent({ type: 'loading', options: opts, source });\r\n\r\n const job = new JobHandle();\r\n this._loading.push(job);\r\n job.addEventListener('notification', (e) => {\r\n this.dispatchEvent(e.slaveEvent);\r\n });\r\n\r\n this._spinner.spin(this._container);\r\n\r\n const onLoadEnd = (anything) => {\r\n const jobIndex = this._loading.indexOf(job);\r\n if (jobIndex !== -1) {\r\n this._loading.splice(jobIndex, 1);\r\n }\r\n this._spinner.stop();\r\n this._refreshTitle();\r\n job.notify({ type: 'loadingDone', anything });\r\n return anything;\r\n };\r\n\r\n return _fetchData(source, opts, job)\r\n .then((data) => _parseData(data, opts, job))\r\n .then((object) => {\r\n const name = this._onLoad(object, opts);\r\n return onLoadEnd(name);\r\n })\r\n .catch((err) => {\r\n this.logger.error('Could not load data');\r\n this.logger.debug(err);\r\n throw onLoadEnd(err);\r\n });\r\n};\r\n\r\n/**\r\n * Unload molecule (delete corresponding visual).\r\n * @param {string=} name - name of the visual\r\n */\r\nMiew.prototype.unload = function (name) {\r\n this._removeVisual(name || this.getCurrentVisual());\r\n this.resetPivot();\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n};\r\n\r\n/**\r\n * Start new animation. Now is broken.\r\n * @param fileData - new data to animate\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._startAnimation = function (fileData) {\r\n this._stopAnimation();\r\n const self = this;\r\n const visual = this._getComplexVisual();\r\n if (visual === null) {\r\n this.logger.error('Unable to start animation - no molecule is loaded.');\r\n return;\r\n }\r\n try {\r\n this._frameInfo = new FrameInfo(\r\n visual.getComplex(),\r\n fileData,\r\n {\r\n onLoadStatusChanged() {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo ? self._frameInfo.isLoading : true,\r\n },\r\n });\r\n },\r\n onError(message) {\r\n self._stopAnimation();\r\n self.logger.error(message);\r\n },\r\n },\r\n );\r\n } catch {\r\n this.logger.error('Animation file does not fit to current complex!');\r\n return;\r\n }\r\n this._continueAnimation();\r\n};\r\n\r\n/**\r\n * Pause current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._pauseAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n this._isAnimating = false;\r\n clearInterval(this._animInterval);\r\n this._animInterval = null;\r\n if (this._frameInfo) {\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: this._isAnimating,\r\n isLoading: this._frameInfo.isLoading,\r\n },\r\n });\r\n }\r\n};\r\n\r\n/**\r\n * Continue current animation after pausing. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._continueAnimation = function () {\r\n this._isAnimating = true;\r\n let minFrameTime = 1000 / settings.now.maxfps;\r\n minFrameTime = Number.isNaN(minFrameTime) ? 0 : minFrameTime;\r\n const self = this;\r\n const { pivot } = self._gfx;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.resetSelectionMask();\r\n visual.rebuildSelectionGeometry();\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n }\r\n this._animInterval = setInterval(() => {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo.isLoading,\r\n },\r\n });\r\n if (self._frameInfo.frameIsReady) {\r\n pivot.updateToFrame(self._frameInfo);\r\n self._updateObjsToFrame(self._frameInfo);\r\n self._refreshTitle(` Frame ${self._frameInfo._currFrame} of ${self._frameInfo._framesCount\r\n } time interval - ${self._frameInfo._timeStep}`);\r\n try {\r\n self._frameInfo.nextFrame();\r\n } catch {\r\n self.logger.error('Error during animation');\r\n self._stopAnimation();\r\n return;\r\n }\r\n self._needRender = true;\r\n }\r\n }, minFrameTime);\r\n};\r\n\r\n/**\r\n * Stop current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._stopAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n clearInterval(this._animInterval);\r\n this._frameInfo.disableEvents();\r\n this._frameInfo = null;\r\n this._animInterval = null;\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: null,\r\n });\r\n};\r\n\r\n/**\r\n * Invoked upon successful loading of some data source\r\n * @param {DataSource} dataSource - Data source for visualization (molecular complex or other)\r\n * @param {object} opts - Options.\r\n * @private\r\n */\r\nMiew.prototype._onLoad = function (dataSource, opts) {\r\n const gfx = this._gfx;\r\n let visualName = null;\r\n\r\n if (opts.animation) {\r\n this._refreshTitle();\r\n this._startAnimation(dataSource);\r\n return null;\r\n }\r\n this._stopAnimation();\r\n if (!opts || !opts.keepRepsInfo) {\r\n this._opts.reps = null;\r\n this._opts._objects = null;\r\n }\r\n\r\n if (dataSource.id === 'Complex') {\r\n const complex = dataSource;\r\n\r\n // update title\r\n if (opts.fileName) {\r\n complex.name = complex.name || removeExtension(opts.fileName).toUpperCase();\r\n } else if (opts.amberFileName) {\r\n complex.name = complex.name || removeExtension(opts.amberFileName).toUpperCase();\r\n } else {\r\n complex.name = `Dynamic ${opts.fileType} molecule`;\r\n }\r\n\r\n visualName = this._addVisual(new ComplexVisual(complex.name, complex));\r\n this._curVisualName = visualName;\r\n\r\n const desc = this.info();\r\n this.logger.info(`Parsed ${opts.fileName} (${\r\n desc.atoms} atoms, ${\r\n desc.bonds} bonds, ${\r\n desc.residues} residues, ${\r\n desc.chains} chains).`);\r\n\r\n if (_.isNumber(this._opts.unit)) {\r\n complex.setCurrentUnit(this._opts.unit);\r\n }\r\n\r\n if (opts.preset) {\r\n // ...removed server access...\r\n } else if (settings.now.autoPreset) {\r\n switch (opts.fileType) {\r\n case 'cml':\r\n this.resetReps('small');\r\n break;\r\n case 'pdb':\r\n case 'mmtf':\r\n case 'cif':\r\n if (hasValidResidues(complex)) {\r\n this.resetReps('macro');\r\n } else {\r\n this.resetReps('small');\r\n }\r\n break;\r\n default:\r\n this.resetReps('default');\r\n break;\r\n }\r\n } else {\r\n this.resetReps('default');\r\n }\r\n } else if (dataSource.id === 'Volume') {\r\n this.resetEd();\r\n visualName = this._onLoadEd(dataSource);\r\n }\r\n\r\n gfx.camera.updateProjectionMatrix();\r\n this._updateFog();\r\n\r\n // reset global transform\r\n gfx.root.resetTransform();\r\n this.resetPivot();\r\n\r\n // set scale to fit everything on the screen\r\n this._objectControls.setScale(settings.now.radiusToFit / this._getBSphereRadius());\r\n\r\n this._resetObjects();\r\n\r\n if (settings.now.autoResolution) {\r\n this._tweakResolution();\r\n }\r\n\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n this._refreshTitle();\r\n\r\n return visualName;\r\n};\r\n\r\nMiew.prototype.resetEd = function () {\r\n if (this._edLoader) {\r\n this._edLoader.abort();\r\n this._edLoader = null;\r\n }\r\n\r\n // free all resources\r\n this._removeVisual(this._getVolumeVisual());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype.loadEd = function (source) {\r\n this.resetEd();\r\n\r\n const TheLoader = _.head(io.loaders.find({ source }));\r\n if (!TheLoader) {\r\n this.logger.error(LOADER_NOT_FOUND);\r\n return Promise.reject(new Error(LOADER_NOT_FOUND));\r\n }\r\n\r\n const loader = this._edLoader = new TheLoader(source, { binary: true });\r\n loader.context = this;\r\n return loader.load().then((data) => {\r\n const TheParser = _.head(io.parsers.find({ format: 'ccp4' }));\r\n if (!TheParser) {\r\n throw new Error(PARSER_NOT_FOUND);\r\n }\r\n const parser = new TheParser(data);\r\n parser.context = this;\r\n return parser.parse().then((dataSource) => {\r\n this._onLoadEd(dataSource);\r\n });\r\n }).catch((error) => {\r\n this.logger.error('Could not load ED data');\r\n this.logger.debug(error);\r\n });\r\n};\r\n\r\nMiew.prototype._onLoadEd = function (dataSource) {\r\n dataSource.normalize();\r\n\r\n const volumeVisual = new VolumeVisual('volume', dataSource);\r\n volumeVisual.getMesh().layers.set(gfxutils.LAYERS.VOLUME); // volume mesh is not visible to common render\r\n const visualName = this._addVisual(volumeVisual);\r\n\r\n this._needRender = true;\r\n return visualName;\r\n};\r\n\r\nMiew.prototype._needRebuild = function () {\r\n let needsRebuild = false;\r\n this._forEachComplexVisual((visual) => {\r\n needsRebuild = needsRebuild || visual.needsRebuild();\r\n });\r\n return needsRebuild;\r\n};\r\n\r\nMiew.prototype._rebuildObjects = function () {\r\n const self = this;\r\n const gfx = this._gfx;\r\n let i;\r\n let n;\r\n\r\n // remove old object geometry\r\n const toRemove = [];\r\n for (i = 0; i < gfx.pivot.children.length; ++i) {\r\n const child = gfx.pivot.children[i];\r\n if (!(child instanceof Visual)) {\r\n toRemove.push(child);\r\n }\r\n }\r\n for (i = 0; i < toRemove.length; ++i) {\r\n toRemove[i].parent.remove(toRemove[i]);\r\n }\r\n\r\n setTimeout(() => {\r\n const objList = self._objects;\r\n for (i = 0, n = objList.length; i < n; ++i) {\r\n const obj = objList[i];\r\n if (obj.needsRebuild) {\r\n obj.build();\r\n }\r\n if (obj.getGeometry()) {\r\n gfx.pivot.add(obj.getGeometry());\r\n }\r\n }\r\n }, 10);\r\n};\r\n\r\nMiew.prototype.changeUnit = function (unitIdx, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n throw new Error('There is no complex to change!');\r\n }\r\n\r\n function currentUnitInfo() {\r\n const unit = visual ? visual.getComplex().getCurrentUnit() : 0;\r\n const type = unit > 0 ? (`Bio molecule ${unit}`) : 'Asymmetric unit';\r\n return `Current unit: ${unit} (${type})`;\r\n }\r\n\r\n if (unitIdx === undefined) {\r\n return currentUnitInfo();\r\n }\r\n if (_.isString(unitIdx)) {\r\n unitIdx = Math.max(parseInt(unitIdx, 10), 0);\r\n }\r\n if (visual.getComplex().setCurrentUnit(unitIdx)) {\r\n this._resetScene();\r\n this._updateInfoPanel();\r\n }\r\n return currentUnitInfo();\r\n};\r\n\r\n/**\r\n * Start to rebuild geometry asynchronously.\r\n */\r\nMiew.prototype.rebuild = function () {\r\n if (this._building) {\r\n this.logger.warn('Miew.rebuild(): already building!');\r\n return;\r\n }\r\n this._building = true;\r\n\r\n this.dispatchEvent({ type: 'rebuilding' });\r\n\r\n this._rebuildObjects();\r\n\r\n this._gfx.renderer2d.reset();\r\n\r\n const rebuildActions = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.needsRebuild()) {\r\n rebuildActions.push(visual.rebuild().then(() => new Promise(((resolve) => {\r\n visual.rebuildSelectionGeometry();\r\n resolve();\r\n }))));\r\n }\r\n });\r\n\r\n // Start asynchronous rebuild\r\n const self = this;\r\n this._spinner.spin(this._container);\r\n Promise.all(rebuildActions).then(() => {\r\n self._spinner.stop();\r\n\r\n self._needRender = true;\r\n\r\n self._refreshTitle();\r\n this.dispatchEvent({ type: 'buildingDone' });\r\n self._building = false;\r\n });\r\n};\r\n\r\n/** Mark all representations for rebuilding */\r\nMiew.prototype.rebuildAll = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setNeedsRebuild();\r\n });\r\n};\r\n\r\nMiew.prototype._refreshTitle = function (appendix) {\r\n let title;\r\n appendix = appendix === undefined ? '' : appendix;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n title = visual.getComplex().name;\r\n const rep = visual.repGet(visual.repCurrent());\r\n title += (rep ? ` – ${rep.mode.name} Mode` : '');\r\n } else {\r\n title = Object.keys(this._visuals).length > 0 ? 'Unknown' : 'No Data';\r\n }\r\n title += appendix;\r\n\r\n this.dispatchEvent({ type: 'titleChanged', data: title });\r\n};\r\n\r\nMiew.prototype.setNeedRender = function () {\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._extractRepresentation = function () {\r\n const changed = [];\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCount() === 0) {\r\n return;\r\n }\r\n\r\n const selector = visual.buildSelectorFromMask(1 << visual.getSelectionBit());\r\n const defPreset = settings.now.presets.default;\r\n const res = visual.repAdd({\r\n selector,\r\n mode: defPreset[0].mode.id,\r\n colorer: defPreset[0].colorer.id,\r\n material: defPreset[0].material.id,\r\n });\r\n if (!res) {\r\n if (visual.repCount() === ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n this.logger.warn(`Number of representations is limited to ${ComplexVisual.NUM_REPRESENTATION_BITS}`);\r\n }\r\n return;\r\n }\r\n\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n visual.repCurrent(res.index);\r\n\r\n changed.push(visual.name);\r\n });\r\n\r\n if (changed.length > 0) {\r\n this.logger.report(`New representation from selection for complexes: ${changed.join(', ')}`);\r\n }\r\n};\r\n\r\n/**\r\n * Change current representation list.\r\n * @param {array} reps - Representation list.\r\n */\r\nMiew.prototype._setReps = function (reps) {\r\n reps = reps || (this._opts && this._opts.reps) || [];\r\n this._forEachComplexVisual((visual) => visual.resetReps(reps));\r\n};\r\n\r\n/**\r\n * Apply existing preset to current scene.\r\n * @param preset\r\n */\r\nMiew.prototype.applyPreset = function (preset) {\r\n const { presets } = settings.now;\r\n const presList = [\r\n preset || settings.defaults.preset,\r\n settings.defaults.preset,\r\n Object.keys(presets)[0],\r\n ];\r\n let reps = null;\r\n for (let i = 0; !reps && i < presList.length; ++i) {\r\n settings.set('preset', presList[i]);\r\n reps = presets[settings.now.preset];\r\n if (!reps) {\r\n this.logger.warn(`Unknown preset \"${settings.now.preset}\"`);\r\n }\r\n }\r\n this._setReps(reps);\r\n};\r\n\r\n/**\r\n * Reset current representation list to initial values.\r\n * @param {string} [preset] - The source preset in case of uninitialized representation list.\r\n */\r\nMiew.prototype.resetReps = function (preset) {\r\n const reps = this._opts && this._opts.reps;\r\n if (reps) {\r\n this._setReps(reps);\r\n } else {\r\n this.applyPreset(preset);\r\n }\r\n};\r\n\r\n/**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\nMiew.prototype.repCount = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repCount() : 0;\r\n};\r\n\r\n/**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {string=} [name] - Complex name. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\nMiew.prototype.repCurrent = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n const newIdx = visual ? visual.repCurrent(index) : -1;\r\n if (index && newIdx !== index) {\r\n this.logger.warn(`Representation ${index} was not found. Current rep remains unchanged.`);\r\n }\r\n return newIdx;\r\n};\r\n\r\n/**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {?object} Representation description.\r\n */\r\nMiew.prototype.rep = function (index, rep) {\r\n const visual = this._getComplexVisual('');\r\n if (!visual) {\r\n return null;\r\n }\r\n const res = visual.rep(index, rep);\r\n if (res.status === 'created') {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n } else if (res.status === 'changed') {\r\n this.dispatchEvent({ type: 'repChanged', index: res.index, name: visual.name });\r\n }\r\n return res.desc;\r\n};\r\n\r\n/**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\nMiew.prototype.repGet = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repGet(index) : null;\r\n};\r\n\r\n/**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {number} Index of the new representation.\r\n */\r\nMiew.prototype.repAdd = function (rep, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return -1;\r\n }\r\n\r\n const res = visual.repAdd(rep);\r\n if (res) {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name });\r\n return res.index;\r\n }\r\n return -1;\r\n};\r\n\r\n/**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\nMiew.prototype.repRemove = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n visual.repRemove(index);\r\n this.dispatchEvent({ type: 'repRemoved', index, name });\r\n};\r\n\r\n/**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\nMiew.prototype.repHide = function (index, hide, name) {\r\n this._needRender = true;\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repHide(index, hide) : null;\r\n};\r\n\r\nMiew.prototype._setEditMode = function (mode) {\r\n this._editMode = mode;\r\n\r\n const elem = this._msgMode;\r\n if (elem) {\r\n elem.style.opacity = (mode === EDIT_MODE.COMPLEX) ? 0.0 : 1.0;\r\n\r\n if (mode !== EDIT_MODE.COMPLEX) {\r\n const t = elem.getElementsByTagName('p')[0];\r\n t.innerHTML = (mode === EDIT_MODE.COMPONENT) ? 'COMPONENT EDIT MODE' : 'FRAGMENT EDIT MODE';\r\n }\r\n }\r\n\r\n this.dispatchEvent({ type: 'editModeChanged', data: mode === EDIT_MODE.COMPLEX });\r\n};\r\n\r\nMiew.prototype._enterComponentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const editors = [];\r\n this._forEachComplexVisual((visual) => {\r\n const editor = visual.beginComponentEdit();\r\n if (editor) {\r\n editors.push(editor);\r\n }\r\n });\r\n\r\n if (editors.length === 0) {\r\n return;\r\n }\r\n\r\n this._editors = editors;\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- ON');\r\n this._setEditMode(EDIT_MODE.COMPONENT);\r\n this._objectControls.keysTranslateObj(true);\r\n};\r\n\r\nMiew.prototype._applyComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._needRender = true;\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._enterFragmentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const selectedVisuals = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual instanceof ComplexVisual\r\n && visual.getSelectionCount() > 0) {\r\n selectedVisuals.push(visual);\r\n }\r\n });\r\n\r\n if (selectedVisuals.length !== 1) {\r\n // either we have no selection or\r\n // we have selected atoms in two or more visuals -- not supported\r\n return;\r\n }\r\n\r\n const editor = selectedVisuals[0].beginFragmentEdit();\r\n if (!editor) {\r\n return;\r\n }\r\n this._editors = [editor];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- ON (single bond)');\r\n this._setEditMode(EDIT_MODE.FRAGMENT);\r\n this._objectControls.allowTranslation(false);\r\n this._objectControls.allowAltObjFreeRotation(editor.isFreeRotationAllowed());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._applyFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onPick = function (event) {\r\n if (!settings.now.picking) {\r\n // picking is disabled\r\n return;\r\n }\r\n\r\n if (this._animInterval !== null) {\r\n // animation playback is on\r\n return;\r\n }\r\n\r\n if (this._editMode === EDIT_MODE.FRAGMENT) {\r\n // prevent picking in fragment edit mode\r\n return;\r\n }\r\n\r\n if (this._objectControls.isEditingAltObj()) {\r\n // prevent picking during component rotation\r\n return;\r\n }\r\n\r\n // update last pick & find complex\r\n let complex = null;\r\n if (event.obj.atom) {\r\n complex = event.obj.atom.residue.getChain().getComplex();\r\n this._lastPick = event.obj.atom;\r\n } else if (event.obj.residue) {\r\n complex = event.obj.residue.getChain().getComplex();\r\n this._lastPick = event.obj.residue;\r\n } else if (event.obj.chain) {\r\n complex = event.obj.chain.getComplex();\r\n this._lastPick = event.obj.chain;\r\n } else if (event.obj.molecule) {\r\n complex = event.obj.molecule.complex;\r\n this._lastPick = event.obj.molecule;\r\n } else {\r\n this._lastPick = null;\r\n }\r\n\r\n function _updateSelection(visual) {\r\n visual.updateSelectionMask(event.obj);\r\n visual.rebuildSelectionGeometry();\r\n }\r\n\r\n // update visual\r\n if (complex) {\r\n const visual = this._getVisualForComplex(complex);\r\n if (visual) {\r\n _updateSelection(visual);\r\n this._needRender = true;\r\n }\r\n } else {\r\n this._forEachComplexVisual(_updateSelection);\r\n this._needRender = true;\r\n }\r\n\r\n this._updateInfoPanel();\r\n this.dispatchEvent(event);\r\n};\r\n\r\nMiew.prototype._onKeyDown = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n // editing keys\r\n if (settings.now.editing) {\r\n switch (event.code) {\r\n case 'KeyC':\r\n this._enterComponentEditMode();\r\n break;\r\n case 'KeyF':\r\n this._enterFragmentEditMode();\r\n break;\r\n case 'KeyA':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._applyComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._applyFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n case 'KeyD':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._discardComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._discardFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n default:\r\n }\r\n }\r\n\r\n // other keys\r\n switch (event.code) {\r\n case 'NumpadAdd':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.expandSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n case 'NumpadSubtract':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.shrinkSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nMiew.prototype._onKeyUp = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n if (event.code === 'KeyX') {\r\n this._extractRepresentation();\r\n }\r\n};\r\n\r\nMiew.prototype._updateInfoPanel = function () {\r\n const info = this._msgAtomInfo.getElementsByTagName('p')[0];\r\n let atom;\r\n let residue;\r\n\r\n let count = 0;\r\n this._forEachComplexVisual((visual) => {\r\n count += visual.getSelectionCount();\r\n });\r\n\r\n while (info.firstChild) {\r\n info.removeChild(info.firstChild);\r\n }\r\n\r\n if (count === 0) {\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n return;\r\n }\r\n\r\n let firstLine = `${String(count)} atom${count !== 1 ? 's' : ''} selected`;\r\n if (this._lastPick !== null) {\r\n firstLine += ', the last pick:';\r\n }\r\n let secondLine = '';\r\n let aName = '';\r\n let coordLine = '';\r\n\r\n if (this._lastPick instanceof Atom) {\r\n atom = this._lastPick;\r\n residue = atom.residue;\r\n\r\n aName = atom.name;\r\n const location = (atom.location !== 32) ? String.fromCharCode(atom.location) : ''; // 32 is code of white-space\r\n secondLine = `${atom.element.fullName} #${atom.serial}${location}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}.`;\r\n secondLine += aName;\r\n\r\n coordLine = `Coord: (${atom.position.x.toFixed(2).toString()},\\\r\n ${atom.position.y.toFixed(2).toString()},\\\r\n ${atom.position.z.toFixed(2).toString()})`;\r\n } else if (this._lastPick instanceof Residue) {\r\n residue = this._lastPick;\r\n\r\n secondLine = `${residue._type._fullName}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}`;\r\n } else if (this._lastPick instanceof Chain) {\r\n secondLine = `chain ${this._lastPick._name}`;\r\n } else if (this._lastPick instanceof Molecule) {\r\n secondLine = `molecule ${this._lastPick._name}`;\r\n }\r\n\r\n info.appendChild(document.createTextNode(firstLine));\r\n\r\n if (secondLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(secondLine));\r\n }\r\n\r\n if (coordLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(coordLine));\r\n }\r\n\r\n this._msgAtomInfo.style.opacity = 1.0;\r\n};\r\n\r\nMiew.prototype._getAltObj = function () {\r\n if (this._editors) {\r\n let altObj = null;\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n const nextAltObj = this._editors[i].getAltObj();\r\n if (nextAltObj.objects.length > 0) {\r\n if (altObj) {\r\n // we have selected atoms in two or more visuals -- not supported\r\n altObj = null;\r\n break;\r\n }\r\n altObj = nextAltObj;\r\n }\r\n }\r\n if (altObj) {\r\n return altObj;\r\n }\r\n }\r\n\r\n return {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n};\r\n\r\nMiew.prototype.resetPivot = (function () {\r\n const boundingBox = new THREE.Box3();\r\n const center = new THREE.Vector3();\r\n\r\n return function () {\r\n boundingBox.makeEmpty();\r\n this._forEachVisual((visual) => {\r\n boundingBox.union(visual.getBoundaries().boundingBox);\r\n });\r\n\r\n boundingBox.getCenter(center);\r\n this._objectControls.setPivot(center.negate());\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotResidue = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (residue) {\r\n const visual = this._getVisualForComplex(residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n if (residue._controlPoint) {\r\n center.copy(residue._controlPoint);\r\n } else {\r\n let x = 0;\r\n let y = 0;\r\n let z = 0;\r\n const amount = residue._atoms.length;\r\n for (let i = 0; i < amount; ++i) {\r\n const p = residue._atoms[i].position;\r\n x += p.x / amount;\r\n y += p.y / amount;\r\n z += p.z / amount;\r\n }\r\n center.set(x, y, z);\r\n }\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotAtom = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (atom) {\r\n const visual = this._getVisualForComplex(atom.residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n center.copy(atom.position);\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.getSelectionCenter = (function () {\r\n const _centerInVisual = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n return function (center, includesAtom, selector) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCenter(_centerInVisual, includesAtom, selector || visual.getSelectionBit())) {\r\n center.add(_centerInVisual);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.negate();\r\n return true;\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotSubset = (function () {\r\n const _center = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n function _includesInCurSelection(atom, selectionBit) {\r\n return atom.mask & (1 << selectionBit);\r\n }\r\n\r\n function _includesInSelector(atom, selector) {\r\n return selector.selector.includesAtom(atom);\r\n }\r\n\r\n return function (selector) {\r\n const includesAtom = (selector) ? _includesInSelector : _includesInCurSelection;\r\n\r\n if (this.getSelectionCenter(_center, includesAtom, selector)) {\r\n this._objectControls.setPivot(_center);\r\n this.dispatchEvent({ type: 'transform' });\r\n } else {\r\n this.logger.warn('selection is empty. Center operation not performed');\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Makes a screenshot.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n * @returns {string} Data URL representing the image contents.\r\n */\r\nMiew.prototype.screenshot = function (width, height) {\r\n const gfx = this._gfx;\r\n const deviceWidth = gfx.renderer.domElement.width;\r\n const deviceHeight = gfx.renderer.domElement.height;\r\n\r\n function fov2Tan(fov) {\r\n return Math.tan(THREE.MathUtils.degToRad(0.5 * fov));\r\n }\r\n\r\n function tan2Fov(tan) {\r\n return THREE.MathUtils.radToDeg(Math.atan(tan)) * 2.0;\r\n }\r\n\r\n function getDataURL() {\r\n let dataURL;\r\n const currBrowser = utils.getBrowser();\r\n\r\n if (currBrowser === utils.browserType.SAFARI) {\r\n const canvas = document.createElement('canvas');\r\n const canvasContext = canvas.getContext('2d');\r\n\r\n canvas.width = width === undefined ? deviceWidth : width;\r\n canvas.height = height === undefined ? deviceHeight : height;\r\n\r\n canvasContext.drawImage(gfx.renderer.domElement, 0, 0, canvas.width, canvas.height);\r\n dataURL = canvas.toDataURL('image/png');\r\n } else {\r\n // Copy current canvas to screenshot\r\n dataURL = gfx.renderer.domElement.toDataURL('image/png');\r\n }\r\n return dataURL;\r\n }\r\n height = height || width;\r\n\r\n let screenshotURI;\r\n if ((width === undefined && height === undefined)\r\n || (width === deviceWidth && height === deviceHeight)) {\r\n // renderer.domElement.toDataURL('image/png') returns flipped image in Safari\r\n // It hasn't been resolved yet, but getScreenshotSafari()\r\n // fixes it using an extra canvas.\r\n screenshotURI = getDataURL();\r\n } else {\r\n const originalAspect = gfx.camera.aspect;\r\n const originalFov = gfx.camera.fov;\r\n const originalTanFov2 = fov2Tan(gfx.camera.fov);\r\n\r\n // screenshot should contain the principal area of interest (a centered square touching screen sides)\r\n const areaOfInterestSize = Math.min(gfx.width, gfx.height);\r\n const areaOfInterestTanFov2 = originalTanFov2 * areaOfInterestSize / gfx.height;\r\n\r\n // set appropriate camera aspect & FOV\r\n const shotAspect = width / height;\r\n gfx.renderer.setPixelRatio(1);\r\n gfx.camera.aspect = shotAspect;\r\n gfx.camera.fov = tan2Fov(areaOfInterestTanFov2 / Math.min(shotAspect, 1.0));\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n // resize canvas to the required size of screenshot\r\n gfx.renderer.setDrawingBufferSize(width, height, 1);\r\n\r\n // make screenshot\r\n this._renderFrame(settings.now.stereo);\r\n screenshotURI = getDataURL();\r\n\r\n // restore original camera & canvas proportions\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.camera.aspect = originalAspect;\r\n gfx.camera.fov = originalFov;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.renderer.setDrawingBufferSize(gfx.width, gfx.height, window.devicePixelRatio);\r\n this._needRender = true;\r\n }\r\n\r\n return screenshotURI;\r\n};\r\n\r\n/**\r\n * Makes screenshot and initiates a download.\r\n * @param {string} [filename] - Name of a file. Default to a 'screenshot-XXXXX.png', where XXXXX is a current\r\n * date/time in seconds.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n */\r\nMiew.prototype.screenshotSave = function (filename, width, height) {\r\n const uri = this.screenshot(width, height);\r\n utils.shotDownload(uri, filename);\r\n};\r\n\r\nMiew.prototype.save = function (opts) {\r\n this._export(opts.fileType).then((dataString) => {\r\n const filename = this._visuals[this._curVisualName]._complex.name;\r\n utils.download(dataString, filename, opts.fileType);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone' });\r\n }).catch((error) => {\r\n this.logger.error('Could not export data');\r\n this.logger.debug(error);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone', error });\r\n });\r\n};\r\n\r\nMiew.prototype._tweakResolution = function () {\r\n const maxPerf = [\r\n ['poor', 100],\r\n ['low', 500],\r\n ['medium', 1000],\r\n ['high', 5000],\r\n ['ultra', Number.MAX_VALUE],\r\n ];\r\n\r\n let atomCount = 0;\r\n this._forEachComplexVisual((visual) => {\r\n atomCount += visual.getComplex().getAtomCount();\r\n });\r\n\r\n if (atomCount > 0) {\r\n const performance = this._gfxScore * 10e5 / atomCount;\r\n // set resolution based on estimated performance\r\n for (let i = 0; i < maxPerf.length; ++i) {\r\n if (performance < maxPerf[i][1]) {\r\n this._autoChangeResolution(maxPerf[i][0]);\r\n break;\r\n }\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._autoChangeResolution = function (resolution) {\r\n if (resolution !== settings.now.resolution) {\r\n this.logger.report(`Your rendering resolution was changed to \"${resolution}\" for best performance.`);\r\n }\r\n settings.now.resolution = resolution;\r\n};\r\n\r\n/**\r\n * Save current settings to cookies.\r\n */\r\nMiew.prototype.saveSettings = function () {\r\n this._cookies.setCookie(this._opts.settingsCookie, JSON.stringify(this.settings.getDiffs(true)));\r\n};\r\n\r\n/**\r\n * Load settings from cookies.\r\n */\r\nMiew.prototype.restoreSettings = function () {\r\n try {\r\n const cookie = this._cookies.getCookie(this._opts.settingsCookie);\r\n const diffs = cookie ? JSON.parse(cookie) : {};\r\n this.settings.applyDiffs(diffs, true);\r\n } catch (e) {\r\n this.logger.error(`Cookies parse error: ${e.message}`);\r\n }\r\n};\r\n\r\n/**\r\n * Reset current settings to the defaults.\r\n */\r\nMiew.prototype.resetSettings = function () {\r\n this.settings.reset();\r\n};\r\n\r\n/*\r\n * DANGEROUS and TEMPORARY. The method should change or disappear in future versions.\r\n * @param {string|object} opts - See {@link Miew} constructor.\r\n * @see {@link Miew#set}, {@link Miew#repAdd}, {@link Miew#rep}.\r\n */\r\nMiew.prototype.setOptions = function (opts) {\r\n if (typeof opts === 'string') {\r\n opts = Miew.options.fromAttr(opts);\r\n }\r\n if (opts.reps) {\r\n this._opts.reps = null;\r\n }\r\n _.merge(this._opts, opts);\r\n if (opts.settings) {\r\n this.set(opts.settings);\r\n }\r\n\r\n this._opts._objects = opts._objects;\r\n this._resetObjects();\r\n\r\n if (opts.load) {\r\n this.load(opts.load, { fileType: opts.type });\r\n }\r\n\r\n if (opts.preset) {\r\n settings.now.preset = opts.preset;\r\n }\r\n\r\n if (opts.reps) {\r\n this.resetReps(opts.preset);\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.getComplex().resetCurrentUnit();\r\n if (_.isNumber(opts.unit)) {\r\n visual.getComplex().setCurrentUnit(opts.unit);\r\n }\r\n this.resetView();\r\n this.rebuildAll();\r\n }\r\n};\r\n\r\nMiew.prototype.info = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return {};\r\n }\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n return {\r\n id: metadata.id || complex.name || 'UNKNOWN',\r\n title: (metadata.title && metadata.title.join(' ')) || 'UNKNOWN DATA',\r\n atoms: complex.getAtomCount(),\r\n bonds: complex.getBondCount(),\r\n residues: complex.getResidueCount(),\r\n chains: complex.getChainCount(),\r\n };\r\n};\r\n\r\n/*\r\n * OBJECTS SEGMENT\r\n */\r\n\r\nMiew.prototype.addObject = function (objData, bThrow) {\r\n let Ctor = null;\r\n\r\n if (objData.type === LinesObject.prototype.type) {\r\n Ctor = LinesObject;\r\n }\r\n\r\n if (Ctor === null) {\r\n throw new Error(`Unknown scene object type - ${objData.type}`);\r\n }\r\n\r\n try {\r\n const newObj = new Ctor(objData.params, objData.opts);\r\n this._addSceneObject(newObj);\r\n } catch (error) {\r\n if (!bThrow) {\r\n this.logger.debug(`Error during scene object creation: ${error.message}`);\r\n } else {\r\n throw error;\r\n }\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._addSceneObject = function (sceneObject) {\r\n const visual = this._getComplexVisual();\r\n if (sceneObject.build && visual) {\r\n sceneObject.build(visual.getComplex());\r\n this._gfx.pivot.add(sceneObject.getGeometry());\r\n }\r\n const objects = this._objects;\r\n objects[objects.length] = sceneObject;\r\n};\r\n\r\nMiew.prototype._updateObjsToFrame = function (frameData) {\r\n const objs = this._objects;\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n if (objs[i].updateToFrame) {\r\n objs[i].updateToFrame(frameData);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._resetObjects = function () {\r\n const objs = this._opts._objects;\r\n\r\n this._objects = [];\r\n if (objs) {\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n this.addObject(objs[i], false);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype.removeObject = function (index) {\r\n const obj = this._objects[index];\r\n if (!obj) {\r\n throw new Error(`Scene object with index ${index} does not exist`);\r\n }\r\n obj.destroy();\r\n this._objects.splice(index, 1);\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Get a string with a URL to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {string} URL\r\n */\r\nMiew.prototype.getURL = function (opts) {\r\n return options.toURL(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n })));\r\n};\r\n\r\n/**\r\n * Get a string with a script to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=true] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=true] - when this flag is true, a view information is included\r\n * @returns {string} script\r\n */\r\nMiew.prototype.getScript = function (opts) {\r\n return options.toScript(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: true,\r\n view: true,\r\n })));\r\n};\r\n\r\n/*\r\n * Generates object that represents the current state of representations list\r\n * @param {boolean} compareWithDefaults - when this flag is true, reps list is compared (if possible)\r\n * to preset's defaults and only diffs are generated\r\n */\r\nMiew.prototype._compareReps = function (complexVisual, compareWithDefaults) {\r\n const ans = {};\r\n let repCount = 0;\r\n\r\n if (complexVisual) {\r\n repCount = complexVisual.repCount();\r\n }\r\n\r\n const currPreset = settings.defaults.presets[settings.now.preset];\r\n let compare = compareWithDefaults;\r\n if (currPreset === undefined || currPreset.length > repCount) {\r\n compare = false;\r\n ans.preset = 'empty';\r\n } else if (settings.now.preset !== settings.defaults.preset) {\r\n ans.preset = settings.now.preset;\r\n }\r\n\r\n const repsDiff = [];\r\n let emptyReps = true;\r\n for (let i = 0, n = repCount; i < n; ++i) {\r\n repsDiff[i] = complexVisual.repGet(i).compare(compare ? currPreset[i] : null);\r\n if (!_.isEmpty(repsDiff[i])) {\r\n emptyReps = false;\r\n }\r\n }\r\n if (!emptyReps) {\r\n ans.reps = repsDiff;\r\n }\r\n return ans;\r\n};\r\n\r\n/*\r\n * Obtain object that represents current state of miew (might be used as options in constructor).\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {Object} State object.\r\n */\r\nMiew.prototype.getState = function (opts) {\r\n const state = {};\r\n\r\n opts = _.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n });\r\n\r\n // load\r\n const visual = this._getComplexVisual();\r\n if (visual !== null) {\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n if (metadata.id) {\r\n const format = metadata.format ? `${metadata.format}:` : '';\r\n state.load = format + metadata.id;\r\n }\r\n const unit = complex.getCurrentUnit();\r\n if (unit !== 1) {\r\n state.unit = unit;\r\n }\r\n }\r\n\r\n // representations\r\n const repsInfo = this._compareReps(visual, opts.compact);\r\n if (repsInfo.preset) {\r\n state.preset = repsInfo.preset;\r\n }\r\n\r\n if (repsInfo.reps) {\r\n state.reps = repsInfo.reps;\r\n }\r\n\r\n // objects\r\n const objects = this._objects;\r\n const objectsState = [];\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n objectsState[i] = objects[i].identify();\r\n }\r\n if (objects.length > 0) {\r\n state._objects = objectsState;\r\n }\r\n\r\n // view\r\n if (opts.view) {\r\n state.view = this.view();\r\n }\r\n\r\n // settings\r\n if (opts.settings) {\r\n const diff = this.settings.getDiffs(false);\r\n if (!_.isEmpty(diff)) {\r\n state.settings = diff;\r\n }\r\n }\r\n\r\n return state;\r\n};\r\n\r\n/**\r\n * Get parameter value.\r\n * @param {string} param - Parameter name or path (e.g. 'modes.BS.atom').\r\n * @param {*=} value - Default value.\r\n * @returns {*} Parameter value.\r\n */\r\nMiew.prototype.get = function (param, value) {\r\n return settings.get(param, value);\r\n};\r\n\r\nMiew.prototype._clipPlaneUpdateValue = function (radius) {\r\n const clipPlaneValue = Math.max(\r\n this._gfx.camera.position.z - radius * settings.now.draft.clipPlaneFactor,\r\n settings.now.camNear,\r\n );\r\n\r\n const opts = { clipPlaneValue };\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions(opts);\r\n });\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setUberOptions(opts);\r\n }\r\n }\r\n if (this._picker !== null) {\r\n this._picker.clipPlaneValue = clipPlaneValue;\r\n }\r\n};\r\n\r\nMiew.prototype._fogFarUpdateValue = function () {\r\n if (this._picker !== null) {\r\n if (this._gfx.scene.fog) {\r\n this._picker.fogFarValue = this._gfx.scene.fog.far;\r\n } else {\r\n this._picker.fogFarValue = undefined;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._updateShadowmapMeshes = function (process) {\r\n this._forEachComplexVisual((visual) => {\r\n const reprList = visual._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n process(repr.geo, repr.material);\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._updateMaterials = function (values, needTraverse = false, process = undefined) {\r\n this._forEachComplexVisual((visual) => visual.setMaterialValues(values, needTraverse, process));\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setValues(values);\r\n obj._line.material.needsUpdate = true;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._fogAlphaChanged = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions({\r\n fogAlpha: settings.now.fogAlpha,\r\n });\r\n });\r\n};\r\n\r\nMiew.prototype._embedWebXR = function () {\r\n // switch off\r\n if (settings.now.stereo !== 'WEBVR') {\r\n if (this.webVR) {\r\n this.webVR.disable();\r\n }\r\n this.webVR = null;\r\n return;\r\n }\r\n // switch on\r\n if (!this.webVR) {\r\n this.webVR = new WebVRPoC(() => {\r\n this._requestAnimationFrame(() => this._onTick());\r\n this._needRender = true;\r\n this._onResize();\r\n });\r\n }\r\n this.webVR.enable(this._gfx);\r\n};\r\n\r\nMiew.prototype._initOnSettingsChanged = function () {\r\n const on = (props, func) => {\r\n props = _.isArray(props) ? props : [props];\r\n props.forEach((prop) => {\r\n this.settings.addEventListener(`change:${prop}`, func);\r\n });\r\n };\r\n\r\n on('modes.VD.frame', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.showFrame(settings.now.modes.VD.frame);\r\n this._needRender = true;\r\n });\r\n\r\n on('modes.VD.isoMode', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n });\r\n\r\n on('bg.color', () => {\r\n this._onBgColorChanged();\r\n });\r\n\r\n on('ao', () => {\r\n const values = { normalsToGBuffer: settings.now.ao };\r\n this._setUberMaterialValues(values);\r\n });\r\n\r\n on('zSprites', () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('fogColor', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('fogColorEnable', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('bg.transparent', (evt) => {\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n // update materials\r\n this._updateMaterials({ fogTransparent: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('draft.clipPlane', (evt) => {\r\n // update materials\r\n this._updateMaterials({ clipPlane: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('shadow.on', (evt) => {\r\n // update materials\r\n const values = { shadowmap: evt.value, shadowmapType: settings.now.shadow.type };\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.shadowMap.enabled = Boolean(values.shadowmap);\r\n }\r\n this._updateMaterials(values, true);\r\n if (values.shadowmap) {\r\n this._updateShadowCamera();\r\n this._updateShadowmapMeshes(meshutils.createShadowmapMaterial);\r\n } else {\r\n this._updateShadowmapMeshes(meshutils.removeShadowmapMaterial);\r\n }\r\n this._needRender = true;\r\n });\r\n\r\n on('shadow.type', (evt) => {\r\n // update materials if shadowmap is enable\r\n if (settings.now.shadow.on) {\r\n this._updateMaterials({ shadowmapType: evt.value }, true);\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on('shadow.radius', (evt) => {\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].shadow !== undefined) {\r\n const light = this._gfx.scene.children[i];\r\n light.shadow.radius = evt.value;\r\n this._needRender = true;\r\n }\r\n }\r\n });\r\n\r\n on('fps', () => {\r\n this._fps.show(settings.now.fps);\r\n });\r\n\r\n on(['fog', 'fogNearFactor', 'fogFarFactor'], () => {\r\n this._updateFog();\r\n this._needRender = true;\r\n });\r\n\r\n on('fogAlpha', () => {\r\n const { fogAlpha } = settings.now;\r\n if (fogAlpha < 0 || fogAlpha > 1) {\r\n this.logger.warn('fogAlpha must belong range [0,1]');\r\n }\r\n this._fogAlphaChanged();\r\n this._needRender = true;\r\n });\r\n\r\n on('autoResolution', (evt) => {\r\n if (evt.value && !this._gfxScore) {\r\n this.logger.warn('Benchmarks are missed, autoresolution will not work! '\r\n + 'Autoresolution should be set during miew startup.');\r\n }\r\n });\r\n\r\n on('stereo', () => {\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n this._needRender = true;\r\n });\r\n\r\n on(['transparency', 'palette'], () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('resolution', () => {\r\n // update complex visuals\r\n this.rebuildAll();\r\n\r\n // update volume visual\r\n const volume = this._getVolumeVisual();\r\n if (volume) {\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on(['axes', 'fxaa', 'ao',\r\n 'outline.on', 'outline.color', 'outline.threshold', 'outline.thickness'], () => {\r\n this._needRender = true;\r\n });\r\n};\r\n\r\n/**\r\n * Set parameter value.\r\n * @param {string|object} params - Parameter name or path (e.g. 'modes.BS.atom') or even settings object.\r\n * @param {*=} value - Value.\r\n */\r\nMiew.prototype.set = function (params, value) {\r\n settings.set(params, value);\r\n};\r\n\r\n/**\r\n * Select atoms with selection string.\r\n * @param {string} expression - string expression of selection\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\nMiew.prototype.select = function (expression, append) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n let sel = expression;\r\n if (_.isString(expression)) {\r\n sel = selectors.parse(expression).selector;\r\n }\r\n\r\n visual.select(sel, append);\r\n this._lastPick = null;\r\n\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n};\r\n\r\nconst VIEW_VERSION = '1';\r\n\r\n/**\r\n * Get or set view info packed into string.\r\n *\r\n * **Note:** view is stored for *left-handed* cs, euler angles are stored in radians and *ZXY-order*,\r\n *\r\n * @param {string=} expression - Optional string encoded the view\r\n */\r\nMiew.prototype.view = function (expression) {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n let transform = [];\r\n const eulerOrder = 'ZXY';\r\n\r\n function encode() {\r\n const pos = pivot.position;\r\n const scale = self._objectControls.getScale() / settings.now.radiusToFit;\r\n const euler = new THREE.Euler();\r\n euler.setFromQuaternion(self._objectControls.getOrientation(), eulerOrder);\r\n transform = [\r\n pos.x, pos.y, pos.z,\r\n scale,\r\n euler.x, euler.y, euler.z,\r\n ];\r\n return VIEW_VERSION + utils.arrayToBase64(transform, Float32Array);\r\n }\r\n\r\n function decode() {\r\n // backwards compatible: old non-versioned view is the 0th version\r\n if (expression.length === 40) {\r\n expression = `0${expression}`;\r\n }\r\n\r\n const version = expression[0];\r\n transform = utils.arrayFromBase64(expression.substr(1), Float32Array);\r\n\r\n // apply adapter for old versions\r\n if (version !== VIEW_VERSION) {\r\n if (version === '0') {\r\n // cancel radiusToFit included in old views\r\n transform[3] /= 8.0;\r\n } else {\r\n // do nothing\r\n self.logger.warn(`Encoded view version mismatch, stored as ${version} vs ${VIEW_VERSION} expected`);\r\n return;\r\n }\r\n }\r\n\r\n const interpolator = self._interpolator;\r\n const srcView = interpolator.createView();\r\n srcView.position.copy(pivot.position);\r\n srcView.scale = self._objectControls.getScale();\r\n srcView.orientation.copy(self._objectControls.getOrientation());\r\n\r\n const dstView = interpolator.createView();\r\n dstView.position.set(transform[0], transform[1], transform[2]);\r\n\r\n // hack to make preset views work after we moved centering offset to visual nodes\r\n // FIXME should only store main pivot offset in preset\r\n if (self._getComplexVisual()) {\r\n dstView.position.sub(self._getComplexVisual().position);\r\n }\r\n\r\n dstView.scale = transform[3]; // eslint-disable-line prefer-destructuring\r\n dstView.orientation.setFromEuler(new THREE.Euler(transform[4], transform[5], transform[6], eulerOrder));\r\n\r\n interpolator.setup(srcView, dstView);\r\n }\r\n\r\n if (typeof expression === 'undefined') {\r\n return encode();\r\n }\r\n decode();\r\n\r\n return expression;\r\n};\r\n\r\n/*\r\n * Update current view due to viewinterpolator state\r\n */\r\nMiew.prototype._updateView = function () {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n\r\n const interpolator = this._interpolator;\r\n if (!interpolator.wasStarted()) {\r\n interpolator.start();\r\n }\r\n\r\n if (!interpolator.isMoving()) {\r\n return;\r\n }\r\n\r\n const res = interpolator.getCurrentView();\r\n if (res.success) {\r\n const curr = res.view;\r\n pivot.position.copy(curr.position);\r\n self._objectControls.setScale(curr.scale * settings.now.radiusToFit);\r\n self._objectControls.setOrientation(curr.orientation);\r\n this.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n }\r\n};\r\n\r\n/**\r\n * Translate object by vector\r\n * @param {number} x - translation value (Ang) along model's X axis\r\n * @param {number} y - translation value (Ang) along model's Y axis\r\n * @param {number} z - translation value (Ang) along model's Z axis\r\n */\r\nMiew.prototype.translate = function (x, y, z) {\r\n this._objectControls.translatePivot(x, y, z);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Rotate object by Euler angles\r\n * @param {number} x - rotation angle around X axis in radians\r\n * @param {number} y - rotation angle around Y axis in radians\r\n * @param {number} z - rotation angle around Z axis in radians\r\n */\r\nMiew.prototype.rotate = function (x, y, z) {\r\n this._objectControls.rotate(new THREE.Quaternion().setFromEuler(new THREE.Euler(x, y, z, 'XYZ')));\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Scale object by factor\r\n * @param {number} factor - scale multiplier, should greater than zero\r\n */\r\nMiew.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n throw new RangeError('Scale should be greater than zero');\r\n }\r\n this._objectControls.scale(factor);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Center view on selection\r\n * @param {empty | subset | string} selector - defines part of molecule which must be centered (\r\n * empty - center on current selection;\r\n * subset - center on picked atom/residue/molecule;\r\n * string - center on atoms correspond to selection string)\r\n */\r\nMiew.prototype.center = function (selector) {\r\n // no arguments - center on current selection;\r\n if (selector === undefined) {\r\n this.setPivotSubset();\r\n this._needRender = true;\r\n return;\r\n }\r\n // subset with atom or residue - center on picked atom/residue;\r\n if (selector.obj !== undefined && ('atom' in selector.obj || 'residue' in selector.obj)) { // from event with selection\r\n if ('atom' in selector.obj) {\r\n this.setPivotAtom(selector.obj.atom);\r\n } else {\r\n this.setPivotResidue(selector.obj.residue);\r\n }\r\n this._needRender = true;\r\n return;\r\n }\r\n // string - center on atoms correspond to selection string\r\n if (selector.obj === undefined && selector !== '') {\r\n const sel = selectors.parse(selector);\r\n if (sel.error === undefined) {\r\n this.setPivotSubset(sel);\r\n this._needRender = true;\r\n return;\r\n }\r\n }\r\n // empty subset or incorrect/empty string - center on all molecule;\r\n this.resetPivot();\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\nMiew.prototype.within = function (selector, radius) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return selectors.None();\r\n }\r\n\r\n if (selector instanceof String) {\r\n selector = selectors.parse(selector);\r\n }\r\n\r\n const res = visual.within(selector, radius);\r\n if (res) {\r\n visual.rebuildSelectionGeometry();\r\n this._needRender = true;\r\n }\r\n return res;\r\n};\r\n\r\n/**\r\n * Get atom position in 2D canvas coords\r\n * @param {string} fullAtomName - full atom name, like A.38.CG\r\n * @returns {Object} {x, y} or false if atom not found\r\n */\r\nMiew.prototype.projected = function (fullAtomName, complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return false;\r\n }\r\n\r\n const atom = visual.getComplex().getAtomByFullname(fullAtomName);\r\n if (atom === null) {\r\n return false;\r\n }\r\n\r\n const pos = atom.position.clone();\r\n // we consider atom position to be affected only by common complex transform\r\n // ignoring any transformations that may add during editing\r\n this._gfx.pivot.updateMatrixWorldRecursive();\r\n this._gfx.camera.updateMatrixWorldRecursive();\r\n this._gfx.pivot.localToWorld(pos);\r\n pos.project(this._gfx.camera);\r\n\r\n return {\r\n x: (pos.x + 1.0) * 0.5 * this._gfx.width,\r\n y: (1.0 - pos.y) * 0.5 * this._gfx.height,\r\n };\r\n};\r\n\r\n/**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n *\r\n * @param {string=} complexName - complex name\r\n */\r\nMiew.prototype.dssp = function (complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return;\r\n }\r\n visual.getComplex().dssp();\r\n\r\n // rebuild dependent representations (cartoon or ss-colored)\r\n visual._reprList.forEach((rep) => {\r\n if (rep.mode.id === 'CA' || rep.colorer.id === 'SS') {\r\n rep.needsRebuild = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype.exportCML = function () {\r\n const self = this;\r\n\r\n function extractRotation(m) {\r\n const xAxis = new THREE.Vector3();\r\n const yAxis = new THREE.Vector3();\r\n const zAxis = new THREE.Vector3();\r\n m.extractBasis(xAxis, yAxis, zAxis);\r\n xAxis.normalize();\r\n yAxis.normalize();\r\n zAxis.normalize();\r\n const retMat = new THREE.Matrix4();\r\n retMat.identity();\r\n retMat.makeBasis(xAxis, yAxis, zAxis);\r\n return retMat;\r\n }\r\n\r\n function updateCMLData(complex) {\r\n const { root } = self._gfx;\r\n const mat = extractRotation(root.matrixWorld);\r\n const v4 = new THREE.Vector4(0, 0, 0, 0);\r\n const vCenter = new THREE.Vector4(0, 0, 0, 0);\r\n let xml = null;\r\n let ap = null;\r\n\r\n // update atoms in cml\r\n complex.forEachAtom((atom) => {\r\n if (atom.xmlNodeRef && atom.xmlNodeRef.xmlNode) {\r\n xml = atom.xmlNodeRef.xmlNode;\r\n ap = atom.position;\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n v4.applyMatrix4(mat);\r\n xml.setAttribute('x3', v4.x.toString());\r\n xml.setAttribute('y3', v4.y.toString());\r\n xml.setAttribute('z3', v4.z.toString());\r\n xml.removeAttribute('x2');\r\n xml.removeAttribute('y2');\r\n }\r\n });\r\n // update stereo groups in cml\r\n complex.forEachSGroup((sGroup) => {\r\n if (sGroup.xmlNodeRef && sGroup.xmlNodeRef.xmlNode) {\r\n xml = sGroup.xmlNodeRef.xmlNode;\r\n ap = sGroup.getPosition();\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n const cp = sGroup.getCentralPoint();\r\n if (cp === null) {\r\n v4.applyMatrix4(mat);\r\n } else {\r\n vCenter.set(cp.x, cp.y, cp.z, 0.0);\r\n v4.add(vCenter);\r\n v4.applyMatrix4(mat); // pos in global space\r\n vCenter.set(cp.x, cp.y, cp.z, 1.0);\r\n vCenter.applyMatrix4(mat);\r\n v4.sub(vCenter);\r\n }\r\n xml.setAttribute('x', v4.x.toString());\r\n xml.setAttribute('y', v4.y.toString());\r\n xml.setAttribute('z', v4.z.toString());\r\n }\r\n });\r\n }\r\n\r\n const visual = self._getComplexVisual();\r\n const complex = visual ? visual.getComplex() : null;\r\n if (complex && complex.originalCML) {\r\n updateCMLData(complex);\r\n\r\n // serialize xml structure to string\r\n const oSerializer = new XMLSerializer();\r\n return oSerializer.serializeToString(complex.originalCML);\r\n }\r\n\r\n return null;\r\n};\r\n\r\n/**\r\n * Reproduce the RCSB PDB Molecule of the Month style by David S. Goodsell\r\n *\r\n * @see http://pdb101.rcsb.org/motm/motm-about\r\n */\r\nMiew.prototype.motm = function () {\r\n settings.set({\r\n fogColorEnable: true,\r\n fogColor: 0x000000,\r\n outline: { on: true, threshold: 0.01 },\r\n bg: { color: 0xffffff },\r\n });\r\n\r\n this._forEachComplexVisual((visual) => {\r\n const rep = [];\r\n const complex = visual.getComplex();\r\n const palette = palettes.get(settings.now.palette);\r\n for (let i = 0; i < complex.getChainCount(); i++) {\r\n const curChainName = complex._chains[i]._name;\r\n const curChainColor = palette.getChainColor(curChainName);\r\n rep[i] = {\r\n selector: `chain ${curChainName}`,\r\n mode: 'VW',\r\n colorer: ['CB', { color: curChainColor, factor: 0.9 }],\r\n material: 'FL',\r\n };\r\n }\r\n visual.resetReps(rep);\r\n });\r\n};\r\n\r\nMiew.prototype.VERSION = (typeof PACKAGE_VERSION !== 'undefined' && PACKAGE_VERSION) || '0.0.0-dev';\r\n\r\n// Uncomment this to get debug trace:\r\n// Miew.prototype.debugTracer = new utils.DebugTracer(Miew.prototype);\r\n\r\n_.assign(Miew, /** @lends Miew */ {\r\n VERSION: Miew.prototype.VERSION,\r\n\r\n registeredPlugins: [],\r\n\r\n // export namespaces // TODO: WIP: refactoring external interface\r\n chem,\r\n io,\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n utils,\r\n gfx: {\r\n Representation,\r\n },\r\n\r\n /**\r\n * Third-party libraries packaged together with Miew.\r\n *\r\n * @property {object} lodash - [Lodash](https://lodash.com/), a modern JavaScript utility library delivering\r\n * modularity, performance & extras.\r\n * @property {object} three - [three.js](https://threejs.org/), JavaScript 3D library.\r\n *\r\n * @example\r\n * var _ = Miew.thirdParty.lodash;\r\n * var opts = _.merge({ ... }, Miew.options.fromURL(window.location.search));\r\n * var miew = new Miew(opts);\r\n */\r\n thirdParty: {\r\n lodash: _,\r\n three: THREE,\r\n },\r\n});\r\n\r\nexport default Miew;\r\n","import palettes from '../gfx/palettes';\r\nimport settings from '../settings';\r\n\r\nconst modeIdDesc = {\r\n $help: [\r\n 'Rendering mode shortcut',\r\n ' BS - balls and sticks mode',\r\n ' LN - lines mode',\r\n ' LC - licorice mode',\r\n ' VW - van der waals mode',\r\n ' TR - trace mode',\r\n ' TU - tube mode',\r\n ' CA - cartoon mode',\r\n ' SA - isosurface mode',\r\n ' QS - quick surface mode',\r\n ' SE - solvent excluded mode',\r\n ' TX - text mode',\r\n ],\r\n BS: {\r\n $help: [\r\n ' Balls and sticks',\r\n ' aromrad = #aromatic radius',\r\n ' atom = #atom radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n CA: {\r\n $help: [\r\n ' Cartoon',\r\n ' arrow = #arrow size',\r\n ' depth = #depth of surface',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = #',\r\n ' width = #secondary width\\n',\r\n ],\r\n },\r\n LN: {\r\n $help: [\r\n ' Lines',\r\n ' atom = #atom radius',\r\n ' chunkarom = ',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' offsarom = \\n',\r\n ],\r\n },\r\n LC: {\r\n $help: [\r\n ' Licorice',\r\n ' aromrad = #aromatic radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n VW: {\r\n $help: [\r\n ' Van der Waals',\r\n ' nothing\\n',\r\n ],\r\n },\r\n TR: {\r\n $help: [\r\n ' Trace',\r\n ' radius = #tube radius\\n',\r\n ],\r\n },\r\n TU: {\r\n $help: [\r\n ' Tube',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = \\n',\r\n ],\r\n },\r\n SA: {\r\n $help: [\r\n ' Surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n QS: {\r\n $help: [\r\n ' Quick surface',\r\n ' isoValue = ',\r\n ' scale = ',\r\n ' wireframe = ',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n SE: {\r\n $help: [\r\n ' Solvent excluded surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n TX: {\r\n $help: [\r\n ' Text mode',\r\n ' template = string that can include \"{{ id }}\"',\r\n ' it will be replaced by value, id can be one of next:',\r\n ' serial, name, type, sequence, residue, chain, hetatm, water\\n',\r\n ' horizontalAlign = {\"left\", \"right\", \"center\"}',\r\n ' verticalAlign = {\"top\", \"bottom\", \"middle\"}',\r\n ' dx = #offset along x',\r\n ' dy = #offset along y',\r\n ' dz = #offset along z',\r\n ' fg = #text color modificator',\r\n ' could be keyword, named color or hex',\r\n ' fg = #back color modificator',\r\n ' could be keyword, named color or hex',\r\n ' showBg = #if set show background',\r\n ' plate under text',\r\n ],\r\n },\r\n};\r\n\r\nconst colorDesc = {\r\n $help: [\r\n 'Coloring mode shortcut',\r\n ' EL - color by element',\r\n ' CH - color by chain',\r\n ' SQ - color by sequence',\r\n ' RT - color by residue type',\r\n ' SS - color by secondary structure',\r\n ' UN - uniform',\r\n ],\r\n UN: {\r\n $help: [\r\n 'Parameters of coloring modes customization',\r\n ' Uniform',\r\n ' color = #RGB->HEX->dec\\n',\r\n ],\r\n color: {\r\n $help: Object.keys(palettes.get(settings.now.palette).namedColors).sort().join('\\n'),\r\n },\r\n },\r\n};\r\n\r\nconst materialDesc = {\r\n $help: [\r\n 'Material shortcut',\r\n ' DF - diffuse',\r\n ' TR - transparent',\r\n ' SF - soft plastic',\r\n ' PL - glossy plastic',\r\n ' ME - metal',\r\n ' GL - glass',\r\n ],\r\n};\r\n\r\nconst addRepDesc = {\r\n $help: [\r\n 'Short (packed) representation description as a set of variables',\r\n ' s=',\r\n ' selector property',\r\n ' m=[!:[,...]]',\r\n ' render mode property',\r\n ' c=[!:[,...]]',\r\n ' color mode property',\r\n ' mt=',\r\n ' material property',\r\n ],\r\n s: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n m: modeIdDesc,\r\n c: colorDesc,\r\n mt: materialDesc,\r\n};\r\n\r\nconst setGetParameterDesc = {\r\n $help: [\r\n 'Parameters of rendering modes customization: modes',\r\n 'Parameters of colorer customization: colorers',\r\n 'Autobuild: autobuild = (|)',\r\n ],\r\n modes: modeIdDesc,\r\n colorers: colorDesc,\r\n};\r\n\r\nconst help = {\r\n $help: [\r\n 'help (| )',\r\n 'You can get detailed information about command options',\r\n ' using \"help cmd.opt.opt.[...]\"\\n',\r\n ' you can use one line comments',\r\n ' everything started from (#|//) will be skipped',\r\n ' Example: >build //some comment\\n',\r\n 'List of available commands:',\r\n ],\r\n reset: {\r\n $help: [\r\n 'Reload current object, delete all representations',\r\n ' Nothing will work until load new object',\r\n ],\r\n },\r\n load: {\r\n $help: [\r\n 'load (||-f [<*.NC FILE URL STRING>])',\r\n ' Load new pdb object from selected source',\r\n ],\r\n PDBID: {\r\n $help: 'pdb id in remote molecule database',\r\n },\r\n URL: {\r\n $help: 'url to source file',\r\n },\r\n f: {\r\n $help: [\r\n 'open file system dialog to fetch local file',\r\n 'optionally you can determine trajectory file',\r\n 'via URL for *.top model',\r\n ],\r\n },\r\n },\r\n clear: {\r\n $help: 'No args. Clear terminal',\r\n },\r\n add: {\r\n $help: [\r\n 'add [] []',\r\n ' Add new item to representation set with',\r\n ' default or params',\r\n ],\r\n REP_NAME: {\r\n $help: 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n rep: {\r\n $help: [\r\n 'rep [|] []',\r\n ' set current representation by name or index',\r\n ' edit current representation by ',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n remove: {\r\n $help: [\r\n 'remove (|)',\r\n 'Remove representation by name or index',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n },\r\n selector: {\r\n $help: [\r\n 'selector ',\r\n ' set selector from EXPRESSION to current representation',\r\n ],\r\n EXPRESSION: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n },\r\n mode: {\r\n $help: [\r\n 'mode [=...]',\r\n ' set rendering mode and apply parameters to current representation',\r\n ],\r\n MODE_ID: modeIdDesc,\r\n },\r\n color: {\r\n $help: [\r\n 'color [=...]',\r\n ' set colorer and apply parameters to current representation',\r\n ],\r\n COLORER_ID: colorDesc,\r\n },\r\n material: {\r\n $help: [\r\n 'material ',\r\n ' set material to current representation',\r\n ],\r\n MATERIAL_ID: materialDesc,\r\n },\r\n build: {\r\n $help: 'build help str',\r\n add: {\r\n $help: 'build.add',\r\n new: {\r\n $help: [\r\n 'add.new',\r\n 'add.new new line 1',\r\n 'add.new new line 2',\r\n 'add.new new line 3',\r\n ],\r\n },\r\n },\r\n del: {\r\n $help: 'build.del',\r\n },\r\n },\r\n list: {\r\n $help: [\r\n 'list [-e|-s||]',\r\n 'Print representations if no args print list of representations',\r\n ' -e expand list and show all representations',\r\n ' -s show all user-registered selectors',\r\n ' | show only current representation',\r\n ],\r\n },\r\n hide: {\r\n $help: [\r\n 'hide (|)',\r\n 'Hide representation referenced in args',\r\n ],\r\n },\r\n show: {\r\n $help: [\r\n 'show (|)',\r\n 'Show representation referenced in args',\r\n ],\r\n },\r\n get: {\r\n $help: [\r\n 'get ',\r\n 'Print value',\r\n ' - path to option use get.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set: {\r\n $help: [\r\n 'set ',\r\n 'Set with ',\r\n ' - path to option use set.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set_save: {\r\n $help: [\r\n 'set_save',\r\n 'Save current settings to cookie',\r\n ],\r\n },\r\n set_restore: {\r\n $help: [\r\n 'set_restore',\r\n 'Load and apply settings from cookie',\r\n ],\r\n },\r\n set_reset: {\r\n $help: [\r\n 'set_reset',\r\n 'Reset current settings to the defaults',\r\n ],\r\n },\r\n preset: {\r\n $help: [\r\n 'preset []',\r\n 'Reset current representation or set preset to ',\r\n ],\r\n PRESET: {\r\n $help: [\r\n 'default',\r\n 'wire',\r\n 'small',\r\n 'macro',\r\n ],\r\n },\r\n },\r\n unit: {\r\n $help: [\r\n 'unit []',\r\n 'Change current biological structure view. Zero value means asymmetric unit,',\r\n 'positive values set an assembly with corresponding number.',\r\n 'Being called with no parameters command prints current unit information.',\r\n ],\r\n },\r\n view: {\r\n $help: [\r\n 'view []',\r\n 'Get current encoded view or set if ENCODED_VIEW placed as argument',\r\n ],\r\n ENCODED_VIEW: {\r\n $help: [\r\n 'encoded view matrix string (binary code)',\r\n ],\r\n },\r\n },\r\n rotate: {\r\n $help: [\r\n 'rotate (x|y|z) [] [(x|y|z) []]...',\r\n 'Rotate scene',\r\n ],\r\n },\r\n scale: {\r\n $help: [\r\n 'scale ',\r\n 'Scale scene',\r\n ],\r\n },\r\n select: {\r\n $help: [\r\n 'select [as ]',\r\n 'Select atoms using selector defined in SELECTOR_STRING',\r\n ' and if SELECTOR_NAME is defined register it in viewer',\r\n ' you can use it later as a complex selector',\r\n ],\r\n },\r\n within: {\r\n $help: [\r\n 'within of as ',\r\n 'Build within named selector',\r\n ' DISTANCE ',\r\n ' SELECTOR_STRING ',\r\n ' SELECTOR_NAME ',\r\n ],\r\n },\r\n url: {\r\n $help: [\r\n 'url [-s] [-v]',\r\n 'Report URL encoded scene',\r\n ' if -s set that include settings in the URL',\r\n ' if -v set that include view in the URL',\r\n ],\r\n },\r\n screenshot: {\r\n $help: [\r\n 'screenshot [ []]',\r\n 'Make a screenshot of the scene',\r\n ' WIDTH in pixels',\r\n ' HEIGHT in pixels, equal to WIDTH by default',\r\n ],\r\n },\r\n line: {\r\n $help: [\r\n 'line [=]',\r\n 'Draw dashed line between two specified atoms',\r\n ],\r\n },\r\n removeobj: {\r\n $help: [\r\n 'removeobj ',\r\n 'Remove scene object by its index. Indices could be obtained by command',\r\n ],\r\n },\r\n listobj: {\r\n $help: [\r\n 'listobj',\r\n 'Display the list of all existing scene objects',\r\n ],\r\n },\r\n};\r\n\r\nexport default help;\r\n","import _ from 'lodash';\r\nimport Miew from './Miew';\r\nimport { parser as parsercli } from './utils/MiewCLIParser';\r\nimport clihelp from './utils/MiewCLIHelp';\r\nimport logger from './utils/logger';\r\nimport utils from './utils';\r\n\r\nconst {\r\n chem: { selectors },\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n} = Miew;\r\n\r\nfunction None() {\r\n}\r\n\r\nconst NULL = (function () {\r\n const obj = new None();\r\n return function () {\r\n return obj;\r\n };\r\n}());\r\n\r\nclass RepresentationMap {\r\n constructor() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n\r\n get(strId) {\r\n return this.representationMap[strId] || this.representationID[strId] || '';\r\n }\r\n\r\n add(strId, index) {\r\n if (strId === -1) {\r\n return 'Can not create representation: there is no data';\r\n }\r\n\r\n if (index !== undefined) {\r\n if (!this.representationMap.hasOwnProperty(strId)) {\r\n this.representationMap[strId.toString()] = index;\r\n this.representationID[index] = strId.toString();\r\n } else {\r\n return 'This name has already existed, registered without name';\r\n }\r\n }\r\n return `Representation ${strId} successfully added`;\r\n }\r\n\r\n remove(index) {\r\n if (index && this.representationID.hasOwnProperty(index)) {\r\n delete this.representationMap[this.representationID[index]];\r\n delete this.representationID[index];\r\n }\r\n\r\n const sortedKeys = Object.keys(this.representationID).sort();\r\n for (const i in sortedKeys) {\r\n if (sortedKeys.hasOwnProperty(i)) {\r\n const id = sortedKeys[i];\r\n if (id > index) {\r\n this.representationID[id - 1] = this.representationID[id];\r\n this.representationMap[this.representationID[id]] -= 1;\r\n delete this.representationID[id];\r\n }\r\n }\r\n }\r\n }\r\n\r\n clear() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n}\r\n\r\nconst representationsStorage = new RepresentationMap();\r\n\r\nfunction keyRemap(key) {\r\n const keys = {\r\n s: 'selector',\r\n m: 'mode',\r\n c: 'colorer',\r\n mt: 'material',\r\n mode: 'modes',\r\n color: 'colorers',\r\n colorer: 'colorers',\r\n select: 'selector',\r\n material: 'materials',\r\n selector: 'selector',\r\n };\r\n const ans = keys[key];\r\n return ans === undefined ? key : ans;\r\n}\r\n\r\nclass CLIUtils {\r\n list(miew, repMap, key) {\r\n let ret = '';\r\n if (miew && repMap !== undefined) {\r\n if (key === undefined || key === '-e') {\r\n const count = miew.repCount();\r\n\r\n for (let i = 0; i < count; i++) {\r\n ret += this.listRep(miew, repMap, i, key);\r\n }\r\n }\r\n }\r\n return ret;\r\n }\r\n\r\n listRep(miew, repMap, repIndex, key) {\r\n let ret = '';\r\n const rep = miew.repGet(repIndex);\r\n if (!rep) {\r\n logger.warn(`Rep ${repIndex} does not exist!`);\r\n return ret;\r\n }\r\n const index = repIndex;\r\n const repName = repMap.get(index);\r\n\r\n const { mode, colorer } = rep;\r\n const selectionStr = rep.selectorString;\r\n const material = rep.materialPreset;\r\n\r\n ret += `#${index} : ${mode.name}${repName === '' ? '' : `, ${repName}`}\\n`;\r\n\r\n if (key !== undefined) {\r\n ret += ` selection : \"${selectionStr}\"\\n`;\r\n ret += ` mode : (${mode.id}), ${mode.name}\\n`;\r\n ret += ` colorer : (${colorer.id}), ${colorer.name}\\n`;\r\n ret += ` material : (${material.id}), ${material.name}\\n`;\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listSelector(miew, context) {\r\n let ret = '';\r\n\r\n for (const k in context) {\r\n if (context.hasOwnProperty(k)) {\r\n ret += `${k} : \"${context[k]}\"\\n`;\r\n }\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listObjs(miew) {\r\n const objs = miew._objects;\r\n\r\n if (!objs || !Array.isArray(objs) || objs.length === 0) {\r\n return 'There are no objects on the scene';\r\n }\r\n\r\n const strList = [];\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n strList[i] = `${i}: ${objs[i].toString()}`;\r\n }\r\n\r\n return strList.join('\\n');\r\n }\r\n\r\n joinHelpStr(helpData) {\r\n if (helpData instanceof Array) {\r\n return helpData.join('\\n');\r\n }\r\n return helpData;\r\n }\r\n\r\n help(path) {\r\n if (_.isUndefined(path)) {\r\n return `${this.joinHelpStr(clihelp.$help)}\\n${_.slice(_.sortBy(_.keys(clihelp)), 1).join(', ')}\\n`;\r\n }\r\n\r\n const helpItem = _.get(clihelp, path);\r\n return _.isUndefined(helpItem) ? this.help() : `${this.joinHelpStr(helpItem.$help)}\\n`;\r\n }\r\n\r\n load(miew, arg) {\r\n if (miew === undefined || arg === undefined || arg === '-f') {\r\n return;\r\n }\r\n miew.awaitWhileCMDisInProcess();\r\n const finish = () => miew.finishAwaitingCMDInProcess();\r\n miew.load(arg).then(finish, finish);\r\n }\r\n\r\n checkArg(key, arg, modificate) {\r\n if (key !== undefined && arg !== undefined) {\r\n if (keyRemap(key) === 'selector') {\r\n const res = selectors.parse(arg);\r\n\r\n if (res.error !== undefined) {\r\n const selExc = { message: res.error };\r\n throw selExc;\r\n }\r\n\r\n if (modificate !== undefined && modificate) {\r\n return res.selector;\r\n }\r\n return arg;\r\n }\r\n\r\n const modificators = {\r\n colorers,\r\n modes,\r\n materials,\r\n };\r\n\r\n let modificator = key;\r\n let temp;\r\n while (modificator !== temp) {\r\n temp = modificator;\r\n modificator = keyRemap(temp);\r\n }\r\n\r\n if (modificators[modificator].get(arg) === undefined) {\r\n const exc = { message: `${arg} is not existed in ${modificator}` };\r\n throw exc;\r\n }\r\n return arg;\r\n }\r\n return NULL;\r\n }\r\n\r\n propagateProp(path, arg) {\r\n if (path !== undefined) {\r\n let argExc = {};\r\n const adapter = options.adapters[typeof _.get(settings.defaults, path)];\r\n if (adapter === undefined) {\r\n const pathExc = { message: `${path} is not existed` };\r\n throw pathExc;\r\n }\r\n\r\n if ((path.endsWith('.color') || path.endsWith('.baseColor')\r\n || path.endsWith('.EL.carbon')) && typeof arg !== 'number') {\r\n arg = palettes.get(settings.now.palette).getNamedColor(arg);\r\n }\r\n\r\n if (path.endsWith('.fg') || path.endsWith('.bg')) {\r\n if (typeof arg !== 'number') {\r\n const val = palettes.get(settings.now.palette).getNamedColor(arg, true);\r\n if (val !== undefined) {\r\n arg = `0x${val.toString(16)}`;\r\n }\r\n } else {\r\n arg = `0x${arg.toString(16)}`;\r\n }\r\n }\r\n\r\n if (path.endsWith('.template')) {\r\n arg = arg.replace(/\\\\n/g, '\\n');// NOSONAR\r\n }\r\n\r\n if (arg !== undefined && adapter(arg) !== arg && adapter(arg) !== (arg > 0)) {\r\n argExc = { message: `${path} must be a \"${typeof _.get(settings.defaults, path)}\"` };\r\n throw argExc;\r\n }\r\n }\r\n return arg;\r\n }\r\n\r\n unquoteString(value) {\r\n return utils.unquoteString(value);\r\n }\r\n}\r\n// repIndexOrRepMap could be RepresentationMap or index\r\n\r\nconst utilFunctions = new CLIUtils();\r\n\r\nfunction CreateObjectPair(a, b) {\r\n const obj = {};\r\n obj[a] = b;\r\n return obj;\r\n}\r\n\r\nfunction ArgList(arg) {\r\n if (arg instanceof this.constructor) {\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n}\r\n\r\nArgList.prototype.append = function (value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n};\r\n\r\nArgList.prototype.remove = function (value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n};\r\n\r\nArgList.prototype.toJSO = function (cliUtils, cmd, arg) {\r\n const res = {};\r\n\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n _.set(res, list[i].id, cliUtils.propagateProp(`${keyRemap(cmd)}.${arg}.${list[i].id}`, list[i].val));\r\n }\r\n\r\n return res;\r\n};\r\n\r\nfunction Arg(_id, _val) {\r\n this.id = _id;\r\n this.val = _val;\r\n}\r\n\r\nconst cliutils = Object.create({});\r\n\r\ncliutils.Arg = Arg;\r\ncliutils.ArgList = ArgList;\r\n\r\ncliutils.miew = null;\r\ncliutils.echo = null;\r\ncliutils.representations = representationsStorage;\r\ncliutils.utils = utilFunctions;\r\n\r\ncliutils._ = _;\r\ncliutils.CreateObjectPair = CreateObjectPair;\r\ncliutils.keyRemap = keyRemap;\r\ncliutils.Context = selectors.Context;\r\ncliutils.ClearContext = selectors.ClearContext;\r\n\r\ncliutils.NULL = NULL;\r\n\r\ncliutils.notimplemented = function () {\r\n return this.NULL;\r\n};\r\n\r\nMiew.prototype.script = function (script, _printCallback, _errorCallback) {\r\n parsercli.yy.miew = this;\r\n parsercli.yy.echo = _printCallback;\r\n parsercli.yy.error = _errorCallback;\r\n if (this.cmdQueue === undefined) {\r\n this.cmdQueue = [];\r\n }\r\n\r\n if (this.commandInAction === undefined) {\r\n this.commandInAction = false;\r\n }\r\n\r\n this.cmdQueue = this.cmdQueue.concat(script.split('\\n'));\r\n};\r\n\r\nMiew.prototype.awaitWhileCMDisInProcess = function () {\r\n this.commandInAction = true;\r\n};\r\n\r\nMiew.prototype.finishAwaitingCMDInProcess = function () {\r\n this.commandInAction = false;\r\n};\r\n\r\nMiew.prototype.isScriptingCommandAvailable = function () {\r\n return this.commandInAction !== undefined\r\n && !this.commandInAction\r\n && this.cmdQueue !== undefined\r\n && this.cmdQueue.length > 0;\r\n};\r\n\r\nMiew.prototype.callNextCmd = function () {\r\n if (this.isScriptingCommandAvailable()) {\r\n const cmd = this.cmdQueue.shift();\r\n\r\n const res = {};\r\n res.success = false;\r\n try {\r\n parsercli.parse(cmd);\r\n res.success = true;\r\n } catch (e) {\r\n res.error = e.message;\r\n parsercli.yy.error(res.error);\r\n this.finishAwaitingCMDInProcess();\r\n }\r\n return res;\r\n }\r\n return '';\r\n};\r\n\r\nparsercli.yy = cliutils;\r\n// workaround for incorrect JISON parser generator for AMD module\r\nparsercli.yy.parseError = parsercli.parseError;\r\n","import Miew from './Miew';\r\nimport './Miew-cli';\r\n\r\nexport default 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\ No newline at end of file diff --git a/packages/miew/dist/Miew.module.js b/packages/miew/dist/Miew.module.js index 4bab14eb..13761d20 100644 --- a/packages/miew/dist/Miew.module.js +++ b/packages/miew/dist/Miew.module.js @@ -1,10 +1,10 @@ -/*! Miew - 3D Molecular Viewer v0.11.1 Copyright (c) 2015-2025 EPAM Systems, Inc. */ -import * as __WEBPACK_EXTERNAL_MODULE_lodash__ from "lodash"; +/*! Miew - 3D Molecular Viewer v0.12.0 Copyright (c) 2015-2026 EPAM Systems, Inc. */ +import { default as __WEBPACK_EXTERNAL_MODULE_lodash_default__ } from "lodash"; import * as __WEBPACK_EXTERNAL_MODULE_three__ from "three"; /******/ var __webpack_modules__ = ({ -/***/ 89: -/***/ ((module) => { +/***/ 89 +(module) { /* eslint-disable */ // DO NOT EDIT! Automatically generated from .jison @@ -351,7 +351,8 @@ var parser = function () { switch (yystate) { case 1: return $$[$0 - 1]; - break; + // removed by dead control flow + case 3: this.$ = yy.miew.reset(false); yy.ClearContext(); @@ -2581,248 +2582,329 @@ var parser = function () { break; case 1: return ''; - break; + // removed by dead control flow + case 2: return ''; - break; + // removed by dead control flow + case 3: return 42; - break; + // removed by dead control flow + case 4: return 35; - break; + // removed by dead control flow + case 5: return 77; - break; + // removed by dead control flow + case 6: return 78; - break; + // removed by dead control flow + case 7: return 78; - break; + // removed by dead control flow + case 8: return 8; - break; + // removed by dead control flow + case 9: return 6; - break; + // removed by dead control flow + case 10: return 82; - break; + // removed by dead control flow + case 11: return 7; - break; + // removed by dead control flow + case 12: return 9; - break; + // removed by dead control flow + case 13: return 59; - break; + // removed by dead control flow + case 14: return 13; - break; + // removed by dead control flow + case 15: return 15; - break; + // removed by dead control flow + case 16: return 17; - break; + // removed by dead control flow + case 17: return 18; - break; + // removed by dead control flow + case 18: return 19; - break; + // removed by dead control flow + case 19: return 20; - break; + // removed by dead control flow + case 20: return 11; - break; + // removed by dead control flow + case 21: return 62; - break; + // removed by dead control flow + case 22: return 64; - break; + // removed by dead control flow + case 23: return 23; - break; + // removed by dead control flow + case 24: return 25; - break; + // removed by dead control flow + case 25: return 26; - break; + // removed by dead control flow + case 26: return 27; - break; + // removed by dead control flow + case 27: return 30; - break; + // removed by dead control flow + case 28: return 34; - break; + // removed by dead control flow + case 29: return 33; - break; + // removed by dead control flow + case 30: return 65; - break; + // removed by dead control flow + case 31: return 66; - break; + // removed by dead control flow + case 32: return 37; - break; + // removed by dead control flow + case 33: return 41; - break; + // removed by dead control flow + case 34: return 43; - break; + // removed by dead control flow + case 35: return 52; - break; + // removed by dead control flow + case 36: return 54; - break; + // removed by dead control flow + case 37: return 55; - break; + // removed by dead control flow + case 38: return 46; - break; + // removed by dead control flow + case 39: return 48; - break; + // removed by dead control flow + case 40: return 45; - break; + // removed by dead control flow + case 41: return 49; - break; + // removed by dead control flow + case 42: return 56; - break; + // removed by dead control flow + case 43: return 58; - break; + // removed by dead control flow + case 44: return 44; - break; + // removed by dead control flow + case 45: return 83; - break; + // removed by dead control flow + case 46: return 84; - break; + // removed by dead control flow + case 47: return 85; - break; + // removed by dead control flow + case 48: return 86; - break; + // removed by dead control flow + case 49: return 87; - break; + // removed by dead control flow + case 50: return 88; - break; + // removed by dead control flow + case 51: return 89; - break; + // removed by dead control flow + case 52: return 90; - break; + // removed by dead control flow + case 53: return 91; - break; + // removed by dead control flow + case 54: return 92; - break; + // removed by dead control flow + case 55: return 93; - break; + // removed by dead control flow + case 56: return 94; - break; + // removed by dead control flow + case 57: return 95; - break; + // removed by dead control flow + case 58: return 70; - break; + // removed by dead control flow + case 59: return 70; - break; + // removed by dead control flow + case 60: return 72; - break; + // removed by dead control flow + case 61: return 72; - break; + // removed by dead control flow + case 62: return 74; - break; + // removed by dead control flow + case 63: return 74; - break; + // removed by dead control flow + case 64: return 74; - break; + // removed by dead control flow + case 65: return 31; - break; + // removed by dead control flow + case 66: return 36; - break; + // removed by dead control flow + case 67: return 96; - break; + // removed by dead control flow + case 68: return 97; - break; + // removed by dead control flow + case 69: return 98; - break; + // removed by dead control flow + case 70: return 99; - break; + // removed by dead control flow + case 71: yy_.yytext = yy.utils.unquoteString(yy_.yytext); return 14; - break; + // removed by dead control flow + case 72: return 38; - break; + // removed by dead control flow + case 73: return 5; - break; + // removed by dead control flow + case 74: return 101; - break; + // removed by dead control flow + case 75: return 103; - break; + // removed by dead control flow + case 76: return '\\'; - break; + // removed by dead control flow + case 77: return 28; - break; + // removed by dead control flow + case 78: return 61; - break; + // removed by dead control flow + case 79: return 29; - break; + // removed by dead control flow + case 80: return 57; - break; + // removed by dead control flow + case 81: return 71; - break; + // removed by dead control flow + } }, rules: [/^(?:\s+)/i, /^(?:[#].*)/i, /^(?:\/\/.*)/i, /^(?:([_A-Z0-9\/\+]+==))/i, /^(?:-?[0-9]+(\.[0-9]+)?\b)/i, /^(?:0[xX][0-9A-F]+\b)/i, /^(?:false\b)/i, /^(?:true\b)/i, /^(?:all\b)/i, /^(?:reset\b)/i, /^(?:clear\b)/i, /^(?:build\b)/i, /^(?:help\b)/i, /^(?:load\b)/i, /^(?:get\b)/i, /^(?:set\b)/i, /^(?:set_save\b)/i, /^(?:set_restore\b)/i, /^(?:set_reset\b)/i, /^(?:preset\b)/i, /^(?:motm\b)/i, /^(?:add\b)/i, /^(?:rep\b)/i, /^(?:remove\b)/i, /^(?:hide\b)/i, /^(?:show\b)/i, /^(?:list\b)/i, /^(?:select\b)/i, /^(?:within\b)/i, /^(?:selector\b)/i, /^(?:mode\b)/i, /^(?:color\b)/i, /^(?:material\b)/i, /^(?:view\b)/i, /^(?:unit\b)/i, /^(?:line\b)/i, /^(?:listobj\b)/i, /^(?:removeobj\b)/i, /^(?:rotate\b)/i, /^(?:translate\b)/i, /^(?:scale\b)/i, /^(?:center\b)/i, /^(?:url\b)/i, /^(?:screenshot\b)/i, /^(?:dssp\b)/i, /^(?:file_list\b)/i, /^(?:file_register\b)/i, /^(?:file_delete\b)/i, /^(?:preset_add\b)/i, /^(?:preset_delete\b)/i, /^(?:preset_update\b)/i, /^(?:preset_rename\b)/i, /^(?:preset_open\b)/i, /^(?:create_scenario\b)/i, /^(?:reset_scenario\b)/i, /^(?:delete_scenario\b)/i, /^(?:add_scenario_item\b)/i, /^(?:list_scenario\b)/i, /^(?:s\b)/i, /^(?:mt\b)/i, /^(?:m\b)/i, /^(?:c\b)/i, /^(?:x\b)/i, /^(?:y\b)/i, /^(?:z\b)/i, /^(?:as\b)/i, /^(?:of\b)/i, /^(?:pdb\b)/i, /^(?:delay\b)/i, /^(?:prst\b)/i, /^(?:desc\b)/i, /^(?:((?:"(?:\\.|[^\\"])*"|'(?:\\.|[^\\'])*')))/i, /^(?:([_A-Z0-9]+))/i, /^(?:$)/i, /^(?:\.)/i, /^(?:\/)/i, /^(?:\\)/i, /^(?:-e\b)/i, /^(?:-f\b)/i, /^(?:-s\b)/i, /^(?:-v\b)/i, /^(?:=)/i], @@ -2847,10 +2929,10 @@ module.exports = { parser: parser }; -/***/ }), +/***/ }, -/***/ 99: -/***/ ((module) => { +/***/ 99 +(module) { /* eslint-disable */ // DO NOT EDIT! Automatically generated from .jison @@ -3002,7 +3084,8 @@ var parser = function () { switch (yystate) { case 1: return $$[$0 - 1]; - break; + // removed by dead control flow + case 3: this.$ = yy.keyword('or')($$[$0 - 2], $$[$0]); break; @@ -3592,65 +3675,85 @@ var parser = function () { break; case 1: return 20; - break; + // removed by dead control flow + case 2: return 7; - break; + // removed by dead control flow + case 3: return 8; - break; + // removed by dead control flow + case 4: return 9; - break; + // removed by dead control flow + case 5: return 12; - break; + // removed by dead control flow + case 6: return 16; - break; + // removed by dead control flow + case 7: return 14; - break; + // removed by dead control flow + case 8: return 10; - break; + // removed by dead control flow + case 9: return 11; - break; + // removed by dead control flow + case 10: return 19; - break; + // removed by dead control flow + case 11: return 21; - break; + // removed by dead control flow + case 12: return '<='; - break; + // removed by dead control flow + case 13: return '>='; - break; + // removed by dead control flow + case 14: return '<'; - break; + // removed by dead control flow + case 15: return '>'; - break; + // removed by dead control flow + case 16: yy_.yytext = yy_.yytext.substr(1, yy_.yyleng - 2); return 24; - break; + // removed by dead control flow + case 17: return 13; - break; + // removed by dead control flow + case 18: return 23; - break; + // removed by dead control flow + case 19: return 5; - break; + // removed by dead control flow + case 20: return 'INVALID'; - break; + // removed by dead control flow + } }, rules: [/^(?:\s+)/i, /^(?:(-?(?:[1-9][0-9]+|[0-9]))\b)/i, /^(?:OR\b)/i, /^(?:AND\b)/i, /^(?:NOT\b)/i, /^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\b)/i, /^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\b)/i, /^(?:((SERIAL|SEQUENCE|RESIDX))\b)/i, /^(?:\()/i, /^(?:\))/i, /^(?:,)/i, /^(?::)/i, /^(?:<=)/i, /^(?:>=)/i, /^(?:<)/i, /^(?:>)/i, /^(?:((?:"(?:\\.|[^\\"])*"|'(?:\\.|[^\\'])*')))/i, /^(?:(@[_A-Z0-9]+))/i, /^(?:([_A-Z0-9]+))/i, /^(?:$)/i, /^(?:.)/i], @@ -3675,10 +3778,10 @@ module.exports = { parser: parser }; -/***/ }), +/***/ }, -/***/ 690: -/***/ (function(__unused_webpack_module, exports) { +/***/ 690 +(__unused_webpack_module, exports) { /* Smooth.js version 0.1.7 @@ -4072,16 +4175,17 @@ Licensed under MIT license (see "Smooth.js MIT license.txt") ( true && exports !== null ? exports : window).Smooth = Smooth; }).call(this); -/***/ }), +/***/ }, -/***/ 660: -/***/ (function(module, exports) { +/***/ 660 +(module, exports) { var __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!function (r, t) { if (true) !(__WEBPACK_AMD_DEFINE_ARRAY__ = [exports], __WEBPACK_AMD_DEFINE_FACTORY__ = (t), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), - __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));else {} + __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));else // removed by dead control flow +{} }(this, function (r) { "use strict"; @@ -4722,7 +4826,7 @@ var __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_ r.encode = Q, r.decode = Y, r.traverse = K, r.fetch = $, r.fetchReduced = _, r.version = er, r.fetchUrl = or, r.fetchReducedUrl = ar, r.encodeMsgpack = o, r.encodeMmtf = R, r.decodeMsgpack = H, r.decodeMmtf = X; }); -/***/ }) +/***/ } /******/ }); /************************************************************************/ @@ -4781,22 +4885,12 @@ var __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_ /******/ })(); /******/ /************************************************************************/ -var __webpack_exports__ = {}; -// EXPORTS -__webpack_require__.d(__webpack_exports__, { - A: () => (/* binding */ src) -}); +;// external {"module":"lodash","commonjs":"lodash","commonjs2":"lodash","amd":"lodash","root":"_"} -;// CONCATENATED MODULE: external {"module":"lodash","commonjs":"lodash","commonjs2":"lodash","amd":"lodash","root":"_"} -var x = (y) => { - var x = {}; __webpack_require__.d(x, y); return x -} -var y = (x) => (() => (x)) -const external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject = x({ ["default"]: () => (__WEBPACK_EXTERNAL_MODULE_lodash__["default"]) }); -;// CONCATENATED MODULE: external {"module":"three","commonjs":"three","commonjs2":"three","amd":"three","root":"THREE"} +;// external {"module":"three","commonjs":"three","commonjs2":"three","amd":"three","root":"THREE"} const external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject = __WEBPACK_EXTERNAL_MODULE_three__; -;// CONCATENATED MODULE: ../../node_modules/spin.js/spin.js +;// ../../node_modules/spin.js/spin.js var __assign = undefined && undefined.__assign || function () { __assign = Object.assign || function (t) { for (var s, i = 1, n = arguments.length; i < n; i++) { @@ -4967,7 +5061,7 @@ function convertOffset(x, y, degrees) { var cos = Math.cos(radians); return [Math.round((x * cos + y * sin) * 1000) / 1000, Math.round((-x * sin + y * cos) * 1000) / 1000]; } -;// CONCATENATED MODULE: ./src/Timer.js +;// ./src/Timer.js //---------------------------------------------------------------------------- // Timer @@ -5006,7 +5100,7 @@ Timer.now = function () { const p = typeof window !== 'undefined' && window.performance; return p && p.now ? p.now.bind(p) : Date.now; }(); -;// CONCATENATED MODULE: ./src/gfx/Stats.js +;// ./src/gfx/Stats.js const { now @@ -5059,7 +5153,7 @@ class Stats { } } /* harmony default export */ const gfx_Stats = (Stats); -;// CONCATENATED MODULE: ./src/utils/EventDispatcher.js +;// ./src/utils/EventDispatcher.js /** * This class introduces the simplest event system. */ @@ -5096,7 +5190,7 @@ EventDispatcher.prototype.addEventListener = function (type, callback, context) function _checkPar(par) { return par[0] === params[0] && par[1] === params[1]; } - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].find(handlers, _checkPar) === undefined) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.find(handlers, _checkPar) === undefined) { handlers.push(params); } }; @@ -5113,10 +5207,10 @@ EventDispatcher.prototype.addEventListener = function (type, callback, context) */ EventDispatcher.prototype.removeEventListener = function (type, callback, context) { const self = this; - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].forEach(self._handlers, (handler, ev) => { - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].remove(handler, values => isUndefOrEqual(type, ev) && isUndefOrEqual(callback, values[0]) && isUndefOrEqual(context, values[1] || self)); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.forEach(self._handlers, (handler, ev) => { + __WEBPACK_EXTERNAL_MODULE_lodash_default__.remove(handler, values => isUndefOrEqual(type, ev) && isUndefOrEqual(callback, values[0]) && isUndefOrEqual(context, values[1] || self)); }); - this._handlers = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].omitBy(self._handlers, handler => handler.length === 0); + this._handlers = __WEBPACK_EXTERNAL_MODULE_lodash_default__.omitBy(self._handlers, handler => handler.length === 0); }; /** @@ -5126,13 +5220,13 @@ EventDispatcher.prototype.removeEventListener = function (type, callback, contex */ EventDispatcher.prototype.dispatchEvent = function (event) { const self = this; - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].forEach(this._handlers[event.type], callback => { + __WEBPACK_EXTERNAL_MODULE_lodash_default__.forEach(this._handlers[event.type], callback => { const context = callback[1] || self; callback[0].apply(context, [event]); }); }; /* harmony default export */ const utils_EventDispatcher = (EventDispatcher); -;// CONCATENATED MODULE: ./src/utils/logger.js +;// ./src/utils/logger.js /** * This module contains class for logging. * Returns an instance of a logger that have already been created. @@ -5175,7 +5269,7 @@ Logger.prototype.instantiate = function () { return new Logger(); }; function verify(number) { - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isNumber(number)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isNumber(number)) { throw new Error('Wrong log level specified!'); } return number; @@ -5187,7 +5281,7 @@ function verify(number) { */ Object.defineProperty(Logger.prototype, 'level', { get() { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].findKey(priorities, value => value === this._priority); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.findKey(priorities, value => value === this._priority); }, set(level) { this._priority = verify(priorities[level]); @@ -5263,7 +5357,7 @@ Logger.prototype._message = function (priority, message) { if (priority < this._priority) { return; } - const level = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].findKey(priorities, value => value === priority); + const level = __WEBPACK_EXTERNAL_MODULE_lodash_default__.findKey(priorities, value => value === priority); message = String(message); if (this.console) { const output = `miew:${level}: ${message}`; @@ -5282,7 +5376,7 @@ Logger.prototype._message = function (priority, message) { }); }; /* harmony default export */ const logger = (new Logger()); -;// CONCATENATED MODULE: ./src/utils.js +;// ./src/utils.js const browserType = { @@ -5363,7 +5457,7 @@ function resolveURL(str) { return new URL(str, window.location).href; } return new URL(str).href; - } catch (error) { + } catch { // IE 11 has a URL object with no constructor available so just try a different approach instead } } @@ -5432,11 +5526,11 @@ function utils_createElement(tag, attrs, content) { * @returns {function} Original class. */ function deriveClass(cls, base, members, statics) { - cls.prototype = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].assign(Object.create(base.prototype), { + cls.prototype = __WEBPACK_EXTERNAL_MODULE_lodash_default__.assign(Object.create(base.prototype), { constructor: cls }, members); if (statics) { - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].assign(cls, statics); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.assign(cls, statics); } return cls; } @@ -5490,16 +5584,13 @@ function DebugTracer(namespace) { let indent = 0; const methods = Object.keys(namespace); function wrap(method_, name_) { - return function () { + return function (...args) { const spaces = DebugTracer.spaces.substr(0, indent * 2); if (enabled) { logger.debug(`${spaces + name_} {`); } indent++; - for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) { - args[_key] = arguments[_key]; - } - const result = method_.apply(this, args); // eslint-disable-line no-invalid-this + const result = method_.apply(this, args); indent--; if (enabled) { logger.debug(`${spaces}} // ${name_}`); @@ -5540,7 +5631,7 @@ function allocateTyped(TypedArrayName, size) { //---------------------------------------------------------------------------- // Float array conversion -function bytesToBase64( /** ArrayBuffer */buffer) { +function bytesToBase64(/** ArrayBuffer */buffer) { const bytes = new Uint8Array(buffer); let binary = ''; for (let i = 0; i < bytes.byteLength; i++) { @@ -5548,7 +5639,7 @@ function bytesToBase64( /** ArrayBuffer */buffer) { } return window.btoa(binary); } -function bytesFromBase64( /** string */str) { +function bytesFromBase64(/** string */str) { const binary = window.atob(str); const bytes = new Uint8Array(binary.length); for (let i = 0; i < bytes.length; ++i) { @@ -5556,10 +5647,10 @@ function bytesFromBase64( /** string */str) { } return bytes.buffer; } -function arrayToBase64( /** number[] */array, /** function */TypedArrayClass) { +function arrayToBase64(/** number[] */array, /** function */TypedArrayClass) { return bytesToBase64(new TypedArrayClass(array).buffer); } -function arrayFromBase64( /** string */str, /** function */TypedArrayClass) { +function arrayFromBase64(/** string */str, /** function */TypedArrayClass) { return Array.prototype.slice.call(new TypedArrayClass(bytesFromBase64(str))); } @@ -5583,7 +5674,7 @@ function compareOptionsWithDefaults(opts, defOpts) { return ''; } function isAlmostPlainObject(o) { - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isPlainObject(o)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isPlainObject(o)) { return true; } const proto = o && Object.getPrototypeOf(o); @@ -5599,14 +5690,14 @@ function isAlmostPlainObject(o) { */ function objectsDiff(src, dst) { const diff = {}; - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].forIn(src, (srcValue, key) => { + __WEBPACK_EXTERNAL_MODULE_lodash_default__.forIn(src, (srcValue, key) => { const dstValue = dst[key]; if (isAlmostPlainObject(srcValue) && isAlmostPlainObject(dstValue)) { const deepDiff = objectsDiff(srcValue, dstValue); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(deepDiff)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(deepDiff)) { diff[key] = deepDiff; } - } else if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEqual(srcValue, dstValue)) { + } else if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEqual(srcValue, dstValue)) { diff[key] = srcValue; } }); @@ -5614,7 +5705,7 @@ function objectsDiff(src, dst) { } function forInRecursive(object, callback) { function iterateThrough(obj, prefix) { - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].forIn(obj, (value, key) => { + __WEBPACK_EXTERNAL_MODULE_lodash_default__.forIn(obj, (value, key) => { const newPref = prefix + (prefix.length > 0 ? '.' : ''); if (value instanceof Object) { iterateThrough(value, newPref + key); @@ -5626,13 +5717,13 @@ function forInRecursive(object, callback) { iterateThrough(object, ''); } function enquoteString(value) { - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(value)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(value)) { return `"${value.replace(/"/g, '\\"')}"`; } return value; } function unquoteString(value) { - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(value)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(value)) { return value; } if (value[0] === '"' && value[value.length - 1] === '"') { @@ -5814,7 +5905,7 @@ function mergeTypedArraysUnsafe(array) { concatTypedArraysUnsafe, mergeTypedArraysUnsafe }); -;// CONCATENATED MODULE: ./src/utils/JobHandle.js +;// ./src/utils/JobHandle.js class JobHandle extends utils_EventDispatcher { constructor() { @@ -5840,7 +5931,7 @@ class JobHandle extends utils_EventDispatcher { }); } } -;// CONCATENATED MODULE: ./src/settings.js +;// ./src/settings.js @@ -6702,32 +6793,32 @@ function Settings() { utils.deriveClass(Settings, utils_EventDispatcher, { defaults: settings_defaults, set(path, value) { - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(path)) { - const oldValue = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(this.now, path); + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(path)) { + const oldValue = __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(this.now, path); if (oldValue !== value) { - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].set(this.now, path, value); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.set(this.now, path, value); this._notifyChange(path, value); } } else { const diff = utils.objectsDiff(path, this.now); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(diff)) { - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge(this.now, diff); + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(diff)) { + __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge(this.now, diff); this._notifyChanges(diff); } } }, get(path, defaultValue) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(this.now, path, defaultValue); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(this.now, path, defaultValue); }, reset() { const diff = utils.objectsDiff(settings_defaults, this.now); - this.now = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].cloneDeep(settings_defaults); + this.now = __WEBPACK_EXTERNAL_MODULE_lodash_default__.cloneDeep(settings_defaults); this.old = null; this._notifyChanges(diff); this._changed = {}; }, checkpoint() { - this.old = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].cloneDeep(this.now); + this.old = __WEBPACK_EXTERNAL_MODULE_lodash_default__.cloneDeep(this.now); this._changed = {}; }, _notifyChange(path, value) { @@ -6750,7 +6841,7 @@ utils.deriveClass(Settings, utils_EventDispatcher, { old, now } = this; - const keys = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].filter(Object.keys(this._changed), key => external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(old, key) !== external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(now, key)); + const keys = __WEBPACK_EXTERNAL_MODULE_lodash_default__.filter(Object.keys(this._changed), key => __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(old, key) !== __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(now, key)); return keys; }, applyDiffs(diffs) { @@ -6770,19 +6861,19 @@ utils.deriveClass(Settings, utils_EventDispatcher, { return diffs; }, setPluginOpts(plugin, opts) { - settings_defaults.plugins[plugin] = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].cloneDeep(opts); - this.now.plugins[plugin] = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].cloneDeep(opts); + settings_defaults.plugins[plugin] = __WEBPACK_EXTERNAL_MODULE_lodash_default__.cloneDeep(opts); + this.now.plugins[plugin] = __WEBPACK_EXTERNAL_MODULE_lodash_default__.cloneDeep(opts); } }); /* harmony default export */ const settings = (new Settings()); -;// CONCATENATED MODULE: ./src/options.js +;// ./src/options.js let repIndex = 0; function asBoolean(value) { - return !(!value || value === '0' || external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(value) && value.toLowerCase() === 'false'); + return !(!value || value === '0' || __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(value) && value.toLowerCase() === 'false'); } const adapters = { string: String, @@ -6895,9 +6986,9 @@ function extractArgs(input, defaultsDict, params) { const pair = arg.split(cL2Ass, 2); const key = decodeURIComponent(pair[0]); const value = decodeURIComponent(pair[1]); - const adapter = adapters[typeof external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(defaults, key)]; + const adapter = adapters[typeof __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(defaults, key)]; if (adapter) { - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].set(opts, key, adapter(value)); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.set(opts, key, adapter(value)); } else { logger.warn(`Unknown argument "${key}" for option "${input}"`); } @@ -6990,20 +7081,20 @@ function _fromArray(entries) { let /** function|string? */action = actions[key]; // unwind shortcuts and aliases - while (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(action)) { + while (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(action)) { key = action; action = actions[key]; } // either set a property or use specialized parser if (!action) { - const adapter = adapters[typeof external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(settings.defaults, key)]; + const adapter = adapters[typeof __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(settings.defaults, key)]; if (adapter) { - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].set(opts, `settings.${key}`, adapter(value)); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.set(opts, `settings.${key}`, adapter(value)); } else { logger.warn(`Unknown option "${key}"`); } - } else if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isFunction(action)) { + } else if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isFunction(action)) { const result = action(value, opts); if (result !== undefined) { opts[key] = result; @@ -7027,7 +7118,7 @@ function _processOptsForURL(opts) { return str.join(cLSep); } function _processArgsForURL(args) { - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArray(args)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isArray(args)) { return args; } if (args.length < 2) { @@ -7040,7 +7131,7 @@ function _processObjForURL(objOpts) { return undefined; } let res = objOpts.type; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArray(objOpts.params) && objOpts.params.length > 0) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isArray(objOpts.params) && objOpts.params.length > 0) { res += `,${objOpts.params.join(',')}`; } if (objOpts.opts) { @@ -7061,7 +7152,7 @@ function toURL(opts) { return; } for (let i = 0, n = repList.length; i < n; ++i) { - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(repList[i])) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(repList[i])) { continue; } checkAndAdd('r', i); @@ -7114,7 +7205,7 @@ function _processOptsForScript(opts) { return str.join(' '); } function _processArgsForScript(args) { - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArray(args)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isArray(args)) { return args; } if (args.length < 2) { @@ -7127,7 +7218,7 @@ function _processObjForScript(objOpts) { return undefined; } let res = objOpts.type; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArray(objOpts.params) && objOpts.params.length > 0) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isArray(objOpts.params) && objOpts.params.length > 0) { res += ` ${objOpts.params.map(utils.enquoteString).join(' ')}`; } if (objOpts.opts) { @@ -7143,7 +7234,7 @@ function _processRepsForScript(rep, index) { repString[strIdx++] = prefix + value; } } - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(rep)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(rep)) { return null; } localAdd('', index); @@ -7203,7 +7294,7 @@ function toScript(opts) { toURL, toScript }); -;// CONCATENATED MODULE: ./src/chem/Atom.js +;// ./src/chem/Atom.js /** * Atom measurements. * @@ -7303,7 +7394,7 @@ class Atom { }; } /* harmony default export */ const chem_Atom = (Atom); -;// CONCATENATED MODULE: ./src/chem/Element.js +;// ./src/chem/Element.js class Element { constructor(number, name, fullName, weight, radius, radiusBonding, hValency) { this.number = number; @@ -7315,39 +7406,32 @@ class Element { this.hydrogenValency = hValency; } static Constants = { - /* eslint-disable no-magic-numbers */ U1: 1, Lead: 2, U2: 3, Wing: 4, U18: 18 - /* eslint-enable no-magic-numbers */ }; - static Role = (() => ({ - /* eslint-disable no-magic-numbers */ + static Role = { N: Element.Constants.U1, CA: Element.Constants.Lead, C: Element.Constants.U2, O: Element.Constants.Wing, SG: Element.Constants.U18 - /* eslint-enable no-magic-numbers */ - }))(); + }; // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. - static ByAtomicNumber = (() => [/* eslint-disable no-magic-numbers */ - null, new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]), new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]), new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]), new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]), new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]), new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]), new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]), new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]), new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]), new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]), new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]), new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]), new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]), new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]), new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]), new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]), new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]), new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]), new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]), new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]), new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]), new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]), new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]), new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]), new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]), new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]), new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]), new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]), new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]), new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]), new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]), new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]), new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]), new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]), new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]), new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]), new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]), new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]), new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]), new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]), new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]), new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]), new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]), new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]), new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]), new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]), new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]), new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]), new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]), new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]), new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]), new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]), new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]), new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]), new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]), new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]), new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]), new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]), new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]), new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]), new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]), new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]), new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]), new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]), new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]), new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]), new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]), new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]), new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]), new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]), new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]), new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]), new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]), new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]), new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]), new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]), new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]), new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]), new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]), new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]), new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]), new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]), new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]), new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]), new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]), new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]), new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]), new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]), new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]), new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]), new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]), new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]), new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]), new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]), new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]), new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]), new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]), new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]), new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]), new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]), new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]), new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]), new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]), new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]), new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]), new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]), new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]), new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]), new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0]) - /* eslint-enable no-magic-numbers */])(); + static ByAtomicNumber = [null, new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]), new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]), new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]), new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]), new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]), new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]), new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]), new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]), new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]), new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]), new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]), new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]), new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]), new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]), new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]), new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]), new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]), new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]), new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]), new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]), new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]), new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]), new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]), new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]), new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]), new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]), new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]), new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]), new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]), new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]), new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]), new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]), new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]), new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]), new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]), new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]), new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]), new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]), new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]), new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]), new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]), new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]), new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]), new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]), new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]), new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]), new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]), new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]), new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]), new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]), new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]), new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]), new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]), new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]), new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]), new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]), new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]), new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]), new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]), new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]), new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]), new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]), new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]), new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]), new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]), new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]), new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]), new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]), new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]), new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]), new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]), new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]), new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]), new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]), new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]), new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]), new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]), new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]), new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]), new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]), new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]), new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]), new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]), new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]), new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]), new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]), new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]), new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]), new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]), new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]), new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]), new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]), new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]), new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]), new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]), new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]), new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]), new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]), new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]), new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]), new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]), new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]), new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]), new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]), new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]), new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]), new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]), new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]), new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0])]; // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. - static ByName = (() => ({ + static ByName = { // Duplicate atomic numbers (isotopes) - /* eslint-disable no-magic-numbers */ + D: new Element(1, 'D', 'Deuterium', 2.014, 1.2, 0.23, [1]), T: new Element(1, 'T', 'Tritium', 3.016, 1.2, 0.23, [1]) - /* eslint-enable no-magic-numbers */ // All regular elements will be added later, automatically - }))(); + }; } (function () { const byAtomicNumber = Element.ByAtomicNumber; @@ -7369,7 +7453,7 @@ Element.getByName = function (element) { return type; }; /* harmony default export */ const chem_Element = (Element); -;// CONCATENATED MODULE: ./src/chem/Bond.js +;// ./src/chem/Bond.js const cBondTypes = { /** Was generated manually */ UNKNOWN: 0, @@ -7544,11 +7628,11 @@ class Bond { firstV.normalize(); return this._fixDir(secondPos, firstV, posGetter); } - static BondType = (() => cBondTypes)(); + static BondType = cBondTypes; } Bond.prototype.BondType = cBondTypes; /* harmony default export */ const chem_Bond = (Bond); -;// CONCATENATED MODULE: ./src/chem/Residue.js +;// ./src/chem/Residue.js @@ -7819,7 +7903,7 @@ class Residue { } } /* harmony default export */ const chem_Residue = (Residue); -;// CONCATENATED MODULE: ./src/chem/ResidueType.js +;// ./src/chem/ResidueType.js /** * Residue type. * @@ -7844,8 +7928,7 @@ class ResidueType { } // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py. - static StandardTypes = (() => ({ - /* eslint-disable no-magic-numbers */ + static StandardTypes = { ALA: new ResidueType('ALA', 'Alanine', 'A'), ARG: new ResidueType('ARG', 'Arginine', 'R'), ASN: new ResidueType('ASN', 'Asparagine', 'N'), @@ -7892,8 +7975,7 @@ class ResidueType { DOD: new ResidueType('DOD', 'Water', ''), UNK: new ResidueType('UNK', 'Unknown', ''), UNL: new ResidueType('UNL', 'Unknown Ligand', '') - /* eslint-enable no-magic-numbers */ - }))(); + }; /** * Enumeration of residue flag values. @@ -7989,7 +8071,7 @@ function _addParam(param, list) { } _addParam('hydrophobicity', hydro); /* harmony default export */ const chem_ResidueType = (ResidueType); -;// CONCATENATED MODULE: ./src/chem/Chain.js +;// ./src/chem/Chain.js @@ -8158,7 +8240,7 @@ class Chain { } } /* harmony default export */ const chem_Chain = (Chain); -;// CONCATENATED MODULE: ./src/chem/StructuralElement.js +;// ./src/chem/StructuralElement.js /** An element of protein secondary structure. */ @@ -8290,7 +8372,7 @@ StructuralElement.genericByType = { [StructuralElementType.HELIX]: StructuralElementGeneric.HELIX }; /* harmony default export */ const chem_StructuralElement = (StructuralElement); -;// CONCATENATED MODULE: ./src/chem/Helix.js +;// ./src/chem/Helix.js const Helix_StructuralElementType = chem_StructuralElement.Type; const typeByPDBHelixClass = { @@ -8342,7 +8424,7 @@ class Helix extends chem_StructuralElement { } } /* harmony default export */ const chem_Helix = (Helix); -;// CONCATENATED MODULE: ./src/chem/Strand.js +;// ./src/chem/Strand.js /** @@ -8416,7 +8498,7 @@ class Strand extends chem_StructuralElement { } } /* harmony default export */ const chem_Strand = (Strand); -;// CONCATENATED MODULE: ./src/chem/Sheet.js +;// ./src/chem/Sheet.js /** @@ -8463,7 +8545,7 @@ class Sheet { } } /* harmony default export */ const chem_Sheet = (Sheet); -;// CONCATENATED MODULE: ./src/chem/SGroup.js +;// ./src/chem/SGroup.js /** @@ -8522,7 +8604,7 @@ class SGroup { /* harmony default export */ const chem_SGroup = (SGroup); // EXTERNAL MODULE: ./src/utils/SelectionParser.js var SelectionParser = __webpack_require__(99); -;// CONCATENATED MODULE: ./src/chem/selectors/selectArgs.js +;// ./src/chem/selectors/selectArgs.js //---------------------------------------------------------------------------- @@ -8653,7 +8735,7 @@ class ValueList extends List { } } -;// CONCATENATED MODULE: ./src/chem/selectors/selectorsBase.js +;// ./src/chem/selectors/selectorsBase.js /** Base class for atom selectors. */ @@ -8706,7 +8788,7 @@ class AllSelector extends Selector { AllSelector.prototype.name = 'All'; AllSelector.prototype.keyword = 'all'; -;// CONCATENATED MODULE: ./src/chem/selectors/selectOps.js +;// ./src/chem/selectors/selectOps.js //---------------------------------------------------------------------------- @@ -8744,7 +8826,7 @@ class InfixOperator extends Selector { } InfixOperator.prototype.priority = 1000; -;// CONCATENATED MODULE: ./src/chem/selectors.js +;// ./src/chem/selectors.js @@ -8761,12 +8843,7 @@ function defineSelector(name, SelectorClass) { const keyword = name.toLowerCase(); SelectorClass.prototype.keyword = keyword; SelectorClass.prototype.name = name; - const factory = function () { - for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) { - args[_key] = arguments[_key]; - } - return new SelectorClass(...args); - }; + const factory = (...args) => new SelectorClass(...args); factory.SelectorClass = SelectorClass; keywords[keyword] = factory; return SelectorClass; @@ -8930,7 +9007,7 @@ SelectionParser.parser.yy = selectors; SelectionParser.parser.yy.parseError = SelectionParser.parser.parseError; // workaround for incorrect JISON parser generator for AMD module /* harmony default export */ const chem_selectors = (selectors); -;// CONCATENATED MODULE: ./src/chem/BiologicalUnit.js +;// ./src/chem/BiologicalUnit.js @@ -9003,7 +9080,7 @@ class BiologicalUnit { finalize() {} } /* harmony default export */ const chem_BiologicalUnit = (BiologicalUnit); -;// CONCATENATED MODULE: ./src/chem/Assembly.js +;// ./src/chem/Assembly.js @@ -9069,7 +9146,7 @@ class Assembly extends chem_BiologicalUnit { } } /* harmony default export */ const chem_Assembly = (Assembly); -;// CONCATENATED MODULE: ./src/chem/Component.js +;// ./src/chem/Component.js /** * This class represents connected component as a part of a complex. * WARNING! The whole component entity is build under the assumption that residues @@ -9219,7 +9296,7 @@ class Component { } } /* harmony default export */ const chem_Component = (Component); -;// CONCATENATED MODULE: ./src/chem/AtomPairs.js +;// ./src/chem/AtomPairs.js const cMaxPairsForHashCode = 32; const cHashTableSize = 1024 * 1024; @@ -9290,7 +9367,7 @@ class AtomPairs { } } /* harmony default export */ const chem_AtomPairs = (AtomPairs); -;// CONCATENATED MODULE: ./src/chem/AutoBond.js +;// ./src/chem/AutoBond.js const cProfileBondBuilder = false; @@ -9472,7 +9549,7 @@ class AutoBond { } } /* harmony default export */ const chem_AutoBond = (AutoBond); -;// CONCATENATED MODULE: ./src/chem/AromaticLoopsMarker.js +;// ./src/chem/AromaticLoopsMarker.js @@ -9704,7 +9781,7 @@ class AromaticLoopsMarker { } } /* harmony default export */ const chem_AromaticLoopsMarker = (AromaticLoopsMarker); -;// CONCATENATED MODULE: ./src/chem/VoxelWorld.js +;// ./src/chem/VoxelWorld.js @@ -9818,8 +9895,8 @@ class VoxelWorld { * @param {Vector3} point - a point in 3D * @returns {number} - index of voxel */ - static _zero = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(0, 0, 0))(); - static _voxel = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3())(); + static _zero = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(0, 0, 0); + static _voxel = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); _findVoxel(point) { const zero = VoxelWorld._zero; const voxel = VoxelWorld._voxel; @@ -9848,9 +9925,9 @@ class VoxelWorld { * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside */ - static _xRange = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector2())(); - static _yRange = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector2())(); - static _zRange = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector2())(); + static _xRange = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector2(); + static _yRange = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector2(); + static _zRange = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector2(); _forEachVoxelWithinRadius(center, radius, process) { const xRange = VoxelWorld._xRange; const yRange = VoxelWorld._yRange; @@ -9906,7 +9983,7 @@ class VoxelWorld { * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside */ - static _vCenter = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3())(); + static _vCenter = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); _forEachVoxelWithinRadiusSimple(center, radius, process) { const xRange = VoxelWorld._xRange; const yRange = VoxelWorld._yRange; @@ -10075,7 +10152,7 @@ class VoxelWorld { } } /* harmony default export */ const chem_VoxelWorld = (VoxelWorld); -;// CONCATENATED MODULE: ./src/chem/HBondInfo.js +;// ./src/chem/HBondInfo.js const MINIMAL_DISTANCE = 0.5; @@ -10309,7 +10386,7 @@ class HBondInfo { return result; } } -;// CONCATENATED MODULE: ./src/chem/SecondaryStructureMap.js +;// ./src/chem/SecondaryStructureMap.js const BridgeType = Object.freeze({ @@ -10736,7 +10813,7 @@ class SecondaryStructureMap { } } SecondaryStructureMap.StructureType = StructureType; -;// CONCATENATED MODULE: ./src/chem/Complex.js +;// ./src/chem/Complex.js @@ -10979,17 +11056,13 @@ class Complex { return this._residueTypes[name] || null; } getUnifiedSerial(chain, serial, iCode) { - /* eslint-disable no-magic-numbers */ const maxSerial = 65536; const chainShift = maxSerial * 256; - /* eslint-enable no-magic-numbers */ return serial + iCode * maxSerial + chain * chainShift; } splitUnifiedSerial(uniSerial) { - /* eslint-disable no-magic-numbers */ const maxSerial = 65536; const chainShift = maxSerial * 256; - /* eslint-enable no-magic-numbers */ const chainId = Math.floor(uniSerial / chainShift); const remnant = uniSerial - chainId * chainShift; const insCode = Math.floor(remnant / maxSerial); @@ -11389,7 +11462,7 @@ class Complex { try { this._voxelWorld = new chem_VoxelWorld(this.getDefaultBoundaries().boundingBox, new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(VOXEL_SIZE, VOXEL_SIZE, VOXEL_SIZE)); this._voxelWorld.addAtoms(this); - } catch (e) { + } catch { logger.warn('Unable to create voxel world'); this._voxelWorld = null; } @@ -11553,7 +11626,7 @@ class Complex { Complex.prototype.id = 'Complex'; Complex.prototype.name = ''; /* harmony default export */ const chem_Complex = (Complex); -;// CONCATENATED MODULE: ./src/chem/Volume.js +;// ./src/chem/Volume.js function pow2ceil(v) { @@ -11804,7 +11877,7 @@ class Volume { } } } - const texture = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.DataTexture(data, width, height, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LuminanceFormat, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.UnsignedByteType, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.UVMapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.ClampToEdgeWrapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.ClampToEdgeWrapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter); + const texture = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.DataTexture(data, width, height, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.RedFormat, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.UnsignedByteType, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.UVMapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.ClampToEdgeWrapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.ClampToEdgeWrapping, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter); texture.needsUpdate = true; return texture; } @@ -11833,7 +11906,7 @@ class Volume { } Volume.prototype.id = 'Volume'; /* harmony default export */ const chem_Volume = (Volume); -;// CONCATENATED MODULE: ./src/chem/Molecule.js +;// ./src/chem/Molecule.js /** * Residue Molecule. * @@ -11872,7 +11945,7 @@ class Molecule { } } /* harmony default export */ const chem_Molecule = (Molecule); -;// CONCATENATED MODULE: ./src/chem.js +;// ./src/chem.js @@ -11907,7 +11980,7 @@ class Molecule { selectors: chem_selectors, Molecule: chem_Molecule }); -;// CONCATENATED MODULE: ./src/gfx/CSS2DObject.js +;// ./src/gfx/CSS2DObject.js /** * @author mrdoob / http://mrdoob.com/ */ @@ -11957,7 +12030,7 @@ class CSS2DObject extends external_module_three_commonjs_three_commonjs2_three_a } } /* harmony default export */ const gfx_CSS2DObject = (CSS2DObject); -;// CONCATENATED MODULE: ./src/gfx/RCGroup.js +;// ./src/gfx/RCGroup.js class RCGroup extends external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Group { raycast(raycaster, intersects) { @@ -12018,14 +12091,13 @@ class RCGroup extends external_module_three_commonjs_three_commonjs2_three_amd_t } } /* harmony default export */ const gfx_RCGroup = (RCGroup); -;// CONCATENATED MODULE: ./src/gfx/shaders/ScreenQuad.vert -const ScreenQuad_namespaceObject = "uniform mat4 projectionMatrix;\r\nuniform mat4 modelViewMatrix;\r\n\r\nattribute vec2 uv;\r\nattribute vec3 position;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vUv = uv;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4( position, 1.0 );\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/ScreenQuadFromTex.frag -const ScreenQuadFromTex_namespaceObject = "precision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform float opacity;\r\n\r\nvoid main() {\r\n vec4 color = texture2D(srcTex, vUv);\r\n gl_FragColor = vec4(color.xyz, color.a * opacity);\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/ScreenQuadFromTexWithDistortion.frag -const ScreenQuadFromTexWithDistortion_namespaceObject = "precision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform float coef;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n float r2 = dot(uv, uv);\r\n vec2 tc = uv * (1.0 + coef * r2);\r\n if (!all(lessThan(abs(tc), vec2(1.0))))\r\n discard;\r\n tc = 0.5 * (tc + 1.0);\r\n gl_FragColor = texture2D(srcTex, tc);\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/gfxutils.js -/* eslint-disable no-magic-numbers */ +;// ./src/gfx/shaders/ScreenQuad.vert +const ScreenQuad_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nuniform mat4 projectionMatrix;\r\nuniform mat4 modelViewMatrix;\r\n\r\nattribute vec2 uv;\r\nattribute vec3 position;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vUv = uv;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4( position, 1.0 );\r\n}\r\n"; +;// ./src/gfx/shaders/ScreenQuadFromTex.frag +const ScreenQuadFromTex_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform float opacity;\r\n\r\nvoid main() {\r\n vec4 color = texture2D(srcTex, vUv);\r\n gl_FragColor = vec4(color.xyz, color.a * opacity);\r\n}\r\n"; +;// ./src/gfx/shaders/ScreenQuadFromTexWithDistortion.frag +const ScreenQuadFromTexWithDistortion_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform float coef;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n float r2 = dot(uv, uv);\r\n vec2 tc = uv * (1.0 + coef * r2);\r\n if (!all(lessThan(abs(tc), vec2(1.0))))\r\n discard;\r\n tc = 0.5 * (tc + 1.0);\r\n gl_FragColor = texture2D(srcTex, tc);\r\n}\r\n"; +;// ./src/gfx/gfxutils.js @@ -12445,7 +12517,7 @@ external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namesp getMiddlePoint, LAYERS }); -;// CONCATENATED MODULE: ./src/Visual.js +;// ./src/Visual.js const _defaultBoundaries = { @@ -12471,7 +12543,7 @@ class Visual extends gfxutils.RCGroup { } } /* harmony default export */ const src_Visual = (Visual); -;// CONCATENATED MODULE: ./src/utils/EntityList.js +;// ./src/utils/EntityList.js function _ensureArray(x) { if (x === null || x === undefined || Array.isArray(x)) { return x; @@ -12490,9 +12562,7 @@ class EntityList { * By default, a single `.id` property is used. * @see EntityList#register */ - constructor() { - let entities = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : []; - let indices = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : ['id']; + constructor(entities = [], indices = ['id']) { this._list = []; this._dict = {}; this._indices = [...indices]; @@ -12659,7 +12729,7 @@ class EntityList { } } /* harmony default export */ const utils_EntityList = (EntityList); -;// CONCATENATED MODULE: ./src/utils/makeContextDependent.js +;// ./src/utils/makeContextDependent.js function makeContextDependent(prototype) { @@ -12677,14 +12747,14 @@ function makeContextDependent(prototype) { }); } /* harmony default export */ const utils_makeContextDependent = (makeContextDependent); -;// CONCATENATED MODULE: ./src/gfx/geometries/SphereCollisionGeo.js +;// ./src/gfx/geometries/SphereCollisionGeo.js class CollisionSphere { constructor(position, radius) { this._position = position; this._radius = radius; } - static _sphere = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Sphere())(); + static _sphere = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Sphere(); raycast(raycaster) { const sphere = CollisionSphere._sphere; sphere.set(this._position, this._radius); @@ -12699,10 +12769,7 @@ class CollisionSphere { } } const SphereCollisionGeo = base => class extends base { - constructor(count) { - for (var _len = arguments.length, args = new Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) { - args[_key - 1] = arguments[_key]; - } + constructor(count, ...args) { super(...args); this._objects = new Array(count); this.boundingSphere = null; @@ -12758,7 +12825,7 @@ const SphereCollisionGeo = base => class extends base { } }; /* harmony default export */ const geometries_SphereCollisionGeo = (SphereCollisionGeo); -;// CONCATENATED MODULE: ./src/gfx/geometries/InstancedSpheresGeometry.js +;// ./src/gfx/geometries/InstancedSpheresGeometry.js @@ -12783,7 +12850,7 @@ function setArrayXYZW(arr, idx, x, y, z, w) { class InstancedSpheresGeometry extends geometries_SphereCollisionGeo(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.InstancedBufferGeometry) { constructor(spheresCount, sphereComplexity, useZSprites) { super(spheresCount); - this._sphGeometry = useZSprites ? new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.PlaneGeometry(2, 2, 1, 1) : new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.SphereBufferGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI); + this._sphGeometry = useZSprites ? new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.PlaneGeometry(2, 2, 1, 1) : new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.SphereGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI); this._init(spheresCount, this._sphGeometry); } setItem(itemIdx, itemPos, itemRad) { @@ -12827,14 +12894,14 @@ class InstancedSpheresGeometry extends geometries_SphereCollisionGeo(external_mo this._offsets = utils.allocateTyped(Float32Array, spheresCount * OFFSET_SIZE); this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE); const alpha = this._alpha = utils.allocateTyped(Float32Array, spheresCount); - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].fill(alpha, 1.0); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.fill(alpha, 1.0); this.setAttribute('offset', new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.InstancedBufferAttribute(this._offsets, OFFSET_SIZE, false, 1)); this.setAttribute('color', new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.InstancedBufferAttribute(this._colors, COLOR_SIZE, false, 1)); this.setAttribute('alphaColor', new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.InstancedBufferAttribute(alpha, 1, false, 1)); } } /* harmony default export */ const geometries_InstancedSpheresGeometry = (InstancedSpheresGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/ChunkedObjectsGeometry.js +;// ./src/gfx/geometries/ChunkedObjectsGeometry.js @@ -12886,7 +12953,7 @@ class ChunkedObjectsGeometry extends external_module_three_commonjs_three_common const chunkSize = this._chunkSize; for (let i = 0, n = chunkIndices.length; i < n; ++i) { const left = chunkIndices[i] * chunkSize; - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].fill(alphaArr, value, left, left + chunkSize); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.fill(alphaArr, value, left, left + chunkSize); } this.getAttribute('alphaColor').needsUpdate = true; } @@ -12941,7 +13008,7 @@ class ChunkedObjectsGeometry extends external_module_three_commonjs_three_common this._normals = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE); this._colors = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE); const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount); - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].fill(alpha, 1.0); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.fill(alpha, 1.0); for (let i = 0; i < chunksCount; ++i) { const offset = i * chunkIndexSize; const posOffset = i * chunkSize; @@ -12958,7 +13025,7 @@ class ChunkedObjectsGeometry extends external_module_three_commonjs_three_common } } /* harmony default export */ const geometries_ChunkedObjectsGeometry = (ChunkedObjectsGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/SimpleSpheresGeometry.js +;// ./src/gfx/geometries/SimpleSpheresGeometry.js @@ -12966,7 +13033,7 @@ class ChunkedObjectsGeometry extends external_module_three_commonjs_three_common const SimpleSpheresGeometry_VEC_SIZE = 3; class SimpleSpheresGeometry extends geometries_SphereCollisionGeo(geometries_ChunkedObjectsGeometry) { constructor(spheresCount, sphereComplexity) { - const sphGeometry = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.SphereBufferGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI); + const sphGeometry = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.SphereGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI); super(spheresCount, sphGeometry, spheresCount); const normals = this._normals; const geoNormals = sphGeometry.attributes.normal.array; @@ -12992,7 +13059,7 @@ class SimpleSpheresGeometry extends geometries_SphereCollisionGeo(geometries_Chu } } /* harmony default export */ const geometries_SimpleSpheresGeometry = (SimpleSpheresGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/Simple2CCylindersGeometry.js +;// ./src/gfx/geometries/Simple2CCylindersGeometry.js @@ -13055,7 +13122,7 @@ class Simple2CCylindersGeometry extends geometries_ChunkedObjectsGeometry { } } /* harmony default export */ const geometries_Simple2CCylindersGeometry = (Simple2CCylindersGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/CylinderBufferGeometry.js +;// ./src/gfx/geometries/CylinderBufferGeometry.js const MAX_POINTS_COUNT_16BIT = 65536; @@ -13079,13 +13146,9 @@ class CylinderBufferGeometry extends external_module_three_commonjs_three_common const vertexCount = (heightSegments + 1) * radialSegments + hasTop * (radialSegments + 1) + hasBottom * (radialSegments + 1); const facesCount = (2 * heightSegments + hasTop + hasBottom) * radialSegments; const heightHalf = height / 2; - - /* eslint-disable no-magic-numbers */ const positions = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3); const normals = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3); const indices = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Uint16BufferAttribute(utils.allocateTyped(Uint16Array, facesCount * PTS_PER_TRIANGLE), 1); - /* eslint-enable no-magic-numbers */ - const uvs = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 2), 2); console.assert(vertexCount < MAX_POINTS_COUNT_16BIT, 'DEBUG: Cylinder Geometry has too many vertices (65536 max).'); let currVtxIdx = 0; @@ -13175,7 +13238,7 @@ class CylinderBufferGeometry extends external_module_three_commonjs_three_common } } /* harmony default export */ const geometries_CylinderBufferGeometry = (CylinderBufferGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/Instanced2CCylindersGeometry.js +;// ./src/gfx/geometries/Instanced2CCylindersGeometry.js @@ -13344,7 +13407,7 @@ class Instanced2CCylindersGeometry extends external_module_three_commonjs_three_ this._color1 = utils.allocateTyped(Float32Array, instanceCount * Instanced2CCylindersGeometry_COLOR_SIZE); this._color2 = utils.allocateTyped(Float32Array, instanceCount * Instanced2CCylindersGeometry_COLOR_SIZE); const alpha = this._alpha = utils.allocateTyped(Float32Array, instanceCount); - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].fill(alpha, 1.0); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.fill(alpha, 1.0); this.setAttribute('matVector1', new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.InstancedBufferAttribute(this._matVector1, Instanced2CCylindersGeometry_OFFSET_SIZE, false, 1)); this.setAttribute('matVector2', new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.InstancedBufferAttribute(this._matVector2, Instanced2CCylindersGeometry_OFFSET_SIZE, false, 1)); this.setAttribute('matVector3', new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.InstancedBufferAttribute(this._matVector3, Instanced2CCylindersGeometry_OFFSET_SIZE, false, 1)); @@ -13362,7 +13425,7 @@ class Instanced2CCylindersGeometry extends external_module_three_commonjs_three_ } } /* harmony default export */ const geometries_Instanced2CCylindersGeometry = (Instanced2CCylindersGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/ExtrudedObjectsGeometry.js +;// ./src/gfx/geometries/ExtrudedObjectsGeometry.js @@ -13415,9 +13478,7 @@ class ExtrudedObjectsGeometry extends geometries_ChunkedObjectsGeometry { tmpShape[i] = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); } } - setItem(itemIdx, matrices) { - let hasSlope = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : false; - let hasCut = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : false; + setItem(itemIdx, matrices, hasSlope = false, hasCut = false) { const ptsCount = this._chunkGeo._positions.length; const ringsCount = this._ringsCount; const chunkStartIdx = ptsCount * this._ringsCount * itemIdx * ExtrudedObjectsGeometry_VEC_SIZE; @@ -13535,7 +13596,7 @@ class ExtrudedObjectsGeometry extends geometries_ChunkedObjectsGeometry { } } /* harmony default export */ const geometries_ExtrudedObjectsGeometry = (ExtrudedObjectsGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/ThickLinesGeometry.js +;// ./src/gfx/geometries/ThickLinesGeometry.js @@ -13622,7 +13683,7 @@ class ThickLinesGeometry extends external_module_three_commonjs_three_commonjs2_ setOpacity(startSegIdx, endSegIdx, value) { const start = startSegIdx * VERTEX_PER_SEGMENT; const end = endSegIdx * VERTEX_PER_SEGMENT; - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].fill(this.alpha, value, end, start); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.fill(this.alpha, value, end, start); this.getAttribute('alphaColor').needsUpdate = true; } getSubsetSegments(startSegmentIdx, segmentsCount) { @@ -13663,7 +13724,7 @@ class ThickLinesGeometry extends external_module_three_commonjs_three_commonjs2_ this._colors = utils.allocateTyped(Float32Array, pointsCount * COL_SIZE); this._directions = utils.allocateTyped(Float32Array, pointsCount * DIR_SIZE); const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount); - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].fill(alpha, 1.0); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.fill(alpha, 1.0); const index = this._index; let indexOffset = 0; let pointOffset = 0; @@ -13683,7 +13744,7 @@ class ThickLinesGeometry extends external_module_three_commonjs_three_commonjs2_ } } /* harmony default export */ const geometries_ThickLinesGeometry = (ThickLinesGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/LinesGeometry.js +;// ./src/gfx/geometries/LinesGeometry.js @@ -13740,7 +13801,7 @@ class LinesGeometry extends geometries_ThickLinesGeometry { } } /* harmony default export */ const geometries_LinesGeometry = (LinesGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/CylinderCollisionGeo.js +;// ./src/gfx/geometries/CylinderCollisionGeo.js @@ -13783,7 +13844,7 @@ class CylinderCollisionGeo extends geometries_ChunkedObjectsGeometry { } } /* harmony default export */ const geometries_CylinderCollisionGeo = (CylinderCollisionGeo); -;// CONCATENATED MODULE: ./src/gfx/geometries/ChunkedLinesGeometry.js +;// ./src/gfx/geometries/ChunkedLinesGeometry.js const COLLISION_RAD = 0.1; @@ -13889,7 +13950,7 @@ class ChunkedLinesGeometry extends geometries_LinesGeometry { } } /* harmony default export */ const geometries_ChunkedLinesGeometry = (ChunkedLinesGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/TwoColorLinesGeometry.js +;// ./src/gfx/geometries/TwoColorLinesGeometry.js @@ -13937,7 +13998,7 @@ class TwoColorLinesGeometry extends geometries_LinesGeometry { // (???)parent = LinesGeometry.prototype; /* harmony default export */ const geometries_TwoColorLinesGeometry = (TwoColorLinesGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/CrossGeometry.js +;// ./src/gfx/geometries/CrossGeometry.js @@ -13965,7 +14026,7 @@ class CrossGeometry extends geometries_SphereCollisionGeo(geometries_ChunkedLine } } /* harmony default export */ const geometries_CrossGeometry = (CrossGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurfaceGeometry.js +;// ./src/gfx/geometries/IsoSurfaceGeometry.js const POS_RAD_SIZE = 4; @@ -14018,7 +14079,7 @@ class IsoSurfaceGeometry extends external_module_three_commonjs_three_commonjs2_ } } /* harmony default export */ const geometries_IsoSurfaceGeometry = (IsoSurfaceGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurfaceMarchCube.js +;// ./src/gfx/geometries/IsoSurfaceMarchCube.js /** @@ -14051,13 +14112,9 @@ class IsoSurfaceMarchCube { this.pointsValuesLinear = null; } } - -/* eslint-disable no-magic-numbers */ IsoSurfaceMarchCube.prototype.striIndicesMarchCube = [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 8, 3, -1, -1, -1, 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1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1]; -/* eslint-enable no-magic-numbers */ - /* harmony default export */ const geometries_IsoSurfaceMarchCube = (IsoSurfaceMarchCube); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurface.js +;// ./src/gfx/geometries/IsoSurface.js @@ -14175,12 +14232,12 @@ class IsoSurface { vertex.lerpVectors(p1, p2, mu); normal.lerpVectors(n1, n2, mu); } - static _triTable = (() => geometries_IsoSurfaceMarchCube.prototype.striIndicesMarchCube)(); + static _triTable = geometries_IsoSurfaceMarchCube.prototype.striIndicesMarchCube; static _arrSize = 12; static _firstIndices = [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3]; static _secondIndices = [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7]; - static _vertexList = (() => createArray(IsoSurface._arrSize))(); - static _normalList = (() => createArray(IsoSurface._arrSize))(); + static _vertexList = createArray(IsoSurface._arrSize); + static _normalList = createArray(IsoSurface._arrSize); _polygonize(grid, isoLevel, triangles) { const { cubeIndex @@ -14277,8 +14334,6 @@ class IsoSurface { for (let y = 0; y < ySize - step; y += step) { let idx = vol.getDirectIdx(0, y, z); for (let x = 0; x < xSize - step; x += step, idx += stepX) { - /* eslint-disable no-multi-spaces */ - /* eslint-disable computed-property-spacing */ gcVal[0] = volData[idx]; gcVal[1] = volData[idx + stepX]; gcVal[3] = volData[idx + stepY]; @@ -14287,8 +14342,6 @@ class IsoSurface { gcVal[5] = volData[idx + stepX + stepZ]; gcVal[7] = volData[idx + stepY + stepZ]; gcVal[6] = volData[idx + stepX + stepY + stepZ]; - /* eslint-enable no-multi-spaces */ - /* eslint-enable computed-property-spacing */ // Determine the index into the edge table which // tells us which vertices are inside of the surface @@ -14569,7 +14622,7 @@ class IsoSurface { } } /* harmony default export */ const geometries_IsoSurface = (IsoSurface); -;// CONCATENATED MODULE: ./src/gfx/geometries/VolumeSurfaceGeometry.js +;// ./src/gfx/geometries/VolumeSurfaceGeometry.js @@ -14676,7 +14729,7 @@ class VolumeSurfaceGeometry extends geometries_IsoSurfaceGeometry { } } /* harmony default export */ const geometries_VolumeSurfaceGeometry = (VolumeSurfaceGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/QuickSurfGeometry.js +;// ./src/gfx/geometries/QuickSurfGeometry.js const { @@ -14809,7 +14862,7 @@ class QuickSurfGeometry extends geometries_VolumeSurfaceGeometry { } } /* harmony default export */ const geometries_QuickSurfGeometry = (QuickSurfGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/ContactSurface.js +;// ./src/gfx/geometries/ContactSurface.js @@ -15352,7 +15405,7 @@ function ContactSurface(packedArrays, boundaries, params, _indexList) { }; } /* harmony default export */ const geometries_ContactSurface = (ContactSurface); -;// CONCATENATED MODULE: ./src/gfx/geometries/ContactSurfaceGeometry.js +;// ./src/gfx/geometries/ContactSurfaceGeometry.js @@ -15381,7 +15434,7 @@ class ContactSurfaceGeometry extends geometries_VolumeSurfaceGeometry { } } /* harmony default export */ const geometries_ContactSurfaceGeometry = (ContactSurfaceGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurfaceAtomColored.js +;// ./src/gfx/geometries/IsoSurfaceAtomColored.js /** @@ -15403,7 +15456,7 @@ class IsoSurfaceAtomColored { } } /* harmony default export */ const geometries_IsoSurfaceAtomColored = (IsoSurfaceAtomColored); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsosurfaceBuildNormals.js +;// ./src/gfx/geometries/IsosurfaceBuildNormals.js @@ -15740,7 +15793,7 @@ class IsosurfaceBuildNormals { } } /* harmony default export */ const geometries_IsosurfaceBuildNormals = (IsosurfaceBuildNormals); -;// CONCATENATED MODULE: ./src/gfx/geometries/IsoSurfaceGeo.js +;// ./src/gfx/geometries/IsoSurfaceGeo.js /** @@ -15785,7 +15838,7 @@ class IsoSurfaceGeo { } } /* harmony default export */ const geometries_IsoSurfaceGeo = (IsoSurfaceGeo); -;// CONCATENATED MODULE: ./src/gfx/geometries/SSIsosurfaceGeometry.js +;// ./src/gfx/geometries/SSIsosurfaceGeometry.js @@ -16176,10 +16229,7 @@ class SSIsosurfaceGeometry extends geometries_IsoSurfaceGeometry { return numIntersectedCells; } getType(letter) { - /* eslint-disable no-magic-numbers */ const atomT = [0, 0, 1, 1, 2, 6, 3, 6, 4, 6, 5, 6, 6, 0, 7, 3, 8, 2, 9, 6, 10, 6, 11, 6, 12, 6, 13, 6, 14, 6, 15, 4, 16, 5, 17, 6, 18, 6, 19, 6, 20, 6, 21, 6, 22, 6, 23, 6, 24, 6, 25, 6, 26, 6, 27, 6, 28, 6, 29, 6, 30, 6, 31, 6, 32, 6, 33, 6, 34, 6, 35, 6, 36, 6, 37, 6, 38, 6, 39, 6, 40, 6, 41, 6, 42, 6, 43, 6, 44, 6, 45, 6, 46, 6, 47, 6, 48, 6, 49, 6, 50, 6, 51, 6, 52, 6, 53, 6, 54, 6, 55, 6, 56, 6, 57, 6, 58, 6, 59, 6, 60, 6, 61, 6, 62, 6, 63, 6, 64, 6, 65, 6, 66, 6, 67, 6, 68, 6, 69, 6, 70, 6, 71, 6, 72, 6, 73, 6, 74, 6, 75, 6, 76, 6, 77, 6, 78, 6, 79, 6, 80, 6, 81, 6, 82, 6, 83, 6, 84, 6, 85, 6, 86, 6, 87, 6, 88, 6, 89, 6, 90, 6, 91, 6, 92, 6, 93, 6, 94, 6, 95, 6, 96, 6, 97, 6, 98, 6, 99, 6, 100, 6, 101, 6, 102, 6, 103, 6, 104, 6, 105, 6, 106, 6, 107, 6, 108, 6, 109, 6]; - /* eslint-enable no-magic-numbers */ - if (letter < 1 || letter > atomT.length / 2 || Object.keys(SSIsosurfaceGeometry_Element.ByAtomicNumber).length * 2 !== atomT.length) { throw new Error('atomT.length should be equal Element.ByAtomicNumber.length * 2'); } @@ -16202,10 +16252,7 @@ class SSIsosurfaceGeometry extends geometries_IsoSurfaceGeometry { const side3 = side2 * side; const vCorner = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); const vDif = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); - /* eslint-disable no-magic-numbers */ const aLot = +1.0e12; - /* eslint-enable no-magic-numbers */ - for (let i = 0; i < side3; i++) { corners[i] = aLot; // to large value } @@ -16564,7 +16611,7 @@ class SSIsosurfaceGeometry extends geometries_IsoSurfaceGeometry { // All code below must be erased from every device and each developer's memory /* harmony default export */ const geometries_SSIsosurfaceGeometry = (SSIsosurfaceGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/LabelsGeometry.js +;// ./src/gfx/geometries/LabelsGeometry.js function createLabel(fieldTxt, className) { @@ -16660,7 +16707,7 @@ class LabelsGeometry extends utils_EventDispatcher { } } /* harmony default export */ const geometries_LabelsGeometry = (LabelsGeometry); -;// CONCATENATED MODULE: ./src/gfx/geometries/geometries.js +;// ./src/gfx/geometries/geometries.js @@ -16687,11 +16734,11 @@ class LabelsGeometry extends utils_EventDispatcher { SSIsosurfaceGeometry: geometries_SSIsosurfaceGeometry, LabelsGeometry: geometries_LabelsGeometry }); -;// CONCATENATED MODULE: ./src/gfx/shaders/Uber.vert -const Uber_namespaceObject = "float INSTANCED_SPRITE_OVERSCALE = 1.3;\r\n\r\nattribute vec3 normal;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n varying vec3 viewNormal;\r\n#endif\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n varying vec3 vNormal;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n attribute vec4 position; // W contains vert pos or neg offset\r\n#else\r\n attribute vec3 position;\r\n#endif\r\n\r\nvarying vec3 vWorldPosition;\r\nvarying vec3 vViewPosition;\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n attribute float alphaColor;\r\n varying float alphaCol;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n attribute vec3 color;\r\n varying vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n attribute vec3 color2;\r\n varying vec3 vColor2;\r\n attribute vec2 uv;\r\n #ifndef CYLINDER_SPRITE\r\n varying vec2 vUv;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_POS\r\n attribute vec4 offset;\r\n #ifdef SPHERE_SPRITE\r\n varying vec4 instOffset;\r\n varying vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n attribute vec4 matVector1;\r\n attribute vec4 matVector2;\r\n attribute vec4 matVector3;\r\n attribute vec4 invmatVector1;\r\n attribute vec4 invmatVector2;\r\n attribute vec4 invmatVector3;\r\n\r\n #ifdef CYLINDER_SPRITE\r\n varying vec4 matVec1;\r\n varying vec4 matVec2;\r\n varying vec4 matVec3;\r\n varying vec4 invmatVec1;\r\n varying vec4 invmatVec2;\r\n varying vec4 invmatVec3;\r\n varying vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\nuniform mat4 modelViewMatrix; // optional\r\nuniform mat4 projectionMatrix; // optional\r\nuniform mat3 normalMatrix; // optional\r\nuniform mat4 modelMatrix; // optional\r\n\r\n#ifdef DASHED_LINE\r\n attribute float lineDistance;\r\n varying float vLineDistance;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n attribute vec3 direction;\r\n uniform mat4 projMatrixInv;\r\n uniform vec2 viewport;\r\n uniform float lineWidth;\r\n\r\n vec4 transform(vec4 coord){\r\n return projectionMatrix * modelViewMatrix * coord;\r\n }\r\n\r\n vec2 project(vec4 device){\r\n vec3 device_normal = device.xyz/device.w;\r\n vec2 clip_pos = (device_normal*0.5+0.5).xy;\r\n return clip_pos * viewport;\r\n }\r\n\r\n vec4 unproject(vec2 screen, float z, float w){\r\n vec2 clip_pos = screen/viewport;\r\n vec2 device_normal = clip_pos*2.0-1.0;\r\n return vec4(device_normal*w, z, w);\r\n }\r\n#endif\r\n\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n alphaCol = alphaColor;\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n vec3 objectNormal = vec3(\r\n dot(normal, matVector1.xyz),\r\n dot(normal, matVector2.xyz),\r\n dot(normal, matVector3.xyz));\r\n#else\r\n vec3 objectNormal = vec3( normal );\r\n#endif\r\n\r\nvec3 transformedNormal = normalMatrix * objectNormal;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n vNormal = normalize(transformedNormal);\r\n#endif\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n viewNormal = normalize(mat3(modelViewMatrix)*objectNormal);\r\n#endif\r\n\r\n vec4 localPos = vec4(position.xyz, 1.0);\r\n vec4 worldPos = modelMatrix * localPos;\r\n vec4 mvPosition = modelViewMatrix * localPos;\r\n\r\n// make thick line offset\r\n#ifdef THICK_LINE\r\n // get screen pos\r\n vec4 dPos = transform(vec4(position.xyz, 1.0));\r\n vec2 sPos = project(dPos);\r\n // move pos forward\r\n vec3 position2 = position.xyz + direction.xyz * 0.5;\r\n // get screen offset pos\r\n vec4 dPos2 = transform(vec4(position2.xyz, 1.0));\r\n vec2 sPos2 = project(dPos2);\r\n // screen line direction\r\n vec2 sDir = normalize(sPos2 - sPos);\r\n // vertex offset (orthogonal to line direction)\r\n vec2 offset1 = vec2(-sDir.y, sDir.x);\r\n // move screen vertex\r\n vec2 newPos = sPos + offset1 * position.w * lineWidth;\r\n // get moved pos in view space\r\n vec4 dNewPos = unproject(newPos, dPos.z, dPos.w);\r\n mvPosition.xyz = (projMatrixInv * dNewPos).xyz;\r\n#endif // THICK_LINE\r\n\r\n#ifdef INSTANCED_POS\r\n #ifdef SPHERE_SPRITE\r\n instOffset = offset;\r\n\r\n vec4 posEye = modelViewMatrix * vec4( offset.xyz, 1.0 );\r\n float scale = length(modelViewMatrix[0]);\r\n mvPosition = posEye + vec4( position.xyz * offset.w * scale * INSTANCED_SPRITE_OVERSCALE, 0.0 );\r\n posEye.w = offset.w * scale;\r\n\r\n spritePosEye = posEye;\r\n #else\r\n localPos = vec4( offset.xyz + position.xyz * offset.w, 1.0 );\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n #ifdef CYLINDER_SPRITE\r\n matVec1 = matVector1;\r\n matVec2 = matVector2;\r\n matVec3 = matVector3;\r\n invmatVec1 = invmatVector1;\r\n invmatVec2 = invmatVector2;\r\n invmatVec3 = invmatVector3;\r\n\r\n // calculate eye coords of cylinder endpoints\r\n vec4 v = vec4(0, -0.5, 0, 1);\r\n vec4 p1 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n v.y = 0.5;\r\n vec4 p2 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n\r\n // sprite is placed at the center of cylinder\r\n vec4 posEye;\r\n posEye.xyz = mix(p1.xyz, p2.xyz, 0.5);\r\n posEye.w = 1.0;\r\n spritePosEye = posEye;\r\n\r\n // cylinder radius in eye space\r\n float rad = length(modelViewMatrix[0]) * length(vec3(matVector1.x, matVector2.x, matVector3.x));\r\n vec2 spriteSize;\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // In ortho projection we skip z coordinate\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy - p1.xy);\r\n\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * (spriteSizeScreen + 2.0 * rad);\r\n #else\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy / p2.z - p1.xy / p1.z);\r\n\r\n // full sprite size in eye coords\r\n float minZ = min(abs(p1.z), abs(p2.z));\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * abs(posEye.z) * (spriteSizeScreen + 2.0 * rad / minZ);\r\n #endif\r\n\r\n mvPosition = posEye + vec4( position.xy * 0.5 * spriteSize, 0, 0 );\r\n #else\r\n localPos = vec4(dot(localPos, matVector1), dot(localPos, matVector2), dot(localPos, matVector3), 1.0);\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n gl_Position = projectionMatrix * mvPosition;\r\n\r\n vWorldPosition = worldPos.xyz;\r\n vViewPosition = - mvPosition.xyz;\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t vec4 worldPosition;\r\n\t // see THREE.WebGLProgram.unrollLoops\r\n\t #pragma unroll_loop_start\r\n\t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirectionalShadowCoord[ i ] = directionalShadowMatrix[ i ] * vec4(vWorldPosition, 1.0);\r\n vDirectionalShadowNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(objectNormal, 0.0))).xyz;\r\n\t }\r\n\t #pragma unroll_loop_end\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n vColor = color.xyz;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n vColor2 = color2;\r\n #ifndef CYLINDER_SPRITE\r\n vUv = uv;\r\n #endif\r\n#endif\r\n\r\n#ifdef DASHED_LINE\r\n vLineDistance = lineDistance;\r\n#endif\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/Uber.frag -const gfx_shaders_Uber_namespaceObject = "#if defined (NORMALS_TO_G_BUFFER)\r\n #define fragColor gl_FragData[0]\r\n#else\r\n #define fragColor gl_FragColor\r\n#endif\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n varying float alphaCol;\r\n#endif\r\n\r\n#ifdef COLOR_FROM_POS\r\n uniform mat4 world2colorMatrix;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform sampler2D directionalShadowMap[ NUM_DIR_LIGHTS ];\r\n uniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ]; //only for sprites\r\n\t\tvarying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tvarying vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n vec4 vDirLightWorldCoord[ NUM_DIR_LIGHTS ];\r\n vec3 vDirLightWorldNormal[ NUM_DIR_LIGHTS ];\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n // We use 4 instead uniform variable or define because this value is used in for(... i < value; ...) with\r\n // unroll_loop and unroll_loop has pattern:\r\n // /#pragma unroll_loop[\\s]+?for \\( int i \\= (\\d+)\\; i < (\\d+)\\; i \\+\\+ \\) \\{([\\s\\S]+?)(?=\\})\\}/g\r\n uniform vec2 samplesKernel[4]; // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n uniform sampler2D noiseTex;\r\n uniform vec2 noiseTexelSize;\r\n uniform vec2 srcTexelSize;\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n varying vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n varying vec3 vColor2;\r\n #ifndef CYLINDER_SPRITE\r\n varying vec2 vUv;\r\n #endif\r\n#endif\r\n\r\nuniform vec3 diffuse;\r\nuniform vec3 emissive;\r\nuniform vec3 specular;\r\nuniform float shininess;\r\nuniform vec3 fixedColor;\r\nuniform float opacity;\r\nuniform float zClipValue;\r\nuniform float clipPlaneValue;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n varying vec3 viewNormal;\r\n#endif\r\n\r\n#define RECIPROCAL_PI 0.31830988618\r\n#define saturate(a) clamp( a, 0.0, 1.0 )\r\n\r\n#ifdef USE_FOG\r\n uniform vec3 fogColor;\r\n uniform float fogAlpha;\r\n uniform float fogNear;\r\n uniform float fogFar;\r\n#endif\r\n\r\nvarying vec3 vWorldPosition; // world position of the pixel (invalid when INSTANCED_SPRITE is defined)\r\nvarying vec3 vViewPosition;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n varying vec3 vNormal;\r\n#endif\r\n\r\n/////////////////////////////////////////// ZSprites ////////////////////////////////////////////////\r\n#if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n uniform float nearPlaneValue;\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n varying vec4 spritePosEye;\r\n#endif\r\n\r\n#if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n uniform float zOffset;\r\n\r\n #if !defined(USE_LIGHTS) || !defined(SHADOWMAP) || !defined(SHADOWMAP_PCF_RAND) || !(NUM_DIR_LIGHTS > 0)\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\r\n float calcDepthForSprites(vec4 pixelPosEye, float zOffset, mat4 projMatrix) {\r\n vec4 pixelPosScreen = projMatrix * pixelPosEye;\r\n return 0.5 * (pixelPosScreen.z / pixelPosScreen.w + 1.0) + zOffset;\r\n }\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n varying vec4 instOffset;\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n\r\n bool intersect_ray_sphere(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray, ray);\r\n float b = dot(ray, origin);\r\n float c = dot(origin, origin) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n // choose nearest point inside frustum\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all spheres the point with smaller 't' is visible\r\n // t1 is always smaller than t2 (from calculations)\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_sphere_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into sphere local coords\r\n origin = pixelPosEye.xyz - spritePosEye.xyz;\r\n origin = (invModelViewMatrix * vec4(origin, 0.0)).xyz / instOffset.w;\r\n\r\n // transform camera orientation vector into sphere local coords\r\n ray = (invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0)).xyz;\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n vec4 v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into sphere local coords\r\n v = invModelViewMatrix * v;\r\n origin = (v.xyz - instOffset.xyz) / instOffset.w;\r\n\r\n // transform vector from camera pos to curPixel into sphere local coords\r\n ray = (invModelViewMatrix * vec4(pixelPosEye, 0.0)).xyz;\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_sphere(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n varying vec4 matVec1;\r\n varying vec4 matVec2;\r\n varying vec4 matVec3;\r\n varying vec4 invmatVec1;\r\n varying vec4 invmatVec2;\r\n varying vec4 invmatVec3;\r\n\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n varying vec4 spritePosEye;\r\n\r\n bool intersect_ray_cylinder(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray.xz, ray.xz);\r\n float b = dot(ray.xz, origin.xz);\r\n float c = dot(origin.xz, origin.xz) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n float halfHeight = 0.5;\r\n\r\n // choose nearest point\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all cylinders the point with smaller 't' is visible\r\n // if it is not outside of cylinnder (t1 is always smaller than t2).\r\n if (p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0 && p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0 && p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_cylinder_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n vec4 v;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye.xyz - spritePosEye.xyz, 0.0);\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform camera orientation vector into cylinder local coords\r\n v = invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into cylinder local coords\r\n v = invModelViewMatrix * v;\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform vector from camera pos to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_cylinder(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n///////////////////////////////////// Pack and unpack ///////////////////////////////////////////////\r\nconst float PackUpscale = 256. / 255.; // fraction -> 0..1 (including 1)\r\nconst float UnpackDownscale = 255. / 256.; // 0..1 -> fraction (excluding 1)\r\n\r\nconst vec3 PackFactors = vec3( 256. * 256. * 256., 256. * 256., 256. );\r\nconst vec4 UnpackFactors = UnpackDownscale / vec4( PackFactors, 1. );\r\n\r\n\r\nconst float ShiftRight8 = 1. / 256.;\r\n\r\nvec4 packDepthToRGBA( const in float v ) {\r\n vec4 r = vec4( fract( v * PackFactors ), v );\r\n r.yzw -= r.xyz * ShiftRight8; // tidy overflow\r\n return r * PackUpscale;\r\n}\r\n\r\nfloat unpackRGBAToDepth( const in vec4 v ) {\r\n return dot( v, UnpackFactors );\r\n}\r\n\r\n////////////////////////////////////////// All Lighting /////////////////////////////////////////////////\r\n#ifdef TOON_SHADING\r\n #define LOW_TOON_BORDER 0.0\r\n #define MEDIUM_TOON_BORDER 0.7\r\n #define HIGH_TOON_BORDER 1.0\r\n\r\n #define MEDIUM_TOON_RANGE 0.5\r\n #define HIGH_TOON_RANGE 0.95\r\n#endif\r\n#if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n struct ReflectedLight {\r\n vec3 directDiffuse;\r\n vec3 directSpecular;\r\n vec3 indirectDiffuse;\r\n };\r\n\r\n struct BlinnPhongMaterial {\r\n vec3 diffuseColor;\r\n vec3 specularColor;\r\n float specularShininess;\r\n };\r\n\r\n struct GeometricContext {\r\n vec3 normal;\r\n vec3 viewDir;\r\n };\r\n\r\n struct DirectionalLight {\r\n vec3 direction;\r\n vec3 color;\r\n };\r\n uniform DirectionalLight directionalLights[ NUM_DIR_LIGHTS ];\r\n\r\n struct DirectionalLightShadow {\r\n vec2 shadowMapSize;\r\n float shadowBias;\r\n float shadowRadius;\r\n };\r\n uniform DirectionalLightShadow directionalLightShadows[ NUM_DIR_LIGHTS ];\r\n\r\n uniform vec3 ambientLightColor;\r\n\r\n /////////////////////////////////////////// Shadowmap ////////////////////////////////////////////////\r\n\r\n #if defined(SHADOWMAP)\r\n \tfloat texture2DCompare( sampler2D depths, vec2 uv, float compare ) {\r\n \t\treturn step( compare, unpackRGBAToDepth( texture2D( depths, uv ) ) );\r\n \t}\r\n\r\n float getShadow( sampler2D shadowMap, DirectionalLightShadow dirLight, vec4 shadowCoord, vec3 vViewPosition, vec3 vNormal ) {\r\n \t float shadow = 0.0;\r\n\r\n // When shadows for sprites will appear use here for them normals as it done for G-buffer\r\n shadowCoord.xyz += dirLight.shadowBias * vNormal;\r\n shadowCoord.xyz /= shadowCoord.w;\r\n\r\n bvec4 inFrustumVec = bvec4 ( shadowCoord.x >= 0.0, shadowCoord.x <= 1.0, shadowCoord.y >= 0.0, shadowCoord.y <= 1.0 );\r\n bool inFrustum = all( inFrustumVec );\r\n bvec2 frustumTestVec = bvec2( inFrustum, shadowCoord.z <= 1.0 );\r\n bool frustumTest = all( frustumTestVec );\r\n\r\n if ( frustumTest ) {\r\n #ifdef SHADOWMAP_BASIC\r\n \t shadow = texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z );\r\n \t#endif\r\n\r\n \t#ifdef SHADOWMAP_PCF_SHARP\r\n \t vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n float dx0 = - texelSize.x * dirLight.shadowRadius;\r\n float dy0 = - texelSize.y * dirLight.shadowRadius;\r\n float dx1 = + texelSize.x * dirLight.shadowRadius;\r\n float dy1 = + texelSize.y * dirLight.shadowRadius;\r\n\r\n shadow = (\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z )\r\n ) * ( 1.0 / 9.0 );\r\n #endif\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n vec4 vUv = ((projectionMatrix * vec4(vViewPosition, 1.0)) + 1.0) / 2.0;\r\n vec2 vUvNoise = vUv.xy / srcTexelSize * noiseTexelSize;\r\n\r\n vec2 noiseVec = normalize(texture2D(noiseTex, vUvNoise).rg);\r\n mat2 mNoise = mat2(noiseVec.x, noiseVec.y, -noiseVec.y, noiseVec.x);\r\n\r\n vec2 offset;\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < 4; i ++ ) { // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n offset = mNoise * ( normalize( samplesKernel[ i ]) * texelSize * dirLight.shadowRadius );\r\n shadow += texture2DCompare( shadowMap, shadowCoord.xy + offset, shadowCoord.z );\r\n }\r\n #pragma unroll_loop_end\r\n shadow /= float( 4 ); // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n #endif\r\n }\r\n return shadow;//(shadow != 1.0) ? 0.5 : 1.0;//vec4(shadow, shadow, shadow, 1.0);\r\n }\r\n #endif\r\n\r\n /////////////////////////////////////////// Lighting /////////////////////////////////////////////////\r\n\r\n vec3 BRDF_Diffuse_Lambert( const in vec3 diffuseColor ) {\r\n return RECIPROCAL_PI * diffuseColor;\r\n } // validated\r\n\r\n vec3 F_Schlick( const in vec3 specularColor, const in float dotLH ) {\r\n // Original approximation by Christophe Schlick '94\r\n //;float fresnel = pow( 1.0 - dotLH, 5.0 );\r\n // Optimized variant (presented by Epic at SIGGRAPH '13)\r\n float fresnel = exp2( ( -5.55473 * dotLH - 6.98316 ) * dotLH );\r\n return ( 1.0 - specularColor ) * fresnel + specularColor;\r\n } // validated\r\n\r\n float G_BlinnPhong_Implicit( /* const in float dotNL, const in float dotNV */ ) {\r\n // geometry term is (n dot l)(n dot v) / 4(n dot l)(n dot v)\r\n return 0.25;\r\n }\r\n\r\n float D_BlinnPhong( const in float shininess, const in float dotNH ) {\r\n return RECIPROCAL_PI * ( shininess * 0.5 + 1.0 ) * pow( dotNH, shininess );\r\n }\r\n\r\n vec3 BRDF_Specular_BlinnPhong( const in DirectionalLight incidentLight, const in GeometricContext geometry, const in vec3 specularColor, const in float shininess ) {\r\n vec3 halfDir = normalize( incidentLight.direction + geometry.viewDir );\r\n float dotNH = saturate(dot( geometry.normal, halfDir ));\r\n float dotLH = saturate(dot( incidentLight.direction, halfDir ));\r\n\r\n vec3 F = F_Schlick( specularColor, dotLH );\r\n float G = G_BlinnPhong_Implicit( /* dotNL, dotNV */ );\r\n float D = D_BlinnPhong( shininess, dotNH );\r\n\r\n return F * ( G * D );\r\n } // validated\r\n\r\n void RE_Direct_BlinnPhong( const in DirectionalLight directLight, const in GeometricContext geometry, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight, float penumbra ) {\r\n\r\n float dotNL = saturate( dot( geometry.normal, directLight.direction ));\r\n #ifdef TOON_SHADING\r\n if(dotNL < MEDIUM_TOON_RANGE){\r\n dotNL = LOW_TOON_BORDER;\r\n }\r\n else if(dotNL < HIGH_TOON_RANGE){\r\n dotNL = MEDIUM_TOON_BORDER;\r\n }\r\n else{\r\n dotNL = HIGH_TOON_BORDER;\r\n }\r\n #endif\r\n\r\n vec3 irradiance = dotNL * directLight.color;\r\n reflectedLight.directDiffuse += penumbra * irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n reflectedLight.directSpecular += penumbra * irradiance * BRDF_Specular_BlinnPhong( directLight, geometry, material.specularColor, material.specularShininess );\r\n }\r\n\r\n void RE_IndirectDiffuse_BlinnPhong( const in vec3 irradiance, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) {\r\n reflectedLight.indirectDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n }\r\n\r\n vec3 calcLighting(const in GeometricContext geometry, const in BlinnPhongMaterial material, vec3 vViewPosition) {\r\n ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ));\r\n vec3 irradiance = ambientLightColor;\r\n\r\n float shadowMask = 1.0;\r\n // see THREE.WebGLProgram.unrollLoops\r\n \t#pragma unroll_loop_start\r\n \t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n \t #ifdef SHADOWMAP\r\n \t shadowMask = getShadow( directionalShadowMap[ i ], directionalLightShadows[ i ], vDirLightWorldCoord[ i ], vViewPosition, vDirLightWorldNormal[ i ] );\r\n #endif\r\n\r\n \t\t if ( shadowMask > 0.0 ) RE_Direct_BlinnPhong( directionalLights[ i ], geometry, material, reflectedLight, shadowMask );\r\n \t\t}\r\n \t\t#pragma unroll_loop_end\r\n\r\n RE_IndirectDiffuse_BlinnPhong(irradiance, material, reflectedLight);\r\n\r\n return saturate(reflectedLight.indirectDiffuse + reflectedLight.directDiffuse + reflectedLight.directSpecular);\r\n }\r\n#endif\r\n\r\n/////////////////////////////////////////// Dashed Line ///////////////////////////////////////////////\r\n#ifdef DASHED_LINE\r\n uniform float dashedLineSize;\r\n uniform float dashedLinePeriod;\r\n varying float vLineDistance;\r\n#endif\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef CLIP_PLANE\r\n if (vViewPosition.z < clipPlaneValue) discard;\r\n#endif\r\n\r\n#ifdef ZCLIP\r\n if (vViewPosition.z < zClipValue) discard;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = vDirectionalShadowCoord[ i ];\r\n vDirLightWorldNormal[ i ] = vDirectionalShadowNormal[ i ];\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n#endif\r\n\r\n vec4 pixelPosWorld = vec4(vWorldPosition, 1.0);\r\n vec4 pixelPosEye;\r\n\r\n#ifdef SPHERE_SPRITE\r\n\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n vec3 normal;\r\n\r\n/* quick-and-dirty method\r\n normal.xy = ' + INSTANCED_SPRITE_OVERSCALE + ' * (2.0 * vUv - 1.0);\r\n float r2 = dot(normal.xy, normal.xy);\r\n if (r2 > 1.0) discard;\r\n float normalZ = sqrt(1.0 - r2);\r\n normal.z = normalZ;\r\n normal = normal * ( -1.0 + 2.0 * float( gl_FrontFacing ) );\r\n pixelPosEye = vec4(spritePosEye.xyz, 1.0);\r\n pixelPosEye.z += spritePosEye.w * normalZ;\r\n*/\r\n\r\n // ray-trace sphere surface\r\n {\r\n vec3 p;\r\n if (!get_sphere_point(-vViewPosition, p, frontFaced)) discard;\r\n vec4 v = vec4(instOffset.xyz + p * instOffset.w, 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n normal = normalize(normalMatrix * p);\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*p);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(p, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n vec3 normal;\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n float cylinderY = 0.0;\r\n\r\n // ray-trace cylinder surface\r\n {\r\n vec3 p;\r\n if (!get_cylinder_point(-vViewPosition, p, frontFaced)) discard;\r\n\r\n cylinderY = 0.5 * (p.y + 1.0);\r\n\r\n vec4 v = vec4(p, 1.0);\r\n v = vec4(dot(v, matVec1), dot(v, matVec2), dot(v, matVec3), 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n\r\n vec3 localNormal = normalize(vec3(p.x, 0.0, p.z));\r\n normal = vec3(\r\n dot(localNormal, matVec1.xyz),\r\n dot(localNormal, matVec2.xyz),\r\n dot(localNormal, matVec3.xyz));\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*normal);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(normal, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n\r\n normal = normalize(normalMatrix * normal);\r\n }\r\n#endif\r\n\r\n #ifdef ATTR_COLOR\r\n vec3 vertexColor = vColor;\r\n #else\r\n vec3 vertexColor = vec3(1.0, 1.0, 1.0);\r\n #endif\r\n\r\n #ifdef ATTR_COLOR2\r\n #ifdef CYLINDER_SPRITE\r\n float colorCoef = cylinderY; // cylinder parameter is calculated from ray-tracing\r\n #else\r\n float colorCoef = vUv.y; // cylinder parameter is interpolated as tex coord\r\n #endif\r\n // choose either color or color2\r\n vertexColor = mix(vColor2, vColor, step(0.5, colorCoef));\r\n #endif\r\n\r\n // negative red component is a special condition\r\n if (vertexColor.x < 0.0) discard;\r\n\r\n #ifdef DASHED_LINE\r\n if ( mod( vLineDistance, dashedLinePeriod ) > dashedLineSize ) discard;\r\n #endif\r\n\r\n // transparency prepass writes only z, so we don't need to calc the color\r\n #ifdef PREPASS_TRANSP\r\n fragColor = vec4(1.0, 1.0, 1.0, 1.0);\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n return;\r\n #endif\r\n\r\n float totalOpacity = opacity;\r\n\r\n #ifdef ATTR_ALPHA_COLOR\r\n totalOpacity *= alphaCol;\r\n #endif\r\n\r\n // discard fully transparent pixels\r\n if (totalOpacity == 0.0) discard;\r\n\r\n #ifdef FAKE_OPACITY\r\n // discard pixels in checker pattern\r\n vec2 dm_coord = floor(gl_FragCoord.xy);\r\n dm_coord = fract(dm_coord * 0.5);\r\n if (totalOpacity < 1.0 && (dm_coord.x < 0.5 ^^ dm_coord.y < 0.5)) discard;\r\n vec4 diffuseColor = vec4(diffuse, 1.0);\r\n #else\r\n vec4 diffuseColor = vec4(diffuse, totalOpacity);\r\n #endif\r\n\r\n float flipNormal;\r\n #if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n flipNormal = 1.0;\r\n #ifdef DOUBLE_SIDED\r\n flipNormal = float( gl_FrontFacing );\r\n #endif\r\n vec3 normal = normalize( vNormal ) * flipNormal;\r\n #endif\r\n\r\n diffuseColor.rgb *= vertexColor;\r\n\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n\r\n #ifdef NORMALS_TO_G_BUFFER\r\n #if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n vec3 viewNormaInColor = viewNormalSprites;\r\n #else\r\n vec3 viewNormaInColor = viewNormal;\r\n float frontFaced = float( gl_FrontFacing );\r\n #endif\r\n // [-1, 1] -> [0, 1]\r\n viewNormaInColor = 0.5 * viewNormaInColor + 0.5;\r\n gl_FragData[1] = vec4(viewNormaInColor, frontFaced);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n vec3 viewDir;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDir = -pixelPosEye.xyz;\r\n #else\r\n viewDir = vViewPosition;\r\n #endif\r\n GeometricContext geometry = GeometricContext(normal, normalize( viewDir ));\r\n BlinnPhongMaterial material = BlinnPhongMaterial(diffuseColor.rgb, specular, shininess);\r\n vec3 outgoingLight = calcLighting(geometry, material, viewDir);\r\n #else\r\n vec3 outgoingLight = diffuseColor.rgb;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_DEPTH\r\n float depth = 0.0;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepthEXT = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n depth = gl_FragDepthEXT;\r\n #else\r\n depth = gl_FragCoord.z;\r\n #endif\r\n fragColor = packDepthToRGBA(depth);\r\n return;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_POS\r\n fragColor = world2colorMatrix * pixelPosWorld;\r\n #else\r\n #ifdef OVERRIDE_COLOR\r\n fragColor = vec4(fixedColor, diffuseColor.a);\r\n #else\r\n fragColor = vec4(outgoingLight, diffuseColor.a);//vec4(vNormal, 1.0);\r\n #endif\r\n\r\n #ifdef USE_FOG\r\n float viewDistance;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDistance = abs(pixelPosEye.z);\r\n #else\r\n viewDistance = vViewPosition.z;\r\n #endif\r\n float fogFactor = smoothstep( fogNear, fogFar, viewDistance) * fogAlpha;\r\n #ifdef FOG_TRANSPARENT\r\n fragColor.a = fragColor.a * (1.0 - fogFactor);\r\n #else\r\n fragColor.rgb = mix( fragColor.rgb, fogColor, fogFactor );\r\n #endif\r\n #endif\r\n\r\n #endif\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/capabilities.js +;// ./src/gfx/shaders/Uber.vert +const Uber_namespaceObject = "/*\r\n * GLSL Version: ES 3.00 (WebGL 2.0 compatible)\r\n * No #version directive in this file (injected by Three.js).\r\n * Use GLSL3 semantics (`in`/`out`).\r\n * Set `glslVersion: THREE.GLSL3` in ShaderMaterial/RawShaderMaterial.\r\n */\r\n\r\nfloat INSTANCED_SPRITE_OVERSCALE = 1.3;\r\n\r\nin vec3 normal;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n out vec3 viewNormal;\r\n#endif\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n out vec3 vNormal;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n in vec4 position; // W contains vert pos or neg offset\r\n#else\r\n in vec3 position;\r\n#endif\r\n\r\nout vec3 vWorldPosition;\r\nout vec3 vViewPosition;\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n in float alphaColor;\r\n out float alphaCol;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ];\r\n\t\tout vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tout vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n in vec3 color;\r\n out vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n in vec3 color2;\r\n out vec3 vColor2;\r\n in vec2 uv;\r\n #ifndef CYLINDER_SPRITE\r\n out vec2 vUv;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_POS\r\n in vec4 offset;\r\n #ifdef SPHERE_SPRITE\r\n out vec4 instOffset;\r\n out vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n in vec4 matVector1;\r\n in vec4 matVector2;\r\n in vec4 matVector3;\r\n in vec4 invmatVector1;\r\n in vec4 invmatVector2;\r\n in vec4 invmatVector3;\r\n\r\n #ifdef CYLINDER_SPRITE\r\n out vec4 matVec1;\r\n out vec4 matVec2;\r\n out vec4 matVec3;\r\n out vec4 invmatVec1;\r\n out vec4 invmatVec2;\r\n out vec4 invmatVec3;\r\n out vec4 spritePosEye;\r\n #endif\r\n#endif\r\n\r\nuniform mat4 modelViewMatrix; // optional\r\nuniform mat4 projectionMatrix; // optional\r\nuniform mat3 normalMatrix; // optional\r\nuniform mat4 modelMatrix; // optional\r\n\r\n#ifdef DASHED_LINE\r\n in float lineDistance;\r\n out float vLineDistance;\r\n#endif\r\n\r\n#ifdef THICK_LINE\r\n in vec3 direction;\r\n uniform mat4 projMatrixInv;\r\n uniform vec2 viewport;\r\n uniform float lineWidth;\r\n\r\n vec4 transform(vec4 coord){\r\n return projectionMatrix * modelViewMatrix * coord;\r\n }\r\n\r\n vec2 project(vec4 device){\r\n vec3 device_normal = device.xyz/device.w;\r\n vec2 clip_pos = (device_normal*0.5+0.5).xy;\r\n return clip_pos * viewport;\r\n }\r\n\r\n vec4 unproject(vec2 screen, float z, float w){\r\n vec2 clip_pos = screen/viewport;\r\n vec2 device_normal = clip_pos*2.0-1.0;\r\n return vec4(device_normal*w, z, w);\r\n }\r\n#endif\r\n\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n alphaCol = alphaColor;\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n vec3 objectNormal = vec3(\r\n dot(normal, matVector1.xyz),\r\n dot(normal, matVector2.xyz),\r\n dot(normal, matVector3.xyz));\r\n#else\r\n vec3 objectNormal = vec3( normal );\r\n#endif\r\n\r\nvec3 transformedNormal = normalMatrix * objectNormal;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n vNormal = normalize(transformedNormal);\r\n#endif\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n viewNormal = normalize(mat3(modelViewMatrix)*objectNormal);\r\n#endif\r\n\r\n vec4 localPos = vec4(position.xyz, 1.0);\r\n vec4 worldPos = modelMatrix * localPos;\r\n vec4 mvPosition = modelViewMatrix * localPos;\r\n\r\n// make thick line offset\r\n#ifdef THICK_LINE\r\n // get screen pos\r\n vec4 dPos = transform(vec4(position.xyz, 1.0));\r\n vec2 sPos = project(dPos);\r\n // move pos forward\r\n vec3 position2 = position.xyz + direction.xyz * 0.5;\r\n // get screen offset pos\r\n vec4 dPos2 = transform(vec4(position2.xyz, 1.0));\r\n vec2 sPos2 = project(dPos2);\r\n // screen line direction\r\n vec2 sDir = normalize(sPos2 - sPos);\r\n // vertex offset (orthogonal to line direction)\r\n vec2 offset1 = vec2(-sDir.y, sDir.x);\r\n // move screen vertex\r\n vec2 newPos = sPos + offset1 * position.w * lineWidth;\r\n // get moved pos in view space\r\n vec4 dNewPos = unproject(newPos, dPos.z, dPos.w);\r\n mvPosition.xyz = (projMatrixInv * dNewPos).xyz;\r\n#endif // THICK_LINE\r\n\r\n#ifdef INSTANCED_POS\r\n #ifdef SPHERE_SPRITE\r\n instOffset = offset;\r\n\r\n vec4 posEye = modelViewMatrix * vec4( offset.xyz, 1.0 );\r\n float scale = length(modelViewMatrix[0]);\r\n mvPosition = posEye + vec4( position.xyz * offset.w * scale * INSTANCED_SPRITE_OVERSCALE, 0.0 );\r\n posEye.w = offset.w * scale;\r\n\r\n spritePosEye = posEye;\r\n #else\r\n localPos = vec4( offset.xyz + position.xyz * offset.w, 1.0 );\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n#ifdef INSTANCED_MATRIX\r\n #ifdef CYLINDER_SPRITE\r\n matVec1 = matVector1;\r\n matVec2 = matVector2;\r\n matVec3 = matVector3;\r\n invmatVec1 = invmatVector1;\r\n invmatVec2 = invmatVector2;\r\n invmatVec3 = invmatVector3;\r\n\r\n // calculate eye coords of cylinder endpoints\r\n vec4 v = vec4(0, -0.5, 0, 1);\r\n vec4 p1 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n v.y = 0.5;\r\n vec4 p2 = modelViewMatrix * vec4(dot(v, matVector1), dot(v, matVector2), dot(v, matVector3), 1.0);\r\n\r\n // sprite is placed at the center of cylinder\r\n vec4 posEye;\r\n posEye.xyz = mix(p1.xyz, p2.xyz, 0.5);\r\n posEye.w = 1.0;\r\n spritePosEye = posEye;\r\n\r\n // cylinder radius in eye space\r\n float rad = length(modelViewMatrix[0]) * length(vec3(matVector1.x, matVector2.x, matVector3.x));\r\n vec2 spriteSize;\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // In ortho projection we skip z coordinate\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy - p1.xy);\r\n\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * (spriteSizeScreen + 2.0 * rad);\r\n #else\r\n // basic sprite size at screen plane (covers only cylinder axis)\r\n vec2 spriteSizeScreen = abs(p2.xy / p2.z - p1.xy / p1.z);\r\n\r\n // full sprite size in eye coords\r\n float minZ = min(abs(p1.z), abs(p2.z));\r\n spriteSize = vec2(1.0, 1.0) * INSTANCED_SPRITE_OVERSCALE * abs(posEye.z) * (spriteSizeScreen + 2.0 * rad / minZ);\r\n #endif\r\n\r\n mvPosition = posEye + vec4( position.xy * 0.5 * spriteSize, 0, 0 );\r\n #else\r\n localPos = vec4(dot(localPos, matVector1), dot(localPos, matVector2), dot(localPos, matVector3), 1.0);\r\n worldPos = modelMatrix * localPos;\r\n mvPosition = modelViewMatrix * localPos;\r\n #endif\r\n#endif\r\n\r\n gl_Position = projectionMatrix * mvPosition;\r\n\r\n vWorldPosition = worldPos.xyz;\r\n vViewPosition = - mvPosition.xyz;\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t vec4 worldPosition;\r\n\t // see THREE.WebGLProgram.unrollLoops\r\n\t #pragma unroll_loop_start\r\n\t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirectionalShadowCoord[ i ] = directionalShadowMatrix[ i ] * vec4(vWorldPosition, 1.0);\r\n vDirectionalShadowNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(objectNormal, 0.0))).xyz;\r\n\t }\r\n\t #pragma unroll_loop_end\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n vColor = color.xyz;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n vColor2 = color2;\r\n #ifndef CYLINDER_SPRITE\r\n vUv = uv;\r\n #endif\r\n#endif\r\n\r\n#ifdef DASHED_LINE\r\n vLineDistance = lineDistance;\r\n#endif\r\n}\r\n"; +;// ./src/gfx/shaders/Uber.frag +const gfx_shaders_Uber_namespaceObject = "/*\r\n * GLSL Version: ES 3.00 (WebGL 2.0 compatible)\r\n * No #version directive in this file (injected by Three.js).\r\n * Use GLSL3 semantics (`in`/`out`, `layout(location=...)`, `texture`).\r\n * Set `glslVersion: THREE.GLSL3` in ShaderMaterial/RawShaderMaterial.\r\n */\r\n\r\n#if defined (NORMALS_TO_G_BUFFER)\r\n layout(location = 0) out vec4 fragColor;\r\n layout(location = 1) out vec4 fragNormal;\r\n#else\r\n out vec4 fragColor;\r\n#endif\r\n\r\n#ifdef ATTR_ALPHA_COLOR\r\n in float alphaCol;\r\n#endif\r\n\r\n#ifdef COLOR_FROM_POS\r\n uniform mat4 world2colorMatrix;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n\t#if NUM_DIR_LIGHTS > 0\r\n\t\tuniform sampler2D directionalShadowMap[ NUM_DIR_LIGHTS ];\r\n uniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ]; //only for sprites\r\n\t\tin vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\r\n\t\tin vec3 vDirectionalShadowNormal[ NUM_DIR_LIGHTS ];\r\n vec4 vDirLightWorldCoord[ NUM_DIR_LIGHTS ];\r\n vec3 vDirLightWorldNormal[ NUM_DIR_LIGHTS ];\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n // We use 4 instead uniform variable or define because this value is used in for(... i < value; ...) with\r\n // unroll_loop and unroll_loop has pattern:\r\n // /#pragma unroll_loop[\\s]+?for \\( int i \\= (\\d+)\\; i < (\\d+)\\; i \\+\\+ \\) \\{([\\s\\S]+?)(?=\\})\\}/g\r\n uniform vec2 samplesKernel[4]; // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n uniform sampler2D noiseTex;\r\n uniform vec2 noiseTexelSize;\r\n uniform vec2 srcTexelSize;\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\t#endif\r\n#endif\r\n\r\n#ifdef ATTR_COLOR\r\n in vec3 vColor;\r\n#endif\r\n\r\n#ifdef ATTR_COLOR2\r\n in vec3 vColor2;\r\n #ifndef CYLINDER_SPRITE\r\n in vec2 vUv;\r\n #endif\r\n#endif\r\n\r\nuniform vec3 diffuse;\r\nuniform vec3 emissive;\r\nuniform vec3 specular;\r\nuniform float shininess;\r\nuniform vec3 fixedColor;\r\nuniform float opacity;\r\nuniform float zClipValue;\r\nuniform float clipPlaneValue;\r\n\r\n#ifdef NORMALS_TO_G_BUFFER\r\n in vec3 viewNormal;\r\n#endif\r\n\r\n#define RECIPROCAL_PI 0.31830988618\r\n#define saturate(a) clamp( a, 0.0, 1.0 )\r\n\r\n#ifdef USE_FOG\r\n uniform vec3 fogColor;\r\n uniform float fogAlpha;\r\n uniform float fogNear;\r\n uniform float fogFar;\r\n#endif\r\n\r\nin vec3 vWorldPosition; // world position of the pixel (invalid when INSTANCED_SPRITE is defined)\r\nin vec3 vViewPosition;\r\n\r\n#if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n in vec3 vNormal;\r\n#endif\r\n\r\n/////////////////////////////////////////// ZSprites ////////////////////////////////////////////////\r\n#if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n uniform float nearPlaneValue;\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n in vec4 spritePosEye;\r\n#endif\r\n\r\n#if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n uniform float zOffset;\r\n\r\n #if !defined(USE_LIGHTS) || !defined(SHADOWMAP) || !defined(SHADOWMAP_PCF_RAND) || !(NUM_DIR_LIGHTS > 0)\r\n uniform mat4 projectionMatrix;\r\n #endif\r\n\r\n float calcDepthForSprites(vec4 pixelPosEye, float zOffset, mat4 projMatrix) {\r\n vec4 pixelPosScreen = projMatrix * pixelPosEye;\r\n return 0.5 * (pixelPosScreen.z / pixelPosScreen.w + 1.0) + zOffset;\r\n }\r\n#endif\r\n\r\n#ifdef SPHERE_SPRITE\r\n in vec4 instOffset;\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n\r\n bool intersect_ray_sphere(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray, ray);\r\n float b = dot(ray, origin);\r\n float c = dot(origin, origin) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n // choose nearest point inside frustum\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all spheres the point with smaller 't' is visible\r\n // t1 is always smaller than t2 (from calculations)\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_sphere_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into sphere local coords\r\n origin = pixelPosEye.xyz - spritePosEye.xyz;\r\n origin = (invModelViewMatrix * vec4(origin, 0.0)).xyz / instOffset.w;\r\n\r\n // transform camera orientation vector into sphere local coords\r\n ray = (invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0)).xyz;\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n vec4 v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into sphere local coords\r\n v = invModelViewMatrix * v;\r\n origin = (v.xyz - instOffset.xyz) / instOffset.w;\r\n\r\n // transform vector from camera pos to curPixel into sphere local coords\r\n ray = (invModelViewMatrix * vec4(pixelPosEye, 0.0)).xyz;\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_sphere(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n in vec4 matVec1;\r\n in vec4 matVec2;\r\n in vec4 matVec3;\r\n in vec4 invmatVec1;\r\n in vec4 invmatVec2;\r\n in vec4 invmatVec3;\r\n\r\n uniform mat4 modelMatrix;\r\n uniform mat4 modelViewMatrix;\r\n uniform mat4 invModelViewMatrix;\r\n uniform mat3 normalMatrix;\r\n\r\n in vec4 spritePosEye;\r\n\r\n bool intersect_ray_cylinder(in vec3 origin, in vec3 ray, out vec3 point, out float frontFaced) {\r\n\r\n // intersect XZ-projected ray with circle\r\n float a = dot(ray.xz, ray.xz);\r\n float b = dot(ray.xz, origin.xz);\r\n float c = dot(origin.xz, origin.xz) - 1.0;\r\n float det = b * b - a * c;\r\n if (det < 0.0) return false;\r\n float t1 = (-b - sqrt(det)) / a;\r\n float t2 = (-b + sqrt(det)) / a;\r\n\r\n // calculate both intersection points\r\n vec3 p1 = origin + ray * t1;\r\n vec3 p2 = origin + ray * t2;\r\n\r\n float halfHeight = 0.5;\r\n\r\n // choose nearest point\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // orthografic camera is used for dirLight sources. So in it for all cylinders the point with smaller 't' is visible\r\n // if it is not outside of cylinnder (t1 is always smaller than t2).\r\n if (p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #else\r\n // for perspective camera first intersection can be in front of near plane. If not intersection is p1 else - p2\r\n // t* = 0.0 corresponds to point of intersection near plane by the ray from camera to curPixel\r\n if (t1 >= 0.0 && p1.y >= -halfHeight && p1.y <= halfHeight) {\r\n point = p1;\r\n frontFaced = 1.0;\r\n return true;\r\n }\r\n if (t2 >= 0.0 && p2.y >= -halfHeight && p2.y <= halfHeight) {\r\n point = p2;\r\n frontFaced = -1.0;\r\n return true;\r\n }\r\n #endif\r\n\r\n return false;\r\n }\r\n\r\n bool get_cylinder_point(in vec3 pixelPosEye, out vec3 point, out float frontFaced) {\r\n vec3 origin, ray;\r\n vec4 v;\r\n\r\n #ifdef ORTHOGRAPHIC_CAMERA\r\n // transform vector from sprite center to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye.xyz - spritePosEye.xyz, 0.0);\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform camera orientation vector into cylinder local coords\r\n v = invModelViewMatrix * vec4(0.0, 0.0, -1.0, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #else\r\n // find point of intersection near plane by the ray from camera to curPixel\r\n v = vec4(-(nearPlaneValue / pixelPosEye.z) * pixelPosEye, 1.0);\r\n\r\n // transform intersection point into cylinder local coords\r\n v = invModelViewMatrix * v;\r\n origin = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n\r\n // transform vector from camera pos to curPixel into cylinder local coords\r\n v = invModelViewMatrix * vec4(pixelPosEye, 0.0);\r\n ray = vec3(dot(v, invmatVec1), dot(v, invmatVec2), dot(v, invmatVec3));\r\n #endif\r\n ray = normalize(ray);\r\n\r\n return intersect_ray_cylinder(origin, ray, point, frontFaced);\r\n }\r\n#endif\r\n\r\n///////////////////////////////////// Pack and unpack ///////////////////////////////////////////////\r\nconst float PackUpscale = 256. / 255.; // fraction -> 0..1 (including 1)\r\nconst float UnpackDownscale = 255. / 256.; // 0..1 -> fraction (excluding 1)\r\n\r\nconst vec3 PackFactors = vec3( 256. * 256. * 256., 256. * 256., 256. );\r\nconst vec4 UnpackFactors = UnpackDownscale / vec4( PackFactors, 1. );\r\n\r\n\r\nconst float ShiftRight8 = 1. / 256.;\r\n\r\nvec4 packDepthToRGBA( const in float v ) {\r\n vec4 r = vec4( fract( v * PackFactors ), v );\r\n r.yzw -= r.xyz * ShiftRight8; // tidy overflow\r\n return r * PackUpscale;\r\n}\r\n\r\nfloat unpackRGBAToDepth( const in vec4 v ) {\r\n return dot( v, UnpackFactors );\r\n}\r\n\r\n////////////////////////////////////////// All Lighting /////////////////////////////////////////////////\r\n#ifdef TOON_SHADING\r\n #define LOW_TOON_BORDER 0.0\r\n #define MEDIUM_TOON_BORDER 0.7\r\n #define HIGH_TOON_BORDER 1.0\r\n\r\n #define MEDIUM_TOON_RANGE 0.5\r\n #define HIGH_TOON_RANGE 0.95\r\n#endif\r\n#if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n struct ReflectedLight {\r\n vec3 directDiffuse;\r\n vec3 directSpecular;\r\n vec3 indirectDiffuse;\r\n };\r\n\r\n struct BlinnPhongMaterial {\r\n vec3 diffuseColor;\r\n vec3 specularColor;\r\n float specularShininess;\r\n };\r\n\r\n struct GeometricContext {\r\n vec3 normal;\r\n vec3 viewDir;\r\n };\r\n\r\n struct DirectionalLight {\r\n vec3 direction;\r\n vec3 color;\r\n };\r\n uniform DirectionalLight directionalLights[ NUM_DIR_LIGHTS ];\r\n\r\n struct DirectionalLightShadow {\r\n vec2 shadowMapSize;\r\n float shadowBias;\r\n float shadowRadius;\r\n };\r\n uniform DirectionalLightShadow directionalLightShadows[ NUM_DIR_LIGHTS ];\r\n\r\n uniform vec3 ambientLightColor;\r\n\r\n /////////////////////////////////////////// Shadowmap ////////////////////////////////////////////////\r\n\r\n #if defined(SHADOWMAP)\r\n \tfloat texture2DCompare( sampler2D depths, vec2 uv, float compare ) {\r\n \t\treturn step( compare, unpackRGBAToDepth( texture( depths, uv ) ) );\r\n \t}\r\n\r\n float getShadow( sampler2D shadowMap, DirectionalLightShadow dirLight, vec4 shadowCoord, vec3 vViewPosition, vec3 vNormal ) {\r\n \t float shadow = 0.0;\r\n\r\n // When shadows for sprites will appear use here for them normals as it done for G-buffer\r\n shadowCoord.xyz += dirLight.shadowBias * vNormal;\r\n shadowCoord.xyz /= shadowCoord.w;\r\n\r\n bvec4 inFrustumVec = bvec4 ( shadowCoord.x >= 0.0, shadowCoord.x <= 1.0, shadowCoord.y >= 0.0, shadowCoord.y <= 1.0 );\r\n bool inFrustum = all( inFrustumVec );\r\n bvec2 frustumTestVec = bvec2( inFrustum, shadowCoord.z <= 1.0 );\r\n bool frustumTest = all( frustumTestVec );\r\n\r\n if ( frustumTest ) {\r\n #ifdef SHADOWMAP_BASIC\r\n \t shadow = texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z );\r\n \t#endif\r\n\r\n \t#ifdef SHADOWMAP_PCF_SHARP\r\n \t vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n float dx0 = - texelSize.x * dirLight.shadowRadius;\r\n float dy0 = - texelSize.y * dirLight.shadowRadius;\r\n float dx1 = + texelSize.x * dirLight.shadowRadius;\r\n float dy1 = + texelSize.y * dirLight.shadowRadius;\r\n\r\n shadow = (\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) +\r\n \ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z )\r\n ) * ( 1.0 / 9.0 );\r\n #endif\r\n\r\n #ifdef SHADOWMAP_PCF_RAND\r\n vec2 texelSize = vec2( 1.0 ) / dirLight.shadowMapSize;\r\n\r\n vec4 vUv = ((projectionMatrix * vec4(vViewPosition, 1.0)) + 1.0) / 2.0;\r\n vec2 vUvNoise = vUv.xy / srcTexelSize * noiseTexelSize;\r\n\r\n vec2 noiseVec = normalize(texture(noiseTex, vUvNoise).rg);\r\n mat2 mNoise = mat2(noiseVec.x, noiseVec.y, -noiseVec.y, noiseVec.x);\r\n\r\n vec2 offset;\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < 4; i ++ ) { // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n offset = mNoise * ( normalize( samplesKernel[ i ]) * texelSize * dirLight.shadowRadius );\r\n shadow += texture2DCompare( shadowMap, shadowCoord.xy + offset, shadowCoord.z );\r\n }\r\n #pragma unroll_loop_end\r\n shadow /= float( 4 ); // 4 is length of _samplesKernel which is defined in UberMaterial.js\r\n #endif\r\n }\r\n return shadow;//(shadow != 1.0) ? 0.5 : 1.0;//vec4(shadow, shadow, shadow, 1.0);\r\n }\r\n #endif\r\n\r\n /////////////////////////////////////////// Lighting /////////////////////////////////////////////////\r\n\r\n vec3 BRDF_Diffuse_Lambert( const in vec3 diffuseColor ) {\r\n return RECIPROCAL_PI * diffuseColor;\r\n } // validated\r\n\r\n vec3 F_Schlick( const in vec3 specularColor, const in float dotLH ) {\r\n // Original approximation by Christophe Schlick '94\r\n //;float fresnel = pow( 1.0 - dotLH, 5.0 );\r\n // Optimized variant (presented by Epic at SIGGRAPH '13)\r\n float fresnel = exp2( ( -5.55473 * dotLH - 6.98316 ) * dotLH );\r\n return ( 1.0 - specularColor ) * fresnel + specularColor;\r\n } // validated\r\n\r\n float G_BlinnPhong_Implicit( /* const in float dotNL, const in float dotNV */ ) {\r\n // geometry term is (n dot l)(n dot v) / 4(n dot l)(n dot v)\r\n return 0.25;\r\n }\r\n\r\n float D_BlinnPhong( const in float shininess, const in float dotNH ) {\r\n return RECIPROCAL_PI * ( shininess * 0.5 + 1.0 ) * pow( dotNH, shininess );\r\n }\r\n\r\n vec3 BRDF_Specular_BlinnPhong( const in DirectionalLight incidentLight, const in GeometricContext geometry, const in vec3 specularColor, const in float shininess ) {\r\n vec3 halfDir = normalize( incidentLight.direction + geometry.viewDir );\r\n float dotNH = saturate(dot( geometry.normal, halfDir ));\r\n float dotLH = saturate(dot( incidentLight.direction, halfDir ));\r\n\r\n vec3 F = F_Schlick( specularColor, dotLH );\r\n float G = G_BlinnPhong_Implicit( /* dotNL, dotNV */ );\r\n float D = D_BlinnPhong( shininess, dotNH );\r\n\r\n return F * ( G * D );\r\n } // validated\r\n\r\n void RE_Direct_BlinnPhong( const in DirectionalLight directLight, const in GeometricContext geometry, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight, float penumbra ) {\r\n\r\n float dotNL = saturate( dot( geometry.normal, directLight.direction ));\r\n #ifdef TOON_SHADING\r\n if(dotNL < MEDIUM_TOON_RANGE){\r\n dotNL = LOW_TOON_BORDER;\r\n }\r\n else if(dotNL < HIGH_TOON_RANGE){\r\n dotNL = MEDIUM_TOON_BORDER;\r\n }\r\n else{\r\n dotNL = HIGH_TOON_BORDER;\r\n }\r\n #endif\r\n\r\n vec3 irradiance = dotNL * directLight.color;\r\n reflectedLight.directDiffuse += penumbra * irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n reflectedLight.directSpecular += penumbra * irradiance * BRDF_Specular_BlinnPhong( directLight, geometry, material.specularColor, material.specularShininess );\r\n }\r\n\r\n void RE_IndirectDiffuse_BlinnPhong( const in vec3 irradiance, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) {\r\n reflectedLight.indirectDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\r\n }\r\n\r\n vec3 calcLighting(const in GeometricContext geometry, const in BlinnPhongMaterial material, vec3 vViewPosition) {\r\n ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ));\r\n vec3 irradiance = ambientLightColor;\r\n\r\n float shadowMask = 1.0;\r\n // see THREE.WebGLProgram.unrollLoops\r\n \t#pragma unroll_loop_start\r\n \t for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n \t #ifdef SHADOWMAP\r\n \t shadowMask = getShadow( directionalShadowMap[ i ], directionalLightShadows[ i ], vDirLightWorldCoord[ i ], vViewPosition, vDirLightWorldNormal[ i ] );\r\n #endif\r\n\r\n \t\t if ( shadowMask > 0.0 ) RE_Direct_BlinnPhong( directionalLights[ i ], geometry, material, reflectedLight, shadowMask );\r\n \t\t}\r\n \t\t#pragma unroll_loop_end\r\n\r\n RE_IndirectDiffuse_BlinnPhong(irradiance, material, reflectedLight);\r\n\r\n return saturate(reflectedLight.indirectDiffuse + reflectedLight.directDiffuse + reflectedLight.directSpecular);\r\n }\r\n#endif\r\n\r\n/////////////////////////////////////////// Dashed Line ///////////////////////////////////////////////\r\n#ifdef DASHED_LINE\r\n uniform float dashedLineSize;\r\n uniform float dashedLinePeriod;\r\n in float vLineDistance;\r\n#endif\r\n\r\n/////////////////////////////////////////// Main ///////////////////////////////////////////////\r\nvoid main() {\r\n\r\n#ifdef CLIP_PLANE\r\n if (vViewPosition.z < clipPlaneValue) discard;\r\n#endif\r\n\r\n#ifdef ZCLIP\r\n if (vViewPosition.z < zClipValue) discard;\r\n#endif\r\n\r\n#if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = vDirectionalShadowCoord[ i ];\r\n vDirLightWorldNormal[ i ] = vDirectionalShadowNormal[ i ];\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n#endif\r\n\r\n vec4 pixelPosWorld = vec4(vWorldPosition, 1.0);\r\n vec4 pixelPosEye;\r\n\r\n#ifdef SPHERE_SPRITE\r\n\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n vec3 normal;\r\n\r\n/* quick-and-dirty method\r\n normal.xy = ' + INSTANCED_SPRITE_OVERSCALE + ' * (2.0 * vUv - 1.0);\r\n float r2 = dot(normal.xy, normal.xy);\r\n if (r2 > 1.0) discard;\r\n float normalZ = sqrt(1.0 - r2);\r\n normal.z = normalZ;\r\n normal = normal * ( -1.0 + 2.0 * float( gl_FrontFacing ) );\r\n pixelPosEye = vec4(spritePosEye.xyz, 1.0);\r\n pixelPosEye.z += spritePosEye.w * normalZ;\r\n*/\r\n\r\n // ray-trace sphere surface\r\n {\r\n vec3 p;\r\n if (!get_sphere_point(-vViewPosition, p, frontFaced)) discard;\r\n vec4 v = vec4(instOffset.xyz + p * instOffset.w, 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n normal = normalize(normalMatrix * p);\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*p);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(p, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n }\r\n#endif\r\n\r\n#ifdef CYLINDER_SPRITE\r\n vec3 normal;\r\n vec3 viewNormalSprites;\r\n float frontFaced = 1.0;\r\n float cylinderY = 0.0;\r\n\r\n // ray-trace cylinder surface\r\n {\r\n vec3 p;\r\n if (!get_cylinder_point(-vViewPosition, p, frontFaced)) discard;\r\n\r\n cylinderY = 0.5 * (p.y + 1.0);\r\n\r\n vec4 v = vec4(p, 1.0);\r\n v = vec4(dot(v, matVec1), dot(v, matVec2), dot(v, matVec3), 1.0);\r\n pixelPosWorld = modelMatrix * v;\r\n pixelPosEye = modelViewMatrix * v;\r\n\r\n vec3 localNormal = normalize(vec3(p.x, 0.0, p.z));\r\n normal = vec3(\r\n dot(localNormal, matVec1.xyz),\r\n dot(localNormal, matVec2.xyz),\r\n dot(localNormal, matVec3.xyz));\r\n #ifdef NORMALS_TO_G_BUFFER\r\n viewNormalSprites = normalize(mat3(modelViewMatrix)*normal);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && defined(SHADOWMAP)\r\n #if NUM_DIR_LIGHTS > 0\r\n // see THREE.WebGLProgram.unrollLoops\r\n #pragma unroll_loop_start\r\n for ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\r\n vDirLightWorldCoord[ i ] = directionalShadowMatrix[ i ] * pixelPosWorld;\r\n vDirLightWorldNormal[ i ] = (directionalShadowMatrix[ i ] * (modelMatrix * vec4(normal, 0.0))).xyz;\r\n }\r\n #pragma unroll_loop_end\r\n #endif\r\n #endif\r\n\r\n normal = normalize(normalMatrix * normal);\r\n }\r\n#endif\r\n\r\n #ifdef ATTR_COLOR\r\n vec3 vertexColor = vColor;\r\n #else\r\n vec3 vertexColor = vec3(1.0, 1.0, 1.0);\r\n #endif\r\n\r\n #ifdef ATTR_COLOR2\r\n #ifdef CYLINDER_SPRITE\r\n float colorCoef = cylinderY; // cylinder parameter is calculated from ray-tracing\r\n #else\r\n float colorCoef = vUv.y; // cylinder parameter is interpolated as tex coord\r\n #endif\r\n // choose either color or color2\r\n vertexColor = mix(vColor2, vColor, step(0.5, colorCoef));\r\n #endif\r\n\r\n // negative red component is a special condition\r\n if (vertexColor.x < 0.0) discard;\r\n\r\n #ifdef DASHED_LINE\r\n if ( mod( vLineDistance, dashedLinePeriod ) > dashedLineSize ) discard;\r\n #endif\r\n\r\n // transparency prepass writes only z, so we don't need to calc the color\r\n #ifdef PREPASS_TRANSP\r\n fragColor = vec4(1.0, 1.0, 1.0, 1.0);\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n return;\r\n #endif\r\n\r\n float totalOpacity = opacity;\r\n\r\n #ifdef ATTR_ALPHA_COLOR\r\n totalOpacity *= alphaCol;\r\n #endif\r\n\r\n // discard fully transparent pixels\r\n if (totalOpacity == 0.0) discard;\r\n\r\n #ifdef FAKE_OPACITY\r\n // discard pixels in checker pattern\r\n vec2 dm_coord = floor(gl_FragCoord.xy);\r\n dm_coord = fract(dm_coord * 0.5);\r\n if (totalOpacity < 1.0 && (dm_coord.x < 0.5 ^^ dm_coord.y < 0.5)) discard;\r\n vec4 diffuseColor = vec4(diffuse, 1.0);\r\n #else\r\n vec4 diffuseColor = vec4(diffuse, totalOpacity);\r\n #endif\r\n\r\n float flipNormal;\r\n #if !defined (SPHERE_SPRITE) && !defined (CYLINDER_SPRITE)\r\n flipNormal = 1.0;\r\n #ifdef DOUBLE_SIDED\r\n flipNormal = float( gl_FrontFacing );\r\n #endif\r\n vec3 normal = normalize( vNormal ) * flipNormal;\r\n #endif\r\n\r\n diffuseColor.rgb *= vertexColor;\r\n\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n #endif\r\n\r\n #ifdef NORMALS_TO_G_BUFFER\r\n #if defined (SPHERE_SPRITE) || defined (CYLINDER_SPRITE)\r\n vec3 viewNormaInColor = viewNormalSprites;\r\n #else\r\n vec3 viewNormaInColor = viewNormal;\r\n float frontFaced = float( gl_FrontFacing );\r\n #endif\r\n // [-1, 1] -> [0, 1]\r\n viewNormaInColor = 0.5 * viewNormaInColor + 0.5;\r\n fragNormal = vec4(viewNormaInColor, frontFaced);\r\n #endif\r\n\r\n #if defined(USE_LIGHTS) && NUM_DIR_LIGHTS > 0\r\n vec3 viewDir;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDir = -pixelPosEye.xyz;\r\n #else\r\n viewDir = vViewPosition;\r\n #endif\r\n GeometricContext geometry = GeometricContext(normal, normalize( viewDir ));\r\n BlinnPhongMaterial material = BlinnPhongMaterial(diffuseColor.rgb, specular, shininess);\r\n vec3 outgoingLight = calcLighting(geometry, material, viewDir);\r\n #else\r\n vec3 outgoingLight = diffuseColor.rgb;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_DEPTH\r\n float depth = 0.0;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n gl_FragDepth = calcDepthForSprites(pixelPosEye, zOffset, projectionMatrix);\r\n depth = gl_FragDepth;\r\n #else\r\n depth = gl_FragCoord.z;\r\n #endif\r\n fragColor = packDepthToRGBA(depth);\r\n return;\r\n #endif\r\n\r\n #ifdef COLOR_FROM_POS\r\n fragColor = world2colorMatrix * pixelPosWorld;\r\n #else\r\n #ifdef OVERRIDE_COLOR\r\n fragColor = vec4(fixedColor, diffuseColor.a);\r\n #else\r\n fragColor = vec4(outgoingLight, diffuseColor.a);//vec4(vNormal, 1.0);\r\n #endif\r\n\r\n #ifdef USE_FOG\r\n float viewDistance;\r\n #if defined(SPHERE_SPRITE) || defined(CYLINDER_SPRITE)\r\n viewDistance = abs(pixelPosEye.z);\r\n #else\r\n viewDistance = vViewPosition.z;\r\n #endif\r\n float fogFactor = smoothstep( fogNear, fogFar, viewDistance) * fogAlpha;\r\n #ifdef FOG_TRANSPARENT\r\n fragColor.a = fragColor.a * (1.0 - fogFactor);\r\n #else\r\n fragColor.rgb = mix( fragColor.rgb, fogColor, fogFactor );\r\n #endif\r\n #endif\r\n\r\n #endif\r\n}\r\n"; +;// ./src/gfx/capabilities.js /* harmony default export */ const capabilities = ({ precision: 'mediump', /** @@ -16702,7 +16749,7 @@ const gfx_shaders_Uber_namespaceObject = "#if defined (NORMALS_TO_G_BUFFER)\r\n this.precision = renderer.capabilities.getMaxPrecision('highp'); } }); -;// CONCATENATED MODULE: ./src/gfx/noiseTexture.js +;// ./src/gfx/noiseTexture.js const noiseWidth = 4; const noiseHeight = 4; @@ -16719,9 +16766,7 @@ noiseTexture.needsUpdate = true; noiseHeight, noiseTexture }); -;// CONCATENATED MODULE: ./src/gfx/shaders/UberMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/UberMaterial.js @@ -16931,9 +16976,10 @@ class UberMaterial extends external_module_three_commonjs_three_commonjs2_three_ // set default values super.setValues({ - uniforms: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.UniformsUtils.clone(defaultUniforms), + glslVersion: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.GLSL3, vertexShader: this.precisionString() + Uber_namespaceObject, fragmentShader: this.precisionString() + gfx_shaders_Uber_namespaceObject, + uniforms: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.UniformsUtils.clone(defaultUniforms), lights: true, fog: true, side: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.DoubleSide @@ -17119,12 +17165,12 @@ class UberMaterial extends external_module_three_commonjs_three_commonjs2_three_ } UberMaterial.prototype.uberOptions = uberOptions; /* harmony default export */ const shaders_UberMaterial = (UberMaterial); -;// CONCATENATED MODULE: ./src/gfx/meshes/UberObject.js +;// ./src/gfx/meshes/UberObject.js /* harmony default export */ function UberObject(SuperClass) { class NewObjectType extends SuperClass { - constructor() { - super(...arguments); + constructor(...rest) { + super(...rest); this.onBeforeRender = NewObjectType.prototype.onBeforeRender; } onBeforeRender(renderer, scene, camera, geometry, material, group) { @@ -17146,13 +17192,13 @@ UberMaterial.prototype.uberOptions = uberOptions; } return NewObjectType; } -;// CONCATENATED MODULE: ./src/gfx/meshes/ZSpriteMesh.js +;// ./src/gfx/meshes/ZSpriteMesh.js const Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Mesh); class ZSpriteMesh extends Mesh { - constructor() { - super(...arguments); + constructor(...rest) { + super(...rest); this.castShadow = true; this.receiveShadow = true; } @@ -17176,7 +17222,7 @@ class ZSpriteMesh extends Mesh { } } /* harmony default export */ const meshes_ZSpriteMesh = (ZSpriteMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/ZClippedMesh.js +;// ./src/gfx/meshes/ZClippedMesh.js const ZClippedMesh_Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Mesh); @@ -17186,9 +17232,9 @@ class ZClippedMesh extends ZClippedMesh_Mesh { this.castShadow = true; this.receiveShadow = true; } - static _mvLength = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3())(); - static _center = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3())(); - static _modelView = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Matrix4())(); + static _mvLength = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); + static _center = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); + static _modelView = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Matrix4(); _onBeforeRender(renderer, scene, camera) { ZClippedMesh_Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera); const geo = this.geometry; @@ -17210,7 +17256,7 @@ class ZClippedMesh extends ZClippedMesh_Mesh { } } /* harmony default export */ const meshes_ZClippedMesh = (ZClippedMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/TextMesh.js +;// ./src/gfx/meshes/TextMesh.js @@ -17243,7 +17289,7 @@ class TextMesh extends external_module_three_commonjs_three_commonjs2_three_amd_ } const item = utils.shallowCloneNode(srcItem); const label = new gfx_CSS2DObject(item); - label.userData = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].clone(userData); + label.userData = __WEBPACK_EXTERNAL_MODULE_lodash_default__.clone(userData); const el = label.getElement(); el.style.visibility = 'visible'; label.source = srcItem; @@ -17272,7 +17318,7 @@ class TextMesh extends external_module_three_commonjs_three_commonjs2_three_amd_ } } /* harmony default export */ const meshes_TextMesh = (TextMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/SimpleMesh.js +;// ./src/gfx/meshes/SimpleMesh.js const SimpleMesh_Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Mesh); @@ -17284,7 +17330,7 @@ class SimpleMesh extends SimpleMesh_Mesh { } } /* harmony default export */ const meshes_SimpleMesh = (SimpleMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/ThickLineMesh.js +;// ./src/gfx/meshes/ThickLineMesh.js const ThickLineMesh_Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Mesh); @@ -17303,19 +17349,19 @@ class ThickLineMesh extends ThickLineMesh_Mesh { } } /* harmony default export */ const meshes_ThickLineMesh = (ThickLineMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/InstancedMesh.js +;// ./src/gfx/meshes/InstancedMesh.js const InstancedMesh_Mesh = UberObject(external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Mesh); class InstancedMesh extends InstancedMesh_Mesh { - constructor() { - super(...arguments); + constructor(...rest) { + super(...rest); this.castShadow = true; this.receiveShadow = true; } } /* harmony default export */ const meshes_InstancedMesh = (InstancedMesh); -;// CONCATENATED MODULE: ./src/gfx/meshes/meshes.js +;// ./src/gfx/meshes/meshes.js @@ -17334,7 +17380,7 @@ class InstancedMesh extends InstancedMesh_Mesh { ThickLineMesh: meshes_ThickLineMesh, Instanced: meshes_InstancedMesh }); -;// CONCATENATED MODULE: ./src/gfx/meshes/MeshCreator.js +;// ./src/gfx/meshes/MeshCreator.js @@ -17457,12 +17503,12 @@ class MeshCreator { } } /* harmony default export */ const meshes_MeshCreator = (MeshCreator); -;// CONCATENATED MODULE: ./src/gfx/meshes/TransformGroup.js +;// ./src/gfx/meshes/TransformGroup.js class TransformGroup extends external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Object3D { - static _inverseMatrix = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Matrix4())(); - static _ray = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Ray())(); + static _inverseMatrix = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Matrix4(); + static _ray = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Ray(); constructor(geometry, geoParams, material, transforms) { super(); this._geometry = geometry; @@ -17532,7 +17578,7 @@ class TransformGroup extends external_module_three_commonjs_three_commonjs2_thre } } /* harmony default export */ const meshes_TransformGroup = (TransformGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/ChemGroup.js +;// ./src/gfx/modes/groups/ChemGroup.js function wrapper(Name, args) { @@ -17591,7 +17637,7 @@ class ChemGroup extends gfx_RCGroup { } } /* harmony default export */ const groups_ChemGroup = (ChemGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsGroup.js +;// ./src/gfx/modes/groups/AtomsGroup.js class AtomsGroup extends groups_ChemGroup { raycast(raycaster, intersects) { @@ -17629,7 +17675,7 @@ class AtomsGroup extends groups_ChemGroup { } } /* harmony default export */ const groups_AtomsGroup = (AtomsGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsSphereGroup.js +;// ./src/gfx/modes/groups/AtomsSphereGroup.js class AtomsSphereGroup extends groups_AtomsGroup { _makeGeoArgs() { @@ -17673,7 +17719,7 @@ class AtomsSphereGroup extends groups_AtomsGroup { } } /* harmony default export */ const groups_AtomsSphereGroup = (AtomsSphereGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsSurfaceGroup.js +;// ./src/gfx/modes/groups/AtomsSurfaceGroup.js class AtomsSurfaceGroup extends groups_AtomsSphereGroup { _makeGeoArgs() { @@ -17692,7 +17738,7 @@ class AtomsSurfaceGroup extends groups_AtomsSphereGroup { } } /* harmony default export */ const groups_AtomsSurfaceGroup = (AtomsSurfaceGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsSASSESGroupStub.js +;// ./src/gfx/modes/groups/AtomsSASSESGroupStub.js /* This is a stub class keep it until SAS/SES is refactored */ @@ -17715,7 +17761,7 @@ class AtomsSASSESGroupStub extends groups_AtomsSphereGroup { } } /* harmony default export */ const groups_AtomsSASSESGroupStub = (AtomsSASSESGroupStub); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AtomsTextGroup.js +;// ./src/gfx/modes/groups/AtomsTextGroup.js function adjustColor(color) { @@ -17859,7 +17905,7 @@ class AtomsTextGroup extends groups_AtomsGroup { } } /* harmony default export */ const groups_AtomsTextGroup = (AtomsTextGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AromaticGroup.js +;// ./src/gfx/modes/groups/AromaticGroup.js function _slerp(omega, v1, v2, t) { @@ -17921,7 +17967,7 @@ class AromaticGroup extends groups_AtomsGroup { } } /* harmony default export */ const groups_AromaticGroup = (AromaticGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AromaticTorusGroup.js +;// ./src/gfx/modes/groups/AromaticTorusGroup.js @@ -17963,7 +18009,7 @@ class AromaticTorusGroup extends groups_AromaticGroup { } } /* harmony default export */ const groups_AromaticTorusGroup = (AromaticTorusGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/AromaticLinesGroup.js +;// ./src/gfx/modes/groups/AromaticLinesGroup.js class AromaticLinesGroup extends groups_AromaticGroup { _build() { @@ -17986,7 +18032,7 @@ class AromaticLinesGroup extends groups_AromaticGroup { } } /* harmony default export */ const groups_AromaticLinesGroup = (AromaticLinesGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/ResiduesGroup.js +;// ./src/gfx/modes/groups/ResiduesGroup.js class ResiduesGroup extends groups_ChemGroup { raycast(raycaster, intersects) { @@ -18024,7 +18070,7 @@ class ResiduesGroup extends groups_ChemGroup { } } /* harmony default export */ const groups_ResiduesGroup = (ResiduesGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/NucleicItemGroup.js +;// ./src/gfx/modes/groups/NucleicItemGroup.js class NucleicItemGroup extends groups_ResiduesGroup { raycast(raycaster, intersects) { @@ -18100,7 +18146,7 @@ class NucleicItemGroup extends groups_ResiduesGroup { } } /* harmony default export */ const groups_NucleicItemGroup = (NucleicItemGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/NucleicCylindersGroup.js +;// ./src/gfx/modes/groups/NucleicCylindersGroup.js class NucleicCylindersGroup extends groups_NucleicItemGroup { _makeGeoArgs() { @@ -18113,7 +18159,7 @@ class NucleicCylindersGroup extends groups_NucleicItemGroup { } } /* harmony default export */ const groups_NucleicCylindersGroup = (NucleicCylindersGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/NucleicSpheresGroup.js +;// ./src/gfx/modes/groups/NucleicSpheresGroup.js class NucleicSpheresGroup extends groups_NucleicItemGroup { _makeGeoArgs() { @@ -18132,7 +18178,7 @@ class NucleicSpheresGroup extends groups_NucleicItemGroup { /* harmony default export */ const groups_NucleicSpheresGroup = (NucleicSpheresGroup); // EXTERNAL MODULE: ./vendor/js/Smooth.js var Smooth = __webpack_require__(690); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/CartoonHelper.js +;// ./src/gfx/modes/groups/CartoonHelper.js @@ -18308,7 +18354,7 @@ class CartoonHelper { } } /* harmony default export */ const groups_CartoonHelper = (CartoonHelper); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/ResiduesSubseqGroup.js +;// ./src/gfx/modes/groups/ResiduesSubseqGroup.js @@ -18370,9 +18416,7 @@ class ResiduesSubseqGroup extends groups_ResiduesGroup { const geo = this._geo; let chunkIdx = 0; const chunkIdc = []; - _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, function (currRes, mtc) { - let hasSlope = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : false; - let hasCut = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : false; + _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, (currRes, mtc, hasSlope = false, hasCut = false) => { const color = colorer.getResidueColor(currRes, parent); chunkIdc[chunkIdx] = currRes._index; geo.setItem(chunkIdx, mtc, hasSlope, hasCut); @@ -18405,7 +18449,7 @@ class ResiduesSubseqGroup extends groups_ResiduesGroup { } } /* harmony default export */ const groups_ResiduesSubseqGroup = (ResiduesSubseqGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/ResiduesTraceGroup.js +;// ./src/gfx/modes/groups/ResiduesTraceGroup.js class ResiduesTraceGroup extends groups_ChemGroup { _makeGeoArgs() { @@ -18529,7 +18573,7 @@ class ResiduesTraceGroup extends groups_ChemGroup { } } /* harmony default export */ const groups_ResiduesTraceGroup = (ResiduesTraceGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/BondsGroup.js +;// ./src/gfx/modes/groups/BondsGroup.js function getCylinderCount(bondOrder) { @@ -18598,7 +18642,7 @@ class BondsGroup extends groups_ChemGroup { } } /* harmony default export */ const groups_BondsGroup = (BondsGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/BondsCylinderGroup.js +;// ./src/gfx/modes/groups/BondsCylinderGroup.js class BondsCylinderGroup extends groups_BondsGroup { @@ -18690,7 +18734,7 @@ class BondsCylinderGroup extends groups_BondsGroup { } } /* harmony default export */ const groups_BondsCylinderGroup = (BondsCylinderGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/BondsLinesGroup.js +;// ./src/gfx/modes/groups/BondsLinesGroup.js const STEP_SIZE = 0.15; @@ -18801,7 +18845,7 @@ class BondsLinesGroup extends groups_BondsGroup { } } /* harmony default export */ const groups_BondsLinesGroup = (BondsLinesGroup); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/groups.js +;// ./src/gfx/modes/groups/groups.js @@ -18828,7 +18872,7 @@ class BondsLinesGroup extends groups_BondsGroup { BondsCylinderGroup: groups_BondsCylinderGroup, BondsLinesGroup: groups_BondsLinesGroup }); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/AtomsProcessor.js +;// ./src/gfx/modes/processors/AtomsProcessor.js class AtomsProcessor extends gfx_RCGroup { constructor(AtomsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -18882,7 +18926,7 @@ class AtomsProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_AtomsProcessor = (AtomsProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/OrphanAtomsProcessor.js +;// ./src/gfx/modes/processors/OrphanAtomsProcessor.js class OrphanAtomsProcessor extends processors_AtomsProcessor { _checkAtom(atom, mask) { @@ -18901,7 +18945,7 @@ class OrphanAtomsProcessor extends processors_AtomsProcessor { } } /* harmony default export */ const processors_OrphanAtomsProcessor = (OrphanAtomsProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/ResiduesProcessor.js +;// ./src/gfx/modes/processors/ResiduesProcessor.js class ResiduesProcessor extends gfx_RCGroup { constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -18953,7 +18997,7 @@ class ResiduesProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_ResiduesProcessor = (ResiduesProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/NucleicProcessor.js +;// ./src/gfx/modes/processors/NucleicProcessor.js class NucleicProcessor extends processors_ResiduesProcessor { _checkResidue(residue, mask) { @@ -18961,7 +19005,7 @@ class NucleicProcessor extends processors_ResiduesProcessor { } } /* harmony default export */ const processors_NucleicProcessor = (NucleicProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/SubseqsProcessor.js +;// ./src/gfx/modes/processors/SubseqsProcessor.js class SubseqsProcessor extends gfx_RCGroup { constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -19015,7 +19059,7 @@ class SubseqsProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_SubseqsProcessor = (SubseqsProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/BondsProcessor.js +;// ./src/gfx/modes/processors/BondsProcessor.js class BondsProcessor extends gfx_RCGroup { constructor(BondsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -19067,7 +19111,7 @@ class BondsProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_BondsProcessor = (BondsProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/AromaticProcessor.js +;// ./src/gfx/modes/processors/AromaticProcessor.js class AromaticProcessor extends gfx_RCGroup { constructor(AromaticGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) { @@ -19127,7 +19171,7 @@ class AromaticProcessor extends gfx_RCGroup { } } /* harmony default export */ const processors_AromaticProcessor = (AromaticProcessor); -;// CONCATENATED MODULE: ./src/gfx/modes/processors/processors.js +;// ./src/gfx/modes/processors/processors.js @@ -19144,7 +19188,7 @@ class AromaticProcessor extends gfx_RCGroup { Bonds: processors_BondsProcessor, Aromatic: processors_AromaticProcessor }); -;// CONCATENATED MODULE: ./src/gfx/modes/groups/GroupsFactory.js +;// ./src/gfx/modes/groups/GroupsFactory.js @@ -19212,7 +19256,7 @@ class GroupsFactory { } } /* harmony default export */ const groups_GroupsFactory = (GroupsFactory); -;// CONCATENATED MODULE: ./src/gfx/modes/Mode.js +;// ./src/gfx/modes/Mode.js @@ -19242,7 +19286,7 @@ class Mode { * Mode options inherited (prototyped) from defaults. * @type {object} */ - this.opts = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts); + this.opts = __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts); } /** @@ -19253,7 +19297,7 @@ class Mode { */ identify() { const diff = utils.objectsDiff(this.opts, this.settings.now.modes[this.id]); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(diff)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(diff)) { return [this.id, diff]; } return this.id; @@ -19267,7 +19311,7 @@ class Mode { for (let i = 0; i < groupCount; ++i) { let currGroup = groupList[i]; let renderParams = {}; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArray(currGroup)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isArray(currGroup)) { renderParams = currGroup[1].call(this); [currGroup] = currGroup; } @@ -19294,7 +19338,7 @@ Mode.prototype.id = '__'; */ Mode.prototype.depGroups = []; /* harmony default export */ const modes_Mode = (Mode); -;// CONCATENATED MODULE: ./src/gfx/modes/LinesMode.js +;// ./src/gfx/modes/LinesMode.js function getRenderParams() { return { @@ -19332,8 +19376,7 @@ LinesMode.prototype.name = 'Lines'; LinesMode.prototype.shortName = 'Lines'; LinesMode.prototype.depGroups = ['ALoopsLines', 'BondsLines', 'OrphanedAtomsCrosses']; /* harmony default export */ const modes_LinesMode = (LinesMode); -;// CONCATENATED MODULE: ./src/gfx/modes/LicoriceMode.js -/* eslint-disable no-magic-numbers */ +;// ./src/gfx/modes/LicoriceMode.js class LicoriceMode extends modes_Mode { static id = 'LC'; @@ -19361,8 +19404,7 @@ LicoriceMode.prototype.name = 'Licorice'; LicoriceMode.prototype.shortName = 'Licorice'; LicoriceMode.prototype.depGroups = ['AtomsSpheres', 'BondsCylinders', 'ALoopsTorus']; /* harmony default export */ const modes_LicoriceMode = (LicoriceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/BallsAndSticksMode.js -/* eslint-disable no-magic-numbers */ +;// ./src/gfx/modes/BallsAndSticksMode.js class BallsAndSticksMode extends modes_Mode { static id = 'BS'; @@ -19390,7 +19432,7 @@ BallsAndSticksMode.prototype.name = 'Balls and Sticks'; BallsAndSticksMode.prototype.shortName = 'Balls'; BallsAndSticksMode.prototype.depGroups = ['AtomsSpheres', 'BondsCylinders', 'ALoopsTorus']; /* harmony default export */ const modes_BallsAndSticksMode = (BallsAndSticksMode); -;// CONCATENATED MODULE: ./src/gfx/modes/VanDerWaalsMode.js +;// ./src/gfx/modes/VanDerWaalsMode.js class VanDerWaalsMode extends modes_Mode { static id = 'VW'; @@ -19403,7 +19445,7 @@ VanDerWaalsMode.prototype.name = 'Van der Waals'; VanDerWaalsMode.prototype.shortName = 'VDW'; VanDerWaalsMode.prototype.depGroups = ['AtomsSpheres']; /* harmony default export */ const modes_VanDerWaalsMode = (VanDerWaalsMode); -;// CONCATENATED MODULE: ./src/gfx/modes/TraceMode.js +;// ./src/gfx/modes/TraceMode.js class TraceMode extends modes_Mode { static id = 'TR'; @@ -19416,7 +19458,7 @@ TraceMode.prototype.name = 'Trace'; TraceMode.prototype.shortName = 'Trace'; TraceMode.prototype.depGroups = ['TraceChains']; /* harmony default export */ const modes_TraceMode = (TraceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/TubeMode.js +;// ./src/gfx/modes/TubeMode.js class TubeMode extends modes_Mode { @@ -19441,7 +19483,7 @@ TubeMode.prototype.name = 'Tube'; TubeMode.prototype.shortName = 'Tube'; TubeMode.prototype.depGroups = ['CartoonChains']; /* harmony default export */ const modes_TubeMode = (TubeMode); -;// CONCATENATED MODULE: ./src/gfx/modes/CartoonMode.js +;// ./src/gfx/modes/CartoonMode.js class CartoonMode extends modes_Mode { @@ -19524,7 +19566,7 @@ CartoonMode.prototype.name = 'Cartoon'; CartoonMode.prototype.shortName = 'Cartoon'; CartoonMode.prototype.depGroups = ['CartoonChains', 'NucleicSpheres', 'NucleicCylinders']; /* harmony default export */ const modes_CartoonMode = (CartoonMode); -;// CONCATENATED MODULE: ./src/gfx/modes/SurfaceMode.js +;// ./src/gfx/modes/SurfaceMode.js const { @@ -19563,7 +19605,7 @@ class SurfaceMode extends modes_Mode { SurfaceMode.prototype.isSurface = true; SurfaceMode.prototype.surfaceNames = []; /* harmony default export */ const modes_SurfaceMode = (SurfaceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/QuickSurfaceMode.js +;// ./src/gfx/modes/QuickSurfaceMode.js class QuickSurfaceMode extends modes_SurfaceMode { static id = 'QS'; @@ -19584,7 +19626,7 @@ QuickSurfaceMode.prototype.name = 'Quick Surface'; QuickSurfaceMode.prototype.shortName = 'Quick Surf'; QuickSurfaceMode.prototype.surfaceNames = ['QuickSurfGeo']; /* harmony default export */ const modes_QuickSurfaceMode = (QuickSurfaceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/IsoSurfaceMode.js +;// ./src/gfx/modes/IsoSurfaceMode.js class IsoSurfaceMode extends modes_SurfaceMode { constructor(excludeProbe, opts) { @@ -19612,7 +19654,7 @@ IsoSurfaceMode.prototype.surfaceNames = ['SASSESSurfaceGeo']; IsoSurfaceMode.prototype._radScale = 1; IsoSurfaceMode.prototype._excludeProbe = false; /* harmony default export */ const modes_IsoSurfaceMode = (IsoSurfaceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/IsoSurfaceSASMode.js +;// ./src/gfx/modes/IsoSurfaceSASMode.js class IsoSurfaceSASMode extends modes_IsoSurfaceMode { static id = 'SA'; @@ -19624,7 +19666,7 @@ IsoSurfaceSASMode.prototype.id = 'SA'; IsoSurfaceSASMode.prototype.name = 'Solvent Accessible Surface'; IsoSurfaceSASMode.prototype.shortName = 'SAS'; /* harmony default export */ const modes_IsoSurfaceSASMode = (IsoSurfaceSASMode); -;// CONCATENATED MODULE: ./src/gfx/modes/IsoSurfaceSESMode.js +;// ./src/gfx/modes/IsoSurfaceSESMode.js class IsoSurfaceSESMode extends modes_IsoSurfaceMode { static id = 'SE'; @@ -19636,7 +19678,7 @@ IsoSurfaceSESMode.prototype.id = 'SE'; IsoSurfaceSESMode.prototype.name = 'Solvent Excluded Surface'; IsoSurfaceSESMode.prototype.shortName = 'SES'; /* harmony default export */ const modes_IsoSurfaceSESMode = (IsoSurfaceSESMode); -;// CONCATENATED MODULE: ./src/gfx/modes/ContactSurfaceMode.js +;// ./src/gfx/modes/ContactSurfaceMode.js class ContactSurfaceMode extends modes_SurfaceMode { static id = 'CS'; @@ -19659,7 +19701,7 @@ ContactSurfaceMode.prototype.shortName = 'Contact Surf'; ContactSurfaceMode.prototype.isSurface = true; ContactSurfaceMode.prototype.surfaceNames = ['ContactSurfaceGeo']; /* harmony default export */ const modes_ContactSurfaceMode = (ContactSurfaceMode); -;// CONCATENATED MODULE: ./src/gfx/modes/TextMode.js +;// ./src/gfx/modes/TextMode.js class TextMode extends modes_Mode { @@ -19668,7 +19710,7 @@ class TextMode extends modes_Mode { return this.opts.template; } getLabelOpts() { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge(this.opts, { + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge(this.opts, { colors: true, adjustColor: true, transparent: true @@ -19680,7 +19722,7 @@ TextMode.prototype.name = 'Text mode'; TextMode.prototype.shortName = 'Text'; TextMode.prototype.depGroups = ['TextLabelsGeo']; /* harmony default export */ const modes_TextMode = (TextMode); -;// CONCATENATED MODULE: ./src/gfx/modes.js +;// ./src/gfx/modes.js @@ -19696,7 +19738,7 @@ TextMode.prototype.depGroups = ['TextLabelsGeo']; const modes = new utils_EntityList([modes_LinesMode, modes_LicoriceMode, modes_BallsAndSticksMode, modes_VanDerWaalsMode, modes_TraceMode, modes_TubeMode, modes_CartoonMode, modes_QuickSurfaceMode, modes_IsoSurfaceSASMode, modes_IsoSurfaceSESMode, modes_ContactSurfaceMode, modes_TextMode]); /* harmony default export */ const gfx_modes = (modes); -;// CONCATENATED MODULE: ./src/gfx/palettes/Palette.js +;// ./src/gfx/palettes/Palette.js function clamp(x, a, b) { return x <= b ? x < 0 ? 0 : x : b; @@ -19719,13 +19761,11 @@ class Palette { this.name = name || 'Custom'; this.id = id || 'CP'; } - getElementColor(name) { - let asIs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; + getElementColor(name, asIs = false) { const color = this.elementColors[name]; return color === undefined && !asIs ? this.defaultElementColor : color; } - getResidueColor(name) { - let asIs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; + getResidueColor(name, asIs = false) { const color = this.residueColors[name]; return color === undefined && !asIs ? this.defaultResidueColor : color; } @@ -19734,8 +19774,7 @@ class Palette { chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F) % this.chainColors.length; return this.chainColors[chain]; } - getSecondaryColor(type) { - let asIs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; + getSecondaryColor(type, asIs = false) { const color = this.secondaryColors[type]; return color === undefined && !asIs ? this.defaultSecondaryColor : color; } @@ -19758,13 +19797,12 @@ class Palette { left = clamp(left, 0, count - 1); return lerpColor(gradient[left], gradient[right], index - left); } - getNamedColor(name) { - let asIs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; + getNamedColor(name, asIs = false) { const color = this.namedColors[name]; return color === undefined && !asIs ? this.defaultNamedColor : color; } } -external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].assign(Palette.prototype, { +__WEBPACK_EXTERNAL_MODULE_lodash_default__.assign(Palette.prototype, { colors: [0xFFFFFF, 0xFF0000, 0x00FF00, 0x0000FF, 0x808080], minRangeColor: 0x000000, midRangeColor: 0x7F7F7F, @@ -19782,8 +19820,6 @@ external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespac ['indianred', 0xcd5c5c], ['lightcoral', 0xf08080], ['salmon', 0xfa8072], ['darksalmon', 0xe9967a], ['lightsalmon', 0xffa07a], ['crimson', 0xdc143c], ['red', 0xff0000], ['firebrick', 0xb22222], ['darkred', 0x8b0000], ['pink', 0xffc0cb], ['lightpink', 0xffb6c1], ['hotpink', 0xff69b4], ['deeppink', 0xff1493], ['mediumvioletred', 0xc71585], ['palevioletred', 0xdb7093], ['coral', 0xff7f50], ['tomato', 0xff6347], ['orangered', 0xff4500], ['darkorange', 0xff8c00], ['orange', 0xffa500], ['gold', 0xffd700], ['yellow', 0xffff00], ['lightyellow', 0xffffe0], ['lemonchiffon', 0xfffacd], ['lightgoldenrodyellow', 0xfafad2], ['papayawhip', 0xffefd5], ['moccasin', 0xffe4b5], ['peachpuff', 0xffdab9], ['palegoldenrod', 0xeee8aa], ['khaki', 0xf0e68c], ['darkkhaki', 0xbdb76b], ['lavender', 0xe6e6fa], ['thistle', 0xd8bfd8], ['plum', 0xdda0dd], ['violet', 0xee82ee], ['orchid', 0xda70d6], ['fuchsia', 0xff00ff], ['magenta', 0xff00ff], ['mediumorchid', 0xba55d3], ['mediumpurple', 0x9370db], ['rebeccapurple', 0x663399], ['blueviolet', 0x8a2be2], ['darkviolet', 0x9400d3], ['darkorchid', 0x9932cc], ['darkmagenta', 0x8b008b], ['purple', 0x800080], ['indigo', 0x4b0082], ['slateblue', 0x6a5acd], ['mediumslateblue', 0x7b68ee], ['darkslateblue', 0x483d8b], ['greenyellow', 0xadff2f], ['chartreuse', 0x7fff00], ['lawngreen', 0x7cfc00], ['lime', 0x00ff00], ['limegreen', 0x32cd32], ['palegreen', 0x98fb98], ['lightgreen', 0x90ee90], ['mediumspringgreen', 0x00fa9a], ['springgreen', 0x00ff7f], ['mediumseagreen', 0x3cb371], ['seagreen', 0x2e8b57], ['forestgreen', 0x228b22], ['green', 0x008000], ['darkgreen', 0x006400], ['yellowgreen', 0x9acd32], ['olivedrab', 0x6b8e23], ['olive', 0x808000], ['darkolivegreen', 0x556b2f], ['mediumaquamarine', 0x66cdaa], ['darkseagreen', 0x8fbc8f], ['lightseagreen', 0x20b2aa], ['darkcyan', 0x008b8b], ['teal', 0x008080], ['aqua', 0x00ffff], ['cyan', 0x00ffff], ['lightcyan', 0xe0ffff], ['paleturquoise', 0xafeeee], ['aquamarine', 0x7fffd4], ['turquoise', 0x40e0d0], ['mediumturquoise', 0x48d1cc], ['darkturquoise', 0x00ced1], ['cadetblue', 0x5f9ea0], ['steelblue', 0x4682b4], ['lightsteelblue', 0xb0c4de], ['powderblue', 0xb0e0e6], ['lightblue', 0xadd8e6], ['skyblue', 0x87ceeb], ['lightskyblue', 0x87cefa], ['deepskyblue', 0x00bfff], ['dodgerblue', 0x1e90ff], ['cornflowerblue', 0x6495ed], ['royalblue', 0x4169e1], ['blue', 0x0000ff], ['mediumblue', 0x0000cd], ['darkblue', 0x00008b], ['navy', 0x000080], ['midnightblue', 0x191970], ['cornsilk', 0xfff8dc], ['blanchedalmond', 0xffebcd], ['bisque', 0xffe4c4], ['navajowhite', 0xffdead], ['wheat', 0xf5deb3], ['burlywood', 0xdeb887], ['tan', 0xd2b48c], ['rosybrown', 0xbc8f8f], ['sandybrown', 0xf4a460], ['goldenrod', 0xdaa520], ['darkgoldenrod', 0xb8860b], ['peru', 0xcd853f], ['chocolate', 0xd2691e], ['saddlebrown', 0x8b4513], ['sienna', 0xa0522d], ['brown', 0xa52a2a], ['maroon', 0x800000], ['white', 0xffffff], ['snow', 0xfffafa], ['honeydew', 0xf0fff0], ['mintcream', 0xf5fffa], ['azure', 0xf0ffff], ['aliceblue', 0xf0f8ff], ['ghostwhite', 0xf8f8ff], ['whitesmoke', 0xf5f5f5], ['seashell', 0xfff5ee], ['beige', 0xf5f5dc], ['oldlace', 0xfdf5e6], ['floralwhite', 0xfffaf0], ['ivory', 0xfffff0], ['antiquewhite', 0xfaebd7], ['linen', 0xfaf0e6], ['lavenderblush', 0xfff0f5], ['mistyrose', 0xffe4e1], ['gainsboro', 0xdcdcdc], ['lightgray', 0xd3d3d3], ['silver', 0xc0c0c0], ['darkgray', 0xa9a9a9], ['gray', 0x808080], ['dimgray', 0x696969], ['lightslategray', 0x778899], ['slategray', 0x708090], ['darkslategray', 0x2f4f4f], ['black', 0x000000] /* eslint-enable no-multi-spaces */], namedColors: {}, - /* eslint-enable no-magic-numbers */ - gradients: { rainbow: [0x0000ff, // blue @@ -19844,13 +19880,12 @@ for (let i = 0, { namedColors[name] = value; } /* harmony default export */ const palettes_Palette = (Palette); -;// CONCATENATED MODULE: ./src/gfx/palettes/cpkPalette.js +;// ./src/gfx/palettes/cpkPalette.js const palette = new palettes_Palette('CPK', 'CP'); // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. palette.elementColors = { - /* eslint-disable no-magic-numbers */ H: 0xFFFFFF, C: 0x202020, N: 0x2060FF, @@ -19865,15 +19900,13 @@ palette.elementColors = { CU: 0xD0D0D0, BR: 0x008800, I: 0x005500 - /* eslint-enable no-magic-numbers */ }; /* harmony default export */ const cpkPalette = (palette); -;// CONCATENATED MODULE: ./src/gfx/palettes/jmolPalette.js +;// ./src/gfx/palettes/jmolPalette.js const jmolPalette_palette = new palettes_Palette('Jmol', 'JM'); -jmolPalette_palette.colors = [/* eslint-disable no-magic-numbers */ -0x0000FF, +jmolPalette_palette.colors = [0x0000FF, // blue 0x0055FF, // @@ -19908,11 +19941,10 @@ jmolPalette_palette.colors = [/* eslint-disable no-magic-numbers */ 0xAB00FF, // 0x5500FF // -/* eslint-enable no-magic-numbers */]; +]; // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. jmolPalette_palette.elementColors = { - /* eslint-disable no-magic-numbers */ H: 0xFFFFFF, D: 0xFFFFC0, T: 0xFFFFA0, @@ -20024,13 +20056,11 @@ jmolPalette_palette.elementColors = { BH: 0xE00038, HS: 0xE6002E, MT: 0xEB0026 - /* eslint-enable no-magic-numbers */ }; jmolPalette_palette.defaultResidueColor = 0xBEA06E; // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py. jmolPalette_palette.residueColors = { - /* eslint-disable no-magic-numbers */ ALA: 0xC8C8C8, ARG: 0x145AFF, ASN: 0x00DCDC, @@ -20069,7 +20099,6 @@ jmolPalette_palette.residueColors = { '+I': 0x80FFFF, '+T': 0xA0FFA0, '+U': 0xFF8080 - /* eslint-enable no-magic-numbers */ }; jmolPalette_palette.chainColors = [ // ' '->0 'A'->1, 'B'->2 @@ -20141,12 +20170,11 @@ jmolPalette_palette.secondaryColors = { rna: 0xFD0162 }; /* harmony default export */ const jmolPalette = (jmolPalette_palette); -;// CONCATENATED MODULE: ./src/gfx/palettes/vmdPalette.js +;// ./src/gfx/palettes/vmdPalette.js const vmdPalette_palette = new palettes_Palette('VMD', 'VM'); -vmdPalette_palette.colors = [/* eslint-disable no-magic-numbers */ -0x0000FF, +vmdPalette_palette.colors = [0x0000FF, // blue 0xFF0000, // red @@ -20177,25 +20205,22 @@ vmdPalette_palette.colors = [/* eslint-disable no-magic-numbers */ 0x804D00, // ochre 0x8080C0 // ice blue -/* eslint-enable no-magic-numbers */]; +]; vmdPalette_palette.defaultElementColor = 0x804D00; // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py. vmdPalette_palette.elementColors = { - /* eslint-disable no-magic-numbers */ H: 0xFFFFFF, C: 0x40BFBF, N: 0x0000FF, O: 0xFF0000, P: 0x808033, S: 0xFFFF00 - /* eslint-enable no-magic-numbers */ }; vmdPalette_palette.defaultResidueColor = 0x40C0C0; // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py. vmdPalette_palette.residueColors = { - /* eslint-disable no-magic-numbers */ ALA: 0x0000FF, ARG: 0xFFFFFF, ASN: 0x808033, @@ -20234,7 +20259,6 @@ vmdPalette_palette.residueColors = { WAT: 0x40C0C0, H2O: 0x40C0C0, HOH: 0x40C0C0 - /* eslint-enable no-magic-numbers */ }; vmdPalette_palette.chainColors = [0xFFFFFF].concat(vmdPalette_palette.colors); const vmdPalette_StructuralElementType = chem_StructuralElement.Type; @@ -20247,14 +20271,14 @@ vmdPalette_palette.secondaryColors = { [vmdPalette_StructuralElementType.TURN]: 0x40C0C0 }; /* harmony default export */ const vmdPalette = (vmdPalette_palette); -;// CONCATENATED MODULE: ./src/gfx/palettes.js +;// ./src/gfx/palettes.js const palettes = new utils_EntityList([cpkPalette, jmolPalette, vmdPalette]); /* harmony default export */ const gfx_palettes = (palettes); -;// CONCATENATED MODULE: ./src/gfx/colorers/Colorer.js +;// ./src/gfx/colorers/Colorer.js @@ -20283,7 +20307,7 @@ class Colorer { * Colorer options inherited (prototyped) from defaults. * @type {object} */ - this.opts = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge(utils.deriveDeep(settings.now.colorers[this.id], true), opts); + this.opts = __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge(utils.deriveDeep(settings.now.colorers[this.id], true), opts); /** * Palette in use. * @type {Palette} @@ -20299,7 +20323,7 @@ class Colorer { */ identify() { const diff = utils.objectsDiff(this.opts, settings.now.colorers[this.id]); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(diff)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(diff)) { return [this.id, diff]; } return this.id; @@ -20313,7 +20337,7 @@ class Colorer { Colorer.prototype.id = '__'; /* harmony default export */ const colorers_Colorer = (Colorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ElementColorer.js +;// ./src/gfx/colorers/ElementColorer.js /** @@ -20345,7 +20369,7 @@ ElementColorer.prototype.id = 'EL'; ElementColorer.prototype.name = 'Element'; ElementColorer.prototype.shortName = 'Element'; /* harmony default export */ const colorers_ElementColorer = (ElementColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ResidueTypeColorer.js +;// ./src/gfx/colorers/ResidueTypeColorer.js /** @@ -20369,7 +20393,7 @@ ResidueTypeColorer.prototype.id = 'RT'; ResidueTypeColorer.prototype.name = 'Residue Type'; ResidueTypeColorer.prototype.shortName = 'Residue'; /* harmony default export */ const colorers_ResidueTypeColorer = (ResidueTypeColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/SequenceColorer.js +;// ./src/gfx/colorers/SequenceColorer.js class SequenceColorer extends colorers_Colorer { static id = 'SQ'; @@ -20390,7 +20414,7 @@ SequenceColorer.prototype.id = 'SQ'; SequenceColorer.prototype.name = 'Sequence'; SequenceColorer.prototype.shortName = 'Sequence'; /* harmony default export */ const colorers_SequenceColorer = (SequenceColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ChainColorer.js +;// ./src/gfx/colorers/ChainColorer.js class ChainColorer extends colorers_Colorer { static id = 'CH'; @@ -20405,7 +20429,7 @@ ChainColorer.prototype.id = 'CH'; ChainColorer.prototype.name = 'Chain'; ChainColorer.prototype.shortName = 'Chain'; /* harmony default export */ const colorers_ChainColorer = (ChainColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/SecondaryStructureColorer.js +;// ./src/gfx/colorers/SecondaryStructureColorer.js class SecondaryStructureColorer extends colorers_Colorer { @@ -20435,7 +20459,7 @@ SecondaryStructureColorer.prototype.id = 'SS'; SecondaryStructureColorer.prototype.name = 'Secondary Structure'; SecondaryStructureColorer.prototype.shortName = 'Structure'; /* harmony default export */ const colorers_SecondaryStructureColorer = (SecondaryStructureColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/UniformColorer.js +;// ./src/gfx/colorers/UniformColorer.js class UniformColorer extends colorers_Colorer { static id = 'UN'; @@ -20450,7 +20474,7 @@ UniformColorer.prototype.id = 'UN'; UniformColorer.prototype.name = 'Uniform'; UniformColorer.prototype.shortName = 'Uniform'; /* harmony default export */ const colorers_UniformColorer = (UniformColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ConditionalColorer.js +;// ./src/gfx/colorers/ConditionalColorer.js @@ -20489,7 +20513,7 @@ ConditionalColorer.prototype.id = 'CO'; ConditionalColorer.prototype.name = 'Conditional'; ConditionalColorer.prototype.shortName = 'Conditional'; /* harmony default export */ const colorers_ConditionalColorer = (ConditionalColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/ConformationColorer.js +;// ./src/gfx/colorers/ConformationColorer.js class ConformationColorer extends colorers_Colorer { static id = 'CF'; @@ -20504,7 +20528,7 @@ ConformationColorer.prototype.id = 'CF'; ConformationColorer.prototype.name = 'Conformation'; ConformationColorer.prototype.shortName = 'Conformation'; /* harmony default export */ const colorers_ConformationColorer = (ConformationColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/TemperatureColorer.js +;// ./src/gfx/colorers/TemperatureColorer.js /** @@ -20559,7 +20583,7 @@ TemperatureColorer.prototype.id = 'TM'; // [T]e[M]perature TemperatureColorer.prototype.name = 'Temperature'; TemperatureColorer.prototype.shortName = 'Temperature'; /* harmony default export */ const colorers_TemperatureColorer = (TemperatureColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/OccupancyColorer.js +;// ./src/gfx/colorers/OccupancyColorer.js /** @@ -20600,7 +20624,7 @@ OccupancyColorer.prototype.id = 'OC'; // [OC]cupancy OccupancyColorer.prototype.name = 'Occupancy'; OccupancyColorer.prototype.shortName = 'Occupancy'; /* harmony default export */ const colorers_OccupancyColorer = (OccupancyColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/HydrophobicityColorer.js +;// ./src/gfx/colorers/HydrophobicityColorer.js class HydrophobicityColorer extends colorers_Colorer { static id = 'HY'; @@ -20622,7 +20646,7 @@ HydrophobicityColorer.prototype.id = 'HY'; HydrophobicityColorer.prototype.name = 'Hydrophobicity'; HydrophobicityColorer.prototype.shortName = 'Hydrophobicity'; /* harmony default export */ const colorers_HydrophobicityColorer = (HydrophobicityColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/MoleculeColorer.js +;// ./src/gfx/colorers/MoleculeColorer.js class MoleculeColorer extends colorers_Colorer { static id = 'MO'; @@ -20642,7 +20666,7 @@ MoleculeColorer.prototype.id = 'MO'; MoleculeColorer.prototype.name = 'Molecule'; MoleculeColorer.prototype.shortName = 'Molecule'; /* harmony default export */ const colorers_MoleculeColorer = (MoleculeColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers/CarbonColorer.js +;// ./src/gfx/colorers/CarbonColorer.js function scaleColor(c, factor) { @@ -20680,7 +20704,7 @@ CarbonColorer.prototype.id = 'CB'; CarbonColorer.prototype.name = 'Carbon'; CarbonColorer.prototype.shortName = 'Carbon'; /* harmony default export */ const colorers_CarbonColorer = (CarbonColorer); -;// CONCATENATED MODULE: ./src/gfx/colorers.js +;// ./src/gfx/colorers.js @@ -20697,7 +20721,7 @@ CarbonColorer.prototype.shortName = 'Carbon'; const colorers = new utils_EntityList([colorers_ElementColorer, colorers_ResidueTypeColorer, colorers_SequenceColorer, colorers_ChainColorer, colorers_SecondaryStructureColorer, colorers_UniformColorer, colorers_ConditionalColorer, colorers_ConformationColorer, colorers_TemperatureColorer, colorers_OccupancyColorer, colorers_HydrophobicityColorer, colorers_MoleculeColorer, colorers_CarbonColorer]); /* harmony default export */ const gfx_colorers = (colorers); -;// CONCATENATED MODULE: ./src/gfx/materials.js +;// ./src/gfx/materials.js function neutralColor(intensity) { @@ -20858,7 +20882,7 @@ const materialList = [{ }]; const materials = new utils_EntityList(materialList); /* harmony default export */ const gfx_materials = (materials); -;// CONCATENATED MODULE: ./src/gfx/meshutils.js +;// ./src/gfx/meshutils.js /** * Utils functions which is worked with meshes * @@ -21060,7 +21084,7 @@ function countTriangles(group) { forEachMeshInGroup, countTriangles }); -;// CONCATENATED MODULE: ./src/gfx/Representation.js +;// ./src/gfx/Representation.js @@ -21205,7 +21229,7 @@ class Representation { // modify mode if (repSettings.mode) { const newMode = repSettings.mode; - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEqual(this.mode.identify(), newMode)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEqual(this.mode.identify(), newMode)) { diff.mode = newMode; this.setMode(mode); } @@ -21214,7 +21238,7 @@ class Representation { // modify colorer if (repSettings.colorer) { const newColorer = repSettings.colorer; - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEqual(this.colorer.identify(), newColorer)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEqual(this.colorer.identify(), newColorer)) { diff.colorer = newColorer; this.colorer = color; } @@ -21223,7 +21247,7 @@ class Representation { // modify material if (repSettings.material) { const newMaterial = repSettings.material; - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEqual(this.materialPreset.id, newMaterial)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEqual(this.materialPreset.id, newMaterial)) { diff.material = newMaterial; this.setMaterialPreset(gfx_materials.get(repSettings.material)); } @@ -21241,7 +21265,7 @@ class Representation { } } /* harmony default export */ const gfx_Representation = (Representation); -;// CONCATENATED MODULE: ./src/ComplexVisualEdit.js +;// ./src/ComplexVisualEdit.js @@ -21561,7 +21585,7 @@ class ComplexFragmentEditor extends ComplexEditor { ComponentEditor: ComplexComponentEditor, FragmentEditor: ComplexFragmentEditor }); -;// CONCATENATED MODULE: ./src/ComplexVisual.js +;// ./src/ComplexVisual.js @@ -21748,7 +21772,7 @@ class ComplexVisual extends src_Visual { const diff = target.change(rep, this._complex, lookupAndCreate(gfx_modes, rep.mode), lookupAndCreate(gfx_colorers, rep.colorer)); // something was changed - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(diff)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(diff)) { target.needsRebuild = true; for (const key in diff) { if (diff.hasOwnProperty(key)) { @@ -21820,7 +21844,7 @@ class ComplexVisual extends src_Visual { // Fill in default values const def = settings.now.presets.default[0]; - const desc = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge({ + const desc = __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge({ selector: def.selector, mode: def.mode, colorer: def.colorer, @@ -22159,7 +22183,8 @@ class ComplexVisual extends src_Visual { throw e; } } - if (false) {} + if (false) // removed by dead control flow +{} } hasGeometry = errorOccured || hasGeometry || gfxutils.groupHasGeometryToRender(repr.geo); if (repr.geo) { @@ -22317,9 +22342,7 @@ class ComplexVisual extends src_Visual { finalizeEdit() { this._editor = null; } - setMaterialValues(values) { - let needTraverse = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; - let process = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : undefined; + setMaterialValues(values, needTraverse = false, process = undefined) { for (let i = 0, n = this._reprList.length; i < n; ++i) { const rep = this._reprList[i]; rep.material.setValues(values); @@ -22377,21 +22400,19 @@ class ComplexVisual extends src_Visual { // 32 bits = 30 bits for reps + 1 for selection + 1 for selection expansion ComplexVisual.NUM_REPRESENTATION_BITS = 30; /* harmony default export */ const src_ComplexVisual = (ComplexVisual); -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeFaces.vert -const VolumeFaces_namespaceObject = "varying vec3 pos;\r\n\r\nvoid main() {\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n pos = position.xyz + 0.5;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n}"; -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeFaces.frag -const gfx_shaders_VolumeFaces_namespaceObject = "varying vec3 pos;\r\n\r\nvoid main() {\r\n gl_FragColor = vec4(pos, 0.5);\r\n}"; -;// CONCATENATED MODULE: ./src/gfx/shaders/Volume.vert -const shaders_Volume_namespaceObject = "varying vec4 screenSpacePos;\r\n\r\nvoid main() {\r\n screenSpacePos = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n gl_Position = screenSpacePos;\r\n}"; -;// CONCATENATED MODULE: ./src/gfx/shaders/Volume.frag -const src_gfx_shaders_Volume_namespaceObject = "uniform mat4 projectionMatrix;\r\n\r\n// 3D volume texture\r\nuniform vec3 volumeDim; // volume dimensions, pixels\r\nuniform sampler2D tileTex; // tiled texture containing all Z-slices of a 3D data\r\nuniform vec2 tileTexSize; // size of tiled texture, pixels\r\nuniform vec2 tileStride; // UV stride between slices in tile tex, pixels\r\n\r\nuniform vec3 boxAngles;//value of angles({x: alpha, y:beta, z:gamma}) types 1 - if angle is obtuse, 0 - if acute\r\nuniform vec3 delta; //Projection box delta's from non-orthogonal origin axes; {x: XY, y : XZ, z: YZ}\r\n\r\nuniform vec3 _isoLevel0;\r\nuniform float _flipV;\r\nuniform sampler2D _BFLeft;\r\nuniform sampler2D _BFRight;\r\nuniform sampler2D _FFLeft;\r\nuniform sampler2D _FFRight;\r\nuniform sampler2D _WFFLeft;\r\nuniform sampler2D _WFFRight;\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\n#define NO_COLOR vec4(0., 0., 0., 0.)\r\n\r\nvec4 sample3DTexture(vec3 texCoord) {\r\n // a pair of Z slices is determined by nearest slice border\r\n float zSliceBorder = floor(texCoord.z * volumeDim.z + 0.5);\r\n float zSliceNumber1 = max(zSliceBorder - 1.0, 0.0);\r\n float zSliceNumber2 = min(zSliceBorder, volumeDim.z - 1.0);\r\n\r\n float rowTiles = floor(tileTexSize.x / tileStride.x);\r\n\r\n // calculate coords in tile texture for both slices\r\n vec2 tileOffset = vec2(mod(zSliceNumber1, rowTiles), floor(zSliceNumber1 / rowTiles));\r\n vec2 texCoordSlice1 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n tileOffset = vec2(mod(zSliceNumber2, rowTiles), floor(zSliceNumber2 / rowTiles));\r\n vec2 texCoordSlice2 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n\r\n // bilinear filtering\r\n vec4 colorSlice1 = texture2D(tileTex, texCoordSlice1);\r\n vec4 colorSlice2 = texture2D(tileTex, texCoordSlice2);\r\n float weightSlice2 = texCoord.z * volumeDim.z - (zSliceNumber1 + 0.5);\r\n return mix(colorSlice1, colorSlice2, weightSlice2);\r\n}\r\n\r\nvec4 sample3DTextureInclined(vec3 boxCoord) { // delta:{ x: XY, y : XZ, z: YZ }\r\n vec3 textCoord = boxCoord;\r\n vec2 currDelta = mix(boxCoord.zz, vec2(1., 1.) - boxCoord.zz, boxAngles.yx) * delta.yz;\r\n\r\n textCoord.y = (boxCoord.y - currDelta.y) / (1. - delta.z);\r\n if (textCoord.y < 0.0 || textCoord.y > 1.0)\r\n return NO_COLOR;\r\n\r\n currDelta.x += mix(textCoord.y, 1.0 - textCoord.y, boxAngles.z) * delta.x;\r\n\r\n textCoord.x = (boxCoord.x - currDelta.x) / (1. - delta.x - delta.y);\r\n if (textCoord.x < 0.0 || textCoord.x > 1.0)\r\n return NO_COLOR;\r\n\r\n return sample3DTexture(textCoord);\r\n}\r\n\r\nfloat CalcColor(vec3 iter, vec3 dir) {\r\n float d = 1. / 128.;\r\n vec3 dx = vec3(d, 0.0, 0.0);\r\n vec3 dy = vec3(0.0, d, 0.0);\r\n vec3 dz = vec3(0.0, 0.0, d);\r\n\r\n // #Opt: coordInc.x:(iter + dx).x > 1. ? 0.: sample3DTextureInclined(iter + dx).x,\r\n vec3 coordInc = mix(\r\n vec3(\r\n sample3DTextureInclined(iter + dx).x,\r\n sample3DTextureInclined(iter + dy).x,\r\n sample3DTextureInclined(iter + dz).x\r\n ),\r\n vec3(0. ,0. , 0.),\r\n vec3(floor((iter + dx).x), floor((iter + dy).y), floor((iter + dz).z))\r\n );\r\n\r\n // #Opt: coordDec.x:(iter - dx).x < 0. ? 0.: sample3DTextureInclined(iter - dx).x,\r\n vec3 coordDec = mix(\r\n vec3(0. ,0. , 0.),\r\n vec3(\r\n sample3DTextureInclined(iter - dx).x,\r\n sample3DTextureInclined(iter - dy).x,\r\n sample3DTextureInclined(iter - dz).x\r\n ),\r\n vec3(ceil((iter - dx).x), ceil((iter - dy).y), ceil((iter - dz).z))\r\n );\r\n\r\n vec3 N = normalize(coordInc - coordDec);\r\n float dif = max(0.0, dot(N, dir));\r\n return dif;\r\n}\r\n\r\nvec3 AccuracyIso(vec3 left, vec3 right, float volLeft, float threshold) {\r\n for (int i = 0; i < 5; i++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if ((volLeft - threshold) * (vol - threshold) < 0.)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec3 CorrectIso(vec3 left, vec3 right, float tr) {\r\n for (int j = 0; j < 5; j++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if (vol < tr)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec4 GetIso1(vec3 start, vec3 back, float molDist, vec3 dir, float tr, int count) {\r\n float vol, stepSize = (float(count) + 2.) / float(STEPS_COUNT);\r\n vec3 step = stepSize * dir, iterator = start, left, right;\r\n vec4 acc = NO_COLOR;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n vol = sample3DTextureInclined(iterator).r;\r\n if (length(iterator - back) <= stepSize || (vol > tr))\r\n break;\r\n }\r\n\r\n if (vol > tr)\r\n acc = vec4(CorrectIso(iterator, iterator - step, tr).xyz, 1.);\r\n\r\n return acc;\r\n}\r\n\r\nfloat easeOut(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return 1.0 - (1.0 - t) * (1.0 - t);\r\n}\r\n\r\nfloat easeIn(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return t * t;\r\n}\r\n\r\nvec3 GetColSimple(float vol) {\r\n float t = easeOut(_isoLevel0.x, _isoLevel0.y, vol);\r\n float s = easeIn(_isoLevel0.y, _isoLevel0.z, vol);\r\n return vec3(0.5, 0.6, 0.7) * (1.0 - t) + 2.0 * vec3(s, 0, 0);\r\n}\r\n\r\nvec4 VolRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 acc = NO_COLOR, iso;\r\n vec3 iterator = start, sumColor = vec3(0., 0., 0.);\r\n float stepSize, alpha, sumAlpha = 0.0, vol, curStepSize, molD;\r\n vec3 step, col, colOld, right;\r\n float tr0 = _isoLevel0.x;\r\n float dif, r, kd, finish;\r\n int count = 0, stopMol = 0;\r\n\r\n for (int k = 0; k < 3; k++) {\r\n stepSize = (float(k) + 2.) / float(STEPS_COUNT);\r\n kd = 140. * tr0 * stepSize;\r\n r = 1. - kd;\r\n step = stepSize * dir;\r\n iso = GetIso1(iterator, back, molDist, dir, tr0, k);\r\n if (iso.a < 0.1 || length(iso.xyz - start) > molDist)\r\n break;\r\n iterator = iso.xyz;\r\n dif = 1.;// CalcColor(iterator, dir);\r\n colOld = GetColSimple(tr0);\r\n curStepSize = stepSize;\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n molD = length(iterator - start);\r\n vol = sample3DTextureInclined(iterator).r;\r\n finish = distance(iterator, back) - stepSize;\r\n if (finish < 0.0 || vol < tr0 || (sumAlpha > 0.97) || molD > molDist)\r\n break;\r\n alpha = (1. - r);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4.* colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n colOld = col;\r\n } // for i\r\n\r\n if (finish < 0.0 || sumAlpha > 0.97)\r\n break;\r\n\r\n if (molD > molDist) {\r\n curStepSize = stepSize - (molD - molDist);\r\n right = iterator - (molD - molDist) * dir;\r\n vol = sample3DTextureInclined(right).r;\r\n } else {\r\n vec3 left = iterator - step;\r\n right = CorrectIso(left, iterator, tr0);\r\n curStepSize = distance(left, right);\r\n vol = tr0;\r\n }\r\n\r\n alpha = (1. - r) * curStepSize / stepSize;\r\n dif = 1.;// CalcColor(right, dir);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * curStepSize / stepSize * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4. * colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n\r\n if (molD > molDist)\r\n break;\r\n } // for k\r\n acc.rgb = 1. * sumColor / sumAlpha;\r\n acc.a = sumAlpha;\r\n return acc;\r\n}\r\n\r\nvec4 VolRender1(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n float stepSize = 1.0 / float(STEPS_COUNT);\r\n float len = length(back - start);\r\n vec3 step = stepSize * dir;\r\n vec3 iterator = start;\r\n float acc = 0.0;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n if (float(i) * stepSize > len)\r\n break;\r\n iterator = iterator + step;\r\n if (sample3DTextureInclined(iterator).r > _isoLevel0.x)\r\n acc += 10. * sample3DTextureInclined(iterator).r / float(STEPS_COUNT);\r\n }\r\n\r\n return vec4(1.,1.,1., acc);\r\n}\r\n\r\nvec4 IsoRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 tst = GetIso1(start, back, 2., dir, _isoLevel0.x, 0);\r\n vec4 col = NO_COLOR;\r\n\r\n if (length(tst.xyz - start) < molDist && tst.a > 0.1) {\r\n float dif = CalcColor(tst.xyz, dir);\r\n dif = 0.9 * dif * dif;\r\n col = vec4(dif, dif, dif, 1);\r\n }\r\n return col;\r\n}\r\n\r\nvec4 VolRender2(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n return sample3DTexture(start);\r\n}\r\n\r\nvoid main() {\r\n vec3 tc = screenSpacePos.xyz / screenSpacePos.w * 0.5 + 0.5;\r\n\r\n if (_flipV > 0.0) {\r\n tc.y = 1.0 - tc.y;\r\n }\r\n\r\n vec3 start;\r\n vec3 back;\r\n vec3 molBack;\r\n if (projectionMatrix[0][2] < 0.0) {\r\n start = texture2D(_FFLeft, tc.xy).xyz;\r\n back = texture2D(_BFLeft, tc.xy).xyz;\r\n molBack = texture2D(_WFFLeft, tc.xy).xyz;\r\n } else {\r\n start = texture2D(_FFRight, tc.xy).xyz;\r\n back = texture2D(_BFRight, tc.xy).xyz;\r\n molBack = texture2D(_WFFRight, tc.xy).xyz;\r\n }\r\n\r\n vec3 dir = normalize(back - start);\r\n\r\n float molDist = 2.0;\r\n if (length(molBack) > 0.001) {\r\n molDist = distance(start, molBack);\r\n }\r\n\r\n #ifdef ISO_MODE\r\n gl_FragColor = IsoRender(start, back, molDist, dir);\r\n #else\r\n gl_FragColor = VolRender(start, back, molDist, dir);\r\n #endif\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeFarPlane.vert -const VolumeFarPlane_namespaceObject = "varying vec4 volPos;\r\nuniform float aspectRatio;\r\nuniform float farZ;\r\nuniform float tanHalfFOV;\r\nuniform mat4 matWorld2Volume;\r\n\r\nvoid main() {\r\n // rescale plane to fill in the whole far plane area seen from camera\r\n vec3 pos = position.xyz;\r\n pos.x = pos.x * tanHalfFOV * farZ * aspectRatio;\r\n pos.y = pos.y * tanHalfFOV * farZ;\r\n // common transformation\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(pos, 1.0);\r\n // calc pos in volume CS\r\n volPos = matWorld2Volume * modelMatrix * vec4(pos, 1.0);\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n volPos = volPos + 0.5;\r\n volPos.w = 0.5;\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeFarPlane.frag -const gfx_shaders_VolumeFarPlane_namespaceObject = "varying vec4 volPos;\r\n\r\nvoid main() {\r\n gl_FragColor = volPos;\r\n}"; -;// CONCATENATED MODULE: ./src/gfx/shaders/VolumeMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/VolumeFaces.vert +const VolumeFaces_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec3 pos;\r\n\r\nvoid main() {\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n pos = position.xyz + 0.5;\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n}"; +;// ./src/gfx/shaders/VolumeFaces.frag +const gfx_shaders_VolumeFaces_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec3 pos;\r\n\r\nvoid main() {\r\n gl_FragColor = vec4(pos, 0.5);\r\n}"; +;// ./src/gfx/shaders/Volume.vert +const shaders_Volume_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\nvoid main() {\r\n screenSpacePos = projectionMatrix * modelViewMatrix * vec4(position, 1.0);\r\n gl_Position = screenSpacePos;\r\n}"; +;// ./src/gfx/shaders/Volume.frag +const src_gfx_shaders_Volume_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nuniform mat4 projectionMatrix;\r\n\r\n// 3D volume texture\r\nuniform vec3 volumeDim; // volume dimensions, pixels\r\nuniform sampler2D tileTex; // tiled texture containing all Z-slices of a 3D data\r\nuniform vec2 tileTexSize; // size of tiled texture, pixels\r\nuniform vec2 tileStride; // UV stride between slices in tile tex, pixels\r\n\r\nuniform vec3 boxAngles;//value of angles({x: alpha, y:beta, z:gamma}) types 1 - if angle is obtuse, 0 - if acute\r\nuniform vec3 delta; //Projection box delta's from non-orthogonal origin axes; {x: XY, y : XZ, z: YZ}\r\n\r\nuniform vec3 _isoLevel0;\r\nuniform float _flipV;\r\nuniform sampler2D _BFLeft;\r\nuniform sampler2D _BFRight;\r\nuniform sampler2D _FFLeft;\r\nuniform sampler2D _FFRight;\r\nuniform sampler2D _WFFLeft;\r\nuniform sampler2D _WFFRight;\r\n\r\nvarying vec4 screenSpacePos;\r\n\r\n#define NO_COLOR vec4(0., 0., 0., 0.)\r\n\r\nvec4 sample3DTexture(vec3 texCoord) {\r\n // a pair of Z slices is determined by nearest slice border\r\n float zSliceBorder = floor(texCoord.z * volumeDim.z + 0.5);\r\n float zSliceNumber1 = max(zSliceBorder - 1.0, 0.0);\r\n float zSliceNumber2 = min(zSliceBorder, volumeDim.z - 1.0);\r\n\r\n float rowTiles = floor(tileTexSize.x / tileStride.x);\r\n\r\n // calculate coords in tile texture for both slices\r\n vec2 tileOffset = vec2(mod(zSliceNumber1, rowTiles), floor(zSliceNumber1 / rowTiles));\r\n vec2 texCoordSlice1 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n tileOffset = vec2(mod(zSliceNumber2, rowTiles), floor(zSliceNumber2 / rowTiles));\r\n vec2 texCoordSlice2 = (texCoord.xy * volumeDim.xy + tileOffset * tileStride) / tileTexSize.xy;\r\n\r\n // bilinear filtering\r\n vec4 colorSlice1 = texture2D(tileTex, texCoordSlice1);\r\n vec4 colorSlice2 = texture2D(tileTex, texCoordSlice2);\r\n float weightSlice2 = texCoord.z * volumeDim.z - (zSliceNumber1 + 0.5);\r\n return mix(colorSlice1, colorSlice2, weightSlice2);\r\n}\r\n\r\nvec4 sample3DTextureInclined(vec3 boxCoord) { // delta:{ x: XY, y : XZ, z: YZ }\r\n vec3 textCoord = boxCoord;\r\n vec2 currDelta = mix(boxCoord.zz, vec2(1., 1.) - boxCoord.zz, boxAngles.yx) * delta.yz;\r\n\r\n textCoord.y = (boxCoord.y - currDelta.y) / (1. - delta.z);\r\n if (textCoord.y < 0.0 || textCoord.y > 1.0)\r\n return NO_COLOR;\r\n\r\n currDelta.x += mix(textCoord.y, 1.0 - textCoord.y, boxAngles.z) * delta.x;\r\n\r\n textCoord.x = (boxCoord.x - currDelta.x) / (1. - delta.x - delta.y);\r\n if (textCoord.x < 0.0 || textCoord.x > 1.0)\r\n return NO_COLOR;\r\n\r\n return sample3DTexture(textCoord);\r\n}\r\n\r\nfloat CalcColor(vec3 iter, vec3 dir) {\r\n float d = 1. / 128.;\r\n vec3 dx = vec3(d, 0.0, 0.0);\r\n vec3 dy = vec3(0.0, d, 0.0);\r\n vec3 dz = vec3(0.0, 0.0, d);\r\n\r\n // #Opt: coordInc.x:(iter + dx).x > 1. ? 0.: sample3DTextureInclined(iter + dx).x,\r\n vec3 coordInc = mix(\r\n vec3(\r\n sample3DTextureInclined(iter + dx).x,\r\n sample3DTextureInclined(iter + dy).x,\r\n sample3DTextureInclined(iter + dz).x\r\n ),\r\n vec3(0. ,0. , 0.),\r\n vec3(floor((iter + dx).x), floor((iter + dy).y), floor((iter + dz).z))\r\n );\r\n\r\n // #Opt: coordDec.x:(iter - dx).x < 0. ? 0.: sample3DTextureInclined(iter - dx).x,\r\n vec3 coordDec = mix(\r\n vec3(0. ,0. , 0.),\r\n vec3(\r\n sample3DTextureInclined(iter - dx).x,\r\n sample3DTextureInclined(iter - dy).x,\r\n sample3DTextureInclined(iter - dz).x\r\n ),\r\n vec3(ceil((iter - dx).x), ceil((iter - dy).y), ceil((iter - dz).z))\r\n );\r\n\r\n vec3 N = normalize(coordInc - coordDec);\r\n float dif = max(0.0, dot(N, dir));\r\n return dif;\r\n}\r\n\r\nvec3 AccuracyIso(vec3 left, vec3 right, float volLeft, float threshold) {\r\n for (int i = 0; i < 5; i++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if ((volLeft - threshold) * (vol - threshold) < 0.)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec3 CorrectIso(vec3 left, vec3 right, float tr) {\r\n for (int j = 0; j < 5; j++) {\r\n vec3 iterator = 0.5 * (left + right);\r\n float vol = sample3DTextureInclined(iterator).r;\r\n if (vol < tr)\r\n right = iterator;\r\n else\r\n left = iterator;\r\n }\r\n return 0.5 * (left + right);\r\n}\r\n\r\nvec4 GetIso1(vec3 start, vec3 back, float molDist, vec3 dir, float tr, int count) {\r\n float vol, stepSize = (float(count) + 2.) / float(STEPS_COUNT);\r\n vec3 step = stepSize * dir, iterator = start, left, right;\r\n vec4 acc = NO_COLOR;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n vol = sample3DTextureInclined(iterator).r;\r\n if (length(iterator - back) <= stepSize || (vol > tr))\r\n break;\r\n }\r\n\r\n if (vol > tr)\r\n acc = vec4(CorrectIso(iterator, iterator - step, tr).xyz, 1.);\r\n\r\n return acc;\r\n}\r\n\r\nfloat easeOut(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return 1.0 - (1.0 - t) * (1.0 - t);\r\n}\r\n\r\nfloat easeIn(float x0, float x1, float x) {\r\n float t = clamp((x - x0) / (x1 - x0), 0.0, 1.0);\r\n return t * t;\r\n}\r\n\r\nvec3 GetColSimple(float vol) {\r\n float t = easeOut(_isoLevel0.x, _isoLevel0.y, vol);\r\n float s = easeIn(_isoLevel0.y, _isoLevel0.z, vol);\r\n return vec3(0.5, 0.6, 0.7) * (1.0 - t) + 2.0 * vec3(s, 0, 0);\r\n}\r\n\r\nvec4 VolRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 acc = NO_COLOR, iso;\r\n vec3 iterator = start, sumColor = vec3(0., 0., 0.);\r\n float stepSize, alpha, sumAlpha = 0.0, vol, curStepSize, molD;\r\n vec3 step, col, colOld, right;\r\n float tr0 = _isoLevel0.x;\r\n float dif, r, kd, finish;\r\n int count = 0, stopMol = 0;\r\n\r\n for (int k = 0; k < 3; k++) {\r\n stepSize = (float(k) + 2.) / float(STEPS_COUNT);\r\n kd = 140. * tr0 * stepSize;\r\n r = 1. - kd;\r\n step = stepSize * dir;\r\n iso = GetIso1(iterator, back, molDist, dir, tr0, k);\r\n if (iso.a < 0.1 || length(iso.xyz - start) > molDist)\r\n break;\r\n iterator = iso.xyz;\r\n dif = 1.;// CalcColor(iterator, dir);\r\n colOld = GetColSimple(tr0);\r\n curStepSize = stepSize;\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n iterator = iterator + step;\r\n molD = length(iterator - start);\r\n vol = sample3DTextureInclined(iterator).r;\r\n finish = distance(iterator, back) - stepSize;\r\n if (finish < 0.0 || vol < tr0 || (sumAlpha > 0.97) || molD > molDist)\r\n break;\r\n alpha = (1. - r);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4.* colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n colOld = col;\r\n } // for i\r\n\r\n if (finish < 0.0 || sumAlpha > 0.97)\r\n break;\r\n\r\n if (molD > molDist) {\r\n curStepSize = stepSize - (molD - molDist);\r\n right = iterator - (molD - molDist) * dir;\r\n vol = sample3DTextureInclined(right).r;\r\n } else {\r\n vec3 left = iterator - step;\r\n right = CorrectIso(left, iterator, tr0);\r\n curStepSize = distance(left, right);\r\n vol = tr0;\r\n }\r\n\r\n alpha = (1. - r) * curStepSize / stepSize;\r\n dif = 1.;// CalcColor(right, dir);\r\n col = GetColSimple(vol);\r\n vol = sample3DTextureInclined(iterator - 0.5 * curStepSize / stepSize * step).r;\r\n vec3 colMid = GetColSimple(vol);\r\n sumColor += (1. - sumAlpha) * (colOld + 4. * colMid + col) * alpha / 6.;\r\n sumAlpha += (1. - sumAlpha) * alpha;// *(1. - 1.0*dif*dif);\r\n\r\n if (molD > molDist)\r\n break;\r\n } // for k\r\n acc.rgb = 1. * sumColor / sumAlpha;\r\n acc.a = sumAlpha;\r\n return acc;\r\n}\r\n\r\nvec4 VolRender1(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n float stepSize = 1.0 / float(STEPS_COUNT);\r\n float len = length(back - start);\r\n vec3 step = stepSize * dir;\r\n vec3 iterator = start;\r\n float acc = 0.0;\r\n\r\n for (int i = 0; i < STEPS_COUNT; i++) {\r\n if (float(i) * stepSize > len)\r\n break;\r\n iterator = iterator + step;\r\n if (sample3DTextureInclined(iterator).r > _isoLevel0.x)\r\n acc += 10. * sample3DTextureInclined(iterator).r / float(STEPS_COUNT);\r\n }\r\n\r\n return vec4(1.,1.,1., acc);\r\n}\r\n\r\nvec4 IsoRender(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n vec4 tst = GetIso1(start, back, 2., dir, _isoLevel0.x, 0);\r\n vec4 col = NO_COLOR;\r\n\r\n if (length(tst.xyz - start) < molDist && tst.a > 0.1) {\r\n float dif = CalcColor(tst.xyz, dir);\r\n dif = 0.9 * dif * dif;\r\n col = vec4(dif, dif, dif, 1);\r\n }\r\n return col;\r\n}\r\n\r\nvec4 VolRender2(vec3 start, vec3 back, float molDist, vec3 dir) {\r\n return sample3DTexture(start);\r\n}\r\n\r\nvoid main() {\r\n vec3 tc = screenSpacePos.xyz / screenSpacePos.w * 0.5 + 0.5;\r\n\r\n if (_flipV > 0.0) {\r\n tc.y = 1.0 - tc.y;\r\n }\r\n\r\n vec3 start;\r\n vec3 back;\r\n vec3 molBack;\r\n if (projectionMatrix[0][2] < 0.0) {\r\n start = texture2D(_FFLeft, tc.xy).xyz;\r\n back = texture2D(_BFLeft, tc.xy).xyz;\r\n molBack = texture2D(_WFFLeft, tc.xy).xyz;\r\n } else {\r\n start = texture2D(_FFRight, tc.xy).xyz;\r\n back = texture2D(_BFRight, tc.xy).xyz;\r\n molBack = texture2D(_WFFRight, tc.xy).xyz;\r\n }\r\n\r\n vec3 dir = normalize(back - start);\r\n\r\n float molDist = 2.0;\r\n if (length(molBack) > 0.001) {\r\n molDist = distance(start, molBack);\r\n }\r\n\r\n #ifdef ISO_MODE\r\n gl_FragColor = IsoRender(start, back, molDist, dir);\r\n #else\r\n gl_FragColor = VolRender(start, back, molDist, dir);\r\n #endif\r\n}\r\n"; +;// ./src/gfx/shaders/VolumeFarPlane.vert +const VolumeFarPlane_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 volPos;\r\nuniform float aspectRatio;\r\nuniform float farZ;\r\nuniform float tanHalfFOV;\r\nuniform mat4 matWorld2Volume;\r\n\r\nvoid main() {\r\n // rescale plane to fill in the whole far plane area seen from camera\r\n vec3 pos = position.xyz;\r\n pos.x = pos.x * tanHalfFOV * farZ * aspectRatio;\r\n pos.y = pos.y * tanHalfFOV * farZ;\r\n // common transformation\r\n gl_Position = projectionMatrix * modelViewMatrix * vec4(pos, 1.0);\r\n // calc pos in volume CS\r\n volPos = matWorld2Volume * modelMatrix * vec4(pos, 1.0);\r\n // we're assuming local position is in [-0.5, 0.5]\r\n // we need to offset it to be represented in RGB\r\n volPos = volPos + 0.5;\r\n volPos.w = 0.5;\r\n}\r\n"; +;// ./src/gfx/shaders/VolumeFarPlane.frag +const gfx_shaders_VolumeFarPlane_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nvarying vec4 volPos;\r\n\r\nvoid main() {\r\n gl_FragColor = volPos;\r\n}"; +;// ./src/gfx/shaders/VolumeMaterial.js @@ -22547,7 +22568,7 @@ class VolumeMaterial extends external_module_three_commonjs_three_commonjs2_thre FrontFacePosMaterial, VolumeMaterial }); -;// CONCATENATED MODULE: ./src/gfx/VolumeMesh.js +;// ./src/gfx/VolumeMesh.js @@ -22589,12 +22610,12 @@ class VolumeMesh extends external_module_three_commonjs_three_commonjs2_three_am geo.setAttribute('position', new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.BufferAttribute(new Float32Array(this.vertices.length * 3), 3)); this.name = 'VolumeMesh'; } - static _corners = (() => [ + static _corners = [ // x, y, z, edge1, edge2, edge3 - [-1, -1, -1, 0, 4, 8], [1, -1, -1, 0, 5, 9], [1, 1, -1, 1, 5, 10], [-1, 1, -1, 1, 4, 11], [-1, -1, 1, 2, 6, 8], [1, -1, 1, 2, 7, 9], [1, 1, 1, 3, 7, 10], [-1, 1, 1, 3, 6, 11]])(); - static _edges = (() => [ + [-1, -1, -1, 0, 4, 8], [1, -1, -1, 0, 5, 9], [1, 1, -1, 1, 5, 10], [-1, 1, -1, 1, 4, 11], [-1, -1, 1, 2, 6, 8], [1, -1, 1, 2, 7, 9], [1, 1, 1, 3, 7, 10], [-1, 1, 1, 3, 6, 11]]; + static _edges = [ // corner1, corner2, center_x, center_y, center_z - [0, 1, 0, -1, -1], [2, 3, 0, 1, -1], [4, 5, 0, -1, 1], [6, 7, 0, 1, 1], [0, 3, -1, 0, -1], [1, 2, 1, 0, -1], [4, 7, -1, 0, 1], [5, 6, 1, 0, 1], [0, 4, -1, -1, 0], [1, 5, 1, -1, 0], [2, 6, -1, 1, 0], [3, 7, 1, 1, 0]])(); + [0, 1, 0, -1, -1], [2, 3, 0, 1, -1], [4, 5, 0, -1, 1], [6, 7, 0, 1, 1], [0, 3, -1, 0, -1], [1, 2, 1, 0, -1], [4, 7, -1, 0, 1], [5, 6, 1, 0, 1], [0, 4, -1, -1, 0], [1, 5, 1, -1, 0], [2, 6, -1, 1, 0], [3, 7, 1, 1, 0]]; static _edgeIntersections = function () { const edgeIntersections = []; for (let j = 0; j < 12; ++j) { @@ -22872,11 +22893,11 @@ class VolumeMesh extends external_module_three_commonjs_three_commonjs2_three_am this.material.uniforms._isoLevel0.value.set(level(kSigma), level(kSigmaMed), level(kSigmaMax)); } static _nearClipPlaneOffset = 0.2; - static _pos = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3())(); - static _norm = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3())(); - static _norm4D = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector4())(); - static _matrixWorldToLocal = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Matrix4())(); - static _clipPlane = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Plane())(); + static _pos = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); + static _norm = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); + static _norm4D = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector4(); + static _matrixWorldToLocal = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Matrix4(); + static _clipPlane = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Plane(); rebuild(camera) { const nearClipPlaneOffset = VolumeMesh._nearClipPlaneOffset; const pos = VolumeMesh._pos; @@ -22909,7 +22930,7 @@ class VolumeMesh extends external_module_three_commonjs_three_commonjs2_three_am } } /* harmony default export */ const gfx_VolumeMesh = (VolumeMesh); -;// CONCATENATED MODULE: ./src/gfx/VolumeBounds.js +;// ./src/gfx/VolumeBounds.js function _flattenArray(input) { @@ -22986,7 +23007,7 @@ class VolumeBounds { } } /* harmony default export */ const gfx_VolumeBounds = (VolumeBounds); -;// CONCATENATED MODULE: ./src/gfx/VolumeFarPlane.js +;// ./src/gfx/VolumeFarPlane.js @@ -23052,7 +23073,7 @@ class VolumeFarPlane { } } /* harmony default export */ const gfx_VolumeFarPlane = (VolumeFarPlane); -;// CONCATENATED MODULE: ./src/VolumeVisual.js +;// ./src/VolumeVisual.js @@ -23088,7 +23109,7 @@ class VolumeVisual extends src_Visual { } } /* harmony default export */ const src_VolumeVisual = (VolumeVisual); -;// CONCATENATED MODULE: ./src/io/loaders/LoaderList.js +;// ./src/io/loaders/LoaderList.js /** @@ -23106,8 +23127,7 @@ class LoaderList extends utils_EntityList { * automatically register at creation time. * @see LoaderList#register */ - constructor() { - let someLoaders = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : []; + constructor(someLoaders = []) { super(someLoaders, ['types']); } @@ -23129,7 +23149,7 @@ class LoaderList extends utils_EntityList { } } /* harmony default export */ const loaders_LoaderList = (LoaderList); -;// CONCATENATED MODULE: ./src/io/loaders/Loader.js +;// ./src/io/loaders/Loader.js class Loader extends utils_EventDispatcher { @@ -23154,7 +23174,7 @@ class Loader extends utils_EventDispatcher { } } utils_makeContextDependent(Loader.prototype); -;// CONCATENATED MODULE: ./src/io/loaders/FileLoader.js +;// ./src/io/loaders/FileLoader.js class FileLoader extends Loader { constructor(source, options) { @@ -23196,7 +23216,7 @@ class FileLoader extends Loader { } } FileLoader.types = ['file', 'blob']; -;// CONCATENATED MODULE: ./src/io/loaders/XHRLoader.js +;// ./src/io/loaders/XHRLoader.js @@ -23241,7 +23261,7 @@ class XHRLoader extends Loader { }); } static canProbablyLoad(source) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(source) && urlStartRegexp.test(source); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(source) && urlStartRegexp.test(source); } static extractName(source) { if (source) { @@ -23252,7 +23272,7 @@ class XHRLoader extends Loader { } } XHRLoader.types = ['url']; -;// CONCATENATED MODULE: ./src/io/loaders/ImmediateLoader.js +;// ./src/io/loaders/ImmediateLoader.js class ImmediateLoader extends Loader { load() { @@ -23268,7 +23288,7 @@ class ImmediateLoader extends Loader { } } ImmediateLoader.types = ['immediate']; -;// CONCATENATED MODULE: ./src/io/loaders.js +;// ./src/io/loaders.js @@ -23276,7 +23296,7 @@ ImmediateLoader.types = ['immediate']; /* harmony default export */ const loaders = (new loaders_LoaderList([ // note: order might be important FileLoader, XHRLoader, ImmediateLoader])); -;// CONCATENATED MODULE: ./src/io/parsers/ParserList.js +;// ./src/io/parsers/ParserList.js /** @@ -23294,8 +23314,7 @@ class ParserList extends utils_EntityList { * automatically register at creation time. * @see ParserList#register */ - constructor() { - let someParsers = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : []; + constructor(someParsers = []) { super(someParsers, ['formats', 'extensions']); } @@ -23322,7 +23341,7 @@ class ParserList extends utils_EntityList { } } /* harmony default export */ const parsers_ParserList = (ParserList); -;// CONCATENATED MODULE: ./src/io/parsers/Parser.js +;// ./src/io/parsers/Parser.js class Parser { constructor(data, options) { @@ -23358,7 +23377,7 @@ class Parser { } } utils_makeContextDependent(Parser.prototype); -;// CONCATENATED MODULE: ./src/io/parsers/pdb/Remark290.js +;// ./src/io/parsers/pdb/Remark290.js /** @@ -23408,7 +23427,7 @@ class Remark290 { } Remark290.prototype.id = 290; /* harmony default export */ const pdb_Remark290 = (Remark290); -;// CONCATENATED MODULE: ./src/io/parsers/pdb/Remark350.js +;// ./src/io/parsers/pdb/Remark350.js const { @@ -23482,7 +23501,7 @@ class Remark350 { } Remark350.prototype.id = 350; /* harmony default export */ const pdb_Remark350 = (Remark350); -;// CONCATENATED MODULE: ./src/io/parsers/PDBStream.js +;// ./src/io/parsers/PDBStream.js /** Helper class for stream-like reading input files. */ class PDBStream { /** @@ -23595,7 +23614,7 @@ class PDBStream { } } /* harmony default export */ const parsers_PDBStream = (PDBStream); -;// CONCATENATED MODULE: ./src/io/parsers/PDBParser.js +;// ./src/io/parsers/PDBParser.js @@ -23657,7 +23676,7 @@ class PDBParser extends Parser { this._options.fileType = 'pdb'; } static canProbablyParse(data) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(data) && pdbStartRegexp.test(data); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(data) && pdbStartRegexp.test(data); } _finalize() { this._fixBondsArray(); @@ -23665,11 +23684,11 @@ class PDBParser extends Parser { // keep crystallographic symmetry transformations const remark290 = this._remarks[290]; - this._complex.symmetry = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(remark290) ? [] : remark290.matrices; + this._complex.symmetry = __WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(remark290) ? [] : remark290.matrices; // add loaded biological assemblies const remark350 = this._remarks[350]; - this._complex.units = this._complex.units.concat(external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(remark350) ? [] : remark350.assemblies); + this._complex.units = this._complex.units.concat(__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(remark350) ? [] : remark350.assemblies); // add loaded macromolecules this._finalizeMolecules(); @@ -23744,8 +23763,6 @@ class PDBParser extends Parser { if (this._modelId !== 1) { return; } - - /* eslint-disable no-magic-numbers */ const het = stream.readCharCode(1) === 0x48; // field names according to wwPDB Format @@ -23764,7 +23781,7 @@ class PDBParser extends Parser { const tempFactor = stream.readFloat(61, 66); const element = stream.readString(77, 78).trim() || nameToElement(name); const charge = stream.readInt(79, 80) || 0; - /* eslint-enable no-magic-numbers */ + // skip waters (there may be lots of them) if (this.settings.now.nowater) { if (resName === 'HOH' || resName === 'WAT') { @@ -23796,14 +23813,11 @@ class PDBParser extends Parser { this._modelId += 1; } _parseCONECT(stream) { - /* eslint-disable no-magic-numbers */ const serial0 = stream.readInt(7, 11); const serial1 = stream.readInt(12, 16); const serial2 = stream.readInt(17, 21); const serial3 = stream.readInt(22, 26); const serial4 = stream.readInt(27, 31); - /* eslint-enable no-magic-numbers */ - const complex = this._complex; // Keep bonds ordered by atom serial @@ -23821,11 +23835,9 @@ class PDBParser extends Parser { } } _parseCOMPND(stream) { - /* eslint-disable no-magic-numbers */ const str = stream.readString(11, 80); const tokenIdx = str.indexOf(':'); this._compndCurrToken = tokenIdx > 0 ? str.substring(0, tokenIdx).trim() : this._compndCurrToken; - /* eslint-enable no-magic-numbers */ // start reading new molecule if (this._compndCurrToken === 'MOL_ID') { @@ -23851,37 +23863,31 @@ class PDBParser extends Parser { } } _parseREMARK(stream) { - /* eslint-disable no-magic-numbers */ const remarkNum = stream.readInt(8, 10); - /* eslint-enable no-magic-numbers */ // create remark parser if needed let remark = this._remarks[remarkNum]; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(remark)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(remark)) { const RemarkParser = remarkParsers[remarkNum]; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isFunction(RemarkParser)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isFunction(RemarkParser)) { this._remarks[remarkNum] = remark = new RemarkParser(this._complex); } } // delegate parsing - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(remark)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(remark)) { remark.parse(stream); } } _parseHELIX(stream) { - /* eslint-disable no-magic-numbers */ const fields = [20, 22, 32, 34]; - /* eslint-enable no-magic-numbers */ this._parseSTRUCTURE(stream, fields, obj => { this._complex.addHelix(obj); this._complex.structures.push(obj); }); } _parseSHEET(stream) { - /* eslint-disable no-magic-numbers */ const fields = [22, 23, 33, 34]; - /* eslint-enable no-magic-numbers */ this._parseSTRUCTURE(stream, fields, obj => { this._complex.addSheet(obj); }); @@ -23893,7 +23899,7 @@ class PDBParser extends Parser { const endIndex = 3; // identify fields: debugging and stuff - /* eslint-disable no-magic-numbers */ + const codeOfS = 0x53; const serialNumber = stream.readInt(8, 10); const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim() @@ -23903,7 +23909,7 @@ class PDBParser extends Parser { const shWidth = stream.readInt(15, 16); const shCur = stream.readInt(42, 45); const shPrev = stream.readInt(57, 60); - /* eslint-enable no-magic-numbers */ + // file fields const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0); const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0); @@ -23961,7 +23967,7 @@ class PDBParser extends Parser { const line = stream.readInt(9, 10) || 1; metadata.title[line - 1] = stream.readString(11, 80).trim(); } - static tagParsers = (() => ({ + static tagParsers = { HEADER: PDBParser.prototype._parseHEADER, 'TITLE ': PDBParser.prototype._parseTITLE, 'ATOM ': PDBParser.prototype._parseATOM, @@ -23983,7 +23989,7 @@ class PDBParser extends Parser { 'ATOM 7': PDBParser.prototype._parseATOM, 'ATOM 8': PDBParser.prototype._parseATOM, 'ATOM 9': PDBParser.prototype._parseATOM - }))(); + }; parseSync() { const stream = new parsers_PDBStream(this._data); const result = this._complex = new PDBParser_Complex(); @@ -23992,7 +23998,7 @@ class PDBParser extends Parser { while (!stream.end()) { const tag = stream.readString(1, TAG_LENGTH); const func = PDBParser.tagParsers[tag]; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isFunction(func)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isFunction(func)) { func.call(this, stream); } stream.next(); @@ -24016,7 +24022,7 @@ class PDBParser extends Parser { PDBParser.formats = ['pdb']; PDBParser.extensions = ['.pdb', '.ent']; /* harmony default export */ const parsers_PDBParser = (PDBParser); -;// CONCATENATED MODULE: ./src/io/parsers/CMLParser.js +;// ./src/io/parsers/CMLParser.js @@ -24046,7 +24052,7 @@ class CMLParser extends Parser { this._options.fileType = 'cml'; } static canProbablyParse(data) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(data) && cmlStartRegexp.test(data); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(data) && cmlStartRegexp.test(data); } _rebuidBondIndexes(atoms, bonds) { const count = atoms.length; @@ -24608,7 +24614,7 @@ CMLParser.extensions = ['.cml']; // EXTERNAL MODULE: ./vendor/js/mmtf.js var mmtf = __webpack_require__(660); var mmtf_default = /*#__PURE__*/__webpack_require__.n(mmtf); -;// CONCATENATED MODULE: ./src/io/parsers/MMTFParser.js +;// ./src/io/parsers/MMTFParser.js @@ -24691,7 +24697,7 @@ class MMTFParser extends Parser { static canProbablyParse(data) { // check if it's binary MessagePack format containing a map (dictionary) // see https://github.com/msgpack/msgpack/blob/master/spec.md - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArrayBuffer(data) && (getFirstByte(data) | 1) === 0xDF; + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isArrayBuffer(data) && (getFirstByte(data) | 1) === 0xDF; } _onModel(_modelData) {} _onChain(chainData) { @@ -24742,14 +24748,14 @@ class MMTFParser extends Parser { } _updateSecStructure(complex, residue, groupData) { const helixClasses = [3, -1, 1, -1, 5]; - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(groupData) && groupData.secStruct === this._ssType) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(groupData) && groupData.secStruct === this._ssType) { residue._secondary = this._ssStruct; if (this._ssStruct) { this._ssStruct.term = residue; } return; } - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(groupData)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(groupData)) { // start new secondary structure const type = secStructToType[groupData.secStruct]; this._ssType = groupData.secStruct; @@ -25036,7 +25042,7 @@ MMTFParser.formats = ['mmtf']; MMTFParser.extensions = ['.mmtf']; MMTFParser.binary = true; /* harmony default export */ const parsers_MMTFParser = (MMTFParser); -;// CONCATENATED MODULE: ./src/io/parsers/ParsingError.js +;// ./src/io/parsers/ParsingError.js class ParsingError extends Error { constructor(message, line, column) { super(`data:${line}:${column}: ${message}`); @@ -25049,7 +25055,7 @@ class ParsingError extends Error { } } /* harmony default export */ const parsers_ParsingError = (ParsingError); -;// CONCATENATED MODULE: ./src/io/parsers/readCIF.js +;// ./src/io/parsers/readCIF.js @@ -25256,7 +25262,7 @@ function readCIF(source) { break; } value = _parseValue(); - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].set(block, key, value); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.set(block, key, value); state = 1; // block continue; } else if (state === 3) { @@ -25283,7 +25289,7 @@ function readCIF(source) { for (let keyIndex = 0; keyIndex < keysCount; ++keyIndex) { value = []; values[keyIndex] = value; - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].set(block, keys[keyIndex], value); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.set(block, keys[keyIndex], value); } state = 4; continue; // parse again in a different state @@ -25324,7 +25330,7 @@ function readCIF(source) { } return result; } -;// CONCATENATED MODULE: ./src/io/parsers/CIFParser.js +;// ./src/io/parsers/CIFParser.js @@ -25360,7 +25366,7 @@ function getTypeFromId(string) { * @return {array, object} array or object */ function arrize(arrayLikeObject) { - if (arrayLikeObject === null || arrayLikeObject === undefined || external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArray(arrayLikeObject)) { + if (arrayLikeObject === null || arrayLikeObject === undefined || __WEBPACK_EXTERNAL_MODULE_lodash_default__.isArray(arrayLikeObject)) { return arrayLikeObject; } return [arrayLikeObject]; @@ -25417,7 +25423,7 @@ function _getOperations(operList) { return ops; } function _extractOperations(assemblyGen, opsDict) { - assemblyGen = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(assemblyGen) ? assemblyGen : `${assemblyGen}`; + assemblyGen = __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(assemblyGen) ? assemblyGen : `${assemblyGen}`; const l = assemblyGen.replace(/\)\s*\(/g, '!').replace(/[()']/g, ''); const groupStr = l.split('!'); const gps = []; @@ -25466,7 +25472,7 @@ class CIFParser extends Parser { this._options.fileType = 'cif'; } static canProbablyParse(data) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(data) && /^\s*data_/i.test(data); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(data) && /^\s*data_/i.test(data); } parseSync() { this.logger.info('Parsing CIF file..'); @@ -25818,7 +25824,7 @@ class CIFParser extends Parser { CIFParser.formats = ['cif', 'mmcif']; CIFParser.extensions = ['.cif', '.mmcif']; /* harmony default export */ const parsers_CIFParser = (CIFParser); -;// CONCATENATED MODULE: ./src/io/parsers/VolumeModel.js +;// ./src/io/parsers/VolumeModel.js @@ -25830,7 +25836,7 @@ const valueType = { }; class VolumeModel { _xyz2crs = []; - _origin = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(0, 0, 0))(); + _origin = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(0, 0, 0); constructor() { this._header = {}; this._boxSize = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); @@ -25848,9 +25854,9 @@ class VolumeModel { this._header.dmax = 0; } _typedCheck() { - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isTypedArray(this._buff)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isTypedArray(this._buff)) { this._buff = this._buff.buffer; - } else if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArrayBuffer(this._buff)) { + } else if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isArrayBuffer(this._buff)) { throw new TypeError('Expected ArrayBuffer or TypedArray'); } } @@ -25905,7 +25911,7 @@ class VolumeModel { return [this._header.extent[this._xyz2crs[0]], this._header.extent[this._xyz2crs[1]], this._header.extent[this._xyz2crs[2]]]; } _getVolumeInfo() { - const volInfo = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].pick(this._header, ['dmean', 'dmin', 'dmax', 'sd', 'delta']); + const volInfo = __WEBPACK_EXTERNAL_MODULE_lodash_default__.pick(this._header, ['dmean', 'dmin', 'dmax', 'sd', 'delta']); volInfo.obtuseAngle = this._header.angles.map(angle => Number(angle >= Math.PI / 2)); return volInfo; } @@ -25941,7 +25947,7 @@ class VolumeModel { } } /* harmony default export */ const parsers_VolumeModel = (VolumeModel); -;// CONCATENATED MODULE: ./src/io/parsers/CCP4Parser.js +;// ./src/io/parsers/CCP4Parser.js const CCP4Header = { @@ -26077,7 +26083,7 @@ CCP4Parser.formats = ['ccp4']; CCP4Parser.extensions = ['.ccp4', '.map', '.mrc']; CCP4Parser.binary = true; /* harmony default export */ const parsers_CCP4Parser = (CCP4Parser); -;// CONCATENATED MODULE: ./src/io/parsers/XYZParser.js +;// ./src/io/parsers/XYZParser.js @@ -26096,7 +26102,7 @@ class XYZParser extends Parser { this._fileName = options.name; } static canProbablyParse(data) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(data) && /^\s*\d+ *\n[^\n]*\n\s*\w{1,3}\s+-?\d/.test(data); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(data) && /^\s*\d+ *\n[^\n]*\n\s*\w{1,3}\s+-?\d/.test(data); } _parseToAtomsInf(source) { const endnAtoms = source.indexOf('\n'); @@ -26165,7 +26171,7 @@ class XYZParser extends Parser { static extensions = ['.xyz']; } /* harmony default export */ const parsers_XYZParser = (XYZParser); -;// CONCATENATED MODULE: ./src/io/parsers/PubChemParser.js +;// ./src/io/parsers/PubChemParser.js @@ -26180,7 +26186,7 @@ class PubChemParser extends Parser { this._options.fileType = 'pubchem+json'; } static canProbablyParse(data) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(data) && data[0] === '{'; + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(data) && data[0] === '{'; } parseSync() { this.logger.info('Parsing PubChem JSON file...'); @@ -26205,7 +26211,7 @@ class PubChemParser extends Parser { if (!elements || aids.length !== elements.length) { throw new Error('Unable to parse atom elements'); } - elements = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].fromPairs(external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].zip(aids, elements)); + elements = __WEBPACK_EXTERNAL_MODULE_lodash_default__.fromPairs(__WEBPACK_EXTERNAL_MODULE_lodash_default__.zip(aids, elements)); const atoms = {}; const coords = complexData.coords && complexData.coords[0]; const model = coords && coords.conformers && coords.conformers[0]; @@ -26238,7 +26244,7 @@ class PubChemParser extends Parser { PubChemParser.formats = ['pubchem', 'pubchem+json', 'pc']; PubChemParser.extensions = ['.json']; /* harmony default export */ const parsers_PubChemParser = (PubChemParser); -;// CONCATENATED MODULE: ./src/io/parsers/SDFStream.js +;// ./src/io/parsers/SDFStream.js class SDFStream { constructor(data) { @@ -26268,7 +26274,7 @@ class SDFStream { findNextDataItem() { let curStr = this.getNextString(); let res = false; - while (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(curStr) && curStr.trim() !== '$$$$') { + while (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(curStr) && curStr.trim() !== '$$$$') { if (curStr.match(/>\s+<(.*)>/)) { res = true; break; @@ -26279,7 +26285,7 @@ class SDFStream { } findNextCompoundStart() { let curStr = this.getCurrentString(); - while (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(curStr) && curStr.trim() !== '$$$$') { + while (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(curStr) && curStr.trim() !== '$$$$') { curStr = this.getNextString(); } this.setStart(++this._currentStringIndx); @@ -26289,7 +26295,7 @@ class SDFStream { return this._currentStringIndx < this._strings.length - 2; } } -;// CONCATENATED MODULE: ./src/io/parsers/SDFParser.js +;// ./src/io/parsers/SDFParser.js @@ -26370,7 +26376,7 @@ class SDFParser extends Parser { this._atomsIndexes = []; } canProbablyParse(data) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(data) && sdfAndMolRegexp.test(data); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(data) && sdfAndMolRegexp.test(data); } _parseHeader(stream) { const molecule = {}; @@ -26605,7 +26611,7 @@ class SDFParser extends Parser { } SDFParser.formats = ['mol', 'sdf']; SDFParser.extensions = ['.mol', '.sdf']; -;// CONCATENATED MODULE: ./src/io/parsers/DSN6Parser.js +;// ./src/io/parsers/DSN6Parser.js @@ -26749,7 +26755,7 @@ DSN6Parser.formats = ['dsn6']; DSN6Parser.extensions = ['.dsn6', '.omap']; DSN6Parser.binary = true; /* harmony default export */ const parsers_DSN6Parser = (DSN6Parser); -;// CONCATENATED MODULE: ./src/io/parsers/GROReader.js +;// ./src/io/parsers/GROReader.js /** @@ -26773,7 +26779,7 @@ class GROReader extends parsers_PDBStream { } } /* harmony default export */ const parsers_GROReader = (GROReader); -;// CONCATENATED MODULE: ./src/io/parsers/GROParser.js +;// ./src/io/parsers/GROParser.js @@ -26830,7 +26836,7 @@ class GROParser extends Parser { * @returns {boolean} true if this file is in ascii, false otherwise */ canProbablyParse(data) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(this._data) && /^\s*[^\n]*\n\s*\d+ *\n\s*\d+[^\n\d]{3}\s*\w+\s*\d+\s*-?\d/.test(data); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(this._data) && /^\s*[^\n]*\n\s*\d+ *\n\s*\d+[^\n\d]{3}\s*\w+\s*\d+\s*-?\d/.test(data); } /** @@ -26978,7 +26984,7 @@ class GROParser extends Parser { GROParser.formats = ['gro']; GROParser.extensions = ['.gro']; /* harmony default export */ const parsers_GROParser = (GROParser); -;// CONCATENATED MODULE: ./src/io/parsers/MOL2Parser.js +;// ./src/io/parsers/MOL2Parser.js @@ -27255,7 +27261,7 @@ class MOL2Parser extends Parser { MOL2Parser.formats = ['mol2']; MOL2Parser.extensions = ['.mol2', '.ml2', '.sy2']; /* harmony default export */ const parsers_MOL2Parser = (MOL2Parser); -;// CONCATENATED MODULE: ./src/io/parsers.js +;// ./src/io/parsers.js @@ -27271,7 +27277,7 @@ MOL2Parser.extensions = ['.mol2', '.ml2', '.sy2']; /* harmony default export */ const parsers = (new parsers_ParserList([ // note: order might be important parsers_PDBParser, parsers_CIFParser, parsers_MMTFParser, parsers_XYZParser, parsers_CMLParser, parsers_PubChemParser, SDFParser, parsers_CCP4Parser, parsers_DSN6Parser, parsers_GROParser, parsers_MOL2Parser])); -;// CONCATENATED MODULE: ./src/io/exporters/ExporterList.js +;// ./src/io/exporters/ExporterList.js /** @@ -27289,8 +27295,7 @@ class ExporterList extends utils_EntityList { * automatically register at creation time. * @see ExporterList#register */ - constructor() { - let someExporters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : []; + constructor(someExporters = []) { super(someExporters, ['formats']); } @@ -27310,7 +27315,7 @@ class ExporterList extends utils_EntityList { } } /* harmony default export */ const exporters_ExporterList = (ExporterList); -;// CONCATENATED MODULE: ./src/io/exporters/Exporter.js +;// ./src/io/exporters/Exporter.js class Exporter { constructor(source, options) { @@ -27340,7 +27345,7 @@ class Exporter { } } utils_makeContextDependent(Exporter.prototype); -;// CONCATENATED MODULE: ./src/io/exporters/PDBResult.js +;// ./src/io/exporters/PDBResult.js class PDBResult { @@ -27370,12 +27375,12 @@ class PDBResult { } else { this._tag = tag; } - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(numeration)) { - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isNumber(numeration)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(numeration)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isNumber(numeration)) { this._tagStrNum = numeration; this._numeration = true; this._fixedNumeration = true; - } else if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isBoolean(numeration)) { + } else if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isBoolean(numeration)) { this._tagStrNum = 0; this._numeration = numeration; this._fixedNumeration = false; @@ -27427,16 +27432,16 @@ class PDBResult { let curStr = this._resultArray[this._currentStr]; let str; const curStrLength = curStr ? curStr.length : 0; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(string)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(string)) { return; } - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isNumber(begin)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isNumber(begin)) { begin = curStrLength + 1; } - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isNumber(end)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isNumber(end)) { end = curStrLength + string.length; } - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(string)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(string)) { str = string.toString(); } else { str = string; @@ -27521,7 +27526,7 @@ class PDBResult { } } } -;// CONCATENATED MODULE: ./src/io/exporters/PDBExporter.js +;// ./src/io/exporters/PDBExporter.js @@ -27554,7 +27559,7 @@ class PDBExporter extends Exporter { for (let i = 0; i < this._tags.length; i++) { const tag = this._tags[i]; const func = this._tagExtractors[tag]; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isFunction(func)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isFunction(func)) { func.call(this, result); } } @@ -27644,7 +27649,7 @@ class PDBExporter extends Exporter { const helices = this._source._helices; for (let i = 0; i < helices.length; i++) { const helix = helices[i]; - const helixClass = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].invert(typeByPDBHelixClass); + const helixClass = __WEBPACK_EXTERNAL_MODULE_lodash_default__.invert(typeByPDBHelixClass); result.newString(); result.writeString(helix.serial, 10, 8); result.writeString(helix.name, 14, 12); @@ -27768,7 +27773,7 @@ class PDBExporter extends Exporter { } PDBExporter.formats = ['pdb']; PDBExporter.SourceClass = chem_Complex; -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBXModel.js +;// ./src/io/exporters/fbx/FBXModel.js const FBX_POS_SIZE = 3; const FBX_NORM_SIZE = 3; @@ -27912,7 +27917,7 @@ class FBXModel { this.setColors(geo.colors, 0, geo.vertsCount, size.color); } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBXGeometry.js +;// ./src/io/exporters/fbx/FBXGeometry.js /** Base class for fbx geometry contains simply organized attributes: positions+normals+colors, indices. */ class FBXGeometry { /** @@ -27943,7 +27948,7 @@ class FBXGeometry { }; } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBX1CGeometry.js +;// ./src/io/exporters/fbx/FBX1CGeometry.js /** @@ -27987,7 +27992,7 @@ class FBX1CGeometry extends FBXGeometry { } } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBX2CCylinder.js +;// ./src/io/exporters/fbx/FBX2CCylinder.js /** @@ -28108,7 +28113,7 @@ class FBX2CCylinder extends FBXGeometry { } } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBXInfoExtractor.js +;// ./src/io/exporters/fbx/FBXInfoExtractor.js @@ -28392,7 +28397,7 @@ class FBXInfoExtractor { * @returns {number} number of model-material pair */ _checkExistingMaterial(material) { - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].findIndex(this._materials, m => external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEqual(m, material)); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.findIndex(this._materials, m => __WEBPACK_EXTERNAL_MODULE_lodash_default__.isEqual(m, material)); } _gatherCylindersColoringInfo(geo) { const instCount = geo.instanceCount; @@ -28466,7 +28471,7 @@ class FBXInfoExtractor { matrix.set(scale, 0, 0, x, 0, scale, 0, y, 0, 0, scale, z, 0, 0, 0, 1); } } -;// CONCATENATED MODULE: ./src/io/exporters/fbx/FBXResult.js +;// ./src/io/exporters/fbx/FBXResult.js // Forming default definitions block const defaultDefinitions = ` Definitions: { @@ -28635,7 +28640,7 @@ class FBXResult { const creator = `Miew FBX Exporter v${this._info.version}`; // Supposed to be an engine return `; FBX 6.1.0 project file -; Created by ${creator} Copyright (c) 2015-2024 EPAM Systems, Inc. +; Created by ${creator} Copyright (c) 2015-2026 EPAM Systems, Inc. ; For support please contact miew@epam.com ; ---------------------------------------------------- @@ -28924,7 +28929,7 @@ Connections: { }`; } } -;// CONCATENATED MODULE: ./src/io/exporters/FBXExporter.js +;// ./src/io/exporters/FBXExporter.js @@ -28955,12 +28960,12 @@ class FBXExporter extends Exporter { } FBXExporter.formats = ['fbx']; FBXExporter.SourceClass = src_ComplexVisual; -;// CONCATENATED MODULE: ./src/io/exporters.js +;// ./src/io/exporters.js /* harmony default export */ const exporters = (new exporters_ExporterList([PDBExporter, FBXExporter])); -;// CONCATENATED MODULE: ./src/io/io.js +;// ./src/io/io.js @@ -28969,7 +28974,7 @@ FBXExporter.SourceClass = src_ComplexVisual; parsers: parsers, exporters: exporters }); -;// CONCATENATED MODULE: ./src/gfx/CSS2DRenderer.js +;// ./src/gfx/CSS2DRenderer.js /** * @author mrdoob / http://mrdoob.com/ */ @@ -29070,19 +29075,19 @@ class CSS2DRenderer { } } /* harmony default export */ const gfx_CSS2DRenderer = (CSS2DRenderer); -;// CONCATENATED MODULE: ./src/utils/getTopWindow.js +;// ./src/utils/getTopWindow.js function getTopWindow() { // intercept the exception if we have cross-origin iframe try { if (window.top.location.href !== undefined) { return window.top; } - } catch (e) { + } catch { // provide fallback } return window; } -;// CONCATENATED MODULE: ./src/ui/ObjectControls.js +;// ./src/ui/ObjectControls.js @@ -29837,7 +29842,7 @@ ObjectControls.prototype.setPivot = function (newPivot) { }); }; /* harmony default export */ const ui_ObjectControls = (ObjectControls); -;// CONCATENATED MODULE: ./src/ui/Picker.js +;// ./src/ui/Picker.js @@ -30058,7 +30063,7 @@ Picker.prototype.dispose = function () { } }; /* harmony default export */ const ui_Picker = (Picker); -;// CONCATENATED MODULE: ./src/gfx/Axes.js +;// ./src/gfx/Axes.js class Axes { constructor(target, targetCamera) { @@ -30099,7 +30104,7 @@ class Axes { } } /* harmony default export */ const gfx_Axes = (Axes); -;// CONCATENATED MODULE: ./src/gfx/FrameInfo.js +;// ./src/gfx/FrameInfo.js const cDataOffset = 12; @@ -30386,7 +30391,7 @@ class FrameInfo { * Returns link to atom pos vector, clone it if needed */ - static _vec = (() => new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3())(); + static _vec = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.Vector3(); getAtomPos(atomIdx) { const vec = FrameInfo._vec; const self = this; @@ -30404,7 +30409,7 @@ class FrameInfo { } } /* harmony default export */ const gfx_FrameInfo = (FrameInfo); -;// CONCATENATED MODULE: ./src/gfx/objects/SceneObject.js +;// ./src/gfx/objects/SceneObject.js @@ -30435,7 +30440,7 @@ class SceneObject { * @type {object} */ this.params = params; - this.opts = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge(utils.deriveDeep(settings.now.objects[this.type], true), opts); + this.opts = __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge(utils.deriveDeep(settings.now.objects[this.type], true), opts); this.needsRebuild = false; this._mesh = null; this.id = null; @@ -30453,7 +30458,7 @@ class SceneObject { params: this.params }; const diff = utils.objectsDiff(this.opts, settings.now.modes[this.id]); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(diff)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(diff)) { result.opts = diff; } return result; @@ -30479,7 +30484,7 @@ class SceneObject { */ SceneObject.prototype.type = '__'; /* harmony default export */ const objects_SceneObject = (SceneObject); -;// CONCATENATED MODULE: ./src/gfx/objects/LinesObj.js +;// ./src/gfx/objects/LinesObj.js @@ -30548,11 +30553,9 @@ class LinesObj extends objects_SceneObject { LinesObj.prototype.constructor = LinesObj; LinesObj.prototype.type = 'line'; /* harmony default export */ const objects_LinesObj = (LinesObj); -;// CONCATENATED MODULE: ./src/gfx/shaders/Outline.frag -const Outline_namespaceObject = "precision highp float;\r\n\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexSize;\r\nuniform vec2 thickness;\r\nvarying vec2 vUv;\r\n\r\n#ifdef DEPTH_OUTLINE\r\n uniform sampler2D srcDepthTex; //depthTexture\r\n uniform vec3 color;\r\n uniform float threshold;\r\n#endif\r\n\r\nvoid main() {\r\n\r\n vec2 pixelSize = thickness / srcTexSize;\r\n\r\n #ifdef DEPTH_OUTLINE\r\n float c00 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,-pixelSize.y)).x;\r\n float c01 = texture2D(srcDepthTex, vUv + vec2(0,-pixelSize.y)).x;\r\n float c02 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,-pixelSize.y)).x;\r\n float c10 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,0)).x;\r\n float c12 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,0)).x;\r\n float c20 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,pixelSize.y)).x;\r\n float c21 = texture2D(srcDepthTex, vUv + vec2(0,pixelSize.y)).x;\r\n float c22 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,pixelSize.y)).x;\r\n\r\n float horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n float vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n float grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n\r\n gl_FragColor = ( grad > threshold ) ? vec4(color.rgb, 1.0) : gl_FragColor = texture2D(srcTex, vUv);\r\n\r\n #else\r\n vec4 c00 = texture2D(srcTex, vUv + vec2(-pixelSize.x,-pixelSize.y));\r\n vec4 c01 = texture2D(srcTex, vUv + vec2(0,-pixelSize.y));\r\n vec4 c02 = texture2D(srcTex, vUv + vec2(pixelSize.x,-pixelSize.y));\r\n vec4 c10 = texture2D(srcTex, vUv + vec2(-pixelSize.x,0));\r\n vec4 c12 = texture2D(srcTex, vUv + vec2(pixelSize.x,0));\r\n vec4 c20 = texture2D(srcTex, vUv + vec2(-pixelSize.x,pixelSize.y));\r\n vec4 c21 = texture2D(srcTex, vUv + vec2(0,pixelSize.y));\r\n vec4 c22 = texture2D(srcTex, vUv + vec2(pixelSize.x,pixelSize.y));\r\n\r\n vec4 horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n vec4 vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n vec4 grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n gl_FragColor = grad;\r\n #endif\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/OutlineMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/Outline.frag +const Outline_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexSize;\r\nuniform vec2 thickness;\r\nvarying vec2 vUv;\r\n\r\n#ifdef DEPTH_OUTLINE\r\n uniform sampler2D srcDepthTex; //depthTexture\r\n uniform vec3 color;\r\n uniform float threshold;\r\n#endif\r\n\r\nvoid main() {\r\n\r\n vec2 pixelSize = thickness / srcTexSize;\r\n\r\n #ifdef DEPTH_OUTLINE\r\n float c00 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,-pixelSize.y)).x;\r\n float c01 = texture2D(srcDepthTex, vUv + vec2(0,-pixelSize.y)).x;\r\n float c02 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,-pixelSize.y)).x;\r\n float c10 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,0)).x;\r\n float c12 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,0)).x;\r\n float c20 = texture2D(srcDepthTex, vUv + vec2(-pixelSize.x,pixelSize.y)).x;\r\n float c21 = texture2D(srcDepthTex, vUv + vec2(0,pixelSize.y)).x;\r\n float c22 = texture2D(srcDepthTex, vUv + vec2(pixelSize.x,pixelSize.y)).x;\r\n\r\n float horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n float vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n float grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n\r\n gl_FragColor = ( grad > threshold ) ? vec4(color.rgb, 1.0) : gl_FragColor = texture2D(srcTex, vUv);\r\n\r\n #else\r\n vec4 c00 = texture2D(srcTex, vUv + vec2(-pixelSize.x,-pixelSize.y));\r\n vec4 c01 = texture2D(srcTex, vUv + vec2(0,-pixelSize.y));\r\n vec4 c02 = texture2D(srcTex, vUv + vec2(pixelSize.x,-pixelSize.y));\r\n vec4 c10 = texture2D(srcTex, vUv + vec2(-pixelSize.x,0));\r\n vec4 c12 = texture2D(srcTex, vUv + vec2(pixelSize.x,0));\r\n vec4 c20 = texture2D(srcTex, vUv + vec2(-pixelSize.x,pixelSize.y));\r\n vec4 c21 = texture2D(srcTex, vUv + vec2(0,pixelSize.y));\r\n vec4 c22 = texture2D(srcTex, vUv + vec2(pixelSize.x,pixelSize.y));\r\n\r\n vec4 horizEdge = - c00 - 2.0 * c01 - c02 + c20 + 2.0 * c21 + c22;\r\n vec4 vertEdge = - c00 - 2.0 * c10 - c20 + c02 + 2.0 * c12 + c22;\r\n\r\n vec4 grad = sqrt(horizEdge * horizEdge + vertEdge * vertEdge);\r\n gl_FragColor = grad;\r\n #endif\r\n}\r\n"; +;// ./src/gfx/shaders/OutlineMaterial.js @@ -30621,11 +30624,9 @@ class OutlineMaterial extends external_module_three_commonjs_three_commonjs2_thr } OutlineMaterial.prototype.depth = false; /* harmony default export */ const shaders_OutlineMaterial = (OutlineMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/FXAA.frag -const FXAA_namespaceObject = "precision highp float;\r\n\r\n// edge end finding algorithm parameters\r\n#define FXAA_QUALITY_PS 8\r\n#define FXAA_QUALITY_P0 1.0\r\n#define FXAA_QUALITY_P1 1.5\r\n#define FXAA_QUALITY_P2 2.0\r\n#define FXAA_QUALITY_P3 2.0\r\n#define FXAA_QUALITY_P4 2.0\r\n#define FXAA_QUALITY_P5 2.0\r\n#define FXAA_QUALITY_P6 4.0\r\n#define FXAA_QUALITY_P7 12.0\r\n// constants\r\nfloat fxaaQualityEdgeThreshold = 0.125;\r\nfloat fxaaQualityEdgeThresholdMin = 0.0625;\r\nfloat fxaaQualitySubpix = 0.7; //0.65;\r\n// global params\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexelSize;\r\nuniform vec3 bgColor;\r\n// from vs\r\nvarying vec2 vUv;\r\n//=====================================================================//\r\n// calc luminance from rgb\r\n//'float FxaaLuma(vec3 rgb) {return rgb.y * (0.587/0.299) + rgb.x; } // Lotte's idea about game luminance\r\nfloat FxaaLuma(vec3 rgb) {return dot(rgb, vec3(0.299, 0.587, 0.114)); } // real luminance calculation\r\n // for non-real scene rendering\r\n// texture sampling by pixel position(coords) and offset(in pixels)\r\n vec3 FxaaTex(sampler2D tex, vec2 pos, vec2 off, vec2 res ) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos + off * res );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos + off * res ).xyz;\r\n #endif\r\n}\r\nvec3 FxaaTexTop(sampler2D tex, vec2 pos) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos).xyz;\r\n #endif\r\n}\r\nvec4 FxaaTexTopAlpha(sampler2D tex, vec2 pos) {\r\n return texture2D( tex, pos);\r\n}\r\n\r\n//=====================================================================//\r\nvoid main() {\r\n // renaming\r\n vec2 posM = vUv;\r\n // get luminance for neighbours\r\n float lumaS = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, 1.0 ), srcTexelSize));\r\n float lumaE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 0.0 ), srcTexelSize));\r\n float lumaN = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, -1.0 ), srcTexelSize));\r\n float lumaW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 0.0 ), srcTexelSize));\r\n float lumaM = FxaaLuma(FxaaTexTop(srcTex, posM));\r\n // find max and min luminance\r\n float rangeMax = max(max(lumaN, lumaW), max(lumaE, max(lumaS, lumaM)));\r\n float rangeMin = min(min(lumaN, lumaW), min(lumaE, min(lumaS, lumaM)));\r\n // calc maximum non-edge range\r\n float rangeMaxScaled = rangeMax * fxaaQualityEdgeThreshold;\r\n float range = rangeMax - rangeMin;\r\n float rangeMaxClamped = max(fxaaQualityEdgeThresholdMin, rangeMaxScaled);\r\n // exit when luma contrast is small (is not edge)\r\n if(range < rangeMaxClamped){\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n return;\r\n }\r\n float subpixRcpRange = 1.0/range;\r\n // note: the sampling coordinates can be calculated in vertex shader but the approach doesn't affect performance\r\n // visibly, thus we decided to leave calculation here for better readability.\r\n // calc other neighbours luminance\r\n float lumaNE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, -1.0 ), srcTexelSize));\r\n float lumaSW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 1.0 ), srcTexelSize));\r\n float lumaSE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 1.0 ), srcTexelSize));\r\n float lumaNW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, -1.0 ), srcTexelSize));\r\n/*--------------span calculation and subpix amount calulation-----------------*/\r\n float lumaNS = lumaN + lumaS;\r\n float lumaWE = lumaW + lumaE;\r\n float subpixNSWE = lumaNS + lumaWE;\r\n float edgeHorz1 = (-2.0 * lumaM) + lumaNS;\r\n float edgeVert1 = (-2.0 * lumaM) + lumaWE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNESE = lumaNE + lumaSE;\r\n float lumaNWNE = lumaNW + lumaNE;\r\n float edgeHorz2 = (-2.0 * lumaE) + lumaNESE;\r\n float edgeVert2 = (-2.0 * lumaN) + lumaNWNE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNWSW = lumaNW + lumaSW;\r\n float lumaSWSE = lumaSW + lumaSE;\r\n float edgeHorz4 = (abs(edgeHorz1) * 2.0) + abs(edgeHorz2);\r\n float edgeVert4 = (abs(edgeVert1) * 2.0) + abs(edgeVert2);\r\n float edgeHorz3 = (-2.0 * lumaW) + lumaNWSW;\r\n float edgeVert3 = (-2.0 * lumaS) + lumaSWSE;\r\n float edgeHorz = abs(edgeHorz3) + edgeHorz4;\r\n float edgeVert = abs(edgeVert3) + edgeVert4;\r\n/*--------------------subpix amount calulation------------------------------*/\r\n float subpixNWSWNESE = lumaNWSW + lumaNESE;\r\n float lengthSign = srcTexelSize.x;\r\n bool horzSpan = edgeHorz >= edgeVert;\r\n // debug code edge span visualization\r\n/*' if (horzSpan)\r\n gl_FragColor = vec4(0.0, 0.0, 1.0, 1.0);\r\n else\r\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\r\n return;*/\r\n float subpixA = subpixNSWE * 2.0 + subpixNWSWNESE;\r\n/*--------------------------------------------------------------------------*/\r\n if(!horzSpan) lumaN = lumaW;\r\n if(!horzSpan) lumaS = lumaE;\r\n if(horzSpan) lengthSign = srcTexelSize.y;\r\n float subpixB = (subpixA * (1.0/12.0)) - lumaM;\r\n/*--------------------------------------------------------------------------*/\r\n float gradientN = lumaN - lumaM;\r\n float gradientS = lumaS - lumaM;\r\n float lumaNN = lumaN + lumaM;\r\n float lumaSS = lumaS + lumaM;\r\n bool pairN = abs(gradientN) >= abs(gradientS);\r\n float gradient = max(abs(gradientN), abs(gradientS));\r\n if(pairN) lengthSign = -lengthSign;\r\n float subpixC = clamp(abs(subpixB) * subpixRcpRange, 0.0, 1.0);\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posB;\r\n posB = posM;\r\n vec2 offNP;\r\n offNP.x = (!horzSpan) ? 0.0 : srcTexelSize.x;\r\n offNP.y = ( horzSpan) ? 0.0 : srcTexelSize.y;\r\n if(!horzSpan) posB.x += lengthSign * 0.5;\r\n if( horzSpan) posB.y += lengthSign * 0.5;\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posN;\r\n posN = posB - offNP * FXAA_QUALITY_P0;\r\n vec2 posP;\r\n posP = posB + offNP * FXAA_QUALITY_P0;\r\n float subpixD = ((-2.0)*subpixC) + 3.0;\r\n float lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN));\r\n float subpixE = subpixC * subpixC;\r\n float lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP));\r\n/*--------------------------------------------------------------------------*/\r\n if(!pairN) lumaNN = lumaSS;\r\n float gradientScaled = gradient * 1.0/4.0;\r\n float lumaMM = lumaM - lumaNN * 0.5;\r\n float subpixF = subpixD * subpixE;\r\n bool lumaMLTZero = lumaMM < 0.0;\r\n/*---------------------looped edge-end search-------------------------------*/\r\n lumaEndN -= lumaNN * 0.5;\r\n lumaEndP -= lumaNN * 0.5;\r\n bool doneN = abs(lumaEndN) >= gradientScaled;\r\n bool doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P1;\r\n bool doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P1;\r\n/*--------------------------------------------------------------------------*/\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P2;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P2;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 3)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P3;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P3;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 4)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P4;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P4;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 5)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P5;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P5;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 6)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P6;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P6;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 7)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P7;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P7;\r\n/*--------------------------------------------------------------------------*/\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n/*----------------calculate subpix offset due to edge ends-------------------*/\r\n float dstN = posM.x - posN.x;\r\n float dstP = posP.x - posM.x;\r\n if(!horzSpan) dstN = posM.y - posN.y;\r\n if(!horzSpan) dstP = posP.y - posM.y;\r\n/*--------------------------------------------------------------------------*/\r\n bool goodSpanN = (lumaEndN < 0.0) != lumaMLTZero;\r\n float spanLength = (dstP + dstN);\r\n bool goodSpanP = (lumaEndP < 0.0) != lumaMLTZero;\r\n float spanLengthRcp = 1.0 / spanLength;\r\n/*--------------------------------------------------------------------------*/\r\n bool directionN = dstN < dstP;\r\n float dst = min(dstN, dstP);\r\n bool goodSpan = directionN ? goodSpanN : goodSpanP;\r\n float subpixG = subpixF * subpixF;\r\n float pixelOffset = (dst * (-spanLengthRcp)) + 0.5;\r\n float subpixH = subpixG * fxaaQualitySubpix;\r\n/*-----------------calc texture offest using subpix-------------------------*/\r\n float pixelOffsetGood = goodSpan ? pixelOffset : 0.0;\r\n float pixelOffsetSubpix = max(pixelOffsetGood, subpixH);\r\n\r\n float offset = pixelOffsetSubpix * lengthSign;\r\n #ifdef BG_TRANSPARENT\r\n // get original texel\r\n vec4 rgbaA = FxaaTexTopAlpha(srcTex, posM);\r\n // calc step to blended texel\r\n vec2 step = sign((!horzSpan) ? vec2 (offset, 0.0) : vec2 (0.0, offset));\r\n // get neighboring texel\r\n vec4 rgbaB = FxaaTexTopAlpha(srcTex, posM + step * srcTexelSize);\r\n // calc blend factor from offset\r\n float f = (!horzSpan) ? offset / srcTexelSize.x : offset / srcTexelSize.y;\r\n f = abs(f);\r\n // calc alpha (special formula to emulate blending with bg)\r\n gl_FragColor.a = 1.0 - mix(1.0 - rgbaA.a, 1.0 - rgbaB.a, f);\r\n // calc color (special formula to emulate blending with bg)\r\n gl_FragColor.rgb = mix(rgbaA.rgb * rgbaA.a, rgbaB.rgb * rgbaB.a, f) / gl_FragColor.a;\r\n #else\r\n if(!horzSpan) {\r\n posM.x += offset;\r\n } else {\r\n posM.y += offset;\r\n }\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n #endif\r\n return;\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/FXAAMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/FXAA.frag +const FXAA_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\n// edge end finding algorithm parameters\r\n#define FXAA_QUALITY_PS 8\r\n#define FXAA_QUALITY_P0 1.0\r\n#define FXAA_QUALITY_P1 1.5\r\n#define FXAA_QUALITY_P2 2.0\r\n#define FXAA_QUALITY_P3 2.0\r\n#define FXAA_QUALITY_P4 2.0\r\n#define FXAA_QUALITY_P5 2.0\r\n#define FXAA_QUALITY_P6 4.0\r\n#define FXAA_QUALITY_P7 12.0\r\n// constants\r\nfloat fxaaQualityEdgeThreshold = 0.125;\r\nfloat fxaaQualityEdgeThresholdMin = 0.0625;\r\nfloat fxaaQualitySubpix = 0.7; //0.65;\r\n// global params\r\nuniform sampler2D srcTex;\r\nuniform vec2 srcTexelSize;\r\nuniform vec3 bgColor;\r\n// from vs\r\nvarying vec2 vUv;\r\n//=====================================================================//\r\n// calc luminance from rgb\r\n//'float FxaaLuma(vec3 rgb) {return rgb.y * (0.587/0.299) + rgb.x; } // Lotte's idea about game luminance\r\nfloat FxaaLuma(vec3 rgb) {return dot(rgb, vec3(0.299, 0.587, 0.114)); } // real luminance calculation\r\n // for non-real scene rendering\r\n// texture sampling by pixel position(coords) and offset(in pixels)\r\n vec3 FxaaTex(sampler2D tex, vec2 pos, vec2 off, vec2 res ) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos + off * res );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos + off * res ).xyz;\r\n #endif\r\n}\r\nvec3 FxaaTexTop(sampler2D tex, vec2 pos) {\r\n #ifdef BG_TRANSPARENT\r\n vec4 color = texture2D( tex, pos );\r\n return mix(color.rgb, bgColor, 1.0 - color.a);\r\n #else\r\n return texture2D( tex, pos).xyz;\r\n #endif\r\n}\r\nvec4 FxaaTexTopAlpha(sampler2D tex, vec2 pos) {\r\n return texture2D( tex, pos);\r\n}\r\n\r\n//=====================================================================//\r\nvoid main() {\r\n // renaming\r\n vec2 posM = vUv;\r\n // get luminance for neighbours\r\n float lumaS = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, 1.0 ), srcTexelSize));\r\n float lumaE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 0.0 ), srcTexelSize));\r\n float lumaN = FxaaLuma(FxaaTex(srcTex, posM, vec2( 0.0, -1.0 ), srcTexelSize));\r\n float lumaW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 0.0 ), srcTexelSize));\r\n float lumaM = FxaaLuma(FxaaTexTop(srcTex, posM));\r\n // find max and min luminance\r\n float rangeMax = max(max(lumaN, lumaW), max(lumaE, max(lumaS, lumaM)));\r\n float rangeMin = min(min(lumaN, lumaW), min(lumaE, min(lumaS, lumaM)));\r\n // calc maximum non-edge range\r\n float rangeMaxScaled = rangeMax * fxaaQualityEdgeThreshold;\r\n float range = rangeMax - rangeMin;\r\n float rangeMaxClamped = max(fxaaQualityEdgeThresholdMin, rangeMaxScaled);\r\n // exit when luma contrast is small (is not edge)\r\n if(range < rangeMaxClamped){\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n return;\r\n }\r\n float subpixRcpRange = 1.0/range;\r\n // note: the sampling coordinates can be calculated in vertex shader but the approach doesn't affect performance\r\n // visibly, thus we decided to leave calculation here for better readability.\r\n // calc other neighbours luminance\r\n float lumaNE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, -1.0 ), srcTexelSize));\r\n float lumaSW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, 1.0 ), srcTexelSize));\r\n float lumaSE = FxaaLuma(FxaaTex(srcTex, posM, vec2( 1.0, 1.0 ), srcTexelSize));\r\n float lumaNW = FxaaLuma(FxaaTex(srcTex, posM, vec2( -1.0, -1.0 ), srcTexelSize));\r\n/*--------------span calculation and subpix amount calulation-----------------*/\r\n float lumaNS = lumaN + lumaS;\r\n float lumaWE = lumaW + lumaE;\r\n float subpixNSWE = lumaNS + lumaWE;\r\n float edgeHorz1 = (-2.0 * lumaM) + lumaNS;\r\n float edgeVert1 = (-2.0 * lumaM) + lumaWE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNESE = lumaNE + lumaSE;\r\n float lumaNWNE = lumaNW + lumaNE;\r\n float edgeHorz2 = (-2.0 * lumaE) + lumaNESE;\r\n float edgeVert2 = (-2.0 * lumaN) + lumaNWNE;\r\n/*--------------------------------------------------------------------------*/\r\n float lumaNWSW = lumaNW + lumaSW;\r\n float lumaSWSE = lumaSW + lumaSE;\r\n float edgeHorz4 = (abs(edgeHorz1) * 2.0) + abs(edgeHorz2);\r\n float edgeVert4 = (abs(edgeVert1) * 2.0) + abs(edgeVert2);\r\n float edgeHorz3 = (-2.0 * lumaW) + lumaNWSW;\r\n float edgeVert3 = (-2.0 * lumaS) + lumaSWSE;\r\n float edgeHorz = abs(edgeHorz3) + edgeHorz4;\r\n float edgeVert = abs(edgeVert3) + edgeVert4;\r\n/*--------------------subpix amount calulation------------------------------*/\r\n float subpixNWSWNESE = lumaNWSW + lumaNESE;\r\n float lengthSign = srcTexelSize.x;\r\n bool horzSpan = edgeHorz >= edgeVert;\r\n // debug code edge span visualization\r\n/*' if (horzSpan)\r\n gl_FragColor = vec4(0.0, 0.0, 1.0, 1.0);\r\n else\r\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\r\n return;*/\r\n float subpixA = subpixNSWE * 2.0 + subpixNWSWNESE;\r\n/*--------------------------------------------------------------------------*/\r\n if(!horzSpan) lumaN = lumaW;\r\n if(!horzSpan) lumaS = lumaE;\r\n if(horzSpan) lengthSign = srcTexelSize.y;\r\n float subpixB = (subpixA * (1.0/12.0)) - lumaM;\r\n/*--------------------------------------------------------------------------*/\r\n float gradientN = lumaN - lumaM;\r\n float gradientS = lumaS - lumaM;\r\n float lumaNN = lumaN + lumaM;\r\n float lumaSS = lumaS + lumaM;\r\n bool pairN = abs(gradientN) >= abs(gradientS);\r\n float gradient = max(abs(gradientN), abs(gradientS));\r\n if(pairN) lengthSign = -lengthSign;\r\n float subpixC = clamp(abs(subpixB) * subpixRcpRange, 0.0, 1.0);\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posB;\r\n posB = posM;\r\n vec2 offNP;\r\n offNP.x = (!horzSpan) ? 0.0 : srcTexelSize.x;\r\n offNP.y = ( horzSpan) ? 0.0 : srcTexelSize.y;\r\n if(!horzSpan) posB.x += lengthSign * 0.5;\r\n if( horzSpan) posB.y += lengthSign * 0.5;\r\n/*--------------------------------------------------------------------------*/\r\n vec2 posN;\r\n posN = posB - offNP * FXAA_QUALITY_P0;\r\n vec2 posP;\r\n posP = posB + offNP * FXAA_QUALITY_P0;\r\n float subpixD = ((-2.0)*subpixC) + 3.0;\r\n float lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN));\r\n float subpixE = subpixC * subpixC;\r\n float lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP));\r\n/*--------------------------------------------------------------------------*/\r\n if(!pairN) lumaNN = lumaSS;\r\n float gradientScaled = gradient * 1.0/4.0;\r\n float lumaMM = lumaM - lumaNN * 0.5;\r\n float subpixF = subpixD * subpixE;\r\n bool lumaMLTZero = lumaMM < 0.0;\r\n/*---------------------looped edge-end search-------------------------------*/\r\n lumaEndN -= lumaNN * 0.5;\r\n lumaEndP -= lumaNN * 0.5;\r\n bool doneN = abs(lumaEndN) >= gradientScaled;\r\n bool doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P1;\r\n bool doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P1;\r\n/*--------------------------------------------------------------------------*/\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P2;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P2;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 3)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P3;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P3;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 4)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P4;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P4;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 5)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P5;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P5;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 6)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P6;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P6;\r\n/*--------------------------------------------------------------------------*/\r\n #if (FXAA_QUALITY_PS > 7)\r\n if(doneNP) {\r\n if(!doneN) lumaEndN = FxaaLuma(FxaaTexTop(srcTex, posN.xy));\r\n if(!doneP) lumaEndP = FxaaLuma(FxaaTexTop(srcTex, posP.xy));\r\n if(!doneN) lumaEndN = lumaEndN - lumaNN * 0.5;\r\n if(!doneP) lumaEndP = lumaEndP - lumaNN * 0.5;\r\n doneN = abs(lumaEndN) >= gradientScaled;\r\n doneP = abs(lumaEndP) >= gradientScaled;\r\n if(!doneN) posN -= offNP * FXAA_QUALITY_P7;\r\n doneNP = (!doneN) || (!doneP);\r\n if(!doneP) posP += offNP * FXAA_QUALITY_P7;\r\n/*--------------------------------------------------------------------------*/\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n #endif\r\n }\r\n/*----------------calculate subpix offset due to edge ends-------------------*/\r\n float dstN = posM.x - posN.x;\r\n float dstP = posP.x - posM.x;\r\n if(!horzSpan) dstN = posM.y - posN.y;\r\n if(!horzSpan) dstP = posP.y - posM.y;\r\n/*--------------------------------------------------------------------------*/\r\n bool goodSpanN = (lumaEndN < 0.0) != lumaMLTZero;\r\n float spanLength = (dstP + dstN);\r\n bool goodSpanP = (lumaEndP < 0.0) != lumaMLTZero;\r\n float spanLengthRcp = 1.0 / spanLength;\r\n/*--------------------------------------------------------------------------*/\r\n bool directionN = dstN < dstP;\r\n float dst = min(dstN, dstP);\r\n bool goodSpan = directionN ? goodSpanN : goodSpanP;\r\n float subpixG = subpixF * subpixF;\r\n float pixelOffset = (dst * (-spanLengthRcp)) + 0.5;\r\n float subpixH = subpixG * fxaaQualitySubpix;\r\n/*-----------------calc texture offest using subpix-------------------------*/\r\n float pixelOffsetGood = goodSpan ? pixelOffset : 0.0;\r\n float pixelOffsetSubpix = max(pixelOffsetGood, subpixH);\r\n\r\n float offset = pixelOffsetSubpix * lengthSign;\r\n #ifdef BG_TRANSPARENT\r\n // get original texel\r\n vec4 rgbaA = FxaaTexTopAlpha(srcTex, posM);\r\n // calc step to blended texel\r\n vec2 step = sign((!horzSpan) ? vec2 (offset, 0.0) : vec2 (0.0, offset));\r\n // get neighboring texel\r\n vec4 rgbaB = FxaaTexTopAlpha(srcTex, posM + step * srcTexelSize);\r\n // calc blend factor from offset\r\n float f = (!horzSpan) ? offset / srcTexelSize.x : offset / srcTexelSize.y;\r\n f = abs(f);\r\n // calc alpha (special formula to emulate blending with bg)\r\n gl_FragColor.a = 1.0 - mix(1.0 - rgbaA.a, 1.0 - rgbaB.a, f);\r\n // calc color (special formula to emulate blending with bg)\r\n gl_FragColor.rgb = mix(rgbaA.rgb * rgbaA.a, rgbaB.rgb * rgbaB.a, f) / gl_FragColor.a;\r\n #else\r\n if(!horzSpan) {\r\n posM.x += offset;\r\n } else {\r\n posM.y += offset;\r\n }\r\n gl_FragColor = FxaaTexTopAlpha(srcTex, posM);\r\n #endif\r\n return;\r\n}\r\n"; +;// ./src/gfx/shaders/FXAAMaterial.js @@ -30678,11 +30679,9 @@ class FXAAMaterial extends external_module_three_commonjs_three_commonjs2_three_ } FXAAMaterial.prototype.bgTransparent = false; /* harmony default export */ const shaders_FXAAMaterial = (FXAAMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/AO.frag -const AO_namespaceObject = "precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 32\r\nuniform vec3 samplesKernel[MAX_SAMPLES_COUNT];\r\nuniform sampler2D noiseTexture;\r\nuniform vec2 noiseTexelSize;\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D depthTexture;\r\nuniform sampler2D normalTexture;\r\nuniform vec2 srcTexelSize;\r\nuniform vec2 camNearFar;\r\nuniform mat4 projMatrix;\r\n\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\nuniform float kernelRadius;\r\nuniform float depthThreshold;\r\nuniform float factor;\r\n\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n // remap coordinates to prevent noise exture rescale\r\n vec2 vUvNoise = vUv / srcTexelSize * noiseTexelSize;\r\n vec4 normalData = texture2D(normalTexture, vUv);\r\n // return for background fragments (their normals are zero vectors)\r\n if (length(normalData.rgb) < EPSILON) {\r\n // 0.0 in alpha component means that it is background fragment\r\n gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);\r\n return;\r\n }\r\n //[0, 1] -> [-1, 1]\r\n vec3 normal = (normalData.rgb * 2.0 - 1.0);\r\n // normalData.a store 1.0 if normal was build for frontfaced surface\r\n // and 0.0 in other case\r\n if (normalData.a < EPSILON) {\r\n normal *= -1.0;\r\n }\r\n // get random vector for sampling sphere rotation\r\n vec3 randN = texture2D(noiseTexture, vUvNoise).rgb * 2.0 - 1.0;\r\n randN = normalize(randN);\r\n // build TBN (randomly rotated around normal)\r\n vec3 tangent = normalize(randN - normal * dot(randN, normal));\r\n vec3 bitangent = cross(tangent, normal);\r\n mat3 TBN = mat3(tangent, bitangent, normal);\r\n // calc AO value\r\n float AO = 0.0;\r\n for (int i = 0 ; i < MAX_SAMPLES_COUNT ; i++) {\r\n // rotate sampling kernel around normal\r\n vec3 reflectedSample = TBN * samplesKernel[i];\r\n // get sample\r\n vec3 samplePos = viewPos + reflectedSample * kernelRadius;\r\n\r\n // project sample to screen to get sample's screen pos\r\n vec4 SampleScrPos = vec4(samplePos, 1.0);\r\n // eye -> clip\r\n SampleScrPos = projMatrix * SampleScrPos;\r\n // normalize\r\n SampleScrPos.xy /= SampleScrPos.w;\r\n //[-1, 1] -> [0, 1]\r\n SampleScrPos.xy = (SampleScrPos.xy + vec2(1.0)) * 0.5;\r\n\r\n // get view z for sample projected to the objct surface\r\n float sampleDepth = CalcViewZ(SampleScrPos.xy);\r\n // calc occlusion made by object surface at the sample\r\n AO += step(samplePos.z, sampleDepth);\r\n }\r\n // calc result AO-map color\r\n AO = 1.0 - max(0.0, AO / float(MAX_SAMPLES_COUNT) * factor);\r\n // write value to AO-map\r\n gl_FragColor = vec4(AO, AO, AO, 1.0);\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/AOMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/AO.frag +const AO_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 32\r\nuniform vec3 samplesKernel[MAX_SAMPLES_COUNT];\r\nuniform sampler2D noiseTexture;\r\nuniform vec2 noiseTexelSize;\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D depthTexture;\r\nuniform sampler2D normalTexture;\r\nuniform vec2 srcTexelSize;\r\nuniform vec2 camNearFar;\r\nuniform mat4 projMatrix;\r\n\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\nuniform float kernelRadius;\r\nuniform float depthThreshold;\r\nuniform float factor;\r\n\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n // remap coordinates to prevent noise exture rescale\r\n vec2 vUvNoise = vUv / srcTexelSize * noiseTexelSize;\r\n vec4 normalData = texture2D(normalTexture, vUv);\r\n // return for background fragments (their normals are zero vectors)\r\n if (length(normalData.rgb) < EPSILON) {\r\n // 0.0 in alpha component means that it is background fragment\r\n gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);\r\n return;\r\n }\r\n //[0, 1] -> [-1, 1]\r\n vec3 normal = (normalData.rgb * 2.0 - 1.0);\r\n // normalData.a store 1.0 if normal was build for frontfaced surface\r\n // and 0.0 in other case\r\n if (normalData.a < EPSILON) {\r\n normal *= -1.0;\r\n }\r\n // get random vector for sampling sphere rotation\r\n vec3 randN = texture2D(noiseTexture, vUvNoise).rgb * 2.0 - 1.0;\r\n randN = normalize(randN);\r\n // build TBN (randomly rotated around normal)\r\n vec3 tangent = normalize(randN - normal * dot(randN, normal));\r\n vec3 bitangent = cross(tangent, normal);\r\n mat3 TBN = mat3(tangent, bitangent, normal);\r\n // calc AO value\r\n float AO = 0.0;\r\n for (int i = 0 ; i < MAX_SAMPLES_COUNT ; i++) {\r\n // rotate sampling kernel around normal\r\n vec3 reflectedSample = TBN * samplesKernel[i];\r\n // get sample\r\n vec3 samplePos = viewPos + reflectedSample * kernelRadius;\r\n\r\n // project sample to screen to get sample's screen pos\r\n vec4 SampleScrPos = vec4(samplePos, 1.0);\r\n // eye -> clip\r\n SampleScrPos = projMatrix * SampleScrPos;\r\n // normalize\r\n SampleScrPos.xy /= SampleScrPos.w;\r\n //[-1, 1] -> [0, 1]\r\n SampleScrPos.xy = (SampleScrPos.xy + vec2(1.0)) * 0.5;\r\n\r\n // get view z for sample projected to the objct surface\r\n float sampleDepth = CalcViewZ(SampleScrPos.xy);\r\n // calc occlusion made by object surface at the sample\r\n AO += step(samplePos.z, sampleDepth);\r\n }\r\n // calc result AO-map color\r\n AO = 1.0 - max(0.0, AO / float(MAX_SAMPLES_COUNT) * factor);\r\n // write value to AO-map\r\n gl_FragColor = vec4(AO, AO, AO, 1.0);\r\n}\r\n"; +;// ./src/gfx/shaders/AOMaterial.js @@ -30763,11 +30762,9 @@ class AOMaterial extends external_module_three_commonjs_three_commonjs2_three_am } } /* harmony default export */ const shaders_AOMaterial = (AOMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/AOHorBlur.frag -const AOHorBlur_namespaceObject = "precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = res;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x + samplesOffsets[i] * srcTexelSize.x, y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb = res.rgb / weightSum;\r\n gl_FragColor = res;\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/AOHorBlurMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/AOHorBlur.frag +const AOHorBlur_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = res;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x + samplesOffsets[i] * srcTexelSize.x, y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x + samplesOffsets[i] * srcTexelSize.x, y )).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb = res.rgb / weightSum;\r\n gl_FragColor = res;\r\n}\r\n"; +;// ./src/gfx/shaders/AOHorBlurMaterial.js @@ -30805,11 +30802,9 @@ class AOHorBlurMaterial extends external_module_three_commonjs_three_commonjs2_t } } /* harmony default export */ const shaders_AOHorBlurMaterial = (AOHorBlurMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/AOVertBlurWithBlend.frag -const AOVertBlurWithBlend_namespaceObject = "precision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nuniform mat4 projMatrix;\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\n#ifdef USE_FOG\r\n uniform vec2 fogNearFar;\r\n uniform vec4 fogColor;\r\n#endif\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 color = texture2D(diffuseTexture, vec2(x, y));\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = color;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x, y + samplesOffsets[i] * srcTexelSize.y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb /= weightSum;\r\n\r\n #if defined(USE_FOG) && !defined(FOG_TRANSPARENT)\r\n // Add fog to the result value\r\n // Proper way to get an image with fog and ao requires formula:\r\n // gl_FragColor = fragColor*AO*(1-fogFactor) + fogColor*fogFactor\r\n // But we have already fogged molecule to add AO too. Let's split the straight formula into our real steps!\r\n // We have: AO, fogFactor, fogColor,\r\n // color = fragColor*(1-fogFactor) + fogColor*fogFactor (it comes from diffuseTexture,\r\n // where molecule has been already drawn with fog)\r\n // Transform:\r\n // fragColor*AO*(1-fogFactor) + fogColor*fogFactor =\r\n // = [fragColor*(1-fogFactor) = color - fogColor*fogFactor] =\r\n // = (color - fogColor*fogFactor)*AO + fogColor*fogFactor =\r\n // = color*AO + fogColor*fogFactor*(1 - AO)\r\n // Result: gl_FragColor = color*AO + fogColor*fogFactor*(1 - AO)\r\n float fogFactor = smoothstep(fogNearFar.x, fogNearFar.y, - viewPos.z) * fogColor.a;\r\n gl_FragColor.rgb = color.rgb * res.rgb + fogColor.rgb * fogFactor *(vec3(1.0, 1.0, 1.0) - res.rgb);\r\n #else\r\n gl_FragColor.rgb = color.rgb * res.rgb;\r\n #endif\r\n gl_FragColor.a = color.a;\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/AOVertBlurWithBlendMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/AOVertBlurWithBlend.frag +const AOVertBlurWithBlend_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n#define EPSILON 0.0000001\r\n\r\n#define MAX_SAMPLES_COUNT 5\r\nuniform float samplesOffsets[MAX_SAMPLES_COUNT];\r\nuniform sampler2D diffuseTexture;\r\nuniform sampler2D aoMap;\r\nuniform sampler2D depthTexture;\r\nuniform vec2 srcTexelSize;\r\n\r\nuniform mat4 projMatrix;\r\nuniform float aspectRatio;\r\nuniform float tanHalfFOV;\r\n\r\n#ifdef USE_FOG\r\n uniform vec2 fogNearFar;\r\n uniform vec4 fogColor;\r\n#endif\r\nvarying vec2 vUv;\r\n\r\nfloat CalcViewZ(vec2 screenPos)\r\n{\r\n float depth = texture2D(depthTexture, screenPos).x;\r\n // [0, 1]->[-1, 1]\r\n float clipedZ = 2.0 * depth - 1.0;\r\n // see THREE.js camera.makeFrustum for projection details\r\n return (-projMatrix[3][2] / (clipedZ + projMatrix[2][2]));\r\n}\r\n\r\nvec3 ViewPosFromDepth(vec2 screenPos)\r\n{\r\n vec3 viewPos;\r\n viewPos.z = CalcViewZ(screenPos);\r\n //[0, 1]->[-1, 1]\r\n vec2 projPos = 2.0 * screenPos - 1.0;\r\n // reconstruct viewposition in right-handed sc with z to viewer\r\n viewPos.xy = vec2(\r\n projPos.x * aspectRatio * tanHalfFOV * abs(viewPos.z),\r\n projPos.y * tanHalfFOV * abs(viewPos.z)\r\n );\r\n return viewPos;\r\n}\r\n\r\nvoid main() {\r\n vec3 viewPos = ViewPosFromDepth(vUv);\r\n float x = vUv.x;\r\n float y = vUv.y;\r\n vec4 color = texture2D(diffuseTexture, vec2(x, y));\r\n vec4 res = vec4(0.0);\r\n res.a = texture2D(aoMap, vec2(x, y )).a;\r\n // return for background fragments (0.0 in alpha component means that it is background fragment)\r\n if (res.a < EPSILON) {\r\n gl_FragColor = color;\r\n return;\r\n }\r\n\r\n float pixelDepth = texture2D(depthTexture, vec2(x, y)).x;\r\n float weightSum = 0.0;\r\n for (int i = 0; i < MAX_SAMPLES_COUNT; ++i) {\r\n if (texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).a < EPSILON) {\r\n continue;\r\n }\r\n vec2 samplePos = vec2(x, y + samplesOffsets[i] * srcTexelSize.y);\r\n float depth = texture2D(depthTexture, samplePos).x;\r\n float weight = (1.0 / (0.0001 + abs(depth - pixelDepth)));\r\n res.rgb += texture2D(aoMap, vec2(x, y + samplesOffsets[i] * srcTexelSize.y)).rgb * weight;\r\n weightSum += weight;\r\n }\r\n res.rgb /= weightSum;\r\n\r\n #if defined(USE_FOG) && !defined(FOG_TRANSPARENT)\r\n // Add fog to the result value\r\n // Proper way to get an image with fog and ao requires formula:\r\n // gl_FragColor = fragColor*AO*(1-fogFactor) + fogColor*fogFactor\r\n // But we have already fogged molecule to add AO too. Let's split the straight formula into our real steps!\r\n // We have: AO, fogFactor, fogColor,\r\n // color = fragColor*(1-fogFactor) + fogColor*fogFactor (it comes from diffuseTexture,\r\n // where molecule has been already drawn with fog)\r\n // Transform:\r\n // fragColor*AO*(1-fogFactor) + fogColor*fogFactor =\r\n // = [fragColor*(1-fogFactor) = color - fogColor*fogFactor] =\r\n // = (color - fogColor*fogFactor)*AO + fogColor*fogFactor =\r\n // = color*AO + fogColor*fogFactor*(1 - AO)\r\n // Result: gl_FragColor = color*AO + fogColor*fogFactor*(1 - AO)\r\n float fogFactor = smoothstep(fogNearFar.x, fogNearFar.y, - viewPos.z) * fogColor.a;\r\n gl_FragColor.rgb = color.rgb * res.rgb + fogColor.rgb * fogFactor *(vec3(1.0, 1.0, 1.0) - res.rgb);\r\n #else\r\n gl_FragColor.rgb = color.rgb * res.rgb;\r\n #endif\r\n gl_FragColor.a = color.a;\r\n}\r\n"; +;// ./src/gfx/shaders/AOVertBlurWithBlendMaterial.js @@ -30891,11 +30886,9 @@ class AOVertBlurWithBlendMaterial extends external_module_three_commonjs_three_c AOVertBlurWithBlendMaterial.prototype.useFog = true; AOVertBlurWithBlendMaterial.prototype.fogTransparent = false; /* harmony default export */ const shaders_AOVertBlurWithBlendMaterial = (AOVertBlurWithBlendMaterial); -;// CONCATENATED MODULE: ./src/gfx/shaders/Anaglyph.frag -const Anaglyph_namespaceObject = "precision highp float;\r\n\r\nuniform sampler2D srcL;\r\nuniform sampler2D srcR;\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vec4 l = texture2D(srcL, vUv);\r\n vec4 r = texture2D(srcR, vUv);\r\n gl_FragColor = vec4(l.r, r.g, r.b, 1.0);\r\n}\r\n"; -;// CONCATENATED MODULE: ./src/gfx/shaders/AnaglyphMaterial.js -/* eslint-disable no-magic-numbers */ -/* eslint-disable guard-for-in */ +;// ./src/gfx/shaders/Anaglyph.frag +const Anaglyph_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nuniform sampler2D srcL;\r\nuniform sampler2D srcR;\r\nvarying vec2 vUv;\r\n\r\nvoid main() {\r\n vec4 l = texture2D(srcL, vUv);\r\n vec4 r = texture2D(srcR, vUv);\r\n gl_FragColor = vec4(l.r, r.g, r.b, 1.0);\r\n}\r\n"; +;// ./src/gfx/shaders/AnaglyphMaterial.js @@ -30923,7 +30916,7 @@ class AnaglyphMaterial extends external_module_three_commonjs_three_commonjs2_th } } /* harmony default export */ const shaders_AnaglyphMaterial = (AnaglyphMaterial); -;// CONCATENATED MODULE: ./src/gfx/ViewInterpolator.js +;// ./src/gfx/ViewInterpolator.js class View { @@ -31005,7 +30998,7 @@ class ViewInterpolator { return new View(); } } -;// CONCATENATED MODULE: ./src/utils/Cookies.js +;// ./src/utils/Cookies.js const MAX_COOKIE_LEN = 4000; @@ -31028,7 +31021,7 @@ function _chunkString(string, chunkLen) { */ function Cookies(context, opts) { this.context = context; - this._opts = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge({ + this._opts = __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge({ path: '/' }, opts); } @@ -31114,7 +31107,7 @@ Cookies.prototype._exists = function (key) { return document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`)); }; /* harmony default export */ const utils_Cookies = (Cookies); -;// CONCATENATED MODULE: ./src/gfx/vr/createWebVRButton.js +;// ./src/gfx/vr/createWebVRButton.js /* * Toggling WebVR is done through button.click because of limitations on calling requestPresent in webVR: * VRDisplay::requestPresent should be called from user gesture: @@ -31128,7 +31121,7 @@ Cookies.prototype._exists = function (key) { button.style.width = '100px'; button.textContent = 'ENTER VR'; let currentSession = null; - function onSessionEnded( /* event */ + function onSessionEnded(/* event */ ) { currentSession.removeEventListener('end', onSessionEnded); button.textContent = 'ENTER VR'; @@ -31206,7 +31199,7 @@ Cookies.prototype._exists = function (key) { stylizeElement(message); return message; } -;// CONCATENATED MODULE: ./src/gfx/vr/WebVRPoC.js +;// ./src/gfx/vr/WebVRPoC.js @@ -31457,9 +31450,9 @@ class WebVRPoC { return gfx && gfx.renderer ? gfx.renderer.domElement : null; } } -;// CONCATENATED MODULE: ./src/gfx/shaders/ScreenQuadFromDistortionTex.frag -const ScreenQuadFromDistortionTex_namespaceObject = "precision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform vec3 aberration;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n \r\n gl_FragColor.r = texture2D(srcTex, 0.5 * (uv * aberration[0] + 1.0)).r;\r\n gl_FragColor.g = texture2D(srcTex, 0.5 * (uv * aberration[1] + 1.0)).g;\r\n gl_FragColor.b = texture2D(srcTex, 0.5 * (uv * aberration[2] + 1.0)).b;\r\n gl_FragColor.a = 1.0;\r\n}"; -;// CONCATENATED MODULE: ./src/Miew.js +;// ./src/gfx/shaders/ScreenQuadFromDistortionTex.frag +const ScreenQuadFromDistortionTex_namespaceObject = "/*\r\n * GLSL Version: ES 1.00 (WebGL 1.0 compatible)\r\n * No #version directive in this file.\r\n * Use GLSL1 semantics (`attribute`/`varying`, `texture2D`, `gl_FragColor`).\r\n * Keep `glslVersion` as default (GLSL1) or set `THREE.GLSL1` explicitly.\r\n */\r\n\r\nprecision highp float;\r\n\r\nvarying vec2 vUv;\r\nuniform sampler2D srcTex;\r\nuniform vec3 aberration;\r\n\r\nvoid main() {\r\n vec2 uv = vUv * 2.0 - 1.0;\r\n \r\n gl_FragColor.r = texture2D(srcTex, 0.5 * (uv * aberration[0] + 1.0)).r;\r\n gl_FragColor.g = texture2D(srcTex, 0.5 * (uv * aberration[1] + 1.0)).g;\r\n gl_FragColor.b = texture2D(srcTex, 0.5 * (uv * aberration[2] + 1.0)).b;\r\n gl_FragColor.a = 1.0;\r\n}"; +;// ./src/Miew.js /* global PACKAGE_VERSION:false */ @@ -31577,7 +31570,7 @@ function chooseFogColor() { */ function Miew(opts) { utils_EventDispatcher.call(this); - this._opts = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge({ + this._opts = __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge({ settingsCookie: 'settings', cookiePath: '/' }, opts); @@ -31586,7 +31579,7 @@ function Miew(opts) { /** @type {ViewInterpolator} */ this._interpolator = new ViewInterpolator(); /** @type {HTMLElement} */ - this._container = opts && opts.container || document.getElementById('miew-container') || external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].head(document.getElementsByClassName('miew-container')) || document.body; + this._container = opts && opts.container || document.getElementById('miew-container') || __WEBPACK_EXTERNAL_MODULE_lodash_default__.head(document.getElementsByClassName('miew-container')) || document.body; /** @type {HTMLElement} */ this._containerRoot = this._container; @@ -31852,12 +31845,6 @@ Miew.prototype._requestAnimationFrame = function (callback) { } requestAnimationFrame(callback); }; -function arezSpritesSupported(context) { - return context.getExtension('EXT_frag_depth'); -} -function isAOSupported(context) { - return context.getExtension('WEBGL_depth_texture') && context.getExtension('WEBGL_draw_buffers'); -} /** * Initialize WebGL and set 3D scene up. @@ -31877,19 +31864,11 @@ Miew.prototype._initGfx = function () { webGLOptions.antialias = true; } gfx.renderer2d = new gfx_CSS2DRenderer(); - gfx.renderer = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGL1Renderer(webGLOptions); + gfx.renderer = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderer(webGLOptions); gfx.renderer.shadowMap.enabled = settings.now.shadow.on; gfx.renderer.shadowMap.autoUpdate = false; gfx.renderer.shadowMap.type = external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.PCFShadowMap; capabilities.init(gfx.renderer); - - // z-sprites and ambient occlusion possibility - if (!arezSpritesSupported(gfx.renderer.getContext())) { - settings.set('zSprites', false); - } - if (!isAOSupported(gfx.renderer.getContext())) { - settings.set('ao', false); - } gfx.renderer.autoClear = false; gfx.renderer.setPixelRatio(window.devicePixelRatio); gfx.renderer.setSize(gfx.width, gfx.height); @@ -31946,10 +31925,8 @@ Miew.prototype._initGfx = function () { format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.RGBAFormat, depthBuffer: true }); - if (gfx.renderer.getContext().getExtension('WEBGL_depth_texture')) { - gfx.offscreenBuf.depthTexture = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.DepthTexture(); - gfx.offscreenBuf.depthTexture.type = external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.UnsignedShortType; - } + gfx.offscreenBuf.depthTexture = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.DepthTexture(); + gfx.offscreenBuf.depthTexture.type = external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.UnsignedShortType; gfx.offscreenBuf2 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderTarget(deviceWidth, deviceHeight, { minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, @@ -31972,35 +31949,31 @@ Miew.prototype._initGfx = function () { gfx.volFFTex = gfx.offscreenBuf4; gfx.volWFFTex = gfx.offscreenBuf; - // use float textures for volume rendering if possible - if (gfx.renderer.getContext().getExtension('OES_texture_float')) { - gfx.offscreenBuf5 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderTarget(deviceWidth, deviceHeight, { - minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, - magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, - format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.RGBAFormat, - type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.FloatType, - depthBuffer: false - }); - gfx.offscreenBuf6 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderTarget(deviceWidth, deviceHeight, { - minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, - magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, - format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.RGBAFormat, - type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.FloatType, - depthBuffer: false - }); - gfx.offscreenBuf7 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderTarget(deviceWidth, deviceHeight, { - minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, - magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, - format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.RGBAFormat, - type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.FloatType, - depthBuffer: true - }); - gfx.volBFTex = gfx.offscreenBuf5; - gfx.volFFTex = gfx.offscreenBuf6; - gfx.volWFFTex = gfx.offscreenBuf7; - } else { - this.logger.warn('Device doesn\'t support OES_texture_float extension'); - } + // use float textures for volume rendering (WebGL2 core feature) + gfx.offscreenBuf5 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderTarget(deviceWidth, deviceHeight, { + minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, + magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, + format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.RGBAFormat, + type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.FloatType, + depthBuffer: false + }); + gfx.offscreenBuf6 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderTarget(deviceWidth, deviceHeight, { + minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, + magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, + format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.RGBAFormat, + type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.FloatType, + depthBuffer: false + }); + gfx.offscreenBuf7 = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderTarget(deviceWidth, deviceHeight, { + minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, + magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, + format: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.RGBAFormat, + type: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.FloatType, + depthBuffer: true + }); + gfx.volBFTex = gfx.offscreenBuf5; + gfx.volFFTex = gfx.offscreenBuf6; + gfx.volWFFTex = gfx.offscreenBuf7; gfx.stereoBufL = new external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.WebGLRenderTarget(deviceWidth, deviceHeight, { minFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, magFilter: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject.LinearFilter, @@ -32522,12 +32495,11 @@ Miew.prototype._setUberMaterialValues = function (values) { Miew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) { const gfx = this._gfx; const gl = gfx.renderer.getContext(); - const ext = gl.getExtension('WEBGL_draw_buffers'); const { properties } = gfx.renderer; if (!on) { - ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, null]); + gl.drawBuffers([gl.COLOR_ATTACHMENT0, null]); return; } @@ -32546,10 +32518,10 @@ Miew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) { fb.width = renderBuffer.width; fb.height = renderBuffer.height; gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT0, gl.TEXTURE_2D, tx, 0); - gl.framebufferTexture2D(gl.FRAMEBUFFER, ext.COLOR_ATTACHMENT1_WEBGL, gl.TEXTURE_2D, tx8, 0); + gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT1, gl.TEXTURE_2D, tx8, 0); - // mapping textures - ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, ext.COLOR_ATTACHMENT1_WEBGL]); + // mapping textures (MRT is core feature in WebGL2) + gl.drawBuffers([gl.COLOR_ATTACHMENT0, gl.COLOR_ATTACHMENT1]); }; Miew.prototype._renderScene = function () { return function (camera, distortion, target) { @@ -33017,7 +32989,7 @@ Miew.prototype.resetView = function () { }); }; Miew.prototype._export = function (format) { - const TheExporter = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].head(io.exporters.find({ + const TheExporter = __WEBPACK_EXTERNAL_MODULE_lodash_default__.head(io.exporters.find({ format })); if (!TheExporter) { @@ -33048,7 +33020,7 @@ const rePdbId = /^(?:(pdb|cif|ccp4|dsn6):\s*)?(\d[a-z\d]{3})$/i; const rePubchem = /^(?:pc|pubchem):\s*([a-z]+)$/i; const reUrlScheme = /^([a-z][a-z\d\-+.]*):/i; function resolveSourceShortcut(source, opts) { - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(source)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(source)) { return source; } @@ -33109,7 +33081,7 @@ function updateBinaryMode(opts) { // detect by format if (opts.fileType !== undefined) { - const TheParser = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].head(io.parsers.find({ + const TheParser = __WEBPACK_EXTERNAL_MODULE_lodash_default__.head(io.parsers.find({ format: opts.fileType })); if (TheParser) { @@ -33121,7 +33093,7 @@ function updateBinaryMode(opts) { // detect by file extension if (binary === undefined && opts.fileExt !== undefined) { - const TheParser = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].head(io.parsers.find({ + const TheParser = __WEBPACK_EXTERNAL_MODULE_lodash_default__.head(io.parsers.find({ ext: opts.fileExt })); if (TheParser) { @@ -33156,7 +33128,7 @@ function _fetchData(source, opts, job) { source = resolveSourceShortcut(source, opts); // detect a proper loader - const TheLoader = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].head(io.loaders.find({ + const TheLoader = __WEBPACK_EXTERNAL_MODULE_lodash_default__.head(io.loaders.find({ type: opts.sourceType, source })); @@ -33168,7 +33140,7 @@ function _fetchData(source, opts, job) { const fileName = opts.fileName || TheLoader.extractName(source); if (fileName) { const [name, fileExt] = utils.splitFileName(fileName); - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].defaults(opts, { + __WEBPACK_EXTERNAL_MODULE_lodash_default__.defaults(opts, { name, fileExt, fileName @@ -33181,15 +33153,15 @@ function _fetchData(source, opts, job) { // FIXME: All new settings retrieved from server are applied after the loading is complete. However, we need some // flags to alter the loading process itself. Here we apply them in advance. Dirty hack. Kill the server, remove // all hacks and everybody's happy. - let newOptions = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(opts, 'preset.expression'); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(newOptions)) { + let newOptions = __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(opts, 'preset.expression'); + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(newOptions)) { newOptions = JSON.parse(newOptions); if (newOptions && newOptions.settings) { const keys = ['singleUnit']; for (let keyIndex = 0, keyCount = keys.length; keyIndex < keyCount; ++keyIndex) { const key = keys[keyIndex]; - const value = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(newOptions.settings, key); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(value)) { + const value = __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(newOptions.settings, key); + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(value)) { settings.set(key, value); } } @@ -33239,7 +33211,7 @@ function _parseData(data, opts, job) { job.notify({ type: 'parsing' }); - const TheParser = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].head(io.parsers.find({ + const TheParser = __WEBPACK_EXTERNAL_MODULE_lodash_default__.head(io.parsers.find({ format: opts.fileType, ext: opts.fileExt, data @@ -33285,7 +33257,7 @@ function _parseData(data, opts, job) { * @returns {Promise} name of the visual that was added to the viewer */ Miew.prototype.load = function (source, opts) { - opts = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge({}, opts, { + opts = __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge({}, opts, { context: this }); @@ -33382,7 +33354,7 @@ Miew.prototype._startAnimation = function (fileData) { self.logger.error(message); } }); - } catch (e) { + } catch { this.logger.error('Animation file does not fit to current complex!'); return; } @@ -33445,7 +33417,7 @@ Miew.prototype._continueAnimation = function () { self._refreshTitle(` Frame ${self._frameInfo._currFrame} of ${self._frameInfo._framesCount} time interval - ${self._frameInfo._timeStep}`); try { self._frameInfo.nextFrame(); - } catch (e) { + } catch { self.logger.error('Error during animation'); self._stopAnimation(); return; @@ -33508,7 +33480,7 @@ Miew.prototype._onLoad = function (dataSource, opts) { this._curVisualName = visualName; const desc = this.info(); this.logger.info(`Parsed ${opts.fileName} (${desc.atoms} atoms, ${desc.bonds} bonds, ${desc.residues} residues, ${desc.chains} chains).`); - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isNumber(this._opts.unit)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isNumber(this._opts.unit)) { complex.setCurrentUnit(this._opts.unit); } if (opts.preset) { @@ -33573,7 +33545,7 @@ Miew.prototype.resetEd = function () { }; Miew.prototype.loadEd = function (source) { this.resetEd(); - const TheLoader = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].head(io.loaders.find({ + const TheLoader = __WEBPACK_EXTERNAL_MODULE_lodash_default__.head(io.loaders.find({ source })); if (!TheLoader) { @@ -33585,7 +33557,7 @@ Miew.prototype.loadEd = function (source) { }); loader.context = this; return loader.load().then(data => { - const TheParser = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].head(io.parsers.find({ + const TheParser = __WEBPACK_EXTERNAL_MODULE_lodash_default__.head(io.parsers.find({ format: 'ccp4' })); if (!TheParser) { @@ -33659,7 +33631,7 @@ Miew.prototype.changeUnit = function (unitIdx, name) { if (unitIdx === undefined) { return currentUnitInfo(); } - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(unitIdx)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(unitIdx)) { unitIdx = Math.max(parseInt(unitIdx, 10), 0); } if (visual.getComplex().setCurrentUnit(unitIdx)) { @@ -33949,7 +33921,7 @@ Miew.prototype._enterComponentEditMode = function () { editors.push(editor); } }); - if (editors === []) { + if (editors.length === 0) { return; } this._editors = editors; @@ -34517,7 +34489,7 @@ Miew.prototype.setOptions = function (opts) { if (opts.reps) { this._opts.reps = null; } - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].merge(this._opts, opts); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.merge(this._opts, opts); if (opts.settings) { this.set(opts.settings); } @@ -34541,7 +34513,7 @@ Miew.prototype.setOptions = function (opts) { const visual = this._getComplexVisual(); if (visual) { visual.getComplex().resetCurrentUnit(); - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isNumber(opts.unit)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isNumber(opts.unit)) { visual.getComplex().setCurrentUnit(opts.unit); } this.resetView(); @@ -34637,7 +34609,7 @@ Miew.prototype.removeObject = function (index) { * @returns {string} URL */ Miew.prototype.getURL = function (opts) { - return options.toURL(this.getState(external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].defaults(opts, { + return options.toURL(this.getState(__WEBPACK_EXTERNAL_MODULE_lodash_default__.defaults(opts, { compact: true, settings: false, view: false @@ -34654,7 +34626,7 @@ Miew.prototype.getURL = function (opts) { * @returns {string} script */ Miew.prototype.getScript = function (opts) { - return options.toScript(this.getState(external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].defaults(opts, { + return options.toScript(this.getState(__WEBPACK_EXTERNAL_MODULE_lodash_default__.defaults(opts, { compact: true, settings: true, view: true @@ -34684,7 +34656,7 @@ Miew.prototype._compareReps = function (complexVisual, compareWithDefaults) { let emptyReps = true; for (let i = 0, n = repCount; i < n; ++i) { repsDiff[i] = complexVisual.repGet(i).compare(compare ? currPreset[i] : null); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(repsDiff[i])) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(repsDiff[i])) { emptyReps = false; } } @@ -34704,7 +34676,7 @@ Miew.prototype._compareReps = function (complexVisual, compareWithDefaults) { */ Miew.prototype.getState = function (opts) { const state = {}; - opts = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].defaults(opts, { + opts = __WEBPACK_EXTERNAL_MODULE_lodash_default__.defaults(opts, { compact: true, settings: false, view: false @@ -34754,7 +34726,7 @@ Miew.prototype.getState = function (opts) { // settings if (opts.settings) { const diff = this.settings.getDiffs(false); - if (!external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isEmpty(diff)) { + if (!__WEBPACK_EXTERNAL_MODULE_lodash_default__.isEmpty(diff)) { state.settings = diff; } } @@ -34806,9 +34778,7 @@ Miew.prototype._updateShadowmapMeshes = function (process) { } }); }; -Miew.prototype._updateMaterials = function (values) { - let needTraverse = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false; - let process = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : undefined; +Miew.prototype._updateMaterials = function (values, needTraverse = false, process = undefined) { this._forEachComplexVisual(visual => visual.setMaterialValues(values, needTraverse, process)); for (let i = 0, n = this._objects.length; i < n; ++i) { const obj = this._objects[i]; @@ -34846,7 +34816,7 @@ Miew.prototype._embedWebXR = function () { }; Miew.prototype._initOnSettingsChanged = function () { const on = (props, func) => { - props = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isArray(props) ? props : [props]; + props = __WEBPACK_EXTERNAL_MODULE_lodash_default__.isArray(props) ? props : [props]; props.forEach(prop => { this.settings.addEventListener(`change:${prop}`, func); }); @@ -34867,21 +34837,12 @@ Miew.prototype._initOnSettingsChanged = function () { this._onBgColorChanged(); }); on('ao', () => { - if (settings.now.ao && !isAOSupported(this._gfx.renderer.getContext())) { - this.logger.warn('Your device or browser does not support ao'); - settings.set('ao', false); - } else { - const values = { - normalsToGBuffer: settings.now.ao - }; - this._setUberMaterialValues(values); - } + const values = { + normalsToGBuffer: settings.now.ao + }; + this._setUberMaterialValues(values); }); on('zSprites', () => { - if (settings.now.zSprites && !arezSpritesSupported(this._gfx.renderer.getContext())) { - this.logger.warn('Your device or browser does not support zSprites'); - settings.set('zSprites', false); - } this.rebuildAll(); }); on('fogColor', () => { @@ -35010,7 +34971,7 @@ Miew.prototype.select = function (expression, append) { return; } let sel = expression; - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isString(expression)) { + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isString(expression)) { sel = Miew_selectors.parse(expression).selector; } visual.select(sel, append); @@ -35379,12 +35340,12 @@ Miew.prototype.motm = function () { visual.resetReps(rep); }); }; -Miew.prototype.VERSION = true && "0.11.1" || 0; +Miew.prototype.VERSION = true && "0.12.0" || 0; // Uncomment this to get debug trace: // Miew.prototype.debugTracer = new utils.DebugTracer(Miew.prototype); -external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].assign(Miew, /** @lends Miew */{ +__WEBPACK_EXTERNAL_MODULE_lodash_default__.assign(Miew, /** @lends Miew */{ VERSION: Miew.prototype.VERSION, registeredPlugins: [], // export namespaces // TODO: WIP: refactoring external interface @@ -35413,14 +35374,14 @@ external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespac * var miew = new Miew(opts); */ thirdParty: { - lodash: external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"], + lodash: __WEBPACK_EXTERNAL_MODULE_lodash_default__, three: external_module_three_commonjs_three_commonjs2_three_amd_three_root_THREE_namespaceObject } }); /* harmony default export */ const src_Miew = (Miew); // EXTERNAL MODULE: ./src/utils/MiewCLIParser.js var MiewCLIParser = __webpack_require__(89); -;// CONCATENATED MODULE: ./src/utils/MiewCLIHelp.js +;// ./src/utils/MiewCLIHelp.js const modeIdDesc = { @@ -35631,7 +35592,7 @@ const help = { } }; /* harmony default export */ const MiewCLIHelp = (help); -;// CONCATENATED MODULE: ./src/Miew-cli.js +;// ./src/Miew-cli.js @@ -35781,11 +35742,11 @@ class CLIUtils { return helpData; } help(path) { - if (external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(path)) { - return `${this.joinHelpStr(MiewCLIHelp.$help)}\n${external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].slice(external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].sortBy(external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].keys(MiewCLIHelp)), 1).join(', ')}\n`; + if (__WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(path)) { + return `${this.joinHelpStr(MiewCLIHelp.$help)}\n${__WEBPACK_EXTERNAL_MODULE_lodash_default__.slice(__WEBPACK_EXTERNAL_MODULE_lodash_default__.sortBy(__WEBPACK_EXTERNAL_MODULE_lodash_default__.keys(MiewCLIHelp)), 1).join(', ')}\n`; } - const helpItem = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(MiewCLIHelp, path); - return external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].isUndefined(helpItem) ? this.help() : `${this.joinHelpStr(helpItem.$help)}\n`; + const helpItem = __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(MiewCLIHelp, path); + return __WEBPACK_EXTERNAL_MODULE_lodash_default__.isUndefined(helpItem) ? this.help() : `${this.joinHelpStr(helpItem.$help)}\n`; } load(miew, arg) { if (miew === undefined || arg === undefined || arg === '-f') { @@ -35834,7 +35795,7 @@ class CLIUtils { propagateProp(path, arg) { if (path !== undefined) { let argExc = {}; - const adapter = Miew_cli_options.adapters[typeof external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(Miew_cli_settings.defaults, path)]; + const adapter = Miew_cli_options.adapters[typeof __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(Miew_cli_settings.defaults, path)]; if (adapter === undefined) { const pathExc = { message: `${path} is not existed` @@ -35859,7 +35820,7 @@ class CLIUtils { } if (arg !== undefined && adapter(arg) !== arg && adapter(arg) !== arg > 0) { argExc = { - message: `${path} must be a "${typeof external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].get(Miew_cli_settings.defaults, path)}"` + message: `${path} must be a "${typeof __WEBPACK_EXTERNAL_MODULE_lodash_default__.get(Miew_cli_settings.defaults, path)}"` }; throw argExc; } @@ -35907,7 +35868,7 @@ ArgList.prototype.toJSO = function (cliUtils, cmd, arg) { const res = {}; const list = this._values; for (let i = 0, n = list.length; i < n; ++i) { - external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"].set(res, list[i].id, cliUtils.propagateProp(`${keyRemap(cmd)}.${arg}.${list[i].id}`, list[i].val)); + __WEBPACK_EXTERNAL_MODULE_lodash_default__.set(res, list[i].id, cliUtils.propagateProp(`${keyRemap(cmd)}.${arg}.${list[i].id}`, list[i].val)); } return res; }; @@ -35922,7 +35883,7 @@ cliutils.miew = null; cliutils.echo = null; cliutils.representations = representationsStorage; cliutils.utils = utilFunctions; -cliutils._ = external_module_lodash_commonjs_lodash_commonjs2_lodash_amd_lodash_root_namespaceObject["default"]; +cliutils._ = __WEBPACK_EXTERNAL_MODULE_lodash_default__; cliutils.CreateObjectPair = CreateObjectPair; cliutils.keyRemap = keyRemap; cliutils.Context = Miew_cli_selectors.Context; @@ -35972,11 +35933,10 @@ src_Miew.prototype.callNextCmd = function () { MiewCLIParser.parser.yy = cliutils; // workaround for incorrect JISON parser generator for AMD module MiewCLIParser.parser.yy.parseError = MiewCLIParser.parser.parseError; -;// CONCATENATED MODULE: ./src/index.js +;// ./src/index.js /* harmony default export */ const src = (src_Miew); -var __webpack_exports__default = __webpack_exports__.A; -export { __webpack_exports__default as default }; +export { src as default }; //# sourceMappingURL=Miew.module.js.map \ No newline at end of file diff --git a/packages/miew/dist/Miew.module.js.map b/packages/miew/dist/Miew.module.js.map index f193adce..5931714b 100644 --- a/packages/miew/dist/Miew.module.js.map +++ b/packages/miew/dist/Miew.module.js.map @@ -1 +1 @@ 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function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.miew.reset(false); yy.ClearContext(); yy.miew.resetReps(\"empty\");\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.miew.rebuild();\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.miew.rebuildAll(); yy.miew.rebuild();\r\nbreak;\r\ncase 6:\r\nthis.$ = yy.echo(yy.utils.help().toString());\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.echo(yy.utils.help($$[$0]).toString());\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.miew.motm();\r\nbreak;\r\ncase 10: case 11:\r\nthis.$ = yy.utils.propagateProp($$[$0]); yy.echo(yy.miew.get($$[$0]).toString());\r\nbreak;\r\ncase 12: case 13:\r\nthis.$ = yy.miew.set($$[$0-1], yy.utils.propagateProp($$[$0-1], $$[$0]));;\r\nbreak;\r\ncase 14:\r\nthis.$ = yy.miew.saveSettings();;\r\nbreak;\r\ncase 15:\r\nthis.$ = yy.miew.restoreSettings();;\r\nbreak;\r\ncase 16:\r\nthis.$ = yy.miew.resetSettings();;\r\nbreak;\r\ncase 17:\r\nthis.$ = yy.miew.resetReps();\r\nbreak;\r\ncase 18:\r\nthis.$ = yy.miew.applyPreset($$[$0]);\r\nbreak;\r\ncase 21:\r\nthis.$ = yy.miew.repRemove($$[$0]); yy.representations.remove($$[$0]);\r\nbreak;\r\ncase 22:\r\nthis.$ = yy.miew.repHide($$[$0]);\r\nbreak;\r\ncase 23:\r\nthis.$ = yy.miew.repHide($$[$0], false);\r\nbreak;\r\ncase 24:\r\nthis.$ = yy.echo(yy.utils.listRep(yy.miew, yy.representations, $$[$0], '-e'));\r\nbreak;\r\ncase 25:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations));\r\nbreak;\r\ncase 26:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations, $$[$0]));\r\nbreak;\r\ncase 27:\r\nthis.$ = yy.echo(yy.utils.listSelector(yy.miew, yy.Context));\r\nbreak;\r\ncase 28:\r\nthis.$ = yy.miew.select(yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0], true));\r\nbreak;\r\ncase 29:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.utils.checkArg($$[$0-3].toLowerCase(), $$[$0-2], true); yy.miew.select(yy.Context[$$[$0].toLowerCase()]);\r\nbreak;\r\ncase 30:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {selector : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0])});\r\nbreak;\r\ncase 31:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.miew.within(yy.utils.checkArg(\"select\", $$[$0-2], true), Number($$[$0-4]));\r\nbreak;\r\ncase 32:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {material : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 35:\r\nthis.$ = yy.echo(yy.miew.view());\r\nbreak;\r\ncase 36: case 37:\r\nthis.$ = yy.miew.view($$[$0]);\r\nbreak;\r\ncase 38:\r\nthis.$ = yy.echo(yy.miew.changeUnit());\r\nbreak;\r\ncase 39:\r\nthis.$ = yy.echo(yy.miew.changeUnit($$[$0]));\r\nbreak;\r\ncase 40:\r\nthis.$ = yy.miew.dssp();\r\nbreak;\r\ncase 41:\r\nthis.$ = yy.miew.scale($$[$0]);\r\nbreak;\r\ncase 42:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.rotate($$[$0][i]['x'] * Math.PI / 180.0, $$[$0][i]['y'] * Math.PI / 180.0, $$[$0][i]['z'] * Math.PI / 180.0)} \r\nbreak;\r\ncase 43:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.translate($$[$0][i]['x'] || 0, $$[$0][i]['y'] || 0, $$[$0][i]['z'] || 0)} \r\nbreak;\r\ncase 44:\r\nthis.$ = yy.miew.center();\r\nbreak;\r\ncase 45:\r\nthis.$ = yy.miew.center($$[$0]);\r\nbreak;\r\ncase 48: case 49:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-1], $$[$0]]}, true);\r\nbreak;\r\ncase 50: case 51:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-2], $$[$0-1]], opts:$$[$0].toJSO(yy.utils, 'objects', 'line')}, true);\r\nbreak;\r\ncase 52:\r\nthis.$ = yy.echo(yy.utils.listObjs(yy.miew));\r\nbreak;\r\ncase 53:\r\nthis.$ = yy.miew.removeObject($$[$0]);\r\nbreak;\r\ncase 54:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: false}));\r\nbreak;\r\ncase 55:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: true}));\r\nbreak;\r\ncase 56:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: false}));\r\nbreak;\r\ncase 57: case 58:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: true}));\r\nbreak;\r\ncase 59:\r\nthis.$ = yy.miew.screenshotSave();\r\nbreak;\r\ncase 60:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0]));\r\nbreak;\r\ncase 61:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0-1]), Number($$[$0]));\r\nbreak;\r\ncase 62: case 63: case 64:\r\nthis.$ = yy.utils.load(yy.miew, $$[$0]); yy.representations.clear();\r\nbreak;\r\ncase 65:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd()));\r\nbreak;\r\ncase 66:\r\nthis.$ = yy.echo(yy.representations.add($$[$0], yy.miew.repAdd()));\r\nbreak;\r\ncase 67:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 68:\r\nthis.$ = yy.echo(yy.representations.add($$[$0-1], yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 69:\r\nthis.$ = yy.miew.rep($$[$0]); yy.miew.repCurrent($$[$0]);\r\nbreak;\r\ncase 70:\r\nthis.$ = yy.miew.rep($$[$0-1], $$[$0]); yy.miew.repCurrent($$[$0-1]);\r\nbreak;\r\ncase 71:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 72:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 73:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 74:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 75:\r\nthis.$ = Number(yy.representations.get($$[$0]));\r\nbreak;\r\ncase 76: case 92:\r\nthis.$ = Number($$[$0]);\r\nbreak;\r\ncase 77:\r\nthis.$ = $$[$0];\r\nbreak;\r\ncase 78:\r\nthis.$ = yy._.assign($$[$0-1], $$[$0]);\r\nbreak;\r\ncase 79:\r\nthis.$ = yy._.assign($$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 80:\r\nthis.$ = yy._.assign($$[$0-3], $$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 81: case 82:\r\nthis.$ = yy.CreateObjectPair($$[$0].key, $$[$0].val);\r\nbreak;\r\ncase 83:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].key, new Array($$[$0-1].val, $$[$0].toJSO(yy.utils, $$[$0-1].key, $$[$0-1].val)));\r\nbreak;\r\ncase 84: case 85:\r\nthis.$ = Object.create({'key': yy.keyRemap($$[$0-2]), 'val': yy.utils.checkArg($$[$0-2], $$[$0])});\r\nbreak;\r\ncase 86:\r\nthis.$ = [$$[$0]];\r\nbreak;\r\ncase 87:\r\nthis.$ = $$[$0-1].concat($$[$0]);\r\nbreak;\r\ncase 88:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].toLowerCase(), Number($$[$0]));\r\nbreak;\r\ncase 89:\r\nthis.$ = new yy.ArgList($$[$0]);\r\nbreak;\r\ncase 90:\r\nthis.$ = $$[$0-1].append($$[$0]);\r\nbreak;\r\ncase 91:\r\nthis.$ = new yy.Arg($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 93:\r\nthis.$ = parseInt($$[$0]);\r\nbreak;\r\ncase 94:\r\nthis.$ = JSON.parse($$[$0]);\r\nbreak;\r\ncase 95: case 96:\r\nthis.$ = String($$[$0]);\r\nbreak;\r\ncase 157: case 158: case 161: case 162: case 163:\r\nthis.$ = $$[$0-2] + $$[$0-1] + $$[$0] //cause of could be color word in path;\r\nbreak;\r\ncase 166:\r\nthis.$ = $$[$0-2] = $$[$0-2] + $$[$0-1] + $$[$0];\r\nbreak;\r\n}\r\n},\r\ntable: 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,[2,90]),{14:$VS,16:197,35:$VT,38:$VU,77:$VV,78:$VW},{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,33:$Ve,34:$Vf,35:[1,199],37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,79:198,80:52,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN},o($V41,[2,84]),o($V31,[2,85]),{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,32:200,33:$Ve,34:$Vf,37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,70:$Vx,72:$Vy,74:$Vz,79:184,80:52,81:185,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN,96:$VO,97:$VP,98:$VQ,99:$VR},{5:[2,80]},o($V31,[2,91]),o($V61,[2,157]),o($V61,[2,158]),{5:[2,31]}],\r\ndefaultActions: {3:[2,2],4:[2,3],7:[2,8],8:[2,9],11:[2,14],12:[2,15],13:[2,16],15:[2,19],16:[2,20],25:[2,33],26:[2,34],29:[2,40],34:[2,46],35:[2,47],37:[2,52],46:[2,1],47:[2,5],107:[2,11],110:[2,18],116:[2,21],119:[2,22],120:[2,23],121:[2,24],122:[2,26],123:[2,27],125:[2,30],127:[2,32],128:[2,36],129:[2,37],130:[2,39],131:[2,41],136:[2,45],139:[2,53],140:[2,62],141:[2,63],142:[2,64],143:[2,164],145:[2,67],158:[2,12],159:[2,13],166:[2,68],174:[2,70],177:[2,57],178:[2,58],179:[2,61],183:[2,29],184:[2,99],185:[2,100],196:[2,80],200:[2,31]},\r\nparseError: function parseError (str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function(match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex () {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin (condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState () {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules () {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState (n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState (condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* ignore whitespace */\r\nbreak;\r\ncase 1:return '';\r\nbreak;\r\ncase 2:return '';\r\nbreak;\r\ncase 3:return 42;\r\nbreak;\r\ncase 4:return 35;\r\nbreak;\r\ncase 5:return 77;\r\nbreak;\r\ncase 6:return 78;\r\nbreak;\r\ncase 7:return 78;\r\nbreak;\r\ncase 8:return 8;\r\nbreak;\r\ncase 9:return 6;\r\nbreak;\r\ncase 10:return 82;\r\nbreak;\r\ncase 11:return 7;\r\nbreak;\r\ncase 12:return 9;\r\nbreak;\r\ncase 13:return 59;\r\nbreak;\r\ncase 14:return 13\r\nbreak;\r\ncase 15:return 15\r\nbreak;\r\ncase 16:return 17\r\nbreak;\r\ncase 17:return 18\r\nbreak;\r\ncase 18:return 19\r\nbreak;\r\ncase 19:return 20\r\nbreak;\r\ncase 20:return 11\r\nbreak;\r\ncase 21:return 62\r\nbreak;\r\ncase 22:return 64\r\nbreak;\r\ncase 23:return 23\r\nbreak;\r\ncase 24:return 25\r\nbreak;\r\ncase 25:return 26\r\nbreak;\r\ncase 26:return 27\r\nbreak;\r\ncase 27:return 30\r\nbreak;\r\ncase 28:return 34\r\nbreak;\r\ncase 29:return 33\r\nbreak;\r\ncase 30:return 65\r\nbreak;\r\ncase 31:return 66\r\nbreak;\r\ncase 32:return 37\r\nbreak;\r\ncase 33:return 41\r\nbreak;\r\ncase 34:return 43\r\nbreak;\r\ncase 35:return 52\r\nbreak;\r\ncase 36:return 54\r\nbreak;\r\ncase 37:return 55\r\nbreak;\r\ncase 38:return 46\r\nbreak;\r\ncase 39:return 48\r\nbreak;\r\ncase 40:return 45\r\nbreak;\r\ncase 41:return 49\r\nbreak;\r\ncase 42:return 56\r\nbreak;\r\ncase 43:return 58;\r\nbreak;\r\ncase 44:return 44\r\nbreak;\r\ncase 45:return 83\r\nbreak;\r\ncase 46:return 84\r\nbreak;\r\ncase 47:return 85\r\nbreak;\r\ncase 48:return 86\r\nbreak;\r\ncase 49:return 87\r\nbreak;\r\ncase 50:return 88\r\nbreak;\r\ncase 51:return 89\r\nbreak;\r\ncase 52:return 90\r\nbreak;\r\ncase 53:return 91\r\nbreak;\r\ncase 54:return 92\r\nbreak;\r\ncase 55:return 93\r\nbreak;\r\ncase 56:return 94\r\nbreak;\r\ncase 57:return 95\r\nbreak;\r\ncase 58:return 70\r\nbreak;\r\ncase 59:return 70\r\nbreak;\r\ncase 60:return 72\r\nbreak;\r\ncase 61:return 72\r\nbreak;\r\ncase 62:return 74\r\nbreak;\r\ncase 63:return 74\r\nbreak;\r\ncase 64:return 74\r\nbreak;\r\ncase 65:return 31\r\nbreak;\r\ncase 66:return 36\r\nbreak;\r\ncase 67:return 96\r\nbreak;\r\ncase 68:return 97\r\nbreak;\r\ncase 69:return 98\r\nbreak;\r\ncase 70:return 99\r\nbreak;\r\ncase 71:yy_.yytext = yy.utils.unquoteString(yy_.yytext); return 14;\r\nbreak;\r\ncase 72:return 38;\r\nbreak;\r\ncase 73:return 5;\r\nbreak;\r\ncase 74:return 101;\r\nbreak;\r\ncase 75:return 103;\r\nbreak;\r\ncase 76:return '\\\\';\r\nbreak;\r\ncase 77:return 28\r\nbreak;\r\ncase 78:return 61\r\nbreak;\r\ncase 79:return 29\r\nbreak;\r\ncase 80:return 57\r\nbreak;\r\ncase 81:return 71\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:[#].*)/i,/^(?:\\/\\/.*)/i,/^(?:([_A-Z0-9\\/\\+]+==))/i,/^(?:-?[0-9]+(\\.[0-9]+)?\\b)/i,/^(?:0[xX][0-9A-F]+\\b)/i,/^(?:false\\b)/i,/^(?:true\\b)/i,/^(?:all\\b)/i,/^(?:reset\\b)/i,/^(?:clear\\b)/i,/^(?:build\\b)/i,/^(?:help\\b)/i,/^(?:load\\b)/i,/^(?:get\\b)/i,/^(?:set\\b)/i,/^(?:set_save\\b)/i,/^(?:set_restore\\b)/i,/^(?:set_reset\\b)/i,/^(?:preset\\b)/i,/^(?:motm\\b)/i,/^(?:add\\b)/i,/^(?:rep\\b)/i,/^(?:remove\\b)/i,/^(?:hide\\b)/i,/^(?:show\\b)/i,/^(?:list\\b)/i,/^(?:select\\b)/i,/^(?:within\\b)/i,/^(?:selector\\b)/i,/^(?:mode\\b)/i,/^(?:color\\b)/i,/^(?:material\\b)/i,/^(?:view\\b)/i,/^(?:unit\\b)/i,/^(?:line\\b)/i,/^(?:listobj\\b)/i,/^(?:removeobj\\b)/i,/^(?:rotate\\b)/i,/^(?:translate\\b)/i,/^(?:scale\\b)/i,/^(?:center\\b)/i,/^(?:url\\b)/i,/^(?:screenshot\\b)/i,/^(?:dssp\\b)/i,/^(?:file_list\\b)/i,/^(?:file_register\\b)/i,/^(?:file_delete\\b)/i,/^(?:preset_add\\b)/i,/^(?:preset_delete\\b)/i,/^(?:preset_update\\b)/i,/^(?:preset_rename\\b)/i,/^(?:preset_open\\b)/i,/^(?:create_scenario\\b)/i,/^(?:reset_scenario\\b)/i,/^(?:delete_scenario\\b)/i,/^(?:add_scenario_item\\b)/i,/^(?:list_scenario\\b)/i,/^(?:s\\b)/i,/^(?:mt\\b)/i,/^(?:m\\b)/i,/^(?:c\\b)/i,/^(?:x\\b)/i,/^(?:y\\b)/i,/^(?:z\\b)/i,/^(?:as\\b)/i,/^(?:of\\b)/i,/^(?:pdb\\b)/i,/^(?:delay\\b)/i,/^(?:prst\\b)/i,/^(?:desc\\b)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:\\.)/i,/^(?:\\/)/i,/^(?:\\\\)/i,/^(?:-e\\b)/i,/^(?:-f\\b)/i,/^(?:-s\\b)/i,/^(?:-v\\b)/i,/^(?:=)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","/* eslint-disable */\r\n// DO NOT EDIT! Automatically generated from .jison\r\n/* parser generated by jison 0.4.18 */\r\n/*\r\n Returns a Parser object of the following structure:\r\n\r\n Parser: {\r\n yy: {}\r\n }\r\n\r\n Parser.prototype: {\r\n yy: {},\r\n trace: function(),\r\n symbols_: {associative list: name ==> number},\r\n terminals_: {associative list: number ==> name},\r\n productions_: [...],\r\n performAction: function anonymous(yytext, yyleng, yylineno, yy, yystate, $$, _$),\r\n table: [...],\r\n defaultActions: {...},\r\n parseError: function(str, hash),\r\n parse: function(input),\r\n\r\n lexer: {\r\n EOF: 1,\r\n parseError: function(str, hash),\r\n setInput: function(input),\r\n input: function(),\r\n unput: function(str),\r\n more: function(),\r\n less: function(n),\r\n pastInput: function(),\r\n upcomingInput: function(),\r\n showPosition: function(),\r\n test_match: function(regex_match_array, rule_index),\r\n next: function(),\r\n lex: function(),\r\n begin: function(condition),\r\n popState: function(),\r\n _currentRules: function(),\r\n topState: function(),\r\n pushState: function(condition),\r\n\r\n options: {\r\n ranges: boolean (optional: true ==> token location info will include a .range[] member)\r\n flex: boolean (optional: true ==> flex-like lexing behaviour where the rules are tested exhaustively to find the longest match)\r\n backtrack_lexer: boolean (optional: true ==> lexer regexes are tested in order and for each matching regex the action code is invoked; the lexer terminates the scan when a token is returned by the action code)\r\n },\r\n\r\n performAction: function(yy, yy_, $avoiding_name_collisions, YY_START),\r\n rules: [...],\r\n conditions: {associative list: name ==> set},\r\n }\r\n }\r\n\r\n\r\n token location info (@$, _$, etc.): {\r\n first_line: n,\r\n last_line: n,\r\n first_column: n,\r\n last_column: n,\r\n range: [start_number, end_number] (where the numbers are indexes into the input string, regular zero-based)\r\n }\r\n\r\n\r\n the parseError function receives a 'hash' object with these members for lexer and parser errors: {\r\n text: (matched text)\r\n token: (the produced terminal token, if any)\r\n line: (yylineno)\r\n }\r\n while parser (grammar) errors will also provide these members, i.e. parser errors deliver a superset of attributes: {\r\n loc: (yylloc)\r\n expected: (string describing the set of expected tokens)\r\n recoverable: (boolean: TRUE when the parser has a error recovery rule available for this particular error)\r\n }\r\n*/\r\nvar parser = (function(){\r\nvar o=function(k,v,o,l){for(o=o||{},l=k.length;l--;o[k[l]]=v);return o},$V0=[1,4],$V1=[1,5],$V2=[1,6],$V3=[1,7],$V4=[1,8],$V5=[1,9],$V6=[1,11],$V7=[1,12],$V8=[5,7,8,11],$V9=[1,17],$Va=[1,22],$Vb=[1,20],$Vc=[1,21],$Vd=[5,7,8,11,19];\r\nvar parser = {trace: function trace() { },\r\nyy: {},\r\nsymbols_: {\"error\":2,\"Program\":3,\"Expression\":4,\"EOF\":5,\"Selector\":6,\"OR\":7,\"AND\":8,\"NOT\":9,\"(\":10,\")\":11,\"SELECTOR\":12,\"NAMED_SELECTOR\":13,\"SELECTOR_RANGED\":14,\"RangeList\":15,\"SELECTOR_NAMED\":16,\"NameList\":17,\"Range\":18,\",\":19,\"NUMBER\":20,\":\":21,\"Name\":22,\"IDENTIFIER\":23,\"STRING\":24,\"$accept\":0,\"$end\":1},\r\nterminals_: {2:\"error\",5:\"EOF\",7:\"OR\",8:\"AND\",9:\"NOT\",10:\"(\",11:\")\",12:\"SELECTOR\",13:\"NAMED_SELECTOR\",14:\"SELECTOR_RANGED\",16:\"SELECTOR_NAMED\",19:\",\",20:\"NUMBER\",21:\":\",23:\"IDENTIFIER\",24:\"STRING\"},\r\nproductions_: [0,[3,2],[4,1],[4,3],[4,3],[4,2],[4,3],[6,1],[6,1],[6,2],[6,2],[15,1],[15,3],[18,1],[18,3],[17,1],[17,3],[22,1],[22,1],[22,1]],\r\nperformAction: function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.keyword('or')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.keyword('and')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.keyword('not')($$[$0]);\r\nbreak;\r\ncase 6:\r\nthis.$ = $$[$0-1];\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.keyword($$[$0])();\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.GetSelector($$[$0].toLowerCase().slice(1, $$[$0].length));\r\nbreak;\r\ncase 9: case 10:\r\nthis.$ = yy.keyword($$[$0-1])($$[$0]);\r\nbreak;\r\ncase 11:\r\nthis.$ = new yy.RangeList($$[$0]);\r\nbreak;\r\ncase 12: case 16:\r\nthis.$ = $$[$0-2].append($$[$0]);\r\nbreak;\r\ncase 13:\r\nthis.$ = new yy.Range(Number($$[$0]));\r\nbreak;\r\ncase 14:\r\nthis.$ = new yy.Range(Number($$[$0-2]), Number($$[$0]));\r\nbreak;\r\ncase 15:\r\nthis.$ = new yy.ValueList($$[$0]);\r\nbreak;\r\n}\r\n},\r\ntable: [{3:1,4:2,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{1:[3]},{5:[1,10],7:$V6,8:$V7},o($V8,[2,2]),{4:13,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:14,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,7]),o($V8,[2,8]),{15:15,18:16,20:$V9},{17:18,20:$Va,22:19,23:$Vb,24:$Vc},{1:[2,1]},{4:23,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:24,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,5]),{7:$V6,8:$V7,11:[1,25]},o($V8,[2,9],{19:[1,26]}),o($Vd,[2,11]),o($Vd,[2,13],{21:[1,27]}),o($V8,[2,10],{19:[1,28]}),o($Vd,[2,15]),o($Vd,[2,17]),o($Vd,[2,18]),o($Vd,[2,19]),o([5,7,11],[2,3],{8:$V7}),o($V8,[2,4]),o($V8,[2,6]),{18:29,20:$V9},{20:[1,30]},{20:$Va,22:31,23:$Vb,24:$Vc},o($Vd,[2,12]),o($Vd,[2,14]),o($Vd,[2,16])],\r\ndefaultActions: {10:[2,1]},\r\nparseError: function parseError(str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function (match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex() {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin(condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState() {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules() {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState(n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState(condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* skip whitespace */\r\nbreak;\r\ncase 1:return 20;\r\nbreak;\r\ncase 2:return 7;\r\nbreak;\r\ncase 3:return 8;\r\nbreak;\r\ncase 4:return 9;\r\nbreak;\r\ncase 5:return 12;\r\nbreak;\r\ncase 6:return 16;\r\nbreak;\r\ncase 7:return 14;\r\nbreak;\r\ncase 8:return 10;\r\nbreak;\r\ncase 9:return 11;\r\nbreak;\r\ncase 10:return 19;\r\nbreak;\r\ncase 11:return 21;\r\nbreak;\r\ncase 12:return '<=';\r\nbreak;\r\ncase 13:return '>=';\r\nbreak;\r\ncase 14:return '<';\r\nbreak;\r\ncase 15:return '>';\r\nbreak;\r\ncase 16:yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2); return 24;\r\nbreak;\r\ncase 17:return 13;\r\nbreak;\r\ncase 18:return 23;\r\nbreak;\r\ncase 19:return 5;\r\nbreak;\r\ncase 20:return 'INVALID';\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:(-?(?:[1-9][0-9]+|[0-9]))\\b)/i,/^(?:OR\\b)/i,/^(?:AND\\b)/i,/^(?:NOT\\b)/i,/^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\\b)/i,/^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\\b)/i,/^(?:((SERIAL|SEQUENCE|RESIDX))\\b)/i,/^(?:\\()/i,/^(?:\\))/i,/^(?:,)/i,/^(?::)/i,/^(?:<=)/i,/^(?:>=)/i,/^(?:<)/i,/^(?:>)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:(@[_A-Z0-9]+))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:.)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","\r\n/*\r\nSmooth.js version 0.1.7\r\n\r\nTurn arrays into smooth functions.\r\n\r\nCopyright 2012 Spencer Cohen\r\nLicensed under MIT license (see \"Smooth.js MIT license.txt\")\r\n*/\r\n\r\n/*Constants (these are accessible by Smooth.WHATEVER in user space)\r\n*/\r\n\r\n(function() {\r\n var AbstractInterpolator, CubicInterpolator, Enum, LinearInterpolator, NearestInterpolator, PI, SincFilterInterpolator, Smooth, clipClamp, clipMirror, clipPeriodic, defaultConfig, getColumn, getType, isValidNumber, k, makeLanczosWindow, makeScaledFunction, makeSincKernel, normalizeScaleTo, shallowCopy, sin, sinc, v, validateNumber, validateVector,\r\n __hasProp = Object.prototype.hasOwnProperty,\r\n __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor; child.__super__ = parent.prototype; return child; };\r\n\r\n Enum = {\r\n /*Interpolation methods\r\n */\r\n METHOD_NEAREST: 'nearest',\r\n METHOD_LINEAR: 'linear',\r\n METHOD_CUBIC: 'cubic',\r\n METHOD_LANCZOS: 'lanczos',\r\n METHOD_SINC: 'sinc',\r\n /*Input clipping modes\r\n */\r\n CLIP_CLAMP: 'clamp',\r\n CLIP_ZERO: 'zero',\r\n CLIP_PERIODIC: 'periodic',\r\n CLIP_MIRROR: 'mirror',\r\n /* Constants for control over the cubic interpolation tension\r\n */\r\n CUBIC_TENSION_DEFAULT: 0,\r\n CUBIC_TENSION_CATMULL_ROM: 0\r\n };\r\n\r\n defaultConfig = {\r\n method: Enum.METHOD_CUBIC,\r\n cubicTension: Enum.CUBIC_TENSION_DEFAULT,\r\n clip: Enum.CLIP_CLAMP,\r\n scaleTo: 0,\r\n sincFilterSize: 2,\r\n sincWindow: void 0\r\n };\r\n\r\n /*Index clipping functions\r\n */\r\n\r\n clipClamp = function(i, n) {\r\n return Math.max(0, Math.min(i, n - 1));\r\n };\r\n\r\n clipPeriodic = function(i, n) {\r\n i = i % n;\r\n if (i < 0) i += n;\r\n return i;\r\n };\r\n\r\n clipMirror = function(i, n) {\r\n var period;\r\n period = 2 * (n - 1);\r\n i = clipPeriodic(i, period);\r\n if (i > n - 1) i = period - i;\r\n return i;\r\n };\r\n\r\n /*\r\n Abstract scalar interpolation class which provides common functionality for all interpolators\r\n \r\n Subclasses must override interpolate().\r\n */\r\n\r\n AbstractInterpolator = (function() {\r\n\r\n function AbstractInterpolator(array, config) {\r\n this.array = array.slice(0);\r\n this.length = this.array.length;\r\n if (!(this.clipHelper = {\r\n clamp: this.clipHelperClamp,\r\n zero: this.clipHelperZero,\r\n periodic: this.clipHelperPeriodic,\r\n mirror: this.clipHelperMirror\r\n }[config.clip])) {\r\n throw \"Invalid clip: \" + config.clip;\r\n }\r\n }\r\n\r\n AbstractInterpolator.prototype.getClippedInput = function(i) {\r\n if ((0 <= i && i < this.length)) {\r\n return this.array[i];\r\n } else {\r\n return this.clipHelper(i);\r\n }\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperClamp = function(i) {\r\n return this.array[clipClamp(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperZero = function(i) {\r\n return 0;\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperPeriodic = function(i) {\r\n return this.array[clipPeriodic(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperMirror = function(i) {\r\n return this.array[clipMirror(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.interpolate = function(t) {\r\n throw 'Subclasses of AbstractInterpolator must override the interpolate() method.';\r\n };\r\n\r\n return AbstractInterpolator;\r\n\r\n })();\r\n\r\n NearestInterpolator = (function(_super) {\r\n\r\n __extends(NearestInterpolator, _super);\r\n\r\n function NearestInterpolator() {\r\n NearestInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n NearestInterpolator.prototype.interpolate = function(t) {\r\n return this.getClippedInput(Math.round(t));\r\n };\r\n\r\n return NearestInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n LinearInterpolator = (function(_super) {\r\n\r\n __extends(LinearInterpolator, _super);\r\n\r\n function LinearInterpolator() {\r\n LinearInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n LinearInterpolator.prototype.interpolate = function(t) {\r\n var k;\r\n k = Math.floor(t);\r\n t -= k;\r\n return (1 - t) * this.getClippedInput(k) + t * this.getClippedInput(k + 1);\r\n };\r\n\r\n return LinearInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n CubicInterpolator = (function(_super) {\r\n\r\n __extends(CubicInterpolator, _super);\r\n\r\n function CubicInterpolator(array, config) {\r\n this.tangentFactor = 1 - Math.max(-1, Math.min(1, config.cubicTension));\r\n CubicInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n CubicInterpolator.prototype.getTangent = function(k) {\r\n return this.tangentFactor * (this.getClippedInput(k + 1) - this.getClippedInput(k - 1)) / 2;\r\n };\r\n\r\n CubicInterpolator.prototype.interpolate = function(t) {\r\n var k, m, p, t2, t3;\r\n k = Math.floor(t);\r\n m = [this.getTangent(k), this.getTangent(k + 1)];\r\n p = [this.getClippedInput(k), this.getClippedInput(k + 1)];\r\n t -= k;\r\n t2 = t * t;\r\n t3 = t * t2;\r\n return (2 * t3 - 3 * t2 + 1) * p[0] + (t3 - 2 * t2 + t) * m[0] + (-2 * t3 + 3 * t2) * p[1] + (t3 - t2) * m[1];\r\n };\r\n\r\n return CubicInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n sin = Math.sin, PI = Math.PI;\r\n\r\n sinc = function(x) {\r\n if (x === 0) {\r\n return 1;\r\n } else {\r\n return sin(PI * x) / (PI * x);\r\n }\r\n };\r\n\r\n makeLanczosWindow = function(a) {\r\n return function(x) {\r\n return sinc(x / a);\r\n };\r\n };\r\n\r\n makeSincKernel = function(window) {\r\n return function(x) {\r\n return sinc(x) * window(x);\r\n };\r\n };\r\n\r\n SincFilterInterpolator = (function(_super) {\r\n\r\n __extends(SincFilterInterpolator, _super);\r\n\r\n function SincFilterInterpolator(array, config) {\r\n SincFilterInterpolator.__super__.constructor.apply(this, arguments);\r\n this.a = config.sincFilterSize;\r\n if (!config.sincWindow) throw 'No sincWindow provided';\r\n this.kernel = makeSincKernel(config.sincWindow);\r\n }\r\n\r\n SincFilterInterpolator.prototype.interpolate = function(t) {\r\n var k, n, sum, _ref, _ref2;\r\n k = Math.floor(t);\r\n sum = 0;\r\n for (n = _ref = k - this.a + 1, _ref2 = k + this.a; _ref <= _ref2 ? n <= _ref2 : n >= _ref2; _ref <= _ref2 ? n++ : n--) {\r\n sum += this.kernel(t - n) * this.getClippedInput(n);\r\n }\r\n return sum;\r\n };\r\n\r\n return SincFilterInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n getColumn = function(arr, i) {\r\n var row, _i, _len, _results;\r\n _results = [];\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n row = arr[_i];\r\n _results.push(row[i]);\r\n }\r\n return _results;\r\n };\r\n\r\n makeScaledFunction = function(f, baseScale, scaleRange) {\r\n var scaleFactor, translation;\r\n if (scaleRange.join === '0,1') {\r\n return f;\r\n } else {\r\n scaleFactor = baseScale / (scaleRange[1] - scaleRange[0]);\r\n translation = scaleRange[0];\r\n return function(t) {\r\n return f(scaleFactor * (t - translation));\r\n };\r\n }\r\n };\r\n\r\n getType = function(x) {\r\n return Object.prototype.toString.call(x).slice('[object '.length, -1);\r\n };\r\n\r\n validateNumber = function(n) {\r\n if (isNaN(n)) throw 'NaN in Smooth() input';\r\n if (getType(n) !== 'Number') throw 'Non-number in Smooth() input';\r\n if (!isFinite(n)) throw 'Infinity in Smooth() input';\r\n };\r\n\r\n validateVector = function(v, dimension) {\r\n var n, _i, _len;\r\n if (getType(v) !== 'Array') throw 'Non-vector in Smooth() input';\r\n if (v.length !== dimension) throw 'Inconsistent dimension in Smooth() input';\r\n for (_i = 0, _len = v.length; _i < _len; _i++) {\r\n n = v[_i];\r\n validateNumber(n);\r\n }\r\n };\r\n\r\n isValidNumber = function(n) {\r\n return (getType(n) === 'Number') && isFinite(n) && !isNaN(n);\r\n };\r\n\r\n normalizeScaleTo = function(s) {\r\n var invalidErr;\r\n invalidErr = \"scaleTo param must be number or array of two numbers\";\r\n switch (getType(s)) {\r\n case 'Number':\r\n if (!isValidNumber(s)) throw invalidErr;\r\n s = [0, s];\r\n break;\r\n case 'Array':\r\n if (s.length !== 2) throw invalidErr;\r\n if (!(isValidNumber(s[0]) && isValidNumber(s[1]))) throw invalidErr;\r\n break;\r\n default:\r\n throw invalidErr;\r\n }\r\n return s;\r\n };\r\n\r\n shallowCopy = function(obj) {\r\n var copy, k, v;\r\n copy = {};\r\n for (k in obj) {\r\n if (!__hasProp.call(obj, k)) continue;\r\n v = obj[k];\r\n copy[k] = v;\r\n }\r\n return copy;\r\n };\r\n\r\n Smooth = function(arr, config) {\r\n var baseDomainEnd, dimension, i, interpolator, interpolatorClass, interpolators, k, n, properties, smoothFunc, v;\r\n if (config == null) config = {};\r\n properties = {};\r\n config = shallowCopy(config);\r\n properties.config = shallowCopy(config);\r\n if (config.scaleTo == null) config.scaleTo = config.period;\r\n if (config.sincFilterSize == null) {\r\n config.sincFilterSize = config.lanczosFilterSize;\r\n }\r\n for (k in defaultConfig) {\r\n if (!__hasProp.call(defaultConfig, k)) continue;\r\n v = defaultConfig[k];\r\n if (config[k] == null) config[k] = v;\r\n }\r\n if (!(interpolatorClass = {\r\n nearest: NearestInterpolator,\r\n linear: LinearInterpolator,\r\n cubic: CubicInterpolator,\r\n lanczos: SincFilterInterpolator,\r\n sinc: SincFilterInterpolator\r\n }[config.method])) {\r\n throw \"Invalid method: \" + config.method;\r\n }\r\n if (config.method === 'lanczos') {\r\n config.sincWindow = makeLanczosWindow(config.sincFilterSize);\r\n }\r\n if (arr.length < 2) throw 'Array must have at least two elements';\r\n properties.count = arr.length;\r\n smoothFunc = (function() {\r\n var _i, _j, _len, _len2;\r\n switch (getType(arr[0])) {\r\n case 'Number':\r\n properties.dimension = 'scalar';\r\n if (Smooth.deepValidation) {\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n n = arr[_i];\r\n validateNumber(n);\r\n }\r\n }\r\n interpolator = new interpolatorClass(arr, config);\r\n return function(t) {\r\n return interpolator.interpolate(t);\r\n };\r\n case 'Array':\r\n properties.dimension = dimension = arr[0].length;\r\n if (!dimension) throw 'Vectors must be non-empty';\r\n if (Smooth.deepValidation) {\r\n for (_j = 0, _len2 = arr.length; _j < _len2; _j++) {\r\n v = arr[_j];\r\n validateVector(v, dimension);\r\n }\r\n }\r\n interpolators = (function() {\r\n var _results;\r\n _results = [];\r\n for (i = 0; 0 <= dimension ? i < dimension : i > dimension; 0 <= dimension ? i++ : i--) {\r\n _results.push(new interpolatorClass(getColumn(arr, i), config));\r\n }\r\n return _results;\r\n })();\r\n return function(t) {\r\n var interpolator, _k, _len3, _results;\r\n _results = [];\r\n for (_k = 0, _len3 = interpolators.length; _k < _len3; _k++) {\r\n interpolator = interpolators[_k];\r\n _results.push(interpolator.interpolate(t));\r\n }\r\n return _results;\r\n };\r\n default:\r\n throw \"Invalid element type: \" + (getType(arr[0]));\r\n }\r\n })();\r\n if (config.clip === 'periodic') {\r\n baseDomainEnd = arr.length;\r\n } else {\r\n baseDomainEnd = arr.length - 1;\r\n }\r\n config.scaleTo || (config.scaleTo = baseDomainEnd);\r\n properties.domain = normalizeScaleTo(config.scaleTo);\r\n smoothFunc = makeScaledFunction(smoothFunc, baseDomainEnd, properties.domain);\r\n properties.domain.sort();\r\n /*copy properties\r\n */\r\n for (k in properties) {\r\n if (!__hasProp.call(properties, k)) continue;\r\n v = properties[k];\r\n smoothFunc[k] = v;\r\n }\r\n return smoothFunc;\r\n };\r\n\r\n for (k in Enum) {\r\n if (!__hasProp.call(Enum, k)) continue;\r\n v = Enum[k];\r\n Smooth[k] = v;\r\n }\r\n\r\n Smooth.deepValidation = true;\r\n\r\n (typeof exports !== \"undefined\" && exports !== null ? exports : window).Smooth = Smooth;\r\n\r\n}).call(this);\r\n","!function(r,t){if(\"function\"==typeof define&&define.amd)define([\"exports\"],t);else if(\"object\"==typeof exports&&\"undefined\"!=typeof module)t(exports);else 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color : color[idx % color.length];\n}\n/**\n * Internal method that draws the individual lines.\n */\nfunction drawLines(el, opts) {\n var borderRadius = (Math.round(opts.corners * opts.width * 500) / 1000) + 'px';\n var shadow = 'none';\n if (opts.shadow === true) {\n shadow = '0 2px 4px #000'; // default shadow\n }\n else if (typeof opts.shadow === 'string') {\n shadow = opts.shadow;\n }\n var shadows = parseBoxShadow(shadow);\n for (var i = 0; i < opts.lines; i++) {\n var degrees = ~~(360 / opts.lines * i + opts.rotate);\n var backgroundLine = document.createElement('div');\n backgroundLine.style.position = 'absolute';\n backgroundLine.style.top = \"\".concat(-opts.width / 2, \"px\");\n backgroundLine.style.width = (opts.length + opts.width) + 'px';\n backgroundLine.style.height = opts.width + 'px';\n backgroundLine.style.background = getColor(opts.fadeColor, i);\n backgroundLine.style.borderRadius = borderRadius;\n backgroundLine.style.transformOrigin = 'left';\n backgroundLine.style.transform = \"rotate(\".concat(degrees, \"deg) translateX(\").concat(opts.radius, \"px)\");\n var delay = i * opts.direction / opts.lines / opts.speed;\n delay -= 1 / opts.speed; // so initial animation state will include trail\n var line = document.createElement('div');\n line.style.width = '100%';\n line.style.height = '100%';\n line.style.background = getColor(opts.color, i);\n line.style.borderRadius = borderRadius;\n line.style.boxShadow = normalizeShadow(shadows, degrees);\n line.style.animation = \"\".concat(1 / opts.speed, \"s linear \").concat(delay, \"s infinite \").concat(opts.animation);\n backgroundLine.appendChild(line);\n el.appendChild(backgroundLine);\n }\n}\nfunction parseBoxShadow(boxShadow) {\n var regex = /^\\s*([a-zA-Z]+\\s+)?(-?\\d+(\\.\\d+)?)([a-zA-Z]*)\\s+(-?\\d+(\\.\\d+)?)([a-zA-Z]*)(.*)$/;\n var shadows = [];\n for (var _i = 0, _a = boxShadow.split(','); _i < _a.length; _i++) {\n var shadow = _a[_i];\n var matches = shadow.match(regex);\n if (matches === null) {\n continue; // invalid syntax\n }\n var x = +matches[2];\n var y = +matches[5];\n var xUnits = matches[4];\n var yUnits = matches[7];\n if (x === 0 && !xUnits) {\n xUnits = yUnits;\n }\n if (y === 0 && !yUnits) {\n yUnits = xUnits;\n }\n if (xUnits !== yUnits) {\n continue; // units must match to use as coordinates\n }\n shadows.push({\n prefix: matches[1] || '', // could have value of 'inset' or undefined\n x: x,\n y: y,\n xUnits: xUnits,\n yUnits: yUnits,\n end: matches[8],\n });\n }\n return shadows;\n}\n/**\n * Modify box-shadow x/y offsets to counteract rotation\n */\nfunction normalizeShadow(shadows, degrees) {\n var normalized = [];\n for (var _i = 0, shadows_1 = shadows; _i < shadows_1.length; _i++) {\n var shadow = shadows_1[_i];\n var xy = convertOffset(shadow.x, shadow.y, degrees);\n normalized.push(shadow.prefix + xy[0] + shadow.xUnits + ' ' + xy[1] + shadow.yUnits + shadow.end);\n }\n return normalized.join(', ');\n}\nfunction convertOffset(x, y, degrees) {\n var radians = degrees * Math.PI / 180;\n var sin = Math.sin(radians);\n var cos = Math.cos(radians);\n return [\n Math.round((x * cos + y * sin) * 1000) / 1000,\n Math.round((-x * sin + y * cos) * 1000) / 1000,\n ];\n}\n","//----------------------------------------------------------------------------\r\n// Timer\r\n\r\nexport default class Timer {\r\n constructor() {\r\n this.startTime = 0;\r\n this.oldTime = 0;\r\n this.elapsedTime = 0;\r\n this.running = false;\r\n }\r\n\r\n start() {\r\n this.startTime = Timer.now();\r\n this.oldTime = this.startTime;\r\n this.running = true;\r\n }\r\n\r\n stop() {\r\n this.getElapsedTime();\r\n this.running = false;\r\n }\r\n\r\n getElapsedTime() {\r\n this.update();\r\n return this.elapsedTime;\r\n }\r\n\r\n update() {\r\n let delta = 0;\r\n if (this.running) {\r\n const newTime = Timer.now();\r\n delta = 0.001 * (newTime - this.oldTime);\r\n this.oldTime = newTime;\r\n this.elapsedTime += delta;\r\n }\r\n\r\n return delta;\r\n }\r\n}\r\n\r\nTimer.now = (function () {\r\n const p = typeof window !== 'undefined' && window.performance;\r\n return (p && p.now) ? p.now.bind(p) : Date.now;\r\n}());\r\n","import Timer from '../Timer';\r\n\r\nconst { now } = Timer;\r\n\r\nfunction createElement(tag, id, css) {\r\n const element = document.createElement(tag);\r\n element.id = id;\r\n element.style.cssText = css;\r\n return element;\r\n}\r\n\r\nclass Stats {\r\n constructor() {\r\n this.domElement = createElement('div', 'stats', 'padding:8px');\r\n this._text = createElement('p', 'fps', 'margin:0;color:silver;font-size:large');\r\n this.domElement.appendChild(this._text);\r\n\r\n this._startTime = now();\r\n this._prevTime = this._startTime;\r\n\r\n this._deltas = new Array(20);\r\n this._index = 0;\r\n this._total = 0.0;\r\n this._count = 0;\r\n }\r\n\r\n end() {\r\n const time = now();\r\n const delta = time - this._startTime;\r\n\r\n if (this._count < this._deltas.length) {\r\n this._count++;\r\n } else {\r\n this._total -= this._deltas[this._index];\r\n }\r\n this._total += delta;\r\n this._deltas[this._index] = delta;\r\n this._index = (this._index + 1) % this._deltas.length;\r\n\r\n this.ms = this._total / this._count;\r\n this.fps = 1000 / this.ms;\r\n\r\n if (time > this._prevTime + 1000) {\r\n this._text.textContent = this.fps.toPrecision(2);\r\n this._prevTime = time;\r\n }\r\n\r\n return time;\r\n }\r\n\r\n update() {\r\n this._startTime = this.end();\r\n }\r\n\r\n show(on) {\r\n if (on === undefined) {\r\n on = true;\r\n }\r\n this.domElement.style.display = on ? 'block' : 'none';\r\n }\r\n}\r\n\r\nexport default Stats;\r\n","/**\r\n * This class introduces the simplest event system.\r\n */\r\n\r\nimport _ from 'lodash';\r\n\r\nfunction isUndefOrEqual(param, value) {\r\n return !param || param === value;\r\n}\r\n\r\n/**\r\n * Creates empty dispatcher.\r\n *\r\n * @exports EventDispatcher\r\n * @constructor\r\n */\r\nfunction EventDispatcher() {\r\n this._handlers = {};\r\n}\r\n\r\n/**\r\n * Binds callback on specific event type. Optional `context` parameter\r\n * could be used as 'this' for the `callback`.\r\n * @param {string} type Event name.\r\n * @param {function} callback Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.addEventListener = function (type, callback, context) {\r\n let handlers = this._handlers[type];\r\n\r\n if (!handlers) {\r\n this._handlers[type] = [];\r\n handlers = this._handlers[type];\r\n }\r\n\r\n const params = [callback, context];\r\n function _checkPar(par) {\r\n return par[0] === params[0] && par[1] === params[1];\r\n }\r\n\r\n if (_.find(handlers, _checkPar) === undefined) {\r\n handlers.push(params);\r\n }\r\n};\r\n\r\n/**\r\n * Removes a previously-bound callback function from an object.\r\n * If no `context` is specified, all versions of the `callback` with different\r\n * contexts will be removed.\r\n * If no `callback` is specified, all callbacks of the `type` will be removed.\r\n * If no `type` is specified, callbacks for all events will be removed.\r\n * @param {?string} [type] Event type.\r\n * @param {function} [callback] Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.removeEventListener = function (type, callback, context) {\r\n const self = this;\r\n _.forEach(self._handlers, (handler, ev) => {\r\n _.remove(handler, (values) => isUndefOrEqual(type, ev)\r\n && isUndefOrEqual(callback, values[0])\r\n && isUndefOrEqual(context, values[1] || self));\r\n });\r\n\r\n this._handlers = _.omitBy(self._handlers, (handler) => handler.length === 0);\r\n};\r\n\r\n/**\r\n * Makes all the callbacks for the specific `event` to trigger.\r\n * @param {Object} event Event.\r\n * @param {string} event.type Type of the event.\r\n */\r\nEventDispatcher.prototype.dispatchEvent = function (event) {\r\n const self = this;\r\n\r\n _.forEach(this._handlers[event.type], (callback) => {\r\n const context = callback[1] || self;\r\n callback[0].apply(context, [event]);\r\n });\r\n};\r\n\r\nexport default EventDispatcher;\r\n","/**\r\n * This module contains class for logging.\r\n * Returns an instance of a logger that have already been created.\r\n * Allows users to log messages for five different levels,\r\n * enable console output and catch signal on each message.\r\n */\r\nimport _ from 'lodash';\r\nimport EventDispatcher from './EventDispatcher';\r\n\r\nconst priorities = {\r\n debug: 0,\r\n info: 1,\r\n report: 2,\r\n warn: 3,\r\n error: 4,\r\n};\r\n\r\n/**\r\n * Create new Logger.\r\n *\r\n * @exports Logger\r\n * @extends EventDispatcher\r\n * @constructor\r\n */\r\nfunction Logger() {\r\n EventDispatcher.call(this);\r\n /** Boolean flag that toggles output to browser console.\r\n * @type {boolean}\r\n */\r\n this.console = false;\r\n this._priority = priorities.warn;\r\n}\r\n\r\nLogger.prototype = Object.create(EventDispatcher.prototype);\r\nLogger.prototype.constructor = Logger;\r\n\r\n/**\r\n * Create new clean instance of the logger.\r\n * @returns {Logger}\r\n */\r\nLogger.prototype.instantiate = function () {\r\n return new Logger();\r\n};\r\n\r\nfunction verify(number) {\r\n if (!_.isNumber(number)) {\r\n throw new Error('Wrong log level specified!');\r\n }\r\n return number;\r\n}\r\n\r\n/**\r\n * @property {string} current threshold for signals and console output.\r\n * @name Logger#level\r\n */\r\nObject.defineProperty(Logger.prototype, 'level', {\r\n get() {\r\n return _.findKey(priorities, (value) => value === this._priority);\r\n },\r\n set(level) {\r\n this._priority = verify(priorities[level]);\r\n },\r\n});\r\n\r\n/**\r\n * Returns the list of all possible level values.\r\n * @returns {Array}\r\n */\r\nLogger.prototype.levels = function () {\r\n return Object.keys(priorities);\r\n};\r\n\r\n/**\r\n * Add new message with specified level.\r\n * @param {string} level - level of the message, must be one of the\r\n * {'debug' | 'info' | 'report' | 'warn' | 'error'}\r\n * @param {string} message\r\n */\r\nLogger.prototype.message = function (level, message) {\r\n const priority = verify(priorities[level]);\r\n this._message(priority, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('debug', ...);\r\n * @param message\r\n */\r\nLogger.prototype.debug = function (message) {\r\n this._message(priorities.debug, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('info', ...);\r\n * @param message\r\n */\r\nLogger.prototype.info = function (message) {\r\n this._message(priorities.info, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('report', ...);\r\n * @param message\r\n */\r\nLogger.prototype.report = function (message) {\r\n this._message(priorities.report, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('warn', ...);\r\n * @param message\r\n */\r\nLogger.prototype.warn = function (message) {\r\n this._message(priorities.warn, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('error', ...);\r\n * @param message\r\n */\r\nLogger.prototype.error = function (message) {\r\n this._message(priorities.error, message);\r\n};\r\n\r\n/**\r\n * Add new message with specified priority.\r\n * @param {number} priority - priority of the message\r\n * @param {string} message\r\n * @private\r\n */\r\nLogger.prototype._message = function (priority, message) {\r\n if (priority < this._priority) {\r\n return;\r\n }\r\n const level = _.findKey(priorities, (value) => value === priority);\r\n message = String(message);\r\n if (this.console) {\r\n const output = `miew:${level}: ${message}`;\r\n if (level === 'error') {\r\n console.error(output); // NOSONAR\r\n } else if (level === 'warn') {\r\n console.warn(output); // NOSONAR\r\n } else {\r\n console.log(output); // NOSONAR\r\n }\r\n }\r\n this.dispatchEvent({ type: 'message', level, message });\r\n};\r\n\r\nexport default new Logger();\r\n","import _ from 'lodash';\r\nimport logger from './utils/logger';\r\n\r\nconst browserType = {\r\n DEFAULT: 0,\r\n SAFARI: 1,\r\n};\r\n//----------------------------------------------------------------------------\r\n// Query string\r\n\r\n/**\r\n * Escape only dangerous chars in a query string component, use a plus instead of a space.\r\n *\r\n * [RFC 3986](https://tools.ietf.org/html/rfc3986) allows the following chars in the query (see 3.4):\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! $ & ' ( ) * + , ; = : @ / ?\r\n *\r\n * For query string elements we need to escape ampersand, equal sign, and plus,\r\n * but encodeURIComponent() function encodes anything except for the following:\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! ' ( ) *\r\n *\r\n * @param {string} text - key or value to encode\r\n * @param {string} excludeExp - regexp for symbols to exclude from encoding\r\n * @returns {string} encoded string\r\n */\r\nfunction encodeQueryComponent(text, excludeExp) {\r\n const encode = (code) => String.fromCharCode(parseInt(code.substr(1), 16));\r\n return encodeURIComponent(text).replace(excludeExp, encode).replace(/%20/g, '+');\r\n}\r\n\r\n/**\r\n * Unescape dangerous chars in a query string component.\r\n *\r\n * @param {string} text - encoded key or value\r\n * @returns {string} decoded string\r\n * @see {@link encodeQueryComponent}\r\n */\r\nfunction decodeQueryComponent(text) {\r\n return decodeURIComponent(text.replace(/\\+/g, ' '));\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Array} array of (key, value) pairs.\r\n */\r\nfunction getUrlParameters(url) {\r\n url = url || window.location.search;\r\n\r\n const query = url.substring(url.indexOf('?') + 1);\r\n const search = /([^&=]+)=?([^&]*)/g;\r\n const result = [];\r\n let match;\r\n\r\n while ((match = search.exec(query)) !== null) { // eslint-disable-line no-cond-assign\r\n result.push([decodeQueryComponent(match[1]), decodeQueryComponent(match[2])]);\r\n }\r\n\r\n return result;\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters as a hash.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Object}\r\n */\r\nfunction getUrlParametersAsDict(url) {\r\n const result = {};\r\n const a = getUrlParameters(url);\r\n for (let i = 0; i < a.length; ++i) {\r\n const [key, value] = a[i];\r\n result[key] = value;\r\n }\r\n return result;\r\n}\r\n\r\nfunction resolveURL(str) {\r\n if (typeof URL !== 'undefined') {\r\n try {\r\n if (typeof window !== 'undefined') {\r\n return new URL(str, window.location).href;\r\n }\r\n return new URL(str).href;\r\n } catch (error) {\r\n // IE 11 has a URL object with no constructor available so just try a different approach instead\r\n }\r\n }\r\n if (typeof document !== 'undefined') {\r\n const anchor = document.createElement('a');\r\n anchor.href = str;\r\n return anchor.href;\r\n }\r\n return str;\r\n}\r\n\r\n/**\r\n * Generates regular expression object that includes all symbols\r\n * listed in the argument\r\n * @param symbolStr {string} - String containing characters list.\r\n * @returns {RegExp} - Regular expression.\r\n */\r\nfunction generateRegExp(symbolStr) {\r\n const symbolList = [];\r\n\r\n for (let i = 0, n = symbolStr.length; i < n; ++i) {\r\n symbolList[symbolList.length] = symbolStr[i].charCodeAt(0).toString(16);\r\n }\r\n\r\n const listStr = symbolList.join('|');\r\n\r\n return new RegExp(`%(?:${listStr})`, 'gi');\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Create HTML element\r\n\r\nfunction createElement(tag, attrs, content) {\r\n const element = document.createElement(tag);\r\n let i;\r\n let n;\r\n if (attrs) {\r\n const keys = Object.keys(attrs);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n element.setAttribute(key, attrs[key]);\r\n }\r\n }\r\n if (content) {\r\n if (!(content instanceof Array)) {\r\n content = [content];\r\n }\r\n for (i = 0, n = content.length; i < n; ++i) {\r\n const child = content[i];\r\n if (typeof child === 'string') {\r\n element.appendChild(document.createTextNode(child));\r\n } else if (child instanceof HTMLElement) {\r\n element.appendChild(child);\r\n }\r\n }\r\n }\r\n return element;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Easy inheritance\r\n\r\n/**\r\n * Derive the class from the base.\r\n * @param cls {function} - Class (constructor) to derive.\r\n * @param base {function} - Class (constructor) to derive from.\r\n * @param members {object=} - Optional instance members to add.\r\n * @param statics {object=} - Optional static class members to add.\r\n * @returns {function} Original class.\r\n */\r\nfunction deriveClass(cls, base, members, statics) {\r\n cls.prototype = _.assign(Object.create(base.prototype), { constructor: cls }, members);\r\n if (statics) {\r\n _.assign(cls, statics);\r\n }\r\n return cls;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Deep prototyping\r\n\r\nfunction deriveDeep(obj, needZeroOwnProperties) {\r\n let res = obj;\r\n let i;\r\n let n;\r\n if (obj instanceof Array) {\r\n res = new Array(obj.length);\r\n for (i = 0, n = obj.length; i < n; ++i) {\r\n res[i] = deriveDeep(obj[i]);\r\n }\r\n } else if (obj instanceof Object) {\r\n res = Object.create(obj);\r\n const keys = Object.keys(obj);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = obj[key];\r\n const copy = deriveDeep(value);\r\n if (copy !== value) {\r\n res[key] = copy;\r\n }\r\n }\r\n if (needZeroOwnProperties && Object.keys(res).length > 0) {\r\n res = Object.create(res);\r\n }\r\n }\r\n return res;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Colors\r\n\r\nfunction hexColor(color) {\r\n const hex = (`0000000${color.toString(16)}`).substr(-6);\r\n return `#${hex}`;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Debug tracing\r\n\r\nfunction DebugTracer(namespace) {\r\n let enabled = false;\r\n\r\n this.enable = function (on) {\r\n enabled = on;\r\n };\r\n\r\n let indent = 0;\r\n const methods = Object.keys(namespace);\r\n\r\n function wrap(method_, name_) {\r\n return function (...args) {\r\n const spaces = DebugTracer.spaces.substr(0, indent * 2);\r\n if (enabled) {\r\n logger.debug(`${spaces + name_} {`);\r\n }\r\n indent++;\r\n const result = method_.apply(this, args); // eslint-disable-line no-invalid-this\r\n indent--;\r\n if (enabled) {\r\n logger.debug(`${spaces}} // ${name_}`);\r\n }\r\n return result;\r\n };\r\n }\r\n\r\n for (let i = 0, n = methods.length; i < n; ++i) {\r\n const name = methods[i];\r\n const method = namespace[name];\r\n if (method instanceof Function && name !== 'constructor') {\r\n namespace[name] = wrap(method, name);\r\n }\r\n }\r\n}\r\n\r\nDebugTracer.spaces = ' ';\r\n\r\nclass OutOfMemoryError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'OutOfMemoryError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction allocateTyped(TypedArrayName, size) {\r\n let result = null;\r\n try {\r\n result = new TypedArrayName(size);\r\n } catch (e) {\r\n if (e instanceof RangeError) {\r\n throw new OutOfMemoryError(e.message);\r\n } else {\r\n throw e;\r\n }\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Float array conversion\r\n\r\nfunction bytesToBase64(/** ArrayBuffer */ buffer) {\r\n const bytes = new Uint8Array(buffer);\r\n let binary = '';\r\n for (let i = 0; i < bytes.byteLength; i++) {\r\n binary += String.fromCharCode(bytes[i]);\r\n }\r\n return window.btoa(binary);\r\n}\r\n\r\nfunction bytesFromBase64(/** string */ str) {\r\n const binary = window.atob(str);\r\n const bytes = new Uint8Array(binary.length);\r\n for (let i = 0; i < bytes.length; ++i) {\r\n bytes[i] = binary[i].charCodeAt(0);\r\n }\r\n return bytes.buffer;\r\n}\r\n\r\nfunction arrayToBase64(/** number[] */ array, /** function */ TypedArrayClass) {\r\n return bytesToBase64(new TypedArrayClass(array).buffer);\r\n}\r\n\r\nfunction arrayFromBase64(/** string */ str, /** function */ TypedArrayClass) {\r\n return Array.prototype.slice.call(new TypedArrayClass(bytesFromBase64(str)));\r\n}\r\n\r\n// NOTE: this is 1-level comparison\r\nfunction compareOptionsWithDefaults(opts, defOpts) {\r\n const optsStr = [];\r\n if (defOpts && opts) {\r\n const keys = Object.keys(opts);\r\n for (let p = 0; p < keys.length; ++p) {\r\n const key = keys[p];\r\n const value = opts[key];\r\n // TODO add processing for tree structure\r\n if (!(value instanceof Object) && typeof defOpts[key] !== 'undefined' && defOpts[key] !== value) {\r\n optsStr.push(`${key}:${value}`);\r\n }\r\n }\r\n if (optsStr.length > 0) {\r\n return `!${optsStr.join()}`;\r\n }\r\n }\r\n return '';\r\n}\r\n\r\nfunction isAlmostPlainObject(o) {\r\n if (_.isPlainObject(o)) {\r\n return true;\r\n }\r\n const proto = o && Object.getPrototypeOf(o);\r\n return !!proto && !proto.hasOwnProperty('constructor') && isAlmostPlainObject(proto);\r\n}\r\n\r\n/**\r\n * Build an object that contains properties (and subproperties) of `src` different from those\r\n * in `dst`. Objects are parsed recursively, other values (including arrays) are compared for\r\n * equality using `_.isEqual()`.\r\n * @param {!object} src - a new object to compare, may contain changed or new properties\r\n * @param {!object} dst - an old reference object\r\n */\r\nfunction objectsDiff(src, dst) {\r\n const diff = {};\r\n _.forIn(src, (srcValue, key) => {\r\n const dstValue = dst[key];\r\n if (isAlmostPlainObject(srcValue) && isAlmostPlainObject(dstValue)) {\r\n const deepDiff = objectsDiff(srcValue, dstValue);\r\n if (!_.isEmpty(deepDiff)) {\r\n diff[key] = deepDiff;\r\n }\r\n } else if (!_.isEqual(srcValue, dstValue)) {\r\n diff[key] = srcValue;\r\n }\r\n });\r\n return diff;\r\n}\r\n\r\nfunction forInRecursive(object, callback) {\r\n function iterateThrough(obj, prefix) {\r\n _.forIn(obj, (value, key) => {\r\n const newPref = prefix + (prefix.length > 0 ? '.' : '');\r\n if (value instanceof Object) {\r\n iterateThrough(value, newPref + key);\r\n } else if (value !== undefined) {\r\n callback(value, newPref + key);\r\n }\r\n });\r\n }\r\n iterateThrough(object, '');\r\n}\r\n\r\nfunction enquoteString(value) {\r\n if (_.isString(value)) {\r\n return `\"${value.replace(/\"/g, '\\\\\"')}\"`;\r\n }\r\n return value;\r\n}\r\n\r\nfunction unquoteString(value) {\r\n if (!_.isString(value)) {\r\n return value;\r\n }\r\n if (value[0] === '\"' && value[value.length - 1] === '\"') {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\\"/g, '\"');\r\n }\r\n if (value[0] === \"'\" && value[value.length - 1] === \"'\") {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\'/g, \"'\");\r\n }\r\n throw new SyntaxError('Incorrect string format, can\\'t unqute it');\r\n}\r\n\r\nfunction getFileExtension(fileName) {\r\n return fileName.slice((Math.max(0, fileName.lastIndexOf('.')) || Infinity));\r\n}\r\n\r\nfunction splitFileName(fileName) {\r\n const ext = getFileExtension(fileName);\r\n const name = fileName.slice(0, fileName.length - ext.length);\r\n return [name, ext];\r\n}\r\n\r\nfunction dataUrlToBlob(url) {\r\n const parts = url.split(/[:;,]/);\r\n const partsCount = parts.length;\r\n if (partsCount >= 3 && parts[partsCount - 2] === 'base64') {\r\n return new Blob([bytesFromBase64(parts[partsCount - 1])]);\r\n }\r\n return null;\r\n}\r\n\r\nfunction getBrowser() {\r\n if (navigator.vendor && navigator.vendor.indexOf('Apple') > -1\r\n && navigator.userAgent\r\n && navigator.userAgent.indexOf('CriOS') === -1\r\n && navigator.userAgent.indexOf('FxiOS') === -1) {\r\n return browserType.SAFARI;\r\n }\r\n return browserType.DEFAULT;\r\n}\r\n\r\nfunction shotOpen(url) {\r\n if (typeof window !== 'undefined') {\r\n window.open().document.write(``);\r\n }\r\n}\r\n\r\nfunction shotDownload(dataUrl, filename) {\r\n if (!dataUrl || dataUrl.substr(0, 5) !== 'data:') {\r\n return;\r\n }\r\n if (!filename) {\r\n filename = ['screenshot-', +new Date(), '.png'].join('');\r\n }\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(dataUrlToBlob(dataUrl), filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(dataUrlToBlob(dataUrl));\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction download(data, filename, type) {\r\n const blobData = new Blob([data]);\r\n\r\n if (!filename) {\r\n filename = ['data', +new Date()].join('');\r\n }\r\n\r\n if (!type) {\r\n filename += blobData.type || '.bin';\r\n } else {\r\n filename += `.${type}`;\r\n }\r\n\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(blobData, filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(blobData);\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction copySubArrays(src, dst, indices, itemSize) {\r\n for (let i = 0, n = indices.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n dst[i * itemSize + j] = src[indices[i] * itemSize + j];\r\n }\r\n }\r\n}\r\n\r\nfunction shallowCloneNode(node) {\r\n const newNode = node.cloneNode(true);\r\n newNode.worldPos = node.worldPos;\r\n // .style property is readonly, so \"newNode.style = node.style;\" won't work (and we don't need it, right?)\r\n return newNode;\r\n}\r\n\r\nconst unquotedStringRE = /^[a-zA-Z0-9_]*$/;\r\nconst enquoteHelper = ['\"', '', '\"'];\r\n\r\n// verify and correct if needed selctor identifier\r\nfunction correctSelectorIdentifier(value) {\r\n if (unquotedStringRE.test(value)) {\r\n return value;\r\n }\r\n // quote incorrect identifier\r\n enquoteHelper[1] = value;\r\n return enquoteHelper.join('');\r\n}\r\n\r\n/**\r\n * Concatenates two TypedArray. Doesn't check null refs o type equality\r\n * Attention! It must be use very rarely because requires memory reallocation every time. Use MergeTypedArraysUnsafe to\r\n * unite array of subarrays.\r\n * @param{TypedArray} first - destination array\r\n * @param{TypedArray} second - source array\r\n * @returns{TypedArray} resulting concatenated array\r\n */\r\nfunction concatTypedArraysUnsafe(first, second) {\r\n const result = new first.constructor(first.length + second.length);\r\n result.set(first);\r\n result.set(second, first.length);\r\n return result;\r\n}\r\n\r\n/**\r\n * Merges array of TypedArray into TypedArray. Doesn't check null refs o type equality\r\n * @param{array} array - source array of subarrays\r\n * @returns{TypedArray} resulting merged array\r\n */\r\nfunction mergeTypedArraysUnsafe(array) {\r\n if (array.length <= 0) {\r\n return null;\r\n }\r\n // count the size\r\n const size = array.reduce((acc, cur) => acc + cur.length, 0);\r\n // create combined array\r\n const result = new array[0].constructor(size);\r\n for (let i = 0, start = 0; i < array.length; i++) {\r\n const count = array[i].length;\r\n result.set(array[i], start);\r\n start += count;\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Exports\r\n\r\nexport default {\r\n browserType,\r\n encodeQueryComponent,\r\n decodeQueryComponent,\r\n getUrlParameters,\r\n getUrlParametersAsDict,\r\n resolveURL,\r\n generateRegExp,\r\n createElement,\r\n deriveClass,\r\n deriveDeep,\r\n hexColor,\r\n DebugTracer,\r\n OutOfMemoryError,\r\n allocateTyped,\r\n bytesFromBase64,\r\n bytesToBase64,\r\n arrayFromBase64,\r\n arrayToBase64,\r\n compareOptionsWithDefaults,\r\n objectsDiff,\r\n forInRecursive,\r\n enquoteString,\r\n unquoteString,\r\n getBrowser,\r\n shotOpen,\r\n shotDownload,\r\n copySubArrays,\r\n shallowCloneNode,\r\n correctSelectorIdentifier,\r\n getFileExtension,\r\n splitFileName,\r\n download,\r\n concatTypedArraysUnsafe,\r\n mergeTypedArraysUnsafe,\r\n};\r\n","import EventDispatcher from './EventDispatcher';\r\n\r\nexport default class JobHandle extends EventDispatcher {\r\n constructor() {\r\n super();\r\n this._shouldCancel = false;\r\n }\r\n\r\n cancel() {\r\n this._shouldCancel = true;\r\n this.dispatchEvent({ type: 'cancel' });\r\n }\r\n\r\n shouldCancel() {\r\n return this._shouldCancel;\r\n }\r\n\r\n // slaves use this to notify master about their events\r\n // master routes these notifications to a single event slot\r\n notify(event) {\r\n this.dispatchEvent({ type: 'notification', slaveEvent: event });\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport utils from './utils';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\n\r\nconst VERSION = 0;\r\n\r\n//----------------------------------------------------------------------------\r\n// DEFAULT SETTINGS\r\n//----------------------------------------------------------------------------\r\n\r\n/**\r\n * Polygonal complexity settings.\r\n *\r\n * @typedef PolyComplexity\r\n * @property {number} poor\r\n * @property {number} low\r\n * @property {number} medium\r\n * @property {number} high\r\n * @property {number} ultra\r\n */\r\n\r\n/**\r\n * @alias SettingsObject\r\n * @namespace\r\n */\r\nconst defaults = {\r\n /**\r\n * Default options for all available modes.\r\n * Use {@link Mode.id} as a dictionary key to access mode options.\r\n *\r\n * Usually you don't need to override these settings. You may specify mode options as a parameter during\r\n * {@link Mode} construction.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {LinesModeOptions} LN - Lines mode options.\r\n * @property {LicoriceModeOptions} LC - Licorice mode options.\r\n * @property {BallsAndSticksModeOptions} BS - Balls and Sticks mode options.\r\n * @property {VanDerWaalsModeOptions} VW - Van der Waals mode options.\r\n * @property {TraceModeOptions} TR - Trace mode options.\r\n * @property {TubeModeOptions} TU - Tube mode options.\r\n * @property {CartoonModeOptions} CA - Cartoon mode options.\r\n * @property {QuickSurfaceModeOptions} QS - Contact Surface mode options.\r\n * @property {IsoSurfaceSASModeOptions} SA - Solvent Accessible Surface mode options.\r\n * @property {IsoSurfaceSESModeOptions} SE - Solvent Excluded Surface mode options.\r\n * @property {ContactSurfaceModeOptions} CS - Contact Surface mode options.\r\n * @property {TextModeOptions} TX - Text mode options.\r\n * @property {VolumeDensityModeOptions} VD - Volume Density mode options.\r\n */\r\n modes: {\r\n //----------------------------------------------------------------------------\r\n // BALLS AND STICKS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Balls and Sticks mode options.\r\n *\r\n * @typedef BallsAndSticksModeOptions\r\n *\r\n * @property {number} atom - Sphere radius as a fraction of Van der Waals atom radius.\r\n * @property {number} bond - Cylinder radius in angstroms.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n BS: {\r\n atom: 0.23,\r\n bond: 0.15,\r\n space: 0.5,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VAN DER WAALS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Van der Waals mode options.\r\n *\r\n * @typedef VanDerWaalsModeOptions\r\n *\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VW: {\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 8,\r\n high: 16,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LINES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Lines mode options.\r\n *\r\n * @typedef LinesModeOptions\r\n *\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {number} offsarom - Offset between bonds and aromatic cycle.\r\n * @property {number} chunkarom - Number of pieces in a-loop arc, corresponding to atom.\r\n * @property {number} atom - Collision radius for atoms picking.\r\n * @property {number} lineWidth - Line width in pixels (not used in thin lines).\r\n */\r\n LN: {\r\n multibond: true,\r\n showarom: true,\r\n offsarom: 0.2,\r\n chunkarom: 10,\r\n atom: 0.23,\r\n lineWidth: 2,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LICORICE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Licorice mode options.\r\n *\r\n * @typedef LicoriceModeOptions\r\n *\r\n * @property {number} bond - Bond cylinder radius.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Poly complexity values for render modes.\r\n */\r\n LC: {\r\n bond: 0.20,\r\n space: 0.0,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SAS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Accessible Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSASModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SA: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Excluded Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSESModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SE: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // QUICK SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Quick Surface mode options.\r\n *\r\n * @typedef QuickSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} scale - Radius scale for the surface being built.\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} gaussLim - Gauss lim for coloring the bigger the value, the smoother our colors are.\r\n * @property {PolyComplexity} gridSpacing - Poly complexity values for render modes. In this case the value\r\n * corresponds to the grid density.\r\n */\r\n QS: {\r\n isoValue: 0.5,\r\n gaussLim: {\r\n poor: 1.5,\r\n low: 2.0,\r\n medium: 2.5,\r\n high: 3.0,\r\n ultra: 4.0,\r\n },\r\n scale: 1.0,\r\n wireframe: false,\r\n gridSpacing: {\r\n poor: 2,\r\n low: 1.5,\r\n medium: 1,\r\n high: 0.5,\r\n ultra: 0.25,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CONTACT SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Contact Surface mode options.\r\n *\r\n * @typedef ContactSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} probeRadius - Probe radius.\r\n * @property {number} probePositions\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Radius scale for the surface being built.\r\n * Poly complexity values for render modes. In this case the value corresponds to the grid density.\r\n */\r\n CS: {\r\n probeRadius: 1.4,\r\n isoValue: 1.5,\r\n wireframe: false,\r\n probePositions: 30,\r\n polyComplexity: {\r\n poor: 0.5,\r\n low: 1.0,\r\n medium: 1.5,\r\n high: 1.75,\r\n ultra: 2.0,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TRACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Trace mode options.\r\n *\r\n * @typedef TraceModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n TR: {\r\n radius: 0.30,\r\n polyComplexity: {\r\n poor: 12,\r\n low: 16,\r\n medium: 32,\r\n high: 64,\r\n ultra: 64,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TUBE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Tube mode options.\r\n *\r\n * @typedef TubeModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {number} tension - Tension for interpolation.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n TU: {\r\n radius: 0.30,\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CARTOON\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Cartoon mode options.\r\n *\r\n * @typedef CartoonModeOptions\r\n *\r\n * @property {number} radius - Standard tube radius.\r\n * @property {number} depth - Height of the secondary structure ribbon.\r\n * @property {number} tension - Tension for interpolation.\r\n * @proprety {object} ss - Secondary structure parameters.\r\n * @proprety {object} ss.helix - Options for helices render.\r\n * @proprety {number} ss.helix.width - Width of the secondary structure ribbon.\r\n * @proprety {number} ss.helix.arrow - Secondary structure's arrow width.\r\n * @proprety {object} ss.strand - Options for strands render.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * polyComplexity must be even for producing symmetric arrows.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n CA: {\r\n radius: 0.30,\r\n depth: 0.25,\r\n ss: {\r\n helix: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n strand: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n },\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TEXT\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Text mode options.\r\n *\r\n * @typedef TextModeOptions\r\n *\r\n * @property {string} template - Format string for building output text.\r\n * @property {string} horizontalAlign - Text alignment ('left', 'right', 'center').\r\n * @property {string} verticalAlign - Vertical text box alignment ('top', 'bottom', 'middle').\r\n * @property {number} dx - Text offset x in angstroms.\r\n * @property {number} dy - Text offset y in angstroms.\r\n * @property {number} dz - Text offset z in angstroms.\r\n * @property {string} fg - Color rule for foreground.\r\n * @property {string} bg - Color rule for background.\r\n * @property {boolean} showBg - Flag, that toggles background rendering.\r\n *\r\n */\r\n TX: {\r\n template: '{{Chain}}.{{Residue}}{{Sequence}}.{{Name}}',\r\n horizontalAlign: 'center',\r\n verticalAlign: 'middle',\r\n dx: 0,\r\n dy: 0,\r\n dz: 1,\r\n fg: 'none',\r\n bg: '0x202020',\r\n showBg: true,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VOLUME DENSITY\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Volume density mode options.\r\n *\r\n * @typedef VolumeDensityModeOptions\r\n *\r\n * @property {number} kSigma - Noise threshold coefficient.\r\n * @property {boolean} frame - flag, that turns on box frame painting.\r\n * @property {boolean} isoMode - flag, that turns on IsoSurface mode instead of Volume Rendering.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VD: {\r\n kSigma: 1.0,\r\n kSigmaMed: 2.0,\r\n kSigmaMax: 4.0,\r\n frame: true,\r\n isoMode: false,\r\n polyComplexity: {\r\n poor: 2,\r\n low: 3,\r\n medium: 4,\r\n high: 8,\r\n ultra: 10,\r\n },\r\n },\r\n },\r\n\r\n /**\r\n * Default options for all available colorers.\r\n * Use {@link Colorer.id} as a dictionary key to access colorer options.\r\n *\r\n * Usually you don't need to override these settings. You may specify colorer options as a parameter during\r\n * {@link Colorer} construction.\r\n *\r\n * Not all colorers have options.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {ElementColorerOptions} EL - Element colorer options.\r\n * @property {SequenceColorerOptions} SQ - Sequence colorer options.\r\n * @property {MoleculeColorerOptions} MO - Molecule colorer options.\r\n * @property {UniformColorerOptions} UN - Uniform colorer options.\r\n * @property {ConditionalColorerOptions} CO - Conditional colorer options.\r\n * @property {TemperatureColorerOptions} TM - Temperature colorer options.\r\n * @property {OccupancyColorerOptions} OC - Occupancy colorer options.\r\n * @property {HydrophobicityColorerOptions} HY - Hydrophobicity colorer options.\r\n */\r\n colorers: {\r\n /**\r\n * Element colorer options.\r\n *\r\n * @typedef ElementColorerOptions\r\n *\r\n * @property {number} carbon - Carbon color or -1 to use default.\r\n */\r\n EL: {\r\n carbon: -1,\r\n },\r\n\r\n /**\r\n * Uniform colorer options.\r\n *\r\n * @typedef UniformColorerOptions\r\n *\r\n * @property {number} color - Single color to paint with.\r\n */\r\n UN: {\r\n color: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Conditional colorer options.\r\n *\r\n * @typedef ConditionalColorerOptions\r\n *\r\n * @property {string} subset - Selector string.\r\n * @property {number} color - Color of selected atoms.\r\n * @property {number} baseColor - Color of other atoms.\r\n */\r\n CO: {\r\n subset: 'charged',\r\n color: 0xFF0000,\r\n baseColor: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Carbon colorer options.\r\n *\r\n * @typedef CarbonColorerOptions\r\n *\r\n * @property {number} color - Single color to paint carbons\r\n * @property {number} factor - Color factor for not carbon atoms.\r\n */\r\n CB: {\r\n color: 0x909090,\r\n factor: 0.6,\r\n },\r\n\r\n /**\r\n * Sequence colorer options.\r\n *\r\n * @typedef SequenceColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n SQ: {\r\n gradient: 'rainbow',\r\n },\r\n\r\n /**\r\n * Temperature colorer options.\r\n *\r\n * @typedef TemperatureColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n * @property {number} min - Minimal temperature.\r\n * @property {number} max - Maximal temperature.\r\n */\r\n TM: {\r\n gradient: 'temp',\r\n min: 5,\r\n max: 40,\r\n },\r\n\r\n /**\r\n * Occupancy colorer options.\r\n *\r\n * @typedef OccupancyColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n OC: {\r\n gradient: 'reds',\r\n },\r\n\r\n /**\r\n * Hydrophobicity colorer options.\r\n *\r\n * @typedef HydrophobicityColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n HY: {\r\n gradient: 'blue-red',\r\n },\r\n\r\n /**\r\n * Molecule colorer options.\r\n *\r\n * @typedef MoleculeColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n MO: {\r\n gradient: 'rainbow',\r\n },\r\n },\r\n\r\n /*\r\n * Use antialiasing in WebGL.\r\n * @type {boolean}\r\n */\r\n antialias: true,\r\n\r\n /*\r\n * Camera field of view in degrees.\r\n * @type {number}\r\n */\r\n camFov: 45.0,\r\n\r\n /*\r\n * Camera near plane distance.\r\n * @type {number}\r\n */\r\n camNear: 0.5,\r\n\r\n /*\r\n * Camera far plane distance.\r\n * @type {number}\r\n */\r\n camFar: 100.0,\r\n\r\n camDistance: 2.5,\r\n\r\n radiusToFit: 1.0,\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogNearFactor: 0.5, // [0, 1]\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogFarFactor: 1, // [0, 1]\r\n fogAlpha: 1.0,\r\n fogColor: 0x000000,\r\n fogColorEnable: false,\r\n\r\n /**\r\n * Palette used for molecule coloring.\r\n * @type {string}\r\n */\r\n palette: 'JM',\r\n\r\n /*\r\n * Geometry resolution.\r\n * @type {string}\r\n */\r\n resolution: 'medium',\r\n\r\n autoResolution: false/* true */,\r\n\r\n autoPreset: true,\r\n\r\n preset: 'default', // TODO: remove 'preset' from settings, implement autodetection\r\n\r\n presets: {\r\n // Default\r\n default: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n empty: [],\r\n\r\n // Wireframe\r\n wire: [{\r\n mode: 'LN',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Small molecules\r\n small: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Proteins, nucleic acids etc.\r\n macro: [{\r\n mode: 'CA',\r\n colorer: 'SS',\r\n selector: 'not hetatm',\r\n material: 'SF',\r\n }, {\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'hetatm and not water',\r\n material: 'SF',\r\n }],\r\n },\r\n\r\n objects: {\r\n line: {\r\n color: 0xFFFFFFFF,\r\n dashSize: 0.3,\r\n gapSize: 0.05,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n\r\n bg: {\r\n color: 0x202020,\r\n transparent: false,\r\n },\r\n\r\n draft: {\r\n clipPlane: false,\r\n clipPlaneFactor: 0.5,\r\n clipPlaneSpeed: 0.00003,\r\n },\r\n\r\n /*\r\n * Separate group for plugins.\r\n * Each plugin handles its field by itself.\r\n */\r\n plugins: {\r\n\r\n },\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n axes: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fog: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fps: true,\r\n\r\n /**\r\n * Switch using of z-sprites for sphere and cylinder geometry\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zSprites: true,\r\n\r\n isoSurfaceFakeOpacity: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n suspendRender: true,\r\n\r\n nowater: false,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autobuild: true,\r\n\r\n /**\r\n * Anti-aliasing.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fxaa: true,\r\n /**\r\n * Outline depths\r\n * @type {boolean}\r\n * @instance\r\n */\r\n outline: {\r\n on: false,\r\n color: 0x000000,\r\n threshold: 0.1,\r\n thickness: 1,\r\n },\r\n\r\n /**\r\n * Ambient Occlusion special effect.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n ao: false,\r\n\r\n /**\r\n * Shadows options.\r\n *\r\n * @property {boolean} shadowMap - enable/disable.\r\n * @property {string} basic/percentage-closer filtering/non-uniform randomizing pcf.\r\n * @property {number} radius for percentage-closer filtering.\r\n */\r\n shadow: {\r\n on: false,\r\n type: 'random'/* basic, pcf, random */,\r\n radius: 1.0,\r\n },\r\n\r\n /**\r\n * Auto-rotation with constant speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n autoRotation: 0.0,\r\n\r\n /**\r\n * Set maximum fps for animation.\r\n * @type {number}\r\n * @instance\r\n */\r\n maxfps: 30,\r\n\r\n /**\r\n * Set fbx output precision.\r\n * @type {number}\r\n * @instance\r\n */\r\n fbxprec: 4,\r\n\r\n /**\r\n * Auto-rotation axis.\r\n *\r\n * - true: complex auto-rotation is about vertical axis\r\n * - false: rotation axis is defined by last user rotation\r\n *\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autoRotationAxisFixed: true,\r\n\r\n /**\r\n * Enable zooming with mouse wheel or pinch gesture.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zooming: true,\r\n\r\n /**\r\n * Enable picking atoms & residues with left mouse button or touch.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n picking: true,\r\n\r\n /**\r\n * Set picking mode ('atom', 'residue', 'chain', 'molecule').\r\n * @type {string}\r\n * @instance\r\n */\r\n pick: 'atom',\r\n\r\n /**\r\n * Make \"component\" and \"fragment\" editing modes available.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n editing: false,\r\n\r\n /**\r\n * Detect aromatic loops.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n aromatic: false,\r\n\r\n /**\r\n * Load only one biological unit from all those described in PDB file.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n singleUnit: true,\r\n\r\n /**\r\n * Set stereo mode ('NONE', 'SIMPLE', 'DISTORTED', 'ANAGLYPH', 'WEBVR').\r\n * @type {string}\r\n * @instance\r\n */\r\n stereo: 'NONE',\r\n\r\n /**\r\n * Enable smooth transition between views\r\n * @type {boolean}\r\n * @instance\r\n */\r\n interpolateViews: true,\r\n\r\n /**\r\n * Set transparency mode ('standard', 'prepass').\r\n * @type {string}\r\n * @instance\r\n */\r\n transparency: 'prepass',\r\n\r\n /**\r\n * Mouse translation speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n translationSpeed: 2,\r\n\r\n debug: {\r\n example: 3.5,\r\n text: 'hello!',\r\n good: true,\r\n ssaoKernelRadius: 0.7,\r\n ssaoFactor: 0.7,\r\n stereoBarrel: 0.25,\r\n },\r\n use: {\r\n multiFile: false,\r\n },\r\n};\r\n\r\n//----------------------------------------------------------------------------\r\n// SETTINGS CLASS\r\n//----------------------------------------------------------------------------\r\n\r\nfunction Settings() {\r\n EventDispatcher.call(this);\r\n\r\n this.old = null;\r\n this.now = {};\r\n this._changed = {};\r\n\r\n this.reset();\r\n}\r\n\r\nutils.deriveClass(Settings, EventDispatcher, {\r\n defaults,\r\n\r\n set(path, value) {\r\n if (_.isString(path)) {\r\n const oldValue = _.get(this.now, path);\r\n if (oldValue !== value) {\r\n _.set(this.now, path, value);\r\n this._notifyChange(path, value);\r\n }\r\n } else {\r\n const diff = utils.objectsDiff(path, this.now);\r\n if (!_.isEmpty(diff)) {\r\n _.merge(this.now, diff);\r\n this._notifyChanges(diff);\r\n }\r\n }\r\n },\r\n\r\n get(path, defaultValue) {\r\n return _.get(this.now, path, defaultValue);\r\n },\r\n\r\n reset() {\r\n const diff = utils.objectsDiff(defaults, this.now);\r\n this.now = _.cloneDeep(defaults);\r\n this.old = null;\r\n this._notifyChanges(diff);\r\n this._changed = {};\r\n },\r\n\r\n checkpoint() {\r\n this.old = _.cloneDeep(this.now);\r\n this._changed = {};\r\n },\r\n\r\n _notifyChange(path, value) {\r\n this._changed[path] = true;\r\n this.dispatchEvent({ type: `change:${path}`, value });\r\n },\r\n\r\n _notifyChanges(diff) {\r\n utils.forInRecursive(diff, (deepValue, deepPath) => {\r\n this._notifyChange(deepPath, deepValue);\r\n });\r\n },\r\n\r\n changed() {\r\n if (!this.old) {\r\n return [];\r\n }\r\n const { old, now } = this;\r\n const keys = _.filter(Object.keys(this._changed), (key) => _.get(old, key) !== _.get(now, key));\r\n return keys;\r\n },\r\n\r\n applyDiffs(diffs) {\r\n if (diffs.hasOwnProperty('VERSION') && diffs.VERSION !== VERSION) {\r\n throw new Error('Settings version does not match!');\r\n }\r\n // VERSION shouldn't be presented inside settings structure\r\n delete diffs.VERSION;\r\n this.reset();\r\n this.set(diffs);\r\n },\r\n\r\n getDiffs(versioned) {\r\n const diffs = utils.objectsDiff(this.now, defaults);\r\n if (versioned) {\r\n diffs.VERSION = VERSION;\r\n }\r\n return diffs;\r\n },\r\n\r\n setPluginOpts(plugin, opts) {\r\n defaults.plugins[plugin] = _.cloneDeep(opts);\r\n this.now.plugins[plugin] = _.cloneDeep(opts);\r\n },\r\n});\r\n\r\nexport default new Settings();\r\n","import _ from 'lodash';\r\nimport settings from './settings';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\n\r\nlet repIndex = 0;\r\n\r\nfunction asBoolean(value) {\r\n return !(!value || value === '0' || (_.isString(value) && value.toLowerCase() === 'false'));\r\n}\r\n\r\nconst adapters = {\r\n string: String,\r\n number: Number,\r\n boolean: asBoolean,\r\n};\r\n\r\n// Level 1 assignment symbol\r\nconst cL1Ass = '=';\r\n\r\nconst cOptsSep = '!';\r\n// Level 2 (options) assignment symbol\r\nconst cL2Ass = ':';\r\n// Level 2 (options) separator symbol\r\nconst cLSep = ',';\r\n\r\nconst cCommonIgnoreSymbols = '$;@/?';\r\n/**\r\n * We may (and should) leave as is for better readability:\r\n *\r\n * $ , ; : @ / ?\r\n */\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n */\r\nfunction getLevel1ExcludedExpr() {\r\n const cLevel1Ignores = ':,';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel1Ignores);\r\n}\r\n\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n * (options, etc, ..)\r\n */\r\nfunction getLevel2ExcludedExpr() {\r\n const cLevel2Ignores = ' ';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel2Ignores);\r\n}\r\n\r\nconst cL1ExclExpr = getLevel1ExcludedExpr();\r\nfunction encodeQueryComponentL1(value) {\r\n return utils.encodeQueryComponent(value, cL1ExclExpr);\r\n}\r\n\r\nconst cL2ExclExpr = getLevel2ExcludedExpr();\r\nfunction encodeQueryComponentL2(value) {\r\n return utils.encodeQueryComponent(value, cL2ExclExpr);\r\n}\r\n\r\nfunction ensureRepList(opts) {\r\n let { reps } = opts;\r\n if (!reps) {\r\n const { presets } = settings.now;\r\n let preset = opts.preset || settings.now.preset;\r\n reps = presets[preset];\r\n if (!reps) {\r\n logger.warn(`Unknown preset \"${preset}\"`);\r\n [preset] = Object.keys(presets);\r\n reps = presets[preset]; // fall back to any preset\r\n }\r\n opts.preset = preset;\r\n opts.reps = utils.deriveDeep(reps, true);\r\n }\r\n}\r\n\r\nfunction ensureRepAssign(opts, prop, value) {\r\n ensureRepList(opts);\r\n const rep = opts.reps[repIndex];\r\n // prop specified twice therefore start new rep by cloning the current\r\n if (rep.hasOwnProperty(prop)) {\r\n repIndex = opts.reps.length;\r\n opts.reps[repIndex] = utils.deriveDeep(rep, true);\r\n }\r\n if (value !== undefined) {\r\n opts.reps[repIndex][prop] = value;\r\n }\r\n}\r\n\r\nfunction addObject(opts, params, options) {\r\n if (opts._objects === undefined) {\r\n opts._objects = [];\r\n }\r\n\r\n const [type, newOpts] = options;\r\n const newObj = {\r\n type,\r\n params,\r\n };\r\n\r\n if (newOpts !== undefined) {\r\n newObj.opts = newOpts;\r\n }\r\n\r\n opts._objects[opts._objects.length] = newObj;\r\n}\r\n\r\nfunction parseParams(str, params) {\r\n const sep = str.indexOf(',');\r\n if (sep >= 0) {\r\n params.push(str.substr(sep + 1).split(','));\r\n return str.substr(0, sep);\r\n }\r\n // keep this untouched if no params were extracted\r\n return str;\r\n}\r\n\r\nfunction extractArgs(input, defaultsDict, params) {\r\n if (input) {\r\n const bang = input.indexOf(cOptsSep);\r\n const inputVal = parseParams(input.substr(0, bang >= 0 ? bang : undefined), params);\r\n if (bang >= 0) {\r\n const args = input.substr(bang + 1).split(cLSep);\r\n input = inputVal;\r\n if (defaultsDict) {\r\n const defaults = defaultsDict[input];\r\n const opts = utils.deriveDeep(defaults, true);\r\n args.forEach((arg) => {\r\n const pair = arg.split(cL2Ass, 2);\r\n const key = decodeURIComponent(pair[0]);\r\n const value = decodeURIComponent(pair[1]);\r\n const adapter = adapters[typeof _.get(defaults, key)];\r\n if (adapter) {\r\n _.set(opts, key, adapter(value));\r\n } else {\r\n logger.warn(`Unknown argument \"${key}\" for option \"${input}\"`);\r\n }\r\n });\r\n if (Object.keys(opts).length > 0) {\r\n input = [input, opts];\r\n }\r\n }\r\n } else {\r\n input = inputVal;\r\n }\r\n }\r\n return input;\r\n}\r\n\r\nconst actions = {\r\n\r\n l: 'load',\r\n load: String,\r\n t: 'type',\r\n type: String,\r\n v: 'view',\r\n view: String,\r\n u: 'unit',\r\n unit: Number,\r\n menu: asBoolean,\r\n\r\n // Commands\r\n\r\n o: 'object',\r\n object(value, opts) {\r\n const params = [];\r\n let options = extractArgs(value, settings.defaults.objects, params);\r\n if (!Array.isArray(options)) {\r\n options = [options];\r\n }\r\n addObject(opts, params[0], options);\r\n },\r\n\r\n p: 'preset',\r\n preset(value, opts) {\r\n opts.preset = value;\r\n opts.reps = null;\r\n ensureRepList(opts);\r\n },\r\n\r\n r: 'rep',\r\n rep(value, opts) {\r\n ensureRepList(opts);\r\n repIndex = Number(value);\r\n // clamp the index to one greater than the last\r\n repIndex = repIndex <= opts.reps.length ? (repIndex < 0 ? 0 : repIndex) : opts.reps.length;\r\n // create a new rep if it is adjacent to the existing ones\r\n if (repIndex === opts.reps.length) {\r\n // if there is no rep to derive from, derive from the first rep of the default\r\n opts.reps[repIndex] = repIndex > 0 ? utils.deriveDeep(opts.reps[repIndex - 1], true)\r\n : utils.deriveDeep(settings.defaults.presets.default[0], true);\r\n }\r\n },\r\n\r\n s: 'select',\r\n select(value, opts) {\r\n ensureRepAssign(opts, 'selector', value);\r\n },\r\n\r\n m: 'mode',\r\n mode(value, opts) {\r\n ensureRepAssign(opts, 'mode', extractArgs(value, settings.defaults.modes));\r\n },\r\n\r\n c: 'color',\r\n color(value, opts) {\r\n ensureRepAssign(opts, 'colorer', extractArgs(value, settings.defaults.colorers));\r\n },\r\n\r\n mt: 'material',\r\n material(value, opts) {\r\n ensureRepAssign(opts, 'material', extractArgs(value, settings.defaults.materials));\r\n },\r\n\r\n dup(value, opts) {\r\n ensureRepList(opts);\r\n const { reps } = opts;\r\n const rep = reps[repIndex];\r\n repIndex = reps.length;\r\n reps[repIndex] = utils.deriveDeep(rep, true);\r\n },\r\n\r\n // Settings shortcuts\r\n\r\n ar: 'autoResolution',\r\n};\r\n\r\nfunction _fromArray(entries) {\r\n repIndex = 0;\r\n\r\n const opts = {};\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const /** string[] */ entry = entries[i];\r\n let /** string? */ key = entry[0];\r\n const /** string? */ value = entry[1];\r\n let /** function|string? */ action = actions[key];\r\n\r\n // unwind shortcuts and aliases\r\n while (_.isString(action)) {\r\n key = action;\r\n action = actions[key];\r\n }\r\n\r\n // either set a property or use specialized parser\r\n if (!action) {\r\n const adapter = adapters[typeof _.get(settings.defaults, key)];\r\n if (adapter) {\r\n _.set(opts, `settings.${key}`, adapter(value));\r\n } else {\r\n logger.warn(`Unknown option \"${key}\"`);\r\n }\r\n } else if (_.isFunction(action)) {\r\n const result = action(value, opts);\r\n if (result !== undefined) {\r\n opts[key] = result;\r\n }\r\n }\r\n }\r\n\r\n return opts;\r\n}\r\n\r\nfunction fromAttr(attr) {\r\n return _fromArray(utils.getUrlParameters(`?${attr || ''}`));\r\n}\r\n\r\nfunction fromURL(url) {\r\n return _fromArray(utils.getUrlParameters(url));\r\n}\r\n\r\nfunction _processOptsForURL(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = encodeQueryComponentL2(key) + cL2Ass + encodeQueryComponentL2(value);\r\n });\r\n return str.join(cLSep);\r\n}\r\n\r\nfunction _processArgsForURL(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]}${cOptsSep}${_processOptsForURL(args[1])}`;\r\n}\r\n\r\nfunction _processObjForURL(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += `,${objOpts.params.join(',')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += cOptsSep + _processOptsForURL(objOpts.opts);\r\n }\r\n return res;\r\n}\r\n\r\nfunction toURL(opts) {\r\n const stringList = [];\r\n let idx = 0;\r\n\r\n function checkAndAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n stringList[idx++] = encodeQueryComponentL1(prefix)\r\n + cL1Ass + encodeQueryComponentL1(value);\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n if (_.isEmpty(repList[i])) {\r\n continue;\r\n }\r\n checkAndAdd('r', i);\r\n checkAndAdd('s', repList[i].selector);\r\n checkAndAdd('m', _processArgsForURL(repList[i].mode));\r\n checkAndAdd('c', _processArgsForURL(repList[i].colorer));\r\n checkAndAdd('mt', _processArgsForURL(repList[i].material));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('o', _processObjForURL(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('l', opts.load);\r\n checkAndAdd('u', opts.unit);\r\n checkAndAdd('p', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n checkAndAdd('v', opts.view);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(key, value);\r\n });\r\n\r\n let url = '';\r\n if (typeof window !== 'undefined') {\r\n const { location } = window;\r\n url = `${location.protocol}//${location.host}${location.pathname}`;\r\n }\r\n if (stringList.length > 0) {\r\n url += `?${stringList.join('&')}`;\r\n }\r\n\r\n return url;\r\n}\r\n\r\nfunction _processOptsForScript(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = `${key}=${utils.enquoteString(value)}`;\r\n });\r\n return str.join(' ');\r\n}\r\n\r\nfunction _processArgsForScript(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]} ${_processOptsForScript(args[1])}`;\r\n}\r\n\r\nfunction _processObjForScript(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += ` ${objOpts.params.map(utils.enquoteString).join(' ')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += ` ${_processOptsForScript(objOpts.opts)}`;\r\n }\r\n return res;\r\n}\r\n\r\nfunction _processRepsForScript(rep, index) {\r\n const repString = [];\r\n let strIdx = 0;\r\n function localAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n repString[strIdx++] = prefix + value;\r\n }\r\n }\r\n if (_.isEmpty(rep)) {\r\n return null;\r\n }\r\n localAdd('', index);\r\n localAdd('s=', utils.enquoteString(rep.selector));\r\n localAdd('m=', _processArgsForScript(rep.mode));\r\n localAdd('c=', _processArgsForScript(rep.colorer));\r\n localAdd('mt=', _processArgsForScript(rep.material));\r\n return repString.join(' ');\r\n}\r\n\r\nfunction toScript(opts) {\r\n const commandsList = [];\r\n let idx = 0;\r\n function checkAndAdd(command, value, saveQuotes) {\r\n if (value !== null && value !== undefined) {\r\n const quote = (typeof value === 'string' && saveQuotes) ? '\"' : '';\r\n commandsList[idx++] = `${command} ${quote}${value}${quote}`.trim();\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n checkAndAdd('rep', _processRepsForScript(repList[i], i));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('', _processObjForScript(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('set', 'autobuild false');\r\n checkAndAdd('load', opts.load, true);\r\n checkAndAdd('unit', opts.unit);\r\n checkAndAdd('preset', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(`set ${key}`, value, true);\r\n });\r\n checkAndAdd('view', opts.view);\r\n checkAndAdd('set', 'autobuild true');\r\n return commandsList.join('\\n');\r\n}\r\n\r\nexport default {\r\n fromURL,\r\n fromAttr,\r\n adapters,\r\n toURL,\r\n toScript,\r\n};\r\n","/**\r\n * Atom measurements.\r\n *\r\n * @param {Residue} residue - (required) Residue containing the atom\r\n * @param {string} name - (required) Name, unique in the residue\r\n * @param {Element} type - (required) Chemical element reference\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n *\r\n * @param {number} role - Role of atom inside monomer: Lead and wing are particularity interesting\r\n * @param {boolean} het - Non-standard residue indicator\r\n *\r\n * @param {number} serial - Serial number, unique in the model\r\n * @param {string} location - Alternative location indicator (usually space or A-Z)\r\n * @param {number} occupancy - Occupancy percentage, from 0 to 1\r\n * @param {number} temperature - Temperature\r\n * @param {number} charge - Charge\r\n *\r\n * @exports Atom\r\n * @constructor\r\n */\r\n\r\nclass Atom {\r\n constructor(residue, name, type, position, role, het, serial, location, occupancy, temperature, charge) {\r\n this.index = -1;\r\n this.residue = residue;\r\n this.name = name;\r\n this.element = type;\r\n this.position = position;\r\n this.role = role;\r\n this.mask = 1 | 0;\r\n\r\n this.het = het;\r\n\r\n this.serial = serial;\r\n this.location = (location || ' ').charCodeAt(0);\r\n this.occupancy = occupancy || 1;\r\n this.temperature = temperature;\r\n this.charge = charge;\r\n this.hydrogenCount = -1; // explicitly invalid\r\n this.radicalCount = 0;\r\n this.valence = -1; // explicitly invalid\r\n\r\n this.bonds = [];\r\n\r\n this.flags = 0x0000;\r\n if (type.name === 'H') {\r\n this.flags |= Atom.Flags.HYDROGEN;\r\n } else if (type.name === 'C') {\r\n this.flags |= Atom.Flags.CARBON;\r\n }\r\n }\r\n\r\n isHet() {\r\n return this.het;\r\n }\r\n\r\n isHydrogen() {\r\n return this.element.number === 1;\r\n }\r\n\r\n getVisualName() {\r\n const { name } = this;\r\n if (name.length > 0) {\r\n return name;\r\n }\r\n return this.element.name.trim();\r\n }\r\n\r\n forEachBond(process) {\r\n const { bonds } = this;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n getFullName() {\r\n let name = '';\r\n if (this.residue !== null) {\r\n if (this.residue._chain !== null) {\r\n name += `${this.residue._chain.getName()}.`;\r\n }\r\n name += `${this.residue._sequence}.`;\r\n }\r\n name += this.name;\r\n return name;\r\n }\r\n\r\n /**\r\n * Enumeration of atom flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n CARBON: 0x0001,\r\n // OXYGEN: 0x0002,\r\n // NITROGEN: 0x0004,\r\n HYDROGEN: 0x0008,\r\n /** Non-polar hydrogen (it is also a HYDROGEN) */\r\n NONPOLARH: 0x1008,\r\n };\r\n}\r\n\r\nexport default Atom;\r\n","class Element {\r\n constructor(number, name, fullName, weight, radius, radiusBonding, hValency) {\r\n this.number = number;\r\n this.name = name;\r\n this.fullName = fullName;\r\n this.weight = weight;\r\n this.radius = radius;\r\n this.radiusBonding = radiusBonding;\r\n this.hydrogenValency = hValency;\r\n }\r\n\r\n static Constants = {\r\n /* eslint-disable no-magic-numbers */\r\n U1: 1,\r\n Lead: 2,\r\n U2: 3,\r\n Wing: 4,\r\n U18: 18,\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n static Role = {\r\n /* eslint-disable no-magic-numbers */\r\n N: Element.Constants.U1,\r\n CA: Element.Constants.Lead,\r\n C: Element.Constants.U2,\r\n O: Element.Constants.Wing,\r\n SG: Element.Constants.U18,\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByAtomicNumber = [\r\n /* eslint-disable no-magic-numbers */\r\n null,\r\n new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]),\r\n new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]),\r\n new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]),\r\n new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]),\r\n new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]),\r\n new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]),\r\n new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]),\r\n new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]),\r\n new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]),\r\n new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]),\r\n new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]),\r\n new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]),\r\n new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]),\r\n new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]),\r\n new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]),\r\n new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]),\r\n new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]),\r\n new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]),\r\n new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]),\r\n new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]),\r\n new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]),\r\n new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]),\r\n new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]),\r\n new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]),\r\n new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]),\r\n new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]),\r\n new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]),\r\n new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]),\r\n new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]),\r\n new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]),\r\n new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]),\r\n new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]),\r\n new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]),\r\n new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]),\r\n new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]),\r\n new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]),\r\n new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]),\r\n new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]),\r\n new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]),\r\n new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]),\r\n new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]),\r\n new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]),\r\n new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]),\r\n new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]),\r\n new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]),\r\n new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]),\r\n new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]),\r\n new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]),\r\n new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]),\r\n new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]),\r\n new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]),\r\n new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]),\r\n new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]),\r\n new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]),\r\n new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]),\r\n new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]),\r\n new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]),\r\n new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]),\r\n new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]),\r\n new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]),\r\n new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]),\r\n new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]),\r\n new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]),\r\n new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]),\r\n new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]),\r\n new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]),\r\n new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]),\r\n new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]),\r\n new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]),\r\n new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]),\r\n new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]),\r\n new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]),\r\n new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]),\r\n new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]),\r\n new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]),\r\n new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]),\r\n new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]),\r\n new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]),\r\n new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]),\r\n new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]),\r\n new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]),\r\n new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]),\r\n new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]),\r\n new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]),\r\n new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]),\r\n new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]),\r\n new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]),\r\n new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]),\r\n new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]),\r\n new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]),\r\n new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]),\r\n new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]),\r\n new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]),\r\n new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]),\r\n new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]),\r\n new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]),\r\n new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]),\r\n new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]),\r\n new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]),\r\n new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]),\r\n new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]),\r\n new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]),\r\n new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]),\r\n new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]),\r\n new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]),\r\n new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]),\r\n new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]),\r\n new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]),\r\n new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0]),\r\n /* eslint-enable no-magic-numbers */\r\n ];\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByName = {\r\n // Duplicate atomic numbers (isotopes)\r\n /* eslint-disable no-magic-numbers */\r\n D: new Element(1, 'D', 'Deuterium', 2.014, 1.2, 0.23, [1]),\r\n T: new Element(1, 'T', 'Tritium', 3.016, 1.2, 0.23, [1]),\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // All regular elements will be added later, automatically\r\n };\r\n}\r\n\r\n(function () {\r\n const byAtomicNumber = Element.ByAtomicNumber;\r\n const byName = Element.ByName;\r\n for (let i = 0, n = byAtomicNumber.length; i < n; ++i) {\r\n const element = byAtomicNumber[i];\r\n if (element) {\r\n byName[element.name] = element;\r\n }\r\n }\r\n}());\r\n\r\n// find atom type by chemical element (or create if missing)\r\nElement.getByName = function (element) {\r\n let type = Element.ByName[element];\r\n if (!type) {\r\n type = Element.ByName[element] = new Element(0, element, 'Unknown', 0, 1.0, 0.01, [0]);\r\n }\r\n return type;\r\n};\r\n\r\nexport default Element;\r\n","const cBondTypes = {\r\n /** Was generated manually */\r\n UNKNOWN: 0,\r\n /** Simple covalent bond */\r\n COVALENT: 1,\r\n /** Aromatic bond */\r\n AROMATIC: 2,\r\n};\r\n\r\nfunction getAtomPos(atom) {\r\n return atom.position;\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Atom} left - The first atom.\r\n * @param {Atom} right - The second atom.\r\n * @param {number} order - Order of current bond.\r\n * @param {number} type - Bond type.\r\n * @param {boolean} fixed - Indicator of a pre-specified connection (in contrast with guessed one).\r\n *\r\n * @exports Bond\r\n * @constructor\r\n */\r\nclass Bond {\r\n constructor(left, right, order, type, fixed) {\r\n this._left = left;\r\n this._right = right;\r\n this._fixed = fixed;\r\n this._index = -1;\r\n if (left > right) {\r\n throw new Error('In a bond atom indices must be in increasing order');\r\n }\r\n this._order = order;\r\n this._type = type;\r\n }\r\n\r\n getLeft() {\r\n return this._left;\r\n }\r\n\r\n getRight() {\r\n return this._right;\r\n }\r\n\r\n getOrder() {\r\n return this._order;\r\n }\r\n\r\n calcLength() {\r\n return this._left.position.distanceTo(this._right.position);\r\n }\r\n\r\n _forEachNeighbour(currAtom, process) {\r\n const { bonds } = currAtom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]._left !== currAtom ? bonds[i]._left : bonds[i]._right);\r\n }\r\n }\r\n\r\n forEachLevelOne(process) {\r\n const left = this._left;\r\n const right = this._right;\r\n this._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n this._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n }\r\n\r\n forEachLevelTwo(process) {\r\n // TODO refactor this piece of an art?\r\n const left = this._left;\r\n const right = this._right;\r\n const self = this;\r\n self._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === left) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n self._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === right) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n }\r\n\r\n _fixDir(refPoint, currDir, posGetter) {\r\n // count atoms to the right and to the left of the current plane\r\n let rightCount = 0;\r\n let leftCount = 0;\r\n const tmpVec = refPoint.clone();\r\n function checkDir(atom) {\r\n tmpVec.copy(posGetter(atom));\r\n tmpVec.sub(refPoint);\r\n const dotProd = currDir.dot(tmpVec);\r\n if (dotProd > 0) {\r\n ++rightCount;\r\n } else {\r\n ++leftCount;\r\n }\r\n }\r\n function checkCarbon(atom) {\r\n if (atom.element.name === 'C') {\r\n checkDir(atom);\r\n }\r\n }\r\n // count all atoms to the left and right of our plane, start from level 1 and carbons\r\n const stages = [\r\n [this.forEachLevelOne, checkCarbon],\r\n [this.forEachLevelOne, checkDir],\r\n [this.forEachLevelTwo, checkCarbon],\r\n [this.forEachLevelTwo, checkDir],\r\n ];\r\n\r\n for (let stageId = 0; stageId < stages.length; ++stageId) {\r\n stages[stageId][0].call(this, stages[stageId][1]);\r\n if (leftCount > rightCount) {\r\n return currDir.multiplyScalar(-1);\r\n }\r\n if (leftCount < rightCount) {\r\n return currDir;\r\n }\r\n }\r\n return currDir;\r\n }\r\n\r\n calcNormalDir(posGetter) {\r\n const left = this._left;\r\n const right = this._right;\r\n let first = left;\r\n let second = right;\r\n posGetter = posGetter === undefined ? getAtomPos : posGetter;\r\n if (left.bonds.length > right.bonds.length) {\r\n first = right;\r\n second = left;\r\n }\r\n let third = first;\r\n let maxNeibs = 0;\r\n const { bonds } = second;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n let another = bonds[i]._left;\r\n if (bonds[i]._left === second) {\r\n another = bonds[i]._right;\r\n }\r\n if (another.bonds.length > maxNeibs && another !== first) {\r\n third = another;\r\n maxNeibs = another.bonds.length;\r\n }\r\n }\r\n const secondPos = posGetter(second);\r\n const firstV = posGetter(first).clone().sub(secondPos);\r\n const secondV = posGetter(third).clone().sub(secondPos);\r\n secondV.crossVectors(firstV, secondV);\r\n if (secondV.lengthSq() < 0.0001) {\r\n secondV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n secondV.normalize();\r\n firstV.crossVectors(secondV, firstV);\r\n if (firstV.lengthSq() < 0.0001) {\r\n firstV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n return this._fixDir(secondPos, firstV, posGetter);\r\n }\r\n\r\n static BondType = cBondTypes;\r\n}\r\n\r\nBond.prototype.BondType = cBondTypes;\r\n\r\nexport default Bond;\r\n","import * as THREE from 'three';\r\nimport Atom from './Atom';\r\nimport Element from './Element';\r\n\r\nconst cNucleicControlNames = ['C3\\'', 'C3*', 'P', 'H5T', 'H3T'];\r\nconst cNucleicWing1Names = ['OP1', 'O1P'];\r\nconst cNucleicWing2Names = ['OP2', 'O2P'];\r\n\r\nconst cCylinderSource = ['C3\\'', 'C3*', 'C1', 'C1\\'', 'C1*', 'P'];\r\nconst cCylinderTarget = [{\r\n types: ['A', 'DA', 'G', 'DG'],\r\n atoms: ['N1'],\r\n}, {\r\n types: ['C', 'DC'],\r\n atoms: ['N3'],\r\n}, {\r\n types: ['T', 'DT', 'U', 'DU'],\r\n atoms: ['O4'],\r\n}];\r\n\r\n/**\r\n * Residue instance.\r\n *\r\n * @param {Chain} chain - Chain this residue belongs to.\r\n * @param {ResidueType} type - Generic residue instance type.\r\n * @param {number} sequence - Sequence ID.\r\n * @param {string} icode - One character insertion code (usually space or A-Z).\r\n *\r\n * @exports Residue\r\n * @constructor\r\n */\r\nclass Residue {\r\n constructor(chain, type, sequence, icode) {\r\n this._chain = chain;\r\n this._component = null;\r\n this._type = type;\r\n this._sequence = sequence;\r\n this._icode = icode;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n\r\n this._atoms = [];\r\n this._secondary = null;\r\n this._firstAtom = null;\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n this._lastAtom = null;\r\n this._controlPoint = null;\r\n this._midPoint = null;\r\n this._wingVector = null;\r\n this._cylinders = null;\r\n this._isValid = true;\r\n this._het = false;\r\n this._molecule = null;\r\n this.temperature = null;\r\n this.occupancy = null;\r\n }\r\n\r\n // Getters and setters\r\n getChain() {\r\n return this._chain;\r\n }\r\n\r\n getMolecule() {\r\n return this._molecule;\r\n }\r\n\r\n getType() {\r\n return this._type;\r\n }\r\n\r\n getSequence() {\r\n return this._sequence;\r\n }\r\n\r\n getSecondary() {\r\n return this._secondary;\r\n }\r\n\r\n getICode() {\r\n return this._icode;\r\n }\r\n\r\n // Other methods\r\n\r\n addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge) {\r\n const atom = new Atom(this, name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n const complex = this._chain.getComplex();\r\n complex.addAtom(atom);\r\n this._atoms.push(atom);\r\n this._het = this._het || het;\r\n return atom;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (process(atoms[i])) {\r\n break;\r\n }\r\n }\r\n }\r\n\r\n _findAtomByName(name) {\r\n let res = null;\r\n this.forEachAtom((atom) => {\r\n if (atom.name === name) {\r\n res = atom;\r\n return true;\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _findFirstAtomInList(names) {\r\n let res = null;\r\n for (let i = 0; i < names.length; ++i) {\r\n res = this._findAtomByName(names[i]);\r\n if (res !== null) {\r\n return res;\r\n }\r\n }\r\n return res;\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n mask &= atoms[i].mask;\r\n }\r\n this._mask = mask;\r\n }\r\n\r\n getCylinderTargetList() {\r\n const type = this._type._name;\r\n for (let i = 0, n = cCylinderTarget.length; i < n; ++i) {\r\n for (let j = 0, m = cCylinderTarget[i].types.length; j < m; ++j) {\r\n if (type === cCylinderTarget[i].types[j]) {\r\n return cCylinderTarget[i].atoms;\r\n }\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n _detectLeadWing(dst, next, getAtomPosition) {\r\n const leadAtom = this._findFirstAtomInList(cNucleicControlNames);\r\n let wingStart = this._findFirstAtomInList(cNucleicWing1Names);\r\n let wingEnd = this._findFirstAtomInList(cNucleicWing2Names);\r\n\r\n if (wingStart === null && next !== null) {\r\n wingStart = next._findFirstAtomInList(cNucleicWing1Names);\r\n }\r\n\r\n if (wingEnd === null && next !== null) {\r\n wingEnd = next._findFirstAtomInList(cNucleicWing2Names);\r\n }\r\n\r\n if (leadAtom === null || wingStart === null || wingEnd === null) {\r\n return;\r\n }\r\n\r\n dst._leadAtom = leadAtom;\r\n dst._controlPoint = getAtomPosition(leadAtom);\r\n dst._wingVector = getAtomPosition(wingEnd).clone().sub(getAtomPosition(wingStart));\r\n dst._isValid = true;\r\n\r\n const cylSource = this._findFirstAtomInList(cCylinderSource);\r\n const targetList = this.getCylinderTargetList();\r\n const cylTarget = targetList !== null ? this._findFirstAtomInList(targetList) : null;\r\n if (cylSource === null || cylTarget === null) {\r\n return;\r\n }\r\n dst._cylinders = [getAtomPosition(cylSource), getAtomPosition(cylTarget)];\r\n }\r\n\r\n calcWing(prevLeadPos, currLeadPos, prevWingPos, prevWing) {\r\n const vectorA = currLeadPos.clone().sub(prevLeadPos);\r\n const vectorB = prevLeadPos.clone().sub(prevWingPos);\r\n vectorB.crossVectors(vectorA, vectorB);\r\n vectorB.crossVectors(vectorA, vectorB).normalize();\r\n if (prevWing !== null && prevWing.length() > 0.0001) {\r\n const needToNegate = vectorB.length() > 0.0001 && Math.abs(prevWing.angleTo(vectorB)) > Math.PI / 2;\r\n if (needToNegate) {\r\n vectorB.negate();\r\n }\r\n }\r\n return vectorB;\r\n }\r\n\r\n _innerFinalize(prevRes, prev, nextRes, dst, chainAsNucleic, getAtomPosition) {\r\n const bFirstInChain = prev === null;\r\n\r\n const lp = getAtomPosition(this._leadAtom);\r\n const currLeadPos = new THREE.Vector3(lp.x, lp.y, lp.z);\r\n if (chainAsNucleic) {\r\n this._detectLeadWing(dst, nextRes, getAtomPosition);\r\n return;\r\n }\r\n\r\n if (bFirstInChain) { // for first one in chain\r\n dst._midPoint = getAtomPosition(this._firstAtom).clone();\r\n } else {\r\n const prevLeadPos = prev._controlPoint; // lead point of previous monomer\r\n dst._midPoint = prevLeadPos.clone().lerp(currLeadPos, 0.5);\r\n dst._wingVector = this.calcWing(prevLeadPos, currLeadPos, getAtomPosition(prevRes._wingAtom), prev._wingVector);\r\n }\r\n dst._controlPoint = currLeadPos;\r\n }\r\n\r\n _finalize2(prev, next, asNucleic) {\r\n // Should be called AFTER first finalize\r\n this._innerFinalize(prev, prev, next, this, asNucleic, (atom) => atom.position);\r\n }\r\n\r\n isConnected(anotherResidue) {\r\n if (this._chain !== anotherResidue._chain) {\r\n return false;\r\n }\r\n if (this === anotherResidue) {\r\n return true;\r\n }\r\n let res = false;\r\n this.forEachAtom((atom) => {\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue === anotherResidue || bond._right.residue === anotherResidue) {\r\n res = true;\r\n return true;\r\n }\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _finalize() {\r\n const self = this;\r\n [this._firstAtom] = this._atoms;\r\n this._lastAtom = this._atoms[this._atoms.length - 1];\r\n\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n\r\n let tempCount = 0;\r\n let temperature = 0; // average temperature\r\n let occupCount = 0;\r\n let occupancy = 0; // average occupancy\r\n this.forEachAtom((a) => {\r\n if (self._leadAtom === null) {\r\n if (a.role === Element.Constants.Lead) {\r\n self._leadAtom = a;\r\n }\r\n }\r\n if (self._wingAtom === null) {\r\n if (a.role === Element.Constants.Wing) {\r\n self._wingAtom = a;\r\n }\r\n }\r\n if (a.temperature) {\r\n temperature += a.temperature;\r\n tempCount++;\r\n }\r\n if (a.occupancy) {\r\n occupancy += a.occupancy;\r\n occupCount++;\r\n }\r\n return (self._leadAtom !== null && self._wingAtom !== null);\r\n });\r\n\r\n if (tempCount > 0) {\r\n this.temperature = temperature / tempCount;\r\n }\r\n if (occupCount > 0) {\r\n this.occupancy = occupancy / occupCount;\r\n }\r\n\r\n // Still try to make monomer look valid\r\n if (this._leadAtom === null || this._wingAtom === null) {\r\n this._isValid = false;\r\n }\r\n if (this._leadAtom === null) {\r\n this._leadAtom = this._firstAtom;\r\n }\r\n if (this._wingAtom === null) {\r\n this._wingAtom = this._lastAtom;\r\n }\r\n }\r\n}\r\n\r\nexport default Residue;\r\n","/**\r\n * Residue type.\r\n *\r\n * Predefined acid or created with HET, HETNAM, etc.\r\n *\r\n * @param {string} name - Short name, either standard (ALA, MET, etc.) or non-standard one.\r\n * @param {string} fullName - Full residue name.\r\n * @param {string} letterCode - 1-letter symbol.\r\n *\r\n * @exports ResidueType\r\n * @constructor\r\n */\r\nclass ResidueType {\r\n constructor(name, fullName, letterCode) {\r\n this._name = name;\r\n this._fullName = fullName;\r\n this.letterCode = letterCode;\r\n this.flags = 0x0000;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\n static StandardTypes = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: new ResidueType('ALA', 'Alanine', 'A'),\r\n ARG: new ResidueType('ARG', 'Arginine', 'R'),\r\n ASN: new ResidueType('ASN', 'Asparagine', 'N'),\r\n ASP: new ResidueType('ASP', 'Aspartic Acid', 'D'),\r\n CYS: new ResidueType('CYS', 'Cysteine', 'C'),\r\n GLN: new ResidueType('GLN', 'Glutamine', 'Q'),\r\n GLU: new ResidueType('GLU', 'Glutamic Acid', 'E'),\r\n GLY: new ResidueType('GLY', 'Glycine', 'G'),\r\n HIS: new ResidueType('HIS', 'Histidine', 'H'),\r\n ILE: new ResidueType('ILE', 'Isoleucine', 'I'),\r\n LEU: new ResidueType('LEU', 'Leucine', 'L'),\r\n LYS: new ResidueType('LYS', 'Lysine', 'K'),\r\n MET: new ResidueType('MET', 'Methionine', 'M'),\r\n PHE: new ResidueType('PHE', 'Phenylalanine', 'F'),\r\n PRO: new ResidueType('PRO', 'Proline', 'P'),\r\n PYL: new ResidueType('PYL', 'Pyrrolysine', 'O'),\r\n SEC: new ResidueType('SEC', 'Selenocysteine', 'U'),\r\n SER: new ResidueType('SER', 'Serine', 'S'),\r\n THR: new ResidueType('THR', 'Threonine', 'T'),\r\n TRP: new ResidueType('TRP', 'Tryptophan', 'W'),\r\n TYR: new ResidueType('TYR', 'Tyrosine', 'Y'),\r\n VAL: new ResidueType('VAL', 'Valine', 'V'),\r\n A: new ResidueType('A', 'Adenine', 'A'),\r\n C: new ResidueType('C', 'Cytosine', 'C'),\r\n G: new ResidueType('G', 'Guanine', 'G'),\r\n I: new ResidueType('I', 'Inosine', 'I'),\r\n T: new ResidueType('T', 'Thymine', 'T'),\r\n U: new ResidueType('U', 'Uracil', 'U'),\r\n DA: new ResidueType('DA', 'Adenine', 'A'),\r\n DC: new ResidueType('DC', 'Cytosine', 'C'),\r\n DG: new ResidueType('DG', 'Guanine', 'G'),\r\n DI: new ResidueType('DI', 'Inosine', 'I'),\r\n DT: new ResidueType('DT', 'Thymine', 'T'),\r\n DU: new ResidueType('DU', 'Uracil', 'U'),\r\n '+A': new ResidueType('+A', 'Adenine', 'A'),\r\n '+C': new ResidueType('+C', 'Cytosine', 'C'),\r\n '+G': new ResidueType('+G', 'Guanine', 'G'),\r\n '+I': new ResidueType('+I', 'Inosine', 'I'),\r\n '+T': new ResidueType('+T', 'Thymine', 'T'),\r\n '+U': new ResidueType('+U', 'Uracil', 'U'),\r\n WAT: new ResidueType('WAT', 'Water', ''),\r\n H2O: new ResidueType('H2O', 'Water', ''),\r\n HOH: new ResidueType('HOH', 'Water', ''),\r\n DOD: new ResidueType('DOD', 'Water', ''),\r\n UNK: new ResidueType('UNK', 'Unknown', ''),\r\n UNL: new ResidueType('UNL', 'Unknown Ligand', ''),\r\n /* eslint-enable no-magic-numbers */\r\n };\r\n\r\n /**\r\n * Enumeration of residue flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n // Amino acids\r\n /** Amino acid residue */\r\n PROTEIN: 0x0001,\r\n /** Basic amino acid residue */\r\n BASIC: 0x0002,\r\n /** Acidic amino acid residue */\r\n ACIDIC: 0x0004,\r\n /** Polar uncharged side chain amino acid residue */\r\n POLAR: 0x0008,\r\n /** Non-polar hydrophobic side chain amino acid residue */\r\n NONPOLAR: 0x0010,\r\n /** Aromatic amino acid residue */\r\n AROMATIC: 0x0020,\r\n\r\n // Nucleic acids\r\n\r\n /** Nucleic residue */\r\n NUCLEIC: 0x0100,\r\n /** Purine nucleic residue */\r\n PURINE: 0x0200,\r\n /** Pyrimidine nucleic residue */\r\n PYRIMIDINE: 0x0400,\r\n /** DNA */\r\n DNA: 0x0800,\r\n /** RNA */\r\n RNA: 0x1000,\r\n\r\n /** Water */\r\n WATER: 0x10000,\r\n };\r\n}\r\n\r\n// Flag combinations\r\nfunction _addFlag(flag, list) {\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const res = ResidueType.StandardTypes[list[i]];\r\n if (res) {\r\n res.flags |= flag;\r\n }\r\n }\r\n}\r\n\r\nconst { Flags } = ResidueType;\r\n_addFlag(Flags.WATER, ['WAT', 'H2O', 'HOH', 'DOD']);\r\n\r\n_addFlag(Flags.PROTEIN, [\r\n 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLY', 'GLU', 'GLN', 'HIS', 'ILE',\r\n 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'PYL', 'SEC', 'SER', 'THR', 'TRP',\r\n 'TYR', 'VAL',\r\n]);\r\n_addFlag(Flags.BASIC, ['ARG', 'HIS', 'LYS']);\r\n_addFlag(Flags.ACIDIC, ['ASP', 'GLU']);\r\n_addFlag(Flags.POLAR, ['ASN', 'CYS', 'GLN', 'SER', 'THR', 'TYR']);\r\n_addFlag(Flags.NONPOLAR, ['ALA', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'VAL', 'GLY']);\r\n_addFlag(Flags.AROMATIC, ['PHE', 'TRP', 'TYR']);\r\n\r\n_addFlag(Flags.NUCLEIC, [\r\n 'A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I',\r\n 'C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U',\r\n]);\r\n_addFlag(Flags.PURINE, ['A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I']);\r\n_addFlag(Flags.PYRIMIDINE, ['C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U']);\r\n_addFlag(Flags.DNA, ['DA', 'DG', 'DI', 'DC', 'DT', 'DU']);\r\n_addFlag(Flags.RNA, ['A', 'G', 'I', 'C', 'T', 'U']);\r\n// Table of kdHydrophobicity\r\nconst hydro = {\r\n ILE: 4.5,\r\n VAL: 4.2,\r\n LEU: 3.8,\r\n PHE: 2.8,\r\n CYS: 2.5,\r\n MET: 1.9,\r\n ALA: 1.8,\r\n GLY: -0.4,\r\n THR: -0.7,\r\n SER: -0.8,\r\n TRP: -0.9,\r\n TYR: -1.3,\r\n PRO: -1.6,\r\n HIS: -3.2,\r\n GLU: -3.5,\r\n GLN: -3.5,\r\n ASP: -3.5,\r\n ASN: -3.5,\r\n LYS: -3.9,\r\n ARG: -4.5,\r\n};\r\n\r\nfunction _addParam(param, list) {\r\n const keys = Object.keys(list);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = list[key];\r\n ResidueType.StandardTypes[key][param] = value;\r\n }\r\n}\r\n\r\n_addParam('hydrophobicity', hydro);\r\n\r\nexport default ResidueType;\r\n","import * as THREE from 'three';\r\nimport Residue from './Residue';\r\nimport ResidueType from './ResidueType';\r\n\r\n/**\r\n * Residues in chain are either amino acid either nucleic acid (and water)\r\n * There might be some modified/mutated residues, which type could not be determined by their name (nucleic or amino); In this\r\n * case firstly program definites the chain type (by well-known residues) and then definites modified/mutated residues\r\n */\r\nconst ChainType = {\r\n UNKNOWN: 0,\r\n PROTEIN: 1,\r\n NUCLEIC: 2,\r\n};\r\n\r\n/**\r\n * Residue chain.\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n * @param {string} name - One character identifier (usually space, A-Z, 0-9, or a-z).\r\n *\r\n * @exports Chain\r\n * @constructor\r\n */\r\nclass Chain {\r\n constructor(complex, name) {\r\n this._complex = complex;\r\n this._name = name;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n this._residues = [];\r\n\r\n this.minSequence = Number.POSITIVE_INFINITY;\r\n this.maxSequence = Number.NEGATIVE_INFINITY;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n _determineType() {\r\n const residues = this._residues;\r\n\r\n const { PROTEIN, NUCLEIC } = ResidueType.Flags;\r\n\r\n this.type = ChainType.UNKNOWN;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const { flags } = residues[i]._type;\r\n\r\n if ((flags & NUCLEIC) !== 0) {\r\n this.type = ChainType.NUCLEIC;\r\n break;\r\n } else if ((flags & PROTEIN) !== 0) {\r\n this.type = ChainType.PROTEIN;\r\n break;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Finds thre residue with specified sequence number and inserion code\r\n * @param {Number} seqNum sequence number\r\n * @param {string} iCode insertion code\r\n * @returns {*} Residue or null if not found\r\n */\r\n findResidue(seqNum, iCode) {\r\n const residues = this._residues;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n if (res._sequence === seqNum && res._icode === iCode) {\r\n return [res, i];\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _finalize() {\r\n this._determineType();\r\n\r\n const residues = this._residues;\r\n\r\n let prev = null;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const next = (i + 1 < n) ? residues[i + 1] : null;\r\n const curr = residues[i];\r\n // TODO: skip invalid residues\r\n if (1 /* curr._isValid */) { // eslint-disable-line no-constant-condition\r\n curr._finalize2(prev, next, this.type === ChainType.NUCLEIC);\r\n prev = curr;\r\n }\r\n }\r\n\r\n // fix very first wing\r\n if (residues.length > 1 && residues[1]._wingVector) {\r\n const p = residues[1]._wingVector;\r\n residues[0]._wingVector = new THREE.Vector3(p.x, p.y, p.z);\r\n } else if (residues.length > 0) {\r\n residues[0]._wingVector = new THREE.Vector3(1, 0, 0);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const residues = this._residues;\r\n let prev = null;\r\n let prevData = null;\r\n const frameRes = frameData._residues;\r\n const n = residues.length;\r\n function getAtomPos(atom) {\r\n return frameData.getAtomPos(atom.index);\r\n }\r\n\r\n for (let i = 0; i < n; ++i) {\r\n const curr = residues[i];\r\n const currData = frameRes[curr._index];\r\n const nextRes = (i + 1 < n) ? residues[i + 1] : null;\r\n curr._innerFinalize(prev, prevData, nextRes, currData, this.type === ChainType.NUCLEIC, getAtomPos);\r\n prev = curr;\r\n prevData = currData;\r\n }\r\n\r\n frameRes[residues[0]._index]._wingVector = n > 1\r\n ? frameRes[residues[1]._index]._wingVector\r\n : new THREE.Vector3(1, 0, 0);\r\n }\r\n\r\n /**\r\n * Create a new residue.\r\n *\r\n * @param {string} name - Residue name.\r\n * @param {number} sequence - Residue sequence number.\r\n * @param {string} iCode - Insertion code.\r\n * @returns {Residue} - Newly created residue instance.\r\n */\r\n addResidue(name, sequence, iCode) {\r\n let type = this._complex.getResidueType(name);\r\n if (type === null) {\r\n type = this._complex.addResidueType(name);\r\n }\r\n const residue = new Residue(this, type, sequence, iCode);\r\n this._complex.addResidue(residue);\r\n this._residues.push(residue);\r\n\r\n if (type.flags & (ResidueType.Flags.NUCLEIC | ResidueType.Flags.PROTEIN)) {\r\n if (this.maxSequence < sequence) {\r\n this.maxSequence = sequence;\r\n }\r\n if (this.minSequence > sequence) {\r\n this.minSequence = sequence;\r\n }\r\n }\r\n\r\n return residue;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this._mask = mask;\r\n }\r\n}\r\n\r\nexport default Chain;\r\n","import Residue from './Residue';\r\n\r\n/** An element of protein secondary structure. */\r\nclass StructuralElement {\r\n /**\r\n * Create a secondary structural element of the specified type.\r\n *\r\n * @param {StructuralElement.Type} type Secondary structure type.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n */\r\n constructor(type, init, term) {\r\n /**\r\n * Secondary structure type.\r\n * @type {StructuralElement.Type}\r\n */\r\n this.type = type;\r\n /**\r\n * Generic secondary structure type.\r\n * @type {StructuralElement.Generic}\r\n */\r\n this.generic = StructuralElement.genericByType[this.type] || 'loop';\r\n /**\r\n * Initial residue.\r\n * @type Residue\r\n */\r\n this.init = init;\r\n /**\r\n * Terminal residue.\r\n * @type Residue\r\n */\r\n this.term = term;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n if (this.init instanceof Residue && this.term instanceof Residue) {\r\n return;\r\n }\r\n\r\n // Link all intermediate residues to this structural element\r\n const start = complex.splitUnifiedSerial(this.init);\r\n const end = complex.splitUnifiedSerial(this.term);\r\n for (let chainId = start.chain; chainId <= end.chain; chainId++) {\r\n for (let serialId = start.serial; serialId <= end.serial; serialId++) {\r\n for (let { iCode } = start; iCode <= end.iCode; iCode++) {\r\n const hashCode = complex.getUnifiedSerial(chainId, serialId, iCode);\r\n if (residueHash[hashCode]) {\r\n residueHash[hashCode]._secondary = this;\r\n }\r\n }\r\n }\r\n }\r\n\r\n // Replace unfined serials by objects\r\n this.init = residueHash[this.init];\r\n this.term = residueHash[this.term];\r\n }\r\n}\r\n\r\n/**\r\n * Specific type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Generic\r\n */\r\nStructuralElement.Type = {\r\n /** A strand of a [beta-sheet](https://en.wikipedia.org/wiki/Beta_sheet). */\r\n STRAND: 'E',\r\n /** An isolated beta-bridge (too small for a beta-sheet). */\r\n BRIDGE: 'B',\r\n\r\n /** A [3/10 helix](https://en.wikipedia.org/wiki/310_helix) (hydrogen bonding is 3 residues apart). */\r\n HELIX_310: 'G',\r\n /** An [alpha-helix](https://en.wikipedia.org/wiki/Alpha_helix) (hydrogen bonding is 4 residues apart). */\r\n HELIX_ALPHA: 'H',\r\n /** A [pi-helix](https://en.wikipedia.org/wiki/Pi_helix) (hydrogen bonding is 5 residues apart). */\r\n HELIX_PI: 'I',\r\n /** A generic helix of unspecified bonding distance. */\r\n HELIX: 'X',\r\n\r\n /** An isolated 3/10-like helical turn. */\r\n TURN_310: '3',\r\n /** An isolated alpha-like helical turn. */\r\n TURN_ALPHA: '4',\r\n /** An isolated pi-like helical turn. */\r\n TURN_PI: '5',\r\n /** An isolated helical [turn](https://en.wikipedia.org/wiki/Turn_(biochemistry)) of unspecified bonding distance. */\r\n TURN: 'T',\r\n\r\n /** A bend (a region of high curvature). */\r\n BEND: 'S',\r\n /** Just a protein section with no particular conformation. */\r\n COIL: 'C',\r\n};\r\n\r\n/**\r\n * Generic type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Type\r\n */\r\nStructuralElement.Generic = {\r\n /** A strand of a sheet. */\r\n STRAND: 'strand',\r\n /** A helix. */\r\n HELIX: 'helix',\r\n /** Just a protein section with no particular conformation. */\r\n LOOP: 'loop',\r\n};\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\nconst StructuralElementGeneric = StructuralElement.Generic;\r\n\r\n/**\r\n * A mapping from specific types to generic ones.\r\n * @type {Object}\r\n */\r\nStructuralElement.genericByType = {\r\n [StructuralElementType.STRAND]: StructuralElementGeneric.STRAND,\r\n [StructuralElementType.HELIX_310]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_ALPHA]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_PI]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX]: StructuralElementGeneric.HELIX,\r\n};\r\n\r\nexport default StructuralElement;\r\n","import StructuralElement from './StructuralElement';\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\nexport const typeByPDBHelixClass = {\r\n 1: StructuralElementType.HELIX_ALPHA,\r\n 3: StructuralElementType.HELIX_PI,\r\n 5: StructuralElementType.HELIX_310,\r\n};\r\n\r\n/**\r\n * Helical secondary structure of a protein.\r\n * @extends StructuralElement\r\n */\r\nclass Helix extends StructuralElement {\r\n /**\r\n * Create a helix.\r\n *\r\n * @param {number} helixClass A helix class according to the\r\n * [PDB Format](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX).\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} serial Serial number of the helix (see PDB Format).\r\n * @param {string} name Helix identifier (see PDB Format).\r\n * @param {string} comment Comment about this helix (see PDB Format).\r\n * @param {number} length Length of this helix, in residues (see PDB Format).\r\n */\r\n constructor(helixClass, init, term, serial, name, comment, length) {\r\n super(typeByPDBHelixClass[helixClass] || StructuralElement.Type.HELIX, init, term);\r\n\r\n /**\r\n * Serial number of the helix (see PDB Format).\r\n * @type {number}\r\n */\r\n this.serial = serial;\r\n /**\r\n * Helix identifier (see PDB Format).\r\n * @type {string}\r\n */\r\n this.name = name;\r\n /**\r\n * Comment about this helix (see PDB Format).\r\n * @type {string}\r\n */\r\n this.comment = comment;\r\n /**\r\n * Length of this helix, in residues (see PDB Format).\r\n * @type {number}\r\n */\r\n this.length = length;\r\n }\r\n}\r\n\r\nexport default Helix;\r\n","import StructuralElement from './StructuralElement';\r\n\r\n/**\r\n * A single strand of a sheet in a protein secondary structure.\r\n * @extends StructuralElement\r\n */\r\nclass Strand extends StructuralElement {\r\n /**\r\n * Create a strand.\r\n *\r\n * @param {Sheet} sheet Parent sheet this strand belongs to.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} sense Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @param {Atom} atomCur Atom in current strand (see PDB Format).\r\n * @param {Atom} atomPrev Atom in previous strand (see PDB Format).\r\n */\r\n constructor(sheet, init, term, sense, atomCur, atomPrev) {\r\n super(StructuralElement.Type.STRAND, init, term);\r\n\r\n /**\r\n * Parent sheet this strand belongs to.\r\n * @type {Sheet}\r\n */\r\n this.sheet = sheet;\r\n /**\r\n * Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @type {number}\r\n */\r\n this.sense = sense;\r\n /**\r\n * Atom in current strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomCur = atomCur;\r\n /**\r\n * Atom in previous strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomPrev = atomPrev;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n *\r\n * @override\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n super._finalize(serialAtomMap, residueHash, complex);\r\n\r\n let as = this.atomCur;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomCur = serialAtomMap[as];\r\n }\r\n as = this.atomPrev;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomPrev = serialAtomMap[as];\r\n }\r\n }\r\n}\r\n\r\nexport default Strand;\r\n","import Strand from './Strand';\r\n\r\n/**\r\n * Sheet secondary structure of a protein.\r\n *\r\n * @param {string} name -\r\n * @param {number} width -\r\n *\r\n * @exports Sheet\r\n * @constructor\r\n */\r\nclass Sheet {\r\n constructor(name, width) {\r\n this._name = name;\r\n this._width = width;\r\n\r\n this._strands = [];\r\n }\r\n\r\n // Getters and setters\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getWidth() {\r\n return this._width;\r\n }\r\n\r\n addStrand(strand) {\r\n this._strands.push(strand);\r\n this._width = this._strands.length;\r\n }\r\n\r\n addEmptyStrand() {\r\n this._strands.push(new Strand(null, null, null, null, null, null));\r\n }\r\n\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n const s = this._strands;\r\n for (let i = 0, n = s.length; i < n; ++i) {\r\n s[i]._finalize(serialAtomMap, residueHash, complex);\r\n }\r\n if (!this._width) {\r\n this._width = s.length;\r\n }\r\n if (s.length !== this._width) {\r\n throw new Error(`Sheet ${this._name} is inconsistent.`);\r\n }\r\n }\r\n}\r\n\r\nexport default Sheet;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Atom measurements.\r\n *\r\n * @param {string} id - SGroup id\r\n * @param {string} name - Name of the group\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n * @param {array} atoms - Atoms group consists of\r\n * @param {object} saveNode - XML node from file for saving\r\n *\r\n * @exports SGroup\r\n * @constructor\r\n */\r\nclass SGroup {\r\n constructor(id, name, position, atoms, saveNode) {\r\n this._id = id;\r\n this._name = name;\r\n this._position = position || new THREE.Vector3();\r\n this._atoms = atoms || [];\r\n this._charge = 0; // default group charge\r\n this._repeat = 1; // how many times group repeated: always > 0\r\n this._center = null;\r\n this.xmlNodeRef = saveNode || null;\r\n }\r\n\r\n /**\r\n * Get atom full name.\r\n * @returns {string} Atom full name.\r\n */\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getPosition() {\r\n return this._position;\r\n }\r\n\r\n getCentralPoint() {\r\n return this._center;\r\n }\r\n\r\n _rebuildSGroupOnAtomChange() {\r\n const nLimon = 100000000;\r\n if (this._center === null) {\r\n return; // nothing to do if we are not relative\r\n }\r\n\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n for (let j = 0, n = this._atoms.length; j < n; j++) {\r\n const aPos = this._atoms[j].position;\r\n bLow.set(Math.min(bLow.x, aPos.x), Math.min(bLow.y, aPos.y), Math.min(bLow.z, aPos.z));\r\n bHight.set(Math.max(bHight.x, aPos.x), Math.max(bHight.y, aPos.y), Math.max(bHight.z, aPos.z));\r\n }\r\n this._center.addVectors(bLow, bHight);\r\n this._center.multiplyScalar(0.5);\r\n }\r\n}\r\n\r\nexport default SGroup;\r\n","import utils from '../../utils';\r\n\r\n//----------------------------------------------------------------------------\r\nclass Range {\r\n constructor(min, max) {\r\n this.min = min;\r\n this.max = typeof max === 'undefined' ? min : max;\r\n }\r\n\r\n includes(value) {\r\n return this.min <= value && value <= this.max;\r\n }\r\n\r\n toString() {\r\n const { min, max } = this;\r\n return min === max ? String(min) : [min, max].join(':');\r\n }\r\n\r\n toJSON() {\r\n return [this.min, this.max];\r\n }\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\nclass List {\r\n constructor(arg) {\r\n if (arg instanceof this.constructor) {\r\n // delegate construction to a different class\r\n // eslint-disable-next-line no-constructor-return\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n }\r\n\r\n append(value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n }\r\n\r\n toString() {\r\n return this._values.join(',');\r\n }\r\n\r\n toJSON() {\r\n const values = this._values;\r\n const result = [];\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n result[i] = value.toJSON ? value.toJSON() : value;\r\n }\r\n return result;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nclass RangeList extends List {\r\n includes(value) {\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n if (list[i].includes(value)) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nconst valuesArray = [];\r\n\r\nclass ValueList extends List {\r\n constructor(arg, upperOnly) {\r\n const list = super(arg);\r\n if (upperOnly) {\r\n this.upperOnly = true;\r\n const values = list._values;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n if (typeof value === 'string') {\r\n values[i] = value.toUpperCase();\r\n }\r\n }\r\n } else {\r\n this.upperOnly = false;\r\n }\r\n // return constructed object\r\n // eslint-disable-next-line no-constructor-return\r\n return list;\r\n }\r\n\r\n includes(value) {\r\n // we do not convert to upper case here for perfomance reasons\r\n // if list is upper case only, value must be converted before it is sent up to here\r\n return this._values.indexOf(value) !== -1;\r\n }\r\n\r\n toString() {\r\n // Quote values that are not correct identifiers\r\n const values = this._values;\r\n valuesArray.length = 0;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n valuesArray[i] = utils.correctSelectorIdentifier(String(values[i]));\r\n }\r\n return valuesArray.join(',');\r\n }\r\n\r\n _validate(value) {\r\n return (this.upperOnly && typeof value === 'string') ? value.toUpperCase() : value;\r\n }\r\n\r\n append(value) {\r\n super.append(this._validate(value));\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n super.remove(this._validate(value));\r\n return this;\r\n }\r\n}\r\n\r\nexport {\r\n Range,\r\n List,\r\n RangeList,\r\n ValueList,\r\n};\r\n","import { RangeList, ValueList } from './selectArgs';\r\n\r\n/** Base class for atom selectors. */\r\nclass Selector {\r\n toString() {\r\n return this.keyword;\r\n }\r\n\r\n toJSON() {\r\n return [this.name];\r\n }\r\n}\r\n\r\nSelector.prototype.name = 'Error';\r\nSelector.prototype.keyword = 'error';\r\n\r\n/** Base class for list-based atom selectors. */\r\nclass ListSelector extends Selector {\r\n constructor(list) {\r\n super();\r\n this.list = list;\r\n }\r\n\r\n toString() {\r\n return `${this.keyword} ${this.list}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.list.toJSON()];\r\n }\r\n}\r\n\r\nclass RangeListSelector extends ListSelector {\r\n constructor(arg) {\r\n super(new RangeList(arg));\r\n }\r\n}\r\n\r\nclass ValueListSelector extends ListSelector {\r\n constructor(arg, caseSensitive) {\r\n super(new ValueList(arg, !caseSensitive));\r\n }\r\n}\r\n\r\nclass NoneSelector extends Selector {\r\n includesAtom(_atom) {\r\n return false;\r\n }\r\n}\r\n\r\nNoneSelector.prototype.name = 'None';\r\nNoneSelector.prototype.keyword = 'none';\r\n\r\nclass AllSelector extends Selector {\r\n includesAtom(_atom) {\r\n return true;\r\n }\r\n}\r\n\r\nAllSelector.prototype.name = 'All';\r\nAllSelector.prototype.keyword = 'all';\r\n\r\nexport {\r\n Selector,\r\n ListSelector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n};\r\n","import { Selector, NoneSelector } from './selectorsBase';\r\n\r\n//----------------------------------------------------------------------------\r\n// Operators\r\n//----------------------------------------------------------------------------\r\nconst none = new NoneSelector();\r\n\r\nclass PrefixOperator extends Selector {\r\n constructor(rhs) {\r\n super();\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nPrefixOperator.prototype.priority = 1;\r\n\r\nclass InfixOperator extends Selector {\r\n constructor(lhs, rhs) {\r\n super();\r\n this.lhs = lhs || none;\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const lhs = this.lhs.priority && this.lhs.priority > this.priority ? `(${this.lhs})` : this.lhs;\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${lhs} ${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.lhs.toJSON(), this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nInfixOperator.prototype.priority = 1000;\r\n\r\nexport { PrefixOperator, InfixOperator };\r\n","import Atom from './Atom';\r\nimport ResidueType from './ResidueType';\r\nimport { parser } from '../utils/SelectionParser';\r\nimport { Range, RangeList, ValueList } from './selectors/selectArgs';\r\nimport { PrefixOperator, InfixOperator } from './selectors/selectOps';\r\nimport {\r\n Selector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n} from './selectors/selectorsBase';\r\n\r\nconst keywords = {};\r\n\r\n//----------------------------------------------------------------------------\r\n// Named selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineSelector(name, SelectorClass) {\r\n const keyword = name.toLowerCase();\r\n SelectorClass.prototype.keyword = keyword;\r\n SelectorClass.prototype.name = name;\r\n\r\n const factory = ((...args) => new SelectorClass(...args));\r\n factory.SelectorClass = SelectorClass;\r\n keywords[keyword] = factory;\r\n\r\n return SelectorClass;\r\n}\r\n\r\ndefineSelector('Serial', class SerialSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.serial);\r\n }\r\n});\r\n\r\ndefineSelector('Name', class NameSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.name);\r\n }\r\n});\r\n\r\ndefineSelector('AltLoc', class AltLocSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(String.fromCharCode(atom.location));\r\n }\r\n});\r\n\r\ndefineSelector('Elem', class ElemSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.element.name);\r\n }\r\n});\r\n\r\ndefineSelector('Residue', class ResidueSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._type._name);\r\n }\r\n});\r\n\r\ndefineSelector('Sequence', class SequenceSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._sequence);\r\n }\r\n});\r\n\r\ndefineSelector('ICode', class ICodeSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._icode);\r\n }\r\n});\r\n\r\ndefineSelector('ResIdx', class ResIdxSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._index);\r\n }\r\n});\r\n\r\ndefineSelector('Chain', class ChainSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._chain._name);\r\n }\r\n});\r\n\r\ndefineSelector('Hetatm', class HetatmSelector extends Selector {\r\n includesAtom(atom) {\r\n return atom.het;\r\n }\r\n});\r\n\r\ndefineSelector('PolarH', class PolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.HYDROGEN;\r\n }\r\n});\r\n\r\ndefineSelector('NonPolarH', class NonPolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.NONPOLARH;\r\n }\r\n});\r\n\r\ndefineSelector('All', AllSelector);\r\n\r\ndefineSelector('None', NoneSelector);\r\n\r\nconst NULL_SELECTOR = keywords.none();\r\n\r\n//----------------------------------------------------------------------------\r\n// Named operators\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineOperator(name, priority, OperatorClass) {\r\n OperatorClass.prototype.priority = priority;\r\n return defineSelector(name, OperatorClass);\r\n}\r\ndefineOperator('Not', 1, class NotOperator extends PrefixOperator {\r\n includesAtom(atom) {\r\n return !this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('And', 2, class AndOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) && this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('Or', 3, class OrOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) || this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\n//----------------------------------------------------------------------------\r\n// Flag selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction byResidueTypeFlag(flag, name) {\r\n return defineSelector(name, class extends Selector {\r\n includesAtom(atom) {\r\n return (atom.residue._type.flags & flag) !== 0;\r\n }\r\n });\r\n}\r\n\r\nbyResidueTypeFlag(ResidueType.Flags.PROTEIN, 'Protein');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC, 'Basic');\r\nbyResidueTypeFlag(ResidueType.Flags.ACIDIC, 'Acidic');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC | ResidueType.Flags.ACIDIC, 'Charged');\r\nbyResidueTypeFlag(ResidueType.Flags.POLAR, 'Polar');\r\nbyResidueTypeFlag(ResidueType.Flags.NONPOLAR, 'NonPolar');\r\nbyResidueTypeFlag(ResidueType.Flags.AROMATIC, 'Aromatic');\r\nbyResidueTypeFlag(ResidueType.Flags.NUCLEIC, 'Nucleic');\r\nbyResidueTypeFlag(ResidueType.Flags.PURINE, 'Purine');\r\nbyResidueTypeFlag(ResidueType.Flags.PYRIMIDINE, 'Pyrimidine');\r\nbyResidueTypeFlag(ResidueType.Flags.WATER, 'Water');\r\n\r\n//----------------------------------------------------------------------------\r\nconst selectors = Object.create(keywords);\r\n\r\nselectors.Selector = Selector;\r\nselectors.RangeListSelector = RangeListSelector;\r\nselectors.ValueListSelector = ValueListSelector;\r\nselectors.Range = Range;\r\nselectors.RangeList = RangeList;\r\nselectors.ValueList = ValueList;\r\nselectors.PrefixOperator = PrefixOperator;\r\nselectors.InfixOperator = InfixOperator;\r\nselectors.Context = Object.create({});\r\n\r\nselectors.GetSelector = function (key) {\r\n if (!selectors.Context.hasOwnProperty(key)) {\r\n const exc = { message: `selector ${key} is not registered` };\r\n throw exc;\r\n }\r\n return selectors.Context[key] || NULL_SELECTOR;\r\n};\r\n\r\nselectors.ClearContext = function () {\r\n Object.keys(selectors.Context).forEach((k) => { delete selectors.Context[k]; });\r\n};\r\n\r\nselectors.keyword = function (key) {\r\n return keywords[key.toLowerCase()] || keywords.none;\r\n};\r\n\r\nselectors.parse = function (str) {\r\n const res = {};\r\n try {\r\n res.selector = parser.parse(str);\r\n } catch (e) {\r\n res.selector = NULL_SELECTOR;\r\n res.error = e.message;\r\n }\r\n return res;\r\n};\r\n\r\nparser.yy = selectors;\r\nparser.yy.parseError = parser.parseError; // workaround for incorrect JISON parser generator for AMD module\r\n\r\nexport default selectors;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\n\r\n/**\r\n * Basic biological unit class.\r\n *\r\n * @exports BiologicalUnit\r\n * @constructor\r\n */\r\nclass BiologicalUnit {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._selector = selectors.keyword('All')();\r\n this._boundaries = {\r\n boundingBox: new THREE.Box3(),\r\n boundingSphere: new THREE.Sphere(),\r\n };\r\n }\r\n\r\n computeBoundaries() {\r\n const atoms = this._complex._atoms;\r\n const n = atoms.length;\r\n const selector = this._selector;\r\n\r\n const { boundingBox } = this._boundaries;\r\n boundingBox.makeEmpty();\r\n if (n === 1) {\r\n boundingBox.expandByPoint(atoms[0].position);\r\n const bbc = new THREE.Vector3();\r\n boundingBox.getCenter(bbc);\r\n const s = 2 * atoms[0].element.radius;\r\n boundingBox.setFromCenterAndSize(bbc, new THREE.Vector3(s, s, s));\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (selector.includesAtom(atoms[i])) {\r\n boundingBox.expandByPoint(atoms[i].position);\r\n }\r\n }\r\n }\r\n\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n if (n === 1) {\r\n this._boundaries.boundingSphere.set(center, atoms[0].element.radius);\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (!selector.includesAtom(atoms[i])) {\r\n continue;\r\n }\r\n const pos = atoms[i].position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n this._boundaries.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n }\r\n\r\n getTransforms() {\r\n return [];\r\n }\r\n\r\n getSelector() {\r\n return this._selector;\r\n }\r\n\r\n getBoundaries() {\r\n return this._boundaries;\r\n }\r\n\r\n finalize() {\r\n }\r\n}\r\n\r\nexport default BiologicalUnit;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\nimport BiologicalUnit from './BiologicalUnit';\r\n\r\n/**\r\n * Biological assembly.\r\n *\r\n * @exports Assembly\r\n * @constructor\r\n */\r\n\r\nclass Assembly extends BiologicalUnit {\r\n constructor(complex) {\r\n super(complex);\r\n this.chains = [];\r\n this.matrices = [];\r\n }\r\n\r\n computeBoundaries() {\r\n super.computeBoundaries();\r\n // fix up the boundaries\r\n const { matrices } = this;\r\n const oldCenter = this._boundaries.boundingSphere.center;\r\n const oldRad = this._boundaries.boundingSphere.radius;\r\n const boundingBox = this._boundaries.boundingBox = new THREE.Box3();\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = matrices.length; i < n; ++i) {\r\n boundingBox.expandByPoint(oldCenter.clone().applyMatrix4(matrices[i]));\r\n }\r\n\r\n const newRad = boundingBox.max.distanceTo(boundingBox.min) / 2 + oldRad;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n this._boundaries.boundingSphere = new THREE.Sphere().set(center, newRad);\r\n boundingBox.max.addScalar(oldRad);\r\n boundingBox.min.subScalar(oldRad);\r\n }\r\n\r\n /**\r\n * Mark a chain as belonging to this biological assembly.\r\n * @param {string} chain - chain identifier, usually a single letter\r\n */\r\n addChain(chain) {\r\n this.chains[this.chains.length] = chain;\r\n }\r\n\r\n /**\r\n * Add a transformation matrix.\r\n * @param {THREE.Matrix4} matrix - transformation matrix\r\n */\r\n addMatrix(matrix) {\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n getTransforms() {\r\n return this.matrices;\r\n }\r\n\r\n finalize() {\r\n if (this.chains.length > 0) {\r\n this._selector = selectors.keyword('Chain')(this.chains);\r\n } else {\r\n this._selector = selectors.keyword('None')();\r\n }\r\n }\r\n}\r\n\r\nexport default Assembly;\r\n","/**\r\n * This class represents connected component as a part of a complex.\r\n * WARNING! The whole component entity is build under the assumption that residues\r\n * are placed in the chains and complex in ascending order of indices\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n *\r\n * @exports Component\r\n * @constructor\r\n */\r\nclass Component {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._index = -1;\r\n this._residueIndices = [];\r\n this._cycles = [];\r\n this._subDivs = [];\r\n this._residueCount = 0;\r\n }\r\n\r\n getResidues() {\r\n return this._complex._residues;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residueCount;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._complex._residues;\r\n const resIdc = this._residueIndices;\r\n for (let idIdc = 0, idCount = resIdc.length; idIdc < idCount; ++idIdc) {\r\n for (let idx = resIdc[idIdc].start, last = resIdc[idIdc].end; idx <= last; ++idx) {\r\n process(residues[idx]);\r\n }\r\n }\r\n }\r\n\r\n setSubDivs(subDivs) {\r\n this._subDivs = subDivs;\r\n let curr = 0;\r\n const resIdc = [];\r\n let resCnt = 0;\r\n for (let i = 0, n = subDivs.length; i < n; ++i) {\r\n if (i === n - 1 || subDivs[i].end + 1 !== subDivs[i + 1].start) {\r\n const { start } = subDivs[curr];\r\n const { end } = subDivs[i];\r\n resIdc[resIdc.length] = {\r\n start,\r\n end,\r\n };\r\n resCnt += end - start + 1;\r\n curr = i + 1;\r\n }\r\n }\r\n\r\n this._residueIndices = resIdc;\r\n this._residueCount = resCnt;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._complex._bonds;\r\n\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue._component === this) {\r\n process(bond);\r\n }\r\n }\r\n }\r\n\r\n update() {\r\n this.forEachCycle((cycle) => {\r\n cycle.update();\r\n });\r\n }\r\n\r\n forEachAtom(process) {\r\n this.forEachResidue((residue) => {\r\n residue.forEachAtom(process);\r\n });\r\n }\r\n\r\n addCycle(cycle) {\r\n this._cycles.push(cycle);\r\n }\r\n\r\n forEachCycle(process) {\r\n const cycles = this._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n process(cycles[i]);\r\n }\r\n }\r\n\r\n markResidues() {\r\n const self = this;\r\n self.forEachResidue((residue) => {\r\n residue._component = self;\r\n });\r\n }\r\n\r\n _forEachSubChain(mask, process) {\r\n const residues = this._complex._residues;\r\n const subs = this._subDivs;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let idx = subs[i].start, last = subs[i].end; idx <= last; ++idx) {\r\n const currRes = residues[idx];\r\n if (mask & currRes._mask && currRes._isValid) {\r\n let end = idx + 1;\r\n for (; end <= last; ++end) {\r\n const endRes = residues[end];\r\n if (!(mask & endRes._mask && endRes._isValid)) {\r\n break;\r\n }\r\n }\r\n process(i, idx, end - 1);\r\n idx = end;\r\n }\r\n }\r\n }\r\n }\r\n\r\n getMaskedSequences(mask) {\r\n const subs = [];\r\n let idx = 0;\r\n this._forEachSubChain(mask, (_subIdx, start, end) => {\r\n subs[idx++] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n\r\n getMaskedSubdivSequences(mask) {\r\n const subs = [];\r\n let currIdx = -1;\r\n let lastSubIdx = -1;\r\n const subDivs = this._subDivs;\r\n\r\n this._forEachSubChain(mask, (subIdx, start, end) => {\r\n if (lastSubIdx !== subIdx) {\r\n ++currIdx;\r\n subs[currIdx] = {\r\n arr: [],\r\n boundaries: subDivs[subIdx],\r\n };\r\n lastSubIdx = subIdx;\r\n }\r\n subs[currIdx].arr[subs[currIdx].arr.length] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n}\r\n\r\nexport default Component;\r\n","import utils from '../utils';\r\n\r\nconst cMaxPairsForHashCode = 32;\r\nconst cHashTableSize = 1024 * 1024;\r\nconst cNumbersPerPair = 4;\r\nconst cMaxNeighbours = 14;\r\nconst cInvalidVal = -1;\r\n// 89237 is a large simple number, can be used for pseudo random hash code create\r\nconst cBigPrime = 89237;\r\n\r\nclass AtomPairs {\r\n constructor(maxPairsEstimate) {\r\n this.numPairs = 0;\r\n this.numMaxPairs = maxPairsEstimate;\r\n this.intBuffer = utils.allocateTyped(Int32Array, maxPairsEstimate * cNumbersPerPair);\r\n for (let i = 0; i < maxPairsEstimate * cNumbersPerPair; i++) {\r\n this.intBuffer[i] = cInvalidVal;\r\n }\r\n this.hashBuffer = utils.allocateTyped(Int32Array, cHashTableSize * cMaxPairsForHashCode);\r\n for (let i = 0; i < cHashTableSize * cMaxPairsForHashCode; i++) {\r\n this.hashBuffer[i] = cInvalidVal;\r\n }\r\n }\r\n\r\n /**\r\n * Destroy all pairs memory\r\n */\r\n destroy() {\r\n this.intBuffer = null;\r\n this.hashBuffer = null;\r\n }\r\n\r\n /**\r\n * Add pair of atoms to collection\r\n * @param {number} indexA - Index of the 1st vertex.\r\n * @param {number} indexB - Index of the 2nd vertex.\r\n */\r\n addPair(indexA, indexB) {\r\n const ia = (indexA < indexB) ? indexA : indexB;\r\n const ib = (indexA > indexB) ? indexA : indexB;\r\n const codeToAdd = ia + (ib << cMaxNeighbours);\r\n\r\n const hashCode = (ia + (ib * cBigPrime)) & (cHashTableSize - 1);\r\n let j = hashCode * cMaxPairsForHashCode;\r\n let apI = 0;\r\n for (; apI < cMaxPairsForHashCode; apI++) {\r\n const code = this.hashBuffer[j + apI];\r\n if (code === cInvalidVal) {\r\n break;\r\n }\r\n if (code === codeToAdd) {\r\n return false;\r\n }\r\n }\r\n // add this new hash code\r\n if (apI >= cMaxPairsForHashCode) {\r\n throw new Error('addPair: increase cMaxPairsForHashCode');\r\n }\r\n this.hashBuffer[j + apI] = codeToAdd;\r\n\r\n // actually add\r\n if (this.numPairs >= this.numMaxPairs) {\r\n throw new Error('addPair: increase num pairs');\r\n }\r\n j = this.numPairs * cNumbersPerPair;\r\n this.intBuffer[j] = ia;\r\n this.intBuffer[j + 1] = ib;\r\n this.intBuffer[j + 2] = codeToAdd;\r\n this.numPairs++;\r\n return true;\r\n }\r\n}\r\n\r\nexport default AtomPairs;\r\n","import AtomPairs from './AtomPairs';\r\nimport Bond from './Bond';\r\n\r\nconst cProfileBondBuilder = false;\r\nconst cEstBondsMultiplier = 4;\r\nconst cSpaceCode = 32;\r\nconst cBondTolerance = 0.45;\r\nconst cVMDTolerance = 0.6;\r\nconst cBondRadInJMOL = true;\r\nconst cEpsilon = 0.001;\r\n\r\n/**\r\n * Get radius used for building bonds.\r\n *\r\n * @param {Atom} atom - Atom object.\r\n * @returns {number} special value for bonding radius for this atom\r\n */\r\nfunction _getBondingRadius(atom) {\r\n const { element } = atom;\r\n if (element) {\r\n return element.radiusBonding;\r\n }\r\n throw new Error('_getBondingRadius: Logic error.');\r\n}\r\n\r\nfunction _isAtomEligible(atom) {\r\n // build for all non-hetatm and for hetatm without bonds\r\n return !atom.isHet() || (atom.bonds && atom.bonds.length === 0);\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Complex} complex molecular complex\r\n\r\n * @exports AutoBond\r\n * @constructor\r\n */\r\nclass AutoBond {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._maxRad = 1.8;\r\n const bBox = this._complex.getDefaultBoundaries().boundingBox;\r\n this._vBoxMin = bBox.min.clone();\r\n this._vBoxMax = bBox.max.clone();\r\n\r\n this._pairCollection = null;\r\n }\r\n\r\n /**\r\n * Add existing pairs of connectors (from pdb file after its reading)\r\n * @returns {number} 0\r\n */\r\n _addExistingPairs() {\r\n const atoms = this._complex.getAtoms();\r\n const numAtoms = atoms.length;\r\n let aInd = 0;\r\n const collection = this._pairCollection;\r\n\r\n for (; aInd < numAtoms; aInd++) {\r\n const { bonds } = atoms[aInd];\r\n const numBondsForAtom = bonds.length;\r\n for (let bInd = 0; bInd < numBondsForAtom; bInd++) {\r\n const bond = bonds[bInd];\r\n const indTo = bond._left.index;\r\n if (indTo === aInd) {\r\n collection.addPair(aInd, bond._right.index);\r\n }\r\n } // for (b) all bonds in atom\r\n } // for (a)\r\n return 0;\r\n }\r\n\r\n _findPairs() {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const atoms = this._complex._atoms;\r\n const atomsNum = atoms.length;\r\n const self = this;\r\n\r\n let rA;\r\n let isHydrogenA;\r\n let posA;\r\n let locationA;\r\n let atomA;\r\n\r\n const processAtom = function (atomB) {\r\n if (isHydrogenA && atomB.isHydrogen()) {\r\n return;\r\n }\r\n\r\n const locationB = atomB.location;\r\n if ((locationA !== cSpaceCode)\r\n && (locationB !== cSpaceCode)\r\n && (locationA !== locationB)) {\r\n return;\r\n }\r\n\r\n const dist2 = posA.distanceToSquared(atomB.position);\r\n const rB = atomB.element.radiusBonding;\r\n const maxAcceptable = cBondRadInJMOL ? rA + rB + cBondTolerance : cVMDTolerance * (rA + rB);\r\n\r\n if (dist2 > (maxAcceptable * maxAcceptable)) {\r\n return;\r\n }\r\n\r\n if (dist2 < cEpsilon) {\r\n return;\r\n }\r\n\r\n self._pairCollection.addPair(atomA.index, atomB.index);\r\n };\r\n\r\n for (let i = 0; i < atomsNum; ++i) {\r\n atomA = atoms[i];\r\n if (!_isAtomEligible(atomA)) {\r\n continue;\r\n }\r\n\r\n rA = atomA.element.radiusBonding;\r\n isHydrogenA = atomA.isHydrogen();\r\n posA = atomA.position;\r\n locationA = atomA.location;\r\n\r\n vw.forEachAtomWithinRadius(posA, 2 * this._maxRad + cBondTolerance, processAtom);\r\n }\r\n }\r\n\r\n _addPairs() {\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0, k = 0; i < this._pairCollection.numPairs; i++, k += 4) {\r\n const iA = this._pairCollection.intBuffer[k];\r\n const iB = this._pairCollection.intBuffer[k + 1];\r\n this._addPair(atoms[iA], atoms[iB]);\r\n }\r\n }\r\n\r\n _addPair(atomA, atomB) {\r\n const bondsA = atomA.bonds;\r\n const indexA = atomA.index;\r\n const indexB = atomB.index;\r\n for (let j = 0, numBonds = bondsA.length; j < numBonds; ++j) {\r\n const bond = bondsA[j];\r\n if (bond._left.index === indexB || bond._right.index === indexB) {\r\n return;\r\n }\r\n }\r\n const left = indexA < indexB ? atomA : atomB;\r\n const right = indexA < indexB ? atomB : atomA;\r\n const newBond = this._complex.addBond(left, right, 0, Bond.BondType.UNKNOWN, false);\r\n bondsA.push(newBond);\r\n atomB.bonds.push(newBond);\r\n }\r\n\r\n build() {\r\n if (cProfileBondBuilder) {\r\n console.time('Bonds Builder');\r\n }\r\n this._buildInner();\r\n\r\n if (cProfileBondBuilder) {\r\n console.timeEnd('Bonds Builder');\r\n }\r\n }\r\n\r\n _buildInner() {\r\n const atoms = this._complex._atoms;\r\n if (atoms.length < 2) {\r\n return;\r\n }\r\n if (atoms[0].index < 0) {\r\n throw new Error('AutoBond: Atoms in complex were not indexed.');\r\n }\r\n\r\n this._calcBoundingBox();\r\n this._pairCollection = new AtomPairs(atoms.length * cEstBondsMultiplier);\r\n this._addExistingPairs();\r\n this._findPairs();\r\n this._addPairs();\r\n }\r\n\r\n _calcBoundingBox() {\r\n const atoms = this._complex._atoms;\r\n const nAtoms = atoms.length;\r\n let maxRad = _getBondingRadius(atoms[0]);\r\n for (let i = 1; i < nAtoms; ++i) {\r\n maxRad = Math.max(maxRad, _getBondingRadius(atoms[i]));\r\n }\r\n this._vBoxMax.addScalar(maxRad);\r\n this._vBoxMin.addScalar(-maxRad);\r\n this._maxRad = maxRad * 1.2;\r\n }\r\n\r\n destroy() {\r\n if (this._pairCollection) {\r\n this._pairCollection.destroy();\r\n }\r\n }\r\n}\r\n\r\nexport default AutoBond;\r\n","import * as THREE from 'three';\r\nimport Bond from './Bond';\r\nimport Element from './Element';\r\n\r\nconst cCrossThresh = 0.1;\r\nconst cAromaticType = Bond.BondType.AROMATIC;\r\nconst cAromaticAtoms = [\r\n Element.ByName.C.number,\r\n Element.ByName.N.number,\r\n // Element.ByName.O.number,\r\n // Element.ByName.S.number,\r\n];\r\n\r\n/** Conditions for bonds:\r\n * - Cross product with each subsequent bond to add is collinear and point to the same direction\r\n * - Each pair of a adjacent bonds belong to not more than one cycle\r\n * - If there is more than one candidates we try them in ascending order of angle values\r\n */\r\n\r\nconst _coDirVectors = (function () {\r\n const v1Tmp = new THREE.Vector3();\r\n const v2Tmp = new THREE.Vector3();\r\n const cp = new THREE.Vector3();\r\n return function (v1, v2) {\r\n v1Tmp.copy(v1).normalize();\r\n v2Tmp.copy(v2).normalize();\r\n cp.crossVectors(v1Tmp, v2Tmp);\r\n if (cp.length() > cCrossThresh) {\r\n return false;\r\n }\r\n // zero vector in out terms must be collinear to any\r\n return v1Tmp.dot(v2Tmp) >= 0;\r\n };\r\n}());\r\n\r\nfunction _insertAscending(arr, val) {\r\n let idx = 0;\r\n while (idx < arr.length && arr[idx] < val) {\r\n ++idx;\r\n }\r\n arr.splice(idx, 0, val);\r\n}\r\n\r\nfunction _anotherAtom(bond, currAtom) {\r\n return bond._left === currAtom ? bond._right : bond._left;\r\n}\r\n\r\nfunction _cosBetween(v1, v2) {\r\n const theta = v1.dot(v2) / (Math.sqrt(v1.lengthSq() * v2.lengthSq()));\r\n return THREE.MathUtils.clamp(theta, -1, 1);\r\n}\r\n\r\nfunction _markAromatic(bond) {\r\n bond._type = cAromaticType;\r\n}\r\n\r\nclass Cycle {\r\n constructor(atomsList) {\r\n this.atoms = atomsList;\r\n this.update();\r\n }\r\n\r\n update() {\r\n const { atoms } = this;\r\n const center = new THREE.Vector3();\r\n const nA = atoms.length;\r\n for (let j = 0; j < nA; ++j) {\r\n center.add(atoms[j].position);\r\n }\r\n center.multiplyScalar(1.0 / nA);\r\n this.center = center;\r\n this.radius = center.distanceTo(atoms[0].position.clone().lerp(atoms[1].position, 0.5));\r\n }\r\n\r\n forEachBond(process) {\r\n const { atoms } = this;\r\n const nA = atoms.length;\r\n let currAtom = atoms[0];\r\n let nextAtom;\r\n\r\n function checkBond(bond) {\r\n if (bond._left === nextAtom || bond._right === nextAtom) {\r\n process(bond);\r\n }\r\n }\r\n\r\n for (let i = 0; i < nA; ++i) {\r\n nextAtom = atoms[(i + 1) % nA];\r\n currAtom.forEachBond(checkBond);\r\n currAtom = nextAtom;\r\n }\r\n }\r\n}\r\n\r\nfunction _isAromatic(bond) {\r\n return bond._type === cAromaticType;\r\n}\r\n\r\nfunction _isPossibleAromatic(bond) {\r\n if (bond.type === cAromaticType) {\r\n return true;\r\n }\r\n const rightIdx = cAromaticAtoms.indexOf(bond._right.element.number);\r\n const leftIdx = cAromaticAtoms.indexOf(bond._left.element.number);\r\n return rightIdx !== -1 && leftIdx !== -1;\r\n}\r\n\r\nfunction _checkCycleSimple(cycle) {\r\n return cycle.length > 3;\r\n}\r\n\r\nfunction _checkCycleComplex(cycle) {\r\n console.assert(cycle.length > 2);\r\n return true;\r\n}\r\n\r\nclass AromaticLoopsMarker {\r\n constructor(complex) {\r\n this._complex = complex;\r\n const bondsData = new Array(complex._bonds.length);\r\n const bondMarks = new Array(complex._bonds.length);\r\n for (let i = 0, n = bondsData.length; i < n; ++i) {\r\n bondsData[i] = [];\r\n bondMarks[i] = false;\r\n }\r\n this._bondsData = bondsData;\r\n this._bondMarks = bondMarks;\r\n this._resetCycles();\r\n }\r\n\r\n _resetCycles() {\r\n this._cycles = [];\r\n this._currIdx = -1;\r\n }\r\n\r\n _haveSameCycle(bondsData, bond1, bond2) {\r\n const arr1 = bondsData[bond1._index];\r\n const arr2 = bondsData[bond2._index];\r\n const n1 = arr1.length;\r\n const n2 = arr2.length;\r\n let i1 = 0;\r\n let i2 = 0;\r\n while (i1 < n1 && i2 < n2) {\r\n if (arr1[i1] === arr2[i2]) {\r\n return true;\r\n }\r\n if (arr1[i1] > arr2[i2]) {\r\n ++i2;\r\n } else {\r\n ++i1;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _tryBond(prevBond, currRight, currDir) {\r\n const bondsOrder = [];\r\n const bondsData = this._bondsData;\r\n const currLeft = _anotherAtom(prevBond, currRight);\r\n const currVec = currRight.position.clone().sub(currLeft.position);\r\n const startAtomRef = this._currStart;\r\n const self = this;\r\n const bondMarks = this._bondMarks;\r\n let checkAromatic = this._checkBond;\r\n bondMarks[prevBond._index] = true;\r\n checkAromatic = checkAromatic === undefined ? _isAromatic : checkAromatic;\r\n currRight.forEachBond((newBond) => {\r\n if (!checkAromatic(newBond)\r\n || newBond === prevBond\r\n || bondMarks[newBond._index]\r\n || self._haveSameCycle(bondsData, prevBond, newBond)) {\r\n return;\r\n }\r\n const anotherAtom = _anotherAtom(newBond, currRight);\r\n const anotherVec = anotherAtom.position.clone().sub(currRight.position);\r\n const val = anotherAtom === startAtomRef ? -2.0 : 1 - _cosBetween(currVec, anotherVec);\r\n const newDir = anotherVec.cross(currVec);\r\n if (!_coDirVectors(newDir, currDir)) {\r\n return;\r\n }\r\n let idx = 0;\r\n while (idx < bondsOrder.length && bondsOrder[idx].val < val) {\r\n ++idx;\r\n }\r\n bondsOrder.splice(idx, 0, { bond: newBond, val, dir: newDir });\r\n });\r\n\r\n for (let i = 0, n = bondsOrder.length; i < n; ++i) {\r\n const { bond } = bondsOrder[i];\r\n const newRight = bond._left === currRight ? bond._right : bond._left;\r\n if (newRight === startAtomRef) {\r\n ++this._currIdx;\r\n this._cycles.push([currRight]);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n if (this._tryBond(bond, newRight, bondsOrder[i].dir)) {\r\n _insertAscending(bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(currRight);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n }\r\n bondMarks[prevBond._index] = false;\r\n return false;\r\n }\r\n\r\n _startCycle(bond) {\r\n // start from left to right\r\n this._currStart = bond._left;\r\n if (this._tryBond(bond, bond._right, new THREE.Vector3())) {\r\n _insertAscending(this._bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(bond._left);\r\n }\r\n }\r\n\r\n _findLoops(checkBond, checkCycle) {\r\n this._checkBond = checkBond;\r\n const complex = this._complex;\r\n const self = this;\r\n\r\n complex.forEachComponent((component) => {\r\n self._resetCycles();\r\n component.forEachBond((bond) => {\r\n if (checkBond(bond)) {\r\n self._startCycle(bond);\r\n }\r\n });\r\n const cycles = self._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n const cycle = cycles[i];\r\n if (!checkCycle(cycle)) {\r\n continue;\r\n }\r\n const newCycle = new Cycle(cycle);\r\n newCycle.forEachBond(_markAromatic);\r\n component.addCycle(newCycle);\r\n }\r\n });\r\n }\r\n\r\n markCycles() {\r\n this._findLoops(_isAromatic, _checkCycleSimple);\r\n }\r\n\r\n detectCycles() {\r\n this._findLoops(_isPossibleAromatic, _checkCycleComplex);\r\n }\r\n}\r\n\r\nexport default AromaticLoopsMarker;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\n/**\r\n * Calculate min & max radius of a sphere slice between zMin & zMax\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {number} zMin - lower bound of the slice\r\n * @param {number} zMax - upper bound of the slice\r\n */\r\nfunction _getSphereSliceRadiusRange(center, radius, zMin, zMax) {\r\n const dzMin = zMin - center.z;\r\n const dzMax = zMax - center.z;\r\n const rzMin = Math.sqrt(Math.max(radius * radius - dzMin * dzMin, 0.0));\r\n const rzMax = Math.sqrt(Math.max(radius * radius - dzMax * dzMax, 0.0));\r\n\r\n const rMin = Math.min(rzMin, rzMax);\r\n let rMax;\r\n\r\n if (zMin <= center.z && zMax >= center.z) {\r\n // sphere's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(rzMin, rzMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * Calculate min & max radius of a circle slice between yMin & yMax.\r\n *\r\n * To maintain analogy with _getSphereSliceRadiusRange we call radius what in fact is\r\n * half-width (along X axis) of the slice, i.e. 1D-sphere radius.\r\n *\r\n * @param {Vector3} center - center of the circle (z can be ignored)\r\n * @param {number} radius - circle radius\r\n * @param {number} yMin - lower bound of the slice\r\n * @param {number} yMax - upper bound of the slice\r\n * @returns {Array} - array of two numbers (min & max radius, or half-width)\r\n */\r\nfunction _getCircleSliceRadiusRange(center, radius, yMin, yMax) {\r\n const dyMin = yMin - center.y;\r\n const dyMax = yMax - center.y;\r\n const ryMin = Math.sqrt(Math.max(radius * radius - dyMin * dyMin, 0.0));\r\n const ryMax = Math.sqrt(Math.max(radius * radius - dyMax * dyMax, 0.0));\r\n\r\n const rMin = Math.min(ryMin, ryMax);\r\n let rMax;\r\n\r\n if (yMin <= center.y && yMax >= center.y) {\r\n // slice's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(ryMin, ryMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * VoxelWorld constructor\r\n *\r\n * @param {Box3} box - bounding box of the volume to be partitioned\r\n * @param {Vector3} vCellSizeHint - target voxel size (actual voxel size may differ from this)\r\n */\r\nclass VoxelWorld {\r\n constructor(box, vCellSizeHint) {\r\n this._box = box.clone();\r\n const size = new THREE.Vector3();\r\n box.getSize(size);\r\n this._count = size.clone().divide(vCellSizeHint).floor().max(new THREE.Vector3(1, 1, 1));\r\n this._last = this._count.clone().subScalar(1);\r\n this._cellSize = size.clone().divide(this._count);\r\n this._cellInnerR = 0.5 * Math.min(Math.min(this._cellSize.x, this._cellSize.y), this._cellSize.z);\r\n this._cellOuterR = 0.5 * Math.sqrt(this._cellSize.dot(this._cellSize));\r\n\r\n // array of voxels, each element contains index of first atom in voxel\r\n const numVoxels = this._count.x * this._count.y * this._count.z;\r\n this._voxels = utils.allocateTyped(Int32Array, numVoxels);\r\n for (let i = 0; i < numVoxels; ++i) {\r\n this._voxels[i] = -1;\r\n }\r\n\r\n // array of atoms that stores multiple single-linked lists\r\n // two elements for each atom: Atom ref, index of next atom (in this array\r\n this._atoms = [];\r\n }\r\n\r\n /**\r\n * Add all atoms from a complex to voxel world\r\n *\r\n * @param {Complex} complex - complex\r\n */\r\n addAtoms(complex) {\r\n const self = this;\r\n\r\n let idx = this._atoms.length;\r\n\r\n // resize array of atoms\r\n this._atoms.length += 2 * complex.getAtomCount();\r\n\r\n complex.forEachAtom((atom) => {\r\n // find which voxel contains this atom\r\n const voxelIdx = self._findVoxel(atom.position);\r\n\r\n // push current atom to the head of voxel's atom list\r\n self._atoms[idx] = atom;\r\n self._atoms[idx + 1] = self._voxels[voxelIdx];\r\n self._voxels[voxelIdx] = idx;\r\n\r\n idx += 2;\r\n });\r\n }\r\n\r\n /**\r\n * Get voxel that contains specified 3D point (we use clamp at the edges)\r\n *\r\n * @param {Vector3} point - a point in 3D\r\n * @returns {number} - index of voxel\r\n */\r\n static _zero = new THREE.Vector3(0, 0, 0);\r\n\r\n static _voxel = new THREE.Vector3();\r\n\r\n _findVoxel(point) {\r\n const zero = VoxelWorld._zero;\r\n const voxel = VoxelWorld._voxel;\r\n voxel.copy(point)\r\n .sub(this._box.min)\r\n .divide(this._cellSize)\r\n .floor()\r\n .clamp(zero, this._last);\r\n return voxel.x + this._count.x * (voxel.y + this._count.y * voxel.z);\r\n }\r\n\r\n /**\r\n * Call a function for each atom in voxel\r\n *\r\n * @param {number} voxel - index of voxel\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomInVoxel(voxel, process) {\r\n for (let i = this._voxels[voxel]; i >= 0; i = this._atoms[i + 1]) {\r\n process(this._atoms[i]);\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _xRange = new THREE.Vector2();\r\n\r\n static _yRange = new THREE.Vector2();\r\n\r\n static _zRange = new THREE.Vector2();\r\n\r\n _forEachVoxelWithinRadius(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n\r\n // switch to a faster method unless cell size is much smaller than sphere radius\r\n if (radius / this._cellInnerR < 10) {\r\n this._forEachVoxelWithinRadiusSimple(center, radius, process);\r\n return;\r\n }\r\n\r\n let rRangeXY;\r\n let rRangeX;\r\n let xVal;\r\n let yVal;\r\n let zVal;\r\n let isInsideX;\r\n let isInsideY;\r\n let isInsideZ;\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor()\r\n .clampScalar(0, this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n\r\n isInsideZ = (center.z - radius <= zVal[0]) && (zVal[1] <= center.z + radius);\r\n\r\n rRangeXY = _getSphereSliceRadiusRange(center, radius, zVal[0], zVal[1]);\r\n\r\n yRange.set(center.y - rRangeXY[1], center.y + rRangeXY[1]);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor()\r\n .clampScalar(0, this._count.y - 1);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n\r\n isInsideY = (center.y - rRangeXY[0] <= yVal[0]) && (yVal[1] <= center.y + rRangeXY[0]);\r\n\r\n rRangeX = _getCircleSliceRadiusRange(center, rRangeXY[1], yVal[0], yVal[1]);\r\n\r\n xRange.set(center.x - rRangeX[1], center.x + rRangeX[1]);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor()\r\n .clampScalar(0, this._count.x - 1);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n isInsideX = (center.x - rRangeX[0] <= xVal[0]) && (xVal[1] <= center.x + rRangeX[0]);\r\n\r\n process(x + this._count.x * (y + this._count.y * z), isInsideX && isInsideY && isInsideZ);\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n * This is a version of method that doesn't try to \"calculate\" what voxels fall inside radius\r\n * but instead just checks all voxels inside sphere's bounding box. This should be faster\r\n * unless cell size is much smaller than sphere radius.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _vCenter = new THREE.Vector3();\r\n\r\n _forEachVoxelWithinRadiusSimple(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n const vCenter = VoxelWorld._vCenter;\r\n\r\n const distTouch2 = (radius + this._cellOuterR) * (radius + this._cellOuterR);\r\n let distInside2 = -1.0;\r\n if (radius > this._cellOuterR) {\r\n distInside2 = (radius - this._cellOuterR) * (radius - this._cellOuterR);\r\n }\r\n\r\n // calculate bounding box for the sphere\r\n xRange.set(center.x - radius, center.x + radius);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor();\r\n xRange.x = Math.min(Math.max(xRange.x, 0), this._count.x - 1);\r\n xRange.y = Math.min(Math.max(xRange.y, 0), this._count.x - 1);\r\n\r\n yRange.set(center.y - radius, center.y + radius);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor();\r\n yRange.x = Math.min(Math.max(yRange.x, 0), this._count.y - 1);\r\n yRange.y = Math.min(Math.max(yRange.y, 0), this._count.y - 1);\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor();\r\n zRange.x = Math.min(Math.max(zRange.x, 0), this._count.z - 1);\r\n zRange.y = Math.min(Math.max(zRange.y, 0), this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n const zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n vCenter.z = 0.5 * (zVal[0] + zVal[1]);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n const yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n vCenter.y = 0.5 * (yVal[0] + yVal[1]);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n const xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n vCenter.x = 0.5 * (xVal[0] + xVal[1]);\r\n\r\n const d2 = center.distanceToSquared(vCenter);\r\n if (d2 <= distTouch2) {\r\n process(x + this._count.x * (y + this._count.y * z), d2 <= distInside2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each atom within given sphere\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinRadius(center, radius, process) {\r\n const self = this;\r\n const r2 = radius * radius;\r\n\r\n self._forEachVoxelWithinRadius(center, radius, (voxel, isInside) => {\r\n if (isInside) {\r\n self._forEachAtomInVoxel(voxel, process);\r\n } else {\r\n self._forEachAtomInVoxel(voxel, (atom) => {\r\n if (center.distanceToSquared(atom.position) <= r2) {\r\n process(atom);\r\n }\r\n });\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by mask\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} mask - bit mask\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromMasked(complex, mask, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by selector\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} selector - selector\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromSelected(complex, selector, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms\r\n *\r\n * @param {function} forEachAtom - enumerator of atoms in the group\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomWithinDistFromGroup(forEachAtom, dist, process) {\r\n const self = this;\r\n const r2 = dist * dist;\r\n\r\n const voxels = [];\r\n const atoms = [];\r\n let idx = 0;\r\n\r\n // build \"within radius\" atom list for each voxel\r\n forEachAtom((atom) => {\r\n self._forEachVoxelWithinRadius(atom.position, dist, (voxel, isInside) => {\r\n if (isInside) {\r\n // this voxel is inside circle -- no check will be required\r\n voxels[voxel] = -1;\r\n } else if (typeof voxels[voxel] === 'undefined') {\r\n // this voxel isn't covered yet -- start building list of atoms\r\n atoms.push(atom);\r\n atoms.push(-1);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n } else if (voxels[voxel] !== -1) {\r\n // this voxel has a list of atoms required for distance check -- add atom to the list\r\n atoms.push(atom);\r\n atoms.push(voxels[voxel]);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n }\r\n });\r\n });\r\n\r\n let voxel;\r\n\r\n const processIfWithin = function (atom) {\r\n if (typeof voxels[voxel] === 'undefined') {\r\n return;\r\n }\r\n\r\n idx = voxels[voxel];\r\n if (idx === -1) {\r\n // this voxel is fully covered\r\n process(atom);\r\n return;\r\n }\r\n\r\n // check distance to each atom within radius from this voxel\r\n for (; idx >= 0; idx = atoms[idx + 1]) {\r\n if (atom.position.distanceToSquared(atoms[idx].position) < r2) {\r\n process(atom);\r\n break;\r\n }\r\n }\r\n };\r\n\r\n // for each marked voxel\r\n for (voxel in voxels) {\r\n if (voxels.hasOwnProperty(voxel)) {\r\n self._forEachAtomInVoxel(voxel, processIfWithin);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default VoxelWorld;\r\n","import ResidueType from './ResidueType';\r\nimport PairCollection from './AtomPairs';\r\n\r\nconst MINIMAL_DISTANCE = 0.5;\r\nconst MIN_HBOND_ENERGY = -9.9;\r\nconst MAX_HBOND_ENERGY = -0.5;\r\nconst COUPLING_CONSTANT = -27.888; // = -332 * 0.42 * 0.2\r\nconst MAX_COUPLING_DISTANCE = 5.0; // how far is the closest atom of a potential partner residue from CA atom\r\nconst MAX_RESIDUES_THRESHOLD = 1000;\r\n\r\nexport default class HBondInfo {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._hbonds = []; // array of bond info for each residue\r\n if (this._complex._residues.length > MAX_RESIDUES_THRESHOLD) {\r\n this._buildVW(); // optimized version using voxel grid\r\n } else {\r\n this._build(); // test all pairs of residues\r\n }\r\n }\r\n\r\n isBond(from, to) {\r\n if (this._hbonds[from]) {\r\n const [acc0, acc1] = this._hbonds[from].acceptor;\r\n if (acc0 && acc0.residue === to && acc0.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n if (acc1 && acc1.residue === to && acc1.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n\r\n for (let i = 0; i < this._complex._residues.length - 1; ++i) {\r\n const ri = this._complex._residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let preri = null;\r\n if (i > 0 && (this._complex._residues[i - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && ri._sequence === this._complex._residues[i - 1]._sequence + 1) {\r\n preri = this._complex._residues[i - 1];\r\n }\r\n\r\n for (let j = i + 1; j < this._complex._residues.length; ++j) {\r\n const rj = this._complex._residues[j];\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = null;\r\n if ((this._complex._residues[j - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && rj._sequence === this._complex._residues[j - 1]._sequence + 1) {\r\n prerj = this._complex._residues[j - 1];\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (j !== i + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _buildVW() {\r\n const self = this;\r\n const residues = this._complex._residues;\r\n let ri;\r\n let preri;\r\n\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const pairs = new PairCollection(this._complex._residues.length * this._complex._residues.length / 2);\r\n\r\n function processAtom(atom) {\r\n const rj = atom.residue;\r\n\r\n if (rj._index === ri._index) {\r\n return;\r\n }\r\n\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n return;\r\n }\r\n\r\n if (!pairs.addPair(ri._index, rj._index)) {\r\n // we've seen this pair\r\n return;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = rj._index > 0 ? residues[rj._index - 1] : null;\r\n if (prerj\r\n && ((prerj.getType().flags & ResidueType.Flags.PROTEIN) === 0 || rj._sequence !== prerj._sequence + 1)) {\r\n prerj = null;\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (rj._index !== ri._index + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n\r\n for (let i = 0; i < residues.length - 1; ++i) {\r\n ri = residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n preri = i > 0 ? residues[i - 1] : null;\r\n if (preri\r\n && ((preri.getType().flags & ResidueType.Flags.PROTEIN) === 0 || ri._sequence !== preri._sequence + 1)) {\r\n preri = null;\r\n }\r\n\r\n vw.forEachAtomWithinRadius(this._residueGetCAlpha(ri), MAX_COUPLING_DISTANCE, processAtom);\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _residueGetCO(res) {\r\n let c = null;\r\n let o = null;\r\n\r\n res.forEachAtom((a) => {\r\n if (a.name === 'C') {\r\n c = a.position;\r\n } else if (a.name === 'O') {\r\n o = a.position;\r\n }\r\n });\r\n\r\n return [c, o];\r\n }\r\n\r\n // TODO Support hydrogen defined in complex\r\n _residueGetNH(prev, res) {\r\n const [c, o] = this._residueGetCO(prev);\r\n\r\n let n;\r\n res.forEachAtom((a) => {\r\n if (a.name === 'N') {\r\n n = a.position;\r\n }\r\n });\r\n\r\n if (c && o && n) {\r\n // calculate hydrogen position\r\n const h = c.clone();\r\n h.sub(o);\r\n h.multiplyScalar(1.0 / h.length());\r\n h.add(n);\r\n\r\n return [n, h];\r\n }\r\n\r\n return [null, null];\r\n }\r\n\r\n _calcHBondEnergy(predonor, donor, acceptor) {\r\n let result = 0;\r\n\r\n if (predonor === null) {\r\n return result;\r\n }\r\n\r\n if (donor.getType().getName() !== 'PRO') {\r\n const [n, h] = this._residueGetNH(predonor, donor);\r\n const [c, o] = this._residueGetCO(acceptor);\r\n\r\n if (n === null || h === null || c === null || o === null) {\r\n return result;\r\n }\r\n\r\n const distanceHO = h.distanceTo(o);\r\n const distanceHC = h.distanceTo(c);\r\n const distanceNC = n.distanceTo(c);\r\n const distanceNO = n.distanceTo(o);\r\n\r\n if (distanceHO < MINIMAL_DISTANCE || distanceHC < MINIMAL_DISTANCE\r\n || distanceNC < MINIMAL_DISTANCE || distanceNO < MINIMAL_DISTANCE) {\r\n result = MIN_HBOND_ENERGY;\r\n } else {\r\n result = COUPLING_CONSTANT / distanceHO - COUPLING_CONSTANT / distanceHC\r\n + COUPLING_CONSTANT / distanceNC - COUPLING_CONSTANT / distanceNO;\r\n }\r\n\r\n // DSSP compatibility mode:\r\n result = Math.round(result * 1000) / 1000;\r\n\r\n if (result < MIN_HBOND_ENERGY) {\r\n result = MIN_HBOND_ENERGY;\r\n }\r\n }\r\n\r\n // update donor\r\n if (typeof this._hbonds[donor._index] === 'undefined') {\r\n this._hbonds[donor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const donorInfo = this._hbonds[donor._index];\r\n\r\n if (donorInfo.acceptor.length < 2) {\r\n donorInfo.acceptor.push({\r\n residue: acceptor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (donorInfo.acceptor.length > 1) {\r\n if (result < donorInfo.acceptor[0].energy) {\r\n donorInfo.acceptor[1].residue = donorInfo.acceptor[0].residue;\r\n donorInfo.acceptor[1].energy = donorInfo.acceptor[0].energy;\r\n donorInfo.acceptor[0].residue = acceptor._index;\r\n donorInfo.acceptor[0].energy = result;\r\n } else if (result < donorInfo.acceptor[1].energy) {\r\n donorInfo.acceptor[1].residue = acceptor._index;\r\n donorInfo.acceptor[1].energy = result;\r\n }\r\n }\r\n\r\n // update acceptor\r\n if (typeof this._hbonds[acceptor._index] === 'undefined') {\r\n this._hbonds[acceptor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const accInfo = this._hbonds[acceptor._index];\r\n\r\n if (accInfo.donor.length < 2) {\r\n accInfo.donor.push({\r\n residue: donor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (accInfo.donor.length > 1) {\r\n if (result < accInfo.donor[0].energy) {\r\n accInfo.donor[1].residue = accInfo.donor[0].residue;\r\n accInfo.donor[1].energy = accInfo.donor[0].energy;\r\n accInfo.donor[0].residue = donor._index;\r\n accInfo.donor[0].energy = result;\r\n } else if (result < accInfo.donor[1].energy) {\r\n accInfo.donor[1].residue = donor._index;\r\n accInfo.donor[1].energy = result;\r\n }\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n","import HBondInfo from './HBondInfo';\r\nimport ResidueType from './ResidueType';\r\n\r\nconst BridgeType = Object.freeze({\r\n NO_BRIDGE: 0,\r\n PARALLEL: 1,\r\n ANTI_PARALLEL: 2,\r\n});\r\n\r\nconst HelixFlag = Object.freeze({\r\n START: 1,\r\n MIDDLE: 2,\r\n END: 3,\r\n START_AND_END: 4,\r\n});\r\n\r\nconst StructureType = Object.freeze({\r\n STRAND: 'E',\r\n BRIDGE: 'B',\r\n HELIX_310: 'G',\r\n HELIX_ALPHA: 'H',\r\n HELIX_PI: 'I',\r\n TURN: 'T',\r\n BEND: 'S',\r\n LOOP: ' ',\r\n});\r\n\r\nexport default class SecondaryStructureMap {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._build();\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n this._hbonds = new HBondInfo(this._complex);\r\n this._ss = []; // DSSP map by residue\r\n\r\n // auxilliary data\r\n this._sheet = [];\r\n this._betaPartners = [];\r\n this._bend = [];\r\n for (let i = 0; i < this._complex.getResidues().length; ++i) {\r\n this._betaPartners[i] = [];\r\n }\r\n this._helixFlags = [];\r\n this._helixFlags[3] = [];\r\n this._helixFlags[4] = [];\r\n this._helixFlags[5] = [];\r\n\r\n // calculate peptide chain lengths\r\n this._chainLengths = [];\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i].getResidues();\r\n let len = 0;\r\n for (; len < chain.length; ++len) {\r\n if ((chain[len].getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n break;\r\n }\r\n }\r\n this._chainLengths[i] = len;\r\n }\r\n\r\n this._buildBetaSheets();\r\n\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n self._buildAlphaHelices(this._complex._chains[i].getResidues(), this._chainLengths[i], false);\r\n }\r\n }\r\n\r\n _buildAlphaHelices(inResidues, chainLength, inPreferPiHelices) {\r\n // Helix and Turn\r\n for (let stride = 3; stride <= 5; ++stride) {\r\n if (inResidues.length < stride) {\r\n break;\r\n }\r\n\r\n for (let i = 0; i + stride < chainLength; ++i) {\r\n if (this._hbonds.isBond(inResidues[i + stride]._index, inResidues[i]._index)\r\n /* && NoChainBreak(res[i], res[i + stride]) */) {\r\n this._helixFlags[stride][inResidues[i + stride]._index] = HelixFlag.END;\r\n for (let j = i + 1; j < i + stride; ++j) {\r\n if (typeof this._helixFlags[stride][inResidues[j]._index] === 'undefined') {\r\n this._helixFlags[stride][inResidues[j]._index] = HelixFlag.MIDDLE;\r\n }\r\n }\r\n\r\n if (this._helixFlags[stride][inResidues[i]._index] === HelixFlag.END) {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START_AND_END;\r\n } else {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 2; i < chainLength - 2; ++i) {\r\n const kappa = this._kappa(inResidues[i - 2], inResidues[i], inResidues[i + 2]);\r\n this._bend[inResidues[i]._index] = (kappa !== 360 && kappa > 70);\r\n }\r\n\r\n for (let i = 1; i + 4 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 4) && this._isHelixStart(inResidues[i - 1]._index, 4)) {\r\n for (let j = i; j <= i + 3; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_ALPHA;\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 3 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 3) && this._isHelixStart(inResidues[i - 1]._index, 3)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 2; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_310;\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 2; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_310;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 5 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 5) && this._isHelixStart(inResidues[i - 1]._index, 5)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 4; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_PI\r\n || (inPreferPiHelices && this._ss[inResidues[j]._index] === StructureType.HELIX_ALPHA);\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 4; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_PI;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 1 < chainLength; ++i) {\r\n if (typeof this._ss[inResidues[i]._index] === 'undefined') {\r\n let isTurn = false;\r\n for (let stride = 3; stride <= 5 && !isTurn; ++stride) {\r\n for (let k = 1; k < stride && !isTurn; ++k) {\r\n isTurn = (i >= k) && this._isHelixStart(inResidues[i - k]._index, stride);\r\n }\r\n }\r\n\r\n if (isTurn) {\r\n this._ss[inResidues[i]._index] = StructureType.TURN;\r\n } else if (this._bend[inResidues[i]._index]) {\r\n this._ss[inResidues[i]._index] = StructureType.BEND;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _cosinusAngle(p1, p2, p3, p4) {\r\n const v12 = p1.clone().sub(p2);\r\n const v34 = p3.clone().sub(p4);\r\n\r\n let result = 0;\r\n\r\n const x = v12.dot(v12) * v34.dot(v34);\r\n if (x > 0) {\r\n result = v12.dot(v34) / Math.sqrt(x);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _kappa(prevPrev, res, nextNext) {\r\n const curCA = this._residueGetCAlpha(res);\r\n const ppCA = this._residueGetCAlpha(prevPrev);\r\n const nnCA = this._residueGetCAlpha(nextNext);\r\n if (curCA === null || ppCA === null || nnCA === null) {\r\n return 180;\r\n }\r\n\r\n const ckap = this._cosinusAngle(curCA, ppCA, nnCA, curCA);\r\n const skap = Math.sqrt(1 - ckap * ckap);\r\n return Math.atan2(skap, ckap) * 180 / Math.PI;\r\n }\r\n\r\n _isHelixStart(res, stride) {\r\n return (this._helixFlags[stride][res] === HelixFlag.START\r\n || this._helixFlags[stride][res] === HelixFlag.START_AND_END);\r\n }\r\n\r\n _buildBetaSheets() {\r\n // find bridges\r\n // check each chain against each other chain, and against itself\r\n const bridges = [];\r\n for (let a = 0; a < this._complex._chains.length; ++a) {\r\n const lenA = this._chainLengths[a];\r\n if (lenA <= 4) {\r\n continue;\r\n }\r\n\r\n const chainA = this._complex._chains[a].getResidues();\r\n\r\n for (let b = a; b < this._complex._chains.length; ++b) {\r\n const lenB = this._chainLengths[b];\r\n if (lenB <= 4) {\r\n continue;\r\n }\r\n\r\n const chainB = this._complex._chains[b].getResidues();\r\n\r\n for (let i = 1; i + 1 < lenA; ++i) {\r\n const ri = chainA[i];\r\n\r\n let j = 1;\r\n if (b === a) {\r\n j = i + 3; // check for self-bridges forward down the chain\r\n }\r\n\r\n for (; j + 1 < lenB; ++j) {\r\n const rj = chainB[j];\r\n\r\n const type = this._testBridge(chainA, i, chainB, j);\r\n if (type === BridgeType.NO_BRIDGE) {\r\n continue;\r\n }\r\n\r\n // there is a bridge, try to attach it to previously found sequence\r\n let found = false;\r\n for (const bridge of bridges) {\r\n if (type !== bridge.type || ri._index !== bridge.i[bridge.i.length - 1] + 1) {\r\n continue;\r\n }\r\n\r\n if (type === BridgeType.PARALLEL && bridge.j[bridge.j.length - 1] + 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.push(rj._index);\r\n found = true;\r\n break;\r\n }\r\n\r\n if (type === BridgeType.ANTI_PARALLEL && bridge.j[0] - 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.unshift(rj._index);\r\n found = true;\r\n break;\r\n }\r\n }\r\n\r\n // this bridge cannot be attached anywhere, start a new sequence\r\n if (!found) {\r\n bridges.push({\r\n type,\r\n i: [ri._index],\r\n chainI: ri.getChain()._index,\r\n j: [rj._index],\r\n chainJ: rj.getChain()._index,\r\n });\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // extend ladders\r\n bridges.sort((a, b) => {\r\n if (a.chainI < b.chainI || (a.chainI === b.chainI && a.i[0] < b.i[0])) {\r\n return -1;\r\n }\r\n return 1;\r\n });\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n for (let j = i + 1; j < bridges.length; ++j) {\r\n const ibi = bridges[i].i[0];\r\n const iei = bridges[i].i[bridges[i].i.length - 1];\r\n const jbi = bridges[i].j[0];\r\n const jei = bridges[i].j[bridges[i].j.length - 1];\r\n const ibj = bridges[j].i[0];\r\n const iej = bridges[j].i[bridges[j].i.length - 1];\r\n const jbj = bridges[j].j[0];\r\n const jej = bridges[j].j[bridges[j].j.length - 1];\r\n\r\n if (bridges[i].type !== bridges[j].type\r\n || this._hasChainBreak(Math.min(ibi, ibj), Math.max(iei, iej))\r\n || this._hasChainBreak(Math.min(jbi, jbj), Math.max(jei, jej))\r\n || ibj - iei >= 6 || (iei >= ibj && ibi <= iej)) {\r\n continue;\r\n }\r\n\r\n let bulge = false;\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bulge = ((jbj - jei < 6 && ibj - iei < 3) || (jbj - jei < 3));\r\n } else {\r\n bulge = ((jbi - jej < 6 && ibj - iei < 3) || (jbi - jej < 3));\r\n }\r\n\r\n if (bulge) {\r\n bridges[i].i = bridges[i].i.concat(bridges[j].i);\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bridges[i].j = bridges[i].j.concat(bridges[j].j);\r\n } else {\r\n bridges[i].j = bridges[j].j.concat(bridges[i].j);\r\n }\r\n bridges.splice(j--, 1);\r\n }\r\n }\r\n }\r\n\r\n // Sheet\r\n const ladderset = new Set();\r\n for (let i = 0; i < bridges.length; ++i) {\r\n ladderset.add(bridges[i]);\r\n }\r\n\r\n let sheet = 1;\r\n let ladder = 0;\r\n while (ladderset.size > 0) {\r\n let bridge = ladderset.values().next().value;\r\n ladderset.delete(bridge);\r\n\r\n const sheetset = new Set();\r\n sheetset.add(bridge);\r\n\r\n let toMove;\r\n do {\r\n toMove = new Set();\r\n for (const a of sheetset.values()) {\r\n for (const b of ladderset.values()) {\r\n if (this._areBridgesLinked(a, b)) {\r\n toMove.add(b);\r\n }\r\n }\r\n }\r\n for (bridge of toMove.values()) {\r\n sheetset.add(bridge);\r\n ladderset.delete(bridge);\r\n }\r\n } while (toMove.size > 0);\r\n\r\n for (bridge of sheetset.values()) {\r\n bridge.ladder = ladder;\r\n bridge.sheet = sheet;\r\n bridge.link = sheetset;\r\n ++ladder;\r\n }\r\n\r\n ++sheet;\r\n }\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n const bridge = bridges[i];\r\n\r\n // find out if any of the i and j set members already have\r\n // a bridge assigned, if so, we're assigning bridge 2\r\n\r\n let betai = 0;\r\n let betaj = 0;\r\n\r\n for (let l = 0; l < bridge.i.length; ++l) {\r\n if (this._betaPartners[bridge.i[l]][0]) {\r\n betai = 1;\r\n break;\r\n }\r\n }\r\n\r\n for (let l = 0; l < bridge.j.length; ++l) {\r\n if (this._betaPartners[bridge.j[l]][0]) {\r\n betaj = 1;\r\n break;\r\n }\r\n }\r\n\r\n let ss = StructureType.BRIDGE;\r\n if (bridge.i.length > 1) {\r\n ss = StructureType.STRAND;\r\n }\r\n\r\n if (bridge.type === BridgeType.PARALLEL) {\r\n let j = 0;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n\r\n j = 0;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n } else {\r\n let j = bridge.j.length - 1;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n\r\n j = bridge.i.length - 1;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n }\r\n\r\n for (let k = bridge.i[0]; k <= bridge.i[bridge.i.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n\r\n for (let k = bridge.j[0]; k <= bridge.j[bridge.j.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _testBridge(chainA, from, chainB, to) {\r\n let result = BridgeType.NO_BRIDGE;\r\n\r\n const a = chainA[from - 1]._index;\r\n const b = chainA[from]._index;\r\n const c = chainA[from + 1]._index;\r\n const d = chainB[to - 1]._index;\r\n const e = chainB[to]._index;\r\n const f = chainB[to + 1]._index;\r\n\r\n const isBond = this._hbonds.isBond.bind(this._hbonds);\r\n if ((isBond(c, e) && isBond(e, a)) || (isBond(f, b) && isBond(b, d))) {\r\n result = BridgeType.PARALLEL;\r\n } else if ((isBond(c, d) && isBond(f, a)) || (isBond(e, b) && isBond(b, e))) {\r\n result = BridgeType.ANTI_PARALLEL;\r\n }\r\n return result;\r\n }\r\n\r\n // return true if any of the residues in bridge a is identical to any of the residues in bridge b\r\n _areBridgesLinked(a, b) {\r\n const ai = new Set(a.i);\r\n const aj = new Set(a.j);\r\n\r\n for (const i of b.i) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n for (const i of b.j) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n }\r\n\r\n _hasChainBreak(from, to) {\r\n for (let i = from + 1; i <= to; ++i) {\r\n if (this._complex._residues[i]._sequence !== this._complex._residues[i - 1]._sequence + 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\nSecondaryStructureMap.StructureType = StructureType;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport Atom from './Atom';\r\nimport Chain from './Chain';\r\nimport Helix from './Helix';\r\nimport Strand from './Strand';\r\nimport Sheet from './Sheet';\r\nimport Component from './Component';\r\nimport ResidueType from './ResidueType';\r\nimport Bond from './Bond';\r\nimport AutoBond from './AutoBond';\r\nimport AromaticLoopsMarker from './AromaticLoopsMarker';\r\nimport BiologicalUnit from './BiologicalUnit';\r\nimport selectors from './selectors';\r\nimport VoxelWorld from './VoxelWorld';\r\nimport SecondaryStructureMap from './SecondaryStructureMap';\r\nimport StructuralElement from './StructuralElement';\r\n\r\nconst VOXEL_SIZE = 5.0;\r\n\r\nconst { StructureType } = SecondaryStructureMap;\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX\r\nconst helixClassMap = {\r\n [StructureType.HELIX_ALPHA]: 1,\r\n [StructureType.HELIX_PI]: 3,\r\n [StructureType.HELIX_310]: 5,\r\n};\r\n\r\nconst loopMap = {\r\n [StructureType.BRIDGE]: StructuralElementType.BRIDGE,\r\n [StructureType.TURN]: StructuralElementType.TURN,\r\n [StructureType.BEND]: StructuralElementType.BEND,\r\n [StructureType.LOOP]: StructuralElementType.COIL,\r\n};\r\n\r\n/**\r\n * The entire complex of the molecules under study.\r\n *\r\n * @exports Complex\r\n * @constructor\r\n */\r\nclass Complex {\r\n constructor() {\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n\r\n this._residueTypes = Object.create(ResidueType.StandardTypes);\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n this._molecules = [];\r\n this._maskNeedsUpdate = false;\r\n\r\n this.metadata = {};\r\n\r\n this.symmetry = [];\r\n this.units = [new BiologicalUnit(this)];\r\n this._currentUnit = 0; // default biological unit is the asymmetric unit\r\n }\r\n\r\n addAtom(atom) {\r\n const index = this._atoms.length;\r\n this._atoms.push(atom);\r\n return index;\r\n }\r\n\r\n addSheet(sheet) {\r\n const index = this._sheets.length;\r\n this._sheets.push(sheet);\r\n return index;\r\n }\r\n\r\n addHelix(helix) {\r\n const index = this._helices.length;\r\n this._helices.push(helix);\r\n return index;\r\n }\r\n\r\n getAtoms() {\r\n return this._atoms;\r\n }\r\n\r\n getBonds() {\r\n return this._bonds;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n addResidue(residue) {\r\n const index = this._residues.length;\r\n this._residues.push(residue);\r\n return index;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n this.forEachChain((chain) => {\r\n chain.updateToFrame(frameData);\r\n });\r\n }\r\n\r\n addResidueType(resName) {\r\n const rt = this._residueTypes[resName] = new ResidueType(resName, 'Unknown', '');\r\n return rt;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n getSGroupCount() {\r\n return this._sgroups.length;\r\n }\r\n\r\n getSGroups() {\r\n return this._sgroups;\r\n }\r\n\r\n /*\r\n Extract atom by its fullname: #chainName#.#residueId#.#atomName#\r\n */\r\n getAtomByFullname(fullName) {\r\n const parts = fullName.split('.');\r\n if (parts.length !== 3) {\r\n return null;\r\n }\r\n\r\n const chainName = parts[0];\r\n const resId = parseInt(parts[1], 10);\r\n if (Number.isNaN(resId)) {\r\n return null;\r\n }\r\n const atomName = parts[2].toUpperCase();\r\n\r\n let currAtom = null;\r\n this.forEachChain((chain) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (chain._name.localeCompare(chainName) === 0) {\r\n chain.forEachResidue((residue) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (residue._sequence === resId) {\r\n residue.forEachAtom((atom) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (atomName.localeCompare(atom.name) === 0) {\r\n currAtom = atom;\r\n }\r\n });\r\n }\r\n });\r\n }\r\n });\r\n\r\n return currAtom;\r\n }\r\n\r\n /**\r\n * Create a new chain.\r\n *\r\n * @param {string} name - Chain name.\r\n * @returns {Chain} - Newly created chain.\r\n */\r\n addChain(name) {\r\n const result = new Chain(this, name);\r\n this._chains.push(result);\r\n return result;\r\n }\r\n\r\n getChain(name) {\r\n for (let i = 0, n = this._chains.length; i < n; ++i) {\r\n const chain = this._chains[i];\r\n if (chain.getName() === name) {\r\n return chain;\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n getChainCount() {\r\n return this._chains.length;\r\n }\r\n\r\n getMolecules() {\r\n return this._molecules;\r\n }\r\n\r\n getMoleculeCount() {\r\n return this._molecules.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n process(atoms[i]);\r\n }\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._bonds;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n forEachChain(process) {\r\n const chains = this._chains;\r\n for (let i = 0, n = chains.length; i < n; ++i) {\r\n process(chains[i]);\r\n }\r\n }\r\n\r\n forEachMolecule(process) {\r\n const molecules = this._molecules;\r\n const n = molecules.length;\r\n for (let i = 0; i < n; ++i) {\r\n process(molecules[i]);\r\n }\r\n }\r\n\r\n forEachSGroup(process) {\r\n const groups = this._sgroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n process(groups[i]);\r\n }\r\n }\r\n\r\n forEachComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n forEachVisibleComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n addBond(left, right, order, type, fixed) {\r\n const bond = new Bond(left, right, order, type, fixed);\r\n this._bonds.push(bond);\r\n return bond;\r\n }\r\n\r\n getBondCount() {\r\n return this._bonds.length;\r\n }\r\n\r\n getResidueType(name) {\r\n return this._residueTypes[name] || null;\r\n }\r\n\r\n getUnifiedSerial(chain, serial, iCode) {\r\n /* eslint-disable no-magic-numbers */\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n /* eslint-enable no-magic-numbers */\r\n return serial + iCode * maxSerial + chain * chainShift;\r\n }\r\n\r\n splitUnifiedSerial(uniSerial) {\r\n /* eslint-disable no-magic-numbers */\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n /* eslint-enable no-magic-numbers */\r\n const chainId = Math.floor(uniSerial / chainShift);\r\n const remnant = uniSerial - chainId * chainShift;\r\n const insCode = Math.floor(remnant / maxSerial);\r\n const ser = remnant - insCode * maxSerial;\r\n return { chain: chainId, serial: ser, iCode: insCode };\r\n }\r\n\r\n _fillCmpEdit() {\r\n const self = this;\r\n const components = this._components;\r\n\r\n function addComp() {\r\n const comp = new Component(self);\r\n comp._index = components.length;\r\n components[comp._index] = comp;\r\n return comp;\r\n }\r\n\r\n this.forEachChain((chain) => {\r\n const residues = chain._residues;\r\n const resCount = residues.length;\r\n if (resCount < 1) {\r\n return;\r\n }\r\n let comp = addComp();\r\n let currStart = residues[0]._index;\r\n\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)\r\n || currRes._index !== nextRes._index - 1) {\r\n // the last condition is broken and incorrect\r\n // the refactoring of the Component is required in order to fix this issue\r\n comp.setSubDivs([{\r\n start: currStart,\r\n end: currRes._index,\r\n }]);\r\n if (nextRes) {\r\n currStart = nextRes._index;\r\n comp = addComp();\r\n }\r\n }\r\n }\r\n });\r\n }\r\n\r\n // This function was added in the moment of despair\r\n // It was the dark times for miew\r\n _fillCmpNoedit() {\r\n const comp = new Component(this);\r\n comp._index = 0;\r\n\r\n const residues = this._residues;\r\n const resCount = residues.length;\r\n if (resCount === 0) {\r\n return;\r\n }\r\n\r\n const currSubDivs = [];\r\n let currStart = 0;\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)) {\r\n // wrap up this interval\r\n currSubDivs[currSubDivs.length] = {\r\n start: currStart,\r\n end: i,\r\n };\r\n if (nextRes) {\r\n currStart = i + 1;\r\n }\r\n }\r\n }\r\n\r\n comp.setSubDivs(currSubDivs);\r\n this._components[comp._index] = comp;\r\n }\r\n\r\n /**\r\n * Fill components information.\r\n * @param {boolean} enableEditing - Restructure Complex to enable per-component editing.\r\n */\r\n _fillComponents(enableEditing) {\r\n if (enableEditing) {\r\n this._fillCmpEdit();\r\n } else {\r\n this._fillCmpNoedit();\r\n }\r\n }\r\n\r\n getCurrentUnit() {\r\n return this._currentUnit;\r\n }\r\n\r\n getDefaultBoundaries() {\r\n return this.units[0].getBoundaries();\r\n }\r\n\r\n getBoundaries() {\r\n return this.units[this._currentUnit].getBoundaries();\r\n }\r\n\r\n getTransforms() {\r\n return this.units[this._currentUnit].getTransforms();\r\n }\r\n\r\n getSelector() {\r\n return this.units[this._currentUnit].getSelector();\r\n }\r\n\r\n resetCurrentUnit() {\r\n this._currentUnit = 0;\r\n this.setCurrentUnit(1);\r\n }\r\n\r\n setCurrentUnit(newUnit) {\r\n if (newUnit !== null && newUnit !== undefined\r\n && newUnit !== this._currentUnit\r\n && newUnit >= 0\r\n && newUnit < this.units.length) {\r\n this._currentUnit = newUnit;\r\n return true;\r\n }\r\n return false;\r\n }\r\n\r\n _computeBounds() {\r\n const { units } = this;\r\n for (let i = 0, n = units.length; i < n; ++i) {\r\n units[i].computeBoundaries();\r\n }\r\n }\r\n\r\n onAtomPositionChanged() {\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n this.forEachComponent((c) => {\r\n c.update();\r\n });\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n this._finalizeBonds();\r\n this.forEachSGroup((s) => {\r\n s._rebuildSGroupOnAtomChange();\r\n });\r\n }\r\n\r\n update() {\r\n if (this._maskNeedsUpdate) {\r\n this.updateStructuresMask();\r\n this._maskNeedsUpdate = false;\r\n }\r\n }\r\n\r\n _finalizeBonds() {\r\n const bonds = this.getBonds();\r\n const n = bonds.length;\r\n for (let i = 0; i < n; ++i) {\r\n bonds[i]._index = i;\r\n }\r\n }\r\n\r\n /**\r\n * Finalizes complex's inner data(i.e. after parsing).\r\n * @param {objects} opts - Build bonds automatically.\r\n * @param {boolean} opts.needAutoBonding - Build bonds automatically.\r\n * @param {boolean} opts.detectAromaticLoops - Find/mark aromatic loops.\r\n * @param {boolean} opts.enableEditing - Restructure Complex to enable per-component editing.\r\n * @param {Array} [opts.serialAtomMap] - Array of atoms ordered by their serials.\r\n */\r\n finalize(opts) {\r\n opts = opts || {};\r\n // Put bonds into atoms\r\n const bonds = this._bonds;\r\n let i;\r\n let n;\r\n // remove invalid bonds\r\n for (i = bonds.length - 1; i >= 0; i--) {\r\n const bond = bonds[i];\r\n if (bond._left === null || bond._right === null) {\r\n bonds.splice(i, 1);\r\n } else {\r\n bond._left.bonds.push(bond);\r\n bond._right.bonds.push(bond);\r\n }\r\n }\r\n\r\n const residues = this._residues;\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._finalize();\r\n }\r\n\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n\r\n // WARNING! this MUST be done BEFORE computeBounds is called\r\n const { units } = this;\r\n for (i = 0, n = units.length; i < n; ++i) {\r\n units[i].finalize();\r\n }\r\n // try setting first biomolecule by defaults\r\n this.setCurrentUnit(1);\r\n\r\n const residueHash = {};\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n // This code is extremely dangerous for non-PDB formats\r\n residueHash[this.getUnifiedSerial(\r\n res.getChain().getName().charCodeAt(0),\r\n res.getSequence(),\r\n res.getICode().charCodeAt(0),\r\n )] = res;\r\n }\r\n\r\n const { structures } = this;\r\n for (i = 0, n = structures.length; i < n; ++i) {\r\n structures[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const helices = this._helices;\r\n for (i = 0, n = helices.length; i < n; ++i) {\r\n helices[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const sheets = this._sheets;\r\n for (i = 0, n = sheets.length; i < n; ++i) {\r\n sheets[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n\r\n const atoms = this._atoms;\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const currAtom = atoms[i];\r\n currAtom.index = i;\r\n }\r\n\r\n if (opts.needAutoBonding) {\r\n // Ignore errors during autobonding\r\n try {\r\n const autoConnector = new AutoBond(this);\r\n autoConnector.build();\r\n autoConnector.destroy();\r\n } catch (e) {\r\n console.warn('Autobonding failed:', e);\r\n }\r\n }\r\n\r\n const chains = this._chains;\r\n for (i = 0, n = chains.length; i < n; ++i) {\r\n chains[i]._index = i;\r\n }\r\n\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._index = i;\r\n }\r\n\r\n // mark non-polar hydrogens\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n if (atom.flags & Atom.Flags.HYDROGEN && atom.bonds.length === 1) {\r\n const bond = atom.bonds[0];\r\n const other = (bond._left !== atom && bond._left) || bond._right;\r\n if (other.flags & Atom.Flags.CARBON) {\r\n atom.flags |= Atom.Flags.NONPOLARH;\r\n }\r\n }\r\n }\r\n\r\n this._finalizeBonds();\r\n this._fillComponents(opts.enableEditing);\r\n\r\n const marker = new AromaticLoopsMarker(this);\r\n marker.markCycles();\r\n if (opts.detectAromaticLoops) { // TODO remove this condition clause, it is for debug purposes only!\r\n marker.detectCycles(); // TODO add conditional detection\r\n }\r\n\r\n this._finalizeMolecules();\r\n }\r\n\r\n _finalizeMolecules() {\r\n // add reference to molecule into residue\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const molecule = this._molecules[i];\r\n const count = molecule.residues.length;\r\n for (let j = 0; j < count; j++) {\r\n const residue = molecule.residues[j];\r\n residue._molecule = molecule;\r\n }\r\n }\r\n }\r\n\r\n updateStructuresMask() {\r\n const updater = (structure) => structure.collectMask();\r\n this.forEachResidue(updater);\r\n this.forEachChain(updater);\r\n this.forEachMolecule(updater);\r\n }\r\n\r\n countAtomsByMask(mask) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n getNumAtomsBySelector(selector) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n resetAtomMask(mask) {\r\n this.forEachAtom((atom) => {\r\n atom.mask = mask;\r\n });\r\n }\r\n\r\n markAtoms(selector, mask) {\r\n const setMask = mask;\r\n const clearMask = ~setMask;\r\n let count = 0;\r\n const totalSelector = selectors.keyword('And')(selector, this.getSelector());\r\n\r\n this.forEachAtom((atom) => {\r\n if (totalSelector.includesAtom(atom)) {\r\n atom.mask |= setMask;\r\n count++;\r\n } else {\r\n atom.mask &= clearMask;\r\n }\r\n });\r\n this._maskNeedsUpdate = true;\r\n\r\n return count;\r\n }\r\n\r\n markAtomsAdditionally(selector, mask) {\r\n const setMask = mask;\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom) && (atom.mask & mask) !== mask) {\r\n atom.mask |= setMask;\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n clearAtomBits(mask) {\r\n const clearMask = ~mask;\r\n this.forEachAtom((atom) => {\r\n atom.mask &= clearMask;\r\n });\r\n const reseter = (a) => {\r\n a._mask &= clearMask;\r\n };\r\n this.forEachAtom(reseter);\r\n this.forEachResidue(reseter);\r\n this.forEachChain(reseter);\r\n this.forEachMolecule(reseter);\r\n }\r\n\r\n getAtomNames() {\r\n if (this.hasOwnProperty('_atomNames')) {\r\n return this._atomNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.name] = 1;\r\n });\r\n this._atomNames = Object.keys(dict);\r\n\r\n return this._atomNames;\r\n }\r\n\r\n getElements() {\r\n if (this.hasOwnProperty('_elements')) {\r\n return this._elements;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.element.name] = 1;\r\n });\r\n this._elements = Object.keys(dict);\r\n\r\n return this._elements;\r\n }\r\n\r\n getResidueNames() {\r\n if (this.hasOwnProperty('_residueNames')) {\r\n return this._residueNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachResidue((res) => {\r\n dict[res._type._name] = 1;\r\n });\r\n this._residueNames = Object.keys(dict);\r\n\r\n return this._residueNames;\r\n }\r\n\r\n getChainNames() {\r\n if (this.hasOwnProperty('_chainNames')) {\r\n return this._chainNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachChain((chain) => {\r\n dict[chain._name] = 1;\r\n });\r\n this._chainNames = Object.keys(dict);\r\n\r\n return this._chainNames;\r\n }\r\n\r\n getAltLocNames() {\r\n if (this.hasOwnProperty('_altlocNames')) {\r\n return this._altlocNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[String.fromCharCode(atom.location)] = 1;\r\n });\r\n this._altlocNames = Object.keys(dict);\r\n\r\n return this._altlocNames;\r\n }\r\n\r\n getVoxelWorld() {\r\n if (!this.hasOwnProperty('_voxelWorld')) {\r\n try {\r\n this._voxelWorld = new VoxelWorld(\r\n this.getDefaultBoundaries().boundingBox,\r\n new THREE.Vector3(VOXEL_SIZE, VOXEL_SIZE, VOXEL_SIZE),\r\n );\r\n this._voxelWorld.addAtoms(this);\r\n } catch (e) {\r\n logger.warn('Unable to create voxel world');\r\n this._voxelWorld = null;\r\n }\r\n }\r\n\r\n return this._voxelWorld;\r\n }\r\n\r\n /**\r\n * Simple function to make unified routine procedure without code duplication.\r\n * @param {Array} srcArray - Source chemical structure array (will be part of resulting chemical structure array).\r\n * @param {Array} dstArray - Resulting chemical structure array.\r\n * @param {number} param - Parameter for processor.\r\n * @param {function} functor - Processor for every element in array.\r\n */\r\n addElement(srcArray, dstArray, param, functor) {\r\n const { length } = srcArray;\r\n for (let i = 0; i < length; ++i) {\r\n const elem = srcArray[i];\r\n functor(elem, param);\r\n dstArray.push(elem);\r\n }\r\n }\r\n\r\n // this function joins multiple complexes into one (this)\r\n // atom, bond, ... objects are reused -- so input complexes are no longer valid\r\n joinComplexes(complexes) {\r\n // clear target complex\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n\r\n const self = this;\r\n let atomBias = 0;\r\n let bondBias = 0;\r\n let residueBias = 0;\r\n let chainBias = 0;\r\n let componentBias = 0;\r\n\r\n function processAtom(atom, bias) {\r\n atom.serial += bias;\r\n atom.index += bias;\r\n }\r\n\r\n function processBond(bond, bias) {\r\n bond._index += bias;\r\n }\r\n\r\n function processResidue(residue, bias) {\r\n residue._index += bias;\r\n }\r\n\r\n function processChain(chain, bias) {\r\n chain._complex = self;\r\n chain._index += bias;\r\n }\r\n\r\n function processComponent(component, bias) {\r\n component._complex = self;\r\n component._index += bias;\r\n }\r\n\r\n /**\r\n * Simple function to do nothing.\r\n */\r\n function doNothing() {\r\n }\r\n\r\n for (let i = 0; i < complexes.length; ++i) {\r\n const c = complexes[i];\r\n this.addElement(c._atoms, this._atoms, atomBias, processAtom);\r\n this.addElement(c._bonds, this._bonds, bondBias, processBond);\r\n this.addElement(c._residues, this._residues, residueBias, processResidue);\r\n this.addElement(c._chains, this._chains, chainBias, processChain);\r\n this.addElement(c._sheets, this._sheets, 0, doNothing);\r\n this.addElement(c._helices, this._helices, 0, doNothing);\r\n this.addElement(c._sgroups, this._sgroups, 0, doNothing);\r\n this.addElement(c._components, this._components, componentBias, processComponent);\r\n this.addElement(c.structures, this.structures, 0, doNothing);\r\n // merge residue types\r\n for (const rt in c._residueTypes) {\r\n if (c._residueTypes.hasOwnProperty(rt)) {\r\n this._residueTypes[rt] = c._residueTypes[rt];\r\n }\r\n }\r\n\r\n atomBias += c._atoms.length;\r\n bondBias += c._bonds.length;\r\n residueBias += c._residues.length;\r\n chainBias += c._chains.length;\r\n componentBias += c._components.length;\r\n }\r\n\r\n this._computeBounds();\r\n }\r\n\r\n /**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n */\r\n dssp() {\r\n const ssMap = new SecondaryStructureMap(this);\r\n\r\n const structures = this.structures = [];\r\n const helices = this._helices = [];\r\n const sheets = this._sheets = [];\r\n\r\n const getSheet = (index) => {\r\n let item = sheets[index];\r\n if (!item) {\r\n item = sheets[index] = new Sheet(String(index), 0);\r\n }\r\n return item;\r\n };\r\n\r\n let lastCode;\r\n let lastSheetIndex;\r\n let lastHelixIndex = 0;\r\n let curStructure = null;\r\n for (let i = 0, n = this._residues.length; i < n; ++i) {\r\n const curCode = ssMap._ss[i];\r\n const curResidue = this._residues[i];\r\n const curSheetIndex = ssMap._sheet[i];\r\n\r\n // expand the last structure\r\n if (curCode === lastCode && curSheetIndex === lastSheetIndex) {\r\n curResidue._secondary = curStructure;\r\n if (curStructure) {\r\n curStructure.term = curResidue;\r\n }\r\n if (curStructure instanceof Helix) {\r\n curStructure.length++;\r\n }\r\n continue;\r\n }\r\n\r\n // create a new structure\r\n const helixClass = helixClassMap[curCode];\r\n const loopType = loopMap[curCode];\r\n if (curCode === StructureType.STRAND) {\r\n const curSheet = getSheet(curSheetIndex);\r\n curStructure = new Strand(curSheet, curResidue, curResidue, 0, null, null);\r\n curSheet.addStrand(curStructure);\r\n } else if (helixClass !== undefined) {\r\n lastHelixIndex++;\r\n curStructure = new Helix(helixClass, curResidue, curResidue, lastHelixIndex, String(lastHelixIndex), '', 1);\r\n helices.push(curStructure);\r\n } else if (loopType !== undefined) {\r\n curStructure = new StructuralElement(loopType, curResidue, curResidue);\r\n } else {\r\n curStructure = null;\r\n }\r\n\r\n if (curStructure) {\r\n structures.push(curStructure);\r\n }\r\n\r\n curResidue._secondary = curStructure;\r\n\r\n lastCode = curCode;\r\n lastSheetIndex = curSheetIndex;\r\n }\r\n\r\n this._sheets = sheets.filter((_sheet) => true); // squeeze sheets array\r\n }\r\n}\r\n\r\nComplex.prototype.id = 'Complex';\r\nComplex.prototype.name = '';\r\n\r\nexport default Complex;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\nfunction pow2ceil(v) {\r\n let p = 2;\r\n v = (v - 1) >> 1;\r\n while (v) {\r\n p <<= 1;\r\n v >>= 1;\r\n }\r\n return p;\r\n}\r\n\r\n/**\r\n * Volume constructor\r\n *\r\n * @param {Object} type - Float32Array, Int8Array, etc...\r\n * @param {Object|Array} dimensions - number of data points on each axis (x, y, z)\r\n * @param {Box3} box - bounding box defining data place in metric space,\r\n * it's corners correspond to extreme data points\r\n * @param {Number} vecSize - dimension of the field data point (1 = scalar, 3 = 3D vector)\r\n * @param {Object} data - typed array of the same type as specified by the 1st parameter,\r\n * layout: point by point along X,\r\n * row by row along Y,\r\n * plane by plane along Z\r\n * @param {Number} volumeInfo - volume info values to define threshold to filter the noise\r\n */\r\n\r\nclass Volume {\r\n constructor(type, dimensions, box, vecSize, data, volumeInfo) {\r\n this._box = box.clone();\r\n this._dimVec = Math.max(Math.floor(vecSize || 1), 1);\r\n this._volumeInfo = volumeInfo;\r\n\r\n if (dimensions instanceof Array) {\r\n [this._dimX, this._dimY, this._dimZ] = dimensions;\r\n } else {\r\n this._dimX = dimensions.x;\r\n this._dimY = dimensions.y;\r\n this._dimZ = dimensions.z;\r\n }\r\n this._dimX = Math.max(Math.floor(this._dimX), 1);\r\n this._dimY = Math.max(Math.floor(this._dimY), 1);\r\n this._dimZ = Math.max(Math.floor(this._dimZ), 1);\r\n\r\n this._rowElements = this._dimVec * this._dimX;\r\n this._planeElements = this._rowElements * this._dimY;\r\n this._totalElements = this._planeElements * this._dimZ;\r\n\r\n this._data = data || utils.allocateTyped(type, this._totalElements);\r\n\r\n // override getter/setter for vector fields\r\n switch (this._dimVec) {\r\n case 1:\r\n break;\r\n\r\n case 2:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n };\r\n break;\r\n\r\n case 3:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1], this._data[idx + 2]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n this._data[idx + 2] = c;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n this._data[idx + 2] += c;\r\n };\r\n break;\r\n\r\n default:\r\n throw new Error('Volume: invalid vector dimension');\r\n }\r\n }\r\n\r\n // default getter assumes it's a scalar field\r\n getValue(x, y, z) {\r\n return this._data[x + y * this._rowElements + z * this._planeElements];\r\n }\r\n\r\n // default setter assumes it's a scalar field\r\n setValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] = val;\r\n }\r\n\r\n // default adder assumes it's a scalar field\r\n addValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] += val;\r\n }\r\n\r\n getDimensions() {\r\n return [this._dimX, this._dimY, this._dimZ];\r\n }\r\n\r\n getBox() {\r\n return this._box;\r\n }\r\n\r\n getVolumeInfo() {\r\n return this._volumeInfo;\r\n }\r\n\r\n getCellSize() {\r\n const boxSize = new THREE.Vector3();\r\n this._box.getSize(boxSize);\r\n const res = new THREE.Vector3();\r\n res.x = this._dimX > 1 ? boxSize.x / (this._dimX - 1) : 0;\r\n res.y = this._dimY > 1 ? boxSize.y / (this._dimY - 1) : 0;\r\n res.z = this._dimZ > 1 ? boxSize.z / (this._dimZ - 1) : 0;\r\n return res;\r\n }\r\n\r\n computeGradient() {\r\n if (this._dimVec !== 1) {\r\n // gradient can only be computed for scalar fields\r\n return null;\r\n }\r\n\r\n // create a 3D vector field of gradients\r\n const gradient = new Volume(Float32Array, [this._dimX, this._dimY, this._dimZ], this._box, 3);\r\n\r\n // calculate cell side lengths\r\n const vl = this.getCellSize();\r\n\r\n // gradient axis scaling values and averaging factors, to correctly\r\n // calculate the gradient for volumes with irregular cell spacing\r\n const vs = new THREE.Vector3(-0.5 / vl.x, -0.5 / vl.y, -0.5 / vl.z);\r\n\r\n // TODO Check for intended bug in VMD (min is zero)\r\n function clamp(val, min, max) {\r\n return Math.min(max, Math.max(min, val));\r\n }\r\n\r\n const xSize = this._dimX;\r\n const ySize = this._dimY;\r\n const zSize = this._dimZ;\r\n const volMap = this._data;\r\n\r\n function _voxelValue(x, y, z) {\r\n return volMap[z * xSize * ySize + y * xSize + x];\r\n }\r\n\r\n for (let zi = 0; zi < zSize; ++zi) {\r\n const zm = clamp(zi - 1, 0, zSize - 1);\r\n const zp = clamp(zi + 1, 0, zSize - 1);\r\n\r\n for (let yi = 0; yi < ySize; ++yi) {\r\n const ym = clamp(yi - 1, 0, ySize - 1);\r\n const yp = clamp(yi + 1, 0, ySize - 1);\r\n\r\n for (let xi = 0; xi < xSize; ++xi) {\r\n const xm = clamp(xi - 1, 0, xSize - 1);\r\n const xp = clamp(xi + 1, 0, xSize - 1);\r\n\r\n // Calculate the volume gradient at each grid cell.\r\n // Gradients are now stored unnormalized, since we need them in pure\r\n // form in order to draw field lines etc. Shading code will now have\r\n // to do renormalization for itself on-the-fly.\r\n\r\n // XXX this gradient is only correct for orthogonal grids, since\r\n // we're using the array index offsets rather to calculate the gradient\r\n // rather than voxel coordinate offsets. This will have to be\r\n // re-worked for non-orthogonal datasets.\r\n\r\n gradient.setValue(\r\n xi,\r\n yi,\r\n zi,\r\n (_voxelValue(xp, yi, zi) - _voxelValue(xm, yi, zi)) * vs.x,\r\n (_voxelValue(xi, yp, zi) - _voxelValue(xi, ym, zi)) * vs.y,\r\n (_voxelValue(xi, yi, zp) - _voxelValue(xi, yi, zm)) * vs.z,\r\n );\r\n }\r\n }\r\n }\r\n\r\n return gradient;\r\n }\r\n\r\n normalize() {\r\n const data = this._data;\r\n\r\n // get min/max\r\n let min = data[0];\r\n let max = data[0];\r\n for (let i = 1; i < data.length; ++i) {\r\n min = Math.min(min, data[i]);\r\n max = Math.max(max, data[i]);\r\n }\r\n\r\n const d = 1.0 / (max - min);\r\n if (d === 0) {\r\n return;\r\n }\r\n\r\n // normalize\r\n for (let i = 0; i < data.length; ++i) {\r\n data[i] = d * (data[i] - min);\r\n }\r\n }\r\n\r\n getTiledTextureStride() {\r\n return [this._dimX + 2, this._dimY + 2];\r\n }\r\n\r\n buildTiledTexture() {\r\n let tilesX = Math.ceil(Math.sqrt(this._dimZ * this._dimY / this._dimX));\r\n\r\n let width = tilesX * (this._dimX + 2) - 1;\r\n width = pow2ceil(width);\r\n tilesX = Math.floor(width / (this._dimX + 2));\r\n\r\n const tilesY = Math.ceil(this._dimZ / tilesX);\r\n let height = tilesY * (this._dimY + 2) - 1;\r\n height = pow2ceil(height);\r\n\r\n const data = new Uint8Array(width * height);\r\n\r\n let src;\r\n let dst;\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // process each pixel row of this tile row\r\n for (let row = 0; row < this._dimY; ++row) {\r\n src = tileRow * tilesX * this._planeElements + row * this._rowElements;\r\n dst = width * (tileRow * (this._dimY + 2) + row);\r\n // copy a series of rows through several XY planes\r\n for (let t = 0; t < tilesX; ++t) {\r\n // copy one row of one XY plane\r\n for (let x = 0; x < this._dimX; ++x) {\r\n data[dst++] = 255.0 * this._data[src++];\r\n }\r\n\r\n // repeat last pixel of previous tile\r\n data[dst++] = 255.0 * this._data[src - 1];\r\n\r\n if (t < tilesX - 1) {\r\n // skip to the same row of next XY plane\r\n src += this._planeElements - this._rowElements;\r\n // repeat first pixel of next tile\r\n data[dst++] = 255.0 * this._data[src];\r\n }\r\n }\r\n }\r\n }\r\n\r\n // fill pixels between tile rows with copy of edge pixels\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // copy last pixel row of this tile row to the following pixel row of the texture\r\n src = width * (tileRow * (this._dimY + 2) + this._dimY - 1);\r\n dst = src + width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n if (tileRow < tilesY - 1) {\r\n // copy first pixel row of next tile row to the preceding pixel row of the texture\r\n src = width * (tileRow + 1) * (this._dimY + 2);\r\n dst = src - width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n }\r\n }\r\n\r\n const texture = new THREE.DataTexture(\r\n data,\r\n width,\r\n height,\r\n THREE.LuminanceFormat,\r\n THREE.UnsignedByteType,\r\n THREE.UVMapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.LinearFilter,\r\n THREE.LinearFilter,\r\n );\r\n texture.needsUpdate = true;\r\n return texture;\r\n }\r\n\r\n /* ********************************************************************************\r\n *\r\n * Methods that provide direct access to internal array (for better performance)\r\n *\r\n ******************************************************************************** */\r\n\r\n getData() {\r\n return this._data;\r\n }\r\n\r\n getDirectIdx(x, y, z) {\r\n return x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n }\r\n\r\n getStrideX() {\r\n return this._dimVec;\r\n }\r\n\r\n getStrideY() {\r\n return this._rowElements;\r\n }\r\n\r\n getStrideZ() {\r\n return this._planeElements;\r\n }\r\n}\r\n\r\nVolume.prototype.id = 'Volume';\r\n\r\nexport default Volume;\r\n","/**\r\n * Residue Molecule.\r\n *\r\n * @param {Complex} complex - Molecular complex this Molecule belongs to.\r\n * @param {String} name - Molecule's name.\r\n * @param {Integer} index - Molecule's index in file.\r\n *\r\n * @exports Molecule\r\n * @constructor\r\n */\r\nclass Molecule {\r\n constructor(complex, name, index) {\r\n this.complex = complex;\r\n this.name = name || '';\r\n this.residues = [];\r\n this.mask = 1 | 0;\r\n this.index = index || -1; // start with 1\r\n }\r\n\r\n forEachResidue(process) {\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this.mask = mask;\r\n }\r\n}\r\n\r\nexport default Molecule;\r\n","import Atom from './chem/Atom';\r\nimport Element from './chem/Element';\r\nimport Bond from './chem/Bond';\r\nimport Residue from './chem/Residue';\r\nimport ResidueType from './chem/ResidueType';\r\nimport Chain from './chem/Chain';\r\nimport Helix from './chem/Helix';\r\nimport Strand from './chem/Strand';\r\nimport Sheet from './chem/Sheet';\r\nimport SGroup from './chem/SGroup';\r\nimport Assembly from './chem/Assembly';\r\nimport Complex from './chem/Complex';\r\nimport Volume from './chem/Volume';\r\nimport VoxelWorld from './chem/VoxelWorld';\r\nimport selectors from './chem/selectors';\r\nimport Molecule from './chem/Molecule';\r\n\r\nexport default {\r\n Atom,\r\n Element,\r\n Bond,\r\n Residue,\r\n ResidueType,\r\n Chain,\r\n Helix,\r\n Strand,\r\n Sheet,\r\n SGroup,\r\n Assembly,\r\n Complex,\r\n Volume,\r\n VoxelWorld,\r\n selectors,\r\n Molecule,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\n\r\nclass CSS2DObject extends THREE.Object3D {\r\n constructor(element) {\r\n super();\r\n const self = this;\r\n this._element = element;\r\n this._element.style.position = 'absolute';\r\n this.addEventListener('removed', () => {\r\n if (self._element.parentNode !== null) {\r\n self._element.parentNode.removeChild(self._element);\r\n }\r\n });\r\n }\r\n\r\n getElement() {\r\n return this._element;\r\n }\r\n\r\n /**\r\n * Sets label transparency.\r\n *\r\n * @param {number} transp - in [0; 1] 1 means fully transparent\r\n */\r\n setTransparency(transp) {\r\n const el = this.getElement();\r\n if (el === null) {\r\n return;\r\n }\r\n if (transp === 1.0) {\r\n el.style.display = 'none';\r\n return;\r\n }\r\n el.style.display = 'inline';\r\n const op = 1.0 - transp;\r\n const top = op.toString();\r\n const op100 = op * 100;\r\n el.style.opacity = top;\r\n el.style.filter = `alpha(opacity=${op100})`; // IE fallback\r\n }\r\n\r\n clone() {\r\n const obj = new CSS2DObject(this._element);\r\n obj.copy(this);\r\n return obj;\r\n }\r\n}\r\n\r\nexport default CSS2DObject;\r\n","import * as THREE from 'three';\r\n\r\nclass RCGroup extends THREE.Group {\r\n raycast(raycaster, intersects) {\r\n if (!this.visible) {\r\n return;\r\n }\r\n\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n children[i].raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].enableSubset) {\r\n children[i].enableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].disableSubset) {\r\n children[i].disableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n isEmpty() {\r\n return this.children.length === 0;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].updateToFrame) {\r\n children[i].updateToFrame(frameData);\r\n }\r\n }\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n Array.prototype.push.apply(totalSubset, children[i].getSubset(mask, innerOnly));\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default RCGroup;\r\n","/* eslint-disable no-magic-numbers */\r\nimport * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport CSS2DObject from './CSS2DObject';\r\nimport RCGroup from './RCGroup';\r\nimport vertexScreenQuadShader from './shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromTex from './shaders/ScreenQuadFromTex.frag';\r\nimport fragmentScreenQuadFromTexWithDistortion from './shaders/ScreenQuadFromTexWithDistortion.frag';\r\n\r\nconst LAYERS = {\r\n DEFAULT: 0, VOLUME: 1, TRANSPARENT: 2, PREPASS_TRANSPARENT: 3, VOLUME_BFPLANE: 4, COLOR_FROM_POSITION: 5, SHADOWMAP: 6,\r\n};\r\n\r\nconst SELECTION_LAYERS = [ // These layers, that are used in the selection by ray casting\r\n LAYERS.DEFAULT, LAYERS.TRANSPARENT,\r\n];\r\n\r\nTHREE.Object3D.prototype.resetTransform = function () {\r\n this.position.set(0, 0, 0);\r\n this.quaternion.set(0, 0, 0, 1);\r\n this.scale.set(1, 1, 1);\r\n};\r\n\r\n// update world matrix of this object and all its ancestors\r\nTHREE.Object3D.prototype.updateMatrixWorldRecursive = function () {\r\n if (this.parent != null) {\r\n this.parent.updateMatrixWorldRecursive();\r\n }\r\n this.updateMatrixWorld();\r\n};\r\n// add object to parent, saving objects' world transform\r\nTHREE.Object3D.prototype.addSavingWorldTransform = (function () {\r\n const _worldMatrixInverse = new THREE.Matrix4();\r\n\r\n return function (object) {\r\n if (object instanceof THREE.Object3D) {\r\n _worldMatrixInverse.copy(this.matrixWorld).invert();\r\n _worldMatrixInverse.multiply(object.matrixWorld);\r\n object.matrix.copy(_worldMatrixInverse);\r\n object.matrix.decompose(object.position, object.quaternion, object.scale);\r\n this.add(object);\r\n }\r\n };\r\n}());\r\n\r\n// render a tiny transparent quad in the center of the screen\r\nTHREE.WebGLRenderer.prototype.renderDummyQuad = (function () {\r\n const _material = new THREE.MeshBasicMaterial({ transparent: true, opacity: 0.0, depthWrite: false });\r\n\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(0.01, 0.01), _material);\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function () {\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuad = (function () {\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(1.0, 1.0));\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function (material) {\r\n _quad.material = material;\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.isIdentity = (function () {\r\n const identity = new THREE.Matrix4();\r\n return function () {\r\n return identity.equals(this);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.applyToPointsArray = function (array, stride, w) {\r\n if (!array || !stride || stride < 3) {\r\n return array;\r\n }\r\n w = w || 0; // use point as normal by default\r\n const e = this.elements;\r\n for (let i = 0; i < array.length; i += stride) {\r\n const x = array[i];\r\n const y = array[i + 1];\r\n const z = array[i + 2];\r\n\r\n const persp = 1 / (e[3] * x + e[7] * y + e[11] * z + e[15]);\r\n\r\n array[i] = (e[0] * x + e[4] * y + e[8] * z + e[12] * w) * persp;\r\n array[i + 1] = (e[1] * x + e[5] * y + e[9] * z + e[13] * w) * persp;\r\n array[i + 2] = (e[2] * x + e[6] * y + e[10] * z + e[14] * w) * persp;\r\n }\r\n return array;\r\n};\r\n\r\nclass ScreenQuadMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n if (params.uniforms === undefined) {\r\n params.uniforms = {};\r\n }\r\n params.uniforms.srcTex = { type: 't', value: null };\r\n params.vertexShader = vertexScreenQuadShader;\r\n params.transparent = false;\r\n params.depthTest = false;\r\n params.depthWrite = false;\r\n super(params);\r\n }\r\n}\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTex = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { opacity: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTex,\r\n transparent: true,\r\n });\r\n\r\n return function (srcTex, opacity) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.transparent = (opacity < 1.0);\r\n _material.uniforms.opacity.value = opacity;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTexWithDistortion = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { coef: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTexWithDistortion,\r\n });\r\n\r\n return function (srcTex, coef) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.uniforms.coef.value = coef;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\n/**\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setMinimalFov = function (angle) {\r\n if (this.aspect >= 1.0) {\r\n this.fov = angle;\r\n } else {\r\n this.fov = THREE.MathUtils.radToDeg(2 * Math.atan(Math.tan(THREE.MathUtils.degToRad(angle) * 0.5) / this.aspect));\r\n }\r\n};\r\n\r\n/**\r\n * @param {THREE.PerspectiveCamera} camera - Base camera for this stereo camera.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.StereoCamera.prototype.updateHalfSized = function (camera, angle) {\r\n const originalAspect = camera.aspect;\r\n const originalFov = camera.fov;\r\n\r\n camera.aspect = originalAspect / 2.0;\r\n camera.setMinimalFov(angle);\r\n camera.updateProjectionMatrix();\r\n\r\n this.update(camera);\r\n\r\n camera.aspect = originalAspect;\r\n camera.fov = originalFov;\r\n camera.updateProjectionMatrix();\r\n};\r\n\r\n/**\r\n * @param {number} radius - Radius of bounding sphere in angstroms to fit on screen.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setDistanceToFit = function (radius, angle) {\r\n this.position.z = radius / Math.sin(0.5 * THREE.MathUtils.degToRad(angle));\r\n};\r\n\r\n/**\r\n * @param {RCGroup} gfxObj - All objects on scene.\r\n * @param {THREE.PerspectiveCamera} camera - Camera used for rendering.\r\n * @param {number} clipPlane - Distance to clip plane.\r\n * @param {number} fogFarPlane - Distance to fog far plane.\r\n */\r\nTHREE.Raycaster.prototype.intersectVisibleObject = function (gfxObj, camera, clipPlane, fogFarPlane) {\r\n const intersects = this.intersectObject(gfxObj, false);\r\n if (intersects.length === 0) {\r\n return null;\r\n }\r\n\r\n // find point closest to camera that doesn't get clipped by camera near plane or clipPlane (if it exists)\r\n const nearPlane = Math.min(camera.near, clipPlane);\r\n let i;\r\n let p = intersects[0];\r\n const v = new THREE.Vector3();\r\n for (i = 0; i < intersects.length; ++i) {\r\n p = intersects[i];\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -nearPlane) {\r\n break;\r\n }\r\n }\r\n if (i === intersects.length) {\r\n return null;\r\n }\r\n\r\n // check that selected intersection point is not clipped by camera far plane or occluded by fog (if it exists)\r\n const farPlane = Math.min(camera.far, fogFarPlane);\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -farPlane) {\r\n return null;\r\n }\r\n return p;\r\n};\r\n\r\nTHREE.Matrix4.prototype.extractScale = (function () {\r\n const _v = new THREE.Vector3();\r\n\r\n return function (scale) {\r\n if (scale === undefined) {\r\n logger.debug('extractScale(): new is too expensive operation to do it on-the-fly');\r\n scale = _v.clone();\r\n }\r\n\r\n const te = this.elements;\r\n scale.x = _v.set(te[0], te[1], te[2]).length();\r\n scale.y = _v.set(te[4], te[5], te[6]).length();\r\n scale.z = _v.set(te[8], te[9], te[10]).length();\r\n\r\n // if determine is negative, we need to invert one scale\r\n const det = this.determinant();\r\n if (det < 0) {\r\n scale.x = -scale.x;\r\n }\r\n return scale;\r\n };\r\n}());\r\n\r\nfunction _calcCylinderMatrix(posBegin, posEnd, radius) {\r\n const posCenter = posBegin.clone().lerp(posEnd, 0.5);\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(radius, posBegin.distanceTo(posEnd), radius);\r\n\r\n const matRotHalf = new THREE.Matrix4();\r\n matRotHalf.makeRotationX(Math.PI / 2);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n const vUp = new THREE.Vector3(0, 1, 0);\r\n matRotLook.lookAt(posCenter, posEnd, vUp);\r\n\r\n matRotLook.multiply(matRotHalf);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(posCenter);\r\n return matRotLook;\r\n}\r\n\r\nfunction _calcChunkMatrix(eye, target, up, rad) {\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(rad.x, rad.y, 0);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n matRotLook.lookAt(eye, target, up);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(eye);\r\n\r\n return matRotLook;\r\n}\r\n\r\nfunction _groupHasGeometryToRender(group) {\r\n let hasGeoms = false;\r\n group.traverse((node) => {\r\n if (node.hasOwnProperty('geometry') || node instanceof CSS2DObject) {\r\n hasGeoms = true;\r\n }\r\n });\r\n return hasGeoms;\r\n}\r\n\r\nfunction _buildDistorionMesh(widthSegments, heightSegements, coef) {\r\n // solve equation r_u = r_d * (1 + k * r_d^2)\r\n // for r_d using iterations\r\n // takes: r_u^2\r\n // returns: r_d / r_u factor that can be used to distort point coords\r\n function calcInverseBarrel(r2) {\r\n const epsilon = 1e-5;\r\n let prevR2 = 0.0;\r\n let curR2 = r2;\r\n let dr = 1.0;\r\n while (Math.abs(curR2 - prevR2) > epsilon) {\r\n dr = 1.0 + coef * curR2;\r\n prevR2 = curR2;\r\n curR2 = r2 / (dr * dr);\r\n }\r\n\r\n return 1.0 / dr;\r\n }\r\n\r\n const geo = new THREE.PlaneGeometry(2.0, 2.0, widthSegments, heightSegements);\r\n\r\n const pos = geo.getAttribute('position');\r\n for (let i = 0; i < pos.count; ++i) {\r\n const x = pos.array[3 * i];\r\n const y = pos.array[3 * i + 1];\r\n const c = calcInverseBarrel(x * x + y * y);\r\n pos.setXY(i, c * x, c * y);\r\n }\r\n\r\n return geo;\r\n}\r\n\r\nTHREE.BufferAttribute.prototype.copyAtList = function (attribute, indexList) {\r\n console.assert(\r\n this.itemSize === attribute.itemSize,\r\n 'DEBUG: BufferAttribute.copyAtList buffers have different item size.',\r\n );\r\n const { itemSize } = this;\r\n for (let i = 0, n = indexList.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n this.array[i * itemSize + j] = attribute.array[indexList[i] * itemSize + j];\r\n }\r\n }\r\n return this;\r\n};\r\n\r\nfunction fillArray(array, value, startIndex, endIndex) {\r\n startIndex = (typeof startIndex !== 'undefined') ? startIndex : 0;\r\n endIndex = (typeof endIndex !== 'undefined') ? endIndex : array.length;\r\n for (let i = startIndex; i < endIndex; ++i) {\r\n array[i] = value;\r\n }\r\n}\r\n\r\n/** @param {THREE.Object3D} object - Parent object. */\r\nfunction removeChildren(object) {\r\n const { children } = object;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n child.parent = null;\r\n child.dispatchEvent({ type: 'removed' });\r\n }\r\n object.children = [];\r\n}\r\n\r\nfunction clearTree(object) {\r\n object.traverse((obj) => {\r\n if (obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line) {\r\n obj.geometry.dispose();\r\n }\r\n });\r\n removeChildren(object);\r\n}\r\n\r\nfunction destroyObject(object) {\r\n clearTree(object);\r\n if (object.parent) {\r\n object.parent.remove(object);\r\n } else {\r\n object.dispatchEvent({ type: 'removed' });\r\n }\r\n}\r\n\r\nfunction belongToSelectLayers(object) {\r\n for (let i = 0; i < SELECTION_LAYERS.length; i++) {\r\n if (((object.layers.mask >> SELECTION_LAYERS[i]) & 1) === 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n}\r\n\r\nfunction processObjRenderOrder(root, idMaterial) {\r\n // set renderOrder to 0 for Backdrop and to 1 in other cases to render Backdrop earlier all other materials\r\n const renderOrder = +(idMaterial !== 'BA');\r\n root.traverse((object) => {\r\n if (object.isGroup) {\r\n object.renderOrder = renderOrder;\r\n }\r\n });\r\n}\r\n\r\nfunction applySelectionMaterial(geo) {\r\n geo.traverse((node) => {\r\n if ('material' in node) {\r\n node.material = node.material.clone(true);\r\n // using z-offset to magically fix selection rendering artifact (on z-sprites)\r\n node.material.setValues({\r\n depthFunc: THREE.LessEqualDepth,\r\n overrideColor: true,\r\n fog: false,\r\n lights: false,\r\n shadowmap: false,\r\n });\r\n node.material.setUberOptions({ fixedColor: new THREE.Color(0xFFFF00), zOffset: -1e-6 });\r\n }\r\n });\r\n}\r\n\r\nfunction getMiddlePoint(point1, point2, optionalTarget) {\r\n const result = optionalTarget || new THREE.Vector3();\r\n\r\n result.set(0, 0, 0);\r\n result.addScaledVector(point1, 0.5);\r\n result.addScaledVector(point2, 0.5);\r\n\r\n return result;\r\n}\r\n\r\n// Monkey-patch for \"InstancedBufferGeometry.instanceCount becomes undefined after copy()\"\r\n// https://github.com/mrdoob/three.js/issues/22151\r\nconst _oldInstancedBufferGeometryCopy = THREE.InstancedBufferGeometry.prototype.copy;\r\n\r\nTHREE.InstancedBufferGeometry.prototype.copy = function (source) {\r\n _oldInstancedBufferGeometryCopy.call(this, source);\r\n if (this.instanceCount === undefined) {\r\n this.instanceCount = Infinity;\r\n }\r\n};\r\n\r\nexport default {\r\n calcCylinderMatrix: _calcCylinderMatrix,\r\n calcChunkMatrix: _calcChunkMatrix,\r\n groupHasGeometryToRender: _groupHasGeometryToRender,\r\n buildDistorionMesh: _buildDistorionMesh,\r\n RCGroup,\r\n fillArray,\r\n clearTree,\r\n destroyObject,\r\n belongToSelectLayers,\r\n processObjRenderOrder,\r\n applySelectionMaterial,\r\n getMiddlePoint,\r\n LAYERS,\r\n};\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfx/gfxutils';\r\n\r\nconst _defaultBoundaries = {\r\n boundingBox: new THREE.Box3(new THREE.Vector3(-1, -1, -1), new THREE.Vector3(1, 1, 1)),\r\n boundingSphere: new THREE.Sphere(new THREE.Vector3(0, 0, 0), 1),\r\n};\r\n\r\nclass Visual extends gfxutils.RCGroup {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this.name = name;\r\n this._dataSource = dataSource;\r\n }\r\n\r\n release() {\r\n if (this.parent) {\r\n this.parent.remove(this);\r\n }\r\n }\r\n\r\n getDataSource() {\r\n return this._dataSource;\r\n }\r\n\r\n getBoundaries() {\r\n return _defaultBoundaries;\r\n }\r\n}\r\n\r\nexport default Visual;\r\n","function _ensureArray(x) {\r\n if (x === null || x === undefined || Array.isArray(x)) {\r\n return x;\r\n }\r\n return [x];\r\n}\r\n\r\n/** An indexed list of objects or classes. */\r\nclass EntityList {\r\n /**\r\n * Create a list of objects.\r\n * The objects can be indexed by one or more properties for the later retrieval.\r\n *\r\n * @param {!Array=} entities A list of objects to automatically register at creation time.\r\n * @param {!Array=} indices A list of property names to use for case-insensitive indexing.\r\n * By default, a single `.id` property is used.\r\n * @see EntityList#register\r\n */\r\n constructor(entities = [], indices = ['id']) {\r\n this._list = [];\r\n this._dict = {};\r\n this._indices = [...indices];\r\n this._indices.forEach((index) => {\r\n this._dict[index] = {};\r\n });\r\n\r\n entities.forEach((entity) => this.register(entity));\r\n }\r\n\r\n /**\r\n * Add a value to the end of a list.\r\n * The list will contain only one copy of the value.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromList\r\n * @see EntityList.registerInDict\r\n */\r\n static registerInList(list, value) {\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n }\r\n\r\n /**\r\n * Remove a value from a list if it is there.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to remove.\r\n * @see EntityList.registerInList\r\n */\r\n static unregisterFromList(list, value) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n }\r\n\r\n /**\r\n * Add a value to a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromDict\r\n * @see EntityList.registerInList\r\n */\r\n static registerInDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key] = dict[key] || [];\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Remove a value from a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.registerInDict\r\n */\r\n static unregisterFromDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key];\r\n if (list) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n if (list.length === 0) {\r\n delete dict[key];\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Add an entity to this list.\r\n *\r\n * @param {!Object} entity An object or a class to register. The object must include all\r\n * properties specified as indices on construction.\r\n * @see EntityList#unregister\r\n */\r\n register(entity) {\r\n EntityList.registerInList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.registerInDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * Remove an entity from this list.\r\n *\r\n * @param {!Object} entity An object or a class to unregister. The object may be\r\n * missing from the list but it must include all properties specified as indices\r\n * on construction.\r\n * @see EntityList#register\r\n */\r\n unregister(entity) {\r\n EntityList.unregisterFromList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.unregisterFromDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * An ordered list of all registered entities.\r\n * It is a read-only copy, use {@link EntityList#register} and {@link EntityList#unregister}\r\n * to modify it.\r\n *\r\n * @type {!Array}\r\n */\r\n get all() {\r\n return [...this._list];\r\n }\r\n\r\n /**\r\n * The first registered entity.\r\n * Use it if you do not care which entity you are referring to.\r\n *\r\n * @type {Object=}\r\n */\r\n get first() {\r\n return this._list[0];\r\n }\r\n\r\n /**\r\n * Retrieve a list of keys for the index.\r\n *\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {!Array} An unordered list of keys in the index, i.e. particular property\r\n * values for all registered entities.\r\n */\r\n keys(index) {\r\n return Object.keys(this._dict[index || this._indices[0]]);\r\n }\r\n\r\n /**\r\n * Retrieve an entity by its key.\r\n *\r\n * @param {string} key A case-insensitive property value to look-up.\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {Object=} An object registered in the index under the key. If there are multiple\r\n * objects under the same key, the first one is returned.\r\n */\r\n get(key, index) {\r\n const dict = this._dict[index || this._indices[0]];\r\n if (dict) {\r\n const values = dict[key && key.toLowerCase()];\r\n return values && values.length > 0 ? values[0] : undefined;\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nexport default EntityList;\r\n","import settings from '../settings';\r\nimport logger from './logger';\r\n\r\nfunction makeContextDependent(prototype) {\r\n Object.defineProperties(prototype, {\r\n logger: {\r\n get() {\r\n return this.context && this.context.logger ? this.context.logger : logger;\r\n },\r\n },\r\n settings: {\r\n get() {\r\n return this.context && this.context.settings ? this.context.settings : settings;\r\n },\r\n },\r\n });\r\n}\r\n\r\nexport default makeContextDependent;\r\n","import * as THREE from 'three';\r\n\r\nclass CollisionSphere {\r\n constructor(position, radius) {\r\n this._position = position;\r\n this._radius = radius;\r\n }\r\n\r\n static _sphere = new THREE.Sphere();\r\n\r\n raycast(raycaster) {\r\n const sphere = CollisionSphere._sphere;\r\n sphere.set(this._position, this._radius);\r\n\r\n const p = new THREE.Vector3();\r\n if (raycaster.ray.intersectSphere(sphere, p)) {\r\n return {\r\n distance: raycaster.ray.origin.distanceTo(p),\r\n point: p,\r\n };\r\n }\r\n return null;\r\n }\r\n}\r\n\r\nconst SphereCollisionGeo = (base) => class extends base {\r\n constructor(count, ...args) {\r\n super(...args);\r\n this._objects = new Array(count);\r\n this.boundingSphere = null;\r\n this.boundingBox = null;\r\n }\r\n\r\n setSphere(idx, position, radius) {\r\n this._objects[idx] = new CollisionSphere(position, radius);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n // TODO raycast with bounding sphere? How to deal with updates?\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const inters = this._objects[i].raycast(raycaster);\r\n if (inters) {\r\n inters.chunkIdx = i;\r\n intersects.push(inters);\r\n }\r\n }\r\n }\r\n\r\n computeBoundingBox() {\r\n const objects = this._objects;\r\n let { boundingBox } = this;\r\n if (boundingBox === null) {\r\n this.boundingBox = boundingBox = new THREE.Box3();\r\n }\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n boundingBox.expandByPoint(objects[i]._position);\r\n }\r\n }\r\n\r\n computeBoundingSphere() {\r\n this.computeBoundingBox();\r\n const objects = this._objects;\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n const pos = objects[i]._position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n if (this.boundingSphere === null) {\r\n this.boundingSphere = new THREE.Sphere();\r\n }\r\n this.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n};\r\nexport default SphereCollisionGeo;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst tmpColor = new THREE.Color();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\nclass InstancedSpheresGeometry extends SphereCollisionGeo(THREE.InstancedBufferGeometry) {\r\n constructor(spheresCount, sphereComplexity, useZSprites) {\r\n super(spheresCount);\r\n this._sphGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new THREE.SphereBufferGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI);\r\n this._init(spheresCount, this._sphGeometry);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n setArrayXYZW(this._offsets, itemIdx * OFFSET_SIZE, itemPos.x, itemPos.y, itemPos.z, itemRad);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n\r\n setColor(itemIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n setArrayXYZ(this._colors, itemIdx * COLOR_SIZE, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('offset').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[chunkIndices[i]] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._sphGeometry);\r\n\r\n copySubArrays(this._offsets, geom._offsets, chunkIndices, OFFSET_SIZE);\r\n copySubArrays(this._colors, geom._colors, chunkIndices, COLOR_SIZE);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(spheresCount, sphereGeo) {\r\n this.copy(sphereGeo);\r\n\r\n this._offsets = utils.allocateTyped(Float32Array, spheresCount * OFFSET_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, spheresCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('offset', new THREE.InstancedBufferAttribute(this._offsets, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._colors, COLOR_SIZE, false, 1));\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(alpha, 1, false, 1));\r\n }\r\n}\r\nexport default InstancedSpheresGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VEC_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n */\r\n\r\nclass ChunkedObjectsGeometry extends THREE.BufferGeometry {\r\n constructor(chunkGeo, chunksCount) {\r\n super();\r\n\r\n if (this.constructor === ChunkedObjectsGeometry) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n\r\n this._chunkGeo = chunkGeo;\r\n\r\n this._init(chunkGeo, chunksCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('normal').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n const idx = i * VEC_SIZE;\r\n colors[idx] = tmpColor.r;\r\n colors[idx + 1] = tmpColor.g;\r\n colors[idx + 2] = tmpColor.b;\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n _.fill(alphaArr, value, left, left + chunkSize);\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n // use THREE.Mesh raycasting interface for the Geometry. The Mesh is\r\n // created with existed geometry and default material, so it doesn't slowdown.\r\n const mesh = new THREE.Mesh();\r\n mesh.geometry = this;\r\n mesh.raycast(raycaster, inters);\r\n\r\n const facesPerChunk = this._chunkGeo.index.count / 3;\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('faceIndex')) {\r\n continue;\r\n }\r\n inters[i].chunkIdx = Math.floor(inters[i].faceIndex / facesPerChunk);\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.BufferGeometry();\r\n this._init.call(geom, this._chunkGeo, instanceCount);\r\n\r\n const srcPos = this._positions;\r\n const srcNorm = this._normals;\r\n const srcColor = this._colors;\r\n\r\n const dstPos = geom._positions;\r\n const dstNorm = geom._normals;\r\n const dstColor = geom._colors;\r\n\r\n const chunkSize = this._chunkSize * VEC_SIZE;\r\n\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const ptIdxBegin = chunkIndices[i] * chunkSize;\r\n const ptIdxEnd = ptIdxBegin + chunkSize;\r\n dstPos.set(srcPos.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstNorm.set(srcNorm.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstColor.set(srcColor.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n }\r\n\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(chunkGeo, chunksCount) {\r\n const chunkSize = this._chunkSize = chunkGeo.attributes.position.count;\r\n const chunkIndex = chunkGeo.index.array;\r\n const chunkIndexSize = chunkIndex.length;\r\n const pointsCount = this._chunkSize * chunksCount;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n const indexSize = chunkIndexSize * chunksCount;\r\n const index = this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, indexSize);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._normals = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n for (let i = 0; i < chunksCount; ++i) {\r\n const offset = i * chunkIndexSize;\r\n const posOffset = i * chunkSize;\r\n index.set(chunkIndex, offset);\r\n for (let j = 0; j < chunkIndexSize; ++j) {\r\n index[offset + j] += posOffset;\r\n }\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, VEC_SIZE));\r\n this.setAttribute('normal', new THREE.BufferAttribute(this._normals, VEC_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, VEC_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n }\r\n}\r\nexport default ChunkedObjectsGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst VEC_SIZE = 3;\r\n\r\nclass SimpleSpheresGeometry extends SphereCollisionGeo(ChunkedObjectsGeometry) {\r\n constructor(spheresCount, sphereComplexity) {\r\n const sphGeometry = new THREE.SphereBufferGeometry(\r\n 1,\r\n sphereComplexity * 2,\r\n sphereComplexity,\r\n 0,\r\n Math.PI * 2,\r\n 0,\r\n Math.PI,\r\n );\r\n super(spheresCount, sphGeometry, spheresCount);\r\n\r\n const normals = this._normals;\r\n const geoNormals = sphGeometry.attributes.normal.array;\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._tmpPositions = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n for (let i = 0; i < spheresCount; ++i) {\r\n normals.set(geoNormals, chunkSize * VEC_SIZE * i);\r\n }\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n const tmpPos = this._tmpPositions;\r\n const chunkSize = this._chunkSize;\r\n const geoPos = this._chunkPos;\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n const idx = i * 3;\r\n tmpPos[idx] = itemPos.x + geoPos[idx] * itemRad;\r\n tmpPos[idx + 1] = itemPos.y + geoPos[idx + 1] * itemRad;\r\n tmpPos[idx + 2] = itemPos.z + geoPos[idx + 2] * itemRad;\r\n }\r\n\r\n this._positions.set(tmpPos, chunkSize * itemIdx * VEC_SIZE);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n}\r\nexport default SimpleSpheresGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst centerPos = new THREE.Vector3();\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass Simple2CCylindersGeometry extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, 2 * instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const firstOffset = chunkSize * 2 * itemIdx * VEC_SIZE;\r\n const secondOffset = firstOffset + chunkSize * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n centerPos.lerpVectors(botPos, topPos, 0.5);\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, centerPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, firstOffset);\r\n\r\n // now shift center to get another part of the cylinder\r\n centerPos.sub(botPos);\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpArray[idx] += centerPos.x;\r\n tmpArray[idx + 1] += centerPos.y;\r\n tmpArray[idx + 2] += centerPos.z;\r\n }\r\n this._positions.set(tmpArray, secondOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, firstOffset);\r\n this._normals.set(tmpArray, secondOffset);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const first = 2 * itemIdx;\r\n super.setColor(first, colorVal1);\r\n\r\n const second = first + 1;\r\n super.setColor(second, colorVal2);\r\n }\r\n}\r\n\r\nexport default Simple2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_POINTS_COUNT_16BIT = 65536;\r\nconst PTS_PER_TRIANGLE = 3;\r\n\r\nclass CylinderBufferGeometry extends THREE.BufferGeometry {\r\n constructor(\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n ) {\r\n super();\r\n\r\n const thetaStart = 0;\r\n const thetaLength = 2 * Math.PI;\r\n\r\n this.type = 'CylinderBufferGeometry';\r\n\r\n this.parameters = {\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n };\r\n\r\n const hasTop = openEnded === false && radiusTop > 0;\r\n const hasBottom = openEnded === false && radiusBottom > 0;\r\n const vertexCount = (heightSegments + 1) * radialSegments\r\n + hasTop * (radialSegments + 1)\r\n + hasBottom * (radialSegments + 1);\r\n const facesCount = (2 * heightSegments + hasTop + hasBottom) * radialSegments;\r\n\r\n const heightHalf = height / 2;\r\n\r\n /* eslint-disable no-magic-numbers */\r\n const positions = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const normals = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const indices = new THREE.Uint16BufferAttribute(utils.allocateTyped(Uint16Array, facesCount * PTS_PER_TRIANGLE), 1);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n const uvs = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 2), 2);\r\n console.assert(vertexCount < MAX_POINTS_COUNT_16BIT, 'DEBUG: Cylinder Geometry has too many vertices (65536 max).');\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n const tanTheta = -(radiusBottom - radiusTop) / height;\r\n\r\n // setup cylinder data\r\n for (let y = 0; y <= heightSegments; y++) {\r\n // faces\r\n if (y !== heightSegments) {\r\n for (let i = 0; i < radialSegments; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + radialSegments + i;\r\n const v3 = currVtxIdx + radialSegments + ((i + 1) % radialSegments);\r\n const v4 = currVtxIdx + ((i + 1) % radialSegments);\r\n\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n // vertices\r\n const v = y / heightSegments;\r\n const radius = v * (radiusBottom - radiusTop) + radiusTop;\r\n\r\n for (let x = 0; x < radialSegments; x++) {\r\n const u = x / radialSegments;\r\n\r\n const vx = radius * Math.sin(u * thetaLength + thetaStart);\r\n const vy = v * height - heightHalf;\r\n const vz = radius * Math.cos(u * thetaLength + thetaStart);\r\n\r\n const normal = new THREE.Vector3(\r\n vx,\r\n Math.sqrt(vx * vx + vz * vz) * tanTheta,\r\n vz,\r\n ).normalize();\r\n\r\n positions.setXYZ(currVtxIdx, vx, vy, vz);\r\n normals.setXYZ(currVtxIdx, normal.x, normal.y, normal.z);\r\n uvs.setXY(currVtxIdx, u, v);\r\n ++currVtxIdx;\r\n }\r\n }\r\n\r\n // top cap\r\n if (hasTop) {\r\n const startTIdx = currVtxIdx;\r\n const lastIdx = currVtxIdx + radialSegments;\r\n for (let fTIdx = 0; fTIdx < radialSegments; ++fTIdx) {\r\n const currSrcIdx = currVtxIdx - radialSegments;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcIdx),\r\n positions.getY(currSrcIdx),\r\n positions.getZ(currSrcIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n\r\n const nextTVtx = startTIdx + ((fTIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, currVtxIdx, nextTVtx, lastIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n ++currVtxIdx;\r\n }\r\n\r\n // bottom cap\r\n if (hasBottom) {\r\n const startBIdx = currVtxIdx;\r\n const lastBIdx = currVtxIdx + radialSegments;\r\n for (let fBIdx = 0; fBIdx < radialSegments; ++fBIdx) {\r\n const currSrcBIdx = fBIdx;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcBIdx),\r\n positions.getY(currSrcBIdx),\r\n positions.getZ(currSrcBIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n\r\n const nextBVtx = startBIdx + ((fBIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, nextBVtx, currVtxIdx, lastBIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, -heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n }\r\n\r\n this.setIndex(indices);\r\n this.setAttribute('position', positions);\r\n this.setAttribute('normal', normals);\r\n this.setAttribute('uv', uvs);\r\n }\r\n\r\n clone() {\r\n const { parameters } = this;\r\n\r\n return new CylinderBufferGeometry(\r\n parameters.radiusTop,\r\n parameters.radiusBottom,\r\n parameters.height,\r\n parameters.radialSegments,\r\n parameters.heightSegments,\r\n parameters.openEnded,\r\n );\r\n }\r\n}\r\n\r\nexport default CylinderBufferGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport CylinderBufferGeometry from './CylinderBufferGeometry';\r\n\r\nconst tmpColor = new THREE.Color();\r\nconst invMatrix = new THREE.Matrix4();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction sortNumber(a, b) {\r\n return a - b;\r\n}\r\n\r\nfunction _prepareCylinderInfo(chunkIndices) {\r\n chunkIndices.sort(sortNumber);\r\n const chunksIdx = [];\r\n const cylinderInfo = [];\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const val = chunkIndices[i];\r\n const even = (val | 0) % 2 === 0;\r\n const newPar = {\r\n first: false,\r\n second: false,\r\n };\r\n if (even) {\r\n newPar.first = true;\r\n newPar.second = i + 1 < n && chunkIndices[i + 1] === chunkIndices[i] + 1;\r\n if (newPar.second) {\r\n ++i;\r\n }\r\n } else {\r\n newPar.second = true;\r\n }\r\n chunksIdx.push(Math.floor(val / 2));\r\n cylinderInfo.push(newPar);\r\n }\r\n return { indices: chunksIdx, cylinderInfo };\r\n}\r\n\r\nfunction _assignOpacity(cylinderInfo, color1, color2) {\r\n for (let i = 0, n = cylinderInfo.length; i < n; ++i) {\r\n const info = cylinderInfo[i];\r\n if (!info.first) {\r\n color1[COLOR_SIZE * i] = -0.5;\r\n }\r\n if (!info.second) {\r\n color2[COLOR_SIZE * i] = -0.5;\r\n }\r\n }\r\n}\r\nclass Instanced2CCylindersGeometry extends THREE.InstancedBufferGeometry {\r\n constructor(instanceCount, polyComplexity, useZSprites, openEnded) {\r\n super();\r\n this._useZSprites = useZSprites;\r\n this._cylGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new CylinderBufferGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, openEnded);\r\n this._init(instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n this._collisionGeo = new Simple2CCylindersGeometry(instanceCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const matrix = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n let me = matrix.elements;\r\n const mtxOffset = itemIdx * OFFSET_SIZE;\r\n\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, itemRad);\r\n setArrayXYZW(this._matVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._matVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._matVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n\r\n if (this._useZSprites) {\r\n invMatrix.copy(matrix).invert();\r\n me = invMatrix.elements;\r\n setArrayXYZW(this._invmatVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._invmatVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._invmatVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n }\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const colorIdx = itemIdx * COLOR_SIZE;\r\n tmpColor.set(colorVal1);\r\n setArrayXYZ(this._color1, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n tmpColor.set(colorVal2);\r\n setArrayXYZ(this._color2, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n computeBoundingSphere() {\r\n this._collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = this._collisionGeo.boundingSphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n this._collisionGeo.computeBoundingBox();\r\n this.boundingBox = this._collisionGeo.boundingBox;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('matVector1').needsUpdate = true;\r\n this.getAttribute('matVector2').needsUpdate = true;\r\n this.getAttribute('matVector3').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('color2').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n if (this._useZSprites) {\r\n this.getAttribute('invmatVector1').needsUpdate = true;\r\n this.getAttribute('invmatVector2').needsUpdate = true;\r\n this.getAttribute('invmatVector3').needsUpdate = true;\r\n }\r\n\r\n this._collisionGeo.finishUpdate();\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[Math.floor(chunkIndices[i] / 2)] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const info = _prepareCylinderInfo(chunkIndices);\r\n const cylinderIndices = info.indices;\r\n const instanceCount = cylinderIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n copySubArrays(this._matVector1, geom._matVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector2, geom._matVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector3, geom._matVector3, cylinderIndices, OFFSET_SIZE);\r\n\r\n if (this._useZSprites) {\r\n copySubArrays(this._invmatVector1, geom._invmatVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector2, geom._invmatVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector3, geom._invmatVector3, cylinderIndices, OFFSET_SIZE);\r\n }\r\n\r\n copySubArrays(this._color1, geom._color1, cylinderIndices, COLOR_SIZE);\r\n copySubArrays(this._color2, geom._color2, cylinderIndices, COLOR_SIZE);\r\n _assignOpacity(info.cylinderInfo, geom._color1, geom._color2);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n getGeoParams() {\r\n return this._cylGeometry.parameters;\r\n }\r\n\r\n _init(instanceCount, cylinderGeo, useZSprites) {\r\n this.copy(cylinderGeo);\r\n this._matVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._color1 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n this._color2 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, instanceCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('matVector1', new THREE.InstancedBufferAttribute(this._matVector1, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector2', new THREE.InstancedBufferAttribute(this._matVector2, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector3', new THREE.InstancedBufferAttribute(this._matVector3, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._color1, COLOR_SIZE, false, 1));\r\n this.setAttribute('color2', new THREE.InstancedBufferAttribute(this._color2, COLOR_SIZE, false, 1));\r\n\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(this._alpha, 1, false, 1));\r\n\r\n if (useZSprites) {\r\n this._invmatVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n\r\n this.setAttribute(\r\n 'invmatVector1',\r\n new THREE.InstancedBufferAttribute(this._invmatVector1, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector2',\r\n new THREE.InstancedBufferAttribute(this._invmatVector2, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector3',\r\n new THREE.InstancedBufferAttribute(this._invmatVector3, OFFSET_SIZE, false, 1),\r\n );\r\n }\r\n }\r\n}\r\n\r\nexport default Instanced2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst TRI_SIZE = 3;\r\nconst tmpPrev = new THREE.Vector3();\r\nconst tmpNext = new THREE.Vector3();\r\nconst tmpRes = new THREE.Vector3();\r\nconst simpleNormal = new THREE.Vector3(1.0, 0.0, 0.0);\r\nconst normalOnCut = new THREE.Vector3();\r\nconst nearRingPt = new THREE.Vector3();\r\n\r\nfunction _createExtrudedChunkGeometry(shape, ringsCount) {\r\n const geo = new THREE.BufferGeometry();\r\n const ptsCount = shape.length;\r\n const totalPts = ptsCount * ringsCount;\r\n const type = totalPts <= 65536 ? Uint16Array : Uint32Array;\r\n const facesPerChunk = (ringsCount - 1) * ptsCount * 2;\r\n const indices = new THREE.BufferAttribute(utils.allocateTyped(type, facesPerChunk * TRI_SIZE), 1);\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n for (let y = 0; y < ringsCount; y++) {\r\n // faces\r\n if (y !== ringsCount - 1) {\r\n for (let i = 0; i < ptsCount; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + ptsCount + i;\r\n const v3 = currVtxIdx + ptsCount + ((i + 1) % ptsCount);\r\n const v4 = currVtxIdx + ((i + 1) % ptsCount);\r\n\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n currVtxIdx += ptsCount;\r\n }\r\n\r\n geo.setIndex(indices);\r\n const pos = utils.allocateTyped(Float32Array, totalPts * VEC_SIZE);\r\n geo.setAttribute('position', new THREE.BufferAttribute(pos, VEC_SIZE));\r\n\r\n geo._positions = shape;\r\n\r\n return geo;\r\n}\r\n\r\nclass ExtrudedObjectsGeometry extends ChunkedObjectsGeometry {\r\n constructor(shape, ringsCount, chunksCount) {\r\n const chunkGeo = _createExtrudedChunkGeometry(shape, ringsCount);\r\n super(chunkGeo, chunksCount);\r\n this._ringsCount = ringsCount;\r\n\r\n const tmpShape = this._tmpShape = [];\r\n for (let i = 0; i < shape.length; ++i) {\r\n tmpShape[i] = new THREE.Vector3();\r\n }\r\n }\r\n\r\n setItem(itemIdx, matrices, hasSlope = false, hasCut = false) {\r\n const ptsCount = this._chunkGeo._positions.length;\r\n const ringsCount = this._ringsCount;\r\n const chunkStartIdx = ptsCount * this._ringsCount * itemIdx * VEC_SIZE;\r\n\r\n this._setPoints(matrices, ptsCount, ringsCount, chunkStartIdx);\r\n\r\n if (hasSlope) {\r\n this._setSlopeNormals(ptsCount, ringsCount, chunkStartIdx);\r\n } else {\r\n this._setBaseNormals(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n\r\n if (hasCut) {\r\n this._addCut(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n }\r\n\r\n _setPoints(matrices, ptsCount, ringsCount, chunkStartIdx) {\r\n const tmpShape = this._tmpShape;\r\n const positions = this._positions;\r\n const shape = this._chunkGeo._positions;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i) {\r\n const mtx = matrices[i];\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpShape[j].copy(shape[j]).applyMatrix4(mtx).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _setBaseNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, false);\r\n }\r\n }\r\n\r\n _setSlopeNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const normals = this._normals;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First ring\r\n // In all cases, besides cut, second ring is coincident to first. So values of first ring's normals doesn't\r\n // matter (In the cut case special handler will be applied later and will set them to correct values)\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n simpleNormal.toArray(normals, vtxIdx);\r\n }\r\n // second ring\r\n // If it isn't first Item we take normals' values from the last ring of the previous item (these rings are coincident)\r\n // else we count normals' values based on next ring information\r\n if (vtxIdx - 2 * nPtsInRing > 0) {\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(normals, vtxIdx - 2 * nPtsInRing).toArray(normals, vtxIdx);\r\n }\r\n } else {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, +nPtsInRing);\r\n vtxIdx += nPtsInRing;\r\n }\r\n // other rings\r\n // we count normals' values based on previous ring information\r\n for (let i = 2; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, -nPtsInRing);\r\n }\r\n }\r\n\r\n // Counting normals:\r\n // - Slope\r\n // Radius changes throught part => normals aren't parallel with the plane contains section points\r\n // normal = vTangentInSectionPlane x vToSuchPointInPrevSection (all vectors are scaled for being 1 in length)\r\n // - No slope\r\n // Radius doesn't change throught part => normals are parallel with the plane contains section points\r\n // normal = vToPrevPointInSection + vToNextPointInSection (all vectors are scaled for being 1 in length)\r\n _countNormalsInRing(ptsCount, vtxIdx, isSlope, shiftToExtraPt) {\r\n const tmpShape = this._tmpShape;\r\n const normals = this._normals;\r\n\r\n tmpShape[0].fromArray(this._positions, vtxIdx);\r\n tmpShape[ptsCount - 1].fromArray(this._positions, vtxIdx + (ptsCount - 1) * VEC_SIZE);\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n if (j < ptsCount - 1) {\r\n tmpShape[j + 1].fromArray(this._positions, vtxIdx + VEC_SIZE);\r\n }\r\n\r\n if (isSlope) {\r\n nearRingPt.fromArray(this._positions, vtxIdx + shiftToExtraPt);\r\n\r\n tmpPrev.subVectors(tmpShape[(j + ptsCount - 1) % ptsCount], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], nearRingPt).normalize();\r\n tmpRes.crossVectors(tmpNext, tmpPrev).normalize().toArray(normals, vtxIdx);\r\n } else {\r\n tmpPrev.subVectors(tmpShape[j], tmpShape[(j + ptsCount - 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpRes.addVectors(tmpPrev, tmpNext).normalize().toArray(normals, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _addCut(ptsCount, ringsCount, chunkStartIdx) {\r\n // Nothing to do if item is flat or only line\r\n if (ptsCount < 3 || ringsCount < 2) {\r\n return;\r\n }\r\n const positions = this._positions;\r\n const normals = this._normals;\r\n const tmpShape = this._tmpShape;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n // Normal to the cut plane is equal to cross product of two vectors which are lying in it\r\n tmpShape[0].fromArray(positions, chunkStartIdx);\r\n tmpShape[1].fromArray(positions, chunkStartIdx + VEC_SIZE);\r\n tmpShape[2].fromArray(positions, chunkStartIdx + 2 * VEC_SIZE);\r\n\r\n tmpPrev.subVectors(tmpShape[1], tmpShape[0]).normalize();\r\n tmpNext.subVectors(tmpShape[1], tmpShape[2]).normalize();\r\n normalOnCut.crossVectors(tmpPrev, tmpNext).normalize();\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First and second rings normals' values are equal to value of normal to the cutting plane\r\n for (let j = 0; j < ptsCount * 2; ++j, vtxIdx += VEC_SIZE) {\r\n normalOnCut.toArray(normals, vtxIdx);\r\n }\r\n if (ringsCount > 2) {\r\n // Third ring points are coincident to first ring points, but have different normals. It makes sharp angle near cut\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(positions, vtxIdx - nPtsInRing).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default ExtrudedObjectsGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VERTEX_PER_SEGMENT = 4;\r\nconst POS_SIZE = 4;\r\nconst DIR_SIZE = 3;\r\nconst COL_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\nconst direction = new THREE.Vector3();\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction getSubset(arr, startSegmentIdx, segmentsCount, elemSize) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT;\r\n const end = start + segmentsCount * VERTEX_PER_SEGMENT;\r\n return arr.subarray(start * elemSize, end * elemSize);\r\n}\r\n\r\n/**\r\n * This class represents lines geometry which consists of screen-aligned narrow quad of variable width.\r\n *\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * collision geometry.\r\n */\r\n\r\nclass ThickLinesGeometry extends THREE.BufferGeometry {\r\n constructor(segmentsCount) {\r\n super();\r\n this._initVertices(segmentsCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n this.getAttribute('direction').needsUpdate = true;\r\n }\r\n\r\n setColor(segmentIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n setSegment(segmentIdx, pos1, pos2) {\r\n direction.subVectors(pos1, pos2);\r\n direction.normalize();\r\n const positions = this._positions;\r\n const directions = this._directions;\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n let dirIdx = segmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n }\r\n\r\n setOpacity(startSegIdx, endSegIdx, value) {\r\n const start = startSegIdx * VERTEX_PER_SEGMENT;\r\n const end = endSegIdx * VERTEX_PER_SEGMENT;\r\n _.fill(this.alpha, value, end, start);\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubsetSegments(startSegmentIdx, segmentsCount) {\r\n return [\r\n getSubset(this._positions, startSegmentIdx, segmentsCount, POS_SIZE),\r\n getSubset(this._directions, startSegmentIdx, segmentsCount, DIR_SIZE),\r\n ];\r\n }\r\n\r\n getSubsetColors(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._colors, startSegmentIdx, segmentsCount, COL_SIZE);\r\n }\r\n\r\n getSubsetOpacities(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._alpha, startSegmentIdx, segmentsCount, 1);\r\n }\r\n\r\n getNumVertexPerSegment() {\r\n return VERTEX_PER_SEGMENT;\r\n }\r\n\r\n getPositionSize() {\r\n return POS_SIZE;\r\n }\r\n\r\n setSegments(startSegmentIdx, positions) {\r\n const startPos = startSegmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n if (positions instanceof Array && positions.length === 2) {\r\n this._positions.set(positions[0], startPos);\r\n const startDir = startSegmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n this._directions.set(positions[1], startDir); // dirs are geo part of vertex\r\n } else {\r\n this._positions.set(positions, startPos);\r\n }\r\n }\r\n\r\n setColors(startSegmentIdx, colors) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n this._colors.set(colors, start);\r\n }\r\n\r\n _initVertices(segmentsCount) {\r\n this._buffersSize = segmentsCount * VERTEX_PER_SEGMENT;\r\n const pointsCount = this._buffersSize;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, segmentsCount * 6);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * POS_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * COL_SIZE);\r\n this._directions = utils.allocateTyped(Float32Array, pointsCount * DIR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n const index = this._index;\r\n let indexOffset = 0;\r\n let pointOffset = 0;\r\n for (let j = 0; j < segmentsCount; j++, indexOffset += 6, pointOffset += VERTEX_PER_SEGMENT) {\r\n index[indexOffset] = pointOffset;\r\n index[indexOffset + 1] = pointOffset + 1;\r\n index[indexOffset + 2] = pointOffset + 3;\r\n index[indexOffset + 3] = pointOffset;\r\n index[indexOffset + 4] = pointOffset + 2;\r\n index[indexOffset + 5] = pointOffset + 3;\r\n }\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, POS_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, COL_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n this.setAttribute('direction', new THREE.BufferAttribute(this._directions, DIR_SIZE));\r\n }\r\n}\r\n\r\nexport default ThickLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport BaseLinesGeometry from './ThickLinesGeometry';\r\n\r\n/**\r\n * This class represents geometry which consists lines. This can build bounding volumes\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n */\r\nclass LinesGeometry extends BaseLinesGeometry {\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n if (boundingBox) {\r\n boundingBox.getCenter(center);\r\n }\r\n const positions = this._positions;\r\n const sphere = this.boundingSphere || new THREE.Sphere();\r\n const size = this._positions.length;\r\n const pos = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n pos.set(positions[i], positions[i + 1], positions[i + 2]);\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n sphere.set(center, Math.sqrt(radiusSquared));\r\n this.boundingSphere = sphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n const positions = this._positions;\r\n const box = new THREE.Box3();\r\n const size = this._positions.length;\r\n const tmpVec = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n tmpVec.set(positions[i], positions[i + 1], positions[i + 2]);\r\n box.expandByPoint(tmpVec);\r\n }\r\n this.boundingBox = box;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n}\r\n\r\nexport default LinesGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass CylinderCollisionGeo extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const itemOffset = chunkSize * itemIdx * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, itemOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, itemOffset);\r\n }\r\n}\r\nexport default CylinderCollisionGeo;\r\n","import LinesGeometry from './LinesGeometry';\r\nimport CylinderCollisionGeo from './CylinderCollisionGeo';\r\n\r\nconst COLLISION_RAD = 0.1;\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n *\r\n * @param {number} chunksCount Total chunks count.\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * @param {boolean} enableCollision Enable or disable collision where each segment is\r\n * a collidable cylinder.\r\n * collision geometry.\r\n */\r\nclass ChunkedLinesGeometry extends LinesGeometry {\r\n constructor(chunksCount, segmentsCount, enableCollision) {\r\n super(chunksCount * segmentsCount);\r\n this._init(segmentsCount);\r\n this._collisionGeo = enableCollision ? new CylinderCollisionGeo(chunksCount * segmentsCount, 3) : null;\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = collisionGeo.boundingSphere;\r\n return;\r\n }\r\n super.computeBoundingSphere();\r\n }\r\n\r\n computeBoundingBox() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingBox();\r\n this.boundingBox = collisionGeo.boundingBox;\r\n return;\r\n }\r\n super.computeBoundingBox();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const collisionGeo = this._collisionGeo;\r\n if (!collisionGeo) {\r\n return;\r\n }\r\n const segCount = this._chunkSize;\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n for (let i = 0, n = intersects.length; i < n; ++i) {\r\n let { chunkIdx } = intersects[i];\r\n if (chunkIdx === undefined) {\r\n continue;\r\n }\r\n chunkIdx = (chunkIdx / segCount) | 0;\r\n intersects[i].chunkIdx = chunkIdx;\r\n }\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n super.setColor(i, colorVal);\r\n }\r\n }\r\n\r\n setSegment(chunkIdx, segIdx, pos1, pos2) {\r\n const chunkSize = this._chunkSize;\r\n const idx = chunkIdx * chunkSize + segIdx;\r\n super.setSegment(idx, pos1, pos2);\r\n if (this._collisionGeo) {\r\n this._collisionGeo.setItem(chunkIdx * chunkSize + segIdx, pos1, pos2, COLLISION_RAD);\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n super.setOpacity(left, left + chunkSize - 1, value);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const chunkSize = this._chunkSize;\r\n const subset = new ChunkedLinesGeometry(instanceCount, chunkSize, false);\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const startSegIdx = chunkIndices[i] * chunkSize;\r\n subset.setSegments(dstPtOffset, this.getSubsetSegments(startSegIdx, chunkSize));\r\n subset.setColors(dstPtOffset, this.getSubsetColors(startSegIdx, chunkSize));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(chunkSize) {\r\n this._chunkSize = chunkSize;\r\n }\r\n}\r\n\r\nexport default ChunkedLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport LinesGeometry from './LinesGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\n\r\nconst COLLISION_RAD = 0.3;\r\nconst tmpVector = new THREE.Vector3();\r\n\r\nclass TwoColorLinesGeometry extends LinesGeometry {\r\n constructor(segmentsCount) {\r\n super(segmentsCount * 2);\r\n this._init(segmentsCount);\r\n this._collisionGeo = new Simple2CCylindersGeometry(segmentsCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos) {\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, COLLISION_RAD);\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n tmpVector.lerpVectors(botPos, topPos, 0.5);\r\n super.setSegment(offset, botPos, tmpVector);\r\n super.setSegment(offset + 1, tmpVector, topPos);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n super.setColor(offset, colorVal1);\r\n super.setColor(offset + 1, colorVal2);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n if (this._collisionGeo) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n getSubset(segmentIndices) {\r\n const instanceCount = segmentIndices.length;\r\n const subset = new TwoColorLinesGeometry(instanceCount, false);\r\n for (let i = 0, n = instanceCount; i < n; ++i) {\r\n const startSegIdx = segmentIndices[i];\r\n subset.setSegments(i, this.getSubsetSegments(startSegIdx, 1));\r\n subset.setColors(i, this.getSubsetColors(startSegIdx, 1));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(segmentsCount) {\r\n this._segCounts = segmentsCount * 2;\r\n }\r\n}\r\n// (???)parent = LinesGeometry.prototype;\r\n\r\nexport default TwoColorLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst vectors = [\r\n new THREE.Vector3(1, 0, 0),\r\n new THREE.Vector3(-1, 0, 0),\r\n new THREE.Vector3(0, 1, 0),\r\n new THREE.Vector3(0, -1, 0),\r\n new THREE.Vector3(0, 0, 1),\r\n new THREE.Vector3(0, 0, -1),\r\n];\r\nconst vecCount = vectors.length;\r\nconst tempPos1 = new THREE.Vector3();\r\nconst tempPos2 = new THREE.Vector3();\r\n\r\nclass CrossGeometry extends SphereCollisionGeo(ChunkedLinesGeometry) {\r\n constructor(chunksCount) {\r\n super(chunksCount, chunksCount, (vecCount / 2) | 0, false);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n\r\n for (let i = 0; i < vecCount / 2; ++i) {\r\n const first = i * 2;\r\n tempPos1.x = itemPos.x + vectors[first].x * itemRad;\r\n tempPos1.y = itemPos.y + vectors[first].y * itemRad;\r\n tempPos1.z = itemPos.z + vectors[first].z * itemRad;\r\n const second = first + 1;\r\n tempPos2.x = itemPos.x + vectors[second].x * itemRad;\r\n tempPos2.y = itemPos.y + vectors[second].y * itemRad;\r\n tempPos2.z = itemPos.z + vectors[second].z * itemRad;\r\n this.setSegment(itemIdx, i, tempPos1, tempPos2);\r\n }\r\n }\r\n}\r\nexport default CrossGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst POS_RAD_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This is a base class for isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\nclass IsoSurfaceGeometry extends THREE.BufferGeometry {\r\n constructor(spheresCount, opts) {\r\n super();\r\n\r\n this._opts = opts;\r\n this.zClip = this._opts.zClip;\r\n this._posRad = utils.allocateTyped(Float32Array, spheresCount * POS_RAD_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n }\r\n\r\n setItem(chunkIdx, pos, radius) {\r\n const posRad = this._posRad;\r\n let idx = POS_RAD_SIZE * chunkIdx;\r\n posRad[idx++] = pos.x;\r\n posRad[idx++] = pos.y;\r\n posRad[idx++] = pos.z;\r\n posRad[idx] = radius;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n let idx = COLOR_SIZE * chunkIdx;\r\n colors[idx++] = tmpColor.r;\r\n colors[idx++] = tmpColor.g;\r\n colors[idx] = tmpColor.b;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n finishUpdate() {\r\n this._build();\r\n }\r\n\r\n setOpacity() {\r\n // not implemented\r\n }\r\n\r\n raycast() {\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\nexport default IsoSurfaceGeometry;\r\n","import utils from '../../utils';\r\n\r\n/**\r\n * Class for marching cube\r\n * Stores 8 points and 8 float values are stored together in linear array\r\n * Int values for has intersection or not - in integer32 linear array\r\n * Int values for bits flags - in integer32 linear array\r\n *\r\n */\r\nclass IsoSurfaceMarchCube {\r\n constructor() {\r\n this.pointsValuesLinear = null;\r\n this.hasIntersection = null;\r\n this.bitsInside = null;\r\n }\r\n\r\n create(numCellsPerSide) {\r\n const vx7000000 = 0x7000000;\r\n const n3 = numCellsPerSide * numCellsPerSide * numCellsPerSide;\r\n if (n3 > vx7000000) {\r\n throw new Error('Too large cube dimension: lead to memory huge uasge');\r\n }\r\n this.pointsValuesLinear = utils.allocateTyped(Float32Array, (2 << (2 + 2)) * n3);\r\n this.hasIntersection = utils.allocateTyped(Int32Array, n3);\r\n this.bitsInside = utils.allocateTyped(Int32Array, n3);\r\n return 0;\r\n }\r\n\r\n destroy() {\r\n this.bitsInside = null;\r\n this.hasIntersection = null;\r\n this.pointsValuesLinear = null;\r\n }\r\n}\r\n\r\n/* eslint-disable no-magic-numbers */\r\nIsoSurfaceMarchCube.prototype.striIndicesMarchCube = [\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 0, 2, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 8, 3, 2, 10, 8, 10, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 8, 11, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 2, 1, 9, 11, 9, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 1, 11, 10, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 10, 1, 0, 8, 10, 8, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 9, 0, 3, 11, 9, 11, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 7, 3, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 1, 9, 4, 7, 1, 7, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 4, 7, 3, 0, 4, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 9, 0, 2, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 8, 4, 7, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 4, 7, 11, 2, 4, 2, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 8, 4, 7, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1, -1, -1, -1, -1,\r\n 3, 10, 1, 3, 11, 10, 7, 8, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4, -1, -1, -1, -1,\r\n 4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 4, 7, 11, 4, 11, 9, 9, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 1, 5, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 5, 4, 8, 3, 5, 3, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 10, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 2, 10, 5, 4, 2, 4, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8, -1, -1, -1, -1,\r\n 9, 5, 4, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 0, 8, 11, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 0, 1, 5, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5, -1, -1, -1, -1,\r\n 10, 3, 11, 10, 1, 3, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10, -1, -1, -1, -1,\r\n 5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 5, 4, 8, 5, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 5, 7, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 3, 0, 9, 5, 3, 5, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 8, 0, 1, 7, 1, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 9, 5, 7, 10, 1, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3, -1, -1, -1, -1,\r\n 8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2, -1, -1, -1, -1,\r\n 2, 10, 5, 2, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 9, 5, 7, 8, 9, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7, -1, -1, -1, -1,\r\n 11, 2, 1, 11, 1, 7, 7, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11, -1, -1, -1, -1,\r\n 5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0, -1,\r\n 11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0, -1,\r\n 11, 10, 5, 7, 11, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 1, 9, 8, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 2, 6, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 1, 2, 6, 3, 0, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 6, 5, 9, 0, 6, 0, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 0, 8, 11, 2, 0, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11, -1, -1, -1, -1,\r\n 6, 3, 11, 6, 5, 3, 5, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9, -1, -1, -1, -1,\r\n 6, 5, 9, 6, 9, 11, 11, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 4, 7, 3, 6, 5, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 5, 10, 6, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 6, 1, 2, 6, 5, 1, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7, -1, -1, -1, -1,\r\n 8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6, -1, -1, -1, -1,\r\n 7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9, -1,\r\n 3, 11, 2, 7, 8, 4, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1,\r\n 9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6, -1,\r\n 8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11, -1,\r\n 0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7, -1,\r\n 6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9, -1, -1, -1, -1,\r\n 10, 4, 9, 6, 4, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 10, 6, 4, 9, 10, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 0, 1, 10, 6, 0, 6, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 1, 4, 9, 1, 2, 4, 2, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4, -1, -1, -1, -1,\r\n 0, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 2, 8, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 4, 9, 10, 6, 4, 11, 2, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6, -1, -1, -1, -1,\r\n 3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1, -1,\r\n 9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3, -1, -1, -1, -1,\r\n 8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1, -1,\r\n 3, 11, 6, 3, 6, 0, 0, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 4, 8, 11, 6, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 10, 6, 7, 8, 10, 8, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10, -1, -1, -1, -1,\r\n 10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0, -1, -1, -1, -1,\r\n 10, 6, 7, 10, 7, 1, 1, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9, -1,\r\n 7, 8, 0, 7, 0, 6, 6, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 3, 2, 6, 7, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7, -1,\r\n 1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11, -1,\r\n 11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1, -1, -1, -1, -1,\r\n 8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6, -1,\r\n 0, 9, 1, 11, 6, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0, -1, -1, -1, -1,\r\n 7, 11, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 9, 8, 3, 1, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 8, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 9, 0, 2, 10, 9, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8, -1, -1, -1, -1,\r\n 7, 2, 3, 6, 2, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 0, 8, 7, 6, 0, 6, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 7, 6, 2, 3, 7, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6, -1, -1, -1, -1,\r\n 10, 7, 6, 10, 1, 7, 1, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8, -1, -1, -1, -1,\r\n 0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7, -1, -1, -1, -1,\r\n 7, 6, 10, 7, 10, 8, 8, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 8, 4, 11, 8, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 3, 0, 6, 0, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 6, 11, 8, 4, 6, 9, 0, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6, -1, -1, -1, -1,\r\n 6, 8, 4, 6, 11, 8, 2, 10, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6, -1, -1, -1, -1,\r\n 4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9, -1, -1, -1, -1,\r\n 10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3, -1,\r\n 8, 2, 3, 8, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8, -1, -1, -1, -1,\r\n 1, 9, 4, 1, 4, 2, 2, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1, -1, -1, -1, -1,\r\n 10, 1, 0, 10, 0, 6, 6, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3, -1,\r\n 10, 9, 4, 6, 10, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 5, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 1, 5, 4, 0, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5, -1, -1, -1, -1,\r\n 9, 5, 4, 10, 1, 2, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5, -1, -1, -1, -1,\r\n 7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2, -1, -1, -1, -1,\r\n 3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6, -1,\r\n 7, 2, 3, 7, 6, 2, 5, 4, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7, -1, -1, -1, -1,\r\n 3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0, -1, -1, -1, -1,\r\n 6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8, -1,\r\n 9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7, -1, -1, -1, -1,\r\n 1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4, -1,\r\n 4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10, -1,\r\n 7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10, -1, -1, -1, -1,\r\n 6, 9, 5, 6, 11, 9, 11, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5, -1, -1, -1, -1,\r\n 0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11, -1, -1, -1, -1,\r\n 6, 11, 3, 6, 3, 5, 5, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6, -1, -1, -1, -1,\r\n 0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10, -1,\r\n 11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5, -1,\r\n 6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3, -1, -1, -1, -1,\r\n 5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2, -1, -1, -1, -1,\r\n 9, 5, 6, 9, 6, 0, 0, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8, -1,\r\n 1, 5, 6, 2, 1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6, -1,\r\n 10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0, -1, -1, -1, -1,\r\n 0, 3, 8, 5, 6, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 5, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 7, 5, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 11, 7, 5, 8, 3, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 11, 7, 5, 10, 11, 1, 9, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1, -1, -1, -1, -1,\r\n 11, 1, 2, 11, 7, 1, 7, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11, -1, -1, -1, -1,\r\n 9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7, -1, -1, -1, -1,\r\n 7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2, -1,\r\n 2, 5, 10, 2, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2, -1, -1, -1, -1,\r\n 9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2, -1,\r\n 1, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 7, 0, 7, 1, 1, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 3, 9, 3, 5, 5, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 7, 5, 9, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 8, 4, 5, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5, -1, -1, -1, -1,\r\n 10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4, -1,\r\n 2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8, -1, -1, -1, -1,\r\n 0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11, -1,\r\n 0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5, -1,\r\n 9, 4, 5, 2, 11, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4, -1, -1, -1, -1,\r\n 5, 10, 2, 5, 2, 4, 4, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9, -1,\r\n 5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 3, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 5, 1, 0, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5, -1, -1, -1, -1,\r\n 9, 4, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 11, 7, 4, 9, 11, 9, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11, -1, -1, -1, -1,\r\n 1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11, -1, -1, -1, -1,\r\n 3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4, -1,\r\n 4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2, -1, -1, -1, -1,\r\n 9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3, -1,\r\n 11, 7, 4, 11, 4, 2, 2, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4, -1, -1, -1, -1,\r\n 2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9, -1, -1, -1, -1,\r\n 9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7, -1,\r\n 3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10, -1,\r\n 1, 10, 2, 8, 7, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 7, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1, -1, -1, -1, -1,\r\n 4, 0, 3, 7, 4, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 8, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1,\r\n 0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1,\r\n 1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n];\r\n/* eslint-enable no-magic-numbers */\r\n\r\nexport default IsoSurfaceMarchCube;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport utils from '../../utils';\r\n\r\nconst edgeTable = [\r\n 0x0, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c,\r\n 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00,\r\n 0x190, 0x99, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c,\r\n 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90,\r\n 0x230, 0x339, 0x33, 0x13a, 0x636, 0x73f, 0x435, 0x53c,\r\n 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30,\r\n 0x3a0, 0x2a9, 0x1a3, 0xaa, 0x7a6, 0x6af, 0x5a5, 0x4ac,\r\n 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0,\r\n 0x460, 0x569, 0x663, 0x76a, 0x66, 0x16f, 0x265, 0x36c,\r\n 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60,\r\n 0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0xff, 0x3f5, 0x2fc,\r\n 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0,\r\n 0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x55, 0x15c,\r\n 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950,\r\n 0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0xcc,\r\n 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0,\r\n 0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc,\r\n 0xcc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0,\r\n 0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c,\r\n 0x15c, 0x55, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650,\r\n 0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc,\r\n 0x2fc, 0x3f5, 0xff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0,\r\n 0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c,\r\n 0x36c, 0x265, 0x16f, 0x66, 0x76a, 0x663, 0x569, 0x460,\r\n 0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac,\r\n 0x4ac, 0x5a5, 0x6af, 0x7a6, 0xaa, 0x1a3, 0x2a9, 0x3a0,\r\n 0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c,\r\n 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x33, 0x339, 0x230,\r\n 0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c,\r\n 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x99, 0x190,\r\n 0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c,\r\n 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x0];\r\n\r\nfunction _voxelGradientFast(v, point, grad) {\r\n const g = v.getValue(point.x, point.y, point.z);\r\n grad.set(g[0], g[1], g[2]);\r\n}\r\n\r\n// Helper class GridCell\r\nclass GridCell {\r\n constructor() {\r\n this._arrSize = 8;\r\n this.p = new Array(this._arrSize);\r\n this.g = new Array(this._arrSize);\r\n this.val = new Array(this._arrSize);\r\n for (let i = 0; i < this._arrSize; ++i) {\r\n this.p[i] = new THREE.Vector3();\r\n this.g[i] = new THREE.Vector3();\r\n }\r\n this.cubeIndex = 0;\r\n }\r\n}\r\n\r\n// Helper class Triangle\r\nclass Triangle {\r\n constructor() {\r\n this.a = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.b = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.c = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n }\r\n}\r\n\r\nfunction createArray(arrSize) {\r\n const arr = new Array(arrSize);\r\n for (let i = 0; i < arrSize; ++i) {\r\n arr[i] = new THREE.Vector3();\r\n }\r\n\r\n return arr;\r\n}\r\n\r\nclass IsoSurface {\r\n constructor() {\r\n this._numTriangles = 0;\r\n this._numVertices = 0;\r\n this._position = [];\r\n this._normals = [];\r\n this._colors = null;\r\n this._indices = [];\r\n this._volumetricData = null;\r\n this._xAxis = new THREE.Vector3();\r\n this._yAxis = new THREE.Vector3();\r\n this._zAxis = new THREE.Vector3();\r\n this._xDir = new THREE.Vector3();\r\n this._yDir = new THREE.Vector3();\r\n this._zDir = new THREE.Vector3();\r\n }\r\n\r\n _prepareAxesAndDirs() {\r\n const volData = this._volumetricData;\r\n\r\n const cellSize = volData.getCellSize();\r\n\r\n // calculate cell axes\r\n const xAxis = this._xAxis;\r\n const yAxis = this._yAxis;\r\n const zAxis = this._zAxis;\r\n const xDir = this._xDir;\r\n const yDir = this._yDir;\r\n const zDir = this._zDir;\r\n\r\n xAxis.set(cellSize.x, 0, 0);\r\n yAxis.set(0, cellSize.y, 0);\r\n zAxis.set(0, 0, cellSize.z);\r\n\r\n xDir.set(1, 0, 0);\r\n yDir.set(0, 1, 0);\r\n zDir.set(0, 0, 1);\r\n\r\n // flip normals if coordinate system is in the wrong handedness\r\n const tmp = new THREE.Vector3();\r\n tmp.crossVectors(xDir, yDir);\r\n if (tmp.dot(zDir) < 0) {\r\n xDir.negate();\r\n yDir.negate();\r\n zDir.negate();\r\n }\r\n\r\n // check that the grid is in the all-positive octant of the coordinate system\r\n if (xDir.x < 0 || xDir.y < 0 || xDir.z < 0\r\n || yDir.x < 0 || yDir.y < 0 || yDir.z < 0\r\n || zDir.x < 0 || zDir.y < 0 || zDir.z < 0) {\r\n return false;\r\n }\r\n\r\n // check that the grid is axis-aligned\r\n const notZero = (axe) => Math.abs(axe) > Number.EPSILON;\r\n return !(notZero(xAxis.y) || notZero(xAxis.z)\r\n || notZero(yAxis.x) || notZero(yAxis.z)\r\n || notZero(zAxis.x) || notZero(zAxis.y));\r\n }\r\n\r\n _vertexInterp(isoLevel, grid, ind1, ind2, vertex, normal) {\r\n const p1 = grid.p[ind1];\r\n const p2 = grid.p[ind2];\r\n const n1 = grid.g[ind1];\r\n const n2 = grid.g[ind2];\r\n const valP1 = grid.val[ind1];\r\n const valP2 = grid.val[ind2];\r\n const isoDiffP1 = isoLevel - valP1;\r\n const diffValP2P1 = valP2 - valP1;\r\n\r\n let mu = 0.0;\r\n\r\n if (Math.abs(diffValP2P1) > 0.0) {\r\n mu = isoDiffP1 / diffValP2P1;\r\n }\r\n mu = mu > 1.0 ? 1.0 : mu;\r\n vertex.lerpVectors(p1, p2, mu);\r\n normal.lerpVectors(n1, n2, mu);\r\n }\r\n\r\n static _triTable = IsoSurfaceMarchCube.prototype.striIndicesMarchCube;\r\n\r\n static _arrSize = 12;\r\n\r\n static _firstIndices = [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3];\r\n\r\n static _secondIndices = [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7];\r\n\r\n static _vertexList = createArray(IsoSurface._arrSize);\r\n\r\n static _normalList = createArray(IsoSurface._arrSize);\r\n\r\n _polygonize(grid, isoLevel, triangles) {\r\n const { cubeIndex } = grid;\r\n let i = 0;\r\n const arrSize = IsoSurface._arrSize;\r\n const firstIndices = IsoSurface._firstIndices;\r\n const secondIndices = IsoSurface._secondIndices;\r\n const vertexList = IsoSurface._vertexList;\r\n const normalList = IsoSurface._normalList;\r\n\r\n for (; i < arrSize; ++i) {\r\n if (edgeTable[cubeIndex] & (1 << i)) {\r\n this._vertexInterp(\r\n isoLevel,\r\n grid,\r\n firstIndices[i],\r\n secondIndices[i],\r\n vertexList[i],\r\n normalList[i],\r\n );\r\n }\r\n }\r\n\r\n let triCount = 0;\r\n const triTblIdx = cubeIndex * 16;\r\n const triTable = IsoSurface._triTable;\r\n\r\n for (i = 0; triTable[triTblIdx + i] !== -1; i += 3) {\r\n triangles[triCount].a.p.copy(vertexList[triTable[triTblIdx + i]]);\r\n triangles[triCount].a.n.copy(normalList[triTable[triTblIdx + i]]);\r\n\r\n triangles[triCount].b.p.copy(vertexList[triTable[triTblIdx + i + 1]]);\r\n triangles[triCount].b.n.copy(normalList[triTable[triTblIdx + i + 1]]);\r\n\r\n triangles[triCount].c.p.copy(vertexList[triTable[triTblIdx + i + 2]]);\r\n triangles[triCount].c.n.copy(normalList[triTable[triTblIdx + i + 2]]);\r\n ++triCount;\r\n }\r\n\r\n return triCount;\r\n }\r\n\r\n _doGridPosNorms(isoValue, step, appendSimple) {\r\n const vol = this._volumetricData;\r\n const volData = this._volumetricData.getData();\r\n const dim = vol.getDimensions();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n const zSize = dim[2];\r\n const stepX = step * vol.getStrideX();\r\n const stepY = step * vol.getStrideY();\r\n const stepZ = step * vol.getStrideZ();\r\n\r\n const gc = new GridCell();\r\n const gcVal = gc.val;\r\n const gcValSize = gc.val.length;\r\n const additions = [\r\n new THREE.Vector3(0, 0, 0), // 0\r\n new THREE.Vector3(step, 0, 0), // 1\r\n new THREE.Vector3(step, step, 0), // 2\r\n new THREE.Vector3(0, step, 0), // 3\r\n new THREE.Vector3(0, 0, step), // 4\r\n new THREE.Vector3(step, 0, step), // 5\r\n new THREE.Vector3(step, step, step), // 6\r\n new THREE.Vector3(0, step, step), // 7\r\n ];\r\n\r\n const tmpTriCount = 5;\r\n const triangles = new Array(tmpTriCount);\r\n for (let j = 0; j < tmpTriCount; ++j) {\r\n triangles[j] = new Triangle();\r\n }\r\n\r\n let appendVertex;\r\n const self = this;\r\n const positions = this._position;\r\n const normals = this._normals;\r\n if (appendSimple) {\r\n // Special case for axis-aligned grid with positive unit vector normals\r\n appendVertex = (function () {\r\n const axis = new THREE.Vector3(self._xAxis.x, self._yAxis.y, self._zAxis.z);\r\n return function (triVertex) {\r\n const vertex = triVertex.p.clone();\r\n vertex.multiply(axis);\r\n positions.push(vertex.add(self._origin));\r\n normals.push(triVertex.n.clone());\r\n };\r\n }());\r\n } else {\r\n appendVertex = (function () {\r\n const posMtx = new THREE.Matrix3();\r\n posMtx.set(\r\n self._xAxis.x,\r\n self._yAxis.x,\r\n self._zAxis.x,\r\n self._xAxis.y,\r\n self._yAxis.y,\r\n self._zAxis.y,\r\n self._xAxis.z,\r\n self._yAxis.z,\r\n self._zAxis.z,\r\n );\r\n const normMtx = new THREE.Matrix3();\r\n normMtx.set(\r\n self._xDir.x,\r\n self._yDir.x,\r\n self._zDir.x,\r\n self._xDir.y,\r\n self._yDir.y,\r\n self._zDir.y,\r\n self._xDir.z,\r\n self._yDir.z,\r\n self._zDir.z,\r\n );\r\n\r\n return function (triVertex) {\r\n positions.push(triVertex.p.clone().applyMatrix3(posMtx).add(self._origin));\r\n normals.push(triVertex.n.clone().applyMatrix3(normMtx));\r\n };\r\n }());\r\n }\r\n const indices = this._indices;\r\n\r\n let globTriCount = 0;\r\n\r\n for (let z = 0; z < (zSize - step); z += step) {\r\n for (let y = 0; y < (ySize - step); y += step) {\r\n let idx = vol.getDirectIdx(0, y, z);\r\n for (let x = 0; x < (xSize - step); x += step, idx += stepX) {\r\n /* eslint-disable no-multi-spaces */\r\n /* eslint-disable computed-property-spacing */\r\n gcVal[0] = volData[idx];\r\n gcVal[1] = volData[idx + stepX];\r\n gcVal[3] = volData[idx + stepY];\r\n gcVal[2] = volData[idx + stepX + stepY];\r\n gcVal[4] = volData[idx + stepZ];\r\n gcVal[5] = volData[idx + stepX + stepZ];\r\n gcVal[7] = volData[idx + stepY + stepZ];\r\n gcVal[6] = volData[idx + stepX + stepY + stepZ];\r\n /* eslint-enable no-multi-spaces */\r\n /* eslint-enable computed-property-spacing */\r\n\r\n // Determine the index into the edge table which\r\n // tells us which vertices are inside of the surface\r\n let cubeIndex = 0;\r\n let i = 0;\r\n for (; i < gcValSize; ++i) {\r\n if (gcVal[i] < isoValue) {\r\n cubeIndex |= (1 << i);\r\n }\r\n }\r\n\r\n if (edgeTable[cubeIndex] === 0) {\r\n continue;\r\n }\r\n\r\n gc.cubeIndex = cubeIndex;\r\n for (i = 0; i < gcValSize; ++i) {\r\n gc.p[i].set(x + additions[i].x, y + additions[i].y, z + additions[i].z);\r\n _voxelGradientFast(this._gradient, gc.p[i], gc.g[i]);\r\n }\r\n\r\n // calculate vertices and facets for this cube,\r\n // calculate normals by interpolating between the negated\r\n // normalized volume gradients for the 8 reference voxels\r\n const triCount = this._polygonize(gc, isoValue, triangles);\r\n globTriCount += triCount;\r\n\r\n // append triangles using different techniques\r\n for (i = 0; i < triCount; ++i) {\r\n indices.push(this._numTriangles * 3);\r\n indices.push(this._numTriangles * 3 + 1);\r\n indices.push(this._numTriangles * 3 + 2);\r\n ++this._numTriangles;\r\n\r\n appendVertex(triangles[i].a);\r\n appendVertex(triangles[i].b);\r\n appendVertex(triangles[i].c);\r\n }\r\n }\r\n }\r\n }\r\n\r\n return globTriCount;\r\n }\r\n\r\n compute(volData, origin, isoValue, step) {\r\n this._volumetricData = volData;\r\n this._origin = origin;\r\n\r\n this._gradient = volData.computeGradient();\r\n\r\n this._doGridPosNorms(isoValue, step, this._prepareAxesAndDirs());\r\n }\r\n\r\n _remapIndices(vertexMap, idcCount) {\r\n const indices = this._indices;\r\n const newIndices = utils.allocateTyped(Uint32Array, idcCount);\r\n for (let i = 0; i < idcCount; ++i) {\r\n indices[i] = vertexMap[indices[i]];\r\n newIndices[i] = indices[i];\r\n }\r\n this._indices = newIndices;\r\n }\r\n\r\n _remapVertices(vertices, normals, count) {\r\n const newPositions = utils.allocateTyped(Float32Array, count * 3);\r\n const newNormals = utils.allocateTyped(Float32Array, count * 3);\r\n for (let i = 0; i < count; ++i) {\r\n const pos = vertices[i];\r\n newPositions[i * 3] = pos.x;\r\n newPositions[i * 3 + 1] = pos.y;\r\n newPositions[i * 3 + 2] = pos.z;\r\n const norm = normals[i].normalize();\r\n newNormals[i * 3] = norm.x;\r\n newNormals[i * 3 + 1] = norm.y;\r\n newNormals[i * 3 + 2] = norm.z;\r\n }\r\n this._position = newPositions;\r\n this._normals = newNormals;\r\n }\r\n\r\n vertexFusion(offset, len) {\r\n const faceVer = this._indices.length;\r\n const vertices = this._position;\r\n const normals = this._normals;\r\n const oldVerCount = vertices.length | 0;\r\n if (faceVer === 0 || oldVerCount === 0) {\r\n return;\r\n }\r\n const vMap = utils.allocateTyped(Uint32Array, oldVerCount);\r\n vMap[0] = 0;\r\n let newVer = 1;\r\n\r\n let i = 1;\r\n for (; i < oldVerCount; ++i) {\r\n const start = newVer - offset < 0 ? 0 : newVer - offset;\r\n const end = start + len > newVer ? newVer : start + len;\r\n let matchedIndex = -1;\r\n\r\n for (let j = start; j < end; ++j) {\r\n if (Math.abs(vertices[i] - vertices[j]) < Number.EPSILON) {\r\n matchedIndex = j;\r\n break;\r\n }\r\n }\r\n\r\n if (matchedIndex !== -1) {\r\n vMap[i] = matchedIndex;\r\n } else {\r\n vertices[newVer].copy(vertices[i]);\r\n normals[newVer].copy(normals[i]);\r\n vMap[i] = newVer;\r\n ++newVer;\r\n }\r\n }\r\n\r\n this._remapIndices(vMap, faceVer);\r\n this._remapVertices(vertices, normals, newVer);\r\n }\r\n\r\n // Assign per-vertex colors from a volumetric texture map (same dimensions as the original volumetric data).\r\n // Along with color dominating atom is determined for each vertex\r\n // and vertices with atom out of \"visible\" subset get filtered out.\r\n // XXX only handles orthogonal volumes currently\r\n setColorVolTex(colorMap, atomMap, atomWeightMap, visibilitySelector) {\r\n let i;\r\n let idx;\r\n const numVerts = this._position.length / 3;\r\n const vertices = this._position;\r\n const origin = this._origin;\r\n const dim = this._volumetricData.getDimensions();\r\n const xs = dim[0] - 1;\r\n const ys = dim[1] - 1;\r\n const zs = dim[2] - 1;\r\n\r\n const colorData = colorMap.getData();\r\n const strideX = colorMap.getStrideX();\r\n const strideY = colorMap.getStrideY();\r\n const strideZ = colorMap.getStrideZ();\r\n\r\n let atomWeightData;\r\n let atomStrideX;\r\n let atomStrideY;\r\n let atomStrideZ;\r\n\r\n if (visibilitySelector !== null) {\r\n atomWeightData = atomWeightMap.getData();\r\n atomStrideX = atomWeightMap.getStrideX();\r\n atomStrideY = atomWeightMap.getStrideY();\r\n atomStrideZ = atomWeightMap.getStrideZ();\r\n }\r\n\r\n const xInv = 1.0 / this._xAxis.x;\r\n const yInv = 1.0 / this._yAxis.y;\r\n const zInv = 1.0 / this._zAxis.z;\r\n\r\n let atomLookup = [];\r\n let atomWeights = [];\r\n const colors = utils.allocateTyped(Float32Array, numVerts * 3);\r\n\r\n function interp(mu, idx1, idx2, c) {\r\n c[0] = (1 - mu) * colorData[idx1] + mu * colorData[idx2];\r\n c[1] = (1 - mu) * colorData[idx1 + 1] + mu * colorData[idx2 + 1];\r\n c[2] = (1 - mu) * colorData[idx1 + 2] + mu * colorData[idx2 + 2];\r\n }\r\n\r\n function collectWeight(ai, coefX, coefY, coefZ) {\r\n const a = atomMap[ai]; // atomWeightMap is a scalar field, so index into atom map should be the same\r\n if (a != null) {\r\n atomLookup[a.index] = a;\r\n const w = coefX * coefY * coefZ * atomWeightData[ai];\r\n if (typeof atomWeights[a.index] === 'undefined') {\r\n atomWeights[a.index] = w;\r\n } else {\r\n atomWeights[a.index] += w;\r\n }\r\n }\r\n }\r\n\r\n const vMap = utils.allocateTyped(Int32Array, numVerts);\r\n let newVerCount = 0;\r\n\r\n for (i = 0; i < numVerts; i++) {\r\n const ind = i * 3;\r\n const vx = (vertices[ind] - origin.x) * xInv;\r\n const vy = (vertices[ind + 1] - origin.y) * yInv;\r\n const vz = (vertices[ind + 2] - origin.z) * zInv;\r\n const x = Math.min(Math.max(vx, 0), xs) | 0;\r\n const y = Math.min(Math.max(vy, 0), ys) | 0;\r\n const z = Math.min(Math.max(vz, 0), zs) | 0;\r\n\r\n const mux = (vx - x);\r\n const muy = (vy - y);\r\n const muz = (vz - z);\r\n\r\n if (visibilitySelector != null) {\r\n // collect atom weights\r\n atomLookup = [];\r\n atomWeights = [];\r\n idx = atomWeightMap.getDirectIdx(x, y, z);\r\n collectWeight(idx, 1 - mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideX, mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideY, 1 - mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideX + atomStrideY, mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideZ, 1 - mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideZ, mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideY + atomStrideZ, 1 - mux, muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideY + atomStrideZ, mux, muy, muz);\r\n\r\n // find dominant atom\r\n let maxWeight = 0.0;\r\n let dominantIdx = -1;\r\n for (const atomIdx in atomWeights) {\r\n if (atomWeights[atomIdx] > maxWeight) {\r\n dominantIdx = atomIdx;\r\n maxWeight = atomWeights[atomIdx];\r\n }\r\n }\r\n\r\n if (dominantIdx < 0 || !visibilitySelector.includesAtom(atomLookup[dominantIdx])) {\r\n // this vertex doesn't belong to visible subset and will be skipped\r\n vMap[i] = -1;\r\n continue;\r\n }\r\n }\r\n\r\n vMap[i] = newVerCount++;\r\n\r\n // color tri-linear interpolation\r\n const dx = (x < xs) ? strideX : 0;\r\n const dy = (y < ys) ? strideY : 0;\r\n const dz = (z < zs) ? strideZ : 0;\r\n\r\n const c0 = [0, 0, 0];\r\n const c1 = [0, 0, 0];\r\n const c2 = [0, 0, 0];\r\n const c3 = [0, 0, 0];\r\n\r\n idx = colorMap.getDirectIdx(x, y, z);\r\n interp(mux, idx, idx + dx, c0);\r\n interp(mux, idx + dy, idx + dx + dy, c1);\r\n interp(mux, idx + dz, idx + dx + dz, c2);\r\n interp(mux, idx + dy + dz, idx + dx + dy + dz, c3);\r\n\r\n const cz0 = [0, 0, 0];\r\n cz0[0] = (1 - muy) * c0[0] + muy * c1[0];\r\n cz0[1] = (1 - muy) * c0[1] + muy * c1[1];\r\n cz0[2] = (1 - muy) * c0[2] + muy * c1[2];\r\n\r\n const cz1 = [0, 0, 0];\r\n cz1[0] = (1 - muy) * c2[0] + muy * c3[0];\r\n cz1[1] = (1 - muy) * c2[1] + muy * c3[1];\r\n cz1[2] = (1 - muy) * c2[2] + muy * c3[2];\r\n\r\n colors[ind] = (1 - muz) * cz0[0] + muz * cz1[0];\r\n colors[ind + 1] = (1 - muz) * cz0[1] + muz * cz1[1];\r\n colors[ind + 2] = (1 - muz) * cz0[2] + muz * cz1[2];\r\n }\r\n this._colors = colors;\r\n\r\n if (visibilitySelector != null) {\r\n // shift visible vertices towards beginning of array\r\n for (i = 0; i < numVerts; ++i) {\r\n const j = vMap[i];\r\n if (j < 0) {\r\n continue;\r\n }\r\n\r\n // assert: j <= i\r\n this._position[j * 3] = this._position[i * 3];\r\n this._position[j * 3 + 1] = this._position[i * 3 + 1];\r\n this._position[j * 3 + 2] = this._position[i * 3 + 2];\r\n this._normals[j * 3] = this._normals[i * 3];\r\n this._normals[j * 3 + 1] = this._normals[i * 3 + 1];\r\n this._normals[j * 3 + 2] = this._normals[i * 3 + 2];\r\n this._colors[j * 3] = this._colors[i * 3];\r\n this._colors[j * 3 + 1] = this._colors[i * 3 + 1];\r\n this._colors[j * 3 + 2] = this._colors[i * 3 + 2];\r\n }\r\n\r\n // rebuild index list\r\n const numTriangles = this._indices.length / 3;\r\n let newTriCount = 0;\r\n for (i = 0; i < numTriangles; ++i) {\r\n const i0 = vMap[this._indices[3 * i]];\r\n const i1 = vMap[this._indices[3 * i + 1]];\r\n const i2 = vMap[this._indices[3 * i + 2]];\r\n if (i0 >= 0 && i1 >= 0 && i2 >= 0) {\r\n this._indices[3 * newTriCount] = i0;\r\n this._indices[3 * newTriCount + 1] = i1;\r\n this._indices[3 * newTriCount + 2] = i2;\r\n ++newTriCount;\r\n }\r\n }\r\n\r\n // shrink arrays to data size\r\n this._position = new Float32Array(this._position.buffer.slice(0, newVerCount * 3 * 4));\r\n this._normals = new Float32Array(this._normals.buffer.slice(0, newVerCount * 3 * 4));\r\n this._colors = new Float32Array(this._colors.buffer.slice(0, newVerCount * 3 * 4));\r\n this._indices = new Uint32Array(this._indices.buffer.slice(0, newTriCount * 3 * 4));\r\n }\r\n }\r\n\r\n toMesh() {\r\n const geo = new THREE.BufferGeometry();\r\n geo.setIndex(new THREE.BufferAttribute(this._indices, 1));\r\n geo.setAttribute('position', new THREE.BufferAttribute(this._position, 3));\r\n geo.setAttribute('normal', new THREE.BufferAttribute(this._normals, 3));\r\n geo.setAttribute('color', new THREE.BufferAttribute(this._colors, 3));\r\n geo.computeBoundingSphere();\r\n return geo;\r\n }\r\n}\r\nexport default IsoSurface;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurface from './IsoSurface';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * This is a base class for volumetric maps based isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass VolumeSurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n const params = this._opts;\r\n this.numVoxels = [128, 128, 128];\r\n this.xAxis = new THREE.Vector3(1.0, 0.0, 0.0);\r\n this.yAxis = new THREE.Vector3(0.0, 1.0, 0.0);\r\n this.zAxis = new THREE.Vector3(0.0, 0.0, 1.0);\r\n\r\n this.origin = new THREE.Vector3(0.0, 0.0, 0.0);\r\n this._visibilitySelector = params.visibilitySelector;\r\n\r\n this._calcSurface(params);\r\n }\r\n\r\n _findMinMax(posRadArray) {\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n const maxPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n const minPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n for (let i = 1; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n for (let itemIdx = 0; itemIdx < itemSize; ++itemIdx) {\r\n const tmpVal = posRadArray[ind + itemIdx];\r\n maxPosRad[itemIdx] = Math.max(tmpVal, maxPosRad[itemIdx]);\r\n minPosRad[itemIdx] = Math.min(tmpVal, minPosRad[itemIdx]);\r\n }\r\n }\r\n return { maxPosRad, minPosRad };\r\n }\r\n\r\n _findNumVoxels(posRadArray, params) {\r\n const { numVoxels } = this;\r\n const minMaxValues = this._findMinMax(posRadArray);\r\n const minCoordRad = minMaxValues.minPosRad;\r\n const maxCoordRad = minMaxValues.maxPosRad;\r\n\r\n // minrad\r\n if (minCoordRad[3] > 4.0) {\r\n params.gridSpacing *= minCoordRad[3];\r\n }\r\n\r\n let gridPadding = params.radScale * maxCoordRad[3] * 1.7;\r\n let padRad = gridPadding;\r\n padRad = 0.65 * Math.sqrt(4.0 / 3.0 * Math.PI * padRad * padRad * padRad);\r\n gridPadding = Math.max(gridPadding, padRad);\r\n\r\n let i = 0;\r\n for (; i < 3; ++i) {\r\n minCoordRad[i] -= gridPadding;\r\n maxCoordRad[i] += gridPadding;\r\n }\r\n\r\n for (i = 0; i < 3; ++i) {\r\n numVoxels[i] = Math.ceil((maxCoordRad[i] - minCoordRad[i]) / params.gridSpacing);\r\n }\r\n this.xAxis.x = (numVoxels[0] - 1) * params.gridSpacing;\r\n this.yAxis.y = (numVoxels[1] - 1) * params.gridSpacing;\r\n this.zAxis.z = (numVoxels[2] - 1) * params.gridSpacing;\r\n\r\n [this.origin.x, this.origin.y, this.origin.z] = minCoordRad;\r\n\r\n return { bbox: minMaxValues, dim: numVoxels };\r\n }\r\n\r\n _makeSurface(surface, params) {\r\n const isoSurf = new IsoSurface();\r\n isoSurf.compute(surface.volMap, this.origin, params.isoValue, 1);\r\n isoSurf.vertexFusion(9, 9);// normalization is included\r\n\r\n if (isoSurf._numTriangles > 0) {\r\n isoSurf.setColorVolTex(surface.volTexMap, surface.atomMap, surface.atomWeightMap, this._visibilitySelector);\r\n this.setIndex(new THREE.BufferAttribute(isoSurf._indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(isoSurf._position, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(isoSurf._normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(isoSurf._colors, 3));\r\n } else { // geometry should have at least empty position attributes to be processed in wireframe mode by three.js\r\n this.setAttribute('position', new THREE.BufferAttribute(utils.allocateTyped(Float32Array, 0), 3));\r\n }\r\n }\r\n\r\n _calcSurface(params) {\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n\r\n if (packedArrays.posRad.length === 0) {\r\n return;\r\n }\r\n const boundaries = this._findNumVoxels(packedArrays.posRad, params);\r\n\r\n const box = new THREE.Box3(\r\n this.origin,\r\n new THREE.Vector3(this.xAxis.x, this.yAxis.y, this.zAxis.z).add(this.origin),\r\n );\r\n const surface = this._computeSurface(packedArrays, box, boundaries, params);\r\n\r\n this._makeSurface(surface, params);\r\n }\r\n}\r\n\r\nexport default VolumeSurfaceGeometry;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass QuickSurfGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n // beware of shifting this multiple times!\r\n this._shiftByOrigin(packedArrays.posRad);\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3),\r\n };\r\n\r\n if (this._visibilitySelector != null) {\r\n surface.atomMap = [];\r\n surface.atomWeightMap = new Volume(Float32Array, this.numVoxels, box);\r\n }\r\n\r\n this.gaussdensity(surface, packedArrays, null, params);\r\n return surface;\r\n }\r\n\r\n gaussdensity(surface, packedArrays, atomicNum, params) {\r\n const numAtoms = packedArrays.posRad.length / 4;\r\n const { posRad, colors } = packedArrays;\r\n const { numVoxels } = this;\r\n const { radScale, gaussLim, gridSpacing } = params;\r\n const invIsoValue = 1.0 / params.isoValue;\r\n const invGridSpacing = 1.0 / gridSpacing;\r\n const maxVoxelX = numVoxels[0] - 1;\r\n const maxVoxelY = numVoxels[1] - 1;\r\n const maxVoxelZ = numVoxels[2] - 1;\r\n // TODO is densityMap and volTexMap initialized?\r\n\r\n const { volMap, volTexMap } = surface;\r\n const volData = volMap.getData();\r\n const strideX = volMap.getStrideX();\r\n\r\n const volTexData = volTexMap.getData();\r\n const texStrideX = volTexMap.getStrideX();\r\n\r\n let atomWeightData;\r\n if (this._visibilitySelector != null) {\r\n atomWeightData = surface.atomWeightMap.getData();\r\n }\r\n\r\n const { atomMap } = surface;\r\n\r\n for (let i = 0; i < numAtoms; ++i) {\r\n const ind = i * 4;\r\n const scaledRad = posRad[ind + 3] * radScale;\r\n const atomicNumFactor = atomicNum === null ? 1.0 : atomicNum[i];\r\n const radInv = 1 / (2 * scaledRad * scaledRad);\r\n let radLim = gaussLim * scaledRad;\r\n const radLim2 = radLim * radLim;\r\n radLim *= invGridSpacing;\r\n\r\n let tmp = posRad[ind] * invGridSpacing;\r\n const xMin = Math.max((tmp - radLim) | 0, 0);\r\n const xMax = Math.min((tmp + radLim) | 0, maxVoxelX);\r\n tmp = posRad[ind + 1] * invGridSpacing;\r\n const yMin = Math.max((tmp - radLim) | 0, 0);\r\n const yMax = Math.min((tmp + radLim) | 0, maxVoxelY);\r\n tmp = posRad[ind + 2] * invGridSpacing;\r\n const zMin = Math.max((tmp - radLim) | 0, 0);\r\n const zMax = Math.min((tmp + radLim) | 0, maxVoxelZ);\r\n\r\n let dz = zMin * gridSpacing - posRad[ind + 2];\r\n for (let z = zMin; z <= zMax; ++z, dz += gridSpacing) {\r\n let dy = yMin * gridSpacing - posRad[ind + 1];\r\n for (let y = yMin; y <= yMax; ++y, dy += gridSpacing) {\r\n const dy2dz2 = dy * dy + dz * dz;\r\n\r\n if (dy2dz2 >= radLim2) {\r\n continue;\r\n }\r\n\r\n let addr = volMap.getDirectIdx(xMin, y, z);\r\n let texAddr = volTexMap.getDirectIdx(xMin, y, z);\r\n let dx = xMin * gridSpacing - posRad[ind];\r\n for (let x = xMin; x <= xMax; ++x, dx += gridSpacing, addr += strideX, texAddr += texStrideX) {\r\n const r2 = dx * dx + dy2dz2;\r\n const expVal = -r2 * radInv;\r\n\r\n let density = Math.exp(expVal) * atomicNumFactor;\r\n\r\n // store most relevant atom (with highest density)\r\n if (this._visibilitySelector != null\r\n && density > atomWeightData[addr]) { // NOSONAR\r\n atomWeightData[addr] = density;\r\n // we use same index into atom map and atomWeightMap\r\n atomMap[addr] = packedArrays.atoms[i];\r\n }\r\n\r\n volData[addr] += density;\r\n\r\n // TODO check for volTexMap routine?\r\n density *= invIsoValue;\r\n const colInd = i * 3;\r\n volTexData[texAddr] += density * colors[colInd];\r\n volTexData[texAddr + 1] += density * colors[colInd + 1];\r\n volTexData[texAddr + 2] += density * colors[colInd + 2];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n _shiftByOrigin(posRadArray) {\r\n const originX = this.origin.x;\r\n const originY = this.origin.y;\r\n const originZ = this.origin.z;\r\n\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n for (let i = 0; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n posRadArray[ind] -= originX;\r\n posRadArray[ind + 1] -= originY;\r\n posRadArray[ind + 2] -= originZ;\r\n }\r\n }\r\n}\r\n\r\nexport default QuickSurfGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * Modifed from SpatialHash\r\n *\r\n * Main differences are:\r\n * - Optimized grid size to ensure we only ever need to look +/-1 cell\r\n * - Aware of atomic radii and will only output atoms within rAtom + rExtra\r\n * (see withinRadii method)\r\n *\r\n * (Uses rounding rather than bitshifting as consequence of arbitrary grid size)\r\n * @class\r\n * @param {Float32Array} posRad - x, y, z coordinates and radiuses\r\n * @param {Float32Array} min - xyz min coordinates\r\n * @param {Float32Array} max - xyz max coordinates\r\n * @param {number} maxDistance - max distance\r\n */\r\nfunction AVHash(posRad, min, max, maxDistance) {\r\n const itemSize = 4;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const minX = min[0];\r\n const minY = min[1];\r\n const minZ = min[2];\r\n\r\n const maxX = max[0];\r\n const maxY = max[1];\r\n const maxZ = max[2];\r\n\r\n function hashFunc(w, minW) {\r\n return Math.floor((w - minW) / maxDistance);\r\n }\r\n\r\n const iDim = hashFunc(maxX, minX) + 1;\r\n const jDim = hashFunc(maxY, minY) + 1;\r\n const kDim = hashFunc(maxZ, minZ) + 1;\r\n\r\n const nCells = iDim * jDim * kDim;\r\n\r\n const jkDim = jDim * kDim;\r\n\r\n /* Get cellID for cartesian x,y,z */\r\n const cellID = function (x, y, z) {\r\n return (((hashFunc(x, minX) * jDim) + hashFunc(y, minY)) * kDim) + hashFunc(z, minZ);\r\n };\r\n\r\n /* Initial building, could probably be optimized further */\r\n const preHash = [];\r\n let i;\r\n let cid;\r\n for (i = 0; i < nAtoms; i++) {\r\n const iIdx = itemSize * i;\r\n cid = cellID(posRad[iIdx], posRad[iIdx + 1], posRad[iIdx + 2]);\r\n\r\n if (preHash[cid] === undefined) {\r\n preHash[cid] = [i];\r\n } else {\r\n preHash[cid].push(i);\r\n }\r\n }\r\n\r\n const cellOffsets = utils.allocateTyped(Uint32Array, nCells);\r\n const cellLengths = utils.allocateTyped(Uint16Array, nCells);\r\n const data = utils.allocateTyped(Uint32Array, nAtoms);\r\n\r\n let offset = 0;\r\n let maxCellLength = 0;\r\n let j;\r\n for (i = 0; i < nCells; i++) {\r\n const start = cellOffsets[i] = offset;\r\n\r\n const subArray = preHash[i];\r\n\r\n if (subArray !== undefined) {\r\n for (j = 0; j < subArray.length; j++) {\r\n data[offset] = subArray[j];\r\n offset++;\r\n }\r\n }\r\n\r\n const cellLength = offset - start;\r\n cellLengths[i] = cellLength;\r\n\r\n if (cellLength > maxCellLength) {\r\n maxCellLength = cellLength;\r\n }\r\n }\r\n\r\n // Maximum number of neighbours we could ever produce (27 adjacent cells of equal population)\r\n this.neighbourListLength = (27 * maxCellLength) + 1;\r\n\r\n /**\r\n * Populate the supplied out array with atom indices that are within rAtom + rExtra\r\n * of x,y,z\r\n *\r\n * -1 in out array indicates the end of the list\r\n *\r\n * @param {number} x - x coordinate\r\n * @param {number} y - y coordinate\r\n * @param {number} z - z coordinate\r\n * @param {number} rExtra - additional radius\r\n * @param {Float32Array} out - pre-allocated output array\r\n * @return {undefined}\r\n */\r\n this.withinRadii = function (x, y, z, rExtra, out) {\r\n let outIdx = 0;\r\n\r\n const nearI = hashFunc(x, minX);\r\n const nearJ = hashFunc(y, minY);\r\n const nearK = hashFunc(z, minZ);\r\n\r\n const loI = Math.max(0, nearI - 1);\r\n const loJ = Math.max(0, nearJ - 1);\r\n const loK = Math.max(0, nearK - 1);\r\n\r\n const hiI = Math.min(iDim - 1, nearI + 1);\r\n const hiJ = Math.min(jDim - 1, nearJ + 1);\r\n const hiK = Math.min(kDim - 1, nearK + 1);\r\n\r\n for (i = loI; i <= hiI; ++i) {\r\n const iOffset = i * jkDim;\r\n\r\n for (j = loJ; j <= hiJ; ++j) {\r\n const jOffset = j * kDim;\r\n\r\n for (let k = loK; k <= hiK; ++k) {\r\n cid = iOffset + jOffset + k;\r\n\r\n const cellStart = cellOffsets[cid];\r\n const cellEnd = cellStart + cellLengths[cid];\r\n\r\n for (let dataIndex = cellStart; dataIndex < cellEnd; dataIndex++) {\r\n const atomIndex = data[dataIndex];\r\n const baseIndex = itemSize * atomIndex;\r\n const dx = posRad[baseIndex] - x;\r\n const dy = posRad[baseIndex + 1] - y;\r\n const dz = posRad[baseIndex + 2] - z;\r\n const rSum = posRad[baseIndex + 3] + rExtra;\r\n\r\n if ((dx * dx + dy * dy + dz * dz) <= (rSum * rSum)) {\r\n out[outIdx++] = data[dataIndex];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n // Add terminator\r\n out[outIdx] = -1;\r\n };\r\n}\r\nfunction ContactSurface(packedArrays, boundaries, params, _indexList) {\r\n // Field generation method adapted from AstexViewer (Mike Hartshorn)\r\n // by Fred Ludlow.\r\n // Other parts based heavily on NGL (Alexander Rose) EDT Surface class\r\n //\r\n // Should work as a drop-in alternative to EDTSurface (though some of\r\n // the EDT paramters are not relevant in this method).\r\n\r\n const itemSize = 4;\r\n const { posRad, colors, atoms } = packedArrays;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const { bbox } = boundaries;\r\n\r\n const min = bbox.minPosRad;\r\n const max = bbox.maxPosRad;\r\n\r\n let r2; // Atom positions, expanded radii (squared)\r\n let maxRadius;\r\n\r\n // Parameters\r\n let probeRadius;\r\n let scaleFactor;\r\n let probePositions;\r\n\r\n // Cache last value for obscured test\r\n let lastClip = -1;\r\n\r\n // Grid params\r\n let dim;\r\n let grid;\r\n let volTex;\r\n let weights;\r\n let weightsMap = null;\r\n let atomMap = null;\r\n let visibilitySelector = null;\r\n\r\n // grid indices -> xyz coords\r\n let gridx;\r\n let gridy;\r\n let gridz;\r\n\r\n // Lookup tables:\r\n let sinTable;\r\n let cosTable;\r\n\r\n // Spatial Hash\r\n let hash;\r\n\r\n // Neighbour array to be filled by hash\r\n let neighbours;\r\n\r\n // Vectors for Torus Projection\r\n const mid = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n1 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n2 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n let ngTorus;\r\n\r\n function uniformArray(TypeName, n, a) {\r\n const array = utils.allocateTyped(TypeName, n);\r\n for (let innI = 0; innI < n; ++innI) {\r\n array[innI] = a;\r\n }\r\n\r\n return array;\r\n }\r\n\r\n function fillGridDim(a, start, step) {\r\n for (let innI = 0; innI < a.length; innI++) {\r\n a[innI] = start + (step * innI);\r\n }\r\n }\r\n\r\n function initializeGrid() {\r\n ({ scaleFactor } = params);\r\n ({ dim } = boundaries);\r\n\r\n ngTorus = Math.min(5, 2 + Math.floor(probeRadius * scaleFactor));\r\n\r\n const gridSize = dim[0] * dim[1] * dim[2];\r\n grid = uniformArray(Float32Array, gridSize, -1001.0);\r\n volTex = utils.allocateTyped(Float32Array, gridSize * 3);\r\n weights = utils.allocateTyped(Float32Array, gridSize);\r\n if (visibilitySelector) {\r\n weightsMap = utils.allocateTyped(Float32Array, gridSize);\r\n atomMap = [];\r\n }\r\n\r\n gridx = utils.allocateTyped(Float32Array, dim[0]);\r\n gridy = utils.allocateTyped(Float32Array, dim[1]);\r\n gridz = utils.allocateTyped(Float32Array, dim[2]);\r\n\r\n fillGridDim(gridx, min[0], 1 / scaleFactor);\r\n fillGridDim(gridy, min[1], 1 / scaleFactor);\r\n fillGridDim(gridz, min[2], 1 / scaleFactor);\r\n }\r\n\r\n function initializeAngleTables() {\r\n let theta = 0.0;\r\n const step = 2 * Math.PI / probePositions;\r\n\r\n cosTable = utils.allocateTyped(Float32Array, probePositions);\r\n sinTable = utils.allocateTyped(Float32Array, probePositions);\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n cosTable[innI] = Math.cos(theta);\r\n sinTable[innI] = Math.sin(theta);\r\n theta += step;\r\n }\r\n }\r\n\r\n function initializeHash() {\r\n hash = new AVHash(posRad, min, max, 2.01 * maxRadius);\r\n neighbours = new Int32Array(hash.neighbourListLength);\r\n }\r\n\r\n function init() {\r\n ({\r\n probeRadius,\r\n scaleFactor,\r\n probePositions,\r\n visibilitySelector,\r\n } = params);\r\n r2 = utils.allocateTyped(Float32Array, nAtoms);\r\n maxRadius = 0;\r\n for (let innI = 0; innI < nAtoms; ++innI) {\r\n const rExt = posRad[innI * itemSize + 3] += probeRadius;\r\n if (rExt > maxRadius) {\r\n maxRadius = rExt;\r\n }\r\n r2[innI] = rExt * rExt;\r\n }\r\n\r\n initializeGrid();\r\n initializeAngleTables();\r\n initializeHash();\r\n\r\n lastClip = -1;\r\n }\r\n\r\n function singleAtomObscures(ai, innX, innY, innZ) {\r\n const innCI = itemSize * ai;\r\n const ra2 = r2[ai];\r\n const dx = posRad[innCI] - innX;\r\n const dy = posRad[innCI + 1] - innY;\r\n const dz = posRad[innCI + 2] - innZ;\r\n const d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n return d2 < ra2;\r\n }\r\n\r\n function obscured(innX, innY, innZ, a, b) {\r\n // Is the point at x,y,z obscured by any of the atoms\r\n // specifeid by indices in neighbours. Ignore indices\r\n // a and b (these are the relevant atoms in projectPoints/Torii)\r\n\r\n // Cache the last clipped atom (as very often the same one in\r\n // subsequent calls)\r\n let ai;\r\n\r\n if (lastClip !== -1) {\r\n ai = lastClip;\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n return ai;\r\n }\r\n lastClip = -1;\r\n }\r\n\r\n let ni = 0;\r\n ai = neighbours[ni];\r\n while (ai >= 0) {\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n lastClip = ai;\r\n return ai;\r\n }\r\n ai = neighbours[++ni];\r\n }\r\n\r\n lastClip = -1;\r\n\r\n return -1;\r\n }\r\n\r\n function projectPoints() {\r\n // For each atom:\r\n // Iterate over a subsection of the grid, for each point:\r\n // If current value < 0.0, unvisited, set positive\r\n //\r\n // In any case: Project this point onto surface of the atomic sphere\r\n // If this projected point is not obscured by any other atom\r\n // Calcualte delta distance and set grid value to minimum of\r\n // itself and delta\r\n\r\n // Should we alias frequently accessed closure constiables??\r\n // Assume JS engine capable of optimizing this\r\n // anyway...\r\n const maxRad = 4.0;\r\n const sigma = (maxRad) / 3;\r\n const sigma2Inv = 1 / (2 * sigma * sigma);\r\n\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innCI = itemSize * innI;\r\n const ax = posRad[innCI];\r\n const ay = posRad[innCI + 1];\r\n const az = posRad[innCI + 2];\r\n const ar = posRad[innCI + 3];\r\n const ar2 = r2[innI];\r\n\r\n hash.withinRadii(ax, ay, az, ar, neighbours);\r\n\r\n // Number of grid points, round this up...\r\n const ng = Math.ceil(ar * scaleFactor);\r\n\r\n // Center of the atom, mapped to grid points (take floor)\r\n const iax = Math.floor(scaleFactor * (ax - min[0]));\r\n const iay = Math.floor(scaleFactor * (ay - min[1]));\r\n const iaz = Math.floor(scaleFactor * (az - min[2]));\r\n\r\n // Extents of grid to consider for this atom\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n // Add two to these points:\r\n // - iax are floor'd values so this ensures coverage\r\n // - these are loop limits (exclusive)\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n const colIdx = innI * 3;\r\n const cr = colors[colIdx];\r\n const cg = colors[colIdx + 1];\r\n const cb = colors[colIdx + 2];\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n const dz = gridz[iz] - az;\r\n const zOffset = dim[1] * dim[0] * iz;\r\n\r\n for (let iy = miny; iy < maxy; iy++) {\r\n const dy = gridy[iy] - ay;\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n\r\n for (let ix = minx; ix < maxx; ix++) {\r\n const idx = ix + zyOffset;\r\n const dx = gridx[ix] - ax;\r\n const d2 = dzy2 + dx * dx;\r\n\r\n if (d2 < ar2) {\r\n const w = Math.exp(-d2 * sigma2Inv);\r\n const cIdx = idx * 3;\r\n volTex[cIdx] += cr * w;\r\n volTex[cIdx + 1] += cg * w;\r\n volTex[cIdx + 2] += cb * w;\r\n weights[idx] += w;\r\n if (visibilitySelector !== null && w > weightsMap[idx]) {\r\n weightsMap[idx] = w;\r\n atomMap[idx] = atoms[innI];\r\n }\r\n\r\n if (grid[idx] < 0.0) {\r\n // Unvisited, make positive\r\n grid[idx] = -grid[idx];\r\n }\r\n // Project on to the surface of the sphere\r\n // sp is the projected point ( dx, dy, dz ) * ( ra / d )\r\n const d = Math.sqrt(d2);\r\n const ap = ar / d;\r\n let spx = dx * ap;\r\n let spy = dy * ap;\r\n let spz = dz * ap;\r\n\r\n spx += ax;\r\n spy += ay;\r\n spz += az;\r\n\r\n if (obscured(spx, spy, spz, innI, -1) === -1) {\r\n const dd = ar - d;\r\n if (dd < grid[idx]) {\r\n grid[idx] = dd;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function normalToLine(out, p) {\r\n out.x = out.y = out.z = 1.0;\r\n if (p.x !== 0) {\r\n out.x = (p.y + p.z) / -p.x;\r\n } else if (p.y !== 0) {\r\n out.y = (p.x + p.z) / -p.y;\r\n } else if (p.z !== 0) {\r\n out.z = (p.x + p.y) / -p.z;\r\n }\r\n return out;\r\n }\r\n\r\n function projectTorus(a, b) {\r\n const aIdx = itemSize * a;\r\n const bIdx = itemSize * b;\r\n const xa = posRad[aIdx];\r\n const ya = posRad[aIdx + 1];\r\n const za = posRad[aIdx + 2];\r\n const r1 = posRad[aIdx + 3];\r\n let dx = mid.x = posRad[bIdx] - xa;\r\n let dy = mid.y = posRad[bIdx + 1] - ya;\r\n let dz = mid.z = posRad[bIdx + 2] - za;\r\n const innR2 = posRad[bIdx + 3];\r\n let d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n // This check now redundant as already done in AVHash.withinRadii\r\n // if( d2 > (( r1 + r2 ) * ( r1 + r2 )) ){ return; }\r\n\r\n const d = Math.sqrt(d2);\r\n\r\n // Find angle between a->b vector and the circle\r\n // of their intersection by cosine rule\r\n const cosA = (r1 * r1 + d * d - innR2 * innR2) / (2.0 * r1 * d);\r\n\r\n // distance along a->b at intersection\r\n const dmp = r1 * cosA;\r\n\r\n mid.normalize();\r\n\r\n // Create normal to line\r\n normalToLine(n1, mid);\r\n n1.normalize();\r\n\r\n // Cross together for second normal vector\r\n n2.crossVectors(mid, n1);\r\n n2.normalize();\r\n\r\n // r is radius of circle of intersection\r\n const rInt = Math.sqrt(r1 * r1 - dmp * dmp);\r\n\r\n n1.multiplyScalar(rInt);\r\n n2.multiplyScalar(rInt);\r\n mid.multiplyScalar(dmp);\r\n\r\n mid.x += xa;\r\n mid.y += ya;\r\n mid.z += za;\r\n\r\n lastClip = -1;\r\n\r\n const ng = ngTorus;\r\n\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n const cost = cosTable[innI];\r\n const sint = sinTable[innI];\r\n\r\n const px = mid.x + cost * n1.x + sint * n2.x;\r\n const py = mid.y + cost * n1.y + sint * n2.y;\r\n const pz = mid.z + cost * n1.z + sint * n2.z;\r\n\r\n if (obscured(px, py, pz, a, b) === -1) {\r\n // As above, iterate over our grid...\r\n // px, py, pz in grid coords\r\n const iax = Math.floor(scaleFactor * (px - min[0]));\r\n const iay = Math.floor(scaleFactor * (py - min[1]));\r\n const iaz = Math.floor(scaleFactor * (pz - min[2]));\r\n\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n dz = pz - gridz[iz];\r\n const zOffset = dim[1] * dim[0] * iz;\r\n for (let iy = miny; iy < maxy; iy++) {\r\n dy = py - gridy[iy];\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n for (let ix = minx; ix < maxx; ix++) {\r\n dx = px - gridx[ix];\r\n d2 = dzy2 + dx * dx;\r\n const idx = ix + zyOffset;\r\n const current = grid[idx];\r\n\r\n if (current > 0.0 && d2 < (current * current)) {\r\n grid[idx] = Math.sqrt(d2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function projectTorii() {\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innIdx = itemSize * innI;\r\n hash.withinRadii(\r\n posRad[innIdx],\r\n posRad[innIdx + 1],\r\n posRad[innIdx + 2],\r\n posRad[innIdx + 3],\r\n neighbours,\r\n );\r\n let ia = 0;\r\n let ni = neighbours[ia];\r\n while (ni >= 0) {\r\n if (innI < ni) {\r\n projectTorus(innI, ni);\r\n }\r\n ni = neighbours[++ia];\r\n }\r\n }\r\n }\r\n\r\n function fixNegatives() {\r\n for (let innI = 0, n = grid.length; innI < n; innI++) {\r\n if (grid[innI] < 0) grid[innI] = 0;\r\n let w = weights[innI];\r\n if (w > 0) {\r\n w = 1 / w;\r\n const innInnI = innI * 3;\r\n volTex[innInnI] *= w;\r\n volTex[innInnI + 1] *= w;\r\n volTex[innInnI + 2] *= w;\r\n }\r\n }\r\n }\r\n\r\n function getVolume() {\r\n // Basic steps are:\r\n // 1) Initialize\r\n // 2) Project points\r\n // 3) Project torii\r\n console.time('ContactSurface.getVolume');\r\n\r\n console.time('ContactSurface.init');\r\n init();\r\n console.timeEnd('ContactSurface.init');\r\n\r\n console.time('ContactSurface.projectPoints');\r\n projectPoints();\r\n console.timeEnd('ContactSurface.projectPoints');\r\n\r\n console.time('ContactSurface.projectTorii');\r\n projectTorii();\r\n console.timeEnd('ContactSurface.projectTorii');\r\n fixNegatives();\r\n console.timeEnd('ContactSurface.getVolume');\r\n }\r\n\r\n this.build = function () {\r\n // type and cutoff left in for compatibility with EDTSurface.getSurface\r\n // function signature\r\n getVolume();\r\n this.volTexMap = volTex;\r\n this.weightsMap = weightsMap;\r\n this.atomMap = atomMap;\r\n this.volMap = grid;\r\n };\r\n}\r\nexport default ContactSurface;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport ContactSurface from './ContactSurface';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'contact' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass ContactSurfaceGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n const contactSurface = new ContactSurface(packedArrays, boundaries, params);\r\n contactSurface.build();\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.volMap),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3, contactSurface.volTexMap),\r\n atomMap: contactSurface.atomMap,\r\n atomWeightMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.weightsMap),\r\n };\r\n return surface;\r\n }\r\n}\r\n\r\nexport default ContactSurfaceGeometry;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for colored atom. Need for atom structure clusterization\r\n *\r\n * @param {Vector3} vCenter Center of atom\r\n * @param {number} radiusAt Radius of atom\r\n */\r\nclass IsoSurfaceAtomColored {\r\n constructor(vCenter, radiusAt) {\r\n this.coord = new THREE.Vector3();\r\n this.coord.copy(vCenter);\r\n this.radius = radiusAt;\r\n this.colorX = 0.99999;\r\n this.colorY = 0.0;\r\n this.colorZ = 0.0;\r\n this.atomType = 0;\r\n this.srcAtom = null;\r\n }\r\n}\r\nexport default IsoSurfaceAtomColored;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n// suppress some JSHint warnings\r\n/* jshint bitwise: false */\r\n\r\n/**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numAtoms - Number of atoms in molecule\r\n * @param {Element} atoms - Array of atoms\r\n * @param {Vector3} vBoxMin - Bounding box min\r\n * @param {Vector3} vBoxMax - Bounding box max\r\n * @param {number} probeRadius - Normals for output\r\n *\r\n */\r\nclass IsosurfaceBuildNormals {\r\n constructor(numAtoms, atoms, vBoxMin, vBoxMax, probeRadius) {\r\n this._numAtoms = numAtoms;\r\n this._atoms = atoms;\r\n this._vBoxMin = new THREE.Vector3();\r\n this._vBoxMax = new THREE.Vector3();\r\n this._vBoxMin.copy(vBoxMin);\r\n this._vBoxMax.copy(vBoxMax);\r\n this._probeRadius = probeRadius;\r\n\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n }\r\n\r\n createVoxels() {\r\n let numAtomsRefs;\r\n let rad;\r\n const ATOM_VOXEL_REF_SCALE = 4.5;\r\n\r\n const numAtoms = this._numAtoms | 0;\r\n const atoms = this._atoms;\r\n const dx = this._vBoxMax.x - this._vBoxMin.x;\r\n const dy = this._vBoxMax.y - this._vBoxMin.y;\r\n const dz = this._vBoxMax.z - this._vBoxMin.z;\r\n let w = (dx < dy) ? dx : dy;\r\n w = (dz < w) ? dz : w;\r\n let maxRad = 0.0;\r\n let aveRad = 0.0;\r\n\r\n let i;\r\n for (i = 0; i < numAtoms; i++) {\r\n rad = (atoms[i].radius + this._probeRadius) * 2.0;\r\n maxRad = (rad > maxRad) ? rad : maxRad;\r\n aveRad += rad;\r\n }\r\n let numCells = Math.floor(w / maxRad);\r\n if (numCells < 2) {\r\n numCells = 2;\r\n }\r\n aveRad /= numAtoms;\r\n\r\n this._numCells = numCells;\r\n this._aveRad = aveRad;\r\n this._maxRad = maxRad;\r\n\r\n const side = numCells;\r\n const side2 = numCells * numCells;\r\n const side3 = numCells * numCells * numCells;\r\n\r\n const xScale = this._xScale = 1.0 / (this._vBoxMax.x - this._vBoxMin.x);\r\n const yScale = this._yScale = 1.0 / (this._vBoxMax.y - this._vBoxMin.y);\r\n const zScale = this._zScale = 1.0 / (this._vBoxMax.z - this._vBoxMin.z);\r\n\r\n // estimate number of individual atom refs in each voxel list\r\n let maxAtomsRefs = 0;\r\n\r\n const xNumVoxMult = xScale * numCells;\r\n const yNumVoxMult = yScale * numCells;\r\n const zNumVoxMult = zScale * numCells;\r\n\r\n for (i = 0; i < numAtoms; i++) {\r\n const radAffect = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n const diaAffect = radAffect * 2.0;\r\n let numVoxX = Math.floor(xNumVoxMult * diaAffect + 0.8);\r\n let numVoxY = Math.floor(yNumVoxMult * diaAffect + 0.8);\r\n let numVoxZ = Math.floor(zNumVoxMult * diaAffect + 0.8);\r\n // avoid case numVox? == 0\r\n // also use loop i <=\r\n numVoxX++;\r\n numVoxY++;\r\n numVoxZ++;\r\n maxAtomsRefs += numVoxX * numVoxY * numVoxZ;\r\n } // for (i)\r\n // maxAtomsRefs = numAtoms * MAX_ATOMS_IN_SINGLE_VOXEL;\r\n\r\n this._voxelList = utils.allocateTyped(Int32Array, side3);\r\n const atomsList = [];\r\n atomsList.length = maxAtomsRefs;\r\n if ((this._voxelList === null) || (atomsList === null)) {\r\n return 0 - 1;\r\n }\r\n // init voxel list\r\n for (i = 0; i < side3; i++) {\r\n this._voxelList[i] = -1;\r\n }\r\n numAtomsRefs = 0;\r\n\r\n // create voxel lists\r\n for (i = 0; i < numAtoms; i++) {\r\n // use multiplier 4 to locate this atom in different voxels\r\n rad = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n let xIndMin = Math.floor((atoms[i].coord.x - this._vBoxMin.x - rad) * numCells * xScale);\r\n let yIndMin = Math.floor((atoms[i].coord.y - this._vBoxMin.y - rad) * numCells * yScale);\r\n let zIndMin = Math.floor((atoms[i].coord.z - this._vBoxMin.z - rad) * numCells * zScale);\r\n let xIndMax = Math.floor((atoms[i].coord.x - this._vBoxMin.x + rad) * numCells * xScale);\r\n let yIndMax = Math.floor((atoms[i].coord.y - this._vBoxMin.y + rad) * numCells * yScale);\r\n let zIndMax = Math.floor((atoms[i].coord.z - this._vBoxMin.z + rad) * numCells * zScale);\r\n\r\n xIndMin = (xIndMin >= 0) ? xIndMin : 0;\r\n yIndMin = (yIndMin >= 0) ? yIndMin : 0;\r\n zIndMin = (zIndMin >= 0) ? zIndMin : 0;\r\n\r\n xIndMax = (xIndMax < numCells) ? xIndMax : (numCells - 1);\r\n yIndMax = (yIndMax < numCells) ? yIndMax : (numCells - 1);\r\n zIndMax = (zIndMax < numCells) ? zIndMax : (numCells - 1);\r\n\r\n for (let z = zIndMin; z <= zIndMax; z++) {\r\n for (let y = yIndMin; y <= yIndMax; y++) {\r\n for (let x = xIndMin; x <= xIndMax; x++) {\r\n // add atom with index \"i\" to this voxel list\r\n const indVoxel = x + y * side + z * side2;\r\n // assert indVoxel >= 0\r\n // assert indVoxel < side3\r\n\r\n // add first\r\n if (this._voxelList[indVoxel] < 0) {\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = 0 - 1;\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n numAtomsRefs++;\r\n // assert numAtomsRefs < maxAtomsRefs - 1\r\n continue;\r\n }\r\n // insert into head of list\r\n const indexNext = this._voxelList[indVoxel];\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = indexNext;\r\n numAtomsRefs++;\r\n } // for (x)\r\n } // for (y)\r\n } // for (z)\r\n } // for (i)\r\n\r\n // convert Array to Int32Array\r\n this._atomsList = Int32Array.from(atomsList);\r\n\r\n return 0;\r\n }\r\n\r\n destroyVoxels() {\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n\r\n this._atoms = null;\r\n this._vertices = null;\r\n this._vBoxMin = null;\r\n this._vBoxMax = null;\r\n }\r\n\r\n /**\r\n * Enumerate all atoms affecting specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n * @param {func(atom)} process - function to call for each atom\r\n */\r\n forEachRelatedAtom(point, process) {\r\n // find corresponding voxel\r\n const xInd = Math.floor((point.x - this._vBoxMin.x) * this._numCells * this._xScale);\r\n const yInd = Math.floor((point.y - this._vBoxMin.y) * this._numCells * this._yScale);\r\n const zInd = Math.floor((point.z - this._vBoxMin.z) * this._numCells * this._zScale);\r\n const indVoxel = xInd + yInd * this._numCells + zInd * this._numCells * this._numCells;\r\n\r\n // run through atoms affecting this voxel\r\n const atoms = this._atoms;\r\n for (let ref = this._voxelList[indVoxel]; ref >= 0; ref = this._atomsList[ref * 2 + 1]) {\r\n const indexAtom = this._atomsList[ref * 2];\r\n process(atoms[indexAtom]);\r\n }\r\n }\r\n\r\n /**\r\n * Get atom closest to specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n *\r\n * @returns {IsoSurfaceAtomColored} atom, or null if not found\r\n */\r\n getClosestAtom(point) {\r\n let closest = null;\r\n let minDist2 = Number.MAX_VALUE;\r\n\r\n this.forEachRelatedAtom(point, (atom) => {\r\n const dist2 = point.distanceToSquared(atom.coord);\r\n if (dist2 < minDist2) {\r\n minDist2 = dist2;\r\n closest = atom;\r\n }\r\n });\r\n\r\n return closest;\r\n }\r\n\r\n /**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} normals - Normals for output\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildNormals(numVertices, vertices, normals) {\r\n const self = this;\r\n let numCloseAtoms = 0;\r\n let vx = 0;\r\n let vy = 0;\r\n let vz = 0;\r\n let dist2;\r\n let vNormalX = 0;\r\n let vNormalY = 0;\r\n let vNormalZ = 0;\r\n let koef = 0;\r\n let w = 0;\r\n const r25 = 2.5;\r\n const r01 = 0.1;\r\n\r\n const maxRadAffect = this._aveRad * r25;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n const expScale = -this._aveRad * r01;\r\n\r\n // some stats\r\n // numSlowAtoms = 0;\r\n\r\n const gatherNormals = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = Math.exp(expScale * koef);\r\n\r\n vNormalX += dx * w;\r\n vNormalY += dy * w;\r\n vNormalZ += dz * w;\r\n numCloseAtoms++;\r\n };\r\n\r\n let maxClosedAtoms = 0;\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n numCloseAtoms = 0;\r\n vNormalX = vNormalY = vNormalZ = 0.0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherNormals);\r\n\r\n maxClosedAtoms = (numCloseAtoms > maxClosedAtoms) ? numCloseAtoms : maxClosedAtoms;\r\n\r\n // normalize vNormal\r\n dist2 = vNormalX * vNormalX + vNormalY * vNormalY + vNormalZ * vNormalZ;\r\n if (numCloseAtoms > 0) {\r\n koef = 1.0 / Math.sqrt(dist2);\r\n vNormalX *= koef;\r\n vNormalY *= koef;\r\n vNormalZ *= koef;\r\n }\r\n normals[i].x = vNormalX;\r\n normals[i].y = vNormalY;\r\n normals[i].z = vNormalZ;\r\n } // for (i) all vertices\r\n\r\n return 0;\r\n }\r\n\r\n /**\r\n * Build vertex colors for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} colors - Colors for output\r\n * @param {number} radiusColorSmoothness - Radius of smoothness sphere\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildColors(numVertices, vertices, colors, radiusColorSmoothness) {\r\n const self = this;\r\n let vx = 0.0;\r\n let vy = 0.0;\r\n let vz = 0.0;\r\n let koef = 0.0;\r\n let w = 0.0;\r\n const KOEF_ADD = 0.8;\r\n\r\n const maxRadAffect = radiusColorSmoothness;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n\r\n let colorsClose = [];\r\n let weights = [];\r\n let weightsSum = 0;\r\n\r\n const gatherColors = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = 1.0 / (KOEF_ADD + koef);\r\n\r\n colorsClose.push([atom.colorX, atom.colorY, atom.colorZ]);\r\n weights.push(w); // save weights for use\r\n weightsSum += w; // calc sum of weights fo further normalization\r\n };\r\n\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n colorsClose = [];\r\n weights = [];\r\n weightsSum = 0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherColors);\r\n\r\n // normalized weighted sum of colors\r\n for (let j = 0; j < colorsClose.length; ++j) {\r\n const weightNormalized = weights[j] / weightsSum;\r\n colors[i].x += colorsClose[j][0] * weightNormalized;\r\n colors[i].y += colorsClose[j][1] * weightNormalized;\r\n colors[i].z += colorsClose[j][2] * weightNormalized;\r\n }\r\n } // for (i) all vertices\r\n return 0;\r\n }\r\n}\r\nexport default IsosurfaceBuildNormals;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for geometry (triangle mesh) representation\r\n *\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices in mesh\r\n * @param {number} maxNumTriangles Maximum possible number of triangles in mesh\r\n * @param {boolean} needVertexColors Obvious\r\n */\r\nclass IsoSurfaceGeo {\r\n constructor(maxNumVertices, maxNumTriangles, needVertexColors) {\r\n this._maxNumVertices = maxNumVertices;\r\n this._maxNumTriangles = maxNumTriangles;\r\n this._vertices = new Array(maxNumVertices);\r\n this._normals = new Array(maxNumVertices);\r\n this._colors = null;\r\n if (needVertexColors) {\r\n this._colors = new Array(maxNumVertices);\r\n }\r\n this._indices = new Array(maxNumTriangles * (1 + 2));\r\n this._numVertices = 0;\r\n this._numTriangles = 0;\r\n\r\n let i;\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._vertices[i] = new THREE.Vector3();\r\n this._normals[i] = new THREE.Vector3();\r\n }\r\n for (i = 0; i < maxNumTriangles * (1 + 2); i++) {\r\n this._indices[i] = -1;\r\n }\r\n if (needVertexColors) {\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._colors[i] = new THREE.Vector3();\r\n }\r\n }\r\n }\r\n\r\n destroy() {\r\n this._vertices = null;\r\n this._normals = null;\r\n this._indices = null;\r\n }\r\n}\r\nexport default IsoSurfaceGeo;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurfaceAtomColored from './IsoSurfaceAtomColored';\r\nimport IsosurfaceBuildNormals from './IsosurfaceBuildNormals';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport IsoSurfaceGeo from './IsoSurfaceGeo';\r\nimport chem from '../../chem';\r\nimport utils from '../../utils';\r\n\r\nconst COLOR_SIZE = 3;\r\nconst HASH_SIZE = 32768;\r\nconst { Element } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass SSIsosurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n // convert geoOut into arrays of positions, indices, normals\r\n this._innerBuild();\r\n const geoOut = this.getGeo();\r\n this.destroy();\r\n this._fromGeo(geoOut);\r\n }\r\n\r\n _fromGeo(geoOut) {\r\n let colors = null;\r\n const positions = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n const normals = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n if (geoOut._colors !== null) {\r\n colors = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n }\r\n const indices = utils.allocateTyped(Uint32Array, (1 + 2) * geoOut._numTriangles);\r\n\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++) {\r\n positions[j + 0] = (geoOut._vertices[i].x);\r\n positions[j + 1] = (geoOut._vertices[i].y);\r\n positions[j + 2] = (geoOut._vertices[i].z);\r\n normals[j + 0] = geoOut._normals[i].x;\r\n normals[j + 1] = geoOut._normals[i].y;\r\n normals[j + 2] = geoOut._normals[i].z;\r\n j += 3;\r\n }\r\n if (colors !== null) {\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++, j += 3) {\r\n colors[j + 0] = geoOut._colors[i].x;\r\n colors[j + 1] = geoOut._colors[i].y;\r\n colors[j + 2] = geoOut._colors[i].z;\r\n }\r\n }\r\n\r\n const numTri3 = geoOut._numTriangles * (1 + 2);\r\n for (let i = 0; i < numTri3; i++) {\r\n indices[i] = geoOut._indices[i];\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(positions, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(colors, 3));\r\n this.computeBoundingBox();\r\n this.computeBoundingSphere();\r\n\r\n geoOut.destroy();\r\n }\r\n\r\n convertToAtomsColored(packedArrays, atomsColored) {\r\n const { atoms, colors } = packedArrays;\r\n for (let i = 0, numAtoms = atoms.length; i < numAtoms; i++) {\r\n const vCenter = atoms[i].position;\r\n const { radius } = atoms[i].element;\r\n atomsColored[i] = new IsoSurfaceAtomColored(vCenter, radius);\r\n const nm = atoms[i].element.number;\r\n atomsColored[i].atomType = this.getType(nm);\r\n let cIdx = COLOR_SIZE * i;\r\n atomsColored[i].colorX = colors[cIdx++];\r\n atomsColored[i].colorY = colors[cIdx++];\r\n atomsColored[i].colorZ = colors[cIdx];\r\n atomsColored[i].srcAtom = atoms[i];\r\n }\r\n }\r\n\r\n getGeo() {\r\n return this.geoOut;\r\n }\r\n\r\n destroy() {\r\n this.atoms = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n }\r\n\r\n /**\r\n * Calculates bounding box for array with spheres (atoms)\r\n *\r\n * @param {Object} atoms Atoms array\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n */\r\n getBoundingBox(atoms, vBoxMin, vBoxMax) {\r\n const bigNum = 10000000.0;\r\n\r\n vBoxMin.x = vBoxMin.y = vBoxMin.z = bigNum;\r\n vBoxMax.x = vBoxMax.y = vBoxMax.z = 0 - bigNum;\r\n\r\n const probeRadius2 = this.probeRadius * this.atomRadiusScale;\r\n let radMax = 0.0;\r\n for (let i = 0, num = atoms.length; i < num; i++) {\r\n const vCenter = atoms[i].coord;\r\n const rad = atoms[i].radius + probeRadius2;\r\n radMax = (rad > radMax) ? rad : radMax;\r\n if (vCenter.x - rad < vBoxMin.x) {\r\n vBoxMin.x = vCenter.x - rad;\r\n }\r\n if (vCenter.y - rad < vBoxMin.y) {\r\n vBoxMin.y = vCenter.y - rad;\r\n }\r\n if (vCenter.z - rad < vBoxMin.z) {\r\n vBoxMin.z = vCenter.z - rad;\r\n }\r\n if (vCenter.x + rad > vBoxMax.x) {\r\n vBoxMax.x = vCenter.x + rad;\r\n }\r\n if (vCenter.y + rad > vBoxMax.y) {\r\n vBoxMax.y = vCenter.y + rad;\r\n }\r\n if (vCenter.z + rad > vBoxMax.z) {\r\n vBoxMax.z = vCenter.z + rad;\r\n }\r\n }\r\n vBoxMin.x -= radMax;\r\n vBoxMin.y -= radMax;\r\n vBoxMin.z -= radMax;\r\n vBoxMax.x += radMax;\r\n vBoxMax.y += radMax;\r\n vBoxMax.z += radMax;\r\n }\r\n\r\n /**\r\n * Calculate (x,y,z) cordinate of the cell corner point\r\n *\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {number} x Cell integer x coordinate\r\n * @param {number} y Cell integer y coordinate\r\n * @param {number} z Cell integer z coordinate\r\n * @param {number} numPoints NUm points in cell on side\r\n * @param {Vector3} vOut Output vector\r\n */\r\n getCornerCoord(vBoxMin, vBoxMax, x, y, z, numPoints, vOut) {\r\n const invNP = 1.0 / (numPoints - 1.0);\r\n const tx = x * invNP;\r\n const ty = y * invNP;\r\n const tz = z * invNP;\r\n\r\n vOut.x = vBoxMin.x * (1.0 - tx) + vBoxMax.x * tx;\r\n vOut.y = vBoxMin.y * (1.0 - ty) + vBoxMax.y * ty;\r\n vOut.z = vBoxMin.z * (1.0 - tz) + vBoxMax.z * tz;\r\n }\r\n\r\n /**\r\n * Calculate point of intersection of sphere surface\r\n * and cell edge, given by [indexA, indexB] line\r\n *\r\n * @param {number} indexA Cell vertex index in [0..11]\r\n * @param {number} indexB Cell vertex index in [0..11]\r\n * @param {array} sign Sign array for all 8 vertices\r\n * @param {object} cube Cube\r\n * @param {number} indexPointValue for value placement\r\n * @param {Vector3} vOut Point of intersection\r\n */\r\n buildEdgePoint(indexA, indexB, sign, cube, indexPointValue, vOut) {\r\n if (sign[indexA] ^ sign[indexB]) {\r\n const cTwentyFour = 24;\r\n const t = (0 - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA])\r\n / (cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexB]\r\n - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA]);\r\n const xa = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 0];\r\n const ya = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 1];\r\n const za = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 2];\r\n const xb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 0];\r\n const yb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 1];\r\n const zb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 2];\r\n\r\n vOut.x = xa * (1.0 - t) + xb * t;\r\n vOut.y = ya * (1.0 - t) + yb * t;\r\n vOut.z = za * (1.0 - t) + zb * t;\r\n }\r\n }\r\n\r\n /**\r\n * Check if triangle is visible (vertices are close to atoms included in visibility set)\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} true if triangle is visible\r\n */\r\n isTriangleVisible(v0, v1, v2) {\r\n const a0 = this.voxelWorld.getClosestAtom(v0);\r\n const a1 = this.voxelWorld.getClosestAtom(v1);\r\n const a2 = this.voxelWorld.getClosestAtom(v2);\r\n if (a0 === null || a1 === null || a2 === null\r\n || a0.srcAtom === null || a1.srcAtom === null || a2.srcAtom === null) {\r\n return false;\r\n }\r\n\r\n return this.visibilitySelector.includesAtom(a0.srcAtom)\r\n && this.visibilitySelector.includesAtom(a1.srcAtom)\r\n && this.visibilitySelector.includesAtom(a2.srcAtom);\r\n }\r\n\r\n /**\r\n * Add triangle to result geometry\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} false if no more triangles can be added\r\n */\r\n addTriangle(v0, v1, v2) {\r\n if (this.visibilitySelector && !this.isTriangleVisible(v0, v1, v2)) {\r\n return true;\r\n }\r\n\r\n const geo = this.geoOut;\r\n\r\n if (geo._numTriangles >= this.maxNumTriangles) {\r\n return false;\r\n }\r\n\r\n // Add vertex with optimize\r\n const indInGeo0 = this.addVertexToGeo(geo, v0);\r\n const indInGeo1 = this.addVertexToGeo(geo, v1);\r\n const indInGeo2 = this.addVertexToGeo(geo, v2);\r\n if ((indInGeo0 | indInGeo1 | indInGeo2) < 0) {\r\n return false;\r\n }\r\n\r\n const itr = 3 * geo._numTriangles;\r\n geo._indices[itr + 0] = indInGeo0;\r\n geo._indices[itr + 1] = indInGeo1;\r\n geo._indices[itr + 2] = indInGeo2;\r\n geo._numTriangles++;\r\n return true;\r\n }\r\n\r\n /**\r\n * Build result geometry (triangle mesh) from marching cube cells\r\n *\r\n * @param {number} meshRes Marchnig cube vertex count on each side\r\n * @param {Vector3} vBoxMin Bounding box point min\r\n * @param {Vector3} vBoxMax Bounding box point max\r\n * @param {number} corners float values array for each cube point\r\n * @param {Vector3} vCellStep vector to next cube cell diagonal point\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} 0, if success (<0) is error\r\n */\r\n buildGeoFromCorners(meshRes, vBoxMin, vBoxMax, corners, vCellStep, cube) {\r\n const arrSize = 12;\r\n const cNumVerts = 8;\r\n const numCells = meshRes - 1;\r\n const side = meshRes;\r\n const side2 = meshRes * meshRes;\r\n\r\n const vaEdges = new Array(arrSize);\r\n for (let i = 0; i < arrSize; i++) {\r\n vaEdges[i] = new THREE.Vector3();\r\n }\r\n const sign = [];\r\n for (let i = 0; i < cNumVerts; i++) {\r\n sign[i] = 1.0;\r\n }\r\n const vCorner = new THREE.Vector3();\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n if (!cube.hasIntersection[indCell]) {\r\n // next cell\r\n indCell++;\r\n continue;\r\n }\r\n const bitsInside = cube.bitsInside[indCell];\r\n\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, meshRes, vCorner);\r\n\r\n const indPointValues = indCell * (2 << (2 + 2));\r\n for (let i = 0, j = 0; i < cNumVerts; i++) {\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.x;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.y;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.z;\r\n }\r\n\r\n cube.pointsValuesLinear[indPointValues + 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 2 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3] += vCellStep.x;\r\n\r\n cube.pointsValuesLinear[indPointValues + 2 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 3 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 2] += vCellStep.z;\r\n\r\n cube.pointsValuesLinear[indPointValues + 4 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 1] += vCellStep.y;\r\n\r\n // now current cell has intersections (from -x to +x) on some cube edges\r\n const indValues = indPointValues + 24;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n sign[i] = (cube.pointsValuesLinear[indValues + i] < 0.0) ? 1 : 0;\r\n }\r\n\r\n this.buildEdgePoint(0, 1, sign, cube, indPointValues, vaEdges[0]);\r\n this.buildEdgePoint(1, 2, sign, cube, indPointValues, vaEdges[1]);\r\n this.buildEdgePoint(2, 3, sign, cube, indPointValues, vaEdges[2]);\r\n this.buildEdgePoint(3, 0, sign, cube, indPointValues, vaEdges[3]);\r\n\r\n this.buildEdgePoint(4, 5, sign, cube, indPointValues, vaEdges[4]);\r\n this.buildEdgePoint(5, 6, sign, cube, indPointValues, vaEdges[5]);\r\n this.buildEdgePoint(6, 7, sign, cube, indPointValues, vaEdges[6]);\r\n this.buildEdgePoint(7, 4, sign, cube, indPointValues, vaEdges[7]);\r\n\r\n this.buildEdgePoint(0, 4, sign, cube, indPointValues, vaEdges[8]);\r\n this.buildEdgePoint(1, 5, sign, cube, indPointValues, vaEdges[9]);\r\n this.buildEdgePoint(2, 6, sign, cube, indPointValues, vaEdges[10]);\r\n this.buildEdgePoint(3, 7, sign, cube, indPointValues, vaEdges[11]);\r\n\r\n const offs = bitsInside * (2 << (1 + 2));\r\n for (let numTri = 0, indTri = 0; numTri < (2 + 2 + 2); numTri++, indTri += 3) {\r\n // s_triIndicesMarchCube is external array, defined in mold_ind.js\r\n const i0 = cube.striIndicesMarchCube[offs + indTri];\r\n if (i0 < 0) {\r\n break;\r\n }\r\n const i1 = cube.striIndicesMarchCube[offs + indTri + 1];\r\n const i2 = cube.striIndicesMarchCube[offs + indTri + 2];\r\n\r\n if (!this.addTriangle(vaEdges[i0], vaEdges[i1], vaEdges[i2])) {\r\n return 0 - 2;\r\n }\r\n } // for numTri\r\n\r\n // next cell (cube)\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return 0;\r\n }\r\n\r\n /**\r\n * Returns number of cell with intersection with at least one sphere.\r\n * Using this number, we can estimate required number of vertices\r\n * and triangles to build result mesh.\r\n *\r\n * @param {number} side Number of points in cube voxels\r\n * @param {number} numCells Number of cells in cube voxels (per direction)\r\n * @param {array} corners Array of float values for cube corner points\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} numIntersectedCells\r\n */\r\n getNumIntersectedCells(side, numCells, corners, cube) {\r\n const side2 = side * side;\r\n const cNumVerts = 8;\r\n let numIntersectedCells = 0;\r\n\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n const cubeValuesIndex = indCell * (2 << (2 + 2)) + 24;\r\n const indCorner = x + indZ + indY;\r\n\r\n cube.pointsValuesLinear[cubeValuesIndex] = corners[indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 1] = corners[indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 2] = corners[indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 3] = corners[indCorner + side];\r\n cube.pointsValuesLinear[cubeValuesIndex + 4] = corners[side2 + indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 5] = corners[side2 + indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 6] = corners[side2 + indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 7] = corners[side2 + indCorner + side];\r\n\r\n // check read exception\r\n // assert(side2 + indCorner + side + 1 < side3);\r\n\r\n // get bit flags inside\r\n let bitsInside = 0;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n if (cube.pointsValuesLinear[cubeValuesIndex + i] < 0.0) {\r\n bitsInside |= (1 << i);\r\n }\r\n }\r\n\r\n if ((bitsInside === 0) || (bitsInside === ((1 << cNumVerts) - 1))) {\r\n cube.hasIntersection[indCell] = false;\r\n } else {\r\n cube.hasIntersection[indCell] = true;\r\n numIntersectedCells++;\r\n }\r\n cube.bitsInside[indCell] = bitsInside;\r\n // next cell\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return numIntersectedCells;\r\n }\r\n\r\n getType(letter) {\r\n /* eslint-disable no-magic-numbers */\r\n const atomT = [0, 0, 1, 1, 2, 6, 3, 6, 4, 6, 5, 6, 6, 0, 7, 3, 8, 2, 9, 6, 10, 6, 11, 6, 12, 6, 13, 6, 14, 6, 15, 4,\r\n 16, 5, 17, 6, 18, 6, 19, 6, 20, 6, 21, 6, 22, 6, 23, 6, 24, 6, 25, 6, 26, 6, 27, 6, 28, 6, 29, 6, 30, 6, 31, 6,\r\n 32, 6, 33, 6, 34, 6, 35, 6, 36, 6, 37, 6, 38, 6, 39, 6, 40, 6, 41, 6, 42, 6, 43, 6, 44, 6, 45, 6, 46, 6, 47, 6,\r\n 48, 6, 49, 6, 50, 6, 51, 6, 52, 6, 53, 6, 54, 6, 55, 6, 56, 6, 57, 6, 58, 6, 59, 6, 60, 6, 61, 6, 62, 6, 63, 6,\r\n 64, 6, 65, 6, 66, 6, 67, 6, 68, 6, 69, 6, 70, 6, 71, 6, 72, 6, 73, 6, 74, 6, 75, 6, 76, 6, 77, 6, 78, 6, 79, 6,\r\n 80, 6, 81, 6, 82, 6, 83, 6, 84, 6, 85, 6, 86, 6, 87, 6, 88, 6, 89, 6, 90, 6, 91, 6, 92, 6, 93, 6, 94, 6, 95, 6,\r\n 96, 6, 97, 6, 98, 6, 99, 6, 100, 6, 101, 6, 102, 6, 103, 6, 104, 6, 105, 6, 106, 6, 107, 6, 108, 6, 109, 6];\r\n /* eslint-enable no-magic-numbers */\r\n\r\n if (letter < 1 || letter > atomT.length / 2\r\n || (Object.keys(Element.ByAtomicNumber).length * 2) !== atomT.length) {\r\n throw new Error('atomT.length should be equal Element.ByAtomicNumber.length * 2');\r\n }\r\n return atomT[letter * 2];\r\n }\r\n\r\n /**\r\n * Calculate values for marching cube grid points\r\n * positive values are outside sphere, negative - is inside\r\n *\r\n * @param {array} corners array of float values\r\n * @param {number} side Number of point in cube in 1 dimennsion\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {array} atoms Array of input atoms\r\n * @param {number} probeRad radius for atom probing\r\n */\r\n calculateGridCorners(corners, side, vBoxMin, vBoxMax, atoms, probeRad) {\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const vCorner = new THREE.Vector3();\r\n const vDif = new THREE.Vector3();\r\n /* eslint-disable no-magic-numbers */\r\n const aLot = +1.0e12;\r\n /* eslint-enable no-magic-numbers */\r\n\r\n for (let i = 0; i < side3; i++) {\r\n corners[i] = aLot; // to large value\r\n }\r\n\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n for (let s = 0, numAtoms = atoms.length; s < numAtoms; s++) {\r\n const atom = atoms[s];\r\n const radius = atom.radius + probeRad;\r\n\r\n const fx = ((atom.coord.x - radius) - vBoxMin.x) * xScale;\r\n const fy = ((atom.coord.y - radius) - vBoxMin.y) * yScale;\r\n const fz = ((atom.coord.z - radius) - vBoxMin.z) * zScale;\r\n\r\n const indXMin = Math.floor(fx);\r\n const indYMin = Math.floor(fy);\r\n const indZMin = Math.floor(fz);\r\n\r\n let indXMax = Math.floor(((atom.coord.x + radius) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((atom.coord.y + radius) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((atom.coord.z + radius) - vBoxMin.z) * zScale);\r\n\r\n indXMax++;\r\n indYMax++;\r\n indZMax++;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let y = indYMin; y <= indYMax; y++) {\r\n const indY = y * side2;\r\n for (let z = indZMin; z <= indZMax; z++) {\r\n const indZ = z * side;\r\n for (let x = indXMin; x <= indXMax; x++) {\r\n const ind = indY + indZ + x;\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, side, vCorner);\r\n vDif.x = vCorner.x - atom.coord.x;\r\n vDif.y = vCorner.y - atom.coord.y;\r\n vDif.z = vCorner.z - atom.coord.z;\r\n const distToSphere = Math.sqrt(vDif.x * vDif.x + vDif.y * vDif.y + vDif.z * vDif.z);\r\n // val: < 0, if inside sphere\r\n // val: > 0, if outside sphere\r\n const val = distToSphere - radius;\r\n if (val < corners[ind]) {\r\n corners[ind] = val;\r\n }\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n } // for (s)\r\n }\r\n\r\n /**\r\n * Create memory pool for vertex hash management\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices (that will be build)\r\n * @param {number} maxNumTriangles Maximum possible number of triangles (that will be build)\r\n * @returns {number} 0, if success. (<0) is non memory\r\n */\r\n createVertexHash(maxNumVertices, maxNumTriangles) {\r\n this.hashLines = utils.allocateTyped(Int32Array, HASH_SIZE * 2);\r\n if (this.hashLines === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < HASH_SIZE; i++) {\r\n this.hashLines[j++] = 0; // num vertices in this hash line\r\n this.hashLines[j++] = 0 - 1; // index of the first entry\r\n }\r\n\r\n this.maxNumVertices = maxNumVertices;\r\n this.maxNumTriangles = maxNumTriangles;\r\n\r\n this.numHashEtriesAllocated = maxNumVertices;\r\n this.hashEntries = utils.allocateTyped(Int32Array, 2 * this.numHashEtriesAllocated);\r\n if (this.hashEntries === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < this.numHashEtriesAllocated; i++) {\r\n this.hashEntries[j++] = 0 - 1; // index of vertex\r\n this.hashEntries[j++] = 0 - 1; // next hash entry index\r\n }\r\n this.numHashEntryIndex = 0;\r\n return 0;\r\n }\r\n\r\n /**\r\n * Allocate and return new hash entry. Just check possible amount.\r\n *\r\n * @returns {number} index of hash entry, that can be used for geometry add vertex functionality\r\n */\r\n getNewHashEntry() {\r\n if (this.numHashEntryIndex < this.numHashEtriesAllocated) {\r\n const i = this.numHashEntryIndex;\r\n this.numHashEntryIndex++;\r\n return i;\r\n }\r\n return 0 - 1;\r\n }\r\n\r\n /**\r\n * Add vertex to geometry structure\r\n * using vertex hash table to quickly check, is this vertex already exist in geometry\r\n *\r\n * @param {object} geoOut Geometry to build\r\n * @param {Vector3} vAdd Vertex to add\r\n * @returns {number} index of added (or existing) vertex in geometry.\r\n */\r\n addVertexToGeo(geoOut, vAdd) {\r\n let entry;\r\n const oneHynberes = 0.01;\r\n const n815851 = 815851;\r\n const n37633 = 37633;\r\n const n2453543 = 2453543;\r\n const r106 = 1.0e-6;\r\n\r\n const hashResolution = this.marCubeResoultion << 2;\r\n const v = new THREE.Vector3();\r\n const ix = Math.floor(hashResolution * (vAdd.x - this.vBoxMin.x) / (this.vBoxMax.x + oneHynberes - this.vBoxMin.x));\r\n const iy = Math.floor(hashResolution * (vAdd.y - this.vBoxMin.y) / (this.vBoxMax.y + oneHynberes - this.vBoxMin.y));\r\n const iz = Math.floor(hashResolution * (vAdd.z - this.vBoxMin.z) / (this.vBoxMax.z + oneHynberes - this.vBoxMin.z));\r\n let iHash = ix * n815851 + iz * n37633 + iy * n2453543;\r\n iHash &= (HASH_SIZE - 1);\r\n const hLineIndex = iHash + iHash;\r\n\r\n // search vertex via hash\r\n // search in hash list\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n for (entry = this.hashLines[hLineIndex + 1]; entry >= 0; entry = this.hashEntries[entry * 2 + 1]) {\r\n const ind = this.hashEntries[entry * 2 + 0]; // vertex index\r\n v.copy(geoOut._vertices[ind]);\r\n v.x -= vAdd.x;\r\n v.y -= vAdd.y;\r\n v.z -= vAdd.z;\r\n const dot2 = v.x * v.x + v.y * v.y + v.z * v.z;\r\n if (dot2 < r106) {\r\n return ind;\r\n } // if (found)\r\n } // for (entry)\r\n } // search\r\n\r\n // add new vertex to geometry\r\n if (geoOut._numVertices >= this.maxNumVertices) {\r\n return 0 - 1;\r\n }\r\n\r\n const iVertAdd = geoOut._numVertices;\r\n geoOut._vertices[iVertAdd].copy(vAdd);\r\n\r\n // add to hash\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n entry = this.getNewHashEntry();\r\n if (entry < 0) {\r\n return 0 - 1;\r\n }\r\n const entryFirst = this.hashLines[hLineIndex + 1];\r\n this.hashLines[hLineIndex + 1] = entry;\r\n this.hashEntries[entry * 2 + 0] = iVertAdd;\r\n this.hashEntries[entry * 2 + 1] = entryFirst;\r\n\r\n this.hashLines[hLineIndex + 0]++; // num vertices in line ++\r\n }\r\n geoOut._numVertices++;\r\n return iVertAdd;\r\n }\r\n\r\n /**\r\n *\r\n * @param {number} side some placeholder description\r\n * @param {number} probeSphereRadius some placeholder description\r\n * @param {object} vBoxMin some placeholder description\r\n * @param {object} vBoxMax some placeholder description\r\n * @param {object} geoOut some placeholder description\r\n * @param {object} corners some placeholder description\r\n * @returns {number} always 0\r\n */\r\n modifyExcludedFromGeo(\r\n side,\r\n probeSphereRadius,\r\n vBoxMin,\r\n vBoxMax,\r\n geoOut,\r\n corners,\r\n ) {\r\n let ind;\r\n let distToSphere;\r\n let distToBorder;\r\n const r11 = 1.1;\r\n\r\n function innerBlockWorkAround() {\r\n if (distToBorder > 0.0) {\r\n // point is inside probe sphere\r\n if (corners[ind] < 0.0) {\r\n corners[ind] = distToBorder; // was inside surface, now is oustide ( > 0)\r\n }\r\n if (distToBorder > corners[ind]) {\r\n corners[ind] = distToBorder; // find positive maximum\r\n }\r\n } else if (distToBorder > corners[ind]) { // point is outside sphere\r\n corners[ind] = distToBorder; // find negative maximum\r\n }\r\n }\r\n\r\n const side2 = side * side;\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n const probeSpRad2 = (probeSphereRadius * 2) * (probeSphereRadius * 2);\r\n const sideInv = 1.0 / (side - 1);\r\n\r\n for (let i = 0; i < geoOut._numVertices; i++) {\r\n const vCenter = geoOut._vertices[i];\r\n\r\n const radEst = probeSphereRadius * r11;\r\n\r\n let indXMin = Math.floor(((vCenter.x - radEst) - vBoxMin.x) * xScale);\r\n let indYMin = Math.floor(((vCenter.y - radEst) - vBoxMin.y) * yScale);\r\n let indZMin = Math.floor(((vCenter.z - radEst) - vBoxMin.z) * zScale);\r\n\r\n let indXMax = Math.floor(((vCenter.x + radEst) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((vCenter.y + radEst) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((vCenter.z + radEst) - vBoxMin.z) * zScale);\r\n\r\n indXMin = (indXMin >= 0) ? indXMin : 0;\r\n indYMin = (indYMin >= 0) ? indYMin : 0;\r\n indZMin = (indZMin >= 0) ? indZMin : 0;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let iy = indYMin; iy <= indYMax; iy++) {\r\n const indY = iy * side2;\r\n for (let iz = indZMin; iz <= indZMax; iz++) {\r\n const indZ = iz * side;\r\n for (let ix = indXMin; ix <= indXMax; ix++) {\r\n ind = indY + indZ + ix;\r\n // getCornerCoord(vBoxMin, vBoxMax, ix, iy, iz, side, &vCorner);\r\n let t = ix * sideInv;\r\n const xCorner = vBoxMin.x * (1.0 - t) + vBoxMax.x * t;\r\n t = iy * sideInv;\r\n const yCorner = vBoxMin.y * (1.0 - t) + vBoxMax.y * t;\r\n t = iz * sideInv;\r\n const zCorner = vBoxMin.z * (1.0 - t) + vBoxMax.z * t;\r\n\r\n const dx = xCorner - vCenter.x;\r\n const dy = yCorner - vCenter.y;\r\n const dz = zCorner - vCenter.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 < probeSpRad2) {\r\n distToSphere = Math.sqrt(dist2);\r\n distToBorder = -(distToSphere - probeSphereRadius);\r\n innerBlockWorkAround();\r\n } // if (dist from corner point to sphere center more 2 radiuses)\r\n } // for (ix)\r\n } // for (iz)\r\n } // for (iy)\r\n } // for (i) all geo vertices\r\n return 0;\r\n }\r\n\r\n _innerBuild() {\r\n let ok;\r\n const expandFactor = 1.2;\r\n\r\n // performance test\r\n // this.performanceTest();\r\n\r\n // Create temporary atoms (but colored)\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n this.complex = this._opts.parent;\r\n this.atoms = packedArrays.atoms;\r\n this.meshResolution = this._opts.gridSpacing;\r\n this.atomRadiusScale = this._opts.radScale;\r\n this.colorMode = this._opts.colorMode;\r\n this.probeRadius = this._opts.probeRadius;\r\n this.useVertexColors = true;\r\n this.excludeProbe = this._opts.excludeProbe;\r\n this.visibilitySelector = this._opts.visibilitySelector;\r\n\r\n this.geoOut = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n this.numHashEtriesAllocated = 0;\r\n this.numHashEntryIndex = 0;\r\n this.maxNumVertices = 0;\r\n this.maxNumTriangles = 0;\r\n\r\n const atomsColored = new Array(this.atoms.length);\r\n this.convertToAtomsColored(packedArrays, atomsColored);\r\n\r\n // find bbox for spheres scene\r\n const vBoxMin = this.vBoxMin = new THREE.Vector3();\r\n const vBoxMax = this.vBoxMax = new THREE.Vector3();\r\n this.getBoundingBox(atomsColored, vBoxMin, vBoxMax);\r\n\r\n const marCubeResoultion = this.marCubeResoultion = this.meshResolution * (2 + 2);\r\n\r\n // build grid corners for Marching cube algorithm\r\n const side = marCubeResoultion;\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const corners = utils.allocateTyped(Float32Array, side3);\r\n const rProbeRadius = this.probeRadius * this.atomRadiusScale;\r\n\r\n this.calculateGridCorners(corners, side, vBoxMin, vBoxMax, atomsColored, rProbeRadius);\r\n\r\n const numCells = marCubeResoultion - 1;\r\n const cube = new IsoSurfaceMarchCube();\r\n ok = cube.create(numCells);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // copy corners to cells\r\n const vCellStep = new THREE.Vector3();\r\n vCellStep.x = (vBoxMax.x - vBoxMin.x) / numCells;\r\n vCellStep.y = (vBoxMax.y - vBoxMin.y) / numCells;\r\n vCellStep.z = (vBoxMax.z - vBoxMin.z) / numCells;\r\n\r\n let numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n let maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n let maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n\r\n // build voxel world (used to check triangle-to-atom tie and to calculate normals and colors)\r\n let probeRadForNormalsColors = rProbeRadius;\r\n if (this.excludeProbe) {\r\n probeRadForNormalsColors = 0.01;\r\n }\r\n this.voxelWorld = new IsosurfaceBuildNormals(\r\n atomsColored.length,\r\n atomsColored,\r\n vBoxMin,\r\n vBoxMax,\r\n probeRadForNormalsColors,\r\n );\r\n this.voxelWorld.createVoxels();\r\n\r\n ok = this.buildGeoFromCorners(marCubeResoultion, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n if (this.excludeProbe) {\r\n // using 3d mesh (geoOut) as a surface points\r\n // move probe sphere and try to minimuze corners values\r\n this.modifyExcludedFromGeo(side, rProbeRadius, vBoxMin, vBoxMax, this.geoOut, corners);\r\n\r\n // delete old builded geo\r\n this.geoOut._vertices = null;\r\n this.geoOut._colors = null;\r\n this.geoOut._indices = null;\r\n this.geoOut._normals = null;\r\n this.geoOut._numVertices = 0;\r\n this.geoOut._numTriangles = 0;\r\n this.geoOut = null;\r\n\r\n // estimage geo vertices budget again\r\n numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n // creates empty new geometry\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // build vertices and triangles from corners values\r\n ok = this.buildGeoFromCorners(side, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n }\r\n\r\n // build vertex normals\r\n this.voxelWorld.buildNormals(this.geoOut._vertices.length, this.geoOut._vertices, this.geoOut._normals);\r\n // More value : more smooth color mixing\r\n // value about 0.7: very rough colors borders\r\n let radiusColorSmoothness = 6.5;\r\n if (this.excludeProbe) {\r\n radiusColorSmoothness -= 1.5;\r\n }\r\n if (this.useVertexColors) {\r\n this.voxelWorld.buildColors(\r\n this.geoOut._vertices.length,\r\n this.geoOut._vertices,\r\n this.geoOut._colors,\r\n radiusColorSmoothness,\r\n );\r\n }\r\n this.voxelWorld.destroyVoxels();\r\n this.voxelWorld = null;\r\n\r\n // remove objects\r\n cube.destroy();\r\n\r\n return ok;\r\n }\r\n}\r\n\r\n// All code below must be erased from every device and each developer's memory\r\n\r\nexport default SSIsosurfaceGeometry;\r\n","import * as THREE from 'three';\r\nimport EventDispatcher from '../../utils/EventDispatcher';\r\n\r\nfunction createLabel(fieldTxt, className) {\r\n const text = document.createElement('div');\r\n text.className = className;\r\n\r\n if (typeof fieldTxt === 'string') {\r\n const spanText = document.createElement('span');\r\n spanText.style.fontSize = '150%';\r\n const strings = fieldTxt.split('\\n');\r\n\r\n for (let i = 0, n = strings.length; i < n; ++i) {\r\n const spanNodeP = document.createElement('span');\r\n const spanNodeText = document.createTextNode(strings[i]);\r\n spanNodeP.appendChild(spanNodeText);\r\n spanText.appendChild(spanNodeP);\r\n if (i < n - 1) {\r\n spanText.appendChild(document.createElement('br'));\r\n }\r\n }\r\n\r\n text.appendChild(spanText);\r\n } else {\r\n text.appendChild(fieldTxt);\r\n }\r\n text.worldPos = new THREE.Vector3();\r\n return text;\r\n}\r\nclass LabelsGeometry extends EventDispatcher {\r\n constructor(instanceCount, opts) {\r\n super();\r\n this._opts = opts;\r\n this.items = [];\r\n this.needsUpdate = false;\r\n\r\n let xTranslation = -50;\r\n let yTranslation = -50;\r\n switch (opts.horizontalAlign) {\r\n case 'left':\r\n xTranslation = 0;\r\n break;\r\n case 'right':\r\n xTranslation = -100;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n switch (opts.verticalAlign) {\r\n case 'top':\r\n yTranslation = -100;\r\n break;\r\n case 'bottom':\r\n yTranslation = 0;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n const deltaPos = new THREE.Vector3(opts.dx || 0, opts.dy || 0, opts.dz || 0);\r\n this.userData = {\r\n translation: `translate(${xTranslation}%, ${yTranslation}%)`,\r\n offset: deltaPos,\r\n };\r\n }\r\n\r\n setItem(itemIdx, itemPos, fieldTxt) {\r\n const opts = this._opts;\r\n const text = this.items[itemIdx] || createLabel(fieldTxt, 'label');\r\n\r\n text.worldPos.copy(itemPos);\r\n text.style.textAlign = opts.horizontalAlign;\r\n text.style.verticalAlign = opts.verticalAlign;\r\n this.items[itemIdx] = text;\r\n }\r\n\r\n setColor(itemIdx, fColor, bColor) {\r\n const text = this.items[itemIdx];\r\n text.opts = {\r\n color: fColor,\r\n background: bColor,\r\n };\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.needsUpdate = true;\r\n this.dispatchEvent({ type: 'update' });\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n }\r\n\r\n // unimplemented functions\r\n raycast() {\r\n }\r\n\r\n setOpacity() {\r\n\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\n\r\nexport default LabelsGeometry;\r\n","import InstancedSpheresGeometry from './InstancedSpheresGeometry';\r\nimport SimpleSpheresGeometry from './SimpleSpheresGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport Instanced2CCylindersGeometry from './Instanced2CCylindersGeometry';\r\nimport ExtrudedObjectsGeometry from './ExtrudedObjectsGeometry';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport TwoColorLinesGeometry from './TwoColorLinesGeometry';\r\nimport CrossGeometry from './CrossGeometry';\r\nimport QuickSurfGeometry from './QuickSurfGeometry';\r\nimport ContactSurfaceGeometry from './ContactSurfaceGeometry';\r\nimport SSIsosurfaceGeometry from './SSIsosurfaceGeometry';\r\nimport LabelsGeometry from './LabelsGeometry';\r\n\r\nexport default {\r\n InstancedSpheresGeometry,\r\n SimpleSpheresGeometry,\r\n Simple2CCylindersGeometry,\r\n Instanced2CCylindersGeometry,\r\n ExtrudedObjectsGeometry,\r\n ChunkedLinesGeometry,\r\n TwoColorLinesGeometry,\r\n CrossGeometry,\r\n QuickSurfGeometry,\r\n ContactSurfaceGeometry,\r\n SSIsosurfaceGeometry,\r\n LabelsGeometry,\r\n};\r\n","export default {\r\n\r\n precision: 'mediump',\r\n\r\n /**\r\n *\r\n * @param {THREE.WebGLRenderer} renderer\r\n */\r\n init(renderer) {\r\n this.precision = renderer.capabilities.getMaxPrecision('highp');\r\n },\r\n};\r\n","import * as THREE from 'three';\r\n\r\nconst noiseWidth = 4;\r\nconst noiseHeight = 4;\r\nconst _noiseData = new Uint8Array([\r\n 24, 52, 0, 255, 254, 145, 0, 255, 122, 0, 0, 255, 7, 170, 0, 255,\r\n 34, 214, 0, 255, 173, 8, 0, 255, 86, 249, 0, 255, 160, 4, 0, 255,\r\n 226, 46, 0, 255, 224, 211, 0, 255, 3, 157, 0, 255, 174, 247, 0, 255,\r\n 12, 182, 0, 255, 220, 216, 0, 255, 1, 109, 0, 255, 253, 154, 0, 255,\r\n]);\r\nconst _noiseWrapS = THREE.RepeatWrapping;\r\nconst _noiseWrapT = THREE.RepeatWrapping;\r\nconst _noiseMinFilter = THREE.NearestFilter;\r\nconst _noiseMagFilter = THREE.NearestFilter;\r\nconst _noiseMapping = THREE.UVMapping;\r\nconst noiseTexture = new THREE.DataTexture(\r\n _noiseData,\r\n noiseWidth,\r\n noiseHeight,\r\n THREE.RGBAFormat,\r\n THREE.UnsignedByteType,\r\n _noiseMapping,\r\n _noiseWrapS,\r\n _noiseWrapT,\r\n _noiseMagFilter,\r\n _noiseMinFilter,\r\n 1,\r\n);\r\nnoiseTexture.needsUpdate = true;\r\n\r\nexport default {\r\n noiseWidth,\r\n noiseHeight,\r\n noiseTexture,\r\n};\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './Uber.vert';\r\nimport fragmentShader from './Uber.frag';\r\nimport capabilities from '../capabilities';\r\nimport noise from '../noiseTexture';\r\n\r\n// Length of _samplesKernel is used in Uber.frag\r\n// If you want to change length of _samplesKernel, please, remember change it in Uber.frag too.\r\n// You can easy find places for replace using word:_samplesKernel\r\nconst _samplesKernel = [\r\n new THREE.Vector2(-0.541978, 0.840393),\r\n new THREE.Vector2(0.125533, -0.992089),\r\n new THREE.Vector2(0.374329, 0.927296),\r\n new THREE.Vector2(-0.105475, 0.994422),\r\n];\r\n\r\nconst defaultUniforms = THREE.UniformsUtils.merge([\r\n\r\n THREE.UniformsLib.fog,\r\n THREE.UniformsLib.lights,\r\n\r\n {\r\n // are updated automatically by three.js (see THREE.ShaderLib.common)\r\n diffuse: { value: new THREE.Color(0xeeeeee) },\r\n opacity: { value: 1.0 },\r\n\r\n specular: { type: 'c', value: new THREE.Color(0x111111) },\r\n shininess: { type: 'f', value: 30 },\r\n fixedColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n zOffset: { type: 'f', value: 0.0 },\r\n zClipValue: { type: 'f', value: 0.0 },\r\n clipPlaneValue: { type: 'f', value: 0.0 },\r\n nearPlaneValue: { type: 'f', value: -0.5 },\r\n invModelViewMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n world2colorMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n dashedLineSize: { type: 'f', value: 0.1 },\r\n dashedLinePeriod: { type: 'f', value: 0.2 },\r\n projMatrixInv: { type: '4fv', value: new THREE.Matrix4() },\r\n viewport: { type: 'v2', value: new THREE.Vector2() },\r\n lineWidth: { type: 'f', value: 2.0 },\r\n // default value must be the same as settings\r\n fogAlpha: { type: 'f', value: 1.0 },\r\n samplesKernel: { type: 'v2v', value: null },\r\n noiseTex: { type: 't', value: null },\r\n noiseTexelSize: { type: 'v2', value: null },\r\n srcTexelSize: { type: 'v2', value: null },\r\n },\r\n\r\n]);\r\n\r\nconst uberOptionNames = [\r\n 'shininess',\r\n 'opacity',\r\n 'zOffset',\r\n 'diffuse',\r\n 'specular',\r\n 'fixedColor',\r\n 'zClipCoef',\r\n 'zClipValue',\r\n 'clipPlaneValue',\r\n 'world2colorMatrix',\r\n 'dashedLineSize',\r\n 'dashedLinePeriod',\r\n 'projMatrixInv',\r\n 'viewport',\r\n 'lineWidth',\r\n 'fogAlpha',\r\n 'samplesKernel',\r\n 'noiseTex',\r\n 'noiseTexelSize',\r\n 'srcTexelSize',\r\n];\r\n\r\n// properties that convert to uniforms\r\nconst uberOptions = {\r\n diffuse: new THREE.Color(0xffffff), // used in phong lighting\r\n specular: new THREE.Color(0x111111), // used in phong lighting\r\n shininess: 30, // used in phong lighting\r\n opacity: 1, // set mesh opacity\r\n fixedColor: new THREE.Color(0xffffff), // color to override (see OVERRIDE_COLOR)\r\n zOffset: 0.0, // used fo zsprites (see SPHERE_SPRITE CYLINDER_SPRITE)\r\n zClipCoef: 2.0, // use for Surfs clipping (mesh param, isn't used in shader) FIXME move to representation param\r\n zClipValue: 0.0, // value to clip Surfs in shader (see ZCLIP)\r\n clipPlaneValue: 0.0, // value to clip scene globally (see CLIPPLANE)\r\n world2colorMatrix: new THREE.Matrix4(),\r\n dashedLineSize: 0.1,\r\n dashedLinePeriod: 0.3,\r\n projMatrixInv: new THREE.Matrix4(),\r\n viewport: new THREE.Vector2(800, 600),\r\n lineWidth: 2.0,\r\n fogAlpha: 1.0,\r\n samplesKernel: _samplesKernel,\r\n noiseTex: noise.noiseTexture,\r\n noiseTexelSize: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight),\r\n srcTexelSize: new THREE.Vector2(1.0 / 800.0, 1.0 / 600.0),\r\n copy(source) {\r\n this.diffuse.copy(source.diffuse);\r\n this.specular.copy(source.specular);\r\n this.shininess = source.shininess;\r\n this.opacity = source.opacity;\r\n this.fixedColor.copy(source.fixedColor);\r\n this.zOffset = source.zOffset;\r\n this.zClipCoef = source.zClipCoef;\r\n this.zClipValue = source.zClipValue;\r\n this.clipPlaneValue = source.clipPlaneValue;\r\n this.world2colorMatrix.copy(source.world2colorMatrix);\r\n this.dashedLineSize = source.dashedLineSize;\r\n this.dashedLinePeriod = source.dashedLinePeriod;\r\n this.projMatrixInv = source.projMatrixInv;\r\n this.viewport = source.viewport;\r\n this.lineWidth = source.lineWidth; // used for thick lines only\r\n this.toonShading = source.toonShading;\r\n this.fogAlpha = source.fogAlpha;\r\n this.samplesKernel = source.samplesKernel;\r\n this.noiseTex = source.noiseTex;\r\n this.noiseTexelSize = source.noiseTexelSize;\r\n this.srcTexelSize = source.srcTexelSize;\r\n },\r\n};\r\n\r\nclass UberMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // add fog\r\n this.fog = true;\r\n // used for instanced geometry\r\n this.instancedPos = false;\r\n this.instancedMatrix = false;\r\n // atoms and links color\r\n this.attrColor = false;\r\n // second link color for cylinders\r\n this.attrColor2 = false;\r\n //\r\n this.attrAlphaColor = false;\r\n // overrides color for all vertices (used in selection)\r\n this.overrideColor = false;\r\n // zsrpites\r\n this.sphereSprite = false;\r\n this.cylinderSprite = false;\r\n // clip Surfs individually\r\n this.zClip = false;\r\n // clip scene with global clip plane\r\n this.clipPlane = false;\r\n // enable fake (chess-like) opacity\r\n this.fakeOpacity = false;\r\n // render only depth, don't take care about the pixel color (used for transparency depth prepass)\r\n this.prepassTransparancy = false;\r\n // used to render pixel positions\r\n this.colorFromPos = false;\r\n // used to render shadowmap\r\n this.shadowmap = false;\r\n // used to describe shadowmap type\r\n this.shadowmapType = 'random';\r\n // used to render pixel view deph\r\n this.colorFromDepth = false;\r\n // mark that rendering is for orthographic camera\r\n this.orthoCam = false;\r\n // used to render dashed line\r\n this.dashedLine = false;\r\n // mark as transparent\r\n this.transparent = true;\r\n // mark as thick lines\r\n this.thickLine = false;\r\n // makes fog begin transparency (required for transparent background)\r\n this.fogTransparent = false;\r\n // used to render surface normals to G buffer for ssao effect\r\n this.normalsToGBuffer = false;\r\n // used for toon material\r\n this.toonShading = false;\r\n\r\n // uber options of \"root\" materials are inherited from single uber-options object that resides in prototype\r\n this.uberOptions = Object.create(UberMaterial.prototype.uberOptions);\r\n\r\n // set default values\r\n super.setValues({\r\n uniforms: THREE.UniformsUtils.clone(defaultUniforms),\r\n vertexShader: this.precisionString() + vertexShader,\r\n fragmentShader: this.precisionString() + fragmentShader,\r\n lights: true,\r\n fog: true,\r\n side: THREE.DoubleSide,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n precisionString() {\r\n const { precision } = capabilities;\r\n const str = `precision ${precision} float;\\n`\r\n + `precision ${precision} int;\\n\\n`;\r\n return str;\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n\r\n this.fragmentShader = source.fragmentShader;\r\n this.vertexShader = source.vertexShader;\r\n\r\n this.uniforms = THREE.UniformsUtils.clone(source.uniforms);\r\n this.defines = { ...source.defines };\r\n this.extensions = source.extensions;\r\n\r\n this.fog = source.fog;\r\n this.instancedPos = source.instancedPos;\r\n this.instancedMatrix = source.instancedMatrix;\r\n this.attrColor = source.attrColor;\r\n this.attrColor2 = source.attrColor2;\r\n this.attrAlphaColor = source.attrAlphaColor;\r\n this.overrideColor = source.overrideColor;\r\n this.sphereSprite = source.sphereSprite;\r\n this.cylinderSprite = source.cylinderSprite;\r\n this.zClip = source.zClip;\r\n this.clipPlane = source.clipPlane;\r\n this.fakeOpacity = source.fakeOpacity;\r\n this.colorFromPos = source.colorFromPos;\r\n this.shadowmap = source.shadowmap;\r\n this.shadowmapType = source.shadowmapType;\r\n this.colorFromDepth = source.colorFromDepth;\r\n this.orthoCam = source.orthoCam;\r\n this.prepassTransparancy = source.prepassTransparancy;\r\n this.dashedLine = source.dashedLine;\r\n this.thickLine = source.thickLine;\r\n this.fogTransparent = source.fogTransparent;\r\n this.normalsToGBuffer = source.normalsToGBuffer;\r\n this.toonShading = source.toonShading;\r\n\r\n this.uberOptions.copy(source.uberOptions);\r\n\r\n return this;\r\n }\r\n\r\n // create copy of this material\r\n // its options are prototyped after this material's options\r\n createInstance() {\r\n const inst = new UberMaterial();\r\n inst.copy(this);\r\n inst.uberOptions = Object.create(this.uberOptions);\r\n return inst;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n const extensions = {};\r\n\r\n if (this.fog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.instancedPos) {\r\n defines.INSTANCED_POS = 1;\r\n }\r\n if (this.instancedMatrix) {\r\n defines.INSTANCED_MATRIX = 1;\r\n }\r\n if (this.attrColor) {\r\n defines.ATTR_COLOR = 1;\r\n }\r\n if (this.attrColor2) {\r\n defines.ATTR_COLOR2 = 1;\r\n }\r\n if (this.attrAlphaColor) {\r\n defines.ATTR_ALPHA_COLOR = 1;\r\n }\r\n if (this.overrideColor) {\r\n defines.OVERRIDE_COLOR = 1;\r\n }\r\n if (this.sphereSprite) {\r\n defines.SPHERE_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.cylinderSprite) {\r\n defines.CYLINDER_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.zClip) {\r\n defines.ZCLIP = 1;\r\n }\r\n if (this.clipPlane) {\r\n defines.CLIP_PLANE = 1;\r\n }\r\n if (this.fakeOpacity) {\r\n defines.FAKE_OPACITY = 1;\r\n }\r\n if (this.lights) {\r\n defines.USE_LIGHTS = 1;\r\n }\r\n if (this.colorFromPos) {\r\n defines.COLOR_FROM_POS = 1;\r\n }\r\n if (this.shadowmap) {\r\n defines.SHADOWMAP = 1;\r\n if (this.shadowmapType === 'pcf') {\r\n defines.SHADOWMAP_PCF_SHARP = 1;\r\n } else if (this.shadowmapType === 'random') {\r\n defines.SHADOWMAP_PCF_RAND = 1;\r\n } else {\r\n defines.SHADOWMAP_BASIC = 1;\r\n }\r\n }\r\n if (this.colorFromDepth) {\r\n defines.COLOR_FROM_DEPTH = 1;\r\n }\r\n if (this.orthoCam) {\r\n defines.ORTHOGRAPHIC_CAMERA = 1;\r\n }\r\n if (this.prepassTransparancy) {\r\n defines.PREPASS_TRANSP = 1;\r\n }\r\n if (this.dashedLine) {\r\n defines.DASHED_LINE = 1;\r\n }\r\n if (this.thickLine) {\r\n defines.THICK_LINE = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n if (this.normalsToGBuffer) {\r\n extensions.drawBuffers = true;\r\n defines.NORMALS_TO_G_BUFFER = 1;\r\n }\r\n if (this.toonShading) {\r\n defines.TOON_SHADING = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n this.extensions = extensions;\r\n }\r\n\r\n setUberOptions(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n for (const key in values) {\r\n if (!values.hasOwnProperty(key)) {\r\n continue;\r\n }\r\n\r\n if (this.uberOptions[key] instanceof THREE.Color) {\r\n this.uberOptions[key] = values[key].clone();\r\n } else {\r\n this.uberOptions[key] = values[key];\r\n }\r\n }\r\n }\r\n\r\n clone(shallow) {\r\n if (!shallow) {\r\n return super.clone();\r\n }\r\n return this.createInstance();\r\n }\r\n\r\n updateUniforms() {\r\n const self = this;\r\n\r\n uberOptionNames.forEach((p) => {\r\n if (self.uniforms.hasOwnProperty(p)) {\r\n if (self.uberOptions[p] instanceof THREE.Color\r\n || self.uberOptions[p] instanceof THREE.Matrix4) {\r\n self.uniforms[p].value = self.uberOptions[p].clone();\r\n } else {\r\n self.uniforms[p].value = self.uberOptions[p];\r\n }\r\n }\r\n });\r\n }\r\n}\r\n\r\nUberMaterial.prototype.uberOptions = uberOptions;\r\n\r\nexport default UberMaterial;\r\n","import UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default function (SuperClass) {\r\n class NewObjectType extends SuperClass {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.onBeforeRender = NewObjectType.prototype.onBeforeRender;\r\n }\r\n\r\n onBeforeRender(renderer, scene, camera, geometry, material, group) {\r\n this._onBeforeRender(renderer, scene, camera, geometry, material, group);\r\n this._update();\r\n }\r\n\r\n _onBeforeRender() {\r\n }\r\n\r\n _update() {\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material instanceof UberMaterial) {\r\n material.updateUniforms();\r\n }\r\n }\r\n }\r\n\r\n return NewObjectType;\r\n}\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZSpriteMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material.uniforms.invModelViewMatrix) {\r\n // NOTE: update of modelViewMatrix inside threejs is done after onBeforeRender call,\r\n // so we have to do it manually in that place\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n // get inverse matrix\r\n material.uniforms.invModelViewMatrix.value.copy(this.modelViewMatrix).invert();\r\n material.uniforms.nearPlaneValue.value = camera.near;\r\n material.uniformsNeedUpdate = true;\r\n }\r\n }\r\n}\r\n\r\nexport default ZSpriteMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZClippedMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n static _mvLength = new THREE.Vector3();\r\n\r\n static _center = new THREE.Vector3();\r\n\r\n static _modelView = new THREE.Matrix4();\r\n\r\n _onBeforeRender(renderer, scene, camera) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n\r\n const geo = this.geometry;\r\n const { material } = this;\r\n if (!geo.zClip || !material.uberOptions) {\r\n return;\r\n }\r\n\r\n const zClipCoef = 0.5;\r\n\r\n const modelView = ZClippedMesh._modelView;\r\n const mvLength = ZClippedMesh._mvLength;\r\n const center = ZClippedMesh._center;\r\n\r\n modelView.multiplyMatrices(this.matrixWorld, camera.matrixWorldInverse);\r\n const s = mvLength.setFromMatrixColumn(modelView, 0).length();\r\n center.copy(geo.boundingSphere.center);\r\n\r\n this.localToWorld(center);\r\n material.uberOptions.zClipValue = camera.position.z - center.z\r\n - s * (zClipCoef * geo.boundingSphere.radius);\r\n }\r\n}\r\n\r\nexport default ZClippedMesh;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from '../CSS2DObject';\r\nimport utils from '../../utils';\r\n\r\nclass TextMesh extends THREE.Group {\r\n constructor(geometry, _material) {\r\n super();\r\n this.geometry = geometry;\r\n\r\n const self = this;\r\n self.initialized = false;\r\n this.geometry.addEventListener('update', () => {\r\n self.update();\r\n });\r\n }\r\n\r\n init() {\r\n const { children } = this;\r\n for (let i = children.length - 1; i >= 0; --i) {\r\n this.remove(children[i]);\r\n }\r\n\r\n const { items, userData } = this.geometry;\r\n for (let i = 0, n = items.length; i < n; ++i) {\r\n const srcItem = items[i];\r\n if (!srcItem) {\r\n continue;\r\n }\r\n const item = utils.shallowCloneNode(srcItem);\r\n const label = new CSS2DObject(item);\r\n label.userData = _.clone(userData);\r\n const el = label.getElement();\r\n el.style.visibility = 'visible';\r\n label.source = srcItem;\r\n this.add(label);\r\n }\r\n this.initialized = true;\r\n }\r\n\r\n update() {\r\n const geo = this.geometry;\r\n if (!geo.needsUpdate) {\r\n return;\r\n }\r\n const { children } = this;\r\n if (!this.initialized) {\r\n this.init();\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n const item = child.source;\r\n child.position.copy(item.worldPos);\r\n child.userData.color = item.opts.color;\r\n child.userData.background = item.opts.background;\r\n }\r\n }\r\n}\r\n\r\nexport default TextMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass SimpleMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default SimpleMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\nconst _viewport = new THREE.Vector2();\r\n\r\nclass ThickLineMesh extends Mesh {\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!material.uberOptions) {\r\n return;\r\n }\r\n\r\n material.uberOptions.projMatrixInv.copy(camera.projectionMatrix).invert();\r\n renderer.getSize(_viewport);\r\n material.uberOptions.viewport.set(_viewport.width, _viewport.height);\r\n }\r\n}\r\n\r\nexport default ThickLineMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass InstancedMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default InstancedMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\nimport ZSpriteMesh from './ZSpriteMesh';\r\nimport ZClippedMesh from './ZClippedMesh';\r\nimport TextMesh from './TextMesh';\r\nimport SimpleMesh from './SimpleMesh';\r\nimport ThickLineMesh from './ThickLineMesh';\r\nimport InstancedMesh from './InstancedMesh';\r\n\r\nexport default {\r\n ZClipped: ZClippedMesh,\r\n ZSprite: ZSpriteMesh,\r\n Text: TextMesh,\r\n Line: UberObject(THREE.Line),\r\n LineSegments: UberObject(THREE.LineSegments),\r\n Mesh: SimpleMesh,\r\n ThickLineMesh,\r\n Instanced: InstancedMesh,\r\n};\r\n","import geometries from '../geometries/geometries';\r\nimport meshes from './meshes';\r\nimport ThickLinesGeometry from '../geometries/ThickLinesGeometry';\r\n\r\nfunction setMatParams(params, uniforms) {\r\n return function (material) {\r\n material.setValues(params);\r\n material.setUberOptions(uniforms);\r\n };\r\n}\r\n\r\nfunction _createInstancedCylinders(useZSprites, openEnded) {\r\n function Geometry(a, b) {\r\n return new geometries.Instanced2CCylindersGeometry(a, b, useZSprites, openEnded);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedMatrix: true,\r\n attrColor: true,\r\n attrColor2: true,\r\n attrAlphaColor: true,\r\n cylinderSprite: useZSprites,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createLineSegmentsGeoTriplet(geo, renderParams) {\r\n const thickLines = geo.prototype instanceof ThickLinesGeometry;\r\n const lineWidth = renderParams.lineWidth || 0;\r\n return {\r\n Geometry: geo,\r\n Object: thickLines ? meshes.ThickLineMesh : meshes.LineSegments,\r\n initMaterial: setMatParams({\r\n lights: false,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n thickLine: thickLines,\r\n }, {\r\n lineWidth,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createSimpleGeoTriplet(geoClass) {\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.Mesh,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createIsoSurfaceGeoTriplet(geoClass, caps, settings, renderParams) {\r\n const surfaceOpts = {\r\n wireframe: !!renderParams.wireframe,\r\n fakeOpacity: settings.now.isoSurfaceFakeOpacity,\r\n zClip: renderParams.zClip,\r\n };\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.ZClipped,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: false,\r\n wireframe: surfaceOpts.wireframe,\r\n fakeOpacity: surfaceOpts.fakeOpacity,\r\n zClip: surfaceOpts.zClip,\r\n }),\r\n };\r\n}\r\n\r\nclass MeshCreator {\r\n static createSpheres(caps, settings) {\r\n const useZSprites = settings.now.zSprites;\r\n function Geometry(a, b) {\r\n return new geometries.InstancedSpheresGeometry(a, b, useZSprites);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedPos: true,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n sphereSprite: useZSprites,\r\n }),\r\n };\r\n }\r\n\r\n static create2CClosedCylinders(_caps, _settings) {\r\n return _createInstancedCylinders(false, false);\r\n }\r\n\r\n static create2CCylinders(caps, settings) {\r\n return _createInstancedCylinders(settings.now.zSprites, true);\r\n }\r\n\r\n static create2CLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.TwoColorLinesGeometry, renderParams);\r\n }\r\n\r\n static createCrosses(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.CrossGeometry, renderParams);\r\n }\r\n\r\n static createExtrudedChains(_caps, _settings) {\r\n return _createSimpleGeoTriplet(geometries.ExtrudedObjectsGeometry);\r\n }\r\n\r\n static createChunkedLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.ChunkedLinesGeometry, renderParams);\r\n }\r\n\r\n static createQuickSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.QuickSurfGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createContactSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.ContactSurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createSASSES(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.SSIsosurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createLabels(_caps, _settings) {\r\n return {\r\n Geometry: geometries.LabelsGeometry,\r\n Object: meshes.Text,\r\n initMaterial() {\r\n },\r\n };\r\n }\r\n}\r\n\r\nexport default MeshCreator;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../gfxutils';\r\n\r\nclass TransformGroup extends THREE.Object3D {\r\n static _inverseMatrix = new THREE.Matrix4();\r\n\r\n static _ray = new THREE.Ray();\r\n\r\n constructor(geometry, geoParams, material, transforms) {\r\n super();\r\n this._geometry = geometry;\r\n this._geoParams = geoParams;\r\n const mat = material.createInstance();\r\n geoParams.initMaterial(mat);\r\n this._material = mat;\r\n this._transforms = transforms.length > 0 ? transforms : [new THREE.Matrix4()];\r\n const meshes = this._createMeshes(geometry);\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n this.add(meshes[i]);\r\n }\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const ray = TransformGroup._ray;\r\n const inverseMatrix = TransformGroup._inverseMatrix;\r\n const { children } = this;\r\n ray.copy(raycaster.ray);\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n\r\n if (!gfxutils.belongToSelectLayers(child)) {\r\n continue;\r\n }\r\n\r\n child.updateMatrixWorld();\r\n const mtx = child.matrixWorld;\r\n inverseMatrix.copy(mtx).invert();\r\n raycaster.ray.copy(ray).applyMatrix4(inverseMatrix);\r\n const childIntersects = [];\r\n this._geometry.raycast(raycaster, childIntersects);\r\n\r\n for (let j = 0, ciCount = childIntersects.length; j < ciCount; ++j) {\r\n const inters = childIntersects[j];\r\n if (inters.point) {\r\n inters.point.applyMatrix4(mtx);\r\n inters.distance = ray.origin.distanceTo(inters.point);\r\n }\r\n inters.object = child;\r\n intersects[intersects.length] = inters;\r\n }\r\n }\r\n raycaster.ray.copy(ray);\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const geos = this._geometry.getSubset(chunkIndices);\r\n const subset = [];\r\n let subIdx = 0;\r\n\r\n for (let i = 0, n = geos.length; i < n; ++i) {\r\n const meshes = this._createMeshes(geos[i]);\r\n for (let j = 0, meshCnt = meshes.length; j < meshCnt; ++j) {\r\n subset[subIdx++] = meshes[j];\r\n }\r\n }\r\n\r\n return subset;\r\n }\r\n\r\n _createMeshes(geometry) {\r\n const transforms = this._transforms;\r\n const Mesh = this._geoParams.Object;\r\n const material = this._material;\r\n const meshes = [];\r\n for (let i = 0, n = transforms.length; i < n; ++i) {\r\n const mesh = new Mesh(geometry, material);\r\n mesh.applyMatrix4(transforms[i]);\r\n meshes[i] = mesh;\r\n }\r\n\r\n return meshes;\r\n }\r\n}\r\n\r\nexport default TransformGroup;\r\n","import RCGroup from '../../RCGroup';\r\nimport TransformGroup from '../../meshes/TransformGroup';\r\n\r\nfunction wrapper(Name, args) {\r\n const params = [Name].concat(args);\r\n return Name.bind(...params);\r\n}\r\n\r\nclass ChemGroup extends RCGroup {\r\n constructor(geoParams, selection, colorer, mode, transforms, polyComplexity, material) {\r\n super();\r\n if (this.constructor === ChemGroup) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n this._selection = selection;\r\n this._mode = mode;\r\n this._colorer = colorer;\r\n this._chunksIdc = selection.chunks;\r\n this._polyComplexity = polyComplexity;\r\n this._geo = new (wrapper(geoParams.Geometry, this._makeGeoArgs()))();\r\n this._mesh = new TransformGroup(this._geo, geoParams, material, transforms);\r\n this.add(this._mesh);\r\n this._build();\r\n }\r\n\r\n _makeGeoArgs() {\r\n throw new Error('ChemGroup subclass must override _makeGeoArgs() method');\r\n }\r\n\r\n /**\r\n * Builds subset geometry by ATOMS index list\r\n *\r\n * @param {Number} mask - Representation mask\r\n * @param {Boolean} innerOnly - if true returns inner bonds only - without halves\r\n * @returns {Array} Subset geometry\r\n */\r\n getSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : false;\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return [];\r\n }\r\n return this._mesh.getSubset(chunksList);\r\n }\r\n\r\n _changeSubsetOpacity(mask, value, innerOnly) {\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return;\r\n }\r\n this._geo.setOpacity(chunksList, value);\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 1.0, innerOnly);\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 0.0, innerOnly);\r\n }\r\n}\r\n\r\nexport default ChemGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass AtomsGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { atoms } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const atomsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const atomIdx = atomsIdc[inters[i].chunkIdx];\r\n if (atomIdx < atoms.length) {\r\n inters[i].atom = atoms[atomIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { atoms } = this._selection;\r\n const atomsIdc = this._chunksIdc;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n if ((atom.mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default AtomsGroup;\r\n","import AtomsGroup from './AtomsGroup';\r\n\r\nclass AtomsSphereGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, atom.position, mode.calcAtomRadius(atom));\r\n geo.setColor(i, colorer.getAtomColor(atom, parent));\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), mode.calcAtomRadius(atom));\r\n if (updateColor) {\r\n geo.setColor(i, frameData.getAtomColor(colorer, atom));\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsSphereGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSurfaceGroup extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n return [n, opts];\r\n }\r\n}\r\nexport default AtomsSurfaceGroup;\r\n","/* This is a stub class keep it until SAS/SES is refactored */\r\n\r\nimport AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSASSESGroupStub extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n opts.selection = this._selection;\r\n opts.colorMode = this._colorer;\r\n return [n, opts];\r\n }\r\n}\r\n\r\nexport default AtomsSASSESGroupStub;\r\n","import AtomsGroup from './AtomsGroup';\r\nimport utils from '../../../utils';\r\n\r\nfunction adjustColor(color) {\r\n let r = (color >> 16) & 255;\r\n let g = (color >> 8) & 255;\r\n let b = color & 255;\r\n\r\n if (0.2126 * r + 0.7152 * g + 0.0722 * b > 127) {\r\n r = r * 3 / 10;\r\n g = g * 3 / 10;\r\n b = b * 3 / 10;\r\n } else {\r\n r = 255 - ((255 - r) * 3 / 10);\r\n g = 255 - ((255 - g) * 3 / 10);\r\n b = 255 - ((255 - b) * 3 / 10);\r\n }\r\n\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nfunction inverseColor(color) {\r\n const r = (color >> 16) & 255;\r\n const g = (color >> 8) & 255;\r\n const b = color & 255;\r\n\r\n return ((255 - r) << 16) | ((255 - g) << 8) | (255 - b);\r\n}\r\n\r\nfunction getAtomText(atom) {\r\n if (atom.name.getNode() !== null) {\r\n return atom.name.getNode();\r\n }\r\n\r\n return atom.getVisualName();\r\n}\r\n\r\nconst colorMappings = {\r\n none(c) {\r\n return c;\r\n },\r\n adjust: adjustColor,\r\n inverse: inverseColor,\r\n};\r\n\r\nfunction propagateColor(color, rule) {\r\n let result;\r\n if (colorMappings.hasOwnProperty(rule)) {\r\n result = utils.hexColor(colorMappings[rule](color));\r\n } else {\r\n const val = parseInt(rule, 16);\r\n if (!Number.isNaN(val) && rule.toLowerCase().startsWith('0x')) {\r\n result = utils.hexColor(val);\r\n } else {\r\n result = '#000000';\r\n }\r\n }\r\n return result;\r\n}\r\n\r\nconst templateMappings = {\r\n serial(a) {\r\n return a.serial;\r\n },\r\n name(a) {\r\n return a.getVisualName();\r\n },\r\n elem(a) {\r\n return a.element.name;\r\n },\r\n residue(a) {\r\n return a.residue.getType().getName();\r\n },\r\n sequence(a) {\r\n return a.residue.getSequence();\r\n },\r\n chain(a) {\r\n return a.residue.getChain().getName();\r\n },\r\n hetatm(a) {\r\n return a.isHet();\r\n },\r\n water(a) {\r\n return a.residue.getType().getName() === 'HOH' || a.residue.getType().getName() === 'WAT';\r\n },\r\n};\r\n\r\nconst parseTemplate = function (atom, str) {\r\n return str.replace(/\\{\\{(\\s*\\w+\\s*)\\}\\}/g, (m) => {\r\n let key = m.replace(/\\s+/g, '');\r\n key = key.substring(2, key.length - 2).toLowerCase();\r\n\r\n if (templateMappings.hasOwnProperty(key)) {\r\n return templateMappings[key](atom);\r\n }\r\n return 'null';\r\n });\r\n};\r\n\r\nclass AtomsTextGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n const opts = this._mode.getLabelOpts();\r\n return [this._selection.chunks.length, opts];\r\n }\r\n\r\n _build() {\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = colorer.getAtomColor(atom, parent);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, atom.position, text);\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = frameData.getAtomColor(colorer, atom);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), text);\r\n if (updateColor) {\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsTextGroup;\r\n","import * as THREE from 'three';\r\nimport AtomsGroup from './AtomsGroup';\r\n\r\nfunction _slerp(omega, v1, v2, t) {\r\n const oSin = Math.sin(omega);\r\n return v1.clone().multiplyScalar(Math.sin((1 - t) * omega) / oSin).addScaledVector(v2, Math.sin(t * omega) / oSin);\r\n}\r\n\r\nclass AromaticGroup extends AtomsGroup {\r\n _buildInner(radOffset, addChunk) {\r\n const chunksToIdx = this._selection.chunks;\r\n\r\n const prevVector = new THREE.Vector3();\r\n const currVector = new THREE.Vector3();\r\n const segmentsHeight = this._segmentsHeight;\r\n const leprStep = 1.0 / segmentsHeight;\r\n const colorer = this._colorer;\r\n\r\n const { cycles, parent } = this._selection;\r\n let chunkIdx = 0;\r\n let currAtomIdx = chunksToIdx[chunkIdx];\r\n\r\n for (let cIdx = 0, cCount = cycles.length; cIdx < cCount; ++cIdx) {\r\n const cycle = cycles[cIdx];\r\n const cycAtoms = cycle.atoms;\r\n const chunkPoints = [];\r\n const tmpDir = [];\r\n const { center } = cycle;\r\n const cycleRad = cycle.radius - radOffset;\r\n const n = cycAtoms.length;\r\n let i = 0;\r\n const prevPos = cycAtoms[n - 1].position;\r\n let currPos = cycAtoms[i].position;\r\n prevVector.subVectors(prevPos, center);\r\n currVector.subVectors(currPos, center);\r\n const upDir = currVector.clone().cross(prevVector).normalize();\r\n\r\n for (; i < n; ++i) {\r\n const omega = prevVector.angleTo(currVector);\r\n tmpDir[i] = _slerp(omega, prevVector, currVector, 0.5).normalize();\r\n currPos = cycAtoms[(i + 1) % n].position;\r\n prevVector.copy(currVector);\r\n currVector.subVectors(currPos, center);\r\n }\r\n\r\n for (i = 0; i < n; ++i) {\r\n if (cycAtoms[i].index !== currAtomIdx) {\r\n continue;\r\n }\r\n const start = tmpDir[i];\r\n const end = tmpDir[(i + 1) % n];\r\n const color = colorer.getAtomColor(cycAtoms[i], parent);\r\n const currAngle = start.angleTo(end);\r\n\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n chunkPoints[j] = _slerp(currAngle, start, end, j * leprStep).multiplyScalar(cycleRad).add(center);\r\n }\r\n\r\n addChunk(chunkIdx++, color, chunkPoints, center, upDir);\r\n currAtomIdx = chunksToIdx[chunkIdx];\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default AromaticGroup;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../../gfxutils';\r\nimport AromaticGroup from './AromaticGroup';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n for (let i = 0; i < parts; ++i) {\r\n const a = -2 * i / parts * Math.PI;\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\nconst { calcChunkMatrix } = gfxutils;\r\n\r\nclass AromaticTorusGroup extends AromaticGroup {\r\n _build() {\r\n const segmentsHeight = this._segmentsHeight;\r\n const torusRad = this._mode.getAromRadius();\r\n const radiusV = new THREE.Vector2(torusRad, torusRad);\r\n const radOffset = this._mode.calcStickRadius() + 2 * torusRad;\r\n const lookAtVector = new THREE.Vector3();\r\n const mtc = [];\r\n const geo = this._geo;\r\n this._buildInner(radOffset, (chunkIdx, color, points, center, upDir) => {\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n const currDir = currPoint.clone().sub(center).cross(upDir);\r\n lookAtVector.addVectors(currPoint, currDir);\r\n mtc[j] = calcChunkMatrix(currPoint, lookAtVector, upDir, radiusV);\r\n }\r\n geo.setItem(chunkIdx, mtc);\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._polyComplexity;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length];\r\n }\r\n}\r\n\r\nexport default AromaticTorusGroup;\r\n","import AromaticGroup from './AromaticGroup';\r\n\r\nclass AromaticLinesGroup extends AromaticGroup {\r\n _build() {\r\n const geo = this._geo;\r\n const radOffset = this._mode.getAromaticOffset();\r\n this._buildInner(radOffset, (chunkIdx, color, points) => {\r\n let prevPt = points[0];// do not replace with start\r\n for (let j = 1; j <= this._segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n geo.setSegment(chunkIdx, j - 1, prevPt, currPoint);\r\n prevPt = currPoint;\r\n }\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._mode.getAromaticArcChunks();\r\n return [this._selection.chunks.length, this._segmentsHeight, true];\r\n }\r\n}\r\n\r\nexport default AromaticLinesGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[inters[i].chunkIdx];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesGroup;\r\n","import ResiduesGroup from './ResiduesGroup';\r\n\r\nclass NucleicItemGroup extends ResiduesGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[Math.floor(inters[i].chunkIdx / 2)];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n let chunkIdx = 0;\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList[chunkIdx++] = 2 * i;\r\n chunksList[chunkIdx++] = 2 * i + 1;\r\n }\r\n }\r\n return chunksList;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finishUpdate();\r\n }\r\n}\r\n\r\nexport default NucleicItemGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicCylindersGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n geo.setItem(chunkIdx, cyl1, cyl2, stickRad);\r\n geo.setColor(chunkIdx, color, color);\r\n }\r\n}\r\n\r\nexport default NucleicCylindersGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicSpheresGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length * 2, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n let idx = chunkIdx * 2;\r\n geo.setItem(idx, cyl1, stickRad);\r\n geo.setColor(idx, color);\r\n idx++;\r\n geo.setItem(idx, cyl2, stickRad);\r\n geo.setColor(idx, color);\r\n }\r\n}\r\n\r\nexport default NucleicSpheresGroup;\r\n","import * as THREE from 'three';\r\nimport { Smooth } from '../../../../vendor/js/Smooth';\r\nimport gfxutils from '../../gfxutils';\r\nimport chem from '../../../chem';\r\n\r\nconst { ResidueType } = chem;\r\n\r\nconst calcMatrix = gfxutils.calcChunkMatrix;\r\n\r\nfunction _buildStructureInterpolator(points, tension) {\r\n const path = Smooth(points, {\r\n method: Smooth.METHOD_CUBIC,\r\n clip: Smooth.CLIP_CLAMP,\r\n cubicTension: tension,\r\n scaleTo: 1,\r\n });\r\n\r\n return function (t, argTrans) {\r\n let transformT = argTrans;\r\n if (transformT === null) {\r\n // map our range to the [second .. last but one]\r\n transformT = function (tt) {\r\n return (tt * ((points.length - 1) - 2) + 1) / (points.length - 1);\r\n };\r\n }\r\n const newt = transformT(t);\r\n const ans = path(newt);\r\n return new THREE.Vector3(ans[0], ans[1], ans[2]);\r\n };\r\n}\r\n\r\nfunction _addPoints(centerPoints, topPoints, idx, residue) {\r\n if (!residue._isValid) {\r\n centerPoints[idx] = centerPoints[idx - 1];\r\n topPoints[idx] = topPoints[idx - 1];\r\n return;\r\n }\r\n const cp = residue._controlPoint;\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n const tp = cp.clone().add(residue._wingVector);\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n}\r\n\r\nfunction _addPointsForLoneResidue(centerPoints, topPoints, idx, residue) {\r\n const nucleic = (residue._type.flags & ResidueType.Flags.NUCLEIC) !== 0;\r\n const nameFrom = nucleic ? 'C5\\'' : 'N';\r\n const nameTo = nucleic ? 'C3\\'' : 'C';\r\n\r\n let posFrom;\r\n let posTo;\r\n residue.forEachAtom((atom) => {\r\n const name = atom.getVisualName();\r\n if (!posFrom && name === nameFrom) {\r\n posFrom = atom.position;\r\n } else if (!posTo && name === nameTo) {\r\n posTo = atom.position;\r\n }\r\n });\r\n\r\n // provide a fallback for unknown residues\r\n if (!(posFrom && posTo)) {\r\n posFrom = residue._firstAtom.position;\r\n posTo = residue._lastAtom.position;\r\n }\r\n\r\n if (posFrom && posTo) {\r\n const shift = posTo.clone().sub(posFrom);\r\n\r\n const wing = residue._wingVector;\r\n const cp = residue._controlPoint;\r\n const tp = cp.clone().add(wing);\r\n\r\n const cpPrev = cp.clone().sub(shift);\r\n const tpPrev = cpPrev.clone().add(wing);\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n ++idx;\r\n\r\n const cpNext = cp.clone().add(shift);\r\n const tpNext = cpNext.clone().add(wing);\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n ++idx;\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n }\r\n}\r\n\r\nfunction _calcPoints(residues, firstIdx, lastIdx, boundaries) {\r\n const left = boundaries.start;\r\n const right = boundaries.end;\r\n function _prevIdx(idx) {\r\n return idx > left && residues[idx - 1]._isValid ? idx - 1 : idx;\r\n }\r\n function _nextIdx(idx) {\r\n return idx < right && residues[idx + 1]._isValid ? idx + 1 : idx;\r\n }\r\n\r\n const topPoints = [];\r\n const centerPoints = [];\r\n let arrIdx = 0;\r\n function _extrapolate2(currIdx, otherIdx) {\r\n const cp = residues[currIdx]._controlPoint.clone().lerp(residues[otherIdx]._controlPoint, -0.25);\r\n const tp = cp.clone().add(residues[currIdx]._wingVector);\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n }\r\n\r\n // a single disconnected residue\r\n const prevIdx = _prevIdx(firstIdx);\r\n const nextIdx = _nextIdx(lastIdx);\r\n if (prevIdx === nextIdx) {\r\n _addPointsForLoneResidue(centerPoints, topPoints, arrIdx, residues[firstIdx]);\r\n return { centerPoints, topPoints };\r\n }\r\n\r\n // Two points (prev-prev and next-next) are added to support edge conditions for cubic splines, they are ignored\r\n // Another two (prev and next) were added to support the outside of the sub chain\r\n\r\n // prev and prev-prev\r\n if (firstIdx === prevIdx) {\r\n // do the extrapolation\r\n _extrapolate2(firstIdx, _nextIdx(firstIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[_prevIdx(prevIdx)]);\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[prevIdx]);\r\n }\r\n\r\n // main loop\r\n for (let idx = firstIdx; idx <= lastIdx; ++idx) {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[idx]);\r\n }\r\n\r\n // next and next-next\r\n if (nextIdx === _nextIdx(nextIdx)) {\r\n // do the extrapolation\r\n _extrapolate2(lastIdx, _prevIdx(lastIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[nextIdx]);\r\n _addPoints(centerPoints, topPoints, arrIdx, residues[_nextIdx(nextIdx)]);\r\n }\r\n return { centerPoints, topPoints };\r\n}\r\n\r\nclass CartoonHelper {\r\n constructor(residues, startIdx, endIdx, segmentsCount, tension, boundaries) {\r\n const pointsArrays = _calcPoints(residues, startIdx, endIdx, boundaries);\r\n this._topInterp = _buildStructureInterpolator(pointsArrays.topPoints, tension);\r\n this._centerInterp = _buildStructureInterpolator(pointsArrays.centerPoints, tension);\r\n\r\n this._shift = 0.5 / (endIdx - startIdx + 2);\r\n this._valueStep = (1.0 - 2 * this._shift) / (2 * (endIdx - startIdx + 1) * (segmentsCount - 1));\r\n this._segmentsCount = segmentsCount;\r\n }\r\n\r\n prepareMatrices(idx, firstRad, secondRad) {\r\n const mtcCount = this._segmentsCount;\r\n const outMtc = new Array(mtcCount);\r\n const currRad = new THREE.Vector2(0, 0);\r\n\r\n const topInterp = this._topInterp;\r\n const cenInterp = this._centerInterp;\r\n\r\n let currentValue = this._shift + this._valueStep * (mtcCount - 1) * idx;\r\n\r\n for (let mtxIdx = 0; mtxIdx < mtcCount; ++mtxIdx) {\r\n const lerpVal = Math.min(1.0, mtxIdx / (mtcCount - 1));\r\n currRad.lerpVectors(firstRad, secondRad, lerpVal);\r\n\r\n const currTop = topInterp(currentValue, null);\r\n const currCenter = cenInterp(currentValue, null);\r\n currentValue += this._valueStep;\r\n const nextCenter = cenInterp(currentValue, null);\r\n\r\n outMtc[mtxIdx] = calcMatrix(currCenter.clone(), nextCenter.clone(), currTop.clone().sub(currCenter), currRad);\r\n }\r\n\r\n return outMtc;\r\n }\r\n}\r\n\r\nexport default CartoonHelper;\r\n","import * as THREE from 'three';\r\nimport ResiduesGroup from './ResiduesGroup';\r\nimport CartoonHelper from './CartoonHelper';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n\r\n for (let i = 0; i < parts; ++i) {\r\n // starts from pi/2 because it's important that points are lied on the angles of arrows (visual issues if not)\r\n const a = Math.PI / 2.0 - 2 * Math.PI * i / parts;\r\n\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\n\r\nfunction _loopThrough(subDiv, residues, segmentsHeight, tension, mode, callback) {\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n const { boundaries } = subDiv[subDivI];\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const idc = [subs[i].start, subs[i].end];\r\n const matrixHelper = new CartoonHelper(residues, idc[0], idc[1], segmentsHeight, tension, boundaries);\r\n let prevLast = null;\r\n const startIdx = subs[i].start * 2;\r\n const endIdx = subs[i].end * 2 + 1;\r\n let prevSecondRad = mode.getResidueRadius(residues[0], 0);\r\n for (let idx = startIdx; idx <= endIdx; ++idx) {\r\n const resIdx = (idx / 2 | 0);\r\n const currRes = residues[resIdx];\r\n const firstRad = mode.getResidueRadius(currRes, idx % 2);\r\n const secondRad = mode.getResidueRadius(currRes, 1 + (idx % 2));\r\n\r\n const mtc = matrixHelper.prepareMatrices(idx - idc[0] * 2, firstRad, secondRad);\r\n mtc.unshift(prevLast === null ? mtc[0] : prevLast);\r\n\r\n // Slope - radius is changed along this residue part\r\n const hasSlope = (firstRad.x !== secondRad.x) || (firstRad.y !== secondRad.y);\r\n // Cut - end radius of previous part not equal to start radius of this part. First section of this part lies in the orthogonal plane\r\n const hasCut = (firstRad.x !== prevSecondRad.x) || (firstRad.y !== prevSecondRad.y);\r\n\r\n callback(currRes, mtc, hasSlope, hasCut);\r\n\r\n prevLast = mtc[segmentsHeight];\r\n prevSecondRad = secondRad;\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ResiduesSubseqGroup extends ResiduesGroup {\r\n _makeGeoArgs() {\r\n const cmpMultiplier = this._mode.getHeightSegmentsRatio();\r\n this._segmentsHeight = this._polyComplexity * cmpMultiplier | 0;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length * 2];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, (currRes, mtc, hasSlope = false, hasCut = false) => {\r\n const color = colorer.getResidueColor(currRes, parent);\r\n chunkIdc[chunkIdx] = currRes._index;\r\n geo.setItem(chunkIdx, mtc, hasSlope, hasCut);\r\n geo.setColor(chunkIdx++, color);\r\n });\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n const frameRes = frameData.getResidues();\r\n let chunkIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n _loopThrough(this._selection.subdivs, frameRes, this._segmentsHeight, tension, mode, (currRes, mtc) => {\r\n geo.setItem(chunkIdx, mtc);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n });\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default ResiduesSubseqGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesTraceGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const subDiv = this._selection.subdivs;\r\n let chunksCount = 0;\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n chunksCount += subs[i].end - subs[i].start;\r\n }\r\n }\r\n return [chunksCount, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n chunkIdc[chunkIdx] = { first: prevRes._index, second: currRes._index };\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n geo.finalize();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n const { residues } = this._selection;\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksToIdx = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const chunk = chunksToIdx[Math.floor(chunkIdx / 2)];\r\n const resIdx = chunkIdx % 2 === 0 ? chunk.first : chunk.second;\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const chunksToIdx = this._chunksIdc;\r\n const { residues } = this._selection;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const chunk = chunksToIdx[i];\r\n if (residues[chunk.first]._mask & mask) {\r\n chunksList.push(i * 2);\r\n }\r\n if (residues[chunk.second]._mask & mask) {\r\n chunksList.push(i * 2 + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesTraceGroup;\r\n","import ChemGroup from './ChemGroup';\r\nimport Bond from '../../../chem/Bond';\r\n\r\nfunction getCylinderCount(bondOrder) {\r\n return bondOrder < 2 ? 1 : bondOrder;\r\n}\r\n\r\nclass BondsGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const drawMultiple = this._mode.drawMultiorderBonds();\r\n const showAromatic = this._mode.showAromaticLoops();\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n let bondsCount = 0;\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n bondsCount += this.getBondOrder(bonds[bondsIdc[i]], drawMultiple, showAromatic);\r\n }\r\n return [bondsCount, this._polyComplexity];\r\n }\r\n\r\n getBondOrder(bond, drawMultiple, showAromatic) {\r\n let bondOrder = 1;\r\n if (drawMultiple && (!showAromatic || bond._type !== Bond.BondType.AROMATIC)) {\r\n bondOrder = getCylinderCount(bond._order);\r\n }\r\n return bondOrder;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const { bonds } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const bondsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const bondIdx = bondsIdc[Math.floor(chunkIdx / 2)];\r\n if (bondIdx < bonds.length) {\r\n const bond = bonds[bondIdx];\r\n inters[i].atom = chunkIdx % 2 === 0 ? bond._left : bond._right;\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask, innerOnly) {\r\n const chunksList = [];\r\n const { bonds } = this._selection;\r\n const chunksToIdx = this._chunksIdc;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const bond = bonds[chunksToIdx[i]];\r\n if ((bond._left.mask & mask) && (!innerOnly || (bond._right.mask & mask))) {\r\n chunksList.push(2 * i);\r\n }\r\n if ((bond._right.mask & mask) && (!innerOnly || (bond._left.mask & mask))) {\r\n chunksList.push(2 * i + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default BondsGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nclass BondsCylinderGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsCylinderGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nconst STEP_SIZE = 0.15;\r\n\r\nclass BondsLinesGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsLinesGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\nimport AtomsSurfaceGroup from './AtomsSurfaceGroup';\r\nimport AtomsSASSESGroupStub from './AtomsSASSESGroupStub';\r\nimport AtomsTextGroup from './AtomsTextGroup';\r\nimport AromaticTorusGroup from './AromaticTorusGroup';\r\nimport AromaticLinesGroup from './AromaticLinesGroup';\r\nimport NucleicCylindersGroup from './NucleicCylindersGroup';\r\nimport NucleicSpheresGroup from './NucleicSpheresGroup';\r\nimport ResiduesSubseqGroup from './ResiduesSubseqGroup';\r\nimport ResiduesTraceGroup from './ResiduesTraceGroup';\r\nimport BondsCylinderGroup from './BondsCylinderGroup';\r\nimport BondsLinesGroup from './BondsLinesGroup';\r\n\r\nexport default {\r\n AtomsSphereGroup,\r\n AtomsSurfaceGroup,\r\n AtomsSASSESGroupStub,\r\n AtomsTextGroup,\r\n AromaticTorusGroup,\r\n AromaticLinesGroup,\r\n NucleicCylindersGroup,\r\n NucleicSpheresGroup,\r\n ResiduesSubseqGroup,\r\n ResiduesTraceGroup,\r\n BondsCylinderGroup,\r\n BondsLinesGroup,\r\n};\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AtomsProcessor extends RCGroup {\r\n constructor(AtomsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n this._mode = mode;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let atomCount = 0;\r\n component.forEachAtom((atom) => {\r\n if (!self._checkAtom(atom, mask)) {\r\n return;\r\n }\r\n atomsIdc[atomCount++] = atom.index;\r\n });\r\n if (atomCount === 0) {\r\n return;\r\n }\r\n const atomsGroup = new AtomsGroup(geoParams, {\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n _checkAtom(atom, mask) {\r\n return atom.mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AtomsProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\n\r\nclass OrphanAtomsProcessor extends AtomsProcessor {\r\n _checkAtom(atom, mask) {\r\n if (!(atom.mask & mask)) {\r\n return false;\r\n }\r\n\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n if ((bonds[i]._left.mask & mask) && (bonds[i]._right.mask & mask)) {\r\n return false;\r\n }\r\n }\r\n return true;\r\n }\r\n}\r\n\r\nexport default OrphanAtomsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass ResiduesProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n component.forEachResidue((residue) => {\r\n if (self._checkResidue(residue, mask)) {\r\n resIdc[chunksCount++] = residue._index;\r\n }\r\n });\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n checkResidue(residue, mask) {\r\n return residue._mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default ResiduesProcessor;\r\n","import ResidueProcessor from './ResiduesProcessor';\r\n\r\nclass NucleicProcessor extends ResidueProcessor {\r\n _checkResidue(residue, mask) {\r\n return mask & residue._mask && residue._cylinders !== null;\r\n }\r\n}\r\nexport default NucleicProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass SubseqsProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const subDivs = component.getMaskedSubdivSequences(mask);\r\n\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n for (let subDivI = 0, subDivN = subDivs.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDivs[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let j = subs[i].start, jEnd = subs[i].end; j <= jEnd; ++j) {\r\n resIdc[chunksCount++] = residues[j]._index;\r\n }\r\n }\r\n }\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n subdivs: subDivs,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default SubseqsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass BondsProcessor extends RCGroup {\r\n constructor(BondsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const bonds = complex.getBonds();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const bondsIdc = [];\r\n let bondsCount = 0;\r\n component.forEachBond((bond) => {\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n if (!(atom1.mask & mask) || !(atom2.mask & mask)) {\r\n return;\r\n }\r\n bondsIdc[bondsCount++] = bond._index;\r\n });\r\n if (bondsCount === 0) {\r\n return;\r\n }\r\n const bondsGroup = new BondsGroup(geoParams, {\r\n bonds,\r\n chunks: bondsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n bondsGroup._component = component;\r\n self.add(bondsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default BondsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AromaticProcessor extends RCGroup {\r\n constructor(AromaticGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n if (!mode.showAromaticLoops()) {\r\n return;\r\n }\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let chunksCount = 0;\r\n const cycles = [];\r\n let cycleIdx = 0;\r\n component.forEachCycle((cycle) => {\r\n const cycAtoms = cycle.atoms;\r\n let perCycle = 0;\r\n for (let i = 0, n = cycAtoms.length; i < n; ++i) {\r\n if ((cycAtoms[i].mask & mask) !== 0) {\r\n ++perCycle;\r\n atomsIdc[chunksCount++] = cycAtoms[i].index;\r\n }\r\n }\r\n if (perCycle > 0) {\r\n cycles[cycleIdx++] = cycle;\r\n }\r\n });\r\n\r\n const atomsGroup = new AromaticGroup(geoParams, {\r\n cycles,\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AromaticProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\nimport OrphanAtomsProcessor from './OrphanAtomsProcessor';\r\nimport ResiduesProcessor from './ResiduesProcessor';\r\nimport NucleicProcessor from './NucleicProcessor';\r\nimport SubseqsProcessor from './SubseqsProcessor';\r\nimport BondsProcessor from './BondsProcessor';\r\nimport AromaticProcessor from './AromaticProcessor';\r\n\r\nexport default {\r\n Atoms: AtomsProcessor,\r\n OrphanAtoms: OrphanAtomsProcessor,\r\n Residues: ResiduesProcessor,\r\n Nucleic: NucleicProcessor,\r\n Subseqs: SubseqsProcessor,\r\n Bonds: BondsProcessor,\r\n Aromatic: AromaticProcessor,\r\n};\r\n","import MeshCreator from '../../meshes/MeshCreator';\r\nimport groups from './groups';\r\nimport processors from '../processors/processors';\r\n\r\nfunction _bakeGroup(triplet, Processor, Group) {\r\n return function (complex, colorer, mode, polyComplexity, mask, material) {\r\n return new Processor(Group, triplet, complex, colorer, mode, polyComplexity, mask, material);\r\n };\r\n}\r\n\r\nclass GroupsFactory {\r\n static AtomsSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static OrphanedAtomsCrosses(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createCrosses(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.OrphanAtoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static BondsCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsCylinderGroup);\r\n }\r\n\r\n static BondsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.create2CLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsLinesGroup);\r\n }\r\n\r\n static CartoonChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesSubseqGroup);\r\n }\r\n\r\n static TraceChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CClosedCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesTraceGroup);\r\n }\r\n\r\n static NucleicSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicSpheresGroup);\r\n }\r\n\r\n static NucleicCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicCylindersGroup);\r\n }\r\n\r\n static ALoopsTorus(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticTorusGroup);\r\n }\r\n\r\n static ALoopsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createChunkedLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticLinesGroup);\r\n }\r\n\r\n static QuickSurfGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createQuickSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static ContactSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createContactSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static SASSESSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createSASSES(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSASSESGroupStub);\r\n }\r\n\r\n static TextLabelsGeo(caps, settings) {\r\n const gfxTriplet = MeshCreator.createLabels(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsTextGroup);\r\n }\r\n}\r\n\r\nexport default GroupsFactory;\r\n","import _ from 'lodash';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport factory from './groups/GroupsFactory';\r\n\r\n/**\r\n * Create new mode.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the mode after its creation.\r\n *\r\n * @exports Mode\r\n * @this Mode\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available modes used for building and displaying molecule geometry.\r\n */\r\nclass Mode {\r\n constructor(opts) {\r\n if (this.constructor === Mode) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Mode options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts);\r\n }\r\n\r\n /**\r\n * Get mode identification, probably with options.\r\n * @returns {string|Array} Mode identifier string ({@link Mode#id}) or two-element array containing both mode\r\n * identifier and options ({@link Mode#opts}).\r\n * Options are returned if they were changed during or after the mode creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, this.settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const polyComplexity = this.opts.polyComplexity ? this.opts.polyComplexity[this.settings.now.resolution] : 0;\r\n const groupList = this.depGroups;\r\n const groupCount = groupList.length;\r\n const group = new gfxutils.RCGroup();\r\n const self = this;\r\n for (let i = 0; i < groupCount; ++i) {\r\n let currGroup = groupList[i];\r\n let renderParams = {};\r\n if (_.isArray(currGroup)) {\r\n renderParams = currGroup[1].call(this);\r\n [currGroup] = currGroup;\r\n }\r\n const Group = factory[currGroup](null, this.settings, renderParams);\r\n const newGroup = new Group(complex, colorer, self, polyComplexity, mask, material);\r\n if (newGroup.children.length > 0) {\r\n group.add(newGroup);\r\n }\r\n }\r\n return group;\r\n }\r\n}\r\n\r\nmakeContextDependent(Mode.prototype);\r\n\r\n/**\r\n* Mode identifier.\r\n* @type {string}\r\n*/\r\nMode.prototype.id = '__';\r\n\r\n/**\r\n * Mode geo groups.\r\n * @type {Array}\r\n */\r\nMode.prototype.depGroups = [];\r\n\r\nexport default Mode;\r\n","import Mode from './Mode';\r\n\r\nfunction getRenderParams() {\r\n return {\r\n lineWidth: this.opts.lineWidth,\r\n };\r\n}\r\n\r\nclass LinesMode extends Mode {\r\n static id = 'LN';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const groups = this.depGroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n groups[i] = [groups[i], getRenderParams];\r\n }\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n\r\n calcAtomRadius() {\r\n return this.opts.atom;\r\n }\r\n\r\n getAromaticOffset() {\r\n return this.opts.offsarom;\r\n }\r\n\r\n getAromaticArcChunks() {\r\n return this.opts.chunkarom;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n}\r\n\r\nLinesMode.prototype.id = 'LN';\r\nLinesMode.prototype.name = 'Lines';\r\nLinesMode.prototype.shortName = 'Lines';\r\nLinesMode.prototype.depGroups = [\r\n 'ALoopsLines',\r\n 'BondsLines',\r\n 'OrphanedAtomsCrosses',\r\n];\r\n\r\nexport default LinesMode;\r\n","/* eslint-disable no-magic-numbers */\r\nimport Mode from './Mode';\r\n\r\nclass LicoriceMode extends Mode {\r\n static id = 'LC';\r\n\r\n calcAtomRadius(_atom) {\r\n return this.opts.bond;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nLicoriceMode.prototype.id = 'LC';\r\nLicoriceMode.prototype.name = 'Licorice';\r\nLicoriceMode.prototype.shortName = 'Licorice';\r\nLicoriceMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default LicoriceMode;\r\n","/* eslint-disable no-magic-numbers */\r\nimport Mode from './Mode';\r\n\r\nclass BallsAndSticksMode extends Mode {\r\n static id = 'BS';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius * this.opts.atom;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nBallsAndSticksMode.prototype.id = 'BS';\r\nBallsAndSticksMode.prototype.name = 'Balls and Sticks';\r\nBallsAndSticksMode.prototype.shortName = 'Balls';\r\nBallsAndSticksMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default BallsAndSticksMode;\r\n","import Mode from './Mode';\r\n\r\nclass VanDerWaalsMode extends Mode {\r\n static id = 'VW';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n}\r\n\r\nVanDerWaalsMode.prototype.id = 'VW';\r\nVanDerWaalsMode.prototype.name = 'Van der Waals';\r\nVanDerWaalsMode.prototype.shortName = 'VDW';\r\nVanDerWaalsMode.prototype.depGroups = ['AtomsSpheres'];\r\n\r\nexport default VanDerWaalsMode;\r\n","import Mode from './Mode';\r\n\r\nclass TraceMode extends Mode {\r\n static id = 'TR';\r\n\r\n calcStickRadius() {\r\n return this.opts.radius;\r\n }\r\n}\r\n\r\nTraceMode.prototype.id = 'TR';\r\nTraceMode.prototype.name = 'Trace';\r\nTraceMode.prototype.shortName = 'Trace';\r\nTraceMode.prototype.depGroups = ['TraceChains'];\r\n\r\nexport default TraceMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass TubeMode extends Mode {\r\n static id = 'TU';\r\n\r\n getResidueRadius(_residue) {\r\n return this.TUBE_RADIUS;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const rad = this.opts.radius;\r\n this.TUBE_RADIUS = new THREE.Vector2(rad, rad);\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nTubeMode.prototype.id = 'TU';\r\nTubeMode.prototype.name = 'Tube';\r\nTubeMode.prototype.shortName = 'Tube';\r\nTubeMode.prototype.depGroups = ['CartoonChains'];\r\n\r\nexport default TubeMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass CartoonMode extends Mode {\r\n static id = 'CA';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n // cache for secondary structure options\r\n this.secCache = {};\r\n }\r\n\r\n getResidueStartRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (!second || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return secOpts.start;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueEndRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (second === null || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return this.ARROW_END;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueRadius(residue, val) {\r\n const startRad = this.getResidueStartRadius(residue);\r\n if (val === 0) {\r\n return startRad;\r\n }\r\n\r\n const endRad = this.getResidueEndRadius(residue);\r\n if (val === 2) {\r\n return endRad;\r\n }\r\n\r\n return startRad.clone().lerp(endRad, val / 2.0);\r\n }\r\n\r\n calcStickRadius(_res) {\r\n return this.opts.radius;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const tubeRad = this.opts.radius;\r\n const secHeight = this.opts.depth;\r\n\r\n this.TUBE_RADIUS = new THREE.Vector2(tubeRad, tubeRad);\r\n this.ARROW_END = new THREE.Vector2(secHeight, tubeRad);\r\n const secCache = {};\r\n const secData = this.opts.ss;\r\n /* eslint-disable guard-for-in */\r\n for (const prop in secData) {\r\n secCache[prop] = {\r\n center: new THREE.Vector2(secHeight, secData[prop].width),\r\n start: new THREE.Vector2(secHeight, secData[prop].arrow),\r\n };\r\n }\r\n this.secCache = secCache;\r\n /* eslint-enable guard-for-in */\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nCartoonMode.prototype.id = 'CA';\r\nCartoonMode.prototype.name = 'Cartoon';\r\nCartoonMode.prototype.shortName = 'Cartoon';\r\nCartoonMode.prototype.depGroups = [\r\n 'CartoonChains',\r\n 'NucleicSpheres',\r\n 'NucleicCylinders',\r\n];\r\n\r\nexport default CartoonMode;\r\n","import chem from '../../chem';\r\nimport Mode from './Mode';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction getRenderParams() {\r\n return {\r\n wireframe: this.opts.wireframe,\r\n zClip: this.opts.zClip,\r\n };\r\n}\r\n\r\nclass SurfaceMode extends Mode {\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const surfaces = this.surfaceNames;\r\n const groups = this.depGroups;\r\n for (let i = 0, n = surfaces.length; i < n; ++i) {\r\n groups[groups.length] = [surfaces[i], getRenderParams];\r\n }\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getVisibilitySelector() {\r\n let visibilitySelector = null;\r\n if (this.opts.subset !== '') {\r\n const res = selectors.parse(this.opts.subset);\r\n if (!res.error) {\r\n visibilitySelector = res.selector;\r\n }\r\n }\r\n return visibilitySelector;\r\n }\r\n}\r\n\r\nSurfaceMode.prototype.isSurface = true;\r\nSurfaceMode.prototype.surfaceNames = [];\r\n\r\nexport default SurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass QuickSurfaceMode extends SurfaceMode {\r\n static id = 'QS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n useBeads: false,\r\n isoValue: this.opts.isoValue,\r\n gaussLim: this.opts.gaussLim[this.settings.now.resolution],\r\n radScale: this.opts.scale,\r\n gridSpacing: this.opts.gridSpacing[this.settings.now.resolution],\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nQuickSurfaceMode.prototype.id = 'QS';\r\nQuickSurfaceMode.prototype.name = 'Quick Surface';\r\nQuickSurfaceMode.prototype.shortName = 'Quick Surf';\r\nQuickSurfaceMode.prototype.surfaceNames = ['QuickSurfGeo'];\r\n\r\nexport default QuickSurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass IsoSurfaceMode extends SurfaceMode {\r\n constructor(excludeProbe, opts) {\r\n super(opts);\r\n this._excludeProbe = excludeProbe;\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getSurfaceOpts() {\r\n return {\r\n gridSpacing: this.opts.polyComplexity[this.settings.now.resolution],\r\n radScale: this._radScale,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n probeRadius: this.opts.probeRadius,\r\n excludeProbe: this._excludeProbe,\r\n };\r\n }\r\n}\r\n\r\nIsoSurfaceMode.prototype.id = 'SU';\r\nIsoSurfaceMode.prototype.name = 'Surface';\r\nIsoSurfaceMode.prototype.shortName = 'Surface';\r\nIsoSurfaceMode.prototype.surfaceNames = ['SASSESSurfaceGeo'];\r\n\r\nIsoSurfaceMode.prototype._radScale = 1;\r\nIsoSurfaceMode.prototype._excludeProbe = false;\r\n\r\nexport default IsoSurfaceMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSASMode extends IsoSurfaceMode {\r\n static id = 'SA';\r\n\r\n constructor(opts) {\r\n super(false, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSASMode.prototype.id = 'SA';\r\nIsoSurfaceSASMode.prototype.name = 'Solvent Accessible Surface';\r\nIsoSurfaceSASMode.prototype.shortName = 'SAS';\r\n\r\nexport default IsoSurfaceSASMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSESMode extends IsoSurfaceMode {\r\n static id = 'SE';\r\n\r\n constructor(opts) {\r\n super(true, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSESMode.prototype.id = 'SE';\r\nIsoSurfaceSESMode.prototype.name = 'Solvent Excluded Surface';\r\nIsoSurfaceSESMode.prototype.shortName = 'SES';\r\n\r\nexport default IsoSurfaceSESMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass ContactSurfaceMode extends SurfaceMode {\r\n static id = 'CS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n probeRadius: this.opts.probeRadius,\r\n radScale: this.opts.polyComplexity[this.settings.now.resolution],\r\n scaleFactor: this.opts.polyComplexity[this.settings.now.resolution],\r\n gridSpacing: 1.0 / this.opts.polyComplexity[this.settings.now.resolution],\r\n isoValue: this.opts.isoValue,\r\n probePositions: this.opts.probePositions,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nContactSurfaceMode.prototype.id = 'CS';\r\nContactSurfaceMode.prototype.name = 'Contact Surface';\r\nContactSurfaceMode.prototype.shortName = 'Contact Surf';\r\nContactSurfaceMode.prototype.isSurface = true;\r\nContactSurfaceMode.prototype.surfaceNames = ['ContactSurfaceGeo'];\r\n\r\nexport default ContactSurfaceMode;\r\n","import _ from 'lodash';\r\nimport Mode from './Mode';\r\n\r\nclass TextMode extends Mode {\r\n static id = 'TX';\r\n\r\n getTemplateOptions() {\r\n return this.opts.template;\r\n }\r\n\r\n getLabelOpts() {\r\n return _.merge(this.opts, {\r\n colors: true,\r\n adjustColor: true,\r\n transparent: true,\r\n });\r\n }\r\n}\r\n\r\nTextMode.prototype.id = 'TX';\r\nTextMode.prototype.name = 'Text mode';\r\nTextMode.prototype.shortName = 'Text';\r\nTextMode.prototype.depGroups = ['TextLabelsGeo'];\r\n\r\nexport default TextMode;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport LinesMode from './modes/LinesMode';\r\nimport LicoriceMode from './modes/LicoriceMode';\r\nimport BallsAndSticksMode from './modes/BallsAndSticksMode';\r\nimport VanDerWaalsMode from './modes/VanDerWaalsMode';\r\nimport TraceMode from './modes/TraceMode';\r\nimport TubeMode from './modes/TubeMode';\r\nimport CartoonMode from './modes/CartoonMode';\r\nimport QuickSurfaceMode from './modes/QuickSurfaceMode';\r\nimport IsoSurfaceSASMode from './modes/IsoSurfaceSASMode';\r\nimport IsoSurfaceSESMode from './modes/IsoSurfaceSESMode';\r\nimport ContactSurfaceMode from './modes/ContactSurfaceMode';\r\nimport TextMode from './modes/TextMode';\r\n\r\nconst modes = new EntityList([\r\n LinesMode,\r\n LicoriceMode,\r\n BallsAndSticksMode,\r\n VanDerWaalsMode,\r\n TraceMode,\r\n TubeMode,\r\n CartoonMode,\r\n QuickSurfaceMode,\r\n IsoSurfaceSASMode,\r\n IsoSurfaceSESMode,\r\n ContactSurfaceMode,\r\n TextMode,\r\n]);\r\n\r\nexport default modes;\r\n","import _ from 'lodash';\r\n\r\nfunction clamp(x, a, b) {\r\n return x <= b ? x < 0 ? 0 : x : b;\r\n}\r\n\r\nfunction lerpColor(c1, c2, alpha) {\r\n const beta = 1 - alpha;\r\n const r1 = (c1 >> 16) & 0xff;\r\n const g1 = (c1 >> 8) & 0xff;\r\n const b1 = c1 & 0xff;\r\n const r2 = (c2 >> 16) & 0xff;\r\n const g2 = (c2 >> 8) & 0xff;\r\n const b2 = c2 & 0xff;\r\n const r = beta * r1 + alpha * r2;\r\n const g = beta * g1 + alpha * g2;\r\n const b = beta * b1 + alpha * b2;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nclass Palette {\r\n constructor(name, id) {\r\n this.name = name || 'Custom';\r\n this.id = id || 'CP';\r\n }\r\n\r\n getElementColor(name, asIs = false) {\r\n const color = this.elementColors[name];\r\n return color === undefined && !asIs ? this.defaultElementColor : color;\r\n }\r\n\r\n getResidueColor(name, asIs = false) {\r\n const color = this.residueColors[name];\r\n return color === undefined && !asIs ? this.defaultResidueColor : color;\r\n }\r\n\r\n getChainColor(name) {\r\n let chain = name.charCodeAt(0);\r\n chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F)\r\n % this.chainColors.length;\r\n return this.chainColors[chain];\r\n }\r\n\r\n getSecondaryColor(type, asIs = false) {\r\n const color = this.secondaryColors[type];\r\n return color === undefined && !asIs ? this.defaultSecondaryColor : color;\r\n }\r\n\r\n getSequentialColor(index) {\r\n const { colors } = this;\r\n const len = colors.length;\r\n return index < 0 ? colors[(index % len) + len] : colors[index % len];\r\n }\r\n\r\n getGradientColor(value, gradientName) {\r\n const gradient = this.gradients[gradientName];\r\n if (!gradient) {\r\n return this.defaultNamedColor;\r\n }\r\n const count = gradient.length;\r\n const index = value * (count - 1);\r\n let left = Math.floor(index);\r\n const right = clamp(left + 1, 0, count - 1);\r\n left = clamp(left, 0, count - 1);\r\n return lerpColor(gradient[left], gradient[right], index - left);\r\n }\r\n\r\n getNamedColor(name, asIs = false) {\r\n const color = this.namedColors[name];\r\n return color === undefined && !asIs ? this.defaultNamedColor : color;\r\n }\r\n}\r\n\r\n_.assign(Palette.prototype, {\r\n colors: [0xFFFFFF, 0xFF0000, 0x00FF00, 0x0000FF, 0x808080],\r\n\r\n minRangeColor: 0x000000,\r\n midRangeColor: 0x7F7F7F,\r\n maxRangeColor: 0xFFFFFF,\r\n\r\n defaultElementColor: 0xFFFFFF,\r\n elementColors: {},\r\n\r\n defaultResidueColor: 0xFFFFFF,\r\n residueColors: {},\r\n\r\n chainColors: [0xFFFFFF],\r\n\r\n defaultSecondaryColor: 0xFFFFFF,\r\n secondaryColors: {},\r\n\r\n defaultGradientColor: 0x000000,\r\n\r\n defaultNamedColor: 0xFFFFFF,\r\n namedColorsArray: [\r\n /* eslint-disable no-multi-spaces */\r\n ['indianred', 0xcd5c5c],\r\n ['lightcoral', 0xf08080],\r\n ['salmon', 0xfa8072],\r\n ['darksalmon', 0xe9967a],\r\n ['lightsalmon', 0xffa07a],\r\n ['crimson', 0xdc143c],\r\n ['red', 0xff0000],\r\n ['firebrick', 0xb22222],\r\n ['darkred', 0x8b0000],\r\n ['pink', 0xffc0cb],\r\n ['lightpink', 0xffb6c1],\r\n ['hotpink', 0xff69b4],\r\n ['deeppink', 0xff1493],\r\n ['mediumvioletred', 0xc71585],\r\n ['palevioletred', 0xdb7093],\r\n ['coral', 0xff7f50],\r\n ['tomato', 0xff6347],\r\n ['orangered', 0xff4500],\r\n ['darkorange', 0xff8c00],\r\n ['orange', 0xffa500],\r\n ['gold', 0xffd700],\r\n ['yellow', 0xffff00],\r\n ['lightyellow', 0xffffe0],\r\n ['lemonchiffon', 0xfffacd],\r\n ['lightgoldenrodyellow', 0xfafad2],\r\n ['papayawhip', 0xffefd5],\r\n ['moccasin', 0xffe4b5],\r\n ['peachpuff', 0xffdab9],\r\n ['palegoldenrod', 0xeee8aa],\r\n ['khaki', 0xf0e68c],\r\n ['darkkhaki', 0xbdb76b],\r\n ['lavender', 0xe6e6fa],\r\n ['thistle', 0xd8bfd8],\r\n ['plum', 0xdda0dd],\r\n ['violet', 0xee82ee],\r\n ['orchid', 0xda70d6],\r\n ['fuchsia', 0xff00ff],\r\n ['magenta', 0xff00ff],\r\n ['mediumorchid', 0xba55d3],\r\n ['mediumpurple', 0x9370db],\r\n ['rebeccapurple', 0x663399],\r\n ['blueviolet', 0x8a2be2],\r\n ['darkviolet', 0x9400d3],\r\n ['darkorchid', 0x9932cc],\r\n ['darkmagenta', 0x8b008b],\r\n ['purple', 0x800080],\r\n ['indigo', 0x4b0082],\r\n ['slateblue', 0x6a5acd],\r\n ['mediumslateblue', 0x7b68ee],\r\n ['darkslateblue', 0x483d8b],\r\n ['greenyellow', 0xadff2f],\r\n ['chartreuse', 0x7fff00],\r\n ['lawngreen', 0x7cfc00],\r\n ['lime', 0x00ff00],\r\n ['limegreen', 0x32cd32],\r\n ['palegreen', 0x98fb98],\r\n ['lightgreen', 0x90ee90],\r\n ['mediumspringgreen', 0x00fa9a],\r\n ['springgreen', 0x00ff7f],\r\n ['mediumseagreen', 0x3cb371],\r\n ['seagreen', 0x2e8b57],\r\n ['forestgreen', 0x228b22],\r\n ['green', 0x008000],\r\n ['darkgreen', 0x006400],\r\n ['yellowgreen', 0x9acd32],\r\n ['olivedrab', 0x6b8e23],\r\n ['olive', 0x808000],\r\n ['darkolivegreen', 0x556b2f],\r\n ['mediumaquamarine', 0x66cdaa],\r\n ['darkseagreen', 0x8fbc8f],\r\n ['lightseagreen', 0x20b2aa],\r\n ['darkcyan', 0x008b8b],\r\n ['teal', 0x008080],\r\n ['aqua', 0x00ffff],\r\n ['cyan', 0x00ffff],\r\n ['lightcyan', 0xe0ffff],\r\n ['paleturquoise', 0xafeeee],\r\n ['aquamarine', 0x7fffd4],\r\n ['turquoise', 0x40e0d0],\r\n ['mediumturquoise', 0x48d1cc],\r\n ['darkturquoise', 0x00ced1],\r\n ['cadetblue', 0x5f9ea0],\r\n ['steelblue', 0x4682b4],\r\n ['lightsteelblue', 0xb0c4de],\r\n ['powderblue', 0xb0e0e6],\r\n ['lightblue', 0xadd8e6],\r\n ['skyblue', 0x87ceeb],\r\n ['lightskyblue', 0x87cefa],\r\n ['deepskyblue', 0x00bfff],\r\n ['dodgerblue', 0x1e90ff],\r\n ['cornflowerblue', 0x6495ed],\r\n ['royalblue', 0x4169e1],\r\n ['blue', 0x0000ff],\r\n ['mediumblue', 0x0000cd],\r\n ['darkblue', 0x00008b],\r\n ['navy', 0x000080],\r\n ['midnightblue', 0x191970],\r\n ['cornsilk', 0xfff8dc],\r\n ['blanchedalmond', 0xffebcd],\r\n ['bisque', 0xffe4c4],\r\n ['navajowhite', 0xffdead],\r\n ['wheat', 0xf5deb3],\r\n ['burlywood', 0xdeb887],\r\n ['tan', 0xd2b48c],\r\n ['rosybrown', 0xbc8f8f],\r\n ['sandybrown', 0xf4a460],\r\n ['goldenrod', 0xdaa520],\r\n ['darkgoldenrod', 0xb8860b],\r\n ['peru', 0xcd853f],\r\n ['chocolate', 0xd2691e],\r\n ['saddlebrown', 0x8b4513],\r\n ['sienna', 0xa0522d],\r\n ['brown', 0xa52a2a],\r\n ['maroon', 0x800000],\r\n ['white', 0xffffff],\r\n ['snow', 0xfffafa],\r\n ['honeydew', 0xf0fff0],\r\n ['mintcream', 0xf5fffa],\r\n ['azure', 0xf0ffff],\r\n ['aliceblue', 0xf0f8ff],\r\n ['ghostwhite', 0xf8f8ff],\r\n ['whitesmoke', 0xf5f5f5],\r\n ['seashell', 0xfff5ee],\r\n ['beige', 0xf5f5dc],\r\n ['oldlace', 0xfdf5e6],\r\n ['floralwhite', 0xfffaf0],\r\n ['ivory', 0xfffff0],\r\n ['antiquewhite', 0xfaebd7],\r\n ['linen', 0xfaf0e6],\r\n ['lavenderblush', 0xfff0f5],\r\n ['mistyrose', 0xffe4e1],\r\n ['gainsboro', 0xdcdcdc],\r\n ['lightgray', 0xd3d3d3],\r\n ['silver', 0xc0c0c0],\r\n ['darkgray', 0xa9a9a9],\r\n ['gray', 0x808080],\r\n ['dimgray', 0x696969],\r\n ['lightslategray', 0x778899],\r\n ['slategray', 0x708090],\r\n ['darkslategray', 0x2f4f4f],\r\n ['black', 0x000000],\r\n /* eslint-enable no-multi-spaces */\r\n ],\r\n\r\n namedColors: {},\r\n /* eslint-enable no-magic-numbers */\r\n\r\n gradients: {\r\n rainbow: [\r\n 0x0000ff, // blue\r\n 0x00ffff, // cyan\r\n 0x00ff00, // green\r\n 0xffff00, // yellow\r\n 0xff0000, // red\r\n ],\r\n temp: [\r\n 0x0000ff, // blue\r\n 0x007fff, // light-blue\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n hot: [\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n cold: [\r\n 0xffffff, // white\r\n 0x007fff, // light-blue\r\n 0x0000ff, // blue\r\n ],\r\n 'blue-red': [\r\n 0x0000ff, // blue\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n reds: [\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n blues: [\r\n 0xffffff, // white\r\n 0x0000ff, // blue\r\n ],\r\n },\r\n});\r\n\r\nconst { namedColorsArray, namedColors } = Palette.prototype;\r\n\r\nfor (let i = 0, { length } = namedColorsArray; i < length; ++i) {\r\n const [name, value] = namedColorsArray[i];\r\n namedColors[name] = value;\r\n}\r\n\r\nexport default Palette;\r\n","import Palette from './Palette';\r\n\r\nconst palette = new Palette('CPK', 'CP');\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n C: 0x202020,\r\n N: 0x2060FF,\r\n O: 0xEE2010,\r\n F: 0x00FF00,\r\n P: 0x8020FF,\r\n S: 0xFFFF00,\r\n CL: 0x00BB00,\r\n FE: 0xD0D0D0,\r\n CO: 0xD0D0D0,\r\n NI: 0xD0D0D0,\r\n CU: 0xD0D0D0,\r\n BR: 0x008800,\r\n I: 0x005500,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('Jmol', 'JM');\r\n\r\npalette.colors = [\r\n /* eslint-disable no-magic-numbers */\r\n 0x0000FF, // blue\r\n 0x0055FF, //\r\n 0x00ABFF, //\r\n 0x00FFFF, // cyan\r\n 0x00FFAB, //\r\n 0x00FF55, //\r\n 0x00FF00, // green\r\n 0x55FF00, //\r\n 0xABFF00, //\r\n 0xFFFF00, // yellow\r\n 0xFFAB00, //\r\n 0xFF5500, //\r\n 0xFF0000, // red\r\n 0xFF0055, //\r\n 0xFF00AB, //\r\n 0xFF00FF, // magenta\r\n 0xAB00FF, //\r\n 0x5500FF, //\r\n /* eslint-enable no-magic-numbers */\r\n];\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n D: 0xFFFFC0,\r\n T: 0xFFFFA0,\r\n HE: 0xD9FFFF,\r\n LI: 0xCC80FF,\r\n BE: 0xC2FF00,\r\n B: 0xFFB5B5,\r\n C: 0x909090,\r\n N: 0x3050F8,\r\n O: 0xFF0D0D,\r\n F: 0x90E050,\r\n NE: 0xB3E3F5,\r\n NA: 0xAB5CF2,\r\n MG: 0x8AFF00,\r\n AL: 0xBFA6A6,\r\n SI: 0xF0C8A0,\r\n P: 0xFF8000,\r\n S: 0xFFFF30,\r\n CL: 0x1FF01F,\r\n AR: 0x80D1E3,\r\n K: 0x8F40D4,\r\n CA: 0x3DFF00,\r\n SC: 0xE6E6E6,\r\n TI: 0xBFC2C7,\r\n V: 0xA6A6AB,\r\n CR: 0x8A99C7,\r\n MN: 0x9C7AC7,\r\n FE: 0xE06633,\r\n CO: 0xF090A0,\r\n NI: 0x50D050,\r\n CU: 0xC88033,\r\n ZN: 0x7D80B0,\r\n GA: 0xC28F8F,\r\n GE: 0x668F8F,\r\n AS: 0xBD80E3,\r\n SE: 0xFFA100,\r\n BR: 0xA62929,\r\n KR: 0x5CB8D1,\r\n RB: 0x702EB0,\r\n SR: 0x00FF00,\r\n Y: 0x94FFFF,\r\n ZR: 0x94E0E0,\r\n NB: 0x73C2C9,\r\n MO: 0x54B5B5,\r\n TC: 0x3B9E9E,\r\n RU: 0x248F8F,\r\n RH: 0x0A7D8C,\r\n PD: 0x006985,\r\n AG: 0xC0C0C0,\r\n CD: 0xFFD98F,\r\n IN: 0xA67573,\r\n SN: 0x668080,\r\n SB: 0x9E63B5,\r\n TE: 0xD47A00,\r\n I: 0x940094,\r\n XE: 0x429EB0,\r\n CS: 0x57178F,\r\n BA: 0x00C900,\r\n LA: 0x70D4FF,\r\n CE: 0xFFFFC7,\r\n PR: 0xD9FFC7,\r\n ND: 0xC7FFC7,\r\n PM: 0xA3FFC7,\r\n SM: 0x8FFFC7,\r\n EU: 0x61FFC7,\r\n GD: 0x45FFC7,\r\n TB: 0x30FFC7,\r\n DY: 0x1FFFC7,\r\n HO: 0x00FF9C,\r\n ER: 0x00E675,\r\n TM: 0x00D452,\r\n YB: 0x00BF38,\r\n LU: 0x00AB24,\r\n HF: 0x4DC2FF,\r\n TA: 0x4DA6FF,\r\n W: 0x2194D6,\r\n RE: 0x267DAB,\r\n OS: 0x266696,\r\n IR: 0x175487,\r\n PT: 0xD0D0E0,\r\n AU: 0xFFD123,\r\n HG: 0xB8B8D0,\r\n TL: 0xA6544D,\r\n PB: 0x575961,\r\n BI: 0x9E4FB5,\r\n PO: 0xAB5C00,\r\n AT: 0x754F45,\r\n RN: 0x428296,\r\n FR: 0x420066,\r\n RA: 0x007D00,\r\n AC: 0x70ABFA,\r\n TH: 0x00BAFF,\r\n PA: 0x00A1FF,\r\n U: 0x008FFF,\r\n NP: 0x0080FF,\r\n PU: 0x006BFF,\r\n AM: 0x545CF2,\r\n CM: 0x785CE3,\r\n BK: 0x8A4FE3,\r\n CF: 0xA136D4,\r\n ES: 0xB31FD4,\r\n FM: 0xB31FBA,\r\n MD: 0xB30DA6,\r\n NO: 0xBD0D87,\r\n LR: 0xC70066,\r\n RF: 0xCC0059,\r\n DB: 0xD1004F,\r\n SG: 0xD90045,\r\n BH: 0xE00038,\r\n HS: 0xE6002E,\r\n MT: 0xEB0026,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.defaultResidueColor = 0xBEA06E;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: 0xC8C8C8,\r\n ARG: 0x145AFF,\r\n ASN: 0x00DCDC,\r\n ASP: 0xE60A0A,\r\n CYS: 0xE6E600,\r\n GLN: 0x00DCDC,\r\n GLU: 0xE60A0A,\r\n GLY: 0xEBEBEB,\r\n HIS: 0x8282D2,\r\n ILE: 0x0F820F,\r\n LEU: 0x0F820F,\r\n LYS: 0x145AFF,\r\n MET: 0xE6E600,\r\n PHE: 0x3232AA,\r\n PRO: 0xDC9682,\r\n SER: 0xFA9600,\r\n THR: 0xFA9600,\r\n TRP: 0xB45AB4,\r\n TYR: 0x3232AA,\r\n VAL: 0x0F820F,\r\n A: 0xA0A0FF,\r\n C: 0xFF8C4B,\r\n G: 0xFF7070,\r\n I: 0x80FFFF,\r\n T: 0xA0FFA0,\r\n U: 0xFF8080,\r\n DA: 0xA0A0FF,\r\n DC: 0xFF8C4B,\r\n DG: 0xFF7070,\r\n DI: 0x80FFFF,\r\n DT: 0xA0FFA0,\r\n DU: 0xFF8080,\r\n '+A': 0xA0A0FF,\r\n '+C': 0xFF8C4B,\r\n '+G': 0xFF7070,\r\n '+I': 0x80FFFF,\r\n '+T': 0xA0FFA0,\r\n '+U': 0xFF8080,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.chainColors = [\r\n // ' '->0 'A'->1, 'B'->2\r\n 0xFFffffff, // ' ' & '0' white\r\n //\r\n 0xFFC0D0FF, // skyblue\r\n 0xFFB0FFB0, // pastel green\r\n 0xFFFFC0C8, // pink\r\n 0xFFFFFF80, // pastel yellow\r\n 0xFFFFC0FF, // pastel magenta\r\n 0xFFB0F0F0, // pastel cyan\r\n 0xFFFFD070, // pastel gold\r\n 0xFFF08080, // lightcoral\r\n\r\n 0xFFF5DEB3, // wheat\r\n 0xFF00BFFF, // deepskyblue\r\n 0xFFCD5C5C, // indianred\r\n 0xFF66CDAA, // mediumaquamarine\r\n 0xFF9ACD32, // yellowgreen\r\n 0xFFEE82EE, // violet\r\n 0xFF00CED1, // darkturquoise\r\n 0xFF00FF7F, // springgreen\r\n 0xFF3CB371, // mediumseagreen\r\n\r\n 0xFF00008B, // darkblue\r\n 0xFFBDB76B, // darkkhaki\r\n 0xFF006400, // darkgreen\r\n 0xFF800000, // maroon\r\n 0xFF808000, // olive\r\n 0xFF800080, // purple\r\n 0xFF008080, // teal\r\n 0xFFB8860B, // darkgoldenrod\r\n 0xFFB22222, // firebrick\r\n];\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xFF0080,\r\n [StructuralElementType.HELIX_PI]: 0x600080,\r\n [StructuralElementType.HELIX_310]: 0xA00080,\r\n [StructuralElementType.STRAND]: 0xFFC800,\r\n [StructuralElementType.TURN]: 0x6080FF,\r\n dna: 0xAE00FE,\r\n rna: 0xFD0162,\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('VMD', 'VM');\r\n\r\npalette.colors = [\r\n /* eslint-disable no-magic-numbers */\r\n 0x0000FF, // blue\r\n 0xFF0000, // red\r\n 0x606060, // gray\r\n 0xFF8000, // orange\r\n 0xFFFF00, // yellow\r\n 0x808033, // tan\r\n 0x999999, // silver\r\n 0x00FF00, // green\r\n 0xFFFFFF, // white\r\n 0xFF9999, // pink\r\n 0x40C0C0, // cyan\r\n 0xA600A6, // purple\r\n 0x80E666, // lime\r\n 0xE666B3, // mauve\r\n 0x804D00, // ochre\r\n 0x8080C0, // ice blue\r\n /* eslint-enable no-magic-numbers */\r\n];\r\n\r\npalette.defaultElementColor = 0x804D00;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n /* eslint-disable no-magic-numbers */\r\n H: 0xFFFFFF,\r\n C: 0x40BFBF,\r\n N: 0x0000FF,\r\n O: 0xFF0000,\r\n P: 0x808033,\r\n S: 0xFFFF00,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.defaultResidueColor = 0x40C0C0;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n /* eslint-disable no-magic-numbers */\r\n ALA: 0x0000FF,\r\n ARG: 0xFFFFFF,\r\n ASN: 0x808033,\r\n ASP: 0xFF0000,\r\n CYS: 0xFFFF00,\r\n GLN: 0xFF8000,\r\n GLU: 0xFF9999,\r\n GLY: 0xFFFFFF,\r\n HIS: 0x40C0C0,\r\n ILE: 0x00FF00,\r\n LEU: 0xFF9999,\r\n LYS: 0x40C0C0,\r\n MET: 0xFFFF00,\r\n PHE: 0xA600A6,\r\n PRO: 0x804C00,\r\n SER: 0xFFFF00,\r\n THR: 0xE666B3,\r\n TRP: 0x999999,\r\n TYR: 0x00FF00,\r\n VAL: 0x808033,\r\n A: 0x0000FF,\r\n C: 0xFF8000,\r\n G: 0xFFFF00,\r\n T: 0xA600A6,\r\n U: 0x00FF00,\r\n DA: 0x0000FF,\r\n DC: 0xFF8000,\r\n DG: 0xFFFF00,\r\n DT: 0xA600A6,\r\n DU: 0x00FF00,\r\n '+A': 0x0000FF,\r\n '+C': 0xFF8000,\r\n '+G': 0xFFFF00,\r\n '+T': 0xA600A6,\r\n '+U': 0x00FF00,\r\n WAT: 0x40C0C0,\r\n H2O: 0x40C0C0,\r\n HOH: 0x40C0C0,\r\n /* eslint-enable no-magic-numbers */\r\n};\r\n\r\npalette.chainColors = [0xFFFFFF].concat(palette.colors);\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xA600A6,\r\n [StructuralElementType.HELIX_310]: 0x0000FF,\r\n [StructuralElementType.HELIX_PI]: 0xFF0000,\r\n [StructuralElementType.STRAND]: 0xFFFF00,\r\n [StructuralElementType.BRIDGE]: 0x808033,\r\n [StructuralElementType.TURN]: 0x40C0C0,\r\n};\r\n\r\nexport default palette;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport cpkPalette from './palettes/cpkPalette';\r\nimport jmolPalette from './palettes/jmolPalette';\r\nimport vmdPalette from './palettes/vmdPalette';\r\n\r\nconst palettes = new EntityList([\r\n cpkPalette,\r\n jmolPalette,\r\n vmdPalette,\r\n]);\r\n\r\nexport default palettes;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport palettes from '../palettes';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports Colorer\r\n * @this Colorer\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available coloring algorithms used for building and displaying molecule geometry.\r\n */\r\nclass Colorer {\r\n constructor(opts) {\r\n if (this.constructor === Colorer) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Colorer options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(settings.now.colorers[this.id], true), opts);\r\n /**\r\n * Palette in use.\r\n * @type {Palette}\r\n */\r\n this.palette = palettes.first;\r\n }\r\n\r\n /**\r\n * Get Colorer identification, probably with options.\r\n * @returns {string|Array} Colorer identifier string ({@link Colorer#id}) or two-element array containing both colorer\r\n * identifier and options ({@link Colorer#opts}).\r\n * Options are returned if they were changed during or after colorer creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, settings.now.colorers[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n}\r\n\r\n/**\r\n * Colorer identifier.\r\n * @type {string}\r\n */\r\n\r\nColorer.prototype.id = '__';\r\n\r\nexport default Colorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Element\r\n *\r\n * @exports ElementColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on chemical element.\r\n */\r\nclass ElementColorer extends Colorer {\r\n static id = 'EL';\r\n\r\n getAtomColor(atom, _complex) {\r\n const type = atom.element.name;\r\n if (type === 'C' && this.opts.carbon >= 0) {\r\n return this.opts.carbon;\r\n }\r\n return this.palette.getElementColor(type);\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nElementColorer.prototype.id = 'EL';\r\nElementColorer.prototype.name = 'Element';\r\nElementColorer.prototype.shortName = 'Element';\r\n\r\nexport default ElementColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Coloring algorithm based on residue type.\r\n *\r\n * @see ResidueType\r\n *\r\n * @exports ResidueTypeColorer\r\n * @constructor\r\n */\r\nclass ResidueTypeColorer extends Colorer {\r\n static id = 'RT';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getResidueColor(residue._type._name);\r\n }\r\n}\r\n\r\nResidueTypeColorer.prototype.id = 'RT';\r\nResidueTypeColorer.prototype.name = 'Residue Type';\r\nResidueTypeColorer.prototype.shortName = 'Residue';\r\n\r\nexport default ResidueTypeColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass SequenceColorer extends Colorer {\r\n static id = 'SQ';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const chain = residue._chain;\r\n if (chain.minSequence === Number.POSITIVE_INFINITY && chain.maxSequence === Number.NEGATIVE_INFINITY) {\r\n return this.palette.defaultNamedColor;\r\n }\r\n const min = chain.minSequence;\r\n const max = chain.maxSequence > min ? chain.maxSequence : min + 1;\r\n return this.palette.getGradientColor((residue._sequence - min) / (max - min), this.opts.gradient);\r\n }\r\n}\r\n\r\nSequenceColorer.prototype.id = 'SQ';\r\nSequenceColorer.prototype.name = 'Sequence';\r\nSequenceColorer.prototype.shortName = 'Sequence';\r\n\r\nexport default SequenceColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ChainColorer extends Colorer {\r\n static id = 'CH';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getChainColor(residue.getChain()._name);\r\n }\r\n}\r\n\r\nChainColorer.prototype.id = 'CH';\r\nChainColorer.prototype.name = 'Chain';\r\nChainColorer.prototype.shortName = 'Chain';\r\n\r\nexport default ChainColorer;\r\n","import Colorer from './Colorer';\r\nimport ResidueType from '../../chem/ResidueType';\r\n\r\nclass SecondaryStructureColorer extends Colorer {\r\n static id = 'SS';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n if (residue._type.flags & ResidueType.Flags.DNA) {\r\n return this.palette.getSecondaryColor('dna');\r\n }\r\n if (residue._type.flags & ResidueType.Flags.RNA) {\r\n return this.palette.getSecondaryColor('rna');\r\n }\r\n const secondary = residue.getSecondary();\r\n if (secondary) {\r\n let color = this.palette.getSecondaryColor(secondary.type, true);\r\n if (color === undefined) {\r\n color = this.palette.getSecondaryColor(secondary.generic);\r\n }\r\n return color;\r\n }\r\n return this.palette.defaultSecondaryColor;\r\n }\r\n}\r\n\r\nSecondaryStructureColorer.prototype.id = 'SS';\r\nSecondaryStructureColorer.prototype.name = 'Secondary Structure';\r\nSecondaryStructureColorer.prototype.shortName = 'Structure';\r\n\r\nexport default SecondaryStructureColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass UniformColorer extends Colorer {\r\n static id = 'UN';\r\n\r\n getAtomColor(_atom, _complex) {\r\n return this.opts.color;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nUniformColorer.prototype.id = 'UN';\r\nUniformColorer.prototype.name = 'Uniform';\r\nUniformColorer.prototype.shortName = 'Uniform';\r\n\r\nexport default UniformColorer;\r\n","import Colorer from './Colorer';\r\nimport selectors from '../../chem/selectors';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports ConditionalColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on a selector string used as a condition.\r\n */\r\nclass ConditionalColorer extends Colorer {\r\n static id = 'CO';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n const parsed = selectors.parse(this.opts.subset);\r\n this._subsetCached = parsed.error ? selectors.none() : parsed.selector;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n return this._subsetCached.includesAtom(atom) ? this.opts.color : this.opts.baseColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const subset = this._subsetCached;\r\n const atoms = residue._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (!subset.includesAtom(atoms[i])) {\r\n return this.opts.baseColor;\r\n }\r\n }\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nConditionalColorer.prototype.id = 'CO';\r\nConditionalColorer.prototype.name = 'Conditional';\r\nConditionalColorer.prototype.shortName = 'Conditional';\r\n\r\nexport default ConditionalColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ConformationColorer extends Colorer {\r\n static id = 'CF';\r\n\r\n getAtomColor(atom, _complex) {\r\n return this.palette.getChainColor(String.fromCharCode(atom.location));\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nConformationColorer.prototype.id = 'CF';\r\nConformationColorer.prototype.name = 'Conformation';\r\nConformationColorer.prototype.shortName = 'Conformation';\r\n\r\nexport default ConformationColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Temperature\r\n *\r\n * @exports TemperatureColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on temperature of chemical element.\r\n */\r\nclass TemperatureColorer extends Colorer {\r\n static id = 'TM';\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n let factor = 1;\r\n if (atom.temperature && opts) {\r\n if (opts.min === opts.max) {\r\n factor = atom.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (atom.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n if (!opts) {\r\n return this.palette.defaultGradientColor;\r\n }\r\n if (residue.temperature) {\r\n let factor = 0;\r\n if (opts.min === opts.max) {\r\n factor = residue.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (residue.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n}\r\n\r\nTemperatureColorer.prototype.id = 'TM'; // [T]e[M]perature\r\nTemperatureColorer.prototype.name = 'Temperature';\r\nTemperatureColorer.prototype.shortName = 'Temperature';\r\n\r\nexport default TemperatureColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Occupancy\r\n *\r\n * @exports OccupancyColorer\r\n * @augments Occupancy\r\n * @constructor\r\n * @classdesc Coloring algorithm based on occupancy of chemical element.\r\n */\r\nclass OccupancyColorer extends Colorer {\r\n static id = 'OC';\r\n\r\n _getColorByOccupancy(occupancy, opts) {\r\n if (occupancy !== undefined) {\r\n const factor = 1 - occupancy;\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(atom.occupancy, opts);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(residue.occupancy, opts);\r\n }\r\n}\r\n\r\nOccupancyColorer.prototype.id = 'OC'; // [OC]cupancy\r\nOccupancyColorer.prototype.name = 'Occupancy';\r\nOccupancyColorer.prototype.shortName = 'Occupancy';\r\n\r\nexport default OccupancyColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass HydrophobicityColorer extends Colorer {\r\n static id = 'HY';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n let color = this.palette.defaultResidueColor;\r\n if (residue._type.hydrophobicity !== undefined) {\r\n // Kyte Doolitle hydro [-4.5,4.5]->[0.1]\r\n const min = -4.5;\r\n const max = 4.5;\r\n color = this.palette.getGradientColor((residue._type.hydrophobicity - min) / (max - min), this.opts.gradient);\r\n }\r\n return color;\r\n }\r\n}\r\n\r\nHydrophobicityColorer.prototype.id = 'HY';\r\nHydrophobicityColorer.prototype.name = 'Hydrophobicity';\r\nHydrophobicityColorer.prototype.shortName = 'Hydrophobicity';\r\n\r\nexport default HydrophobicityColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass MoleculeColorer extends Colorer {\r\n static id = 'MO';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const molecule = residue._molecule;\r\n const count = _complex.getMoleculeCount();\r\n if (count > 1) {\r\n return this.palette.getGradientColor((molecule.index - 1) / (count - 1), this.opts.gradient);\r\n }\r\n return this.palette.getGradientColor(0, this.opts.gradient);\r\n }\r\n}\r\n\r\nMoleculeColorer.prototype.id = 'MO';\r\nMoleculeColorer.prototype.name = 'Molecule';\r\nMoleculeColorer.prototype.shortName = 'Molecule';\r\n\r\nexport default MoleculeColorer;\r\n","import Colorer from './Colorer';\r\nimport Atom from '../../chem/Atom';\r\n\r\nfunction scaleColor(c, factor) {\r\n const r1 = (c >> 16) & 0xff;\r\n const g1 = (c >> 8) & 0xff;\r\n const b1 = c & 0xff;\r\n const r = factor * r1;\r\n const g = factor * g1;\r\n const b = factor * b1;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports CarbonColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on selection carbon atoms.\r\n */\r\nclass CarbonColorer extends Colorer {\r\n static id = 'CB';\r\n\r\n getAtomColor(atom, _complex) {\r\n const colorCarbon = this.opts.color;\r\n const colorNotCarbon = scaleColor(colorCarbon, this.opts.factor);\r\n return (atom.flags & Atom.Flags.CARBON) ? colorCarbon : colorNotCarbon;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nCarbonColorer.prototype.id = 'CB';\r\nCarbonColorer.prototype.name = 'Carbon';\r\nCarbonColorer.prototype.shortName = 'Carbon';\r\n\r\nexport default CarbonColorer;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport ElementColorer from './colorers/ElementColorer';\r\nimport ResidueTypeColorer from './colorers/ResidueTypeColorer';\r\nimport SequenceColorer from './colorers/SequenceColorer';\r\nimport ChainColorer from './colorers/ChainColorer';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\nimport UniformColorer from './colorers/UniformColorer';\r\nimport ConditionalColorer from './colorers/ConditionalColorer';\r\nimport ConformationColorer from './colorers/ConformationColorer';\r\nimport TemperatureColorer from './colorers/TemperatureColorer';\r\nimport OccupancyColorer from './colorers/OccupancyColorer';\r\nimport HydrophobicityColorer from './colorers/HydrophobicityColorer';\r\nimport MoleculeColorer from './colorers/MoleculeColorer';\r\nimport CarbonColorer from './colorers/CarbonColorer';\r\n\r\nconst colorers = new EntityList([\r\n ElementColorer,\r\n ResidueTypeColorer,\r\n SequenceColorer,\r\n ChainColorer,\r\n SecondaryStructureColorer,\r\n UniformColorer,\r\n ConditionalColorer,\r\n ConformationColorer,\r\n TemperatureColorer,\r\n OccupancyColorer,\r\n HydrophobicityColorer,\r\n MoleculeColorer,\r\n CarbonColorer,\r\n]);\r\n\r\nexport default colorers;\r\n","import * as THREE from 'three';\r\nimport EntityList from '../utils/EntityList';\r\n\r\nfunction neutralColor(intensity) {\r\n return new THREE.Color(intensity, intensity, intensity);\r\n}\r\n\r\nconst materialList = [\r\n {\r\n id: 'DF',\r\n name: 'Diffuse',\r\n shortName: 'Diffuse',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'SF',\r\n name: 'Soft Plastic',\r\n shortName: 'Soft',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.1),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'PL',\r\n name: 'Glossy Plastic',\r\n shortName: 'Glossy',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.28),\r\n shininess: 100,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'ME',\r\n name: 'Metal',\r\n shortName: 'Metal',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.55),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TR',\r\n name: 'Transparent',\r\n shortName: 'Transparent',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'GL',\r\n name: 'Glass',\r\n shortName: 'Glass',\r\n uberOptions: {\r\n diffuse: neutralColor(0.50),\r\n specular: neutralColor(0.65),\r\n shininess: 100,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'BA',\r\n name: 'Backdrop',\r\n shortName: 'Backdrop',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: false,\r\n depthWrite: false,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TN',\r\n name: 'Toon',\r\n shortName: 'Toon',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: true,\r\n },\r\n }, {\r\n id: 'FL',\r\n name: 'Flat',\r\n shortName: 'Flat',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 0,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n },\r\n },\r\n];\r\n\r\nconst materials = new EntityList(materialList);\r\n\r\nexport default materials;\r\n","/**\r\n * Utils functions which is worked with meshes\r\n *\r\n * functions for doing something with all/specified meshes\r\n * functions for traversihg tree and create auxiliary meshes for transparency/shadowmaps...\r\n * functions for calculating data connected with meshes\r\n */\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _gatherObjects(root, meshTypes) {\r\n const meshes = [];\r\n root.traverse((object) => {\r\n for (let i = 0; i < meshTypes.length; i++) {\r\n if (object instanceof meshTypes[i]) {\r\n meshes[meshes.length] = object;\r\n break;\r\n }\r\n }\r\n });\r\n return meshes;\r\n}\r\n\r\n// new mesh with the same geometry and specified material values and layer\r\nfunction createDerivativeMesh(mesh, values, layer) {\r\n const material = mesh.material.createInstance();\r\n material.setValues(values);\r\n\r\n const newMesh = new mesh.constructor(mesh.geometry, material);\r\n newMesh.material.needsUpdate = true;\r\n newMesh.applyMatrix4(mesh.matrix);\r\n newMesh.layers.set(layer);\r\n return newMesh;\r\n}\r\n\r\nfunction traverseMeshes(root, meshTypes, func) {\r\n const meshes = _gatherObjects(root, meshTypes);\r\n\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n const mesh = meshes[i];\r\n if (!mesh.parent) {\r\n continue;\r\n }\r\n func(mesh);\r\n }\r\n}\r\n\r\nfunction applyTransformsToMeshes(root, mtc) {\r\n const mtcCount = mtc.length;\r\n if (mtcCount < 1) {\r\n return;\r\n }\r\n\r\n const meshTypes = [THREE.Mesh, THREE.LineSegments, THREE.Line];\r\n traverseMeshes(root, meshTypes, (mesh) => {\r\n mesh.applyMatrix4(mtc[0]);\r\n for (let j = 1; j < mtcCount; ++j) {\r\n const newMesh = new mesh.constructor(mesh.geometry, mesh.material);\r\n mesh.parent.add(newMesh);\r\n newMesh.applyMatrix4(mtc[j]);\r\n }\r\n });\r\n}\r\n\r\nconst processTransparentMaterial = (function () {\r\n const matValues = {\r\n prepassTransparancy: true,\r\n fakeOpacity: false,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n mesh.material.setValues({ prepassTransparancy: false, fakeOpacity: false });\r\n mesh.material.needsUpdate = true;\r\n mesh.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n\r\n const prepassTranspMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n mesh.parent.add(prepassTranspMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst processColFromPosMaterial = (function () {\r\n const matValues = {\r\n colorFromPos: true,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n overrideColor: false,\r\n fogTransparent: false,\r\n attrColor: false,\r\n attrColor2: false,\r\n attrAlphaColor: false,\r\n fakeOpacity: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n const colFromPosMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n mesh.parent.add(colFromPosMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst createShadowmapMaterial = (function () {\r\n const matValues = {\r\n colorFromDepth: true,\r\n orthoCam: true,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (!mesh.receiveShadow && mesh.material.shadowmap) { // remove shadow from non-receivers\r\n mesh.material.setValues({ shadowmap: false });\r\n }\r\n if (!mesh.material.lights) { // skip creating shadowmap meshes for materials without lighting\r\n return;\r\n }\r\n if (!mesh.castShadow) { // skip creating shadowmap meshes for non-casters\r\n return;\r\n }\r\n if (!gfxutils.belongToSelectLayers(mesh)) { // skip creating shadowmap meshes for selection layer\r\n return;\r\n }\r\n\r\n const shadowmapMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.SHADOWMAP);\r\n shadowmapMesh.isShadowmapMesh = true;\r\n mesh.parent.add(shadowmapMesh);\r\n });\r\n };\r\n}());\r\n\r\nfunction removeShadowmapMaterial(root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (mesh.isShadowmapMesh) {\r\n mesh.parent.remove(mesh);\r\n }\r\n });\r\n}\r\n\r\nfunction forEachMeshInGroup(group, process) {\r\n function processObj(object) {\r\n if (object instanceof THREE.Mesh) {\r\n process(object);\r\n }\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n processObj(object.children[i]);\r\n }\r\n }\r\n processObj(group);\r\n}\r\n\r\nfunction _countMeshTriangles(mesh) {\r\n const geom = mesh.geometry;\r\n if (geom instanceof THREE.InstancedBufferGeometry) {\r\n const attribs = geom.attributes;\r\n for (const property in attribs) {\r\n if (attribs.hasOwnProperty(property) && attribs[property] instanceof THREE.InstancedBufferAttribute) {\r\n const currAttr = attribs[property];\r\n const indexSize = geom.index ? geom.index.array.length / 3 : 0;\r\n return indexSize * currAttr.array.length / currAttr.itemSize;\r\n }\r\n }\r\n return 0;\r\n }\r\n if (geom instanceof THREE.BufferGeometry) {\r\n return geom.index ? geom.index.array.length / 3 : 0;\r\n }\r\n return geom.faces ? geom.faces.length : 0;\r\n}\r\n\r\nfunction countTriangles(group) {\r\n let totalCount = 0;\r\n forEachMeshInGroup(group, (mesh) => {\r\n totalCount += _countMeshTriangles(mesh);\r\n });\r\n return totalCount;\r\n}\r\n\r\nexport default {\r\n applyTransformsToMeshes,\r\n processTransparentMaterial,\r\n processColFromPosMaterial,\r\n createShadowmapMaterial,\r\n removeShadowmapMaterial,\r\n forEachMeshInGroup,\r\n countTriangles,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\nimport meshutils from './meshutils';\r\nimport settings from '../settings';\r\nimport materials from './materials';\r\nimport chem from '../chem';\r\n\r\nconst { selectors } = chem;\r\n\r\nclass Representation {\r\n constructor(index, mode, colorer, selector) {\r\n const startMaterialValues = {\r\n clipPlane: settings.now.draft.clipPlane,\r\n fogTransparent: settings.now.bg.transparent,\r\n shadowmap: settings.now.shadow.on,\r\n shadowmapType: settings.now.shadow.type,\r\n };\r\n this.index = index;\r\n this.mode = mode;\r\n this.colorer = colorer;\r\n this.selector = selector;\r\n this.selectorString = '';\r\n this.count = 0;\r\n this.material = new UberMaterial();\r\n this.material.setValues(startMaterialValues);\r\n this.material.setUberOptions({ fogAlpha: settings.now.fogAlpha });\r\n this.materialPreset = materials.first;\r\n this.needsRebuild = true;\r\n this.visible = true;\r\n\r\n // apply mode params & preset\r\n this.setMode(mode);\r\n }\r\n\r\n markAtoms(complex) {\r\n this.count = complex.markAtoms(this.selector, 1 << this.index);\r\n this.needsRebuild = true;\r\n return this.count;\r\n }\r\n\r\n unmarkAtoms(complex) {\r\n complex.clearAtomBits(1 << this.index);\r\n this.count = 0;\r\n }\r\n\r\n setMode(mode) {\r\n this.mode = mode;\r\n }\r\n\r\n setMaterialPreset(preset) {\r\n this.materialPreset = preset;\r\n this.material.setUberOptions(preset.uberOptions);\r\n this.material.setValues(preset.values);\r\n }\r\n\r\n reset() {\r\n this.geo = null;\r\n this.selectionGeo = null;\r\n }\r\n\r\n buildGeometry(complex) {\r\n this.reset();\r\n this.needsRebuild = false;\r\n\r\n if (settings.now.ao) {\r\n this.material.setValues({ normalsToGBuffer: settings.now.ao });\r\n }\r\n\r\n this.geo = this.mode.buildGeometry(complex, this.colorer, 1 << this.index, this.material);\r\n\r\n if (this.material.uberOptions.opacity < 0.99 && settings.now.transparency === 'prepass') {\r\n meshutils.processTransparentMaterial(this.geo, this.material);\r\n }\r\n this.geo.visible = this.visible;\r\n\r\n gfxutils.processObjRenderOrder(this.geo, this.materialPreset.id);\r\n meshutils.processColFromPosMaterial(this.geo, this.material);\r\n\r\n if (settings.now.shadow.on) {\r\n meshutils.createShadowmapMaterial(this.geo, this.material);\r\n }\r\n\r\n return this.geo;\r\n }\r\n\r\n buildSelectionGeometry(mask) {\r\n let sg = null;\r\n\r\n if (this.geo && ('getSubset' in this.geo)) {\r\n const meshes = this.geo.getSubset(mask);\r\n if (meshes && meshes.length > 0) {\r\n sg = new THREE.Group();\r\n sg.matrixAutoUpdate = false;\r\n sg.matrix = this.geo.matrix;\r\n\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n sg.add(m);\r\n }\r\n }\r\n }\r\n\r\n if (sg) {\r\n sg.visible = this.visible;\r\n }\r\n\r\n this.selectionGeo = sg;\r\n return this.selectionGeo;\r\n }\r\n\r\n /**\r\n * Create object that represents difference between current and another rep\r\n * anotherRep could be undefined. In this case everything is reported.\r\n */\r\n compare(repSettings) {\r\n const diff = {};\r\n\r\n const selStr = String(this.selector);\r\n if (!repSettings || selStr.valueOf() !== String(repSettings.selector).valueOf()) {\r\n diff.selector = selStr;\r\n }\r\n\r\n const modeDiff = this.mode.identify();\r\n if (!repSettings || Array.isArray(modeDiff) || modeDiff !== repSettings.mode) {\r\n diff.mode = modeDiff;\r\n }\r\n\r\n const colorerDiff = this.colorer.identify();\r\n if (!repSettings || Array.isArray(colorerDiff) || colorerDiff !== repSettings.colorer) {\r\n diff.colorer = colorerDiff;\r\n }\r\n\r\n if (!repSettings || this.materialPreset.id !== repSettings.material) {\r\n diff.material = this.materialPreset.id;\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n /**\r\n * Change representation. Write fields what was changed into new object, return it.\r\n */\r\n change(repSettings, complex, mode, color) {\r\n const diff = {};\r\n\r\n // modify selector\r\n if (repSettings.selector) {\r\n const newSelectorObject = selectors.parse(repSettings.selector).selector;\r\n const newSelector = String(newSelectorObject);\r\n if (this.selectorString !== newSelector) {\r\n diff.selector = newSelector;\r\n this.selectorString = newSelector;\r\n this.selector = newSelectorObject;\r\n this.markAtoms(complex);\r\n }\r\n }\r\n\r\n // modify mode\r\n if (repSettings.mode) {\r\n const newMode = repSettings.mode;\r\n if (!_.isEqual(this.mode.identify(), newMode)) {\r\n diff.mode = newMode;\r\n this.setMode(mode);\r\n }\r\n }\r\n\r\n // modify colorer\r\n if (repSettings.colorer) {\r\n const newColorer = repSettings.colorer;\r\n if (!_.isEqual(this.colorer.identify(), newColorer)) {\r\n diff.colorer = newColorer;\r\n this.colorer = color;\r\n }\r\n }\r\n\r\n // modify material\r\n if (repSettings.material) {\r\n const newMaterial = repSettings.material;\r\n if (!_.isEqual(this.materialPreset.id, newMaterial)) {\r\n diff.material = newMaterial;\r\n this.setMaterialPreset(materials.get(repSettings.material));\r\n }\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n show(visible) {\r\n this.visible = visible;\r\n if (this.geo) {\r\n this.geo.visible = visible;\r\n }\r\n if (this.selectionGeo) {\r\n this.selectionGeo.visible = visible;\r\n }\r\n }\r\n}\r\n\r\nexport default Representation;\r\n","import * as THREE from 'three';\r\nimport logger from './utils/logger';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport './gfx/modes';\r\n\r\nfunction _traverseComponentGroups(root, component, callback) {\r\n const { children } = root;\r\n if (!children) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n if (child._component === component) {\r\n callback(child);\r\n }\r\n if (child instanceof gfxutils.RCGroup) {\r\n _traverseComponentGroups(child, component, callback);\r\n }\r\n }\r\n}\r\n\r\nfunction ComplexEditor() {\r\n}\r\n\r\nclass ComplexComponentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n // init component matrices\r\n this._componentTransforms = [];\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n const component = complex._components[i];\r\n this._componentTransforms[component._index] = new THREE.Object3D();\r\n }\r\n\r\n this._inProgress = true;\r\n\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const complex = this._complexVisual.getComplex();\r\n\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n this._bakeComponentTransform(complex._components[i]);\r\n }\r\n\r\n complex.onAtomPositionChanged();\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n const visual = this._complexVisual;\r\n const component = visual.getSelectedComponent();\r\n\r\n if (component === null) {\r\n return res;\r\n }\r\n\r\n const selection = this._complexVisual.getSelectionGeo();\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n // find all geo nodes for this component\r\n _traverseComponentGroups(visual, component, (child) => {\r\n res.objects.push(child);\r\n });\r\n\r\n // find all selection nodes for this component\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component') && geo._component === component) {\r\n res.objects.push(geo);\r\n }\r\n }\r\n }\r\n\r\n // add dummy object that stores component transformation\r\n res.objects.push(this._componentTransforms[component._index]);\r\n\r\n const bbmin = new THREE.Vector3(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE);\r\n const bbmax = new THREE.Vector3(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE);\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (j = 0; j < atoms.length; ++j) {\r\n if (atoms[j].mask & selectionMask) {\r\n bbmin.min(atoms[j].position);\r\n bbmax.max(atoms[j].position);\r\n }\r\n }\r\n });\r\n\r\n res.pivot.lerpVectors(bbmin, bbmax, 0.5);\r\n return res;\r\n }\r\n\r\n _bakeComponentTransform(component) {\r\n const t = this._componentTransforms[component._index];\r\n if (t && (!(t.position.x === 0 && t.position.y === 0 && t.position.z === 0)\r\n || !(t.quaternion.x === 0 && t.quaternion.y === 0 && t.quaternion.z === 0 && t.quaternion.w === 1))) {\r\n t.updateMatrix();\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (let j = 0; j < atoms.length; ++j) {\r\n atoms[j].position.applyMatrix4(t.matrix);\r\n }\r\n });\r\n }\r\n }\r\n\r\n _resetComponentTransform() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n for (i = 0; i < this._componentTransforms.length; ++i) {\r\n geo = this._componentTransforms[i];\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n\r\n // reset all geo nodes\r\n for (i = 0; i < visual.children.length; ++i) {\r\n reprNode = visual.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n // reset all selection nodes\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ComplexFragmentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n const atoms = this._getSelectionBorderAtoms();\r\n if (atoms.length < 1 || atoms.length > 2) {\r\n logger.error('Can only edit fragments with one or two bound atoms.');\r\n return false;\r\n }\r\n\r\n this._fragmentBoundAtoms = atoms;\r\n\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n\r\n // hide selected fragment in main model\r\n visual.disableSubset(selectionMask, true);\r\n\r\n // hide selection geo in main model\r\n for (let k = 0; k < selection.children.length; ++k) {\r\n selection.children[k].visible = false;\r\n }\r\n\r\n // create visible fragment representation to rotate\r\n const pivotPos = atoms[0].position.clone();\r\n\r\n if (atoms.length === 2) {\r\n pivotPos.lerp(atoms[1].position, 0.5);\r\n }\r\n\r\n this._fragmentGeo = new THREE.Group();\r\n visual.add(this._fragmentGeo);\r\n this._fragmentGeo.position.copy(pivotPos);\r\n\r\n this._fragmentSelectionGeo = new THREE.Group();\r\n selection.add(this._fragmentSelectionGeo);\r\n this._fragmentSelectionGeo.position.copy(pivotPos);\r\n\r\n const offset = pivotPos.clone();\r\n offset.negate();\r\n\r\n for (let i = 0; i < visual.children.length; ++i) {\r\n const g = visual.children[i];\r\n if (!('getSubset' in g)) {\r\n continue;\r\n }\r\n\r\n const vg = new THREE.Group();\r\n this._fragmentGeo.add(vg);\r\n\r\n const sg = new THREE.Group();\r\n this._fragmentSelectionGeo.add(sg);\r\n\r\n const meshes = g.getSubset(selectionMask, true);\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n vg.add(m);\r\n m.position.copy(offset);\r\n }\r\n\r\n const smeshes = g.getSubset(selectionMask, true);\r\n for (let h = 0; h < smeshes.length; h++) {\r\n const sm = smeshes[h];\r\n sg.add(sm);\r\n sm.position.copy(offset);\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(this._fragmentSelectionGeo);\r\n\r\n this._inProgress = true;\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selectionBit = visual.getSelectionBit();\r\n\r\n const p = this._fragmentGeo.position;\r\n const m = this._fragmentGeo.matrix.clone();\r\n m.multiply(new THREE.Matrix4().makeTranslation(-p.x, -p.y, -p.z));\r\n\r\n this._bakeAtomTransform(m, 1 << selectionBit);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << selectionBit, true);\r\n\r\n visual.getComplex().onAtomPositionChanged();\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n this._fragmentGeo.parent.remove(this._fragmentGeo);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << visual.getSelectionBit(), true);\r\n\r\n // show selection geo in main model (+ remove fragment selection geo)\r\n for (let i = 0; i < selection.children.length; ++i) {\r\n const node = selection.children[i];\r\n if (node.visible) {\r\n selection.remove(node);\r\n } else {\r\n node.visible = true;\r\n }\r\n }\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n isFreeRotationAllowed() {\r\n return (this._fragmentBoundAtoms.length < 2);\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n res.objects.push(this._fragmentGeo, this._fragmentSelectionGeo);\r\n\r\n const boundAtoms = this._fragmentBoundAtoms;\r\n if (boundAtoms.length === 1) {\r\n if (boundAtoms[0].bonds.length === 1) {\r\n // single external bond allows rotation about bond axis\r\n const bond = boundAtoms[0].bonds[0];\r\n res.axis = new THREE.Vector3().subVectors(bond._right.position, bond._left.position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n } else if (boundAtoms.length === 2) {\r\n // two bound atoms allow rotation only about axis running through their centers\r\n res.axis = new THREE.Vector3().subVectors(boundAtoms[1].position, boundAtoms[0].position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _getSelectionBorderAtoms() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n const selectionMask = 1 << this._complexVisual.getSelectionBit();\r\n const atomHash = {};\r\n\r\n complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n atomHash[bond._left.index] = 1;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n atomHash[bond._right.index] = 1;\r\n }\r\n });\r\n\r\n const atoms = [];\r\n const keys = Object.keys(atomHash);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const idx = keys[i];\r\n atoms.push(complex._atoms[idx]);\r\n }\r\n\r\n return atoms;\r\n }\r\n\r\n _bakeAtomTransform(matrix, mask) {\r\n this._complexVisual.getComplex().forEachAtom((atom) => {\r\n if (atom.mask & mask) {\r\n atom.position.applyMatrix4(matrix);\r\n }\r\n });\r\n }\r\n}\r\n\r\nexport default {\r\n ComponentEditor: ComplexComponentEditor,\r\n FragmentEditor: ComplexFragmentEditor,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\nimport chem from './chem';\r\nimport settings from './settings';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport Visual from './Visual';\r\nimport ComplexVisualEdit from './ComplexVisualEdit';\r\nimport meshutils from './gfx/meshutils';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction lookupAndCreate(entityList, specs) {\r\n if (!Array.isArray(specs)) {\r\n specs = [specs];\r\n }\r\n const [id, opts] = specs;\r\n const Entity = entityList.get(id) || entityList.first;\r\n return new Entity(opts);\r\n}\r\n\r\nclass ComplexVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._complex = dataSource;\r\n\r\n /** @type {Representation[]} */\r\n this._reprList = [];\r\n /** @type {?Representation} */\r\n this._repr = null;\r\n this._reprListChanged = true;\r\n\r\n this._selectionBit = 0;\r\n this._reprUsedBits = 0;\r\n this._selectionCount = 0;\r\n\r\n this._selectionGeometry = new THREE.Group();\r\n }\r\n\r\n getBoundaries() {\r\n return this._complex.getBoundaries();\r\n }\r\n\r\n release() {\r\n if (this._selectionGeometry.parent) {\r\n this._selectionGeometry.remove(this._selectionGeometry);\r\n }\r\n Visual.prototype.release.call(this);\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getSelectionCount() {\r\n return this._selectionCount;\r\n }\r\n\r\n getSelectionGeo() {\r\n return this._selectionGeometry;\r\n }\r\n\r\n getSelectionBit() {\r\n return this._selectionBit;\r\n }\r\n\r\n getEditor() {\r\n return this._editor;\r\n }\r\n\r\n resetReps(reps) {\r\n // Create all necessary representations\r\n if (this._complex) {\r\n this._complex.clearAtomBits(~0);\r\n }\r\n this._reprListChanged = true;\r\n this._reprUsedBits = 0;\r\n this._reprList.length = reps.length;\r\n for (let i = 0, n = reps.length; i < n; ++i) {\r\n const rep = reps[i];\r\n\r\n let selector;\r\n let selectorString;\r\n if (typeof rep.selector === 'string') {\r\n selectorString = rep.selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else if (typeof rep.selector === 'undefined') {\r\n selectorString = settings.now.presets.default[0].selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else {\r\n ({ selector } = rep);\r\n selectorString = selector.toString();\r\n }\r\n const mode = lookupAndCreate(modes, rep.mode);\r\n const colorer = lookupAndCreate(colorers, rep.colorer);\r\n const material = materials.get(rep.material) || materials.first;\r\n\r\n this._reprList[i] = new Representation(i, mode, colorer, selector);\r\n this._reprList[i].setMaterialPreset(material);\r\n this._reprList[i].selectorString = selectorString;\r\n\r\n if (this._complex) {\r\n this._complex.markAtoms(selector, 1 << i);\r\n }\r\n\r\n this._reprUsedBits |= 1 << i;\r\n }\r\n this._repr = reps.length > 0 ? this._reprList[0] : null;\r\n\r\n this._selectionBit = reps.length;\r\n this._reprUsedBits |= 1 << this._selectionBit; // selection uses one bit\r\n this._selectionCount = 0;\r\n\r\n if (this._complex) {\r\n this._complex.update();\r\n }\r\n }\r\n\r\n /**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\n repCount() {\r\n return this._reprList.length;\r\n }\r\n\r\n /**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\n repCurrent(index) {\r\n if (index >= 0 && index < this._reprList.length) {\r\n this._repr = this._reprList[index];\r\n } else {\r\n index = this._reprList.indexOf(this._repr);\r\n }\r\n return index;\r\n }\r\n\r\n /**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {Object} {desc, index, status} field desc contains rep description, index - index of correspondent rep,\r\n * status - one of three strings: 'created', 'changed', ''. 'created' means new rep was created during this function,\r\n * 'changed' - rep was changed during this function. '' - something else.\r\n */\r\n rep(index, rep) {\r\n // if index is missing then it is the current\r\n if (!rep && (index === undefined || index instanceof Object)) {\r\n rep = index;\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index > this._reprList.length) {\r\n logger.error(`Rep ${index} does not exist!`);\r\n return null;\r\n }\r\n\r\n // a special case of adding just after the end\r\n if (index === this._reprList.length) {\r\n const res = this.repAdd(rep);\r\n logger.warn(`Rep ${index} does not exist! New representation was created.`);\r\n return { desc: res.desc, index, status: 'created' };\r\n }\r\n\r\n // gather description\r\n const target = this._reprList[index];\r\n const desc = {\r\n selector: target.selectorString,\r\n mode: target.mode.identify(),\r\n colorer: target.colorer.identify(),\r\n material: target.materialPreset.id,\r\n };\r\n\r\n // modification is requested\r\n if (rep) {\r\n // modify\r\n const diff = target.change(\r\n rep,\r\n this._complex,\r\n lookupAndCreate(modes, rep.mode),\r\n lookupAndCreate(colorers, rep.colorer),\r\n );\r\n\r\n // something was changed\r\n if (!_.isEmpty(diff)) {\r\n target.needsRebuild = true;\r\n for (const key in diff) {\r\n if (diff.hasOwnProperty(key)) {\r\n desc[key] = diff[key];\r\n logger.debug(`rep[${index}].${key} changed to ${diff[key]}`);\r\n }\r\n }\r\n\r\n // safety trick: lower resolution for surface modes\r\n if (diff.mode && target.mode.isSurface\r\n && (settings.now.resolution === 'ultra' || settings.now.resolution === 'high')) {\r\n logger.report('Surface resolution was changed to \"medium\" to avoid hang-ups.');\r\n settings.set('resolution', 'medium');\r\n }\r\n return { desc, index, status: 'changed' };\r\n }\r\n }\r\n return { desc, index, status: '' };\r\n }\r\n\r\n /**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\n repGet(index) {\r\n // if index is missing then it is the current\r\n if (index === undefined || index instanceof Object) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return null;\r\n }\r\n\r\n return this._reprList[index];\r\n }\r\n\r\n _getFreeReprIdx() {\r\n let bits = this._reprUsedBits;\r\n for (let i = 0; i <= ComplexVisual.NUM_REPRESENTATION_BITS; ++i, bits >>= 1) {\r\n if ((bits & 1) === 0) {\r\n return i;\r\n }\r\n }\r\n return -1;\r\n }\r\n\r\n /**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {Object} {desc, index} field desc contains added rep description, index - index of this rep.\r\n */\r\n repAdd(rep) {\r\n if (this._reprList.length >= ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n return null;\r\n }\r\n\r\n const newSelectionBit = this._getFreeReprIdx();\r\n if (newSelectionBit < 0) {\r\n return null; // no more slots for representations\r\n }\r\n\r\n const originalSelection = this.buildSelectorFromMask(1 << this._selectionBit);\r\n\r\n // Fill in default values\r\n const def = settings.now.presets.default[0];\r\n const desc = _.merge({\r\n selector: def.selector,\r\n mode: def.mode,\r\n colorer: def.colorer,\r\n material: def.material,\r\n }, rep);\r\n\r\n const selector = (typeof desc.selector === 'string') ? selectors.parse(desc.selector).selector : desc.selector;\r\n const target = new Representation(\r\n this._selectionBit,\r\n lookupAndCreate(modes, desc.mode),\r\n lookupAndCreate(colorers, desc.colorer),\r\n selector,\r\n );\r\n target.selectorString = selector.toString();\r\n target.setMaterialPreset(materials.get(desc.material));\r\n target.markAtoms(this._complex);\r\n this._reprList.push(target);\r\n\r\n // change selection bit\r\n this._selectionBit = newSelectionBit;\r\n this._reprUsedBits |= 1 << this._selectionBit;\r\n\r\n // restore selection using new selection bit\r\n this._complex.markAtoms(originalSelection, 1 << this._selectionBit);\r\n\r\n return { desc, index: this._reprList.length - 1 };\r\n }\r\n\r\n /**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\n repRemove(index) {\r\n if (index === undefined) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // catch out of bounds case\r\n let count = this._reprList.length;\r\n if (index < 0 || index >= count || count <= 1) { // do not allow to remove the single rep\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.unmarkAtoms(this._complex);\r\n this._reprUsedBits &= ~(1 << target.index);\r\n\r\n this._reprList.splice(index, 1);\r\n\r\n // update current rep\r\n if (target === this._repr) {\r\n --count;\r\n index = index < count ? index : count - 1;\r\n this._repr = this._reprList[index];\r\n }\r\n this._reprListChanged = true;\r\n }\r\n\r\n /**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\n repHide(index, hide) {\r\n if (hide === undefined) {\r\n hide = true;\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.show(!hide);\r\n }\r\n\r\n /**\r\n * Select atoms with selector\r\n * @param {Selector} selector - selector\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\n select(selector, append) {\r\n if (append) {\r\n this._selectionCount += this._complex.markAtomsAdditionally(selector, 1 << this._selectionBit);\r\n } else {\r\n this._selectionCount = this._complex.markAtoms(selector, 1 << this._selectionBit);\r\n }\r\n this._complex.updateStructuresMask();\r\n this.rebuildSelectionGeometry();\r\n }\r\n\r\n resetSelectionMask() {\r\n if (this._selectionCount !== 0) {\r\n this._selectionCount = 0;\r\n if (this._complex) {\r\n this._complex.clearAtomBits(1 << this._selectionBit);\r\n }\r\n }\r\n }\r\n\r\n updateSelectionMask(pickedObj) {\r\n const self = this;\r\n const { atom } = pickedObj;\r\n let { residue, chain, molecule } = pickedObj;\r\n const setMask = 1 << this._selectionBit;\r\n const clearMask = ~setMask;\r\n\r\n if (atom) {\r\n residue = atom.residue;\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (atom.mask & setMask) {\r\n atom.mask &= clearMask;\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n if (molecule) {\r\n molecule.mask &= clearMask;\r\n }\r\n this._selectionCount--;\r\n } else {\r\n atom.mask |= setMask;\r\n this._selectionCount++;\r\n\r\n // select residue if all atoms in it are selected\r\n residue.collectMask();\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (residue) {\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (residue._mask & setMask) {\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n residue.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n } else {\r\n residue._mask |= setMask;\r\n residue.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (chain || molecule) {\r\n const obj = chain || molecule;\r\n if (obj._mask & setMask) {\r\n obj._mask &= clearMask;\r\n obj.forEachResidue((r) => {\r\n if (r._mask & setMask) {\r\n r._mask &= clearMask;\r\n r.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n r._mask &= clearMask;\r\n }\r\n });\r\n } else {\r\n obj._mask |= setMask;\r\n obj.forEachResidue((r) => {\r\n if (!(r._mask & setMask)) {\r\n r._mask |= setMask;\r\n r.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n const otherObj = chain ? r.getMolecule() : r.getChain();\r\n if (otherObj) {\r\n otherObj.collectMask();\r\n }\r\n }\r\n });\r\n }\r\n } else {\r\n this.resetSelectionMask();\r\n }\r\n }\r\n\r\n expandSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms to add\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // select marked atoms\r\n const deselectionMask = ~tmpMask;\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask = (atom.mask & deselectionMask) | selectionMask;\r\n ++self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n shrinkSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms neighbouring to unselected ones\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // mark hanging atoms\r\n this._complex.forEachAtom((atom) => {\r\n if ((atom.mask & selectionMask) && (atom.bonds.length === 1)) {\r\n atom.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // deselect marked atoms\r\n const deselectionMask = ~(selectionMask | tmpMask);\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask &= deselectionMask;\r\n --self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n getSelectedComponent() {\r\n const selectionMask = 1 << this._selectionBit;\r\n\r\n let component = null;\r\n let multiple = false;\r\n\r\n // find which component is selected (exclusively)\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & selectionMask) {\r\n if (component === null) {\r\n component = atom.residue._component;\r\n } else if (component !== atom.residue._component) {\r\n multiple = true;\r\n }\r\n }\r\n });\r\n\r\n return multiple ? null : component;\r\n }\r\n\r\n getSelectionCenter(center, includesAtom, selRule) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._complex.forEachAtom((atom) => {\r\n if (includesAtom(atom, selRule)) {\r\n center.add(atom.position);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.applyMatrix4(this.matrix);\r\n return true;\r\n }\r\n\r\n needsRebuild() {\r\n if (this._reprListChanged) {\r\n return true;\r\n }\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n if (repr.needsRebuild) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n /**\r\n * Rebuild molecule geometry asynchronously.\r\n */\r\n rebuild() {\r\n const self = this;\r\n\r\n // Destroy current geometry\r\n gfxutils.clearTree(this);\r\n\r\n return new Promise(((resolve) => {\r\n // Nothing to do?\r\n const complex = self._complex;\r\n if (!complex) {\r\n resolve();\r\n return;\r\n }\r\n\r\n let errorOccured = false;\r\n setTimeout(() => {\r\n console.time('build');\r\n const reprList = self._reprList;\r\n const palette = palettes.get(settings.now.palette) || palettes.first;\r\n let hasGeometry = false;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n repr.colorer.palette = palette;\r\n\r\n if (repr.needsRebuild) {\r\n repr.reset();\r\n\r\n try {\r\n repr.buildGeometry(complex);\r\n } catch (e) {\r\n if (e instanceof utils.OutOfMemoryError) {\r\n repr.needsRebuild = false;\r\n repr.reset();\r\n logger.error(`Not enough memory to build geometry for representation ${repr.index + 1}`);\r\n errorOccured = true;\r\n } else {\r\n throw e;\r\n }\r\n }\r\n\r\n if (DEBUG && !errorOccured) {\r\n logger.debug(`Triangles count: ${meshutils.countTriangles(repr.geo)}`);\r\n }\r\n }\r\n\r\n hasGeometry = errorOccured || hasGeometry || gfxutils.groupHasGeometryToRender(repr.geo);\r\n\r\n if (repr.geo) {\r\n self.add(repr.geo);\r\n }\r\n }\r\n\r\n self._reprListChanged = false;\r\n\r\n console.timeEnd('build');\r\n resolve();\r\n }, 10);\r\n }));\r\n }\r\n\r\n setNeedsRebuild() {\r\n // invalidate all representations\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n reprList[i].needsRebuild = true;\r\n }\r\n }\r\n\r\n rebuildSelectionGeometry() {\r\n const mask = 1 << this._selectionBit;\r\n\r\n gfxutils.clearTree(this._selectionGeometry);\r\n\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const repr = this._reprList[i];\r\n const sg = repr.buildSelectionGeometry(mask);\r\n if (!sg) {\r\n continue;\r\n }\r\n\r\n this._selectionGeometry.add(sg);\r\n for (let j = 0; j < sg.children.length; j++) {\r\n const m = sg.children[j];\r\n\r\n // copy component transform (that's not applied yet)\r\n // TODO make this code obsolete, accessing editor is bad\r\n if (this._editor && this._editor._componentTransforms) {\r\n const t = this._editor._componentTransforms[m._component._index];\r\n if (t) {\r\n m.position.copy(t.position);\r\n m.quaternion.copy(t.quaternion);\r\n }\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(sg);\r\n }\r\n }\r\n\r\n _buildSelectorFromSortedLists(atoms, residues, chains) {\r\n const complex = this._complex;\r\n\r\n function optimizeList(list) {\r\n const result = [];\r\n let k = 0;\r\n let first = NaN;\r\n let last = NaN;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const value = list[i];\r\n if (value === last + 1) {\r\n last = value;\r\n } else {\r\n if (!Number.isNaN(first)) {\r\n result[k++] = new selectors.Range(first, last);\r\n }\r\n first = last = value;\r\n }\r\n }\r\n if (!Number.isNaN(first)) {\r\n result[k] = new selectors.Range(first, last);\r\n }\r\n return result;\r\n }\r\n\r\n let expression = null;\r\n if (chains.length === complex._chains.length) {\r\n expression = selectors.all();\r\n } else {\r\n let selector;\r\n if (chains.length > 0) {\r\n selector = selectors.chain(chains);\r\n expression = expression ? selectors.or(expression, selector) : selector;// NOSONAR\r\n }\r\n if (Object.keys(residues).length > 0) {\r\n for (const ch in residues) {\r\n if (residues.hasOwnProperty(ch)) {\r\n selector = selectors.and(\r\n selectors.chain(ch),\r\n selectors.residx(optimizeList(residues[ch])),\r\n );\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n }\r\n }\r\n if (atoms.length > 0) {\r\n selector = selectors.serial(optimizeList(atoms));\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n\r\n if (!expression) {\r\n expression = selectors.none();\r\n }\r\n }\r\n\r\n return expression;\r\n }\r\n\r\n buildSelectorFromMask(mask) {\r\n const complex = this._complex;\r\n const chains = [];\r\n const residues = {};\r\n const atoms = [];\r\n\r\n complex.forEachChain((chain) => {\r\n if (chain._mask & mask) {\r\n chains.push(chain._name);\r\n }\r\n });\r\n\r\n complex.forEachResidue((residue) => {\r\n if (residue._mask & mask && !(residue._chain._mask & mask)) {\r\n const c = residue._chain._name;\r\n if (!(c in residues)) {\r\n residues[c] = [residue._index];\r\n } else {\r\n residues[c].push(residue._index);\r\n }\r\n }\r\n });\r\n\r\n complex.forEachAtom((atom) => {\r\n if (atom.mask & mask && !(atom.residue._mask & mask)) {\r\n atoms.push(atom.serial);\r\n }\r\n });\r\n\r\n return this._buildSelectorFromSortedLists(atoms, residues, chains);\r\n }\r\n\r\n forSelectedResidues(process) {\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.forEachResidue((residue) => {\r\n if (residue._mask & selectionMask) {\r\n process(residue);\r\n }\r\n });\r\n }\r\n\r\n beginComponentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.ComponentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n beginFragmentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.FragmentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n // should only be called by editors\r\n finalizeEdit() {\r\n this._editor = null;\r\n }\r\n\r\n setMaterialValues(values, needTraverse = false, process = undefined) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setValues(values);\r\n if (needTraverse) {\r\n rep.geo.traverse((object) => {\r\n if (object instanceof THREE.Mesh) {\r\n object.material.setValues(values);\r\n\r\n if (process !== undefined) {\r\n process(object);\r\n }\r\n\r\n object.material.needsUpdate = true;\r\n }\r\n });\r\n }\r\n }\r\n }\r\n\r\n setUberOptions(values) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setUberOptions(values);\r\n }\r\n }\r\n\r\n /**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\n within(selector, radius) {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return false;\r\n }\r\n\r\n // mark atoms of the group as selected\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.markAtoms(selector, selectionMask);\r\n\r\n // mark all atoms within distance as selected\r\n if (vw) {\r\n vw.forEachAtomWithinDistFromMasked(this._complex, selectionMask, Number(radius), (atom) => {\r\n atom.mask |= selectionMask;\r\n });\r\n }\r\n\r\n // update selection count\r\n this._selectionCount = this._complex.countAtomsByMask(selectionMask);\r\n\r\n // update secondary structure mask\r\n this._complex.updateStructuresMask();\r\n\r\n return this.buildSelectorFromMask(selectionMask);\r\n }\r\n}\r\n// 32 bits = 30 bits for reps + 1 for selection + 1 for selection expansion\r\nComplexVisual.NUM_REPRESENTATION_BITS = 30;\r\n\r\nexport default ComplexVisual;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexVolumeFaces from './VolumeFaces.vert';\r\nimport fragmentVolumeFaces from './VolumeFaces.frag';\r\nimport vertexVolume from './Volume.vert';\r\nimport fragmentVolume from './Volume.frag';\r\nimport vertexFarPlane from './VolumeFarPlane.vert';\r\nimport fragmentFarPlane from './VolumeFarPlane.frag';\r\nimport settings from '../../settings';\r\n\r\nconst volumeUniforms = THREE.UniformsUtils.merge([\r\n {\r\n volumeDim: { type: 'v3', value: new THREE.Vector3(512, 512, 512) },\r\n tileTex: { type: 't', value: null },\r\n tileTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n tileStride: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n\r\n boxAngles: { type: 'v3', value: new THREE.Vector3(1, 1, 1) },\r\n delta: { type: 'v3', value: new THREE.Vector3(0, 0, 0) },\r\n\r\n _isoLevel0: { type: 'v2', value: new THREE.Vector3(0.5, 0.75, 1.0) },\r\n _flipV: { type: 'f', value: 0.0 },\r\n _BFLeft: { type: 't', value: null },\r\n _BFRight: { type: 't', value: null },\r\n _FFLeft: { type: 't', value: null },\r\n _FFRight: { type: 't', value: null },\r\n _WFFLeft: { type: 't', value: null },\r\n _WFFRight: { type: 't', value: null },\r\n },\r\n]);\r\n\r\nfunction overrideUniforms(params, defUniforms) {\r\n const uniforms = THREE.UniformsUtils.clone(defUniforms);\r\n for (const p in params) {\r\n if (uniforms.hasOwnProperty(p)) {\r\n uniforms[p].value = params[p];\r\n }\r\n }\r\n return uniforms;\r\n}\r\n\r\nfunction facesPosMaterialParams(params, sideType) {\r\n return {\r\n uniforms: overrideUniforms(params, {}),\r\n vertexShader: vertexVolumeFaces,\r\n fragmentShader: fragmentVolumeFaces,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n side: sideType,\r\n };\r\n}\r\n\r\nclass BackFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const backFaceParams = facesPosMaterialParams(params, THREE.BackSide);\r\n super(backFaceParams);\r\n }\r\n}\r\n\r\nclass ShaderParams {\r\n constructor(params, uniforms, vertexShader, fragmentShader) {\r\n this.uniforms = overrideUniforms(params, uniforms);\r\n this.vertexShader = vertexShader;\r\n this.fragmentShader = fragmentShader;\r\n this.transparent = false;\r\n this.depthTest = false;\r\n this.depthWrite = false;\r\n this.side = THREE.FrontSide;\r\n }\r\n}\r\n\r\nclass BackFacePosMaterialFarPlane extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const matUniforms = THREE.UniformsUtils.merge([\r\n {\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n farZ: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n matWorld2Volume: { type: '4fv', value: new THREE.Matrix4() },\r\n },\r\n ]);\r\n\r\n const shaderParams = new ShaderParams(params, matUniforms, vertexFarPlane, fragmentFarPlane);\r\n super(shaderParams);\r\n }\r\n}\r\n\r\nclass FrontFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const frontFaceParams = facesPosMaterialParams(params, THREE.FrontSide);\r\n super(frontFaceParams);\r\n }\r\n}\r\n\r\nclass VolumeMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const shaderParams = new ShaderParams(params, volumeUniforms, vertexVolume, fragmentVolume);\r\n shaderParams.transparent = true;\r\n shaderParams.depthTest = true;\r\n\r\n super(shaderParams);\r\n this.updateDefines();\r\n }\r\n\r\n updateDefines() {\r\n this.defines = {\r\n ISO_MODE: settings.now.modes.VD.isoMode,\r\n STEPS_COUNT: settings.now.modes.VD.polyComplexity[settings.now.resolution] * 100,\r\n };\r\n this.needsUpdate = true;\r\n }\r\n}\r\n\r\nexport default {\r\n BackFacePosMaterial,\r\n BackFacePosMaterialFarPlane,\r\n FrontFacePosMaterial,\r\n VolumeMaterial,\r\n};\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport settings from '../settings';\r\n\r\nclass VolumeMesh extends THREE.Mesh {\r\n volumeInfo = {}; // data for noise filter\r\n\r\n constructor() {\r\n const geo = new THREE.BufferGeometry();\r\n super(geo);\r\n this.clipPlane = new THREE.Plane();\r\n const size = new THREE.Vector3(0.5, 0.5, 0.5);\r\n this.size = size;\r\n\r\n this.cullFlag = [\r\n true, true, true, true,\r\n true, true, true, true,\r\n false, false, false, false, false, false,\r\n ];\r\n\r\n this.faces = [\r\n { indices: [], norm: new THREE.Vector3(0, 0, -1) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 1) },\r\n { indices: [], norm: new THREE.Vector3(0, -1, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 1, 0) },\r\n { indices: [], norm: new THREE.Vector3(-1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 0) },\r\n ];\r\n\r\n this.vertices = [\r\n new THREE.Vector3(-size.x, -size.y, -size.z),\r\n new THREE.Vector3(-size.x, size.y, -size.z),\r\n new THREE.Vector3(size.x, -size.y, -size.z),\r\n new THREE.Vector3(size.x, size.y, -size.z),\r\n new THREE.Vector3(-size.x, -size.y, size.z),\r\n new THREE.Vector3(-size.x, size.y, size.z),\r\n new THREE.Vector3(size.x, -size.y, size.z),\r\n new THREE.Vector3(size.x, size.y, size.z),\r\n new THREE.Vector3(0.0, 0.0, 0.0), // Placeholder for section\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n ];\r\n\r\n geo.setAttribute('position', new THREE.BufferAttribute(new Float32Array(this.vertices.length * 3), 3));\r\n\r\n this.name = 'VolumeMesh';\r\n }\r\n\r\n static _corners = [\r\n // x, y, z, edge1, edge2, edge3\r\n [-1, -1, -1, 0, 4, 8],\r\n [1, -1, -1, 0, 5, 9],\r\n [1, 1, -1, 1, 5, 10],\r\n [-1, 1, -1, 1, 4, 11],\r\n [-1, -1, 1, 2, 6, 8],\r\n [1, -1, 1, 2, 7, 9],\r\n [1, 1, 1, 3, 7, 10],\r\n [-1, 1, 1, 3, 6, 11],\r\n ];\r\n\r\n static _edges = [\r\n // corner1, corner2, center_x, center_y, center_z\r\n [0, 1, 0, -1, -1],\r\n [2, 3, 0, 1, -1],\r\n [4, 5, 0, -1, 1],\r\n [6, 7, 0, 1, 1],\r\n [0, 3, -1, 0, -1],\r\n [1, 2, 1, 0, -1],\r\n [4, 7, -1, 0, 1],\r\n [5, 6, 1, 0, 1],\r\n [0, 4, -1, -1, 0],\r\n [1, 5, 1, -1, 0],\r\n [2, 6, -1, 1, 0],\r\n [3, 7, 1, 1, 0],\r\n ];\r\n\r\n static _edgeIntersections = (function () {\r\n const edgeIntersections = [];\r\n for (let j = 0; j < 12; ++j) {\r\n edgeIntersections.push(new THREE.Vector3());\r\n }\r\n return edgeIntersections;\r\n }());\r\n\r\n _updateVertices() {\r\n // Algorithm:\r\n // 1. Get plane parameters\r\n // 2. Compute culling flags for all vertices\r\n // 3. If intersection occurs => compute from 3 to 6 intersection points\r\n const corners = VolumeMesh._corners;\r\n const edges = VolumeMesh._edges;\r\n const edgeIntersections = VolumeMesh._edgeIntersections;\r\n\r\n let i;\r\n\r\n const norm = this.clipPlane.normal;\r\n const D = this.clipPlane.constant;\r\n\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n const cornerMark = [0, 0, 0, 0, 0, 0, 0, 0];\r\n const edgeMark = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1];\r\n\r\n const curEdge = new THREE.Vector3();\r\n let curEdgeInter = null;\r\n\r\n function CheckX() {\r\n if (norm.x === 0) return 0;\r\n const x = -(norm.dot(curEdge) + D) / norm.x;\r\n if (-size.x <= x && x <= size.x) {\r\n curEdgeInter.set(x, curEdge.y, curEdge.z);\r\n if (x === size.x) return 2;\r\n if (x === -size.x) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckY() {\r\n if (norm.y === 0) return 0;\r\n const y = -(norm.dot(curEdge) + D) / norm.y;\r\n if (-size.y <= y && y <= size.y) {\r\n curEdgeInter.set(curEdge.x, y, curEdge.z);\r\n if (y === size.y) return 2;\r\n if (y === -size.y) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckZ() {\r\n if (norm.z === 0) return 0;\r\n const z = -(norm.dot(curEdge) + D) / norm.z;\r\n if (-size.z <= z && z <= size.z) {\r\n curEdgeInter.set(curEdge.x, curEdge.y, z);\r\n if (z === size.z) return 2;\r\n if (z === -size.z) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n // for each edge\r\n for (let curEdgeIdx = 0; curEdgeIdx < 12; ++curEdgeIdx) {\r\n const curEdgeSource = edges[curEdgeIdx];\r\n curEdgeInter = edgeIntersections[curEdgeIdx];\r\n\r\n curEdge.set(curEdgeSource[2], curEdgeSource[3], curEdgeSource[4]);\r\n curEdge.multiply(size);\r\n\r\n // calculate intersection point\r\n let flag = 0;\r\n if (curEdgeSource[2] === 0) flag = CheckX();\r\n if (curEdgeSource[3] === 0) flag = CheckY();\r\n if (curEdgeSource[4] === 0) flag = CheckZ();\r\n\r\n // mark corresponding corner (if plane cuts through one)\r\n if (flag === -2) {\r\n cornerMark[curEdgeSource[0]] = 1;\r\n } else if (flag === 2) {\r\n cornerMark[curEdgeSource[1]] = 1;\r\n } else if (flag === 0) {\r\n // edge is not intersected by the plane (doesn't produce a vertex)\r\n edgeMark[curEdgeIdx] = 0;\r\n }\r\n }\r\n\r\n const face = {\r\n indices: [],\r\n norm: norm.clone().negate(),\r\n };\r\n\r\n let nextVertex = 8;\r\n\r\n // for each marked corner\r\n for (i = 0; i < 8; ++i) {\r\n if (cornerMark[i] === 1) {\r\n // add corner as vertex to the face\r\n vert[nextVertex].set(corners[i][0], corners[i][1], corners[i][2]).multiply(size);\r\n face.indices.push(nextVertex++);\r\n // skip adjacent edges\r\n edgeMark[corners[i][3]] = 0;\r\n edgeMark[corners[i][4]] = 0;\r\n edgeMark[corners[i][5]] = 0;\r\n }\r\n }\r\n\r\n // for each edge that has internal intersection\r\n for (i = 0; i < 12; ++i) {\r\n if (edgeMark[i] === 1) {\r\n // add intersection point as vertex to the face\r\n vert[nextVertex].copy(edgeIntersections[i]);\r\n face.indices.push(nextVertex++);\r\n }\r\n }\r\n\r\n this.faces[6] = face;\r\n\r\n const diff = new THREE.Vector3();\r\n const coplanarPoint = new THREE.Vector3();\r\n this.clipPlane.coplanarPoint(coplanarPoint);\r\n for (i = 0; i < vert.length; ++i) {\r\n this.cullFlag[i] = false;\r\n if (i < 8) {\r\n // corners should be culled by clipping plane\r\n diff.subVectors(vert[i], coplanarPoint);\r\n this.cullFlag[i] = (norm.dot(diff) >= 0.0);\r\n } else if (i < 8 + face.indices.length) {\r\n // cross section vertices don't get culled\r\n this.cullFlag[i] = true;\r\n }\r\n }\r\n\r\n // write data to vertex buffer\r\n const positions = this.geometry.getAttribute('position');\r\n let idx = 0;\r\n for (i = 0; i < vert.length; ++i) {\r\n positions.array[idx++] = vert[i].x;\r\n positions.array[idx++] = vert[i].y;\r\n positions.array[idx++] = vert[i].z;\r\n }\r\n positions.needsUpdate = true;\r\n }\r\n\r\n _collectVertices(face, filter) {\r\n let i;\r\n const vert = this.vertices;\r\n face.indices = [];\r\n for (i = 0; i < vert.length; ++i) {\r\n if (this.cullFlag[i] && filter(vert[i])) {\r\n face.indices.push(i);\r\n }\r\n }\r\n }\r\n\r\n _sortIndices(face, right) {\r\n let i;\r\n let j;\r\n const vert = this.vertices;\r\n const angle = [];\r\n\r\n const dir = new THREE.Vector3();\r\n for (i = 1; i < face.indices.length; ++i) {\r\n dir.subVectors(vert[face.indices[i]], vert[face.indices[0]]);\r\n dir.normalize();\r\n dir.cross(right);\r\n dir.negate();\r\n angle[i] = face.norm.dot(dir);\r\n }\r\n\r\n // Exchange sort\r\n for (i = 1; i < face.indices.length - 1; ++i) {\r\n for (j = i + 1; j < face.indices.length; ++j) {\r\n if (angle[j] < angle[i]) {\r\n // swap\r\n let t = angle[i];\r\n angle[i] = angle[j];\r\n angle[j] = t;\r\n\r\n t = face.indices[i];\r\n face.indices[i] = face.indices[j];\r\n face.indices[j] = t;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _updateIndices() {\r\n // Algorithm:\r\n // 1. Get plane vertices (from 3 to 6 vertices)\r\n // 2. Get \"right\" vector in plane\r\n // 3. Sort vertices using Graham-like method\r\n // 4. Create indices\r\n\r\n let i;\r\n let faceIdx;\r\n let face;\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n this._collectVertices(this.faces[0], (vertex) => vertex.z === -size.z);\r\n this._collectVertices(this.faces[1], (vertex) => vertex.z === size.z);\r\n this._collectVertices(this.faces[2], (vertex) => vertex.y === -size.y);\r\n this._collectVertices(this.faces[3], (vertex) => vertex.y === size.y);\r\n this._collectVertices(this.faces[4], (vertex) => vertex.x === -size.x);\r\n this._collectVertices(this.faces[5], (vertex) => vertex.x === size.x);\r\n\r\n const vCenter = new THREE.Vector3();\r\n const vRight = new THREE.Vector3();\r\n const vDir = new THREE.Vector3();\r\n\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n\r\n if (face.indices.length === 0) continue;\r\n\r\n vCenter.set(0, 0, 0);\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vCenter.add(vert[face.indices[i]]);\r\n }\r\n vCenter.multiplyScalar(1.0 / face.indices.length);\r\n vRight.subVectors(vert[face.indices[0]], vCenter);\r\n vRight.normalize();\r\n\r\n const rightProj = [];\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vDir.subVectors(vert[face.indices[i]], vCenter);\r\n rightProj[i] = vDir.dot(vRight);\r\n }\r\n for (i = 1; i < face.indices.length; ++i) {\r\n if (rightProj[i] < rightProj[0]) {\r\n // swap\r\n let t = rightProj[0];\r\n rightProj[0] = rightProj[i];\r\n rightProj[i] = t;\r\n\r\n [t] = face.indices;\r\n face.indices[0] = face.indices[i];\r\n face.indices[i] = t;\r\n }\r\n }\r\n\r\n this._sortIndices(face, vRight);\r\n }\r\n\r\n let numIndices = 0;\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n if (face.indices.length >= 3) {\r\n numIndices += 3 * (face.indices.length - 2);\r\n }\r\n }\r\n let offset = 0;\r\n const indices = new Uint16Array(numIndices);\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n for (i = 0; i < face.indices.length - 2; ++i) {\r\n indices[offset] = face.indices[0]; // eslint-disable-line prefer-destructuring\r\n indices[offset + 1] = face.indices[i + 1];\r\n indices[offset + 2] = face.indices[i + 2];\r\n offset += 3;\r\n }\r\n }\r\n\r\n this.geometry.setIndex(new THREE.BufferAttribute(indices, 1));\r\n }\r\n\r\n setDataSource(dataSource) {\r\n const vm = new VolumeMaterial.VolumeMaterial();\r\n const dim = dataSource.getDimensions();\r\n const stride = dataSource.getTiledTextureStride();\r\n const texture = dataSource.buildTiledTexture();\r\n const bbox = dataSource.getBox();\r\n vm.uniforms.volumeDim.value.set(dim[0], dim[1], dim[2]);\r\n vm.uniforms.tileTex.value = texture;\r\n vm.uniforms.tileTexSize.value.set(texture.image.width, texture.image.height);\r\n vm.uniforms.tileStride.value.set(stride[0], stride[1]);\r\n Object.assign(this.volumeInfo, dataSource.getVolumeInfo());\r\n\r\n const volInfo = this.volumeInfo;\r\n vm.uniforms.delta.value.copy(volInfo.delta);\r\n vm.uniforms.boxAngles.value.set(volInfo.obtuseAngle[0], volInfo.obtuseAngle[1], volInfo.obtuseAngle[2]);\r\n\r\n this.material = vm;\r\n\r\n bbox.getSize(this.scale);\r\n bbox.getCenter(this.position);\r\n }\r\n\r\n _updateIsoLevel() {\r\n const { kSigma, kSigmaMed, kSigmaMax } = settings.now.modes.VD;\r\n const volInfo = this.volumeInfo;\r\n const mean = volInfo.dmean - volInfo.dmin;\r\n const span = volInfo.dmax - volInfo.dmin;\r\n const level = (k) => (mean + k * volInfo.sd) / span;\r\n this.material.uniforms._isoLevel0.value.set(level(kSigma), level(kSigmaMed), level(kSigmaMax));\r\n }\r\n\r\n static _nearClipPlaneOffset = 0.2;\r\n\r\n static _pos = new THREE.Vector3();\r\n\r\n static _norm = new THREE.Vector3();\r\n\r\n static _norm4D = new THREE.Vector4();\r\n\r\n static _matrixWorldToLocal = new THREE.Matrix4();\r\n\r\n static _clipPlane = new THREE.Plane();\r\n\r\n rebuild(camera) {\r\n const nearClipPlaneOffset = VolumeMesh._nearClipPlaneOffset;\r\n const pos = VolumeMesh._pos;\r\n const norm = VolumeMesh._norm;\r\n const norm4D = VolumeMesh._norm4D;\r\n const matrixWorldToLocal = VolumeMesh._matrixWorldToLocal;\r\n const clipPlane = VolumeMesh._clipPlane;\r\n\r\n this._updateIsoLevel();\r\n\r\n // get clip plane in local space\r\n camera.getWorldDirection(norm);\r\n camera.getWorldPosition(pos);\r\n pos.addScaledVector(norm, camera.near + nearClipPlaneOffset);\r\n\r\n // transform pos to local CS\r\n matrixWorldToLocal.copy(this.matrixWorld).invert();\r\n pos.applyMatrix4(matrixWorldToLocal);\r\n\r\n // transform norm to local CS\r\n norm4D.set(norm.x, norm.y, norm.z, 0.0); // NOTE: use homogeneous norm for proper transformation\r\n norm4D.applyMatrix4(matrixWorldToLocal);\r\n norm.copy(norm4D);\r\n norm.normalize();\r\n\r\n clipPlane.setFromNormalAndCoplanarPoint(norm, pos);\r\n\r\n if (!this.clipPlane.equals(clipPlane)) {\r\n this.clipPlane = clipPlane.clone();\r\n this._updateVertices();\r\n this._updateIndices();\r\n }\r\n }\r\n}\r\n\r\nexport default VolumeMesh;\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _flattenArray(input) {\r\n const n = input.length;\r\n const output = new Float32Array(n * 3);\r\n for (let i = 0; i < n; ++i) {\r\n const j = 3 * i;\r\n const v = input[i];\r\n output[j] = v.x;\r\n output[j + 1] = v.y;\r\n output[j + 2] = v.z;\r\n }\r\n return output;\r\n}\r\n\r\nclass VolumeBounds {\r\n static _projectionTable = { // corresponds between (origin axes and angles between them) and between saving vector coordinates\r\n XY: ['x', 2],\r\n XZ: ['y', 1],\r\n YZ: ['z', 0],\r\n };\r\n\r\n constructor(bBox, volInfo) {\r\n const { delta } = volInfo; // {x: XY, y : XZ, z: YZ}\r\n const { obtuseAngle } = volInfo; // 1 - obtuse, 0 - acute\r\n\r\n const bSize = new THREE.Vector3();\r\n bBox.getSize(bSize);\r\n bSize.multiplyScalar(0.5);\r\n\r\n const offsetVert = this._getBaseVertices(delta, obtuseAngle);\r\n\r\n const geometry = new THREE.BufferGeometry();\r\n const vertices = [];\r\n\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(offsetVert[i].clone().multiply(bSize));\r\n vertices.push(offsetVert[(i + 1) % 4].clone().multiply(bSize));\r\n }\r\n const translation = new THREE.Vector3(2 * bSize.x * (1 - delta.x - delta.y), 0, 0);\r\n for (let i = 0; i < 8; i++) {\r\n vertices.push(vertices[i].clone().add(translation));\r\n }\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(vertices[i * 2].clone());\r\n vertices.push(vertices[i * 2 + 8].clone());\r\n }\r\n const center = new THREE.Vector3();\r\n bBox.getCenter(center);\r\n vertices.forEach((vertex) => vertex.add(center)); // pivot shift\r\n\r\n const flatVertices = _flattenArray(vertices);\r\n geometry.setAttribute('position', new THREE.BufferAttribute(flatVertices, 3));\r\n\r\n this._lines = new THREE.LineSegments(geometry, new THREE.LineBasicMaterial({ color: 0xFFFFFF }));\r\n this._lines.layers.set(gfxutils.LAYERS.VOLUME);\r\n }\r\n\r\n // Set one edge (4 points) of frame, from which with parallel transfer the rest of the frame points can be obtained\r\n _getBaseVertices(delta, obtuseAngle) {\r\n const projTable = VolumeBounds._projectionTable;\r\n\r\n const proj = ((index, inv) => { // tricky function to take account of projections: their position(related to box) and sign\r\n const currDelta = delta[projTable[index][0]];\r\n const angleValue = -0.5 * (inv - 1) + inv * obtuseAngle[projTable[index][1]];// inv = 1: alpha; inv = -1: 1 - alpha\r\n return angleValue * currDelta;\r\n });\r\n\r\n const offsetVert = [\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', 1)), -1 + 2 * proj('YZ', 1), -1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', 1)), -1 + 2 * proj('YZ', -1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', -1)), 1 - 2 * proj('YZ', 1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', -1)), 1 - 2 * proj('YZ', -1), -1),\r\n ];\r\n\r\n return offsetVert;\r\n }\r\n\r\n getMesh() {\r\n return this._lines;\r\n }\r\n}\r\n\r\nexport default VolumeBounds;\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport meshes from './meshes/meshes';\r\nimport gfxutils from './gfxutils';\r\n\r\n// Thes geometric far plane is required for correct filling in the BFTexture in case, when far plane cuts the volume\r\n// cube. In cut place of cube there is no correct data in BFTexture and volume rendering integral is calculated\r\n// with errors.\r\n// Far plane cuts the cube in case of large volume scale (zoom), because farplane doesn't change\r\nclass VolumeFarPlane {\r\n // create plane with unit corners coords (for future rescale in vshader according to camera properties)\r\n constructor(volume, width, height) {\r\n const planeGeo = this._initPlaneGeo(width, height);\r\n\r\n const mat = new VolumeMaterial.BackFacePosMaterialFarPlane();\r\n this._plane = new meshes.Mesh(planeGeo, mat);\r\n this._plane.frustumCulled = false;\r\n this._plane.doubleSided = true;\r\n const matWorldToVolume = new THREE.Matrix4();\r\n\r\n this._plane._onBeforeRender = function (_renderer, _scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!volume || !material) {\r\n return;\r\n }\r\n\r\n // count point in world at farplane place\r\n const planeCamPos = new THREE.Vector4(0, 0, -(camera.far - 0.1), 1);\r\n planeCamPos.applyMatrix4(camera.matrixWorld);\r\n\r\n // recalc matrices to make plane be placed as farplane in the World relative to camera\r\n this.matrix.identity();\r\n this.matrix.makeTranslation(planeCamPos.x, planeCamPos.y, planeCamPos.z);\r\n this.matrixWorld.copy(this.matrix);\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n this.normalMatrix.getNormalMatrix(this.modelViewMatrix);\r\n\r\n // build worldToVolume matrix to transform plane into volumeCS (volumeCS coords are written to BackFaceTexture)\r\n const volumeMatrix = volume.matrixWorld;\r\n matWorldToVolume.copy(volumeMatrix).invert();\r\n\r\n // update material props\r\n material.uniforms.aspectRatio.value = camera.aspect;\r\n material.uniforms.farZ.value = camera.far;\r\n material.uniforms.tanHalfFOV.value = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * camera.fov);\r\n material.uniforms.matWorld2Volume.value = matWorldToVolume;\r\n };\r\n\r\n // set it to special layer to draw only into BFTexture\r\n this._plane.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n }\r\n\r\n _initPlaneGeo(width, height) {\r\n const planeGeo = new THREE.BufferGeometry();\r\n\r\n width = width || 1;\r\n height = height || 1;\r\n\r\n const vertices = new Float32Array([\r\n -0.5 * width, 0.5 * height, 0,\r\n 0.5 * width, 0.5 * height, 0,\r\n -0.5 * width, -0.5 * height, 0,\r\n 0.5 * width, -0.5 * height, 0,\r\n ]);\r\n\r\n planeGeo.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n planeGeo.setIndex([0, 2, 1, 2, 3, 1]);\r\n\r\n return planeGeo;\r\n }\r\n\r\n getMesh() {\r\n return this._plane;\r\n }\r\n}\r\n\r\nexport default VolumeFarPlane;\r\n","import * as THREE from 'three';\r\nimport VolumeMesh from './gfx/VolumeMesh';\r\nimport VolumeBounds from './gfx/VolumeBounds';\r\nimport VolumeFarPlane from './gfx/VolumeFarPlane';\r\nimport Visual from './Visual';\r\nimport settings from './settings';\r\n\r\nclass VolumeVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._mesh = new VolumeMesh();\r\n this._mesh.setDataSource(dataSource);\r\n this.add(this._mesh);\r\n\r\n this._frame = new VolumeBounds(this.getBoundaries().boundingBox, this._mesh.volumeInfo);\r\n this.add(this._frame.getMesh());\r\n this.showFrame(settings.now.modes.VD.frame);\r\n\r\n this._farPlane = new VolumeFarPlane(this._mesh, 2, 2);\r\n this.add(this._farPlane.getMesh());\r\n }\r\n\r\n getBoundaries() {\r\n const box = this._dataSource.getBox();\r\n const sphere = new THREE.Sphere();\r\n box.getBoundingSphere(sphere);\r\n\r\n return {\r\n boundingBox: box,\r\n boundingSphere: sphere,\r\n };\r\n }\r\n\r\n getMesh() {\r\n return this._mesh;\r\n }\r\n\r\n showFrame(needShow) {\r\n this._frame.getMesh().material.visible = needShow;\r\n }\r\n}\r\n\r\nexport default VolumeVisual;\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available loaders.\r\n * @extends EntityList\r\n */\r\nclass LoaderList extends EntityList {\r\n /**\r\n * Create a list of loaders.\r\n * The loaders are indexed by supported source types (`.types` property of a Loader\r\n * subclass).\r\n * The loaders can be retrieved later by matching against specs (see {@link LoaderList#find}).\r\n *\r\n * @param {!Array=} someLoaders A list of {@link Loader} subclasses to\r\n * automatically register at creation time.\r\n * @see LoaderList#register\r\n */\r\n constructor(someLoaders = []) {\r\n super(someLoaders, ['types']);\r\n }\r\n\r\n /**\r\n * Find a suitable loader for a source type.\r\n *\r\n * @param {Object} specs Loader specifications.\r\n * @param {string=} specs.type Supported source type.\r\n * @param {*=} specs.source Source to load from.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.type) {\r\n list = this._dict.types[specs.type.toLowerCase()] || [];\r\n } else if (specs.source) {\r\n return this._list.filter((SomeLoader) => SomeLoader.canProbablyLoad && SomeLoader.canProbablyLoad(specs.source));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default LoaderList;\r\n","import EventDispatcher from '../../utils/EventDispatcher';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Loader extends EventDispatcher {\r\n constructor(source, options) {\r\n super();\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n this._agent = null;\r\n }\r\n\r\n load() {\r\n return Promise.reject(new Error('Loading from this source is not implemented'));\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n if (this._agent) {\r\n this._agent.abort();\r\n }\r\n }\r\n\r\n static extractName(_source) {\r\n return undefined;\r\n }\r\n}\r\n\r\nmakeContextDependent(Loader.prototype);\r\n","import Loader from './Loader';\r\n\r\nexport default class FileLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = options.binary === true;\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const blob = this._source;\r\n const reader = this._agent = new FileReader();\r\n\r\n reader.addEventListener('load', () => {\r\n resolve(reader.result);\r\n });\r\n reader.addEventListener('error', () => {\r\n reject(reader.error);\r\n });\r\n reader.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n reader.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n if (this._binary) {\r\n reader.readAsArrayBuffer(blob);\r\n } else {\r\n reader.readAsText(blob);\r\n }\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return (File && source instanceof File) || (Blob && source instanceof Blob);\r\n }\r\n\r\n static extractName(source) {\r\n return source && source.name;\r\n }\r\n}\r\n\r\nFileLoader.types = ['file', 'blob'];\r\n","import _ from 'lodash';\r\nimport Loader from './Loader';\r\n\r\n// we don't need to detect all kinds of URLs, just the evident ones\r\nconst urlStartRegexp = /^(https?|ftp):\\/\\//i;\r\n\r\nexport default class XHRLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = (options.binary === true);\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const url = this._source;\r\n const request = this._agent = new XMLHttpRequest();\r\n\r\n request.addEventListener('load', () => {\r\n if (request.status === 200) {\r\n resolve(request.response);\r\n } else {\r\n reject(new Error(`HTTP ${request.status} while fetching ${url}`));\r\n }\r\n });\r\n request.addEventListener('error', () => {\r\n reject(new Error('HTTP request failed'));\r\n });\r\n request.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n request.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n request.open('GET', url);\r\n if (this._binary) {\r\n request.responseType = 'arraybuffer';\r\n } else {\r\n request.responseType = 'text';\r\n }\r\n request.send();\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return _.isString(source) && urlStartRegexp.test(source);\r\n }\r\n\r\n static extractName(source) {\r\n if (source) {\r\n const last = (source.indexOf('?') + 1 || source.lastIndexOf('#') + 1 || source.length + 1) - 1;\r\n return source.slice(source.lastIndexOf('/', last) + 1, last);\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nXHRLoader.types = ['url'];\r\n","import Loader from './Loader';\r\n\r\nexport default class ImmediateLoader extends Loader {\r\n load() {\r\n return new Promise((resolve) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n resolve(this._source);\r\n });\r\n }\r\n\r\n static canProbablyLoad(_source) {\r\n return false;\r\n }\r\n}\r\n\r\nImmediateLoader.types = ['immediate'];\r\n","import LoaderList from './loaders/LoaderList';\r\n\r\nimport FileLoader from './loaders/FileLoader';\r\nimport XHRLoader from './loaders/XHRLoader';\r\nimport ImmediateLoader from './loaders/ImmediateLoader';\r\n\r\nexport default new LoaderList([\r\n // note: order might be important\r\n FileLoader,\r\n XHRLoader,\r\n ImmediateLoader,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available parsers.\r\n * @extends EntityList\r\n */\r\nclass ParserList extends EntityList {\r\n /**\r\n * Create a list of parsers.\r\n * The parsers are indexed by supported data formats and file extensions (`.formats` and\r\n * `.extensions` properties of a Parser subclass).\r\n * The parsers can be retrieved later by matching against specs (see {@link ParsrerList#find}).\r\n *\r\n * @param {!Array=} someParsers A list of {@link Parser} subclasses to\r\n * automatically register at creation time.\r\n * @see ParserList#register\r\n */\r\n constructor(someParsers = []) {\r\n super(someParsers, ['formats', 'extensions']);\r\n }\r\n\r\n /**\r\n * Find a suitable parser for data.\r\n *\r\n * @param {Object} specs Parser specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {string=} specs.ext Supported filename extension.\r\n * @param {*=} specs.data Data to parse.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n } else if (specs.ext) {\r\n list = this._dict.extensions[specs.ext.toLowerCase()] || [];\r\n }\r\n // autodetect only if no format is forced\r\n if (list.length === 0 && !specs.format && specs.data) {\r\n return this._list.filter((SomeParser) => SomeParser.canProbablyParse && SomeParser.canProbablyParse(specs.data));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ParserList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Parser {\r\n constructor(data, options) {\r\n this._data = data;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n parseSync() {\r\n throw new Error('Parsing this type of data is not implemented');\r\n }\r\n\r\n parse() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Parsing aborted'));\r\n }\r\n return resolve(this.parseSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n // only for volume Parsers\r\n getModel() {\r\n this.model._parseHeader(this._data);\r\n return this.model;\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Parser.prototype);\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 290\".\r\n *\r\n * @exports Remark290\r\n * @constructor\r\n */\r\nclass Remark290 {\r\n constructor() {\r\n /** @type {THREE.Matrix4[]} */\r\n this.matrices = [];\r\n\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (stream.readString(12, 18) === ' SMTRY') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === this.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n }\r\n }\r\n}\r\n\r\nRemark290.prototype.id = 290;\r\n\r\nexport default Remark290;\r\n","import * as THREE from 'three';\r\nimport chem from '../../../chem';\r\n\r\nconst { Assembly } = chem;\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 350\".\r\n *\r\n * @exports Remark350\r\n * @constructor\r\n */\r\nclass Remark350 {\r\n constructor(complex) {\r\n /** @type {Complex} */\r\n this._complex = complex;\r\n /** @type {Assembly[]} */\r\n this.assemblies = [];\r\n\r\n /** @type {?Assembly} */\r\n this._assembly = null;\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?Assembly} */\r\n let assembly = this._assembly;\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (assembly && stream.readString(12, 18) === ' BIOMT') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === assembly.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n } else if (assembly && stream.readString(35, 41) === 'CHAINS:') {\r\n const entries = stream.readString(42, 80).split(',');\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const chain = entries[i].trim();\r\n if (chain.length > 0) {\r\n assembly.addChain(chain);\r\n }\r\n }\r\n } else if (stream.readString(12, 23) === 'BIOMOLECULE:') {\r\n // assert molIndex === this.assemblies.length + 1\r\n this._matrix = null;\r\n this._matrixIndex = -1;\r\n this._assembly = assembly = new Assembly(this._complex);\r\n this.assemblies.push(assembly);\r\n }\r\n }\r\n}\r\n\r\nRemark350.prototype.id = 350;\r\n\r\nexport default Remark350;\r\n","/** Helper class for stream-like reading input files. */\r\nclass PDBStream {\r\n /**\r\n * Create a stream\r\n * @param {String} data Input data\r\n */\r\n constructor(data) {\r\n /** @type String */\r\n this._data = data; // Input file\r\n /** @type Number */\r\n this._start = 0; // Starting position of line\r\n /** @type Number */\r\n this._nextCR = -1; // Position of next CR (0x0D)\r\n /** @type Number */\r\n this._nextLF = -1; // Position of next LF (0x0A)\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n /** @type Number */\r\n this._end = data.length; // End of data\r\n\r\n this.next();\r\n }\r\n\r\n /**\r\n * Reading next line.\r\n * @returns {String} Next line in data (ending with LF or CR)\r\n */\r\n readLine() {\r\n return this._data.slice(this._start, this._next);\r\n }\r\n\r\n /**\r\n * Reading character from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {String} Character from position\r\n */\r\n readChar(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data[pos] : ' ';\r\n }\r\n\r\n /**\r\n * Reading character code from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {Number} Character code from position\r\n */\r\n readCharCode(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data.charCodeAt(pos) : 32;\r\n }\r\n\r\n /**\r\n * Reading string from begin to end points.\r\n * For a reason unknown, numbering assumed not to start from 0, but from 1.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {String} String from begin to end\r\n */\r\n readString(begin, end) {\r\n const from = this._start + begin - 1;\r\n const to = this._start + end;\r\n return this._data.slice(from, to < this._next ? to : this._next);\r\n }\r\n\r\n /**\r\n * Reading integer from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Integer from begin to end\r\n */\r\n readInt(begin, end) {\r\n return parseInt(this.readString(begin, end), 10);\r\n }\r\n\r\n /**\r\n * Reading float from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Float from begin to end\r\n */\r\n readFloat(begin, end) {\r\n return parseFloat(this.readString(begin, end));\r\n }\r\n\r\n /**\r\n * Checking for end of data.\r\n * @returns {boolean} True if data is ended, false otherwise\r\n */\r\n end() {\r\n return this._start >= this._end;\r\n }\r\n\r\n /**\r\n * Procedure to re-arrange current pointers in data.\r\n */\r\n next() {\r\n const start = this._next + 1;\r\n this._start = start < this._end ? start : this._end;\r\n\r\n // support CR, LF, CR+LF line endings\r\n // do not support LF+CR, CR+CR+LF, and other strange combinations\r\n\r\n if (this._start > this._nextCR) {\r\n this._nextCR = (this._data.indexOf('\\r', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n if (this._start > this._nextLF) {\r\n this._nextLF = (this._data.indexOf('\\n', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n this._next = this._nextCR + 1 < this._nextLF ? this._nextCR : this._nextLF;\r\n }\r\n}\r\n\r\nexport default PDBStream;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport Remark290 from './pdb/Remark290';\r\nimport Remark350 from './pdb/Remark350';\r\nimport PDBStream from './PDBStream';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst TAG_LENGTH = 6;\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\n// the most frequently used beginnings; although HEADER is mandatory, it is often missing in handmade files\r\nconst pdbStartRegexp = /^(HEADER\\s|COMPND\\s|REMARK\\s|ATOM {2}|HETATM|MODEL )/i;\r\n\r\nconst remarkParsers = {\r\n // NOTE: please forget the idea to build the method name in runtime, it can be obfuscated.\r\n 290: Remark290,\r\n 350: Remark350,\r\n};\r\n\r\nclass PDBParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._sheet = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._compaundFound = false;\r\n this._biomoleculeFound = false;\r\n this._allowedChainsIDs = null;\r\n this._lastMolId = -1;\r\n\r\n this._remarks = {};\r\n this._remark = null;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n this._compndCurrToken = '';\r\n\r\n this._options.fileType = 'pdb';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && pdbStartRegexp.test(data);\r\n }\r\n\r\n _finalize() {\r\n this._fixBondsArray();\r\n this._fixChains();\r\n\r\n // keep crystallographic symmetry transformations\r\n const remark290 = this._remarks[290];\r\n this._complex.symmetry = _.isUndefined(remark290) ? [] : remark290.matrices;\r\n\r\n // add loaded biological assemblies\r\n const remark350 = this._remarks[350];\r\n this._complex.units = this._complex.units.concat(_.isUndefined(remark350) ? [] : remark350.assemblies);\r\n\r\n // add loaded macromolecules\r\n this._finalizeMolecules();\r\n\r\n // create secondary structure etc.\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _finalizeMolecules() {\r\n // get chains from complex\r\n const chainDict = {};\r\n let i;\r\n const chains = this._complex._chains;\r\n for (i = 0; i < chains.length; ++i) {\r\n const chainObj = chains[i];\r\n const chainName = chainObj._name;\r\n chainDict[chainName] = chainObj;\r\n }\r\n\r\n // aggregate residues from chains\r\n for (i = 0; i < this._molecules.length; i++) {\r\n const m = this._molecules[i];\r\n let residues = [];\r\n for (let j = 0; j < m._chains.length; j++) {\r\n const name = m._chains[j];\r\n const chain = chainDict[name];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, m._name, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _fixChains() {\r\n const idChainMap = {};\r\n const complex = this._complex;\r\n\r\n // prepare\r\n for (let i = 0; i < complex._chains.length; i++) {\r\n const chain = complex._chains[i];\r\n idChainMap[chain._name.charCodeAt(0)] = chain;\r\n }\r\n }\r\n\r\n // FIXME: This function is redundant, CONECT records always follow ATOM and HETATM. Build the map online.\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseATOM(stream) {\r\n if (this._modelId !== 1) {\r\n return;\r\n }\r\n\r\n /* eslint-disable no-magic-numbers */\r\n const het = stream.readCharCode(1) === 0x48;\r\n\r\n // field names according to wwPDB Format\r\n // NOTE: Chimera allows (nonstandard) use of columns 6-11 for the integer atom serial number in ATOM records.\r\n const serial = het ? stream.readInt(7, 11) : stream.readInt(6, 11);\r\n let name = stream.readString(13, 16);\r\n const altLoc = stream.readChar(17);\r\n const resName = stream.readString(18, 20).trim();\r\n const chainID = stream.readChar(22);\r\n const resSeq = stream.readInt(23, 26);\r\n const iCode = stream.readChar(27);\r\n const x = stream.readFloat(31, 38);\r\n const y = stream.readFloat(39, 46);\r\n const z = stream.readFloat(47, 54);\r\n const occupancy = stream.readFloat(55, 60);\r\n const tempFactor = stream.readFloat(61, 66);\r\n const element = stream.readString(77, 78).trim() || nameToElement(name);\r\n const charge = stream.readInt(79, 80) || 0;\r\n /* eslint-enable no-magic-numbers */\r\n // skip waters (there may be lots of them)\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n // PDB uses positional system for atom names. It helps derive element type from the name\r\n // but names may include extra spaces. From this point on we don't need those spaces anymore.\r\n name = name.trim();\r\n\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name]; // FIXME: Maybe should use type as additional index (\" CA \" vs. \"CA \")\r\n\r\n // NOTE: Residues of a particular chain are not required to be listed next to each other.\r\n // https://github.com/biasmv/pv/commit/7319b898b7473ba380c26699e3b028b2b1a7e1a1\r\n let chain = this._chain;\r\n if (!chain || chain.getName() !== chainID) {\r\n this._chain = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n _parseENDMDL() {\r\n this._modelId += 1;\r\n }\r\n\r\n _parseCONECT(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const serial0 = stream.readInt(7, 11);\r\n const serial1 = stream.readInt(12, 16);\r\n const serial2 = stream.readInt(17, 21);\r\n const serial3 = stream.readInt(22, 26);\r\n const serial4 = stream.readInt(27, 31);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n const complex = this._complex;\r\n\r\n // Keep bonds ordered by atom serial\r\n if (serial1 && serial1 > serial0) {\r\n complex.addBond(serial0, serial1, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial2 && serial2 > serial0) {\r\n complex.addBond(serial0, serial2, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial3 && serial3 > serial0) {\r\n complex.addBond(serial0, serial3, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial4 && serial4 > serial0) {\r\n complex.addBond(serial0, serial4, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n }\r\n\r\n _parseCOMPND(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const str = stream.readString(11, 80);\r\n const tokenIdx = str.indexOf(':');\r\n this._compndCurrToken = tokenIdx > 0 ? str.substring(0, tokenIdx).trim() : this._compndCurrToken;\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // start reading new molecule\r\n if (this._compndCurrToken === 'MOL_ID') {\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = parseInt(str.substring(tokenIdx + 1, str.indexOf(';')), 10);\r\n this._molecules.push(this._molecule);\r\n // parse molecule name\r\n } else if (this._compndCurrToken === 'MOLECULE' && this._molecule != null) {\r\n this._molecule._name = str.substring(tokenIdx + 1, str.indexOf(';')).trim();\r\n // parse molecule chains\r\n } else if (this._compndCurrToken === 'CHAIN' && this._molecule != null) {\r\n let chainStr = str.substring(tokenIdx + 1, 80).trim();\r\n const lastChar = chainStr[chainStr.length - 1];\r\n if (lastChar === ';' || lastChar === ',') {\r\n chainStr = chainStr.slice(0, -1);\r\n }\r\n chainStr = chainStr.replace(/\\s+/g, '');\r\n const chains = chainStr.split(',');\r\n this._molecule._chains = this._molecule._chains.concat(chains);\r\n }\r\n }\r\n\r\n _parseREMARK(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const remarkNum = stream.readInt(8, 10);\r\n /* eslint-enable no-magic-numbers */\r\n\r\n // create remark parser if needed\r\n let remark = this._remarks[remarkNum];\r\n if (_.isUndefined(remark)) {\r\n const RemarkParser = remarkParsers[remarkNum];\r\n if (_.isFunction(RemarkParser)) {\r\n this._remarks[remarkNum] = remark = new RemarkParser(this._complex);\r\n }\r\n }\r\n\r\n // delegate parsing\r\n if (!_.isUndefined(remark)) {\r\n remark.parse(stream);\r\n }\r\n }\r\n\r\n _parseHELIX(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const fields = [20, 22, 32, 34];\r\n /* eslint-enable no-magic-numbers */\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addHelix(obj);\r\n this._complex.structures.push(obj);\r\n });\r\n }\r\n\r\n _parseSHEET(stream) {\r\n /* eslint-disable no-magic-numbers */\r\n const fields = [22, 23, 33, 34];\r\n /* eslint-enable no-magic-numbers */\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addSheet(obj);\r\n });\r\n }\r\n\r\n _parseSTRUCTURE(stream, pars, adder) {\r\n const startId = 0;\r\n const startIndex = 1;\r\n const endId = 2;\r\n const endIndex = 3;\r\n\r\n // identify fields: debugging and stuff\r\n /* eslint-disable no-magic-numbers */\r\n const codeOfS = 0x53;\r\n const serialNumber = stream.readInt(8, 10);\r\n const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim()\r\n const comment = stream.readString(41, 70).trim();\r\n const helLength = stream.readInt(72, 76);\r\n const helixClass = stream.readInt(39, 40);\r\n const shWidth = stream.readInt(15, 16);\r\n const shCur = stream.readInt(42, 45);\r\n const shPrev = stream.readInt(57, 60);\r\n /* eslint-enable no-magic-numbers */\r\n // file fields\r\n const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0);\r\n const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0);\r\n const startSequenceNumber = stream.readInt(pars[startIndex], pars[startIndex] + 3);\r\n let iCodeStr = stream.readString(pars[startIndex] + 4, pars[startIndex] + 4);\r\n let startICode = 0;\r\n\r\n if (iCodeStr.length > 0) {\r\n startICode = iCodeStr.charCodeAt(0);\r\n }\r\n const endSequenceNumber = stream.readInt(pars[endIndex], pars[endIndex] + 3);\r\n iCodeStr = stream.readString(pars[endIndex] + 4, pars[endIndex] + 4);\r\n let endICode = 0;\r\n if (iCodeStr.length > 0) {\r\n endICode = iCodeStr.charCodeAt(0);\r\n }\r\n\r\n let obj;\r\n let cs = this._sheet;\r\n if (stream.readCharCode(1) === codeOfS) {\r\n if (cs !== null && cs.getName() !== structureName) {\r\n cs = null;\r\n this._sheet = null;\r\n }\r\n if (cs === null) {\r\n this._sheet = obj = new Sheet(structureName, shWidth);\r\n adder(obj);\r\n } else {\r\n obj = cs;\r\n }\r\n const strand = new Strand(\r\n obj,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n helixClass,\r\n shCur,\r\n shPrev,\r\n );\r\n obj.addStrand(strand);\r\n this._complex.structures.push(strand);\r\n } else {\r\n obj = new Helix(\r\n helixClass,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n serialNumber,\r\n structureName,\r\n comment,\r\n helLength,\r\n );\r\n adder(obj);\r\n }\r\n }\r\n\r\n _parseHEADER(stream) {\r\n const { metadata } = this._complex;\r\n metadata.classification = stream.readString(11, 50).trim();\r\n metadata.date = stream.readString(51, 59).trim();\r\n\r\n const id = stream.readString(63, 66).trim();\r\n metadata.id = id;\r\n if (id) {\r\n this._complex.name = id;\r\n }\r\n metadata.format = 'pdb';\r\n }\r\n\r\n _parseTITLE(stream) {\r\n const { metadata } = this._complex;\r\n metadata.title = metadata.title || [];\r\n\r\n const line = stream.readInt(9, 10) || 1;\r\n metadata.title[line - 1] = stream.readString(11, 80).trim();\r\n }\r\n\r\n static tagParsers = {\r\n HEADER: PDBParser.prototype._parseHEADER,\r\n 'TITLE ': PDBParser.prototype._parseTITLE,\r\n 'ATOM ': PDBParser.prototype._parseATOM,\r\n HETATM: PDBParser.prototype._parseATOM,\r\n ENDMDL: PDBParser.prototype._parseENDMDL,\r\n CONECT: PDBParser.prototype._parseCONECT,\r\n COMPND: PDBParser.prototype._parseCOMPND,\r\n REMARK: PDBParser.prototype._parseREMARK,\r\n // 'SOURCE': PDBParser.prototype._parseSOURCE,\r\n 'HELIX ': PDBParser.prototype._parseHELIX,\r\n 'SHEET ': PDBParser.prototype._parseSHEET,\r\n\r\n // nonstandard extension to allow range 100,000 - 999,999\r\n 'ATOM 1': PDBParser.prototype._parseATOM,\r\n 'ATOM 2': PDBParser.prototype._parseATOM,\r\n 'ATOM 3': PDBParser.prototype._parseATOM,\r\n 'ATOM 4': PDBParser.prototype._parseATOM,\r\n 'ATOM 5': PDBParser.prototype._parseATOM,\r\n 'ATOM 6': PDBParser.prototype._parseATOM,\r\n 'ATOM 7': PDBParser.prototype._parseATOM,\r\n 'ATOM 8': PDBParser.prototype._parseATOM,\r\n 'ATOM 9': PDBParser.prototype._parseATOM,\r\n };\r\n\r\n parseSync() {\r\n const stream = new PDBStream(this._data);\r\n const result = this._complex = new Complex();\r\n\r\n // parse PDB line by line\r\n while (!stream.end()) {\r\n const tag = stream.readString(1, TAG_LENGTH);\r\n const func = PDBParser.tagParsers[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, stream);\r\n }\r\n stream.next();\r\n }\r\n\r\n // Resolve indices and serials to objects\r\n this._finalize();\r\n\r\n // cleanup\r\n this._serialAtomMap = null;\r\n this._sheet = null;\r\n this._residue = null;\r\n this._chain = null;\r\n this._complex = null;\r\n\r\n if (result.getAtomCount() === 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n\r\nPDBParser.formats = ['pdb'];\r\nPDBParser.extensions = ['.pdb', '.ent'];\r\n\r\nexport default PDBParser;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n SGroup,\r\n Bond,\r\n} = chem;\r\n\r\nconst cOrderCharCodes = {\r\n A: 0,\r\n S: 1,\r\n D: 2,\r\n T: 3,\r\n};\r\n\r\nconst cmlStartRegexp = /\\s*<\\?xml\\b[^?>]*\\?>\\s*<(?:cml|molecule)\\b/i;\r\n\r\nclass CMLParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._complex = null;\r\n this._residue = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._lastMolId = -1;\r\n this._readOnlyOneMolecule = false;\r\n this._options.fileType = 'cml';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && cmlStartRegexp.test(data);\r\n }\r\n\r\n _rebuidBondIndexes(atoms, bonds) {\r\n const count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n\r\n const countBonds = bonds.length;\r\n for (let j = 0; j < countBonds; j++) {\r\n const idxs = bonds[j].atomRefs2.split(' ');\r\n if (idxs[0] === atomId) {\r\n bonds[j].start = i;\r\n }\r\n\r\n if (idxs[1] === atomId) {\r\n bonds[j].end = i;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _createSGroup(molecule, moleculeArr) {\r\n const newGroup = new SGroup(\r\n molecule.id,\r\n molecule.fieldData,\r\n new THREE.Vector3(parseFloat(molecule.x), parseFloat(molecule.y), 0),\r\n molecule.atomRefs,\r\n molecule,\r\n );\r\n if (molecule.placement === 'Relative') {\r\n newGroup._center = new THREE.Vector3(0, 0, 0);\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_CHARGE') {\r\n newGroup._charge = parseInt(molecule.fieldData, 10) || 0;\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_COEFFICIENT') {\r\n newGroup._repeat = parseInt(molecule.fieldData, 10) || 1;\r\n }\r\n moleculeArr.push(newGroup);\r\n }\r\n\r\n _extractSGroup(molecule, moleculeArr) {\r\n if (!Array.isArray(moleculeArr)) {\r\n moleculeArr = [];\r\n }\r\n\r\n if (molecule) {\r\n if (Array.isArray(molecule)) {\r\n const count = molecule.length;\r\n for (let i = 0; i < count; i++) {\r\n if (molecule[i].molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule[i].molecule));\r\n }\r\n this._createSGroup(molecule[i], moleculeArr);\r\n }\r\n } else {\r\n if (molecule.molecule) {\r\n if (molecule.molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule.molecule));\r\n }\r\n }\r\n this._createSGroup(molecule, moleculeArr);\r\n }\r\n }\r\n\r\n return moleculeArr;\r\n }\r\n\r\n _extractSGroups(molecule, atoms) {\r\n const moleculeArr = this._extractSGroup(molecule);\r\n\r\n const count = atoms.length;\r\n let i;\r\n let j;\r\n\r\n for (i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n const firstAtomRef = moleculeArr[j]._atoms.split(' ')[0];\r\n if (firstAtomRef === atomId) {\r\n if (!atoms[i].sgroupRef) {\r\n atoms[i].sgroupRef = [];\r\n }\r\n atoms[i].sgroupRef.push(moleculeArr[j]);\r\n }\r\n }\r\n }\r\n // build sGroups centers\r\n let atomMap = {}; // sgrpmap cache\r\n let mapEntry = null;\r\n const nLimon = 100000000;\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n\r\n function cycleFuncInner(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n moleculeArr[j]._atoms.push(mapEntry.a);\r\n }\r\n }\r\n\r\n function cycleFunc(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n bLow.set(Math.min(bLow.x, mapEntry.x), Math.min(bLow.y, mapEntry.y), Math.min(bLow.z, mapEntry.z));\r\n bHight.set(Math.max(bHight.x, mapEntry.x), Math.max(bHight.y, mapEntry.y), Math.max(bHight.z, mapEntry.z));\r\n cycleFuncInner(e);\r\n }\r\n }\r\n\r\n for (i = 0; i < atoms.length; i++) {\r\n atomMap[atoms[i].id] = {};\r\n atomMap[atoms[i].id].x = atoms[i].x2;\r\n if (atoms[i].x3) {\r\n atomMap[atoms[i].id].x = atoms[i].x3;\r\n }\r\n atomMap[atoms[i].id].x = parseFloat(atomMap[atoms[i].id].x);\r\n atomMap[atoms[i].id].y = atoms[i].y2;\r\n if (atoms[i].y3) {\r\n atomMap[atoms[i].id].y = atoms[i].y3;\r\n }\r\n atomMap[atoms[i].id].y = parseFloat(atomMap[atoms[i].id].y);\r\n atomMap[atoms[i].id].z = '0.0';\r\n if (atoms[i].z3) {\r\n atomMap[atoms[i].id].z = atoms[i].z3;\r\n }\r\n atomMap[atoms[i].id].z = parseFloat(atomMap[atoms[i].id].z);\r\n atomMap[atoms[i].id].a = atoms[i];\r\n }\r\n\r\n let atomsRef;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n if (moleculeArr[j]._center !== null) {\r\n bLow.set(nLimon, nLimon, nLimon);\r\n bHight.set(-nLimon, -nLimon, -nLimon);\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFunc);\r\n\r\n moleculeArr[j]._center.addVectors(bLow, bHight);\r\n moleculeArr[j]._center.multiplyScalar(0.5);\r\n } else {\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFuncInner);\r\n }\r\n }\r\n atomMap = null;\r\n }\r\n\r\n _traverseData(dom) {\r\n function isArray(o) {\r\n return Object.prototype.toString.apply(o) === '[object Array]';\r\n }\r\n\r\n function parseNode(xmlNode, result) {\r\n if (xmlNode.nodeName === '#text' && xmlNode.nodeValue.trim() === '') {\r\n return;\r\n }\r\n\r\n const jsonNode = {};\r\n jsonNode.xmlNode = xmlNode;\r\n const existing = result[xmlNode.nodeName];\r\n if (existing) {\r\n if (!isArray(existing)) {\r\n result[xmlNode.nodeName] = [existing, jsonNode];\r\n } else {\r\n result[xmlNode.nodeName].push(jsonNode);\r\n }\r\n } else {\r\n result[xmlNode.nodeName] = jsonNode;\r\n }\r\n\r\n let length;\r\n let i;\r\n if (xmlNode.attributes) {\r\n ({ length } = xmlNode.attributes);\r\n for (i = 0; i < length; i++) {\r\n const attribute = xmlNode.attributes[i];\r\n jsonNode[attribute.nodeName] = attribute.nodeValue;\r\n }\r\n }\r\n\r\n ({ length } = xmlNode.childNodes);\r\n for (i = 0; i < length; i++) {\r\n parseNode(xmlNode.childNodes[i], jsonNode);\r\n }\r\n }\r\n\r\n const result = {};\r\n if (dom.childNodes.length) {\r\n parseNode(dom.childNodes[0], result);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _findSuitableMolecule(data, molSet) {\r\n for (const key in data) {\r\n if (key === 'xmlNode') {\r\n continue;\r\n } else if (key === 'molecule') {\r\n if (data.molecule) {\r\n if (data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n molSet.push(data);\r\n }\r\n if (Array.isArray(data.molecule)) {\r\n for (let i = 0; i < data.molecule.length; i++) {\r\n if (data.molecule[i].atomArray && data.molecule[i].atomArray.atom) {\r\n molSet.push({ molecule: data.molecule[i] });\r\n }\r\n }\r\n }\r\n }\r\n } else if (data[key] && data[key] !== null && typeof (data[key]) === 'object') {\r\n this._findSuitableMolecule(data[key], molSet);\r\n }\r\n }\r\n }\r\n\r\n _selectComponents(text) {\r\n const parser = new DOMParser();\r\n const doc = parser.parseFromString(text, 'application/xml');\r\n const traversedData = this._traverseData(doc);\r\n let rawData;\r\n const self = this;\r\n\r\n function prepareComponentCompound(data) {\r\n let atoms = [];\r\n if (data.molecule && data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n if (!Array.isArray(data.molecule.atomArray.atom)) {\r\n atoms.push(data.molecule.atomArray.atom);\r\n } else {\r\n atoms = data.molecule.atomArray.atom;\r\n }\r\n } else if (!data.molecule) {\r\n const ret = {};\r\n ret.atomLabels = null;\r\n ret.labelsCount = 1;\r\n return ret;\r\n }\r\n\r\n if (data.molecule.molecule) {\r\n self._extractSGroups(data.molecule.molecule, atoms);\r\n }\r\n\r\n let atom;\r\n let count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges = [];\r\n }\r\n\r\n let localBond = [];\r\n if (data.molecule.bondArray && data.molecule.bondArray.bond) {\r\n if (!Array.isArray(data.molecule.bondArray.bond)) {\r\n localBond.push(data.molecule.bondArray.bond);\r\n } else {\r\n localBond = data.molecule.bondArray.bond;\r\n }\r\n }\r\n let bond;\r\n count = localBond.length;\r\n self._rebuidBondIndexes(atoms, localBond);\r\n\r\n function addCurrBond(index) {\r\n bond = localBond[index];\r\n atom = atoms[bond.start];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.end);\r\n atom = atoms[bond.end];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.start);\r\n return true;\r\n }\r\n\r\n for (let i = 0; i < count; i++) {\r\n if (!addCurrBond(i)) {\r\n // ignore invalid bond\r\n continue;\r\n }\r\n const orderAttr = bond.xmlNode.getAttribute('order');\r\n const tc = parseInt(orderAttr, 10);\r\n // the default bond order is unknown\r\n localBond[i].order = 0;\r\n localBond[i].type = Bond.BondType.UNKNOWN;\r\n if (tc > 1) {\r\n localBond[i].order = tc;\r\n } else {\r\n // another option - bond order is a string\r\n const order = cOrderCharCodes[orderAttr];\r\n if (order !== undefined) {\r\n localBond[i].order = order;\r\n if (orderAttr === 'A') {\r\n localBond[i].type = Bond.BondType.AROMATIC;\r\n }\r\n }\r\n }\r\n }\r\n\r\n count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges.sort();\r\n }\r\n\r\n const labels = self._breadWidthSearch(atoms, 0); // for now\r\n\r\n const retStruct = {};\r\n retStruct.atoms = atoms;\r\n retStruct.bonds = localBond;\r\n retStruct.labels = labels.atomLabels;\r\n retStruct.count = Math.min(1, labels.labelsCount); // for now\r\n retStruct.curr = -1;\r\n retStruct.originalCML = doc;\r\n\r\n return retStruct;\r\n }\r\n\r\n if (traversedData.cml) {\r\n rawData = traversedData.cml;\r\n } else {\r\n rawData = traversedData;\r\n }\r\n const retData = [];\r\n const filteredData = [];\r\n this._findSuitableMolecule(rawData, filteredData);\r\n if (this._readOnlyOneMolecule && filteredData.length > 1) {\r\n filteredData.splice(1, filteredData.length - 1);\r\n }\r\n filteredData.forEach((d) => {\r\n const rd = prepareComponentCompound(d);\r\n if (rd.atoms.length > 0) {\r\n retData.push(rd);\r\n }\r\n });\r\n return retData;\r\n }\r\n\r\n _packLabel(compId, molId) {\r\n const shift = 16;\r\n return (molId << shift) + compId;\r\n }\r\n\r\n _unpackLabel(l) {\r\n const shift = 16;\r\n const mask = (1 << shift) - 1;\r\n return { molId: l >>> shift, compId: l & mask };\r\n }\r\n\r\n _breadWidthSearch(atoms, molID) {\r\n const atomLabels = new Array(atoms.length);\r\n\r\n let id;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n atomLabels[id] = this._packLabel(0, molID);\r\n }\r\n\r\n const breadthQueue = [];\r\n let componentID = 0;\r\n let labeledAtoms = atoms.length;\r\n\r\n while (labeledAtoms > 0) {\r\n componentID++;\r\n\r\n let startID = -1;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n if (this._unpackLabel(atomLabels[id]).compId === 0) {\r\n startID = id;\r\n break;\r\n }\r\n }\r\n\r\n if (startID < 0) {\r\n break;\r\n }\r\n\r\n // Bread first search\r\n breadthQueue.push(atoms[startID]);\r\n atomLabels[startID] = this._packLabel(componentID, molID);\r\n labeledAtoms--;\r\n\r\n while (breadthQueue.length > 0) {\r\n const curr = breadthQueue.shift();\r\n if (!curr) {\r\n continue;\r\n }\r\n\r\n for (let i = 0; i < curr.edges.length; i++) {\r\n if (atomLabels[curr.edges[i]] !== componentID) {\r\n breadthQueue.push(atoms[curr.edges[i]]);\r\n atomLabels[curr.edges[i]] = componentID;\r\n labeledAtoms--;\r\n }\r\n }\r\n }\r\n }\r\n const ret = {};\r\n ret.atomLabels = atomLabels;\r\n ret.labelsCount = componentID;\r\n return ret;\r\n }\r\n\r\n _parseBond(eAtom, mainAtom, order, type) {\r\n if (eAtom >= 0) {\r\n const h = [Math.min(eAtom, mainAtom), Math.max(eAtom, mainAtom)];\r\n this._complex.addBond(h[0], h[1], order, type, true);\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseSet(varData) {\r\n const complex = this._complex = new Complex();\r\n const data = varData;\r\n const currentLabel = data.curr;\r\n const { atoms, labels } = data;\r\n let atom = null;\r\n let i;\r\n let j;\r\n const count = atoms.length;\r\n\r\n function addFunc(a) {\r\n a.xmlNodeRef = atom;\r\n if (atom.x2) {\r\n atom.x3 = atom.x2;\r\n delete atom.x2;\r\n }\r\n if (atom.y2) {\r\n atom.y3 = atom.y2;\r\n delete atom.y2;\r\n }\r\n if (!(atom.z3)) {\r\n atom.z3 = '0.0';\r\n }\r\n atom.complexAtom = a;\r\n }\r\n\r\n let chains = {};\r\n // parse atoms in label order\r\n const reorder = [];\r\n for (i = 0; i < count; i++) {\r\n reorder.push(i);\r\n }\r\n reorder.sort((a, b) => labels[a] - labels[b]);\r\n for (i = 0; i < count; i++) {\r\n const atomCharge = 0;\r\n const lLabel = labels[reorder[i]];\r\n if (this._unpackLabel(lLabel).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[reorder[i]];\r\n const atomFullNameStruct = atom.elementType;\r\n\r\n if (atom.sgroupRef) {\r\n const countRef = atom.sgroupRef.length;\r\n for (let k = 0; k < countRef; ++k) {\r\n complex._sgroups.push(atom.sgroupRef[k]);\r\n }\r\n }\r\n\r\n if (atom.x3 || atom.x2) {\r\n const currAtomComp = this._unpackLabel(lLabel).compId;\r\n // use ' ' by default instead of synthetic creation of chain names\r\n const chainID = ' '; //= String.fromCharCode('A'.charCodeAt(0) + currAtomComp);\r\n const resSeq = currAtomComp;\r\n const iCode = ' ';\r\n let strLabel = currAtomComp.toString();\r\n if (strLabel.length === 1) {\r\n strLabel = `0${strLabel}`;\r\n }\r\n const resName = `N${strLabel}`;\r\n let chain = chains[chainID];\r\n if (!chain || chain.getName() !== chainID) {\r\n chains[chainID] = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n // _x, _y, _z, mname, mindex, atomNameFull, atomName, chainID, serial, isHet, atlLocInd, atomNameToTypeF\r\n let xyz = null;\r\n if (atom.x3) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x3), parseFloat(atom.y3), parseFloat(atom.z3));\r\n } else if (atom.x2) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x2), parseFloat(atom.y2), 0);\r\n }\r\n let element = Element.ByName[atom.elementType.toUpperCase()];\r\n if (!element) {\r\n element = (JSON.parse(JSON.stringify(Element.ByName[\r\n Object.keys(Element.ByName)[Object.keys(Element.ByName).length - 1]])));\r\n element.number += 1;\r\n element.name = atom.elementType.toUpperCase();\r\n element.fullName = 'Unknown';\r\n Element.ByName[atom.elementType.toUpperCase()] = element;\r\n }\r\n const atomSerial = parseInt(atom.id.replace(/[^0-9]/, ''), 10);\r\n const added = residue.addAtom(\r\n atomFullNameStruct,\r\n element,\r\n xyz,\r\n Element.Role.SG,\r\n true,\r\n atomSerial,\r\n ' ',\r\n 1.0,\r\n 0.0,\r\n atomCharge,\r\n );\r\n if (atom.hydrogenCount) {\r\n added.hydrogenCount = parseInt(atom.hydrogenCount, 10);\r\n }\r\n if (atom.mrvValence) {\r\n added.valence = parseInt(atom.mrvValence, 10);\r\n }\r\n addFunc(added);\r\n }\r\n }\r\n }\r\n chains = null;// NOSONAR\r\n for (i = 0; i < data.bonds.length; i++) {\r\n const cb = data.bonds[i];\r\n if (this._unpackLabel(labels[cb.start]).molId === this._unpackLabel(currentLabel).molId\r\n && this._unpackLabel(labels[cb.end]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[cb.start];\r\n if (!atom || !(atoms[cb.end])) {\r\n continue; // skip invalid\r\n }\r\n this._parseBond(\r\n parseInt(atom.id.replace(/[^0-9]/, ''), 10),\r\n parseInt(atoms[cb.end].id.replace(/[^0-9]/, ''), 10),\r\n cb.order,\r\n cb.type,\r\n );\r\n }\r\n }\r\n\r\n for (i = 0; i < this._complex.getSGroupCount(); i++) {\r\n const sGrp = this._complex.getSGroups()[i];\r\n for (j = 0; j < sGrp._atoms.length; j++) {\r\n sGrp._atoms[j] = sGrp._atoms[j].complexAtom;\r\n }\r\n }\r\n for (i = 0; i < count; i++) {\r\n if (this._unpackLabel(labels[i]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[i];\r\n atom.complexAtom = null;\r\n delete atom.complexAtom;\r\n }\r\n }\r\n this._complex.originalCML = data.originalCML;\r\n this._fixBondsArray();\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n this._serialAtomMap = null;\r\n this._complex = null;\r\n return complex;\r\n }\r\n\r\n parseSync() {\r\n const complexes = [];\r\n const self = this;\r\n const moleculaSet = this._selectComponents(this._data);\r\n moleculaSet.forEach((molSet) => {\r\n molSet.curr = 2;\r\n if (molSet.count === 0) {\r\n molSet.count = 1;\r\n }\r\n for (let i = 0; i < molSet.count; i++) {\r\n molSet.curr = (i + 1);\r\n complexes.push(self._parseSet(molSet, false));\r\n }\r\n });\r\n\r\n let totalAtomsParsed = 0;\r\n complexes.forEach((c) => {\r\n totalAtomsParsed += c.getAtomCount();\r\n });\r\n if (totalAtomsParsed <= 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n if (complexes.length > 1) {\r\n const joinedComplex = new Complex();\r\n joinedComplex.joinComplexes(complexes);\r\n joinedComplex.originalCML = complexes[0].originalCML;\r\n return joinedComplex;\r\n }\r\n if (complexes.length === 1) {\r\n return complexes[0];\r\n }\r\n return new Complex();\r\n }\r\n}\r\n\r\nCMLParser.formats = ['cml'];\r\nCMLParser.extensions = ['.cml'];\r\n\r\nexport default CMLParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport MMTF from '../../../vendor/js/mmtf';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst {\r\n Complex,\r\n Chain,\r\n Atom,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nclass ArrayComparator {\r\n constructor(original) {\r\n this._original = Array.from(original);\r\n this._original.sort();\r\n\r\n this._sum = 0;\r\n for (let i = 0; i < this._original.length; ++i) {\r\n this._sum += this._original[i];\r\n }\r\n }\r\n\r\n compare(candidate) {\r\n const len = candidate.length;\r\n if (len !== this._original.length) {\r\n return false;\r\n }\r\n\r\n let sum = 0;\r\n let i;\r\n for (i = 0; i < len; ++i) {\r\n sum += candidate[i];\r\n }\r\n\r\n if (sum !== this._sum) {\r\n return false;\r\n }\r\n\r\n const sorted = Array.from(candidate);\r\n sorted.sort();\r\n\r\n for (i = 0; i < len; ++i) {\r\n if (sorted[i] !== this._original[i]) {\r\n return false;\r\n }\r\n }\r\n\r\n return true;\r\n }\r\n}\r\n\r\nArrayComparator.prototype.constructor = ArrayComparator;\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see https://github.com/rcsb/mmtf-javascript/blob/master/src/mmtf-traverse.js\r\nconst secStructToType = [\r\n StructuralElementType.HELIX_PI, // 0\r\n StructuralElementType.BEND, // 1\r\n StructuralElementType.HELIX_ALPHA, // 2\r\n StructuralElementType.STRAND, // 3\r\n StructuralElementType.HELIX_310, // 4\r\n StructuralElementType.BRIDGE, // 5\r\n StructuralElementType.TURN, // 6\r\n StructuralElementType.COIL, // 7\r\n];\r\n\r\nfunction getFirstByte(buf) {\r\n const bytes = new Uint8Array(buf, 0, 1);\r\n return bytes[0];\r\n}\r\n\r\nclass MMTFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'mmtf';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n // check if it's binary MessagePack format containing a map (dictionary)\r\n // see https://github.com/msgpack/msgpack/blob/master/spec.md\r\n return _.isArrayBuffer(data) && ((getFirstByte(data) | 1) === 0xDF);\r\n }\r\n\r\n _onModel(_modelData) {\r\n }\r\n\r\n _onChain(chainData) {\r\n if (chainData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const chain = new Chain(this._complex, chainData.chainName);\r\n this._complex._chains[chainData.chainIndex] = chain;\r\n chain._index = chainData.chainIndex;\r\n }\r\n\r\n _onGroup(groupData) {\r\n if (groupData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n if (this.settings.now.nowater) {\r\n // skip water\r\n if (groupData.groupName === 'HOH' || groupData.groupName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n const chain = this._complex._chains[groupData.chainIndex];\r\n const icode = !groupData.insCode.charCodeAt(0) ? '' : groupData.insCode;\r\n const residue = chain.addResidue(groupData.groupName, groupData.groupId, icode);\r\n residue._index = groupData.groupIndex;\r\n\r\n this._updateSecStructure(this._complex, residue, groupData);\r\n }\r\n\r\n _onAtom(atomData) {\r\n if (atomData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const altLoc = !atomData.altLoc.charCodeAt(0) ? '' : atomData.altLoc;\r\n const atom = new Atom(\r\n atomData.groupIndex, // we store residue index here to replace it later with actual reference\r\n atomData.atomName,\r\n Element.getByName(atomData.element.toUpperCase()),\r\n new THREE.Vector3(atomData.xCoord, atomData.yCoord, atomData.zCoord),\r\n Element.Role[atomData.atomName],\r\n false, // hetero atoms will be marked later\r\n atomData.atomId,\r\n altLoc,\r\n atomData.occupancy,\r\n atomData.bFactor,\r\n atomData.formalCharge,\r\n );\r\n\r\n this._complex._atoms[atomData.atomIndex] = atom;\r\n atom.index = atomData.atomIndex;\r\n\r\n this._serialAtomMap[atomData.atomId] = atom;\r\n }\r\n\r\n _onBond(bondData) {\r\n const right = Math.max(bondData.atomIndex1, bondData.atomIndex2);\r\n if (right >= this._complex._atoms.length) {\r\n return;\r\n }\r\n const left = Math.min(bondData.atomIndex1, bondData.atomIndex2);\r\n this._complex.addBond(\r\n this._complex._atoms[left],\r\n this._complex._atoms[right],\r\n bondData.bondOrder,\r\n Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n\r\n _updateSecStructure(complex, residue, groupData) {\r\n const helixClasses = [3, -1, 1, -1, 5];\r\n\r\n if (!_.isUndefined(groupData) && groupData.secStruct === this._ssType) {\r\n residue._secondary = this._ssStruct;\r\n if (this._ssStruct) {\r\n this._ssStruct.term = residue;\r\n }\r\n return;\r\n }\r\n\r\n if (!_.isUndefined(groupData)) {\r\n // start new secondary structure\r\n const type = secStructToType[groupData.secStruct];\r\n this._ssType = groupData.secStruct;\r\n this._ssStart = residue;\r\n\r\n let struct = null;\r\n switch (this._ssType) {\r\n case -1: // undefined\r\n case 7: // coil\r\n break;\r\n case 0: // pi helix\r\n case 2: // alpha helix\r\n case 4: // 3-10 helix\r\n struct = new Helix(helixClasses[this._ssType], residue, residue, 0, '', '', 0);\r\n complex._helices.push(struct);\r\n break;\r\n case 3: { // extended\r\n const sheet = new Sheet('', 0);\r\n complex._sheets.push(sheet);\r\n struct = new Strand(sheet, residue, residue, 0, null, null);\r\n break;\r\n }\r\n default:\r\n if (type !== undefined) {\r\n struct = new StructuralElement(type, residue, residue);\r\n }\r\n break;\r\n }\r\n\r\n this._ssStruct = struct;\r\n residue._secondary = struct;\r\n if (struct) {\r\n complex.structures.push(struct);\r\n }\r\n }\r\n }\r\n\r\n _updateMolecules(mmtfData) {\r\n const entities = mmtfData.entityList;\r\n if (!entities) {\r\n return;\r\n }\r\n\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < entities.length; i++) {\r\n const entity = entities[i];\r\n const chains = entity.chainIndexList;\r\n let residues = [];\r\n for (let j = 0; j < chains.length; j++) {\r\n const chainIndex = chains[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, entity.description, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n // populate complex with chains, residues and atoms\r\n _traverse(mmtfData) {\r\n const self = this;\r\n\r\n // get metadata\r\n const { metadata } = this._complex;\r\n metadata.id = mmtfData.structureId;\r\n metadata.title = [];\r\n metadata.title[0] = mmtfData.title;\r\n metadata.date = mmtfData.releaseDate;\r\n metadata.format = 'mmtf';\r\n\r\n // create event callback functions\r\n const eventCallbacks = {\r\n onModel(modelData) {\r\n self._onModel(modelData);\r\n },\r\n onChain(chainData) {\r\n self._onChain(chainData);\r\n },\r\n onGroup(groupData) {\r\n self._onGroup(groupData);\r\n },\r\n onAtom(atomData) {\r\n self._onAtom(atomData);\r\n },\r\n onBond(bondData) {\r\n self._onBond(bondData);\r\n },\r\n };\r\n\r\n // temporary variables used during traversal to track secondary structures\r\n this._ssType = -1;\r\n this._ssStruct = null;\r\n this._ssStart = null;\r\n\r\n // traverse the structure and listen to the events\r\n MMTF.traverse(mmtfData, eventCallbacks);\r\n\r\n this._updateSecStructure(this._complex);\r\n this._updateMolecules(mmtfData);\r\n }\r\n\r\n // During traversal atoms and residues don't come sequentially\r\n // so a residue for certain atom can be unavailable. Thus we\r\n // store residue index in atom.\r\n // This function being called after traversal replaces the index\r\n // with actual reference, and also populates atom lists in residues.\r\n _linkAtomsToResidues() {\r\n for (let i = 0; i < this._complex._atoms.length; ++i) {\r\n const atom = this._complex._atoms[i];\r\n const residue = this._complex._residues[atom.residue];\r\n atom.residue = residue;\r\n residue._atoms.push(atom);\r\n }\r\n }\r\n\r\n _findSynonymousChains() {\r\n const named = {};\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!named.hasOwnProperty(name)) {\r\n named[name] = [];\r\n }\r\n\r\n named[name].push(chain._index);\r\n }\r\n\r\n return named;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _parseAssemblyInfo(mmtfData) {\r\n let i;\r\n let j;\r\n let k;\r\n const assemblies = [];\r\n const { logger } = this;\r\n\r\n for (i = 0; i < mmtfData.bioAssemblyList.length; ++i) {\r\n const baInfo = mmtfData.bioAssemblyList[i];\r\n if (baInfo.transformList.length === 0) {\r\n continue;\r\n }\r\n\r\n const chains = baInfo.transformList[0].chainIndexList;\r\n const chainListCheck = new ArrayComparator(chains);\r\n\r\n // build list of chain names\r\n const chainNames = {};\r\n for (j = 0; j < chains.length; ++j) {\r\n chainNames[this._complex._chains[chains[j]].getName()] = 1;\r\n }\r\n\r\n // all chains with the same name should belong to assembly if one of them belongs\r\n const allChains = [];\r\n let name;\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n // just concat arrays -- there should be no duplicates\r\n Array.prototype.push.apply(allChains, this._chainsByName[name]);\r\n }\r\n }\r\n if (!chainListCheck.compare(allChains)) {\r\n // assembly is missing some of the chains\r\n logger.debug('MMTF: Assembly is missing some of the synonymous chains. Skipping...');\r\n }\r\n\r\n const a = new Assembly(this._complex);\r\n\r\n // add chains to assembly\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n a.addChain(name);\r\n }\r\n }\r\n\r\n // add unique matrices to assembly\r\n a.addMatrix(new THREE.Matrix4().fromArray(baInfo.transformList[0].matrix).transpose());\r\n for (j = 1; j < baInfo.transformList.length; ++j) {\r\n const transform = baInfo.transformList[j];\r\n\r\n if (!chainListCheck.compare(transform.chainIndexList)) {\r\n // list of chains for this transform doesn't match that for other transforms\r\n // this is illegal in our structure\r\n logger.debug('MMTF: Chain lists differ for different transforms in one assembly. Skipping...');\r\n continue;\r\n }\r\n\r\n const m = new THREE.Matrix4().fromArray(transform.matrix).transpose();\r\n\r\n // check if matrix is already in the list\r\n for (k = 0; k < a.matrices.length; ++k) {\r\n if (a.matrices[k].equals(m)) {\r\n break;\r\n }\r\n }\r\n\r\n if (k === a.matrices.length) {\r\n a.addMatrix(m);\r\n }\r\n }\r\n\r\n a.finalize();\r\n assemblies.push(a);\r\n }\r\n\r\n return assemblies;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _markHeteroAtoms(mmtfData) {\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < mmtfData.entityList.length; ++i) {\r\n const entity = mmtfData.entityList[i];\r\n if (entity.type !== 'polymer') {\r\n for (let j = 0; j < entity.chainIndexList.length; ++j) {\r\n const chainIndex = entity.chainIndexList[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n for (let k = 0; k < chain._residues.length; ++k) {\r\n const res = chain._residues[k];\r\n for (let m = 0; m < res._atoms.length; ++m) {\r\n res._atoms[m].het = true;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // joins chains with the same name into single chain\r\n _joinSynonymousChains() {\r\n let i;\r\n let j;\r\n\r\n const primaryChainsArray = [];\r\n const primaryChainsHash = {};\r\n\r\n // join chains\r\n for (i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!primaryChainsHash.hasOwnProperty(name)) {\r\n // new name -- this is a primary chain\r\n primaryChainsHash[name] = chain;\r\n chain._index = primaryChainsArray.length; // update index as this array will later replace original chain list\r\n primaryChainsArray.push(chain);\r\n continue;\r\n }\r\n\r\n // this chain should be joined with the primary chain of the same name\r\n const primary = primaryChainsHash[name];\r\n for (j = 0; j < chain._residues.length; ++j) {\r\n const residue = chain._residues[j];\r\n primary._residues.push(residue);\r\n residue._chain = primary;\r\n }\r\n }\r\n\r\n // replace chains list with one containing only primary chains\r\n // dropping references to all chains but primary\r\n this._complex._chains = primaryChainsArray;\r\n }\r\n\r\n parseSync() {\r\n const mmtfData = MMTF.decode(this._data);\r\n\r\n this._complex = new Complex();\r\n this._serialAtomMap = {}; // filled during traversal\r\n\r\n this._traverse(mmtfData);\r\n this._linkAtomsToResidues();\r\n this._markHeteroAtoms(mmtfData);\r\n this._chainsByName = this._findSynonymousChains();\r\n Array.prototype.push.apply(this._complex.units, this._parseAssemblyInfo(mmtfData));\r\n this._joinSynonymousChains();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n return this._complex;\r\n }\r\n}\r\n\r\nMMTFParser.formats = ['mmtf'];\r\nMMTFParser.extensions = ['.mmtf'];\r\nMMTFParser.binary = true;\r\n\r\nexport default MMTFParser;\r\n","class ParsingError extends Error {\r\n constructor(message, line, column) {\r\n super(`data:${line}:${column}: ${message}`);\r\n\r\n if (Error.captureStackTrace) {\r\n Error.captureStackTrace(this, ParsingError);\r\n }\r\n\r\n this.name = 'ParsingError';\r\n this.parseLine = line;\r\n this.parseColumn = column;\r\n }\r\n}\r\n\r\nexport default ParsingError;\r\n","import _ from 'lodash';\r\nimport ParsingError from './ParsingError';\r\n\r\n// Implemented and being tested against: https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax\r\n\r\nfunction _isWhitespace(ch) {\r\n return ch === 32 || ch === 10 || ch === 13 || ch === 9;\r\n}\r\n\r\nfunction _inlineIndexOf(ch0, str, idx) {\r\n const len = str.length;\r\n let ch = -1;\r\n while (idx < len) {\r\n ch = str.charCodeAt(idx);\r\n if (ch === ch0 || ch === 10) {\r\n break;\r\n }\r\n ++idx;\r\n }\r\n return ch === ch0 ? idx : -1;\r\n}\r\n\r\nexport default function readCIF(source) {\r\n let i = 0;\r\n let j = 0;\r\n const n = source.length;\r\n let code = NaN;\r\n let newline = true;\r\n let line = 1;\r\n let column = 1;\r\n let begin;\r\n let state = 0; // 0 - start, 1 - block, 2 - item, 3 - loop, 4 - values, 5 - value\r\n const result = {};\r\n let block = {};\r\n let keys = [];\r\n let keysCount = 0;\r\n let key = '';\r\n let values = [];\r\n let valuesCount = 0;\r\n let value;\r\n\r\n function _parseValue() {\r\n let val;\r\n if ((code === 46 || code === 63) && (i + 1 >= n || _isWhitespace(source.charCodeAt(i + 1)))) { // '.' or '?' .....\r\n // it's a missing value\r\n ++column;\r\n ++i;\r\n return undefined;\r\n }\r\n if (newline && code === 59) { // ';' ......................................................................\r\n // parse multi-line string\r\n j = i;\r\n let lines = 0;\r\n do {\r\n j = _inlineIndexOf(10, source, j + 1); // '\\n'\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated text block found', line, column);\r\n }\r\n ++lines;\r\n } while ((j + 1 < n && source.charCodeAt(j + 1) !== code) || j + 1 >= n);\r\n val = source.substring(i + 1, j).replace(/\\r/g, '');\r\n i = j + 2;\r\n line += lines;\r\n column = 1;\r\n newline = false;\r\n return val;\r\n }\r\n if (code === 39 || code === 34) { // ''' or '\"' ...........................................................\r\n // parse quoted string\r\n j = i;\r\n do {\r\n j = _inlineIndexOf(code, source, j + 1);\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated quoted string found', line, column);\r\n }\r\n } while (j + 1 < n && !_isWhitespace(source.charCodeAt(j + 1)));\r\n val = source.substring(i + 1, j);\r\n column += j - i + 1;\r\n i = j + 1;\r\n return val;\r\n } // ......................................................................................................\r\n // parse until the first whitespace\r\n j = i;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n val = source.substring(i, j);\r\n column += j - i;\r\n i = j;\r\n // try to convert to a number\r\n const num = Number(val);\r\n if (!Number.isNaN(num)) {\r\n return num;\r\n }\r\n // or leave as an unquoted string\r\n return val;\r\n }\r\n\r\n function _storeKey(tag) {\r\n keys[keysCount++] = tag;\r\n }\r\n\r\n function _storeValue(val) {\r\n const keyIndex = valuesCount % keysCount;\r\n values[keyIndex].push(val);\r\n ++valuesCount;\r\n return val;\r\n }\r\n\r\n while (i <= n) {\r\n code = source.charCodeAt(i); // 'NaN' in place of ''\r\n if (code === 13) { // '\\r' .......................................................................................\r\n // just ignore\r\n } else if (code === 10) { // '\\n' ................................................................................\r\n // take note of new lines\r\n newline = true;\r\n ++line;\r\n column = 1;\r\n } else {\r\n // process inline characters\r\n if (code === 32 || code === 9) { // ' ' or '\\t' ................................................................\r\n // just ignore\r\n } else if (code === 35) { // '#' ...............................................................................\r\n // skip the comment until before the end of the line\r\n i = _inlineIndexOf(10, source, i + 1); // '\\n'\r\n if (i === -1) {\r\n break;\r\n } else {\r\n continue; // don't forget to process the new line\r\n }\r\n } else if (state === 0) { // start =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n j = i + 5;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new data block\r\n result[source.substring(begin, i)] = block = {};\r\n state = 1; // block\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Data block name missing', line, column);\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 1) { // block =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n continue; // parse again in a different state\r\n } else if (code === 95) { // '_' .............................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // start new item\r\n key = source.substring(begin, i);\r\n state = 2; // item\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n i += 5;\r\n column += 5;\r\n if (i < n && !_isWhitespace(source.charCodeAt(i))) {\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n } else {\r\n // start new loop\r\n keys = [];\r\n keysCount = 0;\r\n values = [];\r\n valuesCount = 0;\r\n state = 3; // loop\r\n continue; // don't forget to process the whitespace\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 2) { // item ==============================================================================\r\n if (Number.isNaN(code)) {\r\n break;\r\n }\r\n value = _parseValue();\r\n _.set(block, key, value);\r\n state = 1; // block\r\n continue;\r\n } else if (state === 3) { // loop ==============================================================================\r\n if (code === 95) { // '_' ....................................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new key\r\n _storeKey(source.substring(begin, i));\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else { // ..................................................................................................\r\n if (keysCount > 0) {\r\n for (let keyIndex = 0; keyIndex < keysCount; ++keyIndex) {\r\n value = [];\r\n values[keyIndex] = value;\r\n _.set(block, keys[keyIndex], value);\r\n }\r\n state = 4;\r\n continue; // parse again in a different state\r\n }\r\n throw new ParsingError('Data tags are missing inside a loop', line, column);\r\n }\r\n } else if (state === 4) { // values ============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n } else if (code === 95) { // '_' .............................................................................\r\n state = 1; // block\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n state = 1; // block\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n state = 0;\r\n } else { // ..................................................................................................\r\n _storeValue(_parseValue());\r\n }\r\n continue; // parse again in a different state\r\n } else { // ====================================================================================================\r\n throw new ParsingError(`Unexpected internal state ${state}`, line, column);\r\n }\r\n\r\n newline = false;\r\n ++column;\r\n }\r\n ++i;\r\n }\r\n\r\n if (state === 2) { // item\r\n throw new ParsingError(`Unexpected end of file in state ${state}`, line, column);\r\n }\r\n\r\n return result;\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\nimport readCIF from './readCIF';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nconst cRequiredAtomFields = [\r\n 'auth_seq_id',\r\n 'Cartn_x',\r\n 'Cartn_y',\r\n 'Cartn_z',\r\n 'label_atom_id',\r\n];\r\n\r\nconst cSecondaryCoding = {\r\n helx: 'helix',\r\n turn: 'turn',\r\n strn: 'strand',\r\n};\r\n\r\nfunction getTypeFromId(string) {\r\n const typeId = /[A-Za-z]+/.exec(string);\r\n if (!typeId) {\r\n return null;\r\n }\r\n\r\n return cSecondaryCoding[typeId[0].toLowerCase()];\r\n}\r\n\r\n/**\r\n * Make valid object an array\r\n * @param arrayLikeObject\r\n * @return {array, object} array or object\r\n */\r\nfunction arrize(arrayLikeObject) {\r\n if (arrayLikeObject === null || arrayLikeObject === undefined || _.isArray(arrayLikeObject)) {\r\n return arrayLikeObject;\r\n }\r\n return [arrayLikeObject];\r\n}\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\nclass AtomDataError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'AtomDataError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction _getOperations(operList) {\r\n if (!operList) {\r\n return null;\r\n }\r\n const idc = arrize(operList.id);\r\n const { matrix, vector } = operList;\r\n if (!idc || !matrix || !vector) {\r\n return null;\r\n }\r\n\r\n const ops = [];\r\n for (let i = 0, n = idc.length; i < n; ++i) {\r\n const mtx = new THREE.Matrix4();\r\n const { elements } = mtx;\r\n\r\n for (let row = 0; row < 3; ++row) {\r\n const matrixData = matrix[row + 1];\r\n elements[row] = arrize(matrixData[1])[i];\r\n elements[row + 4] = arrize(matrixData[2])[i];\r\n elements[row + 8] = arrize(matrixData[3])[i];\r\n elements[row + 12] = arrize(vector[row + 1])[i];\r\n }\r\n ops[idc[i]] = mtx;\r\n }\r\n return ops;\r\n}\r\n\r\nfunction _extractOperations(assemblyGen, opsDict) {\r\n assemblyGen = _.isString(assemblyGen) ? assemblyGen : `${assemblyGen}`;\r\n const l = assemblyGen.replace(/\\)\\s*\\(/g, '!').replace(/[()']/g, '');\r\n const groupStr = l.split('!');\r\n const gps = [];\r\n\r\n for (let grIdx = 0, grCount = groupStr.length; grIdx < grCount; ++grIdx) {\r\n const gr = groupStr[grIdx].split(',');\r\n const gp = [];\r\n let idx = 0;\r\n for (let i = 0, n = gr.length; i < n; ++i) {\r\n const s = gr[i];\r\n if (s.includes('-')) {\r\n const es = s.split('-');\r\n let j = parseInt(es[0], 10);\r\n const m = parseInt(es[1], 10);\r\n for (; j <= m; ++j) {\r\n gp[idx++] = opsDict[j];\r\n }\r\n } else {\r\n gp[idx++] = opsDict[s];\r\n }\r\n }\r\n gps.push(gp);\r\n }\r\n\r\n // traverse all groups from the end of array and make all mults\r\n const matrices = [];\r\n let cnt = 0;\r\n function traverse(level, mtx) {\r\n for (let ii = 0, nn = gps[level].length; ii < nn; ++ii) {\r\n const newMtx = mtx ? mtx.clone() : new THREE.Matrix4();\r\n newMtx.multiplyMatrices(gps[level][ii], newMtx);\r\n if (level === 0) {\r\n matrices[cnt++] = newMtx;\r\n } else {\r\n traverse(level - 1, newMtx);\r\n }\r\n }\r\n }\r\n traverse(gps.length - 1);\r\n return matrices;\r\n}\r\n\r\nclass CIFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this.asymDict = {};\r\n this.molecules = [];\r\n this._options.fileType = 'cif';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*data_/i.test(data);\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing CIF file..');\r\n const data = readCIF(this._data);\r\n return this._toComplex(data);\r\n }\r\n\r\n /**\r\n * Convert intermediate structure into our valid Complex object\r\n * @param cifData intermediate CIF object\r\n * @returns {Complex} complex\r\n * @private\r\n */\r\n _toComplex(cifData) {\r\n const complex = new Complex();\r\n const complexData = cifData[Object.keys(cifData)[0]];\r\n this._extractAtoms(complex, complexData);\r\n this._extractSecondary(complex, complexData);\r\n this._extractAssemblies(complex, complexData);\r\n this._extractMolecules(complex, complexData);\r\n this._extractMetadata(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n\r\n return complex;\r\n }\r\n\r\n /**\r\n * Extract metadata\r\n * @param complex structure to fill\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n\r\n _extractMetadata(complex, complexData) {\r\n const { metadata } = complex;\r\n metadata.id = complexData.entry.id;\r\n metadata.classification = complexData.struct_keywords.pdbx_keywords;\r\n const databaserev = complexData.database_PDB_rev;\r\n metadata.date = (databaserev && databaserev.date_original) ? databaserev.date_original : '';\r\n metadata.format = 'cif';\r\n metadata.title = [];\r\n metadata.title[0] = complexData.struct.title;\r\n }\r\n\r\n /**\r\n * Extract molecules information from CIF structure (should be called strictly after _extractAtoms)\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractMolecules(complex, complexData) {\r\n const molData = complexData.entity;\r\n const names = arrize(molData.pdbx_description);\r\n const count = names.length;\r\n let i;\r\n\r\n // molecules names from cif\r\n for (i = 0; i < count; i++) {\r\n if (this.molecules[i]) { // molecule was created during atoms processing\r\n this.molecules[i].name = names[i];\r\n } else { // molecule wasn't created, because there is no atom which is contained\r\n this.molecules[i] = { name: names[i], residues: [] };\r\n }\r\n }\r\n\r\n // reorganize molecules for complex and check chains\r\n const molecules = complex.getMolecules();\r\n for (i = 0; i < count; i++) {\r\n const molecule = this.molecules[i];\r\n molecules[i] = new Molecule(complex, molecule.name, i + 1);\r\n molecules[i].residues = molecule.residues;\r\n }\r\n }\r\n\r\n /**\r\n * Extract atom information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAtoms(complex, complexData) {\r\n const atomData = complexData.atom_site;\r\n if (!atomData) {\r\n throw new AtomDataError('CIF parsing error: atom_site is not specified!');\r\n }\r\n\r\n for (let f = 0, n = cRequiredAtomFields.length; f < n; ++f) {\r\n if (!atomData[cRequiredAtomFields[f]]) {\r\n throw new AtomDataError(`CIF parsing error: requires field ${cRequiredAtomFields[f]} not found!`);\r\n }\r\n }\r\n\r\n const { asymDict } = this;\r\n // required fields\r\n const resIdc = arrize(atomData.auth_seq_id);\r\n const x = arrize(atomData.Cartn_x);\r\n const y = arrize(atomData.Cartn_y);\r\n const z = arrize(atomData.Cartn_z);\r\n const names = arrize(atomData.label_atom_id);\r\n const count = names.length;\r\n // optional fields\r\n const group = arrize(atomData.group_PDB) || [];\r\n const chainIdc = arrize(atomData.auth_asym_id) || [];\r\n const chainLabelIdc = arrize(atomData.label_asym_id) || [];\r\n const serials = arrize(atomData.id) || [];\r\n const iCodes = arrize(atomData.pdbx_PDB_ins_code) || [];\r\n const resNames = arrize(atomData.label_comp_id) || [];\r\n const elements = arrize(atomData.type_symbol) || [];\r\n const tempFactors = arrize(atomData.B_iso_or_equiv) || [];\r\n const occupancies = arrize(atomData.occupancy) || [];\r\n const charges = arrize(atomData.pdbx_formal_charge) || [];\r\n const altLocs = arrize(atomData.label_alt_id) || [];\r\n const models = arrize(atomData.pdbx_PDB_model_num) || [];\r\n const molecules = arrize(atomData.label_entity_id) || [];\r\n\r\n let chain = null;\r\n let residue = null;\r\n for (let i = 0; i < count; ++i) {\r\n const model = models[i] || 1;\r\n if (model !== 1) {\r\n continue;\r\n }\r\n const chainID = String(chainIdc[i] || ' ');\r\n\r\n if (!chain || chain.getName() !== chainID) {\r\n chain = complex.getChain(chainID) || complex.addChain(chainID);\r\n }\r\n asymDict[String(chainLabelIdc[i] || ' ')] = chainID;\r\n const resSeq = resIdc[i];\r\n const iCode = String(iCodes[i] || ' ');\r\n const resName = String(resNames[i] || '');\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n residue = chain.addResidue(resName, resSeq, iCode);\r\n\r\n // store residue in appropriate molecule\r\n const moleculeIdx = molecules[i] - 1;\r\n let entity = this.molecules[moleculeIdx];\r\n if (!entity) { // create new molecule if it hasn't been created\r\n this.molecules[moleculeIdx] = { name: '', residues: [] };\r\n entity = this.molecules[moleculeIdx];\r\n }\r\n entity.residues.push(residue);\r\n }\r\n\r\n const name = names[i];\r\n const element = elements[i] || nameToElement(name);\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name.trim()];\r\n const xyz = new THREE.Vector3(x[i], y[i], z[i]);\r\n const het = group[i] === 'HETATM' || false;\r\n const serial = serials[i] || i;\r\n const tempFactor = tempFactors[i] || 0.0;\r\n const occupancy = occupancies[i] || 0.0;\r\n const altLoc = String(altLocs[i] || '');\r\n const charge = charges[i] || 0;\r\n\r\n residue.addAtom(\r\n name,\r\n type,\r\n xyz,\r\n role,\r\n het,\r\n serial,\r\n altLoc,\r\n occupancy,\r\n tempFactor,\r\n charge,\r\n );\r\n }\r\n }\r\n\r\n /**\r\n * Extracts secondary structure information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex - complex to fill\r\n * @param complexData - CIF complex data\r\n * @private\r\n */\r\n _extractSecondary(complex, complexData) {\r\n if (complexData.struct_conf) {\r\n this._extractConfs(complex, complexData.struct_conf);\r\n }\r\n if (complexData.struct_sheet_range) {\r\n this._extractSheets(complex, complexData.struct_sheet_range);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts sheets information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param sheetData\r\n * @private\r\n */\r\n _extractSheets(complex, sheetData) {\r\n const { asymDict } = this;\r\n if (!sheetData.sheet_id || !sheetData.id || !sheetData.beg_label_seq_id || !sheetData.end_label_seq_id\r\n || !sheetData.beg_label_asym_id) {\r\n return;\r\n }\r\n // Strand(sheet, start, end, sense, cur, prev)\r\n const sheets = complex._sheets;\r\n\r\n function getSheet(name) {\r\n const n = sheets.length;\r\n for (let i = 0; i < n; ++i) {\r\n if (sheets[i]._name === name) {\r\n return sheets[i];\r\n }\r\n }\r\n sheets[n] = new Sheet(name, 0);\r\n return sheets[n];\r\n }\r\n\r\n const sheetNames = arrize(sheetData.sheet_id);\r\n const strandNames = arrize(sheetData.id);\r\n const starts = arrize(sheetData.beg_auth_seq_id);\r\n const ends = arrize(sheetData.end_auth_seq_id);\r\n const chains = arrize(sheetData.beg_label_asym_id);\r\n const stICodes = arrize(sheetData.pdbx_beg_PDB_ins_code) || [];\r\n const endICodes = arrize(sheetData.pdbx_end_PDB_ins_code) || [];\r\n\r\n for (let i = 0, n = strandNames.length; i < n; ++i) {\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n const sheet = getSheet(sheetNames[i]);\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n\r\n const strand = new Strand(sheet, start[0], end[0], 0, null, null);\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = strand;\r\n }\r\n sheet.addStrand(strand);\r\n complex.structures.push(strand);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts helix/turn/strand(?) information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param helicesData\r\n * @private\r\n */\r\n _extractConfs(complex, helicesData) {\r\n const { asymDict } = this;\r\n if (!helicesData.conf_type_id || !helicesData.beg_label_seq_id || !helicesData.end_label_seq_id\r\n || !helicesData.beg_label_asym_id) {\r\n return;\r\n }\r\n\r\n const types = arrize(helicesData.conf_type_id);\r\n const starts = arrize(helicesData.beg_auth_seq_id);\r\n const stICodes = arrize(helicesData.pdbx_beg_PDB_ins_code) || [];\r\n const ends = arrize(helicesData.end_auth_seq_id);\r\n const endICodes = arrize(helicesData.pdbx_end_PDB_ins_code) || [];\r\n const comments = arrize(helicesData.details) || [];\r\n const lengths = arrize(helicesData.pdbx_PDB_helix_length) || [];\r\n const helixClasses = arrize(helicesData.pdbx_PDB_helix_class) || [];\r\n const names = arrize(helicesData.id) || [];\r\n const chains = arrize(helicesData.beg_label_asym_id);\r\n\r\n for (let i = 0, n = types.length; i < n; ++i) {\r\n const type = getTypeFromId(types[i]);\r\n if (!type) {\r\n continue;\r\n }\r\n const name = names[i] || types[i];\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n const comment = comments[i] || '';\r\n const length = lengths[i] || 0;\r\n const helixClass = helixClasses[i] || ' ';\r\n let struct;\r\n if (type === 'helix') {\r\n const idx = complex._helices.length;\r\n struct = new Helix(helixClass, start[0], end[0], idx, name, comment, length);\r\n complex.addHelix(struct);\r\n complex.structures.push(struct);\r\n } else if (type === 'turn') {\r\n struct = new StructuralElement(StructuralElement.Type.TURN, start[0], end[0]);\r\n complex.structures.push(struct);\r\n } else {\r\n struct = null;\r\n }\r\n if (!struct) {\r\n continue;\r\n }\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = struct;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Extract biological assemblies information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAssemblies(complex, complexData) {\r\n const { asymDict } = this;\r\n const asmGen = complexData.pdbx_struct_assembly_gen;\r\n if (!asmGen) {\r\n return;\r\n }\r\n\r\n const asmIdx = arrize(asmGen.assembly_id);\r\n const asmOper = arrize(asmGen.oper_expression);\r\n const asmList = arrize(asmGen.asym_id_list);\r\n if (!asmIdx || !asmOper || !asmList) {\r\n return;\r\n }\r\n\r\n const operList = _getOperations(complexData.pdbx_struct_oper_list);\r\n if (!operList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = asmIdx.length; i < n; ++i) {\r\n const asm = new Assembly(complex);\r\n const assemblyOps = _extractOperations(asmOper[i], operList);\r\n const entries = asmList[i].split(',');\r\n for (let ii = 0, nn = entries.length; ii < nn; ++ii) {\r\n const chain = entries[ii].trim();\r\n if (chain.length > 0) {\r\n asm.addChain(asymDict[chain]);\r\n }\r\n }\r\n asm.matrices = assemblyOps;\r\n complex.units.push(asm);\r\n }\r\n }\r\n}\r\n\r\nCIFParser.formats = ['cif', 'mmcif'];\r\nCIFParser.extensions = ['.cif', '.mmcif'];\r\n\r\nexport default CIFParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Volume from '../../chem/Volume';\r\n\r\nexport const valueType = {\r\n singular: 0,\r\n vector: 1,\r\n array: 2,\r\n buffer: 3,\r\n};\r\n\r\nclass VolumeModel {\r\n _xyz2crs = [];\r\n\r\n _origin = new THREE.Vector3(0, 0, 0);\r\n\r\n constructor() {\r\n this._header = {};\r\n this._boxSize = new THREE.Vector3();\r\n this._boxStart = new THREE.Vector3();\r\n this._header.delta = {};\r\n this._header.extent = [];\r\n this._header.nstart = [];\r\n this._header.grid = [];\r\n this._header.crs2xyz = [];\r\n this._header.cellDims = new THREE.Vector3();\r\n this._header.angles = [];\r\n this._header.origin = new THREE.Vector3(0, 0, 0);\r\n this._header.dmin = 0;\r\n this._header.dmean = 0;\r\n this._header.dmax = 0;\r\n }\r\n\r\n _typedCheck() {\r\n if (_.isTypedArray(this._buff)) {\r\n this._buff = this._buff.buffer;\r\n } else if (!_.isArrayBuffer(this._buff)) {\r\n throw new TypeError('Expected ArrayBuffer or TypedArray');\r\n }\r\n }\r\n\r\n _fillHeader(headerFormat, arrays) {\r\n for (const key in headerFormat) {\r\n if (headerFormat.hasOwnProperty(key)) {\r\n switch (headerFormat[key][0]) {\r\n case valueType.singular:\r\n this._header[key] = arrays[headerFormat[key][1]][headerFormat[key][2]];\r\n break;\r\n\r\n case valueType.array:\r\n this._parseArray(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.vector:\r\n this._parseVector(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.buffer:\r\n this._header[key] = new Uint8Array(\r\n arrays[headerFormat[key][1]],\r\n [headerFormat[key][2]] * 4,\r\n [headerFormat[key][3]] * 4,\r\n );\r\n break;\r\n\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _parseVector(vector, arr, pos) {\r\n [vector.x, vector.y, vector.z] = [arr[pos], arr[pos + 1], arr[pos + 2]];\r\n }\r\n\r\n _parseArray(vector, arr, pos) {\r\n vector[0] = arr[pos];\r\n vector[1] = arr[pos + 1];\r\n vector[2] = arr[pos + 2];\r\n }\r\n\r\n _parseHeader(_buffer) {}\r\n\r\n _setAxisIndices() {}\r\n\r\n _setOrigins() {}\r\n\r\n _getAxis() {\r\n const header = this._header;\r\n\r\n const xScale = header.cellDims.x / header.grid[0];\r\n const yScale = header.cellDims.y / header.grid[1];\r\n const zScale = header.cellDims.z / header.grid[2];\r\n\r\n const [alpha, beta, gamma] = header.angles;\r\n\r\n const z1 = Math.cos(beta);\r\n const z2 = (Math.cos(alpha) - Math.cos(beta)\r\n * Math.cos(gamma)) / Math.sin(gamma);\r\n const z3 = Math.sqrt(1.0 - z1 * z1 - z2 * z2);\r\n\r\n const xaxis = new THREE.Vector3(xScale, 0, 0);\r\n const yaxis = new THREE.Vector3(Math.cos(gamma) * yScale, Math.sin(gamma) * yScale, 0);\r\n const zaxis = new THREE.Vector3(z1 * zScale, z2 * zScale, z3 * zScale);\r\n\r\n return [xaxis, yaxis, zaxis];\r\n }\r\n\r\n _getXYZdim() {\r\n return [this._header.extent[this._xyz2crs[0]],\r\n this._header.extent[this._xyz2crs[1]],\r\n this._header.extent[this._xyz2crs[2]]];\r\n }\r\n\r\n _getVolumeInfo() {\r\n const volInfo = _.pick(this._header, ['dmean', 'dmin', 'dmax', 'sd', 'delta']);\r\n volInfo.obtuseAngle = this._header.angles.map((angle) => Number(angle >= (Math.PI / 2)));\r\n return volInfo;\r\n }\r\n\r\n _setBoxParams(xaxis, yaxis, zaxis) {\r\n // if axes are not orthogonal, the origins might not match with box coordinates - need to make shift\r\n let shiftX = 0;\r\n let shiftY = 0;\r\n const [alpha, beta, gamma] = this._header.angles;\r\n\r\n if (gamma >= Math.PI / 2) {\r\n shiftX += Math.abs(yaxis.x);\r\n }\r\n if (beta >= Math.PI / 2) {\r\n shiftX += Math.abs(zaxis.x);\r\n }\r\n if (alpha >= Math.PI / 2) {\r\n shiftY += Math.abs(zaxis.y);\r\n }\r\n\r\n this._boxStart = new THREE.Vector3(this._origin.x - shiftX, this._origin.y - shiftY, this._origin.z);\r\n this._boxSize = new THREE.Vector3(\r\n Math.abs(xaxis.x) + Math.abs(yaxis.x) + Math.abs(zaxis.x),\r\n Math.abs(yaxis.y) + Math.abs(zaxis.y),\r\n Math.abs(zaxis.z),\r\n );\r\n\r\n const delta = (axe, proj) => (Math.abs(axe[proj]) / this._boxSize[proj]);\r\n this._header.delta.x = delta(yaxis, 'x');\r\n this._header.delta.y = delta(zaxis, 'x');\r\n this._header.delta.z = delta(zaxis, 'y');\r\n }\r\n\r\n _getXYZbox() {\r\n return new THREE.Box3(this._boxStart.clone(), this._boxStart.clone().add(this._boxSize));\r\n }\r\n\r\n _toXYZData() {}\r\n\r\n parse(data) {\r\n this._parseHeader(data);\r\n this._setOrigins();\r\n return new Volume(Float32Array, this._getXYZdim(), this._getXYZbox(), 1, this._toXYZData(), this._getVolumeInfo());\r\n }\r\n}\r\n\r\nexport default VolumeModel;\r\n","import Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\nconst CCP4Header = {\r\n extent: [valueType.array, 'u32', 0],\r\n type: [valueType.singular, 'u32', 3],\r\n nstart: [valueType.array, 'i32', 4],\r\n grid: [valueType.array, 'u32', 7],\r\n cellDims: [valueType.vector, 'f32', 10],\r\n angles: [valueType.array, 'f32', 13],\r\n crs2xyz: [valueType.array, 'i32', 16],\r\n dmin: [valueType.singular, 'f32', 19],\r\n dmax: [valueType.singular, 'f32', 20],\r\n dmean: [valueType.singular, 'f32', 21],\r\n ispg: [valueType.singular, 'u32', 22],\r\n nsymbt: [valueType.singular, 'u32', 23],\r\n lksflg: [valueType.singular, 'u32', 24],\r\n customData: [valueType.buffer, 'buffer', 25, 9],\r\n origin: [valueType.vector, 'f32', 34],\r\n map: [valueType.buffer, 'buffer', 52, 1],\r\n machine: [valueType.singular, 'u32', 53],\r\n sd: [valueType.singular, 'f32', 54],\r\n nlabel: [valueType.singular, 'f32', 55],\r\n label: [valueType.buffer, 'buffer', 56, 200],\r\n};\r\n\r\nclass Ccp4Model extends VolumeModel {\r\n // read header (http://www.ccp4.ac.uk/html/maplib.html)\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n const arrays = {};\r\n arrays.u32 = new Uint32Array(this._buff, 0, 56);\r\n arrays.i32 = new Int32Array(this._buff, 0, 56);\r\n arrays.f32 = new Float32Array(this._buff, 0, 56);\r\n arrays.buffer = this._buff;\r\n const header = this._header;\r\n\r\n this._fillHeader(CCP4Header, arrays);\r\n\r\n // calculate non-orthogonal unit cell coordinates\r\n header.angles.forEach((angle, i, a) => { a[i] *= Math.PI / 180.0; });\r\n }\r\n\r\n _setAxisIndices() {\r\n const header = this._header;\r\n\r\n if (header.cellDims.x === 0.0 && header.cellDims.y === 0.0 && header.cellDims.z === 0.0) {\r\n header.cellDims.set(1.0, 1.0, 1.0);\r\n }\r\n // Apply header conversion\r\n // Mapping between CCP4 column, row, section and VMD x, y, z.\r\n const { crs2xyz } = this._header;\r\n if (crs2xyz[0] === 0 && crs2xyz[1] === 0 && crs2xyz[2] === 0) {\r\n crs2xyz[0] = 1;\r\n crs2xyz[1] = 2;\r\n crs2xyz[2] = 3;\r\n }\r\n\r\n const xyz2crs = this._xyz2crs;\r\n xyz2crs[crs2xyz[0] - 1] = 0; // column\r\n xyz2crs[crs2xyz[1] - 1] = 1; // row\r\n xyz2crs[crs2xyz[2] - 1] = 2; // section\r\n }\r\n\r\n _setOrigins() {\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n const header = this._header;\r\n const xyz2crs = this._xyz2crs;\r\n // Handle both MRC-2000 and older format maps\r\n if (header.origin.x === 0.0 && header.origin.y === 0.0 && header.origin.z === 0.0) {\r\n this._origin.addScaledVector(xaxis, header.nstart[xyz2crs[0]]);\r\n this._origin.addScaledVector(yaxis, header.nstart[xyz2crs[1]]);\r\n this._origin.addScaledVector(zaxis, header.nstart[xyz2crs[2]]);\r\n } else {\r\n this._origin = header.origin;\r\n // Use ORIGIN records rather than old n[xyz]start records\r\n // http://www2.mrc-lmb.cam.ac.uk/image2000.html\r\n // XXX the ORIGIN field is only used by the EM community, and\r\n // has undefined meaning for non-orthogonal maps and/or non-cubic voxels, etc.\r\n }\r\n xaxis.multiplyScalar(header.extent[xyz2crs[0]] - 1);\r\n yaxis.multiplyScalar(header.extent[xyz2crs[1]] - 1);\r\n zaxis.multiplyScalar(header.extent[xyz2crs[2]] - 1);\r\n\r\n if (header.type === 2) {\r\n this._data = new Float32Array(\r\n this._buff,\r\n 1024 + header.nsymbt,\r\n header.extent[0] * header.extent[1] * header.extent[2],\r\n );\r\n } else {\r\n throw new Error(`CCP4: Unsupported format ${header.type}`);\r\n }\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const data = this._data;\r\n const xyz2crs = this._xyz2crs;\r\n const xyzData = new Float32Array(data.length);\r\n\r\n const dim = this._getXYZdim();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n\r\n let crsIdx = 0;\r\n const coord = [];\r\n let x;\r\n let y;\r\n let z;\r\n for (coord[2] = 0; coord[2] < header.extent[2]; coord[2]++) { // Site\r\n for (coord[1] = 0; coord[1] < header.extent[1]; coord[1]++) { // Row\r\n for (coord[0] = 0; coord[0] < header.extent[0]; coord[0]++, crsIdx++) { // Column\r\n x = coord[xyz2crs[0]];\r\n y = coord[xyz2crs[1]];\r\n z = coord[xyz2crs[2]];\r\n xyzData[x + xSize * (y + ySize * z)] = data[crsIdx];\r\n }\r\n }\r\n }\r\n\r\n return xyzData;\r\n }\r\n}\r\n\r\nclass CCP4Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'ccp4';\r\n this.model = new Ccp4Model();\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false; // Autodetection is not implemented yet\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nCCP4Parser.formats = ['ccp4'];\r\nCCP4Parser.extensions = ['.ccp4', '.map', '.mrc'];\r\nCCP4Parser.binary = true;\r\n\r\nexport default CCP4Parser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element, Molecule } = chem;\r\n\r\nclass XYZParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n this._options.fileType = 'xyz';\r\n this._fileName = options.name;\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*\\d+ *\\n[^\\n]*\\n\\s*\\w{1,3}\\s+-?\\d/.test(data);\r\n }\r\n\r\n _parseToAtomsInf(source) {\r\n const endnAtoms = source.indexOf('\\n');\r\n const nAtoms = parseInt(source.substring(0, endnAtoms), 10);\r\n const endComment = source.indexOf('\\n', endnAtoms + 1);\r\n let comment = source.slice(endnAtoms + 1, endComment).trim();\r\n if (comment.length === 0) {\r\n comment = this._fileName;\r\n }\r\n\r\n const startAtomsInf = endComment + source.substring(endComment).search(/\\S/);\r\n this._atomsInf = source.substring(startAtomsInf).split(/[\\s,]*\\n[\\s,]*/);\r\n if (!Number.isNaN(nAtoms) && (this._atomsInf.length - 1 !== nAtoms)) {\r\n this._complex.error = {\r\n message: 'wrong number of atoms',\r\n };\r\n return;\r\n }\r\n\r\n this._complex.metadata.format = 'xyz';\r\n this._complex.name = comment;\r\n }\r\n\r\n _parseAtomsInf() {\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n\r\n const chain = this._complex.addChain('A');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0; i < this._atomsInf.length - 1; i++) {\r\n const words = this._atomsInf[i].split(/[\\s,]+/);\r\n\r\n if (words.length !== 4) {\r\n this._complex.error = {\r\n message: 'missed parameters',\r\n };\r\n break;\r\n }\r\n\r\n const serial = i + 1;\r\n const name = words[0];\r\n const xyz = new THREE.Vector3(parseFloat(words[1]), parseFloat(words[2]), parseFloat(words[3]));\r\n const type = Element.getByName(name);\r\n const role = undefined;\r\n\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n const molecule = new Molecule(this._complex, this._complex.name, 1);\r\n molecule.residues = residue;\r\n this._complex._molecules[0] = molecule;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n\r\n this._parseToAtomsInf(this._data);\r\n this._parseAtomsInf();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n return result;\r\n }\r\n\r\n static formats = ['xyz'];\r\n\r\n static extensions = ['.xyz'];\r\n}\r\n\r\nexport default XYZParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element } = chem;\r\n\r\nclass PubChemParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'pubchem+json';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && data[0] === '{';\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing PubChem JSON file...');\r\n return this._toComplex(JSON.parse(this._data));\r\n }\r\n\r\n _toComplex(jsonData) {\r\n const complex = new Complex();\r\n const complexData = jsonData.PC_Compounds && jsonData.PC_Compounds[0];\r\n if (complexData) {\r\n this._extractAtoms(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n }\r\n return complex;\r\n }\r\n\r\n _extractAtoms(complex, complexData) {\r\n let aids = complexData.atoms && complexData.atoms.aid;\r\n let elements = aids && complexData.atoms.element;\r\n if (!elements || aids.length !== elements.length) {\r\n throw new Error('Unable to parse atom elements');\r\n }\r\n elements = _.fromPairs(_.zip(aids, elements));\r\n const atoms = {};\r\n\r\n const coords = complexData.coords && complexData.coords[0];\r\n const model = coords && coords.conformers && coords.conformers[0];\r\n const xs = model && model.x;\r\n const ys = model && model.y;\r\n const zs = (model && model.z) || [];\r\n aids = coords && coords.aid;\r\n if (!aids || !xs || !ys) {\r\n throw new Error('Coordinates are not found in the file');\r\n }\r\n\r\n const chain = complex.addChain(' ');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0, n = aids.length; i < n; ++i) {\r\n const aid = aids[i];\r\n const element = Element.ByAtomicNumber[elements[aid]];\r\n const xyz = new THREE.Vector3(xs[i], ys[i], zs[i] || 0.0);\r\n atoms[aid] = residue.addAtom(element.name, element, xyz, undefined, true, aid, ' ', 1.0, 0.0, 0);\r\n }\r\n\r\n const aids1 = complexData.bonds && complexData.bonds.aid1;\r\n const aids2 = complexData.bonds && complexData.bonds.aid2;\r\n const orders = (complexData.bonds && complexData.bonds.order) || [];\r\n if (!aids1 || !aids2 || aids1.length !== aids2.length) {\r\n return;\r\n }\r\n\r\n for (let j = 0, m = aids1.length; j < m; ++j) {\r\n complex.addBond(atoms[aids1[j]], atoms[aids2[j]], orders[j] || 1, 0, true);\r\n }\r\n }\r\n}\r\n\r\nPubChemParser.formats = ['pubchem', 'pubchem+json', 'pc'];\r\nPubChemParser.extensions = ['.json'];\r\n\r\nexport default PubChemParser;\r\n","import _ from 'lodash';\r\n\r\nexport default class SDFStream {\r\n constructor(data) {\r\n this._strings = data.split(/\\r?\\n|\\r/);\r\n this._currentStart = 0;\r\n this._currentStringIndx = 0;\r\n }\r\n\r\n setStart(start) {\r\n if (start >= this._strings.length) {\r\n this._currentStart = this._strings.length - 1;\r\n this._currentStringIndx = this._strings.length - 1;\r\n } else {\r\n this._currentStart = start;\r\n this._currentStringIndx = start;\r\n }\r\n }\r\n\r\n getNextString() {\r\n return this._strings[++this._currentStringIndx];\r\n }\r\n\r\n getCurrentString() {\r\n return this._strings[this._currentStringIndx];\r\n }\r\n\r\n getStringFromStart(numb) {\r\n this._currentStringIndx = this._currentStart + numb;\r\n return this._strings[this._currentStart + numb];\r\n }\r\n\r\n findNextDataItem() {\r\n let curStr = this.getNextString();\r\n let res = false;\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n if (curStr.match(/>\\s+<(.*)>/)) {\r\n res = true;\r\n break;\r\n }\r\n curStr = this.getNextString();\r\n }\r\n\r\n return res;\r\n }\r\n\r\n findNextCompoundStart() {\r\n let curStr = this.getCurrentString();\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n curStr = this.getNextString();\r\n }\r\n this.setStart(++this._currentStringIndx);\r\n return this.probablyHaveDataToParse();\r\n }\r\n\r\n probablyHaveDataToParse() {\r\n return this._currentStringIndx < this._strings.length - 2;\r\n }\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport SDFStream from './SDFStream';\r\nimport Assembly from '../../chem/Assembly';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst chargeMap = [0, 3, 2, 1, 0, -1, -2, -3];\r\nconst orderMap = [0, 1, 2, 3, 1, 1, 1, 2];\r\nconst typeMap = [\r\n Bond.BondType.UNKNOWN, // 0 - error\r\n Bond.BondType.COVALENT, // 1 - single\r\n Bond.BondType.COVALENT, // 2 - double\r\n Bond.BondType.COVALENT, // 3 - triple\r\n Bond.BondType.AROMATIC, // 4 - aromatic\r\n Bond.BondType.UNKNOWN, // 5 - single or double\r\n Bond.BondType.AROMATIC, // 6 - single or aromatic\r\n Bond.BondType.AROMATIC, // 7 - double or aromatic\r\n // 8 - any\r\n // 9 - coordination\r\n // 10 - hydrogen\r\n];\r\n\r\nconst sdfAndMolRegexp = /.*(M\\s\\sEND).*|.*(^$$$$).*|.*>\\s+<(.+)>.*/;\r\nconst sdfRegExp = /.*($$$$).*|.*>\\s+<(.+)>.*/;\r\n\r\nconst fileFormat = { SDF: 'sdf', MOL: 'mol' };\r\n\r\nconst possibleNameTags = ['PUBCHEM_IUPAC_TRADITIONAL_NAME', /PUBCHEM_(.+)_NAME/, /(.+)name/, /(.+)NAME/];\r\nconst possibleIDTags = ['PUBCHEM_COMPOUND_CID', 'id', 'ID', /.*CID/, /.*ID/, /.*id/];\r\nconst possibleTitleTags = ['msg', 'MSG', 'message', 'title', 'description', 'desc'];\r\nconst tagsNames = ['name', 'id', 'title'];\r\nconst tags = { name: possibleNameTags, id: possibleIDTags, title: possibleTitleTags };\r\n\r\nfunction buildChainID(index) {\r\n if (!index) {\r\n return 'A';\r\n }\r\n\r\n const codes = [];\r\n while (index) {\r\n codes.push(65 + (index % 26));\r\n index = Math.trunc(index / 26);\r\n }\r\n if (codes.length > 1) {\r\n codes.reverse();\r\n codes[0] -= 1;\r\n }\r\n\r\n return String.fromCharCode(...codes);\r\n}\r\n\r\nexport default class SDFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._format = 'sdf';\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._molecules = null;\r\n this._metadata = {};\r\n this._metadata.molecules = [];\r\n this._currentMolProps = {};\r\n this._compoundIndx = -1;\r\n this._assemblies = [];\r\n this._atomsParsed = 0;\r\n this._atomsIndexes = [];\r\n }\r\n\r\n canProbablyParse(data) {\r\n return _.isString(data) && sdfAndMolRegexp.test(data);\r\n }\r\n\r\n _parseHeader(stream) {\r\n const molecule = {};\r\n molecule.name = stream.getStringFromStart(0);\r\n const date = parseInt(stream.getStringFromStart(1).substr(10, 6).trim(), 10);\r\n molecule.date = date.toString() || '';\r\n molecule.title = stream.getStringFromStart(2);\r\n this._metadata.molecules.push(molecule);\r\n }\r\n\r\n _parseAtoms(stream, atomsNum) {\r\n let curStr;\r\n let serial = this._atomsParsed;\r\n\r\n // each molecule = chain\\residue\r\n const chainID = buildChainID(this._compoundIndx);\r\n const resName = 'UNK';\r\n const resSeq = 1;\r\n\r\n this._chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = this._chain.addResidue(resName, resSeq, ' ');\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n curStr = stream.getNextString();\r\n serial++;\r\n const x = parseFloat(curStr.substr(0, 10));\r\n const y = parseFloat(curStr.substr(10, 10));\r\n const z = parseFloat(curStr.substr(20, 10));\r\n const charge = chargeMap[parseInt(curStr.substr(36, 3), 10)];\r\n const xyz = new THREE.Vector3(x, y, z);\r\n let name = curStr.substr(31, 3).trim().toUpperCase();\r\n const type = Element.getByName(name);\r\n if (!this._atomsIndexes[name]) {\r\n this._atomsIndexes[name] = 0;\r\n }\r\n this._atomsIndexes[name] += 1;\r\n name += this._atomsIndexes[name]; // every atom need to have unique name.\r\n\r\n this._residue.addAtom(name, type, xyz, undefined, true, serial, ' ', 1.0, 0.0, charge);\r\n }\r\n }\r\n\r\n _parseBonds(stream, bondsNum) {\r\n let curStr;\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n curStr = stream.getNextString();\r\n let atom1 = parseInt(curStr.substr(0, 3), 10) + this._atomsParsed;\r\n let atom2 = parseInt(curStr.substr(3, 3), 10) + this._atomsParsed;\r\n const bondType = parseInt(curStr.substr(6, 3), 10);\r\n\r\n if (atom1 > atom2) {\r\n [atom1, atom2] = [atom2, atom1];\r\n }\r\n this._complex.addBond(\r\n atom1,\r\n atom2,\r\n orderMap[bondType] || 1,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _parseMOL(stream) {\r\n this._compoundIndx++;\r\n\r\n this._parseHeader(stream);\r\n const countsLine = stream.getStringFromStart(3);\r\n const atomsNum = parseInt(countsLine.substr(0, 3), 10);\r\n const bondsNum = parseInt(countsLine.substr(3, 3), 10);\r\n this._parseAtoms(stream, atomsNum);\r\n this._parseBonds(stream, bondsNum);\r\n\r\n this._atomsParsed += atomsNum;\r\n\r\n this._metadata.molecules[this._compoundIndx]._residues = [];\r\n this._metadata.molecules[this._compoundIndx]._residues.push(this._residue);\r\n }\r\n\r\n _parseDataItem(stream) {\r\n const tag = stream.getCurrentString();\r\n\r\n let data = [];\r\n let curStr = stream.getNextString();\r\n\r\n // read data\r\n while (curStr.trim() !== '') {\r\n data.push(curStr);\r\n curStr = stream.getNextString();\r\n }\r\n if (data.length === 1) {\r\n [data] = data;\r\n }\r\n this._currentMolProps[tag.replace(/[<>]/g, '').trim()] = data;\r\n }\r\n\r\n _parseCompound(stream) {\r\n this._parseMOL(stream);\r\n\r\n // parse data items block\r\n if (this._format === fileFormat.SDF) {\r\n this._currentMolProps = {};\r\n while (stream.findNextDataItem()) {\r\n this._parseDataItem(stream);\r\n }\r\n if (Object.keys(this._currentMolProps).length !== 0) {\r\n const molecule = this._metadata.molecules[this._compoundIndx];\r\n molecule.props = this._currentMolProps;\r\n this._tryToUpdateMoleculeData(molecule);\r\n }\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n console.log('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _buildAssemblies() {\r\n const chains = this._complex._chains;\r\n\r\n if (chains.length === 1) {\r\n return this._assemblies;\r\n }\r\n\r\n for (let i = 0; i < chains.length; i++) {\r\n const assembly = new Assembly(this._complex);\r\n const matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n assembly.addChain(chains[i]._name);\r\n this._assemblies.push(assembly);\r\n }\r\n\r\n return this._assemblies;\r\n }\r\n\r\n _buildMolecules() {\r\n this._complex._molecules = [];\r\n const { molecules } = this._metadata;\r\n for (let i = 0; i < molecules.length; i++) {\r\n const molecule = new Molecule(this._complex, molecules[i].name, i + 1);\r\n molecule.residues = molecules[i]._residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n\r\n return this._complex._molecules;\r\n }\r\n\r\n _searchTag(tag, props) {\r\n for (let i = 0; i < props.length; i++) {\r\n if ((tag instanceof RegExp && tag.test(props[i].tag)) || tag === props[i].tag) {\r\n return props[i].data;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToFind(tagsList, props) {\r\n for (let j = 0; j < tagsList.length; j++) {\r\n const res = this._searchTag(tagsList[j], props);\r\n if (res) {\r\n return res;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToUpdateMoleculeData(molecule) {\r\n let res = false;\r\n for (let i = 0; i < tagsNames.length; i++) {\r\n const tagPossibleNames = tags[tagsNames[i]];\r\n const data = this._tryToFind(tagPossibleNames, molecule.props);\r\n if (data) {\r\n molecule[tagsNames[i]] = data;\r\n res = true;\r\n }\r\n }\r\n\r\n molecule.name = molecule.name || molecule.id;\r\n if (molecule.name.match(/^\\d+$/)) {\r\n molecule.name = `CID: ${molecule.name}`;\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _finalizeMetadata() {\r\n const { molecules } = this._metadata;\r\n const { metadata } = this._complex;\r\n const complex = this._complex;\r\n\r\n if (molecules.length === 1) {\r\n complex.name = molecules[0].name;\r\n metadata.title = molecules[0].title;\r\n metadata.date = molecules[0].date;\r\n metadata.properties = molecules[0].props;\r\n } else if (molecules.length > 1) {\r\n metadata.molecules = [];\r\n for (let i = 0; i < molecules.length; i++) {\r\n metadata.molecules.push({\r\n name: molecules[i].name, date: molecules[i].date, title: molecules[i].title, properties: molecules[i].props,\r\n });\r\n }\r\n }\r\n }\r\n\r\n _finalize() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n this._complex._finalizeBonds();\r\n this._fixBondsArray();\r\n this._finalizeMetadata();\r\n this._buildAssemblies();\r\n this._complex.units = this._complex.units.concat(this._assemblies);\r\n this._buildMolecules();\r\n this._complex.finalize({\r\n needAutoBonding: false, detectAromaticLoops: false, enableEditing: false, serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n defineFormat(data) {\r\n let format;\r\n if (sdfRegExp.test(data)) {\r\n format = fileFormat.SDF;\r\n } else {\r\n format = fileFormat.MOL;\r\n }\r\n\r\n return format;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const stream = new SDFStream(this._data);\r\n\r\n this._format = this.defineFormat(this._data);\r\n result.metadata.format = this._format;\r\n\r\n do {\r\n this._parseCompound(stream);\r\n } while (stream.findNextCompoundStart());\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nSDFParser.formats = ['mol', 'sdf'];\r\nSDFParser.extensions = ['.mol', '.sdf'];\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\n// http://www.uoxray.uoregon.edu/tnt/manual/node104.html\r\nconst DSN6Header = {\r\n nstart: [valueType.array, 'i16', 0],\r\n extent: [valueType.array, 'i16', 3],\r\n grid: [valueType.array, 'i16', 6],\r\n cellDims: [valueType.vector, 'i16', 9],\r\n angles: [valueType.array, 'i16', 12],\r\n div: [valueType.singular, 'i16', 15],\r\n adder: [valueType.singular, 'i16', 16],\r\n scaleFactor: [valueType.singular, 'i16', 17],\r\n};\r\n\r\nclass DSN6Model extends VolumeModel {\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n\r\n const arrays = {};\r\n arrays.i16 = new Int16Array(this._buff);\r\n\r\n // check and reverse if big endian\r\n if (arrays.i16[18] !== 100) {\r\n for (let i = 0, n = arrays.i16.length; i < n; ++i) {\r\n const val = arrays.i16[i];\r\n arrays.i16[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff);\r\n }\r\n }\r\n if (arrays.i16[18] !== 100) {\r\n throw new Error('DSN6: Incorrect format ');\r\n }\r\n\r\n const header = this._header;\r\n\r\n this._fillHeader(DSN6Header, arrays);\r\n header.cellDims.multiplyScalar(1.0 / header.scaleFactor);\r\n header.angles.forEach((angle, i, a) => { a[i] *= (Math.PI / 180.0) / header.scaleFactor; });\r\n header.div /= 100;\r\n }\r\n\r\n _setAxisIndices() {\r\n this._xyz2crs[0] = 0;\r\n this._xyz2crs[1] = 1;\r\n this._xyz2crs[2] = 2;\r\n }\r\n\r\n _setOrigins() {\r\n const header = this._header;\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n this._origin.addScaledVector(xaxis, header.nstart[0]);\r\n this._origin.addScaledVector(yaxis, header.nstart[1]);\r\n this._origin.addScaledVector(zaxis, header.nstart[2]);\r\n\r\n xaxis.multiplyScalar(header.extent[0]);\r\n yaxis.multiplyScalar(header.extent[1]);\r\n zaxis.multiplyScalar(header.extent[2]);\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _pointCalculate(xyzData, byteBuffer, z, y, x, pos, i) {\r\n const header = this._header;\r\n\r\n if (x < header.extent[0] && y < header.extent[1] && z < header.extent[2]) {\r\n const idx = x + header.extent[0] * (y + header.extent[1] * z);\r\n xyzData[idx] = (byteBuffer[pos.counter] - header.adder) / header.div;\r\n ++pos.counter;\r\n } else {\r\n pos.counter += 8 - i;\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n _blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos) {\r\n for (let k = 0; k < 8; ++k) {\r\n const z = 8 * zBlock + k;\r\n for (let j = 0; j < 8; ++j) {\r\n const y = 8 * yBlock + j;\r\n let inRange = true;\r\n let i = 0;\r\n while (inRange && i < 8) {\r\n const x = 8 * xBlock + i;\r\n inRange = this._pointCalculate(xyzData, byteBuffer, z, y, x, pos, i);\r\n i++;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const byteBuffer = new Uint8Array(this._buff);\r\n const xyzData = new Float32Array(header.extent[0] * header.extent[1] * header.extent[2]);\r\n\r\n const blocks = new THREE.Vector3(header.extent[0] / 8, header.extent[1] / 8, header.extent[2] / 8);\r\n\r\n const pos = {};\r\n pos.counter = 512;\r\n\r\n for (let zBlock = 0; zBlock < blocks.z; ++zBlock) {\r\n for (let yBlock = 0; yBlock < blocks.y; ++yBlock) {\r\n for (let xBlock = 0; xBlock < blocks.x; ++xBlock) {\r\n this._blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos);\r\n }\r\n }\r\n }\r\n this._calculateInfoParams(xyzData);\r\n return xyzData;\r\n }\r\n\r\n _calculateInfoParams(xyzData) {\r\n this._header.dmean /= xyzData.length;\r\n let dispersion = 0;\r\n let minDensity = xyzData[0];\r\n let maxDensity = xyzData[0];\r\n for (let j = 0; j < xyzData.length; j++) {\r\n dispersion += (this._header.dmean - xyzData[j]) ** 2;\r\n\r\n if (xyzData[j] < minDensity) {\r\n minDensity = xyzData[j];\r\n }\r\n if (xyzData[j] > maxDensity) {\r\n maxDensity = xyzData[j];\r\n }\r\n }\r\n this._header.sd = Math.sqrt(dispersion / xyzData.length);\r\n this._header.dmax = maxDensity;\r\n this._header.dmin = minDensity;\r\n }\r\n}\r\n\r\nclass DSN6Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'dsn6';\r\n this.model = new DSN6Model();\r\n }\r\n\r\n static canParse(data, options) {\r\n if (!data) {\r\n return false;\r\n }\r\n return data instanceof ArrayBuffer && Parser.checkDataTypeOptions(options, 'dsn6');\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false;\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nDSN6Parser.formats = ['dsn6'];\r\nDSN6Parser.extensions = ['.dsn6', '.omap'];\r\nDSN6Parser.binary = true;\r\n\r\nexport default DSN6Parser;\r\n","import PDBStream from './PDBStream';\r\n\r\n/**\r\n * Little helper class for GRO Parser usage.\r\n * @extends PDBStream\r\n */\r\nclass GROReader extends PDBStream {\r\n constructor(data) {\r\n super(data);\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n this.next();\r\n }\r\n\r\n /**\r\n * Getting end of string.\r\n * @returns {Number} Pointer to end of string\r\n */\r\n getNext() {\r\n return this._next;\r\n }\r\n}\r\n\r\nexport default GROReader;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport GROReader from './GROReader';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Molecule,\r\n} = chem;\r\n\r\n/**\r\n * Gromos87 file format parser.\r\n * @extends Parser\r\n */\r\nclass GROParser extends Parser {\r\n /**\r\n * Create parser for .gro file format\r\n *\r\n * @param {String} data Input file\r\n * @param {String} options Input options (optional field)\r\n */\r\n constructor(data, options) {\r\n super(data, options);\r\n /** @type Date */\r\n this._time = null; // Time in ps, optional field for animations\r\n /** @type Number */\r\n this._numAtoms = null; // Number of atoms in complex\r\n /** @type Number */\r\n this._residueNumber = null; // Number of exact residue\r\n /** @type String */\r\n this._residueName = ''; // Scientific name of exact residue\r\n /** @type String */\r\n this._atomName = ''; // Scientific name of exact atom\r\n /** @type Number */\r\n this._atomNumber = null; // Sorted number of exact atom\r\n /** @type Array */\r\n this._atomPosition = []; // Array which contains x, y, z position of exact atom\r\n /** @type Array */\r\n this._atomVelocity = []; // Array which contains x, y, z velocity of exact atom (optional)\r\n /** @type Complex */\r\n this._complex = null; // Complex structure for unified molecule representation\r\n /** @type Vector3 */\r\n this._molecules = []; // Molecules array\r\n /** @type Molecule */\r\n this._molecule = null; // Single molecule\r\n /** @type String */\r\n this._options.filetype = 'gro'; // Extension of data file.\r\n }\r\n\r\n /**\r\n * General check for possibility of parsing.\r\n * @param {String} data - Input file\r\n * @returns {boolean} true if this file is in ascii, false otherwise\r\n */\r\n canProbablyParse(data) {\r\n return _.isString(this._data) && /^\\s*[^\\n]*\\n\\s*\\d+ *\\n\\s*\\d+[^\\n\\d]{3}\\s*\\w+\\s*\\d+\\s*-?\\d/.test(data);\r\n }\r\n\r\n /**\r\n * Parsing title of molecule complex.\r\n * NOTE: that names are ESTIMATES, there is no strict rules in Gromos87 standard for first line in input file.\r\n * @param {GROReader} line - Line containing title and time.\r\n */\r\n _parseTitle(line) {\r\n const { metadata } = this._complex;\r\n metadata.id = line.readLine().trim();\r\n metadata.name = metadata.id.slice(metadata.id.lastIndexOf('\\\\') + 1, metadata.id.lastIndexOf('.'));\r\n metadata.format = 'gro';\r\n }\r\n\r\n /**\r\n * Parsing line containing number of atoms information.\r\n * @param {GROReader} line - Line containing number of atoms.\r\n */\r\n _parseNumberOfAtoms(line) {\r\n this._numAtoms = line.readInt(0, line.getNext());\r\n if (Number.isNaN(this._numAtoms)) {\r\n throw new Error('Line 2 is not representing atom number. Consider checking input file');\r\n }\r\n }\r\n\r\n /**\r\n * Parsing line containing information about residues, atoms etc. Also information about box vectors.\r\n * Format of atoms MUST (by Gromos87 standard) be this: (note that numbering starts not from 0, but from 1!)\r\n * ResidueNumber[1 - 5] ResidueName[6 - 10] AtomName[11 - 15] AtomNumber[16 - 20] Position[21 - 45] Velocity[46 - 69]\r\n * @param {GROReader} line - Line containing information about atom.\r\n */\r\n _parseAtom(line) {\r\n this._residueNumber = line.readInt(1, 5);\r\n this._residueName = line.readString(6, 10).trim();\r\n this._atomName = line.readString(11, 15).trim();\r\n this._atomNumber = line.readInt(16, 20);\r\n const positionX = line.readFloat(21, 28) * 10;\r\n const positionY = line.readFloat(29, 36) * 10;\r\n const positionZ = line.readFloat(37, 45) * 10;\r\n if (Number.isNaN(positionX) || Number.isNaN(positionY) || Number.isNaN(positionZ)) {\r\n this._complex.error = {\r\n message: `Atom position is invalid in \"${line.readLine()}\"`,\r\n };\r\n return;\r\n }\r\n /* const velocityX = line.readFloat(46, 53);\r\n const velocityY = line.readFloat(54, 61);\r\n const velocityZ = line.readFloat(62, 69); */\r\n /* Adding residue and atom to complex structure */\r\n const type = Element.getByName(this._atomName[0]); /* MAGIC 0. REASONS: This name is something like \"CA\", where\r\n C - is an element an A is something else. But what about Calcium? */\r\n if (type.fullName === 'Unknown') {\r\n this._complex.error = {\r\n message: `${this._atomName[0]} hasn't been recognised as an atom name.`,\r\n };\r\n return;\r\n }\r\n const role = Element.Role[this._atomName];\r\n /* Firstly, create a dummy chain */\r\n let chain = this._chain;\r\n if (!chain) {\r\n this._chain = chain = this._complex.addChain('A');\r\n }\r\n /* Secondly, add residue to that chain */\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== this._residueNumber) {\r\n this._residue = residue = chain.addResidue(this._residueName, this._residueNumber, ' ');\r\n }\r\n /* Lastly, add atom to that residue */\r\n this._atomPosition = new THREE.Vector3(positionX, positionY, positionZ);\r\n /* Adding default constants to correct atom addition process */\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n residue.addAtom(this._atomName, type, this._atomPosition, role, het, this._atomNumber, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n /**\r\n * Some finalizing procedures. In '.gro' file format there is only 1 chain and 1 molecule.\r\n */\r\n _finalize() {\r\n const molecule = new Molecule(this._complex, this._complex.metadata.name, 1);\r\n // aggregate residues from chain\r\n molecule.residues = this._chain._residues;\r\n molecule._chains = this._chain;\r\n this._complex._molecules[0] = molecule;\r\n this._molecules.push(molecule);\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n /**\r\n * Main parsing procedure.\r\n * @returns {Complex} Complex structure for visualizing.\r\n */\r\n parseSync() {\r\n /* Create \"Complex\" variable */\r\n const result = this._complex = new Complex();\r\n /* Parse input file line-by-line */\r\n const reader = new GROReader(this._data);\r\n let counter = 0; /* Simple counter regarding to format of .gro file */\r\n /* First two lines - technical information, other lines - Atoms */\r\n this._parseTitle(reader);\r\n reader.next();\r\n this._parseNumberOfAtoms(reader);\r\n reader.next();\r\n for (counter = 0; counter < this._numAtoms; ++counter) {\r\n if (!reader.end()) {\r\n this._parseAtom(reader);\r\n reader.next();\r\n } else break;\r\n }\r\n /* If number of atoms in second line is less then actual atoms in file */\r\n if (counter < this._numAtoms) {\r\n this._complex.error = {\r\n message: 'File ended unexpectedly.',\r\n };\r\n }\r\n /* Catch errors occurred in parsing process */\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n\r\n /* Finalizing data */\r\n this._finalize();\r\n\r\n /* Cleaning up */\r\n this._atomPosition = null;\r\n this._complex = null;\r\n this._molecules = null;\r\n this._molecule = null;\r\n\r\n /* Return resulting Complex variable */\r\n return result;\r\n }\r\n}\r\n\r\nGROParser.formats = ['gro'];\r\nGROParser.extensions = ['.gro'];\r\n\r\nexport default GROParser;\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst orderMap = {\r\n un: 0,\r\n 1: 1,\r\n 2: 2,\r\n 3: 3,\r\n ar: 1,\r\n am: 1,\r\n nc: 0,\r\n du: 1,\r\n};\r\nconst typeMap = {\r\n un: Bond.BondType.UNKNOWN, // unknown (cannot be determined from the parameter tables)\r\n 1: Bond.BondType.COVALENT, // single\r\n 2: Bond.BondType.COVALENT, // double\r\n 3: Bond.BondType.COVALENT, // triple\r\n ar: Bond.BondType.AROMATIC, // aromatic\r\n am: Bond.BondType.COVALENT, // amide\r\n nc: Bond.BondType.UNKNOWN, // not connected\r\n du: Bond.BondType.COVALENT, // dummy\r\n};\r\n\r\nconst resNumberRegex = /\\d+$/;\r\nconst spacesRegex = /\\s+/;\r\n\r\nfunction splitToFields(str) {\r\n return str.trim().split(spacesRegex);\r\n}\r\n/* There is no jsdoc documentation because of eslint corrections:\r\n * not all Parser methods are implemented\r\n */\r\n\r\nclass MOL2Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._compoundIndx = -1;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n\r\n this._currPosIdx = 0;\r\n this._currStartIdx = 0;\r\n\r\n this._serialAtomMap = {};\r\n\r\n this._options.fileType = 'mol2';\r\n }\r\n\r\n _parseRawStrings(data) {\r\n return data.split(/\\r?\\n|\\r/);\r\n }\r\n\r\n _toStringFromStart(numb, MOL2Data) {\r\n const newPosIdx = this._currStartIdx + numb;\r\n this._currPosIdx = (newPosIdx < MOL2Data.length) ? newPosIdx : this._currStartIdx;\r\n }\r\n\r\n _toHeaderString(header, MOL2Data) {\r\n this._toStringFromStart(0, MOL2Data);\r\n while (this._currPosIdx < MOL2Data.length) {\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`)) {\r\n return;\r\n }\r\n this._currPosIdx++;\r\n }\r\n this._toStringFromStart(0, MOL2Data);\r\n }\r\n\r\n _toStringFromHeader(header, numb, MOL2Data) {\r\n this._toHeaderString(header, MOL2Data);\r\n const newPosIdx = this._currPosIdx + numb;\r\n\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`) && newPosIdx < MOL2Data.length) {\r\n this._currPosIdx = newPosIdx;\r\n }\r\n }\r\n\r\n _setStart(startPos, MOL2Data) {\r\n if (startPos >= MOL2Data.length) {\r\n this._currStartIdx = this._currPosIdx = MOL2Data.length - 1;\r\n } else {\r\n this._currStartIdx = this._currPosIdx = startPos;\r\n }\r\n }\r\n\r\n _probablyHaveDataToParse(MOL2Data) {\r\n return this._currPosIdx < MOL2Data.length - 2;\r\n }\r\n\r\n _findNextCompoundStart(MOL2Data) {\r\n while (this._currPosIdx < MOL2Data.length && MOL2Data[this._currPosIdx].trim() !== '@MOLECULE>') {\r\n this._currPosIdx++;\r\n }\r\n this._setStart(++this._currPosIdx, MOL2Data);\r\n return this._probablyHaveDataToParse(MOL2Data);\r\n }\r\n\r\n _parseMolecule(MOL2Data) {\r\n this._toHeaderString('MOLECULE', MOL2Data);\r\n\r\n const { metadata } = this._complex;\r\n metadata.name = MOL2Data[++this._currPosIdx];\r\n metadata.format = 'mol2';\r\n\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = this._compoundIndx + 1;\r\n this._molecules.push(this._molecule);\r\n }\r\n\r\n /* Atom format description:\r\n * atomId atomName x y z element [resSeq [resName [charge [statusBit]]]]\r\n * statusBits is the internal SYBYL status bits associated with the atom.\r\n * These should never be set by the user.\r\n * Source: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf\r\n */\r\n _parseAtoms(atomsNum, MOL2Data) {\r\n this._toHeaderString('ATOM', MOL2Data);\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 6) {\r\n throw new Error('MOL2 parsing error: Not enough information to create atom!');\r\n }\r\n const atomId = parseInt(parsedStr[0], 10);\r\n const atomName = parsedStr[1];\r\n\r\n const x = parseFloat(parsedStr[2]);\r\n const y = parseFloat(parsedStr[3]);\r\n const z = parseFloat(parsedStr[4]);\r\n\r\n const element = parsedStr[5].split('.')[0].toUpperCase();\r\n\r\n let charge = 0;\r\n if (parsedStr.length >= 9) {\r\n charge = parseFloat(parsedStr[8]) || 0.0;\r\n }\r\n\r\n let chain = this._chain;\r\n if (!chain) {\r\n // .mol2 may contain information about multiple molecules, but they can't be visualized\r\n // at the same time now. There is no need to create different chain IDs then.\r\n this._chain = chain = this._complex.getChain('A') || this._complex.addChain('A');\r\n this._residue = null;\r\n }\r\n if (!this._setResidue(parsedStr)) {\r\n continue;\r\n }\r\n\r\n // These fields are not listed in mol2 format. Set them default.\r\n // Atoms and het atoms doesn't differ in .mol2,\r\n // but het atoms have special residues. It can be used in next updates\r\n const het = false;\r\n const altLoc = ' ';\r\n const occupancy = 1.0;\r\n const tempFactor = 0.0;\r\n const type = Element.getByName(element);\r\n const role = Element.Role[atomName];\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n this._residue.addAtom(atomName, type, xyz, role, het, atomId, altLoc, occupancy, tempFactor, charge);\r\n }\r\n }\r\n\r\n _setResidue(parsedStr) {\r\n let resSeq = 1;\r\n let resName = 'UNK'; // The same meaning has '<0>' in some mol2 files\r\n\r\n if (parsedStr.length >= 7) {\r\n resSeq = parseInt(parsedStr[6], 10);\r\n }\r\n if (parsedStr.length >= 8 && parsedStr[7] !== '<0>') {\r\n resName = parsedStr[7].replace(resNumberRegex, '');\r\n }\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return false;\r\n }\r\n }\r\n const residue = this._residue;\r\n const chain = this._chain;\r\n if (!residue || residue.getSequence() !== resSeq) {\r\n this._residue = chain.addResidue(resName, resSeq, 'A');\r\n }\r\n return true;\r\n }\r\n\r\n /* Bond format description\r\n * bondId originAtomId targetAtomId bondType [statusBits]\r\n */\r\n _parseBonds(bondsNum, MOL2Data) {\r\n this._toHeaderString('BOND', MOL2Data);\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 3) {\r\n throw new Error('MOL2 parsing error: Missing information about bonds!');\r\n }\r\n\r\n let originAtomId = parseInt(parsedStr[1], 10);\r\n let targetAtomId = parseInt(parsedStr[2], 10);\r\n const bondType = parsedStr[3];\r\n\r\n if (originAtomId > targetAtomId) {\r\n [originAtomId, targetAtomId] = [targetAtomId, originAtomId];\r\n }\r\n this._complex.addBond(\r\n originAtomId,\r\n targetAtomId,\r\n orderMap[bondType] || 0,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _fixSerialAtoms() {\r\n const atoms = this._complex._atoms;\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n this._serialAtomMap[atom.serial] = atom;\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n if (Object.keys(serialAtomMap).length === 0) {\r\n throw new Error('MOL2 parsing error: Missing atom information!');\r\n }\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _finalizeMolecules() {\r\n // Get chain from complex\r\n const chain = this._complex._chains[0];\r\n this._complex._molecules = [];\r\n\r\n // Aggregate residues from chains\r\n // (to be precise from the chain 'A')\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const currMolecule = this._molecules[i];\r\n const molResidues = chain._residues;\r\n const molecule = new Molecule(this._complex, currMolecule._name, i + 1);\r\n molecule.residues = molResidues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _finalize() {\r\n this._complex._finalizeBonds();\r\n this._fixSerialAtoms();\r\n this._fixBondsArray();\r\n this._finalizeMolecules();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _parseCompound(MOL2Data) {\r\n this._compoundIndx++;\r\n this._parseMolecule(MOL2Data);\r\n\r\n // Ignoring comments and everything before @MOLECULE block\r\n this._toStringFromHeader('MOLECULE', 2, MOL2Data);\r\n\r\n const parsedStr = MOL2Data[this._currPosIdx].trim().split(spacesRegex);\r\n const atomsNum = parsedStr[0];\r\n const bondsNum = parsedStr[1];\r\n\r\n this._parseAtoms(atomsNum, MOL2Data);\r\n this._parseBonds(bondsNum, MOL2Data);\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const MOL2Data = this._parseRawStrings(this._data);\r\n do {\r\n this._parseCompound(MOL2Data);\r\n } while (this._findNextCompoundStart(MOL2Data));\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nMOL2Parser.formats = ['mol2'];\r\nMOL2Parser.extensions = ['.mol2', '.ml2', '.sy2'];\r\n\r\nexport default MOL2Parser;\r\n","import ParserList from './parsers/ParserList';\r\n\r\nimport PDBParser from './parsers/PDBParser';\r\nimport CMLParser from './parsers/CMLParser';\r\nimport MMTFParser from './parsers/MMTFParser';\r\nimport CIFParser from './parsers/CIFParser';\r\nimport CCP4Parser from './parsers/CCP4Parser';\r\nimport XYZParser from './parsers/XYZParser';\r\nimport PubChemParser from './parsers/PubChemParser';\r\nimport SDFParser from './parsers/SDFParser';\r\nimport DSN6Parser from './parsers/DSN6Parser';\r\nimport GROParser from './parsers/GROParser';\r\nimport MOL2Parser from './parsers/MOL2Parser';\r\n\r\nexport default new ParserList([\r\n // note: order might be important\r\n PDBParser,\r\n CIFParser,\r\n MMTFParser,\r\n XYZParser,\r\n CMLParser,\r\n PubChemParser,\r\n SDFParser,\r\n CCP4Parser,\r\n DSN6Parser,\r\n GROParser,\r\n MOL2Parser,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available exporters.\r\n * @extends EntityList\r\n */\r\nclass ExporterList extends EntityList {\r\n /**\r\n * Create a list of exporters.\r\n * The exporters are indexed by supported data formats (`.formats` and\r\n * `.extensions` properties of a Exporter subclass).\r\n * The Exporters can be retrieved later by matching against specs (see {@link ExporterList#find}).\r\n *\r\n * @param {!Array=} someExporters A list of {@link Exporter} subclasses to\r\n * automatically register at creation time.\r\n * @see ExporterList#register\r\n */\r\n constructor(someExporters = []) {\r\n super(someExporters, ['formats']);\r\n }\r\n\r\n /**\r\n * Find a suitable exporter for data.\r\n *\r\n * @param {Object} specs Exporter specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {*=} specs.data Data to export.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ExporterList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Exporter {\r\n constructor(source, options) {\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n exportSync() {\r\n throw new Error('Exporting to this source is not implemented');\r\n }\r\n\r\n export() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Export aborted'));\r\n }\r\n return resolve(this.exportSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Exporter.prototype);\r\n","import _ from 'lodash';\r\nimport { Matrix4 } from 'three';\r\n\r\nexport default class PDBResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._currentStr = -1;\r\n this._tag = null;\r\n this._fixedNumeration = false;\r\n this._numeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n\r\n getResult() {\r\n this.writeString('\\n', 81, 81);\r\n return this._resultArray.join('');\r\n }\r\n\r\n _currentStrLength() {\r\n const curStr = this._resultArray[this._currentStr];\r\n return curStr ? curStr.length : 0;\r\n }\r\n\r\n // numeration can be number or boolean\r\n // if numeration is number then just put this number to 8-10 pos in string\r\n // if numeration is boolean then increase number for all new strings\r\n newTag(tag, numeration) {\r\n if (!tag) {\r\n this._tag = null;\r\n } else {\r\n this._tag = tag;\r\n }\r\n if (!_.isUndefined(numeration)) {\r\n if (_.isNumber(numeration)) {\r\n this._tagStrNum = numeration;\r\n this._numeration = true;\r\n this._fixedNumeration = true;\r\n } else if (_.isBoolean(numeration)) {\r\n this._tagStrNum = 0;\r\n this._numeration = numeration;\r\n this._fixedNumeration = false;\r\n }\r\n } else {\r\n this._numeration = false;\r\n this._fixedNumeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n }\r\n\r\n newString(tag) {\r\n this.writeString('\\n', 81, 81);\r\n this._currentStr++;\r\n this._resultArray.push('');\r\n\r\n if (tag) {\r\n this.writeString(tag, 1, 6);\r\n } else if (this._tag) {\r\n this.writeString(this._tag, 1, 6);\r\n }\r\n\r\n if (this._numeration) {\r\n if (!this._fixedNumeration) {\r\n this._tagStrNum++;\r\n }\r\n if (this._tagStrNum !== 1) {\r\n this.writeString(this._tagStrNum.toString(), 10, 8);\r\n }\r\n }\r\n }\r\n\r\n writeEntireString(string, maxStrPos, concat) {\r\n if (!maxStrPos) {\r\n maxStrPos = 81;\r\n }\r\n for (let j = 0; j < string.length; j++) {\r\n if (this._currentStrLength() === maxStrPos && j !== string.length - 1) {\r\n this.newString();\r\n if (concat) { // pretty hardcoddy\r\n this.writeString(concat.tag, concat.begin, concat.end);\r\n }\r\n }\r\n if (string[j] === '\\n') {\r\n this.newString();\r\n } else {\r\n this.writeString(string[j]);\r\n }\r\n }\r\n }\r\n\r\n writeString(string, begin, end) {\r\n let curStr = this._resultArray[this._currentStr];\r\n let str;\r\n\r\n const curStrLength = curStr ? curStr.length : 0;\r\n\r\n if (_.isUndefined(string)) {\r\n return;\r\n }\r\n\r\n if (!_.isNumber(begin)) {\r\n begin = curStrLength + 1;\r\n }\r\n\r\n if (!_.isNumber(end)) {\r\n end = curStrLength + string.length;\r\n }\r\n\r\n if (!_.isString(string)) {\r\n str = string.toString();\r\n } else {\r\n str = string;\r\n }\r\n\r\n const finish = begin < end ? end : begin;\r\n const start = begin < end ? begin : end;\r\n\r\n if (str.length > Math.abs(begin - end) + 1) {\r\n str = str.substr(0, Math.abs(begin - end + 1));\r\n }\r\n\r\n // spaces before start of new data\r\n if (start > curStrLength + 1) {\r\n this._resultArray[this._currentStr] += ' '.repeat(start - curStrLength - 1);\r\n } else if (start <= curStrLength) {\r\n const cStr = this._resultArray[this._currentStr];\r\n this._resultArray[this._currentStr] = cStr.slice(0, start - 1);\r\n }\r\n\r\n // if reverse order\r\n // reverse order of end and begin means that user wants to align text right\r\n if (end < begin) {\r\n const len = begin - end + 1;\r\n str = ' '.repeat(len - str.length) + str;\r\n }\r\n\r\n // some hardcode fix for space between string numeration and data\r\n // (see pdb file format description)\r\n if (start === 11 && this._numeration && this._tagStrNum !== 1) {\r\n str = ` ${str}`;\r\n }\r\n\r\n // append new data to string\r\n this._resultArray[this._currentStr] += str;\r\n curStr = this._resultArray[this._currentStr];\r\n\r\n if (finish > curStr.length) {\r\n this._resultArray[this._currentStr] += ' '.repeat(finish - curStr.length);\r\n }\r\n }\r\n\r\n writeBondsArray(bonds, atom) {\r\n const bondsArrays = this._getSubArrays(bonds, 4);\r\n\r\n for (let k = 0; k < bondsArrays.length; k++) {\r\n this.newString();\r\n this.writeString(atom.serial, 11, 7);\r\n\r\n for (let j = 0; j < bondsArrays[k].length; j++) {\r\n const serial = (bondsArrays[k][j]._left.serial === atom.serial)\r\n ? bondsArrays[k][j]._right.serial : bondsArrays[k][j]._left.serial;\r\n\r\n this.writeString(serial, 16 + 5 * j, 12 + 5 * j);\r\n }\r\n }\r\n }\r\n\r\n _getSubArrays(arr, subArraySize) {\r\n const subArrays = [];\r\n for (let i = 0; i < arr.length; i += subArraySize) {\r\n subArrays.push(arr.slice(i, i + subArraySize));\r\n }\r\n return subArrays;\r\n }\r\n\r\n // function for writing matrix in Remark290 and Remark350 tags\r\n // (see pdb file description)\r\n writeMatrix(matrix, matrixIndx, tag) {\r\n for (let j = 0; j < 3; j++) {\r\n this.newString();\r\n this.writeString(tag, 14, 18);\r\n this.writeString((j + 1).toString(), 19, 19);\r\n this.writeString(matrixIndx.toString(), 23, 20);\r\n for (let k = 0; k < 3; k++) {\r\n const numb = parseFloat(matrix.elements[j * 4 + k]).toFixed(6);\r\n this.writeString(numb.toString(), 33 + k * 10, 24 + k * 10);\r\n }\r\n\r\n const numb = parseFloat(matrix.elements[j * 4 + 3]).toFixed(5);\r\n this.writeString(numb.toString(), 68, 55);\r\n }\r\n }\r\n\r\n writeMatrices(matrices, string) {\r\n if (!matrices) {\r\n return;\r\n }\r\n const matrix = new Matrix4();\r\n for (let j = 0; j < matrices.length; j++) {\r\n matrix.copy(matrices[j]).transpose();\r\n this.writeMatrix(matrix, j + 1, string);\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport Complex from '../../chem/Complex';\r\nimport Exporter from './Exporter';\r\nimport PDBResult from './PDBResult';\r\nimport Assembly from '../../chem/Assembly';\r\nimport { typeByPDBHelixClass } from '../../chem/Helix';\r\n\r\nexport default class PDBExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n this._tags = ['HEADER', 'TITLE', 'COMPND', 'REMARK', 'HELIX', 'SHEET', 'ATOM and HETATM', 'CONECT'];\r\n this._result = null;\r\n this._tagExtractors = {\r\n HEADER: this._extractHEADER,\r\n TITLE: this._extractTITLE,\r\n 'ATOM and HETATM': this._extractATOM,\r\n CONECT: this._extractCONECT,\r\n COMPND: this._extractCOMPND,\r\n REMARK: this._extractREMARK,\r\n HELIX: this._extractHELIX,\r\n SHEET: this._extractSHEET,\r\n };\r\n this._stringForRemark350 = 'COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN\\n'\r\n + 'BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE\\n'\r\n + 'MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS\\n'\r\n + 'GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND\\n'\r\n + 'CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.';\r\n\r\n this._stringForRemark290 = 'CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS\\n'\r\n + 'THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM\\n'\r\n + 'RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY\\n'\r\n + 'RELATED MOLECULES.';\r\n }\r\n\r\n exportSync() {\r\n const result = new PDBResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n for (let i = 0; i < this._tags.length; i++) {\r\n const tag = this._tags[i];\r\n const func = this._tagExtractors[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, result);\r\n }\r\n }\r\n\r\n this._result = result.getResult();\r\n\r\n return this._result;\r\n }\r\n\r\n _extractHEADER(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n result.newTag('HEADER');\r\n result.newString();\r\n if (metadata.classification) {\r\n result.writeString(metadata.classification, 11, 50);\r\n }\r\n if (metadata.date) {\r\n result.writeString(metadata.date, 51, 59);\r\n }\r\n if (metadata.id) {\r\n result.writeString(metadata.id, 63, 66);\r\n }\r\n }\r\n\r\n _extractTITLE(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n if (!metadata.title) {\r\n return;\r\n }\r\n result.newTag('TITLE', true);\r\n for (let i = 0; i < metadata.title.length; i++) {\r\n result.newString();\r\n result.writeString(metadata.title[i], 11, 80);\r\n }\r\n }\r\n\r\n _extractCONECT(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n\r\n const atoms = this._source._atoms;\r\n result.newTag('CONECT');\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const fixedBonds = atoms[i].bonds.filter((bond) => bond._fixed);\r\n if (fixedBonds.length !== 0) {\r\n result.writeBondsArray(fixedBonds.reverse(), atoms[i]);\r\n }\r\n }\r\n }\r\n\r\n _extractSHEET(result) {\r\n if (!this._source._sheets) {\r\n return;\r\n }\r\n\r\n result.newTag('SHEET');\r\n\r\n const sheets = this._source._sheets;\r\n for (let i = 0; i < sheets.length; i++) {\r\n if (sheets[i]._strands) {\r\n const strands = sheets[i]._strands;\r\n for (let j = 0; j < strands.length; j++) {\r\n result.newString();\r\n result.writeString(j + 1, 10, 8);\r\n result.writeString(sheets[i]._name, 14, 12);\r\n result.writeString(strands.length, 16, 15);\r\n result.writeString(strands[j].init._type._name, 18, 20);\r\n result.writeString(strands[j].init._chain._name, 22, 22);\r\n result.writeString(strands[j].init._sequence, 26, 23);\r\n result.writeString(strands[j].init._icode, 27, 27);\r\n result.writeString(strands[j].term._type._name, 29, 31);\r\n result.writeString(strands[j].init._chain._name, 33, 33);\r\n result.writeString(strands[j].term._sequence, 37, 34);\r\n result.writeString(strands[j].term._icode, 38, 38);\r\n result.writeString(strands[j].sense, 40, 39);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _extractHELIX(result) {\r\n if (!this._source._helices) {\r\n return;\r\n }\r\n\r\n result.newTag('HELIX');\r\n const helices = this._source._helices;\r\n for (let i = 0; i < helices.length; i++) {\r\n const helix = helices[i];\r\n const helixClass = _.invert(typeByPDBHelixClass);\r\n result.newString();\r\n result.writeString(helix.serial, 10, 8);\r\n result.writeString(helix.name, 14, 12);\r\n result.writeString(helix.init._type._name, 16, 18);\r\n result.writeString(helix.init._chain._name, 20, 20);\r\n result.writeString(helix.init._sequence, 25, 22);\r\n result.writeString(helix.init._icode, 26, 26);\r\n result.writeString(helix.term._type._name, 28, 30);\r\n result.writeString(helix.term._chain._name, 32, 32);\r\n result.writeString(helix.term._sequence, 37, 34);\r\n result.writeString(helix.term._icode, 38, 38);\r\n result.writeString(helixClass[helix.type], 40, 39);\r\n result.writeString(helix.comment, 41, 70);\r\n result.writeString(helix.length, 76, 72);\r\n }\r\n }\r\n\r\n _extractATOM(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n const atoms = this._source._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const tag = atoms[i].het ? 'HETATM' : 'ATOM';\r\n result.newString(tag);\r\n const startIndx = (atoms[i].element.name.length > 1 || atoms[i].name.length > 3) ? 13 : 14;\r\n result.writeString(atoms[i].serial, 11, 7);\r\n result.writeString(atoms[i].name, startIndx, 16);\r\n result.writeString(String.fromCharCode(atoms[i].location), 17, 17);\r\n result.writeString(atoms[i].residue._type._name, 20, 18);\r\n result.writeString(atoms[i].residue._chain._name, 22, 22);\r\n result.writeString(atoms[i].residue._sequence, 26, 23);\r\n result.writeString(atoms[i].residue._icode, 27, 27);\r\n result.writeString(atoms[i].position.x.toFixed(3), 38, 31);\r\n result.writeString(atoms[i].position.y.toFixed(3), 46, 39);\r\n result.writeString(atoms[i].position.z.toFixed(3), 54, 47);\r\n result.writeString(atoms[i].occupancy.toFixed(2), 60, 55);\r\n result.writeString(atoms[i].temperature.toFixed(2), 66, 61);\r\n result.writeString(atoms[i].element.name, 78, 77);\r\n if (atoms[i].charge) {\r\n result.writeString(atoms[i].charge, 79, 80);\r\n }\r\n }\r\n }\r\n\r\n _extractCOMPND(result) {\r\n if (!this._source._molecules) {\r\n return;\r\n }\r\n const molecules = this._source._molecules;\r\n result.newTag('COMPND', true);\r\n\r\n for (let i = 0; i < molecules.length; i++) {\r\n const chains = this._getMoleculeChains(molecules[i]);\r\n result.newString();\r\n result.writeString(`MOL_ID: ${molecules[i].index};`, 11, 80);\r\n result.newString();\r\n result.writeString(`MOLECULE: ${molecules[i].name};`, 11, 80);\r\n result.newString();\r\n result.writeString('CHAIN: ', 11, 18);\r\n const chainsString = `${chains.join(', ')};`;\r\n result.writeEntireString(chainsString, 81);\r\n }\r\n }\r\n\r\n _extractREMARK(result) {\r\n this._Remark290(result);\r\n this._Remark350(result);\r\n }\r\n\r\n _Remark290(result) {\r\n if (!this._source.symmetry) {\r\n return;\r\n }\r\n\r\n if (this._source.symmetry.length !== 0) {\r\n const matrices = this._source.symmetry;\r\n result.newTag('REMARK', 290);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark290);\r\n result.writeMatrices(matrices, 'SMTRY');\r\n result.newString();\r\n result.newString();\r\n result.writeString('REMARK: NULL', 11, 80);\r\n }\r\n }\r\n\r\n _Remark350(result) {\r\n if (!this._source.units) {\r\n return;\r\n }\r\n const { units } = this._source;\r\n let biomolIndx = 0;\r\n\r\n result.newTag('REMARK', 350);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark350);\r\n\r\n const assemblies = units.filter((unit) => unit instanceof Assembly);\r\n\r\n for (let i = 0; i < assemblies.length; i++) {\r\n result.newString();\r\n result.newString();\r\n biomolIndx++;\r\n result.writeString(`BIOMOLECULE: ${biomolIndx}`, 11, 80);\r\n const chains = assemblies[i].chains.join(', ');\r\n result.newString();\r\n result.writeString('APPLY THE FOLLOWING TO CHAINS: ');\r\n result.writeEntireString(chains, 69, { tag: 'AND CHAINS: ', begin: 31, end: 42 });\r\n\r\n const { matrices } = assemblies[i];\r\n result.writeMatrices(matrices, 'BIOMT');\r\n }\r\n }\r\n\r\n _getMoleculeChains(molecule) {\r\n function getChainName(residue) {\r\n return residue._chain._name;\r\n }\r\n const chainNames = molecule.residues.map(getChainName);\r\n return chainNames.filter((item, pos) => chainNames.indexOf(item) === pos);\r\n }\r\n}\r\n\r\nPDBExporter.formats = ['pdb'];\r\nPDBExporter.SourceClass = Complex;\r\n","import * as THREE from 'three';\r\n\r\nconst FBX_POS_SIZE = 3;\r\nconst FBX_NORM_SIZE = 3;\r\nconst FBX_COL_SIZE = 4;\r\n\r\nfunction copyFbxPoint3(src, srcIdx, dst, dstIdx) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n}\r\n\r\nfunction copyFbxPoint4(src, srcIdx, dst, dstIdx, value) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n dst[dstIdx + 3] = value;\r\n}\r\n\r\nconst vector4 = new THREE.Vector4();\r\nfunction copyTransformedPoint3(src, srcIdx, dst, dstIdx, opts) {\r\n vector4.set(src[srcIdx], src[srcIdx + 1], src[srcIdx + 2], opts.w);\r\n vector4.applyMatrix4(opts.matrix);\r\n dst[dstIdx] = vector4.x;\r\n dst[dstIdx + 1] = vector4.y;\r\n dst[dstIdx + 2] = vector4.z;\r\n}\r\n\r\nfunction setSubArray(src, dst, count, copyFunctor, functorOpts) {\r\n if ((dst.array.length - dst.start) / dst.stride < count\r\n || (src.array.length - src.start) / src.stride < count) {\r\n return; // we've got no space\r\n }\r\n if (src.stride === dst.stride) { // stride is the same\r\n dst.array.set(src.array, dst.start);\r\n } else {\r\n let idx = dst.start;\r\n let arridx = src.start;\r\n for (let i = 0; i < count; ++i, idx += dst.stride, arridx += src.stride) {\r\n copyFunctor(src.array, arridx, dst.array, idx, functorOpts);\r\n }\r\n }\r\n}\r\n\r\nexport default class FBXModel {\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.lastPos = 0;\r\n this.lastNorm = 0;\r\n this.lastCol = 0;\r\n this.lastIdx = 0;\r\n }\r\n\r\n init(vertsCount, indsCount) {\r\n this.positions = new Float32Array(vertsCount * FBX_POS_SIZE);\r\n this.normals = new Float32Array(vertsCount * FBX_NORM_SIZE);\r\n this.colors = new Float32Array(vertsCount * FBX_COL_SIZE);\r\n this.indices = new Int32Array(indsCount);\r\n }\r\n\r\n setPositions(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.positions,\r\n start: this.lastPos,\r\n stride: FBX_POS_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setTransformedPositions(array, start, count, stride, matrix) {\r\n let idx = this.lastPos;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 1 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_POS_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.positions, idx, opts);\r\n }\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setNormals(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.normals,\r\n start: this.lastNorm,\r\n stride: FBX_NORM_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setTransformedNormals(array, start, count, stride, matrix) {\r\n let idx = this.lastNorm;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 0 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_NORM_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.normals, idx, opts);\r\n }\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setColors(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.colors,\r\n start: this.lastCol,\r\n stride: FBX_COL_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint4, 1);\r\n this.lastCol += count * FBX_COL_SIZE;\r\n }\r\n\r\n setIndices(array, start, count) {\r\n this.indices.set(array, this.lastIdx);\r\n this.lastIdx += count;\r\n }\r\n\r\n setShiftedIndices(array, count, shift) {\r\n const shifted = array.map((x) => x + shift);\r\n this.setIndices(shifted, 0, count);\r\n }\r\n\r\n getVerticesNumber() {\r\n return this.lastPos / FBX_POS_SIZE;\r\n }\r\n\r\n addInstance(matrix, geo) {\r\n // add indices at first to take old number of vertices for shift\r\n const currentCount = this.getVerticesNumber();\r\n this.setShiftedIndices(geo.indices, geo.indices.length, currentCount);\r\n // simply write vertices at empty space\r\n const size = geo.itemSize;\r\n this.setTransformedPositions(geo.positions, 0, geo.vertsCount, size.position, matrix);\r\n this.setTransformedNormals(geo.normals, 0, geo.vertsCount, size.normal, matrix);\r\n this.setColors(geo.colors, 0, geo.vertsCount, size.color);\r\n }\r\n}\r\n","/** Base class for fbx geometry contains simply organized attributes: positions+normals+colors, indices. */\r\nexport default class FBXGeometry {\r\n /**\r\n * Create a base geo with necessary members.\r\n */\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.vertsCount = 0;\r\n this.itemSize = null;\r\n }\r\n\r\n /**\r\n * Initialize base geo storing items info from attributes.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n const { attributes } = geo;\r\n // save item size\r\n this.itemSize = {\r\n position: attributes.position.itemSize,\r\n normal: attributes.normal.itemSize,\r\n color: attributes.color.itemSize,\r\n };\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes and creates colors filled with defined value.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX1CGeometry extends FBXGeometry {\r\n /**\r\n * Initialize geo storing positions, normals, indices and create colors.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n super.init(geo, _info);\r\n const {\r\n attributes: {\r\n position,\r\n normal,\r\n },\r\n index,\r\n } = geo;\r\n // copy vertices attributes\r\n this.vertsCount = position.count;\r\n this.positions = position.array;\r\n this.normals = normal.array;\r\n // create color array\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n // indices\r\n this.indices = index.array;\r\n }\r\n\r\n /**\r\n * Set defined color for all items in color attribute\r\n * @param {Object} color - THREE.Color.\r\n */\r\n setColors(color) {\r\n let offset = 0;\r\n for (let i = 0, l = this.colors.length, cl = this.itemSize.color; i < l; i += cl) {\r\n this.colors[offset++] = color.r;\r\n this.colors[offset++] = color.g;\r\n this.colors[offset++] = color.b;\r\n }\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes from cylinder geometry and creates colors filled with two\r\n * defined values.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX2CCylinder extends FBXGeometry {\r\n constructor() {\r\n super();\r\n this._cutRawStart = 0;\r\n this._cutRawEnd = 0;\r\n this._facesPerSlice = 0;\r\n }\r\n\r\n /**\r\n * Initialize geo by creating new attributes, because we extend number of vertices to make cylinder two-colored.\r\n * Indices remain the same. We process open- end close-ended cylinders and consider cylinders od 2 segments\r\n * in height ONLY.\r\n * NOTE: cylinder consists of 2 height segments and stores parts in the order: tube, topCap, bottomCap\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n * @param {Object} info - information needed for geo extend\r\n */\r\n init(geo, info) {\r\n super.init(geo, info);\r\n const {\r\n attributes: {\r\n position,\r\n },\r\n index,\r\n } = geo;\r\n // extend vertices arrays\r\n this.vertsCount = position.count + info.addPerCylinder;\r\n this._facesPerSlice = info.addPerCylinder;\r\n this.positions = new Float32Array(this.vertsCount * position.itemSize);\r\n this.normals = new Float32Array(this.vertsCount * this.itemSize.normal);\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n this._extendVertices(geo, info);\r\n // number of indices stays the same\r\n this.indices = new Uint32Array(index.count);\r\n this._extendIndices(geo, info);\r\n }\r\n\r\n /** Extend vertex attributes to have one more slice to make sharp middle startColor-endColor line. */\r\n _extendVertices(geo, info) {\r\n const { position } = geo.attributes;\r\n const { normal } = geo.attributes;\r\n const geoParams = geo.getGeoParams();\r\n const cutRaw = 1; // we expect cylinders of 2 segments in height => so half segment = 1\r\n this._cutRawStart = cutRaw * geoParams.radialSegments;\r\n this._cutRawEnd = this._cutRawStart + info.addPerCylinder;\r\n { // write first half of cylinder\r\n let temp = position.array.slice(0, this._cutRawEnd * position.itemSize);\r\n this.positions.set(temp, 0);\r\n temp = normal.array.slice(0, this._cutRawEnd * normal.itemSize);\r\n this.normals.set(temp, 0);\r\n }\r\n { // write second part of cylinder\r\n let temp = position.array.slice(this._cutRawStart * position.itemSize, position.array.length);\r\n this.positions.set(temp, this._cutRawEnd * position.itemSize);\r\n temp = normal.array.slice(this._cutRawStart * normal.itemSize, normal.array.length);\r\n this.normals.set(temp, this._cutRawEnd * normal.itemSize);\r\n }\r\n }\r\n\r\n /** Shift values of second part (+caps) indices by newly added vertices count. Number of faces remains the same. */\r\n _extendIndices(geo, info) {\r\n const { index } = geo;\r\n const indicesPerQuad = 6; // quad = 2 triangles => 6 indices\r\n const startToShift = info.addPerCylinder * indicesPerQuad;\r\n const shift = info.addPerCylinder;\r\n let shifted = index.array.slice(startToShift, index.count);\r\n shifted = shifted.map((x) => x + shift); // shift only the endings\r\n this.indices.set(index.array, 0);\r\n this.indices.set(shifted, startToShift);\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {number} start - start color index\r\n * @param {number} end - start color index\r\n * @param {array} array - array of colors\r\n * @param {array} color - color value components\r\n */\r\n _setColorRange(start, end, array, color) {\r\n const colorSize = color.length;\r\n for (let i = start; i < end; i += colorSize) {\r\n array.set(color, i);\r\n }\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {Object} color1 - THREE.Color.\r\n * @param {Object} color2 - THREE.Color.\r\n */\r\n setColors(color1, color2) {\r\n const colorSize = this.itemSize.color;\r\n const part1End = this._cutRawEnd * colorSize;\r\n const part2End = part1End * 2;\r\n this._setColorRange(0, part1End, this.colors, color1.toArray());\r\n this._setColorRange(part1End, part2End, this.colors, color2.toArray());\r\n if (part2End < this.colors.length) { // cylinder has caps, lets paint them\r\n const capSize = (this._facesPerSlice + 1) * colorSize;\r\n const cap1End = part2End + capSize;\r\n this._setColorRange(part2End, cap1End, this.colors, color2.toArray());\r\n const cap2End = cap1End + capSize; // should be equal to this.colors.length;\r\n this._setColorRange(cap1End, cap2End, this.colors, color1.toArray());\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\n\r\nimport utils from '../../../utils';\r\nimport gfxutils from '../../../gfx/gfxutils';\r\nimport logger from '../../../utils/logger';\r\n\r\nimport FBXModel from './FBXModel';\r\nimport ThickLineMesh from '../../../gfx/meshes/ThickLineMesh';\r\nimport ZSpriteMesh from '../../../gfx/meshes/ZSpriteMesh';\r\nimport InstancedSpheresGeometry from '../../../gfx/geometries/InstancedSpheresGeometry';\r\nimport Instanced2CCylindersGeometry from '../../../gfx/geometries/Instanced2CCylindersGeometry';\r\nimport FBX1CGeometry from './FBX1CGeometry';\r\nimport FBX2CCylinder from './FBX2CCylinder';\r\n\r\nexport default class FBXInfoExtractor {\r\n constructor() {\r\n this._materials = [];\r\n this._models = [];\r\n }\r\n\r\n process(data) {\r\n this._extractModelsAndMaterials(data);\r\n const models = this._flattenModels();\r\n\r\n return {\r\n name: data.name,\r\n models,\r\n materials: this._materials,\r\n };\r\n }\r\n\r\n /**\r\n * Extract fbx object information from ComplexVisual\r\n * @param {object} data - complexVisual to get geometry info from\r\n */\r\n _extractModelsAndMaterials(data) {\r\n const layersOfInterest = new THREE.Layers();\r\n layersOfInterest.set(gfxutils.LAYERS.DEFAULT);\r\n layersOfInterest.enable(gfxutils.LAYERS.TRANSPARENT);\r\n data.traverse((object) => {\r\n if (object instanceof THREE.Mesh && object.layers.test(layersOfInterest) && this.checkExportAbility(object)) {\r\n if (object.geometry.type === 'InstancedBufferGeometry') {\r\n this._collectInstancedGeoInfo(object);\r\n } else {\r\n this._collectGeoInfo(object);\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Reworking indices buffer, see https://banexdevblog.wordpress.com/2014/06/23/a-quick-tutorial-about-the-fbx-ascii-format/\r\n * basically, every triangle in Miew has been represented hat way (e.g.) : 0,1,7, but we must (for FBX) rework that\r\n * into: 0,1,-8.\r\n * @param {array} indices - belongs to [0, maxVertIndex]\r\n */\r\n _reworkIndices(indices) {\r\n const faceSize = 3;\r\n for (let i = faceSize - 1; i < indices.length; i += faceSize) {\r\n indices[i] *= -1;\r\n indices[i]--;\r\n }\r\n }\r\n\r\n /**\r\n * Combine geometry from several models having the same material into one Model and finally prepare indices\r\n * @returns {array} models, combined by material id\r\n */\r\n _flattenModels() {\r\n let overallVertsCount = 0;\r\n function shift(x) {\r\n return x + overallVertsCount;\r\n }\r\n const combined = [];\r\n // flatten models geometry\r\n for (let i = 0, n = this._models.length; i < n; i++) {\r\n const models = this._models[i];\r\n let indices = [];\r\n let positions = [];\r\n let normals = [];\r\n let colors = [];\r\n // reorganize every attributes as array of arrays\r\n overallVertsCount = 0;\r\n for (let j = 0; j < models.length; j++) {\r\n const m = models[j];\r\n indices.push(m.indices.map(shift));\r\n overallVertsCount += m.getVerticesNumber();\r\n positions.push(m.positions);\r\n normals.push(m.normals);\r\n colors.push(m.colors);\r\n }\r\n // join all subarrays into one\r\n indices = utils.mergeTypedArraysUnsafe(indices);\r\n this._reworkIndices(indices);\r\n positions = utils.mergeTypedArraysUnsafe(positions);\r\n normals = utils.mergeTypedArraysUnsafe(normals);\r\n colors = utils.mergeTypedArraysUnsafe(colors);\r\n combined.push({\r\n indices,\r\n positions,\r\n normals,\r\n colors,\r\n verticesCount: overallVertsCount,\r\n });\r\n }\r\n return combined;\r\n }\r\n\r\n /**\r\n * Check ability to export the kind of mesh.\r\n * @param {object} mesh - given mesh to check\r\n * @returns {boolean} result of check\r\n */\r\n checkExportAbility(mesh) {\r\n // check mesh on not being empty\r\n if (mesh.geometry.attributes.position.count === 0) {\r\n return false;\r\n }\r\n // check type of mesh\r\n // if (mesh.geometry.isInstancedBufferGeometry && settings.now.zSprites) {\r\n if (mesh instanceof ZSpriteMesh) {\r\n logger.warn('Currently we cannot export \\'sprites\\' modes, like BS, WV, LC. Please turn of settings \\'zSprites\\' and try again');\r\n return false;\r\n }\r\n if (mesh instanceof ThickLineMesh) {\r\n logger.warn('Currently we cannot export Lines mode');\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n /**\r\n * Save geometry info from common mesh, like Surface or Cartoon\r\n */\r\n _collectGeoInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n normal,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const vertCount = position.count;\r\n model.init(vertCount, index.count);\r\n if (matrix.isIdentity()) {\r\n model.setPositions(position.array, 0, vertCount, position.itemSize);\r\n model.setNormals(normal.array, 0, vertCount, normal.itemSize);\r\n } else {\r\n model.setTransformedPositions(position.array, 0, vertCount, position.itemSize, matrix);\r\n model.setTransformedNormals(normal.array, 0, vertCount, normal.itemSize, matrix);\r\n }\r\n model.setColors(color.array, 0, vertCount, color.itemSize);\r\n model.setIndices(index.array, 0, index.count);\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Collect instanced spheres geometry and materials.\r\n * @param {object} mesh - mesh with instanced spheres info\r\n */\r\n _collectSpheresInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount, instCount * indsCount);\r\n const geo = new FBX1CGeometry();\r\n geo.init(mesh.geometry);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const sphereColor = new THREE.Color();\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n sphereColor.fromArray(color.array, colorIdx);\r\n geo.setColors(sphereColor);\r\n // add instance to the model\r\n this._getSphereInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Getting all instanced cylinders from given mesh.\r\n * Divide cylinder (add additional vertexes) for prettiness therefore algorithm is a bit complicated\r\n * @param {object} mesh - given mesh with instanced cylinders\r\n */\r\n _collectCylindersInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n color2,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const oneCCylinder = new FBX1CGeometry();\r\n oneCCylinder.init(mesh.geometry);\r\n const splittingInfo = this._gatherCylindersColoringInfo(mesh.geometry);\r\n let twoCCylinder = null;\r\n if (splittingInfo.needToSplit > 0) {\r\n twoCCylinder = new FBX2CCylinder();\r\n twoCCylinder.init(mesh.geometry, splittingInfo);\r\n }\r\n const additionalVertsCount = splittingInfo.addPerCylinder * splittingInfo.needToSplit;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount + additionalVertsCount, instCount * indsCount);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const colorStart = new THREE.Color();\r\n const colorEnd = new THREE.Color();\r\n let geo = {};\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n if (splittingInfo.is2Colored[instanceIndex]) {\r\n // .color2 contains starting color, and .color contains starting color (see uber.frag ATTR_COLOR2)\r\n colorStart.fromArray(color2.array, colorIdx);\r\n colorEnd.fromArray(color.array, colorIdx);\r\n if (twoCCylinder) {\r\n twoCCylinder.setColors(colorStart, colorEnd);\r\n geo = twoCCylinder;\r\n }\r\n } else {\r\n // has one color per cylinder\r\n colorStart.fromArray(color.array, colorIdx);\r\n oneCCylinder.setColors(colorStart);\r\n geo = oneCCylinder;\r\n }\r\n // add instance to the model\r\n this._getCylinderInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Adding model to pool of models or extend existing ones\r\n * @param {object} model - model to add\r\n * @param {object} material - material to add\r\n */\r\n _addToPool(model, material) {\r\n const materialIdx = this._checkExistingMaterial(material);\r\n if (materialIdx < 0) { // new model-material pair\r\n this._models.push([model]);\r\n this._materials.push(material);\r\n } else { // add model to existing model-material pair\r\n const models = this._models[materialIdx];\r\n models.push(model);\r\n }\r\n }\r\n\r\n /**\r\n * Checking if given material already was registered in materials pool (no need to create new one)\r\n * @param {object} material - given material\r\n * @returns {number} number of model-material pair\r\n */\r\n _checkExistingMaterial(material) {\r\n return _.findIndex(this._materials, (m) => _.isEqual(m, material));\r\n }\r\n\r\n _gatherCylindersColoringInfo(geo) {\r\n const instCount = geo.instanceCount;\r\n const color1 = geo.attributes.color.array;\r\n const color2 = geo.attributes.color2.array;\r\n const stride = geo.attributes.color.itemSize;\r\n const is2Colored = new Array(instCount);\r\n // analyze color instance attributes\r\n let needToSplit = 0;\r\n let colIdx = 0;\r\n for (let i = 0; i < instCount; i++, colIdx += stride) {\r\n const differs = (Math.abs(color1[colIdx] - color2[colIdx]) > 0.0000001) // compare ending colors\r\n || (Math.abs(color1[colIdx + 1] - color2[colIdx + 1]) > 0.0000001)\r\n || (Math.abs(color1[colIdx + 2] - color2[colIdx + 2]) > 0.0000001);\r\n is2Colored[i] = differs;\r\n needToSplit += differs; // count number of 2-colored cylinders\r\n }\r\n // calc number of vertices to add into 2-colored\r\n const geoParams = geo.getGeoParams();\r\n const addPerCylinder = geoParams.radialSegments;\r\n return { is2Colored, needToSplit, addPerCylinder };\r\n }\r\n\r\n /**\r\n * Collect instanced models and materials.\r\n * @param {object} mesh - given mesh with instanced something (spheres or cylinders)\r\n */\r\n _collectInstancedGeoInfo(mesh) {\r\n if (mesh.geometry instanceof InstancedSpheresGeometry) {\r\n this._collectSpheresInfo(mesh);\r\n } else if (mesh.geometry instanceof Instanced2CCylindersGeometry) {\r\n this._collectCylindersInfo(mesh);\r\n }\r\n }\r\n\r\n /**\r\n * Collect Material info from given mesh.\r\n * @param {object} mesh - given mesh with material info\r\n * @returns {object} material\r\n */\r\n _collectMaterialInfo(mesh) {\r\n const { uberOptions } = mesh.material;\r\n return ({\r\n diffuse: uberOptions.diffuse.toArray(),\r\n opacity: uberOptions.opacity,\r\n shininess: uberOptions.shininess,\r\n specular: uberOptions.specular.toArray(),\r\n });\r\n }\r\n\r\n _getCylinderInstanceMatrix(geo, instIdx, matrix) {\r\n const matVector1 = geo.attributes.matVector1.array;\r\n const matVector2 = geo.attributes.matVector2.array;\r\n const matVector3 = geo.attributes.matVector3.array;\r\n const idxOffset = instIdx * 4; // used 4 because offset arrays are stored in quads\r\n matrix.set(\r\n matVector1[idxOffset],\r\n matVector1[idxOffset + 1],\r\n matVector1[idxOffset + 2],\r\n matVector1[idxOffset + 3],\r\n matVector2[idxOffset],\r\n matVector2[idxOffset + 1],\r\n matVector2[idxOffset + 2],\r\n matVector2[idxOffset + 3],\r\n matVector3[idxOffset],\r\n matVector3[idxOffset + 1],\r\n matVector3[idxOffset + 2],\r\n matVector3[idxOffset + 3],\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n\r\n _getSphereInstanceMatrix(geo, instIdx, matrix) {\r\n const { offset } = geo.attributes;\r\n const idx = instIdx * offset.itemSize;\r\n const x = offset.array[idx];\r\n const y = offset.array[idx + 1];\r\n const z = offset.array[idx + 2];\r\n const scale = offset.array[idx + 3];\r\n matrix.set(\r\n scale,\r\n 0,\r\n 0,\r\n x,\r\n 0,\r\n scale,\r\n 0,\r\n y,\r\n 0,\r\n 0,\r\n scale,\r\n z,\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n}\r\n","// Forming default definitions block\r\nconst defaultDefinitions = `\r\nDefinitions: {\r\n Version: 100\r\n Count: 3\r\n ObjectType: \"Model\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Geometry\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Material\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Pose\" {\r\n Count: 1\r\n }\r\n ObjectType: \"GlobalSettings\" {\r\n Count: 1\r\n }\r\n} `;\r\n\r\n// Default model properties\r\nconst defaultProperties = `Properties60: {\r\n Property: \"QuaternionInterpolate\", \"bool\", \"\",0\r\n Property: \"Visibility\", \"Visibility\", \"A\",1\r\n Property: \"Lcl Translation\", \"Lcl Translation\", \"A\",0.000000000000000,0.000000000000000,-1789.238037109375000\r\n Property: \"Lcl Rotation\", \"Lcl Rotation\", \"A\",0.000009334667643,-0.000000000000000,0.000000000000000\r\n Property: \"Lcl Scaling\", \"Lcl Scaling\", \"A\",1.000000000000000,1.000000000000000,1.000000000000000\r\n Property: \"RotationOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationActive\", \"bool\", \"\",0\r\n Property: \"TranslationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMinX\", \"bool\", \"\",0\r\n Property: \"TranslationMinY\", \"bool\", \"\",0\r\n Property: \"TranslationMinZ\", \"bool\", \"\",0\r\n Property: \"TranslationMaxX\", \"bool\", \"\",0\r\n Property: \"TranslationMaxY\", \"bool\", \"\",0\r\n Property: \"TranslationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationOrder\", \"enum\", \"\",0\r\n Property: \"RotationSpaceForLimitOnly\", \"bool\", \"\",0\r\n Property: \"AxisLen\", \"double\", \"\",10\r\n Property: \"PreRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"PostRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationActive\", \"bool\", \"\",0\r\n Property: \"RotationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMinX\", \"bool\", \"\",0\r\n Property: \"RotationMinY\", \"bool\", \"\",0\r\n Property: \"RotationMinZ\", \"bool\", \"\",0\r\n Property: \"RotationMaxX\", \"bool\", \"\",0\r\n Property: \"RotationMaxY\", \"bool\", \"\",0\r\n Property: \"RotationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationStiffnessX\", \"double\", \"\",0\r\n Property: \"RotationStiffnessY\", \"double\", \"\",0\r\n Property: \"RotationStiffnessZ\", \"double\", \"\",0\r\n Property: \"MinDampRangeX\", \"double\", \"\",0\r\n Property: \"MinDampRangeY\", \"double\", \"\",0\r\n Property: \"MinDampRangeZ\", \"double\", \"\",0\r\n Property: \"MaxDampRangeX\", \"double\", \"\",0\r\n Property: \"MaxDampRangeY\", \"double\", \"\",0\r\n Property: \"MaxDampRangeZ\", \"double\", \"\",0\r\n Property: \"MinDampStrengthX\", \"double\", \"\",0\r\n Property: \"MinDampStrengthY\", \"double\", \"\",0\r\n Property: \"MinDampStrengthZ\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthX\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthY\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthZ\", \"double\", \"\",0\r\n Property: \"PreferedAngleX\", \"double\", \"\",0\r\n Property: \"PreferedAngleY\", \"double\", \"\",0\r\n Property: \"PreferedAngleZ\", \"double\", \"\",0\r\n Property: \"InheritType\", \"enum\", \"\",0\r\n Property: \"ScalingActive\", \"bool\", \"\",0\r\n Property: \"ScalingMin\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMax\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMinX\", \"bool\", \"\",0\r\n Property: \"ScalingMinY\", \"bool\", \"\",0\r\n Property: \"ScalingMinZ\", \"bool\", \"\",0\r\n Property: \"ScalingMaxX\", \"bool\", \"\",0\r\n Property: \"ScalingMaxY\", \"bool\", \"\",0\r\n Property: \"ScalingMaxZ\", \"bool\", \"\",0\r\n Property: \"GeometricTranslation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricScaling\", \"Vector3D\", \"\",1,1,1\r\n Property: \"LookAtProperty\", \"object\", \"\"\r\n Property: \"UpVectorProperty\", \"object\", \"\"\r\n Property: \"Show\", \"bool\", \"\",1\r\n Property: \"NegativePercentShapeSupport\", \"bool\", \"\",1\r\n Property: \"DefaultAttributeIndex\", \"int\", \"\",0\r\n Property: \"Color\", \"Color\", \"A+\",0,0,0\r\n Property: \"Size\", \"double\", \"\",100\r\n Property: \"Look\", \"enum\", \"\",1\r\n }`;\r\n\r\n// Default materials layer\r\nconst defaultMaterialLayer = `\r\n LayerElementMaterial: 0 {\r\n Version: 101\r\n Name: \"\"\r\n MappingInformationType: \"AllSame\"\r\n ReferenceInformationType: \"Direct\"\r\n Materials: 0\r\n }`;\r\n\r\n// Default layers block\r\nconst defaultLayerBlock = `\r\n Layer: 0 {\r\n Version: 100\r\n LayerElement: {\r\n Type: \"LayerElementNormal\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementColor\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementMaterial\"\r\n TypedIndex: 0\r\n }\r\n }`;\r\n\r\n/**\r\n * globalSettings info in output file.\r\n */\r\nconst globalSettings = `GlobalSettings: {\r\n Version: 1000\r\n Properties60: {\r\n Property: \"UpAxis\", \"int\", \"\",1\r\n Property: \"UpAxisSign\", \"int\", \"\",1\r\n Property: \"FrontAxis\", \"int\", \"\",2\r\n Property: \"FrontAxisSign\", \"int\", \"\",1\r\n Property: \"CoordAxis\", \"int\", \"\",0\r\n Property: \"CoordAxisSign\", \"int\", \"\",1\r\n Property: \"UnitScaleFactor\", \"double\", \"\",1\r\n }\r\n }`;\r\n\r\nexport default class FBXResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._info = null;\r\n }\r\n\r\n getResult(info) {\r\n this._info = info;\r\n this._resultArray.push(this._writeHeader());\r\n this._resultArray.push(this._writeDefinitions());\r\n this._resultArray.push(this._writeObjects(info.models, info.materials));\r\n this._resultArray.push(this._writeRelations());\r\n this._resultArray.push(this._writeConnections()); // connections between models and materials)\r\n this._info = null;\r\n return this._resultArray.join('');\r\n }\r\n\r\n /**\r\n * Add FBXHeader info to output file.\r\n * Some fields are really confusing, but it seems that all listed fields are very informative\r\n */\r\n _writeHeader() {\r\n const FBXHeaderVersion = 1003; // 1003 is some number which appears to present in many 6.1 ASCII files\r\n const FBXVersion = 6100; // Mandatory and only supported version\r\n const date = new Date();\r\n const timeStampVersion = 1000;\r\n const creator = `Miew FBX Exporter v${this._info.version}`; // Supposed to be an engine\r\n\r\n return `; FBX 6.1.0 project file\r\n; Created by ${creator} Copyright (c) 2015-2024 EPAM Systems, Inc.\r\n; For support please contact miew@epam.com\r\n; ----------------------------------------------------\r\n\r\nFBXHeaderExtension: {\r\n FBXHeaderVersion: ${FBXHeaderVersion}\r\n FBXVersion: ${FBXVersion}\r\n CreationTimeStamp: {\r\n Version: ${timeStampVersion}\r\n Year: ${date.getFullYear()}\r\n Month: ${date.getMonth() + 1}\r\n Day: ${date.getDate()}\r\n Hour: ${date.getHours()}\r\n Minute: ${date.getMinutes()}\r\n Second: ${date.getSeconds()}\r\n Millisecond: ${date.getMilliseconds()}\r\n }\r\n Creator: \"${creator}\"\r\n OtherFlags: {\r\n FlagPLE: 0\r\n }\r\n}\r\nCreationTime: \"${date}\"\r\nCreator: \"${creator}\"\r\n`;\r\n }\r\n\r\n /**\r\n * Add Definitions info to output file.\r\n * Not exactly sure if this section is template section (as it is in 7.4+) or it should every time be like this\r\n */\r\n _writeDefinitions() {\r\n return `\r\n; Object definitions\r\n;------------------------------------------------------------------\r\n\r\n${defaultDefinitions}\r\n`;\r\n }\r\n\r\n /**\r\n * Adding gathered information about Models to resulting string.\r\n * Reminder - there may be more then 1 model in scene, but we must place materials after ALL models.\r\n * @returns {string} string containing all models (vertices, indices, colors, normals etc)\r\n */\r\n _models() {\r\n const modelVersion = 232;\r\n let allModels = '';\r\n const { models } = this._info;\r\n for (let i = 0; i < models.length; ++i) {\r\n const model = models[i];\r\n const vertCount = model.verticesCount;\r\n allModels += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n Version: ${modelVersion}\r\n ${defaultProperties}\r\n ${this._verticesIndices(model.positions, model.indices)}\r\n ${this._normalLayer(model.normals)}\r\n ${this._colorLayer(model.colors, vertCount)}\r\n ${defaultMaterialLayer}\r\n ${defaultLayerBlock}\r\n }`;\r\n }\r\n return allModels;\r\n }\r\n\r\n /**\r\n * Add Material info to result\r\n */\r\n _materials() {\r\n const materialVersion = 102;\r\n let allMaterials = '';\r\n const { materials } = this._info;\r\n for (let i = 0; i < materials.length; ++i) {\r\n const material = materials[i];\r\n allMaterials += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n Version: ${materialVersion}\r\n ShadingModel: \"lambert\"\r\n MultiLayer: 0\r\n ${this._materialProperties(material)}\r\n }`;\r\n }\r\n return allMaterials;\r\n }\r\n\r\n /**\r\n * Add Objects info to output file.\r\n */\r\n _writeObjects() {\r\n return `\r\n; Object properties\r\n;------------------------------------------------------------------\r\n\r\nObjects: {\r\n ${this._models()}\r\n ${this._materials()}\r\n ${globalSettings}\r\n}\r\n`;\r\n }\r\n\r\n /**\r\n * Add Relations info to output file.\r\n */\r\n _writeRelations() {\r\n let modelsList = '';\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n }`;\r\n }\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n }`;\r\n }\r\n\r\n return `\r\n; Object relations\r\n;------------------------------------------------------------------\r\n\r\nRelations: {\r\n ${modelsList}\r\n Model: \"Model::Producer Perspective\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Top\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Bottom\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Front\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Back\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Right\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Left\", \"Camera\" {\r\n }\r\n Model: \"Model::Camera Switcher\", \"CameraSwitcher\" {\r\n }\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Add Connections info to output file.\r\n */\r\n _writeConnections() {\r\n let modelsList = '';\r\n const { name } = this._info;\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Connect: \"OO\", \"Model::${name}_${i}\", \"Model::Scene\"`;\r\n }\r\n\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Connect: \"OO\", \"Material::${name}_${i}_default\", \"Model::${name}_${i}\"`;\r\n }\r\n\r\n return `\r\n; Object connections\r\n;------------------------------------------------------------------\r\n\r\nConnections: {\r\n ${modelsList}\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Write float array to string with limited precision\r\n * @param {Float32Array} array - array to be fixed\r\n * @returns {String} String with fixed floats\r\n */\r\n _floatArrayToString(array) {\r\n const str = [];\r\n for (let i = 0; i < array.length; ++i) {\r\n str[i] = array[i].toFixed(6);\r\n }\r\n return str.join(',');\r\n }\r\n\r\n /**\r\n * Adding color layer to resulting file\r\n * @param {Float32Array} colorArray attribute\r\n * @param {number} vertCount - number of vertices in the model\r\n * @returns {string} color layer info\r\n */\r\n _colorLayer(colorArray, vertCount) {\r\n const layerElementColorNumber = 0;\r\n const layerElementColorVersion = 101;\r\n const layerElementColorName = '';\r\n const colorsStr = this._floatArrayToString(colorArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n // As said [..Array(...)] - fastest and easiest way to produce [0, 1, .....] array\r\n const colorIndices = [...Array(vertCount).keys()];\r\n return `\r\n LayerElementColor: ${layerElementColorNumber} {\r\n Version: ${layerElementColorVersion}\r\n Name: \"${layerElementColorName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Colors: ${colorsStr}\r\n ColorIndex: ${colorIndices}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding normal layer to resulting file\r\n * @param {Float32Array} normalArray attribute\r\n * @returns {string} normal layer info\r\n */\r\n _normalLayer(normalArray) {\r\n const layerElementNormalNumber = 0;\r\n const layerElementNormalVersion = 101;\r\n const layerElementNormalName = '';\r\n const normalsStr = this._floatArrayToString(normalArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n return `\r\n LayerElementNormal: ${layerElementNormalNumber} {\r\n Version: ${layerElementNormalVersion}\r\n Name: \"${layerElementNormalName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Normals: ${normalsStr}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding vertices and indices to resulting string\r\n * @return {string} resulting string in FBX notation\r\n */\r\n _verticesIndices(positions, indices) {\r\n const multiLayer = 0;\r\n const multiTake = 1;\r\n const shading = 'Y';\r\n const culling = 'CullingOff';\r\n const geometryVersion = 124;\r\n const vertStr = this._floatArrayToString(positions);\r\n /* About _correctArrayNotation: Float32Arrays will contains only Float32 numbers, which implies that it will be floating points with 17 numbers after point.\r\n * We cannot (and it's logically incorrect) save all this information, so we convert this Float32Array into Array-like object with numbers with only 6 numbers after point\r\n * Reminder - this is big memory loss (as we must save at one moment two arrays with similar information) */\r\n return `MultiLayer: ${multiLayer}\r\n MultiTake: ${multiTake}\r\n Shading: ${shading}\r\n Culling: \"${culling}\"\r\n Vertices: ${vertStr}\r\n PolygonVertexIndex: ${indices}\r\n GeometryVersion: ${geometryVersion}`;\r\n }\r\n\r\n /**\r\n * Forming material properties block.\r\n * @param {Object} material - given material of model\r\n * @returns {String} material properties string\r\n */\r\n _materialProperties(material) {\r\n return `Properties60: {\r\n Property: \"ShadingModel\", \"KString\", \"\", \"Lambert\"\r\n Property: \"MultiLayer\", \"bool\", \"\",0\r\n Property: \"EmissiveColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"EmissiveFactor\", \"double\", \"\",0.0000\r\n Property: \"AmbientColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"AmbientFactor\", \"double\", \"\",0.0000\r\n Property: \"DiffuseColor\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"DiffuseFactor\", \"double\", \"\",1.0000\r\n Property: \"Bump\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TransparentColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"TransparencyFactor\", \"double\", \"\",0.0000\r\n Property: \"SpecularColor\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"SpecularFactor\", \"double\", \"\",1.0000\r\n Property: \"ShininessExponent\", \"double\", \"\",${material.shininess}\r\n Property: \"ReflectionColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"ReflectionFactor\", \"double\", \"\",1\r\n Property: \"Ambient\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"Diffuse\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"Specular\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"Shininess\", \"double\", \"\",${material.shininess}\r\n Property: \"Opacity\", \"double\", \"\",${material.opacity}\r\n Property: \"Reflectivity\", \"double\", \"\",0\r\n }`;\r\n }\r\n}\r\n","import Exporter from './Exporter';\r\nimport FBXInfoExtractor from './fbx/FBXInfoExtractor';\r\nimport FBXResult from './fbx/FBXResult';\r\nimport ComplexVisual from '../../ComplexVisual';\r\n\r\nexport default class FBXExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n // Data\r\n this._data = source;\r\n this._version = options.miewVersion || '0.0-UNSPECIFIED';\r\n this._extractor = new FBXInfoExtractor();\r\n }\r\n\r\n /**\r\n * Entry point to exporter.\r\n */\r\n exportSync() {\r\n // Creating mandatory blocks\r\n const result = new FBXResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n const info = this._extractor.process(this._data);\r\n info.version = this._version;\r\n this._result = result.getResult(info);\r\n return this._result;\r\n }\r\n}\r\n\r\nFBXExporter.formats = ['fbx'];\r\nFBXExporter.SourceClass = ComplexVisual;\r\n","import ExporterList from './exporters/ExporterList';\r\n\r\nimport PDBExporter from './exporters/PDBExporter';\r\nimport FBXExporter from './exporters/FBXExporter';\r\n\r\nexport default new ExporterList([\r\n PDBExporter,\r\n FBXExporter,\r\n]);\r\n","import loaders from './loaders';\r\nimport parsers from './parsers';\r\nimport exporters from './exporters';\r\n\r\nexport default {\r\n loaders,\r\n parsers,\r\n exporters,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from './CSS2DObject';\r\n\r\nconst tempColor = new THREE.Color();\r\n\r\nclass CSS2DRenderer {\r\n constructor() {\r\n this._width = 0;\r\n this._height = 0;\r\n this._widthHalf = 0;\r\n this._heightHalf = 0;\r\n\r\n this._vector = new THREE.Vector3();\r\n this._viewMatrix = new THREE.Matrix4();\r\n this._projectionMatrix = new THREE.Matrix4();\r\n\r\n this._domElement = document.createElement('div');\r\n this._domElement.style.overflow = 'hidden';\r\n this._domElement.style.position = 'absolute';\r\n this._domElement.style.top = '0';\r\n this._domElement.style.zIndex = '0'; // start a new Stacking Context to enclose all z-ordered children\r\n this._domElement.style.pointerEvents = 'none';\r\n }\r\n\r\n getElement() {\r\n return this._domElement;\r\n }\r\n\r\n reset() {\r\n const myNode = this.getElement();\r\n while (myNode.firstChild) {\r\n myNode.removeChild(myNode.firstChild);\r\n }\r\n }\r\n\r\n setSize(width, height) {\r\n this._width = width;\r\n this._height = height;\r\n\r\n this._widthHalf = this._width / 2;\r\n this._heightHalf = this._height / 2;\r\n\r\n this._domElement.style.width = `${width}px`;\r\n this._domElement.style.height = `${height}px`;\r\n }\r\n\r\n _renderObject(object, camera, scene) {\r\n function lerpColorAsHex(a, b, t) {\r\n tempColor.setHex(a);\r\n tempColor.lerp(b, t);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n function colorAsHex(a) {\r\n tempColor.setHex(a);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n if (object instanceof CSS2DObject) {\r\n this._vector.setFromMatrixPosition(object.matrixWorld);\r\n\r\n if (object.userData !== undefined && object.userData.offset !== undefined) {\r\n const localOffset = new THREE.Vector3(object.userData.offset.x, object.userData.offset.y, 0);\r\n this._vector.add(localOffset.multiplyScalar(object.matrixWorld.getMaxScaleOnAxis()));\r\n }\r\n\r\n this._vector.applyMatrix4(this._viewMatrix);\r\n\r\n const visibility = this._vector.z > -camera.near ? 'hidden' : 'visible';\r\n const zIndex = 10000 * (camera.far - (-this._vector.z)) / (camera.far - camera.near);\r\n\r\n const element = object.getElement();\r\n if (typeof scene.fog === 'undefined') {\r\n element.style.color = colorAsHex(object.userData.color);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = colorAsHex(object.userData.background);\r\n }\r\n } else {\r\n const fogFactor = THREE.MathUtils.smoothstep(-this._vector.z, scene.fog.near, scene.fog.far);\r\n element.style.color = lerpColorAsHex(object.userData.color, scene.fog.color, fogFactor);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = lerpColorAsHex(object.userData.background, scene.fog.color, fogFactor);\r\n }\r\n }\r\n\r\n this._vector.applyMatrix4(this._projectionMatrix);\r\n\r\n const style = `${object.userData !== {} ? object.userData.translation : 'translate(-50%, -50%) '\r\n }translate(${this._vector.x * this._widthHalf + this._widthHalf}px,${\r\n -this._vector.y * this._heightHalf + this._heightHalf}px)`;\r\n element.style.visibility = visibility;\r\n element.style.WebkitTransform = style;\r\n element.style.MozTransform = style;\r\n element.style.oTransform = style;\r\n element.style.transform = style;\r\n element.style.zIndex = Number(zIndex).toFixed(0);\r\n\r\n if (element.parentNode !== this._domElement) {\r\n this._domElement.appendChild(element);\r\n }\r\n }\r\n\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n this._renderObject(object.children[i], camera, scene);\r\n }\r\n }\r\n\r\n render(scene, camera) {\r\n scene.updateMatrixWorld();\r\n\r\n if (camera.parent === null) {\r\n camera.updateMatrixWorld();\r\n }\r\n\r\n camera.matrixWorldInverse.copy(camera.matrixWorld).invert();\r\n\r\n this._viewMatrix.copy(camera.matrixWorldInverse);\r\n this._projectionMatrix.copy(camera.projectionMatrix);\r\n\r\n this._renderObject(scene, camera, scene);\r\n }\r\n}\r\nexport default CSS2DRenderer;\r\n","export default function getTopWindow() {\r\n // intercept the exception if we have cross-origin iframe\r\n try {\r\n if (window.top.location.href !== undefined) {\r\n return window.top;\r\n }\r\n } catch (e) {\r\n // provide fallback\r\n }\r\n return window;\r\n}\r\n","import * as THREE from 'three';\r\nimport Timer from '../Timer';\r\nimport settings from '../settings';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\nimport getTopWindow from '../utils/getTopWindow';\r\n\r\nconst VK_LEFT = 37;\r\nconst VK_UP = 38;\r\nconst VK_RIGHT = 39;\r\nconst VK_DOWN = 40;\r\n\r\nconst STATE = {\r\n NONE: -1, ROTATE: 0, TRANSLATE: 1, SCALE: 2, TRANSLATE_PIVOT: 3,\r\n};\r\n\r\n// pausing for this amount of time before releasing mouse button prevents inertial rotation (seconds)\r\nconst FULL_STOP_THRESHOLD = 0.1;\r\n\r\nconst quaternion = new THREE.Quaternion();\r\nconst matrix4 = new THREE.Matrix4();\r\n\r\n// pivot -- local offset of the rotation pivot point\r\nfunction ObjectHandler(objects, camera, pivot, options) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n this.camera = camera;\r\n this.pivot = pivot;\r\n this.axis = new THREE.Vector3(0, 0, 1);\r\n this.options = options;\r\n\r\n this.lastRotation = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n}\r\n\r\nObjectHandler.prototype._rotate = (function () {\r\n const p = new THREE.Vector3();\r\n const q = new THREE.Quaternion();\r\n const s = new THREE.Vector3();\r\n\r\n const m = new THREE.Matrix4();\r\n\r\n return function (quat) {\r\n const zeroPivot = (this.pivot.x === 0.0 && this.pivot.y === 0.0 && this.pivot.z === 0.0);\r\n\r\n m.copy(this.object.matrix);\r\n\r\n if (zeroPivot) {\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n } else {\r\n m.multiply(matrix4.makeTranslation(this.pivot.x, this.pivot.y, this.pivot.z));\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n m.multiply(matrix4.makeTranslation(-this.pivot.x, -this.pivot.y, -this.pivot.z));\r\n }\r\n\r\n m.decompose(p, q, s);\r\n\r\n // update objects\r\n if (!zeroPivot) {\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].position.copy(p);\r\n }\r\n }\r\n\r\n for (let j = 0; j < this.objects.length; ++j) {\r\n this.objects[j].quaternion.copy(q);\r\n this.objects[j].updateMatrix();\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.setObjects = function (objects) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n};\r\n\r\nObjectHandler.prototype.rotate = (function () {\r\n const rot = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n\r\n return function (quat, mousePrevPos, mouseCurPos, aboutAxis) {\r\n this.mouse2rotation(rot, mousePrevPos, mouseCurPos, aboutAxis);\r\n quat.setFromAxisAngle(rot.axis, rot.angle);\r\n\r\n if (rot.angle) {\r\n this._rotate(quat);\r\n }\r\n\r\n this.lastRotation = rot;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.translate = (function () {\r\n const dir = new THREE.Vector3();\r\n const pivot = new THREE.Vector3();\r\n\r\n return function (delta) {\r\n // reverse-project viewport movement to view coords (compensate for screen aspect ratio)\r\n dir.set(\r\n delta.x / this.camera.projectionMatrix.elements[0],\r\n delta.y / this.camera.projectionMatrix.elements[5],\r\n 0,\r\n );\r\n let dist = dir.length();\r\n dir.normalize();\r\n\r\n // transform movement direction to object local coords\r\n dir.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // visible translate distance shouldn't depend on camera-to-object distance\r\n pivot.copy(this.pivot);\r\n this.object.localToWorld(pivot);\r\n dist *= Math.abs(pivot.z - this.camera.position.z);\r\n\r\n // visible translate distance shouldn't depend on object scale\r\n dist /= this.object.matrixWorld.getMaxScaleOnAxis();\r\n\r\n // all objects are translated similar to principal object\r\n // (we assume they all have identical pivot and scale)\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].translateOnAxis(dir, dist);\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.update = (function () {\r\n const axis = new THREE.Vector3();\r\n\r\n return function (timeSinceLastUpdate, timeSinceMove) {\r\n if (settings.now.autoRotation !== 0.0) {\r\n // auto-rotation with constant speed\r\n\r\n // if rotation axis is fixed or hasn't been defined yet\r\n if (settings.now.autoRotationAxisFixed || this.lastRotation.axis.length() === 0.0) {\r\n // use Y-axis (transformed to local object coords)\r\n axis.set(0, 1, 0).transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n } else {\r\n // use axis defined by last user rotation\r\n axis.copy(this.lastRotation.axis);\r\n }\r\n\r\n this._rotate(quaternion.setFromAxisAngle(axis, settings.now.autoRotation * timeSinceLastUpdate));\r\n return true;\r\n }\r\n\r\n if (this.options.intertia && this.lastRotation.angle) {\r\n // inertial object rotation\r\n const angle = this.lastRotation.angle * ((1.0 - this.options.dynamicDampingFactor) ** (40.0 * timeSinceMove));\r\n\r\n if (Math.abs(angle) <= this.options.intertiaThreshold) {\r\n this.lastRotation.angle = 0.0;\r\n } else {\r\n this._rotate(quaternion.setFromAxisAngle(this.lastRotation.axis, angle));\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.stop = function () {\r\n this.lastRotation.angle = 0.0;\r\n};\r\n\r\n// calculate (axis, angle) pair from mouse/touch movement\r\nObjectHandler.prototype.mouse2rotation = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n const eye = new THREE.Vector3();\r\n const eyeDirection = new THREE.Vector3();\r\n\r\n const cameraUpDirection = new THREE.Vector3();\r\n const cameraSidewaysDirection = new THREE.Vector3();\r\n\r\n const moveDirection = new THREE.Vector3();\r\n\r\n const mouseDelta = new THREE.Vector2();\r\n\r\n return function (rot, mousePrev, mouseCur, aboutAxis) {\r\n if (aboutAxis) {\r\n rot.axis.copy(this.axis);\r\n rot.angle = this.options.axisRotateFactor * (mouseCur.y - mousePrev.y);\r\n\r\n /* cool method that allows rotation around Z axis to be \"tied\" to mouse cursor\r\n\r\n res.axis.copy(this.axis);\r\n\r\n var pivot = this.pivot.clone();\r\n this.object.localToWorld(pivot);\r\n pivot.project(this.camera);\r\n\r\n var v1 = new THREE.Vector3(mousePrev.x, mousePrev.y, this.camera.position.z);\r\n v1.sub(pivot);\r\n var v2 = new THREE.Vector3(mouseCur.x, mouseCur.y, this.camera.position.z);\r\n v2.sub(pivot);\r\n\r\n v1.sub(res.axis.clone().multiplyScalar(v1.dot(res.axis)));\r\n v2.sub(res.axis.clone().multiplyScalar(v2.dot(res.axis)));\r\n\r\n var abs = v1.length() * v2.length();\r\n if (abs > 0) {\r\n res.angle = res.axis.dot(v1.cross(v2)) / abs;\r\n }\r\n */\r\n } else {\r\n mouseDelta.subVectors(mouseCur, mousePrev);\r\n const angle = mouseDelta.length();\r\n if (angle === 0.0) {\r\n return;\r\n }\r\n\r\n center.copy(this.pivot);\r\n this.object.localToWorld(center);\r\n eye.subVectors(this.camera.position, center);\r\n eyeDirection.copy(eye).normalize();\r\n\r\n cameraUpDirection.copy(this.camera.up).normalize();\r\n cameraSidewaysDirection.crossVectors(cameraUpDirection, eyeDirection).normalize();\r\n\r\n cameraUpDirection.setLength(mouseDelta.y);\r\n cameraSidewaysDirection.setLength(mouseDelta.x);\r\n\r\n moveDirection.copy(cameraUpDirection.add(cameraSidewaysDirection));\r\n\r\n rot.axis.crossVectors(moveDirection, eye);\r\n\r\n rot.angle = -angle * this.options.rotateFactor;\r\n }\r\n\r\n rot.axis.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // make sure angle is always positive (thus 'axis' defines both axis and direction of rotation)\r\n if (rot.angle < 0.0) {\r\n rot.axis.negate();\r\n rot.angle = -rot.angle;\r\n }\r\n };\r\n}());\r\n\r\nfunction ObjectControls(object, objectPivot, camera, domElement, getAltObj) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.object = object;\r\n this.objectPivot = objectPivot;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.getAltObj = getAltObj;\r\n\r\n // API\r\n\r\n this.enabled = true;\r\n this.hotkeysEnabled = true;\r\n\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n\r\n this.options = {\r\n rotateFactor: Math.PI, // full screen slide (along short side) would roughly mean 180 deg. rotation\r\n axisRotateFactor: 4 * Math.PI, // full screen slide (along short side) would roughly mean 720 deg. rotation\r\n intertia: true,\r\n dynamicDampingFactor: 0.1,\r\n intertiaThreshold: 1e-3,\r\n };\r\n\r\n // internals\r\n\r\n this._state = STATE.NONE;\r\n\r\n this._mousePrevPos = new THREE.Vector2();\r\n this._mouseCurPos = new THREE.Vector2();\r\n\r\n this._mainObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._altObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._affectedObj = this._mainObj;\r\n this._isAltObjFreeRotationAllowed = true;\r\n this._isTranslationAllowed = true;\r\n this._isKeysTranslatingObj = false;\r\n\r\n this._pressedKeys = [];\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n this._lastUpdateTime = this._clock.getElapsedTime();\r\n\r\n // events\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousewheel',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'DOMMouseScroll',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseout',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchmove',\r\n handler(e) {\r\n self.touchmove(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keydown',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keyup',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'blur',\r\n handler() {\r\n self.resetKeys();\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'contextmenu',\r\n handler(e) {\r\n self.contextmenu(e);\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n\r\n this.resetKeys();\r\n\r\n // force an update at start\r\n this.update();\r\n}\r\n\r\n// methods\r\n\r\nObjectControls.prototype = Object.create(EventDispatcher.prototype);\r\nObjectControls.prototype.constructor = ObjectControls;\r\n\r\nObjectControls.prototype.resetKeys = function () {\r\n this._pressedKeys[VK_LEFT] = false;\r\n this._pressedKeys[VK_UP] = false;\r\n this._pressedKeys[VK_RIGHT] = false;\r\n this._pressedKeys[VK_DOWN] = false;\r\n};\r\n\r\nObjectControls.prototype.contextmenu = function (e) {\r\n e.stopPropagation();\r\n e.preventDefault();\r\n};\r\n\r\nObjectControls.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nObjectControls.prototype.enable = function (enable) {\r\n this.enabled = enable;\r\n};\r\n\r\nObjectControls.prototype.enableHotkeys = function (enable) {\r\n this.hotkeysEnabled = enable;\r\n};\r\n\r\nObjectControls.prototype.allowTranslation = function (allow) {\r\n this._isTranslationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.allowAltObjFreeRotation = function (allow) {\r\n this._isAltObjFreeRotationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.keysTranslateObj = function (on) {\r\n this._isKeysTranslatingObj = on;\r\n};\r\n\r\nObjectControls.prototype.isEditingAltObj = function () {\r\n return ((this._state === STATE.ROTATE) || (this._state === STATE.TRANSLATE))\r\n && (this._affectedObj === this._altObj);\r\n};\r\n\r\n// convert page coords of mouse/touch to uniform coords with smaller side being [-0.5, 0.5]\r\n// (uniform coords keep direct proportion with screen distance travelled by mouse regardless of screen aspect ratio)\r\nObjectControls.prototype.convertMouseToOnCircle = function (coords, pageX, pageY) {\r\n const screenSize = Math.min(this.screen.width, this.screen.height);\r\n\r\n if (screenSize === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n ((pageX - this.screen.width * 0.5 - this.screen.left) / screenSize),\r\n ((0.5 * this.screen.height + this.screen.top - pageY) / screenSize),\r\n );\r\n};\r\n\r\n// convert page coords of mouse/touch to viewport coords with both sides being [-1, 1]\r\n// (those are non-uniform coords affected by screen aspect ratio)\r\nObjectControls.prototype.convertMouseToViewport = function (coords, pageX, pageY) {\r\n if (this.screen.width === 0 || this.screen.height === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n (2.0 * (pageX - this.screen.width * 0.5 - this.screen.left) / this.screen.width),\r\n (2.0 * (0.5 * this.screen.height + this.screen.top - pageY) / this.screen.height),\r\n );\r\n};\r\n\r\nObjectControls.prototype.stop = function () {\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n};\r\n\r\n// rotate object based on latest mouse/touch movement\r\nObjectControls.prototype.rotateByMouse = (function () {\r\n const quat = new THREE.Quaternion();\r\n\r\n return function (aboutZAxis) {\r\n this._affectedObj.rotate(quat, this._mousePrevPos, this._mouseCurPos, aboutZAxis);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n };\r\n}());\r\n\r\n// rotate object by specified quaternion\r\nObjectControls.prototype.rotate = function (quat) {\r\n this.object.quaternion.multiply(quat);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n};\r\n\r\n// get object's orientation\r\nObjectControls.prototype.getOrientation = function () {\r\n return this.object.quaternion;\r\n};\r\n\r\n// set object's orientation\r\nObjectControls.prototype.setOrientation = function (quat) {\r\n this.object.quaternion.copy(quat);\r\n};\r\n\r\n// translate object based on latest mouse/touch movement\r\nObjectControls.prototype.translate = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this._affectedObj.translate(delta);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n };\r\n}());\r\n\r\n// get object scale\r\nObjectControls.prototype.getScale = function () {\r\n return this.object.scale.x;\r\n};\r\n\r\n// set uniform object scale\r\nObjectControls.prototype.setScale = function (scale) {\r\n this.object.scale.set(scale, scale, scale);\r\n};\r\n\r\n// scale object by factor (factor should be greater than zero)\r\nObjectControls.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n return;\r\n }\r\n this.setScale(this.object.scale.x * factor);\r\n this.dispatchEvent({ type: 'change', action: 'zoom', factor });\r\n};\r\n\r\nObjectControls.prototype.update = (function () {\r\n const shift = new THREE.Vector2();\r\n\r\n return function () {\r\n const curTime = this._clock.getElapsedTime();\r\n const timeSinceLastUpdate = curTime - this._lastUpdateTime;\r\n\r\n // update object handler\r\n if (this._state === STATE.NONE) {\r\n const timeSinceMove = curTime - this._lastMouseMoveTime;\r\n if (this._mainObj.update(timeSinceLastUpdate, timeSinceMove)\r\n || this._altObj.update(timeSinceLastUpdate, timeSinceMove)) {\r\n this.dispatchEvent({ type: 'change', action: 'auto' });\r\n }\r\n }\r\n\r\n // apply arrow keys\r\n if (this._isKeysTranslatingObj) {\r\n const speedX = Number(this._pressedKeys[VK_RIGHT]) - Number(this._pressedKeys[VK_LEFT]);\r\n const speedY = Number(this._pressedKeys[VK_UP]) - Number(this._pressedKeys[VK_DOWN]);\r\n if (speedX !== 0.0 || speedY !== 0.0) {\r\n const delta = timeSinceLastUpdate;\r\n\r\n // update object translation\r\n const altObj = this.getAltObj();\r\n if (altObj.objects.length > 0) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n\r\n shift.set(delta * speedX, delta * speedY);\r\n this._altObj.translate(shift);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n }\r\n }\r\n }\r\n\r\n this._lastUpdateTime = curTime;\r\n };\r\n}());\r\n\r\nObjectControls.prototype.reset = function () {\r\n this._state = STATE.NONE;\r\n\r\n this.object.quaternion.copy(quaternion.set(0, 0, 0, 1));\r\n};\r\n\r\n// listeners\r\n\r\nObjectControls.prototype.mousedown = function (event) {\r\n if (this.enabled === false || this._state !== STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (this._state === STATE.NONE) {\r\n if (event.button === 0) {\r\n this._affectedObj.stop(); // can edit only one object at a time\r\n\r\n let workWithAltObj = false;\r\n\r\n if (event.altKey) {\r\n const altObj = this.getAltObj();\r\n workWithAltObj = (altObj.objects.length > 0);\r\n if (workWithAltObj) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n this._affectedObj = workWithAltObj ? this._altObj : this._mainObj;\r\n\r\n this._state = (workWithAltObj && event.ctrlKey && this._isTranslationAllowed) ? STATE.TRANSLATE : STATE.ROTATE;\r\n } else if (event.button === 2) {\r\n this._state = STATE.TRANSLATE_PIVOT;\r\n }\r\n }\r\n\r\n if (this._state === STATE.ROTATE) {\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n\r\n if (this._state === STATE.TRANSLATE || this._state === STATE.TRANSLATE_PIVOT) {\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousemove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this.rotateByMouse((event.altKey && !this._isAltObjFreeRotationAllowed) || event.shiftKey);\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.TRANSLATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translate();\r\n break;\r\n\r\n case STATE.TRANSLATE_PIVOT:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translatePivotByMouse();\r\n break;\r\n\r\n default: break;\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousewheel = function (event) {\r\n if (this.enabled === false || !settings.now.zooming || this._state !== STATE.NONE || event.shiftKey) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n\r\n let delta = 0;\r\n\r\n if (event.wheelDelta) {\r\n // WebKit / Opera / Explorer 9\r\n delta = event.wheelDelta / 40;\r\n } else if (event.detail) {\r\n // Firefox\r\n delta = -event.detail / 3;\r\n }\r\n\r\n let factor = 1.0 + delta * 0.05;\r\n factor = Math.max(factor, 0.01);\r\n this.scale(factor);\r\n};\r\n\r\nObjectControls.prototype.mouseup = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n this._state = STATE.NONE;\r\n\r\n if (this._clock.getElapsedTime() - this._lastMouseMoveTime > FULL_STOP_THRESHOLD) {\r\n this._affectedObj.stop();\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchstartend = function (event) {\r\n if (this.enabled === false) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (event.touches.length) {\r\n case 1:\r\n this._state = STATE.ROTATE;\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n break;\r\n\r\n case 2: {\r\n // prevent inertial rotation\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n\r\n this._state = STATE.SCALE;\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = this._touchDistanceStart = Math.sqrt(dx * dx + dy * dy);\r\n this._scaleStart = this.object.scale.x;\r\n break;\r\n }\r\n\r\n default:\r\n this._state = STATE.NONE;\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchmove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this.rotateByMouse(false);\r\n\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.SCALE:\r\n if (settings.now.zooming) {\r\n // update scale\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = Math.sqrt(dx * dx + dy * dy);\r\n const newScale = this._scaleStart * this._touchDistanceCur / this._touchDistanceStart;\r\n const factor = newScale / this.object.scale.x;\r\n this.scale(factor);\r\n }\r\n break;\r\n\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.keydownup = function (event) {\r\n if (this.enabled === false || this.hotkeysEnabled === false) {\r\n return;\r\n }\r\n\r\n switch (event.keyCode) {\r\n case VK_LEFT:\r\n case VK_UP:\r\n case VK_RIGHT:\r\n case VK_DOWN:\r\n this._pressedKeys[event.keyCode] = (event.type === 'keydown');\r\n event.preventDefault();\r\n event.stopPropagation();\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.getKeyBindObject = function () {\r\n return getTopWindow();\r\n};\r\n\r\nObjectControls.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nObjectControls.prototype.translatePivotByMouse = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this.translatePivotInWorld(settings.now.translationSpeed * delta.x, settings.now.translationSpeed * delta.y, 0);\r\n };\r\n}());\r\n\r\n// Translate in WorldCS, translation is scaled with root scale matrix\r\nObjectControls.prototype.translatePivotInWorld = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.applyMatrix4(this.object.matrixWorld);\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n pos.applyMatrix4(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Translate in ModelCS, x, y, z are Ang\r\nObjectControls.prototype.translatePivot = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Set pivot\r\nObjectControls.prototype.setPivot = function (newPivot) {\r\n this.objectPivot.position.copy(newPivot);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\nexport default ObjectControls;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\nimport Timer from '../Timer';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\n\r\nfunction Picker(gfxObj, camera, domElement) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.gfxObj = gfxObj;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n this._lastMousePos = new THREE.Vector2(0, 0);\r\n this._mouseTotalDist = 0.0;\r\n this._lastClickBeginTime = -1000.0;\r\n this._lastClickPos = new THREE.Vector2(0, 0);\r\n this._clickBeginTime = 0.0;\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstart(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchend(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n}\r\n\r\nPicker.prototype = Object.create(EventDispatcher.prototype);\r\nPicker.prototype.constructor = Picker;\r\n\r\nPicker.prototype.reset = function () {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n};\r\n\r\nPicker.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nPicker.prototype.pickObject = function (screenPos) {\r\n if (!this.gfxObj) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n const { gfxObj } = this;\r\n const rayCaster = new THREE.Raycaster();\r\n rayCaster.ray.origin.setFromMatrixPosition(this.camera.matrixWorld);\r\n rayCaster.ray.direction.set(screenPos.x, screenPos.y, 0.5).unproject(this.camera).sub(rayCaster.ray.origin).normalize();\r\n\r\n const clipPlane = (settings.now.draft.clipPlane && this.clipPlaneValue) ? this.clipPlaneValue : Infinity;\r\n const fogFarPlane = (settings.now.fog && this.fogFarValue) ? this.fogFarValue : Infinity;\r\n const point = rayCaster.intersectVisibleObject(gfxObj, this.camera, clipPlane, fogFarPlane);\r\n if (!point) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n let picked = {};\r\n if (point.residue || point.atom) {\r\n const residue = point.residue || point.atom.residue;\r\n if (settings.now.pick === 'chain') {\r\n picked = { chain: residue.getChain() };\r\n } else if (settings.now.pick === 'molecule') {\r\n picked = { molecule: residue.getMolecule() };\r\n } else if (point.residue || settings.now.pick === 'residue') {\r\n picked = { residue };\r\n } else if (point.atom) {\r\n picked = { atom: point.atom };\r\n }\r\n }\r\n this.picked = picked;\r\n this.dispatchEvent({ type: 'newpick', obj: picked });\r\n};\r\n\r\nPicker.prototype.getMouseInViewport = function (pageX, pageY) {\r\n return new THREE.Vector2(\r\n (pageX - this.screen.left) / this.screen.width * 2 - 1,\r\n -(pageY - this.screen.top) / this.screen.height * 2 + 1,\r\n );\r\n};\r\n\r\nPicker.prototype.mousedown = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n this._lastMousePos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist = 0.0;\r\n this._clickBeginTime = this._clock.getElapsedTime();\r\n }\r\n};\r\n\r\nPicker.prototype.mousemove = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n const pos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist += pos.sub(this._lastMousePos).length();\r\n};\r\n\r\nPicker.prototype.mouseup = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n if (this._mouseTotalDist < 0.01) {\r\n const curTime = this._clock.getElapsedTime();\r\n const curPos = this.getMouseInViewport(event.pageX, event.pageY);\r\n\r\n const timeSinceLastClickBegin = curTime - this._lastClickBeginTime;\r\n if (timeSinceLastClickBegin < 0.7) {\r\n const clickDist = new THREE.Vector2().subVectors(curPos, this._lastClickPos);\r\n if (clickDist.length() < 0.01) {\r\n // it's a double click\r\n this.dispatchEvent({ type: 'dblclick', obj: this.picked });\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = -1000; // this click cannot serve as first click in double-click\r\n return;\r\n }\r\n }\r\n\r\n setTimeout(() => {\r\n self.pickObject(curPos);\r\n }, 0);\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = this._clickBeginTime;\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.touchstart = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 1) {\r\n this._lastTouchdownPos = this.getMouseInViewport(event.touches[0].pageX, event.touches[0].pageY);\r\n }\r\n};\r\n\r\nPicker.prototype.touchend = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 0\r\n && event.changedTouches.length === 1) {\r\n const pos = this.getMouseInViewport(event.changedTouches[0].pageX, event.changedTouches[0].pageY);\r\n const dist = pos.sub(this._lastTouchdownPos).length();\r\n if (dist < 0.01) {\r\n setTimeout(() => {\r\n self.pickObject(self._lastTouchdownPos);\r\n }, 0);\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nexport default Picker;\r\n","import * as THREE from 'three';\r\n\r\nclass Axes {\r\n constructor(target, targetCamera) {\r\n this._target = target;\r\n this._targetCamera = targetCamera;\r\n this._camera = new THREE.PerspectiveCamera(targetCamera.fov, targetCamera.aspect, 1, 100);\r\n this._object = new THREE.AxesHelper(1);\r\n this._scene = new THREE.Scene();\r\n this._scene.add(this._object);\r\n this._full = new THREE.Vector2();\r\n\r\n this._update();\r\n }\r\n\r\n _update() {\r\n const { fov } = this._targetCamera;\r\n const camera = this._camera;\r\n camera.aspect = this._targetCamera.aspect;\r\n camera.setMinimalFov(fov);\r\n camera.setDistanceToFit(1.0, fov);\r\n camera.updateProjectionMatrix();\r\n\r\n this._object.quaternion.copy(this._target.quaternion);\r\n }\r\n\r\n render(renderer) {\r\n this._update();\r\n\r\n renderer.getSize(this._full);\r\n const width = this._full.width * 0.25;\r\n const height = this._full.height * 0.25;\r\n\r\n const { autoClear } = renderer;\r\n renderer.autoClear = false;\r\n renderer.setViewport(0.0, 0.0, width, height);\r\n renderer.clear(false, true, false);\r\n renderer.render(this._scene, this._camera);\r\n renderer.setViewport(0, 0, this._full.width, this._full.height);\r\n renderer.autoClear = autoClear;\r\n }\r\n}\r\nexport default Axes;\r\n","import * as THREE from 'three';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\n\r\nconst cDataOffset = 12;\r\nconst cFirstMask = 0x0FFFFF00;\r\nconst cFirstShift = 8;\r\nconst cSecMask1 = 0x000000FF;\r\nconst cSecShift1 = 12;\r\nconst cSecMask2 = 0xFFF00000;\r\nconst cSecShift2 = 20;\r\nconst cThirdMask = 0x000FFFFF;\r\nconst cStrMask = 0xF0000000;\r\nconst cStrShift = 28;\r\nconst c219 = 1 << 19;\r\nconst c220 = 1 << 20;\r\n\r\nconst cHelixIdx = 1;\r\nconst cSheetIdx = 2;\r\nconst secTypes = ['helix', 'strand'];\r\nconst cSecNames = ['fs', 'ps', 'ns', 'us'];\r\n\r\nfunction _createSecondary(strArray, complex) {\r\n const residues = complex._residues;\r\n const nRes = residues.length;\r\n const resid = new Uint8Array(nRes);\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, n = strArray.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n resid[atom.residue._index] = strArray[i];\r\n }\r\n\r\n const secondary = [];\r\n let rIdx = 0;\r\n while (rIdx < nRes) {\r\n if (resid[rIdx] !== 0) {\r\n const start = rIdx;\r\n const val = resid[rIdx];\r\n while (rIdx < nRes - 1 && resid[rIdx + 1] === val\r\n && residues[rIdx].isConnected(residues[rIdx + 1])) {\r\n ++rIdx;\r\n }\r\n secondary.push({ start, end: rIdx, type: secTypes[val - 1] });\r\n }\r\n ++rIdx;\r\n }\r\n return secondary;\r\n}\r\n\r\nfunction fromUInt20ToInt20(uint20) {\r\n return uint20 >= c219 ? uint20 - c220 : uint20;\r\n}\r\n\r\nclass FrameInfo {\r\n constructor(complex, payload, callbacks) {\r\n this._complex = complex;\r\n this._secondary = null;\r\n this.isLoading = false;\r\n this._framesRange = {\r\n start: 0,\r\n end: -1,\r\n };\r\n this.frameIsReady = false;\r\n this._buffer = null;\r\n this._frameRequest = null;\r\n this._callbacks = callbacks;\r\n if (typeof payload === 'function') {\r\n this._framesRequestLength = 1;\r\n this._downloadDataFn = payload;\r\n } else {\r\n this.parseBinaryData(payload, true);\r\n }\r\n this.reset();\r\n this.setFrame(0);\r\n }\r\n\r\n _prepareBuffer(framesStart, framesEnd) {\r\n if (framesStart === undefined || framesStart === null) {\r\n framesStart = 0;\r\n }\r\n if (framesEnd === undefined || framesEnd === null) {\r\n framesEnd = framesStart + this._framesRequestLength;\r\n }\r\n if (this._framesCount !== undefined) {\r\n framesEnd = Math.min(this._framesCount - 1, framesEnd);\r\n }\r\n if (this._downloadDataFn) {\r\n const self = this;\r\n const onDone = function (data) {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n self._buffer = {\r\n data,\r\n state: 'ready',\r\n start: framesStart,\r\n end: framesEnd,\r\n };\r\n if (self._frameRequest !== null) {\r\n const idx = self._frameRequest;\r\n self._frameRequest = null;\r\n self.setFrame(idx);\r\n }\r\n };\r\n const onFail = function () {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onError === 'function') {\r\n self._callbacks.onError('Streaming failed');\r\n }\r\n };\r\n if (!this._buffer) {\r\n this._buffer = {};\r\n }\r\n this._buffer.state = 'downloading';\r\n this.isLoading = true;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n this._downloadDataFn({ start: framesStart, end: framesEnd + 1 }, onDone, onFail);\r\n }\r\n }\r\n\r\n _parseBuffer() {\r\n if (this._buffer && this._buffer.state === 'ready') {\r\n this._framesRange = {\r\n start: this._buffer.start,\r\n end: this._buffer.end,\r\n };\r\n this.parseBinaryData(this._buffer.data, false);\r\n let _bufferRequestStart = (this._buffer.end + 1) % this._framesCount;\r\n if (_bufferRequestStart >= this._framesCount) {\r\n _bufferRequestStart = 0;\r\n }\r\n this._buffer = {\r\n state: 'none',\r\n };\r\n this._prepareBuffer(_bufferRequestStart, _bufferRequestStart + this._framesRequestLength);\r\n if (this._frameRequest !== null) {\r\n const idx = this._frameRequest;\r\n this._frameRequest = null;\r\n this.setFrame(idx);\r\n }\r\n }\r\n }\r\n\r\n parseBinaryData(arrayBuffer) {\r\n const dataView = new DataView(arrayBuffer);\r\n let offset = 0;\r\n const atomsCount = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const framesCount = dataView.getUint32(offset, true);\r\n this._framesCount = framesCount;\r\n this._framesRange.end = this._framesRange.end > 0\r\n ? Math.min(this._framesRange.end, framesCount - 1) : framesCount - 1;\r\n offset += 4;\r\n this._atomsCount = atomsCount;\r\n const maxSize = 1024 * 1024; // 1 MB\r\n this._framesRequestLength = Math.ceil(maxSize / (atomsCount * 8));\r\n const chunkedFramesCount = this._framesRange.end - this._framesRange.start + 1;\r\n if (atomsCount !== this._complex._atoms.length\r\n || arrayBuffer.byteLength !== cDataOffset + chunkedFramesCount * atomsCount * 8) {\r\n throw new Error();\r\n }\r\n const complex = this._complex;\r\n let timeStep = dataView.getUint32(offset, true);\r\n let iName = 0;\r\n while (timeStep > 1000 && iName < cSecNames.length - 1) {\r\n timeStep /= 1000;\r\n ++iName;\r\n }\r\n\r\n this._timeStep = `${timeStep.toString()} ${cSecNames[iName]}`;\r\n offset += 4;\r\n const secondary = [];\r\n const posData = new Float32Array(chunkedFramesCount * atomsCount * 3);\r\n let coordIdx = 0;\r\n const secondaryArr = new Int8Array(atomsCount);\r\n for (let j = 0; j < chunkedFramesCount; ++j) {\r\n for (let i = 0; i < atomsCount; ++i) {\r\n const hiWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const loWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const str = (loWord & cStrMask) >>> cStrShift;\r\n const x = fromUInt20ToInt20(((loWord & cFirstMask) >>> cFirstShift) >> 0);\r\n const y = fromUInt20ToInt20((((loWord & cSecMask1) << cSecShift1)\r\n | ((hiWord & cSecMask2) >>> cSecShift2)) >> 0);\r\n const z = fromUInt20ToInt20((hiWord & cThirdMask) >> 0);\r\n secondaryArr[i] = 0;\r\n if (str > 0 && str < 4) {\r\n secondaryArr[i] = cHelixIdx;\r\n } else if (str === 4) {\r\n secondaryArr[i] = cSheetIdx;\r\n }\r\n posData[coordIdx++] = x / 100;\r\n posData[coordIdx++] = y / 100;\r\n posData[coordIdx++] = z / 100;\r\n }\r\n secondary.push(_createSecondary(secondaryArr, complex));\r\n }\r\n this._secondaryData = secondary;\r\n this._data = posData;\r\n }\r\n\r\n nextFrame() {\r\n this.setFrame((this._currFrame + 1) % this._framesCount);\r\n }\r\n\r\n needsColorUpdate(colorer) {\r\n return colorer instanceof SecondaryStructureColorer;\r\n }\r\n\r\n getAtomColor(colorer, atom) {\r\n return colorer.getResidueColor(this._residues[atom.residue._index], this._complex);\r\n }\r\n\r\n getResidueColor(colorer, residue) {\r\n return colorer.getResidueColor(this._residues[residue._index], this._complex);\r\n }\r\n\r\n _updateSecondary() {\r\n let i;\r\n const myResidues = this._residues;\r\n let n = myResidues.length;\r\n for (i = 0; i < n; ++i) {\r\n myResidues[i]._secondary = null;\r\n }\r\n const sec = this._secondaryData[this._currFrame - this._framesRange.start];\r\n for (i = 0, n = sec.length; i < n; ++i) {\r\n const oldSec = sec[i];\r\n const { start, end } = oldSec;\r\n const nSec = {\r\n _start: myResidues[start],\r\n _end: myResidues[end],\r\n type: oldSec.type,\r\n generic: oldSec.generic,\r\n };\r\n for (let j = start; j <= end; ++j) {\r\n myResidues[j]._secondary = nSec;\r\n }\r\n }\r\n }\r\n\r\n reset() {\r\n const compRes = this._complex._residues;\r\n const n = compRes.length;\r\n this._residues = new Array(n);\r\n const myResidues = this._residues;\r\n const getSec = function () {\r\n return this._secondary;\r\n };\r\n for (let i = 0; i < n; ++i) {\r\n myResidues[i] = {\r\n _type: compRes[i]._type,\r\n _isValid: compRes[i]._isValid,\r\n _controlPoint: null,\r\n _wingVector: null,\r\n _secondary: null,\r\n getSecondary: getSec,\r\n };\r\n }\r\n }\r\n\r\n setFrame(frameIdx) {\r\n this.frameIsReady = false;\r\n if (frameIdx >= this._framesRange.start && frameIdx <= this._framesRange.end) {\r\n this._currFrame = frameIdx;\r\n this._cachedResidues = false;\r\n this._updateSecondary();\r\n this.frameIsReady = true;\r\n } else {\r\n this._frameRequest = frameIdx;\r\n if (!this._buffer) {\r\n this._prepareBuffer(frameIdx);\r\n } else {\r\n const self = this;\r\n switch (this._buffer.state) {\r\n case 'none':\r\n this._prepareBuffer(frameIdx);\r\n break;\r\n case 'ready':\r\n self._parseBuffer();\r\n break;\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n disableEvents() {\r\n this._callbacks = null;\r\n }\r\n\r\n /**\r\n * Returns link to atom pos vector, clone it if needed\r\n */\r\n\r\n static _vec = new THREE.Vector3();\r\n\r\n getAtomPos(atomIdx) {\r\n const vec = FrameInfo._vec;\r\n const self = this;\r\n const data = self._data;\r\n const idx = (self._atomsCount * (self._currFrame - self._framesRange.start) + atomIdx) * 3;\r\n vec.set(data[idx], data[idx + 1], data[idx + 2]);\r\n return vec;\r\n }\r\n\r\n getResidues() {\r\n if (this._cachedResidues) {\r\n return this._residues;\r\n }\r\n this._complex.updateToFrame(this);\r\n return this._residues;\r\n }\r\n}\r\nexport default FrameInfo;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\n\r\n/**\r\n * Create new scene object.\r\n *\r\n * @param {array=} params - Object required params.\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports SceneObject\r\n * @this SceneObject\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all scene objects that are not reps.\r\n */\r\nclass SceneObject {\r\n constructor(params, opts) {\r\n if (this.constructor === SceneObject) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Object's options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.params = params;\r\n this.opts = _.merge(utils.deriveDeep(settings.now.objects[this.type], true), opts);\r\n this.needsRebuild = false;\r\n this._mesh = null;\r\n this.id = null;\r\n }\r\n\r\n /**\r\n * Get object identification, probably with options.\r\n * @returns {Object} field type contains type information, params - object's formal parameters,\r\n * opts - changed options\r\n * Options are returned if they were changed during or after object creation.\r\n */\r\n identify() {\r\n const result = {\r\n type: this.type,\r\n params: this.params,\r\n };\r\n const diff = utils.objectsDiff(this.opts, settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n result.opts = diff;\r\n }\r\n return result;\r\n }\r\n\r\n toString() {\r\n const paramsStr = `o=${this.type},${this.params.join(',')}`;\r\n const optsStr = utils.compareOptionsWithDefaults(this.opts, settings.defaults.objects[this.type]);\r\n return paramsStr + optsStr;\r\n }\r\n\r\n getGeometry() {\r\n return this._mesh;\r\n }\r\n\r\n destroy() {\r\n if (this._mesh) {\r\n gfxutils.destroyObject(this._mesh);\r\n }\r\n }\r\n}\r\n\r\n/**\r\n * Scene object identifier.\r\n * @type {string}\r\n */\r\nSceneObject.prototype.type = '__';\r\n\r\nexport default SceneObject;\r\n","import * as THREE from 'three';\r\nimport SceneObject from './SceneObject';\r\nimport meshutils from '../meshutils';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\nimport meshes from '../meshes/meshes';\r\nimport settings from '../../settings';\r\n\r\nclass LinesObj extends SceneObject {\r\n constructor(params, opts) {\r\n super(params, opts);\r\n if (params.length < 2) {\r\n throw new Error('Wrong number of argumets on line object creation!');\r\n }\r\n [this._id1, this._id2] = params;\r\n }\r\n\r\n _getAtomFromName(complex, atomId) {\r\n const err = ' - Wrong atom format it must be \\'#CHAIN_NAME.#RESIDUE_NUMBER.#ATOM_NAME\\' (e.g. \\'A.38.CO1\\')';\r\n const atom1 = complex.getAtomByFullname(atomId);\r\n if (!atom1) {\r\n throw new Error(atomId + err);\r\n }\r\n return atom1;\r\n }\r\n\r\n build(complex) {\r\n const geom = new THREE.BufferGeometry();\r\n this._atom1 = this._getAtomFromName(complex, this._id1);\r\n this._atom2 = this._getAtomFromName(complex, this._id2);\r\n\r\n const p1 = this._atom1.position;\r\n const p2 = this._atom2.position;\r\n const vertices = new Float32Array([\r\n p1.x, p1.y, p1.z,\r\n p2.x, p2.y, p2.z,\r\n ]);\r\n\r\n geom.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n geom.computeBoundingBox();\r\n\r\n this._line = new meshes.Line(geom, new UberMaterial({\r\n lights: false,\r\n overrideColor: true,\r\n dashedLine: true,\r\n fogTransparent: settings.now.bg.transparent,\r\n }));\r\n this._line.computeLineDistances();\r\n this._line.material.setUberOptions({\r\n fixedColor: new THREE.Color(this.opts.color),\r\n dashedLineSize: this.opts.dashSize,\r\n dashedLinePeriod: this.opts.dashSize + this.opts.gapSize,\r\n });\r\n this._line.material.updateUniforms();\r\n\r\n this._line.raycast = function (_raycaster, _intersects) {};\r\n this._mesh = this._line;\r\n const transforms = complex.getTransforms();\r\n if (transforms.length > 0) {\r\n this._mesh = new THREE.Group();\r\n this._mesh.add(this._line);\r\n meshutils.applyTransformsToMeshes(this._mesh, transforms);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n if (!this._atom1 || !this._atom2 || !this._line) {\r\n return;\r\n }\r\n\r\n const geo = this._line.geometry;\r\n geo.vertices[0].copy(frameData.getAtomPos(this._atom1.index));\r\n geo.vertices[1].copy(frameData.getAtomPos(this._atom2.index));\r\n this._line.computeLineDistances();\r\n geo.computeBoundingSphere();\r\n\r\n geo.verticesNeedUpdate = true;\r\n }\r\n}\r\n\r\nLinesObj.prototype.constructor = LinesObj;\r\nLinesObj.prototype.type = 'line';\r\n\r\nexport default LinesObj;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Outline.frag';\r\n\r\nclass OutlineMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n // add depth outline\r\n super(params);\r\n\r\n const settings = {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcDepthTex: { type: 't', value: null },\r\n srcTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n color: { type: 'v3', value: null },\r\n threshold: { type: 'f', value: null },\r\n opacity: { type: 'f', value: 1.0 },\r\n thickness: { type: 'v2', value: new THREE.Vector2(1, 1) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: true,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n\r\n this.setValues(settings);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n const defines = {};\r\n\r\n if (this.depth) {\r\n defines.DEPTH_OUTLINE = 1;\r\n }\r\n\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nOutlineMaterial.prototype.depth = false;\r\n\r\nexport default OutlineMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './FXAA.frag';\r\n\r\nclass FXAAMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n bgColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.bgTransparent) {\r\n defines.BG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nFXAAMaterial.prototype.bgTransparent = false;\r\n\r\nexport default FXAAMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AO.frag';\r\nimport noise from '../noiseTexture';\r\n\r\nconst _samplesKernel = [\r\n // hemisphere samples adopted to sphere\r\n new THREE.Vector3(0.295184, 0.077723, 0.068429),\r\n new THREE.Vector3(-0.271976, -0.365221, 0.838363),\r\n new THREE.Vector3(0.547713, 0.467576, 0.488515),\r\n new THREE.Vector3(0.662808, -0.031733, 0.584758),\r\n new THREE.Vector3(-0.025717, 0.218955, 0.657094),\r\n new THREE.Vector3(-0.310153, -0.365223, 0.370701),\r\n new THREE.Vector3(-0.101407, -0.006313, 0.747665),\r\n new THREE.Vector3(-0.769138, 0.360399, 0.086847),\r\n new THREE.Vector3(-0.271988, -0.275140, 0.905353),\r\n new THREE.Vector3(0.096740, -0.566901, 0.700151),\r\n new THREE.Vector3(0.562872, -0.735136, 0.094647),\r\n new THREE.Vector3(0.379877, 0.359278, 0.190061),\r\n new THREE.Vector3(0.519064, -0.023055, 0.405068),\r\n new THREE.Vector3(-0.301036, 0.114696, 0.088885),\r\n new THREE.Vector3(-0.282922, 0.598305, 0.487214),\r\n new THREE.Vector3(-0.181859, 0.251670, 0.679702),\r\n new THREE.Vector3(-0.191463, -0.635818, 0.512919),\r\n new THREE.Vector3(-0.293655, 0.427423, 0.078921),\r\n new THREE.Vector3(-0.267983, 0.680534, 0.132880),\r\n new THREE.Vector3(0.139611, 0.319637, 0.477439),\r\n new THREE.Vector3(-0.352086, 0.311040, 0.653913),\r\n new THREE.Vector3(0.321032, 0.805279, 0.487345),\r\n new THREE.Vector3(0.073516, 0.820734, 0.414183),\r\n new THREE.Vector3(-0.155324, 0.589983, 0.411460),\r\n new THREE.Vector3(0.335976, 0.170782, 0.527627),\r\n new THREE.Vector3(0.463460, -0.355658, 0.167689),\r\n new THREE.Vector3(0.222654, 0.596550, 0.769406),\r\n new THREE.Vector3(0.922138, -0.042070, 0.147555),\r\n new THREE.Vector3(-0.727050, -0.329192, 0.369826),\r\n new THREE.Vector3(-0.090731, 0.533820, 0.463767),\r\n new THREE.Vector3(-0.323457, -0.876559, 0.238524),\r\n new THREE.Vector3(-0.663277, -0.372384, 0.342856),\r\n];\r\n\r\nclass AOMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n noiseTexture: { type: 't', value: noise.noiseTexture },\r\n noiseTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight) },\r\n diffuseTexture: { type: 't', value: null },\r\n normalTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n camNearFar: { type: 'v2', value: new THREE.Vector2(1.0, 10.0) },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n samplesKernel: { type: 'v3v', value: _samplesKernel },\r\n kernelRadius: { type: 'f', value: 1.0 },\r\n depthThreshold: { type: 'f', value: 1.0 },\r\n factor: { type: 'f', value: 1.0 },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOHorBlur.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOHorBlurMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOHorBlurMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOVertBlurWithBlend.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOVertBlurWithBlendMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n diffuseTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n fogNearFar: { type: 'v2', value: new THREE.Vector2(100.0, 100.0) },\r\n fogColor: { type: 'v4', value: new THREE.Vector4(0.0, 0.5, 0.0, 1.0) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.useFog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nAOVertBlurWithBlendMaterial.prototype.useFog = true;\r\nAOVertBlurWithBlendMaterial.prototype.fogTransparent = false;\r\n\r\nexport default AOVertBlurWithBlendMaterial;\r\n","/* eslint-disable no-magic-numbers */\r\n/* eslint-disable guard-for-in */\r\nimport * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Anaglyph.frag';\r\n\r\nclass AnaglyphMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n const settings = {\r\n uniforms: {\r\n srcL: { type: 't', value: null },\r\n srcR: { type: 't', value: null },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n this.setValues(settings);\r\n }\r\n}\r\n\r\nexport default AnaglyphMaterial;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\n\r\nclass View {\r\n constructor() {\r\n this.position = new THREE.Vector3(0, 0, 0);\r\n this.scale = 1;\r\n this.orientation = new THREE.Quaternion(0, 0, 0, 1);\r\n }\r\n\r\n set(position, scale, orientation) {\r\n this.position = position;\r\n this.scale = scale;\r\n this.orientation = orientation;\r\n }\r\n}\r\n\r\nconst _transitionTime = 1.5; // in seconds\r\n\r\nexport default class ViewInterpolator {\r\n setup(startView, endView) {\r\n this._startTime = undefined;\r\n this._endTime = undefined;\r\n this._isPaused = false;\r\n\r\n this._srcView = startView;\r\n this._dstView = endView;\r\n this._isMoving = false;\r\n }\r\n\r\n isMoving() {\r\n return this._isMoving;\r\n }\r\n\r\n wasStarted() {\r\n return typeof this._startTime !== 'undefined' && typeof this._endTime !== 'undefined';\r\n }\r\n\r\n start() {\r\n this._startTime = Date.now();\r\n const transTime = settings.now.interpolateViews ? _transitionTime * 1000 : 0;\r\n this._endTime = this._startTime + transTime;\r\n this._isMoving = true;\r\n }\r\n\r\n getCurrentView() {\r\n if (typeof this._srcView === 'undefined' || typeof this._dstView === 'undefined'\r\n || !this._isMoving || !this.wasStarted()) {\r\n return { success: false };\r\n }\r\n\r\n let view = this.createView();\r\n const time = Date.now();\r\n if (time > this._endTime) {\r\n view = this._dstView;\r\n this.reset();\r\n return { success: true, view };\r\n }\r\n\r\n const factor = (time - this._startTime) / (this._endTime - this._startTime);\r\n view.position.copy(this._srcView.position);\r\n view.position.lerp(this._dstView.position, factor);\r\n view.scale = (1 - factor) * this._srcView.scale + factor * this._dstView.scale;\r\n view.orientation.copy(this._srcView.orientation);\r\n view.orientation.slerp(this._dstView.orientation, factor);\r\n return { success: true, view };\r\n }\r\n\r\n reset() {\r\n this._startTime = this._endTime = 0;\r\n this._isMoving = false;\r\n }\r\n\r\n pause() {\r\n if (!this._isPaused) {\r\n this.setup(this.getCurrentView().view, this._dstView);\r\n this._isPaused = true;\r\n }\r\n }\r\n\r\n resume() {\r\n this._isPaused = false;\r\n }\r\n\r\n createView() {\r\n return new View();\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport makeContextDependent from './makeContextDependent';\r\n\r\nconst MAX_COOKIE_LEN = 4000;\r\nconst COUNT_SUFFIX = 'Cnt';\r\n\r\nfunction _chunkString(string, chunkLen) {\r\n const l = string.length;\r\n const chunks = [];\r\n for (let c = 0, lc = 0; lc < l; c++, lc += chunkLen) {\r\n chunks[c] = string.slice(lc, lc + chunkLen);\r\n }\r\n return chunks;\r\n}\r\n\r\n/**\r\n * Create new context dependent Cookie holder object.\r\n * @param context\r\n * @param {Object} opts - options\r\n * @param {string} opts.path - cookie path\r\n * @constructor\r\n */\r\nfunction Cookies(context, opts) {\r\n this.context = context;\r\n this._opts = _.merge({\r\n path: '/',\r\n }, opts);\r\n}\r\n\r\nmakeContextDependent(Cookies.prototype);\r\n\r\n/**\r\n * Remove cookie by the name.\r\n * @param key\r\n */\r\nCookies.prototype.removeCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n this._removeSimpleCookie(key);\r\n return;\r\n }\r\n this._removeSimpleCookie(cntKey);\r\n cntVal = parseInt(cntVal, 10);\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._removeSimpleCookie(key + i);\r\n }\r\n};\r\n\r\n/**\r\n * Set new cookie value. Automatically splits\r\n * values that are too large into multiple cookies.\r\n * @param key\r\n * @param value\r\n */\r\nCookies.prototype.setCookie = function (key, value) {\r\n this.removeCookie(key);\r\n value = encodeURIComponent(value);\r\n const values = _chunkString(value, MAX_COOKIE_LEN - key.length - 1);\r\n const cntVal = values.length;\r\n if (cntVal === 1) {\r\n this._setSimpleCookie(key, value);\r\n return;\r\n }\r\n const cntKey = this._toCount(key);\r\n this._setSimpleCookie(cntKey, cntVal.toString());\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._setSimpleCookie(key + i, values[i]);\r\n }\r\n};\r\n\r\n/**\r\n * Obtain the value of a compound cookie.\r\n * @param key\r\n */\r\nCookies.prototype.getCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n return this._getSimpleCookie(key);\r\n }\r\n cntVal = parseInt(cntVal, 10);\r\n const value = [];\r\n for (let i = 0; i < cntVal; ++i) {\r\n value[i] = this._getSimpleCookie(key + i);\r\n }\r\n return value.join('');\r\n};\r\n\r\nCookies.prototype._toCount = function (key) {\r\n return key + COUNT_SUFFIX;\r\n};\r\n\r\nCookies.prototype._removeSimpleCookie = function (key) {\r\n document.cookie = `${key}=; expires=Thu, 01 Jan 1970 00:00:01 GMT;`;\r\n};\r\n\r\nCookies.prototype._getExpirationDate = function () {\r\n const today = new Date();\r\n const EXP_PERIOD_YEARS = 10;\r\n today.setFullYear(today.getFullYear() + EXP_PERIOD_YEARS);\r\n return today;\r\n};\r\n\r\nCookies.prototype._setSimpleCookie = function (key, value) {\r\n document.cookie = `${key}=${value\r\n };expires=${this._getExpirationDate().toUTCString()\r\n };path=${this._opts.path}`;\r\n};\r\n\r\nCookies.prototype._getSimpleCookie = function (key) {\r\n const matches = document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n return matches ? decodeURIComponent(matches[1]) : '';\r\n};\r\n\r\nCookies.prototype._exists = function (key) {\r\n return document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n};\r\n\r\nexport default Cookies;\r\n","/*\r\n * Toggling WebVR is done through button.click because of limitations on calling requestPresent in webVR:\r\n * VRDisplay::requestPresent should be called from user gesture:\r\n * https://developer.mozilla.org/en-US/docs/Web/API/VRDisplay/requestPresent\r\n */\r\nexport default function (webVRPoC) {\r\n function showEnterVR(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'pointer';\r\n button.style.left = 'calc(50% - 50px)';\r\n button.style.width = '100px';\r\n\r\n button.textContent = 'ENTER VR';\r\n\r\n let currentSession = null;\r\n\r\n function onSessionEnded(/* event */) {\r\n currentSession.removeEventListener('end', onSessionEnded);\r\n button.textContent = 'ENTER VR';\r\n currentSession = null;\r\n }\r\n\r\n function onSessionStarted(session) {\r\n session.addEventListener('end', onSessionEnded);\r\n webVRPoC._gfx.renderer.xr.setReferenceSpaceType('local');\r\n webVRPoC._gfx.renderer.xr.setSession(session);\r\n button.textContent = 'EXIT VR';\r\n currentSession = session;\r\n }\r\n\r\n button.onmouseenter = function () { button.style.opacity = '1.0'; };\r\n button.onmouseleave = function () { button.style.opacity = '0.5'; };\r\n\r\n button.onclick = function () {\r\n if (currentSession === null) {\r\n // WebXR's requestReferenceSpace only works if the corresponding feature\r\n // was requested at session creation time. For simplicity, just ask for\r\n // the interesting ones as optional features, but be aware that the\r\n // requestReferenceSpace call will fail if it turns out to be unavailable.\r\n // ('local' is always available for immersive sessions and doesn't need to\r\n // be requested separately.)\r\n\r\n const sessionInit = { optionalFeatures: ['local-floor', 'bounded-floor'] };\r\n navigator.xr.requestSession('immersive-vr', sessionInit).then(onSessionStarted);\r\n webVRPoC.moveSceneBehindHeadset();\r\n } else {\r\n currentSession.end();\r\n }\r\n };\r\n }\r\n\r\n function showWebXRNotFound(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'auto';\r\n button.style.left = 'calc(50% - 75px)';\r\n button.style.width = '150px';\r\n button.textContent = 'VR NOT FOUND';\r\n button.onmouseenter = null;\r\n button.onmouseleave = null;\r\n button.onclick = null;\r\n }\r\n\r\n function stylizeElement(element) {\r\n element.style.position = 'absolute';\r\n element.style.bottom = '20px';\r\n element.style.padding = '12px 6px';\r\n element.style.border = '1px solid #fff';\r\n element.style.borderRadius = '4px';\r\n element.style.background = 'transparent';\r\n element.style.color = '#fff';\r\n element.style.font = 'normal 13px sans-serif';\r\n element.style.textAlign = 'center';\r\n element.style.opacity = '0.5';\r\n element.style.outline = 'none';\r\n element.style.zIndex = '999';\r\n }\r\n\r\n if ('xr' in navigator) {\r\n const button = document.createElement('button');\r\n button.style.display = 'none';\r\n stylizeElement(button);\r\n navigator.xr.isSessionSupported('immersive-vr').then((supported) => (\r\n supported ? showEnterVR(button) : showWebXRNotFound(button)\r\n ));\r\n return button;\r\n }\r\n const message = document.createElement('a');\r\n message.href = 'https://webvr.info';\r\n message.innerHTML = 'WEBXR NOT SUPPORTED';\r\n message.style.left = 'calc(50% - 90px)';\r\n message.style.width = '180px';\r\n message.style.textDecoration = 'none';\r\n stylizeElement(message);\r\n return message;\r\n}\r\n","import * as THREE from 'three';\r\nimport createWebVRButton from './createWebVRButton';\r\nimport gfxutils from '../gfxutils';\r\nimport logger from '../../utils/logger';\r\nimport settings from '../../settings';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default class WebVRPoC {\r\n constructor(onToggle) {\r\n this._mainCamera = new THREE.PerspectiveCamera();\r\n this._button = null;\r\n this._onToggle = onToggle;\r\n\r\n this._molContainer = new gfxutils.RCGroup();\r\n this._user = new gfxutils.RCGroup();\r\n this._scalingPivot = new THREE.Object3D();\r\n this._user.add(this._scalingPivot);\r\n\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n this._pressedGripsCounter = 0;\r\n this._distance = 0;\r\n\r\n this._gfx = null;\r\n }\r\n\r\n startScalingByControllers() {\r\n // reset scale\r\n this._distance = this._controller1.position.distanceTo(this._controller2.position);\r\n gfxutils.getMiddlePoint(this._controller1.position, this._controller2.position, this._scalingPivot.position);\r\n this._scalingPivot.scale.set(1, 1, 1);\r\n this._scalingPivot.updateMatrix();\r\n this._scalingPivot.updateMatrixWorld();\r\n // link molecule to pivot\r\n this._scalingPivot.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n stopScalingByControllers() {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n handleGripsDown(event) {\r\n this._pressedGripsCounter++;\r\n if (this._pressedGripsCounter === 2) {\r\n this.startScalingByControllers();\r\n } else if (this._pressedGripsCounter === 1) {\r\n event.target.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n handleGripsUp(event) {\r\n this._pressedGripsCounter--;\r\n if (this._pressedGripsCounter === 1) {\r\n this.stopScalingByControllers();\r\n // reattach molecule to other controller\r\n const anotherController = event.target === this._controller1 ? this._controller2 : this._controller1;\r\n anotherController.addSavingWorldTransform(this._molContainer);\r\n } else if (this._pressedGripsCounter === 0) {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n enable(gfx) {\r\n if (!gfx) {\r\n logger.warn('WebVR couldn\\'t be enabled, because gfx is not defined');\r\n return;\r\n }\r\n this._gfx = gfx;\r\n const { renderer, camera } = gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n if (!camera) {\r\n throw new Error('No camera is available to toggle WebVR');\r\n }\r\n\r\n // enable xr in renderer\r\n renderer.xr.enabled = true;\r\n // add button for turning vr mode\r\n if (!this._button) {\r\n this._button = createWebVRButton(this);\r\n document.body.appendChild(this._button);\r\n } else {\r\n this._button.style.display = 'block';\r\n }\r\n // store fog setting\r\n this._mainFog = settings.now.fog;\r\n settings.set('fog', false);\r\n\r\n this._plugVRNodesIntoScene(gfx, renderer);\r\n this._setControllersListeners();\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n _plugVRNodesIntoScene(gfx, renderer) {\r\n // store common scene camera\r\n this._mainCamera.copy(gfx.camera);\r\n // add hierarchical structure for webVR into scene\r\n gfx.scene.add(this._user);\r\n // turn on webvr transformation\r\n gfx.scene.add(this._molContainer);\r\n this._molContainer.add(gfx.root);\r\n\r\n this._controller1 = renderer.xr.getController(0);\r\n this._controller2 = renderer.xr.getController(1);\r\n const mesh = this._createControllerMesh();\r\n this._controller1.add(mesh);\r\n this._controller2.add(mesh.clone());\r\n this._user.add(this._controller1);\r\n this._user.add(this._controller2);\r\n }\r\n\r\n _setControllersListeners() {\r\n this._controller1.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n\r\n this._controller1.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n }\r\n\r\n disable() {\r\n if (!this._gfx) {\r\n return;\r\n }\r\n const { renderer, camera } = this._gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n\r\n // nullify webxr callback for animation frame\r\n renderer.setAnimationLoop(null);\r\n const session = renderer.xr.getSession();\r\n if (session) {\r\n session.end();\r\n }\r\n renderer.xr.enabled = false;\r\n // remove button of VR entering\r\n if (this._button) {\r\n this._button.style.display = 'none';\r\n }\r\n // restore fog param\r\n settings.set('fog', this._mainFog);\r\n\r\n this._unplugVRNodesFromScene(camera);\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(false);\r\n }\r\n }\r\n\r\n _unplugVRNodesFromScene(camera) {\r\n // restore common camera\r\n if (this._mainCamera && camera) {\r\n camera.copy(this._mainCamera);\r\n }\r\n // turn off webvr transformation\r\n const root = this._molContainer.children[0];\r\n if (root) {\r\n this._gfx.scene.add(root);\r\n }\r\n this._molContainer.parent.remove(this._molContainer);\r\n if (this._user) {\r\n this._gfx.scene.remove(this._user);\r\n }\r\n // free scene nodes\r\n this._molContainer = null;\r\n this._user = null;\r\n this._scalingPivot = null;\r\n this._user = null;\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n }\r\n\r\n _createControllerMesh() {\r\n // visualize controllers with cylinders\r\n const geometry = new THREE.CylinderGeometry(0.04, 0.04, 0.3);\r\n const material = new UberMaterial({ lights: false, overrideColor: true });\r\n material.setUberOptions({ fixedColor: new THREE.Color(0x4444ff) });\r\n material.updateUniforms();\r\n const cylinder = new THREE.Mesh(geometry, material);\r\n cylinder.rotateX(-Math.PI / 2);\r\n return cylinder;\r\n }\r\n\r\n updateMoleculeScale() {\r\n if (!this._controller1 || !this._controller2) {\r\n return;\r\n }\r\n\r\n const self = this;\r\n // update molecule scaling by controllers\r\n if (self._pressedGripsCounter === 2) {\r\n // recalc scaling pivot\r\n gfxutils.getMiddlePoint(self._controller1.position, self._controller2.position, self._scalingPivot.position);\r\n // recalc scaler\r\n const dist = self._controller1.position.distanceTo(self._controller2.position);\r\n const scaler = dist / self._distance;\r\n self._scalingPivot.scale.multiplyScalar(scaler);\r\n // save cur distance for next frame\r\n self._distance = dist;\r\n }\r\n }\r\n\r\n /**\r\n * Reposition molecule right before the camera.\r\n * @note The proper way is to initiate headset in the place of common Miew's camera.\r\n * But threejs limitations on setting new XRReferenceSpace enforce the molecule repositioning\r\n * Hope, something will change.\r\n */\r\n moveSceneBehindHeadset() {\r\n const gfx = this._gfx;\r\n const { camera } = gfx;\r\n\r\n // set container position in camera space\r\n const container = this._molContainer;\r\n container.matrix.identity();\r\n container.position.set(0, 0, -4.0);\r\n container.updateMatrix();\r\n\r\n // update container world matrix\r\n container.matrixWorld.multiplyMatrices(camera.matrixWorld, container.matrix);\r\n // readd to scene\r\n gfx.scene.addSavingWorldTransform(container);\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n getCanvas() {\r\n const gfx = this._gfx;\r\n return (gfx && gfx.renderer) ? gfx.renderer.domElement : null;\r\n }\r\n}\r\n","/* global PACKAGE_VERSION:false */\r\nimport _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport { Spinner } from 'spin.js';\r\nimport Stats from './gfx/Stats';\r\nimport utils from './utils';\r\nimport JobHandle from './utils/JobHandle';\r\nimport options from './options';\r\nimport settings from './settings';\r\nimport chem from './chem';\r\nimport Visual from './Visual';\r\nimport ComplexVisual from './ComplexVisual';\r\nimport Complex from './chem/Complex';\r\nimport VolumeVisual from './VolumeVisual';\r\nimport io from './io/io';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport CSS2DRenderer from './gfx/CSS2DRenderer';\r\nimport ObjectControls from './ui/ObjectControls';\r\nimport Picker from './ui/Picker';\r\nimport Axes from './gfx/Axes';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport meshutils from './gfx/meshutils';\r\nimport FrameInfo from './gfx/FrameInfo';\r\nimport meshes from './gfx/meshes/meshes';\r\nimport LinesObject from './gfx/objects/LinesObj';\r\nimport UberMaterial from './gfx/shaders/UberMaterial';\r\nimport OutlineMaterial from './gfx/shaders/OutlineMaterial';\r\nimport FXAAMaterial from './gfx/shaders/FXAAMaterial';\r\nimport AOMaterial from './gfx/shaders/AOMaterial';\r\nimport AOHorBlurMaterial from './gfx/shaders/AOHorBlurMaterial';\r\nimport AOVertBlurWithBlendMaterial from './gfx/shaders/AOVertBlurWithBlendMaterial';\r\nimport AnaglyphMaterial from './gfx/shaders/AnaglyphMaterial';\r\nimport VolumeMaterial from './gfx/shaders/VolumeMaterial';\r\nimport ViewInterpolator from './gfx/ViewInterpolator';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\nimport logger from './utils/logger';\r\nimport Cookies from './utils/Cookies';\r\nimport capabilities from './gfx/capabilities';\r\nimport WebVRPoC from './gfx/vr/WebVRPoC';\r\nimport vertexScreenQuadShader from './gfx/shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromDistTex from './gfx/shaders/ScreenQuadFromDistortionTex.frag';\r\nimport getTopWindow from './utils/getTopWindow';\r\n\r\nconst {\r\n selectors,\r\n Atom,\r\n Residue,\r\n Chain,\r\n Molecule,\r\n} = chem;\r\n\r\nconst EDIT_MODE = { COMPLEX: 0, COMPONENT: 1, FRAGMENT: 2 };\r\n\r\nconst LOADER_NOT_FOUND = 'Could not find suitable loader for this source';\r\nconst PARSER_NOT_FOUND = 'Could not find suitable parser for this source';\r\n\r\n// Color management changed a lot in threejs 152+ version.\r\n// To keep miew colors we disable the new color management system\r\nTHREE.ColorManagement.enabled = false;\r\n\r\nconst { createElement } = utils;\r\n\r\nfunction updateFogRange(fog, center, radius) {\r\n fog.near = center - radius * settings.now.fogNearFactor;\r\n fog.far = center + radius * settings.now.fogFarFactor;\r\n}\r\n\r\nfunction removeExtension(fileName) {\r\n const dot = fileName.lastIndexOf('.');\r\n if (dot >= 0) {\r\n fileName = fileName.substr(0, dot);\r\n }\r\n return fileName;\r\n}\r\n\r\nfunction hasValidResidues(complex) {\r\n let hasValidRes = false;\r\n complex.forEachComponent((component) => {\r\n component.forEachResidue((residue) => {\r\n if (residue._isValid) {\r\n hasValidRes = true;\r\n }\r\n });\r\n });\r\n return hasValidRes;\r\n}\r\n\r\nfunction reportProgress(log, action, percent) {\r\n const TOTAL_PERCENT = 100;\r\n if (percent !== undefined) {\r\n log.debug(`${action}... ${Math.floor(percent * TOTAL_PERCENT)}%`);\r\n } else {\r\n log.debug(`${action}...`);\r\n }\r\n}\r\n\r\nfunction chooseFogColor() {\r\n return settings.now.fogColorEnable ? settings.now.fogColor : settings.now.bg.color;\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\n/**\r\n * Main 3D Molecular Viewer class.\r\n *\r\n * @param {object} opts - Viewer options.\r\n * @param {HTMLElement=} opts.container - DOM element that serves as a viewer container.\r\n * @param {object=} opts.settings - An object with properties to override default settings.\r\n * @param {string=} opts.settingsCookie='settings' - The name of the cookie to save current settings to.\r\n * @param {string=} opts.cookiePath='/' - The path option for cookies. Defaults to root.\r\n *\r\n * @exports Miew\r\n * @constructor\r\n */\r\nfunction Miew(opts) {\r\n EventDispatcher.call(this);\r\n this._opts = _.merge({\r\n settingsCookie: 'settings',\r\n cookiePath: '/',\r\n }, opts);\r\n /** @type {?object} */\r\n this._gfx = null;\r\n /** @type {ViewInterpolator} */\r\n this._interpolator = new ViewInterpolator();\r\n /** @type {HTMLElement} */\r\n this._container = (opts && opts.container)\r\n || document.getElementById('miew-container')\r\n || _.head(document.getElementsByClassName('miew-container'))\r\n || document.body;\r\n /** @type {HTMLElement} */\r\n this._containerRoot = this._container;\r\n\r\n /** @type {boolean} */\r\n this._running = false;\r\n /** @type {boolean} */\r\n this._halting = false;\r\n /** @type {boolean} */\r\n this._building = false;\r\n /** @type {boolean} */\r\n this._needRender = true;\r\n /** @type {boolean} */\r\n this._hotKeysEnabled = true;\r\n\r\n /** @type {Settings} */\r\n this.settings = settings;\r\n const log = logger;\r\n log.console = DEBUG;\r\n log.level = DEBUG ? 'debug' : 'info';\r\n /**\r\n * @type {Logger}\r\n * @example\r\n * miew.logger.addEventListener('message', function _onLogMessage(evt) {\r\n * console.log(evt.message);\r\n * });\r\n */\r\n this.logger = log;\r\n\r\n this._cookies = new Cookies(this);\r\n this.restoreSettings();\r\n if (opts && opts.settings) {\r\n this.settings.set(opts.settings);\r\n }\r\n\r\n /** @type {?Spinner} */\r\n this._spinner = null;\r\n /** @type {JobHandle[]} */\r\n this._loading = [];\r\n /** @type {?number}\r\n * @deprecated until Animation system refactoring\r\n */\r\n this._animInterval = null;\r\n\r\n /** @type {object} */\r\n this._visuals = {};\r\n /** @type {?string} */\r\n this._curVisualName = null;\r\n\r\n /** @type {array} */\r\n this._objects = [];\r\n\r\n /** @type {object} */\r\n this._sourceWindow = null;\r\n\r\n this.reset();\r\n\r\n if (this._repr) {\r\n log.debug(`Selected ${this._repr.mode.name} mode with ${this._repr.colorer.name} colorer.`);\r\n }\r\n\r\n const self = this;\r\n Miew.registeredPlugins.forEach((plugin) => {\r\n plugin.call(self);\r\n });\r\n\r\n this._initOnSettingsChanged();\r\n}\r\n\r\nMiew.prototype = Object.create(EventDispatcher.prototype);\r\nMiew.prototype.constructor = Miew;\r\n\r\nMiew.prototype.getMaxRepresentationCount = function () {\r\n return ComplexVisual.NUM_REPRESENTATION_BITS;\r\n};\r\n\r\n/**\r\n * Replace viewer container contents with a DOM element.\r\n * @param {HTMLElement} container - parent container.\r\n * @param {HTMLElement} element - DOM element to show.\r\n * @private\r\n */\r\nfunction _setContainerContents(container, element) {\r\n const parent = container;\r\n while (parent.firstChild) {\r\n parent.removeChild(parent.firstChild);\r\n }\r\n parent.appendChild(element);\r\n}\r\n\r\n/**\r\n * Update Shadow Camera target position and frustum.\r\n * @private\r\n */\r\nMiew.prototype._updateShadowCamera = (function () {\r\n const shadowMatrix = new THREE.Matrix4();\r\n const direction = new THREE.Vector3();\r\n const OBB = { center: new THREE.Vector3(), halfSize: new THREE.Vector3() };\r\n\r\n return function () {\r\n this._gfx.scene.updateMatrixWorld();\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = this._gfx.scene.children[i];\r\n shadowMatrix.copy(light.shadow.camera.matrixWorldInverse);\r\n this.getOBB(shadowMatrix, OBB);\r\n\r\n direction.subVectors(light.target.position, light.position);\r\n light.position.subVectors(OBB.center, direction);\r\n light.target.position.copy(OBB.center);\r\n\r\n light.shadow.bias = 0.09;\r\n light.shadow.camera.bottom = -OBB.halfSize.y;\r\n light.shadow.camera.top = OBB.halfSize.y;\r\n light.shadow.camera.right = OBB.halfSize.x;\r\n light.shadow.camera.left = -OBB.halfSize.x;\r\n light.shadow.camera.near = direction.length() - OBB.halfSize.z;\r\n light.shadow.camera.far = direction.length() + OBB.halfSize.z;\r\n\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Initialize the viewer.\r\n * @returns {boolean} true on success.\r\n * @throws Forwards exception raised during initialization.\r\n * @see Miew#term\r\n */\r\nMiew.prototype.init = function () {\r\n const container = this._container;\r\n const elem = utils.createElement('div', { class: 'miew-canvas' });\r\n _setContainerContents(container, elem);\r\n this._container = elem;\r\n\r\n const frag = document.createDocumentFragment();\r\n frag.appendChild(this._msgMode = createElement(\r\n 'div',\r\n { class: 'mode-message overlay' },\r\n createElement('p', {}, 'COMPONENT EDIT MODE'),\r\n ));\r\n frag.appendChild(this._msgAtomInfo = createElement(\r\n 'div',\r\n { class: 'atom-info overlay' },\r\n createElement('p', {}, ''),\r\n ));\r\n container.appendChild(frag);\r\n\r\n if (this._gfx !== null) { // block double init\r\n return true;\r\n }\r\n\r\n const self = this;\r\n this._showMessage('Viewer is being initialized...');\r\n try {\r\n this._initGfx();\r\n\r\n this._initListeners();\r\n this._spinner = new Spinner({\r\n lines: 13,\r\n length: 28,\r\n width: 14,\r\n radius: 42,\r\n color: '#fff',\r\n zIndex: 700,\r\n });\r\n\r\n const target = getTopWindow();\r\n target.addEventListener('keydown', (event) => {\r\n self._onKeyDown(event);\r\n });\r\n\r\n target.addEventListener('keyup', (event) => {\r\n self._onKeyUp(event);\r\n });\r\n\r\n this._objectControls = new ObjectControls(\r\n this._gfx.root,\r\n this._gfx.pivot,\r\n this._gfx.camera,\r\n this._gfx.renderer.domElement,\r\n () => self._getAltObj(),\r\n );\r\n this._objectControls.addEventListener('change', (e) => {\r\n if (settings.now.shadow.on) {\r\n self._updateShadowCamera();\r\n }\r\n // route rotate, zoom, translate and translatePivot events to the external API\r\n switch (e.action) {\r\n case 'rotate':\r\n self.dispatchEvent({ type: 'rotate', quaternion: e.quaternion });\r\n break;\r\n case 'zoom':\r\n self.dispatchEvent({ type: 'zoom', factor: e.factor });\r\n break;\r\n default:\r\n self.dispatchEvent({ type: e.action });\r\n }\r\n self.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n });\r\n\r\n const gfx = this._gfx;\r\n this._picker = new Picker(gfx.root, gfx.camera, gfx.renderer.domElement);\r\n this._picker.addEventListener('newpick', (event) => {\r\n self._onPick(event);\r\n });\r\n this._picker.addEventListener('dblclick', (event) => {\r\n self.center(event);\r\n });\r\n } catch (error) {\r\n if (error.name === 'TypeError' && error.message === 'Cannot read property \\'getExtension\\' of null') {\r\n this._showMessage('Could not create WebGL context.');\r\n } else if (error.message.search(/webgl/i) > 1) {\r\n this._showMessage(error.message);\r\n } else {\r\n this._showMessage('Viewer initialization failed.');\r\n throw error;\r\n }\r\n return false;\r\n }\r\n\r\n // automatically load default file\r\n const file = this._opts && this._opts.load;\r\n if (file) {\r\n const type = this._opts && this._opts.type;\r\n this.load(file, { fileType: type, keepRepsInfo: true });\r\n }\r\n\r\n return true;\r\n};\r\n\r\n/**\r\n * Terminate the viewer completely.\r\n * @see Miew#init\r\n */\r\nMiew.prototype.term = function () {\r\n this._showMessage('Viewer has been terminated.');\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n this.halt();\r\n this._gfx = null;\r\n};\r\n\r\n/**\r\n * Display message inside the viewer container, hiding WebGL canvas.\r\n * @param {string} msg - Message to show.\r\n * @private\r\n */\r\nMiew.prototype._showMessage = function (msg) {\r\n const element = document.createElement('div');\r\n element.setAttribute('class', 'miew-message');\r\n element.appendChild(document.createElement('p')).appendChild(document.createTextNode(msg));\r\n _setContainerContents(this._container, element);\r\n};\r\n\r\n/**\r\n * Display WebGL canvas inside the viewer container, hiding any message shown.\r\n * @private\r\n */\r\nMiew.prototype._showCanvas = function () {\r\n _setContainerContents(this._container, this._gfx.renderer.domElement);\r\n};\r\n\r\nMiew.prototype._requestAnimationFrame = function (callback) {\r\n const { xr } = this._gfx.renderer;\r\n if (xr && xr.enabled) {\r\n this._gfx.renderer.setAnimationLoop(callback);\r\n return;\r\n }\r\n requestAnimationFrame(callback);\r\n};\r\n\r\nfunction arezSpritesSupported(context) {\r\n return context.getExtension('EXT_frag_depth');\r\n}\r\n\r\nfunction isAOSupported(context) {\r\n return (context.getExtension('WEBGL_depth_texture')\r\n && context.getExtension('WEBGL_draw_buffers'));\r\n}\r\n\r\n/**\r\n * Initialize WebGL and set 3D scene up.\r\n * @private\r\n */\r\nMiew.prototype._initGfx = function () {\r\n const gfx = {\r\n width: this._container.clientWidth,\r\n height: this._container.clientHeight,\r\n };\r\n\r\n const webGLOptions = { preserveDrawingBuffer: true, alpha: true, premultipliedAlpha: false };\r\n if (settings.now.antialias) {\r\n webGLOptions.antialias = true;\r\n }\r\n\r\n gfx.renderer2d = new CSS2DRenderer();\r\n\r\n gfx.renderer = new THREE.WebGL1Renderer(webGLOptions);\r\n gfx.renderer.shadowMap.enabled = settings.now.shadow.on;\r\n gfx.renderer.shadowMap.autoUpdate = false;\r\n gfx.renderer.shadowMap.type = THREE.PCFShadowMap;\r\n capabilities.init(gfx.renderer);\r\n\r\n // z-sprites and ambient occlusion possibility\r\n if (!arezSpritesSupported(gfx.renderer.getContext())) {\r\n settings.set('zSprites', false);\r\n }\r\n if (!isAOSupported(gfx.renderer.getContext())) {\r\n settings.set('ao', false);\r\n }\r\n\r\n gfx.renderer.autoClear = false;\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n gfx.camera = new THREE.PerspectiveCamera(\r\n settings.now.camFov,\r\n gfx.width / gfx.height,\r\n settings.now.camNear,\r\n settings.now.camFar,\r\n );\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.position.z = settings.now.camDistance;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n\r\n gfx.stereoCam = new THREE.StereoCamera();\r\n\r\n gfx.scene = new THREE.Scene();\r\n\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color, settings.now.camNear, settings.now.camFar);\r\n\r\n gfx.root = new gfxutils.RCGroup();\r\n gfx.scene.add(gfx.root);\r\n\r\n gfx.pivot = new gfxutils.RCGroup();\r\n gfx.root.add(gfx.pivot);\r\n\r\n gfx.selectionScene = new THREE.Scene();\r\n gfx.selectionRoot = new THREE.Group();\r\n gfx.selectionRoot.matrixAutoUpdate = false;\r\n gfx.selectionScene.add(gfx.selectionRoot);\r\n\r\n gfx.selectionPivot = new THREE.Group();\r\n gfx.selectionPivot.matrixAutoUpdate = false;\r\n gfx.selectionRoot.add(gfx.selectionPivot);\r\n\r\n const light12 = new THREE.DirectionalLight(0xffffff, 0.45);\r\n light12.position.set(0, 0.414, 1);\r\n light12.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n light12.castShadow = true;\r\n light12.shadow.bias = 0.09;\r\n light12.shadow.radius = settings.now.shadow.radius;\r\n light12.shadow.camera.layers.set(gfxutils.LAYERS.SHADOWMAP);\r\n\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n const shadowMapSize = Math.max(gfx.width, gfx.height) * pixelRatio;\r\n light12.shadow.mapSize.width = shadowMapSize;\r\n light12.shadow.mapSize.height = shadowMapSize;\r\n light12.target.position.set(0.0, 0.0, 0.0);\r\n gfx.scene.add(light12);\r\n gfx.scene.add(light12.target);\r\n\r\n const light3 = new THREE.AmbientLight(0x666666);\r\n light3.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.scene.add(light3);\r\n\r\n // add axes\r\n gfx.axes = new Axes(gfx.root, gfx.camera);\r\n const deviceWidth = gfx.width * pixelRatio;\r\n const deviceHeight = gfx.height * pixelRatio;\r\n\r\n gfx.offscreenBuf = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat, depthBuffer: true,\r\n },\r\n );\r\n\r\n if (gfx.renderer.getContext().getExtension('WEBGL_depth_texture')) {\r\n gfx.offscreenBuf.depthTexture = new THREE.DepthTexture();\r\n gfx.offscreenBuf.depthTexture.type = THREE.UnsignedShortType;\r\n }\r\n\r\n gfx.offscreenBuf2 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf3 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf4 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf3;\r\n gfx.volFFTex = gfx.offscreenBuf4;\r\n gfx.volWFFTex = gfx.offscreenBuf;\r\n\r\n // use float textures for volume rendering if possible\r\n if (gfx.renderer.getContext().getExtension('OES_texture_float')) {\r\n gfx.offscreenBuf5 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf6 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf7 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf5;\r\n gfx.volFFTex = gfx.offscreenBuf6;\r\n gfx.volWFFTex = gfx.offscreenBuf7;\r\n } else {\r\n this.logger.warn('Device doesn\\'t support OES_texture_float extension');\r\n }\r\n\r\n gfx.stereoBufL = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.stereoBufR = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n this._gfx = gfx;\r\n this._showCanvas();\r\n\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n\r\n this._container.appendChild(gfx.renderer2d.getElement());\r\n\r\n // add FPS counter\r\n const stats = new Stats();\r\n stats.domElement.style.position = 'absolute';\r\n stats.domElement.style.right = '0';\r\n stats.domElement.style.bottom = '0';\r\n this._container.appendChild(stats.domElement);\r\n this._fps = stats;\r\n this._fps.show(settings.now.fps);\r\n};\r\n\r\n/**\r\n * Setup event listeners.\r\n * @private\r\n */\r\nMiew.prototype._initListeners = function () {\r\n const self = this;\r\n window.addEventListener('resize', () => {\r\n self._onResize();\r\n });\r\n};\r\n\r\n/**\r\n * Try to add numbers to the base name to make it unique among visuals\r\n * @private\r\n */\r\nMiew.prototype._makeUniqueVisualName = function (baseName) {\r\n if (!baseName) {\r\n return Math.random().toString();\r\n }\r\n\r\n let name = baseName;\r\n let suffix = 1;\r\n while (this._visuals.hasOwnProperty(name)) {\r\n name = `${baseName} (${suffix.toString()})`;\r\n suffix++;\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Add visual to the viewer\r\n * @private\r\n */\r\nMiew.prototype._addVisual = function (visual) {\r\n if (!visual) {\r\n return null;\r\n }\r\n\r\n // change visual name in order to make it unique\r\n const name = this._makeUniqueVisualName(visual.name);\r\n visual.name = name;\r\n\r\n this._visuals[name] = visual;\r\n this._gfx.pivot.add(visual);\r\n if (visual.getSelectionGeo) {\r\n this._gfx.selectionPivot.add(visual.getSelectionGeo());\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Remove visual from the viewer\r\n * @private\r\n */\r\nMiew.prototype._removeVisual = function (visual) {\r\n let name = '';\r\n let obj = null;\r\n if (visual instanceof Visual) {\r\n ({ name } = visual);\r\n obj = visual;\r\n } else if (typeof visual === 'string') {\r\n name = visual;\r\n obj = this._visuals[name];\r\n }\r\n\r\n if (!obj || !this._visuals.hasOwnProperty(name) || this._visuals[name] !== obj) {\r\n return;\r\n }\r\n\r\n if (name === this._curVisualName) {\r\n this._curVisualName = undefined;\r\n }\r\n\r\n delete this._visuals[name];\r\n obj.release(); // removes nodes from scene\r\n\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Call specified function for each Visual\r\n * @private\r\n */\r\nMiew.prototype._forEachVisual = function (callback) {\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Release (destroy) all visuals in the scene\r\n * @private\r\n */\r\nMiew.prototype._releaseAllVisuals = function () {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n this._visuals[name].release();\r\n }\r\n }\r\n\r\n this._visuals = {};\r\n};\r\n\r\n/**\r\n * Call specified function for each ComplexVisual\r\n * @private\r\n */\r\nMiew.prototype._forEachComplexVisual = function (callback) {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)\r\n && this._visuals[name] instanceof ComplexVisual) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual with specified name, or current (if not found), or any, or null\r\n * @private\r\n */\r\nMiew.prototype._getComplexVisual = function (name) {\r\n name = name || this._curVisualName;\r\n let any = null;\r\n let named = null;\r\n this._forEachComplexVisual((visual) => {\r\n any = visual;\r\n if (visual.name === name) {\r\n named = visual;\r\n }\r\n });\r\n return named || any;\r\n};\r\n\r\n/**\r\n * Returns first found VolumeVisual (no more than one should be present actually)\r\n * @private\r\n */\r\nMiew.prototype._getVolumeVisual = function () {\r\n let any = null;\r\n this._forEachVisual((visual) => {\r\n if (visual instanceof VolumeVisual) {\r\n any = visual;\r\n }\r\n });\r\n return any;\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual corresponding to specified complex\r\n * @private\r\n */\r\nMiew.prototype._getVisualForComplex = function (complex) {\r\n if (!complex) {\r\n return null;\r\n }\r\n\r\n let found = null;\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getComplex() === complex) {\r\n found = visual;\r\n }\r\n });\r\n return found;\r\n};\r\n\r\n/*\r\n * Get a list of names of visuals currently shown by the viewer\r\n */\r\nMiew.prototype.getVisuals = function () {\r\n return Object.keys(this._visuals);\r\n};\r\n\r\n/*\r\n * Get complex visuals count\r\n */\r\nMiew.prototype.getComplexVisualsCount = function () {\r\n let count = 0;\r\n this._forEachComplexVisual(() => count++);\r\n return count;\r\n};\r\n\r\n/*\r\n * Get current visual\r\n */\r\nMiew.prototype.getCurrentVisual = function () {\r\n return this._curVisualName;\r\n};\r\n\r\n/*\r\n * Set current visual.\r\n * All further operations will be performed on this visual (complex) if not stated otherwise.\r\n */\r\nMiew.prototype.setCurrentVisual = function (name) {\r\n if (!this._visuals[name]) {\r\n return;\r\n }\r\n\r\n this._curVisualName = name;\r\n};\r\n\r\n/**\r\n * Run the viewer, start processing update/render frames periodically.\r\n * Has no effect if already running.\r\n * @see Miew#halt\r\n */\r\nMiew.prototype.run = function () {\r\n if (!this._running) {\r\n this._running = true;\r\n if (this._halting) {\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._objectControls.enable(true);\r\n this._interpolator.resume();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to stop.\r\n * Will be processed during the next frame.\r\n * @see Miew#run\r\n */\r\nMiew.prototype.halt = function () {\r\n if (this._running) {\r\n this._discardComponentEdit();\r\n this._discardFragmentEdit();\r\n this._objectControls.enable(false);\r\n this._interpolator.pause();\r\n this._halting = true;\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to start / stop responsing\r\n * on hot keys.\r\n * @param enabled - start (true) or stop (false) response on hot keys.\r\n */\r\nMiew.prototype.enableHotKeys = function (enabled) {\r\n this._hotKeysEnabled = enabled;\r\n this._objectControls.enableHotkeys(enabled);\r\n};\r\n\r\n/**\r\n * Callback which processes window resize.\r\n * @private\r\n */\r\nMiew.prototype._onResize = function () {\r\n const gfx = this._gfx;\r\n if (!gfx) {\r\n return;\r\n }\r\n\r\n this._needRender = true;\r\n\r\n gfx.width = this._container.clientWidth;\r\n gfx.height = this._container.clientHeight;\r\n\r\n gfx.camera.aspect = gfx.width / gfx.height;\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n this.dispatchEvent({ type: 'resize' });\r\n};\r\n\r\nMiew.prototype._resizeOffscreenBuffers = function (width, height, stereo) {\r\n const gfx = this._gfx;\r\n stereo = stereo || 'NONE';\r\n const isAnaglyph = (stereo === 'NONE' || stereo === 'ANAGLYPH');\r\n const multi = isAnaglyph ? 1 : 0.5;\r\n gfx.offscreenBuf.setSize(multi * width, height);\r\n gfx.offscreenBuf2.setSize(multi * width, height);\r\n gfx.offscreenBuf3.setSize(multi * width, height);\r\n gfx.offscreenBuf4.setSize(multi * width, height);\r\n if (gfx.offscreenBuf5) {\r\n gfx.offscreenBuf5.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf6) {\r\n gfx.offscreenBuf6.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf7) {\r\n gfx.offscreenBuf7.setSize(multi * width, height);\r\n }\r\n if (isAnaglyph) {\r\n gfx.stereoBufL.setSize(width, height);\r\n gfx.stereoBufR.setSize(width, height);\r\n }\r\n};\r\n\r\n/**\r\n * Callback which processes update/render frames.\r\n * @private\r\n */\r\nMiew.prototype._onTick = function () {\r\n if (this._halting) {\r\n this._running = false;\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._fps.update();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n\r\n this._onUpdate();\r\n if (this._needRender) {\r\n this._onRender();\r\n this._needRender = !settings.now.suspendRender || settings.now.stereo === 'WEBVR';\r\n }\r\n};\r\n\r\nMiew.prototype._getBSphereRadius = function () {\r\n // calculate radius that would include all visuals\r\n let radius = 0;\r\n this._forEachVisual((visual) => {\r\n radius = Math.max(radius, visual.getBoundaries().boundingSphere.radius);\r\n });\r\n return radius * this._objectControls.getScale();\r\n};\r\n\r\n/**\r\n * Calculate bounding box that would include all visuals and being axis aligned in world defined by\r\n * transformation matrix: matrix\r\n * @param {Matrix4} matrix - transformation matrix.\r\n * @param {object} OBB - calculating bounding box.\r\n * @param {Vector3} OBB.center - OBB center.\r\n * @param {Vector3} OBB.halfSize - half magnitude of OBB sizes.\r\n */\r\nMiew.prototype.getOBB = (function () {\r\n const _bSphereForOneVisual = new THREE.Sphere();\r\n const _bBoxForOneVisual = new THREE.Box3();\r\n const _bBox = new THREE.Box3();\r\n\r\n const _invMatrix = new THREE.Matrix4();\r\n\r\n const _points = [\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n ];\r\n\r\n return function (matrix, OBB) {\r\n _bBox.makeEmpty();\r\n\r\n this._forEachVisual((visual) => {\r\n _bSphereForOneVisual.copy(visual.getBoundaries().boundingSphere);\r\n _bSphereForOneVisual.applyMatrix4(visual.matrixWorld).applyMatrix4(matrix);\r\n _bSphereForOneVisual.getBoundingBox(_bBoxForOneVisual);\r\n _bBox.union(_bBoxForOneVisual);\r\n });\r\n _bBox.getCenter(OBB.center);\r\n\r\n _invMatrix.copy(matrix).invert();\r\n OBB.center.applyMatrix4(_invMatrix);\r\n\r\n const { min } = _bBox;\r\n const { max } = _bBox;\r\n _points[0].set(min.x, min.y, min.z); // 000\r\n _points[1].set(max.x, min.y, min.z); // 100\r\n _points[2].set(min.x, max.y, min.z); // 010\r\n _points[3].set(min.x, min.y, max.z); // 001\r\n for (let i = 0, l = _points.length; i < l; i++) {\r\n _points[i].applyMatrix4(_invMatrix);\r\n }\r\n\r\n OBB.halfSize.set(\r\n Math.abs(_points[0].x - _points[1].x),\r\n Math.abs(_points[0].y - _points[2].y),\r\n Math.abs(_points[0].z - _points[3].z),\r\n ).multiplyScalar(0.5);\r\n };\r\n}());\r\n\r\nMiew.prototype._updateFog = function () {\r\n const gfx = this._gfx;\r\n\r\n if (settings.now.fog) {\r\n if (typeof gfx.scene.fog === 'undefined' || gfx.scene.fog === null) {\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color);\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n updateFogRange(gfx.scene.fog, gfx.camera.position.z, this._getBSphereRadius());\r\n } else if (gfx.scene.fog) {\r\n gfx.scene.fog = undefined;\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n};\r\n\r\nMiew.prototype._onUpdate = function () {\r\n if (this.isScriptingCommandAvailable !== undefined && this.isScriptingCommandAvailable() && !this._building) {\r\n this.callNextCmd();\r\n }\r\n\r\n this._objectControls.update();\r\n\r\n this._forEachComplexVisual((visual) => {\r\n visual.getComplex().update();\r\n });\r\n\r\n if (settings.now.autobuild && !this._loading.length && !this._building && this._needRebuild()) {\r\n this.rebuild();\r\n }\r\n\r\n if (!this._loading.length && !this._building && !this._needRebuild()) {\r\n this._updateView();\r\n }\r\n\r\n this._updateFog();\r\n\r\n if (this._gfx.renderer.xr.enabled) {\r\n this.webVR.updateMoleculeScale();\r\n }\r\n};\r\n\r\nMiew.prototype._onRender = function () {\r\n const gfx = this._gfx;\r\n\r\n // update all matrices\r\n gfx.scene.updateMatrixWorld();\r\n gfx.camera.updateMatrixWorld();\r\n\r\n this._clipPlaneUpdateValue(this._getBSphereRadius());\r\n this._fogFarUpdateValue();\r\n\r\n gfx.renderer.setRenderTarget(null);\r\n gfx.renderer.clear();\r\n\r\n this._renderFrame(settings.now.stereo);\r\n};\r\n\r\nMiew.prototype._renderFrame = (function () {\r\n const _anaglyphMat = new AnaglyphMaterial();\r\n const _size = new THREE.Vector2();\r\n\r\n return function (stereo) {\r\n const gfx = this._gfx;\r\n const { renderer } = gfx;\r\n\r\n renderer.getSize(_size);\r\n\r\n if (stereo !== 'NONE') {\r\n gfx.camera.focus = gfx.camera.position.z; // set focus to the center of the object\r\n gfx.stereoCam.aspect = 1.0;\r\n\r\n // in anaglyph mode we render full-size image for each eye\r\n // while in other stereo modes only half-size (two images on the screen)\r\n if (stereo === 'ANAGLYPH') {\r\n gfx.stereoCam.update(gfx.camera);\r\n } else {\r\n gfx.stereoCam.updateHalfSized(gfx.camera, settings.now.camFov);\r\n }\r\n }\r\n\r\n // resize offscreen buffers to match the target\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n this._resizeOffscreenBuffers(_size.width * pixelRatio, _size.height * pixelRatio, stereo);\r\n\r\n this._renderShadowMap();\r\n\r\n switch (stereo) {\r\n case 'WEBVR':\r\n case 'NONE':\r\n this._renderScene(gfx.camera, false);\r\n break;\r\n case 'SIMPLE':\r\n case 'DISTORTED':\r\n renderer.setScissorTest(true);\r\n\r\n renderer.setScissor(0, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(0, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraL, stereo === 'DISTORTED');\r\n\r\n renderer.setScissor(_size.width / 2, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(_size.width / 2, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraR, stereo === 'DISTORTED');\r\n\r\n renderer.setScissorTest(false);\r\n break;\r\n case 'ANAGLYPH':\r\n this._renderScene(this._gfx.stereoCam.cameraL, false, gfx.stereoBufL);\r\n this._renderScene(this._gfx.stereoCam.cameraR, false, gfx.stereoBufR);\r\n renderer.setRenderTarget(null);\r\n _anaglyphMat.uniforms.srcL.value = gfx.stereoBufL.texture;\r\n _anaglyphMat.uniforms.srcR.value = gfx.stereoBufR.texture;\r\n gfx.renderer.renderScreenQuad(_anaglyphMat);\r\n break;\r\n default:\r\n }\r\n\r\n gfx.renderer2d.render(gfx.scene, gfx.camera);\r\n\r\n if (settings.now.axes && gfx.axes && !gfx.renderer.xr.enabled) {\r\n gfx.axes.render(renderer);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._onBgColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx) {\r\n if (gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onFogColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx && gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._setUberMaterialValues = function (values) {\r\n this._gfx.root.traverse((obj) => {\r\n if ((obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line)\r\n && obj.material instanceof UberMaterial) {\r\n obj.material.setValues(values);\r\n obj.material.needsUpdate = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) {\r\n const gfx = this._gfx;\r\n const gl = gfx.renderer.getContext();\r\n const ext = gl.getExtension('WEBGL_draw_buffers');\r\n const { properties } = gfx.renderer;\r\n\r\n if (!on) {\r\n ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, null]);\r\n return;\r\n }\r\n\r\n // take extra texture from Texture Buffer\r\n gfx.renderer.setRenderTarget(textureBuffer);\r\n const tx8 = properties.get(textureBuffer.texture).__webglTexture;\r\n gl.bindTexture(gl.TEXTURE_2D, tx8);\r\n\r\n // take texture and framebuffer from renderbuffer\r\n gfx.renderer.setRenderTarget(renderBuffer);\r\n const fb = properties.get(renderBuffer).__webglFramebuffer;\r\n const tx = properties.get(renderBuffer.texture).__webglTexture;\r\n\r\n // set framebuffer\r\n gl.bindFramebuffer(gl.FRAMEBUFFER, fb);\r\n fb.width = renderBuffer.width;\r\n fb.height = renderBuffer.height;\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT0, gl.TEXTURE_2D, tx, 0);\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, ext.COLOR_ATTACHMENT1_WEBGL, gl.TEXTURE_2D, tx8, 0);\r\n\r\n // mapping textures\r\n ext.drawBuffersWEBGL([gl.COLOR_ATTACHMENT0, ext.COLOR_ATTACHMENT1_WEBGL]);\r\n};\r\n\r\nMiew.prototype._renderScene = (function () {\r\n return function (camera, distortion, target) {\r\n distortion = distortion || false;\r\n target = target || null;\r\n\r\n const gfx = this._gfx;\r\n\r\n // render to offscreen buffer\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.clear();\r\n if (gfx.renderer.xr.enabled) {\r\n gfx.renderer.render(gfx.scene, camera);\r\n return;\r\n }\r\n\r\n // clean buffer for normals texture\r\n gfx.renderer.setClearColor(0x000000, 0.0);\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf4);\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.clear();\r\n\r\n const bHaveComplexes = (this._getComplexVisual() !== null);\r\n const volumeVisual = this._getVolumeVisual();\r\n const ssao = bHaveComplexes && settings.now.ao;\r\n\r\n if (ssao) {\r\n this._enableMRT(true, gfx.offscreenBuf, gfx.offscreenBuf4);\r\n }\r\n\r\n if (settings.now.transparency === 'prepass') {\r\n this._renderWithPrepassTransparency(camera, gfx.offscreenBuf);\r\n } else if (settings.now.transparency === 'standard') {\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n }\r\n\r\n if (ssao) {\r\n this._enableMRT(false, null, null);\r\n }\r\n\r\n // when fxaa we should get resulting image in temp off-screen buff2 for further postprocessing with fxaa filter\r\n // otherwise we render to canvas\r\n const outline = bHaveComplexes && settings.now.outline.on;\r\n const fxaa = bHaveComplexes && settings.now.fxaa;\r\n const volume = (volumeVisual !== null) && (volumeVisual.getMesh().material != null);\r\n let dstBuffer = (ssao || outline || volume || fxaa || distortion) ? gfx.offscreenBuf2 : target;\r\n let srcBuffer = gfx.offscreenBuf;\r\n\r\n if (ssao) {\r\n this._performAO(\r\n srcBuffer,\r\n gfx.offscreenBuf4,\r\n gfx.offscreenBuf.depthTexture,\r\n dstBuffer,\r\n gfx.offscreenBuf3,\r\n gfx.offscreenBuf2,\r\n );\r\n if (!fxaa && !distortion && !volume && !outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = target;\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n } else {\r\n // just copy color buffer to dst buffer\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n\r\n // outline\r\n if (outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = (volume || fxaa || distortion) ? gfx.offscreenBuf3 : target;\r\n if (srcBuffer != null) {\r\n this._renderOutline(camera, gfx.offscreenBuf, srcBuffer, dstBuffer);\r\n }\r\n }\r\n\r\n // render selected part with outline material\r\n this._renderSelection(camera, gfx.offscreenBuf, dstBuffer);\r\n\r\n if (volume) {\r\n // copy current picture to the buffer that retains depth-data of the original molecule render\r\n // so that volume renderer could use depth-test\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n dstBuffer = gfx.offscreenBuf;\r\n this._renderVolume(volumeVisual, camera, dstBuffer, gfx.volBFTex, gfx.volFFTex, gfx.volWFFTex);\r\n\r\n // if this is the last stage -- copy image to target\r\n if (!fxaa && !distortion) {\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n }\r\n }\r\n\r\n srcBuffer = dstBuffer;\r\n\r\n if (fxaa) {\r\n dstBuffer = distortion ? gfx.offscreenBuf4 : target;\r\n this._performFXAA(srcBuffer, dstBuffer);\r\n srcBuffer = dstBuffer;\r\n }\r\n\r\n if (distortion) {\r\n dstBuffer = target;\r\n this._performDistortion(srcBuffer, dstBuffer, true);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._performDistortion = (function () {\r\n const _scene = new THREE.Scene();\r\n const _camera = new THREE.OrthographicCamera(-1.0, 1.0, 1.0, -1.0, -500, 1000);\r\n\r\n const _material = new THREE.RawShaderMaterial({\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n aberration: { type: 'fv3', value: new THREE.Vector3(1.0) },\r\n },\r\n vertexShader: vertexScreenQuadShader,\r\n fragmentShader: fragmentScreenQuadFromDistTex,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n const _geo = gfxutils.buildDistorionMesh(10, 10, settings.now.debug.stereoBarrel);\r\n _scene.add(new meshes.Mesh(_geo, _material));\r\n\r\n return function (srcBuffer, targetBuffer, mesh) {\r\n this._gfx.renderer.setRenderTarget(targetBuffer);\r\n this._gfx.renderer.clear();\r\n\r\n if (mesh) {\r\n _material.uniforms.srcTex.value = srcBuffer.texture;\r\n _material.uniforms.aberration.value.set(0.995, 1.0, 1.01);\r\n this._gfx.renderer.render(_scene, _camera);\r\n } else {\r\n this._gfx.renderer.renderScreenQuadFromTexWithDistortion(srcBuffer, settings.now.debug.stereoBarrel);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._renderOutline = (function () {\r\n const _outlineMaterial = new OutlineMaterial({ depth: true });\r\n\r\n return function (camera, srcDepthBuffer, srcColorBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcColorBuffer.texture;\r\n _outlineMaterial.uniforms.srcDepthTex.value = srcDepthBuffer.depthTexture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcDepthBuffer.width, srcDepthBuffer.height);\r\n _outlineMaterial.uniforms.color.value = new THREE.Color(settings.now.outline.color);\r\n _outlineMaterial.uniforms.threshold.value = settings.now.outline.threshold;\r\n _outlineMaterial.uniforms.thickness.value = new THREE.Vector2(\r\n settings.now.outline.thickness,\r\n settings.now.outline.thickness,\r\n );\r\n\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._renderShadowMap = (function () {\r\n const pars = { minFilter: THREE.NearestFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat };\r\n\r\n return function () {\r\n if (!settings.now.shadow.on) {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n const currentRenderTarget = gfx.renderer.getRenderTarget();\r\n const activeCubeFace = gfx.renderer.getActiveCubeFace();\r\n const activeMipmapLevel = gfx.renderer.getActiveMipmapLevel();\r\n\r\n const _state = gfx.renderer.state;\r\n\r\n // Set GL state for depth map.\r\n _state.setBlending(THREE.NoBlending);\r\n _state.buffers.color.setClear(1, 1, 1, 1);\r\n _state.buffers.depth.setTest(true);\r\n _state.setScissorTest(false);\r\n\r\n for (let i = 0; i < gfx.scene.children.length; i++) {\r\n if (gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = gfx.scene.children[i];\r\n\r\n if (light.shadow.map == null) {\r\n light.shadow.map = new THREE.WebGLRenderTarget(light.shadow.mapSize.width, light.shadow.mapSize.height, pars);\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n light.shadow.updateMatrices(light);\r\n\r\n gfx.renderer.setRenderTarget(light.shadow.map);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.render(gfx.scene, light.shadow.camera);\r\n }\r\n }\r\n gfx.renderer.setRenderTarget(currentRenderTarget, activeCubeFace, activeMipmapLevel);\r\n };\r\n}());\r\n\r\n/**\r\n * Check if there is selection which must be rendered or not.\r\n * @private\r\n * @returns {boolean} true on existing selection to render\r\n */\r\nMiew.prototype._hasSelectionToRender = function () {\r\n const selPivot = this._gfx.selectionPivot;\r\n\r\n for (let i = 0; i < selPivot.children.length; i++) {\r\n const selPivotChild = selPivot.children[i];\r\n if (selPivotChild.children.length > 0) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n};\r\n\r\nMiew.prototype._renderSelection = (function () {\r\n const _outlineMaterial = new OutlineMaterial();\r\n\r\n return function (camera, srcBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // clear offscreen buffer (leave z-buffer intact)\r\n gfx.renderer.setClearColor('black', 0);\r\n\r\n // render selection to offscreen buffer\r\n gfx.renderer.setRenderTarget(srcBuffer);\r\n gfx.renderer.clear(true, false, false);\r\n if (self._hasSelectionToRender()) {\r\n gfx.selectionRoot.matrix = gfx.root.matrix;\r\n gfx.selectionPivot.matrix = gfx.pivot.matrix;\r\n gfx.renderer.render(gfx.selectionScene, camera);\r\n } else {\r\n // just render something to force \"target clear\" operation to finish\r\n gfx.renderer.renderDummyQuad();\r\n }\r\n\r\n // overlay to screen\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 0.6);\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcBuffer.width, srcBuffer.height);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._checkVolumeRenderingSupport = function (renderTarget) {\r\n if (!renderTarget) {\r\n return false;\r\n }\r\n const gfx = this._gfx;\r\n const oldRT = gfx.renderer.getRenderTarget();\r\n\r\n gfx.renderer.setRenderTarget(renderTarget);\r\n const context = gfx.renderer.getContext();\r\n const result = context.checkFramebufferStatus(context.FRAMEBUFFER);\r\n gfx.renderer.setRenderTarget(oldRT);\r\n if (result !== context.FRAMEBUFFER_COMPLETE) {\r\n // floatFrameBufferWarning = ;\r\n this.logger.warn('Device doesn\\'t support electron density rendering');\r\n return false;\r\n }\r\n return true;\r\n};\r\n\r\nMiew.prototype._renderVolume = (function () {\r\n const volumeBFMat = new VolumeMaterial.BackFacePosMaterial();\r\n const volumeFFMat = new VolumeMaterial.FrontFacePosMaterial();\r\n const cubeOffsetMat = new THREE.Matrix4().makeTranslation(0.5, 0.5, 0.5);\r\n const world2colorMat = new THREE.Matrix4();\r\n\r\n let volumeRenderingSupported;\r\n\r\n return function (volumeVisual, camera, dstBuf, tmpBuf1, tmpBuf2, tmpBuf3) {\r\n const gfx = this._gfx;\r\n\r\n if (typeof volumeRenderingSupported === 'undefined') {\r\n volumeRenderingSupported = this._checkVolumeRenderingSupport(tmpBuf1);\r\n }\r\n\r\n if (!volumeRenderingSupported) {\r\n return;\r\n }\r\n\r\n const mesh = volumeVisual.getMesh();\r\n\r\n mesh.rebuild(gfx.camera);\r\n\r\n // use main camera to prepare special textures to be used by volumetric rendering\r\n // these textures have the size of the window and are stored in offscreen buffers\r\n gfx.renderer.setClearColor('black', 0);\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n // draw plane with its own material, because it differs slightly from volumeBFMat\r\n camera.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeBFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeFFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.scene.overrideMaterial = null;\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n\r\n // prepare texture that contains molecule positions\r\n world2colorMat.copy(mesh.matrixWorld).invert();\r\n UberMaterial.prototype.uberOptions.world2colorMatrix.multiplyMatrices(cubeOffsetMat, world2colorMat);\r\n camera.layers.set(gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // render volume\r\n const vm = mesh.material;\r\n vm.uniforms._BFRight.value = tmpBuf1.texture;\r\n vm.uniforms._FFRight.value = tmpBuf2.texture;\r\n vm.uniforms._WFFRight.value = tmpBuf3.texture;\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.renderer.setRenderTarget(dstBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\n/* Render scene with 'ZPrepass transparency Effect'\r\n * Idea: transparent objects are rendered in two passes. The first one writes result only into depth buffer.\r\n * The second pass reads depth buffer and writes only to color buffer. The method results in\r\n * correct image of front part of the semi-transparent objects, but we can see only front transparent objects\r\n * and opaque objects inside, there is no transparent objects inside.\r\n * Notes: 1. Opaque objects should be rendered strictly before semi-transparent ones.\r\n * 2. Realization doesn't use camera layers because scene traversing is used for material changes and\r\n * we can use it to select needed meshes and don't complicate meshes builders with layers\r\n */\r\nMiew.prototype._renderWithPrepassTransparency = (function () {\r\n return function (camera, targetBuffer) {\r\n const gfx = this._gfx;\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n\r\n // opaque objects\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // transparent objects z prepass\r\n camera.layers.set(gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n gfx.renderer.getContext().colorMask(false, false, false, false); // don't update color buffer\r\n gfx.renderer.render(gfx.scene, camera);\r\n gfx.renderer.getContext().colorMask(true, true, true, true); // update color buffer\r\n\r\n // transparent objects color pass\r\n camera.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // restore default layer\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\nMiew.prototype._performFXAA = (function () {\r\n const _fxaaMaterial = new FXAAMaterial();\r\n\r\n return function (srcBuffer, targetBuffer) {\r\n if (typeof srcBuffer === 'undefined' || typeof targetBuffer === 'undefined') {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n\r\n // clear canvas\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.clear();\r\n\r\n // do fxaa processing of offscreen buff2\r\n _fxaaMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _fxaaMaterial.uniforms.srcTexelSize.value.set(1.0 / srcBuffer.width, 1.0 / srcBuffer.height);\r\n _fxaaMaterial.uniforms.bgColor.value.set(settings.now.bg.color);\r\n\r\n if (_fxaaMaterial.bgTransparent !== settings.now.bg.transparent) {\r\n _fxaaMaterial.setValues({ bgTransparent: settings.now.bg.transparent });\r\n _fxaaMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.renderScreenQuad(_fxaaMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._performAO = (function () {\r\n const _aoMaterial = new AOMaterial();\r\n const _horBlurMaterial = new AOHorBlurMaterial();\r\n const _vertBlurMaterial = new AOVertBlurWithBlendMaterial();\r\n\r\n const _scale = new THREE.Vector3();\r\n return function (srcColorBuffer, normalBuffer, srcDepthTexture, targetBuffer, tempBuffer, tempBuffer1) {\r\n if (!srcColorBuffer || !normalBuffer || !srcDepthTexture || !targetBuffer || !tempBuffer || !tempBuffer1) {\r\n return;\r\n }\r\n const gfx = this._gfx;\r\n const tanHalfFOV = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * gfx.camera.fov);\r\n\r\n _aoMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _aoMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _aoMaterial.uniforms.normalTexture.value = normalBuffer.texture;\r\n _aoMaterial.uniforms.srcTexelSize.value.set(1.0 / srcColorBuffer.width, 1.0 / srcColorBuffer.height);\r\n _aoMaterial.uniforms.camNearFar.value.set(gfx.camera.near, gfx.camera.far);\r\n _aoMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _aoMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _aoMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n gfx.root.matrix.extractScale(_scale);\r\n _aoMaterial.uniforms.kernelRadius.value = settings.now.debug.ssaoKernelRadius * _scale.x;\r\n _aoMaterial.uniforms.depthThreshold.value = 2.0 * this._getBSphereRadius(); // diameter\r\n _aoMaterial.uniforms.factor.value = settings.now.debug.ssaoFactor;\r\n // N: should be tempBuffer1 for proper use of buffers (see buffers using outside the function)\r\n gfx.renderer.setRenderTarget(tempBuffer1);\r\n gfx.renderer.renderScreenQuad(_aoMaterial);\r\n\r\n _horBlurMaterial.uniforms.aoMap.value = tempBuffer1.texture;\r\n _horBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer1.width, 1.0 / tempBuffer1.height);\r\n _horBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n gfx.renderer.setRenderTarget(tempBuffer);\r\n gfx.renderer.renderScreenQuad(_horBlurMaterial);\r\n\r\n _vertBlurMaterial.uniforms.aoMap.value = tempBuffer.texture;\r\n _vertBlurMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _vertBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer.width, 1.0 / tempBuffer.height);\r\n _vertBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _vertBlurMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _vertBlurMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _vertBlurMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n const { fog } = gfx.scene;\r\n if (fog) {\r\n _vertBlurMaterial.uniforms.fogNearFar.value.set(fog.near, fog.far);\r\n _vertBlurMaterial.uniforms.fogColor.value.set(fog.color.r, fog.color.g, fog.color.b, settings.now.fogAlpha);\r\n }\r\n if ((_vertBlurMaterial.useFog !== settings.now.fog)\r\n || (_vertBlurMaterial.fogTransparent !== settings.now.bg.transparent)) {\r\n _vertBlurMaterial.setValues({ useFog: settings.now.fog, fogTransparent: settings.now.bg.transparent });\r\n _vertBlurMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_vertBlurMaterial);\r\n };\r\n}());\r\n\r\n/**\r\n * Reset the viewer, unload molecules.\r\n * @param {boolean=} keepReps - Keep representations while resetting viewer state.\r\n */\r\nMiew.prototype.reset = function (/* keepReps */) {\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._lastPick = null;\r\n\r\n this._releaseAllVisuals();\r\n\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._resetObjects();\r\n\r\n if (this._gfx) {\r\n gfxutils.clearTree(this._gfx.pivot);\r\n this._gfx.renderer2d.reset();\r\n }\r\n\r\n this.setNeedRender();\r\n};\r\n\r\nMiew.prototype._resetScene = function () {\r\n this._objectControls.reset();\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n this.resetReps();\r\n this.resetPivot();\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype.resetView = function () {\r\n // reset controls\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._resetScene();\r\n\r\n // reset selection\r\n this._forEachComplexVisual((visual) => {\r\n visual.updateSelectionMask({});\r\n visual.rebuildSelectionGeometry();\r\n });\r\n};\r\n\r\nMiew.prototype._export = function (format) {\r\n const TheExporter = _.head(io.exporters.find({ format }));\r\n if (!TheExporter) {\r\n this.logger.error('Could not find suitable exporter for this source');\r\n return Promise.reject(new Error('Could not find suitable exporter for this source'));\r\n }\r\n this.dispatchEvent({ type: 'exporting' });\r\n\r\n if (this._visuals[this._curVisualName] instanceof ComplexVisual) {\r\n let dataSource = null;\r\n if (TheExporter.SourceClass === ComplexVisual) {\r\n dataSource = this._visuals[this._curVisualName];\r\n } else if (TheExporter.SourceClass === Complex) {\r\n dataSource = this._visuals[this._curVisualName]._complex;\r\n }\r\n const exporter = new TheExporter(dataSource, { miewVersion: Miew.VERSION });\r\n return exporter.export().then((data) => data);\r\n }\r\n if (this._visuals[this._curVisualName] instanceof VolumeVisual) {\r\n return Promise.reject(new Error('Sorry, exporter for volume data not implemented yet'));\r\n }\r\n return Promise.reject(new Error('Unexpected format of data'));\r\n};\r\n\r\nconst rePdbId = /^(?:(pdb|cif|ccp4|dsn6):\\s*)?(\\d[a-z\\d]{3})$/i;\r\nconst rePubchem = /^(?:pc|pubchem):\\s*([a-z]+)$/i;\r\nconst reUrlScheme = /^([a-z][a-z\\d\\-+.]*):/i;\r\n\r\nfunction resolveSourceShortcut(source, opts) {\r\n if (!_.isString(source)) {\r\n return source;\r\n }\r\n\r\n // e.g. \"cif:1CRN\"\r\n const matchesPdbId = rePdbId.exec(source);\r\n if (matchesPdbId) {\r\n let [, format = 'pdb', id] = matchesPdbId;\r\n\r\n format = format.toLowerCase();\r\n id = id.toUpperCase();\r\n\r\n switch (format) {\r\n case 'pdb':\r\n source = `https://files.rcsb.org/download/${id}.pdb`;\r\n break;\r\n case 'cif':\r\n source = `https://files.rcsb.org/download/${id}.cif`;\r\n break;\r\n case 'ccp4':\r\n source = `https://www.ebi.ac.uk/pdbe/coordinates/files/${id.toLowerCase()}.ccp4`;\r\n break;\r\n case 'dsn6':\r\n source = `https://edmaps.rcsb.org/maps/${id.toLowerCase()}_2fofc.dsn6`;\r\n break;\r\n default:\r\n throw new Error('Unexpected data format shortcut');\r\n }\r\n\r\n opts.fileType = format;\r\n opts.fileName = `${id}.${format}`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // e.g. \"pc:aspirin\"\r\n const matchesPubchem = rePubchem.exec(source);\r\n if (matchesPubchem) {\r\n const compound = matchesPubchem[1].toLowerCase();\r\n source = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${compound}/JSON?record_type=3d`;\r\n opts.fileType = 'pubchem';\r\n opts.fileName = `${compound}.json`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // otherwise is should be an URL\r\n if (opts.sourceType === 'url' || opts.sourceType === undefined) {\r\n opts.sourceType = 'url';\r\n\r\n // e.g. \"./data/1CRN.pdb\"\r\n if (!reUrlScheme.test(source)) {\r\n source = utils.resolveURL(source);\r\n }\r\n }\r\n\r\n return source;\r\n}\r\n\r\nfunction updateBinaryMode(opts) {\r\n let { binary } = opts;\r\n\r\n // detect by format\r\n if (opts.fileType !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n } else {\r\n throw new Error('Could not find suitable parser for this format');\r\n }\r\n }\r\n\r\n // detect by file extension\r\n if (binary === undefined && opts.fileExt !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ ext: opts.fileExt }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n }\r\n }\r\n\r\n // temporary workaround for animation\r\n if (opts.fileExt !== undefined && opts.fileExt.toLowerCase() === '.man') {\r\n opts.binary = true;\r\n opts.animation = true; // who cares?\r\n }\r\n\r\n // update if detected\r\n if (binary !== undefined) {\r\n if (opts.binary !== undefined && opts.binary !== binary) {\r\n opts.context.logger.warn('Overriding incorrect binary mode');\r\n }\r\n }\r\n\r\n opts.binary = binary || false;\r\n}\r\n\r\nfunction _fetchData(source, opts, job) {\r\n return new Promise(((resolve) => {\r\n if (job.shouldCancel()) {\r\n throw new Error('Operation cancelled');\r\n }\r\n job.notify({ type: 'fetching' });\r\n\r\n // allow for source shortcuts\r\n source = resolveSourceShortcut(source, opts);\r\n\r\n // detect a proper loader\r\n const TheLoader = _.head(io.loaders.find({ type: opts.sourceType, source }));\r\n if (!TheLoader) {\r\n throw new Error(LOADER_NOT_FOUND);\r\n }\r\n\r\n // split file name\r\n const fileName = opts.fileName || TheLoader.extractName(source);\r\n if (fileName) {\r\n const [name, fileExt] = utils.splitFileName(fileName);\r\n _.defaults(opts, { name, fileExt, fileName });\r\n }\r\n\r\n // should it be text or binary?\r\n updateBinaryMode(opts);\r\n\r\n // FIXME: All new settings retrieved from server are applied after the loading is complete. However, we need some\r\n // flags to alter the loading process itself. Here we apply them in advance. Dirty hack. Kill the server, remove\r\n // all hacks and everybody's happy.\r\n let newOptions = _.get(opts, 'preset.expression');\r\n if (!_.isUndefined(newOptions)) {\r\n newOptions = JSON.parse(newOptions);\r\n if (newOptions && newOptions.settings) {\r\n const keys = ['singleUnit'];\r\n for (let keyIndex = 0, keyCount = keys.length; keyIndex < keyCount; ++keyIndex) {\r\n const key = keys[keyIndex];\r\n const value = _.get(newOptions.settings, key);\r\n if (!_.isUndefined(value)) {\r\n settings.set(key, value);\r\n }\r\n }\r\n }\r\n }\r\n\r\n // create a loader\r\n const loader = new TheLoader(source, opts);\r\n loader.context = opts.context;\r\n job.addEventListener('cancel', () => loader.abort());\r\n\r\n loader.addEventListener('progress', (event) => {\r\n if (event.lengthComputable && event.total > 0) {\r\n reportProgress(loader.logger, 'Fetching', event.loaded / event.total);\r\n } else {\r\n reportProgress(loader.logger, 'Fetching');\r\n }\r\n });\r\n\r\n console.time('fetch');\r\n const promise = loader.load()\r\n .then((data) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.info('Fetching finished');\r\n job.notify({ type: 'fetchingDone', data });\r\n return data;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Fetching failed');\r\n job.notify({ type: 'fetchingDone', error });\r\n throw error;\r\n });\r\n resolve(promise);\r\n }));\r\n}\r\n\r\nfunction _parseData(data, opts, job) {\r\n if (job.shouldCancel()) {\r\n return Promise.reject(new Error('Operation cancelled'));\r\n }\r\n\r\n job.notify({ type: 'parsing' });\r\n\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType, ext: opts.fileExt, data }));\r\n if (!TheParser) {\r\n return Promise.reject(new Error('Could not find suitable parser'));\r\n }\r\n\r\n const parser = new TheParser(data, opts);\r\n parser.context = opts.context;\r\n job.addEventListener('cancel', () => parser.abort());\r\n\r\n console.time('parse');\r\n return parser.parse()\r\n .then((dataSet) => {\r\n console.timeEnd('parse');\r\n job.notify({ type: 'parsingDone', data: dataSet });\r\n return dataSet;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('parse');\r\n opts.error = error;\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Parsing failed');\r\n job.notify({ type: 'parsingDone', error });\r\n throw error;\r\n });\r\n}\r\n\r\n/**\r\n * Load molecule asynchronously.\r\n * @param {string|File} source - Molecule source to load (e.g. PDB ID, URL or File object).\r\n * @param {object=} opts - Options.\r\n * @param {string=} opts.sourceType - Data source type (e.g. 'url', 'file').\r\n * @param {string=} opts.fileType - Data contents type (e.g. 'pdb', 'cml').\r\n * @param {string=} opts.mdFile - .nc file path.\r\n * @param {boolean=} opts.keepRepsInfo - prevent reset of object and reps information.\r\n * @returns {Promise} name of the visual that was added to the viewer\r\n */\r\nMiew.prototype.load = function (source, opts) {\r\n opts = _.merge({}, opts, {\r\n context: this,\r\n });\r\n\r\n // for a single-file scenario\r\n if (!this.settings.now.use.multiFile) {\r\n // abort all loaders in progress\r\n if (this._loading.length) {\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n }\r\n\r\n // reset\r\n if (!opts.animation) { // FIXME: sometimes it is set AFTERWARDS!\r\n this.reset(true);\r\n }\r\n }\r\n\r\n this._interpolator.reset();\r\n\r\n this.dispatchEvent({ type: 'loading', options: opts, source });\r\n\r\n const job = new JobHandle();\r\n this._loading.push(job);\r\n job.addEventListener('notification', (e) => {\r\n this.dispatchEvent(e.slaveEvent);\r\n });\r\n\r\n this._spinner.spin(this._container);\r\n\r\n const onLoadEnd = (anything) => {\r\n const jobIndex = this._loading.indexOf(job);\r\n if (jobIndex !== -1) {\r\n this._loading.splice(jobIndex, 1);\r\n }\r\n this._spinner.stop();\r\n this._refreshTitle();\r\n job.notify({ type: 'loadingDone', anything });\r\n return anything;\r\n };\r\n\r\n return _fetchData(source, opts, job)\r\n .then((data) => _parseData(data, opts, job))\r\n .then((object) => {\r\n const name = this._onLoad(object, opts);\r\n return onLoadEnd(name);\r\n })\r\n .catch((err) => {\r\n this.logger.error('Could not load data');\r\n this.logger.debug(err);\r\n throw onLoadEnd(err);\r\n });\r\n};\r\n\r\n/**\r\n * Unload molecule (delete corresponding visual).\r\n * @param {string=} name - name of the visual\r\n */\r\nMiew.prototype.unload = function (name) {\r\n this._removeVisual(name || this.getCurrentVisual());\r\n this.resetPivot();\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n};\r\n\r\n/**\r\n * Start new animation. Now is broken.\r\n * @param fileData - new data to animate\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._startAnimation = function (fileData) {\r\n this._stopAnimation();\r\n const self = this;\r\n const visual = this._getComplexVisual();\r\n if (visual === null) {\r\n this.logger.error('Unable to start animation - no molecule is loaded.');\r\n return;\r\n }\r\n try {\r\n this._frameInfo = new FrameInfo(\r\n visual.getComplex(),\r\n fileData,\r\n {\r\n onLoadStatusChanged() {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo ? self._frameInfo.isLoading : true,\r\n },\r\n });\r\n },\r\n onError(message) {\r\n self._stopAnimation();\r\n self.logger.error(message);\r\n },\r\n },\r\n );\r\n } catch (e) {\r\n this.logger.error('Animation file does not fit to current complex!');\r\n return;\r\n }\r\n this._continueAnimation();\r\n};\r\n\r\n/**\r\n * Pause current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._pauseAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n this._isAnimating = false;\r\n clearInterval(this._animInterval);\r\n this._animInterval = null;\r\n if (this._frameInfo) {\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: this._isAnimating,\r\n isLoading: this._frameInfo.isLoading,\r\n },\r\n });\r\n }\r\n};\r\n\r\n/**\r\n * Continue current animation after pausing. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._continueAnimation = function () {\r\n this._isAnimating = true;\r\n let minFrameTime = 1000 / settings.now.maxfps;\r\n minFrameTime = Number.isNaN(minFrameTime) ? 0 : minFrameTime;\r\n const self = this;\r\n const { pivot } = self._gfx;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.resetSelectionMask();\r\n visual.rebuildSelectionGeometry();\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n }\r\n this._animInterval = setInterval(() => {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo.isLoading,\r\n },\r\n });\r\n if (self._frameInfo.frameIsReady) {\r\n pivot.updateToFrame(self._frameInfo);\r\n self._updateObjsToFrame(self._frameInfo);\r\n self._refreshTitle(` Frame ${self._frameInfo._currFrame} of ${self._frameInfo._framesCount\r\n } time interval - ${self._frameInfo._timeStep}`);\r\n try {\r\n self._frameInfo.nextFrame();\r\n } catch (e) {\r\n self.logger.error('Error during animation');\r\n self._stopAnimation();\r\n return;\r\n }\r\n self._needRender = true;\r\n }\r\n }, minFrameTime);\r\n};\r\n\r\n/**\r\n * Stop current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._stopAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n clearInterval(this._animInterval);\r\n this._frameInfo.disableEvents();\r\n this._frameInfo = null;\r\n this._animInterval = null;\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: null,\r\n });\r\n};\r\n\r\n/**\r\n * Invoked upon successful loading of some data source\r\n * @param {DataSource} dataSource - Data source for visualization (molecular complex or other)\r\n * @param {object} opts - Options.\r\n * @private\r\n */\r\nMiew.prototype._onLoad = function (dataSource, opts) {\r\n const gfx = this._gfx;\r\n let visualName = null;\r\n\r\n if (opts.animation) {\r\n this._refreshTitle();\r\n this._startAnimation(dataSource);\r\n return null;\r\n }\r\n this._stopAnimation();\r\n if (!opts || !opts.keepRepsInfo) {\r\n this._opts.reps = null;\r\n this._opts._objects = null;\r\n }\r\n\r\n if (dataSource.id === 'Complex') {\r\n const complex = dataSource;\r\n\r\n // update title\r\n if (opts.fileName) {\r\n complex.name = complex.name || removeExtension(opts.fileName).toUpperCase();\r\n } else if (opts.amberFileName) {\r\n complex.name = complex.name || removeExtension(opts.amberFileName).toUpperCase();\r\n } else {\r\n complex.name = `Dynamic ${opts.fileType} molecule`;\r\n }\r\n\r\n visualName = this._addVisual(new ComplexVisual(complex.name, complex));\r\n this._curVisualName = visualName;\r\n\r\n const desc = this.info();\r\n this.logger.info(`Parsed ${opts.fileName} (${\r\n desc.atoms} atoms, ${\r\n desc.bonds} bonds, ${\r\n desc.residues} residues, ${\r\n desc.chains} chains).`);\r\n\r\n if (_.isNumber(this._opts.unit)) {\r\n complex.setCurrentUnit(this._opts.unit);\r\n }\r\n\r\n if (opts.preset) {\r\n // ...removed server access...\r\n } else if (settings.now.autoPreset) {\r\n switch (opts.fileType) {\r\n case 'cml':\r\n this.resetReps('small');\r\n break;\r\n case 'pdb':\r\n case 'mmtf':\r\n case 'cif':\r\n if (hasValidResidues(complex)) {\r\n this.resetReps('macro');\r\n } else {\r\n this.resetReps('small');\r\n }\r\n break;\r\n default:\r\n this.resetReps('default');\r\n break;\r\n }\r\n } else {\r\n this.resetReps('default');\r\n }\r\n } else if (dataSource.id === 'Volume') {\r\n this.resetEd();\r\n visualName = this._onLoadEd(dataSource);\r\n }\r\n\r\n gfx.camera.updateProjectionMatrix();\r\n this._updateFog();\r\n\r\n // reset global transform\r\n gfx.root.resetTransform();\r\n this.resetPivot();\r\n\r\n // set scale to fit everything on the screen\r\n this._objectControls.setScale(settings.now.radiusToFit / this._getBSphereRadius());\r\n\r\n this._resetObjects();\r\n\r\n if (settings.now.autoResolution) {\r\n this._tweakResolution();\r\n }\r\n\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n this._refreshTitle();\r\n\r\n return visualName;\r\n};\r\n\r\nMiew.prototype.resetEd = function () {\r\n if (this._edLoader) {\r\n this._edLoader.abort();\r\n this._edLoader = null;\r\n }\r\n\r\n // free all resources\r\n this._removeVisual(this._getVolumeVisual());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype.loadEd = function (source) {\r\n this.resetEd();\r\n\r\n const TheLoader = _.head(io.loaders.find({ source }));\r\n if (!TheLoader) {\r\n this.logger.error(LOADER_NOT_FOUND);\r\n return Promise.reject(new Error(LOADER_NOT_FOUND));\r\n }\r\n\r\n const loader = this._edLoader = new TheLoader(source, { binary: true });\r\n loader.context = this;\r\n return loader.load().then((data) => {\r\n const TheParser = _.head(io.parsers.find({ format: 'ccp4' }));\r\n if (!TheParser) {\r\n throw new Error(PARSER_NOT_FOUND);\r\n }\r\n const parser = new TheParser(data);\r\n parser.context = this;\r\n return parser.parse().then((dataSource) => {\r\n this._onLoadEd(dataSource);\r\n });\r\n }).catch((error) => {\r\n this.logger.error('Could not load ED data');\r\n this.logger.debug(error);\r\n });\r\n};\r\n\r\nMiew.prototype._onLoadEd = function (dataSource) {\r\n dataSource.normalize();\r\n\r\n const volumeVisual = new VolumeVisual('volume', dataSource);\r\n volumeVisual.getMesh().layers.set(gfxutils.LAYERS.VOLUME); // volume mesh is not visible to common render\r\n const visualName = this._addVisual(volumeVisual);\r\n\r\n this._needRender = true;\r\n return visualName;\r\n};\r\n\r\nMiew.prototype._needRebuild = function () {\r\n let needsRebuild = false;\r\n this._forEachComplexVisual((visual) => {\r\n needsRebuild = needsRebuild || visual.needsRebuild();\r\n });\r\n return needsRebuild;\r\n};\r\n\r\nMiew.prototype._rebuildObjects = function () {\r\n const self = this;\r\n const gfx = this._gfx;\r\n let i;\r\n let n;\r\n\r\n // remove old object geometry\r\n const toRemove = [];\r\n for (i = 0; i < gfx.pivot.children.length; ++i) {\r\n const child = gfx.pivot.children[i];\r\n if (!(child instanceof Visual)) {\r\n toRemove.push(child);\r\n }\r\n }\r\n for (i = 0; i < toRemove.length; ++i) {\r\n toRemove[i].parent.remove(toRemove[i]);\r\n }\r\n\r\n setTimeout(() => {\r\n const objList = self._objects;\r\n for (i = 0, n = objList.length; i < n; ++i) {\r\n const obj = objList[i];\r\n if (obj.needsRebuild) {\r\n obj.build();\r\n }\r\n if (obj.getGeometry()) {\r\n gfx.pivot.add(obj.getGeometry());\r\n }\r\n }\r\n }, 10);\r\n};\r\n\r\nMiew.prototype.changeUnit = function (unitIdx, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n throw new Error('There is no complex to change!');\r\n }\r\n\r\n function currentUnitInfo() {\r\n const unit = visual ? visual.getComplex().getCurrentUnit() : 0;\r\n const type = unit > 0 ? (`Bio molecule ${unit}`) : 'Asymmetric unit';\r\n return `Current unit: ${unit} (${type})`;\r\n }\r\n\r\n if (unitIdx === undefined) {\r\n return currentUnitInfo();\r\n }\r\n if (_.isString(unitIdx)) {\r\n unitIdx = Math.max(parseInt(unitIdx, 10), 0);\r\n }\r\n if (visual.getComplex().setCurrentUnit(unitIdx)) {\r\n this._resetScene();\r\n this._updateInfoPanel();\r\n }\r\n return currentUnitInfo();\r\n};\r\n\r\n/**\r\n * Start to rebuild geometry asynchronously.\r\n */\r\nMiew.prototype.rebuild = function () {\r\n if (this._building) {\r\n this.logger.warn('Miew.rebuild(): already building!');\r\n return;\r\n }\r\n this._building = true;\r\n\r\n this.dispatchEvent({ type: 'rebuilding' });\r\n\r\n this._rebuildObjects();\r\n\r\n this._gfx.renderer2d.reset();\r\n\r\n const rebuildActions = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.needsRebuild()) {\r\n rebuildActions.push(visual.rebuild().then(() => new Promise(((resolve) => {\r\n visual.rebuildSelectionGeometry();\r\n resolve();\r\n }))));\r\n }\r\n });\r\n\r\n // Start asynchronous rebuild\r\n const self = this;\r\n this._spinner.spin(this._container);\r\n Promise.all(rebuildActions).then(() => {\r\n self._spinner.stop();\r\n\r\n self._needRender = true;\r\n\r\n self._refreshTitle();\r\n this.dispatchEvent({ type: 'buildingDone' });\r\n self._building = false;\r\n });\r\n};\r\n\r\n/** Mark all representations for rebuilding */\r\nMiew.prototype.rebuildAll = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setNeedsRebuild();\r\n });\r\n};\r\n\r\nMiew.prototype._refreshTitle = function (appendix) {\r\n let title;\r\n appendix = appendix === undefined ? '' : appendix;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n title = visual.getComplex().name;\r\n const rep = visual.repGet(visual.repCurrent());\r\n title += (rep ? ` – ${rep.mode.name} Mode` : '');\r\n } else {\r\n title = Object.keys(this._visuals).length > 0 ? 'Unknown' : 'No Data';\r\n }\r\n title += appendix;\r\n\r\n this.dispatchEvent({ type: 'titleChanged', data: title });\r\n};\r\n\r\nMiew.prototype.setNeedRender = function () {\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._extractRepresentation = function () {\r\n const changed = [];\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCount() === 0) {\r\n return;\r\n }\r\n\r\n const selector = visual.buildSelectorFromMask(1 << visual.getSelectionBit());\r\n const defPreset = settings.now.presets.default;\r\n const res = visual.repAdd({\r\n selector,\r\n mode: defPreset[0].mode.id,\r\n colorer: defPreset[0].colorer.id,\r\n material: defPreset[0].material.id,\r\n });\r\n if (!res) {\r\n if (visual.repCount() === ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n this.logger.warn(`Number of representations is limited to ${ComplexVisual.NUM_REPRESENTATION_BITS}`);\r\n }\r\n return;\r\n }\r\n\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n visual.repCurrent(res.index);\r\n\r\n changed.push(visual.name);\r\n });\r\n\r\n if (changed.length > 0) {\r\n this.logger.report(`New representation from selection for complexes: ${changed.join(', ')}`);\r\n }\r\n};\r\n\r\n/**\r\n * Change current representation list.\r\n * @param {array} reps - Representation list.\r\n */\r\nMiew.prototype._setReps = function (reps) {\r\n reps = reps || (this._opts && this._opts.reps) || [];\r\n this._forEachComplexVisual((visual) => visual.resetReps(reps));\r\n};\r\n\r\n/**\r\n * Apply existing preset to current scene.\r\n * @param preset\r\n */\r\nMiew.prototype.applyPreset = function (preset) {\r\n const { presets } = settings.now;\r\n const presList = [\r\n preset || settings.defaults.preset,\r\n settings.defaults.preset,\r\n Object.keys(presets)[0],\r\n ];\r\n let reps = null;\r\n for (let i = 0; !reps && i < presList.length; ++i) {\r\n settings.set('preset', presList[i]);\r\n reps = presets[settings.now.preset];\r\n if (!reps) {\r\n this.logger.warn(`Unknown preset \"${settings.now.preset}\"`);\r\n }\r\n }\r\n this._setReps(reps);\r\n};\r\n\r\n/**\r\n * Reset current representation list to initial values.\r\n * @param {string} [preset] - The source preset in case of uninitialized representation list.\r\n */\r\nMiew.prototype.resetReps = function (preset) {\r\n const reps = this._opts && this._opts.reps;\r\n if (reps) {\r\n this._setReps(reps);\r\n } else {\r\n this.applyPreset(preset);\r\n }\r\n};\r\n\r\n/**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\nMiew.prototype.repCount = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repCount() : 0;\r\n};\r\n\r\n/**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {string=} [name] - Complex name. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\nMiew.prototype.repCurrent = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n const newIdx = visual ? visual.repCurrent(index) : -1;\r\n if (index && newIdx !== index) {\r\n this.logger.warn(`Representation ${index} was not found. Current rep remains unchanged.`);\r\n }\r\n return newIdx;\r\n};\r\n\r\n/**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {?object} Representation description.\r\n */\r\nMiew.prototype.rep = function (index, rep) {\r\n const visual = this._getComplexVisual('');\r\n if (!visual) {\r\n return null;\r\n }\r\n const res = visual.rep(index, rep);\r\n if (res.status === 'created') {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n } else if (res.status === 'changed') {\r\n this.dispatchEvent({ type: 'repChanged', index: res.index, name: visual.name });\r\n }\r\n return res.desc;\r\n};\r\n\r\n/**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\nMiew.prototype.repGet = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repGet(index) : null;\r\n};\r\n\r\n/**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {number} Index of the new representation.\r\n */\r\nMiew.prototype.repAdd = function (rep, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return -1;\r\n }\r\n\r\n const res = visual.repAdd(rep);\r\n if (res) {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name });\r\n return res.index;\r\n }\r\n return -1;\r\n};\r\n\r\n/**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\nMiew.prototype.repRemove = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n visual.repRemove(index);\r\n this.dispatchEvent({ type: 'repRemoved', index, name });\r\n};\r\n\r\n/**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\nMiew.prototype.repHide = function (index, hide, name) {\r\n this._needRender = true;\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repHide(index, hide) : null;\r\n};\r\n\r\nMiew.prototype._setEditMode = function (mode) {\r\n this._editMode = mode;\r\n\r\n const elem = this._msgMode;\r\n if (elem) {\r\n elem.style.opacity = (mode === EDIT_MODE.COMPLEX) ? 0.0 : 1.0;\r\n\r\n if (mode !== EDIT_MODE.COMPLEX) {\r\n const t = elem.getElementsByTagName('p')[0];\r\n t.innerHTML = (mode === EDIT_MODE.COMPONENT) ? 'COMPONENT EDIT MODE' : 'FRAGMENT EDIT MODE';\r\n }\r\n }\r\n\r\n this.dispatchEvent({ type: 'editModeChanged', data: mode === EDIT_MODE.COMPLEX });\r\n};\r\n\r\nMiew.prototype._enterComponentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const editors = [];\r\n this._forEachComplexVisual((visual) => {\r\n const editor = visual.beginComponentEdit();\r\n if (editor) {\r\n editors.push(editor);\r\n }\r\n });\r\n\r\n if (editors === []) {\r\n return;\r\n }\r\n\r\n this._editors = editors;\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- ON');\r\n this._setEditMode(EDIT_MODE.COMPONENT);\r\n this._objectControls.keysTranslateObj(true);\r\n};\r\n\r\nMiew.prototype._applyComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._needRender = true;\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._enterFragmentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const selectedVisuals = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual instanceof ComplexVisual\r\n && visual.getSelectionCount() > 0) {\r\n selectedVisuals.push(visual);\r\n }\r\n });\r\n\r\n if (selectedVisuals.length !== 1) {\r\n // either we have no selection or\r\n // we have selected atoms in two or more visuals -- not supported\r\n return;\r\n }\r\n\r\n const editor = selectedVisuals[0].beginFragmentEdit();\r\n if (!editor) {\r\n return;\r\n }\r\n this._editors = [editor];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- ON (single bond)');\r\n this._setEditMode(EDIT_MODE.FRAGMENT);\r\n this._objectControls.allowTranslation(false);\r\n this._objectControls.allowAltObjFreeRotation(editor.isFreeRotationAllowed());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._applyFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onPick = function (event) {\r\n if (!settings.now.picking) {\r\n // picking is disabled\r\n return;\r\n }\r\n\r\n if (this._animInterval !== null) {\r\n // animation playback is on\r\n return;\r\n }\r\n\r\n if (this._editMode === EDIT_MODE.FRAGMENT) {\r\n // prevent picking in fragment edit mode\r\n return;\r\n }\r\n\r\n if (this._objectControls.isEditingAltObj()) {\r\n // prevent picking during component rotation\r\n return;\r\n }\r\n\r\n // update last pick & find complex\r\n let complex = null;\r\n if (event.obj.atom) {\r\n complex = event.obj.atom.residue.getChain().getComplex();\r\n this._lastPick = event.obj.atom;\r\n } else if (event.obj.residue) {\r\n complex = event.obj.residue.getChain().getComplex();\r\n this._lastPick = event.obj.residue;\r\n } else if (event.obj.chain) {\r\n complex = event.obj.chain.getComplex();\r\n this._lastPick = event.obj.chain;\r\n } else if (event.obj.molecule) {\r\n complex = event.obj.molecule.complex;\r\n this._lastPick = event.obj.molecule;\r\n } else {\r\n this._lastPick = null;\r\n }\r\n\r\n function _updateSelection(visual) {\r\n visual.updateSelectionMask(event.obj);\r\n visual.rebuildSelectionGeometry();\r\n }\r\n\r\n // update visual\r\n if (complex) {\r\n const visual = this._getVisualForComplex(complex);\r\n if (visual) {\r\n _updateSelection(visual);\r\n this._needRender = true;\r\n }\r\n } else {\r\n this._forEachComplexVisual(_updateSelection);\r\n this._needRender = true;\r\n }\r\n\r\n this._updateInfoPanel();\r\n this.dispatchEvent(event);\r\n};\r\n\r\nMiew.prototype._onKeyDown = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n // editing keys\r\n if (settings.now.editing) {\r\n switch (event.code) {\r\n case 'KeyC':\r\n this._enterComponentEditMode();\r\n break;\r\n case 'KeyF':\r\n this._enterFragmentEditMode();\r\n break;\r\n case 'KeyA':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._applyComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._applyFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n case 'KeyD':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._discardComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._discardFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n default:\r\n }\r\n }\r\n\r\n // other keys\r\n switch (event.code) {\r\n case 'NumpadAdd':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.expandSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n case 'NumpadSubtract':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.shrinkSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nMiew.prototype._onKeyUp = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n if (event.code === 'KeyX') {\r\n this._extractRepresentation();\r\n }\r\n};\r\n\r\nMiew.prototype._updateInfoPanel = function () {\r\n const info = this._msgAtomInfo.getElementsByTagName('p')[0];\r\n let atom;\r\n let residue;\r\n\r\n let count = 0;\r\n this._forEachComplexVisual((visual) => {\r\n count += visual.getSelectionCount();\r\n });\r\n\r\n while (info.firstChild) {\r\n info.removeChild(info.firstChild);\r\n }\r\n\r\n if (count === 0) {\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n return;\r\n }\r\n\r\n let firstLine = `${String(count)} atom${count !== 1 ? 's' : ''} selected`;\r\n if (this._lastPick !== null) {\r\n firstLine += ', the last pick:';\r\n }\r\n let secondLine = '';\r\n let aName = '';\r\n let coordLine = '';\r\n\r\n if (this._lastPick instanceof Atom) {\r\n atom = this._lastPick;\r\n residue = atom.residue;\r\n\r\n aName = atom.name;\r\n const location = (atom.location !== 32) ? String.fromCharCode(atom.location) : ''; // 32 is code of white-space\r\n secondLine = `${atom.element.fullName} #${atom.serial}${location}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}.`;\r\n secondLine += aName;\r\n\r\n coordLine = `Coord: (${atom.position.x.toFixed(2).toString()},\\\r\n ${atom.position.y.toFixed(2).toString()},\\\r\n ${atom.position.z.toFixed(2).toString()})`;\r\n } else if (this._lastPick instanceof Residue) {\r\n residue = this._lastPick;\r\n\r\n secondLine = `${residue._type._fullName}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}`;\r\n } else if (this._lastPick instanceof Chain) {\r\n secondLine = `chain ${this._lastPick._name}`;\r\n } else if (this._lastPick instanceof Molecule) {\r\n secondLine = `molecule ${this._lastPick._name}`;\r\n }\r\n\r\n info.appendChild(document.createTextNode(firstLine));\r\n\r\n if (secondLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(secondLine));\r\n }\r\n\r\n if (coordLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(coordLine));\r\n }\r\n\r\n this._msgAtomInfo.style.opacity = 1.0;\r\n};\r\n\r\nMiew.prototype._getAltObj = function () {\r\n if (this._editors) {\r\n let altObj = null;\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n const nextAltObj = this._editors[i].getAltObj();\r\n if (nextAltObj.objects.length > 0) {\r\n if (altObj) {\r\n // we have selected atoms in two or more visuals -- not supported\r\n altObj = null;\r\n break;\r\n }\r\n altObj = nextAltObj;\r\n }\r\n }\r\n if (altObj) {\r\n return altObj;\r\n }\r\n }\r\n\r\n return {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n};\r\n\r\nMiew.prototype.resetPivot = (function () {\r\n const boundingBox = new THREE.Box3();\r\n const center = new THREE.Vector3();\r\n\r\n return function () {\r\n boundingBox.makeEmpty();\r\n this._forEachVisual((visual) => {\r\n boundingBox.union(visual.getBoundaries().boundingBox);\r\n });\r\n\r\n boundingBox.getCenter(center);\r\n this._objectControls.setPivot(center.negate());\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotResidue = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (residue) {\r\n const visual = this._getVisualForComplex(residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n if (residue._controlPoint) {\r\n center.copy(residue._controlPoint);\r\n } else {\r\n let x = 0;\r\n let y = 0;\r\n let z = 0;\r\n const amount = residue._atoms.length;\r\n for (let i = 0; i < amount; ++i) {\r\n const p = residue._atoms[i].position;\r\n x += p.x / amount;\r\n y += p.y / amount;\r\n z += p.z / amount;\r\n }\r\n center.set(x, y, z);\r\n }\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotAtom = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (atom) {\r\n const visual = this._getVisualForComplex(atom.residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n center.copy(atom.position);\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.getSelectionCenter = (function () {\r\n const _centerInVisual = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n return function (center, includesAtom, selector) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCenter(_centerInVisual, includesAtom, selector || visual.getSelectionBit())) {\r\n center.add(_centerInVisual);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.negate();\r\n return true;\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotSubset = (function () {\r\n const _center = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n function _includesInCurSelection(atom, selectionBit) {\r\n return atom.mask & (1 << selectionBit);\r\n }\r\n\r\n function _includesInSelector(atom, selector) {\r\n return selector.selector.includesAtom(atom);\r\n }\r\n\r\n return function (selector) {\r\n const includesAtom = (selector) ? _includesInSelector : _includesInCurSelection;\r\n\r\n if (this.getSelectionCenter(_center, includesAtom, selector)) {\r\n this._objectControls.setPivot(_center);\r\n this.dispatchEvent({ type: 'transform' });\r\n } else {\r\n this.logger.warn('selection is empty. Center operation not performed');\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Makes a screenshot.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n * @returns {string} Data URL representing the image contents.\r\n */\r\nMiew.prototype.screenshot = function (width, height) {\r\n const gfx = this._gfx;\r\n const deviceWidth = gfx.renderer.domElement.width;\r\n const deviceHeight = gfx.renderer.domElement.height;\r\n\r\n function fov2Tan(fov) {\r\n return Math.tan(THREE.MathUtils.degToRad(0.5 * fov));\r\n }\r\n\r\n function tan2Fov(tan) {\r\n return THREE.MathUtils.radToDeg(Math.atan(tan)) * 2.0;\r\n }\r\n\r\n function getDataURL() {\r\n let dataURL;\r\n const currBrowser = utils.getBrowser();\r\n\r\n if (currBrowser === utils.browserType.SAFARI) {\r\n const canvas = document.createElement('canvas');\r\n const canvasContext = canvas.getContext('2d');\r\n\r\n canvas.width = width === undefined ? deviceWidth : width;\r\n canvas.height = height === undefined ? deviceHeight : height;\r\n\r\n canvasContext.drawImage(gfx.renderer.domElement, 0, 0, canvas.width, canvas.height);\r\n dataURL = canvas.toDataURL('image/png');\r\n } else {\r\n // Copy current canvas to screenshot\r\n dataURL = gfx.renderer.domElement.toDataURL('image/png');\r\n }\r\n return dataURL;\r\n }\r\n height = height || width;\r\n\r\n let screenshotURI;\r\n if ((width === undefined && height === undefined)\r\n || (width === deviceWidth && height === deviceHeight)) {\r\n // renderer.domElement.toDataURL('image/png') returns flipped image in Safari\r\n // It hasn't been resolved yet, but getScreenshotSafari()\r\n // fixes it using an extra canvas.\r\n screenshotURI = getDataURL();\r\n } else {\r\n const originalAspect = gfx.camera.aspect;\r\n const originalFov = gfx.camera.fov;\r\n const originalTanFov2 = fov2Tan(gfx.camera.fov);\r\n\r\n // screenshot should contain the principal area of interest (a centered square touching screen sides)\r\n const areaOfInterestSize = Math.min(gfx.width, gfx.height);\r\n const areaOfInterestTanFov2 = originalTanFov2 * areaOfInterestSize / gfx.height;\r\n\r\n // set appropriate camera aspect & FOV\r\n const shotAspect = width / height;\r\n gfx.renderer.setPixelRatio(1);\r\n gfx.camera.aspect = shotAspect;\r\n gfx.camera.fov = tan2Fov(areaOfInterestTanFov2 / Math.min(shotAspect, 1.0));\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n // resize canvas to the required size of screenshot\r\n gfx.renderer.setDrawingBufferSize(width, height, 1);\r\n\r\n // make screenshot\r\n this._renderFrame(settings.now.stereo);\r\n screenshotURI = getDataURL();\r\n\r\n // restore original camera & canvas proportions\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.camera.aspect = originalAspect;\r\n gfx.camera.fov = originalFov;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.renderer.setDrawingBufferSize(gfx.width, gfx.height, window.devicePixelRatio);\r\n this._needRender = true;\r\n }\r\n\r\n return screenshotURI;\r\n};\r\n\r\n/**\r\n * Makes screenshot and initiates a download.\r\n * @param {string} [filename] - Name of a file. Default to a 'screenshot-XXXXX.png', where XXXXX is a current\r\n * date/time in seconds.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n */\r\nMiew.prototype.screenshotSave = function (filename, width, height) {\r\n const uri = this.screenshot(width, height);\r\n utils.shotDownload(uri, filename);\r\n};\r\n\r\nMiew.prototype.save = function (opts) {\r\n this._export(opts.fileType).then((dataString) => {\r\n const filename = this._visuals[this._curVisualName]._complex.name;\r\n utils.download(dataString, filename, opts.fileType);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone' });\r\n }).catch((error) => {\r\n this.logger.error('Could not export data');\r\n this.logger.debug(error);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone', error });\r\n });\r\n};\r\n\r\nMiew.prototype._tweakResolution = function () {\r\n const maxPerf = [\r\n ['poor', 100],\r\n ['low', 500],\r\n ['medium', 1000],\r\n ['high', 5000],\r\n ['ultra', Number.MAX_VALUE],\r\n ];\r\n\r\n let atomCount = 0;\r\n this._forEachComplexVisual((visual) => {\r\n atomCount += visual.getComplex().getAtomCount();\r\n });\r\n\r\n if (atomCount > 0) {\r\n const performance = this._gfxScore * 10e5 / atomCount;\r\n // set resolution based on estimated performance\r\n for (let i = 0; i < maxPerf.length; ++i) {\r\n if (performance < maxPerf[i][1]) {\r\n this._autoChangeResolution(maxPerf[i][0]);\r\n break;\r\n }\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._autoChangeResolution = function (resolution) {\r\n if (resolution !== settings.now.resolution) {\r\n this.logger.report(`Your rendering resolution was changed to \"${resolution}\" for best performance.`);\r\n }\r\n settings.now.resolution = resolution;\r\n};\r\n\r\n/**\r\n * Save current settings to cookies.\r\n */\r\nMiew.prototype.saveSettings = function () {\r\n this._cookies.setCookie(this._opts.settingsCookie, JSON.stringify(this.settings.getDiffs(true)));\r\n};\r\n\r\n/**\r\n * Load settings from cookies.\r\n */\r\nMiew.prototype.restoreSettings = function () {\r\n try {\r\n const cookie = this._cookies.getCookie(this._opts.settingsCookie);\r\n const diffs = cookie ? JSON.parse(cookie) : {};\r\n this.settings.applyDiffs(diffs, true);\r\n } catch (e) {\r\n this.logger.error(`Cookies parse error: ${e.message}`);\r\n }\r\n};\r\n\r\n/**\r\n * Reset current settings to the defaults.\r\n */\r\nMiew.prototype.resetSettings = function () {\r\n this.settings.reset();\r\n};\r\n\r\n/*\r\n * DANGEROUS and TEMPORARY. The method should change or disappear in future versions.\r\n * @param {string|object} opts - See {@link Miew} constructor.\r\n * @see {@link Miew#set}, {@link Miew#repAdd}, {@link Miew#rep}.\r\n */\r\nMiew.prototype.setOptions = function (opts) {\r\n if (typeof opts === 'string') {\r\n opts = Miew.options.fromAttr(opts);\r\n }\r\n if (opts.reps) {\r\n this._opts.reps = null;\r\n }\r\n _.merge(this._opts, opts);\r\n if (opts.settings) {\r\n this.set(opts.settings);\r\n }\r\n\r\n this._opts._objects = opts._objects;\r\n this._resetObjects();\r\n\r\n if (opts.load) {\r\n this.load(opts.load, { fileType: opts.type });\r\n }\r\n\r\n if (opts.preset) {\r\n settings.now.preset = opts.preset;\r\n }\r\n\r\n if (opts.reps) {\r\n this.resetReps(opts.preset);\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.getComplex().resetCurrentUnit();\r\n if (_.isNumber(opts.unit)) {\r\n visual.getComplex().setCurrentUnit(opts.unit);\r\n }\r\n this.resetView();\r\n this.rebuildAll();\r\n }\r\n};\r\n\r\nMiew.prototype.info = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return {};\r\n }\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n return {\r\n id: metadata.id || complex.name || 'UNKNOWN',\r\n title: (metadata.title && metadata.title.join(' ')) || 'UNKNOWN DATA',\r\n atoms: complex.getAtomCount(),\r\n bonds: complex.getBondCount(),\r\n residues: complex.getResidueCount(),\r\n chains: complex.getChainCount(),\r\n };\r\n};\r\n\r\n/*\r\n * OBJECTS SEGMENT\r\n */\r\n\r\nMiew.prototype.addObject = function (objData, bThrow) {\r\n let Ctor = null;\r\n\r\n if (objData.type === LinesObject.prototype.type) {\r\n Ctor = LinesObject;\r\n }\r\n\r\n if (Ctor === null) {\r\n throw new Error(`Unknown scene object type - ${objData.type}`);\r\n }\r\n\r\n try {\r\n const newObj = new Ctor(objData.params, objData.opts);\r\n this._addSceneObject(newObj);\r\n } catch (error) {\r\n if (!bThrow) {\r\n this.logger.debug(`Error during scene object creation: ${error.message}`);\r\n } else {\r\n throw error;\r\n }\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._addSceneObject = function (sceneObject) {\r\n const visual = this._getComplexVisual();\r\n if (sceneObject.build && visual) {\r\n sceneObject.build(visual.getComplex());\r\n this._gfx.pivot.add(sceneObject.getGeometry());\r\n }\r\n const objects = this._objects;\r\n objects[objects.length] = sceneObject;\r\n};\r\n\r\nMiew.prototype._updateObjsToFrame = function (frameData) {\r\n const objs = this._objects;\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n if (objs[i].updateToFrame) {\r\n objs[i].updateToFrame(frameData);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._resetObjects = function () {\r\n const objs = this._opts._objects;\r\n\r\n this._objects = [];\r\n if (objs) {\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n this.addObject(objs[i], false);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype.removeObject = function (index) {\r\n const obj = this._objects[index];\r\n if (!obj) {\r\n throw new Error(`Scene object with index ${index} does not exist`);\r\n }\r\n obj.destroy();\r\n this._objects.splice(index, 1);\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Get a string with a URL to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {string} URL\r\n */\r\nMiew.prototype.getURL = function (opts) {\r\n return options.toURL(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n })));\r\n};\r\n\r\n/**\r\n * Get a string with a script to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=true] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=true] - when this flag is true, a view information is included\r\n * @returns {string} script\r\n */\r\nMiew.prototype.getScript = function (opts) {\r\n return options.toScript(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: true,\r\n view: true,\r\n })));\r\n};\r\n\r\n/*\r\n * Generates object that represents the current state of representations list\r\n * @param {boolean} compareWithDefaults - when this flag is true, reps list is compared (if possible)\r\n * to preset's defaults and only diffs are generated\r\n */\r\nMiew.prototype._compareReps = function (complexVisual, compareWithDefaults) {\r\n const ans = {};\r\n let repCount = 0;\r\n\r\n if (complexVisual) {\r\n repCount = complexVisual.repCount();\r\n }\r\n\r\n const currPreset = settings.defaults.presets[settings.now.preset];\r\n let compare = compareWithDefaults;\r\n if (currPreset === undefined || currPreset.length > repCount) {\r\n compare = false;\r\n ans.preset = 'empty';\r\n } else if (settings.now.preset !== settings.defaults.preset) {\r\n ans.preset = settings.now.preset;\r\n }\r\n\r\n const repsDiff = [];\r\n let emptyReps = true;\r\n for (let i = 0, n = repCount; i < n; ++i) {\r\n repsDiff[i] = complexVisual.repGet(i).compare(compare ? currPreset[i] : null);\r\n if (!_.isEmpty(repsDiff[i])) {\r\n emptyReps = false;\r\n }\r\n }\r\n if (!emptyReps) {\r\n ans.reps = repsDiff;\r\n }\r\n return ans;\r\n};\r\n\r\n/*\r\n * Obtain object that represents current state of miew (might be used as options in constructor).\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {Object} State object.\r\n */\r\nMiew.prototype.getState = function (opts) {\r\n const state = {};\r\n\r\n opts = _.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n });\r\n\r\n // load\r\n const visual = this._getComplexVisual();\r\n if (visual !== null) {\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n if (metadata.id) {\r\n const format = metadata.format ? `${metadata.format}:` : '';\r\n state.load = format + metadata.id;\r\n }\r\n const unit = complex.getCurrentUnit();\r\n if (unit !== 1) {\r\n state.unit = unit;\r\n }\r\n }\r\n\r\n // representations\r\n const repsInfo = this._compareReps(visual, opts.compact);\r\n if (repsInfo.preset) {\r\n state.preset = repsInfo.preset;\r\n }\r\n\r\n if (repsInfo.reps) {\r\n state.reps = repsInfo.reps;\r\n }\r\n\r\n // objects\r\n const objects = this._objects;\r\n const objectsState = [];\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n objectsState[i] = objects[i].identify();\r\n }\r\n if (objects.length > 0) {\r\n state._objects = objectsState;\r\n }\r\n\r\n // view\r\n if (opts.view) {\r\n state.view = this.view();\r\n }\r\n\r\n // settings\r\n if (opts.settings) {\r\n const diff = this.settings.getDiffs(false);\r\n if (!_.isEmpty(diff)) {\r\n state.settings = diff;\r\n }\r\n }\r\n\r\n return state;\r\n};\r\n\r\n/**\r\n * Get parameter value.\r\n * @param {string} param - Parameter name or path (e.g. 'modes.BS.atom').\r\n * @param {*=} value - Default value.\r\n * @returns {*} Parameter value.\r\n */\r\nMiew.prototype.get = function (param, value) {\r\n return settings.get(param, value);\r\n};\r\n\r\nMiew.prototype._clipPlaneUpdateValue = function (radius) {\r\n const clipPlaneValue = Math.max(\r\n this._gfx.camera.position.z - radius * settings.now.draft.clipPlaneFactor,\r\n settings.now.camNear,\r\n );\r\n\r\n const opts = { clipPlaneValue };\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions(opts);\r\n });\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setUberOptions(opts);\r\n }\r\n }\r\n if (this._picker !== null) {\r\n this._picker.clipPlaneValue = clipPlaneValue;\r\n }\r\n};\r\n\r\nMiew.prototype._fogFarUpdateValue = function () {\r\n if (this._picker !== null) {\r\n if (this._gfx.scene.fog) {\r\n this._picker.fogFarValue = this._gfx.scene.fog.far;\r\n } else {\r\n this._picker.fogFarValue = undefined;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._updateShadowmapMeshes = function (process) {\r\n this._forEachComplexVisual((visual) => {\r\n const reprList = visual._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n process(repr.geo, repr.material);\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._updateMaterials = function (values, needTraverse = false, process = undefined) {\r\n this._forEachComplexVisual((visual) => visual.setMaterialValues(values, needTraverse, process));\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setValues(values);\r\n obj._line.material.needsUpdate = true;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._fogAlphaChanged = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions({\r\n fogAlpha: settings.now.fogAlpha,\r\n });\r\n });\r\n};\r\n\r\nMiew.prototype._embedWebXR = function () {\r\n // switch off\r\n if (settings.now.stereo !== 'WEBVR') {\r\n if (this.webVR) {\r\n this.webVR.disable();\r\n }\r\n this.webVR = null;\r\n return;\r\n }\r\n // switch on\r\n if (!this.webVR) {\r\n this.webVR = new WebVRPoC(() => {\r\n this._requestAnimationFrame(() => this._onTick());\r\n this._needRender = true;\r\n this._onResize();\r\n });\r\n }\r\n this.webVR.enable(this._gfx);\r\n};\r\n\r\nMiew.prototype._initOnSettingsChanged = function () {\r\n const on = (props, func) => {\r\n props = _.isArray(props) ? props : [props];\r\n props.forEach((prop) => {\r\n this.settings.addEventListener(`change:${prop}`, func);\r\n });\r\n };\r\n\r\n on('modes.VD.frame', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.showFrame(settings.now.modes.VD.frame);\r\n this._needRender = true;\r\n });\r\n\r\n on('modes.VD.isoMode', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n });\r\n\r\n on('bg.color', () => {\r\n this._onBgColorChanged();\r\n });\r\n\r\n on('ao', () => {\r\n if (settings.now.ao && !isAOSupported(this._gfx.renderer.getContext())) {\r\n this.logger.warn('Your device or browser does not support ao');\r\n settings.set('ao', false);\r\n } else {\r\n const values = { normalsToGBuffer: settings.now.ao };\r\n this._setUberMaterialValues(values);\r\n }\r\n });\r\n\r\n on('zSprites', () => {\r\n if (settings.now.zSprites && !arezSpritesSupported(this._gfx.renderer.getContext())) {\r\n this.logger.warn('Your device or browser does not support zSprites');\r\n settings.set('zSprites', false);\r\n }\r\n this.rebuildAll();\r\n });\r\n\r\n on('fogColor', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('fogColorEnable', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('bg.transparent', (evt) => {\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n // update materials\r\n this._updateMaterials({ fogTransparent: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('draft.clipPlane', (evt) => {\r\n // update materials\r\n this._updateMaterials({ clipPlane: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('shadow.on', (evt) => {\r\n // update materials\r\n const values = { shadowmap: evt.value, shadowmapType: settings.now.shadow.type };\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.shadowMap.enabled = Boolean(values.shadowmap);\r\n }\r\n this._updateMaterials(values, true);\r\n if (values.shadowmap) {\r\n this._updateShadowCamera();\r\n this._updateShadowmapMeshes(meshutils.createShadowmapMaterial);\r\n } else {\r\n this._updateShadowmapMeshes(meshutils.removeShadowmapMaterial);\r\n }\r\n this._needRender = true;\r\n });\r\n\r\n on('shadow.type', (evt) => {\r\n // update materials if shadowmap is enable\r\n if (settings.now.shadow.on) {\r\n this._updateMaterials({ shadowmapType: evt.value }, true);\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on('shadow.radius', (evt) => {\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].shadow !== undefined) {\r\n const light = this._gfx.scene.children[i];\r\n light.shadow.radius = evt.value;\r\n this._needRender = true;\r\n }\r\n }\r\n });\r\n\r\n on('fps', () => {\r\n this._fps.show(settings.now.fps);\r\n });\r\n\r\n on(['fog', 'fogNearFactor', 'fogFarFactor'], () => {\r\n this._updateFog();\r\n this._needRender = true;\r\n });\r\n\r\n on('fogAlpha', () => {\r\n const { fogAlpha } = settings.now;\r\n if (fogAlpha < 0 || fogAlpha > 1) {\r\n this.logger.warn('fogAlpha must belong range [0,1]');\r\n }\r\n this._fogAlphaChanged();\r\n this._needRender = true;\r\n });\r\n\r\n on('autoResolution', (evt) => {\r\n if (evt.value && !this._gfxScore) {\r\n this.logger.warn('Benchmarks are missed, autoresolution will not work! '\r\n + 'Autoresolution should be set during miew startup.');\r\n }\r\n });\r\n\r\n on('stereo', () => {\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n this._needRender = true;\r\n });\r\n\r\n on(['transparency', 'palette'], () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('resolution', () => {\r\n // update complex visuals\r\n this.rebuildAll();\r\n\r\n // update volume visual\r\n const volume = this._getVolumeVisual();\r\n if (volume) {\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on(['axes', 'fxaa', 'ao',\r\n 'outline.on', 'outline.color', 'outline.threshold', 'outline.thickness'], () => {\r\n this._needRender = true;\r\n });\r\n};\r\n\r\n/**\r\n * Set parameter value.\r\n * @param {string|object} params - Parameter name or path (e.g. 'modes.BS.atom') or even settings object.\r\n * @param {*=} value - Value.\r\n */\r\nMiew.prototype.set = function (params, value) {\r\n settings.set(params, value);\r\n};\r\n\r\n/**\r\n * Select atoms with selection string.\r\n * @param {string} expression - string expression of selection\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\nMiew.prototype.select = function (expression, append) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n let sel = expression;\r\n if (_.isString(expression)) {\r\n sel = selectors.parse(expression).selector;\r\n }\r\n\r\n visual.select(sel, append);\r\n this._lastPick = null;\r\n\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n};\r\n\r\nconst VIEW_VERSION = '1';\r\n\r\n/**\r\n * Get or set view info packed into string.\r\n *\r\n * **Note:** view is stored for *left-handed* cs, euler angles are stored in radians and *ZXY-order*,\r\n *\r\n * @param {string=} expression - Optional string encoded the view\r\n */\r\nMiew.prototype.view = function (expression) {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n let transform = [];\r\n const eulerOrder = 'ZXY';\r\n\r\n function encode() {\r\n const pos = pivot.position;\r\n const scale = self._objectControls.getScale() / settings.now.radiusToFit;\r\n const euler = new THREE.Euler();\r\n euler.setFromQuaternion(self._objectControls.getOrientation(), eulerOrder);\r\n transform = [\r\n pos.x, pos.y, pos.z,\r\n scale,\r\n euler.x, euler.y, euler.z,\r\n ];\r\n return VIEW_VERSION + utils.arrayToBase64(transform, Float32Array);\r\n }\r\n\r\n function decode() {\r\n // backwards compatible: old non-versioned view is the 0th version\r\n if (expression.length === 40) {\r\n expression = `0${expression}`;\r\n }\r\n\r\n const version = expression[0];\r\n transform = utils.arrayFromBase64(expression.substr(1), Float32Array);\r\n\r\n // apply adapter for old versions\r\n if (version !== VIEW_VERSION) {\r\n if (version === '0') {\r\n // cancel radiusToFit included in old views\r\n transform[3] /= 8.0;\r\n } else {\r\n // do nothing\r\n self.logger.warn(`Encoded view version mismatch, stored as ${version} vs ${VIEW_VERSION} expected`);\r\n return;\r\n }\r\n }\r\n\r\n const interpolator = self._interpolator;\r\n const srcView = interpolator.createView();\r\n srcView.position.copy(pivot.position);\r\n srcView.scale = self._objectControls.getScale();\r\n srcView.orientation.copy(self._objectControls.getOrientation());\r\n\r\n const dstView = interpolator.createView();\r\n dstView.position.set(transform[0], transform[1], transform[2]);\r\n\r\n // hack to make preset views work after we moved centering offset to visual nodes\r\n // FIXME should only store main pivot offset in preset\r\n if (self._getComplexVisual()) {\r\n dstView.position.sub(self._getComplexVisual().position);\r\n }\r\n\r\n dstView.scale = transform[3]; // eslint-disable-line prefer-destructuring\r\n dstView.orientation.setFromEuler(new THREE.Euler(transform[4], transform[5], transform[6], eulerOrder));\r\n\r\n interpolator.setup(srcView, dstView);\r\n }\r\n\r\n if (typeof expression === 'undefined') {\r\n return encode();\r\n }\r\n decode();\r\n\r\n return expression;\r\n};\r\n\r\n/*\r\n * Update current view due to viewinterpolator state\r\n */\r\nMiew.prototype._updateView = function () {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n\r\n const interpolator = this._interpolator;\r\n if (!interpolator.wasStarted()) {\r\n interpolator.start();\r\n }\r\n\r\n if (!interpolator.isMoving()) {\r\n return;\r\n }\r\n\r\n const res = interpolator.getCurrentView();\r\n if (res.success) {\r\n const curr = res.view;\r\n pivot.position.copy(curr.position);\r\n self._objectControls.setScale(curr.scale * settings.now.radiusToFit);\r\n self._objectControls.setOrientation(curr.orientation);\r\n this.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n }\r\n};\r\n\r\n/**\r\n * Translate object by vector\r\n * @param {number} x - translation value (Ang) along model's X axis\r\n * @param {number} y - translation value (Ang) along model's Y axis\r\n * @param {number} z - translation value (Ang) along model's Z axis\r\n */\r\nMiew.prototype.translate = function (x, y, z) {\r\n this._objectControls.translatePivot(x, y, z);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Rotate object by Euler angles\r\n * @param {number} x - rotation angle around X axis in radians\r\n * @param {number} y - rotation angle around Y axis in radians\r\n * @param {number} z - rotation angle around Z axis in radians\r\n */\r\nMiew.prototype.rotate = function (x, y, z) {\r\n this._objectControls.rotate(new THREE.Quaternion().setFromEuler(new THREE.Euler(x, y, z, 'XYZ')));\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Scale object by factor\r\n * @param {number} factor - scale multiplier, should greater than zero\r\n */\r\nMiew.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n throw new RangeError('Scale should be greater than zero');\r\n }\r\n this._objectControls.scale(factor);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Center view on selection\r\n * @param {empty | subset | string} selector - defines part of molecule which must be centered (\r\n * empty - center on current selection;\r\n * subset - center on picked atom/residue/molecule;\r\n * string - center on atoms correspond to selection string)\r\n */\r\nMiew.prototype.center = function (selector) {\r\n // no arguments - center on current selection;\r\n if (selector === undefined) {\r\n this.setPivotSubset();\r\n this._needRender = true;\r\n return;\r\n }\r\n // subset with atom or residue - center on picked atom/residue;\r\n if (selector.obj !== undefined && ('atom' in selector.obj || 'residue' in selector.obj)) { // from event with selection\r\n if ('atom' in selector.obj) {\r\n this.setPivotAtom(selector.obj.atom);\r\n } else {\r\n this.setPivotResidue(selector.obj.residue);\r\n }\r\n this._needRender = true;\r\n return;\r\n }\r\n // string - center on atoms correspond to selection string\r\n if (selector.obj === undefined && selector !== '') {\r\n const sel = selectors.parse(selector);\r\n if (sel.error === undefined) {\r\n this.setPivotSubset(sel);\r\n this._needRender = true;\r\n return;\r\n }\r\n }\r\n // empty subset or incorrect/empty string - center on all molecule;\r\n this.resetPivot();\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\nMiew.prototype.within = function (selector, radius) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return selectors.None();\r\n }\r\n\r\n if (selector instanceof String) {\r\n selector = selectors.parse(selector);\r\n }\r\n\r\n const res = visual.within(selector, radius);\r\n if (res) {\r\n visual.rebuildSelectionGeometry();\r\n this._needRender = true;\r\n }\r\n return res;\r\n};\r\n\r\n/**\r\n * Get atom position in 2D canvas coords\r\n * @param {string} fullAtomName - full atom name, like A.38.CG\r\n * @returns {Object} {x, y} or false if atom not found\r\n */\r\nMiew.prototype.projected = function (fullAtomName, complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return false;\r\n }\r\n\r\n const atom = visual.getComplex().getAtomByFullname(fullAtomName);\r\n if (atom === null) {\r\n return false;\r\n }\r\n\r\n const pos = atom.position.clone();\r\n // we consider atom position to be affected only by common complex transform\r\n // ignoring any transformations that may add during editing\r\n this._gfx.pivot.updateMatrixWorldRecursive();\r\n this._gfx.camera.updateMatrixWorldRecursive();\r\n this._gfx.pivot.localToWorld(pos);\r\n pos.project(this._gfx.camera);\r\n\r\n return {\r\n x: (pos.x + 1.0) * 0.5 * this._gfx.width,\r\n y: (1.0 - pos.y) * 0.5 * this._gfx.height,\r\n };\r\n};\r\n\r\n/**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n *\r\n * @param {string=} complexName - complex name\r\n */\r\nMiew.prototype.dssp = function (complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return;\r\n }\r\n visual.getComplex().dssp();\r\n\r\n // rebuild dependent representations (cartoon or ss-colored)\r\n visual._reprList.forEach((rep) => {\r\n if (rep.mode.id === 'CA' || rep.colorer.id === 'SS') {\r\n rep.needsRebuild = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype.exportCML = function () {\r\n const self = this;\r\n\r\n function extractRotation(m) {\r\n const xAxis = new THREE.Vector3();\r\n const yAxis = new THREE.Vector3();\r\n const zAxis = new THREE.Vector3();\r\n m.extractBasis(xAxis, yAxis, zAxis);\r\n xAxis.normalize();\r\n yAxis.normalize();\r\n zAxis.normalize();\r\n const retMat = new THREE.Matrix4();\r\n retMat.identity();\r\n retMat.makeBasis(xAxis, yAxis, zAxis);\r\n return retMat;\r\n }\r\n\r\n function updateCMLData(complex) {\r\n const { root } = self._gfx;\r\n const mat = extractRotation(root.matrixWorld);\r\n const v4 = new THREE.Vector4(0, 0, 0, 0);\r\n const vCenter = new THREE.Vector4(0, 0, 0, 0);\r\n let xml = null;\r\n let ap = null;\r\n\r\n // update atoms in cml\r\n complex.forEachAtom((atom) => {\r\n if (atom.xmlNodeRef && atom.xmlNodeRef.xmlNode) {\r\n xml = atom.xmlNodeRef.xmlNode;\r\n ap = atom.position;\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n v4.applyMatrix4(mat);\r\n xml.setAttribute('x3', v4.x.toString());\r\n xml.setAttribute('y3', v4.y.toString());\r\n xml.setAttribute('z3', v4.z.toString());\r\n xml.removeAttribute('x2');\r\n xml.removeAttribute('y2');\r\n }\r\n });\r\n // update stereo groups in cml\r\n complex.forEachSGroup((sGroup) => {\r\n if (sGroup.xmlNodeRef && sGroup.xmlNodeRef.xmlNode) {\r\n xml = sGroup.xmlNodeRef.xmlNode;\r\n ap = sGroup.getPosition();\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n const cp = sGroup.getCentralPoint();\r\n if (cp === null) {\r\n v4.applyMatrix4(mat);\r\n } else {\r\n vCenter.set(cp.x, cp.y, cp.z, 0.0);\r\n v4.add(vCenter);\r\n v4.applyMatrix4(mat); // pos in global space\r\n vCenter.set(cp.x, cp.y, cp.z, 1.0);\r\n vCenter.applyMatrix4(mat);\r\n v4.sub(vCenter);\r\n }\r\n xml.setAttribute('x', v4.x.toString());\r\n xml.setAttribute('y', v4.y.toString());\r\n xml.setAttribute('z', v4.z.toString());\r\n }\r\n });\r\n }\r\n\r\n const visual = self._getComplexVisual();\r\n const complex = visual ? visual.getComplex() : null;\r\n if (complex && complex.originalCML) {\r\n updateCMLData(complex);\r\n\r\n // serialize xml structure to string\r\n const oSerializer = new XMLSerializer();\r\n return oSerializer.serializeToString(complex.originalCML);\r\n }\r\n\r\n return null;\r\n};\r\n\r\n/**\r\n * Reproduce the RCSB PDB Molecule of the Month style by David S. Goodsell\r\n *\r\n * @see http://pdb101.rcsb.org/motm/motm-about\r\n */\r\nMiew.prototype.motm = function () {\r\n settings.set({\r\n fogColorEnable: true,\r\n fogColor: 0x000000,\r\n outline: { on: true, threshold: 0.01 },\r\n bg: { color: 0xffffff },\r\n });\r\n\r\n this._forEachComplexVisual((visual) => {\r\n const rep = [];\r\n const complex = visual.getComplex();\r\n const palette = palettes.get(settings.now.palette);\r\n for (let i = 0; i < complex.getChainCount(); i++) {\r\n const curChainName = complex._chains[i]._name;\r\n const curChainColor = palette.getChainColor(curChainName);\r\n rep[i] = {\r\n selector: `chain ${curChainName}`,\r\n mode: 'VW',\r\n colorer: ['CB', { color: curChainColor, factor: 0.9 }],\r\n material: 'FL',\r\n };\r\n }\r\n visual.resetReps(rep);\r\n });\r\n};\r\n\r\nMiew.prototype.VERSION = (typeof PACKAGE_VERSION !== 'undefined' && PACKAGE_VERSION) || '0.0.0-dev';\r\n\r\n// Uncomment this to get debug trace:\r\n// Miew.prototype.debugTracer = new utils.DebugTracer(Miew.prototype);\r\n\r\n_.assign(Miew, /** @lends Miew */ {\r\n VERSION: Miew.prototype.VERSION,\r\n\r\n registeredPlugins: [],\r\n\r\n // export namespaces // TODO: WIP: refactoring external interface\r\n chem,\r\n io,\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n utils,\r\n gfx: {\r\n Representation,\r\n },\r\n\r\n /**\r\n * Third-party libraries packaged together with Miew.\r\n *\r\n * @property {object} lodash - [Lodash](https://lodash.com/), a modern JavaScript utility library delivering\r\n * modularity, performance & extras.\r\n * @property {object} three - [three.js](https://threejs.org/), JavaScript 3D library.\r\n *\r\n * @example\r\n * var _ = Miew.thirdParty.lodash;\r\n * var opts = _.merge({ ... }, Miew.options.fromURL(window.location.search));\r\n * var miew = new Miew(opts);\r\n */\r\n thirdParty: {\r\n lodash: _,\r\n three: THREE,\r\n },\r\n});\r\n\r\nexport default Miew;\r\n","import palettes from '../gfx/palettes';\r\nimport settings from '../settings';\r\n\r\nconst modeIdDesc = {\r\n $help: [\r\n 'Rendering mode shortcut',\r\n ' BS - balls and sticks mode',\r\n ' LN - lines mode',\r\n ' LC - licorice mode',\r\n ' VW - van der waals mode',\r\n ' TR - trace mode',\r\n ' TU - tube mode',\r\n ' CA - cartoon mode',\r\n ' SA - isosurface mode',\r\n ' QS - quick surface mode',\r\n ' SE - solvent excluded mode',\r\n ' TX - text mode',\r\n ],\r\n BS: {\r\n $help: [\r\n ' Balls and sticks',\r\n ' aromrad = #aromatic radius',\r\n ' atom = #atom radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n CA: {\r\n $help: [\r\n ' Cartoon',\r\n ' arrow = #arrow size',\r\n ' depth = #depth of surface',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = #',\r\n ' width = #secondary width\\n',\r\n ],\r\n },\r\n LN: {\r\n $help: [\r\n ' Lines',\r\n ' atom = #atom radius',\r\n ' chunkarom = ',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' offsarom = \\n',\r\n ],\r\n },\r\n LC: {\r\n $help: [\r\n ' Licorice',\r\n ' aromrad = #aromatic radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n VW: {\r\n $help: [\r\n ' Van der Waals',\r\n ' nothing\\n',\r\n ],\r\n },\r\n TR: {\r\n $help: [\r\n ' Trace',\r\n ' radius = #tube radius\\n',\r\n ],\r\n },\r\n TU: {\r\n $help: [\r\n ' Tube',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = \\n',\r\n ],\r\n },\r\n SA: {\r\n $help: [\r\n ' Surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n QS: {\r\n $help: [\r\n ' Quick surface',\r\n ' isoValue = ',\r\n ' scale = ',\r\n ' wireframe = ',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n SE: {\r\n $help: [\r\n ' Solvent excluded surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n TX: {\r\n $help: [\r\n ' Text mode',\r\n ' template = string that can include \"{{ id }}\"',\r\n ' it will be replaced by value, id can be one of next:',\r\n ' serial, name, type, sequence, residue, chain, hetatm, water\\n',\r\n ' horizontalAlign = {\"left\", \"right\", \"center\"}',\r\n ' verticalAlign = {\"top\", \"bottom\", \"middle\"}',\r\n ' dx = #offset along x',\r\n ' dy = #offset along y',\r\n ' dz = #offset along z',\r\n ' fg = #text color modificator',\r\n ' could be keyword, named color or hex',\r\n ' fg = #back color modificator',\r\n ' could be keyword, named color or hex',\r\n ' showBg = #if set show background',\r\n ' plate under text',\r\n ],\r\n },\r\n};\r\n\r\nconst colorDesc = {\r\n $help: [\r\n 'Coloring mode shortcut',\r\n ' EL - color by element',\r\n ' CH - color by chain',\r\n ' SQ - color by sequence',\r\n ' RT - color by residue type',\r\n ' SS - color by secondary structure',\r\n ' UN - uniform',\r\n ],\r\n UN: {\r\n $help: [\r\n 'Parameters of coloring modes customization',\r\n ' Uniform',\r\n ' color = #RGB->HEX->dec\\n',\r\n ],\r\n color: {\r\n $help: Object.keys(palettes.get(settings.now.palette).namedColors).sort().join('\\n'),\r\n },\r\n },\r\n};\r\n\r\nconst materialDesc = {\r\n $help: [\r\n 'Material shortcut',\r\n ' DF - diffuse',\r\n ' TR - transparent',\r\n ' SF - soft plastic',\r\n ' PL - glossy plastic',\r\n ' ME - metal',\r\n ' GL - glass',\r\n ],\r\n};\r\n\r\nconst addRepDesc = {\r\n $help: [\r\n 'Short (packed) representation description as a set of variables',\r\n ' s=',\r\n ' selector property',\r\n ' m=[!:[,...]]',\r\n ' render mode property',\r\n ' c=[!:[,...]]',\r\n ' color mode property',\r\n ' mt=',\r\n ' material property',\r\n ],\r\n s: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n m: modeIdDesc,\r\n c: colorDesc,\r\n mt: materialDesc,\r\n};\r\n\r\nconst setGetParameterDesc = {\r\n $help: [\r\n 'Parameters of rendering modes customization: modes',\r\n 'Parameters of colorer customization: colorers',\r\n 'Autobuild: autobuild = (|)',\r\n ],\r\n modes: modeIdDesc,\r\n colorers: colorDesc,\r\n};\r\n\r\nconst help = {\r\n $help: [\r\n 'help (| )',\r\n 'You can get detailed information about command options',\r\n ' using \"help cmd.opt.opt.[...]\"\\n',\r\n ' you can use one line comments',\r\n ' everything started from (#|//) will be skipped',\r\n ' Example: >build //some comment\\n',\r\n 'List of available commands:',\r\n ],\r\n reset: {\r\n $help: [\r\n 'Reload current object, delete all representations',\r\n ' Nothing will work until load new object',\r\n ],\r\n },\r\n load: {\r\n $help: [\r\n 'load (||-f [<*.NC FILE URL STRING>])',\r\n ' Load new pdb object from selected source',\r\n ],\r\n PDBID: {\r\n $help: 'pdb id in remote molecule database',\r\n },\r\n URL: {\r\n $help: 'url to source file',\r\n },\r\n f: {\r\n $help: [\r\n 'open file system dialog to fetch local file',\r\n 'optionally you can determine trajectory file',\r\n 'via URL for *.top model',\r\n ],\r\n },\r\n },\r\n clear: {\r\n $help: 'No args. Clear terminal',\r\n },\r\n add: {\r\n $help: [\r\n 'add [] []',\r\n ' Add new item to representation set with',\r\n ' default or params',\r\n ],\r\n REP_NAME: {\r\n $help: 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n rep: {\r\n $help: [\r\n 'rep [|] []',\r\n ' set current representation by name or index',\r\n ' edit current representation by ',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n remove: {\r\n $help: [\r\n 'remove (|)',\r\n 'Remove representation by name or index',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n },\r\n selector: {\r\n $help: [\r\n 'selector ',\r\n ' set selector from EXPRESSION to current representation',\r\n ],\r\n EXPRESSION: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n },\r\n mode: {\r\n $help: [\r\n 'mode [=...]',\r\n ' set rendering mode and apply parameters to current representation',\r\n ],\r\n MODE_ID: modeIdDesc,\r\n },\r\n color: {\r\n $help: [\r\n 'color [=...]',\r\n ' set colorer and apply parameters to current representation',\r\n ],\r\n COLORER_ID: colorDesc,\r\n },\r\n material: {\r\n $help: [\r\n 'material ',\r\n ' set material to current representation',\r\n ],\r\n MATERIAL_ID: materialDesc,\r\n },\r\n build: {\r\n $help: 'build help str',\r\n add: {\r\n $help: 'build.add',\r\n new: {\r\n $help: [\r\n 'add.new',\r\n 'add.new new line 1',\r\n 'add.new new line 2',\r\n 'add.new new line 3',\r\n ],\r\n },\r\n },\r\n del: {\r\n $help: 'build.del',\r\n },\r\n },\r\n list: {\r\n $help: [\r\n 'list [-e|-s||]',\r\n 'Print representations if no args print list of representations',\r\n ' -e expand list and show all representations',\r\n ' -s show all user-registered selectors',\r\n ' | show only current representation',\r\n ],\r\n },\r\n hide: {\r\n $help: [\r\n 'hide (|)',\r\n 'Hide representation referenced in args',\r\n ],\r\n },\r\n show: {\r\n $help: [\r\n 'show (|)',\r\n 'Show representation referenced in args',\r\n ],\r\n },\r\n get: {\r\n $help: [\r\n 'get ',\r\n 'Print value',\r\n ' - path to option use get.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set: {\r\n $help: [\r\n 'set ',\r\n 'Set with ',\r\n ' - path to option use set.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set_save: {\r\n $help: [\r\n 'set_save',\r\n 'Save current settings to cookie',\r\n ],\r\n },\r\n set_restore: {\r\n $help: [\r\n 'set_restore',\r\n 'Load and apply settings from cookie',\r\n ],\r\n },\r\n set_reset: {\r\n $help: [\r\n 'set_reset',\r\n 'Reset current settings to the defaults',\r\n ],\r\n },\r\n preset: {\r\n $help: [\r\n 'preset []',\r\n 'Reset current representation or set preset to ',\r\n ],\r\n PRESET: {\r\n $help: [\r\n 'default',\r\n 'wire',\r\n 'small',\r\n 'macro',\r\n ],\r\n },\r\n },\r\n unit: {\r\n $help: [\r\n 'unit []',\r\n 'Change current biological structure view. Zero value means asymmetric unit,',\r\n 'positive values set an assembly with corresponding number.',\r\n 'Being called with no parameters command prints current unit information.',\r\n ],\r\n },\r\n view: {\r\n $help: [\r\n 'view []',\r\n 'Get current encoded view or set if ENCODED_VIEW placed as argument',\r\n ],\r\n ENCODED_VIEW: {\r\n $help: [\r\n 'encoded view matrix string (binary code)',\r\n ],\r\n },\r\n },\r\n rotate: {\r\n $help: [\r\n 'rotate (x|y|z) [] [(x|y|z) []]...',\r\n 'Rotate scene',\r\n ],\r\n },\r\n scale: {\r\n $help: [\r\n 'scale ',\r\n 'Scale scene',\r\n ],\r\n },\r\n select: {\r\n $help: [\r\n 'select [as ]',\r\n 'Select atoms using selector defined in SELECTOR_STRING',\r\n ' and if SELECTOR_NAME is defined register it in viewer',\r\n ' you can use it later as a complex selector',\r\n ],\r\n },\r\n within: {\r\n $help: [\r\n 'within of as ',\r\n 'Build within named selector',\r\n ' DISTANCE ',\r\n ' SELECTOR_STRING ',\r\n ' SELECTOR_NAME ',\r\n ],\r\n },\r\n url: {\r\n $help: [\r\n 'url [-s] [-v]',\r\n 'Report URL encoded scene',\r\n ' if -s set that include settings in the URL',\r\n ' if -v set that include view in the URL',\r\n ],\r\n },\r\n screenshot: {\r\n $help: [\r\n 'screenshot [ []]',\r\n 'Make a screenshot of the scene',\r\n ' WIDTH in pixels',\r\n ' HEIGHT in pixels, equal to WIDTH by default',\r\n ],\r\n },\r\n line: {\r\n $help: [\r\n 'line [=]',\r\n 'Draw dashed line between two specified atoms',\r\n ],\r\n },\r\n removeobj: {\r\n $help: [\r\n 'removeobj ',\r\n 'Remove scene object by its index. Indices could be obtained by command',\r\n ],\r\n },\r\n listobj: {\r\n $help: [\r\n 'listobj',\r\n 'Display the list of all existing scene objects',\r\n ],\r\n },\r\n};\r\n\r\nexport default help;\r\n","import _ from 'lodash';\r\nimport Miew from './Miew';\r\nimport { parser as parsercli } from './utils/MiewCLIParser';\r\nimport clihelp from './utils/MiewCLIHelp';\r\nimport logger from './utils/logger';\r\nimport utils from './utils';\r\n\r\nconst {\r\n chem: { selectors },\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n} = Miew;\r\n\r\nfunction None() {\r\n}\r\n\r\nconst NULL = (function () {\r\n const obj = new None();\r\n return function () {\r\n return obj;\r\n };\r\n}());\r\n\r\nclass RepresentationMap {\r\n constructor() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n\r\n get(strId) {\r\n return this.representationMap[strId] || this.representationID[strId] || '';\r\n }\r\n\r\n add(strId, index) {\r\n if (strId === -1) {\r\n return 'Can not create representation: there is no data';\r\n }\r\n\r\n if (index !== undefined) {\r\n if (!this.representationMap.hasOwnProperty(strId)) {\r\n this.representationMap[strId.toString()] = index;\r\n this.representationID[index] = strId.toString();\r\n } else {\r\n return 'This name has already existed, registered without name';\r\n }\r\n }\r\n return `Representation ${strId} successfully added`;\r\n }\r\n\r\n remove(index) {\r\n if (index && this.representationID.hasOwnProperty(index)) {\r\n delete this.representationMap[this.representationID[index]];\r\n delete this.representationID[index];\r\n }\r\n\r\n const sortedKeys = Object.keys(this.representationID).sort();\r\n for (const i in sortedKeys) {\r\n if (sortedKeys.hasOwnProperty(i)) {\r\n const id = sortedKeys[i];\r\n if (id > index) {\r\n this.representationID[id - 1] = this.representationID[id];\r\n this.representationMap[this.representationID[id]] -= 1;\r\n delete this.representationID[id];\r\n }\r\n }\r\n }\r\n }\r\n\r\n clear() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n}\r\n\r\nconst representationsStorage = new RepresentationMap();\r\n\r\nfunction keyRemap(key) {\r\n const keys = {\r\n s: 'selector',\r\n m: 'mode',\r\n c: 'colorer',\r\n mt: 'material',\r\n mode: 'modes',\r\n color: 'colorers',\r\n colorer: 'colorers',\r\n select: 'selector',\r\n material: 'materials',\r\n selector: 'selector',\r\n };\r\n const ans = keys[key];\r\n return ans === undefined ? key : ans;\r\n}\r\n\r\nclass CLIUtils {\r\n list(miew, repMap, key) {\r\n let ret = '';\r\n if (miew && repMap !== undefined) {\r\n if (key === undefined || key === '-e') {\r\n const count = miew.repCount();\r\n\r\n for (let i = 0; i < count; i++) {\r\n ret += this.listRep(miew, repMap, i, key);\r\n }\r\n }\r\n }\r\n return ret;\r\n }\r\n\r\n listRep(miew, repMap, repIndex, key) {\r\n let ret = '';\r\n const rep = miew.repGet(repIndex);\r\n if (!rep) {\r\n logger.warn(`Rep ${repIndex} does not exist!`);\r\n return ret;\r\n }\r\n const index = repIndex;\r\n const repName = repMap.get(index);\r\n\r\n const { mode, colorer } = rep;\r\n const selectionStr = rep.selectorString;\r\n const material = rep.materialPreset;\r\n\r\n ret += `#${index} : ${mode.name}${repName === '' ? '' : `, ${repName}`}\\n`;\r\n\r\n if (key !== undefined) {\r\n ret += ` selection : \"${selectionStr}\"\\n`;\r\n ret += ` mode : (${mode.id}), ${mode.name}\\n`;\r\n ret += ` colorer : (${colorer.id}), ${colorer.name}\\n`;\r\n ret += ` material : (${material.id}), ${material.name}\\n`;\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listSelector(miew, context) {\r\n let ret = '';\r\n\r\n for (const k in context) {\r\n if (context.hasOwnProperty(k)) {\r\n ret += `${k} : \"${context[k]}\"\\n`;\r\n }\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listObjs(miew) {\r\n const objs = miew._objects;\r\n\r\n if (!objs || !Array.isArray(objs) || objs.length === 0) {\r\n return 'There are no objects on the scene';\r\n }\r\n\r\n const strList = [];\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n strList[i] = `${i}: ${objs[i].toString()}`;\r\n }\r\n\r\n return strList.join('\\n');\r\n }\r\n\r\n joinHelpStr(helpData) {\r\n if (helpData instanceof Array) {\r\n return helpData.join('\\n');\r\n }\r\n return helpData;\r\n }\r\n\r\n help(path) {\r\n if (_.isUndefined(path)) {\r\n return `${this.joinHelpStr(clihelp.$help)}\\n${_.slice(_.sortBy(_.keys(clihelp)), 1).join(', ')}\\n`;\r\n }\r\n\r\n const helpItem = _.get(clihelp, path);\r\n return _.isUndefined(helpItem) ? this.help() : `${this.joinHelpStr(helpItem.$help)}\\n`;\r\n }\r\n\r\n load(miew, arg) {\r\n if (miew === undefined || arg === undefined || arg === '-f') {\r\n return;\r\n }\r\n miew.awaitWhileCMDisInProcess();\r\n const finish = () => miew.finishAwaitingCMDInProcess();\r\n miew.load(arg).then(finish, finish);\r\n }\r\n\r\n checkArg(key, arg, modificate) {\r\n if (key !== undefined && arg !== undefined) {\r\n if (keyRemap(key) === 'selector') {\r\n const res = selectors.parse(arg);\r\n\r\n if (res.error !== undefined) {\r\n const selExc = { message: res.error };\r\n throw selExc;\r\n }\r\n\r\n if (modificate !== undefined && modificate) {\r\n return res.selector;\r\n }\r\n return arg;\r\n }\r\n\r\n const modificators = {\r\n colorers,\r\n modes,\r\n materials,\r\n };\r\n\r\n let modificator = key;\r\n let temp;\r\n while (modificator !== temp) {\r\n temp = modificator;\r\n modificator = keyRemap(temp);\r\n }\r\n\r\n if (modificators[modificator].get(arg) === undefined) {\r\n const exc = { message: `${arg} is not existed in ${modificator}` };\r\n throw exc;\r\n }\r\n return arg;\r\n }\r\n return NULL;\r\n }\r\n\r\n propagateProp(path, arg) {\r\n if (path !== undefined) {\r\n let argExc = {};\r\n const adapter = options.adapters[typeof _.get(settings.defaults, path)];\r\n if (adapter === undefined) {\r\n const pathExc = { message: `${path} is not existed` };\r\n throw pathExc;\r\n }\r\n\r\n if ((path.endsWith('.color') || path.endsWith('.baseColor')\r\n || path.endsWith('.EL.carbon')) && typeof arg !== 'number') {\r\n arg = palettes.get(settings.now.palette).getNamedColor(arg);\r\n }\r\n\r\n if (path.endsWith('.fg') || path.endsWith('.bg')) {\r\n if (typeof arg !== 'number') {\r\n const val = palettes.get(settings.now.palette).getNamedColor(arg, true);\r\n if (val !== undefined) {\r\n arg = `0x${val.toString(16)}`;\r\n }\r\n } else {\r\n arg = `0x${arg.toString(16)}`;\r\n }\r\n }\r\n\r\n if (path.endsWith('.template')) {\r\n arg = arg.replace(/\\\\n/g, '\\n');// NOSONAR\r\n }\r\n\r\n if (arg !== undefined && adapter(arg) !== arg && adapter(arg) !== (arg > 0)) {\r\n argExc = { message: `${path} must be a \"${typeof _.get(settings.defaults, path)}\"` };\r\n throw argExc;\r\n }\r\n }\r\n return arg;\r\n }\r\n\r\n unquoteString(value) {\r\n return utils.unquoteString(value);\r\n }\r\n}\r\n// repIndexOrRepMap could be RepresentationMap or index\r\n\r\nconst utilFunctions = new CLIUtils();\r\n\r\nfunction CreateObjectPair(a, b) {\r\n const obj = {};\r\n obj[a] = b;\r\n return obj;\r\n}\r\n\r\nfunction ArgList(arg) {\r\n if (arg instanceof this.constructor) {\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n}\r\n\r\nArgList.prototype.append = function (value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n};\r\n\r\nArgList.prototype.remove = function (value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n};\r\n\r\nArgList.prototype.toJSO = function (cliUtils, cmd, arg) {\r\n const res = {};\r\n\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n _.set(res, list[i].id, cliUtils.propagateProp(`${keyRemap(cmd)}.${arg}.${list[i].id}`, list[i].val));\r\n }\r\n\r\n return res;\r\n};\r\n\r\nfunction Arg(_id, _val) {\r\n this.id = _id;\r\n this.val = _val;\r\n}\r\n\r\nconst cliutils = Object.create({});\r\n\r\ncliutils.Arg = Arg;\r\ncliutils.ArgList = ArgList;\r\n\r\ncliutils.miew = null;\r\ncliutils.echo = null;\r\ncliutils.representations = representationsStorage;\r\ncliutils.utils = utilFunctions;\r\n\r\ncliutils._ = _;\r\ncliutils.CreateObjectPair = CreateObjectPair;\r\ncliutils.keyRemap = keyRemap;\r\ncliutils.Context = selectors.Context;\r\ncliutils.ClearContext = selectors.ClearContext;\r\n\r\ncliutils.NULL = NULL;\r\n\r\ncliutils.notimplemented = function () {\r\n return this.NULL;\r\n};\r\n\r\nMiew.prototype.script = function (script, _printCallback, _errorCallback) {\r\n parsercli.yy.miew = this;\r\n parsercli.yy.echo = _printCallback;\r\n parsercli.yy.error = _errorCallback;\r\n if (this.cmdQueue === undefined) {\r\n this.cmdQueue = [];\r\n }\r\n\r\n if (this.commandInAction === undefined) {\r\n this.commandInAction = false;\r\n }\r\n\r\n this.cmdQueue = this.cmdQueue.concat(script.split('\\n'));\r\n};\r\n\r\nMiew.prototype.awaitWhileCMDisInProcess = function () {\r\n this.commandInAction = true;\r\n};\r\n\r\nMiew.prototype.finishAwaitingCMDInProcess = function () {\r\n this.commandInAction = false;\r\n};\r\n\r\nMiew.prototype.isScriptingCommandAvailable = function () {\r\n return this.commandInAction !== undefined\r\n && !this.commandInAction\r\n && this.cmdQueue !== undefined\r\n && this.cmdQueue.length > 0;\r\n};\r\n\r\nMiew.prototype.callNextCmd = function () {\r\n if (this.isScriptingCommandAvailable()) {\r\n const cmd = this.cmdQueue.shift();\r\n\r\n const res = {};\r\n res.success = false;\r\n try {\r\n parsercli.parse(cmd);\r\n res.success = true;\r\n } catch (e) {\r\n res.error = e.message;\r\n parsercli.yy.error(res.error);\r\n this.finishAwaitingCMDInProcess();\r\n }\r\n return res;\r\n }\r\n return '';\r\n};\r\n\r\nparsercli.yy = cliutils;\r\n// workaround for incorrect JISON parser generator for AMD module\r\nparsercli.yy.parseError = parsercli.parseError;\r\n","import Miew from './Miew';\r\nimport './Miew-cli';\r\n\r\nexport default 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function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.miew.reset(false); yy.ClearContext(); yy.miew.resetReps(\"empty\");\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.miew.rebuild();\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.miew.rebuildAll(); yy.miew.rebuild();\r\nbreak;\r\ncase 6:\r\nthis.$ = yy.echo(yy.utils.help().toString());\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.echo(yy.utils.help($$[$0]).toString());\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.miew.motm();\r\nbreak;\r\ncase 10: case 11:\r\nthis.$ = yy.utils.propagateProp($$[$0]); yy.echo(yy.miew.get($$[$0]).toString());\r\nbreak;\r\ncase 12: case 13:\r\nthis.$ = yy.miew.set($$[$0-1], yy.utils.propagateProp($$[$0-1], $$[$0]));;\r\nbreak;\r\ncase 14:\r\nthis.$ = yy.miew.saveSettings();;\r\nbreak;\r\ncase 15:\r\nthis.$ = yy.miew.restoreSettings();;\r\nbreak;\r\ncase 16:\r\nthis.$ = yy.miew.resetSettings();;\r\nbreak;\r\ncase 17:\r\nthis.$ = yy.miew.resetReps();\r\nbreak;\r\ncase 18:\r\nthis.$ = yy.miew.applyPreset($$[$0]);\r\nbreak;\r\ncase 21:\r\nthis.$ = yy.miew.repRemove($$[$0]); yy.representations.remove($$[$0]);\r\nbreak;\r\ncase 22:\r\nthis.$ = yy.miew.repHide($$[$0]);\r\nbreak;\r\ncase 23:\r\nthis.$ = yy.miew.repHide($$[$0], false);\r\nbreak;\r\ncase 24:\r\nthis.$ = yy.echo(yy.utils.listRep(yy.miew, yy.representations, $$[$0], '-e'));\r\nbreak;\r\ncase 25:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations));\r\nbreak;\r\ncase 26:\r\nthis.$ = yy.echo(yy.utils.list(yy.miew, yy.representations, $$[$0]));\r\nbreak;\r\ncase 27:\r\nthis.$ = yy.echo(yy.utils.listSelector(yy.miew, yy.Context));\r\nbreak;\r\ncase 28:\r\nthis.$ = yy.miew.select(yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0], true));\r\nbreak;\r\ncase 29:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.utils.checkArg($$[$0-3].toLowerCase(), $$[$0-2], true); yy.miew.select(yy.Context[$$[$0].toLowerCase()]);\r\nbreak;\r\ncase 30:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {selector : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0])});\r\nbreak;\r\ncase 31:\r\nthis.$ = yy.Context[$$[$0].toLowerCase()] = yy.miew.within(yy.utils.checkArg(\"select\", $$[$0-2], true), Number($$[$0-4]));\r\nbreak;\r\ncase 32:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {material : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 35:\r\nthis.$ = yy.echo(yy.miew.view());\r\nbreak;\r\ncase 36: case 37:\r\nthis.$ = yy.miew.view($$[$0]);\r\nbreak;\r\ncase 38:\r\nthis.$ = yy.echo(yy.miew.changeUnit());\r\nbreak;\r\ncase 39:\r\nthis.$ = yy.echo(yy.miew.changeUnit($$[$0]));\r\nbreak;\r\ncase 40:\r\nthis.$ = yy.miew.dssp();\r\nbreak;\r\ncase 41:\r\nthis.$ = yy.miew.scale($$[$0]);\r\nbreak;\r\ncase 42:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.rotate($$[$0][i]['x'] * Math.PI / 180.0, $$[$0][i]['y'] * Math.PI / 180.0, $$[$0][i]['z'] * Math.PI / 180.0)} \r\nbreak;\r\ncase 43:\r\n for (var i = 0, n = $$[$0].length; i < n; i++) {yy.miew.translate($$[$0][i]['x'] || 0, $$[$0][i]['y'] || 0, $$[$0][i]['z'] || 0)} \r\nbreak;\r\ncase 44:\r\nthis.$ = yy.miew.center();\r\nbreak;\r\ncase 45:\r\nthis.$ = yy.miew.center($$[$0]);\r\nbreak;\r\ncase 48: case 49:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-1], $$[$0]]}, true);\r\nbreak;\r\ncase 50: case 51:\r\nthis.$ = yy.miew.addObject({type: 'line', params: [$$[$0-2], $$[$0-1]], opts:$$[$0].toJSO(yy.utils, 'objects', 'line')}, true);\r\nbreak;\r\ncase 52:\r\nthis.$ = yy.echo(yy.utils.listObjs(yy.miew));\r\nbreak;\r\ncase 53:\r\nthis.$ = yy.miew.removeObject($$[$0]);\r\nbreak;\r\ncase 54:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: false}));\r\nbreak;\r\ncase 55:\r\nthis.$ = yy.echo(yy.miew.getURL({view: false, settings: true}));\r\nbreak;\r\ncase 56:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: false}));\r\nbreak;\r\ncase 57: case 58:\r\nthis.$ = yy.echo(yy.miew.getURL({view: true, settings: true}));\r\nbreak;\r\ncase 59:\r\nthis.$ = yy.miew.screenshotSave();\r\nbreak;\r\ncase 60:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0]));\r\nbreak;\r\ncase 61:\r\nthis.$ = yy.miew.screenshotSave('', Number($$[$0-1]), Number($$[$0]));\r\nbreak;\r\ncase 62: case 63: case 64:\r\nthis.$ = yy.utils.load(yy.miew, $$[$0]); yy.representations.clear();\r\nbreak;\r\ncase 65:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd()));\r\nbreak;\r\ncase 66:\r\nthis.$ = yy.echo(yy.representations.add($$[$0], yy.miew.repAdd()));\r\nbreak;\r\ncase 67:\r\nthis.$ = yy.echo(yy.representations.add(yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 68:\r\nthis.$ = yy.echo(yy.representations.add($$[$0-1], yy.miew.repAdd($$[$0])));\r\nbreak;\r\ncase 69:\r\nthis.$ = yy.miew.rep($$[$0]); yy.miew.repCurrent($$[$0]);\r\nbreak;\r\ncase 70:\r\nthis.$ = yy.miew.rep($$[$0-1], $$[$0]); yy.miew.repCurrent($$[$0-1]);\r\nbreak;\r\ncase 71:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 72:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {mode : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 73:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : yy.utils.checkArg($$[$0-1].toLowerCase(), $$[$0].toUpperCase())});\r\nbreak;\r\ncase 74:\r\nthis.$ = yy.miew.rep(yy.miew.repCurrent(), {colorer : new Array(yy.utils.checkArg($$[$0-2].toLowerCase(), $$[$0-1].toUpperCase()), $$[$0].toJSO(yy.utils, $$[$0-2], $$[$0-1].toUpperCase()))});\r\nbreak;\r\ncase 75:\r\nthis.$ = Number(yy.representations.get($$[$0]));\r\nbreak;\r\ncase 76: case 92:\r\nthis.$ = Number($$[$0]);\r\nbreak;\r\ncase 77:\r\nthis.$ = $$[$0];\r\nbreak;\r\ncase 78:\r\nthis.$ = yy._.assign($$[$0-1], $$[$0]);\r\nbreak;\r\ncase 79:\r\nthis.$ = yy._.assign($$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 80:\r\nthis.$ = yy._.assign($$[$0-3], $$[$0-2], $$[$0-1], $$[$0]);\r\nbreak;\r\ncase 81: case 82:\r\nthis.$ = yy.CreateObjectPair($$[$0].key, $$[$0].val);\r\nbreak;\r\ncase 83:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].key, new Array($$[$0-1].val, $$[$0].toJSO(yy.utils, $$[$0-1].key, $$[$0-1].val)));\r\nbreak;\r\ncase 84: case 85:\r\nthis.$ = Object.create({'key': yy.keyRemap($$[$0-2]), 'val': yy.utils.checkArg($$[$0-2], $$[$0])});\r\nbreak;\r\ncase 86:\r\nthis.$ = [$$[$0]];\r\nbreak;\r\ncase 87:\r\nthis.$ = $$[$0-1].concat($$[$0]);\r\nbreak;\r\ncase 88:\r\nthis.$ = yy.CreateObjectPair($$[$0-1].toLowerCase(), Number($$[$0]));\r\nbreak;\r\ncase 89:\r\nthis.$ = new yy.ArgList($$[$0]);\r\nbreak;\r\ncase 90:\r\nthis.$ = $$[$0-1].append($$[$0]);\r\nbreak;\r\ncase 91:\r\nthis.$ = new yy.Arg($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 93:\r\nthis.$ = parseInt($$[$0]);\r\nbreak;\r\ncase 94:\r\nthis.$ = JSON.parse($$[$0]);\r\nbreak;\r\ncase 95: case 96:\r\nthis.$ = String($$[$0]);\r\nbreak;\r\ncase 157: case 158: case 161: case 162: case 163:\r\nthis.$ = $$[$0-2] + $$[$0-1] + $$[$0] //cause of could be color word in path;\r\nbreak;\r\ncase 166:\r\nthis.$ = $$[$0-2] = $$[$0-2] + $$[$0-1] + $$[$0];\r\nbreak;\r\n}\r\n},\r\ntable: 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,[2,90]),{14:$VS,16:197,35:$VT,38:$VU,77:$VV,78:$VW},{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,33:$Ve,34:$Vf,35:[1,199],37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,79:198,80:52,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN},o($V41,[2,84]),o($V31,[2,85]),{6:$V0,7:$V1,9:$V2,13:$V3,15:$V4,17:$V5,18:$V6,19:$V7,20:$V8,23:$V9,25:$Va,26:$Vb,27:$Vc,30:$Vd,32:200,33:$Ve,34:$Vf,37:$Vg,38:$Vh,41:$Vi,43:$Vj,45:$Vk,46:$Vl,49:$Vm,52:$Vn,54:$Vo,55:$Vp,56:$Vq,58:$Vr,59:$Vs,62:$Vt,64:$Vu,65:$Vv,66:$Vw,70:$Vx,72:$Vy,74:$Vz,79:184,80:52,81:185,82:$VA,83:$VB,84:$VC,85:$VD,86:$VE,87:$VF,88:$VG,89:$VH,90:$VI,91:$VJ,92:$VK,93:$VL,94:$VM,95:$VN,96:$VO,97:$VP,98:$VQ,99:$VR},{5:[2,80]},o($V31,[2,91]),o($V61,[2,157]),o($V61,[2,158]),{5:[2,31]}],\r\ndefaultActions: {3:[2,2],4:[2,3],7:[2,8],8:[2,9],11:[2,14],12:[2,15],13:[2,16],15:[2,19],16:[2,20],25:[2,33],26:[2,34],29:[2,40],34:[2,46],35:[2,47],37:[2,52],46:[2,1],47:[2,5],107:[2,11],110:[2,18],116:[2,21],119:[2,22],120:[2,23],121:[2,24],122:[2,26],123:[2,27],125:[2,30],127:[2,32],128:[2,36],129:[2,37],130:[2,39],131:[2,41],136:[2,45],139:[2,53],140:[2,62],141:[2,63],142:[2,64],143:[2,164],145:[2,67],158:[2,12],159:[2,13],166:[2,68],174:[2,70],177:[2,57],178:[2,58],179:[2,61],183:[2,29],184:[2,99],185:[2,100],196:[2,80],200:[2,31]},\r\nparseError: function parseError (str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function(match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex () {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin (condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState () {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules () {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState (n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState (condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* ignore whitespace */\r\nbreak;\r\ncase 1:return '';\r\nbreak;\r\ncase 2:return '';\r\nbreak;\r\ncase 3:return 42;\r\nbreak;\r\ncase 4:return 35;\r\nbreak;\r\ncase 5:return 77;\r\nbreak;\r\ncase 6:return 78;\r\nbreak;\r\ncase 7:return 78;\r\nbreak;\r\ncase 8:return 8;\r\nbreak;\r\ncase 9:return 6;\r\nbreak;\r\ncase 10:return 82;\r\nbreak;\r\ncase 11:return 7;\r\nbreak;\r\ncase 12:return 9;\r\nbreak;\r\ncase 13:return 59;\r\nbreak;\r\ncase 14:return 13\r\nbreak;\r\ncase 15:return 15\r\nbreak;\r\ncase 16:return 17\r\nbreak;\r\ncase 17:return 18\r\nbreak;\r\ncase 18:return 19\r\nbreak;\r\ncase 19:return 20\r\nbreak;\r\ncase 20:return 11\r\nbreak;\r\ncase 21:return 62\r\nbreak;\r\ncase 22:return 64\r\nbreak;\r\ncase 23:return 23\r\nbreak;\r\ncase 24:return 25\r\nbreak;\r\ncase 25:return 26\r\nbreak;\r\ncase 26:return 27\r\nbreak;\r\ncase 27:return 30\r\nbreak;\r\ncase 28:return 34\r\nbreak;\r\ncase 29:return 33\r\nbreak;\r\ncase 30:return 65\r\nbreak;\r\ncase 31:return 66\r\nbreak;\r\ncase 32:return 37\r\nbreak;\r\ncase 33:return 41\r\nbreak;\r\ncase 34:return 43\r\nbreak;\r\ncase 35:return 52\r\nbreak;\r\ncase 36:return 54\r\nbreak;\r\ncase 37:return 55\r\nbreak;\r\ncase 38:return 46\r\nbreak;\r\ncase 39:return 48\r\nbreak;\r\ncase 40:return 45\r\nbreak;\r\ncase 41:return 49\r\nbreak;\r\ncase 42:return 56\r\nbreak;\r\ncase 43:return 58;\r\nbreak;\r\ncase 44:return 44\r\nbreak;\r\ncase 45:return 83\r\nbreak;\r\ncase 46:return 84\r\nbreak;\r\ncase 47:return 85\r\nbreak;\r\ncase 48:return 86\r\nbreak;\r\ncase 49:return 87\r\nbreak;\r\ncase 50:return 88\r\nbreak;\r\ncase 51:return 89\r\nbreak;\r\ncase 52:return 90\r\nbreak;\r\ncase 53:return 91\r\nbreak;\r\ncase 54:return 92\r\nbreak;\r\ncase 55:return 93\r\nbreak;\r\ncase 56:return 94\r\nbreak;\r\ncase 57:return 95\r\nbreak;\r\ncase 58:return 70\r\nbreak;\r\ncase 59:return 70\r\nbreak;\r\ncase 60:return 72\r\nbreak;\r\ncase 61:return 72\r\nbreak;\r\ncase 62:return 74\r\nbreak;\r\ncase 63:return 74\r\nbreak;\r\ncase 64:return 74\r\nbreak;\r\ncase 65:return 31\r\nbreak;\r\ncase 66:return 36\r\nbreak;\r\ncase 67:return 96\r\nbreak;\r\ncase 68:return 97\r\nbreak;\r\ncase 69:return 98\r\nbreak;\r\ncase 70:return 99\r\nbreak;\r\ncase 71:yy_.yytext = yy.utils.unquoteString(yy_.yytext); return 14;\r\nbreak;\r\ncase 72:return 38;\r\nbreak;\r\ncase 73:return 5;\r\nbreak;\r\ncase 74:return 101;\r\nbreak;\r\ncase 75:return 103;\r\nbreak;\r\ncase 76:return '\\\\';\r\nbreak;\r\ncase 77:return 28\r\nbreak;\r\ncase 78:return 61\r\nbreak;\r\ncase 79:return 29\r\nbreak;\r\ncase 80:return 57\r\nbreak;\r\ncase 81:return 71\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:[#].*)/i,/^(?:\\/\\/.*)/i,/^(?:([_A-Z0-9\\/\\+]+==))/i,/^(?:-?[0-9]+(\\.[0-9]+)?\\b)/i,/^(?:0[xX][0-9A-F]+\\b)/i,/^(?:false\\b)/i,/^(?:true\\b)/i,/^(?:all\\b)/i,/^(?:reset\\b)/i,/^(?:clear\\b)/i,/^(?:build\\b)/i,/^(?:help\\b)/i,/^(?:load\\b)/i,/^(?:get\\b)/i,/^(?:set\\b)/i,/^(?:set_save\\b)/i,/^(?:set_restore\\b)/i,/^(?:set_reset\\b)/i,/^(?:preset\\b)/i,/^(?:motm\\b)/i,/^(?:add\\b)/i,/^(?:rep\\b)/i,/^(?:remove\\b)/i,/^(?:hide\\b)/i,/^(?:show\\b)/i,/^(?:list\\b)/i,/^(?:select\\b)/i,/^(?:within\\b)/i,/^(?:selector\\b)/i,/^(?:mode\\b)/i,/^(?:color\\b)/i,/^(?:material\\b)/i,/^(?:view\\b)/i,/^(?:unit\\b)/i,/^(?:line\\b)/i,/^(?:listobj\\b)/i,/^(?:removeobj\\b)/i,/^(?:rotate\\b)/i,/^(?:translate\\b)/i,/^(?:scale\\b)/i,/^(?:center\\b)/i,/^(?:url\\b)/i,/^(?:screenshot\\b)/i,/^(?:dssp\\b)/i,/^(?:file_list\\b)/i,/^(?:file_register\\b)/i,/^(?:file_delete\\b)/i,/^(?:preset_add\\b)/i,/^(?:preset_delete\\b)/i,/^(?:preset_update\\b)/i,/^(?:preset_rename\\b)/i,/^(?:preset_open\\b)/i,/^(?:create_scenario\\b)/i,/^(?:reset_scenario\\b)/i,/^(?:delete_scenario\\b)/i,/^(?:add_scenario_item\\b)/i,/^(?:list_scenario\\b)/i,/^(?:s\\b)/i,/^(?:mt\\b)/i,/^(?:m\\b)/i,/^(?:c\\b)/i,/^(?:x\\b)/i,/^(?:y\\b)/i,/^(?:z\\b)/i,/^(?:as\\b)/i,/^(?:of\\b)/i,/^(?:pdb\\b)/i,/^(?:delay\\b)/i,/^(?:prst\\b)/i,/^(?:desc\\b)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:\\.)/i,/^(?:\\/)/i,/^(?:\\\\)/i,/^(?:-e\\b)/i,/^(?:-f\\b)/i,/^(?:-s\\b)/i,/^(?:-v\\b)/i,/^(?:=)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","/* eslint-disable */\r\n// DO NOT EDIT! Automatically generated from .jison\r\n/* parser generated by jison 0.4.18 */\r\n/*\r\n Returns a Parser object of the following structure:\r\n\r\n Parser: {\r\n yy: {}\r\n }\r\n\r\n Parser.prototype: {\r\n yy: {},\r\n trace: function(),\r\n symbols_: {associative list: name ==> number},\r\n terminals_: {associative list: number ==> name},\r\n productions_: [...],\r\n performAction: function anonymous(yytext, yyleng, yylineno, yy, yystate, $$, _$),\r\n table: [...],\r\n defaultActions: {...},\r\n parseError: function(str, hash),\r\n parse: function(input),\r\n\r\n lexer: {\r\n EOF: 1,\r\n parseError: function(str, hash),\r\n setInput: function(input),\r\n input: function(),\r\n unput: function(str),\r\n more: function(),\r\n less: function(n),\r\n pastInput: function(),\r\n upcomingInput: function(),\r\n showPosition: function(),\r\n test_match: function(regex_match_array, rule_index),\r\n next: function(),\r\n lex: function(),\r\n begin: function(condition),\r\n popState: function(),\r\n _currentRules: function(),\r\n topState: function(),\r\n pushState: function(condition),\r\n\r\n options: {\r\n ranges: boolean (optional: true ==> token location info will include a .range[] member)\r\n flex: boolean (optional: true ==> flex-like lexing behaviour where the rules are tested exhaustively to find the longest match)\r\n backtrack_lexer: boolean (optional: true ==> lexer regexes are tested in order and for each matching regex the action code is invoked; the lexer terminates the scan when a token is returned by the action code)\r\n },\r\n\r\n performAction: function(yy, yy_, $avoiding_name_collisions, YY_START),\r\n rules: [...],\r\n conditions: {associative list: name ==> set},\r\n }\r\n }\r\n\r\n\r\n token location info (@$, _$, etc.): {\r\n first_line: n,\r\n last_line: n,\r\n first_column: n,\r\n last_column: n,\r\n range: [start_number, end_number] (where the numbers are indexes into the input string, regular zero-based)\r\n }\r\n\r\n\r\n the parseError function receives a 'hash' object with these members for lexer and parser errors: {\r\n text: (matched text)\r\n token: (the produced terminal token, if any)\r\n line: (yylineno)\r\n }\r\n while parser (grammar) errors will also provide these members, i.e. parser errors deliver a superset of attributes: {\r\n loc: (yylloc)\r\n expected: (string describing the set of expected tokens)\r\n recoverable: (boolean: TRUE when the parser has a error recovery rule available for this particular error)\r\n }\r\n*/\r\nvar parser = (function(){\r\nvar o=function(k,v,o,l){for(o=o||{},l=k.length;l--;o[k[l]]=v);return o},$V0=[1,4],$V1=[1,5],$V2=[1,6],$V3=[1,7],$V4=[1,8],$V5=[1,9],$V6=[1,11],$V7=[1,12],$V8=[5,7,8,11],$V9=[1,17],$Va=[1,22],$Vb=[1,20],$Vc=[1,21],$Vd=[5,7,8,11,19];\r\nvar parser = {trace: function trace() { },\r\nyy: {},\r\nsymbols_: {\"error\":2,\"Program\":3,\"Expression\":4,\"EOF\":5,\"Selector\":6,\"OR\":7,\"AND\":8,\"NOT\":9,\"(\":10,\")\":11,\"SELECTOR\":12,\"NAMED_SELECTOR\":13,\"SELECTOR_RANGED\":14,\"RangeList\":15,\"SELECTOR_NAMED\":16,\"NameList\":17,\"Range\":18,\",\":19,\"NUMBER\":20,\":\":21,\"Name\":22,\"IDENTIFIER\":23,\"STRING\":24,\"$accept\":0,\"$end\":1},\r\nterminals_: {2:\"error\",5:\"EOF\",7:\"OR\",8:\"AND\",9:\"NOT\",10:\"(\",11:\")\",12:\"SELECTOR\",13:\"NAMED_SELECTOR\",14:\"SELECTOR_RANGED\",16:\"SELECTOR_NAMED\",19:\",\",20:\"NUMBER\",21:\":\",23:\"IDENTIFIER\",24:\"STRING\"},\r\nproductions_: [0,[3,2],[4,1],[4,3],[4,3],[4,2],[4,3],[6,1],[6,1],[6,2],[6,2],[15,1],[15,3],[18,1],[18,3],[17,1],[17,3],[22,1],[22,1],[22,1]],\r\nperformAction: function anonymous(yytext, yyleng, yylineno, yy, yystate /* action[1] */, $$ /* vstack */, _$ /* lstack */) {\r\n/* this == yyval */\r\n\r\nvar $0 = $$.length - 1;\r\nswitch (yystate) {\r\ncase 1:\r\n return $$[$0-1]; \r\nbreak;\r\ncase 3:\r\nthis.$ = yy.keyword('or')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 4:\r\nthis.$ = yy.keyword('and')($$[$0-2], $$[$0]);\r\nbreak;\r\ncase 5:\r\nthis.$ = yy.keyword('not')($$[$0]);\r\nbreak;\r\ncase 6:\r\nthis.$ = $$[$0-1];\r\nbreak;\r\ncase 7:\r\nthis.$ = yy.keyword($$[$0])();\r\nbreak;\r\ncase 8:\r\nthis.$ = yy.GetSelector($$[$0].toLowerCase().slice(1, $$[$0].length));\r\nbreak;\r\ncase 9: case 10:\r\nthis.$ = yy.keyword($$[$0-1])($$[$0]);\r\nbreak;\r\ncase 11:\r\nthis.$ = new yy.RangeList($$[$0]);\r\nbreak;\r\ncase 12: case 16:\r\nthis.$ = $$[$0-2].append($$[$0]);\r\nbreak;\r\ncase 13:\r\nthis.$ = new yy.Range(Number($$[$0]));\r\nbreak;\r\ncase 14:\r\nthis.$ = new yy.Range(Number($$[$0-2]), Number($$[$0]));\r\nbreak;\r\ncase 15:\r\nthis.$ = new yy.ValueList($$[$0]);\r\nbreak;\r\n}\r\n},\r\ntable: [{3:1,4:2,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{1:[3]},{5:[1,10],7:$V6,8:$V7},o($V8,[2,2]),{4:13,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:14,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,7]),o($V8,[2,8]),{15:15,18:16,20:$V9},{17:18,20:$Va,22:19,23:$Vb,24:$Vc},{1:[2,1]},{4:23,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},{4:24,6:3,9:$V0,10:$V1,12:$V2,13:$V3,14:$V4,16:$V5},o($V8,[2,5]),{7:$V6,8:$V7,11:[1,25]},o($V8,[2,9],{19:[1,26]}),o($Vd,[2,11]),o($Vd,[2,13],{21:[1,27]}),o($V8,[2,10],{19:[1,28]}),o($Vd,[2,15]),o($Vd,[2,17]),o($Vd,[2,18]),o($Vd,[2,19]),o([5,7,11],[2,3],{8:$V7}),o($V8,[2,4]),o($V8,[2,6]),{18:29,20:$V9},{20:[1,30]},{20:$Va,22:31,23:$Vb,24:$Vc},o($Vd,[2,12]),o($Vd,[2,14]),o($Vd,[2,16])],\r\ndefaultActions: {10:[2,1]},\r\nparseError: function parseError(str, hash) {\r\n if (hash.recoverable) {\r\n this.trace(str);\r\n } else {\r\n var error = new Error(str);\r\n error.hash = hash;\r\n throw error;\r\n }\r\n},\r\nparse: function parse(input) {\r\n var self = this, stack = [0], tstack = [], vstack = [null], lstack = [], table = this.table, yytext = '', yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;\r\n var args = lstack.slice.call(arguments, 1);\r\n var lexer = Object.create(this.lexer);\r\n var sharedState = { yy: {} };\r\n for (var k in this.yy) {\r\n if (Object.prototype.hasOwnProperty.call(this.yy, k)) {\r\n sharedState.yy[k] = this.yy[k];\r\n }\r\n }\r\n lexer.setInput(input, sharedState.yy);\r\n sharedState.yy.lexer = lexer;\r\n sharedState.yy.parser = this;\r\n if (typeof lexer.yylloc == 'undefined') {\r\n lexer.yylloc = {};\r\n }\r\n var yyloc = lexer.yylloc;\r\n lstack.push(yyloc);\r\n var ranges = lexer.options && lexer.options.ranges;\r\n if (typeof sharedState.yy.parseError === 'function') {\r\n this.parseError = sharedState.yy.parseError;\r\n } else {\r\n this.parseError = Object.getPrototypeOf(this).parseError;\r\n }\r\n function popStack(n) {\r\n stack.length = stack.length - 2 * n;\r\n vstack.length = vstack.length - n;\r\n lstack.length = lstack.length - n;\r\n }\r\n function lex() {\r\n var token;\r\n token = tstack.pop() || lexer.lex() || EOF;\r\n if (typeof token !== 'number') {\r\n if (token instanceof Array) {\r\n tstack = token;\r\n token = tstack.pop();\r\n }\r\n token = self.symbols_[token] || token;\r\n }\r\n return token;\r\n }\r\n var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;\r\n while (true) {\r\n state = stack[stack.length - 1];\r\n if (this.defaultActions[state]) {\r\n action = this.defaultActions[state];\r\n } else {\r\n if (symbol === null || typeof symbol == 'undefined') {\r\n symbol = lex();\r\n }\r\n action = table[state] && table[state][symbol];\r\n }\r\n if (typeof action === 'undefined' || !action.length || !action[0]) {\r\n var errStr = '';\r\n expected = [];\r\n for (p in table[state]) {\r\n if (this.terminals_[p] && p > TERROR) {\r\n expected.push('\\'' + this.terminals_[p] + '\\'');\r\n }\r\n }\r\n if (lexer.showPosition) {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ':\\n' + lexer.showPosition() + '\\nExpecting ' + expected.join(', ') + ', got \\'' + (this.terminals_[symbol] || symbol) + '\\'';\r\n } else {\r\n errStr = 'Parse error on line ' + (yylineno + 1) + ': Unexpected ' + (symbol == EOF ? 'end of input' : '\\'' + (this.terminals_[symbol] || symbol) + '\\'');\r\n }\r\n this.parseError(errStr, {\r\n text: lexer.match,\r\n token: this.terminals_[symbol] || symbol,\r\n line: lexer.yylineno,\r\n loc: yyloc,\r\n expected: expected\r\n });\r\n }\r\n if (action[0] instanceof Array && action.length > 1) {\r\n throw new Error('Parse Error: multiple actions possible at state: ' + state + ', token: ' + symbol);\r\n }\r\n switch (action[0]) {\r\n case 1:\r\n stack.push(symbol);\r\n vstack.push(lexer.yytext);\r\n lstack.push(lexer.yylloc);\r\n stack.push(action[1]);\r\n symbol = null;\r\n if (!preErrorSymbol) {\r\n yyleng = lexer.yyleng;\r\n yytext = lexer.yytext;\r\n yylineno = lexer.yylineno;\r\n yyloc = lexer.yylloc;\r\n if (recovering > 0) {\r\n recovering--;\r\n }\r\n } else {\r\n symbol = preErrorSymbol;\r\n preErrorSymbol = null;\r\n }\r\n break;\r\n case 2:\r\n len = this.productions_[action[1]][1];\r\n yyval.$ = vstack[vstack.length - len];\r\n yyval._$ = {\r\n first_line: lstack[lstack.length - (len || 1)].first_line,\r\n last_line: lstack[lstack.length - 1].last_line,\r\n first_column: lstack[lstack.length - (len || 1)].first_column,\r\n last_column: lstack[lstack.length - 1].last_column\r\n };\r\n if (ranges) {\r\n yyval._$.range = [\r\n lstack[lstack.length - (len || 1)].range[0],\r\n lstack[lstack.length - 1].range[1]\r\n ];\r\n }\r\n r = this.performAction.apply(yyval, [\r\n yytext,\r\n yyleng,\r\n yylineno,\r\n sharedState.yy,\r\n action[1],\r\n vstack,\r\n lstack\r\n ].concat(args));\r\n if (typeof r !== 'undefined') {\r\n return r;\r\n }\r\n if (len) {\r\n stack = stack.slice(0, -1 * len * 2);\r\n vstack = vstack.slice(0, -1 * len);\r\n lstack = lstack.slice(0, -1 * len);\r\n }\r\n stack.push(this.productions_[action[1]][0]);\r\n vstack.push(yyval.$);\r\n lstack.push(yyval._$);\r\n newState = table[stack[stack.length - 2]][stack[stack.length - 1]];\r\n stack.push(newState);\r\n break;\r\n case 3:\r\n return true;\r\n }\r\n }\r\n return true;\r\n}};\r\n\r\n\r\n/* generated by jison-lex 0.3.4 */\r\nvar lexer = (function(){\r\nvar lexer = ({\r\n\r\nEOF:1,\r\n\r\nparseError:function parseError(str, hash) {\r\n if (this.yy.parser) {\r\n this.yy.parser.parseError(str, hash);\r\n } else {\r\n throw new Error(str);\r\n }\r\n },\r\n\r\n// resets the lexer, sets new input\r\nsetInput:function (input, yy) {\r\n this.yy = yy || this.yy || {};\r\n this._input = input;\r\n this._more = this._backtrack = this.done = false;\r\n this.yylineno = this.yyleng = 0;\r\n this.yytext = this.matched = this.match = '';\r\n this.conditionStack = ['INITIAL'];\r\n this.yylloc = {\r\n first_line: 1,\r\n first_column: 0,\r\n last_line: 1,\r\n last_column: 0\r\n };\r\n if (this.options.ranges) {\r\n this.yylloc.range = [0,0];\r\n }\r\n this.offset = 0;\r\n return this;\r\n },\r\n\r\n// consumes and returns one char from the input\r\ninput:function () {\r\n var ch = this._input[0];\r\n this.yytext += ch;\r\n this.yyleng++;\r\n this.offset++;\r\n this.match += ch;\r\n this.matched += ch;\r\n var lines = ch.match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno++;\r\n this.yylloc.last_line++;\r\n } else {\r\n this.yylloc.last_column++;\r\n }\r\n if (this.options.ranges) {\r\n this.yylloc.range[1]++;\r\n }\r\n\r\n this._input = this._input.slice(1);\r\n return ch;\r\n },\r\n\r\n// unshifts one char (or a string) into the input\r\nunput:function (ch) {\r\n var len = ch.length;\r\n var lines = ch.split(/(?:\\r\\n?|\\n)/g);\r\n\r\n this._input = ch + this._input;\r\n this.yytext = this.yytext.substr(0, this.yytext.length - len);\r\n //this.yyleng -= len;\r\n this.offset -= len;\r\n var oldLines = this.match.split(/(?:\\r\\n?|\\n)/g);\r\n this.match = this.match.substr(0, this.match.length - 1);\r\n this.matched = this.matched.substr(0, this.matched.length - 1);\r\n\r\n if (lines.length - 1) {\r\n this.yylineno -= lines.length - 1;\r\n }\r\n var r = this.yylloc.range;\r\n\r\n this.yylloc = {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.first_column,\r\n last_column: lines ?\r\n (lines.length === oldLines.length ? this.yylloc.first_column : 0)\r\n + oldLines[oldLines.length - lines.length].length - lines[0].length :\r\n this.yylloc.first_column - len\r\n };\r\n\r\n if (this.options.ranges) {\r\n this.yylloc.range = [r[0], r[0] + this.yyleng - len];\r\n }\r\n this.yyleng = this.yytext.length;\r\n return this;\r\n },\r\n\r\n// When called from action, caches matched text and appends it on next action\r\nmore:function () {\r\n this._more = true;\r\n return this;\r\n },\r\n\r\n// When called from action, signals the lexer that this rule fails to match the input, so the next matching rule (regex) should be tested instead.\r\nreject:function () {\r\n if (this.options.backtrack_lexer) {\r\n this._backtrack = true;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n\r\n }\r\n return this;\r\n },\r\n\r\n// retain first n characters of the match\r\nless:function (n) {\r\n this.unput(this.match.slice(n));\r\n },\r\n\r\n// displays already matched input, i.e. for error messages\r\npastInput:function () {\r\n var past = this.matched.substr(0, this.matched.length - this.match.length);\r\n return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays upcoming input, i.e. for error messages\r\nupcomingInput:function () {\r\n var next = this.match;\r\n if (next.length < 20) {\r\n next += this._input.substr(0, 20-next.length);\r\n }\r\n return (next.substr(0,20) + (next.length > 20 ? '...' : '')).replace(/\\n/g, \"\");\r\n },\r\n\r\n// displays the character position where the lexing error occurred, i.e. for error messages\r\nshowPosition:function () {\r\n var pre = this.pastInput();\r\n var c = new Array(pre.length + 1).join(\"-\");\r\n return pre + this.upcomingInput() + \"\\n\" + c + \"^\";\r\n },\r\n\r\n// test the lexed token: return FALSE when not a match, otherwise return token\r\ntest_match:function (match, indexed_rule) {\r\n var token,\r\n lines,\r\n backup;\r\n\r\n if (this.options.backtrack_lexer) {\r\n // save context\r\n backup = {\r\n yylineno: this.yylineno,\r\n yylloc: {\r\n first_line: this.yylloc.first_line,\r\n last_line: this.last_line,\r\n first_column: this.yylloc.first_column,\r\n last_column: this.yylloc.last_column\r\n },\r\n yytext: this.yytext,\r\n match: this.match,\r\n matches: this.matches,\r\n matched: this.matched,\r\n yyleng: this.yyleng,\r\n offset: this.offset,\r\n _more: this._more,\r\n _input: this._input,\r\n yy: this.yy,\r\n conditionStack: this.conditionStack.slice(0),\r\n done: this.done\r\n };\r\n if (this.options.ranges) {\r\n backup.yylloc.range = this.yylloc.range.slice(0);\r\n }\r\n }\r\n\r\n lines = match[0].match(/(?:\\r\\n?|\\n).*/g);\r\n if (lines) {\r\n this.yylineno += lines.length;\r\n }\r\n this.yylloc = {\r\n first_line: this.yylloc.last_line,\r\n last_line: this.yylineno + 1,\r\n first_column: this.yylloc.last_column,\r\n last_column: lines ?\r\n lines[lines.length - 1].length - lines[lines.length - 1].match(/\\r?\\n?/)[0].length :\r\n this.yylloc.last_column + match[0].length\r\n };\r\n this.yytext += match[0];\r\n this.match += match[0];\r\n this.matches = match;\r\n this.yyleng = this.yytext.length;\r\n if (this.options.ranges) {\r\n this.yylloc.range = [this.offset, this.offset += this.yyleng];\r\n }\r\n this._more = false;\r\n this._backtrack = false;\r\n this._input = this._input.slice(match[0].length);\r\n this.matched += match[0];\r\n token = this.performAction.call(this, this.yy, this, indexed_rule, this.conditionStack[this.conditionStack.length - 1]);\r\n if (this.done && this._input) {\r\n this.done = false;\r\n }\r\n if (token) {\r\n return token;\r\n } else if (this._backtrack) {\r\n // recover context\r\n for (var k in backup) {\r\n this[k] = backup[k];\r\n }\r\n return false; // rule action called reject() implying the next rule should be tested instead.\r\n }\r\n return false;\r\n },\r\n\r\n// return next match in input\r\nnext:function () {\r\n if (this.done) {\r\n return this.EOF;\r\n }\r\n if (!this._input) {\r\n this.done = true;\r\n }\r\n\r\n var token,\r\n match,\r\n tempMatch,\r\n index;\r\n if (!this._more) {\r\n this.yytext = '';\r\n this.match = '';\r\n }\r\n var rules = this._currentRules();\r\n for (var i = 0; i < rules.length; i++) {\r\n tempMatch = this._input.match(this.rules[rules[i]]);\r\n if (tempMatch && (!match || tempMatch[0].length > match[0].length)) {\r\n match = tempMatch;\r\n index = i;\r\n if (this.options.backtrack_lexer) {\r\n token = this.test_match(tempMatch, rules[i]);\r\n if (token !== false) {\r\n return token;\r\n } else if (this._backtrack) {\r\n match = false;\r\n continue; // rule action called reject() implying a rule MISmatch.\r\n } else {\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n } else if (!this.options.flex) {\r\n break;\r\n }\r\n }\r\n }\r\n if (match) {\r\n token = this.test_match(match, rules[index]);\r\n if (token !== false) {\r\n return token;\r\n }\r\n // else: this is a lexer rule which consumes input without producing a token (e.g. whitespace)\r\n return false;\r\n }\r\n if (this._input === \"\") {\r\n return this.EOF;\r\n } else {\r\n return this.parseError('Lexical error on line ' + (this.yylineno + 1) + '. Unrecognized text.\\n' + this.showPosition(), {\r\n text: \"\",\r\n token: null,\r\n line: this.yylineno\r\n });\r\n }\r\n },\r\n\r\n// return next match that has a token\r\nlex:function lex() {\r\n var r = this.next();\r\n if (r) {\r\n return r;\r\n } else {\r\n return this.lex();\r\n }\r\n },\r\n\r\n// activates a new lexer condition state (pushes the new lexer condition state onto the condition stack)\r\nbegin:function begin(condition) {\r\n this.conditionStack.push(condition);\r\n },\r\n\r\n// pop the previously active lexer condition state off the condition stack\r\npopState:function popState() {\r\n var n = this.conditionStack.length - 1;\r\n if (n > 0) {\r\n return this.conditionStack.pop();\r\n } else {\r\n return this.conditionStack[0];\r\n }\r\n },\r\n\r\n// produce the lexer rule set which is active for the currently active lexer condition state\r\n_currentRules:function _currentRules() {\r\n if (this.conditionStack.length && this.conditionStack[this.conditionStack.length - 1]) {\r\n return this.conditions[this.conditionStack[this.conditionStack.length - 1]].rules;\r\n } else {\r\n return this.conditions[\"INITIAL\"].rules;\r\n }\r\n },\r\n\r\n// return the currently active lexer condition state; when an index argument is provided it produces the N-th previous condition state, if available\r\ntopState:function topState(n) {\r\n n = this.conditionStack.length - 1 - Math.abs(n || 0);\r\n if (n >= 0) {\r\n return this.conditionStack[n];\r\n } else {\r\n return \"INITIAL\";\r\n }\r\n },\r\n\r\n// alias for begin(condition)\r\npushState:function pushState(condition) {\r\n this.begin(condition);\r\n },\r\n\r\n// return the number of states currently on the stack\r\nstateStackSize:function stateStackSize() {\r\n return this.conditionStack.length;\r\n },\r\noptions: {\"case-insensitive\":true},\r\nperformAction: function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) {\r\nvar YYSTATE=YY_START;\r\nswitch($avoiding_name_collisions) {\r\ncase 0:/* skip whitespace */\r\nbreak;\r\ncase 1:return 20;\r\nbreak;\r\ncase 2:return 7;\r\nbreak;\r\ncase 3:return 8;\r\nbreak;\r\ncase 4:return 9;\r\nbreak;\r\ncase 5:return 12;\r\nbreak;\r\ncase 6:return 16;\r\nbreak;\r\ncase 7:return 14;\r\nbreak;\r\ncase 8:return 10;\r\nbreak;\r\ncase 9:return 11;\r\nbreak;\r\ncase 10:return 19;\r\nbreak;\r\ncase 11:return 21;\r\nbreak;\r\ncase 12:return '<=';\r\nbreak;\r\ncase 13:return '>=';\r\nbreak;\r\ncase 14:return '<';\r\nbreak;\r\ncase 15:return '>';\r\nbreak;\r\ncase 16:yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2); return 24;\r\nbreak;\r\ncase 17:return 13;\r\nbreak;\r\ncase 18:return 23;\r\nbreak;\r\ncase 19:return 5;\r\nbreak;\r\ncase 20:return 'INVALID';\r\nbreak;\r\n}\r\n},\r\nrules: [/^(?:\\s+)/i,/^(?:(-?(?:[1-9][0-9]+|[0-9]))\\b)/i,/^(?:OR\\b)/i,/^(?:AND\\b)/i,/^(?:NOT\\b)/i,/^(?:((ALL|NONE|HETATM|PROTEIN|BASIC|ACIDIC|CHARGED|POLAR|NONPOLAR|AROMATIC|NUCLEIC|PURINE|PYRIMIDINE|WATER|POLARH|NONPOLARH))\\b)/i,/^(?:((NAME|ELEM|TYPE|RESIDUE|ICODE|CHAIN|ALTLOC))\\b)/i,/^(?:((SERIAL|SEQUENCE|RESIDX))\\b)/i,/^(?:\\()/i,/^(?:\\))/i,/^(?:,)/i,/^(?::)/i,/^(?:<=)/i,/^(?:>=)/i,/^(?:<)/i,/^(?:>)/i,/^(?:((?:\"(?:\\\\.|[^\\\\\"])*\"|'(?:\\\\.|[^\\\\'])*')))/i,/^(?:(@[_A-Z0-9]+))/i,/^(?:([_A-Z0-9]+))/i,/^(?:$)/i,/^(?:.)/i],\r\nconditions: {\"INITIAL\":{\"rules\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],\"inclusive\":true}}\r\n});\r\nreturn lexer;\r\n})();\r\nparser.lexer = lexer;\r\nfunction Parser () {\r\n this.yy = {};\r\n}\r\nParser.prototype = parser;parser.Parser = Parser;\r\nreturn new Parser;\r\n})();\r\n\r\nmodule.exports = {parser: parser};\r\n","\r\n/*\r\nSmooth.js version 0.1.7\r\n\r\nTurn arrays into smooth functions.\r\n\r\nCopyright 2012 Spencer Cohen\r\nLicensed under MIT license (see \"Smooth.js MIT license.txt\")\r\n*/\r\n\r\n/*Constants (these are accessible by Smooth.WHATEVER in user space)\r\n*/\r\n\r\n(function() {\r\n var AbstractInterpolator, CubicInterpolator, Enum, LinearInterpolator, NearestInterpolator, PI, SincFilterInterpolator, Smooth, clipClamp, clipMirror, clipPeriodic, defaultConfig, getColumn, getType, isValidNumber, k, makeLanczosWindow, makeScaledFunction, makeSincKernel, normalizeScaleTo, shallowCopy, sin, sinc, v, validateNumber, validateVector,\r\n __hasProp = Object.prototype.hasOwnProperty,\r\n __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor; child.__super__ = parent.prototype; return child; };\r\n\r\n Enum = {\r\n /*Interpolation methods\r\n */\r\n METHOD_NEAREST: 'nearest',\r\n METHOD_LINEAR: 'linear',\r\n METHOD_CUBIC: 'cubic',\r\n METHOD_LANCZOS: 'lanczos',\r\n METHOD_SINC: 'sinc',\r\n /*Input clipping modes\r\n */\r\n CLIP_CLAMP: 'clamp',\r\n CLIP_ZERO: 'zero',\r\n CLIP_PERIODIC: 'periodic',\r\n CLIP_MIRROR: 'mirror',\r\n /* Constants for control over the cubic interpolation tension\r\n */\r\n CUBIC_TENSION_DEFAULT: 0,\r\n CUBIC_TENSION_CATMULL_ROM: 0\r\n };\r\n\r\n defaultConfig = {\r\n method: Enum.METHOD_CUBIC,\r\n cubicTension: Enum.CUBIC_TENSION_DEFAULT,\r\n clip: Enum.CLIP_CLAMP,\r\n scaleTo: 0,\r\n sincFilterSize: 2,\r\n sincWindow: void 0\r\n };\r\n\r\n /*Index clipping functions\r\n */\r\n\r\n clipClamp = function(i, n) {\r\n return Math.max(0, Math.min(i, n - 1));\r\n };\r\n\r\n clipPeriodic = function(i, n) {\r\n i = i % n;\r\n if (i < 0) i += n;\r\n return i;\r\n };\r\n\r\n clipMirror = function(i, n) {\r\n var period;\r\n period = 2 * (n - 1);\r\n i = clipPeriodic(i, period);\r\n if (i > n - 1) i = period - i;\r\n return i;\r\n };\r\n\r\n /*\r\n Abstract scalar interpolation class which provides common functionality for all interpolators\r\n \r\n Subclasses must override interpolate().\r\n */\r\n\r\n AbstractInterpolator = (function() {\r\n\r\n function AbstractInterpolator(array, config) {\r\n this.array = array.slice(0);\r\n this.length = this.array.length;\r\n if (!(this.clipHelper = {\r\n clamp: this.clipHelperClamp,\r\n zero: this.clipHelperZero,\r\n periodic: this.clipHelperPeriodic,\r\n mirror: this.clipHelperMirror\r\n }[config.clip])) {\r\n throw \"Invalid clip: \" + config.clip;\r\n }\r\n }\r\n\r\n AbstractInterpolator.prototype.getClippedInput = function(i) {\r\n if ((0 <= i && i < this.length)) {\r\n return this.array[i];\r\n } else {\r\n return this.clipHelper(i);\r\n }\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperClamp = function(i) {\r\n return this.array[clipClamp(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperZero = function(i) {\r\n return 0;\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperPeriodic = function(i) {\r\n return this.array[clipPeriodic(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.clipHelperMirror = function(i) {\r\n return this.array[clipMirror(i, this.length)];\r\n };\r\n\r\n AbstractInterpolator.prototype.interpolate = function(t) {\r\n throw 'Subclasses of AbstractInterpolator must override the interpolate() method.';\r\n };\r\n\r\n return AbstractInterpolator;\r\n\r\n })();\r\n\r\n NearestInterpolator = (function(_super) {\r\n\r\n __extends(NearestInterpolator, _super);\r\n\r\n function NearestInterpolator() {\r\n NearestInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n NearestInterpolator.prototype.interpolate = function(t) {\r\n return this.getClippedInput(Math.round(t));\r\n };\r\n\r\n return NearestInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n LinearInterpolator = (function(_super) {\r\n\r\n __extends(LinearInterpolator, _super);\r\n\r\n function LinearInterpolator() {\r\n LinearInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n LinearInterpolator.prototype.interpolate = function(t) {\r\n var k;\r\n k = Math.floor(t);\r\n t -= k;\r\n return (1 - t) * this.getClippedInput(k) + t * this.getClippedInput(k + 1);\r\n };\r\n\r\n return LinearInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n CubicInterpolator = (function(_super) {\r\n\r\n __extends(CubicInterpolator, _super);\r\n\r\n function CubicInterpolator(array, config) {\r\n this.tangentFactor = 1 - Math.max(-1, Math.min(1, config.cubicTension));\r\n CubicInterpolator.__super__.constructor.apply(this, arguments);\r\n }\r\n\r\n CubicInterpolator.prototype.getTangent = function(k) {\r\n return this.tangentFactor * (this.getClippedInput(k + 1) - this.getClippedInput(k - 1)) / 2;\r\n };\r\n\r\n CubicInterpolator.prototype.interpolate = function(t) {\r\n var k, m, p, t2, t3;\r\n k = Math.floor(t);\r\n m = [this.getTangent(k), this.getTangent(k + 1)];\r\n p = [this.getClippedInput(k), this.getClippedInput(k + 1)];\r\n t -= k;\r\n t2 = t * t;\r\n t3 = t * t2;\r\n return (2 * t3 - 3 * t2 + 1) * p[0] + (t3 - 2 * t2 + t) * m[0] + (-2 * t3 + 3 * t2) * p[1] + (t3 - t2) * m[1];\r\n };\r\n\r\n return CubicInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n sin = Math.sin, PI = Math.PI;\r\n\r\n sinc = function(x) {\r\n if (x === 0) {\r\n return 1;\r\n } else {\r\n return sin(PI * x) / (PI * x);\r\n }\r\n };\r\n\r\n makeLanczosWindow = function(a) {\r\n return function(x) {\r\n return sinc(x / a);\r\n };\r\n };\r\n\r\n makeSincKernel = function(window) {\r\n return function(x) {\r\n return sinc(x) * window(x);\r\n };\r\n };\r\n\r\n SincFilterInterpolator = (function(_super) {\r\n\r\n __extends(SincFilterInterpolator, _super);\r\n\r\n function SincFilterInterpolator(array, config) {\r\n SincFilterInterpolator.__super__.constructor.apply(this, arguments);\r\n this.a = config.sincFilterSize;\r\n if (!config.sincWindow) throw 'No sincWindow provided';\r\n this.kernel = makeSincKernel(config.sincWindow);\r\n }\r\n\r\n SincFilterInterpolator.prototype.interpolate = function(t) {\r\n var k, n, sum, _ref, _ref2;\r\n k = Math.floor(t);\r\n sum = 0;\r\n for (n = _ref = k - this.a + 1, _ref2 = k + this.a; _ref <= _ref2 ? n <= _ref2 : n >= _ref2; _ref <= _ref2 ? n++ : n--) {\r\n sum += this.kernel(t - n) * this.getClippedInput(n);\r\n }\r\n return sum;\r\n };\r\n\r\n return SincFilterInterpolator;\r\n\r\n })(AbstractInterpolator);\r\n\r\n getColumn = function(arr, i) {\r\n var row, _i, _len, _results;\r\n _results = [];\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n row = arr[_i];\r\n _results.push(row[i]);\r\n }\r\n return _results;\r\n };\r\n\r\n makeScaledFunction = function(f, baseScale, scaleRange) {\r\n var scaleFactor, translation;\r\n if (scaleRange.join === '0,1') {\r\n return f;\r\n } else {\r\n scaleFactor = baseScale / (scaleRange[1] - scaleRange[0]);\r\n translation = scaleRange[0];\r\n return function(t) {\r\n return f(scaleFactor * (t - translation));\r\n };\r\n }\r\n };\r\n\r\n getType = function(x) {\r\n return Object.prototype.toString.call(x).slice('[object '.length, -1);\r\n };\r\n\r\n validateNumber = function(n) {\r\n if (isNaN(n)) throw 'NaN in Smooth() input';\r\n if (getType(n) !== 'Number') throw 'Non-number in Smooth() input';\r\n if (!isFinite(n)) throw 'Infinity in Smooth() input';\r\n };\r\n\r\n validateVector = function(v, dimension) {\r\n var n, _i, _len;\r\n if (getType(v) !== 'Array') throw 'Non-vector in Smooth() input';\r\n if (v.length !== dimension) throw 'Inconsistent dimension in Smooth() input';\r\n for (_i = 0, _len = v.length; _i < _len; _i++) {\r\n n = v[_i];\r\n validateNumber(n);\r\n }\r\n };\r\n\r\n isValidNumber = function(n) {\r\n return (getType(n) === 'Number') && isFinite(n) && !isNaN(n);\r\n };\r\n\r\n normalizeScaleTo = function(s) {\r\n var invalidErr;\r\n invalidErr = \"scaleTo param must be number or array of two numbers\";\r\n switch (getType(s)) {\r\n case 'Number':\r\n if (!isValidNumber(s)) throw invalidErr;\r\n s = [0, s];\r\n break;\r\n case 'Array':\r\n if (s.length !== 2) throw invalidErr;\r\n if (!(isValidNumber(s[0]) && isValidNumber(s[1]))) throw invalidErr;\r\n break;\r\n default:\r\n throw invalidErr;\r\n }\r\n return s;\r\n };\r\n\r\n shallowCopy = function(obj) {\r\n var copy, k, v;\r\n copy = {};\r\n for (k in obj) {\r\n if (!__hasProp.call(obj, k)) continue;\r\n v = obj[k];\r\n copy[k] = v;\r\n }\r\n return copy;\r\n };\r\n\r\n Smooth = function(arr, config) {\r\n var baseDomainEnd, dimension, i, interpolator, interpolatorClass, interpolators, k, n, properties, smoothFunc, v;\r\n if (config == null) config = {};\r\n properties = {};\r\n config = shallowCopy(config);\r\n properties.config = shallowCopy(config);\r\n if (config.scaleTo == null) config.scaleTo = config.period;\r\n if (config.sincFilterSize == null) {\r\n config.sincFilterSize = config.lanczosFilterSize;\r\n }\r\n for (k in defaultConfig) {\r\n if (!__hasProp.call(defaultConfig, k)) continue;\r\n v = defaultConfig[k];\r\n if (config[k] == null) config[k] = v;\r\n }\r\n if (!(interpolatorClass = {\r\n nearest: NearestInterpolator,\r\n linear: LinearInterpolator,\r\n cubic: CubicInterpolator,\r\n lanczos: SincFilterInterpolator,\r\n sinc: SincFilterInterpolator\r\n }[config.method])) {\r\n throw \"Invalid method: \" + config.method;\r\n }\r\n if (config.method === 'lanczos') {\r\n config.sincWindow = makeLanczosWindow(config.sincFilterSize);\r\n }\r\n if (arr.length < 2) throw 'Array must have at least two elements';\r\n properties.count = arr.length;\r\n smoothFunc = (function() {\r\n var _i, _j, _len, _len2;\r\n switch (getType(arr[0])) {\r\n case 'Number':\r\n properties.dimension = 'scalar';\r\n if (Smooth.deepValidation) {\r\n for (_i = 0, _len = arr.length; _i < _len; _i++) {\r\n n = arr[_i];\r\n validateNumber(n);\r\n }\r\n }\r\n interpolator = new interpolatorClass(arr, config);\r\n return function(t) {\r\n return interpolator.interpolate(t);\r\n };\r\n case 'Array':\r\n properties.dimension = dimension = arr[0].length;\r\n if (!dimension) throw 'Vectors must be non-empty';\r\n if (Smooth.deepValidation) {\r\n for (_j = 0, _len2 = arr.length; _j < _len2; _j++) {\r\n v = arr[_j];\r\n validateVector(v, dimension);\r\n }\r\n }\r\n interpolators = (function() {\r\n var _results;\r\n _results = [];\r\n for (i = 0; 0 <= dimension ? i < dimension : i > dimension; 0 <= dimension ? i++ : i--) {\r\n _results.push(new interpolatorClass(getColumn(arr, i), config));\r\n }\r\n return _results;\r\n })();\r\n return function(t) {\r\n var interpolator, _k, _len3, _results;\r\n _results = [];\r\n for (_k = 0, _len3 = interpolators.length; _k < _len3; _k++) {\r\n interpolator = interpolators[_k];\r\n _results.push(interpolator.interpolate(t));\r\n }\r\n return _results;\r\n };\r\n default:\r\n throw \"Invalid element type: \" + (getType(arr[0]));\r\n }\r\n })();\r\n if (config.clip === 'periodic') {\r\n baseDomainEnd = arr.length;\r\n } else {\r\n baseDomainEnd = arr.length - 1;\r\n }\r\n config.scaleTo || (config.scaleTo = baseDomainEnd);\r\n properties.domain = normalizeScaleTo(config.scaleTo);\r\n smoothFunc = makeScaledFunction(smoothFunc, baseDomainEnd, properties.domain);\r\n properties.domain.sort();\r\n /*copy properties\r\n */\r\n for (k in properties) {\r\n if (!__hasProp.call(properties, k)) continue;\r\n v = properties[k];\r\n smoothFunc[k] = v;\r\n }\r\n return smoothFunc;\r\n };\r\n\r\n for (k in Enum) {\r\n if (!__hasProp.call(Enum, k)) continue;\r\n v = Enum[k];\r\n Smooth[k] = v;\r\n }\r\n\r\n Smooth.deepValidation = true;\r\n\r\n (typeof exports !== \"undefined\" && exports !== null ? exports : window).Smooth = Smooth;\r\n\r\n}).call(this);\r\n","!function(r,t){if(\"function\"==typeof define&&define.amd)define([\"exports\"],t);else if(\"object\"==typeof exports&&\"undefined\"!=typeof module)t(exports);else t(r.MMTF=r.MMTF||{})}(this,function(r){\"use strict\";function t(r,t,n){for(var e=(r.byteLength,0),i=n.length;i>e;e++){var o=n.charCodeAt(e);if(128>o)r.setUint8(t++,o>>>0&127|0);else if(2048>o)r.setUint8(t++,o>>>6&31|192),r.setUint8(t++,o>>>0&63|128);else if(65536>o)r.setUint8(t++,o>>>12&15|224),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128);else{if(!(1114112>o))throw new Error(\"bad codepoint \"+o);r.setUint8(t++,o>>>18&7|240),r.setUint8(t++,o>>>12&63|128),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128)}}}function n(r){for(var t=0,n=0,e=r.length;e>n;n++){var i=r.charCodeAt(n);if(128>i)t+=1;else if(2048>i)t+=2;else if(65536>i)t+=3;else{if(!(1114112>i))throw new Error(\"bad codepoint \"+i);t+=4}}return t}function e(r,i,o){var a=typeof r;if(\"string\"===a){var u=n(r);if(32>u)return i.setUint8(o,160|u),t(i,o+1,r),1+u;if(256>u)return i.setUint8(o,217),i.setUint8(o+1,u),t(i,o+2,r),2+u;if(65536>u)return 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'50%',\n left: '50%',\n shadow: '0 0 1px transparent', // prevent aliased lines\n position: 'absolute',\n};\nvar Spinner = /** @class */ (function () {\n function Spinner(opts) {\n if (opts === void 0) { opts = {}; }\n this.opts = __assign(__assign({}, defaults), opts);\n }\n /**\n * Adds the spinner to the given target element. If this instance is already\n * spinning, it is automatically removed from its previous target by calling\n * stop() internally.\n */\n Spinner.prototype.spin = function (target) {\n this.stop();\n this.el = document.createElement('div');\n this.el.className = this.opts.className;\n this.el.setAttribute('role', 'progressbar');\n this.el.style.position = this.opts.position;\n this.el.style.width = \"0\";\n this.el.style.zIndex = this.opts.zIndex.toString();\n this.el.style.left = this.opts.left;\n this.el.style.top = this.opts.top;\n this.el.style.transform = \"scale(\".concat(this.opts.scale, \")\");\n if (target) {\n target.insertBefore(this.el, target.firstChild || null);\n }\n drawLines(this.el, this.opts);\n return this;\n };\n /**\n * Stops and removes the Spinner.\n * Stopped spinners may be reused by calling spin() again.\n */\n Spinner.prototype.stop = function () {\n if (this.el) {\n if (this.el.parentNode) {\n this.el.parentNode.removeChild(this.el);\n }\n this.el = undefined;\n }\n return this;\n };\n return Spinner;\n}());\nexport { Spinner };\n/**\n * Returns the line color from the given string or array.\n */\nfunction getColor(color, idx) {\n return typeof color == 'string' ? color : color[idx % color.length];\n}\n/**\n * Internal method that draws the individual lines.\n */\nfunction drawLines(el, opts) {\n var borderRadius = (Math.round(opts.corners * opts.width * 500) / 1000) + 'px';\n var shadow = 'none';\n if (opts.shadow === true) {\n shadow = '0 2px 4px #000'; // default shadow\n }\n else if (typeof opts.shadow === 'string') {\n shadow = opts.shadow;\n }\n var shadows = parseBoxShadow(shadow);\n for (var i = 0; i < opts.lines; i++) {\n var degrees = ~~(360 / opts.lines * i + opts.rotate);\n var backgroundLine = document.createElement('div');\n backgroundLine.style.position = 'absolute';\n backgroundLine.style.top = \"\".concat(-opts.width / 2, \"px\");\n backgroundLine.style.width = (opts.length + opts.width) + 'px';\n backgroundLine.style.height = opts.width + 'px';\n backgroundLine.style.background = getColor(opts.fadeColor, i);\n backgroundLine.style.borderRadius = borderRadius;\n backgroundLine.style.transformOrigin = 'left';\n backgroundLine.style.transform = \"rotate(\".concat(degrees, \"deg) translateX(\").concat(opts.radius, \"px)\");\n var delay = i * opts.direction / opts.lines / opts.speed;\n delay -= 1 / opts.speed; // so initial animation state will include trail\n var line = document.createElement('div');\n line.style.width = '100%';\n line.style.height = '100%';\n line.style.background = getColor(opts.color, i);\n line.style.borderRadius = borderRadius;\n line.style.boxShadow = normalizeShadow(shadows, degrees);\n line.style.animation = \"\".concat(1 / opts.speed, \"s linear \").concat(delay, \"s infinite \").concat(opts.animation);\n backgroundLine.appendChild(line);\n el.appendChild(backgroundLine);\n }\n}\nfunction parseBoxShadow(boxShadow) {\n var regex = /^\\s*([a-zA-Z]+\\s+)?(-?\\d+(\\.\\d+)?)([a-zA-Z]*)\\s+(-?\\d+(\\.\\d+)?)([a-zA-Z]*)(.*)$/;\n var shadows = [];\n for (var _i = 0, _a = boxShadow.split(','); _i < _a.length; _i++) {\n var shadow = _a[_i];\n var matches = shadow.match(regex);\n if (matches === null) {\n continue; // invalid syntax\n }\n var x = +matches[2];\n var y = +matches[5];\n var xUnits = matches[4];\n var yUnits = matches[7];\n if (x === 0 && !xUnits) {\n xUnits = yUnits;\n }\n if (y === 0 && !yUnits) {\n yUnits = xUnits;\n }\n if (xUnits !== yUnits) {\n continue; // units must match to use as coordinates\n }\n shadows.push({\n prefix: matches[1] || '', // could have value of 'inset' or undefined\n x: x,\n y: y,\n xUnits: xUnits,\n yUnits: yUnits,\n end: matches[8],\n });\n }\n return shadows;\n}\n/**\n * Modify box-shadow x/y offsets to counteract rotation\n */\nfunction normalizeShadow(shadows, degrees) {\n var normalized = [];\n for (var _i = 0, shadows_1 = shadows; _i < shadows_1.length; _i++) {\n var shadow = shadows_1[_i];\n var xy = convertOffset(shadow.x, shadow.y, degrees);\n normalized.push(shadow.prefix + xy[0] + shadow.xUnits + ' ' + xy[1] + shadow.yUnits + shadow.end);\n }\n return normalized.join(', ');\n}\nfunction convertOffset(x, y, degrees) {\n var radians = degrees * Math.PI / 180;\n var sin = Math.sin(radians);\n var cos = Math.cos(radians);\n return [\n Math.round((x * cos + y * sin) * 1000) / 1000,\n Math.round((-x * sin + y * cos) * 1000) / 1000,\n ];\n}\n","//----------------------------------------------------------------------------\r\n// Timer\r\n\r\nexport default class Timer {\r\n constructor() {\r\n this.startTime = 0;\r\n this.oldTime = 0;\r\n this.elapsedTime = 0;\r\n this.running = false;\r\n }\r\n\r\n start() {\r\n this.startTime = Timer.now();\r\n this.oldTime = this.startTime;\r\n this.running = true;\r\n }\r\n\r\n stop() {\r\n this.getElapsedTime();\r\n this.running = false;\r\n }\r\n\r\n getElapsedTime() {\r\n this.update();\r\n return this.elapsedTime;\r\n }\r\n\r\n update() {\r\n let delta = 0;\r\n if (this.running) {\r\n const newTime = Timer.now();\r\n delta = 0.001 * (newTime - this.oldTime);\r\n this.oldTime = newTime;\r\n this.elapsedTime += delta;\r\n }\r\n\r\n return delta;\r\n }\r\n}\r\n\r\nTimer.now = (function () {\r\n const p = typeof window !== 'undefined' && window.performance;\r\n return (p && p.now) ? p.now.bind(p) : Date.now;\r\n}());\r\n","import Timer from '../Timer';\r\n\r\nconst { now } = Timer;\r\n\r\nfunction createElement(tag, id, css) {\r\n const element = document.createElement(tag);\r\n element.id = id;\r\n element.style.cssText = css;\r\n return element;\r\n}\r\n\r\nclass Stats {\r\n constructor() {\r\n this.domElement = createElement('div', 'stats', 'padding:8px');\r\n this._text = createElement('p', 'fps', 'margin:0;color:silver;font-size:large');\r\n this.domElement.appendChild(this._text);\r\n\r\n this._startTime = now();\r\n this._prevTime = this._startTime;\r\n\r\n this._deltas = new Array(20);\r\n this._index = 0;\r\n this._total = 0.0;\r\n this._count = 0;\r\n }\r\n\r\n end() {\r\n const time = now();\r\n const delta = time - this._startTime;\r\n\r\n if (this._count < this._deltas.length) {\r\n this._count++;\r\n } else {\r\n this._total -= this._deltas[this._index];\r\n }\r\n this._total += delta;\r\n this._deltas[this._index] = delta;\r\n this._index = (this._index + 1) % this._deltas.length;\r\n\r\n this.ms = this._total / this._count;\r\n this.fps = 1000 / this.ms;\r\n\r\n if (time > this._prevTime + 1000) {\r\n this._text.textContent = this.fps.toPrecision(2);\r\n this._prevTime = time;\r\n }\r\n\r\n return time;\r\n }\r\n\r\n update() {\r\n this._startTime = this.end();\r\n }\r\n\r\n show(on) {\r\n if (on === undefined) {\r\n on = true;\r\n }\r\n this.domElement.style.display = on ? 'block' : 'none';\r\n }\r\n}\r\n\r\nexport default Stats;\r\n","/**\r\n * This class introduces the simplest event system.\r\n */\r\n\r\nimport _ from 'lodash';\r\n\r\nfunction isUndefOrEqual(param, value) {\r\n return !param || param === value;\r\n}\r\n\r\n/**\r\n * Creates empty dispatcher.\r\n *\r\n * @exports EventDispatcher\r\n * @constructor\r\n */\r\nfunction EventDispatcher() {\r\n this._handlers = {};\r\n}\r\n\r\n/**\r\n * Binds callback on specific event type. Optional `context` parameter\r\n * could be used as 'this' for the `callback`.\r\n * @param {string} type Event name.\r\n * @param {function} callback Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.addEventListener = function (type, callback, context) {\r\n let handlers = this._handlers[type];\r\n\r\n if (!handlers) {\r\n this._handlers[type] = [];\r\n handlers = this._handlers[type];\r\n }\r\n\r\n const params = [callback, context];\r\n function _checkPar(par) {\r\n return par[0] === params[0] && par[1] === params[1];\r\n }\r\n\r\n if (_.find(handlers, _checkPar) === undefined) {\r\n handlers.push(params);\r\n }\r\n};\r\n\r\n/**\r\n * Removes a previously-bound callback function from an object.\r\n * If no `context` is specified, all versions of the `callback` with different\r\n * contexts will be removed.\r\n * If no `callback` is specified, all callbacks of the `type` will be removed.\r\n * If no `type` is specified, callbacks for all events will be removed.\r\n * @param {?string} [type] Event type.\r\n * @param {function} [callback] Callback function.\r\n * @param {Object} [context] 'This' object for the callback.\r\n */\r\nEventDispatcher.prototype.removeEventListener = function (type, callback, context) {\r\n const self = this;\r\n _.forEach(self._handlers, (handler, ev) => {\r\n _.remove(handler, (values) => isUndefOrEqual(type, ev)\r\n && isUndefOrEqual(callback, values[0])\r\n && isUndefOrEqual(context, values[1] || self));\r\n });\r\n\r\n this._handlers = _.omitBy(self._handlers, (handler) => handler.length === 0);\r\n};\r\n\r\n/**\r\n * Makes all the callbacks for the specific `event` to trigger.\r\n * @param {Object} event Event.\r\n * @param {string} event.type Type of the event.\r\n */\r\nEventDispatcher.prototype.dispatchEvent = function (event) {\r\n const self = this;\r\n\r\n _.forEach(this._handlers[event.type], (callback) => {\r\n const context = callback[1] || self;\r\n callback[0].apply(context, [event]);\r\n });\r\n};\r\n\r\nexport default EventDispatcher;\r\n","/**\r\n * This module contains class for logging.\r\n * Returns an instance of a logger that have already been created.\r\n * Allows users to log messages for five different levels,\r\n * enable console output and catch signal on each message.\r\n */\r\nimport _ from 'lodash';\r\nimport EventDispatcher from './EventDispatcher';\r\n\r\nconst priorities = {\r\n debug: 0,\r\n info: 1,\r\n report: 2,\r\n warn: 3,\r\n error: 4,\r\n};\r\n\r\n/**\r\n * Create new Logger.\r\n *\r\n * @exports Logger\r\n * @extends EventDispatcher\r\n * @constructor\r\n */\r\nfunction Logger() {\r\n EventDispatcher.call(this);\r\n /** Boolean flag that toggles output to browser console.\r\n * @type {boolean}\r\n */\r\n this.console = false;\r\n this._priority = priorities.warn;\r\n}\r\n\r\nLogger.prototype = Object.create(EventDispatcher.prototype);\r\nLogger.prototype.constructor = Logger;\r\n\r\n/**\r\n * Create new clean instance of the logger.\r\n * @returns {Logger}\r\n */\r\nLogger.prototype.instantiate = function () {\r\n return new Logger();\r\n};\r\n\r\nfunction verify(number) {\r\n if (!_.isNumber(number)) {\r\n throw new Error('Wrong log level specified!');\r\n }\r\n return number;\r\n}\r\n\r\n/**\r\n * @property {string} current threshold for signals and console output.\r\n * @name Logger#level\r\n */\r\nObject.defineProperty(Logger.prototype, 'level', {\r\n get() {\r\n return _.findKey(priorities, (value) => value === this._priority);\r\n },\r\n set(level) {\r\n this._priority = verify(priorities[level]);\r\n },\r\n});\r\n\r\n/**\r\n * Returns the list of all possible level values.\r\n * @returns {Array}\r\n */\r\nLogger.prototype.levels = function () {\r\n return Object.keys(priorities);\r\n};\r\n\r\n/**\r\n * Add new message with specified level.\r\n * @param {string} level - level of the message, must be one of the\r\n * {'debug' | 'info' | 'report' | 'warn' | 'error'}\r\n * @param {string} message\r\n */\r\nLogger.prototype.message = function (level, message) {\r\n const priority = verify(priorities[level]);\r\n this._message(priority, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('debug', ...);\r\n * @param message\r\n */\r\nLogger.prototype.debug = function (message) {\r\n this._message(priorities.debug, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('info', ...);\r\n * @param message\r\n */\r\nLogger.prototype.info = function (message) {\r\n this._message(priorities.info, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('report', ...);\r\n * @param message\r\n */\r\nLogger.prototype.report = function (message) {\r\n this._message(priorities.report, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('warn', ...);\r\n * @param message\r\n */\r\nLogger.prototype.warn = function (message) {\r\n this._message(priorities.warn, message);\r\n};\r\n\r\n/**\r\n * Shortcut for message('error', ...);\r\n * @param message\r\n */\r\nLogger.prototype.error = function (message) {\r\n this._message(priorities.error, message);\r\n};\r\n\r\n/**\r\n * Add new message with specified priority.\r\n * @param {number} priority - priority of the message\r\n * @param {string} message\r\n * @private\r\n */\r\nLogger.prototype._message = function (priority, message) {\r\n if (priority < this._priority) {\r\n return;\r\n }\r\n const level = _.findKey(priorities, (value) => value === priority);\r\n message = String(message);\r\n if (this.console) {\r\n const output = `miew:${level}: ${message}`;\r\n if (level === 'error') {\r\n console.error(output); // NOSONAR\r\n } else if (level === 'warn') {\r\n console.warn(output); // NOSONAR\r\n } else {\r\n console.log(output); // NOSONAR\r\n }\r\n }\r\n this.dispatchEvent({ type: 'message', level, message });\r\n};\r\n\r\nexport default new Logger();\r\n","import _ from 'lodash';\r\nimport logger from './utils/logger';\r\n\r\nconst browserType = {\r\n DEFAULT: 0,\r\n SAFARI: 1,\r\n};\r\n//----------------------------------------------------------------------------\r\n// Query string\r\n\r\n/**\r\n * Escape only dangerous chars in a query string component, use a plus instead of a space.\r\n *\r\n * [RFC 3986](https://tools.ietf.org/html/rfc3986) allows the following chars in the query (see 3.4):\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! $ & ' ( ) * + , ; = : @ / ?\r\n *\r\n * For query string elements we need to escape ampersand, equal sign, and plus,\r\n * but encodeURIComponent() function encodes anything except for the following:\r\n *\r\n * A-Z a-z 0-9 - _ . ~ ! ' ( ) *\r\n *\r\n * @param {string} text - key or value to encode\r\n * @param {string} excludeExp - regexp for symbols to exclude from encoding\r\n * @returns {string} encoded string\r\n */\r\nfunction encodeQueryComponent(text, excludeExp) {\r\n const encode = (code) => String.fromCharCode(parseInt(code.substr(1), 16));\r\n return encodeURIComponent(text).replace(excludeExp, encode).replace(/%20/g, '+');\r\n}\r\n\r\n/**\r\n * Unescape dangerous chars in a query string component.\r\n *\r\n * @param {string} text - encoded key or value\r\n * @returns {string} decoded string\r\n * @see {@link encodeQueryComponent}\r\n */\r\nfunction decodeQueryComponent(text) {\r\n return decodeURIComponent(text.replace(/\\+/g, ' '));\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Array} array of (key, value) pairs.\r\n */\r\nfunction getUrlParameters(url) {\r\n url = url || window.location.search;\r\n\r\n const query = url.substring(url.indexOf('?') + 1);\r\n const search = /([^&=]+)=?([^&]*)/g;\r\n const result = [];\r\n let match;\r\n\r\n while ((match = search.exec(query)) !== null) { // eslint-disable-line no-cond-assign\r\n result.push([decodeQueryComponent(match[1]), decodeQueryComponent(match[2])]);\r\n }\r\n\r\n return result;\r\n}\r\n\r\n/**\r\n * Parse URL and extract an array of parameters as a hash.\r\n * @param {string?} url - URL or query string to parse\r\n * @returns {Object}\r\n */\r\nfunction getUrlParametersAsDict(url) {\r\n const result = {};\r\n const a = getUrlParameters(url);\r\n for (let i = 0; i < a.length; ++i) {\r\n const [key, value] = a[i];\r\n result[key] = value;\r\n }\r\n return result;\r\n}\r\n\r\nfunction resolveURL(str) {\r\n if (typeof URL !== 'undefined') {\r\n try {\r\n if (typeof window !== 'undefined') {\r\n return new URL(str, window.location).href;\r\n }\r\n return new URL(str).href;\r\n } catch {\r\n // IE 11 has a URL object with no constructor available so just try a different approach instead\r\n }\r\n }\r\n if (typeof document !== 'undefined') {\r\n const anchor = document.createElement('a');\r\n anchor.href = str;\r\n return anchor.href;\r\n }\r\n return str;\r\n}\r\n\r\n/**\r\n * Generates regular expression object that includes all symbols\r\n * listed in the argument\r\n * @param symbolStr {string} - String containing characters list.\r\n * @returns {RegExp} - Regular expression.\r\n */\r\nfunction generateRegExp(symbolStr) {\r\n const symbolList = [];\r\n\r\n for (let i = 0, n = symbolStr.length; i < n; ++i) {\r\n symbolList[symbolList.length] = symbolStr[i].charCodeAt(0).toString(16);\r\n }\r\n\r\n const listStr = symbolList.join('|');\r\n\r\n return new RegExp(`%(?:${listStr})`, 'gi');\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Create HTML element\r\n\r\nfunction createElement(tag, attrs, content) {\r\n const element = document.createElement(tag);\r\n let i;\r\n let n;\r\n if (attrs) {\r\n const keys = Object.keys(attrs);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n element.setAttribute(key, attrs[key]);\r\n }\r\n }\r\n if (content) {\r\n if (!(content instanceof Array)) {\r\n content = [content];\r\n }\r\n for (i = 0, n = content.length; i < n; ++i) {\r\n const child = content[i];\r\n if (typeof child === 'string') {\r\n element.appendChild(document.createTextNode(child));\r\n } else if (child instanceof HTMLElement) {\r\n element.appendChild(child);\r\n }\r\n }\r\n }\r\n return element;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Easy inheritance\r\n\r\n/**\r\n * Derive the class from the base.\r\n * @param cls {function} - Class (constructor) to derive.\r\n * @param base {function} - Class (constructor) to derive from.\r\n * @param members {object=} - Optional instance members to add.\r\n * @param statics {object=} - Optional static class members to add.\r\n * @returns {function} Original class.\r\n */\r\nfunction deriveClass(cls, base, members, statics) {\r\n cls.prototype = _.assign(Object.create(base.prototype), { constructor: cls }, members);\r\n if (statics) {\r\n _.assign(cls, statics);\r\n }\r\n return cls;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Deep prototyping\r\n\r\nfunction deriveDeep(obj, needZeroOwnProperties) {\r\n let res = obj;\r\n let i;\r\n let n;\r\n if (obj instanceof Array) {\r\n res = new Array(obj.length);\r\n for (i = 0, n = obj.length; i < n; ++i) {\r\n res[i] = deriveDeep(obj[i]);\r\n }\r\n } else if (obj instanceof Object) {\r\n res = Object.create(obj);\r\n const keys = Object.keys(obj);\r\n for (i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = obj[key];\r\n const copy = deriveDeep(value);\r\n if (copy !== value) {\r\n res[key] = copy;\r\n }\r\n }\r\n if (needZeroOwnProperties && Object.keys(res).length > 0) {\r\n res = Object.create(res);\r\n }\r\n }\r\n return res;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Colors\r\n\r\nfunction hexColor(color) {\r\n const hex = (`0000000${color.toString(16)}`).substr(-6);\r\n return `#${hex}`;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Debug tracing\r\n\r\nfunction DebugTracer(namespace) {\r\n let enabled = false;\r\n\r\n this.enable = function (on) {\r\n enabled = on;\r\n };\r\n\r\n let indent = 0;\r\n const methods = Object.keys(namespace);\r\n\r\n function wrap(method_, name_) {\r\n return function (...args) {\r\n const spaces = DebugTracer.spaces.substr(0, indent * 2);\r\n if (enabled) {\r\n logger.debug(`${spaces + name_} {`);\r\n }\r\n indent++;\r\n const result = method_.apply(this, args);\r\n indent--;\r\n if (enabled) {\r\n logger.debug(`${spaces}} // ${name_}`);\r\n }\r\n return result;\r\n };\r\n }\r\n\r\n for (let i = 0, n = methods.length; i < n; ++i) {\r\n const name = methods[i];\r\n const method = namespace[name];\r\n if (method instanceof Function && name !== 'constructor') {\r\n namespace[name] = wrap(method, name);\r\n }\r\n }\r\n}\r\n\r\nDebugTracer.spaces = ' ';\r\n\r\nclass OutOfMemoryError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'OutOfMemoryError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction allocateTyped(TypedArrayName, size) {\r\n let result = null;\r\n try {\r\n result = new TypedArrayName(size);\r\n } catch (e) {\r\n if (e instanceof RangeError) {\r\n throw new OutOfMemoryError(e.message);\r\n } else {\r\n throw e;\r\n }\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Float array conversion\r\n\r\nfunction bytesToBase64(/** ArrayBuffer */ buffer) {\r\n const bytes = new Uint8Array(buffer);\r\n let binary = '';\r\n for (let i = 0; i < bytes.byteLength; i++) {\r\n binary += String.fromCharCode(bytes[i]);\r\n }\r\n return window.btoa(binary);\r\n}\r\n\r\nfunction bytesFromBase64(/** string */ str) {\r\n const binary = window.atob(str);\r\n const bytes = new Uint8Array(binary.length);\r\n for (let i = 0; i < bytes.length; ++i) {\r\n bytes[i] = binary[i].charCodeAt(0);\r\n }\r\n return bytes.buffer;\r\n}\r\n\r\nfunction arrayToBase64(/** number[] */ array, /** function */ TypedArrayClass) {\r\n return bytesToBase64(new TypedArrayClass(array).buffer);\r\n}\r\n\r\nfunction arrayFromBase64(/** string */ str, /** function */ TypedArrayClass) {\r\n return Array.prototype.slice.call(new TypedArrayClass(bytesFromBase64(str)));\r\n}\r\n\r\n// NOTE: this is 1-level comparison\r\nfunction compareOptionsWithDefaults(opts, defOpts) {\r\n const optsStr = [];\r\n if (defOpts && opts) {\r\n const keys = Object.keys(opts);\r\n for (let p = 0; p < keys.length; ++p) {\r\n const key = keys[p];\r\n const value = opts[key];\r\n // TODO add processing for tree structure\r\n if (!(value instanceof Object) && typeof defOpts[key] !== 'undefined' && defOpts[key] !== value) {\r\n optsStr.push(`${key}:${value}`);\r\n }\r\n }\r\n if (optsStr.length > 0) {\r\n return `!${optsStr.join()}`;\r\n }\r\n }\r\n return '';\r\n}\r\n\r\nfunction isAlmostPlainObject(o) {\r\n if (_.isPlainObject(o)) {\r\n return true;\r\n }\r\n const proto = o && Object.getPrototypeOf(o);\r\n return !!proto && !proto.hasOwnProperty('constructor') && isAlmostPlainObject(proto);\r\n}\r\n\r\n/**\r\n * Build an object that contains properties (and subproperties) of `src` different from those\r\n * in `dst`. Objects are parsed recursively, other values (including arrays) are compared for\r\n * equality using `_.isEqual()`.\r\n * @param {!object} src - a new object to compare, may contain changed or new properties\r\n * @param {!object} dst - an old reference object\r\n */\r\nfunction objectsDiff(src, dst) {\r\n const diff = {};\r\n _.forIn(src, (srcValue, key) => {\r\n const dstValue = dst[key];\r\n if (isAlmostPlainObject(srcValue) && isAlmostPlainObject(dstValue)) {\r\n const deepDiff = objectsDiff(srcValue, dstValue);\r\n if (!_.isEmpty(deepDiff)) {\r\n diff[key] = deepDiff;\r\n }\r\n } else if (!_.isEqual(srcValue, dstValue)) {\r\n diff[key] = srcValue;\r\n }\r\n });\r\n return diff;\r\n}\r\n\r\nfunction forInRecursive(object, callback) {\r\n function iterateThrough(obj, prefix) {\r\n _.forIn(obj, (value, key) => {\r\n const newPref = prefix + (prefix.length > 0 ? '.' : '');\r\n if (value instanceof Object) {\r\n iterateThrough(value, newPref + key);\r\n } else if (value !== undefined) {\r\n callback(value, newPref + key);\r\n }\r\n });\r\n }\r\n iterateThrough(object, '');\r\n}\r\n\r\nfunction enquoteString(value) {\r\n if (_.isString(value)) {\r\n return `\"${value.replace(/\"/g, '\\\\\"')}\"`;\r\n }\r\n return value;\r\n}\r\n\r\nfunction unquoteString(value) {\r\n if (!_.isString(value)) {\r\n return value;\r\n }\r\n if (value[0] === '\"' && value[value.length - 1] === '\"') {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\\"/g, '\"');\r\n }\r\n if (value[0] === \"'\" && value[value.length - 1] === \"'\") {\r\n value = value.slice(1, value.length - 1);\r\n return value.replace(/\\\\'/g, \"'\");\r\n }\r\n throw new SyntaxError('Incorrect string format, can\\'t unqute it');\r\n}\r\n\r\nfunction getFileExtension(fileName) {\r\n return fileName.slice((Math.max(0, fileName.lastIndexOf('.')) || Infinity));\r\n}\r\n\r\nfunction splitFileName(fileName) {\r\n const ext = getFileExtension(fileName);\r\n const name = fileName.slice(0, fileName.length - ext.length);\r\n return [name, ext];\r\n}\r\n\r\nfunction dataUrlToBlob(url) {\r\n const parts = url.split(/[:;,]/);\r\n const partsCount = parts.length;\r\n if (partsCount >= 3 && parts[partsCount - 2] === 'base64') {\r\n return new Blob([bytesFromBase64(parts[partsCount - 1])]);\r\n }\r\n return null;\r\n}\r\n\r\nfunction getBrowser() {\r\n if (navigator.vendor && navigator.vendor.indexOf('Apple') > -1\r\n && navigator.userAgent\r\n && navigator.userAgent.indexOf('CriOS') === -1\r\n && navigator.userAgent.indexOf('FxiOS') === -1) {\r\n return browserType.SAFARI;\r\n }\r\n return browserType.DEFAULT;\r\n}\r\n\r\nfunction shotOpen(url) {\r\n if (typeof window !== 'undefined') {\r\n window.open().document.write(``);\r\n }\r\n}\r\n\r\nfunction shotDownload(dataUrl, filename) {\r\n if (!dataUrl || dataUrl.substr(0, 5) !== 'data:') {\r\n return;\r\n }\r\n if (!filename) {\r\n filename = ['screenshot-', +new Date(), '.png'].join('');\r\n }\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(dataUrlToBlob(dataUrl), filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(dataUrlToBlob(dataUrl));\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction download(data, filename, type) {\r\n const blobData = new Blob([data]);\r\n\r\n if (!filename) {\r\n filename = ['data', +new Date()].join('');\r\n }\r\n\r\n if (!type) {\r\n filename += blobData.type || '.bin';\r\n } else {\r\n filename += `.${type}`;\r\n }\r\n\r\n if (typeof window !== 'undefined' && window.navigator && window.navigator.msSaveBlob) {\r\n window.navigator.msSaveBlob(blobData, filename);\r\n } else if (typeof document !== 'undefined') {\r\n const link = document.createElement('a');\r\n link.download = filename;\r\n link.innerHTML = 'download';\r\n link.href = window.URL.createObjectURL(blobData);\r\n document.body.appendChild(link);\r\n link.click();\r\n document.body.removeChild(link);\r\n }\r\n}\r\n\r\nfunction copySubArrays(src, dst, indices, itemSize) {\r\n for (let i = 0, n = indices.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n dst[i * itemSize + j] = src[indices[i] * itemSize + j];\r\n }\r\n }\r\n}\r\n\r\nfunction shallowCloneNode(node) {\r\n const newNode = node.cloneNode(true);\r\n newNode.worldPos = node.worldPos;\r\n // .style property is readonly, so \"newNode.style = node.style;\" won't work (and we don't need it, right?)\r\n return newNode;\r\n}\r\n\r\nconst unquotedStringRE = /^[a-zA-Z0-9_]*$/;\r\nconst enquoteHelper = ['\"', '', '\"'];\r\n\r\n// verify and correct if needed selctor identifier\r\nfunction correctSelectorIdentifier(value) {\r\n if (unquotedStringRE.test(value)) {\r\n return value;\r\n }\r\n // quote incorrect identifier\r\n enquoteHelper[1] = value;\r\n return enquoteHelper.join('');\r\n}\r\n\r\n/**\r\n * Concatenates two TypedArray. Doesn't check null refs o type equality\r\n * Attention! It must be use very rarely because requires memory reallocation every time. Use MergeTypedArraysUnsafe to\r\n * unite array of subarrays.\r\n * @param{TypedArray} first - destination array\r\n * @param{TypedArray} second - source array\r\n * @returns{TypedArray} resulting concatenated array\r\n */\r\nfunction concatTypedArraysUnsafe(first, second) {\r\n const result = new first.constructor(first.length + second.length);\r\n result.set(first);\r\n result.set(second, first.length);\r\n return result;\r\n}\r\n\r\n/**\r\n * Merges array of TypedArray into TypedArray. Doesn't check null refs o type equality\r\n * @param{array} array - source array of subarrays\r\n * @returns{TypedArray} resulting merged array\r\n */\r\nfunction mergeTypedArraysUnsafe(array) {\r\n if (array.length <= 0) {\r\n return null;\r\n }\r\n // count the size\r\n const size = array.reduce((acc, cur) => acc + cur.length, 0);\r\n // create combined array\r\n const result = new array[0].constructor(size);\r\n for (let i = 0, start = 0; i < array.length; i++) {\r\n const count = array[i].length;\r\n result.set(array[i], start);\r\n start += count;\r\n }\r\n return result;\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n// Exports\r\n\r\nexport default {\r\n browserType,\r\n encodeQueryComponent,\r\n decodeQueryComponent,\r\n getUrlParameters,\r\n getUrlParametersAsDict,\r\n resolveURL,\r\n generateRegExp,\r\n createElement,\r\n deriveClass,\r\n deriveDeep,\r\n hexColor,\r\n DebugTracer,\r\n OutOfMemoryError,\r\n allocateTyped,\r\n bytesFromBase64,\r\n bytesToBase64,\r\n arrayFromBase64,\r\n arrayToBase64,\r\n compareOptionsWithDefaults,\r\n objectsDiff,\r\n forInRecursive,\r\n enquoteString,\r\n unquoteString,\r\n getBrowser,\r\n shotOpen,\r\n shotDownload,\r\n copySubArrays,\r\n shallowCloneNode,\r\n correctSelectorIdentifier,\r\n getFileExtension,\r\n splitFileName,\r\n download,\r\n concatTypedArraysUnsafe,\r\n mergeTypedArraysUnsafe,\r\n};\r\n","import EventDispatcher from './EventDispatcher';\r\n\r\nexport default class JobHandle extends EventDispatcher {\r\n constructor() {\r\n super();\r\n this._shouldCancel = false;\r\n }\r\n\r\n cancel() {\r\n this._shouldCancel = true;\r\n this.dispatchEvent({ type: 'cancel' });\r\n }\r\n\r\n shouldCancel() {\r\n return this._shouldCancel;\r\n }\r\n\r\n // slaves use this to notify master about their events\r\n // master routes these notifications to a single event slot\r\n notify(event) {\r\n this.dispatchEvent({ type: 'notification', slaveEvent: event });\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport utils from './utils';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\n\r\nconst VERSION = 0;\r\n\r\n//----------------------------------------------------------------------------\r\n// DEFAULT SETTINGS\r\n//----------------------------------------------------------------------------\r\n\r\n/**\r\n * Polygonal complexity settings.\r\n *\r\n * @typedef PolyComplexity\r\n * @property {number} poor\r\n * @property {number} low\r\n * @property {number} medium\r\n * @property {number} high\r\n * @property {number} ultra\r\n */\r\n\r\n/**\r\n * @alias SettingsObject\r\n * @namespace\r\n */\r\nconst defaults = {\r\n /**\r\n * Default options for all available modes.\r\n * Use {@link Mode.id} as a dictionary key to access mode options.\r\n *\r\n * Usually you don't need to override these settings. You may specify mode options as a parameter during\r\n * {@link Mode} construction.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {LinesModeOptions} LN - Lines mode options.\r\n * @property {LicoriceModeOptions} LC - Licorice mode options.\r\n * @property {BallsAndSticksModeOptions} BS - Balls and Sticks mode options.\r\n * @property {VanDerWaalsModeOptions} VW - Van der Waals mode options.\r\n * @property {TraceModeOptions} TR - Trace mode options.\r\n * @property {TubeModeOptions} TU - Tube mode options.\r\n * @property {CartoonModeOptions} CA - Cartoon mode options.\r\n * @property {QuickSurfaceModeOptions} QS - Contact Surface mode options.\r\n * @property {IsoSurfaceSASModeOptions} SA - Solvent Accessible Surface mode options.\r\n * @property {IsoSurfaceSESModeOptions} SE - Solvent Excluded Surface mode options.\r\n * @property {ContactSurfaceModeOptions} CS - Contact Surface mode options.\r\n * @property {TextModeOptions} TX - Text mode options.\r\n * @property {VolumeDensityModeOptions} VD - Volume Density mode options.\r\n */\r\n modes: {\r\n //----------------------------------------------------------------------------\r\n // BALLS AND STICKS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Balls and Sticks mode options.\r\n *\r\n * @typedef BallsAndSticksModeOptions\r\n *\r\n * @property {number} atom - Sphere radius as a fraction of Van der Waals atom radius.\r\n * @property {number} bond - Cylinder radius in angstroms.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n BS: {\r\n atom: 0.23,\r\n bond: 0.15,\r\n space: 0.5,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VAN DER WAALS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Van der Waals mode options.\r\n *\r\n * @typedef VanDerWaalsModeOptions\r\n *\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VW: {\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 8,\r\n high: 16,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LINES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Lines mode options.\r\n *\r\n * @typedef LinesModeOptions\r\n *\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {number} offsarom - Offset between bonds and aromatic cycle.\r\n * @property {number} chunkarom - Number of pieces in a-loop arc, corresponding to atom.\r\n * @property {number} atom - Collision radius for atoms picking.\r\n * @property {number} lineWidth - Line width in pixels (not used in thin lines).\r\n */\r\n LN: {\r\n multibond: true,\r\n showarom: true,\r\n offsarom: 0.2,\r\n chunkarom: 10,\r\n atom: 0.23,\r\n lineWidth: 2,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // LICORICE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Licorice mode options.\r\n *\r\n * @typedef LicoriceModeOptions\r\n *\r\n * @property {number} bond - Bond cylinder radius.\r\n * @property {number} space - Fraction of the space around one cylinder. Zero means that cylinder fills all\r\n * available space.\r\n * @property {boolean} multibond - Flag, that toggles rendering of multiple ordered bonds.\r\n * @property {number} aromrad - Minor radius of a torus for aromatic loops.\r\n * @property {boolean} showarom - Flag, that toggles rendering of aromatic loops.\r\n * @property {PolyComplexity} polyComplexity - Poly complexity values for render modes.\r\n */\r\n LC: {\r\n bond: 0.20,\r\n space: 0.0,\r\n multibond: true,\r\n aromrad: 0.1,\r\n showarom: true,\r\n polyComplexity: {\r\n poor: 3,\r\n low: 4,\r\n medium: 6,\r\n high: 12,\r\n ultra: 32,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SAS\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Accessible Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSASModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SA: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // SURFACE SES\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Solvent Excluded Surface mode options.\r\n *\r\n * @typedef IsoSurfaceSESModeOptions\r\n *\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {number} probeRadius - Radius of the probe.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n SE: {\r\n zClip: false,\r\n probeRadius: 1.5,\r\n subset: '',\r\n wireframe: false,\r\n polyComplexity: {\r\n poor: 6,\r\n low: 8,\r\n medium: 16,\r\n high: 30,\r\n ultra: 60,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // QUICK SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Quick Surface mode options.\r\n *\r\n * @typedef QuickSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} scale - Radius scale for the surface being built.\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} gaussLim - Gauss lim for coloring the bigger the value, the smoother our colors are.\r\n * @property {PolyComplexity} gridSpacing - Poly complexity values for render modes. In this case the value\r\n * corresponds to the grid density.\r\n */\r\n QS: {\r\n isoValue: 0.5,\r\n gaussLim: {\r\n poor: 1.5,\r\n low: 2.0,\r\n medium: 2.5,\r\n high: 3.0,\r\n ultra: 4.0,\r\n },\r\n scale: 1.0,\r\n wireframe: false,\r\n gridSpacing: {\r\n poor: 2,\r\n low: 1.5,\r\n medium: 1,\r\n high: 0.5,\r\n ultra: 0.25,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CONTACT SURFACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Contact Surface mode options.\r\n *\r\n * @typedef ContactSurfaceModeOptions\r\n *\r\n * @property {number} isoValue - Isovalue of the surface to extract.\r\n * @property {number} probeRadius - Probe radius.\r\n * @property {number} probePositions\r\n * @property {boolean} zClip - Flag, that toggles z-clipping.\r\n * @property {string} subset - Only parts of surface close to selected atoms will be visible.\r\n * Empty string means whole surface is visible.\r\n * @property {boolean} wireframe - Flag that specifies whether or not surface rendered in wireframe mode.\r\n * @property {PolyComplexity} polyComplexity - Radius scale for the surface being built.\r\n * Poly complexity values for render modes. In this case the value corresponds to the grid density.\r\n */\r\n CS: {\r\n probeRadius: 1.4,\r\n isoValue: 1.5,\r\n wireframe: false,\r\n probePositions: 30,\r\n polyComplexity: {\r\n poor: 0.5,\r\n low: 1.0,\r\n medium: 1.5,\r\n high: 1.75,\r\n ultra: 2.0,\r\n },\r\n subset: '',\r\n zClip: false,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TRACE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Trace mode options.\r\n *\r\n * @typedef TraceModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n TR: {\r\n radius: 0.30,\r\n polyComplexity: {\r\n poor: 12,\r\n low: 16,\r\n medium: 32,\r\n high: 64,\r\n ultra: 64,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TUBE\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Tube mode options.\r\n *\r\n * @typedef TubeModeOptions\r\n *\r\n * @property {number} radius - Cylinder radius.\r\n * @property {number} tension - Tension for interpolation.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n TU: {\r\n radius: 0.30,\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // CARTOON\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Cartoon mode options.\r\n *\r\n * @typedef CartoonModeOptions\r\n *\r\n * @property {number} radius - Standard tube radius.\r\n * @property {number} depth - Height of the secondary structure ribbon.\r\n * @property {number} tension - Tension for interpolation.\r\n * @proprety {object} ss - Secondary structure parameters.\r\n * @proprety {object} ss.helix - Options for helices render.\r\n * @proprety {number} ss.helix.width - Width of the secondary structure ribbon.\r\n * @proprety {number} ss.helix.arrow - Secondary structure's arrow width.\r\n * @proprety {object} ss.strand - Options for strands render.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n * polyComplexity must be even for producing symmetric arrows.\r\n * @property {number} heightSegmentsRatio - Poly complexity multiplier for height segments.\r\n */\r\n CA: {\r\n radius: 0.30,\r\n depth: 0.25,\r\n ss: {\r\n helix: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n strand: {\r\n width: 1.0,\r\n arrow: 2.0,\r\n },\r\n },\r\n heightSegmentsRatio: 1.5,\r\n tension: -0.7,\r\n polyComplexity: {\r\n poor: 4,\r\n low: 6,\r\n medium: 10,\r\n high: 18,\r\n ultra: 34,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // TEXT\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Text mode options.\r\n *\r\n * @typedef TextModeOptions\r\n *\r\n * @property {string} template - Format string for building output text.\r\n * @property {string} horizontalAlign - Text alignment ('left', 'right', 'center').\r\n * @property {string} verticalAlign - Vertical text box alignment ('top', 'bottom', 'middle').\r\n * @property {number} dx - Text offset x in angstroms.\r\n * @property {number} dy - Text offset y in angstroms.\r\n * @property {number} dz - Text offset z in angstroms.\r\n * @property {string} fg - Color rule for foreground.\r\n * @property {string} bg - Color rule for background.\r\n * @property {boolean} showBg - Flag, that toggles background rendering.\r\n *\r\n */\r\n TX: {\r\n template: '{{Chain}}.{{Residue}}{{Sequence}}.{{Name}}',\r\n horizontalAlign: 'center',\r\n verticalAlign: 'middle',\r\n dx: 0,\r\n dy: 0,\r\n dz: 1,\r\n fg: 'none',\r\n bg: '0x202020',\r\n showBg: true,\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n // VOLUME DENSITY\r\n //----------------------------------------------------------------------------\r\n\r\n /**\r\n * Volume density mode options.\r\n *\r\n * @typedef VolumeDensityModeOptions\r\n *\r\n * @property {number} kSigma - Noise threshold coefficient.\r\n * @property {boolean} frame - flag, that turns on box frame painting.\r\n * @property {boolean} isoMode - flag, that turns on IsoSurface mode instead of Volume Rendering.\r\n * @property {PolyComplexity} polyComplexity - Polygonal complexity settings for different resolutions.\r\n */\r\n VD: {\r\n kSigma: 1.0,\r\n kSigmaMed: 2.0,\r\n kSigmaMax: 4.0,\r\n frame: true,\r\n isoMode: false,\r\n polyComplexity: {\r\n poor: 2,\r\n low: 3,\r\n medium: 4,\r\n high: 8,\r\n ultra: 10,\r\n },\r\n },\r\n },\r\n\r\n /**\r\n * Default options for all available colorers.\r\n * Use {@link Colorer.id} as a dictionary key to access colorer options.\r\n *\r\n * Usually you don't need to override these settings. You may specify colorer options as a parameter during\r\n * {@link Colorer} construction.\r\n *\r\n * Not all colorers have options.\r\n *\r\n * @memberof SettingsObject#\r\n * @type {Object.}\r\n *\r\n * @property {ElementColorerOptions} EL - Element colorer options.\r\n * @property {SequenceColorerOptions} SQ - Sequence colorer options.\r\n * @property {MoleculeColorerOptions} MO - Molecule colorer options.\r\n * @property {UniformColorerOptions} UN - Uniform colorer options.\r\n * @property {ConditionalColorerOptions} CO - Conditional colorer options.\r\n * @property {TemperatureColorerOptions} TM - Temperature colorer options.\r\n * @property {OccupancyColorerOptions} OC - Occupancy colorer options.\r\n * @property {HydrophobicityColorerOptions} HY - Hydrophobicity colorer options.\r\n */\r\n colorers: {\r\n /**\r\n * Element colorer options.\r\n *\r\n * @typedef ElementColorerOptions\r\n *\r\n * @property {number} carbon - Carbon color or -1 to use default.\r\n */\r\n EL: {\r\n carbon: -1,\r\n },\r\n\r\n /**\r\n * Uniform colorer options.\r\n *\r\n * @typedef UniformColorerOptions\r\n *\r\n * @property {number} color - Single color to paint with.\r\n */\r\n UN: {\r\n color: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Conditional colorer options.\r\n *\r\n * @typedef ConditionalColorerOptions\r\n *\r\n * @property {string} subset - Selector string.\r\n * @property {number} color - Color of selected atoms.\r\n * @property {number} baseColor - Color of other atoms.\r\n */\r\n CO: {\r\n subset: 'charged',\r\n color: 0xFF0000,\r\n baseColor: 0xFFFFFF,\r\n },\r\n\r\n /**\r\n * Carbon colorer options.\r\n *\r\n * @typedef CarbonColorerOptions\r\n *\r\n * @property {number} color - Single color to paint carbons\r\n * @property {number} factor - Color factor for not carbon atoms.\r\n */\r\n CB: {\r\n color: 0x909090,\r\n factor: 0.6,\r\n },\r\n\r\n /**\r\n * Sequence colorer options.\r\n *\r\n * @typedef SequenceColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n SQ: {\r\n gradient: 'rainbow',\r\n },\r\n\r\n /**\r\n * Temperature colorer options.\r\n *\r\n * @typedef TemperatureColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n * @property {number} min - Minimal temperature.\r\n * @property {number} max - Maximal temperature.\r\n */\r\n TM: {\r\n gradient: 'temp',\r\n min: 5,\r\n max: 40,\r\n },\r\n\r\n /**\r\n * Occupancy colorer options.\r\n *\r\n * @typedef OccupancyColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n OC: {\r\n gradient: 'reds',\r\n },\r\n\r\n /**\r\n * Hydrophobicity colorer options.\r\n *\r\n * @typedef HydrophobicityColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n HY: {\r\n gradient: 'blue-red',\r\n },\r\n\r\n /**\r\n * Molecule colorer options.\r\n *\r\n * @typedef MoleculeColorerOptions\r\n *\r\n * @property {string} gradient - Name of gradient to use.\r\n */\r\n MO: {\r\n gradient: 'rainbow',\r\n },\r\n },\r\n\r\n /*\r\n * Use antialiasing in WebGL.\r\n * @type {boolean}\r\n */\r\n antialias: true,\r\n\r\n /*\r\n * Camera field of view in degrees.\r\n * @type {number}\r\n */\r\n camFov: 45.0,\r\n\r\n /*\r\n * Camera near plane distance.\r\n * @type {number}\r\n */\r\n camNear: 0.5,\r\n\r\n /*\r\n * Camera far plane distance.\r\n * @type {number}\r\n */\r\n camFar: 100.0,\r\n\r\n camDistance: 2.5,\r\n\r\n radiusToFit: 1.0,\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogNearFactor: 0.5, // [0, 1]\r\n\r\n /**\r\n * @type {number}\r\n * @instance\r\n */\r\n fogFarFactor: 1, // [0, 1]\r\n fogAlpha: 1.0,\r\n fogColor: 0x000000,\r\n fogColorEnable: false,\r\n\r\n /**\r\n * Palette used for molecule coloring.\r\n * @type {string}\r\n */\r\n palette: 'JM',\r\n\r\n /*\r\n * Geometry resolution.\r\n * @type {string}\r\n */\r\n resolution: 'medium',\r\n\r\n autoResolution: false/* true */,\r\n\r\n autoPreset: true,\r\n\r\n preset: 'default', // TODO: remove 'preset' from settings, implement autodetection\r\n\r\n presets: {\r\n // Default\r\n default: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n empty: [],\r\n\r\n // Wireframe\r\n wire: [{\r\n mode: 'LN',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Small molecules\r\n small: [{\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'all',\r\n material: 'SF',\r\n }],\r\n\r\n // Proteins, nucleic acids etc.\r\n macro: [{\r\n mode: 'CA',\r\n colorer: 'SS',\r\n selector: 'not hetatm',\r\n material: 'SF',\r\n }, {\r\n mode: 'BS',\r\n colorer: 'EL',\r\n selector: 'hetatm and not water',\r\n material: 'SF',\r\n }],\r\n },\r\n\r\n objects: {\r\n line: {\r\n color: 0xFFFFFFFF,\r\n dashSize: 0.3,\r\n gapSize: 0.05,\r\n },\r\n },\r\n\r\n //----------------------------------------------------------------------------\r\n\r\n bg: {\r\n color: 0x202020,\r\n transparent: false,\r\n },\r\n\r\n draft: {\r\n clipPlane: false,\r\n clipPlaneFactor: 0.5,\r\n clipPlaneSpeed: 0.00003,\r\n },\r\n\r\n /*\r\n * Separate group for plugins.\r\n * Each plugin handles its field by itself.\r\n */\r\n plugins: {\r\n\r\n },\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n axes: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fog: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fps: true,\r\n\r\n /**\r\n * Switch using of z-sprites for sphere and cylinder geometry\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zSprites: true,\r\n\r\n isoSurfaceFakeOpacity: true,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n suspendRender: true,\r\n\r\n nowater: false,\r\n\r\n /**\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autobuild: true,\r\n\r\n /**\r\n * Anti-aliasing.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n fxaa: true,\r\n /**\r\n * Outline depths\r\n * @type {boolean}\r\n * @instance\r\n */\r\n outline: {\r\n on: false,\r\n color: 0x000000,\r\n threshold: 0.1,\r\n thickness: 1,\r\n },\r\n\r\n /**\r\n * Ambient Occlusion special effect.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n ao: false,\r\n\r\n /**\r\n * Shadows options.\r\n *\r\n * @property {boolean} shadowMap - enable/disable.\r\n * @property {string} basic/percentage-closer filtering/non-uniform randomizing pcf.\r\n * @property {number} radius for percentage-closer filtering.\r\n */\r\n shadow: {\r\n on: false,\r\n type: 'random'/* basic, pcf, random */,\r\n radius: 1.0,\r\n },\r\n\r\n /**\r\n * Auto-rotation with constant speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n autoRotation: 0.0,\r\n\r\n /**\r\n * Set maximum fps for animation.\r\n * @type {number}\r\n * @instance\r\n */\r\n maxfps: 30,\r\n\r\n /**\r\n * Set fbx output precision.\r\n * @type {number}\r\n * @instance\r\n */\r\n fbxprec: 4,\r\n\r\n /**\r\n * Auto-rotation axis.\r\n *\r\n * - true: complex auto-rotation is about vertical axis\r\n * - false: rotation axis is defined by last user rotation\r\n *\r\n * @type {boolean}\r\n * @instance\r\n */\r\n autoRotationAxisFixed: true,\r\n\r\n /**\r\n * Enable zooming with mouse wheel or pinch gesture.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n zooming: true,\r\n\r\n /**\r\n * Enable picking atoms & residues with left mouse button or touch.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n picking: true,\r\n\r\n /**\r\n * Set picking mode ('atom', 'residue', 'chain', 'molecule').\r\n * @type {string}\r\n * @instance\r\n */\r\n pick: 'atom',\r\n\r\n /**\r\n * Make \"component\" and \"fragment\" editing modes available.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n editing: false,\r\n\r\n /**\r\n * Detect aromatic loops.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n aromatic: false,\r\n\r\n /**\r\n * Load only one biological unit from all those described in PDB file.\r\n * @type {boolean}\r\n * @instance\r\n */\r\n singleUnit: true,\r\n\r\n /**\r\n * Set stereo mode ('NONE', 'SIMPLE', 'DISTORTED', 'ANAGLYPH', 'WEBVR').\r\n * @type {string}\r\n * @instance\r\n */\r\n stereo: 'NONE',\r\n\r\n /**\r\n * Enable smooth transition between views\r\n * @type {boolean}\r\n * @instance\r\n */\r\n interpolateViews: true,\r\n\r\n /**\r\n * Set transparency mode ('standard', 'prepass').\r\n * @type {string}\r\n * @instance\r\n */\r\n transparency: 'prepass',\r\n\r\n /**\r\n * Mouse translation speed.\r\n * @type {number}\r\n * @instance\r\n */\r\n translationSpeed: 2,\r\n\r\n debug: {\r\n example: 3.5,\r\n text: 'hello!',\r\n good: true,\r\n ssaoKernelRadius: 0.7,\r\n ssaoFactor: 0.7,\r\n stereoBarrel: 0.25,\r\n },\r\n use: {\r\n multiFile: false,\r\n },\r\n};\r\n\r\n//----------------------------------------------------------------------------\r\n// SETTINGS CLASS\r\n//----------------------------------------------------------------------------\r\n\r\nfunction Settings() {\r\n EventDispatcher.call(this);\r\n\r\n this.old = null;\r\n this.now = {};\r\n this._changed = {};\r\n\r\n this.reset();\r\n}\r\n\r\nutils.deriveClass(Settings, EventDispatcher, {\r\n defaults,\r\n\r\n set(path, value) {\r\n if (_.isString(path)) {\r\n const oldValue = _.get(this.now, path);\r\n if (oldValue !== value) {\r\n _.set(this.now, path, value);\r\n this._notifyChange(path, value);\r\n }\r\n } else {\r\n const diff = utils.objectsDiff(path, this.now);\r\n if (!_.isEmpty(diff)) {\r\n _.merge(this.now, diff);\r\n this._notifyChanges(diff);\r\n }\r\n }\r\n },\r\n\r\n get(path, defaultValue) {\r\n return _.get(this.now, path, defaultValue);\r\n },\r\n\r\n reset() {\r\n const diff = utils.objectsDiff(defaults, this.now);\r\n this.now = _.cloneDeep(defaults);\r\n this.old = null;\r\n this._notifyChanges(diff);\r\n this._changed = {};\r\n },\r\n\r\n checkpoint() {\r\n this.old = _.cloneDeep(this.now);\r\n this._changed = {};\r\n },\r\n\r\n _notifyChange(path, value) {\r\n this._changed[path] = true;\r\n this.dispatchEvent({ type: `change:${path}`, value });\r\n },\r\n\r\n _notifyChanges(diff) {\r\n utils.forInRecursive(diff, (deepValue, deepPath) => {\r\n this._notifyChange(deepPath, deepValue);\r\n });\r\n },\r\n\r\n changed() {\r\n if (!this.old) {\r\n return [];\r\n }\r\n const { old, now } = this;\r\n const keys = _.filter(Object.keys(this._changed), (key) => _.get(old, key) !== _.get(now, key));\r\n return keys;\r\n },\r\n\r\n applyDiffs(diffs) {\r\n if (diffs.hasOwnProperty('VERSION') && diffs.VERSION !== VERSION) {\r\n throw new Error('Settings version does not match!');\r\n }\r\n // VERSION shouldn't be presented inside settings structure\r\n delete diffs.VERSION;\r\n this.reset();\r\n this.set(diffs);\r\n },\r\n\r\n getDiffs(versioned) {\r\n const diffs = utils.objectsDiff(this.now, defaults);\r\n if (versioned) {\r\n diffs.VERSION = VERSION;\r\n }\r\n return diffs;\r\n },\r\n\r\n setPluginOpts(plugin, opts) {\r\n defaults.plugins[plugin] = _.cloneDeep(opts);\r\n this.now.plugins[plugin] = _.cloneDeep(opts);\r\n },\r\n});\r\n\r\nexport default new Settings();\r\n","import _ from 'lodash';\r\nimport settings from './settings';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\n\r\nlet repIndex = 0;\r\n\r\nfunction asBoolean(value) {\r\n return !(!value || value === '0' || (_.isString(value) && value.toLowerCase() === 'false'));\r\n}\r\n\r\nconst adapters = {\r\n string: String,\r\n number: Number,\r\n boolean: asBoolean,\r\n};\r\n\r\n// Level 1 assignment symbol\r\nconst cL1Ass = '=';\r\n\r\nconst cOptsSep = '!';\r\n// Level 2 (options) assignment symbol\r\nconst cL2Ass = ':';\r\n// Level 2 (options) separator symbol\r\nconst cLSep = ',';\r\n\r\nconst cCommonIgnoreSymbols = '$;@/?';\r\n/**\r\n * We may (and should) leave as is for better readability:\r\n *\r\n * $ , ; : @ / ?\r\n */\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n */\r\nfunction getLevel1ExcludedExpr() {\r\n const cLevel1Ignores = ':,';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel1Ignores);\r\n}\r\n\r\n/**\r\n * Generate regular expression for symbols excluded for first level encryption\r\n * (options, etc, ..)\r\n */\r\nfunction getLevel2ExcludedExpr() {\r\n const cLevel2Ignores = ' ';\r\n return utils.generateRegExp(cCommonIgnoreSymbols + cLevel2Ignores);\r\n}\r\n\r\nconst cL1ExclExpr = getLevel1ExcludedExpr();\r\nfunction encodeQueryComponentL1(value) {\r\n return utils.encodeQueryComponent(value, cL1ExclExpr);\r\n}\r\n\r\nconst cL2ExclExpr = getLevel2ExcludedExpr();\r\nfunction encodeQueryComponentL2(value) {\r\n return utils.encodeQueryComponent(value, cL2ExclExpr);\r\n}\r\n\r\nfunction ensureRepList(opts) {\r\n let { reps } = opts;\r\n if (!reps) {\r\n const { presets } = settings.now;\r\n let preset = opts.preset || settings.now.preset;\r\n reps = presets[preset];\r\n if (!reps) {\r\n logger.warn(`Unknown preset \"${preset}\"`);\r\n [preset] = Object.keys(presets);\r\n reps = presets[preset]; // fall back to any preset\r\n }\r\n opts.preset = preset;\r\n opts.reps = utils.deriveDeep(reps, true);\r\n }\r\n}\r\n\r\nfunction ensureRepAssign(opts, prop, value) {\r\n ensureRepList(opts);\r\n const rep = opts.reps[repIndex];\r\n // prop specified twice therefore start new rep by cloning the current\r\n if (rep.hasOwnProperty(prop)) {\r\n repIndex = opts.reps.length;\r\n opts.reps[repIndex] = utils.deriveDeep(rep, true);\r\n }\r\n if (value !== undefined) {\r\n opts.reps[repIndex][prop] = value;\r\n }\r\n}\r\n\r\nfunction addObject(opts, params, options) {\r\n if (opts._objects === undefined) {\r\n opts._objects = [];\r\n }\r\n\r\n const [type, newOpts] = options;\r\n const newObj = {\r\n type,\r\n params,\r\n };\r\n\r\n if (newOpts !== undefined) {\r\n newObj.opts = newOpts;\r\n }\r\n\r\n opts._objects[opts._objects.length] = newObj;\r\n}\r\n\r\nfunction parseParams(str, params) {\r\n const sep = str.indexOf(',');\r\n if (sep >= 0) {\r\n params.push(str.substr(sep + 1).split(','));\r\n return str.substr(0, sep);\r\n }\r\n // keep this untouched if no params were extracted\r\n return str;\r\n}\r\n\r\nfunction extractArgs(input, defaultsDict, params) {\r\n if (input) {\r\n const bang = input.indexOf(cOptsSep);\r\n const inputVal = parseParams(input.substr(0, bang >= 0 ? bang : undefined), params);\r\n if (bang >= 0) {\r\n const args = input.substr(bang + 1).split(cLSep);\r\n input = inputVal;\r\n if (defaultsDict) {\r\n const defaults = defaultsDict[input];\r\n const opts = utils.deriveDeep(defaults, true);\r\n args.forEach((arg) => {\r\n const pair = arg.split(cL2Ass, 2);\r\n const key = decodeURIComponent(pair[0]);\r\n const value = decodeURIComponent(pair[1]);\r\n const adapter = adapters[typeof _.get(defaults, key)];\r\n if (adapter) {\r\n _.set(opts, key, adapter(value));\r\n } else {\r\n logger.warn(`Unknown argument \"${key}\" for option \"${input}\"`);\r\n }\r\n });\r\n if (Object.keys(opts).length > 0) {\r\n input = [input, opts];\r\n }\r\n }\r\n } else {\r\n input = inputVal;\r\n }\r\n }\r\n return input;\r\n}\r\n\r\nconst actions = {\r\n\r\n l: 'load',\r\n load: String,\r\n t: 'type',\r\n type: String,\r\n v: 'view',\r\n view: String,\r\n u: 'unit',\r\n unit: Number,\r\n menu: asBoolean,\r\n\r\n // Commands\r\n\r\n o: 'object',\r\n object(value, opts) {\r\n const params = [];\r\n let options = extractArgs(value, settings.defaults.objects, params);\r\n if (!Array.isArray(options)) {\r\n options = [options];\r\n }\r\n addObject(opts, params[0], options);\r\n },\r\n\r\n p: 'preset',\r\n preset(value, opts) {\r\n opts.preset = value;\r\n opts.reps = null;\r\n ensureRepList(opts);\r\n },\r\n\r\n r: 'rep',\r\n rep(value, opts) {\r\n ensureRepList(opts);\r\n repIndex = Number(value);\r\n // clamp the index to one greater than the last\r\n repIndex = repIndex <= opts.reps.length ? (repIndex < 0 ? 0 : repIndex) : opts.reps.length;\r\n // create a new rep if it is adjacent to the existing ones\r\n if (repIndex === opts.reps.length) {\r\n // if there is no rep to derive from, derive from the first rep of the default\r\n opts.reps[repIndex] = repIndex > 0 ? utils.deriveDeep(opts.reps[repIndex - 1], true)\r\n : utils.deriveDeep(settings.defaults.presets.default[0], true);\r\n }\r\n },\r\n\r\n s: 'select',\r\n select(value, opts) {\r\n ensureRepAssign(opts, 'selector', value);\r\n },\r\n\r\n m: 'mode',\r\n mode(value, opts) {\r\n ensureRepAssign(opts, 'mode', extractArgs(value, settings.defaults.modes));\r\n },\r\n\r\n c: 'color',\r\n color(value, opts) {\r\n ensureRepAssign(opts, 'colorer', extractArgs(value, settings.defaults.colorers));\r\n },\r\n\r\n mt: 'material',\r\n material(value, opts) {\r\n ensureRepAssign(opts, 'material', extractArgs(value, settings.defaults.materials));\r\n },\r\n\r\n dup(value, opts) {\r\n ensureRepList(opts);\r\n const { reps } = opts;\r\n const rep = reps[repIndex];\r\n repIndex = reps.length;\r\n reps[repIndex] = utils.deriveDeep(rep, true);\r\n },\r\n\r\n // Settings shortcuts\r\n\r\n ar: 'autoResolution',\r\n};\r\n\r\nfunction _fromArray(entries) {\r\n repIndex = 0;\r\n\r\n const opts = {};\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const /** string[] */ entry = entries[i];\r\n let /** string? */ key = entry[0];\r\n const /** string? */ value = entry[1];\r\n let /** function|string? */ action = actions[key];\r\n\r\n // unwind shortcuts and aliases\r\n while (_.isString(action)) {\r\n key = action;\r\n action = actions[key];\r\n }\r\n\r\n // either set a property or use specialized parser\r\n if (!action) {\r\n const adapter = adapters[typeof _.get(settings.defaults, key)];\r\n if (adapter) {\r\n _.set(opts, `settings.${key}`, adapter(value));\r\n } else {\r\n logger.warn(`Unknown option \"${key}\"`);\r\n }\r\n } else if (_.isFunction(action)) {\r\n const result = action(value, opts);\r\n if (result !== undefined) {\r\n opts[key] = result;\r\n }\r\n }\r\n }\r\n\r\n return opts;\r\n}\r\n\r\nfunction fromAttr(attr) {\r\n return _fromArray(utils.getUrlParameters(`?${attr || ''}`));\r\n}\r\n\r\nfunction fromURL(url) {\r\n return _fromArray(utils.getUrlParameters(url));\r\n}\r\n\r\nfunction _processOptsForURL(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = encodeQueryComponentL2(key) + cL2Ass + encodeQueryComponentL2(value);\r\n });\r\n return str.join(cLSep);\r\n}\r\n\r\nfunction _processArgsForURL(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]}${cOptsSep}${_processOptsForURL(args[1])}`;\r\n}\r\n\r\nfunction _processObjForURL(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += `,${objOpts.params.join(',')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += cOptsSep + _processOptsForURL(objOpts.opts);\r\n }\r\n return res;\r\n}\r\n\r\nfunction toURL(opts) {\r\n const stringList = [];\r\n let idx = 0;\r\n\r\n function checkAndAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n stringList[idx++] = encodeQueryComponentL1(prefix)\r\n + cL1Ass + encodeQueryComponentL1(value);\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n if (_.isEmpty(repList[i])) {\r\n continue;\r\n }\r\n checkAndAdd('r', i);\r\n checkAndAdd('s', repList[i].selector);\r\n checkAndAdd('m', _processArgsForURL(repList[i].mode));\r\n checkAndAdd('c', _processArgsForURL(repList[i].colorer));\r\n checkAndAdd('mt', _processArgsForURL(repList[i].material));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('o', _processObjForURL(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('l', opts.load);\r\n checkAndAdd('u', opts.unit);\r\n checkAndAdd('p', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n checkAndAdd('v', opts.view);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(key, value);\r\n });\r\n\r\n let url = '';\r\n if (typeof window !== 'undefined') {\r\n const { location } = window;\r\n url = `${location.protocol}//${location.host}${location.pathname}`;\r\n }\r\n if (stringList.length > 0) {\r\n url += `?${stringList.join('&')}`;\r\n }\r\n\r\n return url;\r\n}\r\n\r\nfunction _processOptsForScript(opts) {\r\n const str = [];\r\n let i = 0;\r\n utils.forInRecursive(opts, (value, key) => {\r\n str[i++] = `${key}=${utils.enquoteString(value)}`;\r\n });\r\n return str.join(' ');\r\n}\r\n\r\nfunction _processArgsForScript(args) {\r\n if (!_.isArray(args)) {\r\n return args;\r\n }\r\n if (args.length < 2) {\r\n return args[0];\r\n }\r\n return `${args[0]} ${_processOptsForScript(args[1])}`;\r\n}\r\n\r\nfunction _processObjForScript(objOpts) {\r\n if (!objOpts || !objOpts.type) {\r\n return undefined;\r\n }\r\n let res = objOpts.type;\r\n if (_.isArray(objOpts.params) && objOpts.params.length > 0) {\r\n res += ` ${objOpts.params.map(utils.enquoteString).join(' ')}`;\r\n }\r\n if (objOpts.opts) {\r\n res += ` ${_processOptsForScript(objOpts.opts)}`;\r\n }\r\n return res;\r\n}\r\n\r\nfunction _processRepsForScript(rep, index) {\r\n const repString = [];\r\n let strIdx = 0;\r\n function localAdd(prefix, value) {\r\n if (value !== null && value !== undefined) {\r\n repString[strIdx++] = prefix + value;\r\n }\r\n }\r\n if (_.isEmpty(rep)) {\r\n return null;\r\n }\r\n localAdd('', index);\r\n localAdd('s=', utils.enquoteString(rep.selector));\r\n localAdd('m=', _processArgsForScript(rep.mode));\r\n localAdd('c=', _processArgsForScript(rep.colorer));\r\n localAdd('mt=', _processArgsForScript(rep.material));\r\n return repString.join(' ');\r\n}\r\n\r\nfunction toScript(opts) {\r\n const commandsList = [];\r\n let idx = 0;\r\n function checkAndAdd(command, value, saveQuotes) {\r\n if (value !== null && value !== undefined) {\r\n const quote = (typeof value === 'string' && saveQuotes) ? '\"' : '';\r\n commandsList[idx++] = `${command} ${quote}${value}${quote}`.trim();\r\n }\r\n }\r\n\r\n function addReps(repList) {\r\n if (!repList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = repList.length; i < n; ++i) {\r\n checkAndAdd('rep', _processRepsForScript(repList[i], i));\r\n }\r\n }\r\n\r\n function addObjects(objList) {\r\n if (!objList) {\r\n return;\r\n }\r\n for (let i = 0, n = objList.length; i < n; ++i) {\r\n checkAndAdd('', _processObjForScript(objList[i]));\r\n }\r\n }\r\n\r\n checkAndAdd('set', 'autobuild false');\r\n checkAndAdd('load', opts.load, true);\r\n checkAndAdd('unit', opts.unit);\r\n checkAndAdd('preset', opts.preset);\r\n addReps(opts.reps);\r\n addObjects(opts._objects);\r\n\r\n utils.forInRecursive(opts.settings, (value, key) => {\r\n // I heard these lines in the whispers of the Gods\r\n // Handle preset setting in reps\r\n if (key === 'preset') {\r\n return;\r\n }\r\n checkAndAdd(`set ${key}`, value, true);\r\n });\r\n checkAndAdd('view', opts.view);\r\n checkAndAdd('set', 'autobuild true');\r\n return commandsList.join('\\n');\r\n}\r\n\r\nexport default {\r\n fromURL,\r\n fromAttr,\r\n adapters,\r\n toURL,\r\n toScript,\r\n};\r\n","/**\r\n * Atom measurements.\r\n *\r\n * @param {Residue} residue - (required) Residue containing the atom\r\n * @param {string} name - (required) Name, unique in the residue\r\n * @param {Element} type - (required) Chemical element reference\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n *\r\n * @param {number} role - Role of atom inside monomer: Lead and wing are particularity interesting\r\n * @param {boolean} het - Non-standard residue indicator\r\n *\r\n * @param {number} serial - Serial number, unique in the model\r\n * @param {string} location - Alternative location indicator (usually space or A-Z)\r\n * @param {number} occupancy - Occupancy percentage, from 0 to 1\r\n * @param {number} temperature - Temperature\r\n * @param {number} charge - Charge\r\n *\r\n * @exports Atom\r\n * @constructor\r\n */\r\n\r\nclass Atom {\r\n constructor(residue, name, type, position, role, het, serial, location, occupancy, temperature, charge) {\r\n this.index = -1;\r\n this.residue = residue;\r\n this.name = name;\r\n this.element = type;\r\n this.position = position;\r\n this.role = role;\r\n this.mask = 1 | 0;\r\n\r\n this.het = het;\r\n\r\n this.serial = serial;\r\n this.location = (location || ' ').charCodeAt(0);\r\n this.occupancy = occupancy || 1;\r\n this.temperature = temperature;\r\n this.charge = charge;\r\n this.hydrogenCount = -1; // explicitly invalid\r\n this.radicalCount = 0;\r\n this.valence = -1; // explicitly invalid\r\n\r\n this.bonds = [];\r\n\r\n this.flags = 0x0000;\r\n if (type.name === 'H') {\r\n this.flags |= Atom.Flags.HYDROGEN;\r\n } else if (type.name === 'C') {\r\n this.flags |= Atom.Flags.CARBON;\r\n }\r\n }\r\n\r\n isHet() {\r\n return this.het;\r\n }\r\n\r\n isHydrogen() {\r\n return this.element.number === 1;\r\n }\r\n\r\n getVisualName() {\r\n const { name } = this;\r\n if (name.length > 0) {\r\n return name;\r\n }\r\n return this.element.name.trim();\r\n }\r\n\r\n forEachBond(process) {\r\n const { bonds } = this;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n getFullName() {\r\n let name = '';\r\n if (this.residue !== null) {\r\n if (this.residue._chain !== null) {\r\n name += `${this.residue._chain.getName()}.`;\r\n }\r\n name += `${this.residue._sequence}.`;\r\n }\r\n name += this.name;\r\n return name;\r\n }\r\n\r\n /**\r\n * Enumeration of atom flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n CARBON: 0x0001,\r\n // OXYGEN: 0x0002,\r\n // NITROGEN: 0x0004,\r\n HYDROGEN: 0x0008,\r\n /** Non-polar hydrogen (it is also a HYDROGEN) */\r\n NONPOLARH: 0x1008,\r\n };\r\n}\r\n\r\nexport default Atom;\r\n","class Element {\r\n constructor(number, name, fullName, weight, radius, radiusBonding, hValency) {\r\n this.number = number;\r\n this.name = name;\r\n this.fullName = fullName;\r\n this.weight = weight;\r\n this.radius = radius;\r\n this.radiusBonding = radiusBonding;\r\n this.hydrogenValency = hValency;\r\n }\r\n\r\n static Constants = {\r\n\r\n U1: 1,\r\n Lead: 2,\r\n U2: 3,\r\n Wing: 4,\r\n U18: 18,\r\n\r\n };\r\n\r\n static Role = {\r\n\r\n N: Element.Constants.U1,\r\n CA: Element.Constants.Lead,\r\n C: Element.Constants.U2,\r\n O: Element.Constants.Wing,\r\n SG: Element.Constants.U18,\r\n\r\n };\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByAtomicNumber = [\r\n\r\n null,\r\n new Element(1, 'H', 'Hydrogen', 1.008, 1.2, 0.23, [1]),\r\n new Element(2, 'HE', 'Helium', 4.003, 1.4, 0.93, [0]),\r\n new Element(3, 'LI', 'Lithium', 6.941, 1.82, 0.68, [1]),\r\n new Element(4, 'BE', 'Beryllium', 9.012, 1.7, 0.35, [2]),\r\n new Element(5, 'B', 'Boron', 10.81, 2.08, 0.83, [3]),\r\n new Element(6, 'C', 'Carbon', 12.011, 1.95, 0.68, [4]),\r\n new Element(7, 'N', 'Nitrogen', 14.007, 1.85, 0.68, [3, 5]),\r\n new Element(8, 'O', 'Oxygen', 15.999, 1.7, 0.68, [2, 4]),\r\n new Element(9, 'F', 'Fluorine', 18.998, 1.73, 0.64, [1]),\r\n new Element(10, 'NE', 'Neon', 20.18, 1.54, 1.12, [0]),\r\n new Element(11, 'NA', 'Sodium', 22.99, 2.27, 0.97, [1]),\r\n new Element(12, 'MG', 'Magnesium', 24.305, 1.73, 1.1, [2]),\r\n new Element(13, 'AL', 'Aluminum', 26.981, 2.05, 1.35, [3]),\r\n new Element(14, 'SI', 'Silicon', 28.086, 2.1, 1.2, [4]),\r\n new Element(15, 'P', 'Phosphorus', 30.974, 2.08, 0.75, [3, 5]),\r\n new Element(16, 'S', 'Sulfur', 32.07, 2, 1.02, [2, 4, 6]),\r\n new Element(17, 'CL', 'Chlorine', 35.453, 1.97, 0.99, [1, 3, 5, 7]),\r\n new Element(18, 'AR', 'Argon', 39.948, 1.88, 1.57, [0]),\r\n new Element(19, 'K', 'Potassium', 39.1, 2.75, 1.33, [1]),\r\n new Element(20, 'CA', 'Calcium', 40.08, 1.973, 0.99, [2]),\r\n new Element(21, 'SC', 'Scandium', 44.956, 1.7, 1.44, [0]),\r\n new Element(22, 'TI', 'Titanium', 47.88, 1.7, 1.47, [0]),\r\n new Element(23, 'V', 'Vanadium', 50.941, 1.7, 1.33, [0]),\r\n new Element(24, 'CR', 'Chromium', 52, 1.7, 1.35, [0]),\r\n new Element(25, 'MN', 'Manganese', 54.938, 1.7, 1.35, [0]),\r\n new Element(26, 'FE', 'Iron', 55.847, 1.7, 1.34, [0]),\r\n new Element(27, 'CO', 'Cobalt', 58.93, 1.7, 1.33, [0]),\r\n new Element(28, 'NI', 'Nickel', 58.69, 1.63, 1.5, [0]),\r\n new Element(29, 'CU', 'Copper', 63.55, 1.4, 1.52, [0]),\r\n new Element(30, 'ZN', 'Zinc', 65.39, 1.39, 1.45, [0]),\r\n new Element(31, 'GA', 'Gallium', 69.72, 1.87, 1.22, [3]),\r\n new Element(32, 'GE', 'Germanium', 72.61, 1.7, 1.17, [4]),\r\n new Element(33, 'AS', 'Arsenic', 74.92, 1.85, 1.21, [3, 5]),\r\n new Element(34, 'SE', 'Selenium', 78.96, 1.9, 1.22, [2, 4, 6]),\r\n new Element(35, 'BR', 'Bromine', 79.9, 2.1, 1.21, [1, 3, 5, 7]),\r\n new Element(36, 'KR', 'Krypton', 83.8, 2.02, 1.91, [0]),\r\n new Element(37, 'RB', 'Rubidium', 85.47, 1.7, 1.47, [1]),\r\n new Element(38, 'SR', 'Strontium', 87.62, 1.7, 1.12, [2]),\r\n new Element(39, 'Y', 'Yttrium', 88.91, 1.7, 1.78, [0]),\r\n new Element(40, 'ZR', 'Zirconium', 91.22, 1.7, 1.56, [0]),\r\n new Element(41, 'NB', 'Niobium', 92.91, 1.7, 1.48, [0]),\r\n new Element(42, 'MO', 'Molybdenum', 95.94, 1.7, 1.47, [0]),\r\n new Element(43, 'TC', 'Technetium', 98.91, 1.7, 1.35, [0]),\r\n new Element(44, 'RU', 'Ruthenium', 101.07, 1.7, 1.4, [0]),\r\n new Element(45, 'RH', 'Rhodium', 102.91, 1.7, 1.45, [0]),\r\n new Element(46, 'PD', 'Palladium', 106.42, 1.63, 1.5, [0]),\r\n new Element(47, 'AG', 'Silver', 107.87, 1.72, 1.59, [0]),\r\n new Element(48, 'CD', 'Cadmium', 112.41, 1.58, 1.69, [0]),\r\n new Element(49, 'IN', 'Indium', 114.82, 1.93, 1.63, [3]),\r\n new Element(50, 'SN', 'Tin', 118.71, 2.17, 1.46, [2, 4]),\r\n new Element(51, 'SB', 'Antimony', 121.75, 2.2, 1.46, [3, 5]),\r\n new Element(52, 'TE', 'Tellurium', 127.6, 2.06, 1.47, [2, 4, 6]),\r\n new Element(53, 'I', 'Iodine', 126.91, 2.15, 1.4, [1, 3, 5, 7]),\r\n new Element(54, 'XE', 'Xenon', 131.29, 2.16, 1.98, [0]),\r\n new Element(55, 'CS', 'Cesium', 132.91, 1.7, 1.67, [1]),\r\n new Element(56, 'BA', 'Barium', 137.33, 1.7, 1.34, [2]),\r\n new Element(57, 'LA', 'Lanthanum', 138.91, 1.7, 1.87, [0]),\r\n new Element(58, 'CE', 'Cerium', 140.12, 1.7, 1.83, [0]),\r\n new Element(59, 'PR', 'Praseodymium', 140.91, 1.7, 1.82, [0]),\r\n new Element(60, 'ND', 'Neodymium', 144.24, 1.7, 1.81, [0]),\r\n new Element(61, 'PM', 'Promethium', 144.9, 1.7, 1.8, [0]),\r\n new Element(62, 'SM', 'Samarium', 150.36, 1.7, 1.8, [0]),\r\n new Element(63, 'EU', 'Europium', 151.96, 1.7, 1.99, [0]),\r\n new Element(64, 'GD', 'Gadolinium', 157.25, 1.7, 1.79, [0]),\r\n new Element(65, 'TB', 'Terbium', 158.93, 1.7, 1.76, [0]),\r\n new Element(66, 'DY', 'Dysprosium', 162.5, 1.7, 1.75, [0]),\r\n new Element(67, 'HO', 'Holmium', 164.93, 1.7, 1.74, [0]),\r\n new Element(68, 'ER', 'Erbium', 167.26, 1.7, 1.73, [0]),\r\n new Element(69, 'TM', 'Thulium', 168.93, 1.7, 1.72, [0]),\r\n new Element(70, 'YB', 'Ytterbium', 173.04, 1.7, 1.94, [0]),\r\n new Element(71, 'LU', 'Lutetium', 174.97, 1.7, 1.72, [0]),\r\n new Element(72, 'HF', 'Hafnium', 178.49, 1.7, 1.57, [0]),\r\n new Element(73, 'TA', 'Tantalum', 180.95, 1.7, 1.43, [0]),\r\n new Element(74, 'W', 'Tungsten', 183.85, 1.7, 1.37, [0]),\r\n new Element(75, 'RE', 'Rhenium', 186.21, 1.7, 1.35, [0]),\r\n new Element(76, 'OS', 'Osmium', 190.2, 1.7, 1.37, [0]),\r\n new Element(77, 'IR', 'Iridium', 192.22, 1.7, 1.32, [0]),\r\n new Element(78, 'PT', 'Platinum', 195.08, 1.72, 1.5, [0]),\r\n new Element(79, 'AU', 'Gold', 196.97, 1.66, 1.5, [0]),\r\n new Element(80, 'HG', 'Mercury', 200.59, 1.55, 1.7, [0]),\r\n new Element(81, 'TL', 'Thallium', 204.38, 1.96, 1.55, [1, 3]),\r\n new Element(82, 'PB', 'Lead', 207.2, 2.02, 1.54, [2, 4]),\r\n new Element(83, 'BI', 'Bismuth', 208.98, 1.7, 1.54, [3, 5]),\r\n new Element(84, 'PO', 'Polonium', 210, 1.7, 1.68, [2, 4, 6]),\r\n new Element(85, 'AT', 'Astatine', 210, 1.7, 1.7, [1, 3, 5, 7]),\r\n new Element(86, 'RN', 'Radon', 222, 1.7, 2.4, [0]),\r\n new Element(87, 'FR', 'Francium', 223, 1.7, 2, [1]),\r\n new Element(88, 'RA', 'Radium', 226.03, 1.7, 1.9, [2]),\r\n new Element(89, 'AC', 'Actinium', 227.03, 1.7, 1.88, [0]),\r\n new Element(90, 'TH', 'Thorium', 232.04, 1.7, 1.79, [0]),\r\n new Element(91, 'PA', 'Protactinium', 231.04, 1.7, 1.61, [0]),\r\n new Element(92, 'U', 'Uranium', 238.03, 1.86, 1.58, [0]),\r\n new Element(93, 'NP', 'Neptunium', 237.05, 1.7, 1.55, [0]),\r\n new Element(94, 'PU', 'Plutonium', 239.1, 1.7, 1.53, [0]),\r\n new Element(95, 'AM', 'Americium', 243.1, 1.7, 1.51, [0]),\r\n new Element(96, 'CM', 'Curium', 247.1, 1.7, 1.5, [0]),\r\n new Element(97, 'BK', 'Berkelium', 247.1, 1.7, 1.5, [0]),\r\n new Element(98, 'CF', 'Californium', 252.1, 1.7, 1.5, [0]),\r\n new Element(99, 'ES', 'Einsteinium', 252.1, 1.7, 1.5, [0]),\r\n new Element(100, 'FM', 'Fermium', 257.1, 1.7, 1.5, [0]),\r\n new Element(101, 'MD', 'Mendelevium', 256.1, 1.7, 1.5, [0]),\r\n new Element(102, 'NO', 'Nobelium', 259.1, 1.7, 1.5, [0]),\r\n new Element(103, 'LR', 'Lawrencium', 260.1, 1.7, 1.5, [0]),\r\n new Element(104, 'RF', 'Rutherfordium', 261, 1.7, 1.6, [0]),\r\n new Element(105, 'DB', 'Dubnium', 262, 1.7, 1.6, [0]),\r\n new Element(106, 'SG', 'Seaborgium', 263, 1.7, 1.6, [0]),\r\n new Element(107, 'BH', 'Bohrium', 262, 1.7, 1.6, [0]),\r\n new Element(108, 'HS', 'Hassium', 265, 1.7, 1.6, [0]),\r\n new Element(109, 'MT', 'Meitnerium', 268, 1.7, 1.6, [0]),\r\n\r\n ];\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\n static ByName = {\r\n // Duplicate atomic numbers (isotopes)\r\n\r\n D: new Element(1, 'D', 'Deuterium', 2.014, 1.2, 0.23, [1]),\r\n T: new Element(1, 'T', 'Tritium', 3.016, 1.2, 0.23, [1]),\r\n\r\n // All regular elements will be added later, automatically\r\n };\r\n}\r\n\r\n(function () {\r\n const byAtomicNumber = Element.ByAtomicNumber;\r\n const byName = Element.ByName;\r\n for (let i = 0, n = byAtomicNumber.length; i < n; ++i) {\r\n const element = byAtomicNumber[i];\r\n if (element) {\r\n byName[element.name] = element;\r\n }\r\n }\r\n}());\r\n\r\n// find atom type by chemical element (or create if missing)\r\nElement.getByName = function (element) {\r\n let type = Element.ByName[element];\r\n if (!type) {\r\n type = Element.ByName[element] = new Element(0, element, 'Unknown', 0, 1.0, 0.01, [0]);\r\n }\r\n return type;\r\n};\r\n\r\nexport default Element;\r\n","const cBondTypes = {\r\n /** Was generated manually */\r\n UNKNOWN: 0,\r\n /** Simple covalent bond */\r\n COVALENT: 1,\r\n /** Aromatic bond */\r\n AROMATIC: 2,\r\n};\r\n\r\nfunction getAtomPos(atom) {\r\n return atom.position;\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Atom} left - The first atom.\r\n * @param {Atom} right - The second atom.\r\n * @param {number} order - Order of current bond.\r\n * @param {number} type - Bond type.\r\n * @param {boolean} fixed - Indicator of a pre-specified connection (in contrast with guessed one).\r\n *\r\n * @exports Bond\r\n * @constructor\r\n */\r\nclass Bond {\r\n constructor(left, right, order, type, fixed) {\r\n this._left = left;\r\n this._right = right;\r\n this._fixed = fixed;\r\n this._index = -1;\r\n if (left > right) {\r\n throw new Error('In a bond atom indices must be in increasing order');\r\n }\r\n this._order = order;\r\n this._type = type;\r\n }\r\n\r\n getLeft() {\r\n return this._left;\r\n }\r\n\r\n getRight() {\r\n return this._right;\r\n }\r\n\r\n getOrder() {\r\n return this._order;\r\n }\r\n\r\n calcLength() {\r\n return this._left.position.distanceTo(this._right.position);\r\n }\r\n\r\n _forEachNeighbour(currAtom, process) {\r\n const { bonds } = currAtom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]._left !== currAtom ? bonds[i]._left : bonds[i]._right);\r\n }\r\n }\r\n\r\n forEachLevelOne(process) {\r\n const left = this._left;\r\n const right = this._right;\r\n this._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n this._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n process(atom);\r\n });\r\n }\r\n\r\n forEachLevelTwo(process) {\r\n // TODO refactor this piece of an art?\r\n const left = this._left;\r\n const right = this._right;\r\n const self = this;\r\n self._forEachNeighbour(left, (atom) => {\r\n if (atom === right) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === left) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n self._forEachNeighbour(right, (atom) => {\r\n if (atom === left) {\r\n return;\r\n }\r\n self._forEachNeighbour(atom, (l2Atom) => {\r\n if (l2Atom === right) {\r\n return;\r\n }\r\n process(l2Atom);\r\n });\r\n });\r\n }\r\n\r\n _fixDir(refPoint, currDir, posGetter) {\r\n // count atoms to the right and to the left of the current plane\r\n let rightCount = 0;\r\n let leftCount = 0;\r\n const tmpVec = refPoint.clone();\r\n function checkDir(atom) {\r\n tmpVec.copy(posGetter(atom));\r\n tmpVec.sub(refPoint);\r\n const dotProd = currDir.dot(tmpVec);\r\n if (dotProd > 0) {\r\n ++rightCount;\r\n } else {\r\n ++leftCount;\r\n }\r\n }\r\n function checkCarbon(atom) {\r\n if (atom.element.name === 'C') {\r\n checkDir(atom);\r\n }\r\n }\r\n // count all atoms to the left and right of our plane, start from level 1 and carbons\r\n const stages = [\r\n [this.forEachLevelOne, checkCarbon],\r\n [this.forEachLevelOne, checkDir],\r\n [this.forEachLevelTwo, checkCarbon],\r\n [this.forEachLevelTwo, checkDir],\r\n ];\r\n\r\n for (let stageId = 0; stageId < stages.length; ++stageId) {\r\n stages[stageId][0].call(this, stages[stageId][1]);\r\n if (leftCount > rightCount) {\r\n return currDir.multiplyScalar(-1);\r\n }\r\n if (leftCount < rightCount) {\r\n return currDir;\r\n }\r\n }\r\n return currDir;\r\n }\r\n\r\n calcNormalDir(posGetter) {\r\n const left = this._left;\r\n const right = this._right;\r\n let first = left;\r\n let second = right;\r\n posGetter = posGetter === undefined ? getAtomPos : posGetter;\r\n if (left.bonds.length > right.bonds.length) {\r\n first = right;\r\n second = left;\r\n }\r\n let third = first;\r\n let maxNeibs = 0;\r\n const { bonds } = second;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n let another = bonds[i]._left;\r\n if (bonds[i]._left === second) {\r\n another = bonds[i]._right;\r\n }\r\n if (another.bonds.length > maxNeibs && another !== first) {\r\n third = another;\r\n maxNeibs = another.bonds.length;\r\n }\r\n }\r\n const secondPos = posGetter(second);\r\n const firstV = posGetter(first).clone().sub(secondPos);\r\n const secondV = posGetter(third).clone().sub(secondPos);\r\n secondV.crossVectors(firstV, secondV);\r\n if (secondV.lengthSq() < 0.0001) {\r\n secondV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n secondV.normalize();\r\n firstV.crossVectors(secondV, firstV);\r\n if (firstV.lengthSq() < 0.0001) {\r\n firstV.set(0, 1, 0);\r\n }\r\n firstV.normalize();\r\n return this._fixDir(secondPos, firstV, posGetter);\r\n }\r\n\r\n static BondType = cBondTypes;\r\n}\r\n\r\nBond.prototype.BondType = cBondTypes;\r\n\r\nexport default Bond;\r\n","import * as THREE from 'three';\r\nimport Atom from './Atom';\r\nimport Element from './Element';\r\n\r\nconst cNucleicControlNames = ['C3\\'', 'C3*', 'P', 'H5T', 'H3T'];\r\nconst cNucleicWing1Names = ['OP1', 'O1P'];\r\nconst cNucleicWing2Names = ['OP2', 'O2P'];\r\n\r\nconst cCylinderSource = ['C3\\'', 'C3*', 'C1', 'C1\\'', 'C1*', 'P'];\r\nconst cCylinderTarget = [{\r\n types: ['A', 'DA', 'G', 'DG'],\r\n atoms: ['N1'],\r\n}, {\r\n types: ['C', 'DC'],\r\n atoms: ['N3'],\r\n}, {\r\n types: ['T', 'DT', 'U', 'DU'],\r\n atoms: ['O4'],\r\n}];\r\n\r\n/**\r\n * Residue instance.\r\n *\r\n * @param {Chain} chain - Chain this residue belongs to.\r\n * @param {ResidueType} type - Generic residue instance type.\r\n * @param {number} sequence - Sequence ID.\r\n * @param {string} icode - One character insertion code (usually space or A-Z).\r\n *\r\n * @exports Residue\r\n * @constructor\r\n */\r\nclass Residue {\r\n constructor(chain, type, sequence, icode) {\r\n this._chain = chain;\r\n this._component = null;\r\n this._type = type;\r\n this._sequence = sequence;\r\n this._icode = icode;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n\r\n this._atoms = [];\r\n this._secondary = null;\r\n this._firstAtom = null;\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n this._lastAtom = null;\r\n this._controlPoint = null;\r\n this._midPoint = null;\r\n this._wingVector = null;\r\n this._cylinders = null;\r\n this._isValid = true;\r\n this._het = false;\r\n this._molecule = null;\r\n this.temperature = null;\r\n this.occupancy = null;\r\n }\r\n\r\n // Getters and setters\r\n getChain() {\r\n return this._chain;\r\n }\r\n\r\n getMolecule() {\r\n return this._molecule;\r\n }\r\n\r\n getType() {\r\n return this._type;\r\n }\r\n\r\n getSequence() {\r\n return this._sequence;\r\n }\r\n\r\n getSecondary() {\r\n return this._secondary;\r\n }\r\n\r\n getICode() {\r\n return this._icode;\r\n }\r\n\r\n // Other methods\r\n\r\n addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge) {\r\n const atom = new Atom(this, name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n const complex = this._chain.getComplex();\r\n complex.addAtom(atom);\r\n this._atoms.push(atom);\r\n this._het = this._het || het;\r\n return atom;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (process(atoms[i])) {\r\n break;\r\n }\r\n }\r\n }\r\n\r\n _findAtomByName(name) {\r\n let res = null;\r\n this.forEachAtom((atom) => {\r\n if (atom.name === name) {\r\n res = atom;\r\n return true;\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _findFirstAtomInList(names) {\r\n let res = null;\r\n for (let i = 0; i < names.length; ++i) {\r\n res = this._findAtomByName(names[i]);\r\n if (res !== null) {\r\n return res;\r\n }\r\n }\r\n return res;\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n mask &= atoms[i].mask;\r\n }\r\n this._mask = mask;\r\n }\r\n\r\n getCylinderTargetList() {\r\n const type = this._type._name;\r\n for (let i = 0, n = cCylinderTarget.length; i < n; ++i) {\r\n for (let j = 0, m = cCylinderTarget[i].types.length; j < m; ++j) {\r\n if (type === cCylinderTarget[i].types[j]) {\r\n return cCylinderTarget[i].atoms;\r\n }\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n _detectLeadWing(dst, next, getAtomPosition) {\r\n const leadAtom = this._findFirstAtomInList(cNucleicControlNames);\r\n let wingStart = this._findFirstAtomInList(cNucleicWing1Names);\r\n let wingEnd = this._findFirstAtomInList(cNucleicWing2Names);\r\n\r\n if (wingStart === null && next !== null) {\r\n wingStart = next._findFirstAtomInList(cNucleicWing1Names);\r\n }\r\n\r\n if (wingEnd === null && next !== null) {\r\n wingEnd = next._findFirstAtomInList(cNucleicWing2Names);\r\n }\r\n\r\n if (leadAtom === null || wingStart === null || wingEnd === null) {\r\n return;\r\n }\r\n\r\n dst._leadAtom = leadAtom;\r\n dst._controlPoint = getAtomPosition(leadAtom);\r\n dst._wingVector = getAtomPosition(wingEnd).clone().sub(getAtomPosition(wingStart));\r\n dst._isValid = true;\r\n\r\n const cylSource = this._findFirstAtomInList(cCylinderSource);\r\n const targetList = this.getCylinderTargetList();\r\n const cylTarget = targetList !== null ? this._findFirstAtomInList(targetList) : null;\r\n if (cylSource === null || cylTarget === null) {\r\n return;\r\n }\r\n dst._cylinders = [getAtomPosition(cylSource), getAtomPosition(cylTarget)];\r\n }\r\n\r\n calcWing(prevLeadPos, currLeadPos, prevWingPos, prevWing) {\r\n const vectorA = currLeadPos.clone().sub(prevLeadPos);\r\n const vectorB = prevLeadPos.clone().sub(prevWingPos);\r\n vectorB.crossVectors(vectorA, vectorB);\r\n vectorB.crossVectors(vectorA, vectorB).normalize();\r\n if (prevWing !== null && prevWing.length() > 0.0001) {\r\n const needToNegate = vectorB.length() > 0.0001 && Math.abs(prevWing.angleTo(vectorB)) > Math.PI / 2;\r\n if (needToNegate) {\r\n vectorB.negate();\r\n }\r\n }\r\n return vectorB;\r\n }\r\n\r\n _innerFinalize(prevRes, prev, nextRes, dst, chainAsNucleic, getAtomPosition) {\r\n const bFirstInChain = prev === null;\r\n\r\n const lp = getAtomPosition(this._leadAtom);\r\n const currLeadPos = new THREE.Vector3(lp.x, lp.y, lp.z);\r\n if (chainAsNucleic) {\r\n this._detectLeadWing(dst, nextRes, getAtomPosition);\r\n return;\r\n }\r\n\r\n if (bFirstInChain) { // for first one in chain\r\n dst._midPoint = getAtomPosition(this._firstAtom).clone();\r\n } else {\r\n const prevLeadPos = prev._controlPoint; // lead point of previous monomer\r\n dst._midPoint = prevLeadPos.clone().lerp(currLeadPos, 0.5);\r\n dst._wingVector = this.calcWing(prevLeadPos, currLeadPos, getAtomPosition(prevRes._wingAtom), prev._wingVector);\r\n }\r\n dst._controlPoint = currLeadPos;\r\n }\r\n\r\n _finalize2(prev, next, asNucleic) {\r\n // Should be called AFTER first finalize\r\n this._innerFinalize(prev, prev, next, this, asNucleic, (atom) => atom.position);\r\n }\r\n\r\n isConnected(anotherResidue) {\r\n if (this._chain !== anotherResidue._chain) {\r\n return false;\r\n }\r\n if (this === anotherResidue) {\r\n return true;\r\n }\r\n let res = false;\r\n this.forEachAtom((atom) => {\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue === anotherResidue || bond._right.residue === anotherResidue) {\r\n res = true;\r\n return true;\r\n }\r\n }\r\n return false;\r\n });\r\n return res;\r\n }\r\n\r\n _finalize() {\r\n const self = this;\r\n [this._firstAtom] = this._atoms;\r\n this._lastAtom = this._atoms[this._atoms.length - 1];\r\n\r\n this._leadAtom = null;\r\n this._wingAtom = null;\r\n\r\n let tempCount = 0;\r\n let temperature = 0; // average temperature\r\n let occupCount = 0;\r\n let occupancy = 0; // average occupancy\r\n this.forEachAtom((a) => {\r\n if (self._leadAtom === null) {\r\n if (a.role === Element.Constants.Lead) {\r\n self._leadAtom = a;\r\n }\r\n }\r\n if (self._wingAtom === null) {\r\n if (a.role === Element.Constants.Wing) {\r\n self._wingAtom = a;\r\n }\r\n }\r\n if (a.temperature) {\r\n temperature += a.temperature;\r\n tempCount++;\r\n }\r\n if (a.occupancy) {\r\n occupancy += a.occupancy;\r\n occupCount++;\r\n }\r\n return (self._leadAtom !== null && self._wingAtom !== null);\r\n });\r\n\r\n if (tempCount > 0) {\r\n this.temperature = temperature / tempCount;\r\n }\r\n if (occupCount > 0) {\r\n this.occupancy = occupancy / occupCount;\r\n }\r\n\r\n // Still try to make monomer look valid\r\n if (this._leadAtom === null || this._wingAtom === null) {\r\n this._isValid = false;\r\n }\r\n if (this._leadAtom === null) {\r\n this._leadAtom = this._firstAtom;\r\n }\r\n if (this._wingAtom === null) {\r\n this._wingAtom = this._lastAtom;\r\n }\r\n }\r\n}\r\n\r\nexport default Residue;\r\n","/**\r\n * Residue type.\r\n *\r\n * Predefined acid or created with HET, HETNAM, etc.\r\n *\r\n * @param {string} name - Short name, either standard (ALA, MET, etc.) or non-standard one.\r\n * @param {string} fullName - Full residue name.\r\n * @param {string} letterCode - 1-letter symbol.\r\n *\r\n * @exports ResidueType\r\n * @constructor\r\n */\r\nclass ResidueType {\r\n constructor(name, fullName, letterCode) {\r\n this._name = name;\r\n this._fullName = fullName;\r\n this.letterCode = letterCode;\r\n this.flags = 0x0000;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n // DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\n static StandardTypes = {\r\n\r\n ALA: new ResidueType('ALA', 'Alanine', 'A'),\r\n ARG: new ResidueType('ARG', 'Arginine', 'R'),\r\n ASN: new ResidueType('ASN', 'Asparagine', 'N'),\r\n ASP: new ResidueType('ASP', 'Aspartic Acid', 'D'),\r\n CYS: new ResidueType('CYS', 'Cysteine', 'C'),\r\n GLN: new ResidueType('GLN', 'Glutamine', 'Q'),\r\n GLU: new ResidueType('GLU', 'Glutamic Acid', 'E'),\r\n GLY: new ResidueType('GLY', 'Glycine', 'G'),\r\n HIS: new ResidueType('HIS', 'Histidine', 'H'),\r\n ILE: new ResidueType('ILE', 'Isoleucine', 'I'),\r\n LEU: new ResidueType('LEU', 'Leucine', 'L'),\r\n LYS: new ResidueType('LYS', 'Lysine', 'K'),\r\n MET: new ResidueType('MET', 'Methionine', 'M'),\r\n PHE: new ResidueType('PHE', 'Phenylalanine', 'F'),\r\n PRO: new ResidueType('PRO', 'Proline', 'P'),\r\n PYL: new ResidueType('PYL', 'Pyrrolysine', 'O'),\r\n SEC: new ResidueType('SEC', 'Selenocysteine', 'U'),\r\n SER: new ResidueType('SER', 'Serine', 'S'),\r\n THR: new ResidueType('THR', 'Threonine', 'T'),\r\n TRP: new ResidueType('TRP', 'Tryptophan', 'W'),\r\n TYR: new ResidueType('TYR', 'Tyrosine', 'Y'),\r\n VAL: new ResidueType('VAL', 'Valine', 'V'),\r\n A: new ResidueType('A', 'Adenine', 'A'),\r\n C: new ResidueType('C', 'Cytosine', 'C'),\r\n G: new ResidueType('G', 'Guanine', 'G'),\r\n I: new ResidueType('I', 'Inosine', 'I'),\r\n T: new ResidueType('T', 'Thymine', 'T'),\r\n U: new ResidueType('U', 'Uracil', 'U'),\r\n DA: new ResidueType('DA', 'Adenine', 'A'),\r\n DC: new ResidueType('DC', 'Cytosine', 'C'),\r\n DG: new ResidueType('DG', 'Guanine', 'G'),\r\n DI: new ResidueType('DI', 'Inosine', 'I'),\r\n DT: new ResidueType('DT', 'Thymine', 'T'),\r\n DU: new ResidueType('DU', 'Uracil', 'U'),\r\n '+A': new ResidueType('+A', 'Adenine', 'A'),\r\n '+C': new ResidueType('+C', 'Cytosine', 'C'),\r\n '+G': new ResidueType('+G', 'Guanine', 'G'),\r\n '+I': new ResidueType('+I', 'Inosine', 'I'),\r\n '+T': new ResidueType('+T', 'Thymine', 'T'),\r\n '+U': new ResidueType('+U', 'Uracil', 'U'),\r\n WAT: new ResidueType('WAT', 'Water', ''),\r\n H2O: new ResidueType('H2O', 'Water', ''),\r\n HOH: new ResidueType('HOH', 'Water', ''),\r\n DOD: new ResidueType('DOD', 'Water', ''),\r\n UNK: new ResidueType('UNK', 'Unknown', ''),\r\n UNL: new ResidueType('UNL', 'Unknown Ligand', ''),\r\n\r\n };\r\n\r\n /**\r\n * Enumeration of residue flag values.\r\n *\r\n * @enum {number}\r\n * @readonly\r\n */\r\n static Flags = {\r\n // Amino acids\r\n /** Amino acid residue */\r\n PROTEIN: 0x0001,\r\n /** Basic amino acid residue */\r\n BASIC: 0x0002,\r\n /** Acidic amino acid residue */\r\n ACIDIC: 0x0004,\r\n /** Polar uncharged side chain amino acid residue */\r\n POLAR: 0x0008,\r\n /** Non-polar hydrophobic side chain amino acid residue */\r\n NONPOLAR: 0x0010,\r\n /** Aromatic amino acid residue */\r\n AROMATIC: 0x0020,\r\n\r\n // Nucleic acids\r\n\r\n /** Nucleic residue */\r\n NUCLEIC: 0x0100,\r\n /** Purine nucleic residue */\r\n PURINE: 0x0200,\r\n /** Pyrimidine nucleic residue */\r\n PYRIMIDINE: 0x0400,\r\n /** DNA */\r\n DNA: 0x0800,\r\n /** RNA */\r\n RNA: 0x1000,\r\n\r\n /** Water */\r\n WATER: 0x10000,\r\n };\r\n}\r\n\r\n// Flag combinations\r\nfunction _addFlag(flag, list) {\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const res = ResidueType.StandardTypes[list[i]];\r\n if (res) {\r\n res.flags |= flag;\r\n }\r\n }\r\n}\r\n\r\nconst { Flags } = ResidueType;\r\n_addFlag(Flags.WATER, ['WAT', 'H2O', 'HOH', 'DOD']);\r\n\r\n_addFlag(Flags.PROTEIN, [\r\n 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLY', 'GLU', 'GLN', 'HIS', 'ILE',\r\n 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'PYL', 'SEC', 'SER', 'THR', 'TRP',\r\n 'TYR', 'VAL',\r\n]);\r\n_addFlag(Flags.BASIC, ['ARG', 'HIS', 'LYS']);\r\n_addFlag(Flags.ACIDIC, ['ASP', 'GLU']);\r\n_addFlag(Flags.POLAR, ['ASN', 'CYS', 'GLN', 'SER', 'THR', 'TYR']);\r\n_addFlag(Flags.NONPOLAR, ['ALA', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'VAL', 'GLY']);\r\n_addFlag(Flags.AROMATIC, ['PHE', 'TRP', 'TYR']);\r\n\r\n_addFlag(Flags.NUCLEIC, [\r\n 'A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I',\r\n 'C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U',\r\n]);\r\n_addFlag(Flags.PURINE, ['A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I']);\r\n_addFlag(Flags.PYRIMIDINE, ['C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U']);\r\n_addFlag(Flags.DNA, ['DA', 'DG', 'DI', 'DC', 'DT', 'DU']);\r\n_addFlag(Flags.RNA, ['A', 'G', 'I', 'C', 'T', 'U']);\r\n// Table of kdHydrophobicity\r\nconst hydro = {\r\n ILE: 4.5,\r\n VAL: 4.2,\r\n LEU: 3.8,\r\n PHE: 2.8,\r\n CYS: 2.5,\r\n MET: 1.9,\r\n ALA: 1.8,\r\n GLY: -0.4,\r\n THR: -0.7,\r\n SER: -0.8,\r\n TRP: -0.9,\r\n TYR: -1.3,\r\n PRO: -1.6,\r\n HIS: -3.2,\r\n GLU: -3.5,\r\n GLN: -3.5,\r\n ASP: -3.5,\r\n ASN: -3.5,\r\n LYS: -3.9,\r\n ARG: -4.5,\r\n};\r\n\r\nfunction _addParam(param, list) {\r\n const keys = Object.keys(list);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const key = keys[i];\r\n const value = list[key];\r\n ResidueType.StandardTypes[key][param] = value;\r\n }\r\n}\r\n\r\n_addParam('hydrophobicity', hydro);\r\n\r\nexport default ResidueType;\r\n","import * as THREE from 'three';\r\nimport Residue from './Residue';\r\nimport ResidueType from './ResidueType';\r\n\r\n/**\r\n * Residues in chain are either amino acid either nucleic acid (and water)\r\n * There might be some modified/mutated residues, which type could not be determined by their name (nucleic or amino); In this\r\n * case firstly program definites the chain type (by well-known residues) and then definites modified/mutated residues\r\n */\r\nconst ChainType = {\r\n UNKNOWN: 0,\r\n PROTEIN: 1,\r\n NUCLEIC: 2,\r\n};\r\n\r\n/**\r\n * Residue chain.\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n * @param {string} name - One character identifier (usually space, A-Z, 0-9, or a-z).\r\n *\r\n * @exports Chain\r\n * @constructor\r\n */\r\nclass Chain {\r\n constructor(complex, name) {\r\n this._complex = complex;\r\n this._name = name;\r\n this._mask = 1 | 0;\r\n this._index = -1;\r\n this._residues = [];\r\n\r\n this.minSequence = Number.POSITIVE_INFINITY;\r\n this.maxSequence = Number.NEGATIVE_INFINITY;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n _determineType() {\r\n const residues = this._residues;\r\n\r\n const { PROTEIN, NUCLEIC } = ResidueType.Flags;\r\n\r\n this.type = ChainType.UNKNOWN;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const { flags } = residues[i]._type;\r\n\r\n if ((flags & NUCLEIC) !== 0) {\r\n this.type = ChainType.NUCLEIC;\r\n break;\r\n } else if ((flags & PROTEIN) !== 0) {\r\n this.type = ChainType.PROTEIN;\r\n break;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Finds thre residue with specified sequence number and inserion code\r\n * @param {Number} seqNum sequence number\r\n * @param {string} iCode insertion code\r\n * @returns {*} Residue or null if not found\r\n */\r\n findResidue(seqNum, iCode) {\r\n const residues = this._residues;\r\n\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n if (res._sequence === seqNum && res._icode === iCode) {\r\n return [res, i];\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _finalize() {\r\n this._determineType();\r\n\r\n const residues = this._residues;\r\n\r\n let prev = null;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n const next = (i + 1 < n) ? residues[i + 1] : null;\r\n const curr = residues[i];\r\n // TODO: skip invalid residues\r\n if (1 /* curr._isValid */) { // eslint-disable-line no-constant-condition\r\n curr._finalize2(prev, next, this.type === ChainType.NUCLEIC);\r\n prev = curr;\r\n }\r\n }\r\n\r\n // fix very first wing\r\n if (residues.length > 1 && residues[1]._wingVector) {\r\n const p = residues[1]._wingVector;\r\n residues[0]._wingVector = new THREE.Vector3(p.x, p.y, p.z);\r\n } else if (residues.length > 0) {\r\n residues[0]._wingVector = new THREE.Vector3(1, 0, 0);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const residues = this._residues;\r\n let prev = null;\r\n let prevData = null;\r\n const frameRes = frameData._residues;\r\n const n = residues.length;\r\n function getAtomPos(atom) {\r\n return frameData.getAtomPos(atom.index);\r\n }\r\n\r\n for (let i = 0; i < n; ++i) {\r\n const curr = residues[i];\r\n const currData = frameRes[curr._index];\r\n const nextRes = (i + 1 < n) ? residues[i + 1] : null;\r\n curr._innerFinalize(prev, prevData, nextRes, currData, this.type === ChainType.NUCLEIC, getAtomPos);\r\n prev = curr;\r\n prevData = currData;\r\n }\r\n\r\n frameRes[residues[0]._index]._wingVector = n > 1\r\n ? frameRes[residues[1]._index]._wingVector\r\n : new THREE.Vector3(1, 0, 0);\r\n }\r\n\r\n /**\r\n * Create a new residue.\r\n *\r\n * @param {string} name - Residue name.\r\n * @param {number} sequence - Residue sequence number.\r\n * @param {string} iCode - Insertion code.\r\n * @returns {Residue} - Newly created residue instance.\r\n */\r\n addResidue(name, sequence, iCode) {\r\n let type = this._complex.getResidueType(name);\r\n if (type === null) {\r\n type = this._complex.addResidueType(name);\r\n }\r\n const residue = new Residue(this, type, sequence, iCode);\r\n this._complex.addResidue(residue);\r\n this._residues.push(residue);\r\n\r\n if (type.flags & (ResidueType.Flags.NUCLEIC | ResidueType.Flags.PROTEIN)) {\r\n if (this.maxSequence < sequence) {\r\n this.maxSequence = sequence;\r\n }\r\n if (this.minSequence > sequence) {\r\n this.minSequence = sequence;\r\n }\r\n }\r\n\r\n return residue;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this._mask = mask;\r\n }\r\n}\r\n\r\nexport default Chain;\r\n","import Residue from './Residue';\r\n\r\n/** An element of protein secondary structure. */\r\nclass StructuralElement {\r\n /**\r\n * Create a secondary structural element of the specified type.\r\n *\r\n * @param {StructuralElement.Type} type Secondary structure type.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n */\r\n constructor(type, init, term) {\r\n /**\r\n * Secondary structure type.\r\n * @type {StructuralElement.Type}\r\n */\r\n this.type = type;\r\n /**\r\n * Generic secondary structure type.\r\n * @type {StructuralElement.Generic}\r\n */\r\n this.generic = StructuralElement.genericByType[this.type] || 'loop';\r\n /**\r\n * Initial residue.\r\n * @type Residue\r\n */\r\n this.init = init;\r\n /**\r\n * Terminal residue.\r\n * @type Residue\r\n */\r\n this.term = term;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n if (this.init instanceof Residue && this.term instanceof Residue) {\r\n return;\r\n }\r\n\r\n // Link all intermediate residues to this structural element\r\n const start = complex.splitUnifiedSerial(this.init);\r\n const end = complex.splitUnifiedSerial(this.term);\r\n for (let chainId = start.chain; chainId <= end.chain; chainId++) {\r\n for (let serialId = start.serial; serialId <= end.serial; serialId++) {\r\n for (let { iCode } = start; iCode <= end.iCode; iCode++) {\r\n const hashCode = complex.getUnifiedSerial(chainId, serialId, iCode);\r\n if (residueHash[hashCode]) {\r\n residueHash[hashCode]._secondary = this;\r\n }\r\n }\r\n }\r\n }\r\n\r\n // Replace unfined serials by objects\r\n this.init = residueHash[this.init];\r\n this.term = residueHash[this.term];\r\n }\r\n}\r\n\r\n/**\r\n * Specific type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Generic\r\n */\r\nStructuralElement.Type = {\r\n /** A strand of a [beta-sheet](https://en.wikipedia.org/wiki/Beta_sheet). */\r\n STRAND: 'E',\r\n /** An isolated beta-bridge (too small for a beta-sheet). */\r\n BRIDGE: 'B',\r\n\r\n /** A [3/10 helix](https://en.wikipedia.org/wiki/310_helix) (hydrogen bonding is 3 residues apart). */\r\n HELIX_310: 'G',\r\n /** An [alpha-helix](https://en.wikipedia.org/wiki/Alpha_helix) (hydrogen bonding is 4 residues apart). */\r\n HELIX_ALPHA: 'H',\r\n /** A [pi-helix](https://en.wikipedia.org/wiki/Pi_helix) (hydrogen bonding is 5 residues apart). */\r\n HELIX_PI: 'I',\r\n /** A generic helix of unspecified bonding distance. */\r\n HELIX: 'X',\r\n\r\n /** An isolated 3/10-like helical turn. */\r\n TURN_310: '3',\r\n /** An isolated alpha-like helical turn. */\r\n TURN_ALPHA: '4',\r\n /** An isolated pi-like helical turn. */\r\n TURN_PI: '5',\r\n /** An isolated helical [turn](https://en.wikipedia.org/wiki/Turn_(biochemistry)) of unspecified bonding distance. */\r\n TURN: 'T',\r\n\r\n /** A bend (a region of high curvature). */\r\n BEND: 'S',\r\n /** Just a protein section with no particular conformation. */\r\n COIL: 'C',\r\n};\r\n\r\n/**\r\n * Generic type of a secondary structural element.\r\n * @enum {string}\r\n * @see StructuralElement.Type\r\n */\r\nStructuralElement.Generic = {\r\n /** A strand of a sheet. */\r\n STRAND: 'strand',\r\n /** A helix. */\r\n HELIX: 'helix',\r\n /** Just a protein section with no particular conformation. */\r\n LOOP: 'loop',\r\n};\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\nconst StructuralElementGeneric = StructuralElement.Generic;\r\n\r\n/**\r\n * A mapping from specific types to generic ones.\r\n * @type {Object}\r\n */\r\nStructuralElement.genericByType = {\r\n [StructuralElementType.STRAND]: StructuralElementGeneric.STRAND,\r\n [StructuralElementType.HELIX_310]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_ALPHA]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX_PI]: StructuralElementGeneric.HELIX,\r\n [StructuralElementType.HELIX]: StructuralElementGeneric.HELIX,\r\n};\r\n\r\nexport default StructuralElement;\r\n","import StructuralElement from './StructuralElement';\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\nexport const typeByPDBHelixClass = {\r\n 1: StructuralElementType.HELIX_ALPHA,\r\n 3: StructuralElementType.HELIX_PI,\r\n 5: StructuralElementType.HELIX_310,\r\n};\r\n\r\n/**\r\n * Helical secondary structure of a protein.\r\n * @extends StructuralElement\r\n */\r\nclass Helix extends StructuralElement {\r\n /**\r\n * Create a helix.\r\n *\r\n * @param {number} helixClass A helix class according to the\r\n * [PDB Format](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX).\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} serial Serial number of the helix (see PDB Format).\r\n * @param {string} name Helix identifier (see PDB Format).\r\n * @param {string} comment Comment about this helix (see PDB Format).\r\n * @param {number} length Length of this helix, in residues (see PDB Format).\r\n */\r\n constructor(helixClass, init, term, serial, name, comment, length) {\r\n super(typeByPDBHelixClass[helixClass] || StructuralElement.Type.HELIX, init, term);\r\n\r\n /**\r\n * Serial number of the helix (see PDB Format).\r\n * @type {number}\r\n */\r\n this.serial = serial;\r\n /**\r\n * Helix identifier (see PDB Format).\r\n * @type {string}\r\n */\r\n this.name = name;\r\n /**\r\n * Comment about this helix (see PDB Format).\r\n * @type {string}\r\n */\r\n this.comment = comment;\r\n /**\r\n * Length of this helix, in residues (see PDB Format).\r\n * @type {number}\r\n */\r\n this.length = length;\r\n }\r\n}\r\n\r\nexport default Helix;\r\n","import StructuralElement from './StructuralElement';\r\n\r\n/**\r\n * A single strand of a sheet in a protein secondary structure.\r\n * @extends StructuralElement\r\n */\r\nclass Strand extends StructuralElement {\r\n /**\r\n * Create a strand.\r\n *\r\n * @param {Sheet} sheet Parent sheet this strand belongs to.\r\n * @param {Residue} init Initial residue.\r\n * @param {Residue} term Terminal residue.\r\n * @param {number} sense Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @param {Atom} atomCur Atom in current strand (see PDB Format).\r\n * @param {Atom} atomPrev Atom in previous strand (see PDB Format).\r\n */\r\n constructor(sheet, init, term, sense, atomCur, atomPrev) {\r\n super(StructuralElement.Type.STRAND, init, term);\r\n\r\n /**\r\n * Parent sheet this strand belongs to.\r\n * @type {Sheet}\r\n */\r\n this.sheet = sheet;\r\n /**\r\n * Sense of strand with respect to previous strand in the sheet.\r\n * - 0 if the first strand,\r\n * - 1 if parallel, and\r\n * - -1 if anti-parallel.\r\n * @type {number}\r\n */\r\n this.sense = sense;\r\n /**\r\n * Atom in current strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomCur = atomCur;\r\n /**\r\n * Atom in previous strand (see PDB Format).\r\n * @type {Atom}\r\n */\r\n this.atomPrev = atomPrev;\r\n }\r\n\r\n /**\r\n * An internal method for making a final pass over the complex to set all required references.\r\n *\r\n * **NOTE:** I'm sorry. It's a legacy code waiting for refactoring.\r\n * Just copying it as-is right now and hoping for the best.\r\n *\r\n * @param {object} serialAtomMap A dictionary of atoms\r\n * @param {object} residueHash A dictionary of hashed residues to check.\r\n * @param {Complex} complex The molecular complex this element belongs to.\r\n *\r\n * @override\r\n */\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n super._finalize(serialAtomMap, residueHash, complex);\r\n\r\n let as = this.atomCur;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomCur = serialAtomMap[as];\r\n }\r\n as = this.atomPrev;\r\n if (as !== null && !Number.isNaN(as)) {\r\n this.atomPrev = serialAtomMap[as];\r\n }\r\n }\r\n}\r\n\r\nexport default Strand;\r\n","import Strand from './Strand';\r\n\r\n/**\r\n * Sheet secondary structure of a protein.\r\n *\r\n * @param {string} name -\r\n * @param {number} width -\r\n *\r\n * @exports Sheet\r\n * @constructor\r\n */\r\nclass Sheet {\r\n constructor(name, width) {\r\n this._name = name;\r\n this._width = width;\r\n\r\n this._strands = [];\r\n }\r\n\r\n // Getters and setters\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getWidth() {\r\n return this._width;\r\n }\r\n\r\n addStrand(strand) {\r\n this._strands.push(strand);\r\n this._width = this._strands.length;\r\n }\r\n\r\n addEmptyStrand() {\r\n this._strands.push(new Strand(null, null, null, null, null, null));\r\n }\r\n\r\n _finalize(serialAtomMap, residueHash, complex) {\r\n const s = this._strands;\r\n for (let i = 0, n = s.length; i < n; ++i) {\r\n s[i]._finalize(serialAtomMap, residueHash, complex);\r\n }\r\n if (!this._width) {\r\n this._width = s.length;\r\n }\r\n if (s.length !== this._width) {\r\n throw new Error(`Sheet ${this._name} is inconsistent.`);\r\n }\r\n }\r\n}\r\n\r\nexport default Sheet;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Atom measurements.\r\n *\r\n * @param {string} id - SGroup id\r\n * @param {string} name - Name of the group\r\n * @param {THREE.Vector3} position - Registered coordinates\r\n * @param {array} atoms - Atoms group consists of\r\n * @param {object} saveNode - XML node from file for saving\r\n *\r\n * @exports SGroup\r\n * @constructor\r\n */\r\nclass SGroup {\r\n constructor(id, name, position, atoms, saveNode) {\r\n this._id = id;\r\n this._name = name;\r\n this._position = position || new THREE.Vector3();\r\n this._atoms = atoms || [];\r\n this._charge = 0; // default group charge\r\n this._repeat = 1; // how many times group repeated: always > 0\r\n this._center = null;\r\n this.xmlNodeRef = saveNode || null;\r\n }\r\n\r\n /**\r\n * Get atom full name.\r\n * @returns {string} Atom full name.\r\n */\r\n getName() {\r\n return this._name;\r\n }\r\n\r\n getPosition() {\r\n return this._position;\r\n }\r\n\r\n getCentralPoint() {\r\n return this._center;\r\n }\r\n\r\n _rebuildSGroupOnAtomChange() {\r\n const nLimon = 100000000;\r\n if (this._center === null) {\r\n return; // nothing to do if we are not relative\r\n }\r\n\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n for (let j = 0, n = this._atoms.length; j < n; j++) {\r\n const aPos = this._atoms[j].position;\r\n bLow.set(Math.min(bLow.x, aPos.x), Math.min(bLow.y, aPos.y), Math.min(bLow.z, aPos.z));\r\n bHight.set(Math.max(bHight.x, aPos.x), Math.max(bHight.y, aPos.y), Math.max(bHight.z, aPos.z));\r\n }\r\n this._center.addVectors(bLow, bHight);\r\n this._center.multiplyScalar(0.5);\r\n }\r\n}\r\n\r\nexport default SGroup;\r\n","import utils from '../../utils';\r\n\r\n//----------------------------------------------------------------------------\r\nclass Range {\r\n constructor(min, max) {\r\n this.min = min;\r\n this.max = typeof max === 'undefined' ? min : max;\r\n }\r\n\r\n includes(value) {\r\n return this.min <= value && value <= this.max;\r\n }\r\n\r\n toString() {\r\n const { min, max } = this;\r\n return min === max ? String(min) : [min, max].join(':');\r\n }\r\n\r\n toJSON() {\r\n return [this.min, this.max];\r\n }\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\nclass List {\r\n constructor(arg) {\r\n if (arg instanceof this.constructor) {\r\n // delegate construction to a different class\r\n // eslint-disable-next-line no-constructor-return\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n }\r\n\r\n append(value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n }\r\n\r\n toString() {\r\n return this._values.join(',');\r\n }\r\n\r\n toJSON() {\r\n const values = this._values;\r\n const result = [];\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n result[i] = value.toJSON ? value.toJSON() : value;\r\n }\r\n return result;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nclass RangeList extends List {\r\n includes(value) {\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n if (list[i].includes(value)) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\n//----------------------------------------------------------------------------\r\n\r\nconst valuesArray = [];\r\n\r\nclass ValueList extends List {\r\n constructor(arg, upperOnly) {\r\n const list = super(arg);\r\n if (upperOnly) {\r\n this.upperOnly = true;\r\n const values = list._values;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n const value = values[i];\r\n if (typeof value === 'string') {\r\n values[i] = value.toUpperCase();\r\n }\r\n }\r\n } else {\r\n this.upperOnly = false;\r\n }\r\n // return constructed object\r\n // eslint-disable-next-line no-constructor-return\r\n return list;\r\n }\r\n\r\n includes(value) {\r\n // we do not convert to upper case here for perfomance reasons\r\n // if list is upper case only, value must be converted before it is sent up to here\r\n return this._values.indexOf(value) !== -1;\r\n }\r\n\r\n toString() {\r\n // Quote values that are not correct identifiers\r\n const values = this._values;\r\n valuesArray.length = 0;\r\n for (let i = 0, n = values.length; i < n; ++i) {\r\n valuesArray[i] = utils.correctSelectorIdentifier(String(values[i]));\r\n }\r\n return valuesArray.join(',');\r\n }\r\n\r\n _validate(value) {\r\n return (this.upperOnly && typeof value === 'string') ? value.toUpperCase() : value;\r\n }\r\n\r\n append(value) {\r\n super.append(this._validate(value));\r\n return this;\r\n }\r\n\r\n remove(value) {\r\n super.remove(this._validate(value));\r\n return this;\r\n }\r\n}\r\n\r\nexport {\r\n Range,\r\n List,\r\n RangeList,\r\n ValueList,\r\n};\r\n","import { RangeList, ValueList } from './selectArgs';\r\n\r\n/** Base class for atom selectors. */\r\nclass Selector {\r\n toString() {\r\n return this.keyword;\r\n }\r\n\r\n toJSON() {\r\n return [this.name];\r\n }\r\n}\r\n\r\nSelector.prototype.name = 'Error';\r\nSelector.prototype.keyword = 'error';\r\n\r\n/** Base class for list-based atom selectors. */\r\nclass ListSelector extends Selector {\r\n constructor(list) {\r\n super();\r\n this.list = list;\r\n }\r\n\r\n toString() {\r\n return `${this.keyword} ${this.list}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.list.toJSON()];\r\n }\r\n}\r\n\r\nclass RangeListSelector extends ListSelector {\r\n constructor(arg) {\r\n super(new RangeList(arg));\r\n }\r\n}\r\n\r\nclass ValueListSelector extends ListSelector {\r\n constructor(arg, caseSensitive) {\r\n super(new ValueList(arg, !caseSensitive));\r\n }\r\n}\r\n\r\nclass NoneSelector extends Selector {\r\n includesAtom(_atom) {\r\n return false;\r\n }\r\n}\r\n\r\nNoneSelector.prototype.name = 'None';\r\nNoneSelector.prototype.keyword = 'none';\r\n\r\nclass AllSelector extends Selector {\r\n includesAtom(_atom) {\r\n return true;\r\n }\r\n}\r\n\r\nAllSelector.prototype.name = 'All';\r\nAllSelector.prototype.keyword = 'all';\r\n\r\nexport {\r\n Selector,\r\n ListSelector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n};\r\n","import { Selector, NoneSelector } from './selectorsBase';\r\n\r\n//----------------------------------------------------------------------------\r\n// Operators\r\n//----------------------------------------------------------------------------\r\nconst none = new NoneSelector();\r\n\r\nclass PrefixOperator extends Selector {\r\n constructor(rhs) {\r\n super();\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nPrefixOperator.prototype.priority = 1;\r\n\r\nclass InfixOperator extends Selector {\r\n constructor(lhs, rhs) {\r\n super();\r\n this.lhs = lhs || none;\r\n this.rhs = rhs || none;\r\n }\r\n\r\n toString() {\r\n const lhs = this.lhs.priority && this.lhs.priority > this.priority ? `(${this.lhs})` : this.lhs;\r\n const rhs = this.rhs.priority && this.rhs.priority > this.priority ? `(${this.rhs})` : this.rhs;\r\n return `${lhs} ${this.keyword} ${rhs}`;\r\n }\r\n\r\n toJSON() {\r\n return [this.name, this.lhs.toJSON(), this.rhs.toJSON()];\r\n }\r\n}\r\n\r\nInfixOperator.prototype.priority = 1000;\r\n\r\nexport { PrefixOperator, InfixOperator };\r\n","import Atom from './Atom';\r\nimport ResidueType from './ResidueType';\r\nimport { parser } from '../utils/SelectionParser';\r\nimport { Range, RangeList, ValueList } from './selectors/selectArgs';\r\nimport { PrefixOperator, InfixOperator } from './selectors/selectOps';\r\nimport {\r\n Selector,\r\n RangeListSelector,\r\n ValueListSelector,\r\n NoneSelector,\r\n AllSelector,\r\n} from './selectors/selectorsBase';\r\n\r\nconst keywords = {};\r\n\r\n//----------------------------------------------------------------------------\r\n// Named selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineSelector(name, SelectorClass) {\r\n const keyword = name.toLowerCase();\r\n SelectorClass.prototype.keyword = keyword;\r\n SelectorClass.prototype.name = name;\r\n\r\n const factory = ((...args) => new SelectorClass(...args));\r\n factory.SelectorClass = SelectorClass;\r\n keywords[keyword] = factory;\r\n\r\n return SelectorClass;\r\n}\r\n\r\ndefineSelector('Serial', class SerialSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.serial);\r\n }\r\n});\r\n\r\ndefineSelector('Name', class NameSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.name);\r\n }\r\n});\r\n\r\ndefineSelector('AltLoc', class AltLocSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(String.fromCharCode(atom.location));\r\n }\r\n});\r\n\r\ndefineSelector('Elem', class ElemSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.element.name);\r\n }\r\n});\r\n\r\ndefineSelector('Residue', class ResidueSelector extends ValueListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._type._name);\r\n }\r\n});\r\n\r\ndefineSelector('Sequence', class SequenceSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._sequence);\r\n }\r\n});\r\n\r\ndefineSelector('ICode', class ICodeSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._icode);\r\n }\r\n});\r\n\r\ndefineSelector('ResIdx', class ResIdxSelector extends RangeListSelector {\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._index);\r\n }\r\n});\r\n\r\ndefineSelector('Chain', class ChainSelector extends ValueListSelector {\r\n constructor(arg) {\r\n super(arg, true);\r\n }\r\n\r\n includesAtom(atom) {\r\n return this.list.includes(atom.residue._chain._name);\r\n }\r\n});\r\n\r\ndefineSelector('Hetatm', class HetatmSelector extends Selector {\r\n includesAtom(atom) {\r\n return atom.het;\r\n }\r\n});\r\n\r\ndefineSelector('PolarH', class PolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.HYDROGEN;\r\n }\r\n});\r\n\r\ndefineSelector('NonPolarH', class NonPolarHSelector extends Selector {\r\n includesAtom(atom) {\r\n return (atom.flags & Atom.Flags.NONPOLARH) === Atom.Flags.NONPOLARH;\r\n }\r\n});\r\n\r\ndefineSelector('All', AllSelector);\r\n\r\ndefineSelector('None', NoneSelector);\r\n\r\nconst NULL_SELECTOR = keywords.none();\r\n\r\n//----------------------------------------------------------------------------\r\n// Named operators\r\n//----------------------------------------------------------------------------\r\n\r\nfunction defineOperator(name, priority, OperatorClass) {\r\n OperatorClass.prototype.priority = priority;\r\n return defineSelector(name, OperatorClass);\r\n}\r\ndefineOperator('Not', 1, class NotOperator extends PrefixOperator {\r\n includesAtom(atom) {\r\n return !this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('And', 2, class AndOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) && this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\ndefineOperator('Or', 3, class OrOperator extends InfixOperator {\r\n includesAtom(atom) {\r\n return this.lhs.includesAtom(atom) || this.rhs.includesAtom(atom);\r\n }\r\n});\r\n\r\n//----------------------------------------------------------------------------\r\n// Flag selectors\r\n//----------------------------------------------------------------------------\r\n\r\nfunction byResidueTypeFlag(flag, name) {\r\n return defineSelector(name, class extends Selector {\r\n includesAtom(atom) {\r\n return (atom.residue._type.flags & flag) !== 0;\r\n }\r\n });\r\n}\r\n\r\nbyResidueTypeFlag(ResidueType.Flags.PROTEIN, 'Protein');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC, 'Basic');\r\nbyResidueTypeFlag(ResidueType.Flags.ACIDIC, 'Acidic');\r\nbyResidueTypeFlag(ResidueType.Flags.BASIC | ResidueType.Flags.ACIDIC, 'Charged');\r\nbyResidueTypeFlag(ResidueType.Flags.POLAR, 'Polar');\r\nbyResidueTypeFlag(ResidueType.Flags.NONPOLAR, 'NonPolar');\r\nbyResidueTypeFlag(ResidueType.Flags.AROMATIC, 'Aromatic');\r\nbyResidueTypeFlag(ResidueType.Flags.NUCLEIC, 'Nucleic');\r\nbyResidueTypeFlag(ResidueType.Flags.PURINE, 'Purine');\r\nbyResidueTypeFlag(ResidueType.Flags.PYRIMIDINE, 'Pyrimidine');\r\nbyResidueTypeFlag(ResidueType.Flags.WATER, 'Water');\r\n\r\n//----------------------------------------------------------------------------\r\nconst selectors = Object.create(keywords);\r\n\r\nselectors.Selector = Selector;\r\nselectors.RangeListSelector = RangeListSelector;\r\nselectors.ValueListSelector = ValueListSelector;\r\nselectors.Range = Range;\r\nselectors.RangeList = RangeList;\r\nselectors.ValueList = ValueList;\r\nselectors.PrefixOperator = PrefixOperator;\r\nselectors.InfixOperator = InfixOperator;\r\nselectors.Context = Object.create({});\r\n\r\nselectors.GetSelector = function (key) {\r\n if (!selectors.Context.hasOwnProperty(key)) {\r\n const exc = { message: `selector ${key} is not registered` };\r\n throw exc;\r\n }\r\n return selectors.Context[key] || NULL_SELECTOR;\r\n};\r\n\r\nselectors.ClearContext = function () {\r\n Object.keys(selectors.Context).forEach((k) => { delete selectors.Context[k]; });\r\n};\r\n\r\nselectors.keyword = function (key) {\r\n return keywords[key.toLowerCase()] || keywords.none;\r\n};\r\n\r\nselectors.parse = function (str) {\r\n const res = {};\r\n try {\r\n res.selector = parser.parse(str);\r\n } catch (e) {\r\n res.selector = NULL_SELECTOR;\r\n res.error = e.message;\r\n }\r\n return res;\r\n};\r\n\r\nparser.yy = selectors;\r\nparser.yy.parseError = parser.parseError; // workaround for incorrect JISON parser generator for AMD module\r\n\r\nexport default selectors;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\n\r\n/**\r\n * Basic biological unit class.\r\n *\r\n * @exports BiologicalUnit\r\n * @constructor\r\n */\r\nclass BiologicalUnit {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._selector = selectors.keyword('All')();\r\n this._boundaries = {\r\n boundingBox: new THREE.Box3(),\r\n boundingSphere: new THREE.Sphere(),\r\n };\r\n }\r\n\r\n computeBoundaries() {\r\n const atoms = this._complex._atoms;\r\n const n = atoms.length;\r\n const selector = this._selector;\r\n\r\n const { boundingBox } = this._boundaries;\r\n boundingBox.makeEmpty();\r\n if (n === 1) {\r\n boundingBox.expandByPoint(atoms[0].position);\r\n const bbc = new THREE.Vector3();\r\n boundingBox.getCenter(bbc);\r\n const s = 2 * atoms[0].element.radius;\r\n boundingBox.setFromCenterAndSize(bbc, new THREE.Vector3(s, s, s));\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (selector.includesAtom(atoms[i])) {\r\n boundingBox.expandByPoint(atoms[i].position);\r\n }\r\n }\r\n }\r\n\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n if (n === 1) {\r\n this._boundaries.boundingSphere.set(center, atoms[0].element.radius);\r\n } else {\r\n for (let i = 0; i < n; ++i) {\r\n if (!selector.includesAtom(atoms[i])) {\r\n continue;\r\n }\r\n const pos = atoms[i].position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n this._boundaries.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n }\r\n\r\n getTransforms() {\r\n return [];\r\n }\r\n\r\n getSelector() {\r\n return this._selector;\r\n }\r\n\r\n getBoundaries() {\r\n return this._boundaries;\r\n }\r\n\r\n finalize() {\r\n }\r\n}\r\n\r\nexport default BiologicalUnit;\r\n","import * as THREE from 'three';\r\nimport selectors from './selectors';\r\nimport BiologicalUnit from './BiologicalUnit';\r\n\r\n/**\r\n * Biological assembly.\r\n *\r\n * @exports Assembly\r\n * @constructor\r\n */\r\n\r\nclass Assembly extends BiologicalUnit {\r\n constructor(complex) {\r\n super(complex);\r\n this.chains = [];\r\n this.matrices = [];\r\n }\r\n\r\n computeBoundaries() {\r\n super.computeBoundaries();\r\n // fix up the boundaries\r\n const { matrices } = this;\r\n const oldCenter = this._boundaries.boundingSphere.center;\r\n const oldRad = this._boundaries.boundingSphere.radius;\r\n const boundingBox = this._boundaries.boundingBox = new THREE.Box3();\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = matrices.length; i < n; ++i) {\r\n boundingBox.expandByPoint(oldCenter.clone().applyMatrix4(matrices[i]));\r\n }\r\n\r\n const newRad = boundingBox.max.distanceTo(boundingBox.min) / 2 + oldRad;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n this._boundaries.boundingSphere = new THREE.Sphere().set(center, newRad);\r\n boundingBox.max.addScalar(oldRad);\r\n boundingBox.min.subScalar(oldRad);\r\n }\r\n\r\n /**\r\n * Mark a chain as belonging to this biological assembly.\r\n * @param {string} chain - chain identifier, usually a single letter\r\n */\r\n addChain(chain) {\r\n this.chains[this.chains.length] = chain;\r\n }\r\n\r\n /**\r\n * Add a transformation matrix.\r\n * @param {THREE.Matrix4} matrix - transformation matrix\r\n */\r\n addMatrix(matrix) {\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n getTransforms() {\r\n return this.matrices;\r\n }\r\n\r\n finalize() {\r\n if (this.chains.length > 0) {\r\n this._selector = selectors.keyword('Chain')(this.chains);\r\n } else {\r\n this._selector = selectors.keyword('None')();\r\n }\r\n }\r\n}\r\n\r\nexport default Assembly;\r\n","/**\r\n * This class represents connected component as a part of a complex.\r\n * WARNING! The whole component entity is build under the assumption that residues\r\n * are placed in the chains and complex in ascending order of indices\r\n *\r\n * @param {Complex} complex - Molecular complex this chain belongs to.\r\n *\r\n * @exports Component\r\n * @constructor\r\n */\r\nclass Component {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._index = -1;\r\n this._residueIndices = [];\r\n this._cycles = [];\r\n this._subDivs = [];\r\n this._residueCount = 0;\r\n }\r\n\r\n getResidues() {\r\n return this._complex._residues;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residueCount;\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._complex._residues;\r\n const resIdc = this._residueIndices;\r\n for (let idIdc = 0, idCount = resIdc.length; idIdc < idCount; ++idIdc) {\r\n for (let idx = resIdc[idIdc].start, last = resIdc[idIdc].end; idx <= last; ++idx) {\r\n process(residues[idx]);\r\n }\r\n }\r\n }\r\n\r\n setSubDivs(subDivs) {\r\n this._subDivs = subDivs;\r\n let curr = 0;\r\n const resIdc = [];\r\n let resCnt = 0;\r\n for (let i = 0, n = subDivs.length; i < n; ++i) {\r\n if (i === n - 1 || subDivs[i].end + 1 !== subDivs[i + 1].start) {\r\n const { start } = subDivs[curr];\r\n const { end } = subDivs[i];\r\n resIdc[resIdc.length] = {\r\n start,\r\n end,\r\n };\r\n resCnt += end - start + 1;\r\n curr = i + 1;\r\n }\r\n }\r\n\r\n this._residueIndices = resIdc;\r\n this._residueCount = resCnt;\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._complex._bonds;\r\n\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n const bond = bonds[i];\r\n if (bond._left.residue._component === this) {\r\n process(bond);\r\n }\r\n }\r\n }\r\n\r\n update() {\r\n this.forEachCycle((cycle) => {\r\n cycle.update();\r\n });\r\n }\r\n\r\n forEachAtom(process) {\r\n this.forEachResidue((residue) => {\r\n residue.forEachAtom(process);\r\n });\r\n }\r\n\r\n addCycle(cycle) {\r\n this._cycles.push(cycle);\r\n }\r\n\r\n forEachCycle(process) {\r\n const cycles = this._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n process(cycles[i]);\r\n }\r\n }\r\n\r\n markResidues() {\r\n const self = this;\r\n self.forEachResidue((residue) => {\r\n residue._component = self;\r\n });\r\n }\r\n\r\n _forEachSubChain(mask, process) {\r\n const residues = this._complex._residues;\r\n const subs = this._subDivs;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let idx = subs[i].start, last = subs[i].end; idx <= last; ++idx) {\r\n const currRes = residues[idx];\r\n if (mask & currRes._mask && currRes._isValid) {\r\n let end = idx + 1;\r\n for (; end <= last; ++end) {\r\n const endRes = residues[end];\r\n if (!(mask & endRes._mask && endRes._isValid)) {\r\n break;\r\n }\r\n }\r\n process(i, idx, end - 1);\r\n idx = end;\r\n }\r\n }\r\n }\r\n }\r\n\r\n getMaskedSequences(mask) {\r\n const subs = [];\r\n let idx = 0;\r\n this._forEachSubChain(mask, (_subIdx, start, end) => {\r\n subs[idx++] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n\r\n getMaskedSubdivSequences(mask) {\r\n const subs = [];\r\n let currIdx = -1;\r\n let lastSubIdx = -1;\r\n const subDivs = this._subDivs;\r\n\r\n this._forEachSubChain(mask, (subIdx, start, end) => {\r\n if (lastSubIdx !== subIdx) {\r\n ++currIdx;\r\n subs[currIdx] = {\r\n arr: [],\r\n boundaries: subDivs[subIdx],\r\n };\r\n lastSubIdx = subIdx;\r\n }\r\n subs[currIdx].arr[subs[currIdx].arr.length] = { start, end };\r\n });\r\n\r\n return subs;\r\n }\r\n}\r\n\r\nexport default Component;\r\n","import utils from '../utils';\r\n\r\nconst cMaxPairsForHashCode = 32;\r\nconst cHashTableSize = 1024 * 1024;\r\nconst cNumbersPerPair = 4;\r\nconst cMaxNeighbours = 14;\r\nconst cInvalidVal = -1;\r\n// 89237 is a large simple number, can be used for pseudo random hash code create\r\nconst cBigPrime = 89237;\r\n\r\nclass AtomPairs {\r\n constructor(maxPairsEstimate) {\r\n this.numPairs = 0;\r\n this.numMaxPairs = maxPairsEstimate;\r\n this.intBuffer = utils.allocateTyped(Int32Array, maxPairsEstimate * cNumbersPerPair);\r\n for (let i = 0; i < maxPairsEstimate * cNumbersPerPair; i++) {\r\n this.intBuffer[i] = cInvalidVal;\r\n }\r\n this.hashBuffer = utils.allocateTyped(Int32Array, cHashTableSize * cMaxPairsForHashCode);\r\n for (let i = 0; i < cHashTableSize * cMaxPairsForHashCode; i++) {\r\n this.hashBuffer[i] = cInvalidVal;\r\n }\r\n }\r\n\r\n /**\r\n * Destroy all pairs memory\r\n */\r\n destroy() {\r\n this.intBuffer = null;\r\n this.hashBuffer = null;\r\n }\r\n\r\n /**\r\n * Add pair of atoms to collection\r\n * @param {number} indexA - Index of the 1st vertex.\r\n * @param {number} indexB - Index of the 2nd vertex.\r\n */\r\n addPair(indexA, indexB) {\r\n const ia = (indexA < indexB) ? indexA : indexB;\r\n const ib = (indexA > indexB) ? indexA : indexB;\r\n const codeToAdd = ia + (ib << cMaxNeighbours);\r\n\r\n const hashCode = (ia + (ib * cBigPrime)) & (cHashTableSize - 1);\r\n let j = hashCode * cMaxPairsForHashCode;\r\n let apI = 0;\r\n for (; apI < cMaxPairsForHashCode; apI++) {\r\n const code = this.hashBuffer[j + apI];\r\n if (code === cInvalidVal) {\r\n break;\r\n }\r\n if (code === codeToAdd) {\r\n return false;\r\n }\r\n }\r\n // add this new hash code\r\n if (apI >= cMaxPairsForHashCode) {\r\n throw new Error('addPair: increase cMaxPairsForHashCode');\r\n }\r\n this.hashBuffer[j + apI] = codeToAdd;\r\n\r\n // actually add\r\n if (this.numPairs >= this.numMaxPairs) {\r\n throw new Error('addPair: increase num pairs');\r\n }\r\n j = this.numPairs * cNumbersPerPair;\r\n this.intBuffer[j] = ia;\r\n this.intBuffer[j + 1] = ib;\r\n this.intBuffer[j + 2] = codeToAdd;\r\n this.numPairs++;\r\n return true;\r\n }\r\n}\r\n\r\nexport default AtomPairs;\r\n","import AtomPairs from './AtomPairs';\r\nimport Bond from './Bond';\r\n\r\nconst cProfileBondBuilder = false;\r\nconst cEstBondsMultiplier = 4;\r\nconst cSpaceCode = 32;\r\nconst cBondTolerance = 0.45;\r\nconst cVMDTolerance = 0.6;\r\nconst cBondRadInJMOL = true;\r\nconst cEpsilon = 0.001;\r\n\r\n/**\r\n * Get radius used for building bonds.\r\n *\r\n * @param {Atom} atom - Atom object.\r\n * @returns {number} special value for bonding radius for this atom\r\n */\r\nfunction _getBondingRadius(atom) {\r\n const { element } = atom;\r\n if (element) {\r\n return element.radiusBonding;\r\n }\r\n throw new Error('_getBondingRadius: Logic error.');\r\n}\r\n\r\nfunction _isAtomEligible(atom) {\r\n // build for all non-hetatm and for hetatm without bonds\r\n return !atom.isHet() || (atom.bonds && atom.bonds.length === 0);\r\n}\r\n\r\n/**\r\n * Bond between atoms.\r\n *\r\n * @param {Complex} complex molecular complex\r\n\r\n * @exports AutoBond\r\n * @constructor\r\n */\r\nclass AutoBond {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._maxRad = 1.8;\r\n const bBox = this._complex.getDefaultBoundaries().boundingBox;\r\n this._vBoxMin = bBox.min.clone();\r\n this._vBoxMax = bBox.max.clone();\r\n\r\n this._pairCollection = null;\r\n }\r\n\r\n /**\r\n * Add existing pairs of connectors (from pdb file after its reading)\r\n * @returns {number} 0\r\n */\r\n _addExistingPairs() {\r\n const atoms = this._complex.getAtoms();\r\n const numAtoms = atoms.length;\r\n let aInd = 0;\r\n const collection = this._pairCollection;\r\n\r\n for (; aInd < numAtoms; aInd++) {\r\n const { bonds } = atoms[aInd];\r\n const numBondsForAtom = bonds.length;\r\n for (let bInd = 0; bInd < numBondsForAtom; bInd++) {\r\n const bond = bonds[bInd];\r\n const indTo = bond._left.index;\r\n if (indTo === aInd) {\r\n collection.addPair(aInd, bond._right.index);\r\n }\r\n } // for (b) all bonds in atom\r\n } // for (a)\r\n return 0;\r\n }\r\n\r\n _findPairs() {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const atoms = this._complex._atoms;\r\n const atomsNum = atoms.length;\r\n const self = this;\r\n\r\n let rA;\r\n let isHydrogenA;\r\n let posA;\r\n let locationA;\r\n let atomA;\r\n\r\n const processAtom = function (atomB) {\r\n if (isHydrogenA && atomB.isHydrogen()) {\r\n return;\r\n }\r\n\r\n const locationB = atomB.location;\r\n if ((locationA !== cSpaceCode)\r\n && (locationB !== cSpaceCode)\r\n && (locationA !== locationB)) {\r\n return;\r\n }\r\n\r\n const dist2 = posA.distanceToSquared(atomB.position);\r\n const rB = atomB.element.radiusBonding;\r\n const maxAcceptable = cBondRadInJMOL ? rA + rB + cBondTolerance : cVMDTolerance * (rA + rB);\r\n\r\n if (dist2 > (maxAcceptable * maxAcceptable)) {\r\n return;\r\n }\r\n\r\n if (dist2 < cEpsilon) {\r\n return;\r\n }\r\n\r\n self._pairCollection.addPair(atomA.index, atomB.index);\r\n };\r\n\r\n for (let i = 0; i < atomsNum; ++i) {\r\n atomA = atoms[i];\r\n if (!_isAtomEligible(atomA)) {\r\n continue;\r\n }\r\n\r\n rA = atomA.element.radiusBonding;\r\n isHydrogenA = atomA.isHydrogen();\r\n posA = atomA.position;\r\n locationA = atomA.location;\r\n\r\n vw.forEachAtomWithinRadius(posA, 2 * this._maxRad + cBondTolerance, processAtom);\r\n }\r\n }\r\n\r\n _addPairs() {\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0, k = 0; i < this._pairCollection.numPairs; i++, k += 4) {\r\n const iA = this._pairCollection.intBuffer[k];\r\n const iB = this._pairCollection.intBuffer[k + 1];\r\n this._addPair(atoms[iA], atoms[iB]);\r\n }\r\n }\r\n\r\n _addPair(atomA, atomB) {\r\n const bondsA = atomA.bonds;\r\n const indexA = atomA.index;\r\n const indexB = atomB.index;\r\n for (let j = 0, numBonds = bondsA.length; j < numBonds; ++j) {\r\n const bond = bondsA[j];\r\n if (bond._left.index === indexB || bond._right.index === indexB) {\r\n return;\r\n }\r\n }\r\n const left = indexA < indexB ? atomA : atomB;\r\n const right = indexA < indexB ? atomB : atomA;\r\n const newBond = this._complex.addBond(left, right, 0, Bond.BondType.UNKNOWN, false);\r\n bondsA.push(newBond);\r\n atomB.bonds.push(newBond);\r\n }\r\n\r\n build() {\r\n if (cProfileBondBuilder) {\r\n console.time('Bonds Builder');\r\n }\r\n this._buildInner();\r\n\r\n if (cProfileBondBuilder) {\r\n console.timeEnd('Bonds Builder');\r\n }\r\n }\r\n\r\n _buildInner() {\r\n const atoms = this._complex._atoms;\r\n if (atoms.length < 2) {\r\n return;\r\n }\r\n if (atoms[0].index < 0) {\r\n throw new Error('AutoBond: Atoms in complex were not indexed.');\r\n }\r\n\r\n this._calcBoundingBox();\r\n this._pairCollection = new AtomPairs(atoms.length * cEstBondsMultiplier);\r\n this._addExistingPairs();\r\n this._findPairs();\r\n this._addPairs();\r\n }\r\n\r\n _calcBoundingBox() {\r\n const atoms = this._complex._atoms;\r\n const nAtoms = atoms.length;\r\n let maxRad = _getBondingRadius(atoms[0]);\r\n for (let i = 1; i < nAtoms; ++i) {\r\n maxRad = Math.max(maxRad, _getBondingRadius(atoms[i]));\r\n }\r\n this._vBoxMax.addScalar(maxRad);\r\n this._vBoxMin.addScalar(-maxRad);\r\n this._maxRad = maxRad * 1.2;\r\n }\r\n\r\n destroy() {\r\n if (this._pairCollection) {\r\n this._pairCollection.destroy();\r\n }\r\n }\r\n}\r\n\r\nexport default AutoBond;\r\n","import * as THREE from 'three';\r\nimport Bond from './Bond';\r\nimport Element from './Element';\r\n\r\nconst cCrossThresh = 0.1;\r\nconst cAromaticType = Bond.BondType.AROMATIC;\r\nconst cAromaticAtoms = [\r\n Element.ByName.C.number,\r\n Element.ByName.N.number,\r\n // Element.ByName.O.number,\r\n // Element.ByName.S.number,\r\n];\r\n\r\n/** Conditions for bonds:\r\n * - Cross product with each subsequent bond to add is collinear and point to the same direction\r\n * - Each pair of a adjacent bonds belong to not more than one cycle\r\n * - If there is more than one candidates we try them in ascending order of angle values\r\n */\r\n\r\nconst _coDirVectors = (function () {\r\n const v1Tmp = new THREE.Vector3();\r\n const v2Tmp = new THREE.Vector3();\r\n const cp = new THREE.Vector3();\r\n return function (v1, v2) {\r\n v1Tmp.copy(v1).normalize();\r\n v2Tmp.copy(v2).normalize();\r\n cp.crossVectors(v1Tmp, v2Tmp);\r\n if (cp.length() > cCrossThresh) {\r\n return false;\r\n }\r\n // zero vector in out terms must be collinear to any\r\n return v1Tmp.dot(v2Tmp) >= 0;\r\n };\r\n}());\r\n\r\nfunction _insertAscending(arr, val) {\r\n let idx = 0;\r\n while (idx < arr.length && arr[idx] < val) {\r\n ++idx;\r\n }\r\n arr.splice(idx, 0, val);\r\n}\r\n\r\nfunction _anotherAtom(bond, currAtom) {\r\n return bond._left === currAtom ? bond._right : bond._left;\r\n}\r\n\r\nfunction _cosBetween(v1, v2) {\r\n const theta = v1.dot(v2) / (Math.sqrt(v1.lengthSq() * v2.lengthSq()));\r\n return THREE.MathUtils.clamp(theta, -1, 1);\r\n}\r\n\r\nfunction _markAromatic(bond) {\r\n bond._type = cAromaticType;\r\n}\r\n\r\nclass Cycle {\r\n constructor(atomsList) {\r\n this.atoms = atomsList;\r\n this.update();\r\n }\r\n\r\n update() {\r\n const { atoms } = this;\r\n const center = new THREE.Vector3();\r\n const nA = atoms.length;\r\n for (let j = 0; j < nA; ++j) {\r\n center.add(atoms[j].position);\r\n }\r\n center.multiplyScalar(1.0 / nA);\r\n this.center = center;\r\n this.radius = center.distanceTo(atoms[0].position.clone().lerp(atoms[1].position, 0.5));\r\n }\r\n\r\n forEachBond(process) {\r\n const { atoms } = this;\r\n const nA = atoms.length;\r\n let currAtom = atoms[0];\r\n let nextAtom;\r\n\r\n function checkBond(bond) {\r\n if (bond._left === nextAtom || bond._right === nextAtom) {\r\n process(bond);\r\n }\r\n }\r\n\r\n for (let i = 0; i < nA; ++i) {\r\n nextAtom = atoms[(i + 1) % nA];\r\n currAtom.forEachBond(checkBond);\r\n currAtom = nextAtom;\r\n }\r\n }\r\n}\r\n\r\nfunction _isAromatic(bond) {\r\n return bond._type === cAromaticType;\r\n}\r\n\r\nfunction _isPossibleAromatic(bond) {\r\n if (bond.type === cAromaticType) {\r\n return true;\r\n }\r\n const rightIdx = cAromaticAtoms.indexOf(bond._right.element.number);\r\n const leftIdx = cAromaticAtoms.indexOf(bond._left.element.number);\r\n return rightIdx !== -1 && leftIdx !== -1;\r\n}\r\n\r\nfunction _checkCycleSimple(cycle) {\r\n return cycle.length > 3;\r\n}\r\n\r\nfunction _checkCycleComplex(cycle) {\r\n console.assert(cycle.length > 2);\r\n return true;\r\n}\r\n\r\nclass AromaticLoopsMarker {\r\n constructor(complex) {\r\n this._complex = complex;\r\n const bondsData = new Array(complex._bonds.length);\r\n const bondMarks = new Array(complex._bonds.length);\r\n for (let i = 0, n = bondsData.length; i < n; ++i) {\r\n bondsData[i] = [];\r\n bondMarks[i] = false;\r\n }\r\n this._bondsData = bondsData;\r\n this._bondMarks = bondMarks;\r\n this._resetCycles();\r\n }\r\n\r\n _resetCycles() {\r\n this._cycles = [];\r\n this._currIdx = -1;\r\n }\r\n\r\n _haveSameCycle(bondsData, bond1, bond2) {\r\n const arr1 = bondsData[bond1._index];\r\n const arr2 = bondsData[bond2._index];\r\n const n1 = arr1.length;\r\n const n2 = arr2.length;\r\n let i1 = 0;\r\n let i2 = 0;\r\n while (i1 < n1 && i2 < n2) {\r\n if (arr1[i1] === arr2[i2]) {\r\n return true;\r\n }\r\n if (arr1[i1] > arr2[i2]) {\r\n ++i2;\r\n } else {\r\n ++i1;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _tryBond(prevBond, currRight, currDir) {\r\n const bondsOrder = [];\r\n const bondsData = this._bondsData;\r\n const currLeft = _anotherAtom(prevBond, currRight);\r\n const currVec = currRight.position.clone().sub(currLeft.position);\r\n const startAtomRef = this._currStart;\r\n const self = this;\r\n const bondMarks = this._bondMarks;\r\n let checkAromatic = this._checkBond;\r\n bondMarks[prevBond._index] = true;\r\n checkAromatic = checkAromatic === undefined ? _isAromatic : checkAromatic;\r\n currRight.forEachBond((newBond) => {\r\n if (!checkAromatic(newBond)\r\n || newBond === prevBond\r\n || bondMarks[newBond._index]\r\n || self._haveSameCycle(bondsData, prevBond, newBond)) {\r\n return;\r\n }\r\n const anotherAtom = _anotherAtom(newBond, currRight);\r\n const anotherVec = anotherAtom.position.clone().sub(currRight.position);\r\n const val = anotherAtom === startAtomRef ? -2.0 : 1 - _cosBetween(currVec, anotherVec);\r\n const newDir = anotherVec.cross(currVec);\r\n if (!_coDirVectors(newDir, currDir)) {\r\n return;\r\n }\r\n let idx = 0;\r\n while (idx < bondsOrder.length && bondsOrder[idx].val < val) {\r\n ++idx;\r\n }\r\n bondsOrder.splice(idx, 0, { bond: newBond, val, dir: newDir });\r\n });\r\n\r\n for (let i = 0, n = bondsOrder.length; i < n; ++i) {\r\n const { bond } = bondsOrder[i];\r\n const newRight = bond._left === currRight ? bond._right : bond._left;\r\n if (newRight === startAtomRef) {\r\n ++this._currIdx;\r\n this._cycles.push([currRight]);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n if (this._tryBond(bond, newRight, bondsOrder[i].dir)) {\r\n _insertAscending(bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(currRight);\r\n bondMarks[prevBond._index] = false;\r\n return true;\r\n }\r\n }\r\n bondMarks[prevBond._index] = false;\r\n return false;\r\n }\r\n\r\n _startCycle(bond) {\r\n // start from left to right\r\n this._currStart = bond._left;\r\n if (this._tryBond(bond, bond._right, new THREE.Vector3())) {\r\n _insertAscending(this._bondsData[bond._index], this._currIdx);\r\n this._cycles[this._currIdx].push(bond._left);\r\n }\r\n }\r\n\r\n _findLoops(checkBond, checkCycle) {\r\n this._checkBond = checkBond;\r\n const complex = this._complex;\r\n const self = this;\r\n\r\n complex.forEachComponent((component) => {\r\n self._resetCycles();\r\n component.forEachBond((bond) => {\r\n if (checkBond(bond)) {\r\n self._startCycle(bond);\r\n }\r\n });\r\n const cycles = self._cycles;\r\n for (let i = 0, n = cycles.length; i < n; ++i) {\r\n const cycle = cycles[i];\r\n if (!checkCycle(cycle)) {\r\n continue;\r\n }\r\n const newCycle = new Cycle(cycle);\r\n newCycle.forEachBond(_markAromatic);\r\n component.addCycle(newCycle);\r\n }\r\n });\r\n }\r\n\r\n markCycles() {\r\n this._findLoops(_isAromatic, _checkCycleSimple);\r\n }\r\n\r\n detectCycles() {\r\n this._findLoops(_isPossibleAromatic, _checkCycleComplex);\r\n }\r\n}\r\n\r\nexport default AromaticLoopsMarker;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\n/**\r\n * Calculate min & max radius of a sphere slice between zMin & zMax\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {number} zMin - lower bound of the slice\r\n * @param {number} zMax - upper bound of the slice\r\n */\r\nfunction _getSphereSliceRadiusRange(center, radius, zMin, zMax) {\r\n const dzMin = zMin - center.z;\r\n const dzMax = zMax - center.z;\r\n const rzMin = Math.sqrt(Math.max(radius * radius - dzMin * dzMin, 0.0));\r\n const rzMax = Math.sqrt(Math.max(radius * radius - dzMax * dzMax, 0.0));\r\n\r\n const rMin = Math.min(rzMin, rzMax);\r\n let rMax;\r\n\r\n if (zMin <= center.z && zMax >= center.z) {\r\n // sphere's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(rzMin, rzMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * Calculate min & max radius of a circle slice between yMin & yMax.\r\n *\r\n * To maintain analogy with _getSphereSliceRadiusRange we call radius what in fact is\r\n * half-width (along X axis) of the slice, i.e. 1D-sphere radius.\r\n *\r\n * @param {Vector3} center - center of the circle (z can be ignored)\r\n * @param {number} radius - circle radius\r\n * @param {number} yMin - lower bound of the slice\r\n * @param {number} yMax - upper bound of the slice\r\n * @returns {Array} - array of two numbers (min & max radius, or half-width)\r\n */\r\nfunction _getCircleSliceRadiusRange(center, radius, yMin, yMax) {\r\n const dyMin = yMin - center.y;\r\n const dyMax = yMax - center.y;\r\n const ryMin = Math.sqrt(Math.max(radius * radius - dyMin * dyMin, 0.0));\r\n const ryMax = Math.sqrt(Math.max(radius * radius - dyMax * dyMax, 0.0));\r\n\r\n const rMin = Math.min(ryMin, ryMax);\r\n let rMax;\r\n\r\n if (yMin <= center.y && yMax >= center.y) {\r\n // slice's main diameter is inside slice\r\n rMax = radius;\r\n } else {\r\n rMax = Math.max(ryMin, ryMax);\r\n }\r\n\r\n return [rMin, rMax];\r\n}\r\n\r\n/**\r\n * VoxelWorld constructor\r\n *\r\n * @param {Box3} box - bounding box of the volume to be partitioned\r\n * @param {Vector3} vCellSizeHint - target voxel size (actual voxel size may differ from this)\r\n */\r\nclass VoxelWorld {\r\n constructor(box, vCellSizeHint) {\r\n this._box = box.clone();\r\n const size = new THREE.Vector3();\r\n box.getSize(size);\r\n this._count = size.clone().divide(vCellSizeHint).floor().max(new THREE.Vector3(1, 1, 1));\r\n this._last = this._count.clone().subScalar(1);\r\n this._cellSize = size.clone().divide(this._count);\r\n this._cellInnerR = 0.5 * Math.min(Math.min(this._cellSize.x, this._cellSize.y), this._cellSize.z);\r\n this._cellOuterR = 0.5 * Math.sqrt(this._cellSize.dot(this._cellSize));\r\n\r\n // array of voxels, each element contains index of first atom in voxel\r\n const numVoxels = this._count.x * this._count.y * this._count.z;\r\n this._voxels = utils.allocateTyped(Int32Array, numVoxels);\r\n for (let i = 0; i < numVoxels; ++i) {\r\n this._voxels[i] = -1;\r\n }\r\n\r\n // array of atoms that stores multiple single-linked lists\r\n // two elements for each atom: Atom ref, index of next atom (in this array\r\n this._atoms = [];\r\n }\r\n\r\n /**\r\n * Add all atoms from a complex to voxel world\r\n *\r\n * @param {Complex} complex - complex\r\n */\r\n addAtoms(complex) {\r\n const self = this;\r\n\r\n let idx = this._atoms.length;\r\n\r\n // resize array of atoms\r\n this._atoms.length += 2 * complex.getAtomCount();\r\n\r\n complex.forEachAtom((atom) => {\r\n // find which voxel contains this atom\r\n const voxelIdx = self._findVoxel(atom.position);\r\n\r\n // push current atom to the head of voxel's atom list\r\n self._atoms[idx] = atom;\r\n self._atoms[idx + 1] = self._voxels[voxelIdx];\r\n self._voxels[voxelIdx] = idx;\r\n\r\n idx += 2;\r\n });\r\n }\r\n\r\n /**\r\n * Get voxel that contains specified 3D point (we use clamp at the edges)\r\n *\r\n * @param {Vector3} point - a point in 3D\r\n * @returns {number} - index of voxel\r\n */\r\n static _zero = new THREE.Vector3(0, 0, 0);\r\n\r\n static _voxel = new THREE.Vector3();\r\n\r\n _findVoxel(point) {\r\n const zero = VoxelWorld._zero;\r\n const voxel = VoxelWorld._voxel;\r\n voxel.copy(point)\r\n .sub(this._box.min)\r\n .divide(this._cellSize)\r\n .floor()\r\n .clamp(zero, this._last);\r\n return voxel.x + this._count.x * (voxel.y + this._count.y * voxel.z);\r\n }\r\n\r\n /**\r\n * Call a function for each atom in voxel\r\n *\r\n * @param {number} voxel - index of voxel\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomInVoxel(voxel, process) {\r\n for (let i = this._voxels[voxel]; i >= 0; i = this._atoms[i + 1]) {\r\n process(this._atoms[i]);\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _xRange = new THREE.Vector2();\r\n\r\n static _yRange = new THREE.Vector2();\r\n\r\n static _zRange = new THREE.Vector2();\r\n\r\n _forEachVoxelWithinRadius(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n\r\n // switch to a faster method unless cell size is much smaller than sphere radius\r\n if (radius / this._cellInnerR < 10) {\r\n this._forEachVoxelWithinRadiusSimple(center, radius, process);\r\n return;\r\n }\r\n\r\n let rRangeXY;\r\n let rRangeX;\r\n let xVal;\r\n let yVal;\r\n let zVal;\r\n let isInsideX;\r\n let isInsideY;\r\n let isInsideZ;\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor()\r\n .clampScalar(0, this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n\r\n isInsideZ = (center.z - radius <= zVal[0]) && (zVal[1] <= center.z + radius);\r\n\r\n rRangeXY = _getSphereSliceRadiusRange(center, radius, zVal[0], zVal[1]);\r\n\r\n yRange.set(center.y - rRangeXY[1], center.y + rRangeXY[1]);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor()\r\n .clampScalar(0, this._count.y - 1);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n\r\n isInsideY = (center.y - rRangeXY[0] <= yVal[0]) && (yVal[1] <= center.y + rRangeXY[0]);\r\n\r\n rRangeX = _getCircleSliceRadiusRange(center, rRangeXY[1], yVal[0], yVal[1]);\r\n\r\n xRange.set(center.x - rRangeX[1], center.x + rRangeX[1]);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor()\r\n .clampScalar(0, this._count.x - 1);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n isInsideX = (center.x - rRangeX[0] <= xVal[0]) && (xVal[1] <= center.x + rRangeX[0]);\r\n\r\n process(x + this._count.x * (y + this._count.y * z), isInsideX && isInsideY && isInsideZ);\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each voxel that is touched by given sphere. Callback also takes flag\r\n * isInside specifying whether voxel lies inside the sphere entirely.\r\n * This is a version of method that doesn't try to \"calculate\" what voxels fall inside radius\r\n * but instead just checks all voxels inside sphere's bounding box. This should be faster\r\n * unless cell size is much smaller than sphere radius.\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(number,bool)} process - function to call that takes voxel index and boolean isInside\r\n */\r\n\r\n static _vCenter = new THREE.Vector3();\r\n\r\n _forEachVoxelWithinRadiusSimple(center, radius, process) {\r\n const xRange = VoxelWorld._xRange;\r\n const yRange = VoxelWorld._yRange;\r\n const zRange = VoxelWorld._zRange;\r\n const vCenter = VoxelWorld._vCenter;\r\n\r\n const distTouch2 = (radius + this._cellOuterR) * (radius + this._cellOuterR);\r\n let distInside2 = -1.0;\r\n if (radius > this._cellOuterR) {\r\n distInside2 = (radius - this._cellOuterR) * (radius - this._cellOuterR);\r\n }\r\n\r\n // calculate bounding box for the sphere\r\n xRange.set(center.x - radius, center.x + radius);\r\n xRange.subScalar(this._box.min.x)\r\n .divideScalar(this._cellSize.x)\r\n .floor();\r\n xRange.x = Math.min(Math.max(xRange.x, 0), this._count.x - 1);\r\n xRange.y = Math.min(Math.max(xRange.y, 0), this._count.x - 1);\r\n\r\n yRange.set(center.y - radius, center.y + radius);\r\n yRange.subScalar(this._box.min.y)\r\n .divideScalar(this._cellSize.y)\r\n .floor();\r\n yRange.x = Math.min(Math.max(yRange.x, 0), this._count.y - 1);\r\n yRange.y = Math.min(Math.max(yRange.y, 0), this._count.y - 1);\r\n\r\n zRange.set(center.z - radius, center.z + radius);\r\n zRange.subScalar(this._box.min.z)\r\n .divideScalar(this._cellSize.z)\r\n .floor();\r\n zRange.x = Math.min(Math.max(zRange.x, 0), this._count.z - 1);\r\n zRange.y = Math.min(Math.max(zRange.y, 0), this._count.z - 1);\r\n\r\n for (let z = zRange.x; z <= zRange.y; ++z) {\r\n const zVal = [this._box.min.z + z * this._cellSize.z,\r\n this._box.min.z + (z + 1) * this._cellSize.z];\r\n vCenter.z = 0.5 * (zVal[0] + zVal[1]);\r\n\r\n for (let y = yRange.x; y <= yRange.y; ++y) {\r\n const yVal = [this._box.min.y + y * this._cellSize.y,\r\n this._box.min.y + (y + 1) * this._cellSize.y];\r\n vCenter.y = 0.5 * (yVal[0] + yVal[1]);\r\n\r\n for (let { x } = xRange; x <= xRange.y; ++x) {\r\n const xVal = [this._box.min.x + x * this._cellSize.x,\r\n this._box.min.x + (x + 1) * this._cellSize.x];\r\n vCenter.x = 0.5 * (xVal[0] + xVal[1]);\r\n\r\n const d2 = center.distanceToSquared(vCenter);\r\n if (d2 <= distTouch2) {\r\n process(x + this._count.x * (y + this._count.y * z), d2 <= distInside2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Call a function for each atom within given sphere\r\n *\r\n * @param {Vector3} center - center of the sphere\r\n * @param {number} radius - sphere radius\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinRadius(center, radius, process) {\r\n const self = this;\r\n const r2 = radius * radius;\r\n\r\n self._forEachVoxelWithinRadius(center, radius, (voxel, isInside) => {\r\n if (isInside) {\r\n self._forEachAtomInVoxel(voxel, process);\r\n } else {\r\n self._forEachAtomInVoxel(voxel, (atom) => {\r\n if (center.distanceToSquared(atom.position) <= r2) {\r\n process(atom);\r\n }\r\n });\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by mask\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} mask - bit mask\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromMasked(complex, mask, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms defined by selector\r\n *\r\n * @param {Complex} complex - complex\r\n * @param {number} selector - selector\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n forEachAtomWithinDistFromSelected(complex, selector, dist, process) {\r\n this._forEachAtomWithinDistFromGroup((atomProc) => {\r\n complex.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n atomProc(atom);\r\n }\r\n });\r\n }, dist, process);\r\n }\r\n\r\n /**\r\n * Call a function for each atom of given complex within given distance from group of atoms\r\n *\r\n * @param {function} forEachAtom - enumerator of atoms in the group\r\n * @param {number} dist - distance\r\n * @param {function(Atom)} process - function to call\r\n */\r\n _forEachAtomWithinDistFromGroup(forEachAtom, dist, process) {\r\n const self = this;\r\n const r2 = dist * dist;\r\n\r\n const voxels = [];\r\n const atoms = [];\r\n let idx = 0;\r\n\r\n // build \"within radius\" atom list for each voxel\r\n forEachAtom((atom) => {\r\n self._forEachVoxelWithinRadius(atom.position, dist, (voxel, isInside) => {\r\n if (isInside) {\r\n // this voxel is inside circle -- no check will be required\r\n voxels[voxel] = -1;\r\n } else if (typeof voxels[voxel] === 'undefined') {\r\n // this voxel isn't covered yet -- start building list of atoms\r\n atoms.push(atom);\r\n atoms.push(-1);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n } else if (voxels[voxel] !== -1) {\r\n // this voxel has a list of atoms required for distance check -- add atom to the list\r\n atoms.push(atom);\r\n atoms.push(voxels[voxel]);\r\n voxels[voxel] = idx;\r\n idx += 2;\r\n }\r\n });\r\n });\r\n\r\n let voxel;\r\n\r\n const processIfWithin = function (atom) {\r\n if (typeof voxels[voxel] === 'undefined') {\r\n return;\r\n }\r\n\r\n idx = voxels[voxel];\r\n if (idx === -1) {\r\n // this voxel is fully covered\r\n process(atom);\r\n return;\r\n }\r\n\r\n // check distance to each atom within radius from this voxel\r\n for (; idx >= 0; idx = atoms[idx + 1]) {\r\n if (atom.position.distanceToSquared(atoms[idx].position) < r2) {\r\n process(atom);\r\n break;\r\n }\r\n }\r\n };\r\n\r\n // for each marked voxel\r\n for (voxel in voxels) {\r\n if (voxels.hasOwnProperty(voxel)) {\r\n self._forEachAtomInVoxel(voxel, processIfWithin);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default VoxelWorld;\r\n","import ResidueType from './ResidueType';\r\nimport PairCollection from './AtomPairs';\r\n\r\nconst MINIMAL_DISTANCE = 0.5;\r\nconst MIN_HBOND_ENERGY = -9.9;\r\nconst MAX_HBOND_ENERGY = -0.5;\r\nconst COUPLING_CONSTANT = -27.888; // = -332 * 0.42 * 0.2\r\nconst MAX_COUPLING_DISTANCE = 5.0; // how far is the closest atom of a potential partner residue from CA atom\r\nconst MAX_RESIDUES_THRESHOLD = 1000;\r\n\r\nexport default class HBondInfo {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._hbonds = []; // array of bond info for each residue\r\n if (this._complex._residues.length > MAX_RESIDUES_THRESHOLD) {\r\n this._buildVW(); // optimized version using voxel grid\r\n } else {\r\n this._build(); // test all pairs of residues\r\n }\r\n }\r\n\r\n isBond(from, to) {\r\n if (this._hbonds[from]) {\r\n const [acc0, acc1] = this._hbonds[from].acceptor;\r\n if (acc0 && acc0.residue === to && acc0.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n if (acc1 && acc1.residue === to && acc1.energy < MAX_HBOND_ENERGY) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n\r\n for (let i = 0; i < this._complex._residues.length - 1; ++i) {\r\n const ri = this._complex._residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let preri = null;\r\n if (i > 0 && (this._complex._residues[i - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && ri._sequence === this._complex._residues[i - 1]._sequence + 1) {\r\n preri = this._complex._residues[i - 1];\r\n }\r\n\r\n for (let j = i + 1; j < this._complex._residues.length; ++j) {\r\n const rj = this._complex._residues[j];\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = null;\r\n if ((this._complex._residues[j - 1].getType().flags & ResidueType.Flags.PROTEIN)\r\n && rj._sequence === this._complex._residues[j - 1]._sequence + 1) {\r\n prerj = this._complex._residues[j - 1];\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (j !== i + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _buildVW() {\r\n const self = this;\r\n const residues = this._complex._residues;\r\n let ri;\r\n let preri;\r\n\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return;\r\n }\r\n\r\n const pairs = new PairCollection(this._complex._residues.length * this._complex._residues.length / 2);\r\n\r\n function processAtom(atom) {\r\n const rj = atom.residue;\r\n\r\n if (rj._index === ri._index) {\r\n return;\r\n }\r\n\r\n if ((rj.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n return;\r\n }\r\n\r\n if (!pairs.addPair(ri._index, rj._index)) {\r\n // we've seen this pair\r\n return;\r\n }\r\n\r\n // get predecessor in chain\r\n let prerj = rj._index > 0 ? residues[rj._index - 1] : null;\r\n if (prerj\r\n && ((prerj.getType().flags & ResidueType.Flags.PROTEIN) === 0 || rj._sequence !== prerj._sequence + 1)) {\r\n prerj = null;\r\n }\r\n\r\n self._calcHBondEnergy(preri, ri, rj);\r\n if (rj._index !== ri._index + 1) {\r\n self._calcHBondEnergy(prerj, rj, ri);\r\n }\r\n }\r\n\r\n for (let i = 0; i < residues.length - 1; ++i) {\r\n ri = residues[i];\r\n if ((ri.getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n continue;\r\n }\r\n\r\n // get predecessor in chain\r\n preri = i > 0 ? residues[i - 1] : null;\r\n if (preri\r\n && ((preri.getType().flags & ResidueType.Flags.PROTEIN) === 0 || ri._sequence !== preri._sequence + 1)) {\r\n preri = null;\r\n }\r\n\r\n vw.forEachAtomWithinRadius(this._residueGetCAlpha(ri), MAX_COUPLING_DISTANCE, processAtom);\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _residueGetCO(res) {\r\n let c = null;\r\n let o = null;\r\n\r\n res.forEachAtom((a) => {\r\n if (a.name === 'C') {\r\n c = a.position;\r\n } else if (a.name === 'O') {\r\n o = a.position;\r\n }\r\n });\r\n\r\n return [c, o];\r\n }\r\n\r\n // TODO Support hydrogen defined in complex\r\n _residueGetNH(prev, res) {\r\n const [c, o] = this._residueGetCO(prev);\r\n\r\n let n;\r\n res.forEachAtom((a) => {\r\n if (a.name === 'N') {\r\n n = a.position;\r\n }\r\n });\r\n\r\n if (c && o && n) {\r\n // calculate hydrogen position\r\n const h = c.clone();\r\n h.sub(o);\r\n h.multiplyScalar(1.0 / h.length());\r\n h.add(n);\r\n\r\n return [n, h];\r\n }\r\n\r\n return [null, null];\r\n }\r\n\r\n _calcHBondEnergy(predonor, donor, acceptor) {\r\n let result = 0;\r\n\r\n if (predonor === null) {\r\n return result;\r\n }\r\n\r\n if (donor.getType().getName() !== 'PRO') {\r\n const [n, h] = this._residueGetNH(predonor, donor);\r\n const [c, o] = this._residueGetCO(acceptor);\r\n\r\n if (n === null || h === null || c === null || o === null) {\r\n return result;\r\n }\r\n\r\n const distanceHO = h.distanceTo(o);\r\n const distanceHC = h.distanceTo(c);\r\n const distanceNC = n.distanceTo(c);\r\n const distanceNO = n.distanceTo(o);\r\n\r\n if (distanceHO < MINIMAL_DISTANCE || distanceHC < MINIMAL_DISTANCE\r\n || distanceNC < MINIMAL_DISTANCE || distanceNO < MINIMAL_DISTANCE) {\r\n result = MIN_HBOND_ENERGY;\r\n } else {\r\n result = COUPLING_CONSTANT / distanceHO - COUPLING_CONSTANT / distanceHC\r\n + COUPLING_CONSTANT / distanceNC - COUPLING_CONSTANT / distanceNO;\r\n }\r\n\r\n // DSSP compatibility mode:\r\n result = Math.round(result * 1000) / 1000;\r\n\r\n if (result < MIN_HBOND_ENERGY) {\r\n result = MIN_HBOND_ENERGY;\r\n }\r\n }\r\n\r\n // update donor\r\n if (typeof this._hbonds[donor._index] === 'undefined') {\r\n this._hbonds[donor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const donorInfo = this._hbonds[donor._index];\r\n\r\n if (donorInfo.acceptor.length < 2) {\r\n donorInfo.acceptor.push({\r\n residue: acceptor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (donorInfo.acceptor.length > 1) {\r\n if (result < donorInfo.acceptor[0].energy) {\r\n donorInfo.acceptor[1].residue = donorInfo.acceptor[0].residue;\r\n donorInfo.acceptor[1].energy = donorInfo.acceptor[0].energy;\r\n donorInfo.acceptor[0].residue = acceptor._index;\r\n donorInfo.acceptor[0].energy = result;\r\n } else if (result < donorInfo.acceptor[1].energy) {\r\n donorInfo.acceptor[1].residue = acceptor._index;\r\n donorInfo.acceptor[1].energy = result;\r\n }\r\n }\r\n\r\n // update acceptor\r\n if (typeof this._hbonds[acceptor._index] === 'undefined') {\r\n this._hbonds[acceptor._index] = {\r\n donor: [],\r\n acceptor: [],\r\n };\r\n }\r\n const accInfo = this._hbonds[acceptor._index];\r\n\r\n if (accInfo.donor.length < 2) {\r\n accInfo.donor.push({\r\n residue: donor._index,\r\n energy: result,\r\n });\r\n }\r\n\r\n if (accInfo.donor.length > 1) {\r\n if (result < accInfo.donor[0].energy) {\r\n accInfo.donor[1].residue = accInfo.donor[0].residue;\r\n accInfo.donor[1].energy = accInfo.donor[0].energy;\r\n accInfo.donor[0].residue = donor._index;\r\n accInfo.donor[0].energy = result;\r\n } else if (result < accInfo.donor[1].energy) {\r\n accInfo.donor[1].residue = donor._index;\r\n accInfo.donor[1].energy = result;\r\n }\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n","import HBondInfo from './HBondInfo';\r\nimport ResidueType from './ResidueType';\r\n\r\nconst BridgeType = Object.freeze({\r\n NO_BRIDGE: 0,\r\n PARALLEL: 1,\r\n ANTI_PARALLEL: 2,\r\n});\r\n\r\nconst HelixFlag = Object.freeze({\r\n START: 1,\r\n MIDDLE: 2,\r\n END: 3,\r\n START_AND_END: 4,\r\n});\r\n\r\nconst StructureType = Object.freeze({\r\n STRAND: 'E',\r\n BRIDGE: 'B',\r\n HELIX_310: 'G',\r\n HELIX_ALPHA: 'H',\r\n HELIX_PI: 'I',\r\n TURN: 'T',\r\n BEND: 'S',\r\n LOOP: ' ',\r\n});\r\n\r\nexport default class SecondaryStructureMap {\r\n constructor(complex) {\r\n this._complex = complex;\r\n this._build();\r\n }\r\n\r\n _build() {\r\n const self = this;\r\n this._hbonds = new HBondInfo(this._complex);\r\n this._ss = []; // DSSP map by residue\r\n\r\n // auxilliary data\r\n this._sheet = [];\r\n this._betaPartners = [];\r\n this._bend = [];\r\n for (let i = 0; i < this._complex.getResidues().length; ++i) {\r\n this._betaPartners[i] = [];\r\n }\r\n this._helixFlags = [];\r\n this._helixFlags[3] = [];\r\n this._helixFlags[4] = [];\r\n this._helixFlags[5] = [];\r\n\r\n // calculate peptide chain lengths\r\n this._chainLengths = [];\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i].getResidues();\r\n let len = 0;\r\n for (; len < chain.length; ++len) {\r\n if ((chain[len].getType().flags & ResidueType.Flags.PROTEIN) === 0) {\r\n break;\r\n }\r\n }\r\n this._chainLengths[i] = len;\r\n }\r\n\r\n this._buildBetaSheets();\r\n\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n self._buildAlphaHelices(this._complex._chains[i].getResidues(), this._chainLengths[i], false);\r\n }\r\n }\r\n\r\n _buildAlphaHelices(inResidues, chainLength, inPreferPiHelices) {\r\n // Helix and Turn\r\n for (let stride = 3; stride <= 5; ++stride) {\r\n if (inResidues.length < stride) {\r\n break;\r\n }\r\n\r\n for (let i = 0; i + stride < chainLength; ++i) {\r\n if (this._hbonds.isBond(inResidues[i + stride]._index, inResidues[i]._index)\r\n /* && NoChainBreak(res[i], res[i + stride]) */) {\r\n this._helixFlags[stride][inResidues[i + stride]._index] = HelixFlag.END;\r\n for (let j = i + 1; j < i + stride; ++j) {\r\n if (typeof this._helixFlags[stride][inResidues[j]._index] === 'undefined') {\r\n this._helixFlags[stride][inResidues[j]._index] = HelixFlag.MIDDLE;\r\n }\r\n }\r\n\r\n if (this._helixFlags[stride][inResidues[i]._index] === HelixFlag.END) {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START_AND_END;\r\n } else {\r\n this._helixFlags[stride][inResidues[i]._index] = HelixFlag.START;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 2; i < chainLength - 2; ++i) {\r\n const kappa = this._kappa(inResidues[i - 2], inResidues[i], inResidues[i + 2]);\r\n this._bend[inResidues[i]._index] = (kappa !== 360 && kappa > 70);\r\n }\r\n\r\n for (let i = 1; i + 4 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 4) && this._isHelixStart(inResidues[i - 1]._index, 4)) {\r\n for (let j = i; j <= i + 3; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_ALPHA;\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 3 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 3) && this._isHelixStart(inResidues[i - 1]._index, 3)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 2; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_310;\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 2; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_310;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 5 < chainLength; ++i) {\r\n if (this._isHelixStart(inResidues[i]._index, 5) && this._isHelixStart(inResidues[i - 1]._index, 5)) {\r\n let empty = true;\r\n for (let j = i; empty && j <= i + 4; ++j) {\r\n empty = typeof this._ss[inResidues[j]._index] === 'undefined'\r\n || this._ss[inResidues[j]._index] === StructureType.HELIX_PI\r\n || (inPreferPiHelices && this._ss[inResidues[j]._index] === StructureType.HELIX_ALPHA);\r\n }\r\n if (empty) {\r\n for (let j = i; j <= i + 4; ++j) {\r\n this._ss[inResidues[j]._index] = StructureType.HELIX_PI;\r\n }\r\n }\r\n }\r\n }\r\n\r\n for (let i = 1; i + 1 < chainLength; ++i) {\r\n if (typeof this._ss[inResidues[i]._index] === 'undefined') {\r\n let isTurn = false;\r\n for (let stride = 3; stride <= 5 && !isTurn; ++stride) {\r\n for (let k = 1; k < stride && !isTurn; ++k) {\r\n isTurn = (i >= k) && this._isHelixStart(inResidues[i - k]._index, stride);\r\n }\r\n }\r\n\r\n if (isTurn) {\r\n this._ss[inResidues[i]._index] = StructureType.TURN;\r\n } else if (this._bend[inResidues[i]._index]) {\r\n this._ss[inResidues[i]._index] = StructureType.BEND;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _residueGetCAlpha(res) {\r\n for (let i = 0; i < res._atoms.length; ++i) {\r\n const { name } = res._atoms[i];\r\n if (name === 'CA'\r\n || name === 'C1') {\r\n return res._atoms[i].position;\r\n }\r\n }\r\n\r\n return null;\r\n }\r\n\r\n _cosinusAngle(p1, p2, p3, p4) {\r\n const v12 = p1.clone().sub(p2);\r\n const v34 = p3.clone().sub(p4);\r\n\r\n let result = 0;\r\n\r\n const x = v12.dot(v12) * v34.dot(v34);\r\n if (x > 0) {\r\n result = v12.dot(v34) / Math.sqrt(x);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _kappa(prevPrev, res, nextNext) {\r\n const curCA = this._residueGetCAlpha(res);\r\n const ppCA = this._residueGetCAlpha(prevPrev);\r\n const nnCA = this._residueGetCAlpha(nextNext);\r\n if (curCA === null || ppCA === null || nnCA === null) {\r\n return 180;\r\n }\r\n\r\n const ckap = this._cosinusAngle(curCA, ppCA, nnCA, curCA);\r\n const skap = Math.sqrt(1 - ckap * ckap);\r\n return Math.atan2(skap, ckap) * 180 / Math.PI;\r\n }\r\n\r\n _isHelixStart(res, stride) {\r\n return (this._helixFlags[stride][res] === HelixFlag.START\r\n || this._helixFlags[stride][res] === HelixFlag.START_AND_END);\r\n }\r\n\r\n _buildBetaSheets() {\r\n // find bridges\r\n // check each chain against each other chain, and against itself\r\n const bridges = [];\r\n for (let a = 0; a < this._complex._chains.length; ++a) {\r\n const lenA = this._chainLengths[a];\r\n if (lenA <= 4) {\r\n continue;\r\n }\r\n\r\n const chainA = this._complex._chains[a].getResidues();\r\n\r\n for (let b = a; b < this._complex._chains.length; ++b) {\r\n const lenB = this._chainLengths[b];\r\n if (lenB <= 4) {\r\n continue;\r\n }\r\n\r\n const chainB = this._complex._chains[b].getResidues();\r\n\r\n for (let i = 1; i + 1 < lenA; ++i) {\r\n const ri = chainA[i];\r\n\r\n let j = 1;\r\n if (b === a) {\r\n j = i + 3; // check for self-bridges forward down the chain\r\n }\r\n\r\n for (; j + 1 < lenB; ++j) {\r\n const rj = chainB[j];\r\n\r\n const type = this._testBridge(chainA, i, chainB, j);\r\n if (type === BridgeType.NO_BRIDGE) {\r\n continue;\r\n }\r\n\r\n // there is a bridge, try to attach it to previously found sequence\r\n let found = false;\r\n for (const bridge of bridges) {\r\n if (type !== bridge.type || ri._index !== bridge.i[bridge.i.length - 1] + 1) {\r\n continue;\r\n }\r\n\r\n if (type === BridgeType.PARALLEL && bridge.j[bridge.j.length - 1] + 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.push(rj._index);\r\n found = true;\r\n break;\r\n }\r\n\r\n if (type === BridgeType.ANTI_PARALLEL && bridge.j[0] - 1 === rj._index) {\r\n bridge.i.push(ri._index);\r\n bridge.j.unshift(rj._index);\r\n found = true;\r\n break;\r\n }\r\n }\r\n\r\n // this bridge cannot be attached anywhere, start a new sequence\r\n if (!found) {\r\n bridges.push({\r\n type,\r\n i: [ri._index],\r\n chainI: ri.getChain()._index,\r\n j: [rj._index],\r\n chainJ: rj.getChain()._index,\r\n });\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // extend ladders\r\n bridges.sort((a, b) => {\r\n if (a.chainI < b.chainI || (a.chainI === b.chainI && a.i[0] < b.i[0])) {\r\n return -1;\r\n }\r\n return 1;\r\n });\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n for (let j = i + 1; j < bridges.length; ++j) {\r\n const ibi = bridges[i].i[0];\r\n const iei = bridges[i].i[bridges[i].i.length - 1];\r\n const jbi = bridges[i].j[0];\r\n const jei = bridges[i].j[bridges[i].j.length - 1];\r\n const ibj = bridges[j].i[0];\r\n const iej = bridges[j].i[bridges[j].i.length - 1];\r\n const jbj = bridges[j].j[0];\r\n const jej = bridges[j].j[bridges[j].j.length - 1];\r\n\r\n if (bridges[i].type !== bridges[j].type\r\n || this._hasChainBreak(Math.min(ibi, ibj), Math.max(iei, iej))\r\n || this._hasChainBreak(Math.min(jbi, jbj), Math.max(jei, jej))\r\n || ibj - iei >= 6 || (iei >= ibj && ibi <= iej)) {\r\n continue;\r\n }\r\n\r\n let bulge = false;\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bulge = ((jbj - jei < 6 && ibj - iei < 3) || (jbj - jei < 3));\r\n } else {\r\n bulge = ((jbi - jej < 6 && ibj - iei < 3) || (jbi - jej < 3));\r\n }\r\n\r\n if (bulge) {\r\n bridges[i].i = bridges[i].i.concat(bridges[j].i);\r\n if (bridges[i].type === BridgeType.PARALLEL) {\r\n bridges[i].j = bridges[i].j.concat(bridges[j].j);\r\n } else {\r\n bridges[i].j = bridges[j].j.concat(bridges[i].j);\r\n }\r\n bridges.splice(j--, 1);\r\n }\r\n }\r\n }\r\n\r\n // Sheet\r\n const ladderset = new Set();\r\n for (let i = 0; i < bridges.length; ++i) {\r\n ladderset.add(bridges[i]);\r\n }\r\n\r\n let sheet = 1;\r\n let ladder = 0;\r\n while (ladderset.size > 0) {\r\n let bridge = ladderset.values().next().value;\r\n ladderset.delete(bridge);\r\n\r\n const sheetset = new Set();\r\n sheetset.add(bridge);\r\n\r\n let toMove;\r\n do {\r\n toMove = new Set();\r\n for (const a of sheetset.values()) {\r\n for (const b of ladderset.values()) {\r\n if (this._areBridgesLinked(a, b)) {\r\n toMove.add(b);\r\n }\r\n }\r\n }\r\n for (bridge of toMove.values()) {\r\n sheetset.add(bridge);\r\n ladderset.delete(bridge);\r\n }\r\n } while (toMove.size > 0);\r\n\r\n for (bridge of sheetset.values()) {\r\n bridge.ladder = ladder;\r\n bridge.sheet = sheet;\r\n bridge.link = sheetset;\r\n ++ladder;\r\n }\r\n\r\n ++sheet;\r\n }\r\n\r\n for (let i = 0; i < bridges.length; ++i) {\r\n const bridge = bridges[i];\r\n\r\n // find out if any of the i and j set members already have\r\n // a bridge assigned, if so, we're assigning bridge 2\r\n\r\n let betai = 0;\r\n let betaj = 0;\r\n\r\n for (let l = 0; l < bridge.i.length; ++l) {\r\n if (this._betaPartners[bridge.i[l]][0]) {\r\n betai = 1;\r\n break;\r\n }\r\n }\r\n\r\n for (let l = 0; l < bridge.j.length; ++l) {\r\n if (this._betaPartners[bridge.j[l]][0]) {\r\n betaj = 1;\r\n break;\r\n }\r\n }\r\n\r\n let ss = StructureType.BRIDGE;\r\n if (bridge.i.length > 1) {\r\n ss = StructureType.STRAND;\r\n }\r\n\r\n if (bridge.type === BridgeType.PARALLEL) {\r\n let j = 0;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n\r\n j = 0;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j++],\r\n ladder: bridge.ladder,\r\n parallel: true,\r\n };\r\n }\r\n } else {\r\n let j = bridge.j.length - 1;\r\n for (let k = 0; k < bridge.i.length; ++k) {\r\n this._betaPartners[bridge.i[k]][betai] = {\r\n residue: bridge.j[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n\r\n j = bridge.i.length - 1;\r\n for (let k = 0; k < bridge.j.length; ++k) {\r\n this._betaPartners[bridge.j[k]][betaj] = {\r\n residue: bridge.i[j--],\r\n ladder: bridge.ladder,\r\n parallel: false,\r\n };\r\n }\r\n }\r\n\r\n for (let k = bridge.i[0]; k <= bridge.i[bridge.i.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n\r\n for (let k = bridge.j[0]; k <= bridge.j[bridge.j.length - 1]; ++k) {\r\n if (this._ss[k] !== StructureType.STRAND) {\r\n this._ss[k] = ss;\r\n this._sheet[k] = bridge.sheet;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _testBridge(chainA, from, chainB, to) {\r\n let result = BridgeType.NO_BRIDGE;\r\n\r\n const a = chainA[from - 1]._index;\r\n const b = chainA[from]._index;\r\n const c = chainA[from + 1]._index;\r\n const d = chainB[to - 1]._index;\r\n const e = chainB[to]._index;\r\n const f = chainB[to + 1]._index;\r\n\r\n const isBond = this._hbonds.isBond.bind(this._hbonds);\r\n if ((isBond(c, e) && isBond(e, a)) || (isBond(f, b) && isBond(b, d))) {\r\n result = BridgeType.PARALLEL;\r\n } else if ((isBond(c, d) && isBond(f, a)) || (isBond(e, b) && isBond(b, e))) {\r\n result = BridgeType.ANTI_PARALLEL;\r\n }\r\n return result;\r\n }\r\n\r\n // return true if any of the residues in bridge a is identical to any of the residues in bridge b\r\n _areBridgesLinked(a, b) {\r\n const ai = new Set(a.i);\r\n const aj = new Set(a.j);\r\n\r\n for (const i of b.i) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n for (const i of b.j) {\r\n if (ai.has(i) || aj.has(i)) {\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n }\r\n\r\n _hasChainBreak(from, to) {\r\n for (let i = from + 1; i <= to; ++i) {\r\n if (this._complex._residues[i]._sequence !== this._complex._residues[i - 1]._sequence + 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n}\r\n\r\nSecondaryStructureMap.StructureType = StructureType;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport Atom from './Atom';\r\nimport Chain from './Chain';\r\nimport Helix from './Helix';\r\nimport Strand from './Strand';\r\nimport Sheet from './Sheet';\r\nimport Component from './Component';\r\nimport ResidueType from './ResidueType';\r\nimport Bond from './Bond';\r\nimport AutoBond from './AutoBond';\r\nimport AromaticLoopsMarker from './AromaticLoopsMarker';\r\nimport BiologicalUnit from './BiologicalUnit';\r\nimport selectors from './selectors';\r\nimport VoxelWorld from './VoxelWorld';\r\nimport SecondaryStructureMap from './SecondaryStructureMap';\r\nimport StructuralElement from './StructuralElement';\r\n\r\nconst VOXEL_SIZE = 5.0;\r\n\r\nconst { StructureType } = SecondaryStructureMap;\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX\r\nconst helixClassMap = {\r\n [StructureType.HELIX_ALPHA]: 1,\r\n [StructureType.HELIX_PI]: 3,\r\n [StructureType.HELIX_310]: 5,\r\n};\r\n\r\nconst loopMap = {\r\n [StructureType.BRIDGE]: StructuralElementType.BRIDGE,\r\n [StructureType.TURN]: StructuralElementType.TURN,\r\n [StructureType.BEND]: StructuralElementType.BEND,\r\n [StructureType.LOOP]: StructuralElementType.COIL,\r\n};\r\n\r\n/**\r\n * The entire complex of the molecules under study.\r\n *\r\n * @exports Complex\r\n * @constructor\r\n */\r\nclass Complex {\r\n constructor() {\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n\r\n this._residueTypes = Object.create(ResidueType.StandardTypes);\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n this._molecules = [];\r\n this._maskNeedsUpdate = false;\r\n\r\n this.metadata = {};\r\n\r\n this.symmetry = [];\r\n this.units = [new BiologicalUnit(this)];\r\n this._currentUnit = 0; // default biological unit is the asymmetric unit\r\n }\r\n\r\n addAtom(atom) {\r\n const index = this._atoms.length;\r\n this._atoms.push(atom);\r\n return index;\r\n }\r\n\r\n addSheet(sheet) {\r\n const index = this._sheets.length;\r\n this._sheets.push(sheet);\r\n return index;\r\n }\r\n\r\n addHelix(helix) {\r\n const index = this._helices.length;\r\n this._helices.push(helix);\r\n return index;\r\n }\r\n\r\n getAtoms() {\r\n return this._atoms;\r\n }\r\n\r\n getBonds() {\r\n return this._bonds;\r\n }\r\n\r\n getAtomCount() {\r\n return this._atoms.length;\r\n }\r\n\r\n addResidue(residue) {\r\n const index = this._residues.length;\r\n this._residues.push(residue);\r\n return index;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n this.forEachChain((chain) => {\r\n chain.updateToFrame(frameData);\r\n });\r\n }\r\n\r\n addResidueType(resName) {\r\n const rt = this._residueTypes[resName] = new ResidueType(resName, 'Unknown', '');\r\n return rt;\r\n }\r\n\r\n getResidueCount() {\r\n return this._residues.length;\r\n }\r\n\r\n getResidues() {\r\n return this._residues;\r\n }\r\n\r\n getSGroupCount() {\r\n return this._sgroups.length;\r\n }\r\n\r\n getSGroups() {\r\n return this._sgroups;\r\n }\r\n\r\n /*\r\n Extract atom by its fullname: #chainName#.#residueId#.#atomName#\r\n */\r\n getAtomByFullname(fullName) {\r\n const parts = fullName.split('.');\r\n if (parts.length !== 3) {\r\n return null;\r\n }\r\n\r\n const chainName = parts[0];\r\n const resId = parseInt(parts[1], 10);\r\n if (Number.isNaN(resId)) {\r\n return null;\r\n }\r\n const atomName = parts[2].toUpperCase();\r\n\r\n let currAtom = null;\r\n this.forEachChain((chain) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (chain._name.localeCompare(chainName) === 0) {\r\n chain.forEachResidue((residue) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (residue._sequence === resId) {\r\n residue.forEachAtom((atom) => {\r\n if (currAtom) {\r\n return;\r\n }\r\n if (atomName.localeCompare(atom.name) === 0) {\r\n currAtom = atom;\r\n }\r\n });\r\n }\r\n });\r\n }\r\n });\r\n\r\n return currAtom;\r\n }\r\n\r\n /**\r\n * Create a new chain.\r\n *\r\n * @param {string} name - Chain name.\r\n * @returns {Chain} - Newly created chain.\r\n */\r\n addChain(name) {\r\n const result = new Chain(this, name);\r\n this._chains.push(result);\r\n return result;\r\n }\r\n\r\n getChain(name) {\r\n for (let i = 0, n = this._chains.length; i < n; ++i) {\r\n const chain = this._chains[i];\r\n if (chain.getName() === name) {\r\n return chain;\r\n }\r\n }\r\n return null;\r\n }\r\n\r\n getChainCount() {\r\n return this._chains.length;\r\n }\r\n\r\n getMolecules() {\r\n return this._molecules;\r\n }\r\n\r\n getMoleculeCount() {\r\n return this._molecules.length;\r\n }\r\n\r\n forEachAtom(process) {\r\n const atoms = this._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n process(atoms[i]);\r\n }\r\n }\r\n\r\n forEachBond(process) {\r\n const bonds = this._bonds;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n process(bonds[i]);\r\n }\r\n }\r\n\r\n forEachResidue(process) {\r\n const residues = this._residues;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n forEachChain(process) {\r\n const chains = this._chains;\r\n for (let i = 0, n = chains.length; i < n; ++i) {\r\n process(chains[i]);\r\n }\r\n }\r\n\r\n forEachMolecule(process) {\r\n const molecules = this._molecules;\r\n const n = molecules.length;\r\n for (let i = 0; i < n; ++i) {\r\n process(molecules[i]);\r\n }\r\n }\r\n\r\n forEachSGroup(process) {\r\n const groups = this._sgroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n process(groups[i]);\r\n }\r\n }\r\n\r\n forEachComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n forEachVisibleComponent(process) {\r\n const components = this._components;\r\n for (let i = 0, n = components.length; i < n; ++i) {\r\n process(components[i]);\r\n }\r\n }\r\n\r\n addBond(left, right, order, type, fixed) {\r\n const bond = new Bond(left, right, order, type, fixed);\r\n this._bonds.push(bond);\r\n return bond;\r\n }\r\n\r\n getBondCount() {\r\n return this._bonds.length;\r\n }\r\n\r\n getResidueType(name) {\r\n return this._residueTypes[name] || null;\r\n }\r\n\r\n getUnifiedSerial(chain, serial, iCode) {\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n return serial + iCode * maxSerial + chain * chainShift;\r\n }\r\n\r\n splitUnifiedSerial(uniSerial) {\r\n const maxSerial = 65536;\r\n const chainShift = maxSerial * 256;\r\n const chainId = Math.floor(uniSerial / chainShift);\r\n const remnant = uniSerial - chainId * chainShift;\r\n const insCode = Math.floor(remnant / maxSerial);\r\n const ser = remnant - insCode * maxSerial;\r\n return { chain: chainId, serial: ser, iCode: insCode };\r\n }\r\n\r\n _fillCmpEdit() {\r\n const self = this;\r\n const components = this._components;\r\n\r\n function addComp() {\r\n const comp = new Component(self);\r\n comp._index = components.length;\r\n components[comp._index] = comp;\r\n return comp;\r\n }\r\n\r\n this.forEachChain((chain) => {\r\n const residues = chain._residues;\r\n const resCount = residues.length;\r\n if (resCount < 1) {\r\n return;\r\n }\r\n let comp = addComp();\r\n let currStart = residues[0]._index;\r\n\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)\r\n || currRes._index !== nextRes._index - 1) {\r\n // the last condition is broken and incorrect\r\n // the refactoring of the Component is required in order to fix this issue\r\n comp.setSubDivs([{\r\n start: currStart,\r\n end: currRes._index,\r\n }]);\r\n if (nextRes) {\r\n currStart = nextRes._index;\r\n comp = addComp();\r\n }\r\n }\r\n }\r\n });\r\n }\r\n\r\n // This function was added in the moment of despair\r\n // It was the dark times for miew\r\n _fillCmpNoedit() {\r\n const comp = new Component(this);\r\n comp._index = 0;\r\n\r\n const residues = this._residues;\r\n const resCount = residues.length;\r\n if (resCount === 0) {\r\n return;\r\n }\r\n\r\n const currSubDivs = [];\r\n let currStart = 0;\r\n for (let i = 0; i < resCount; ++i) {\r\n const currRes = residues[i];\r\n currRes._component = comp;\r\n\r\n const nextRes = i === resCount - 1 ? null : residues[i + 1];\r\n if (!nextRes\r\n || !currRes.isConnected(nextRes)) {\r\n // wrap up this interval\r\n currSubDivs[currSubDivs.length] = {\r\n start: currStart,\r\n end: i,\r\n };\r\n if (nextRes) {\r\n currStart = i + 1;\r\n }\r\n }\r\n }\r\n\r\n comp.setSubDivs(currSubDivs);\r\n this._components[comp._index] = comp;\r\n }\r\n\r\n /**\r\n * Fill components information.\r\n * @param {boolean} enableEditing - Restructure Complex to enable per-component editing.\r\n */\r\n _fillComponents(enableEditing) {\r\n if (enableEditing) {\r\n this._fillCmpEdit();\r\n } else {\r\n this._fillCmpNoedit();\r\n }\r\n }\r\n\r\n getCurrentUnit() {\r\n return this._currentUnit;\r\n }\r\n\r\n getDefaultBoundaries() {\r\n return this.units[0].getBoundaries();\r\n }\r\n\r\n getBoundaries() {\r\n return this.units[this._currentUnit].getBoundaries();\r\n }\r\n\r\n getTransforms() {\r\n return this.units[this._currentUnit].getTransforms();\r\n }\r\n\r\n getSelector() {\r\n return this.units[this._currentUnit].getSelector();\r\n }\r\n\r\n resetCurrentUnit() {\r\n this._currentUnit = 0;\r\n this.setCurrentUnit(1);\r\n }\r\n\r\n setCurrentUnit(newUnit) {\r\n if (newUnit !== null && newUnit !== undefined\r\n && newUnit !== this._currentUnit\r\n && newUnit >= 0\r\n && newUnit < this.units.length) {\r\n this._currentUnit = newUnit;\r\n return true;\r\n }\r\n return false;\r\n }\r\n\r\n _computeBounds() {\r\n const { units } = this;\r\n for (let i = 0, n = units.length; i < n; ++i) {\r\n units[i].computeBoundaries();\r\n }\r\n }\r\n\r\n onAtomPositionChanged() {\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n this.forEachComponent((c) => {\r\n c.update();\r\n });\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n this._finalizeBonds();\r\n this.forEachSGroup((s) => {\r\n s._rebuildSGroupOnAtomChange();\r\n });\r\n }\r\n\r\n update() {\r\n if (this._maskNeedsUpdate) {\r\n this.updateStructuresMask();\r\n this._maskNeedsUpdate = false;\r\n }\r\n }\r\n\r\n _finalizeBonds() {\r\n const bonds = this.getBonds();\r\n const n = bonds.length;\r\n for (let i = 0; i < n; ++i) {\r\n bonds[i]._index = i;\r\n }\r\n }\r\n\r\n /**\r\n * Finalizes complex's inner data(i.e. after parsing).\r\n * @param {objects} opts - Build bonds automatically.\r\n * @param {boolean} opts.needAutoBonding - Build bonds automatically.\r\n * @param {boolean} opts.detectAromaticLoops - Find/mark aromatic loops.\r\n * @param {boolean} opts.enableEditing - Restructure Complex to enable per-component editing.\r\n * @param {Array} [opts.serialAtomMap] - Array of atoms ordered by their serials.\r\n */\r\n finalize(opts) {\r\n opts = opts || {};\r\n // Put bonds into atoms\r\n const bonds = this._bonds;\r\n let i;\r\n let n;\r\n // remove invalid bonds\r\n for (i = bonds.length - 1; i >= 0; i--) {\r\n const bond = bonds[i];\r\n if (bond._left === null || bond._right === null) {\r\n bonds.splice(i, 1);\r\n } else {\r\n bond._left.bonds.push(bond);\r\n bond._right.bonds.push(bond);\r\n }\r\n }\r\n\r\n const residues = this._residues;\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._finalize();\r\n }\r\n\r\n this.forEachChain((a) => {\r\n a._finalize();\r\n });\r\n\r\n // WARNING! this MUST be done BEFORE computeBounds is called\r\n const { units } = this;\r\n for (i = 0, n = units.length; i < n; ++i) {\r\n units[i].finalize();\r\n }\r\n // try setting first biomolecule by defaults\r\n this.setCurrentUnit(1);\r\n\r\n const residueHash = {};\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n const res = residues[i];\r\n // This code is extremely dangerous for non-PDB formats\r\n residueHash[this.getUnifiedSerial(\r\n res.getChain().getName().charCodeAt(0),\r\n res.getSequence(),\r\n res.getICode().charCodeAt(0),\r\n )] = res;\r\n }\r\n\r\n const { structures } = this;\r\n for (i = 0, n = structures.length; i < n; ++i) {\r\n structures[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const helices = this._helices;\r\n for (i = 0, n = helices.length; i < n; ++i) {\r\n helices[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n const sheets = this._sheets;\r\n for (i = 0, n = sheets.length; i < n; ++i) {\r\n sheets[i]._finalize(opts.serialAtomMap, residueHash, this);\r\n }\r\n\r\n // Update bounding sphere and box\r\n this._computeBounds();\r\n\r\n const atoms = this._atoms;\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const currAtom = atoms[i];\r\n currAtom.index = i;\r\n }\r\n\r\n if (opts.needAutoBonding) {\r\n // Ignore errors during autobonding\r\n try {\r\n const autoConnector = new AutoBond(this);\r\n autoConnector.build();\r\n autoConnector.destroy();\r\n } catch (e) {\r\n console.warn('Autobonding failed:', e);\r\n }\r\n }\r\n\r\n const chains = this._chains;\r\n for (i = 0, n = chains.length; i < n; ++i) {\r\n chains[i]._index = i;\r\n }\r\n\r\n for (i = 0, n = residues.length; i < n; ++i) {\r\n residues[i]._index = i;\r\n }\r\n\r\n // mark non-polar hydrogens\r\n for (i = 0, n = atoms.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n if (atom.flags & Atom.Flags.HYDROGEN && atom.bonds.length === 1) {\r\n const bond = atom.bonds[0];\r\n const other = (bond._left !== atom && bond._left) || bond._right;\r\n if (other.flags & Atom.Flags.CARBON) {\r\n atom.flags |= Atom.Flags.NONPOLARH;\r\n }\r\n }\r\n }\r\n\r\n this._finalizeBonds();\r\n this._fillComponents(opts.enableEditing);\r\n\r\n const marker = new AromaticLoopsMarker(this);\r\n marker.markCycles();\r\n if (opts.detectAromaticLoops) { // TODO remove this condition clause, it is for debug purposes only!\r\n marker.detectCycles(); // TODO add conditional detection\r\n }\r\n\r\n this._finalizeMolecules();\r\n }\r\n\r\n _finalizeMolecules() {\r\n // add reference to molecule into residue\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const molecule = this._molecules[i];\r\n const count = molecule.residues.length;\r\n for (let j = 0; j < count; j++) {\r\n const residue = molecule.residues[j];\r\n residue._molecule = molecule;\r\n }\r\n }\r\n }\r\n\r\n updateStructuresMask() {\r\n const updater = (structure) => structure.collectMask();\r\n this.forEachResidue(updater);\r\n this.forEachChain(updater);\r\n this.forEachMolecule(updater);\r\n }\r\n\r\n countAtomsByMask(mask) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if ((atom.mask & mask) !== 0) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n getNumAtomsBySelector(selector) {\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom)) {\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n resetAtomMask(mask) {\r\n this.forEachAtom((atom) => {\r\n atom.mask = mask;\r\n });\r\n }\r\n\r\n markAtoms(selector, mask) {\r\n const setMask = mask;\r\n const clearMask = ~setMask;\r\n let count = 0;\r\n const totalSelector = selectors.keyword('And')(selector, this.getSelector());\r\n\r\n this.forEachAtom((atom) => {\r\n if (totalSelector.includesAtom(atom)) {\r\n atom.mask |= setMask;\r\n count++;\r\n } else {\r\n atom.mask &= clearMask;\r\n }\r\n });\r\n this._maskNeedsUpdate = true;\r\n\r\n return count;\r\n }\r\n\r\n markAtomsAdditionally(selector, mask) {\r\n const setMask = mask;\r\n let count = 0;\r\n\r\n this.forEachAtom((atom) => {\r\n if (selector.includesAtom(atom) && (atom.mask & mask) !== mask) {\r\n atom.mask |= setMask;\r\n count++;\r\n }\r\n });\r\n\r\n return count;\r\n }\r\n\r\n clearAtomBits(mask) {\r\n const clearMask = ~mask;\r\n this.forEachAtom((atom) => {\r\n atom.mask &= clearMask;\r\n });\r\n const reseter = (a) => {\r\n a._mask &= clearMask;\r\n };\r\n this.forEachAtom(reseter);\r\n this.forEachResidue(reseter);\r\n this.forEachChain(reseter);\r\n this.forEachMolecule(reseter);\r\n }\r\n\r\n getAtomNames() {\r\n if (this.hasOwnProperty('_atomNames')) {\r\n return this._atomNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.name] = 1;\r\n });\r\n this._atomNames = Object.keys(dict);\r\n\r\n return this._atomNames;\r\n }\r\n\r\n getElements() {\r\n if (this.hasOwnProperty('_elements')) {\r\n return this._elements;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[atom.element.name] = 1;\r\n });\r\n this._elements = Object.keys(dict);\r\n\r\n return this._elements;\r\n }\r\n\r\n getResidueNames() {\r\n if (this.hasOwnProperty('_residueNames')) {\r\n return this._residueNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachResidue((res) => {\r\n dict[res._type._name] = 1;\r\n });\r\n this._residueNames = Object.keys(dict);\r\n\r\n return this._residueNames;\r\n }\r\n\r\n getChainNames() {\r\n if (this.hasOwnProperty('_chainNames')) {\r\n return this._chainNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachChain((chain) => {\r\n dict[chain._name] = 1;\r\n });\r\n this._chainNames = Object.keys(dict);\r\n\r\n return this._chainNames;\r\n }\r\n\r\n getAltLocNames() {\r\n if (this.hasOwnProperty('_altlocNames')) {\r\n return this._altlocNames;\r\n }\r\n\r\n const dict = {};\r\n this.forEachAtom((atom) => {\r\n dict[String.fromCharCode(atom.location)] = 1;\r\n });\r\n this._altlocNames = Object.keys(dict);\r\n\r\n return this._altlocNames;\r\n }\r\n\r\n getVoxelWorld() {\r\n if (!this.hasOwnProperty('_voxelWorld')) {\r\n try {\r\n this._voxelWorld = new VoxelWorld(\r\n this.getDefaultBoundaries().boundingBox,\r\n new THREE.Vector3(VOXEL_SIZE, VOXEL_SIZE, VOXEL_SIZE),\r\n );\r\n this._voxelWorld.addAtoms(this);\r\n } catch {\r\n logger.warn('Unable to create voxel world');\r\n this._voxelWorld = null;\r\n }\r\n }\r\n\r\n return this._voxelWorld;\r\n }\r\n\r\n /**\r\n * Simple function to make unified routine procedure without code duplication.\r\n * @param {Array} srcArray - Source chemical structure array (will be part of resulting chemical structure array).\r\n * @param {Array} dstArray - Resulting chemical structure array.\r\n * @param {number} param - Parameter for processor.\r\n * @param {function} functor - Processor for every element in array.\r\n */\r\n addElement(srcArray, dstArray, param, functor) {\r\n const { length } = srcArray;\r\n for (let i = 0; i < length; ++i) {\r\n const elem = srcArray[i];\r\n functor(elem, param);\r\n dstArray.push(elem);\r\n }\r\n }\r\n\r\n // this function joins multiple complexes into one (this)\r\n // atom, bond, ... objects are reused -- so input complexes are no longer valid\r\n joinComplexes(complexes) {\r\n // clear target complex\r\n this._chains = [];\r\n this._components = [];\r\n this._helices = [];\r\n this._sheets = [];\r\n this.structures = [];\r\n this._atoms = [];\r\n this._residues = [];\r\n this._bonds = [];\r\n this._sgroups = [];\r\n\r\n const self = this;\r\n let atomBias = 0;\r\n let bondBias = 0;\r\n let residueBias = 0;\r\n let chainBias = 0;\r\n let componentBias = 0;\r\n\r\n function processAtom(atom, bias) {\r\n atom.serial += bias;\r\n atom.index += bias;\r\n }\r\n\r\n function processBond(bond, bias) {\r\n bond._index += bias;\r\n }\r\n\r\n function processResidue(residue, bias) {\r\n residue._index += bias;\r\n }\r\n\r\n function processChain(chain, bias) {\r\n chain._complex = self;\r\n chain._index += bias;\r\n }\r\n\r\n function processComponent(component, bias) {\r\n component._complex = self;\r\n component._index += bias;\r\n }\r\n\r\n /**\r\n * Simple function to do nothing.\r\n */\r\n function doNothing() {\r\n }\r\n\r\n for (let i = 0; i < complexes.length; ++i) {\r\n const c = complexes[i];\r\n this.addElement(c._atoms, this._atoms, atomBias, processAtom);\r\n this.addElement(c._bonds, this._bonds, bondBias, processBond);\r\n this.addElement(c._residues, this._residues, residueBias, processResidue);\r\n this.addElement(c._chains, this._chains, chainBias, processChain);\r\n this.addElement(c._sheets, this._sheets, 0, doNothing);\r\n this.addElement(c._helices, this._helices, 0, doNothing);\r\n this.addElement(c._sgroups, this._sgroups, 0, doNothing);\r\n this.addElement(c._components, this._components, componentBias, processComponent);\r\n this.addElement(c.structures, this.structures, 0, doNothing);\r\n // merge residue types\r\n for (const rt in c._residueTypes) {\r\n if (c._residueTypes.hasOwnProperty(rt)) {\r\n this._residueTypes[rt] = c._residueTypes[rt];\r\n }\r\n }\r\n\r\n atomBias += c._atoms.length;\r\n bondBias += c._bonds.length;\r\n residueBias += c._residues.length;\r\n chainBias += c._chains.length;\r\n componentBias += c._components.length;\r\n }\r\n\r\n this._computeBounds();\r\n }\r\n\r\n /**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n */\r\n dssp() {\r\n const ssMap = new SecondaryStructureMap(this);\r\n\r\n const structures = this.structures = [];\r\n const helices = this._helices = [];\r\n const sheets = this._sheets = [];\r\n\r\n const getSheet = (index) => {\r\n let item = sheets[index];\r\n if (!item) {\r\n item = sheets[index] = new Sheet(String(index), 0);\r\n }\r\n return item;\r\n };\r\n\r\n let lastCode;\r\n let lastSheetIndex;\r\n let lastHelixIndex = 0;\r\n let curStructure = null;\r\n for (let i = 0, n = this._residues.length; i < n; ++i) {\r\n const curCode = ssMap._ss[i];\r\n const curResidue = this._residues[i];\r\n const curSheetIndex = ssMap._sheet[i];\r\n\r\n // expand the last structure\r\n if (curCode === lastCode && curSheetIndex === lastSheetIndex) {\r\n curResidue._secondary = curStructure;\r\n if (curStructure) {\r\n curStructure.term = curResidue;\r\n }\r\n if (curStructure instanceof Helix) {\r\n curStructure.length++;\r\n }\r\n continue;\r\n }\r\n\r\n // create a new structure\r\n const helixClass = helixClassMap[curCode];\r\n const loopType = loopMap[curCode];\r\n if (curCode === StructureType.STRAND) {\r\n const curSheet = getSheet(curSheetIndex);\r\n curStructure = new Strand(curSheet, curResidue, curResidue, 0, null, null);\r\n curSheet.addStrand(curStructure);\r\n } else if (helixClass !== undefined) {\r\n lastHelixIndex++;\r\n curStructure = new Helix(helixClass, curResidue, curResidue, lastHelixIndex, String(lastHelixIndex), '', 1);\r\n helices.push(curStructure);\r\n } else if (loopType !== undefined) {\r\n curStructure = new StructuralElement(loopType, curResidue, curResidue);\r\n } else {\r\n curStructure = null;\r\n }\r\n\r\n if (curStructure) {\r\n structures.push(curStructure);\r\n }\r\n\r\n curResidue._secondary = curStructure;\r\n\r\n lastCode = curCode;\r\n lastSheetIndex = curSheetIndex;\r\n }\r\n\r\n this._sheets = sheets.filter((_sheet) => true); // squeeze sheets array\r\n }\r\n}\r\n\r\nComplex.prototype.id = 'Complex';\r\nComplex.prototype.name = '';\r\n\r\nexport default Complex;\r\n","import * as THREE from 'three';\r\nimport utils from '../utils';\r\n\r\nfunction pow2ceil(v) {\r\n let p = 2;\r\n v = (v - 1) >> 1;\r\n while (v) {\r\n p <<= 1;\r\n v >>= 1;\r\n }\r\n return p;\r\n}\r\n\r\n/**\r\n * Volume constructor\r\n *\r\n * @param {Object} type - Float32Array, Int8Array, etc...\r\n * @param {Object|Array} dimensions - number of data points on each axis (x, y, z)\r\n * @param {Box3} box - bounding box defining data place in metric space,\r\n * it's corners correspond to extreme data points\r\n * @param {Number} vecSize - dimension of the field data point (1 = scalar, 3 = 3D vector)\r\n * @param {Object} data - typed array of the same type as specified by the 1st parameter,\r\n * layout: point by point along X,\r\n * row by row along Y,\r\n * plane by plane along Z\r\n * @param {Number} volumeInfo - volume info values to define threshold to filter the noise\r\n */\r\n\r\nclass Volume {\r\n constructor(type, dimensions, box, vecSize, data, volumeInfo) {\r\n this._box = box.clone();\r\n this._dimVec = Math.max(Math.floor(vecSize || 1), 1);\r\n this._volumeInfo = volumeInfo;\r\n\r\n if (dimensions instanceof Array) {\r\n [this._dimX, this._dimY, this._dimZ] = dimensions;\r\n } else {\r\n this._dimX = dimensions.x;\r\n this._dimY = dimensions.y;\r\n this._dimZ = dimensions.z;\r\n }\r\n this._dimX = Math.max(Math.floor(this._dimX), 1);\r\n this._dimY = Math.max(Math.floor(this._dimY), 1);\r\n this._dimZ = Math.max(Math.floor(this._dimZ), 1);\r\n\r\n this._rowElements = this._dimVec * this._dimX;\r\n this._planeElements = this._rowElements * this._dimY;\r\n this._totalElements = this._planeElements * this._dimZ;\r\n\r\n this._data = data || utils.allocateTyped(type, this._totalElements);\r\n\r\n // override getter/setter for vector fields\r\n switch (this._dimVec) {\r\n case 1:\r\n break;\r\n\r\n case 2:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n };\r\n break;\r\n\r\n case 3:\r\n this.getValue = function (x, y, z) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n return [this._data[idx], this._data[idx + 1], this._data[idx + 2]];\r\n };\r\n\r\n this.setValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] = a;\r\n this._data[idx + 1] = b;\r\n this._data[idx + 2] = c;\r\n };\r\n\r\n this.addValue = function (x, y, z, a, b, c) {\r\n const idx = x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n this._data[idx] += a;\r\n this._data[idx + 1] += b;\r\n this._data[idx + 2] += c;\r\n };\r\n break;\r\n\r\n default:\r\n throw new Error('Volume: invalid vector dimension');\r\n }\r\n }\r\n\r\n // default getter assumes it's a scalar field\r\n getValue(x, y, z) {\r\n return this._data[x + y * this._rowElements + z * this._planeElements];\r\n }\r\n\r\n // default setter assumes it's a scalar field\r\n setValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] = val;\r\n }\r\n\r\n // default adder assumes it's a scalar field\r\n addValue(x, y, z, val) {\r\n this._data[x + y * this._rowElements + z * this._planeElements] += val;\r\n }\r\n\r\n getDimensions() {\r\n return [this._dimX, this._dimY, this._dimZ];\r\n }\r\n\r\n getBox() {\r\n return this._box;\r\n }\r\n\r\n getVolumeInfo() {\r\n return this._volumeInfo;\r\n }\r\n\r\n getCellSize() {\r\n const boxSize = new THREE.Vector3();\r\n this._box.getSize(boxSize);\r\n const res = new THREE.Vector3();\r\n res.x = this._dimX > 1 ? boxSize.x / (this._dimX - 1) : 0;\r\n res.y = this._dimY > 1 ? boxSize.y / (this._dimY - 1) : 0;\r\n res.z = this._dimZ > 1 ? boxSize.z / (this._dimZ - 1) : 0;\r\n return res;\r\n }\r\n\r\n computeGradient() {\r\n if (this._dimVec !== 1) {\r\n // gradient can only be computed for scalar fields\r\n return null;\r\n }\r\n\r\n // create a 3D vector field of gradients\r\n const gradient = new Volume(Float32Array, [this._dimX, this._dimY, this._dimZ], this._box, 3);\r\n\r\n // calculate cell side lengths\r\n const vl = this.getCellSize();\r\n\r\n // gradient axis scaling values and averaging factors, to correctly\r\n // calculate the gradient for volumes with irregular cell spacing\r\n const vs = new THREE.Vector3(-0.5 / vl.x, -0.5 / vl.y, -0.5 / vl.z);\r\n\r\n // TODO Check for intended bug in VMD (min is zero)\r\n function clamp(val, min, max) {\r\n return Math.min(max, Math.max(min, val));\r\n }\r\n\r\n const xSize = this._dimX;\r\n const ySize = this._dimY;\r\n const zSize = this._dimZ;\r\n const volMap = this._data;\r\n\r\n function _voxelValue(x, y, z) {\r\n return volMap[z * xSize * ySize + y * xSize + x];\r\n }\r\n\r\n for (let zi = 0; zi < zSize; ++zi) {\r\n const zm = clamp(zi - 1, 0, zSize - 1);\r\n const zp = clamp(zi + 1, 0, zSize - 1);\r\n\r\n for (let yi = 0; yi < ySize; ++yi) {\r\n const ym = clamp(yi - 1, 0, ySize - 1);\r\n const yp = clamp(yi + 1, 0, ySize - 1);\r\n\r\n for (let xi = 0; xi < xSize; ++xi) {\r\n const xm = clamp(xi - 1, 0, xSize - 1);\r\n const xp = clamp(xi + 1, 0, xSize - 1);\r\n\r\n // Calculate the volume gradient at each grid cell.\r\n // Gradients are now stored unnormalized, since we need them in pure\r\n // form in order to draw field lines etc. Shading code will now have\r\n // to do renormalization for itself on-the-fly.\r\n\r\n // XXX this gradient is only correct for orthogonal grids, since\r\n // we're using the array index offsets rather to calculate the gradient\r\n // rather than voxel coordinate offsets. This will have to be\r\n // re-worked for non-orthogonal datasets.\r\n\r\n gradient.setValue(\r\n xi,\r\n yi,\r\n zi,\r\n (_voxelValue(xp, yi, zi) - _voxelValue(xm, yi, zi)) * vs.x,\r\n (_voxelValue(xi, yp, zi) - _voxelValue(xi, ym, zi)) * vs.y,\r\n (_voxelValue(xi, yi, zp) - _voxelValue(xi, yi, zm)) * vs.z,\r\n );\r\n }\r\n }\r\n }\r\n\r\n return gradient;\r\n }\r\n\r\n normalize() {\r\n const data = this._data;\r\n\r\n // get min/max\r\n let min = data[0];\r\n let max = data[0];\r\n for (let i = 1; i < data.length; ++i) {\r\n min = Math.min(min, data[i]);\r\n max = Math.max(max, data[i]);\r\n }\r\n\r\n const d = 1.0 / (max - min);\r\n if (d === 0) {\r\n return;\r\n }\r\n\r\n // normalize\r\n for (let i = 0; i < data.length; ++i) {\r\n data[i] = d * (data[i] - min);\r\n }\r\n }\r\n\r\n getTiledTextureStride() {\r\n return [this._dimX + 2, this._dimY + 2];\r\n }\r\n\r\n buildTiledTexture() {\r\n let tilesX = Math.ceil(Math.sqrt(this._dimZ * this._dimY / this._dimX));\r\n\r\n let width = tilesX * (this._dimX + 2) - 1;\r\n width = pow2ceil(width);\r\n tilesX = Math.floor(width / (this._dimX + 2));\r\n\r\n const tilesY = Math.ceil(this._dimZ / tilesX);\r\n let height = tilesY * (this._dimY + 2) - 1;\r\n height = pow2ceil(height);\r\n\r\n const data = new Uint8Array(width * height);\r\n\r\n let src;\r\n let dst;\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // process each pixel row of this tile row\r\n for (let row = 0; row < this._dimY; ++row) {\r\n src = tileRow * tilesX * this._planeElements + row * this._rowElements;\r\n dst = width * (tileRow * (this._dimY + 2) + row);\r\n // copy a series of rows through several XY planes\r\n for (let t = 0; t < tilesX; ++t) {\r\n // copy one row of one XY plane\r\n for (let x = 0; x < this._dimX; ++x) {\r\n data[dst++] = 255.0 * this._data[src++];\r\n }\r\n\r\n // repeat last pixel of previous tile\r\n data[dst++] = 255.0 * this._data[src - 1];\r\n\r\n if (t < tilesX - 1) {\r\n // skip to the same row of next XY plane\r\n src += this._planeElements - this._rowElements;\r\n // repeat first pixel of next tile\r\n data[dst++] = 255.0 * this._data[src];\r\n }\r\n }\r\n }\r\n }\r\n\r\n // fill pixels between tile rows with copy of edge pixels\r\n for (let tileRow = 0; tileRow < tilesY; ++tileRow) {\r\n // copy last pixel row of this tile row to the following pixel row of the texture\r\n src = width * (tileRow * (this._dimY + 2) + this._dimY - 1);\r\n dst = src + width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n if (tileRow < tilesY - 1) {\r\n // copy first pixel row of next tile row to the preceding pixel row of the texture\r\n src = width * (tileRow + 1) * (this._dimY + 2);\r\n dst = src - width;\r\n for (let x = 0; x < width; ++x) {\r\n data[dst++] = data[src++];\r\n }\r\n }\r\n }\r\n\r\n const texture = new THREE.DataTexture(\r\n data,\r\n width,\r\n height,\r\n THREE.RedFormat,\r\n THREE.UnsignedByteType,\r\n THREE.UVMapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.ClampToEdgeWrapping,\r\n THREE.LinearFilter,\r\n THREE.LinearFilter,\r\n );\r\n texture.needsUpdate = true;\r\n return texture;\r\n }\r\n\r\n /* ********************************************************************************\r\n *\r\n * Methods that provide direct access to internal array (for better performance)\r\n *\r\n ******************************************************************************** */\r\n\r\n getData() {\r\n return this._data;\r\n }\r\n\r\n getDirectIdx(x, y, z) {\r\n return x * this._dimVec + y * this._rowElements + z * this._planeElements;\r\n }\r\n\r\n getStrideX() {\r\n return this._dimVec;\r\n }\r\n\r\n getStrideY() {\r\n return this._rowElements;\r\n }\r\n\r\n getStrideZ() {\r\n return this._planeElements;\r\n }\r\n}\r\n\r\nVolume.prototype.id = 'Volume';\r\n\r\nexport default Volume;\r\n","/**\r\n * Residue Molecule.\r\n *\r\n * @param {Complex} complex - Molecular complex this Molecule belongs to.\r\n * @param {String} name - Molecule's name.\r\n * @param {Integer} index - Molecule's index in file.\r\n *\r\n * @exports Molecule\r\n * @constructor\r\n */\r\nclass Molecule {\r\n constructor(complex, name, index) {\r\n this.complex = complex;\r\n this.name = name || '';\r\n this.residues = [];\r\n this.mask = 1 | 0;\r\n this.index = index || -1; // start with 1\r\n }\r\n\r\n forEachResidue(process) {\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n process(residues[i]);\r\n }\r\n }\r\n\r\n collectMask() {\r\n let mask = 0xffffffff;\r\n const { residues } = this;\r\n for (let i = 0, n = residues.length; i < n; ++i) {\r\n mask &= residues[i]._mask;\r\n }\r\n this.mask = mask;\r\n }\r\n}\r\n\r\nexport default Molecule;\r\n","import Atom from './chem/Atom';\r\nimport Element from './chem/Element';\r\nimport Bond from './chem/Bond';\r\nimport Residue from './chem/Residue';\r\nimport ResidueType from './chem/ResidueType';\r\nimport Chain from './chem/Chain';\r\nimport Helix from './chem/Helix';\r\nimport Strand from './chem/Strand';\r\nimport Sheet from './chem/Sheet';\r\nimport SGroup from './chem/SGroup';\r\nimport Assembly from './chem/Assembly';\r\nimport Complex from './chem/Complex';\r\nimport Volume from './chem/Volume';\r\nimport VoxelWorld from './chem/VoxelWorld';\r\nimport selectors from './chem/selectors';\r\nimport Molecule from './chem/Molecule';\r\n\r\nexport default {\r\n Atom,\r\n Element,\r\n Bond,\r\n Residue,\r\n ResidueType,\r\n Chain,\r\n Helix,\r\n Strand,\r\n Sheet,\r\n SGroup,\r\n Assembly,\r\n Complex,\r\n Volume,\r\n VoxelWorld,\r\n selectors,\r\n Molecule,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\n\r\nclass CSS2DObject extends THREE.Object3D {\r\n constructor(element) {\r\n super();\r\n const self = this;\r\n this._element = element;\r\n this._element.style.position = 'absolute';\r\n this.addEventListener('removed', () => {\r\n if (self._element.parentNode !== null) {\r\n self._element.parentNode.removeChild(self._element);\r\n }\r\n });\r\n }\r\n\r\n getElement() {\r\n return this._element;\r\n }\r\n\r\n /**\r\n * Sets label transparency.\r\n *\r\n * @param {number} transp - in [0; 1] 1 means fully transparent\r\n */\r\n setTransparency(transp) {\r\n const el = this.getElement();\r\n if (el === null) {\r\n return;\r\n }\r\n if (transp === 1.0) {\r\n el.style.display = 'none';\r\n return;\r\n }\r\n el.style.display = 'inline';\r\n const op = 1.0 - transp;\r\n const top = op.toString();\r\n const op100 = op * 100;\r\n el.style.opacity = top;\r\n el.style.filter = `alpha(opacity=${op100})`; // IE fallback\r\n }\r\n\r\n clone() {\r\n const obj = new CSS2DObject(this._element);\r\n obj.copy(this);\r\n return obj;\r\n }\r\n}\r\n\r\nexport default CSS2DObject;\r\n","import * as THREE from 'three';\r\n\r\nclass RCGroup extends THREE.Group {\r\n raycast(raycaster, intersects) {\r\n if (!this.visible) {\r\n return;\r\n }\r\n\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n children[i].raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].enableSubset) {\r\n children[i].enableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].disableSubset) {\r\n children[i].disableSubset(mask, innerOnly);\r\n }\r\n }\r\n }\r\n\r\n isEmpty() {\r\n return this.children.length === 0;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].updateToFrame) {\r\n children[i].updateToFrame(frameData);\r\n }\r\n }\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n Array.prototype.push.apply(totalSubset, children[i].getSubset(mask, innerOnly));\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default RCGroup;\r\n","import * as THREE from 'three';\r\nimport logger from '../utils/logger';\r\nimport CSS2DObject from './CSS2DObject';\r\nimport RCGroup from './RCGroup';\r\nimport vertexScreenQuadShader from './shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromTex from './shaders/ScreenQuadFromTex.frag';\r\nimport fragmentScreenQuadFromTexWithDistortion from './shaders/ScreenQuadFromTexWithDistortion.frag';\r\n\r\nconst LAYERS = {\r\n DEFAULT: 0, VOLUME: 1, TRANSPARENT: 2, PREPASS_TRANSPARENT: 3, VOLUME_BFPLANE: 4, COLOR_FROM_POSITION: 5, SHADOWMAP: 6,\r\n};\r\n\r\nconst SELECTION_LAYERS = [ // These layers, that are used in the selection by ray casting\r\n LAYERS.DEFAULT, LAYERS.TRANSPARENT,\r\n];\r\n\r\nTHREE.Object3D.prototype.resetTransform = function () {\r\n this.position.set(0, 0, 0);\r\n this.quaternion.set(0, 0, 0, 1);\r\n this.scale.set(1, 1, 1);\r\n};\r\n\r\n// update world matrix of this object and all its ancestors\r\nTHREE.Object3D.prototype.updateMatrixWorldRecursive = function () {\r\n if (this.parent != null) {\r\n this.parent.updateMatrixWorldRecursive();\r\n }\r\n this.updateMatrixWorld();\r\n};\r\n// add object to parent, saving objects' world transform\r\nTHREE.Object3D.prototype.addSavingWorldTransform = (function () {\r\n const _worldMatrixInverse = new THREE.Matrix4();\r\n\r\n return function (object) {\r\n if (object instanceof THREE.Object3D) {\r\n _worldMatrixInverse.copy(this.matrixWorld).invert();\r\n _worldMatrixInverse.multiply(object.matrixWorld);\r\n object.matrix.copy(_worldMatrixInverse);\r\n object.matrix.decompose(object.position, object.quaternion, object.scale);\r\n this.add(object);\r\n }\r\n };\r\n}());\r\n\r\n// render a tiny transparent quad in the center of the screen\r\nTHREE.WebGLRenderer.prototype.renderDummyQuad = (function () {\r\n const _material = new THREE.MeshBasicMaterial({ transparent: true, opacity: 0.0, depthWrite: false });\r\n\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(0.01, 0.01), _material);\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function () {\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuad = (function () {\r\n const _scene = new THREE.Scene();\r\n const _quad = new THREE.Mesh(new THREE.PlaneGeometry(1.0, 1.0));\r\n _scene.add(_quad);\r\n\r\n const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);\r\n _camera.position.z = 100;\r\n\r\n return function (material) {\r\n _quad.material = material;\r\n this.render(_scene, _camera);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.isIdentity = (function () {\r\n const identity = new THREE.Matrix4();\r\n return function () {\r\n return identity.equals(this);\r\n };\r\n}());\r\n\r\nTHREE.Matrix4.prototype.applyToPointsArray = function (array, stride, w) {\r\n if (!array || !stride || stride < 3) {\r\n return array;\r\n }\r\n w = w || 0; // use point as normal by default\r\n const e = this.elements;\r\n for (let i = 0; i < array.length; i += stride) {\r\n const x = array[i];\r\n const y = array[i + 1];\r\n const z = array[i + 2];\r\n\r\n const persp = 1 / (e[3] * x + e[7] * y + e[11] * z + e[15]);\r\n\r\n array[i] = (e[0] * x + e[4] * y + e[8] * z + e[12] * w) * persp;\r\n array[i + 1] = (e[1] * x + e[5] * y + e[9] * z + e[13] * w) * persp;\r\n array[i + 2] = (e[2] * x + e[6] * y + e[10] * z + e[14] * w) * persp;\r\n }\r\n return array;\r\n};\r\n\r\nclass ScreenQuadMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n if (params.uniforms === undefined) {\r\n params.uniforms = {};\r\n }\r\n params.uniforms.srcTex = { type: 't', value: null };\r\n params.vertexShader = vertexScreenQuadShader;\r\n params.transparent = false;\r\n params.depthTest = false;\r\n params.depthWrite = false;\r\n super(params);\r\n }\r\n}\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTex = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { opacity: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTex,\r\n transparent: true,\r\n });\r\n\r\n return function (srcTex, opacity) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.transparent = (opacity < 1.0);\r\n _material.uniforms.opacity.value = opacity;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\nTHREE.WebGLRenderer.prototype.renderScreenQuadFromTexWithDistortion = (function () {\r\n const _material = new ScreenQuadMaterial({\r\n uniforms: { coef: { type: 'f', value: 1.0 } },\r\n fragmentShader: fragmentScreenQuadFromTexWithDistortion,\r\n });\r\n\r\n return function (srcTex, coef) {\r\n _material.uniforms.srcTex.value = srcTex;\r\n _material.uniforms.coef.value = coef;\r\n this.renderScreenQuad(_material);\r\n };\r\n}());\r\n\r\n/**\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setMinimalFov = function (angle) {\r\n if (this.aspect >= 1.0) {\r\n this.fov = angle;\r\n } else {\r\n this.fov = THREE.MathUtils.radToDeg(2 * Math.atan(Math.tan(THREE.MathUtils.degToRad(angle) * 0.5) / this.aspect));\r\n }\r\n};\r\n\r\n/**\r\n * @param {THREE.PerspectiveCamera} camera - Base camera for this stereo camera.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.StereoCamera.prototype.updateHalfSized = function (camera, angle) {\r\n const originalAspect = camera.aspect;\r\n const originalFov = camera.fov;\r\n\r\n camera.aspect = originalAspect / 2.0;\r\n camera.setMinimalFov(angle);\r\n camera.updateProjectionMatrix();\r\n\r\n this.update(camera);\r\n\r\n camera.aspect = originalAspect;\r\n camera.fov = originalFov;\r\n camera.updateProjectionMatrix();\r\n};\r\n\r\n/**\r\n * @param {number} radius - Radius of bounding sphere in angstroms to fit on screen.\r\n * @param {number} angle - Field of view in degrees.\r\n */\r\nTHREE.PerspectiveCamera.prototype.setDistanceToFit = function (radius, angle) {\r\n this.position.z = radius / Math.sin(0.5 * THREE.MathUtils.degToRad(angle));\r\n};\r\n\r\n/**\r\n * @param {RCGroup} gfxObj - All objects on scene.\r\n * @param {THREE.PerspectiveCamera} camera - Camera used for rendering.\r\n * @param {number} clipPlane - Distance to clip plane.\r\n * @param {number} fogFarPlane - Distance to fog far plane.\r\n */\r\nTHREE.Raycaster.prototype.intersectVisibleObject = function (gfxObj, camera, clipPlane, fogFarPlane) {\r\n const intersects = this.intersectObject(gfxObj, false);\r\n if (intersects.length === 0) {\r\n return null;\r\n }\r\n\r\n // find point closest to camera that doesn't get clipped by camera near plane or clipPlane (if it exists)\r\n const nearPlane = Math.min(camera.near, clipPlane);\r\n let i;\r\n let p = intersects[0];\r\n const v = new THREE.Vector3();\r\n for (i = 0; i < intersects.length; ++i) {\r\n p = intersects[i];\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -nearPlane) {\r\n break;\r\n }\r\n }\r\n if (i === intersects.length) {\r\n return null;\r\n }\r\n\r\n // check that selected intersection point is not clipped by camera far plane or occluded by fog (if it exists)\r\n const farPlane = Math.min(camera.far, fogFarPlane);\r\n v.copy(p.point);\r\n v.applyMatrix4(camera.matrixWorldInverse);\r\n if (v.z <= -farPlane) {\r\n return null;\r\n }\r\n return p;\r\n};\r\n\r\nTHREE.Matrix4.prototype.extractScale = (function () {\r\n const _v = new THREE.Vector3();\r\n\r\n return function (scale) {\r\n if (scale === undefined) {\r\n logger.debug('extractScale(): new is too expensive operation to do it on-the-fly');\r\n scale = _v.clone();\r\n }\r\n\r\n const te = this.elements;\r\n scale.x = _v.set(te[0], te[1], te[2]).length();\r\n scale.y = _v.set(te[4], te[5], te[6]).length();\r\n scale.z = _v.set(te[8], te[9], te[10]).length();\r\n\r\n // if determine is negative, we need to invert one scale\r\n const det = this.determinant();\r\n if (det < 0) {\r\n scale.x = -scale.x;\r\n }\r\n return scale;\r\n };\r\n}());\r\n\r\nfunction _calcCylinderMatrix(posBegin, posEnd, radius) {\r\n const posCenter = posBegin.clone().lerp(posEnd, 0.5);\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(radius, posBegin.distanceTo(posEnd), radius);\r\n\r\n const matRotHalf = new THREE.Matrix4();\r\n matRotHalf.makeRotationX(Math.PI / 2);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n const vUp = new THREE.Vector3(0, 1, 0);\r\n matRotLook.lookAt(posCenter, posEnd, vUp);\r\n\r\n matRotLook.multiply(matRotHalf);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(posCenter);\r\n return matRotLook;\r\n}\r\n\r\nfunction _calcChunkMatrix(eye, target, up, rad) {\r\n const matScale = new THREE.Matrix4();\r\n matScale.makeScale(rad.x, rad.y, 0);\r\n\r\n const matRotLook = new THREE.Matrix4();\r\n matRotLook.lookAt(eye, target, up);\r\n matRotLook.multiply(matScale);\r\n matRotLook.setPosition(eye);\r\n\r\n return matRotLook;\r\n}\r\n\r\nfunction _groupHasGeometryToRender(group) {\r\n let hasGeoms = false;\r\n group.traverse((node) => {\r\n if (node.hasOwnProperty('geometry') || node instanceof CSS2DObject) {\r\n hasGeoms = true;\r\n }\r\n });\r\n return hasGeoms;\r\n}\r\n\r\nfunction _buildDistorionMesh(widthSegments, heightSegements, coef) {\r\n // solve equation r_u = r_d * (1 + k * r_d^2)\r\n // for r_d using iterations\r\n // takes: r_u^2\r\n // returns: r_d / r_u factor that can be used to distort point coords\r\n function calcInverseBarrel(r2) {\r\n const epsilon = 1e-5;\r\n let prevR2 = 0.0;\r\n let curR2 = r2;\r\n let dr = 1.0;\r\n while (Math.abs(curR2 - prevR2) > epsilon) {\r\n dr = 1.0 + coef * curR2;\r\n prevR2 = curR2;\r\n curR2 = r2 / (dr * dr);\r\n }\r\n\r\n return 1.0 / dr;\r\n }\r\n\r\n const geo = new THREE.PlaneGeometry(2.0, 2.0, widthSegments, heightSegements);\r\n\r\n const pos = geo.getAttribute('position');\r\n for (let i = 0; i < pos.count; ++i) {\r\n const x = pos.array[3 * i];\r\n const y = pos.array[3 * i + 1];\r\n const c = calcInverseBarrel(x * x + y * y);\r\n pos.setXY(i, c * x, c * y);\r\n }\r\n\r\n return geo;\r\n}\r\n\r\nTHREE.BufferAttribute.prototype.copyAtList = function (attribute, indexList) {\r\n console.assert(\r\n this.itemSize === attribute.itemSize,\r\n 'DEBUG: BufferAttribute.copyAtList buffers have different item size.',\r\n );\r\n const { itemSize } = this;\r\n for (let i = 0, n = indexList.length; i < n; ++i) {\r\n for (let j = 0; j < itemSize; ++j) {\r\n this.array[i * itemSize + j] = attribute.array[indexList[i] * itemSize + j];\r\n }\r\n }\r\n return this;\r\n};\r\n\r\nfunction fillArray(array, value, startIndex, endIndex) {\r\n startIndex = (typeof startIndex !== 'undefined') ? startIndex : 0;\r\n endIndex = (typeof endIndex !== 'undefined') ? endIndex : array.length;\r\n for (let i = startIndex; i < endIndex; ++i) {\r\n array[i] = value;\r\n }\r\n}\r\n\r\n/** @param {THREE.Object3D} object - Parent object. */\r\nfunction removeChildren(object) {\r\n const { children } = object;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n child.parent = null;\r\n child.dispatchEvent({ type: 'removed' });\r\n }\r\n object.children = [];\r\n}\r\n\r\nfunction clearTree(object) {\r\n object.traverse((obj) => {\r\n if (obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line) {\r\n obj.geometry.dispose();\r\n }\r\n });\r\n removeChildren(object);\r\n}\r\n\r\nfunction destroyObject(object) {\r\n clearTree(object);\r\n if (object.parent) {\r\n object.parent.remove(object);\r\n } else {\r\n object.dispatchEvent({ type: 'removed' });\r\n }\r\n}\r\n\r\nfunction belongToSelectLayers(object) {\r\n for (let i = 0; i < SELECTION_LAYERS.length; i++) {\r\n if (((object.layers.mask >> SELECTION_LAYERS[i]) & 1) === 1) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n}\r\n\r\nfunction processObjRenderOrder(root, idMaterial) {\r\n // set renderOrder to 0 for Backdrop and to 1 in other cases to render Backdrop earlier all other materials\r\n const renderOrder = +(idMaterial !== 'BA');\r\n root.traverse((object) => {\r\n if (object.isGroup) {\r\n object.renderOrder = renderOrder;\r\n }\r\n });\r\n}\r\n\r\nfunction applySelectionMaterial(geo) {\r\n geo.traverse((node) => {\r\n if ('material' in node) {\r\n node.material = node.material.clone(true);\r\n // using z-offset to magically fix selection rendering artifact (on z-sprites)\r\n node.material.setValues({\r\n depthFunc: THREE.LessEqualDepth,\r\n overrideColor: true,\r\n fog: false,\r\n lights: false,\r\n shadowmap: false,\r\n });\r\n node.material.setUberOptions({ fixedColor: new THREE.Color(0xFFFF00), zOffset: -1e-6 });\r\n }\r\n });\r\n}\r\n\r\nfunction getMiddlePoint(point1, point2, optionalTarget) {\r\n const result = optionalTarget || new THREE.Vector3();\r\n\r\n result.set(0, 0, 0);\r\n result.addScaledVector(point1, 0.5);\r\n result.addScaledVector(point2, 0.5);\r\n\r\n return result;\r\n}\r\n\r\n// Monkey-patch for \"InstancedBufferGeometry.instanceCount becomes undefined after copy()\"\r\n// https://github.com/mrdoob/three.js/issues/22151\r\nconst _oldInstancedBufferGeometryCopy = THREE.InstancedBufferGeometry.prototype.copy;\r\n\r\nTHREE.InstancedBufferGeometry.prototype.copy = function (source) {\r\n _oldInstancedBufferGeometryCopy.call(this, source);\r\n if (this.instanceCount === undefined) {\r\n this.instanceCount = Infinity;\r\n }\r\n};\r\n\r\nexport default {\r\n calcCylinderMatrix: _calcCylinderMatrix,\r\n calcChunkMatrix: _calcChunkMatrix,\r\n groupHasGeometryToRender: _groupHasGeometryToRender,\r\n buildDistorionMesh: _buildDistorionMesh,\r\n RCGroup,\r\n fillArray,\r\n clearTree,\r\n destroyObject,\r\n belongToSelectLayers,\r\n processObjRenderOrder,\r\n applySelectionMaterial,\r\n getMiddlePoint,\r\n LAYERS,\r\n};\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfx/gfxutils';\r\n\r\nconst _defaultBoundaries = {\r\n boundingBox: new THREE.Box3(new THREE.Vector3(-1, -1, -1), new THREE.Vector3(1, 1, 1)),\r\n boundingSphere: new THREE.Sphere(new THREE.Vector3(0, 0, 0), 1),\r\n};\r\n\r\nclass Visual extends gfxutils.RCGroup {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this.name = name;\r\n this._dataSource = dataSource;\r\n }\r\n\r\n release() {\r\n if (this.parent) {\r\n this.parent.remove(this);\r\n }\r\n }\r\n\r\n getDataSource() {\r\n return this._dataSource;\r\n }\r\n\r\n getBoundaries() {\r\n return _defaultBoundaries;\r\n }\r\n}\r\n\r\nexport default Visual;\r\n","function _ensureArray(x) {\r\n if (x === null || x === undefined || Array.isArray(x)) {\r\n return x;\r\n }\r\n return [x];\r\n}\r\n\r\n/** An indexed list of objects or classes. */\r\nclass EntityList {\r\n /**\r\n * Create a list of objects.\r\n * The objects can be indexed by one or more properties for the later retrieval.\r\n *\r\n * @param {!Array=} entities A list of objects to automatically register at creation time.\r\n * @param {!Array=} indices A list of property names to use for case-insensitive indexing.\r\n * By default, a single `.id` property is used.\r\n * @see EntityList#register\r\n */\r\n constructor(entities = [], indices = ['id']) {\r\n this._list = [];\r\n this._dict = {};\r\n this._indices = [...indices];\r\n this._indices.forEach((index) => {\r\n this._dict[index] = {};\r\n });\r\n\r\n entities.forEach((entity) => this.register(entity));\r\n }\r\n\r\n /**\r\n * Add a value to the end of a list.\r\n * The list will contain only one copy of the value.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromList\r\n * @see EntityList.registerInDict\r\n */\r\n static registerInList(list, value) {\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n }\r\n\r\n /**\r\n * Remove a value from a list if it is there.\r\n *\r\n * @param {!Array} list An array.\r\n * @param {*} value A value to remove.\r\n * @see EntityList.registerInList\r\n */\r\n static unregisterFromList(list, value) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n }\r\n\r\n /**\r\n * Add a value to a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.unregisterFromDict\r\n * @see EntityList.registerInList\r\n */\r\n static registerInDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key] = dict[key] || [];\r\n if (!list.includes(value)) {\r\n list.push(value);\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Remove a value from a dictionary.\r\n * The value may be stored under multiple different keys (aliases).\r\n * There might be multiples values stored under the same key.\r\n *\r\n * @param {!Object} dict A dictionary.\r\n * @param {!Array} keys An array of keys.\r\n * @param {*} value A value to add.\r\n * @see EntityList.registerInDict\r\n */\r\n static unregisterFromDict(dict, keys, value) {\r\n keys.forEach((key) => {\r\n key = key.toLowerCase();\r\n const list = dict[key];\r\n if (list) {\r\n const pos = list.indexOf(value);\r\n if (pos !== -1) {\r\n list.splice(pos, 1);\r\n }\r\n if (list.length === 0) {\r\n delete dict[key];\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Add an entity to this list.\r\n *\r\n * @param {!Object} entity An object or a class to register. The object must include all\r\n * properties specified as indices on construction.\r\n * @see EntityList#unregister\r\n */\r\n register(entity) {\r\n EntityList.registerInList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.registerInDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * Remove an entity from this list.\r\n *\r\n * @param {!Object} entity An object or a class to unregister. The object may be\r\n * missing from the list but it must include all properties specified as indices\r\n * on construction.\r\n * @see EntityList#register\r\n */\r\n unregister(entity) {\r\n EntityList.unregisterFromList(this._list, entity);\r\n this._indices.forEach((index) => {\r\n EntityList.unregisterFromDict(this._dict[index], _ensureArray(entity[index]), entity);\r\n });\r\n }\r\n\r\n /**\r\n * An ordered list of all registered entities.\r\n * It is a read-only copy, use {@link EntityList#register} and {@link EntityList#unregister}\r\n * to modify it.\r\n *\r\n * @type {!Array}\r\n */\r\n get all() {\r\n return [...this._list];\r\n }\r\n\r\n /**\r\n * The first registered entity.\r\n * Use it if you do not care which entity you are referring to.\r\n *\r\n * @type {Object=}\r\n */\r\n get first() {\r\n return this._list[0];\r\n }\r\n\r\n /**\r\n * Retrieve a list of keys for the index.\r\n *\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {!Array} An unordered list of keys in the index, i.e. particular property\r\n * values for all registered entities.\r\n */\r\n keys(index) {\r\n return Object.keys(this._dict[index || this._indices[0]]);\r\n }\r\n\r\n /**\r\n * Retrieve an entity by its key.\r\n *\r\n * @param {string} key A case-insensitive property value to look-up.\r\n * @param {string=} index One of the indices specified during the list construction. If omitted,\r\n * the first of the indices is used.\r\n * @returns {Object=} An object registered in the index under the key. If there are multiple\r\n * objects under the same key, the first one is returned.\r\n */\r\n get(key, index) {\r\n const dict = this._dict[index || this._indices[0]];\r\n if (dict) {\r\n const values = dict[key && key.toLowerCase()];\r\n return values && values.length > 0 ? values[0] : undefined;\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nexport default EntityList;\r\n","import settings from '../settings';\r\nimport logger from './logger';\r\n\r\nfunction makeContextDependent(prototype) {\r\n Object.defineProperties(prototype, {\r\n logger: {\r\n get() {\r\n return this.context && this.context.logger ? this.context.logger : logger;\r\n },\r\n },\r\n settings: {\r\n get() {\r\n return this.context && this.context.settings ? this.context.settings : settings;\r\n },\r\n },\r\n });\r\n}\r\n\r\nexport default makeContextDependent;\r\n","import * as THREE from 'three';\r\n\r\nclass CollisionSphere {\r\n constructor(position, radius) {\r\n this._position = position;\r\n this._radius = radius;\r\n }\r\n\r\n static _sphere = new THREE.Sphere();\r\n\r\n raycast(raycaster) {\r\n const sphere = CollisionSphere._sphere;\r\n sphere.set(this._position, this._radius);\r\n\r\n const p = new THREE.Vector3();\r\n if (raycaster.ray.intersectSphere(sphere, p)) {\r\n return {\r\n distance: raycaster.ray.origin.distanceTo(p),\r\n point: p,\r\n };\r\n }\r\n return null;\r\n }\r\n}\r\n\r\nconst SphereCollisionGeo = (base) => class extends base {\r\n constructor(count, ...args) {\r\n super(...args);\r\n this._objects = new Array(count);\r\n this.boundingSphere = null;\r\n this.boundingBox = null;\r\n }\r\n\r\n setSphere(idx, position, radius) {\r\n this._objects[idx] = new CollisionSphere(position, radius);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n // TODO raycast with bounding sphere? How to deal with updates?\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const inters = this._objects[i].raycast(raycaster);\r\n if (inters) {\r\n inters.chunkIdx = i;\r\n intersects.push(inters);\r\n }\r\n }\r\n }\r\n\r\n computeBoundingBox() {\r\n const objects = this._objects;\r\n let { boundingBox } = this;\r\n if (boundingBox === null) {\r\n this.boundingBox = boundingBox = new THREE.Box3();\r\n }\r\n boundingBox.makeEmpty();\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n boundingBox.expandByPoint(objects[i]._position);\r\n }\r\n }\r\n\r\n computeBoundingSphere() {\r\n this.computeBoundingBox();\r\n const objects = this._objects;\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n boundingBox.getCenter(center);\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n const pos = objects[i]._position;\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n if (this.boundingSphere === null) {\r\n this.boundingSphere = new THREE.Sphere();\r\n }\r\n this.boundingSphere.set(center, Math.sqrt(radiusSquared));\r\n }\r\n};\r\nexport default SphereCollisionGeo;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst tmpColor = new THREE.Color();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\nclass InstancedSpheresGeometry extends SphereCollisionGeo(THREE.InstancedBufferGeometry) {\r\n constructor(spheresCount, sphereComplexity, useZSprites) {\r\n super(spheresCount);\r\n this._sphGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new THREE.SphereGeometry(1, sphereComplexity * 2, sphereComplexity, 0, Math.PI * 2, 0, Math.PI);\r\n this._init(spheresCount, this._sphGeometry);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n setArrayXYZW(this._offsets, itemIdx * OFFSET_SIZE, itemPos.x, itemPos.y, itemPos.z, itemRad);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n\r\n setColor(itemIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n setArrayXYZ(this._colors, itemIdx * COLOR_SIZE, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('offset').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[chunkIndices[i]] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._sphGeometry);\r\n\r\n copySubArrays(this._offsets, geom._offsets, chunkIndices, OFFSET_SIZE);\r\n copySubArrays(this._colors, geom._colors, chunkIndices, COLOR_SIZE);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(spheresCount, sphereGeo) {\r\n this.copy(sphereGeo);\r\n\r\n this._offsets = utils.allocateTyped(Float32Array, spheresCount * OFFSET_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, spheresCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('offset', new THREE.InstancedBufferAttribute(this._offsets, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._colors, COLOR_SIZE, false, 1));\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(alpha, 1, false, 1));\r\n }\r\n}\r\nexport default InstancedSpheresGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VEC_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n */\r\n\r\nclass ChunkedObjectsGeometry extends THREE.BufferGeometry {\r\n constructor(chunkGeo, chunksCount) {\r\n super();\r\n\r\n if (this.constructor === ChunkedObjectsGeometry) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n\r\n this._chunkGeo = chunkGeo;\r\n\r\n this._init(chunkGeo, chunksCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('normal').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n const idx = i * VEC_SIZE;\r\n colors[idx] = tmpColor.r;\r\n colors[idx + 1] = tmpColor.g;\r\n colors[idx + 2] = tmpColor.b;\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n _.fill(alphaArr, value, left, left + chunkSize);\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n // use THREE.Mesh raycasting interface for the Geometry. The Mesh is\r\n // created with existed geometry and default material, so it doesn't slowdown.\r\n const mesh = new THREE.Mesh();\r\n mesh.geometry = this;\r\n mesh.raycast(raycaster, inters);\r\n\r\n const facesPerChunk = this._chunkGeo.index.count / 3;\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('faceIndex')) {\r\n continue;\r\n }\r\n inters[i].chunkIdx = Math.floor(inters[i].faceIndex / facesPerChunk);\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const geom = new THREE.BufferGeometry();\r\n this._init.call(geom, this._chunkGeo, instanceCount);\r\n\r\n const srcPos = this._positions;\r\n const srcNorm = this._normals;\r\n const srcColor = this._colors;\r\n\r\n const dstPos = geom._positions;\r\n const dstNorm = geom._normals;\r\n const dstColor = geom._colors;\r\n\r\n const chunkSize = this._chunkSize * VEC_SIZE;\r\n\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const ptIdxBegin = chunkIndices[i] * chunkSize;\r\n const ptIdxEnd = ptIdxBegin + chunkSize;\r\n dstPos.set(srcPos.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstNorm.set(srcNorm.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n dstColor.set(srcColor.subarray(ptIdxBegin, ptIdxEnd), dstPtOffset);\r\n }\r\n\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n _init(chunkGeo, chunksCount) {\r\n const chunkSize = this._chunkSize = chunkGeo.attributes.position.count;\r\n const chunkIndex = chunkGeo.index.array;\r\n const chunkIndexSize = chunkIndex.length;\r\n const pointsCount = this._chunkSize * chunksCount;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n const indexSize = chunkIndexSize * chunksCount;\r\n const index = this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, indexSize);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._normals = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * VEC_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n for (let i = 0; i < chunksCount; ++i) {\r\n const offset = i * chunkIndexSize;\r\n const posOffset = i * chunkSize;\r\n index.set(chunkIndex, offset);\r\n for (let j = 0; j < chunkIndexSize; ++j) {\r\n index[offset + j] += posOffset;\r\n }\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, VEC_SIZE));\r\n this.setAttribute('normal', new THREE.BufferAttribute(this._normals, VEC_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, VEC_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n }\r\n}\r\nexport default ChunkedObjectsGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst VEC_SIZE = 3;\r\n\r\nclass SimpleSpheresGeometry extends SphereCollisionGeo(ChunkedObjectsGeometry) {\r\n constructor(spheresCount, sphereComplexity) {\r\n const sphGeometry = new THREE.SphereGeometry(\r\n 1,\r\n sphereComplexity * 2,\r\n sphereComplexity,\r\n 0,\r\n Math.PI * 2,\r\n 0,\r\n Math.PI,\r\n );\r\n super(spheresCount, sphGeometry, spheresCount);\r\n\r\n const normals = this._normals;\r\n const geoNormals = sphGeometry.attributes.normal.array;\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._tmpPositions = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n for (let i = 0; i < spheresCount; ++i) {\r\n normals.set(geoNormals, chunkSize * VEC_SIZE * i);\r\n }\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n const tmpPos = this._tmpPositions;\r\n const chunkSize = this._chunkSize;\r\n const geoPos = this._chunkPos;\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n const idx = i * 3;\r\n tmpPos[idx] = itemPos.x + geoPos[idx] * itemRad;\r\n tmpPos[idx + 1] = itemPos.y + geoPos[idx + 1] * itemRad;\r\n tmpPos[idx + 2] = itemPos.z + geoPos[idx + 2] * itemRad;\r\n }\r\n\r\n this._positions.set(tmpPos, chunkSize * itemIdx * VEC_SIZE);\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n }\r\n}\r\nexport default SimpleSpheresGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst centerPos = new THREE.Vector3();\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass Simple2CCylindersGeometry extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, 2 * instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const firstOffset = chunkSize * 2 * itemIdx * VEC_SIZE;\r\n const secondOffset = firstOffset + chunkSize * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n centerPos.lerpVectors(botPos, topPos, 0.5);\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, centerPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, firstOffset);\r\n\r\n // now shift center to get another part of the cylinder\r\n centerPos.sub(botPos);\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpArray[idx] += centerPos.x;\r\n tmpArray[idx + 1] += centerPos.y;\r\n tmpArray[idx + 2] += centerPos.z;\r\n }\r\n this._positions.set(tmpArray, secondOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, firstOffset);\r\n this._normals.set(tmpArray, secondOffset);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const first = 2 * itemIdx;\r\n super.setColor(first, colorVal1);\r\n\r\n const second = first + 1;\r\n super.setColor(second, colorVal2);\r\n }\r\n}\r\n\r\nexport default Simple2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_POINTS_COUNT_16BIT = 65536;\r\nconst PTS_PER_TRIANGLE = 3;\r\n\r\nclass CylinderBufferGeometry extends THREE.BufferGeometry {\r\n constructor(\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n ) {\r\n super();\r\n\r\n const thetaStart = 0;\r\n const thetaLength = 2 * Math.PI;\r\n\r\n this.type = 'CylinderBufferGeometry';\r\n\r\n this.parameters = {\r\n radiusTop,\r\n radiusBottom,\r\n height,\r\n radialSegments,\r\n heightSegments,\r\n openEnded,\r\n };\r\n\r\n const hasTop = openEnded === false && radiusTop > 0;\r\n const hasBottom = openEnded === false && radiusBottom > 0;\r\n const vertexCount = (heightSegments + 1) * radialSegments\r\n + hasTop * (radialSegments + 1)\r\n + hasBottom * (radialSegments + 1);\r\n const facesCount = (2 * heightSegments + hasTop + hasBottom) * radialSegments;\r\n\r\n const heightHalf = height / 2;\r\n\r\n const positions = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const normals = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 3), 3);\r\n const indices = new THREE.Uint16BufferAttribute(utils.allocateTyped(Uint16Array, facesCount * PTS_PER_TRIANGLE), 1);\r\n\r\n const uvs = new THREE.BufferAttribute(utils.allocateTyped(Float32Array, vertexCount * 2), 2);\r\n console.assert(vertexCount < MAX_POINTS_COUNT_16BIT, 'DEBUG: Cylinder Geometry has too many vertices (65536 max).');\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n const tanTheta = -(radiusBottom - radiusTop) / height;\r\n\r\n // setup cylinder data\r\n for (let y = 0; y <= heightSegments; y++) {\r\n // faces\r\n if (y !== heightSegments) {\r\n for (let i = 0; i < radialSegments; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + radialSegments + i;\r\n const v3 = currVtxIdx + radialSegments + ((i + 1) % radialSegments);\r\n const v4 = currVtxIdx + ((i + 1) % radialSegments);\r\n\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n // vertices\r\n const v = y / heightSegments;\r\n const radius = v * (radiusBottom - radiusTop) + radiusTop;\r\n\r\n for (let x = 0; x < radialSegments; x++) {\r\n const u = x / radialSegments;\r\n\r\n const vx = radius * Math.sin(u * thetaLength + thetaStart);\r\n const vy = v * height - heightHalf;\r\n const vz = radius * Math.cos(u * thetaLength + thetaStart);\r\n\r\n const normal = new THREE.Vector3(\r\n vx,\r\n Math.sqrt(vx * vx + vz * vz) * tanTheta,\r\n vz,\r\n ).normalize();\r\n\r\n positions.setXYZ(currVtxIdx, vx, vy, vz);\r\n normals.setXYZ(currVtxIdx, normal.x, normal.y, normal.z);\r\n uvs.setXY(currVtxIdx, u, v);\r\n ++currVtxIdx;\r\n }\r\n }\r\n\r\n // top cap\r\n if (hasTop) {\r\n const startTIdx = currVtxIdx;\r\n const lastIdx = currVtxIdx + radialSegments;\r\n for (let fTIdx = 0; fTIdx < radialSegments; ++fTIdx) {\r\n const currSrcIdx = currVtxIdx - radialSegments;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcIdx),\r\n positions.getY(currSrcIdx),\r\n positions.getZ(currSrcIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n\r\n const nextTVtx = startTIdx + ((fTIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, currVtxIdx, nextTVtx, lastIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, 1, 0);\r\n uvs.setXY(currVtxIdx, 1, 1);\r\n ++currVtxIdx;\r\n }\r\n\r\n // bottom cap\r\n if (hasBottom) {\r\n const startBIdx = currVtxIdx;\r\n const lastBIdx = currVtxIdx + radialSegments;\r\n for (let fBIdx = 0; fBIdx < radialSegments; ++fBIdx) {\r\n const currSrcBIdx = fBIdx;\r\n positions.setXYZ(\r\n currVtxIdx,\r\n positions.getX(currSrcBIdx),\r\n positions.getY(currSrcBIdx),\r\n positions.getZ(currSrcBIdx),\r\n );\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n\r\n const nextBVtx = startBIdx + ((fBIdx + 1) % radialSegments);\r\n indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, nextBVtx, currVtxIdx, lastBIdx);\r\n currFaceIdx++;\r\n currVtxIdx++;\r\n }\r\n\r\n positions.setXYZ(currVtxIdx, 0, -heightHalf, 0);\r\n normals.setXYZ(currVtxIdx, 0, -1, 0);\r\n uvs.setXY(currVtxIdx, 0, 0);\r\n }\r\n\r\n this.setIndex(indices);\r\n this.setAttribute('position', positions);\r\n this.setAttribute('normal', normals);\r\n this.setAttribute('uv', uvs);\r\n }\r\n\r\n clone() {\r\n const { parameters } = this;\r\n\r\n return new CylinderBufferGeometry(\r\n parameters.radiusTop,\r\n parameters.radiusBottom,\r\n parameters.height,\r\n parameters.radialSegments,\r\n parameters.heightSegments,\r\n parameters.openEnded,\r\n );\r\n }\r\n}\r\n\r\nexport default CylinderBufferGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport CylinderBufferGeometry from './CylinderBufferGeometry';\r\n\r\nconst tmpColor = new THREE.Color();\r\nconst invMatrix = new THREE.Matrix4();\r\n\r\nconst OFFSET_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst { copySubArrays } = utils;\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction sortNumber(a, b) {\r\n return a - b;\r\n}\r\n\r\nfunction _prepareCylinderInfo(chunkIndices) {\r\n chunkIndices.sort(sortNumber);\r\n const chunksIdx = [];\r\n const cylinderInfo = [];\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const val = chunkIndices[i];\r\n const even = (val | 0) % 2 === 0;\r\n const newPar = {\r\n first: false,\r\n second: false,\r\n };\r\n if (even) {\r\n newPar.first = true;\r\n newPar.second = i + 1 < n && chunkIndices[i + 1] === chunkIndices[i] + 1;\r\n if (newPar.second) {\r\n ++i;\r\n }\r\n } else {\r\n newPar.second = true;\r\n }\r\n chunksIdx.push(Math.floor(val / 2));\r\n cylinderInfo.push(newPar);\r\n }\r\n return { indices: chunksIdx, cylinderInfo };\r\n}\r\n\r\nfunction _assignOpacity(cylinderInfo, color1, color2) {\r\n for (let i = 0, n = cylinderInfo.length; i < n; ++i) {\r\n const info = cylinderInfo[i];\r\n if (!info.first) {\r\n color1[COLOR_SIZE * i] = -0.5;\r\n }\r\n if (!info.second) {\r\n color2[COLOR_SIZE * i] = -0.5;\r\n }\r\n }\r\n}\r\nclass Instanced2CCylindersGeometry extends THREE.InstancedBufferGeometry {\r\n constructor(instanceCount, polyComplexity, useZSprites, openEnded) {\r\n super();\r\n this._useZSprites = useZSprites;\r\n this._cylGeometry = useZSprites ? new THREE.PlaneGeometry(2, 2, 1, 1)\r\n : new CylinderBufferGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, openEnded);\r\n this._init(instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n this._collisionGeo = new Simple2CCylindersGeometry(instanceCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const matrix = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n let me = matrix.elements;\r\n const mtxOffset = itemIdx * OFFSET_SIZE;\r\n\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, itemRad);\r\n setArrayXYZW(this._matVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._matVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._matVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n\r\n if (this._useZSprites) {\r\n invMatrix.copy(matrix).invert();\r\n me = invMatrix.elements;\r\n setArrayXYZW(this._invmatVector1, mtxOffset, me[0], me[4], me[8], me[12]);\r\n setArrayXYZW(this._invmatVector2, mtxOffset, me[1], me[5], me[9], me[13]);\r\n setArrayXYZW(this._invmatVector3, mtxOffset, me[2], me[6], me[10], me[14]);\r\n }\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const colorIdx = itemIdx * COLOR_SIZE;\r\n tmpColor.set(colorVal1);\r\n setArrayXYZ(this._color1, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n tmpColor.set(colorVal2);\r\n setArrayXYZ(this._color2, colorIdx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n computeBoundingSphere() {\r\n this._collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = this._collisionGeo.boundingSphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n this._collisionGeo.computeBoundingBox();\r\n this.boundingBox = this._collisionGeo.boundingBox;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('matVector1').needsUpdate = true;\r\n this.getAttribute('matVector2').needsUpdate = true;\r\n this.getAttribute('matVector3').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('color2').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n if (this._useZSprites) {\r\n this.getAttribute('invmatVector1').needsUpdate = true;\r\n this.getAttribute('invmatVector2').needsUpdate = true;\r\n this.getAttribute('invmatVector3').needsUpdate = true;\r\n }\r\n\r\n this._collisionGeo.finishUpdate();\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const alphaArr = this._alpha;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n alphaArr[Math.floor(chunkIndices[i] / 2)] = value;\r\n }\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const info = _prepareCylinderInfo(chunkIndices);\r\n const cylinderIndices = info.indices;\r\n const instanceCount = cylinderIndices.length;\r\n const geom = new THREE.InstancedBufferGeometry();\r\n this._init.call(geom, instanceCount, this._cylGeometry, this._useZSprites);\r\n\r\n copySubArrays(this._matVector1, geom._matVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector2, geom._matVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._matVector3, geom._matVector3, cylinderIndices, OFFSET_SIZE);\r\n\r\n if (this._useZSprites) {\r\n copySubArrays(this._invmatVector1, geom._invmatVector1, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector2, geom._invmatVector2, cylinderIndices, OFFSET_SIZE);\r\n copySubArrays(this._invmatVector3, geom._invmatVector3, cylinderIndices, OFFSET_SIZE);\r\n }\r\n\r\n copySubArrays(this._color1, geom._color1, cylinderIndices, COLOR_SIZE);\r\n copySubArrays(this._color2, geom._color2, cylinderIndices, COLOR_SIZE);\r\n _assignOpacity(info.cylinderInfo, geom._color1, geom._color2);\r\n geom.boundingSphere = this.boundingSphere;\r\n geom.boundingBox = this.boundingBox;\r\n return [geom];\r\n }\r\n\r\n getGeoParams() {\r\n return this._cylGeometry.parameters;\r\n }\r\n\r\n _init(instanceCount, cylinderGeo, useZSprites) {\r\n this.copy(cylinderGeo);\r\n this._matVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._matVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._color1 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n this._color2 = utils.allocateTyped(Float32Array, instanceCount * COLOR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, instanceCount);\r\n _.fill(alpha, 1.0);\r\n\r\n this.setAttribute('matVector1', new THREE.InstancedBufferAttribute(this._matVector1, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector2', new THREE.InstancedBufferAttribute(this._matVector2, OFFSET_SIZE, false, 1));\r\n this.setAttribute('matVector3', new THREE.InstancedBufferAttribute(this._matVector3, OFFSET_SIZE, false, 1));\r\n this.setAttribute('color', new THREE.InstancedBufferAttribute(this._color1, COLOR_SIZE, false, 1));\r\n this.setAttribute('color2', new THREE.InstancedBufferAttribute(this._color2, COLOR_SIZE, false, 1));\r\n\r\n this.setAttribute('alphaColor', new THREE.InstancedBufferAttribute(this._alpha, 1, false, 1));\r\n\r\n if (useZSprites) {\r\n this._invmatVector1 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector2 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n this._invmatVector3 = utils.allocateTyped(Float32Array, instanceCount * OFFSET_SIZE);\r\n\r\n this.setAttribute(\r\n 'invmatVector1',\r\n new THREE.InstancedBufferAttribute(this._invmatVector1, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector2',\r\n new THREE.InstancedBufferAttribute(this._invmatVector2, OFFSET_SIZE, false, 1),\r\n );\r\n this.setAttribute(\r\n 'invmatVector3',\r\n new THREE.InstancedBufferAttribute(this._invmatVector3, OFFSET_SIZE, false, 1),\r\n );\r\n }\r\n }\r\n}\r\n\r\nexport default Instanced2CCylindersGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst TRI_SIZE = 3;\r\nconst tmpPrev = new THREE.Vector3();\r\nconst tmpNext = new THREE.Vector3();\r\nconst tmpRes = new THREE.Vector3();\r\nconst simpleNormal = new THREE.Vector3(1.0, 0.0, 0.0);\r\nconst normalOnCut = new THREE.Vector3();\r\nconst nearRingPt = new THREE.Vector3();\r\n\r\nfunction _createExtrudedChunkGeometry(shape, ringsCount) {\r\n const geo = new THREE.BufferGeometry();\r\n const ptsCount = shape.length;\r\n const totalPts = ptsCount * ringsCount;\r\n const type = totalPts <= 65536 ? Uint16Array : Uint32Array;\r\n const facesPerChunk = (ringsCount - 1) * ptsCount * 2;\r\n const indices = new THREE.BufferAttribute(utils.allocateTyped(type, facesPerChunk * TRI_SIZE), 1);\r\n\r\n let currVtxIdx = 0;\r\n let currFaceIdx = 0;\r\n for (let y = 0; y < ringsCount; y++) {\r\n // faces\r\n if (y !== ringsCount - 1) {\r\n for (let i = 0; i < ptsCount; i++) {\r\n const v1 = currVtxIdx + i;\r\n const v2 = currVtxIdx + ptsCount + i;\r\n const v3 = currVtxIdx + ptsCount + ((i + 1) % ptsCount);\r\n const v4 = currVtxIdx + ((i + 1) % ptsCount);\r\n\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v1, v4, v2);\r\n currFaceIdx++;\r\n indices.setXYZ(currFaceIdx * TRI_SIZE, v2, v4, v3);\r\n currFaceIdx++;\r\n }\r\n }\r\n\r\n currVtxIdx += ptsCount;\r\n }\r\n\r\n geo.setIndex(indices);\r\n const pos = utils.allocateTyped(Float32Array, totalPts * VEC_SIZE);\r\n geo.setAttribute('position', new THREE.BufferAttribute(pos, VEC_SIZE));\r\n\r\n geo._positions = shape;\r\n\r\n return geo;\r\n}\r\n\r\nclass ExtrudedObjectsGeometry extends ChunkedObjectsGeometry {\r\n constructor(shape, ringsCount, chunksCount) {\r\n const chunkGeo = _createExtrudedChunkGeometry(shape, ringsCount);\r\n super(chunkGeo, chunksCount);\r\n this._ringsCount = ringsCount;\r\n\r\n const tmpShape = this._tmpShape = [];\r\n for (let i = 0; i < shape.length; ++i) {\r\n tmpShape[i] = new THREE.Vector3();\r\n }\r\n }\r\n\r\n setItem(itemIdx, matrices, hasSlope = false, hasCut = false) {\r\n const ptsCount = this._chunkGeo._positions.length;\r\n const ringsCount = this._ringsCount;\r\n const chunkStartIdx = ptsCount * this._ringsCount * itemIdx * VEC_SIZE;\r\n\r\n this._setPoints(matrices, ptsCount, ringsCount, chunkStartIdx);\r\n\r\n if (hasSlope) {\r\n this._setSlopeNormals(ptsCount, ringsCount, chunkStartIdx);\r\n } else {\r\n this._setBaseNormals(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n\r\n if (hasCut) {\r\n this._addCut(ptsCount, ringsCount, chunkStartIdx);\r\n }\r\n }\r\n\r\n _setPoints(matrices, ptsCount, ringsCount, chunkStartIdx) {\r\n const tmpShape = this._tmpShape;\r\n const positions = this._positions;\r\n const shape = this._chunkGeo._positions;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i) {\r\n const mtx = matrices[i];\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpShape[j].copy(shape[j]).applyMatrix4(mtx).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _setBaseNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n for (let i = 0, vtxIdx = chunkStartIdx; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, false);\r\n }\r\n }\r\n\r\n _setSlopeNormals(ptsCount, ringsCount, chunkStartIdx) {\r\n const normals = this._normals;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First ring\r\n // In all cases, besides cut, second ring is coincident to first. So values of first ring's normals doesn't\r\n // matter (In the cut case special handler will be applied later and will set them to correct values)\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n simpleNormal.toArray(normals, vtxIdx);\r\n }\r\n // second ring\r\n // If it isn't first Item we take normals' values from the last ring of the previous item (these rings are coincident)\r\n // else we count normals' values based on next ring information\r\n if (vtxIdx - 2 * nPtsInRing > 0) {\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(normals, vtxIdx - 2 * nPtsInRing).toArray(normals, vtxIdx);\r\n }\r\n } else {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, +nPtsInRing);\r\n vtxIdx += nPtsInRing;\r\n }\r\n // other rings\r\n // we count normals' values based on previous ring information\r\n for (let i = 2; i < ringsCount; ++i, vtxIdx += nPtsInRing) {\r\n this._countNormalsInRing(ptsCount, vtxIdx, true, -nPtsInRing);\r\n }\r\n }\r\n\r\n // Counting normals:\r\n // - Slope\r\n // Radius changes throught part => normals aren't parallel with the plane contains section points\r\n // normal = vTangentInSectionPlane x vToSuchPointInPrevSection (all vectors are scaled for being 1 in length)\r\n // - No slope\r\n // Radius doesn't change throught part => normals are parallel with the plane contains section points\r\n // normal = vToPrevPointInSection + vToNextPointInSection (all vectors are scaled for being 1 in length)\r\n _countNormalsInRing(ptsCount, vtxIdx, isSlope, shiftToExtraPt) {\r\n const tmpShape = this._tmpShape;\r\n const normals = this._normals;\r\n\r\n tmpShape[0].fromArray(this._positions, vtxIdx);\r\n tmpShape[ptsCount - 1].fromArray(this._positions, vtxIdx + (ptsCount - 1) * VEC_SIZE);\r\n\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n if (j < ptsCount - 1) {\r\n tmpShape[j + 1].fromArray(this._positions, vtxIdx + VEC_SIZE);\r\n }\r\n\r\n if (isSlope) {\r\n nearRingPt.fromArray(this._positions, vtxIdx + shiftToExtraPt);\r\n\r\n tmpPrev.subVectors(tmpShape[(j + ptsCount - 1) % ptsCount], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], nearRingPt).normalize();\r\n tmpRes.crossVectors(tmpNext, tmpPrev).normalize().toArray(normals, vtxIdx);\r\n } else {\r\n tmpPrev.subVectors(tmpShape[j], tmpShape[(j + ptsCount - 1) % ptsCount]).normalize();\r\n tmpNext.subVectors(tmpShape[j], tmpShape[(j + 1) % ptsCount]).normalize();\r\n tmpRes.addVectors(tmpPrev, tmpNext).normalize().toArray(normals, vtxIdx);\r\n }\r\n }\r\n }\r\n\r\n _addCut(ptsCount, ringsCount, chunkStartIdx) {\r\n // Nothing to do if item is flat or only line\r\n if (ptsCount < 3 || ringsCount < 2) {\r\n return;\r\n }\r\n const positions = this._positions;\r\n const normals = this._normals;\r\n const tmpShape = this._tmpShape;\r\n const nPtsInRing = ptsCount * VEC_SIZE;\r\n\r\n // Normal to the cut plane is equal to cross product of two vectors which are lying in it\r\n tmpShape[0].fromArray(positions, chunkStartIdx);\r\n tmpShape[1].fromArray(positions, chunkStartIdx + VEC_SIZE);\r\n tmpShape[2].fromArray(positions, chunkStartIdx + 2 * VEC_SIZE);\r\n\r\n tmpPrev.subVectors(tmpShape[1], tmpShape[0]).normalize();\r\n tmpNext.subVectors(tmpShape[1], tmpShape[2]).normalize();\r\n normalOnCut.crossVectors(tmpPrev, tmpNext).normalize();\r\n\r\n let vtxIdx = chunkStartIdx;\r\n // First and second rings normals' values are equal to value of normal to the cutting plane\r\n for (let j = 0; j < ptsCount * 2; ++j, vtxIdx += VEC_SIZE) {\r\n normalOnCut.toArray(normals, vtxIdx);\r\n }\r\n if (ringsCount > 2) {\r\n // Third ring points are coincident to first ring points, but have different normals. It makes sharp angle near cut\r\n for (let j = 0; j < ptsCount; ++j, vtxIdx += VEC_SIZE) {\r\n tmpRes.fromArray(positions, vtxIdx - nPtsInRing).toArray(positions, vtxIdx);\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default ExtrudedObjectsGeometry;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst MAX_IDC_16BIT = 65535;\r\nconst VERTEX_PER_SEGMENT = 4;\r\nconst POS_SIZE = 4;\r\nconst DIR_SIZE = 3;\r\nconst COL_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\nconst direction = new THREE.Vector3();\r\n\r\nfunction setArrayXYZ(arr, idx, x, y, z) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n}\r\n\r\nfunction setArrayXYZW(arr, idx, x, y, z, w) {\r\n arr[idx] = x;\r\n arr[idx + 1] = y;\r\n arr[idx + 2] = z;\r\n arr[idx + 3] = w;\r\n}\r\n\r\nfunction getSubset(arr, startSegmentIdx, segmentsCount, elemSize) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT;\r\n const end = start + segmentsCount * VERTEX_PER_SEGMENT;\r\n return arr.subarray(start * elemSize, end * elemSize);\r\n}\r\n\r\n/**\r\n * This class represents lines geometry which consists of screen-aligned narrow quad of variable width.\r\n *\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * collision geometry.\r\n */\r\n\r\nclass ThickLinesGeometry extends THREE.BufferGeometry {\r\n constructor(segmentsCount) {\r\n super();\r\n this._initVertices(segmentsCount);\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.getAttribute('position').needsUpdate = true;\r\n this.getAttribute('color').needsUpdate = true;\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n this.getAttribute('direction').needsUpdate = true;\r\n }\r\n\r\n setColor(segmentIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n idx += COL_SIZE;\r\n setArrayXYZ(this._colors, idx, tmpColor.r, tmpColor.g, tmpColor.b);\r\n }\r\n\r\n setSegment(segmentIdx, pos1, pos2) {\r\n direction.subVectors(pos1, pos2);\r\n direction.normalize();\r\n const positions = this._positions;\r\n const directions = this._directions;\r\n let idx = segmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n let dirIdx = segmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos1.x, pos1.y, pos1.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, 0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n idx += POS_SIZE;\r\n dirIdx += DIR_SIZE;\r\n setArrayXYZW(positions, idx, pos2.x, pos2.y, pos2.z, -0.5);\r\n setArrayXYZ(directions, dirIdx, direction.x, direction.y, direction.z);\r\n }\r\n\r\n setOpacity(startSegIdx, endSegIdx, value) {\r\n const start = startSegIdx * VERTEX_PER_SEGMENT;\r\n const end = endSegIdx * VERTEX_PER_SEGMENT;\r\n _.fill(this.alpha, value, end, start);\r\n this.getAttribute('alphaColor').needsUpdate = true;\r\n }\r\n\r\n getSubsetSegments(startSegmentIdx, segmentsCount) {\r\n return [\r\n getSubset(this._positions, startSegmentIdx, segmentsCount, POS_SIZE),\r\n getSubset(this._directions, startSegmentIdx, segmentsCount, DIR_SIZE),\r\n ];\r\n }\r\n\r\n getSubsetColors(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._colors, startSegmentIdx, segmentsCount, COL_SIZE);\r\n }\r\n\r\n getSubsetOpacities(startSegmentIdx, segmentsCount) {\r\n return getSubset(this._alpha, startSegmentIdx, segmentsCount, 1);\r\n }\r\n\r\n getNumVertexPerSegment() {\r\n return VERTEX_PER_SEGMENT;\r\n }\r\n\r\n getPositionSize() {\r\n return POS_SIZE;\r\n }\r\n\r\n setSegments(startSegmentIdx, positions) {\r\n const startPos = startSegmentIdx * VERTEX_PER_SEGMENT * POS_SIZE;\r\n if (positions instanceof Array && positions.length === 2) {\r\n this._positions.set(positions[0], startPos);\r\n const startDir = startSegmentIdx * VERTEX_PER_SEGMENT * DIR_SIZE;\r\n this._directions.set(positions[1], startDir); // dirs are geo part of vertex\r\n } else {\r\n this._positions.set(positions, startPos);\r\n }\r\n }\r\n\r\n setColors(startSegmentIdx, colors) {\r\n const start = startSegmentIdx * VERTEX_PER_SEGMENT * COL_SIZE;\r\n this._colors.set(colors, start);\r\n }\r\n\r\n _initVertices(segmentsCount) {\r\n this._buffersSize = segmentsCount * VERTEX_PER_SEGMENT;\r\n const pointsCount = this._buffersSize;\r\n const use32bitIndex = pointsCount > MAX_IDC_16BIT;\r\n this._index = utils.allocateTyped(use32bitIndex ? Uint32Array : Uint16Array, segmentsCount * 6);\r\n this._positions = utils.allocateTyped(Float32Array, pointsCount * POS_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, pointsCount * COL_SIZE);\r\n this._directions = utils.allocateTyped(Float32Array, pointsCount * DIR_SIZE);\r\n const alpha = this._alpha = utils.allocateTyped(Float32Array, pointsCount);\r\n _.fill(alpha, 1.0);\r\n\r\n const index = this._index;\r\n let indexOffset = 0;\r\n let pointOffset = 0;\r\n for (let j = 0; j < segmentsCount; j++, indexOffset += 6, pointOffset += VERTEX_PER_SEGMENT) {\r\n index[indexOffset] = pointOffset;\r\n index[indexOffset + 1] = pointOffset + 1;\r\n index[indexOffset + 2] = pointOffset + 3;\r\n index[indexOffset + 3] = pointOffset;\r\n index[indexOffset + 4] = pointOffset + 2;\r\n index[indexOffset + 5] = pointOffset + 3;\r\n }\r\n this.setIndex(new THREE.BufferAttribute(this._index, 1));\r\n\r\n this.setAttribute('position', new THREE.BufferAttribute(this._positions, POS_SIZE));\r\n this.setAttribute('color', new THREE.BufferAttribute(this._colors, COL_SIZE));\r\n this.setAttribute('alphaColor', new THREE.BufferAttribute(alpha, 1));\r\n this.setAttribute('direction', new THREE.BufferAttribute(this._directions, DIR_SIZE));\r\n }\r\n}\r\n\r\nexport default ThickLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport BaseLinesGeometry from './ThickLinesGeometry';\r\n\r\n/**\r\n * This class represents geometry which consists lines. This can build bounding volumes\r\n * @constructor\r\n *\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n */\r\nclass LinesGeometry extends BaseLinesGeometry {\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const { boundingBox } = this;\r\n // Build bounding sphere\r\n let radiusSquared = 0.0;\r\n const center = new THREE.Vector3();\r\n if (boundingBox) {\r\n boundingBox.getCenter(center);\r\n }\r\n const positions = this._positions;\r\n const sphere = this.boundingSphere || new THREE.Sphere();\r\n const size = this._positions.length;\r\n const pos = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n pos.set(positions[i], positions[i + 1], positions[i + 2]);\r\n const lengthSquared = center.distanceToSquared(pos);\r\n if (radiusSquared < lengthSquared) {\r\n radiusSquared = lengthSquared;\r\n }\r\n }\r\n sphere.set(center, Math.sqrt(radiusSquared));\r\n this.boundingSphere = sphere;\r\n }\r\n\r\n computeBoundingBox() {\r\n const positions = this._positions;\r\n const box = new THREE.Box3();\r\n const size = this._positions.length;\r\n const tmpVec = new THREE.Vector3();\r\n const posSize = this.getPositionSize();\r\n for (let i = 0; i < size; i += posSize) {\r\n tmpVec.set(positions[i], positions[i + 1], positions[i + 2]);\r\n box.expandByPoint(tmpVec);\r\n }\r\n this.boundingBox = box;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n}\r\n\r\nexport default LinesGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport ChunkedObjectsGeometry from './ChunkedObjectsGeometry';\r\n\r\nconst VEC_SIZE = 3;\r\nconst tmpVector = new THREE.Vector3();\r\nconst normMtx = new THREE.Matrix3();\r\n\r\nclass CylinderCollisionGeo extends ChunkedObjectsGeometry {\r\n constructor(instanceCount, polyComplexity) {\r\n const cylGeometry = new THREE.CylinderGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);\r\n super(cylGeometry, instanceCount);\r\n\r\n const chunkSize = this._chunkSize;\r\n this._chunkPos = this._chunkGeo.attributes.position.array;\r\n this._chunkNorms = this._chunkGeo.attributes.normal.array;\r\n this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos, itemRad) {\r\n const chunkSize = this._chunkSize;\r\n const itemOffset = chunkSize * itemIdx * VEC_SIZE;\r\n\r\n const tmpArray = this._tmpVector;\r\n const geoPos = this._chunkPos;\r\n const geoNorm = this._chunkNorms;\r\n\r\n const mtx1 = gfxutils.calcCylinderMatrix(botPos, topPos, itemRad);\r\n normMtx.getNormalMatrix(mtx1);\r\n let idx;\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoPos, idx);\r\n tmpVector.applyMatrix4(mtx1);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._positions.set(tmpArray, itemOffset);\r\n\r\n for (let i = 0; i < chunkSize; ++i) {\r\n idx = i * VEC_SIZE;\r\n tmpVector.fromArray(geoNorm, idx);\r\n tmpVector.applyMatrix3(normMtx);\r\n tmpVector.toArray(tmpArray, idx);\r\n }\r\n this._normals.set(tmpArray, itemOffset);\r\n }\r\n}\r\nexport default CylinderCollisionGeo;\r\n","import LinesGeometry from './LinesGeometry';\r\nimport CylinderCollisionGeo from './CylinderCollisionGeo';\r\n\r\nconst COLLISION_RAD = 0.1;\r\n\r\n/**\r\n * This class represents geometry which consists of separate chunks.\r\n * Each chunk has same index and similar geometry with equal points and faces count.\r\n * Each chunk has by default only one color.\r\n * @constructor\r\n *\r\n * @param {number} chunksCount Total chunks count.\r\n * @param {number} segmentsCount Number of segments per chunk.\r\n * @param {boolean} enableCollision Enable or disable collision where each segment is\r\n * a collidable cylinder.\r\n * collision geometry.\r\n */\r\nclass ChunkedLinesGeometry extends LinesGeometry {\r\n constructor(chunksCount, segmentsCount, enableCollision) {\r\n super(chunksCount * segmentsCount);\r\n this._init(segmentsCount);\r\n this._collisionGeo = enableCollision ? new CylinderCollisionGeo(chunksCount * segmentsCount, 3) : null;\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n computeBoundingSphere() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingSphere();\r\n this.boundingSphere = collisionGeo.boundingSphere;\r\n return;\r\n }\r\n super.computeBoundingSphere();\r\n }\r\n\r\n computeBoundingBox() {\r\n const collisionGeo = this._collisionGeo;\r\n if (collisionGeo) {\r\n collisionGeo.computeBoundingBox();\r\n this.boundingBox = collisionGeo.boundingBox;\r\n return;\r\n }\r\n super.computeBoundingBox();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const collisionGeo = this._collisionGeo;\r\n if (!collisionGeo) {\r\n return;\r\n }\r\n const segCount = this._chunkSize;\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n for (let i = 0, n = intersects.length; i < n; ++i) {\r\n let { chunkIdx } = intersects[i];\r\n if (chunkIdx === undefined) {\r\n continue;\r\n }\r\n chunkIdx = (chunkIdx / segCount) | 0;\r\n intersects[i].chunkIdx = chunkIdx;\r\n }\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = chunkIdx * chunkSize, end = i + chunkSize; i < end; ++i) {\r\n super.setColor(i, colorVal);\r\n }\r\n }\r\n\r\n setSegment(chunkIdx, segIdx, pos1, pos2) {\r\n const chunkSize = this._chunkSize;\r\n const idx = chunkIdx * chunkSize + segIdx;\r\n super.setSegment(idx, pos1, pos2);\r\n if (this._collisionGeo) {\r\n this._collisionGeo.setItem(chunkIdx * chunkSize + segIdx, pos1, pos2, COLLISION_RAD);\r\n }\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n setOpacity(chunkIndices, value) {\r\n const chunkSize = this._chunkSize;\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const left = chunkIndices[i] * chunkSize;\r\n super.setOpacity(left, left + chunkSize - 1, value);\r\n }\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const instanceCount = chunkIndices.length;\r\n const chunkSize = this._chunkSize;\r\n const subset = new ChunkedLinesGeometry(instanceCount, chunkSize, false);\r\n for (let i = 0, n = chunkIndices.length; i < n; ++i) {\r\n const dstPtOffset = i * chunkSize;\r\n const startSegIdx = chunkIndices[i] * chunkSize;\r\n subset.setSegments(dstPtOffset, this.getSubsetSegments(startSegIdx, chunkSize));\r\n subset.setColors(dstPtOffset, this.getSubsetColors(startSegIdx, chunkSize));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(chunkSize) {\r\n this._chunkSize = chunkSize;\r\n }\r\n}\r\n\r\nexport default ChunkedLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport LinesGeometry from './LinesGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\n\r\nconst COLLISION_RAD = 0.3;\r\nconst tmpVector = new THREE.Vector3();\r\n\r\nclass TwoColorLinesGeometry extends LinesGeometry {\r\n constructor(segmentsCount) {\r\n super(segmentsCount * 2);\r\n this._init(segmentsCount);\r\n this._collisionGeo = new Simple2CCylindersGeometry(segmentsCount, 3);\r\n }\r\n\r\n setItem(itemIdx, botPos, topPos) {\r\n this._collisionGeo.setItem(itemIdx, botPos, topPos, COLLISION_RAD);\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n tmpVector.lerpVectors(botPos, topPos, 0.5);\r\n super.setSegment(offset, botPos, tmpVector);\r\n super.setSegment(offset + 1, tmpVector, topPos);\r\n }\r\n\r\n setColor(itemIdx, colorVal1, colorVal2) {\r\n const offset = 2 * itemIdx;// there are two points per segment\r\n super.setColor(offset, colorVal1);\r\n super.setColor(offset + 1, colorVal2);\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n if (this._collisionGeo) {\r\n this._collisionGeo.raycast(raycaster, intersects);\r\n }\r\n }\r\n\r\n getSubset(segmentIndices) {\r\n const instanceCount = segmentIndices.length;\r\n const subset = new TwoColorLinesGeometry(instanceCount, false);\r\n for (let i = 0, n = instanceCount; i < n; ++i) {\r\n const startSegIdx = segmentIndices[i];\r\n subset.setSegments(i, this.getSubsetSegments(startSegIdx, 1));\r\n subset.setColors(i, this.getSubsetColors(startSegIdx, 1));\r\n }\r\n\r\n subset.boundingSphere = this.boundingSphere;\r\n subset.boundingBox = this.boundingBox;\r\n return [subset];\r\n }\r\n\r\n _init(segmentsCount) {\r\n this._segCounts = segmentsCount * 2;\r\n }\r\n}\r\n// (???)parent = LinesGeometry.prototype;\r\n\r\nexport default TwoColorLinesGeometry;\r\n","import * as THREE from 'three';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport SphereCollisionGeo from './SphereCollisionGeo';\r\n\r\nconst vectors = [\r\n new THREE.Vector3(1, 0, 0),\r\n new THREE.Vector3(-1, 0, 0),\r\n new THREE.Vector3(0, 1, 0),\r\n new THREE.Vector3(0, -1, 0),\r\n new THREE.Vector3(0, 0, 1),\r\n new THREE.Vector3(0, 0, -1),\r\n];\r\nconst vecCount = vectors.length;\r\nconst tempPos1 = new THREE.Vector3();\r\nconst tempPos2 = new THREE.Vector3();\r\n\r\nclass CrossGeometry extends SphereCollisionGeo(ChunkedLinesGeometry) {\r\n constructor(chunksCount) {\r\n super(chunksCount, chunksCount, (vecCount / 2) | 0, false);\r\n }\r\n\r\n setItem(itemIdx, itemPos, itemRad) {\r\n this.setSphere(itemIdx, itemPos, itemRad);\r\n\r\n for (let i = 0; i < vecCount / 2; ++i) {\r\n const first = i * 2;\r\n tempPos1.x = itemPos.x + vectors[first].x * itemRad;\r\n tempPos1.y = itemPos.y + vectors[first].y * itemRad;\r\n tempPos1.z = itemPos.z + vectors[first].z * itemRad;\r\n const second = first + 1;\r\n tempPos2.x = itemPos.x + vectors[second].x * itemRad;\r\n tempPos2.y = itemPos.y + vectors[second].y * itemRad;\r\n tempPos2.z = itemPos.z + vectors[second].z * itemRad;\r\n this.setSegment(itemIdx, i, tempPos1, tempPos2);\r\n }\r\n }\r\n}\r\nexport default CrossGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\nconst POS_RAD_SIZE = 4;\r\nconst COLOR_SIZE = 3;\r\nconst tmpColor = new THREE.Color();\r\n\r\n/**\r\n * This is a base class for isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\nclass IsoSurfaceGeometry extends THREE.BufferGeometry {\r\n constructor(spheresCount, opts) {\r\n super();\r\n\r\n this._opts = opts;\r\n this.zClip = this._opts.zClip;\r\n this._posRad = utils.allocateTyped(Float32Array, spheresCount * POS_RAD_SIZE);\r\n this._colors = utils.allocateTyped(Float32Array, spheresCount * COLOR_SIZE);\r\n }\r\n\r\n setItem(chunkIdx, pos, radius) {\r\n const posRad = this._posRad;\r\n let idx = POS_RAD_SIZE * chunkIdx;\r\n posRad[idx++] = pos.x;\r\n posRad[idx++] = pos.y;\r\n posRad[idx++] = pos.z;\r\n posRad[idx] = radius;\r\n }\r\n\r\n setColor(chunkIdx, colorVal) {\r\n tmpColor.set(colorVal);\r\n const colors = this._colors;\r\n let idx = COLOR_SIZE * chunkIdx;\r\n colors[idx++] = tmpColor.r;\r\n colors[idx++] = tmpColor.g;\r\n colors[idx] = tmpColor.b;\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n this.computeBoundingSphere();\r\n }\r\n\r\n finishUpdate() {\r\n this._build();\r\n }\r\n\r\n setOpacity() {\r\n // not implemented\r\n }\r\n\r\n raycast() {\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\nexport default IsoSurfaceGeometry;\r\n","import utils from '../../utils';\r\n\r\n/**\r\n * Class for marching cube\r\n * Stores 8 points and 8 float values are stored together in linear array\r\n * Int values for has intersection or not - in integer32 linear array\r\n * Int values for bits flags - in integer32 linear array\r\n *\r\n */\r\nclass IsoSurfaceMarchCube {\r\n constructor() {\r\n this.pointsValuesLinear = null;\r\n this.hasIntersection = null;\r\n this.bitsInside = null;\r\n }\r\n\r\n create(numCellsPerSide) {\r\n const vx7000000 = 0x7000000;\r\n const n3 = numCellsPerSide * numCellsPerSide * numCellsPerSide;\r\n if (n3 > vx7000000) {\r\n throw new Error('Too large cube dimension: lead to memory huge uasge');\r\n }\r\n this.pointsValuesLinear = utils.allocateTyped(Float32Array, (2 << (2 + 2)) * n3);\r\n this.hasIntersection = utils.allocateTyped(Int32Array, n3);\r\n this.bitsInside = utils.allocateTyped(Int32Array, n3);\r\n return 0;\r\n }\r\n\r\n destroy() {\r\n this.bitsInside = null;\r\n this.hasIntersection = null;\r\n this.pointsValuesLinear = null;\r\n }\r\n}\r\n\r\nIsoSurfaceMarchCube.prototype.striIndicesMarchCube = [\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 0, 2, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 8, 3, 2, 10, 8, 10, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 8, 11, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 2, 1, 9, 11, 9, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 1, 11, 10, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 10, 1, 0, 8, 10, 8, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 9, 0, 3, 11, 9, 11, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 7, 3, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 1, 9, 4, 7, 1, 7, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 4, 7, 3, 0, 4, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 2, 10, 9, 0, 2, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 8, 4, 7, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 4, 7, 11, 2, 4, 2, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 8, 4, 7, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1, -1, -1, -1, -1,\r\n 3, 10, 1, 3, 11, 10, 7, 8, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4, -1, -1, -1, -1,\r\n 4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 4, 7, 11, 4, 11, 9, 9, 11, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 1, 5, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 5, 4, 8, 3, 5, 3, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 10, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 2, 10, 5, 4, 2, 4, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8, -1, -1, -1, -1,\r\n 9, 5, 4, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 11, 2, 0, 8, 11, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 5, 4, 0, 1, 5, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5, -1, -1, -1, -1,\r\n 10, 3, 11, 10, 1, 3, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10, -1, -1, -1, -1,\r\n 5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3, -1, -1, -1, -1,\r\n 5, 4, 8, 5, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 5, 7, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 3, 0, 9, 5, 3, 5, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 8, 0, 1, 7, 1, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 7, 8, 9, 5, 7, 10, 1, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3, -1, -1, -1, -1,\r\n 8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2, -1, -1, -1, -1,\r\n 2, 10, 5, 2, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 9, 5, 7, 8, 9, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7, -1, -1, -1, -1,\r\n 11, 2, 1, 11, 1, 7, 7, 1, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11, -1, -1, -1, -1,\r\n 5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0, -1,\r\n 11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0, -1,\r\n 11, 10, 5, 7, 11, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 8, 3, 1, 9, 8, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 2, 6, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 5, 1, 2, 6, 3, 0, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 6, 5, 9, 0, 6, 0, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 0, 8, 11, 2, 0, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11, -1, -1, -1, -1,\r\n 6, 3, 11, 6, 5, 3, 5, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9, -1, -1, -1, -1,\r\n 6, 5, 9, 6, 9, 11, 11, 9, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 3, 0, 4, 7, 3, 6, 5, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 5, 10, 6, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4, -1, -1, -1, -1,\r\n 6, 1, 2, 6, 5, 1, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7, -1, -1, -1, -1,\r\n 8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6, -1, -1, -1, -1,\r\n 7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9, -1,\r\n 3, 11, 2, 7, 8, 4, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11, -1, -1, -1, -1,\r\n 0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1,\r\n 9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6, -1,\r\n 8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6, -1, -1, -1, -1,\r\n 5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11, -1,\r\n 0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7, -1,\r\n 6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9, -1, -1, -1, -1,\r\n 10, 4, 9, 6, 4, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 10, 6, 4, 9, 10, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 0, 1, 10, 6, 0, 6, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 1, 4, 9, 1, 2, 4, 2, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4, -1, -1, -1, -1,\r\n 0, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 3, 2, 8, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 4, 9, 10, 6, 4, 11, 2, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6, -1, -1, -1, -1,\r\n 3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10, -1, -1, -1, -1,\r\n 6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1, -1,\r\n 9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3, -1, -1, -1, -1,\r\n 8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1, -1,\r\n 3, 11, 6, 3, 6, 0, 0, 6, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 4, 8, 11, 6, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 10, 6, 7, 8, 10, 8, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10, -1, -1, -1, -1,\r\n 10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0, -1, -1, -1, -1,\r\n 10, 6, 7, 10, 7, 1, 1, 7, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9, -1,\r\n 7, 8, 0, 7, 0, 6, 6, 0, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 3, 2, 6, 7, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7, -1, -1, -1, -1,\r\n 2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7, -1,\r\n 1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11, -1,\r\n 11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1, -1, -1, -1, -1,\r\n 8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6, -1,\r\n 0, 9, 1, 11, 6, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0, -1, -1, -1, -1,\r\n 7, 11, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 8, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 9, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 9, 8, 3, 1, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 1, 2, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 8, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 9, 0, 2, 10, 9, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8, -1, -1, -1, -1,\r\n 7, 2, 3, 6, 2, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 7, 0, 8, 7, 6, 0, 6, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 7, 6, 2, 3, 7, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6, -1, -1, -1, -1,\r\n 10, 7, 6, 10, 1, 7, 1, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8, -1, -1, -1, -1,\r\n 0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7, -1, -1, -1, -1,\r\n 7, 6, 10, 7, 10, 8, 8, 10, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 8, 4, 11, 8, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 3, 0, 6, 0, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 6, 11, 8, 4, 6, 9, 0, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6, -1, -1, -1, -1,\r\n 6, 8, 4, 6, 11, 8, 2, 10, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6, -1, -1, -1, -1,\r\n 4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9, -1, -1, -1, -1,\r\n 10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3, -1,\r\n 8, 2, 3, 8, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8, -1, -1, -1, -1,\r\n 1, 9, 4, 1, 4, 2, 2, 4, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1, -1, -1, -1, -1,\r\n 10, 1, 0, 10, 0, 6, 6, 0, 4, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3, -1,\r\n 10, 9, 4, 6, 10, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 5, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 5, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 1, 5, 4, 0, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5, -1, -1, -1, -1,\r\n 9, 5, 4, 10, 1, 2, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5, -1, -1, -1, -1,\r\n 7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2, -1, -1, -1, -1,\r\n 3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6, -1,\r\n 7, 2, 3, 7, 6, 2, 5, 4, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7, -1, -1, -1, -1,\r\n 3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0, -1, -1, -1, -1,\r\n 6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8, -1,\r\n 9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7, -1, -1, -1, -1,\r\n 1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4, -1,\r\n 4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10, -1,\r\n 7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10, -1, -1, -1, -1,\r\n 6, 9, 5, 6, 11, 9, 11, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5, -1, -1, -1, -1,\r\n 0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11, -1, -1, -1, -1,\r\n 6, 11, 3, 6, 3, 5, 5, 3, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6, -1, -1, -1, -1,\r\n 0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10, -1,\r\n 11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5, -1,\r\n 6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3, -1, -1, -1, -1,\r\n 5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2, -1, -1, -1, -1,\r\n 9, 5, 6, 9, 6, 0, 0, 6, 2, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8, -1,\r\n 1, 5, 6, 2, 1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6, -1,\r\n 10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0, -1, -1, -1, -1,\r\n 0, 3, 8, 5, 6, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 5, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 7, 5, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 5, 10, 11, 7, 5, 8, 3, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 11, 7, 5, 10, 11, 1, 9, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1, -1, -1, -1, -1,\r\n 11, 1, 2, 11, 7, 1, 7, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11, -1, -1, -1, -1,\r\n 9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7, -1, -1, -1, -1,\r\n 7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2, -1,\r\n 2, 5, 10, 2, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5, -1, -1, -1, -1,\r\n 9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2, -1, -1, -1, -1,\r\n 9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2, -1,\r\n 1, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 7, 0, 7, 1, 1, 7, 5, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 0, 3, 9, 3, 5, 5, 3, 7, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 8, 7, 5, 9, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 8, 4, 5, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0, -1, -1, -1, -1,\r\n 0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5, -1, -1, -1, -1,\r\n 10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4, -1,\r\n 2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8, -1, -1, -1, -1,\r\n 0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11, -1,\r\n 0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5, -1,\r\n 9, 4, 5, 2, 11, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4, -1, -1, -1, -1,\r\n 5, 10, 2, 5, 2, 4, 4, 2, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9, -1,\r\n 5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 3, 5, 1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 4, 5, 1, 0, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5, -1, -1, -1, -1,\r\n 9, 4, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 11, 7, 4, 9, 11, 9, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11, -1, -1, -1, -1,\r\n 1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11, -1, -1, -1, -1,\r\n 3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4, -1,\r\n 4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2, -1, -1, -1, -1,\r\n 9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3, -1,\r\n 11, 7, 4, 11, 4, 2, 2, 4, 0, -1, -1, -1, -1, -1, -1, -1,\r\n 11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4, -1, -1, -1, -1,\r\n 2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9, -1, -1, -1, -1,\r\n 9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7, -1,\r\n 3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10, -1,\r\n 1, 10, 2, 8, 7, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 7, 1, 3, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1, -1, -1, -1, -1,\r\n 4, 0, 3, 7, 4, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 4, 8, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1,\r\n 0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1,\r\n 9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1,\r\n 1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,\r\n];\r\n\r\nexport default IsoSurfaceMarchCube;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport utils from '../../utils';\r\n\r\nconst edgeTable = [\r\n 0x0, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c,\r\n 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00,\r\n 0x190, 0x99, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c,\r\n 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90,\r\n 0x230, 0x339, 0x33, 0x13a, 0x636, 0x73f, 0x435, 0x53c,\r\n 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30,\r\n 0x3a0, 0x2a9, 0x1a3, 0xaa, 0x7a6, 0x6af, 0x5a5, 0x4ac,\r\n 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0,\r\n 0x460, 0x569, 0x663, 0x76a, 0x66, 0x16f, 0x265, 0x36c,\r\n 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60,\r\n 0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0xff, 0x3f5, 0x2fc,\r\n 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0,\r\n 0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x55, 0x15c,\r\n 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950,\r\n 0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0xcc,\r\n 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0,\r\n 0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc,\r\n 0xcc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0,\r\n 0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c,\r\n 0x15c, 0x55, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650,\r\n 0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc,\r\n 0x2fc, 0x3f5, 0xff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0,\r\n 0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c,\r\n 0x36c, 0x265, 0x16f, 0x66, 0x76a, 0x663, 0x569, 0x460,\r\n 0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac,\r\n 0x4ac, 0x5a5, 0x6af, 0x7a6, 0xaa, 0x1a3, 0x2a9, 0x3a0,\r\n 0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c,\r\n 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x33, 0x339, 0x230,\r\n 0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c,\r\n 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x99, 0x190,\r\n 0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c,\r\n 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x0];\r\n\r\nfunction _voxelGradientFast(v, point, grad) {\r\n const g = v.getValue(point.x, point.y, point.z);\r\n grad.set(g[0], g[1], g[2]);\r\n}\r\n\r\n// Helper class GridCell\r\nclass GridCell {\r\n constructor() {\r\n this._arrSize = 8;\r\n this.p = new Array(this._arrSize);\r\n this.g = new Array(this._arrSize);\r\n this.val = new Array(this._arrSize);\r\n for (let i = 0; i < this._arrSize; ++i) {\r\n this.p[i] = new THREE.Vector3();\r\n this.g[i] = new THREE.Vector3();\r\n }\r\n this.cubeIndex = 0;\r\n }\r\n}\r\n\r\n// Helper class Triangle\r\nclass Triangle {\r\n constructor() {\r\n this.a = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.b = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n\r\n this.c = {\r\n p: new THREE.Vector3(),\r\n n: new THREE.Vector3(),\r\n };\r\n }\r\n}\r\n\r\nfunction createArray(arrSize) {\r\n const arr = new Array(arrSize);\r\n for (let i = 0; i < arrSize; ++i) {\r\n arr[i] = new THREE.Vector3();\r\n }\r\n\r\n return arr;\r\n}\r\n\r\nclass IsoSurface {\r\n constructor() {\r\n this._numTriangles = 0;\r\n this._numVertices = 0;\r\n this._position = [];\r\n this._normals = [];\r\n this._colors = null;\r\n this._indices = [];\r\n this._volumetricData = null;\r\n this._xAxis = new THREE.Vector3();\r\n this._yAxis = new THREE.Vector3();\r\n this._zAxis = new THREE.Vector3();\r\n this._xDir = new THREE.Vector3();\r\n this._yDir = new THREE.Vector3();\r\n this._zDir = new THREE.Vector3();\r\n }\r\n\r\n _prepareAxesAndDirs() {\r\n const volData = this._volumetricData;\r\n\r\n const cellSize = volData.getCellSize();\r\n\r\n // calculate cell axes\r\n const xAxis = this._xAxis;\r\n const yAxis = this._yAxis;\r\n const zAxis = this._zAxis;\r\n const xDir = this._xDir;\r\n const yDir = this._yDir;\r\n const zDir = this._zDir;\r\n\r\n xAxis.set(cellSize.x, 0, 0);\r\n yAxis.set(0, cellSize.y, 0);\r\n zAxis.set(0, 0, cellSize.z);\r\n\r\n xDir.set(1, 0, 0);\r\n yDir.set(0, 1, 0);\r\n zDir.set(0, 0, 1);\r\n\r\n // flip normals if coordinate system is in the wrong handedness\r\n const tmp = new THREE.Vector3();\r\n tmp.crossVectors(xDir, yDir);\r\n if (tmp.dot(zDir) < 0) {\r\n xDir.negate();\r\n yDir.negate();\r\n zDir.negate();\r\n }\r\n\r\n // check that the grid is in the all-positive octant of the coordinate system\r\n if (xDir.x < 0 || xDir.y < 0 || xDir.z < 0\r\n || yDir.x < 0 || yDir.y < 0 || yDir.z < 0\r\n || zDir.x < 0 || zDir.y < 0 || zDir.z < 0) {\r\n return false;\r\n }\r\n\r\n // check that the grid is axis-aligned\r\n const notZero = (axe) => Math.abs(axe) > Number.EPSILON;\r\n return !(notZero(xAxis.y) || notZero(xAxis.z)\r\n || notZero(yAxis.x) || notZero(yAxis.z)\r\n || notZero(zAxis.x) || notZero(zAxis.y));\r\n }\r\n\r\n _vertexInterp(isoLevel, grid, ind1, ind2, vertex, normal) {\r\n const p1 = grid.p[ind1];\r\n const p2 = grid.p[ind2];\r\n const n1 = grid.g[ind1];\r\n const n2 = grid.g[ind2];\r\n const valP1 = grid.val[ind1];\r\n const valP2 = grid.val[ind2];\r\n const isoDiffP1 = isoLevel - valP1;\r\n const diffValP2P1 = valP2 - valP1;\r\n\r\n let mu = 0.0;\r\n\r\n if (Math.abs(diffValP2P1) > 0.0) {\r\n mu = isoDiffP1 / diffValP2P1;\r\n }\r\n mu = mu > 1.0 ? 1.0 : mu;\r\n vertex.lerpVectors(p1, p2, mu);\r\n normal.lerpVectors(n1, n2, mu);\r\n }\r\n\r\n static _triTable = IsoSurfaceMarchCube.prototype.striIndicesMarchCube;\r\n\r\n static _arrSize = 12;\r\n\r\n static _firstIndices = [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3];\r\n\r\n static _secondIndices = [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7];\r\n\r\n static _vertexList = createArray(IsoSurface._arrSize);\r\n\r\n static _normalList = createArray(IsoSurface._arrSize);\r\n\r\n _polygonize(grid, isoLevel, triangles) {\r\n const { cubeIndex } = grid;\r\n let i = 0;\r\n const arrSize = IsoSurface._arrSize;\r\n const firstIndices = IsoSurface._firstIndices;\r\n const secondIndices = IsoSurface._secondIndices;\r\n const vertexList = IsoSurface._vertexList;\r\n const normalList = IsoSurface._normalList;\r\n\r\n for (; i < arrSize; ++i) {\r\n if (edgeTable[cubeIndex] & (1 << i)) {\r\n this._vertexInterp(\r\n isoLevel,\r\n grid,\r\n firstIndices[i],\r\n secondIndices[i],\r\n vertexList[i],\r\n normalList[i],\r\n );\r\n }\r\n }\r\n\r\n let triCount = 0;\r\n const triTblIdx = cubeIndex * 16;\r\n const triTable = IsoSurface._triTable;\r\n\r\n for (i = 0; triTable[triTblIdx + i] !== -1; i += 3) {\r\n triangles[triCount].a.p.copy(vertexList[triTable[triTblIdx + i]]);\r\n triangles[triCount].a.n.copy(normalList[triTable[triTblIdx + i]]);\r\n\r\n triangles[triCount].b.p.copy(vertexList[triTable[triTblIdx + i + 1]]);\r\n triangles[triCount].b.n.copy(normalList[triTable[triTblIdx + i + 1]]);\r\n\r\n triangles[triCount].c.p.copy(vertexList[triTable[triTblIdx + i + 2]]);\r\n triangles[triCount].c.n.copy(normalList[triTable[triTblIdx + i + 2]]);\r\n ++triCount;\r\n }\r\n\r\n return triCount;\r\n }\r\n\r\n _doGridPosNorms(isoValue, step, appendSimple) {\r\n const vol = this._volumetricData;\r\n const volData = this._volumetricData.getData();\r\n const dim = vol.getDimensions();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n const zSize = dim[2];\r\n const stepX = step * vol.getStrideX();\r\n const stepY = step * vol.getStrideY();\r\n const stepZ = step * vol.getStrideZ();\r\n\r\n const gc = new GridCell();\r\n const gcVal = gc.val;\r\n const gcValSize = gc.val.length;\r\n const additions = [\r\n new THREE.Vector3(0, 0, 0), // 0\r\n new THREE.Vector3(step, 0, 0), // 1\r\n new THREE.Vector3(step, step, 0), // 2\r\n new THREE.Vector3(0, step, 0), // 3\r\n new THREE.Vector3(0, 0, step), // 4\r\n new THREE.Vector3(step, 0, step), // 5\r\n new THREE.Vector3(step, step, step), // 6\r\n new THREE.Vector3(0, step, step), // 7\r\n ];\r\n\r\n const tmpTriCount = 5;\r\n const triangles = new Array(tmpTriCount);\r\n for (let j = 0; j < tmpTriCount; ++j) {\r\n triangles[j] = new Triangle();\r\n }\r\n\r\n let appendVertex;\r\n const self = this;\r\n const positions = this._position;\r\n const normals = this._normals;\r\n if (appendSimple) {\r\n // Special case for axis-aligned grid with positive unit vector normals\r\n appendVertex = (function () {\r\n const axis = new THREE.Vector3(self._xAxis.x, self._yAxis.y, self._zAxis.z);\r\n return function (triVertex) {\r\n const vertex = triVertex.p.clone();\r\n vertex.multiply(axis);\r\n positions.push(vertex.add(self._origin));\r\n normals.push(triVertex.n.clone());\r\n };\r\n }());\r\n } else {\r\n appendVertex = (function () {\r\n const posMtx = new THREE.Matrix3();\r\n posMtx.set(\r\n self._xAxis.x,\r\n self._yAxis.x,\r\n self._zAxis.x,\r\n self._xAxis.y,\r\n self._yAxis.y,\r\n self._zAxis.y,\r\n self._xAxis.z,\r\n self._yAxis.z,\r\n self._zAxis.z,\r\n );\r\n const normMtx = new THREE.Matrix3();\r\n normMtx.set(\r\n self._xDir.x,\r\n self._yDir.x,\r\n self._zDir.x,\r\n self._xDir.y,\r\n self._yDir.y,\r\n self._zDir.y,\r\n self._xDir.z,\r\n self._yDir.z,\r\n self._zDir.z,\r\n );\r\n\r\n return function (triVertex) {\r\n positions.push(triVertex.p.clone().applyMatrix3(posMtx).add(self._origin));\r\n normals.push(triVertex.n.clone().applyMatrix3(normMtx));\r\n };\r\n }());\r\n }\r\n const indices = this._indices;\r\n\r\n let globTriCount = 0;\r\n\r\n for (let z = 0; z < (zSize - step); z += step) {\r\n for (let y = 0; y < (ySize - step); y += step) {\r\n let idx = vol.getDirectIdx(0, y, z);\r\n for (let x = 0; x < (xSize - step); x += step, idx += stepX) {\r\n gcVal[0] = volData[idx];\r\n gcVal[1] = volData[idx + stepX];\r\n gcVal[3] = volData[idx + stepY];\r\n gcVal[2] = volData[idx + stepX + stepY];\r\n gcVal[4] = volData[idx + stepZ];\r\n gcVal[5] = volData[idx + stepX + stepZ];\r\n gcVal[7] = volData[idx + stepY + stepZ];\r\n gcVal[6] = volData[idx + stepX + stepY + stepZ];\r\n\r\n // Determine the index into the edge table which\r\n // tells us which vertices are inside of the surface\r\n let cubeIndex = 0;\r\n let i = 0;\r\n for (; i < gcValSize; ++i) {\r\n if (gcVal[i] < isoValue) {\r\n cubeIndex |= (1 << i);\r\n }\r\n }\r\n\r\n if (edgeTable[cubeIndex] === 0) {\r\n continue;\r\n }\r\n\r\n gc.cubeIndex = cubeIndex;\r\n for (i = 0; i < gcValSize; ++i) {\r\n gc.p[i].set(x + additions[i].x, y + additions[i].y, z + additions[i].z);\r\n _voxelGradientFast(this._gradient, gc.p[i], gc.g[i]);\r\n }\r\n\r\n // calculate vertices and facets for this cube,\r\n // calculate normals by interpolating between the negated\r\n // normalized volume gradients for the 8 reference voxels\r\n const triCount = this._polygonize(gc, isoValue, triangles);\r\n globTriCount += triCount;\r\n\r\n // append triangles using different techniques\r\n for (i = 0; i < triCount; ++i) {\r\n indices.push(this._numTriangles * 3);\r\n indices.push(this._numTriangles * 3 + 1);\r\n indices.push(this._numTriangles * 3 + 2);\r\n ++this._numTriangles;\r\n\r\n appendVertex(triangles[i].a);\r\n appendVertex(triangles[i].b);\r\n appendVertex(triangles[i].c);\r\n }\r\n }\r\n }\r\n }\r\n\r\n return globTriCount;\r\n }\r\n\r\n compute(volData, origin, isoValue, step) {\r\n this._volumetricData = volData;\r\n this._origin = origin;\r\n\r\n this._gradient = volData.computeGradient();\r\n\r\n this._doGridPosNorms(isoValue, step, this._prepareAxesAndDirs());\r\n }\r\n\r\n _remapIndices(vertexMap, idcCount) {\r\n const indices = this._indices;\r\n const newIndices = utils.allocateTyped(Uint32Array, idcCount);\r\n for (let i = 0; i < idcCount; ++i) {\r\n indices[i] = vertexMap[indices[i]];\r\n newIndices[i] = indices[i];\r\n }\r\n this._indices = newIndices;\r\n }\r\n\r\n _remapVertices(vertices, normals, count) {\r\n const newPositions = utils.allocateTyped(Float32Array, count * 3);\r\n const newNormals = utils.allocateTyped(Float32Array, count * 3);\r\n for (let i = 0; i < count; ++i) {\r\n const pos = vertices[i];\r\n newPositions[i * 3] = pos.x;\r\n newPositions[i * 3 + 1] = pos.y;\r\n newPositions[i * 3 + 2] = pos.z;\r\n const norm = normals[i].normalize();\r\n newNormals[i * 3] = norm.x;\r\n newNormals[i * 3 + 1] = norm.y;\r\n newNormals[i * 3 + 2] = norm.z;\r\n }\r\n this._position = newPositions;\r\n this._normals = newNormals;\r\n }\r\n\r\n vertexFusion(offset, len) {\r\n const faceVer = this._indices.length;\r\n const vertices = this._position;\r\n const normals = this._normals;\r\n const oldVerCount = vertices.length | 0;\r\n if (faceVer === 0 || oldVerCount === 0) {\r\n return;\r\n }\r\n const vMap = utils.allocateTyped(Uint32Array, oldVerCount);\r\n vMap[0] = 0;\r\n let newVer = 1;\r\n\r\n let i = 1;\r\n for (; i < oldVerCount; ++i) {\r\n const start = newVer - offset < 0 ? 0 : newVer - offset;\r\n const end = start + len > newVer ? newVer : start + len;\r\n let matchedIndex = -1;\r\n\r\n for (let j = start; j < end; ++j) {\r\n if (Math.abs(vertices[i] - vertices[j]) < Number.EPSILON) {\r\n matchedIndex = j;\r\n break;\r\n }\r\n }\r\n\r\n if (matchedIndex !== -1) {\r\n vMap[i] = matchedIndex;\r\n } else {\r\n vertices[newVer].copy(vertices[i]);\r\n normals[newVer].copy(normals[i]);\r\n vMap[i] = newVer;\r\n ++newVer;\r\n }\r\n }\r\n\r\n this._remapIndices(vMap, faceVer);\r\n this._remapVertices(vertices, normals, newVer);\r\n }\r\n\r\n // Assign per-vertex colors from a volumetric texture map (same dimensions as the original volumetric data).\r\n // Along with color dominating atom is determined for each vertex\r\n // and vertices with atom out of \"visible\" subset get filtered out.\r\n // XXX only handles orthogonal volumes currently\r\n setColorVolTex(colorMap, atomMap, atomWeightMap, visibilitySelector) {\r\n let i;\r\n let idx;\r\n const numVerts = this._position.length / 3;\r\n const vertices = this._position;\r\n const origin = this._origin;\r\n const dim = this._volumetricData.getDimensions();\r\n const xs = dim[0] - 1;\r\n const ys = dim[1] - 1;\r\n const zs = dim[2] - 1;\r\n\r\n const colorData = colorMap.getData();\r\n const strideX = colorMap.getStrideX();\r\n const strideY = colorMap.getStrideY();\r\n const strideZ = colorMap.getStrideZ();\r\n\r\n let atomWeightData;\r\n let atomStrideX;\r\n let atomStrideY;\r\n let atomStrideZ;\r\n\r\n if (visibilitySelector !== null) {\r\n atomWeightData = atomWeightMap.getData();\r\n atomStrideX = atomWeightMap.getStrideX();\r\n atomStrideY = atomWeightMap.getStrideY();\r\n atomStrideZ = atomWeightMap.getStrideZ();\r\n }\r\n\r\n const xInv = 1.0 / this._xAxis.x;\r\n const yInv = 1.0 / this._yAxis.y;\r\n const zInv = 1.0 / this._zAxis.z;\r\n\r\n let atomLookup = [];\r\n let atomWeights = [];\r\n const colors = utils.allocateTyped(Float32Array, numVerts * 3);\r\n\r\n function interp(mu, idx1, idx2, c) {\r\n c[0] = (1 - mu) * colorData[idx1] + mu * colorData[idx2];\r\n c[1] = (1 - mu) * colorData[idx1 + 1] + mu * colorData[idx2 + 1];\r\n c[2] = (1 - mu) * colorData[idx1 + 2] + mu * colorData[idx2 + 2];\r\n }\r\n\r\n function collectWeight(ai, coefX, coefY, coefZ) {\r\n const a = atomMap[ai]; // atomWeightMap is a scalar field, so index into atom map should be the same\r\n if (a != null) {\r\n atomLookup[a.index] = a;\r\n const w = coefX * coefY * coefZ * atomWeightData[ai];\r\n if (typeof atomWeights[a.index] === 'undefined') {\r\n atomWeights[a.index] = w;\r\n } else {\r\n atomWeights[a.index] += w;\r\n }\r\n }\r\n }\r\n\r\n const vMap = utils.allocateTyped(Int32Array, numVerts);\r\n let newVerCount = 0;\r\n\r\n for (i = 0; i < numVerts; i++) {\r\n const ind = i * 3;\r\n const vx = (vertices[ind] - origin.x) * xInv;\r\n const vy = (vertices[ind + 1] - origin.y) * yInv;\r\n const vz = (vertices[ind + 2] - origin.z) * zInv;\r\n const x = Math.min(Math.max(vx, 0), xs) | 0;\r\n const y = Math.min(Math.max(vy, 0), ys) | 0;\r\n const z = Math.min(Math.max(vz, 0), zs) | 0;\r\n\r\n const mux = (vx - x);\r\n const muy = (vy - y);\r\n const muz = (vz - z);\r\n\r\n if (visibilitySelector != null) {\r\n // collect atom weights\r\n atomLookup = [];\r\n atomWeights = [];\r\n idx = atomWeightMap.getDirectIdx(x, y, z);\r\n collectWeight(idx, 1 - mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideX, mux, 1 - muy, 1 - muz);\r\n collectWeight(idx + atomStrideY, 1 - mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideX + atomStrideY, mux, muy, 1 - muz);\r\n collectWeight(idx + atomStrideZ, 1 - mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideZ, mux, 1 - muy, muz);\r\n collectWeight(idx + atomStrideY + atomStrideZ, 1 - mux, muy, muz);\r\n collectWeight(idx + atomStrideX + atomStrideY + atomStrideZ, mux, muy, muz);\r\n\r\n // find dominant atom\r\n let maxWeight = 0.0;\r\n let dominantIdx = -1;\r\n for (const atomIdx in atomWeights) {\r\n if (atomWeights[atomIdx] > maxWeight) {\r\n dominantIdx = atomIdx;\r\n maxWeight = atomWeights[atomIdx];\r\n }\r\n }\r\n\r\n if (dominantIdx < 0 || !visibilitySelector.includesAtom(atomLookup[dominantIdx])) {\r\n // this vertex doesn't belong to visible subset and will be skipped\r\n vMap[i] = -1;\r\n continue;\r\n }\r\n }\r\n\r\n vMap[i] = newVerCount++;\r\n\r\n // color tri-linear interpolation\r\n const dx = (x < xs) ? strideX : 0;\r\n const dy = (y < ys) ? strideY : 0;\r\n const dz = (z < zs) ? strideZ : 0;\r\n\r\n const c0 = [0, 0, 0];\r\n const c1 = [0, 0, 0];\r\n const c2 = [0, 0, 0];\r\n const c3 = [0, 0, 0];\r\n\r\n idx = colorMap.getDirectIdx(x, y, z);\r\n interp(mux, idx, idx + dx, c0);\r\n interp(mux, idx + dy, idx + dx + dy, c1);\r\n interp(mux, idx + dz, idx + dx + dz, c2);\r\n interp(mux, idx + dy + dz, idx + dx + dy + dz, c3);\r\n\r\n const cz0 = [0, 0, 0];\r\n cz0[0] = (1 - muy) * c0[0] + muy * c1[0];\r\n cz0[1] = (1 - muy) * c0[1] + muy * c1[1];\r\n cz0[2] = (1 - muy) * c0[2] + muy * c1[2];\r\n\r\n const cz1 = [0, 0, 0];\r\n cz1[0] = (1 - muy) * c2[0] + muy * c3[0];\r\n cz1[1] = (1 - muy) * c2[1] + muy * c3[1];\r\n cz1[2] = (1 - muy) * c2[2] + muy * c3[2];\r\n\r\n colors[ind] = (1 - muz) * cz0[0] + muz * cz1[0];\r\n colors[ind + 1] = (1 - muz) * cz0[1] + muz * cz1[1];\r\n colors[ind + 2] = (1 - muz) * cz0[2] + muz * cz1[2];\r\n }\r\n this._colors = colors;\r\n\r\n if (visibilitySelector != null) {\r\n // shift visible vertices towards beginning of array\r\n for (i = 0; i < numVerts; ++i) {\r\n const j = vMap[i];\r\n if (j < 0) {\r\n continue;\r\n }\r\n\r\n // assert: j <= i\r\n this._position[j * 3] = this._position[i * 3];\r\n this._position[j * 3 + 1] = this._position[i * 3 + 1];\r\n this._position[j * 3 + 2] = this._position[i * 3 + 2];\r\n this._normals[j * 3] = this._normals[i * 3];\r\n this._normals[j * 3 + 1] = this._normals[i * 3 + 1];\r\n this._normals[j * 3 + 2] = this._normals[i * 3 + 2];\r\n this._colors[j * 3] = this._colors[i * 3];\r\n this._colors[j * 3 + 1] = this._colors[i * 3 + 1];\r\n this._colors[j * 3 + 2] = this._colors[i * 3 + 2];\r\n }\r\n\r\n // rebuild index list\r\n const numTriangles = this._indices.length / 3;\r\n let newTriCount = 0;\r\n for (i = 0; i < numTriangles; ++i) {\r\n const i0 = vMap[this._indices[3 * i]];\r\n const i1 = vMap[this._indices[3 * i + 1]];\r\n const i2 = vMap[this._indices[3 * i + 2]];\r\n if (i0 >= 0 && i1 >= 0 && i2 >= 0) {\r\n this._indices[3 * newTriCount] = i0;\r\n this._indices[3 * newTriCount + 1] = i1;\r\n this._indices[3 * newTriCount + 2] = i2;\r\n ++newTriCount;\r\n }\r\n }\r\n\r\n // shrink arrays to data size\r\n this._position = new Float32Array(this._position.buffer.slice(0, newVerCount * 3 * 4));\r\n this._normals = new Float32Array(this._normals.buffer.slice(0, newVerCount * 3 * 4));\r\n this._colors = new Float32Array(this._colors.buffer.slice(0, newVerCount * 3 * 4));\r\n this._indices = new Uint32Array(this._indices.buffer.slice(0, newTriCount * 3 * 4));\r\n }\r\n }\r\n\r\n toMesh() {\r\n const geo = new THREE.BufferGeometry();\r\n geo.setIndex(new THREE.BufferAttribute(this._indices, 1));\r\n geo.setAttribute('position', new THREE.BufferAttribute(this._position, 3));\r\n geo.setAttribute('normal', new THREE.BufferAttribute(this._normals, 3));\r\n geo.setAttribute('color', new THREE.BufferAttribute(this._colors, 3));\r\n geo.computeBoundingSphere();\r\n return geo;\r\n }\r\n}\r\nexport default IsoSurface;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurface from './IsoSurface';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * This is a base class for volumetric maps based isosurface algorithms.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass VolumeSurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n const params = this._opts;\r\n this.numVoxels = [128, 128, 128];\r\n this.xAxis = new THREE.Vector3(1.0, 0.0, 0.0);\r\n this.yAxis = new THREE.Vector3(0.0, 1.0, 0.0);\r\n this.zAxis = new THREE.Vector3(0.0, 0.0, 1.0);\r\n\r\n this.origin = new THREE.Vector3(0.0, 0.0, 0.0);\r\n this._visibilitySelector = params.visibilitySelector;\r\n\r\n this._calcSurface(params);\r\n }\r\n\r\n _findMinMax(posRadArray) {\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n const maxPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n const minPosRad = [posRadArray[0], posRadArray[1], posRadArray[2], posRadArray[3]];\r\n for (let i = 1; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n for (let itemIdx = 0; itemIdx < itemSize; ++itemIdx) {\r\n const tmpVal = posRadArray[ind + itemIdx];\r\n maxPosRad[itemIdx] = Math.max(tmpVal, maxPosRad[itemIdx]);\r\n minPosRad[itemIdx] = Math.min(tmpVal, minPosRad[itemIdx]);\r\n }\r\n }\r\n return { maxPosRad, minPosRad };\r\n }\r\n\r\n _findNumVoxels(posRadArray, params) {\r\n const { numVoxels } = this;\r\n const minMaxValues = this._findMinMax(posRadArray);\r\n const minCoordRad = minMaxValues.minPosRad;\r\n const maxCoordRad = minMaxValues.maxPosRad;\r\n\r\n // minrad\r\n if (minCoordRad[3] > 4.0) {\r\n params.gridSpacing *= minCoordRad[3];\r\n }\r\n\r\n let gridPadding = params.radScale * maxCoordRad[3] * 1.7;\r\n let padRad = gridPadding;\r\n padRad = 0.65 * Math.sqrt(4.0 / 3.0 * Math.PI * padRad * padRad * padRad);\r\n gridPadding = Math.max(gridPadding, padRad);\r\n\r\n let i = 0;\r\n for (; i < 3; ++i) {\r\n minCoordRad[i] -= gridPadding;\r\n maxCoordRad[i] += gridPadding;\r\n }\r\n\r\n for (i = 0; i < 3; ++i) {\r\n numVoxels[i] = Math.ceil((maxCoordRad[i] - minCoordRad[i]) / params.gridSpacing);\r\n }\r\n this.xAxis.x = (numVoxels[0] - 1) * params.gridSpacing;\r\n this.yAxis.y = (numVoxels[1] - 1) * params.gridSpacing;\r\n this.zAxis.z = (numVoxels[2] - 1) * params.gridSpacing;\r\n\r\n [this.origin.x, this.origin.y, this.origin.z] = minCoordRad;\r\n\r\n return { bbox: minMaxValues, dim: numVoxels };\r\n }\r\n\r\n _makeSurface(surface, params) {\r\n const isoSurf = new IsoSurface();\r\n isoSurf.compute(surface.volMap, this.origin, params.isoValue, 1);\r\n isoSurf.vertexFusion(9, 9);// normalization is included\r\n\r\n if (isoSurf._numTriangles > 0) {\r\n isoSurf.setColorVolTex(surface.volTexMap, surface.atomMap, surface.atomWeightMap, this._visibilitySelector);\r\n this.setIndex(new THREE.BufferAttribute(isoSurf._indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(isoSurf._position, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(isoSurf._normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(isoSurf._colors, 3));\r\n } else { // geometry should have at least empty position attributes to be processed in wireframe mode by three.js\r\n this.setAttribute('position', new THREE.BufferAttribute(utils.allocateTyped(Float32Array, 0), 3));\r\n }\r\n }\r\n\r\n _calcSurface(params) {\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n\r\n if (packedArrays.posRad.length === 0) {\r\n return;\r\n }\r\n const boundaries = this._findNumVoxels(packedArrays.posRad, params);\r\n\r\n const box = new THREE.Box3(\r\n this.origin,\r\n new THREE.Vector3(this.xAxis.x, this.yAxis.y, this.zAxis.z).add(this.origin),\r\n );\r\n const surface = this._computeSurface(packedArrays, box, boundaries, params);\r\n\r\n this._makeSurface(surface, params);\r\n }\r\n}\r\n\r\nexport default VolumeSurfaceGeometry;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass QuickSurfGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n // beware of shifting this multiple times!\r\n this._shiftByOrigin(packedArrays.posRad);\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3),\r\n };\r\n\r\n if (this._visibilitySelector != null) {\r\n surface.atomMap = [];\r\n surface.atomWeightMap = new Volume(Float32Array, this.numVoxels, box);\r\n }\r\n\r\n this.gaussdensity(surface, packedArrays, null, params);\r\n return surface;\r\n }\r\n\r\n gaussdensity(surface, packedArrays, atomicNum, params) {\r\n const numAtoms = packedArrays.posRad.length / 4;\r\n const { posRad, colors } = packedArrays;\r\n const { numVoxels } = this;\r\n const { radScale, gaussLim, gridSpacing } = params;\r\n const invIsoValue = 1.0 / params.isoValue;\r\n const invGridSpacing = 1.0 / gridSpacing;\r\n const maxVoxelX = numVoxels[0] - 1;\r\n const maxVoxelY = numVoxels[1] - 1;\r\n const maxVoxelZ = numVoxels[2] - 1;\r\n // TODO is densityMap and volTexMap initialized?\r\n\r\n const { volMap, volTexMap } = surface;\r\n const volData = volMap.getData();\r\n const strideX = volMap.getStrideX();\r\n\r\n const volTexData = volTexMap.getData();\r\n const texStrideX = volTexMap.getStrideX();\r\n\r\n let atomWeightData;\r\n if (this._visibilitySelector != null) {\r\n atomWeightData = surface.atomWeightMap.getData();\r\n }\r\n\r\n const { atomMap } = surface;\r\n\r\n for (let i = 0; i < numAtoms; ++i) {\r\n const ind = i * 4;\r\n const scaledRad = posRad[ind + 3] * radScale;\r\n const atomicNumFactor = atomicNum === null ? 1.0 : atomicNum[i];\r\n const radInv = 1 / (2 * scaledRad * scaledRad);\r\n let radLim = gaussLim * scaledRad;\r\n const radLim2 = radLim * radLim;\r\n radLim *= invGridSpacing;\r\n\r\n let tmp = posRad[ind] * invGridSpacing;\r\n const xMin = Math.max((tmp - radLim) | 0, 0);\r\n const xMax = Math.min((tmp + radLim) | 0, maxVoxelX);\r\n tmp = posRad[ind + 1] * invGridSpacing;\r\n const yMin = Math.max((tmp - radLim) | 0, 0);\r\n const yMax = Math.min((tmp + radLim) | 0, maxVoxelY);\r\n tmp = posRad[ind + 2] * invGridSpacing;\r\n const zMin = Math.max((tmp - radLim) | 0, 0);\r\n const zMax = Math.min((tmp + radLim) | 0, maxVoxelZ);\r\n\r\n let dz = zMin * gridSpacing - posRad[ind + 2];\r\n for (let z = zMin; z <= zMax; ++z, dz += gridSpacing) {\r\n let dy = yMin * gridSpacing - posRad[ind + 1];\r\n for (let y = yMin; y <= yMax; ++y, dy += gridSpacing) {\r\n const dy2dz2 = dy * dy + dz * dz;\r\n\r\n if (dy2dz2 >= radLim2) {\r\n continue;\r\n }\r\n\r\n let addr = volMap.getDirectIdx(xMin, y, z);\r\n let texAddr = volTexMap.getDirectIdx(xMin, y, z);\r\n let dx = xMin * gridSpacing - posRad[ind];\r\n for (let x = xMin; x <= xMax; ++x, dx += gridSpacing, addr += strideX, texAddr += texStrideX) {\r\n const r2 = dx * dx + dy2dz2;\r\n const expVal = -r2 * radInv;\r\n\r\n let density = Math.exp(expVal) * atomicNumFactor;\r\n\r\n // store most relevant atom (with highest density)\r\n if (this._visibilitySelector != null\r\n && density > atomWeightData[addr]) { // NOSONAR\r\n atomWeightData[addr] = density;\r\n // we use same index into atom map and atomWeightMap\r\n atomMap[addr] = packedArrays.atoms[i];\r\n }\r\n\r\n volData[addr] += density;\r\n\r\n // TODO check for volTexMap routine?\r\n density *= invIsoValue;\r\n const colInd = i * 3;\r\n volTexData[texAddr] += density * colors[colInd];\r\n volTexData[texAddr + 1] += density * colors[colInd + 1];\r\n volTexData[texAddr + 2] += density * colors[colInd + 2];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n _shiftByOrigin(posRadArray) {\r\n const originX = this.origin.x;\r\n const originY = this.origin.y;\r\n const originZ = this.origin.z;\r\n\r\n const itemSize = 4;\r\n const itemsCount = posRadArray.length / itemSize;\r\n for (let i = 0; i < itemsCount; ++i) {\r\n const ind = i * itemSize;\r\n\r\n posRadArray[ind] -= originX;\r\n posRadArray[ind + 1] -= originY;\r\n posRadArray[ind + 2] -= originZ;\r\n }\r\n }\r\n}\r\n\r\nexport default QuickSurfGeometry;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n/**\r\n * Modifed from SpatialHash\r\n *\r\n * Main differences are:\r\n * - Optimized grid size to ensure we only ever need to look +/-1 cell\r\n * - Aware of atomic radii and will only output atoms within rAtom + rExtra\r\n * (see withinRadii method)\r\n *\r\n * (Uses rounding rather than bitshifting as consequence of arbitrary grid size)\r\n * @class\r\n * @param {Float32Array} posRad - x, y, z coordinates and radiuses\r\n * @param {Float32Array} min - xyz min coordinates\r\n * @param {Float32Array} max - xyz max coordinates\r\n * @param {number} maxDistance - max distance\r\n */\r\nfunction AVHash(posRad, min, max, maxDistance) {\r\n const itemSize = 4;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const minX = min[0];\r\n const minY = min[1];\r\n const minZ = min[2];\r\n\r\n const maxX = max[0];\r\n const maxY = max[1];\r\n const maxZ = max[2];\r\n\r\n function hashFunc(w, minW) {\r\n return Math.floor((w - minW) / maxDistance);\r\n }\r\n\r\n const iDim = hashFunc(maxX, minX) + 1;\r\n const jDim = hashFunc(maxY, minY) + 1;\r\n const kDim = hashFunc(maxZ, minZ) + 1;\r\n\r\n const nCells = iDim * jDim * kDim;\r\n\r\n const jkDim = jDim * kDim;\r\n\r\n /* Get cellID for cartesian x,y,z */\r\n const cellID = function (x, y, z) {\r\n return (((hashFunc(x, minX) * jDim) + hashFunc(y, minY)) * kDim) + hashFunc(z, minZ);\r\n };\r\n\r\n /* Initial building, could probably be optimized further */\r\n const preHash = [];\r\n let i;\r\n let cid;\r\n for (i = 0; i < nAtoms; i++) {\r\n const iIdx = itemSize * i;\r\n cid = cellID(posRad[iIdx], posRad[iIdx + 1], posRad[iIdx + 2]);\r\n\r\n if (preHash[cid] === undefined) {\r\n preHash[cid] = [i];\r\n } else {\r\n preHash[cid].push(i);\r\n }\r\n }\r\n\r\n const cellOffsets = utils.allocateTyped(Uint32Array, nCells);\r\n const cellLengths = utils.allocateTyped(Uint16Array, nCells);\r\n const data = utils.allocateTyped(Uint32Array, nAtoms);\r\n\r\n let offset = 0;\r\n let maxCellLength = 0;\r\n let j;\r\n for (i = 0; i < nCells; i++) {\r\n const start = cellOffsets[i] = offset;\r\n\r\n const subArray = preHash[i];\r\n\r\n if (subArray !== undefined) {\r\n for (j = 0; j < subArray.length; j++) {\r\n data[offset] = subArray[j];\r\n offset++;\r\n }\r\n }\r\n\r\n const cellLength = offset - start;\r\n cellLengths[i] = cellLength;\r\n\r\n if (cellLength > maxCellLength) {\r\n maxCellLength = cellLength;\r\n }\r\n }\r\n\r\n // Maximum number of neighbours we could ever produce (27 adjacent cells of equal population)\r\n this.neighbourListLength = (27 * maxCellLength) + 1;\r\n\r\n /**\r\n * Populate the supplied out array with atom indices that are within rAtom + rExtra\r\n * of x,y,z\r\n *\r\n * -1 in out array indicates the end of the list\r\n *\r\n * @param {number} x - x coordinate\r\n * @param {number} y - y coordinate\r\n * @param {number} z - z coordinate\r\n * @param {number} rExtra - additional radius\r\n * @param {Float32Array} out - pre-allocated output array\r\n * @return {undefined}\r\n */\r\n this.withinRadii = function (x, y, z, rExtra, out) {\r\n let outIdx = 0;\r\n\r\n const nearI = hashFunc(x, minX);\r\n const nearJ = hashFunc(y, minY);\r\n const nearK = hashFunc(z, minZ);\r\n\r\n const loI = Math.max(0, nearI - 1);\r\n const loJ = Math.max(0, nearJ - 1);\r\n const loK = Math.max(0, nearK - 1);\r\n\r\n const hiI = Math.min(iDim - 1, nearI + 1);\r\n const hiJ = Math.min(jDim - 1, nearJ + 1);\r\n const hiK = Math.min(kDim - 1, nearK + 1);\r\n\r\n for (i = loI; i <= hiI; ++i) {\r\n const iOffset = i * jkDim;\r\n\r\n for (j = loJ; j <= hiJ; ++j) {\r\n const jOffset = j * kDim;\r\n\r\n for (let k = loK; k <= hiK; ++k) {\r\n cid = iOffset + jOffset + k;\r\n\r\n const cellStart = cellOffsets[cid];\r\n const cellEnd = cellStart + cellLengths[cid];\r\n\r\n for (let dataIndex = cellStart; dataIndex < cellEnd; dataIndex++) {\r\n const atomIndex = data[dataIndex];\r\n const baseIndex = itemSize * atomIndex;\r\n const dx = posRad[baseIndex] - x;\r\n const dy = posRad[baseIndex + 1] - y;\r\n const dz = posRad[baseIndex + 2] - z;\r\n const rSum = posRad[baseIndex + 3] + rExtra;\r\n\r\n if ((dx * dx + dy * dy + dz * dz) <= (rSum * rSum)) {\r\n out[outIdx++] = data[dataIndex];\r\n }\r\n }\r\n }\r\n }\r\n }\r\n // Add terminator\r\n out[outIdx] = -1;\r\n };\r\n}\r\nfunction ContactSurface(packedArrays, boundaries, params, _indexList) {\r\n // Field generation method adapted from AstexViewer (Mike Hartshorn)\r\n // by Fred Ludlow.\r\n // Other parts based heavily on NGL (Alexander Rose) EDT Surface class\r\n //\r\n // Should work as a drop-in alternative to EDTSurface (though some of\r\n // the EDT paramters are not relevant in this method).\r\n\r\n const itemSize = 4;\r\n const { posRad, colors, atoms } = packedArrays;\r\n const nAtoms = posRad.length / itemSize;\r\n\r\n const { bbox } = boundaries;\r\n\r\n const min = bbox.minPosRad;\r\n const max = bbox.maxPosRad;\r\n\r\n let r2; // Atom positions, expanded radii (squared)\r\n let maxRadius;\r\n\r\n // Parameters\r\n let probeRadius;\r\n let scaleFactor;\r\n let probePositions;\r\n\r\n // Cache last value for obscured test\r\n let lastClip = -1;\r\n\r\n // Grid params\r\n let dim;\r\n let grid;\r\n let volTex;\r\n let weights;\r\n let weightsMap = null;\r\n let atomMap = null;\r\n let visibilitySelector = null;\r\n\r\n // grid indices -> xyz coords\r\n let gridx;\r\n let gridy;\r\n let gridz;\r\n\r\n // Lookup tables:\r\n let sinTable;\r\n let cosTable;\r\n\r\n // Spatial Hash\r\n let hash;\r\n\r\n // Neighbour array to be filled by hash\r\n let neighbours;\r\n\r\n // Vectors for Torus Projection\r\n const mid = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n1 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n const n2 = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n let ngTorus;\r\n\r\n function uniformArray(TypeName, n, a) {\r\n const array = utils.allocateTyped(TypeName, n);\r\n for (let innI = 0; innI < n; ++innI) {\r\n array[innI] = a;\r\n }\r\n\r\n return array;\r\n }\r\n\r\n function fillGridDim(a, start, step) {\r\n for (let innI = 0; innI < a.length; innI++) {\r\n a[innI] = start + (step * innI);\r\n }\r\n }\r\n\r\n function initializeGrid() {\r\n ({ scaleFactor } = params);\r\n ({ dim } = boundaries);\r\n\r\n ngTorus = Math.min(5, 2 + Math.floor(probeRadius * scaleFactor));\r\n\r\n const gridSize = dim[0] * dim[1] * dim[2];\r\n grid = uniformArray(Float32Array, gridSize, -1001.0);\r\n volTex = utils.allocateTyped(Float32Array, gridSize * 3);\r\n weights = utils.allocateTyped(Float32Array, gridSize);\r\n if (visibilitySelector) {\r\n weightsMap = utils.allocateTyped(Float32Array, gridSize);\r\n atomMap = [];\r\n }\r\n\r\n gridx = utils.allocateTyped(Float32Array, dim[0]);\r\n gridy = utils.allocateTyped(Float32Array, dim[1]);\r\n gridz = utils.allocateTyped(Float32Array, dim[2]);\r\n\r\n fillGridDim(gridx, min[0], 1 / scaleFactor);\r\n fillGridDim(gridy, min[1], 1 / scaleFactor);\r\n fillGridDim(gridz, min[2], 1 / scaleFactor);\r\n }\r\n\r\n function initializeAngleTables() {\r\n let theta = 0.0;\r\n const step = 2 * Math.PI / probePositions;\r\n\r\n cosTable = utils.allocateTyped(Float32Array, probePositions);\r\n sinTable = utils.allocateTyped(Float32Array, probePositions);\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n cosTable[innI] = Math.cos(theta);\r\n sinTable[innI] = Math.sin(theta);\r\n theta += step;\r\n }\r\n }\r\n\r\n function initializeHash() {\r\n hash = new AVHash(posRad, min, max, 2.01 * maxRadius);\r\n neighbours = new Int32Array(hash.neighbourListLength);\r\n }\r\n\r\n function init() {\r\n ({\r\n probeRadius,\r\n scaleFactor,\r\n probePositions,\r\n visibilitySelector,\r\n } = params);\r\n r2 = utils.allocateTyped(Float32Array, nAtoms);\r\n maxRadius = 0;\r\n for (let innI = 0; innI < nAtoms; ++innI) {\r\n const rExt = posRad[innI * itemSize + 3] += probeRadius;\r\n if (rExt > maxRadius) {\r\n maxRadius = rExt;\r\n }\r\n r2[innI] = rExt * rExt;\r\n }\r\n\r\n initializeGrid();\r\n initializeAngleTables();\r\n initializeHash();\r\n\r\n lastClip = -1;\r\n }\r\n\r\n function singleAtomObscures(ai, innX, innY, innZ) {\r\n const innCI = itemSize * ai;\r\n const ra2 = r2[ai];\r\n const dx = posRad[innCI] - innX;\r\n const dy = posRad[innCI + 1] - innY;\r\n const dz = posRad[innCI + 2] - innZ;\r\n const d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n return d2 < ra2;\r\n }\r\n\r\n function obscured(innX, innY, innZ, a, b) {\r\n // Is the point at x,y,z obscured by any of the atoms\r\n // specifeid by indices in neighbours. Ignore indices\r\n // a and b (these are the relevant atoms in projectPoints/Torii)\r\n\r\n // Cache the last clipped atom (as very often the same one in\r\n // subsequent calls)\r\n let ai;\r\n\r\n if (lastClip !== -1) {\r\n ai = lastClip;\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n return ai;\r\n }\r\n lastClip = -1;\r\n }\r\n\r\n let ni = 0;\r\n ai = neighbours[ni];\r\n while (ai >= 0) {\r\n if (ai !== a && ai !== b && singleAtomObscures(ai, innX, innY, innZ)) {\r\n lastClip = ai;\r\n return ai;\r\n }\r\n ai = neighbours[++ni];\r\n }\r\n\r\n lastClip = -1;\r\n\r\n return -1;\r\n }\r\n\r\n function projectPoints() {\r\n // For each atom:\r\n // Iterate over a subsection of the grid, for each point:\r\n // If current value < 0.0, unvisited, set positive\r\n //\r\n // In any case: Project this point onto surface of the atomic sphere\r\n // If this projected point is not obscured by any other atom\r\n // Calcualte delta distance and set grid value to minimum of\r\n // itself and delta\r\n\r\n // Should we alias frequently accessed closure constiables??\r\n // Assume JS engine capable of optimizing this\r\n // anyway...\r\n const maxRad = 4.0;\r\n const sigma = (maxRad) / 3;\r\n const sigma2Inv = 1 / (2 * sigma * sigma);\r\n\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innCI = itemSize * innI;\r\n const ax = posRad[innCI];\r\n const ay = posRad[innCI + 1];\r\n const az = posRad[innCI + 2];\r\n const ar = posRad[innCI + 3];\r\n const ar2 = r2[innI];\r\n\r\n hash.withinRadii(ax, ay, az, ar, neighbours);\r\n\r\n // Number of grid points, round this up...\r\n const ng = Math.ceil(ar * scaleFactor);\r\n\r\n // Center of the atom, mapped to grid points (take floor)\r\n const iax = Math.floor(scaleFactor * (ax - min[0]));\r\n const iay = Math.floor(scaleFactor * (ay - min[1]));\r\n const iaz = Math.floor(scaleFactor * (az - min[2]));\r\n\r\n // Extents of grid to consider for this atom\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n // Add two to these points:\r\n // - iax are floor'd values so this ensures coverage\r\n // - these are loop limits (exclusive)\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n const colIdx = innI * 3;\r\n const cr = colors[colIdx];\r\n const cg = colors[colIdx + 1];\r\n const cb = colors[colIdx + 2];\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n const dz = gridz[iz] - az;\r\n const zOffset = dim[1] * dim[0] * iz;\r\n\r\n for (let iy = miny; iy < maxy; iy++) {\r\n const dy = gridy[iy] - ay;\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n\r\n for (let ix = minx; ix < maxx; ix++) {\r\n const idx = ix + zyOffset;\r\n const dx = gridx[ix] - ax;\r\n const d2 = dzy2 + dx * dx;\r\n\r\n if (d2 < ar2) {\r\n const w = Math.exp(-d2 * sigma2Inv);\r\n const cIdx = idx * 3;\r\n volTex[cIdx] += cr * w;\r\n volTex[cIdx + 1] += cg * w;\r\n volTex[cIdx + 2] += cb * w;\r\n weights[idx] += w;\r\n if (visibilitySelector !== null && w > weightsMap[idx]) {\r\n weightsMap[idx] = w;\r\n atomMap[idx] = atoms[innI];\r\n }\r\n\r\n if (grid[idx] < 0.0) {\r\n // Unvisited, make positive\r\n grid[idx] = -grid[idx];\r\n }\r\n // Project on to the surface of the sphere\r\n // sp is the projected point ( dx, dy, dz ) * ( ra / d )\r\n const d = Math.sqrt(d2);\r\n const ap = ar / d;\r\n let spx = dx * ap;\r\n let spy = dy * ap;\r\n let spz = dz * ap;\r\n\r\n spx += ax;\r\n spy += ay;\r\n spz += az;\r\n\r\n if (obscured(spx, spy, spz, innI, -1) === -1) {\r\n const dd = ar - d;\r\n if (dd < grid[idx]) {\r\n grid[idx] = dd;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function normalToLine(out, p) {\r\n out.x = out.y = out.z = 1.0;\r\n if (p.x !== 0) {\r\n out.x = (p.y + p.z) / -p.x;\r\n } else if (p.y !== 0) {\r\n out.y = (p.x + p.z) / -p.y;\r\n } else if (p.z !== 0) {\r\n out.z = (p.x + p.y) / -p.z;\r\n }\r\n return out;\r\n }\r\n\r\n function projectTorus(a, b) {\r\n const aIdx = itemSize * a;\r\n const bIdx = itemSize * b;\r\n const xa = posRad[aIdx];\r\n const ya = posRad[aIdx + 1];\r\n const za = posRad[aIdx + 2];\r\n const r1 = posRad[aIdx + 3];\r\n let dx = mid.x = posRad[bIdx] - xa;\r\n let dy = mid.y = posRad[bIdx + 1] - ya;\r\n let dz = mid.z = posRad[bIdx + 2] - za;\r\n const innR2 = posRad[bIdx + 3];\r\n let d2 = dx * dx + dy * dy + dz * dz;\r\n\r\n // This check now redundant as already done in AVHash.withinRadii\r\n // if( d2 > (( r1 + r2 ) * ( r1 + r2 )) ){ return; }\r\n\r\n const d = Math.sqrt(d2);\r\n\r\n // Find angle between a->b vector and the circle\r\n // of their intersection by cosine rule\r\n const cosA = (r1 * r1 + d * d - innR2 * innR2) / (2.0 * r1 * d);\r\n\r\n // distance along a->b at intersection\r\n const dmp = r1 * cosA;\r\n\r\n mid.normalize();\r\n\r\n // Create normal to line\r\n normalToLine(n1, mid);\r\n n1.normalize();\r\n\r\n // Cross together for second normal vector\r\n n2.crossVectors(mid, n1);\r\n n2.normalize();\r\n\r\n // r is radius of circle of intersection\r\n const rInt = Math.sqrt(r1 * r1 - dmp * dmp);\r\n\r\n n1.multiplyScalar(rInt);\r\n n2.multiplyScalar(rInt);\r\n mid.multiplyScalar(dmp);\r\n\r\n mid.x += xa;\r\n mid.y += ya;\r\n mid.z += za;\r\n\r\n lastClip = -1;\r\n\r\n const ng = ngTorus;\r\n\r\n for (let innI = 0; innI < probePositions; innI++) {\r\n const cost = cosTable[innI];\r\n const sint = sinTable[innI];\r\n\r\n const px = mid.x + cost * n1.x + sint * n2.x;\r\n const py = mid.y + cost * n1.y + sint * n2.y;\r\n const pz = mid.z + cost * n1.z + sint * n2.z;\r\n\r\n if (obscured(px, py, pz, a, b) === -1) {\r\n // As above, iterate over our grid...\r\n // px, py, pz in grid coords\r\n const iax = Math.floor(scaleFactor * (px - min[0]));\r\n const iay = Math.floor(scaleFactor * (py - min[1]));\r\n const iaz = Math.floor(scaleFactor * (pz - min[2]));\r\n\r\n const minx = Math.max(0, iax - ng);\r\n const miny = Math.max(0, iay - ng);\r\n const minz = Math.max(0, iaz - ng);\r\n\r\n const maxx = Math.min(dim[0], iax + ng + 2);\r\n const maxy = Math.min(dim[1], iay + ng + 2);\r\n const maxz = Math.min(dim[2], iaz + ng + 2);\r\n\r\n for (let iz = minz; iz < maxz; iz++) {\r\n dz = pz - gridz[iz];\r\n const zOffset = dim[1] * dim[0] * iz;\r\n for (let iy = miny; iy < maxy; iy++) {\r\n dy = py - gridy[iy];\r\n const dzy2 = dz * dz + dy * dy;\r\n const zyOffset = zOffset + dim[0] * iy;\r\n for (let ix = minx; ix < maxx; ix++) {\r\n dx = px - gridx[ix];\r\n d2 = dzy2 + dx * dx;\r\n const idx = ix + zyOffset;\r\n const current = grid[idx];\r\n\r\n if (current > 0.0 && d2 < (current * current)) {\r\n grid[idx] = Math.sqrt(d2);\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n function projectTorii() {\r\n for (let innI = 0; innI < nAtoms; innI++) {\r\n const innIdx = itemSize * innI;\r\n hash.withinRadii(\r\n posRad[innIdx],\r\n posRad[innIdx + 1],\r\n posRad[innIdx + 2],\r\n posRad[innIdx + 3],\r\n neighbours,\r\n );\r\n let ia = 0;\r\n let ni = neighbours[ia];\r\n while (ni >= 0) {\r\n if (innI < ni) {\r\n projectTorus(innI, ni);\r\n }\r\n ni = neighbours[++ia];\r\n }\r\n }\r\n }\r\n\r\n function fixNegatives() {\r\n for (let innI = 0, n = grid.length; innI < n; innI++) {\r\n if (grid[innI] < 0) grid[innI] = 0;\r\n let w = weights[innI];\r\n if (w > 0) {\r\n w = 1 / w;\r\n const innInnI = innI * 3;\r\n volTex[innInnI] *= w;\r\n volTex[innInnI + 1] *= w;\r\n volTex[innInnI + 2] *= w;\r\n }\r\n }\r\n }\r\n\r\n function getVolume() {\r\n // Basic steps are:\r\n // 1) Initialize\r\n // 2) Project points\r\n // 3) Project torii\r\n console.time('ContactSurface.getVolume');\r\n\r\n console.time('ContactSurface.init');\r\n init();\r\n console.timeEnd('ContactSurface.init');\r\n\r\n console.time('ContactSurface.projectPoints');\r\n projectPoints();\r\n console.timeEnd('ContactSurface.projectPoints');\r\n\r\n console.time('ContactSurface.projectTorii');\r\n projectTorii();\r\n console.timeEnd('ContactSurface.projectTorii');\r\n fixNegatives();\r\n console.timeEnd('ContactSurface.getVolume');\r\n }\r\n\r\n this.build = function () {\r\n // type and cutoff left in for compatibility with EDTSurface.getSurface\r\n // function signature\r\n getVolume();\r\n this.volTexMap = volTex;\r\n this.weightsMap = weightsMap;\r\n this.atomMap = atomMap;\r\n this.volMap = grid;\r\n };\r\n}\r\nexport default ContactSurface;\r\n","import VolumeSurfaceGeometry from './VolumeSurfaceGeometry';\r\nimport ContactSurface from './ContactSurface';\r\nimport chem from '../../chem';\r\n\r\nconst { Volume } = chem;\r\n\r\n/**\r\n * This class implements 'contact' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass ContactSurfaceGeometry extends VolumeSurfaceGeometry {\r\n _computeSurface(packedArrays, box, boundaries, params) {\r\n const contactSurface = new ContactSurface(packedArrays, boundaries, params);\r\n contactSurface.build();\r\n\r\n const surface = {\r\n volMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.volMap),\r\n volTexMap: new Volume(Float32Array, this.numVoxels, box, 3, contactSurface.volTexMap),\r\n atomMap: contactSurface.atomMap,\r\n atomWeightMap: new Volume(Float32Array, this.numVoxels, box, 1, contactSurface.weightsMap),\r\n };\r\n return surface;\r\n }\r\n}\r\n\r\nexport default ContactSurfaceGeometry;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for colored atom. Need for atom structure clusterization\r\n *\r\n * @param {Vector3} vCenter Center of atom\r\n * @param {number} radiusAt Radius of atom\r\n */\r\nclass IsoSurfaceAtomColored {\r\n constructor(vCenter, radiusAt) {\r\n this.coord = new THREE.Vector3();\r\n this.coord.copy(vCenter);\r\n this.radius = radiusAt;\r\n this.colorX = 0.99999;\r\n this.colorY = 0.0;\r\n this.colorZ = 0.0;\r\n this.atomType = 0;\r\n this.srcAtom = null;\r\n }\r\n}\r\nexport default IsoSurfaceAtomColored;\r\n","import * as THREE from 'three';\r\nimport utils from '../../utils';\r\n\r\n// suppress some JSHint warnings\r\n/* jshint bitwise: false */\r\n\r\n/**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numAtoms - Number of atoms in molecule\r\n * @param {Element} atoms - Array of atoms\r\n * @param {Vector3} vBoxMin - Bounding box min\r\n * @param {Vector3} vBoxMax - Bounding box max\r\n * @param {number} probeRadius - Normals for output\r\n *\r\n */\r\nclass IsosurfaceBuildNormals {\r\n constructor(numAtoms, atoms, vBoxMin, vBoxMax, probeRadius) {\r\n this._numAtoms = numAtoms;\r\n this._atoms = atoms;\r\n this._vBoxMin = new THREE.Vector3();\r\n this._vBoxMax = new THREE.Vector3();\r\n this._vBoxMin.copy(vBoxMin);\r\n this._vBoxMax.copy(vBoxMax);\r\n this._probeRadius = probeRadius;\r\n\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n }\r\n\r\n createVoxels() {\r\n let numAtomsRefs;\r\n let rad;\r\n const ATOM_VOXEL_REF_SCALE = 4.5;\r\n\r\n const numAtoms = this._numAtoms | 0;\r\n const atoms = this._atoms;\r\n const dx = this._vBoxMax.x - this._vBoxMin.x;\r\n const dy = this._vBoxMax.y - this._vBoxMin.y;\r\n const dz = this._vBoxMax.z - this._vBoxMin.z;\r\n let w = (dx < dy) ? dx : dy;\r\n w = (dz < w) ? dz : w;\r\n let maxRad = 0.0;\r\n let aveRad = 0.0;\r\n\r\n let i;\r\n for (i = 0; i < numAtoms; i++) {\r\n rad = (atoms[i].radius + this._probeRadius) * 2.0;\r\n maxRad = (rad > maxRad) ? rad : maxRad;\r\n aveRad += rad;\r\n }\r\n let numCells = Math.floor(w / maxRad);\r\n if (numCells < 2) {\r\n numCells = 2;\r\n }\r\n aveRad /= numAtoms;\r\n\r\n this._numCells = numCells;\r\n this._aveRad = aveRad;\r\n this._maxRad = maxRad;\r\n\r\n const side = numCells;\r\n const side2 = numCells * numCells;\r\n const side3 = numCells * numCells * numCells;\r\n\r\n const xScale = this._xScale = 1.0 / (this._vBoxMax.x - this._vBoxMin.x);\r\n const yScale = this._yScale = 1.0 / (this._vBoxMax.y - this._vBoxMin.y);\r\n const zScale = this._zScale = 1.0 / (this._vBoxMax.z - this._vBoxMin.z);\r\n\r\n // estimate number of individual atom refs in each voxel list\r\n let maxAtomsRefs = 0;\r\n\r\n const xNumVoxMult = xScale * numCells;\r\n const yNumVoxMult = yScale * numCells;\r\n const zNumVoxMult = zScale * numCells;\r\n\r\n for (i = 0; i < numAtoms; i++) {\r\n const radAffect = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n const diaAffect = radAffect * 2.0;\r\n let numVoxX = Math.floor(xNumVoxMult * diaAffect + 0.8);\r\n let numVoxY = Math.floor(yNumVoxMult * diaAffect + 0.8);\r\n let numVoxZ = Math.floor(zNumVoxMult * diaAffect + 0.8);\r\n // avoid case numVox? == 0\r\n // also use loop i <=\r\n numVoxX++;\r\n numVoxY++;\r\n numVoxZ++;\r\n maxAtomsRefs += numVoxX * numVoxY * numVoxZ;\r\n } // for (i)\r\n // maxAtomsRefs = numAtoms * MAX_ATOMS_IN_SINGLE_VOXEL;\r\n\r\n this._voxelList = utils.allocateTyped(Int32Array, side3);\r\n const atomsList = [];\r\n atomsList.length = maxAtomsRefs;\r\n if ((this._voxelList === null) || (atomsList === null)) {\r\n return 0 - 1;\r\n }\r\n // init voxel list\r\n for (i = 0; i < side3; i++) {\r\n this._voxelList[i] = -1;\r\n }\r\n numAtomsRefs = 0;\r\n\r\n // create voxel lists\r\n for (i = 0; i < numAtoms; i++) {\r\n // use multiplier 4 to locate this atom in different voxels\r\n rad = (atoms[i].radius + this._probeRadius) * ATOM_VOXEL_REF_SCALE;\r\n let xIndMin = Math.floor((atoms[i].coord.x - this._vBoxMin.x - rad) * numCells * xScale);\r\n let yIndMin = Math.floor((atoms[i].coord.y - this._vBoxMin.y - rad) * numCells * yScale);\r\n let zIndMin = Math.floor((atoms[i].coord.z - this._vBoxMin.z - rad) * numCells * zScale);\r\n let xIndMax = Math.floor((atoms[i].coord.x - this._vBoxMin.x + rad) * numCells * xScale);\r\n let yIndMax = Math.floor((atoms[i].coord.y - this._vBoxMin.y + rad) * numCells * yScale);\r\n let zIndMax = Math.floor((atoms[i].coord.z - this._vBoxMin.z + rad) * numCells * zScale);\r\n\r\n xIndMin = (xIndMin >= 0) ? xIndMin : 0;\r\n yIndMin = (yIndMin >= 0) ? yIndMin : 0;\r\n zIndMin = (zIndMin >= 0) ? zIndMin : 0;\r\n\r\n xIndMax = (xIndMax < numCells) ? xIndMax : (numCells - 1);\r\n yIndMax = (yIndMax < numCells) ? yIndMax : (numCells - 1);\r\n zIndMax = (zIndMax < numCells) ? zIndMax : (numCells - 1);\r\n\r\n for (let z = zIndMin; z <= zIndMax; z++) {\r\n for (let y = yIndMin; y <= yIndMax; y++) {\r\n for (let x = xIndMin; x <= xIndMax; x++) {\r\n // add atom with index \"i\" to this voxel list\r\n const indVoxel = x + y * side + z * side2;\r\n // assert indVoxel >= 0\r\n // assert indVoxel < side3\r\n\r\n // add first\r\n if (this._voxelList[indVoxel] < 0) {\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = 0 - 1;\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n numAtomsRefs++;\r\n // assert numAtomsRefs < maxAtomsRefs - 1\r\n continue;\r\n }\r\n // insert into head of list\r\n const indexNext = this._voxelList[indVoxel];\r\n this._voxelList[indVoxel] = numAtomsRefs;\r\n atomsList[numAtomsRefs * 2 + 0] = i;\r\n atomsList[numAtomsRefs * 2 + 1] = indexNext;\r\n numAtomsRefs++;\r\n } // for (x)\r\n } // for (y)\r\n } // for (z)\r\n } // for (i)\r\n\r\n // convert Array to Int32Array\r\n this._atomsList = Int32Array.from(atomsList);\r\n\r\n return 0;\r\n }\r\n\r\n destroyVoxels() {\r\n this._atomsList = null;\r\n this._voxelList = null;\r\n\r\n this._atoms = null;\r\n this._vertices = null;\r\n this._vBoxMin = null;\r\n this._vBoxMax = null;\r\n }\r\n\r\n /**\r\n * Enumerate all atoms affecting specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n * @param {func(atom)} process - function to call for each atom\r\n */\r\n forEachRelatedAtom(point, process) {\r\n // find corresponding voxel\r\n const xInd = Math.floor((point.x - this._vBoxMin.x) * this._numCells * this._xScale);\r\n const yInd = Math.floor((point.y - this._vBoxMin.y) * this._numCells * this._yScale);\r\n const zInd = Math.floor((point.z - this._vBoxMin.z) * this._numCells * this._zScale);\r\n const indVoxel = xInd + yInd * this._numCells + zInd * this._numCells * this._numCells;\r\n\r\n // run through atoms affecting this voxel\r\n const atoms = this._atoms;\r\n for (let ref = this._voxelList[indVoxel]; ref >= 0; ref = this._atomsList[ref * 2 + 1]) {\r\n const indexAtom = this._atomsList[ref * 2];\r\n process(atoms[indexAtom]);\r\n }\r\n }\r\n\r\n /**\r\n * Get atom closest to specified point\r\n *\r\n * @param {Vector3} point - point in 3D\r\n *\r\n * @returns {IsoSurfaceAtomColored} atom, or null if not found\r\n */\r\n getClosestAtom(point) {\r\n let closest = null;\r\n let minDist2 = Number.MAX_VALUE;\r\n\r\n this.forEachRelatedAtom(point, (atom) => {\r\n const dist2 = point.distanceToSquared(atom.coord);\r\n if (dist2 < minDist2) {\r\n minDist2 = dist2;\r\n closest = atom;\r\n }\r\n });\r\n\r\n return closest;\r\n }\r\n\r\n /**\r\n * Build normals for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} normals - Normals for output\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildNormals(numVertices, vertices, normals) {\r\n const self = this;\r\n let numCloseAtoms = 0;\r\n let vx = 0;\r\n let vy = 0;\r\n let vz = 0;\r\n let dist2;\r\n let vNormalX = 0;\r\n let vNormalY = 0;\r\n let vNormalZ = 0;\r\n let koef = 0;\r\n let w = 0;\r\n const r25 = 2.5;\r\n const r01 = 0.1;\r\n\r\n const maxRadAffect = this._aveRad * r25;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n const expScale = -this._aveRad * r01;\r\n\r\n // some stats\r\n // numSlowAtoms = 0;\r\n\r\n const gatherNormals = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = Math.exp(expScale * koef);\r\n\r\n vNormalX += dx * w;\r\n vNormalY += dy * w;\r\n vNormalZ += dz * w;\r\n numCloseAtoms++;\r\n };\r\n\r\n let maxClosedAtoms = 0;\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n numCloseAtoms = 0;\r\n vNormalX = vNormalY = vNormalZ = 0.0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherNormals);\r\n\r\n maxClosedAtoms = (numCloseAtoms > maxClosedAtoms) ? numCloseAtoms : maxClosedAtoms;\r\n\r\n // normalize vNormal\r\n dist2 = vNormalX * vNormalX + vNormalY * vNormalY + vNormalZ * vNormalZ;\r\n if (numCloseAtoms > 0) {\r\n koef = 1.0 / Math.sqrt(dist2);\r\n vNormalX *= koef;\r\n vNormalY *= koef;\r\n vNormalZ *= koef;\r\n }\r\n normals[i].x = vNormalX;\r\n normals[i].y = vNormalY;\r\n normals[i].z = vNormalZ;\r\n } // for (i) all vertices\r\n\r\n return 0;\r\n }\r\n\r\n /**\r\n * Build vertex colors for isosurface, using atoms information\r\n *\r\n * @param {number} numVertices - Number of vertices in final geometry (to render)\r\n * @param {Vector3} vertices - Geometry vertices (3d coordinates array)\r\n * @param {Vector3} colors - Colors for output\r\n * @param {number} radiusColorSmoothness - Radius of smoothness sphere\r\n *\r\n * @returns {number} 0, if success\r\n */\r\n buildColors(numVertices, vertices, colors, radiusColorSmoothness) {\r\n const self = this;\r\n let vx = 0.0;\r\n let vy = 0.0;\r\n let vz = 0.0;\r\n let koef = 0.0;\r\n let w = 0.0;\r\n const KOEF_ADD = 0.8;\r\n\r\n const maxRadAffect = radiusColorSmoothness;\r\n const maxRadAffect2 = maxRadAffect * maxRadAffect;\r\n\r\n let colorsClose = [];\r\n let weights = [];\r\n let weightsSum = 0;\r\n\r\n const gatherColors = function (atom) {\r\n const dx = vx - atom.coord.x;\r\n const dy = vy - atom.coord.y;\r\n const dz = vz - atom.coord.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 > maxRadAffect2) {\r\n return;\r\n }\r\n\r\n // get weight for gaussian smoothing\r\n const rad = atom.radius + self._probeRadius;\r\n koef = dist2 - (rad * rad);\r\n if (koef < 0.0) {\r\n koef = -koef;\r\n }\r\n w = 1.0 / (KOEF_ADD + koef);\r\n\r\n colorsClose.push([atom.colorX, atom.colorY, atom.colorZ]);\r\n weights.push(w); // save weights for use\r\n weightsSum += w; // calc sum of weights fo further normalization\r\n };\r\n\r\n // process all vertices, one by one\r\n for (let i = 0; i < numVertices; i++) {\r\n vx = vertices[i].x;\r\n vy = vertices[i].y;\r\n vz = vertices[i].z;\r\n\r\n colorsClose = [];\r\n weights = [];\r\n weightsSum = 0;\r\n\r\n this.forEachRelatedAtom(vertices[i], gatherColors);\r\n\r\n // normalized weighted sum of colors\r\n for (let j = 0; j < colorsClose.length; ++j) {\r\n const weightNormalized = weights[j] / weightsSum;\r\n colors[i].x += colorsClose[j][0] * weightNormalized;\r\n colors[i].y += colorsClose[j][1] * weightNormalized;\r\n colors[i].z += colorsClose[j][2] * weightNormalized;\r\n }\r\n } // for (i) all vertices\r\n return 0;\r\n }\r\n}\r\nexport default IsosurfaceBuildNormals;\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Class for geometry (triangle mesh) representation\r\n *\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices in mesh\r\n * @param {number} maxNumTriangles Maximum possible number of triangles in mesh\r\n * @param {boolean} needVertexColors Obvious\r\n */\r\nclass IsoSurfaceGeo {\r\n constructor(maxNumVertices, maxNumTriangles, needVertexColors) {\r\n this._maxNumVertices = maxNumVertices;\r\n this._maxNumTriangles = maxNumTriangles;\r\n this._vertices = new Array(maxNumVertices);\r\n this._normals = new Array(maxNumVertices);\r\n this._colors = null;\r\n if (needVertexColors) {\r\n this._colors = new Array(maxNumVertices);\r\n }\r\n this._indices = new Array(maxNumTriangles * (1 + 2));\r\n this._numVertices = 0;\r\n this._numTriangles = 0;\r\n\r\n let i;\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._vertices[i] = new THREE.Vector3();\r\n this._normals[i] = new THREE.Vector3();\r\n }\r\n for (i = 0; i < maxNumTriangles * (1 + 2); i++) {\r\n this._indices[i] = -1;\r\n }\r\n if (needVertexColors) {\r\n for (i = 0; i < maxNumVertices; i++) {\r\n this._colors[i] = new THREE.Vector3();\r\n }\r\n }\r\n }\r\n\r\n destroy() {\r\n this._vertices = null;\r\n this._normals = null;\r\n this._indices = null;\r\n }\r\n}\r\nexport default IsoSurfaceGeo;\r\n","import * as THREE from 'three';\r\nimport IsoSurfaceGeometry from './IsoSurfaceGeometry';\r\nimport IsoSurfaceAtomColored from './IsoSurfaceAtomColored';\r\nimport IsosurfaceBuildNormals from './IsosurfaceBuildNormals';\r\nimport IsoSurfaceMarchCube from './IsoSurfaceMarchCube';\r\nimport IsoSurfaceGeo from './IsoSurfaceGeo';\r\nimport chem from '../../chem';\r\nimport utils from '../../utils';\r\n\r\nconst COLOR_SIZE = 3;\r\nconst HASH_SIZE = 32768;\r\nconst { Element } = chem;\r\n\r\n/**\r\n * This class implements 'quick' isosurface geometry generation algorithm.\r\n * @param spheresCount - number of atoms/spheres\r\n * @param opts - geometry specific options\r\n * @constructor\r\n */\r\n\r\nclass SSIsosurfaceGeometry extends IsoSurfaceGeometry {\r\n _build() {\r\n // convert geoOut into arrays of positions, indices, normals\r\n this._innerBuild();\r\n const geoOut = this.getGeo();\r\n this.destroy();\r\n this._fromGeo(geoOut);\r\n }\r\n\r\n _fromGeo(geoOut) {\r\n let colors = null;\r\n const positions = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n const normals = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n if (geoOut._colors !== null) {\r\n colors = utils.allocateTyped(Float32Array, (1 + 2) * geoOut._numVertices);\r\n }\r\n const indices = utils.allocateTyped(Uint32Array, (1 + 2) * geoOut._numTriangles);\r\n\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++) {\r\n positions[j + 0] = (geoOut._vertices[i].x);\r\n positions[j + 1] = (geoOut._vertices[i].y);\r\n positions[j + 2] = (geoOut._vertices[i].z);\r\n normals[j + 0] = geoOut._normals[i].x;\r\n normals[j + 1] = geoOut._normals[i].y;\r\n normals[j + 2] = geoOut._normals[i].z;\r\n j += 3;\r\n }\r\n if (colors !== null) {\r\n for (let i = 0, j = 0; i < geoOut._numVertices; i++, j += 3) {\r\n colors[j + 0] = geoOut._colors[i].x;\r\n colors[j + 1] = geoOut._colors[i].y;\r\n colors[j + 2] = geoOut._colors[i].z;\r\n }\r\n }\r\n\r\n const numTri3 = geoOut._numTriangles * (1 + 2);\r\n for (let i = 0; i < numTri3; i++) {\r\n indices[i] = geoOut._indices[i];\r\n }\r\n\r\n this.setIndex(new THREE.BufferAttribute(indices, 1));\r\n this.setAttribute('position', new THREE.BufferAttribute(positions, 3));\r\n this.setAttribute('normal', new THREE.BufferAttribute(normals, 3));\r\n this.setAttribute('color', new THREE.BufferAttribute(colors, 3));\r\n this.computeBoundingBox();\r\n this.computeBoundingSphere();\r\n\r\n geoOut.destroy();\r\n }\r\n\r\n convertToAtomsColored(packedArrays, atomsColored) {\r\n const { atoms, colors } = packedArrays;\r\n for (let i = 0, numAtoms = atoms.length; i < numAtoms; i++) {\r\n const vCenter = atoms[i].position;\r\n const { radius } = atoms[i].element;\r\n atomsColored[i] = new IsoSurfaceAtomColored(vCenter, radius);\r\n const nm = atoms[i].element.number;\r\n atomsColored[i].atomType = this.getType(nm);\r\n let cIdx = COLOR_SIZE * i;\r\n atomsColored[i].colorX = colors[cIdx++];\r\n atomsColored[i].colorY = colors[cIdx++];\r\n atomsColored[i].colorZ = colors[cIdx];\r\n atomsColored[i].srcAtom = atoms[i];\r\n }\r\n }\r\n\r\n getGeo() {\r\n return this.geoOut;\r\n }\r\n\r\n destroy() {\r\n this.atoms = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n }\r\n\r\n /**\r\n * Calculates bounding box for array with spheres (atoms)\r\n *\r\n * @param {Object} atoms Atoms array\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n */\r\n getBoundingBox(atoms, vBoxMin, vBoxMax) {\r\n const bigNum = 10000000.0;\r\n\r\n vBoxMin.x = vBoxMin.y = vBoxMin.z = bigNum;\r\n vBoxMax.x = vBoxMax.y = vBoxMax.z = 0 - bigNum;\r\n\r\n const probeRadius2 = this.probeRadius * this.atomRadiusScale;\r\n let radMax = 0.0;\r\n for (let i = 0, num = atoms.length; i < num; i++) {\r\n const vCenter = atoms[i].coord;\r\n const rad = atoms[i].radius + probeRadius2;\r\n radMax = (rad > radMax) ? rad : radMax;\r\n if (vCenter.x - rad < vBoxMin.x) {\r\n vBoxMin.x = vCenter.x - rad;\r\n }\r\n if (vCenter.y - rad < vBoxMin.y) {\r\n vBoxMin.y = vCenter.y - rad;\r\n }\r\n if (vCenter.z - rad < vBoxMin.z) {\r\n vBoxMin.z = vCenter.z - rad;\r\n }\r\n if (vCenter.x + rad > vBoxMax.x) {\r\n vBoxMax.x = vCenter.x + rad;\r\n }\r\n if (vCenter.y + rad > vBoxMax.y) {\r\n vBoxMax.y = vCenter.y + rad;\r\n }\r\n if (vCenter.z + rad > vBoxMax.z) {\r\n vBoxMax.z = vCenter.z + rad;\r\n }\r\n }\r\n vBoxMin.x -= radMax;\r\n vBoxMin.y -= radMax;\r\n vBoxMin.z -= radMax;\r\n vBoxMax.x += radMax;\r\n vBoxMax.y += radMax;\r\n vBoxMax.z += radMax;\r\n }\r\n\r\n /**\r\n * Calculate (x,y,z) cordinate of the cell corner point\r\n *\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {number} x Cell integer x coordinate\r\n * @param {number} y Cell integer y coordinate\r\n * @param {number} z Cell integer z coordinate\r\n * @param {number} numPoints NUm points in cell on side\r\n * @param {Vector3} vOut Output vector\r\n */\r\n getCornerCoord(vBoxMin, vBoxMax, x, y, z, numPoints, vOut) {\r\n const invNP = 1.0 / (numPoints - 1.0);\r\n const tx = x * invNP;\r\n const ty = y * invNP;\r\n const tz = z * invNP;\r\n\r\n vOut.x = vBoxMin.x * (1.0 - tx) + vBoxMax.x * tx;\r\n vOut.y = vBoxMin.y * (1.0 - ty) + vBoxMax.y * ty;\r\n vOut.z = vBoxMin.z * (1.0 - tz) + vBoxMax.z * tz;\r\n }\r\n\r\n /**\r\n * Calculate point of intersection of sphere surface\r\n * and cell edge, given by [indexA, indexB] line\r\n *\r\n * @param {number} indexA Cell vertex index in [0..11]\r\n * @param {number} indexB Cell vertex index in [0..11]\r\n * @param {array} sign Sign array for all 8 vertices\r\n * @param {object} cube Cube\r\n * @param {number} indexPointValue for value placement\r\n * @param {Vector3} vOut Point of intersection\r\n */\r\n buildEdgePoint(indexA, indexB, sign, cube, indexPointValue, vOut) {\r\n if (sign[indexA] ^ sign[indexB]) {\r\n const cTwentyFour = 24;\r\n const t = (0 - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA])\r\n / (cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexB]\r\n - cube.pointsValuesLinear[indexPointValue + cTwentyFour + indexA]);\r\n const xa = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 0];\r\n const ya = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 1];\r\n const za = cube.pointsValuesLinear[indexPointValue + indexA * (2 + 1) + 2];\r\n const xb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 0];\r\n const yb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 1];\r\n const zb = cube.pointsValuesLinear[indexPointValue + indexB * (2 + 1) + 2];\r\n\r\n vOut.x = xa * (1.0 - t) + xb * t;\r\n vOut.y = ya * (1.0 - t) + yb * t;\r\n vOut.z = za * (1.0 - t) + zb * t;\r\n }\r\n }\r\n\r\n /**\r\n * Check if triangle is visible (vertices are close to atoms included in visibility set)\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} true if triangle is visible\r\n */\r\n isTriangleVisible(v0, v1, v2) {\r\n const a0 = this.voxelWorld.getClosestAtom(v0);\r\n const a1 = this.voxelWorld.getClosestAtom(v1);\r\n const a2 = this.voxelWorld.getClosestAtom(v2);\r\n if (a0 === null || a1 === null || a2 === null\r\n || a0.srcAtom === null || a1.srcAtom === null || a2.srcAtom === null) {\r\n return false;\r\n }\r\n\r\n return this.visibilitySelector.includesAtom(a0.srcAtom)\r\n && this.visibilitySelector.includesAtom(a1.srcAtom)\r\n && this.visibilitySelector.includesAtom(a2.srcAtom);\r\n }\r\n\r\n /**\r\n * Add triangle to result geometry\r\n *\r\n * @param {Vector3} v0 Vertex #0\r\n * @param {Vector3} v1 Vertex #1\r\n * @param {Vector3} v2 Vertex #2\r\n * @returns {boolean} false if no more triangles can be added\r\n */\r\n addTriangle(v0, v1, v2) {\r\n if (this.visibilitySelector && !this.isTriangleVisible(v0, v1, v2)) {\r\n return true;\r\n }\r\n\r\n const geo = this.geoOut;\r\n\r\n if (geo._numTriangles >= this.maxNumTriangles) {\r\n return false;\r\n }\r\n\r\n // Add vertex with optimize\r\n const indInGeo0 = this.addVertexToGeo(geo, v0);\r\n const indInGeo1 = this.addVertexToGeo(geo, v1);\r\n const indInGeo2 = this.addVertexToGeo(geo, v2);\r\n if ((indInGeo0 | indInGeo1 | indInGeo2) < 0) {\r\n return false;\r\n }\r\n\r\n const itr = 3 * geo._numTriangles;\r\n geo._indices[itr + 0] = indInGeo0;\r\n geo._indices[itr + 1] = indInGeo1;\r\n geo._indices[itr + 2] = indInGeo2;\r\n geo._numTriangles++;\r\n return true;\r\n }\r\n\r\n /**\r\n * Build result geometry (triangle mesh) from marching cube cells\r\n *\r\n * @param {number} meshRes Marchnig cube vertex count on each side\r\n * @param {Vector3} vBoxMin Bounding box point min\r\n * @param {Vector3} vBoxMax Bounding box point max\r\n * @param {number} corners float values array for each cube point\r\n * @param {Vector3} vCellStep vector to next cube cell diagonal point\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} 0, if success (<0) is error\r\n */\r\n buildGeoFromCorners(meshRes, vBoxMin, vBoxMax, corners, vCellStep, cube) {\r\n const arrSize = 12;\r\n const cNumVerts = 8;\r\n const numCells = meshRes - 1;\r\n const side = meshRes;\r\n const side2 = meshRes * meshRes;\r\n\r\n const vaEdges = new Array(arrSize);\r\n for (let i = 0; i < arrSize; i++) {\r\n vaEdges[i] = new THREE.Vector3();\r\n }\r\n const sign = [];\r\n for (let i = 0; i < cNumVerts; i++) {\r\n sign[i] = 1.0;\r\n }\r\n const vCorner = new THREE.Vector3();\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n if (!cube.hasIntersection[indCell]) {\r\n // next cell\r\n indCell++;\r\n continue;\r\n }\r\n const bitsInside = cube.bitsInside[indCell];\r\n\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, meshRes, vCorner);\r\n\r\n const indPointValues = indCell * (2 << (2 + 2));\r\n for (let i = 0, j = 0; i < cNumVerts; i++) {\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.x;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.y;\r\n cube.pointsValuesLinear[indPointValues + j++] = vCorner.z;\r\n }\r\n\r\n cube.pointsValuesLinear[indPointValues + 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 2 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3] += vCellStep.x;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3] += vCellStep.x;\r\n\r\n cube.pointsValuesLinear[indPointValues + 2 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 3 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 2] += vCellStep.z;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 2] += vCellStep.z;\r\n\r\n cube.pointsValuesLinear[indPointValues + 4 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 5 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 6 * 3 + 1] += vCellStep.y;\r\n cube.pointsValuesLinear[indPointValues + 7 * 3 + 1] += vCellStep.y;\r\n\r\n // now current cell has intersections (from -x to +x) on some cube edges\r\n const indValues = indPointValues + 24;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n sign[i] = (cube.pointsValuesLinear[indValues + i] < 0.0) ? 1 : 0;\r\n }\r\n\r\n this.buildEdgePoint(0, 1, sign, cube, indPointValues, vaEdges[0]);\r\n this.buildEdgePoint(1, 2, sign, cube, indPointValues, vaEdges[1]);\r\n this.buildEdgePoint(2, 3, sign, cube, indPointValues, vaEdges[2]);\r\n this.buildEdgePoint(3, 0, sign, cube, indPointValues, vaEdges[3]);\r\n\r\n this.buildEdgePoint(4, 5, sign, cube, indPointValues, vaEdges[4]);\r\n this.buildEdgePoint(5, 6, sign, cube, indPointValues, vaEdges[5]);\r\n this.buildEdgePoint(6, 7, sign, cube, indPointValues, vaEdges[6]);\r\n this.buildEdgePoint(7, 4, sign, cube, indPointValues, vaEdges[7]);\r\n\r\n this.buildEdgePoint(0, 4, sign, cube, indPointValues, vaEdges[8]);\r\n this.buildEdgePoint(1, 5, sign, cube, indPointValues, vaEdges[9]);\r\n this.buildEdgePoint(2, 6, sign, cube, indPointValues, vaEdges[10]);\r\n this.buildEdgePoint(3, 7, sign, cube, indPointValues, vaEdges[11]);\r\n\r\n const offs = bitsInside * (2 << (1 + 2));\r\n for (let numTri = 0, indTri = 0; numTri < (2 + 2 + 2); numTri++, indTri += 3) {\r\n // s_triIndicesMarchCube is external array, defined in mold_ind.js\r\n const i0 = cube.striIndicesMarchCube[offs + indTri];\r\n if (i0 < 0) {\r\n break;\r\n }\r\n const i1 = cube.striIndicesMarchCube[offs + indTri + 1];\r\n const i2 = cube.striIndicesMarchCube[offs + indTri + 2];\r\n\r\n if (!this.addTriangle(vaEdges[i0], vaEdges[i1], vaEdges[i2])) {\r\n return 0 - 2;\r\n }\r\n } // for numTri\r\n\r\n // next cell (cube)\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return 0;\r\n }\r\n\r\n /**\r\n * Returns number of cell with intersection with at least one sphere.\r\n * Using this number, we can estimate required number of vertices\r\n * and triangles to build result mesh.\r\n *\r\n * @param {number} side Number of points in cube voxels\r\n * @param {number} numCells Number of cells in cube voxels (per direction)\r\n * @param {array} corners Array of float values for cube corner points\r\n * @param {object} cube IsoSurfaceMarchCube object\r\n * @returns {number} numIntersectedCells\r\n */\r\n getNumIntersectedCells(side, numCells, corners, cube) {\r\n const side2 = side * side;\r\n const cNumVerts = 8;\r\n let numIntersectedCells = 0;\r\n\r\n let indCell = 0;\r\n let indY = 0;\r\n for (let y = 0; y < numCells; y++, indY += side2) {\r\n let indZ = 0;\r\n for (let z = 0; z < numCells; z++, indZ += side) {\r\n for (let x = 0; x < numCells; x++) {\r\n const cubeValuesIndex = indCell * (2 << (2 + 2)) + 24;\r\n const indCorner = x + indZ + indY;\r\n\r\n cube.pointsValuesLinear[cubeValuesIndex] = corners[indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 1] = corners[indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 2] = corners[indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 3] = corners[indCorner + side];\r\n cube.pointsValuesLinear[cubeValuesIndex + 4] = corners[side2 + indCorner];\r\n cube.pointsValuesLinear[cubeValuesIndex + 5] = corners[side2 + indCorner + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 6] = corners[side2 + indCorner + side + 1];\r\n cube.pointsValuesLinear[cubeValuesIndex + 7] = corners[side2 + indCorner + side];\r\n\r\n // check read exception\r\n // assert(side2 + indCorner + side + 1 < side3);\r\n\r\n // get bit flags inside\r\n let bitsInside = 0;\r\n for (let i = 0; i < cNumVerts; ++i) {\r\n if (cube.pointsValuesLinear[cubeValuesIndex + i] < 0.0) {\r\n bitsInside |= (1 << i);\r\n }\r\n }\r\n\r\n if ((bitsInside === 0) || (bitsInside === ((1 << cNumVerts) - 1))) {\r\n cube.hasIntersection[indCell] = false;\r\n } else {\r\n cube.hasIntersection[indCell] = true;\r\n numIntersectedCells++;\r\n }\r\n cube.bitsInside[indCell] = bitsInside;\r\n // next cell\r\n indCell++;\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n return numIntersectedCells;\r\n }\r\n\r\n getType(letter) {\r\n const atomT = [0, 0, 1, 1, 2, 6, 3, 6, 4, 6, 5, 6, 6, 0, 7, 3, 8, 2, 9, 6, 10, 6, 11, 6, 12, 6, 13, 6, 14, 6, 15, 4,\r\n 16, 5, 17, 6, 18, 6, 19, 6, 20, 6, 21, 6, 22, 6, 23, 6, 24, 6, 25, 6, 26, 6, 27, 6, 28, 6, 29, 6, 30, 6, 31, 6,\r\n 32, 6, 33, 6, 34, 6, 35, 6, 36, 6, 37, 6, 38, 6, 39, 6, 40, 6, 41, 6, 42, 6, 43, 6, 44, 6, 45, 6, 46, 6, 47, 6,\r\n 48, 6, 49, 6, 50, 6, 51, 6, 52, 6, 53, 6, 54, 6, 55, 6, 56, 6, 57, 6, 58, 6, 59, 6, 60, 6, 61, 6, 62, 6, 63, 6,\r\n 64, 6, 65, 6, 66, 6, 67, 6, 68, 6, 69, 6, 70, 6, 71, 6, 72, 6, 73, 6, 74, 6, 75, 6, 76, 6, 77, 6, 78, 6, 79, 6,\r\n 80, 6, 81, 6, 82, 6, 83, 6, 84, 6, 85, 6, 86, 6, 87, 6, 88, 6, 89, 6, 90, 6, 91, 6, 92, 6, 93, 6, 94, 6, 95, 6,\r\n 96, 6, 97, 6, 98, 6, 99, 6, 100, 6, 101, 6, 102, 6, 103, 6, 104, 6, 105, 6, 106, 6, 107, 6, 108, 6, 109, 6];\r\n\r\n if (letter < 1 || letter > atomT.length / 2\r\n || (Object.keys(Element.ByAtomicNumber).length * 2) !== atomT.length) {\r\n throw new Error('atomT.length should be equal Element.ByAtomicNumber.length * 2');\r\n }\r\n return atomT[letter * 2];\r\n }\r\n\r\n /**\r\n * Calculate values for marching cube grid points\r\n * positive values are outside sphere, negative - is inside\r\n *\r\n * @param {array} corners array of float values\r\n * @param {number} side Number of point in cube in 1 dimennsion\r\n * @param {Vector3} vBoxMin Bounding box min point\r\n * @param {Vector3} vBoxMax Bounding box max point\r\n * @param {array} atoms Array of input atoms\r\n * @param {number} probeRad radius for atom probing\r\n */\r\n calculateGridCorners(corners, side, vBoxMin, vBoxMax, atoms, probeRad) {\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const vCorner = new THREE.Vector3();\r\n const vDif = new THREE.Vector3();\r\n\r\n const aLot = +1.0e12;\r\n\r\n for (let i = 0; i < side3; i++) {\r\n corners[i] = aLot; // to large value\r\n }\r\n\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n for (let s = 0, numAtoms = atoms.length; s < numAtoms; s++) {\r\n const atom = atoms[s];\r\n const radius = atom.radius + probeRad;\r\n\r\n const fx = ((atom.coord.x - radius) - vBoxMin.x) * xScale;\r\n const fy = ((atom.coord.y - radius) - vBoxMin.y) * yScale;\r\n const fz = ((atom.coord.z - radius) - vBoxMin.z) * zScale;\r\n\r\n const indXMin = Math.floor(fx);\r\n const indYMin = Math.floor(fy);\r\n const indZMin = Math.floor(fz);\r\n\r\n let indXMax = Math.floor(((atom.coord.x + radius) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((atom.coord.y + radius) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((atom.coord.z + radius) - vBoxMin.z) * zScale);\r\n\r\n indXMax++;\r\n indYMax++;\r\n indZMax++;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let y = indYMin; y <= indYMax; y++) {\r\n const indY = y * side2;\r\n for (let z = indZMin; z <= indZMax; z++) {\r\n const indZ = z * side;\r\n for (let x = indXMin; x <= indXMax; x++) {\r\n const ind = indY + indZ + x;\r\n this.getCornerCoord(vBoxMin, vBoxMax, x, y, z, side, vCorner);\r\n vDif.x = vCorner.x - atom.coord.x;\r\n vDif.y = vCorner.y - atom.coord.y;\r\n vDif.z = vCorner.z - atom.coord.z;\r\n const distToSphere = Math.sqrt(vDif.x * vDif.x + vDif.y * vDif.y + vDif.z * vDif.z);\r\n // val: < 0, if inside sphere\r\n // val: > 0, if outside sphere\r\n const val = distToSphere - radius;\r\n if (val < corners[ind]) {\r\n corners[ind] = val;\r\n }\r\n } // for (x)\r\n } // for (z)\r\n } // for (y)\r\n } // for (s)\r\n }\r\n\r\n /**\r\n * Create memory pool for vertex hash management\r\n *\r\n * @param {number} maxNumVertices Maximum possible number of vertices (that will be build)\r\n * @param {number} maxNumTriangles Maximum possible number of triangles (that will be build)\r\n * @returns {number} 0, if success. (<0) is non memory\r\n */\r\n createVertexHash(maxNumVertices, maxNumTriangles) {\r\n this.hashLines = utils.allocateTyped(Int32Array, HASH_SIZE * 2);\r\n if (this.hashLines === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < HASH_SIZE; i++) {\r\n this.hashLines[j++] = 0; // num vertices in this hash line\r\n this.hashLines[j++] = 0 - 1; // index of the first entry\r\n }\r\n\r\n this.maxNumVertices = maxNumVertices;\r\n this.maxNumTriangles = maxNumTriangles;\r\n\r\n this.numHashEtriesAllocated = maxNumVertices;\r\n this.hashEntries = utils.allocateTyped(Int32Array, 2 * this.numHashEtriesAllocated);\r\n if (this.hashEntries === null) {\r\n return 0 - 1;\r\n }\r\n for (let i = 0, j = 0; i < this.numHashEtriesAllocated; i++) {\r\n this.hashEntries[j++] = 0 - 1; // index of vertex\r\n this.hashEntries[j++] = 0 - 1; // next hash entry index\r\n }\r\n this.numHashEntryIndex = 0;\r\n return 0;\r\n }\r\n\r\n /**\r\n * Allocate and return new hash entry. Just check possible amount.\r\n *\r\n * @returns {number} index of hash entry, that can be used for geometry add vertex functionality\r\n */\r\n getNewHashEntry() {\r\n if (this.numHashEntryIndex < this.numHashEtriesAllocated) {\r\n const i = this.numHashEntryIndex;\r\n this.numHashEntryIndex++;\r\n return i;\r\n }\r\n return 0 - 1;\r\n }\r\n\r\n /**\r\n * Add vertex to geometry structure\r\n * using vertex hash table to quickly check, is this vertex already exist in geometry\r\n *\r\n * @param {object} geoOut Geometry to build\r\n * @param {Vector3} vAdd Vertex to add\r\n * @returns {number} index of added (or existing) vertex in geometry.\r\n */\r\n addVertexToGeo(geoOut, vAdd) {\r\n let entry;\r\n const oneHynberes = 0.01;\r\n const n815851 = 815851;\r\n const n37633 = 37633;\r\n const n2453543 = 2453543;\r\n const r106 = 1.0e-6;\r\n\r\n const hashResolution = this.marCubeResoultion << 2;\r\n const v = new THREE.Vector3();\r\n const ix = Math.floor(hashResolution * (vAdd.x - this.vBoxMin.x) / (this.vBoxMax.x + oneHynberes - this.vBoxMin.x));\r\n const iy = Math.floor(hashResolution * (vAdd.y - this.vBoxMin.y) / (this.vBoxMax.y + oneHynberes - this.vBoxMin.y));\r\n const iz = Math.floor(hashResolution * (vAdd.z - this.vBoxMin.z) / (this.vBoxMax.z + oneHynberes - this.vBoxMin.z));\r\n let iHash = ix * n815851 + iz * n37633 + iy * n2453543;\r\n iHash &= (HASH_SIZE - 1);\r\n const hLineIndex = iHash + iHash;\r\n\r\n // search vertex via hash\r\n // search in hash list\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n for (entry = this.hashLines[hLineIndex + 1]; entry >= 0; entry = this.hashEntries[entry * 2 + 1]) {\r\n const ind = this.hashEntries[entry * 2 + 0]; // vertex index\r\n v.copy(geoOut._vertices[ind]);\r\n v.x -= vAdd.x;\r\n v.y -= vAdd.y;\r\n v.z -= vAdd.z;\r\n const dot2 = v.x * v.x + v.y * v.y + v.z * v.z;\r\n if (dot2 < r106) {\r\n return ind;\r\n } // if (found)\r\n } // for (entry)\r\n } // search\r\n\r\n // add new vertex to geometry\r\n if (geoOut._numVertices >= this.maxNumVertices) {\r\n return 0 - 1;\r\n }\r\n\r\n const iVertAdd = geoOut._numVertices;\r\n geoOut._vertices[iVertAdd].copy(vAdd);\r\n\r\n // add to hash\r\n if (this.vBoxMin !== null && this.vBoxMax !== null) {\r\n entry = this.getNewHashEntry();\r\n if (entry < 0) {\r\n return 0 - 1;\r\n }\r\n const entryFirst = this.hashLines[hLineIndex + 1];\r\n this.hashLines[hLineIndex + 1] = entry;\r\n this.hashEntries[entry * 2 + 0] = iVertAdd;\r\n this.hashEntries[entry * 2 + 1] = entryFirst;\r\n\r\n this.hashLines[hLineIndex + 0]++; // num vertices in line ++\r\n }\r\n geoOut._numVertices++;\r\n return iVertAdd;\r\n }\r\n\r\n /**\r\n *\r\n * @param {number} side some placeholder description\r\n * @param {number} probeSphereRadius some placeholder description\r\n * @param {object} vBoxMin some placeholder description\r\n * @param {object} vBoxMax some placeholder description\r\n * @param {object} geoOut some placeholder description\r\n * @param {object} corners some placeholder description\r\n * @returns {number} always 0\r\n */\r\n modifyExcludedFromGeo(\r\n side,\r\n probeSphereRadius,\r\n vBoxMin,\r\n vBoxMax,\r\n geoOut,\r\n corners,\r\n ) {\r\n let ind;\r\n let distToSphere;\r\n let distToBorder;\r\n const r11 = 1.1;\r\n\r\n function innerBlockWorkAround() {\r\n if (distToBorder > 0.0) {\r\n // point is inside probe sphere\r\n if (corners[ind] < 0.0) {\r\n corners[ind] = distToBorder; // was inside surface, now is oustide ( > 0)\r\n }\r\n if (distToBorder > corners[ind]) {\r\n corners[ind] = distToBorder; // find positive maximum\r\n }\r\n } else if (distToBorder > corners[ind]) { // point is outside sphere\r\n corners[ind] = distToBorder; // find negative maximum\r\n }\r\n }\r\n\r\n const side2 = side * side;\r\n const xScale = (side - 1) / (vBoxMax.x - vBoxMin.x);\r\n const yScale = (side - 1) / (vBoxMax.y - vBoxMin.y);\r\n const zScale = (side - 1) / (vBoxMax.z - vBoxMin.z);\r\n\r\n const probeSpRad2 = (probeSphereRadius * 2) * (probeSphereRadius * 2);\r\n const sideInv = 1.0 / (side - 1);\r\n\r\n for (let i = 0; i < geoOut._numVertices; i++) {\r\n const vCenter = geoOut._vertices[i];\r\n\r\n const radEst = probeSphereRadius * r11;\r\n\r\n let indXMin = Math.floor(((vCenter.x - radEst) - vBoxMin.x) * xScale);\r\n let indYMin = Math.floor(((vCenter.y - radEst) - vBoxMin.y) * yScale);\r\n let indZMin = Math.floor(((vCenter.z - radEst) - vBoxMin.z) * zScale);\r\n\r\n let indXMax = Math.floor(((vCenter.x + radEst) - vBoxMin.x) * xScale);\r\n let indYMax = Math.floor(((vCenter.y + radEst) - vBoxMin.y) * yScale);\r\n let indZMax = Math.floor(((vCenter.z + radEst) - vBoxMin.z) * zScale);\r\n\r\n indXMin = (indXMin >= 0) ? indXMin : 0;\r\n indYMin = (indYMin >= 0) ? indYMin : 0;\r\n indZMin = (indZMin >= 0) ? indZMin : 0;\r\n indXMax = (indXMax <= (side - 1)) ? indXMax : (side - 1);\r\n indYMax = (indYMax <= (side - 1)) ? indYMax : (side - 1);\r\n indZMax = (indZMax <= (side - 1)) ? indZMax : (side - 1);\r\n\r\n for (let iy = indYMin; iy <= indYMax; iy++) {\r\n const indY = iy * side2;\r\n for (let iz = indZMin; iz <= indZMax; iz++) {\r\n const indZ = iz * side;\r\n for (let ix = indXMin; ix <= indXMax; ix++) {\r\n ind = indY + indZ + ix;\r\n // getCornerCoord(vBoxMin, vBoxMax, ix, iy, iz, side, &vCorner);\r\n let t = ix * sideInv;\r\n const xCorner = vBoxMin.x * (1.0 - t) + vBoxMax.x * t;\r\n t = iy * sideInv;\r\n const yCorner = vBoxMin.y * (1.0 - t) + vBoxMax.y * t;\r\n t = iz * sideInv;\r\n const zCorner = vBoxMin.z * (1.0 - t) + vBoxMax.z * t;\r\n\r\n const dx = xCorner - vCenter.x;\r\n const dy = yCorner - vCenter.y;\r\n const dz = zCorner - vCenter.z;\r\n const dist2 = dx * dx + dy * dy + dz * dz;\r\n if (dist2 < probeSpRad2) {\r\n distToSphere = Math.sqrt(dist2);\r\n distToBorder = -(distToSphere - probeSphereRadius);\r\n innerBlockWorkAround();\r\n } // if (dist from corner point to sphere center more 2 radiuses)\r\n } // for (ix)\r\n } // for (iz)\r\n } // for (iy)\r\n } // for (i) all geo vertices\r\n return 0;\r\n }\r\n\r\n _innerBuild() {\r\n let ok;\r\n const expandFactor = 1.2;\r\n\r\n // performance test\r\n // this.performanceTest();\r\n\r\n // Create temporary atoms (but colored)\r\n const packedArrays = {\r\n posRad: this._posRad,\r\n colors: this._colors,\r\n atoms: this._opts.atoms,\r\n };\r\n this.complex = this._opts.parent;\r\n this.atoms = packedArrays.atoms;\r\n this.meshResolution = this._opts.gridSpacing;\r\n this.atomRadiusScale = this._opts.radScale;\r\n this.colorMode = this._opts.colorMode;\r\n this.probeRadius = this._opts.probeRadius;\r\n this.useVertexColors = true;\r\n this.excludeProbe = this._opts.excludeProbe;\r\n this.visibilitySelector = this._opts.visibilitySelector;\r\n\r\n this.geoOut = null;\r\n\r\n this.hashLines = null;\r\n this.hashEntries = null;\r\n this.numHashEtriesAllocated = 0;\r\n this.numHashEntryIndex = 0;\r\n this.maxNumVertices = 0;\r\n this.maxNumTriangles = 0;\r\n\r\n const atomsColored = new Array(this.atoms.length);\r\n this.convertToAtomsColored(packedArrays, atomsColored);\r\n\r\n // find bbox for spheres scene\r\n const vBoxMin = this.vBoxMin = new THREE.Vector3();\r\n const vBoxMax = this.vBoxMax = new THREE.Vector3();\r\n this.getBoundingBox(atomsColored, vBoxMin, vBoxMax);\r\n\r\n const marCubeResoultion = this.marCubeResoultion = this.meshResolution * (2 + 2);\r\n\r\n // build grid corners for Marching cube algorithm\r\n const side = marCubeResoultion;\r\n const side2 = side * side;\r\n const side3 = side2 * side;\r\n const corners = utils.allocateTyped(Float32Array, side3);\r\n const rProbeRadius = this.probeRadius * this.atomRadiusScale;\r\n\r\n this.calculateGridCorners(corners, side, vBoxMin, vBoxMax, atomsColored, rProbeRadius);\r\n\r\n const numCells = marCubeResoultion - 1;\r\n const cube = new IsoSurfaceMarchCube();\r\n ok = cube.create(numCells);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // copy corners to cells\r\n const vCellStep = new THREE.Vector3();\r\n vCellStep.x = (vBoxMax.x - vBoxMin.x) / numCells;\r\n vCellStep.y = (vBoxMax.y - vBoxMin.y) / numCells;\r\n vCellStep.z = (vBoxMax.z - vBoxMin.z) / numCells;\r\n\r\n let numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n let maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n let maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n\r\n // build voxel world (used to check triangle-to-atom tie and to calculate normals and colors)\r\n let probeRadForNormalsColors = rProbeRadius;\r\n if (this.excludeProbe) {\r\n probeRadForNormalsColors = 0.01;\r\n }\r\n this.voxelWorld = new IsosurfaceBuildNormals(\r\n atomsColored.length,\r\n atomsColored,\r\n vBoxMin,\r\n vBoxMax,\r\n probeRadForNormalsColors,\r\n );\r\n this.voxelWorld.createVoxels();\r\n\r\n ok = this.buildGeoFromCorners(marCubeResoultion, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n if (this.excludeProbe) {\r\n // using 3d mesh (geoOut) as a surface points\r\n // move probe sphere and try to minimuze corners values\r\n this.modifyExcludedFromGeo(side, rProbeRadius, vBoxMin, vBoxMax, this.geoOut, corners);\r\n\r\n // delete old builded geo\r\n this.geoOut._vertices = null;\r\n this.geoOut._colors = null;\r\n this.geoOut._indices = null;\r\n this.geoOut._normals = null;\r\n this.geoOut._numVertices = 0;\r\n this.geoOut._numTriangles = 0;\r\n this.geoOut = null;\r\n\r\n // estimage geo vertices budget again\r\n numIntersectedCellsEstim = this.getNumIntersectedCells(side, numCells, corners, cube);\r\n maxNumVertices = Math.floor(numIntersectedCellsEstim * expandFactor);\r\n maxNumTriangles = Math.floor(numIntersectedCellsEstim * expandFactor * 2);\r\n\r\n // creates empty new geometry\r\n this.geoOut = new IsoSurfaceGeo(maxNumVertices, maxNumTriangles, this.useVertexColors);\r\n ok = this.createVertexHash(maxNumVertices, maxNumTriangles);\r\n if (ok < 0) {\r\n return ok;\r\n }\r\n // build vertices and triangles from corners values\r\n ok = this.buildGeoFromCorners(side, vBoxMin, vBoxMax, corners, vCellStep, cube);\r\n }\r\n\r\n // build vertex normals\r\n this.voxelWorld.buildNormals(this.geoOut._vertices.length, this.geoOut._vertices, this.geoOut._normals);\r\n // More value : more smooth color mixing\r\n // value about 0.7: very rough colors borders\r\n let radiusColorSmoothness = 6.5;\r\n if (this.excludeProbe) {\r\n radiusColorSmoothness -= 1.5;\r\n }\r\n if (this.useVertexColors) {\r\n this.voxelWorld.buildColors(\r\n this.geoOut._vertices.length,\r\n this.geoOut._vertices,\r\n this.geoOut._colors,\r\n radiusColorSmoothness,\r\n );\r\n }\r\n this.voxelWorld.destroyVoxels();\r\n this.voxelWorld = null;\r\n\r\n // remove objects\r\n cube.destroy();\r\n\r\n return ok;\r\n }\r\n}\r\n\r\n// All code below must be erased from every device and each developer's memory\r\n\r\nexport default SSIsosurfaceGeometry;\r\n","import * as THREE from 'three';\r\nimport EventDispatcher from '../../utils/EventDispatcher';\r\n\r\nfunction createLabel(fieldTxt, className) {\r\n const text = document.createElement('div');\r\n text.className = className;\r\n\r\n if (typeof fieldTxt === 'string') {\r\n const spanText = document.createElement('span');\r\n spanText.style.fontSize = '150%';\r\n const strings = fieldTxt.split('\\n');\r\n\r\n for (let i = 0, n = strings.length; i < n; ++i) {\r\n const spanNodeP = document.createElement('span');\r\n const spanNodeText = document.createTextNode(strings[i]);\r\n spanNodeP.appendChild(spanNodeText);\r\n spanText.appendChild(spanNodeP);\r\n if (i < n - 1) {\r\n spanText.appendChild(document.createElement('br'));\r\n }\r\n }\r\n\r\n text.appendChild(spanText);\r\n } else {\r\n text.appendChild(fieldTxt);\r\n }\r\n text.worldPos = new THREE.Vector3();\r\n return text;\r\n}\r\nclass LabelsGeometry extends EventDispatcher {\r\n constructor(instanceCount, opts) {\r\n super();\r\n this._opts = opts;\r\n this.items = [];\r\n this.needsUpdate = false;\r\n\r\n let xTranslation = -50;\r\n let yTranslation = -50;\r\n switch (opts.horizontalAlign) {\r\n case 'left':\r\n xTranslation = 0;\r\n break;\r\n case 'right':\r\n xTranslation = -100;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n switch (opts.verticalAlign) {\r\n case 'top':\r\n yTranslation = -100;\r\n break;\r\n case 'bottom':\r\n yTranslation = 0;\r\n break;\r\n default:\r\n break;\r\n }\r\n\r\n const deltaPos = new THREE.Vector3(opts.dx || 0, opts.dy || 0, opts.dz || 0);\r\n this.userData = {\r\n translation: `translate(${xTranslation}%, ${yTranslation}%)`,\r\n offset: deltaPos,\r\n };\r\n }\r\n\r\n setItem(itemIdx, itemPos, fieldTxt) {\r\n const opts = this._opts;\r\n const text = this.items[itemIdx] || createLabel(fieldTxt, 'label');\r\n\r\n text.worldPos.copy(itemPos);\r\n text.style.textAlign = opts.horizontalAlign;\r\n text.style.verticalAlign = opts.verticalAlign;\r\n this.items[itemIdx] = text;\r\n }\r\n\r\n setColor(itemIdx, fColor, bColor) {\r\n const text = this.items[itemIdx];\r\n text.opts = {\r\n color: fColor,\r\n background: bColor,\r\n };\r\n }\r\n\r\n startUpdate() {\r\n return true;\r\n }\r\n\r\n finishUpdate() {\r\n this.needsUpdate = true;\r\n this.dispatchEvent({ type: 'update' });\r\n }\r\n\r\n finalize() {\r\n this.finishUpdate();\r\n }\r\n\r\n // unimplemented functions\r\n raycast() {\r\n }\r\n\r\n setOpacity() {\r\n\r\n }\r\n\r\n getSubset() {\r\n return [];\r\n }\r\n}\r\n\r\nexport default LabelsGeometry;\r\n","import InstancedSpheresGeometry from './InstancedSpheresGeometry';\r\nimport SimpleSpheresGeometry from './SimpleSpheresGeometry';\r\nimport Simple2CCylindersGeometry from './Simple2CCylindersGeometry';\r\nimport Instanced2CCylindersGeometry from './Instanced2CCylindersGeometry';\r\nimport ExtrudedObjectsGeometry from './ExtrudedObjectsGeometry';\r\nimport ChunkedLinesGeometry from './ChunkedLinesGeometry';\r\nimport TwoColorLinesGeometry from './TwoColorLinesGeometry';\r\nimport CrossGeometry from './CrossGeometry';\r\nimport QuickSurfGeometry from './QuickSurfGeometry';\r\nimport ContactSurfaceGeometry from './ContactSurfaceGeometry';\r\nimport SSIsosurfaceGeometry from './SSIsosurfaceGeometry';\r\nimport LabelsGeometry from './LabelsGeometry';\r\n\r\nexport default {\r\n InstancedSpheresGeometry,\r\n SimpleSpheresGeometry,\r\n Simple2CCylindersGeometry,\r\n Instanced2CCylindersGeometry,\r\n ExtrudedObjectsGeometry,\r\n ChunkedLinesGeometry,\r\n TwoColorLinesGeometry,\r\n CrossGeometry,\r\n QuickSurfGeometry,\r\n ContactSurfaceGeometry,\r\n SSIsosurfaceGeometry,\r\n LabelsGeometry,\r\n};\r\n","export default {\r\n\r\n precision: 'mediump',\r\n\r\n /**\r\n *\r\n * @param {THREE.WebGLRenderer} renderer\r\n */\r\n init(renderer) {\r\n this.precision = renderer.capabilities.getMaxPrecision('highp');\r\n },\r\n};\r\n","import * as THREE from 'three';\r\n\r\nconst noiseWidth = 4;\r\nconst noiseHeight = 4;\r\nconst _noiseData = new Uint8Array([\r\n 24, 52, 0, 255, 254, 145, 0, 255, 122, 0, 0, 255, 7, 170, 0, 255,\r\n 34, 214, 0, 255, 173, 8, 0, 255, 86, 249, 0, 255, 160, 4, 0, 255,\r\n 226, 46, 0, 255, 224, 211, 0, 255, 3, 157, 0, 255, 174, 247, 0, 255,\r\n 12, 182, 0, 255, 220, 216, 0, 255, 1, 109, 0, 255, 253, 154, 0, 255,\r\n]);\r\nconst _noiseWrapS = THREE.RepeatWrapping;\r\nconst _noiseWrapT = THREE.RepeatWrapping;\r\nconst _noiseMinFilter = THREE.NearestFilter;\r\nconst _noiseMagFilter = THREE.NearestFilter;\r\nconst _noiseMapping = THREE.UVMapping;\r\nconst noiseTexture = new THREE.DataTexture(\r\n _noiseData,\r\n noiseWidth,\r\n noiseHeight,\r\n THREE.RGBAFormat,\r\n THREE.UnsignedByteType,\r\n _noiseMapping,\r\n _noiseWrapS,\r\n _noiseWrapT,\r\n _noiseMagFilter,\r\n _noiseMinFilter,\r\n 1,\r\n);\r\nnoiseTexture.needsUpdate = true;\r\n\r\nexport default {\r\n noiseWidth,\r\n noiseHeight,\r\n noiseTexture,\r\n};\r\n","import * as THREE from 'three';\r\nimport vertexShader from './Uber.vert';\r\nimport fragmentShader from './Uber.frag';\r\nimport capabilities from '../capabilities';\r\nimport noise from '../noiseTexture';\r\n\r\n// Length of _samplesKernel is used in Uber.frag\r\n// If you want to change length of _samplesKernel, please, remember change it in Uber.frag too.\r\n// You can easy find places for replace using word:_samplesKernel\r\nconst _samplesKernel = [\r\n new THREE.Vector2(-0.541978, 0.840393),\r\n new THREE.Vector2(0.125533, -0.992089),\r\n new THREE.Vector2(0.374329, 0.927296),\r\n new THREE.Vector2(-0.105475, 0.994422),\r\n];\r\n\r\nconst defaultUniforms = THREE.UniformsUtils.merge([\r\n\r\n THREE.UniformsLib.fog,\r\n THREE.UniformsLib.lights,\r\n\r\n {\r\n // are updated automatically by three.js (see THREE.ShaderLib.common)\r\n diffuse: { value: new THREE.Color(0xeeeeee) },\r\n opacity: { value: 1.0 },\r\n\r\n specular: { type: 'c', value: new THREE.Color(0x111111) },\r\n shininess: { type: 'f', value: 30 },\r\n fixedColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n zOffset: { type: 'f', value: 0.0 },\r\n zClipValue: { type: 'f', value: 0.0 },\r\n clipPlaneValue: { type: 'f', value: 0.0 },\r\n nearPlaneValue: { type: 'f', value: -0.5 },\r\n invModelViewMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n world2colorMatrix: { type: '4fv', value: new THREE.Matrix4() },\r\n dashedLineSize: { type: 'f', value: 0.1 },\r\n dashedLinePeriod: { type: 'f', value: 0.2 },\r\n projMatrixInv: { type: '4fv', value: new THREE.Matrix4() },\r\n viewport: { type: 'v2', value: new THREE.Vector2() },\r\n lineWidth: { type: 'f', value: 2.0 },\r\n // default value must be the same as settings\r\n fogAlpha: { type: 'f', value: 1.0 },\r\n samplesKernel: { type: 'v2v', value: null },\r\n noiseTex: { type: 't', value: null },\r\n noiseTexelSize: { type: 'v2', value: null },\r\n srcTexelSize: { type: 'v2', value: null },\r\n },\r\n\r\n]);\r\n\r\nconst uberOptionNames = [\r\n 'shininess',\r\n 'opacity',\r\n 'zOffset',\r\n 'diffuse',\r\n 'specular',\r\n 'fixedColor',\r\n 'zClipCoef',\r\n 'zClipValue',\r\n 'clipPlaneValue',\r\n 'world2colorMatrix',\r\n 'dashedLineSize',\r\n 'dashedLinePeriod',\r\n 'projMatrixInv',\r\n 'viewport',\r\n 'lineWidth',\r\n 'fogAlpha',\r\n 'samplesKernel',\r\n 'noiseTex',\r\n 'noiseTexelSize',\r\n 'srcTexelSize',\r\n];\r\n\r\n// properties that convert to uniforms\r\nconst uberOptions = {\r\n diffuse: new THREE.Color(0xffffff), // used in phong lighting\r\n specular: new THREE.Color(0x111111), // used in phong lighting\r\n shininess: 30, // used in phong lighting\r\n opacity: 1, // set mesh opacity\r\n fixedColor: new THREE.Color(0xffffff), // color to override (see OVERRIDE_COLOR)\r\n zOffset: 0.0, // used fo zsprites (see SPHERE_SPRITE CYLINDER_SPRITE)\r\n zClipCoef: 2.0, // use for Surfs clipping (mesh param, isn't used in shader) FIXME move to representation param\r\n zClipValue: 0.0, // value to clip Surfs in shader (see ZCLIP)\r\n clipPlaneValue: 0.0, // value to clip scene globally (see CLIPPLANE)\r\n world2colorMatrix: new THREE.Matrix4(),\r\n dashedLineSize: 0.1,\r\n dashedLinePeriod: 0.3,\r\n projMatrixInv: new THREE.Matrix4(),\r\n viewport: new THREE.Vector2(800, 600),\r\n lineWidth: 2.0,\r\n fogAlpha: 1.0,\r\n samplesKernel: _samplesKernel,\r\n noiseTex: noise.noiseTexture,\r\n noiseTexelSize: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight),\r\n srcTexelSize: new THREE.Vector2(1.0 / 800.0, 1.0 / 600.0),\r\n copy(source) {\r\n this.diffuse.copy(source.diffuse);\r\n this.specular.copy(source.specular);\r\n this.shininess = source.shininess;\r\n this.opacity = source.opacity;\r\n this.fixedColor.copy(source.fixedColor);\r\n this.zOffset = source.zOffset;\r\n this.zClipCoef = source.zClipCoef;\r\n this.zClipValue = source.zClipValue;\r\n this.clipPlaneValue = source.clipPlaneValue;\r\n this.world2colorMatrix.copy(source.world2colorMatrix);\r\n this.dashedLineSize = source.dashedLineSize;\r\n this.dashedLinePeriod = source.dashedLinePeriod;\r\n this.projMatrixInv = source.projMatrixInv;\r\n this.viewport = source.viewport;\r\n this.lineWidth = source.lineWidth; // used for thick lines only\r\n this.toonShading = source.toonShading;\r\n this.fogAlpha = source.fogAlpha;\r\n this.samplesKernel = source.samplesKernel;\r\n this.noiseTex = source.noiseTex;\r\n this.noiseTexelSize = source.noiseTexelSize;\r\n this.srcTexelSize = source.srcTexelSize;\r\n },\r\n};\r\n\r\nclass UberMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // add fog\r\n this.fog = true;\r\n // used for instanced geometry\r\n this.instancedPos = false;\r\n this.instancedMatrix = false;\r\n // atoms and links color\r\n this.attrColor = false;\r\n // second link color for cylinders\r\n this.attrColor2 = false;\r\n //\r\n this.attrAlphaColor = false;\r\n // overrides color for all vertices (used in selection)\r\n this.overrideColor = false;\r\n // zsrpites\r\n this.sphereSprite = false;\r\n this.cylinderSprite = false;\r\n // clip Surfs individually\r\n this.zClip = false;\r\n // clip scene with global clip plane\r\n this.clipPlane = false;\r\n // enable fake (chess-like) opacity\r\n this.fakeOpacity = false;\r\n // render only depth, don't take care about the pixel color (used for transparency depth prepass)\r\n this.prepassTransparancy = false;\r\n // used to render pixel positions\r\n this.colorFromPos = false;\r\n // used to render shadowmap\r\n this.shadowmap = false;\r\n // used to describe shadowmap type\r\n this.shadowmapType = 'random';\r\n // used to render pixel view deph\r\n this.colorFromDepth = false;\r\n // mark that rendering is for orthographic camera\r\n this.orthoCam = false;\r\n // used to render dashed line\r\n this.dashedLine = false;\r\n // mark as transparent\r\n this.transparent = true;\r\n // mark as thick lines\r\n this.thickLine = false;\r\n // makes fog begin transparency (required for transparent background)\r\n this.fogTransparent = false;\r\n // used to render surface normals to G buffer for ssao effect\r\n this.normalsToGBuffer = false;\r\n // used for toon material\r\n this.toonShading = false;\r\n\r\n // uber options of \"root\" materials are inherited from single uber-options object that resides in prototype\r\n this.uberOptions = Object.create(UberMaterial.prototype.uberOptions);\r\n\r\n // set default values\r\n super.setValues({\r\n glslVersion: THREE.GLSL3,\r\n vertexShader: this.precisionString() + vertexShader,\r\n fragmentShader: this.precisionString() + fragmentShader,\r\n uniforms: THREE.UniformsUtils.clone(defaultUniforms),\r\n lights: true,\r\n fog: true,\r\n side: THREE.DoubleSide,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n precisionString() {\r\n const { precision } = capabilities;\r\n const str = `precision ${precision} float;\\n`\r\n + `precision ${precision} int;\\n\\n`;\r\n return str;\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n\r\n this.fragmentShader = source.fragmentShader;\r\n this.vertexShader = source.vertexShader;\r\n\r\n this.uniforms = THREE.UniformsUtils.clone(source.uniforms);\r\n this.defines = { ...source.defines };\r\n this.extensions = source.extensions;\r\n\r\n this.fog = source.fog;\r\n this.instancedPos = source.instancedPos;\r\n this.instancedMatrix = source.instancedMatrix;\r\n this.attrColor = source.attrColor;\r\n this.attrColor2 = source.attrColor2;\r\n this.attrAlphaColor = source.attrAlphaColor;\r\n this.overrideColor = source.overrideColor;\r\n this.sphereSprite = source.sphereSprite;\r\n this.cylinderSprite = source.cylinderSprite;\r\n this.zClip = source.zClip;\r\n this.clipPlane = source.clipPlane;\r\n this.fakeOpacity = source.fakeOpacity;\r\n this.colorFromPos = source.colorFromPos;\r\n this.shadowmap = source.shadowmap;\r\n this.shadowmapType = source.shadowmapType;\r\n this.colorFromDepth = source.colorFromDepth;\r\n this.orthoCam = source.orthoCam;\r\n this.prepassTransparancy = source.prepassTransparancy;\r\n this.dashedLine = source.dashedLine;\r\n this.thickLine = source.thickLine;\r\n this.fogTransparent = source.fogTransparent;\r\n this.normalsToGBuffer = source.normalsToGBuffer;\r\n this.toonShading = source.toonShading;\r\n\r\n this.uberOptions.copy(source.uberOptions);\r\n\r\n return this;\r\n }\r\n\r\n // create copy of this material\r\n // its options are prototyped after this material's options\r\n createInstance() {\r\n const inst = new UberMaterial();\r\n inst.copy(this);\r\n inst.uberOptions = Object.create(this.uberOptions);\r\n return inst;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n const extensions = {};\r\n\r\n if (this.fog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.instancedPos) {\r\n defines.INSTANCED_POS = 1;\r\n }\r\n if (this.instancedMatrix) {\r\n defines.INSTANCED_MATRIX = 1;\r\n }\r\n if (this.attrColor) {\r\n defines.ATTR_COLOR = 1;\r\n }\r\n if (this.attrColor2) {\r\n defines.ATTR_COLOR2 = 1;\r\n }\r\n if (this.attrAlphaColor) {\r\n defines.ATTR_ALPHA_COLOR = 1;\r\n }\r\n if (this.overrideColor) {\r\n defines.OVERRIDE_COLOR = 1;\r\n }\r\n if (this.sphereSprite) {\r\n defines.SPHERE_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.cylinderSprite) {\r\n defines.CYLINDER_SPRITE = 1;\r\n extensions.fragDepth = true;\r\n }\r\n if (this.zClip) {\r\n defines.ZCLIP = 1;\r\n }\r\n if (this.clipPlane) {\r\n defines.CLIP_PLANE = 1;\r\n }\r\n if (this.fakeOpacity) {\r\n defines.FAKE_OPACITY = 1;\r\n }\r\n if (this.lights) {\r\n defines.USE_LIGHTS = 1;\r\n }\r\n if (this.colorFromPos) {\r\n defines.COLOR_FROM_POS = 1;\r\n }\r\n if (this.shadowmap) {\r\n defines.SHADOWMAP = 1;\r\n if (this.shadowmapType === 'pcf') {\r\n defines.SHADOWMAP_PCF_SHARP = 1;\r\n } else if (this.shadowmapType === 'random') {\r\n defines.SHADOWMAP_PCF_RAND = 1;\r\n } else {\r\n defines.SHADOWMAP_BASIC = 1;\r\n }\r\n }\r\n if (this.colorFromDepth) {\r\n defines.COLOR_FROM_DEPTH = 1;\r\n }\r\n if (this.orthoCam) {\r\n defines.ORTHOGRAPHIC_CAMERA = 1;\r\n }\r\n if (this.prepassTransparancy) {\r\n defines.PREPASS_TRANSP = 1;\r\n }\r\n if (this.dashedLine) {\r\n defines.DASHED_LINE = 1;\r\n }\r\n if (this.thickLine) {\r\n defines.THICK_LINE = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n if (this.normalsToGBuffer) {\r\n extensions.drawBuffers = true;\r\n defines.NORMALS_TO_G_BUFFER = 1;\r\n }\r\n if (this.toonShading) {\r\n defines.TOON_SHADING = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n this.extensions = extensions;\r\n }\r\n\r\n setUberOptions(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n for (const key in values) {\r\n if (!values.hasOwnProperty(key)) {\r\n continue;\r\n }\r\n\r\n if (this.uberOptions[key] instanceof THREE.Color) {\r\n this.uberOptions[key] = values[key].clone();\r\n } else {\r\n this.uberOptions[key] = values[key];\r\n }\r\n }\r\n }\r\n\r\n clone(shallow) {\r\n if (!shallow) {\r\n return super.clone();\r\n }\r\n return this.createInstance();\r\n }\r\n\r\n updateUniforms() {\r\n const self = this;\r\n\r\n uberOptionNames.forEach((p) => {\r\n if (self.uniforms.hasOwnProperty(p)) {\r\n if (self.uberOptions[p] instanceof THREE.Color\r\n || self.uberOptions[p] instanceof THREE.Matrix4) {\r\n self.uniforms[p].value = self.uberOptions[p].clone();\r\n } else {\r\n self.uniforms[p].value = self.uberOptions[p];\r\n }\r\n }\r\n });\r\n }\r\n}\r\n\r\nUberMaterial.prototype.uberOptions = uberOptions;\r\n\r\nexport default UberMaterial;\r\n","import UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default function (SuperClass) {\r\n class NewObjectType extends SuperClass {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.onBeforeRender = NewObjectType.prototype.onBeforeRender;\r\n }\r\n\r\n onBeforeRender(renderer, scene, camera, geometry, material, group) {\r\n this._onBeforeRender(renderer, scene, camera, geometry, material, group);\r\n this._update();\r\n }\r\n\r\n _onBeforeRender() {\r\n }\r\n\r\n _update() {\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material instanceof UberMaterial) {\r\n material.updateUniforms();\r\n }\r\n }\r\n }\r\n\r\n return NewObjectType;\r\n}\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZSpriteMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n const { material } = this;\r\n if (!material) {\r\n return;\r\n }\r\n\r\n if (material.uniforms.invModelViewMatrix) {\r\n // NOTE: update of modelViewMatrix inside threejs is done after onBeforeRender call,\r\n // so we have to do it manually in that place\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n // get inverse matrix\r\n material.uniforms.invModelViewMatrix.value.copy(this.modelViewMatrix).invert();\r\n material.uniforms.nearPlaneValue.value = camera.near;\r\n material.uniformsNeedUpdate = true;\r\n }\r\n }\r\n}\r\n\r\nexport default ZSpriteMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass ZClippedMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n\r\n static _mvLength = new THREE.Vector3();\r\n\r\n static _center = new THREE.Vector3();\r\n\r\n static _modelView = new THREE.Matrix4();\r\n\r\n _onBeforeRender(renderer, scene, camera) {\r\n Mesh.prototype._onBeforeRender.call(this, renderer, scene, camera);\r\n\r\n const geo = this.geometry;\r\n const { material } = this;\r\n if (!geo.zClip || !material.uberOptions) {\r\n return;\r\n }\r\n\r\n const zClipCoef = 0.5;\r\n\r\n const modelView = ZClippedMesh._modelView;\r\n const mvLength = ZClippedMesh._mvLength;\r\n const center = ZClippedMesh._center;\r\n\r\n modelView.multiplyMatrices(this.matrixWorld, camera.matrixWorldInverse);\r\n const s = mvLength.setFromMatrixColumn(modelView, 0).length();\r\n center.copy(geo.boundingSphere.center);\r\n\r\n this.localToWorld(center);\r\n material.uberOptions.zClipValue = camera.position.z - center.z\r\n - s * (zClipCoef * geo.boundingSphere.radius);\r\n }\r\n}\r\n\r\nexport default ZClippedMesh;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from '../CSS2DObject';\r\nimport utils from '../../utils';\r\n\r\nclass TextMesh extends THREE.Group {\r\n constructor(geometry, _material) {\r\n super();\r\n this.geometry = geometry;\r\n\r\n const self = this;\r\n self.initialized = false;\r\n this.geometry.addEventListener('update', () => {\r\n self.update();\r\n });\r\n }\r\n\r\n init() {\r\n const { children } = this;\r\n for (let i = children.length - 1; i >= 0; --i) {\r\n this.remove(children[i]);\r\n }\r\n\r\n const { items, userData } = this.geometry;\r\n for (let i = 0, n = items.length; i < n; ++i) {\r\n const srcItem = items[i];\r\n if (!srcItem) {\r\n continue;\r\n }\r\n const item = utils.shallowCloneNode(srcItem);\r\n const label = new CSS2DObject(item);\r\n label.userData = _.clone(userData);\r\n const el = label.getElement();\r\n el.style.visibility = 'visible';\r\n label.source = srcItem;\r\n this.add(label);\r\n }\r\n this.initialized = true;\r\n }\r\n\r\n update() {\r\n const geo = this.geometry;\r\n if (!geo.needsUpdate) {\r\n return;\r\n }\r\n const { children } = this;\r\n if (!this.initialized) {\r\n this.init();\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n const item = child.source;\r\n child.position.copy(item.worldPos);\r\n child.userData.color = item.opts.color;\r\n child.userData.background = item.opts.background;\r\n }\r\n }\r\n}\r\n\r\nexport default TextMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass SimpleMesh extends Mesh {\r\n constructor(geometry, material) {\r\n super(geometry, material);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default SimpleMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\nconst _viewport = new THREE.Vector2();\r\n\r\nclass ThickLineMesh extends Mesh {\r\n _onBeforeRender(renderer, scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!material.uberOptions) {\r\n return;\r\n }\r\n\r\n material.uberOptions.projMatrixInv.copy(camera.projectionMatrix).invert();\r\n renderer.getSize(_viewport);\r\n material.uberOptions.viewport.set(_viewport.width, _viewport.height);\r\n }\r\n}\r\n\r\nexport default ThickLineMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\n\r\nconst Mesh = UberObject(THREE.Mesh);\r\n\r\nclass InstancedMesh extends Mesh {\r\n constructor(...rest) {\r\n super(...rest);\r\n this.castShadow = true;\r\n this.receiveShadow = true;\r\n }\r\n}\r\n\r\nexport default InstancedMesh;\r\n","import * as THREE from 'three';\r\nimport UberObject from './UberObject';\r\nimport ZSpriteMesh from './ZSpriteMesh';\r\nimport ZClippedMesh from './ZClippedMesh';\r\nimport TextMesh from './TextMesh';\r\nimport SimpleMesh from './SimpleMesh';\r\nimport ThickLineMesh from './ThickLineMesh';\r\nimport InstancedMesh from './InstancedMesh';\r\n\r\nexport default {\r\n ZClipped: ZClippedMesh,\r\n ZSprite: ZSpriteMesh,\r\n Text: TextMesh,\r\n Line: UberObject(THREE.Line),\r\n LineSegments: UberObject(THREE.LineSegments),\r\n Mesh: SimpleMesh,\r\n ThickLineMesh,\r\n Instanced: InstancedMesh,\r\n};\r\n","import geometries from '../geometries/geometries';\r\nimport meshes from './meshes';\r\nimport ThickLinesGeometry from '../geometries/ThickLinesGeometry';\r\n\r\nfunction setMatParams(params, uniforms) {\r\n return function (material) {\r\n material.setValues(params);\r\n material.setUberOptions(uniforms);\r\n };\r\n}\r\n\r\nfunction _createInstancedCylinders(useZSprites, openEnded) {\r\n function Geometry(a, b) {\r\n return new geometries.Instanced2CCylindersGeometry(a, b, useZSprites, openEnded);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedMatrix: true,\r\n attrColor: true,\r\n attrColor2: true,\r\n attrAlphaColor: true,\r\n cylinderSprite: useZSprites,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createLineSegmentsGeoTriplet(geo, renderParams) {\r\n const thickLines = geo.prototype instanceof ThickLinesGeometry;\r\n const lineWidth = renderParams.lineWidth || 0;\r\n return {\r\n Geometry: geo,\r\n Object: thickLines ? meshes.ThickLineMesh : meshes.LineSegments,\r\n initMaterial: setMatParams({\r\n lights: false,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n thickLine: thickLines,\r\n }, {\r\n lineWidth,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createSimpleGeoTriplet(geoClass) {\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.Mesh,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n }),\r\n };\r\n}\r\n\r\nfunction _createIsoSurfaceGeoTriplet(geoClass, caps, settings, renderParams) {\r\n const surfaceOpts = {\r\n wireframe: !!renderParams.wireframe,\r\n fakeOpacity: settings.now.isoSurfaceFakeOpacity,\r\n zClip: renderParams.zClip,\r\n };\r\n return {\r\n Geometry: geoClass,\r\n Object: meshes.ZClipped,\r\n initMaterial: setMatParams({\r\n attrColor: true,\r\n attrAlphaColor: false,\r\n wireframe: surfaceOpts.wireframe,\r\n fakeOpacity: surfaceOpts.fakeOpacity,\r\n zClip: surfaceOpts.zClip,\r\n }),\r\n };\r\n}\r\n\r\nclass MeshCreator {\r\n static createSpheres(caps, settings) {\r\n const useZSprites = settings.now.zSprites;\r\n function Geometry(a, b) {\r\n return new geometries.InstancedSpheresGeometry(a, b, useZSprites);\r\n }\r\n return {\r\n Geometry,\r\n Object: useZSprites ? meshes.ZSprite : meshes.Instanced,\r\n initMaterial: setMatParams({\r\n instancedPos: true,\r\n attrColor: true,\r\n attrAlphaColor: true,\r\n sphereSprite: useZSprites,\r\n }),\r\n };\r\n }\r\n\r\n static create2CClosedCylinders(_caps, _settings) {\r\n return _createInstancedCylinders(false, false);\r\n }\r\n\r\n static create2CCylinders(caps, settings) {\r\n return _createInstancedCylinders(settings.now.zSprites, true);\r\n }\r\n\r\n static create2CLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.TwoColorLinesGeometry, renderParams);\r\n }\r\n\r\n static createCrosses(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.CrossGeometry, renderParams);\r\n }\r\n\r\n static createExtrudedChains(_caps, _settings) {\r\n return _createSimpleGeoTriplet(geometries.ExtrudedObjectsGeometry);\r\n }\r\n\r\n static createChunkedLines(_caps, _settings, renderParams) {\r\n return _createLineSegmentsGeoTriplet(geometries.ChunkedLinesGeometry, renderParams);\r\n }\r\n\r\n static createQuickSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.QuickSurfGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createContactSurface(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.ContactSurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createSASSES(caps, settings, renderParams) {\r\n return _createIsoSurfaceGeoTriplet(geometries.SSIsosurfaceGeometry, caps, settings, renderParams);\r\n }\r\n\r\n static createLabels(_caps, _settings) {\r\n return {\r\n Geometry: geometries.LabelsGeometry,\r\n Object: meshes.Text,\r\n initMaterial() {\r\n },\r\n };\r\n }\r\n}\r\n\r\nexport default MeshCreator;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../gfxutils';\r\n\r\nclass TransformGroup extends THREE.Object3D {\r\n static _inverseMatrix = new THREE.Matrix4();\r\n\r\n static _ray = new THREE.Ray();\r\n\r\n constructor(geometry, geoParams, material, transforms) {\r\n super();\r\n this._geometry = geometry;\r\n this._geoParams = geoParams;\r\n const mat = material.createInstance();\r\n geoParams.initMaterial(mat);\r\n this._material = mat;\r\n this._transforms = transforms.length > 0 ? transforms : [new THREE.Matrix4()];\r\n const meshes = this._createMeshes(geometry);\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n this.add(meshes[i]);\r\n }\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const ray = TransformGroup._ray;\r\n const inverseMatrix = TransformGroup._inverseMatrix;\r\n const { children } = this;\r\n ray.copy(raycaster.ray);\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n\r\n if (!gfxutils.belongToSelectLayers(child)) {\r\n continue;\r\n }\r\n\r\n child.updateMatrixWorld();\r\n const mtx = child.matrixWorld;\r\n inverseMatrix.copy(mtx).invert();\r\n raycaster.ray.copy(ray).applyMatrix4(inverseMatrix);\r\n const childIntersects = [];\r\n this._geometry.raycast(raycaster, childIntersects);\r\n\r\n for (let j = 0, ciCount = childIntersects.length; j < ciCount; ++j) {\r\n const inters = childIntersects[j];\r\n if (inters.point) {\r\n inters.point.applyMatrix4(mtx);\r\n inters.distance = ray.origin.distanceTo(inters.point);\r\n }\r\n inters.object = child;\r\n intersects[intersects.length] = inters;\r\n }\r\n }\r\n raycaster.ray.copy(ray);\r\n }\r\n\r\n getSubset(chunkIndices) {\r\n const geos = this._geometry.getSubset(chunkIndices);\r\n const subset = [];\r\n let subIdx = 0;\r\n\r\n for (let i = 0, n = geos.length; i < n; ++i) {\r\n const meshes = this._createMeshes(geos[i]);\r\n for (let j = 0, meshCnt = meshes.length; j < meshCnt; ++j) {\r\n subset[subIdx++] = meshes[j];\r\n }\r\n }\r\n\r\n return subset;\r\n }\r\n\r\n _createMeshes(geometry) {\r\n const transforms = this._transforms;\r\n const Mesh = this._geoParams.Object;\r\n const material = this._material;\r\n const meshes = [];\r\n for (let i = 0, n = transforms.length; i < n; ++i) {\r\n const mesh = new Mesh(geometry, material);\r\n mesh.applyMatrix4(transforms[i]);\r\n meshes[i] = mesh;\r\n }\r\n\r\n return meshes;\r\n }\r\n}\r\n\r\nexport default TransformGroup;\r\n","import RCGroup from '../../RCGroup';\r\nimport TransformGroup from '../../meshes/TransformGroup';\r\n\r\nfunction wrapper(Name, args) {\r\n const params = [Name].concat(args);\r\n return Name.bind(...params);\r\n}\r\n\r\nclass ChemGroup extends RCGroup {\r\n constructor(geoParams, selection, colorer, mode, transforms, polyComplexity, material) {\r\n super();\r\n if (this.constructor === ChemGroup) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n this._selection = selection;\r\n this._mode = mode;\r\n this._colorer = colorer;\r\n this._chunksIdc = selection.chunks;\r\n this._polyComplexity = polyComplexity;\r\n this._geo = new (wrapper(geoParams.Geometry, this._makeGeoArgs()))();\r\n this._mesh = new TransformGroup(this._geo, geoParams, material, transforms);\r\n this.add(this._mesh);\r\n this._build();\r\n }\r\n\r\n _makeGeoArgs() {\r\n throw new Error('ChemGroup subclass must override _makeGeoArgs() method');\r\n }\r\n\r\n /**\r\n * Builds subset geometry by ATOMS index list\r\n *\r\n * @param {Number} mask - Representation mask\r\n * @param {Boolean} innerOnly - if true returns inner bonds only - without halves\r\n * @returns {Array} Subset geometry\r\n */\r\n getSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : false;\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return [];\r\n }\r\n return this._mesh.getSubset(chunksList);\r\n }\r\n\r\n _changeSubsetOpacity(mask, value, innerOnly) {\r\n const chunksList = this._calcChunksList(mask, innerOnly);\r\n if (chunksList.length === 0) {\r\n return;\r\n }\r\n this._geo.setOpacity(chunksList, value);\r\n }\r\n\r\n enableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 1.0, innerOnly);\r\n }\r\n\r\n disableSubset(mask, innerOnly) {\r\n innerOnly = innerOnly !== undefined ? innerOnly : true;\r\n this._changeSubsetOpacity(mask, 0.0, innerOnly);\r\n }\r\n}\r\n\r\nexport default ChemGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass AtomsGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { atoms } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const atomsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const atomIdx = atomsIdc[inters[i].chunkIdx];\r\n if (atomIdx < atoms.length) {\r\n inters[i].atom = atoms[atomIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { atoms } = this._selection;\r\n const atomsIdc = this._chunksIdc;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n if ((atom.mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default AtomsGroup;\r\n","import AtomsGroup from './AtomsGroup';\r\n\r\nclass AtomsSphereGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, atom.position, mode.calcAtomRadius(atom));\r\n geo.setColor(i, colorer.getAtomColor(atom, parent));\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), mode.calcAtomRadius(atom));\r\n if (updateColor) {\r\n geo.setColor(i, frameData.getAtomColor(colorer, atom));\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsSphereGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSurfaceGroup extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n return [n, opts];\r\n }\r\n}\r\nexport default AtomsSurfaceGroup;\r\n","/* This is a stub class keep it until SAS/SES is refactored */\r\n\r\nimport AtomsSphereGroup from './AtomsSphereGroup';\r\n\r\nclass AtomsSASSESGroupStub extends AtomsSphereGroup {\r\n _makeGeoArgs() {\r\n const selectedAtoms = [];\r\n const { atoms, chunks } = this._selection;\r\n const n = chunks.length;\r\n for (let i = 0; i < n; ++i) {\r\n selectedAtoms[i] = atoms[chunks[i]];\r\n }\r\n const opts = this._mode.getSurfaceOpts();\r\n opts.atoms = selectedAtoms;\r\n opts.selection = this._selection;\r\n opts.colorMode = this._colorer;\r\n return [n, opts];\r\n }\r\n}\r\n\r\nexport default AtomsSASSESGroupStub;\r\n","import AtomsGroup from './AtomsGroup';\r\nimport utils from '../../../utils';\r\n\r\nfunction adjustColor(color) {\r\n let r = (color >> 16) & 255;\r\n let g = (color >> 8) & 255;\r\n let b = color & 255;\r\n\r\n if (0.2126 * r + 0.7152 * g + 0.0722 * b > 127) {\r\n r = r * 3 / 10;\r\n g = g * 3 / 10;\r\n b = b * 3 / 10;\r\n } else {\r\n r = 255 - ((255 - r) * 3 / 10);\r\n g = 255 - ((255 - g) * 3 / 10);\r\n b = 255 - ((255 - b) * 3 / 10);\r\n }\r\n\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nfunction inverseColor(color) {\r\n const r = (color >> 16) & 255;\r\n const g = (color >> 8) & 255;\r\n const b = color & 255;\r\n\r\n return ((255 - r) << 16) | ((255 - g) << 8) | (255 - b);\r\n}\r\n\r\nfunction getAtomText(atom) {\r\n if (atom.name.getNode() !== null) {\r\n return atom.name.getNode();\r\n }\r\n\r\n return atom.getVisualName();\r\n}\r\n\r\nconst colorMappings = {\r\n none(c) {\r\n return c;\r\n },\r\n adjust: adjustColor,\r\n inverse: inverseColor,\r\n};\r\n\r\nfunction propagateColor(color, rule) {\r\n let result;\r\n if (colorMappings.hasOwnProperty(rule)) {\r\n result = utils.hexColor(colorMappings[rule](color));\r\n } else {\r\n const val = parseInt(rule, 16);\r\n if (!Number.isNaN(val) && rule.toLowerCase().startsWith('0x')) {\r\n result = utils.hexColor(val);\r\n } else {\r\n result = '#000000';\r\n }\r\n }\r\n return result;\r\n}\r\n\r\nconst templateMappings = {\r\n serial(a) {\r\n return a.serial;\r\n },\r\n name(a) {\r\n return a.getVisualName();\r\n },\r\n elem(a) {\r\n return a.element.name;\r\n },\r\n residue(a) {\r\n return a.residue.getType().getName();\r\n },\r\n sequence(a) {\r\n return a.residue.getSequence();\r\n },\r\n chain(a) {\r\n return a.residue.getChain().getName();\r\n },\r\n hetatm(a) {\r\n return a.isHet();\r\n },\r\n water(a) {\r\n return a.residue.getType().getName() === 'HOH' || a.residue.getType().getName() === 'WAT';\r\n },\r\n};\r\n\r\nconst parseTemplate = function (atom, str) {\r\n return str.replace(/\\{\\{(\\s*\\w+\\s*)\\}\\}/g, (m) => {\r\n let key = m.replace(/\\s+/g, '');\r\n key = key.substring(2, key.length - 2).toLowerCase();\r\n\r\n if (templateMappings.hasOwnProperty(key)) {\r\n return templateMappings[key](atom);\r\n }\r\n return 'null';\r\n });\r\n};\r\n\r\nclass AtomsTextGroup extends AtomsGroup {\r\n _makeGeoArgs() {\r\n const opts = this._mode.getLabelOpts();\r\n return [this._selection.chunks.length, opts];\r\n }\r\n\r\n _build() {\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = colorer.getAtomColor(atom, parent);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, atom.position, text);\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const opts = this._mode.getLabelOpts();\r\n const atomsIdc = this._selection.chunks;\r\n const { atoms } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = atomsIdc.length; i < n; ++i) {\r\n const atom = atoms[atomsIdc[i]];\r\n const text = opts.template ? parseTemplate(atom, opts.template) : getAtomText(atom);\r\n if (!text) {\r\n continue;\r\n }\r\n const color = frameData.getAtomColor(colorer, atom);\r\n const fgColor = parseInt(propagateColor(color, opts.fg).substring(1), 16);\r\n const bgColor = opts.showBg ? parseInt(propagateColor(color, opts.bg).substring(1), 16) : 'transparent';\r\n geo.setItem(i, frameData.getAtomPos(atomsIdc[i]), text);\r\n if (updateColor) {\r\n geo.setColor(i, fgColor, bgColor);\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default AtomsTextGroup;\r\n","import * as THREE from 'three';\r\nimport AtomsGroup from './AtomsGroup';\r\n\r\nfunction _slerp(omega, v1, v2, t) {\r\n const oSin = Math.sin(omega);\r\n return v1.clone().multiplyScalar(Math.sin((1 - t) * omega) / oSin).addScaledVector(v2, Math.sin(t * omega) / oSin);\r\n}\r\n\r\nclass AromaticGroup extends AtomsGroup {\r\n _buildInner(radOffset, addChunk) {\r\n const chunksToIdx = this._selection.chunks;\r\n\r\n const prevVector = new THREE.Vector3();\r\n const currVector = new THREE.Vector3();\r\n const segmentsHeight = this._segmentsHeight;\r\n const leprStep = 1.0 / segmentsHeight;\r\n const colorer = this._colorer;\r\n\r\n const { cycles, parent } = this._selection;\r\n let chunkIdx = 0;\r\n let currAtomIdx = chunksToIdx[chunkIdx];\r\n\r\n for (let cIdx = 0, cCount = cycles.length; cIdx < cCount; ++cIdx) {\r\n const cycle = cycles[cIdx];\r\n const cycAtoms = cycle.atoms;\r\n const chunkPoints = [];\r\n const tmpDir = [];\r\n const { center } = cycle;\r\n const cycleRad = cycle.radius - radOffset;\r\n const n = cycAtoms.length;\r\n let i = 0;\r\n const prevPos = cycAtoms[n - 1].position;\r\n let currPos = cycAtoms[i].position;\r\n prevVector.subVectors(prevPos, center);\r\n currVector.subVectors(currPos, center);\r\n const upDir = currVector.clone().cross(prevVector).normalize();\r\n\r\n for (; i < n; ++i) {\r\n const omega = prevVector.angleTo(currVector);\r\n tmpDir[i] = _slerp(omega, prevVector, currVector, 0.5).normalize();\r\n currPos = cycAtoms[(i + 1) % n].position;\r\n prevVector.copy(currVector);\r\n currVector.subVectors(currPos, center);\r\n }\r\n\r\n for (i = 0; i < n; ++i) {\r\n if (cycAtoms[i].index !== currAtomIdx) {\r\n continue;\r\n }\r\n const start = tmpDir[i];\r\n const end = tmpDir[(i + 1) % n];\r\n const color = colorer.getAtomColor(cycAtoms[i], parent);\r\n const currAngle = start.angleTo(end);\r\n\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n chunkPoints[j] = _slerp(currAngle, start, end, j * leprStep).multiplyScalar(cycleRad).add(center);\r\n }\r\n\r\n addChunk(chunkIdx++, color, chunkPoints, center, upDir);\r\n currAtomIdx = chunksToIdx[chunkIdx];\r\n }\r\n }\r\n }\r\n}\r\n\r\nexport default AromaticGroup;\r\n","import * as THREE from 'three';\r\nimport gfxutils from '../../gfxutils';\r\nimport AromaticGroup from './AromaticGroup';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n for (let i = 0; i < parts; ++i) {\r\n const a = -2 * i / parts * Math.PI;\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\nconst { calcChunkMatrix } = gfxutils;\r\n\r\nclass AromaticTorusGroup extends AromaticGroup {\r\n _build() {\r\n const segmentsHeight = this._segmentsHeight;\r\n const torusRad = this._mode.getAromRadius();\r\n const radiusV = new THREE.Vector2(torusRad, torusRad);\r\n const radOffset = this._mode.calcStickRadius() + 2 * torusRad;\r\n const lookAtVector = new THREE.Vector3();\r\n const mtc = [];\r\n const geo = this._geo;\r\n this._buildInner(radOffset, (chunkIdx, color, points, center, upDir) => {\r\n for (let j = 0; j <= segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n const currDir = currPoint.clone().sub(center).cross(upDir);\r\n lookAtVector.addVectors(currPoint, currDir);\r\n mtc[j] = calcChunkMatrix(currPoint, lookAtVector, upDir, radiusV);\r\n }\r\n geo.setItem(chunkIdx, mtc);\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._polyComplexity;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length];\r\n }\r\n}\r\n\r\nexport default AromaticTorusGroup;\r\n","import AromaticGroup from './AromaticGroup';\r\n\r\nclass AromaticLinesGroup extends AromaticGroup {\r\n _build() {\r\n const geo = this._geo;\r\n const radOffset = this._mode.getAromaticOffset();\r\n this._buildInner(radOffset, (chunkIdx, color, points) => {\r\n let prevPt = points[0];// do not replace with start\r\n for (let j = 1; j <= this._segmentsHeight; ++j) {\r\n const currPoint = points[j];\r\n geo.setSegment(chunkIdx, j - 1, prevPt, currPoint);\r\n prevPt = currPoint;\r\n }\r\n geo.setColor(chunkIdx, color);\r\n });\r\n geo.finalize();\r\n }\r\n\r\n _makeGeoArgs() {\r\n this._segmentsHeight = this._mode.getAromaticArcChunks();\r\n return [this._selection.chunks.length, this._segmentsHeight, true];\r\n }\r\n}\r\n\r\nexport default AromaticLinesGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesGroup extends ChemGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[inters[i].chunkIdx];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList.push(i);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesGroup;\r\n","import ResiduesGroup from './ResiduesGroup';\r\n\r\nclass NucleicItemGroup extends ResiduesGroup {\r\n raycast(raycaster, intersects) {\r\n const { residues } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const resIdx = chunksIdc[Math.floor(inters[i].chunkIdx / 2)];\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finalize();\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n let chunkIdx = 0;\r\n const { residues } = this._selection;\r\n const resIdc = this._chunksIdc;\r\n\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n if ((res._mask & mask) !== 0) {\r\n chunksList[chunkIdx++] = 2 * i;\r\n chunksList[chunkIdx++] = 2 * i + 1;\r\n }\r\n }\r\n return chunksList;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const stickRad = this._mode.calcStickRadius();\r\n let chunkIdx = 0;\r\n\r\n const resIdc = this._selection.chunks;\r\n for (let i = 0, n = resIdc.length; i < n; ++i) {\r\n const res = residues[resIdc[i]];\r\n const color = colorer.getResidueColor(res, parent);\r\n this._processItem(chunkIdx++, res._cylinders[0], res._cylinders[1], stickRad, color);\r\n }\r\n geo.finishUpdate();\r\n }\r\n}\r\n\r\nexport default NucleicItemGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicCylindersGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n geo.setItem(chunkIdx, cyl1, cyl2, stickRad);\r\n geo.setColor(chunkIdx, color, color);\r\n }\r\n}\r\n\r\nexport default NucleicCylindersGroup;\r\n","import NucleicItemGroup from './NucleicItemGroup';\r\n\r\nclass NucleicSpheresGroup extends NucleicItemGroup {\r\n _makeGeoArgs() {\r\n return [this._selection.chunks.length * 2, this._polyComplexity];\r\n }\r\n\r\n _processItem(chunkIdx, cyl1, cyl2, stickRad, color) {\r\n const geo = this._geo;\r\n let idx = chunkIdx * 2;\r\n geo.setItem(idx, cyl1, stickRad);\r\n geo.setColor(idx, color);\r\n idx++;\r\n geo.setItem(idx, cyl2, stickRad);\r\n geo.setColor(idx, color);\r\n }\r\n}\r\n\r\nexport default NucleicSpheresGroup;\r\n","import * as THREE from 'three';\r\nimport { Smooth } from '../../../../vendor/js/Smooth';\r\nimport gfxutils from '../../gfxutils';\r\nimport chem from '../../../chem';\r\n\r\nconst { ResidueType } = chem;\r\n\r\nconst calcMatrix = gfxutils.calcChunkMatrix;\r\n\r\nfunction _buildStructureInterpolator(points, tension) {\r\n const path = Smooth(points, {\r\n method: Smooth.METHOD_CUBIC,\r\n clip: Smooth.CLIP_CLAMP,\r\n cubicTension: tension,\r\n scaleTo: 1,\r\n });\r\n\r\n return function (t, argTrans) {\r\n let transformT = argTrans;\r\n if (transformT === null) {\r\n // map our range to the [second .. last but one]\r\n transformT = function (tt) {\r\n return (tt * ((points.length - 1) - 2) + 1) / (points.length - 1);\r\n };\r\n }\r\n const newt = transformT(t);\r\n const ans = path(newt);\r\n return new THREE.Vector3(ans[0], ans[1], ans[2]);\r\n };\r\n}\r\n\r\nfunction _addPoints(centerPoints, topPoints, idx, residue) {\r\n if (!residue._isValid) {\r\n centerPoints[idx] = centerPoints[idx - 1];\r\n topPoints[idx] = topPoints[idx - 1];\r\n return;\r\n }\r\n const cp = residue._controlPoint;\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n const tp = cp.clone().add(residue._wingVector);\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n}\r\n\r\nfunction _addPointsForLoneResidue(centerPoints, topPoints, idx, residue) {\r\n const nucleic = (residue._type.flags & ResidueType.Flags.NUCLEIC) !== 0;\r\n const nameFrom = nucleic ? 'C5\\'' : 'N';\r\n const nameTo = nucleic ? 'C3\\'' : 'C';\r\n\r\n let posFrom;\r\n let posTo;\r\n residue.forEachAtom((atom) => {\r\n const name = atom.getVisualName();\r\n if (!posFrom && name === nameFrom) {\r\n posFrom = atom.position;\r\n } else if (!posTo && name === nameTo) {\r\n posTo = atom.position;\r\n }\r\n });\r\n\r\n // provide a fallback for unknown residues\r\n if (!(posFrom && posTo)) {\r\n posFrom = residue._firstAtom.position;\r\n posTo = residue._lastAtom.position;\r\n }\r\n\r\n if (posFrom && posTo) {\r\n const shift = posTo.clone().sub(posFrom);\r\n\r\n const wing = residue._wingVector;\r\n const cp = residue._controlPoint;\r\n const tp = cp.clone().add(wing);\r\n\r\n const cpPrev = cp.clone().sub(shift);\r\n const tpPrev = cpPrev.clone().add(wing);\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n centerPoints[idx] = [cpPrev.x, cpPrev.y, cpPrev.z];\r\n topPoints[idx] = [tpPrev.x, tpPrev.y, tpPrev.z];\r\n ++idx;\r\n\r\n centerPoints[idx] = [cp.x, cp.y, cp.z];\r\n topPoints[idx] = [tp.x, tp.y, tp.z];\r\n ++idx;\r\n\r\n const cpNext = cp.clone().add(shift);\r\n const tpNext = cpNext.clone().add(wing);\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n ++idx;\r\n centerPoints[idx] = [cpNext.x, cpNext.y, cpNext.z];\r\n topPoints[idx] = [tpNext.x, tpNext.y, tpNext.z];\r\n }\r\n}\r\n\r\nfunction _calcPoints(residues, firstIdx, lastIdx, boundaries) {\r\n const left = boundaries.start;\r\n const right = boundaries.end;\r\n function _prevIdx(idx) {\r\n return idx > left && residues[idx - 1]._isValid ? idx - 1 : idx;\r\n }\r\n function _nextIdx(idx) {\r\n return idx < right && residues[idx + 1]._isValid ? idx + 1 : idx;\r\n }\r\n\r\n const topPoints = [];\r\n const centerPoints = [];\r\n let arrIdx = 0;\r\n function _extrapolate2(currIdx, otherIdx) {\r\n const cp = residues[currIdx]._controlPoint.clone().lerp(residues[otherIdx]._controlPoint, -0.25);\r\n const tp = cp.clone().add(residues[currIdx]._wingVector);\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n centerPoints[arrIdx] = [cp.x, cp.y, cp.z];\r\n topPoints[arrIdx++] = [tp.x, tp.y, tp.z];\r\n }\r\n\r\n // a single disconnected residue\r\n const prevIdx = _prevIdx(firstIdx);\r\n const nextIdx = _nextIdx(lastIdx);\r\n if (prevIdx === nextIdx) {\r\n _addPointsForLoneResidue(centerPoints, topPoints, arrIdx, residues[firstIdx]);\r\n return { centerPoints, topPoints };\r\n }\r\n\r\n // Two points (prev-prev and next-next) are added to support edge conditions for cubic splines, they are ignored\r\n // Another two (prev and next) were added to support the outside of the sub chain\r\n\r\n // prev and prev-prev\r\n if (firstIdx === prevIdx) {\r\n // do the extrapolation\r\n _extrapolate2(firstIdx, _nextIdx(firstIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[_prevIdx(prevIdx)]);\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[prevIdx]);\r\n }\r\n\r\n // main loop\r\n for (let idx = firstIdx; idx <= lastIdx; ++idx) {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[idx]);\r\n }\r\n\r\n // next and next-next\r\n if (nextIdx === _nextIdx(nextIdx)) {\r\n // do the extrapolation\r\n _extrapolate2(lastIdx, _prevIdx(lastIdx));\r\n } else {\r\n _addPoints(centerPoints, topPoints, arrIdx++, residues[nextIdx]);\r\n _addPoints(centerPoints, topPoints, arrIdx, residues[_nextIdx(nextIdx)]);\r\n }\r\n return { centerPoints, topPoints };\r\n}\r\n\r\nclass CartoonHelper {\r\n constructor(residues, startIdx, endIdx, segmentsCount, tension, boundaries) {\r\n const pointsArrays = _calcPoints(residues, startIdx, endIdx, boundaries);\r\n this._topInterp = _buildStructureInterpolator(pointsArrays.topPoints, tension);\r\n this._centerInterp = _buildStructureInterpolator(pointsArrays.centerPoints, tension);\r\n\r\n this._shift = 0.5 / (endIdx - startIdx + 2);\r\n this._valueStep = (1.0 - 2 * this._shift) / (2 * (endIdx - startIdx + 1) * (segmentsCount - 1));\r\n this._segmentsCount = segmentsCount;\r\n }\r\n\r\n prepareMatrices(idx, firstRad, secondRad) {\r\n const mtcCount = this._segmentsCount;\r\n const outMtc = new Array(mtcCount);\r\n const currRad = new THREE.Vector2(0, 0);\r\n\r\n const topInterp = this._topInterp;\r\n const cenInterp = this._centerInterp;\r\n\r\n let currentValue = this._shift + this._valueStep * (mtcCount - 1) * idx;\r\n\r\n for (let mtxIdx = 0; mtxIdx < mtcCount; ++mtxIdx) {\r\n const lerpVal = Math.min(1.0, mtxIdx / (mtcCount - 1));\r\n currRad.lerpVectors(firstRad, secondRad, lerpVal);\r\n\r\n const currTop = topInterp(currentValue, null);\r\n const currCenter = cenInterp(currentValue, null);\r\n currentValue += this._valueStep;\r\n const nextCenter = cenInterp(currentValue, null);\r\n\r\n outMtc[mtxIdx] = calcMatrix(currCenter.clone(), nextCenter.clone(), currTop.clone().sub(currCenter), currRad);\r\n }\r\n\r\n return outMtc;\r\n }\r\n}\r\n\r\nexport default CartoonHelper;\r\n","import * as THREE from 'three';\r\nimport ResiduesGroup from './ResiduesGroup';\r\nimport CartoonHelper from './CartoonHelper';\r\n\r\nfunction _createShape(rad, parts) {\r\n const pts = [];\r\n\r\n for (let i = 0; i < parts; ++i) {\r\n // starts from pi/2 because it's important that points are lied on the angles of arrows (visual issues if not)\r\n const a = Math.PI / 2.0 - 2 * Math.PI * i / parts;\r\n\r\n pts.push(new THREE.Vector3(Math.cos(a) * rad, Math.sin(a) * rad, 0));\r\n }\r\n return pts;\r\n}\r\n\r\nfunction _loopThrough(subDiv, residues, segmentsHeight, tension, mode, callback) {\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n const { boundaries } = subDiv[subDivI];\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const idc = [subs[i].start, subs[i].end];\r\n const matrixHelper = new CartoonHelper(residues, idc[0], idc[1], segmentsHeight, tension, boundaries);\r\n let prevLast = null;\r\n const startIdx = subs[i].start * 2;\r\n const endIdx = subs[i].end * 2 + 1;\r\n let prevSecondRad = mode.getResidueRadius(residues[0], 0);\r\n for (let idx = startIdx; idx <= endIdx; ++idx) {\r\n const resIdx = (idx / 2 | 0);\r\n const currRes = residues[resIdx];\r\n const firstRad = mode.getResidueRadius(currRes, idx % 2);\r\n const secondRad = mode.getResidueRadius(currRes, 1 + (idx % 2));\r\n\r\n const mtc = matrixHelper.prepareMatrices(idx - idc[0] * 2, firstRad, secondRad);\r\n mtc.unshift(prevLast === null ? mtc[0] : prevLast);\r\n\r\n // Slope - radius is changed along this residue part\r\n const hasSlope = (firstRad.x !== secondRad.x) || (firstRad.y !== secondRad.y);\r\n // Cut - end radius of previous part not equal to start radius of this part. First section of this part lies in the orthogonal plane\r\n const hasCut = (firstRad.x !== prevSecondRad.x) || (firstRad.y !== prevSecondRad.y);\r\n\r\n callback(currRes, mtc, hasSlope, hasCut);\r\n\r\n prevLast = mtc[segmentsHeight];\r\n prevSecondRad = secondRad;\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ResiduesSubseqGroup extends ResiduesGroup {\r\n _makeGeoArgs() {\r\n const cmpMultiplier = this._mode.getHeightSegmentsRatio();\r\n this._segmentsHeight = this._polyComplexity * cmpMultiplier | 0;\r\n return [_createShape(1.0, this._polyComplexity), this._segmentsHeight + 1, this._selection.chunks.length * 2];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n _loopThrough(this._selection.subdivs, residues, this._segmentsHeight, tension, mode, (currRes, mtc, hasSlope = false, hasCut = false) => {\r\n const color = colorer.getResidueColor(currRes, parent);\r\n chunkIdc[chunkIdx] = currRes._index;\r\n geo.setItem(chunkIdx, mtc, hasSlope, hasCut);\r\n geo.setColor(chunkIdx++, color);\r\n });\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const tension = mode.getTension();\r\n const geo = this._geo;\r\n const frameRes = frameData.getResidues();\r\n let chunkIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n _loopThrough(this._selection.subdivs, frameRes, this._segmentsHeight, tension, mode, (currRes, mtc) => {\r\n geo.setItem(chunkIdx, mtc);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n });\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default ResiduesSubseqGroup;\r\n","import ChemGroup from './ChemGroup';\r\n\r\nclass ResiduesTraceGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const subDiv = this._selection.subdivs;\r\n let chunksCount = 0;\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n chunksCount += subs[i].end - subs[i].start;\r\n }\r\n }\r\n return [chunksCount, this._polyComplexity];\r\n }\r\n\r\n _build() {\r\n const { residues, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const chunkIdc = [];\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n chunkIdc[chunkIdx] = { first: prevRes._index, second: currRes._index };\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n this._chunksIdc = chunkIdc;\r\n geo.finalize();\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n\r\n const residues = frameData.getResidues();\r\n const { parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n let chunkIdx = 0;\r\n const subDiv = this._selection.subdivs;\r\n const stickRad = mode.calcStickRadius();\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n\r\n for (let subDivI = 0, subDivN = subDiv.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDiv[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n const startIdx = subs[i].start;\r\n const endIdx = subs[i].end;\r\n let prevRes = residues[startIdx];\r\n for (let idx = startIdx + 1; idx <= endIdx; ++idx) {\r\n const currRes = residues[idx];\r\n geo.setItem(chunkIdx, prevRes._controlPoint, currRes._controlPoint, stickRad);\r\n if (updateColor) {\r\n geo.setColor(chunkIdx, colorer.getResidueColor(prevRes, parent), colorer.getResidueColor(currRes, parent));\r\n }\r\n chunkIdx++;\r\n prevRes = currRes;\r\n }\r\n }\r\n }\r\n\r\n geo.finalize();\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const inters = [];\r\n const { residues } = this._selection;\r\n this._mesh.raycast(raycaster, inters);\r\n const chunksToIdx = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const chunk = chunksToIdx[Math.floor(chunkIdx / 2)];\r\n const resIdx = chunkIdx % 2 === 0 ? chunk.first : chunk.second;\r\n if (resIdx < residues.length) {\r\n inters[i].residue = residues[resIdx];\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask) {\r\n const chunksList = [];\r\n const chunksToIdx = this._chunksIdc;\r\n const { residues } = this._selection;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const chunk = chunksToIdx[i];\r\n if (residues[chunk.first]._mask & mask) {\r\n chunksList.push(i * 2);\r\n }\r\n if (residues[chunk.second]._mask & mask) {\r\n chunksList.push(i * 2 + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default ResiduesTraceGroup;\r\n","import ChemGroup from './ChemGroup';\r\nimport Bond from '../../../chem/Bond';\r\n\r\nfunction getCylinderCount(bondOrder) {\r\n return bondOrder < 2 ? 1 : bondOrder;\r\n}\r\n\r\nclass BondsGroup extends ChemGroup {\r\n _makeGeoArgs() {\r\n const drawMultiple = this._mode.drawMultiorderBonds();\r\n const showAromatic = this._mode.showAromaticLoops();\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n let bondsCount = 0;\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n bondsCount += this.getBondOrder(bonds[bondsIdc[i]], drawMultiple, showAromatic);\r\n }\r\n return [bondsCount, this._polyComplexity];\r\n }\r\n\r\n getBondOrder(bond, drawMultiple, showAromatic) {\r\n let bondOrder = 1;\r\n if (drawMultiple && (!showAromatic || bond._type !== Bond.BondType.AROMATIC)) {\r\n bondOrder = getCylinderCount(bond._order);\r\n }\r\n return bondOrder;\r\n }\r\n\r\n raycast(raycaster, intersects) {\r\n const { bonds } = this._selection;\r\n const inters = [];\r\n this._mesh.raycast(raycaster, inters);\r\n const bondsIdc = this._chunksIdc;\r\n // process inters array - arr object references\r\n for (let i = 0, n = inters.length; i < n; ++i) {\r\n if (!inters[i].hasOwnProperty('chunkIdx')) {\r\n continue;\r\n }\r\n const { chunkIdx } = inters[i];\r\n const bondIdx = bondsIdc[Math.floor(chunkIdx / 2)];\r\n if (bondIdx < bonds.length) {\r\n const bond = bonds[bondIdx];\r\n inters[i].atom = chunkIdx % 2 === 0 ? bond._left : bond._right;\r\n intersects.push(inters[i]);\r\n }\r\n }\r\n }\r\n\r\n _calcChunksList(mask, innerOnly) {\r\n const chunksList = [];\r\n const { bonds } = this._selection;\r\n const chunksToIdx = this._chunksIdc;\r\n for (let i = 0, n = chunksToIdx.length; i < n; ++i) {\r\n const bond = bonds[chunksToIdx[i]];\r\n if ((bond._left.mask & mask) && (!innerOnly || (bond._right.mask & mask))) {\r\n chunksList.push(2 * i);\r\n }\r\n if ((bond._right.mask & mask) && (!innerOnly || (bond._left.mask & mask))) {\r\n chunksList.push(2 * i + 1);\r\n }\r\n }\r\n return chunksList;\r\n }\r\n}\r\n\r\nexport default BondsGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nclass BondsCylinderGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const stickRad = mode.calcStickRadius();\r\n const emptyOffset = mode.calcSpaceFraction();\r\n let normDir;\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n normDir = bond.calcNormalDir();\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n const minRad = Math.min(mode.calcAtomRadius(atom1), mode.calcAtomRadius(atom2));\r\n const dist = 2 * minRad / order;\r\n const currStickRad = drawMultiple ? Math.min(stickRad, dist * 0.5 * (1.0 - emptyOffset)) : stickRad;\r\n\r\n for (let j = 0; j < order; ++j) {\r\n const scale = dist * (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n leftPos.copy(a1Pos);\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.copy(a2Pos);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos, currStickRad);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsCylinderGroup;\r\n","import * as THREE from 'three';\r\nimport BondsGroup from './BondsGroup';\r\n\r\nconst STEP_SIZE = 0.15;\r\n\r\nclass BondsLinesGroup extends BondsGroup {\r\n _build() {\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds, parent } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const chunksToIdx = [];\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = atom1.position;\r\n const a2Pos = atom2.position;\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n chunksToIdx[currBondIdx] = bond._index;\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n geo.setColor(currBondIdx++, colorer.getAtomColor(atom1, parent), colorer.getAtomColor(atom2, parent));\r\n }\r\n }\r\n geo.finalize();\r\n this._chunksIdc = chunksToIdx;\r\n }\r\n\r\n updateToFrame(frameData) {\r\n // This method looks like a copy paste. However, it\r\n // was decided to postpone animation refactoring until GFX is fixed.\r\n const bondsIdc = this._selection.chunks;\r\n const { bonds } = this._selection;\r\n const mode = this._mode;\r\n const colorer = this._colorer;\r\n const geo = this._geo;\r\n const drawMultiple = mode.drawMultiorderBonds();\r\n const showAromatic = mode.showAromaticLoops();\r\n\r\n const bondDir = new THREE.Vector3();\r\n\r\n const leftPos = new THREE.Vector3();\r\n const rightPos = new THREE.Vector3();\r\n let currBondIdx = 0;\r\n const updateColor = frameData.needsColorUpdate(colorer);\r\n for (let i = 0, n = bondsIdc.length; i < n; ++i) {\r\n const bond = bonds[bondsIdc[i]];\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n const a1Pos = frameData.getAtomPos(atom1.index).clone();\r\n const a2Pos = frameData.getAtomPos(atom2.index);\r\n const a1Hangs = atom1.bonds.length === 1;\r\n const a2Hangs = atom2.bonds.length === 1;\r\n bondDir.subVectors(a2Pos, a1Pos);\r\n const len = bondDir.length();\r\n const normDir = bond.calcNormalDir();\r\n\r\n const order = this.getBondOrder(bond, drawMultiple, showAromatic);\r\n\r\n for (let j = 0; j < order; ++j) {\r\n leftPos.copy(a1Pos);\r\n rightPos.copy(a2Pos);\r\n let scale = (order % 2 === 0\r\n ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))\r\n : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)));\r\n if (order === 2 && (!a1Hangs && !a2Hangs)) {\r\n scale -= 0.5;\r\n scale *= -1;\r\n }\r\n\r\n if (!a1Hangs && !a2Hangs && order > 1 && scale !== 0) {\r\n leftPos.lerpVectors(a1Pos, a2Pos, STEP_SIZE / (len));\r\n rightPos.lerpVectors(a1Pos, a2Pos, 1.0 - STEP_SIZE / (len));\r\n }\r\n\r\n scale *= STEP_SIZE;\r\n\r\n leftPos.addScaledVector(normDir, scale);\r\n rightPos.addScaledVector(normDir, scale);\r\n geo.setItem(currBondIdx, leftPos, rightPos);\r\n if (updateColor) {\r\n geo.setColor(currBondIdx, frameData.getAtomColor(colorer, atom1), frameData.getAtomColor(colorer, atom2));\r\n }\r\n currBondIdx++;\r\n }\r\n }\r\n geo.finalize();\r\n }\r\n}\r\n\r\nexport default BondsLinesGroup;\r\n","import AtomsSphereGroup from './AtomsSphereGroup';\r\nimport AtomsSurfaceGroup from './AtomsSurfaceGroup';\r\nimport AtomsSASSESGroupStub from './AtomsSASSESGroupStub';\r\nimport AtomsTextGroup from './AtomsTextGroup';\r\nimport AromaticTorusGroup from './AromaticTorusGroup';\r\nimport AromaticLinesGroup from './AromaticLinesGroup';\r\nimport NucleicCylindersGroup from './NucleicCylindersGroup';\r\nimport NucleicSpheresGroup from './NucleicSpheresGroup';\r\nimport ResiduesSubseqGroup from './ResiduesSubseqGroup';\r\nimport ResiduesTraceGroup from './ResiduesTraceGroup';\r\nimport BondsCylinderGroup from './BondsCylinderGroup';\r\nimport BondsLinesGroup from './BondsLinesGroup';\r\n\r\nexport default {\r\n AtomsSphereGroup,\r\n AtomsSurfaceGroup,\r\n AtomsSASSESGroupStub,\r\n AtomsTextGroup,\r\n AromaticTorusGroup,\r\n AromaticLinesGroup,\r\n NucleicCylindersGroup,\r\n NucleicSpheresGroup,\r\n ResiduesSubseqGroup,\r\n ResiduesTraceGroup,\r\n BondsCylinderGroup,\r\n BondsLinesGroup,\r\n};\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AtomsProcessor extends RCGroup {\r\n constructor(AtomsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n this._mode = mode;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let atomCount = 0;\r\n component.forEachAtom((atom) => {\r\n if (!self._checkAtom(atom, mask)) {\r\n return;\r\n }\r\n atomsIdc[atomCount++] = atom.index;\r\n });\r\n if (atomCount === 0) {\r\n return;\r\n }\r\n const atomsGroup = new AtomsGroup(geoParams, {\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n _checkAtom(atom, mask) {\r\n return atom.mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AtomsProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\n\r\nclass OrphanAtomsProcessor extends AtomsProcessor {\r\n _checkAtom(atom, mask) {\r\n if (!(atom.mask & mask)) {\r\n return false;\r\n }\r\n\r\n const { bonds } = atom;\r\n for (let i = 0, n = bonds.length; i < n; ++i) {\r\n if ((bonds[i]._left.mask & mask) && (bonds[i]._right.mask & mask)) {\r\n return false;\r\n }\r\n }\r\n return true;\r\n }\r\n}\r\n\r\nexport default OrphanAtomsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass ResiduesProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n component.forEachResidue((residue) => {\r\n if (self._checkResidue(residue, mask)) {\r\n resIdc[chunksCount++] = residue._index;\r\n }\r\n });\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n checkResidue(residue, mask) {\r\n return residue._mask & mask;\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default ResiduesProcessor;\r\n","import ResidueProcessor from './ResiduesProcessor';\r\n\r\nclass NucleicProcessor extends ResidueProcessor {\r\n _checkResidue(residue, mask) {\r\n return mask & residue._mask && residue._cylinders !== null;\r\n }\r\n}\r\nexport default NucleicProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass SubseqsProcessor extends RCGroup {\r\n constructor(ResidueGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const residues = complex.getResidues();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const subDivs = component.getMaskedSubdivSequences(mask);\r\n\r\n let chunksCount = 0;\r\n const resIdc = [];\r\n for (let subDivI = 0, subDivN = subDivs.length; subDivI < subDivN; ++subDivI) {\r\n const subs = subDivs[subDivI].arr;\r\n for (let i = 0, n = subs.length; i < n; ++i) {\r\n for (let j = subs[i].start, jEnd = subs[i].end; j <= jEnd; ++j) {\r\n resIdc[chunksCount++] = residues[j]._index;\r\n }\r\n }\r\n }\r\n\r\n if (chunksCount === 0) {\r\n return;\r\n }\r\n const residuesGroup = new ResidueGroup(geoParams, {\r\n residues,\r\n chunks: resIdc,\r\n subdivs: subDivs,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n residuesGroup._component = component;\r\n self.add(residuesGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default SubseqsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass BondsProcessor extends RCGroup {\r\n constructor(BondsGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const bonds = complex.getBonds();\r\n const transforms = complex.getTransforms();\r\n\r\n complex.forEachComponent((component) => {\r\n const bondsIdc = [];\r\n let bondsCount = 0;\r\n component.forEachBond((bond) => {\r\n const atom1 = bond._left;\r\n const atom2 = bond._right;\r\n if (!(atom1.mask & mask) || !(atom2.mask & mask)) {\r\n return;\r\n }\r\n bondsIdc[bondsCount++] = bond._index;\r\n });\r\n if (bondsCount === 0) {\r\n return;\r\n }\r\n const bondsGroup = new BondsGroup(geoParams, {\r\n bonds,\r\n chunks: bondsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n bondsGroup._component = component;\r\n self.add(bondsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default BondsProcessor;\r\n","import RCGroup from '../../RCGroup';\r\n\r\nclass AromaticProcessor extends RCGroup {\r\n constructor(AromaticGroup, geoParams, complex, colorer, mode, polyComplexity, mask, material) {\r\n super();\r\n const self = this;\r\n this._complex = complex;\r\n const atoms = complex.getAtoms();\r\n const transforms = complex.getTransforms();\r\n if (!mode.showAromaticLoops()) {\r\n return;\r\n }\r\n\r\n complex.forEachComponent((component) => {\r\n const atomsIdc = [];\r\n let chunksCount = 0;\r\n const cycles = [];\r\n let cycleIdx = 0;\r\n component.forEachCycle((cycle) => {\r\n const cycAtoms = cycle.atoms;\r\n let perCycle = 0;\r\n for (let i = 0, n = cycAtoms.length; i < n; ++i) {\r\n if ((cycAtoms[i].mask & mask) !== 0) {\r\n ++perCycle;\r\n atomsIdc[chunksCount++] = cycAtoms[i].index;\r\n }\r\n }\r\n if (perCycle > 0) {\r\n cycles[cycleIdx++] = cycle;\r\n }\r\n });\r\n\r\n const atomsGroup = new AromaticGroup(geoParams, {\r\n cycles,\r\n atoms,\r\n chunks: atomsIdc,\r\n parent: complex,\r\n }, colorer, mode, transforms, polyComplexity, material);\r\n atomsGroup._component = component;\r\n self.add(atomsGroup);\r\n });\r\n }\r\n\r\n getSubset(mask, innerOnly) {\r\n const totalSubset = [];\r\n const { children } = this;\r\n let meshIdx = 0;\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n if (children[i].getSubset) {\r\n const chSubset = children[i].getSubset(mask, innerOnly);\r\n for (let j = 0, m = chSubset.length; j < m; ++j) {\r\n const subsetEl = chSubset[j];\r\n subsetEl._component = children[i]._component;\r\n totalSubset[meshIdx++] = subsetEl;\r\n }\r\n }\r\n }\r\n return totalSubset;\r\n }\r\n}\r\n\r\nexport default AromaticProcessor;\r\n","import AtomsProcessor from './AtomsProcessor';\r\nimport OrphanAtomsProcessor from './OrphanAtomsProcessor';\r\nimport ResiduesProcessor from './ResiduesProcessor';\r\nimport NucleicProcessor from './NucleicProcessor';\r\nimport SubseqsProcessor from './SubseqsProcessor';\r\nimport BondsProcessor from './BondsProcessor';\r\nimport AromaticProcessor from './AromaticProcessor';\r\n\r\nexport default {\r\n Atoms: AtomsProcessor,\r\n OrphanAtoms: OrphanAtomsProcessor,\r\n Residues: ResiduesProcessor,\r\n Nucleic: NucleicProcessor,\r\n Subseqs: SubseqsProcessor,\r\n Bonds: BondsProcessor,\r\n Aromatic: AromaticProcessor,\r\n};\r\n","import MeshCreator from '../../meshes/MeshCreator';\r\nimport groups from './groups';\r\nimport processors from '../processors/processors';\r\n\r\nfunction _bakeGroup(triplet, Processor, Group) {\r\n return function (complex, colorer, mode, polyComplexity, mask, material) {\r\n return new Processor(Group, triplet, complex, colorer, mode, polyComplexity, mask, material);\r\n };\r\n}\r\n\r\nclass GroupsFactory {\r\n static AtomsSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static OrphanedAtomsCrosses(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createCrosses(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.OrphanAtoms, groups.AtomsSphereGroup);\r\n }\r\n\r\n static BondsCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsCylinderGroup);\r\n }\r\n\r\n static BondsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.create2CLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Bonds, groups.BondsLinesGroup);\r\n }\r\n\r\n static CartoonChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesSubseqGroup);\r\n }\r\n\r\n static TraceChains(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CClosedCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Subseqs, groups.ResiduesTraceGroup);\r\n }\r\n\r\n static NucleicSpheres(caps, settings) {\r\n const gfxTriplet = MeshCreator.createSpheres(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicSpheresGroup);\r\n }\r\n\r\n static NucleicCylinders(caps, settings) {\r\n const gfxTriplet = MeshCreator.create2CCylinders(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Nucleic, groups.NucleicCylindersGroup);\r\n }\r\n\r\n static ALoopsTorus(caps, settings) {\r\n const gfxTriplet = MeshCreator.createExtrudedChains(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticTorusGroup);\r\n }\r\n\r\n static ALoopsLines(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createChunkedLines(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Aromatic, groups.AromaticLinesGroup);\r\n }\r\n\r\n static QuickSurfGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createQuickSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static ContactSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createContactSurface(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSurfaceGroup);\r\n }\r\n\r\n static SASSESSurfaceGeo(caps, settings, renderParams) {\r\n const gfxTriplet = MeshCreator.createSASSES(caps, settings, renderParams);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsSASSESGroupStub);\r\n }\r\n\r\n static TextLabelsGeo(caps, settings) {\r\n const gfxTriplet = MeshCreator.createLabels(caps, settings);\r\n\r\n return _bakeGroup(gfxTriplet, processors.Atoms, groups.AtomsTextGroup);\r\n }\r\n}\r\n\r\nexport default GroupsFactory;\r\n","import _ from 'lodash';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\nimport factory from './groups/GroupsFactory';\r\n\r\n/**\r\n * Create new mode.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the mode after its creation.\r\n *\r\n * @exports Mode\r\n * @this Mode\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available modes used for building and displaying molecule geometry.\r\n */\r\nclass Mode {\r\n constructor(opts) {\r\n if (this.constructor === Mode) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Mode options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts);\r\n }\r\n\r\n /**\r\n * Get mode identification, probably with options.\r\n * @returns {string|Array} Mode identifier string ({@link Mode#id}) or two-element array containing both mode\r\n * identifier and options ({@link Mode#opts}).\r\n * Options are returned if they were changed during or after the mode creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, this.settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const polyComplexity = this.opts.polyComplexity ? this.opts.polyComplexity[this.settings.now.resolution] : 0;\r\n const groupList = this.depGroups;\r\n const groupCount = groupList.length;\r\n const group = new gfxutils.RCGroup();\r\n const self = this;\r\n for (let i = 0; i < groupCount; ++i) {\r\n let currGroup = groupList[i];\r\n let renderParams = {};\r\n if (_.isArray(currGroup)) {\r\n renderParams = currGroup[1].call(this);\r\n [currGroup] = currGroup;\r\n }\r\n const Group = factory[currGroup](null, this.settings, renderParams);\r\n const newGroup = new Group(complex, colorer, self, polyComplexity, mask, material);\r\n if (newGroup.children.length > 0) {\r\n group.add(newGroup);\r\n }\r\n }\r\n return group;\r\n }\r\n}\r\n\r\nmakeContextDependent(Mode.prototype);\r\n\r\n/**\r\n* Mode identifier.\r\n* @type {string}\r\n*/\r\nMode.prototype.id = '__';\r\n\r\n/**\r\n * Mode geo groups.\r\n * @type {Array}\r\n */\r\nMode.prototype.depGroups = [];\r\n\r\nexport default Mode;\r\n","import Mode from './Mode';\r\n\r\nfunction getRenderParams() {\r\n return {\r\n lineWidth: this.opts.lineWidth,\r\n };\r\n}\r\n\r\nclass LinesMode extends Mode {\r\n static id = 'LN';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const groups = this.depGroups;\r\n for (let i = 0, n = groups.length; i < n; ++i) {\r\n groups[i] = [groups[i], getRenderParams];\r\n }\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n\r\n calcAtomRadius() {\r\n return this.opts.atom;\r\n }\r\n\r\n getAromaticOffset() {\r\n return this.opts.offsarom;\r\n }\r\n\r\n getAromaticArcChunks() {\r\n return this.opts.chunkarom;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n}\r\n\r\nLinesMode.prototype.id = 'LN';\r\nLinesMode.prototype.name = 'Lines';\r\nLinesMode.prototype.shortName = 'Lines';\r\nLinesMode.prototype.depGroups = [\r\n 'ALoopsLines',\r\n 'BondsLines',\r\n 'OrphanedAtomsCrosses',\r\n];\r\n\r\nexport default LinesMode;\r\n","import Mode from './Mode';\r\n\r\nclass LicoriceMode extends Mode {\r\n static id = 'LC';\r\n\r\n calcAtomRadius(_atom) {\r\n return this.opts.bond;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nLicoriceMode.prototype.id = 'LC';\r\nLicoriceMode.prototype.name = 'Licorice';\r\nLicoriceMode.prototype.shortName = 'Licorice';\r\nLicoriceMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default LicoriceMode;\r\n","import Mode from './Mode';\r\n\r\nclass BallsAndSticksMode extends Mode {\r\n static id = 'BS';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius * this.opts.atom;\r\n }\r\n\r\n calcStickRadius() {\r\n return this.opts.bond;\r\n }\r\n\r\n getAromRadius() {\r\n return this.opts.aromrad;\r\n }\r\n\r\n showAromaticLoops() {\r\n return this.opts.showarom;\r\n }\r\n\r\n calcSpaceFraction() {\r\n return this.opts.space;\r\n }\r\n\r\n drawMultiorderBonds() {\r\n return this.opts.multibond;\r\n }\r\n}\r\n\r\nBallsAndSticksMode.prototype.id = 'BS';\r\nBallsAndSticksMode.prototype.name = 'Balls and Sticks';\r\nBallsAndSticksMode.prototype.shortName = 'Balls';\r\nBallsAndSticksMode.prototype.depGroups = [\r\n 'AtomsSpheres',\r\n 'BondsCylinders',\r\n 'ALoopsTorus',\r\n];\r\n\r\nexport default BallsAndSticksMode;\r\n","import Mode from './Mode';\r\n\r\nclass VanDerWaalsMode extends Mode {\r\n static id = 'VW';\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n}\r\n\r\nVanDerWaalsMode.prototype.id = 'VW';\r\nVanDerWaalsMode.prototype.name = 'Van der Waals';\r\nVanDerWaalsMode.prototype.shortName = 'VDW';\r\nVanDerWaalsMode.prototype.depGroups = ['AtomsSpheres'];\r\n\r\nexport default VanDerWaalsMode;\r\n","import Mode from './Mode';\r\n\r\nclass TraceMode extends Mode {\r\n static id = 'TR';\r\n\r\n calcStickRadius() {\r\n return this.opts.radius;\r\n }\r\n}\r\n\r\nTraceMode.prototype.id = 'TR';\r\nTraceMode.prototype.name = 'Trace';\r\nTraceMode.prototype.shortName = 'Trace';\r\nTraceMode.prototype.depGroups = ['TraceChains'];\r\n\r\nexport default TraceMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass TubeMode extends Mode {\r\n static id = 'TU';\r\n\r\n getResidueRadius(_residue) {\r\n return this.TUBE_RADIUS;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const rad = this.opts.radius;\r\n this.TUBE_RADIUS = new THREE.Vector2(rad, rad);\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nTubeMode.prototype.id = 'TU';\r\nTubeMode.prototype.name = 'Tube';\r\nTubeMode.prototype.shortName = 'Tube';\r\nTubeMode.prototype.depGroups = ['CartoonChains'];\r\n\r\nexport default TubeMode;\r\n","import * as THREE from 'three';\r\nimport Mode from './Mode';\r\n\r\nclass CartoonMode extends Mode {\r\n static id = 'CA';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n // cache for secondary structure options\r\n this.secCache = {};\r\n }\r\n\r\n getResidueStartRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (!second || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return secOpts.start;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueEndRadius(residue) {\r\n const second = residue.getSecondary();\r\n if (second === null || !second.generic) {\r\n return this.TUBE_RADIUS;\r\n }\r\n const secOpts = this.secCache[second.generic];\r\n if (!secOpts) {\r\n return this.TUBE_RADIUS;\r\n }\r\n if (second.term === residue) {\r\n return this.ARROW_END;\r\n }\r\n return secOpts.center;\r\n }\r\n\r\n getResidueRadius(residue, val) {\r\n const startRad = this.getResidueStartRadius(residue);\r\n if (val === 0) {\r\n return startRad;\r\n }\r\n\r\n const endRad = this.getResidueEndRadius(residue);\r\n if (val === 2) {\r\n return endRad;\r\n }\r\n\r\n return startRad.clone().lerp(endRad, val / 2.0);\r\n }\r\n\r\n calcStickRadius(_res) {\r\n return this.opts.radius;\r\n }\r\n\r\n getHeightSegmentsRatio() {\r\n return this.opts.heightSegmentsRatio;\r\n }\r\n\r\n getTension() {\r\n return this.opts.tension;\r\n }\r\n\r\n buildGeometry(complex, colorer, mask, material) {\r\n const tubeRad = this.opts.radius;\r\n const secHeight = this.opts.depth;\r\n\r\n this.TUBE_RADIUS = new THREE.Vector2(tubeRad, tubeRad);\r\n this.ARROW_END = new THREE.Vector2(secHeight, tubeRad);\r\n const secCache = {};\r\n const secData = this.opts.ss;\r\n /* eslint-disable guard-for-in */\r\n for (const prop in secData) {\r\n secCache[prop] = {\r\n center: new THREE.Vector2(secHeight, secData[prop].width),\r\n start: new THREE.Vector2(secHeight, secData[prop].arrow),\r\n };\r\n }\r\n this.secCache = secCache;\r\n /* eslint-enable guard-for-in */\r\n\r\n return Mode.prototype.buildGeometry.call(this, complex, colorer, mask, material);\r\n }\r\n}\r\n\r\nCartoonMode.prototype.id = 'CA';\r\nCartoonMode.prototype.name = 'Cartoon';\r\nCartoonMode.prototype.shortName = 'Cartoon';\r\nCartoonMode.prototype.depGroups = [\r\n 'CartoonChains',\r\n 'NucleicSpheres',\r\n 'NucleicCylinders',\r\n];\r\n\r\nexport default CartoonMode;\r\n","import chem from '../../chem';\r\nimport Mode from './Mode';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction getRenderParams() {\r\n return {\r\n wireframe: this.opts.wireframe,\r\n zClip: this.opts.zClip,\r\n };\r\n}\r\n\r\nclass SurfaceMode extends Mode {\r\n constructor(opts) {\r\n super(opts);\r\n this.depGroups = this.depGroups.slice(0); // clone depGroups to prevent prototype edits\r\n const surfaces = this.surfaceNames;\r\n const groups = this.depGroups;\r\n for (let i = 0, n = surfaces.length; i < n; ++i) {\r\n groups[groups.length] = [surfaces[i], getRenderParams];\r\n }\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getVisibilitySelector() {\r\n let visibilitySelector = null;\r\n if (this.opts.subset !== '') {\r\n const res = selectors.parse(this.opts.subset);\r\n if (!res.error) {\r\n visibilitySelector = res.selector;\r\n }\r\n }\r\n return visibilitySelector;\r\n }\r\n}\r\n\r\nSurfaceMode.prototype.isSurface = true;\r\nSurfaceMode.prototype.surfaceNames = [];\r\n\r\nexport default SurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass QuickSurfaceMode extends SurfaceMode {\r\n static id = 'QS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n useBeads: false,\r\n isoValue: this.opts.isoValue,\r\n gaussLim: this.opts.gaussLim[this.settings.now.resolution],\r\n radScale: this.opts.scale,\r\n gridSpacing: this.opts.gridSpacing[this.settings.now.resolution],\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nQuickSurfaceMode.prototype.id = 'QS';\r\nQuickSurfaceMode.prototype.name = 'Quick Surface';\r\nQuickSurfaceMode.prototype.shortName = 'Quick Surf';\r\nQuickSurfaceMode.prototype.surfaceNames = ['QuickSurfGeo'];\r\n\r\nexport default QuickSurfaceMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass IsoSurfaceMode extends SurfaceMode {\r\n constructor(excludeProbe, opts) {\r\n super(opts);\r\n this._excludeProbe = excludeProbe;\r\n }\r\n\r\n calcAtomRadius(atom) {\r\n return atom.element.radius;\r\n }\r\n\r\n getSurfaceOpts() {\r\n return {\r\n gridSpacing: this.opts.polyComplexity[this.settings.now.resolution],\r\n radScale: this._radScale,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n probeRadius: this.opts.probeRadius,\r\n excludeProbe: this._excludeProbe,\r\n };\r\n }\r\n}\r\n\r\nIsoSurfaceMode.prototype.id = 'SU';\r\nIsoSurfaceMode.prototype.name = 'Surface';\r\nIsoSurfaceMode.prototype.shortName = 'Surface';\r\nIsoSurfaceMode.prototype.surfaceNames = ['SASSESSurfaceGeo'];\r\n\r\nIsoSurfaceMode.prototype._radScale = 1;\r\nIsoSurfaceMode.prototype._excludeProbe = false;\r\n\r\nexport default IsoSurfaceMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSASMode extends IsoSurfaceMode {\r\n static id = 'SA';\r\n\r\n constructor(opts) {\r\n super(false, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSASMode.prototype.id = 'SA';\r\nIsoSurfaceSASMode.prototype.name = 'Solvent Accessible Surface';\r\nIsoSurfaceSASMode.prototype.shortName = 'SAS';\r\n\r\nexport default IsoSurfaceSASMode;\r\n","import IsoSurfaceMode from './IsoSurfaceMode';\r\n\r\nclass IsoSurfaceSESMode extends IsoSurfaceMode {\r\n static id = 'SE';\r\n\r\n constructor(opts) {\r\n super(true, opts);\r\n }\r\n}\r\n\r\nIsoSurfaceSESMode.prototype.id = 'SE';\r\nIsoSurfaceSESMode.prototype.name = 'Solvent Excluded Surface';\r\nIsoSurfaceSESMode.prototype.shortName = 'SES';\r\n\r\nexport default IsoSurfaceSESMode;\r\n","import SurfaceMode from './SurfaceMode';\r\n\r\nclass ContactSurfaceMode extends SurfaceMode {\r\n static id = 'CS';\r\n\r\n getSurfaceOpts() {\r\n return {\r\n probeRadius: this.opts.probeRadius,\r\n radScale: this.opts.polyComplexity[this.settings.now.resolution],\r\n scaleFactor: this.opts.polyComplexity[this.settings.now.resolution],\r\n gridSpacing: 1.0 / this.opts.polyComplexity[this.settings.now.resolution],\r\n isoValue: this.opts.isoValue,\r\n probePositions: this.opts.probePositions,\r\n zClip: this.opts.zClip,\r\n visibilitySelector: this.getVisibilitySelector(),\r\n };\r\n }\r\n}\r\n\r\nContactSurfaceMode.prototype.id = 'CS';\r\nContactSurfaceMode.prototype.name = 'Contact Surface';\r\nContactSurfaceMode.prototype.shortName = 'Contact Surf';\r\nContactSurfaceMode.prototype.isSurface = true;\r\nContactSurfaceMode.prototype.surfaceNames = ['ContactSurfaceGeo'];\r\n\r\nexport default ContactSurfaceMode;\r\n","import _ from 'lodash';\r\nimport Mode from './Mode';\r\n\r\nclass TextMode extends Mode {\r\n static id = 'TX';\r\n\r\n getTemplateOptions() {\r\n return this.opts.template;\r\n }\r\n\r\n getLabelOpts() {\r\n return _.merge(this.opts, {\r\n colors: true,\r\n adjustColor: true,\r\n transparent: true,\r\n });\r\n }\r\n}\r\n\r\nTextMode.prototype.id = 'TX';\r\nTextMode.prototype.name = 'Text mode';\r\nTextMode.prototype.shortName = 'Text';\r\nTextMode.prototype.depGroups = ['TextLabelsGeo'];\r\n\r\nexport default TextMode;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport LinesMode from './modes/LinesMode';\r\nimport LicoriceMode from './modes/LicoriceMode';\r\nimport BallsAndSticksMode from './modes/BallsAndSticksMode';\r\nimport VanDerWaalsMode from './modes/VanDerWaalsMode';\r\nimport TraceMode from './modes/TraceMode';\r\nimport TubeMode from './modes/TubeMode';\r\nimport CartoonMode from './modes/CartoonMode';\r\nimport QuickSurfaceMode from './modes/QuickSurfaceMode';\r\nimport IsoSurfaceSASMode from './modes/IsoSurfaceSASMode';\r\nimport IsoSurfaceSESMode from './modes/IsoSurfaceSESMode';\r\nimport ContactSurfaceMode from './modes/ContactSurfaceMode';\r\nimport TextMode from './modes/TextMode';\r\n\r\nconst modes = new EntityList([\r\n LinesMode,\r\n LicoriceMode,\r\n BallsAndSticksMode,\r\n VanDerWaalsMode,\r\n TraceMode,\r\n TubeMode,\r\n CartoonMode,\r\n QuickSurfaceMode,\r\n IsoSurfaceSASMode,\r\n IsoSurfaceSESMode,\r\n ContactSurfaceMode,\r\n TextMode,\r\n]);\r\n\r\nexport default modes;\r\n","import _ from 'lodash';\r\n\r\nfunction clamp(x, a, b) {\r\n return x <= b ? x < 0 ? 0 : x : b;\r\n}\r\n\r\nfunction lerpColor(c1, c2, alpha) {\r\n const beta = 1 - alpha;\r\n const r1 = (c1 >> 16) & 0xff;\r\n const g1 = (c1 >> 8) & 0xff;\r\n const b1 = c1 & 0xff;\r\n const r2 = (c2 >> 16) & 0xff;\r\n const g2 = (c2 >> 8) & 0xff;\r\n const b2 = c2 & 0xff;\r\n const r = beta * r1 + alpha * r2;\r\n const g = beta * g1 + alpha * g2;\r\n const b = beta * b1 + alpha * b2;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\nclass Palette {\r\n constructor(name, id) {\r\n this.name = name || 'Custom';\r\n this.id = id || 'CP';\r\n }\r\n\r\n getElementColor(name, asIs = false) {\r\n const color = this.elementColors[name];\r\n return color === undefined && !asIs ? this.defaultElementColor : color;\r\n }\r\n\r\n getResidueColor(name, asIs = false) {\r\n const color = this.residueColors[name];\r\n return color === undefined && !asIs ? this.defaultResidueColor : color;\r\n }\r\n\r\n getChainColor(name) {\r\n let chain = name.charCodeAt(0);\r\n chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F)\r\n % this.chainColors.length;\r\n return this.chainColors[chain];\r\n }\r\n\r\n getSecondaryColor(type, asIs = false) {\r\n const color = this.secondaryColors[type];\r\n return color === undefined && !asIs ? this.defaultSecondaryColor : color;\r\n }\r\n\r\n getSequentialColor(index) {\r\n const { colors } = this;\r\n const len = colors.length;\r\n return index < 0 ? colors[(index % len) + len] : colors[index % len];\r\n }\r\n\r\n getGradientColor(value, gradientName) {\r\n const gradient = this.gradients[gradientName];\r\n if (!gradient) {\r\n return this.defaultNamedColor;\r\n }\r\n const count = gradient.length;\r\n const index = value * (count - 1);\r\n let left = Math.floor(index);\r\n const right = clamp(left + 1, 0, count - 1);\r\n left = clamp(left, 0, count - 1);\r\n return lerpColor(gradient[left], gradient[right], index - left);\r\n }\r\n\r\n getNamedColor(name, asIs = false) {\r\n const color = this.namedColors[name];\r\n return color === undefined && !asIs ? this.defaultNamedColor : color;\r\n }\r\n}\r\n\r\n_.assign(Palette.prototype, {\r\n colors: [0xFFFFFF, 0xFF0000, 0x00FF00, 0x0000FF, 0x808080],\r\n\r\n minRangeColor: 0x000000,\r\n midRangeColor: 0x7F7F7F,\r\n maxRangeColor: 0xFFFFFF,\r\n\r\n defaultElementColor: 0xFFFFFF,\r\n elementColors: {},\r\n\r\n defaultResidueColor: 0xFFFFFF,\r\n residueColors: {},\r\n\r\n chainColors: [0xFFFFFF],\r\n\r\n defaultSecondaryColor: 0xFFFFFF,\r\n secondaryColors: {},\r\n\r\n defaultGradientColor: 0x000000,\r\n\r\n defaultNamedColor: 0xFFFFFF,\r\n namedColorsArray: [\r\n /* eslint-disable no-multi-spaces */\r\n ['indianred', 0xcd5c5c],\r\n ['lightcoral', 0xf08080],\r\n ['salmon', 0xfa8072],\r\n ['darksalmon', 0xe9967a],\r\n ['lightsalmon', 0xffa07a],\r\n ['crimson', 0xdc143c],\r\n ['red', 0xff0000],\r\n ['firebrick', 0xb22222],\r\n ['darkred', 0x8b0000],\r\n ['pink', 0xffc0cb],\r\n ['lightpink', 0xffb6c1],\r\n ['hotpink', 0xff69b4],\r\n ['deeppink', 0xff1493],\r\n ['mediumvioletred', 0xc71585],\r\n ['palevioletred', 0xdb7093],\r\n ['coral', 0xff7f50],\r\n ['tomato', 0xff6347],\r\n ['orangered', 0xff4500],\r\n ['darkorange', 0xff8c00],\r\n ['orange', 0xffa500],\r\n ['gold', 0xffd700],\r\n ['yellow', 0xffff00],\r\n ['lightyellow', 0xffffe0],\r\n ['lemonchiffon', 0xfffacd],\r\n ['lightgoldenrodyellow', 0xfafad2],\r\n ['papayawhip', 0xffefd5],\r\n ['moccasin', 0xffe4b5],\r\n ['peachpuff', 0xffdab9],\r\n ['palegoldenrod', 0xeee8aa],\r\n ['khaki', 0xf0e68c],\r\n ['darkkhaki', 0xbdb76b],\r\n ['lavender', 0xe6e6fa],\r\n ['thistle', 0xd8bfd8],\r\n ['plum', 0xdda0dd],\r\n ['violet', 0xee82ee],\r\n ['orchid', 0xda70d6],\r\n ['fuchsia', 0xff00ff],\r\n ['magenta', 0xff00ff],\r\n ['mediumorchid', 0xba55d3],\r\n ['mediumpurple', 0x9370db],\r\n ['rebeccapurple', 0x663399],\r\n ['blueviolet', 0x8a2be2],\r\n ['darkviolet', 0x9400d3],\r\n ['darkorchid', 0x9932cc],\r\n ['darkmagenta', 0x8b008b],\r\n ['purple', 0x800080],\r\n ['indigo', 0x4b0082],\r\n ['slateblue', 0x6a5acd],\r\n ['mediumslateblue', 0x7b68ee],\r\n ['darkslateblue', 0x483d8b],\r\n ['greenyellow', 0xadff2f],\r\n ['chartreuse', 0x7fff00],\r\n ['lawngreen', 0x7cfc00],\r\n ['lime', 0x00ff00],\r\n ['limegreen', 0x32cd32],\r\n ['palegreen', 0x98fb98],\r\n ['lightgreen', 0x90ee90],\r\n ['mediumspringgreen', 0x00fa9a],\r\n ['springgreen', 0x00ff7f],\r\n ['mediumseagreen', 0x3cb371],\r\n ['seagreen', 0x2e8b57],\r\n ['forestgreen', 0x228b22],\r\n ['green', 0x008000],\r\n ['darkgreen', 0x006400],\r\n ['yellowgreen', 0x9acd32],\r\n ['olivedrab', 0x6b8e23],\r\n ['olive', 0x808000],\r\n ['darkolivegreen', 0x556b2f],\r\n ['mediumaquamarine', 0x66cdaa],\r\n ['darkseagreen', 0x8fbc8f],\r\n ['lightseagreen', 0x20b2aa],\r\n ['darkcyan', 0x008b8b],\r\n ['teal', 0x008080],\r\n ['aqua', 0x00ffff],\r\n ['cyan', 0x00ffff],\r\n ['lightcyan', 0xe0ffff],\r\n ['paleturquoise', 0xafeeee],\r\n ['aquamarine', 0x7fffd4],\r\n ['turquoise', 0x40e0d0],\r\n ['mediumturquoise', 0x48d1cc],\r\n ['darkturquoise', 0x00ced1],\r\n ['cadetblue', 0x5f9ea0],\r\n ['steelblue', 0x4682b4],\r\n ['lightsteelblue', 0xb0c4de],\r\n ['powderblue', 0xb0e0e6],\r\n ['lightblue', 0xadd8e6],\r\n ['skyblue', 0x87ceeb],\r\n ['lightskyblue', 0x87cefa],\r\n ['deepskyblue', 0x00bfff],\r\n ['dodgerblue', 0x1e90ff],\r\n ['cornflowerblue', 0x6495ed],\r\n ['royalblue', 0x4169e1],\r\n ['blue', 0x0000ff],\r\n ['mediumblue', 0x0000cd],\r\n ['darkblue', 0x00008b],\r\n ['navy', 0x000080],\r\n ['midnightblue', 0x191970],\r\n ['cornsilk', 0xfff8dc],\r\n ['blanchedalmond', 0xffebcd],\r\n ['bisque', 0xffe4c4],\r\n ['navajowhite', 0xffdead],\r\n ['wheat', 0xf5deb3],\r\n ['burlywood', 0xdeb887],\r\n ['tan', 0xd2b48c],\r\n ['rosybrown', 0xbc8f8f],\r\n ['sandybrown', 0xf4a460],\r\n ['goldenrod', 0xdaa520],\r\n ['darkgoldenrod', 0xb8860b],\r\n ['peru', 0xcd853f],\r\n ['chocolate', 0xd2691e],\r\n ['saddlebrown', 0x8b4513],\r\n ['sienna', 0xa0522d],\r\n ['brown', 0xa52a2a],\r\n ['maroon', 0x800000],\r\n ['white', 0xffffff],\r\n ['snow', 0xfffafa],\r\n ['honeydew', 0xf0fff0],\r\n ['mintcream', 0xf5fffa],\r\n ['azure', 0xf0ffff],\r\n ['aliceblue', 0xf0f8ff],\r\n ['ghostwhite', 0xf8f8ff],\r\n ['whitesmoke', 0xf5f5f5],\r\n ['seashell', 0xfff5ee],\r\n ['beige', 0xf5f5dc],\r\n ['oldlace', 0xfdf5e6],\r\n ['floralwhite', 0xfffaf0],\r\n ['ivory', 0xfffff0],\r\n ['antiquewhite', 0xfaebd7],\r\n ['linen', 0xfaf0e6],\r\n ['lavenderblush', 0xfff0f5],\r\n ['mistyrose', 0xffe4e1],\r\n ['gainsboro', 0xdcdcdc],\r\n ['lightgray', 0xd3d3d3],\r\n ['silver', 0xc0c0c0],\r\n ['darkgray', 0xa9a9a9],\r\n ['gray', 0x808080],\r\n ['dimgray', 0x696969],\r\n ['lightslategray', 0x778899],\r\n ['slategray', 0x708090],\r\n ['darkslategray', 0x2f4f4f],\r\n ['black', 0x000000],\r\n /* eslint-enable no-multi-spaces */\r\n ],\r\n\r\n namedColors: {},\r\n\r\n gradients: {\r\n rainbow: [\r\n 0x0000ff, // blue\r\n 0x00ffff, // cyan\r\n 0x00ff00, // green\r\n 0xffff00, // yellow\r\n 0xff0000, // red\r\n ],\r\n temp: [\r\n 0x0000ff, // blue\r\n 0x007fff, // light-blue\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n hot: [\r\n 0xffffff, // white\r\n 0xff7f00, // orange\r\n 0xff0000, // red\r\n ],\r\n cold: [\r\n 0xffffff, // white\r\n 0x007fff, // light-blue\r\n 0x0000ff, // blue\r\n ],\r\n 'blue-red': [\r\n 0x0000ff, // blue\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n reds: [\r\n 0xffffff, // white\r\n 0xff0000, // red\r\n ],\r\n blues: [\r\n 0xffffff, // white\r\n 0x0000ff, // blue\r\n ],\r\n },\r\n});\r\n\r\nconst { namedColorsArray, namedColors } = Palette.prototype;\r\n\r\nfor (let i = 0, { length } = namedColorsArray; i < length; ++i) {\r\n const [name, value] = namedColorsArray[i];\r\n namedColors[name] = value;\r\n}\r\n\r\nexport default Palette;\r\n","import Palette from './Palette';\r\n\r\nconst palette = new Palette('CPK', 'CP');\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n C: 0x202020,\r\n N: 0x2060FF,\r\n O: 0xEE2010,\r\n F: 0x00FF00,\r\n P: 0x8020FF,\r\n S: 0xFFFF00,\r\n CL: 0x00BB00,\r\n FE: 0xD0D0D0,\r\n CO: 0xD0D0D0,\r\n NI: 0xD0D0D0,\r\n CU: 0xD0D0D0,\r\n BR: 0x008800,\r\n I: 0x005500,\r\n\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('Jmol', 'JM');\r\n\r\npalette.colors = [\r\n\r\n 0x0000FF, // blue\r\n 0x0055FF, //\r\n 0x00ABFF, //\r\n 0x00FFFF, // cyan\r\n 0x00FFAB, //\r\n 0x00FF55, //\r\n 0x00FF00, // green\r\n 0x55FF00, //\r\n 0xABFF00, //\r\n 0xFFFF00, // yellow\r\n 0xFFAB00, //\r\n 0xFF5500, //\r\n 0xFF0000, // red\r\n 0xFF0055, //\r\n 0xFF00AB, //\r\n 0xFF00FF, // magenta\r\n 0xAB00FF, //\r\n 0x5500FF, //\r\n\r\n];\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n D: 0xFFFFC0,\r\n T: 0xFFFFA0,\r\n HE: 0xD9FFFF,\r\n LI: 0xCC80FF,\r\n BE: 0xC2FF00,\r\n B: 0xFFB5B5,\r\n C: 0x909090,\r\n N: 0x3050F8,\r\n O: 0xFF0D0D,\r\n F: 0x90E050,\r\n NE: 0xB3E3F5,\r\n NA: 0xAB5CF2,\r\n MG: 0x8AFF00,\r\n AL: 0xBFA6A6,\r\n SI: 0xF0C8A0,\r\n P: 0xFF8000,\r\n S: 0xFFFF30,\r\n CL: 0x1FF01F,\r\n AR: 0x80D1E3,\r\n K: 0x8F40D4,\r\n CA: 0x3DFF00,\r\n SC: 0xE6E6E6,\r\n TI: 0xBFC2C7,\r\n V: 0xA6A6AB,\r\n CR: 0x8A99C7,\r\n MN: 0x9C7AC7,\r\n FE: 0xE06633,\r\n CO: 0xF090A0,\r\n NI: 0x50D050,\r\n CU: 0xC88033,\r\n ZN: 0x7D80B0,\r\n GA: 0xC28F8F,\r\n GE: 0x668F8F,\r\n AS: 0xBD80E3,\r\n SE: 0xFFA100,\r\n BR: 0xA62929,\r\n KR: 0x5CB8D1,\r\n RB: 0x702EB0,\r\n SR: 0x00FF00,\r\n Y: 0x94FFFF,\r\n ZR: 0x94E0E0,\r\n NB: 0x73C2C9,\r\n MO: 0x54B5B5,\r\n TC: 0x3B9E9E,\r\n RU: 0x248F8F,\r\n RH: 0x0A7D8C,\r\n PD: 0x006985,\r\n AG: 0xC0C0C0,\r\n CD: 0xFFD98F,\r\n IN: 0xA67573,\r\n SN: 0x668080,\r\n SB: 0x9E63B5,\r\n TE: 0xD47A00,\r\n I: 0x940094,\r\n XE: 0x429EB0,\r\n CS: 0x57178F,\r\n BA: 0x00C900,\r\n LA: 0x70D4FF,\r\n CE: 0xFFFFC7,\r\n PR: 0xD9FFC7,\r\n ND: 0xC7FFC7,\r\n PM: 0xA3FFC7,\r\n SM: 0x8FFFC7,\r\n EU: 0x61FFC7,\r\n GD: 0x45FFC7,\r\n TB: 0x30FFC7,\r\n DY: 0x1FFFC7,\r\n HO: 0x00FF9C,\r\n ER: 0x00E675,\r\n TM: 0x00D452,\r\n YB: 0x00BF38,\r\n LU: 0x00AB24,\r\n HF: 0x4DC2FF,\r\n TA: 0x4DA6FF,\r\n W: 0x2194D6,\r\n RE: 0x267DAB,\r\n OS: 0x266696,\r\n IR: 0x175487,\r\n PT: 0xD0D0E0,\r\n AU: 0xFFD123,\r\n HG: 0xB8B8D0,\r\n TL: 0xA6544D,\r\n PB: 0x575961,\r\n BI: 0x9E4FB5,\r\n PO: 0xAB5C00,\r\n AT: 0x754F45,\r\n RN: 0x428296,\r\n FR: 0x420066,\r\n RA: 0x007D00,\r\n AC: 0x70ABFA,\r\n TH: 0x00BAFF,\r\n PA: 0x00A1FF,\r\n U: 0x008FFF,\r\n NP: 0x0080FF,\r\n PU: 0x006BFF,\r\n AM: 0x545CF2,\r\n CM: 0x785CE3,\r\n BK: 0x8A4FE3,\r\n CF: 0xA136D4,\r\n ES: 0xB31FD4,\r\n FM: 0xB31FBA,\r\n MD: 0xB30DA6,\r\n NO: 0xBD0D87,\r\n LR: 0xC70066,\r\n RF: 0xCC0059,\r\n DB: 0xD1004F,\r\n SG: 0xD90045,\r\n BH: 0xE00038,\r\n HS: 0xE6002E,\r\n MT: 0xEB0026,\r\n\r\n};\r\n\r\npalette.defaultResidueColor = 0xBEA06E;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n\r\n ALA: 0xC8C8C8,\r\n ARG: 0x145AFF,\r\n ASN: 0x00DCDC,\r\n ASP: 0xE60A0A,\r\n CYS: 0xE6E600,\r\n GLN: 0x00DCDC,\r\n GLU: 0xE60A0A,\r\n GLY: 0xEBEBEB,\r\n HIS: 0x8282D2,\r\n ILE: 0x0F820F,\r\n LEU: 0x0F820F,\r\n LYS: 0x145AFF,\r\n MET: 0xE6E600,\r\n PHE: 0x3232AA,\r\n PRO: 0xDC9682,\r\n SER: 0xFA9600,\r\n THR: 0xFA9600,\r\n TRP: 0xB45AB4,\r\n TYR: 0x3232AA,\r\n VAL: 0x0F820F,\r\n A: 0xA0A0FF,\r\n C: 0xFF8C4B,\r\n G: 0xFF7070,\r\n I: 0x80FFFF,\r\n T: 0xA0FFA0,\r\n U: 0xFF8080,\r\n DA: 0xA0A0FF,\r\n DC: 0xFF8C4B,\r\n DG: 0xFF7070,\r\n DI: 0x80FFFF,\r\n DT: 0xA0FFA0,\r\n DU: 0xFF8080,\r\n '+A': 0xA0A0FF,\r\n '+C': 0xFF8C4B,\r\n '+G': 0xFF7070,\r\n '+I': 0x80FFFF,\r\n '+T': 0xA0FFA0,\r\n '+U': 0xFF8080,\r\n\r\n};\r\n\r\npalette.chainColors = [\r\n // ' '->0 'A'->1, 'B'->2\r\n 0xFFffffff, // ' ' & '0' white\r\n //\r\n 0xFFC0D0FF, // skyblue\r\n 0xFFB0FFB0, // pastel green\r\n 0xFFFFC0C8, // pink\r\n 0xFFFFFF80, // pastel yellow\r\n 0xFFFFC0FF, // pastel magenta\r\n 0xFFB0F0F0, // pastel cyan\r\n 0xFFFFD070, // pastel gold\r\n 0xFFF08080, // lightcoral\r\n\r\n 0xFFF5DEB3, // wheat\r\n 0xFF00BFFF, // deepskyblue\r\n 0xFFCD5C5C, // indianred\r\n 0xFF66CDAA, // mediumaquamarine\r\n 0xFF9ACD32, // yellowgreen\r\n 0xFFEE82EE, // violet\r\n 0xFF00CED1, // darkturquoise\r\n 0xFF00FF7F, // springgreen\r\n 0xFF3CB371, // mediumseagreen\r\n\r\n 0xFF00008B, // darkblue\r\n 0xFFBDB76B, // darkkhaki\r\n 0xFF006400, // darkgreen\r\n 0xFF800000, // maroon\r\n 0xFF808000, // olive\r\n 0xFF800080, // purple\r\n 0xFF008080, // teal\r\n 0xFFB8860B, // darkgoldenrod\r\n 0xFFB22222, // firebrick\r\n];\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xFF0080,\r\n [StructuralElementType.HELIX_PI]: 0x600080,\r\n [StructuralElementType.HELIX_310]: 0xA00080,\r\n [StructuralElementType.STRAND]: 0xFFC800,\r\n [StructuralElementType.TURN]: 0x6080FF,\r\n dna: 0xAE00FE,\r\n rna: 0xFD0162,\r\n};\r\n\r\nexport default palette;\r\n","import Palette from './Palette';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst palette = new Palette('VMD', 'VM');\r\n\r\npalette.colors = [\r\n\r\n 0x0000FF, // blue\r\n 0xFF0000, // red\r\n 0x606060, // gray\r\n 0xFF8000, // orange\r\n 0xFFFF00, // yellow\r\n 0x808033, // tan\r\n 0x999999, // silver\r\n 0x00FF00, // green\r\n 0xFFFFFF, // white\r\n 0xFF9999, // pink\r\n 0x40C0C0, // cyan\r\n 0xA600A6, // purple\r\n 0x80E666, // lime\r\n 0xE666B3, // mauve\r\n 0x804D00, // ochre\r\n 0x8080C0, // ice blue\r\n\r\n];\r\n\r\npalette.defaultElementColor = 0x804D00;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from atom_types.csv by atom_types.py.\r\npalette.elementColors = {\r\n\r\n H: 0xFFFFFF,\r\n C: 0x40BFBF,\r\n N: 0x0000FF,\r\n O: 0xFF0000,\r\n P: 0x808033,\r\n S: 0xFFFF00,\r\n\r\n};\r\n\r\npalette.defaultResidueColor = 0x40C0C0;\r\n\r\n// DO NOT EDIT MANUALLY! Autogenerated from residue_types.csv by residue_types.py.\r\npalette.residueColors = {\r\n\r\n ALA: 0x0000FF,\r\n ARG: 0xFFFFFF,\r\n ASN: 0x808033,\r\n ASP: 0xFF0000,\r\n CYS: 0xFFFF00,\r\n GLN: 0xFF8000,\r\n GLU: 0xFF9999,\r\n GLY: 0xFFFFFF,\r\n HIS: 0x40C0C0,\r\n ILE: 0x00FF00,\r\n LEU: 0xFF9999,\r\n LYS: 0x40C0C0,\r\n MET: 0xFFFF00,\r\n PHE: 0xA600A6,\r\n PRO: 0x804C00,\r\n SER: 0xFFFF00,\r\n THR: 0xE666B3,\r\n TRP: 0x999999,\r\n TYR: 0x00FF00,\r\n VAL: 0x808033,\r\n A: 0x0000FF,\r\n C: 0xFF8000,\r\n G: 0xFFFF00,\r\n T: 0xA600A6,\r\n U: 0x00FF00,\r\n DA: 0x0000FF,\r\n DC: 0xFF8000,\r\n DG: 0xFFFF00,\r\n DT: 0xA600A6,\r\n DU: 0x00FF00,\r\n '+A': 0x0000FF,\r\n '+C': 0xFF8000,\r\n '+G': 0xFFFF00,\r\n '+T': 0xA600A6,\r\n '+U': 0x00FF00,\r\n WAT: 0x40C0C0,\r\n H2O: 0x40C0C0,\r\n HOH: 0x40C0C0,\r\n\r\n};\r\n\r\npalette.chainColors = [0xFFFFFF].concat(palette.colors);\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\npalette.secondaryColors = {\r\n [StructuralElementType.HELIX_ALPHA]: 0xA600A6,\r\n [StructuralElementType.HELIX_310]: 0x0000FF,\r\n [StructuralElementType.HELIX_PI]: 0xFF0000,\r\n [StructuralElementType.STRAND]: 0xFFFF00,\r\n [StructuralElementType.BRIDGE]: 0x808033,\r\n [StructuralElementType.TURN]: 0x40C0C0,\r\n};\r\n\r\nexport default palette;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport cpkPalette from './palettes/cpkPalette';\r\nimport jmolPalette from './palettes/jmolPalette';\r\nimport vmdPalette from './palettes/vmdPalette';\r\n\r\nconst palettes = new EntityList([\r\n cpkPalette,\r\n jmolPalette,\r\n vmdPalette,\r\n]);\r\n\r\nexport default palettes;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport palettes from '../palettes';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports Colorer\r\n * @this Colorer\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all available coloring algorithms used for building and displaying molecule geometry.\r\n */\r\nclass Colorer {\r\n constructor(opts) {\r\n if (this.constructor === Colorer) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Colorer options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.opts = _.merge(utils.deriveDeep(settings.now.colorers[this.id], true), opts);\r\n /**\r\n * Palette in use.\r\n * @type {Palette}\r\n */\r\n this.palette = palettes.first;\r\n }\r\n\r\n /**\r\n * Get Colorer identification, probably with options.\r\n * @returns {string|Array} Colorer identifier string ({@link Colorer#id}) or two-element array containing both colorer\r\n * identifier and options ({@link Colorer#opts}).\r\n * Options are returned if they were changed during or after colorer creation.\r\n */\r\n identify() {\r\n const diff = utils.objectsDiff(this.opts, settings.now.colorers[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n return [this.id, diff];\r\n }\r\n return this.id;\r\n }\r\n}\r\n\r\n/**\r\n * Colorer identifier.\r\n * @type {string}\r\n */\r\n\r\nColorer.prototype.id = '__';\r\n\r\nexport default Colorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Element\r\n *\r\n * @exports ElementColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on chemical element.\r\n */\r\nclass ElementColorer extends Colorer {\r\n static id = 'EL';\r\n\r\n getAtomColor(atom, _complex) {\r\n const type = atom.element.name;\r\n if (type === 'C' && this.opts.carbon >= 0) {\r\n return this.opts.carbon;\r\n }\r\n return this.palette.getElementColor(type);\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nElementColorer.prototype.id = 'EL';\r\nElementColorer.prototype.name = 'Element';\r\nElementColorer.prototype.shortName = 'Element';\r\n\r\nexport default ElementColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Coloring algorithm based on residue type.\r\n *\r\n * @see ResidueType\r\n *\r\n * @exports ResidueTypeColorer\r\n * @constructor\r\n */\r\nclass ResidueTypeColorer extends Colorer {\r\n static id = 'RT';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getResidueColor(residue._type._name);\r\n }\r\n}\r\n\r\nResidueTypeColorer.prototype.id = 'RT';\r\nResidueTypeColorer.prototype.name = 'Residue Type';\r\nResidueTypeColorer.prototype.shortName = 'Residue';\r\n\r\nexport default ResidueTypeColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass SequenceColorer extends Colorer {\r\n static id = 'SQ';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const chain = residue._chain;\r\n if (chain.minSequence === Number.POSITIVE_INFINITY && chain.maxSequence === Number.NEGATIVE_INFINITY) {\r\n return this.palette.defaultNamedColor;\r\n }\r\n const min = chain.minSequence;\r\n const max = chain.maxSequence > min ? chain.maxSequence : min + 1;\r\n return this.palette.getGradientColor((residue._sequence - min) / (max - min), this.opts.gradient);\r\n }\r\n}\r\n\r\nSequenceColorer.prototype.id = 'SQ';\r\nSequenceColorer.prototype.name = 'Sequence';\r\nSequenceColorer.prototype.shortName = 'Sequence';\r\n\r\nexport default SequenceColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ChainColorer extends Colorer {\r\n static id = 'CH';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n return this.palette.getChainColor(residue.getChain()._name);\r\n }\r\n}\r\n\r\nChainColorer.prototype.id = 'CH';\r\nChainColorer.prototype.name = 'Chain';\r\nChainColorer.prototype.shortName = 'Chain';\r\n\r\nexport default ChainColorer;\r\n","import Colorer from './Colorer';\r\nimport ResidueType from '../../chem/ResidueType';\r\n\r\nclass SecondaryStructureColorer extends Colorer {\r\n static id = 'SS';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n if (residue._type.flags & ResidueType.Flags.DNA) {\r\n return this.palette.getSecondaryColor('dna');\r\n }\r\n if (residue._type.flags & ResidueType.Flags.RNA) {\r\n return this.palette.getSecondaryColor('rna');\r\n }\r\n const secondary = residue.getSecondary();\r\n if (secondary) {\r\n let color = this.palette.getSecondaryColor(secondary.type, true);\r\n if (color === undefined) {\r\n color = this.palette.getSecondaryColor(secondary.generic);\r\n }\r\n return color;\r\n }\r\n return this.palette.defaultSecondaryColor;\r\n }\r\n}\r\n\r\nSecondaryStructureColorer.prototype.id = 'SS';\r\nSecondaryStructureColorer.prototype.name = 'Secondary Structure';\r\nSecondaryStructureColorer.prototype.shortName = 'Structure';\r\n\r\nexport default SecondaryStructureColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass UniformColorer extends Colorer {\r\n static id = 'UN';\r\n\r\n getAtomColor(_atom, _complex) {\r\n return this.opts.color;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nUniformColorer.prototype.id = 'UN';\r\nUniformColorer.prototype.name = 'Uniform';\r\nUniformColorer.prototype.shortName = 'Uniform';\r\n\r\nexport default UniformColorer;\r\n","import Colorer from './Colorer';\r\nimport selectors from '../../chem/selectors';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports ConditionalColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on a selector string used as a condition.\r\n */\r\nclass ConditionalColorer extends Colorer {\r\n static id = 'CO';\r\n\r\n constructor(opts) {\r\n super(opts);\r\n const parsed = selectors.parse(this.opts.subset);\r\n this._subsetCached = parsed.error ? selectors.none() : parsed.selector;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n return this._subsetCached.includesAtom(atom) ? this.opts.color : this.opts.baseColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const subset = this._subsetCached;\r\n const atoms = residue._atoms;\r\n for (let i = 0, n = atoms.length; i < n; ++i) {\r\n if (!subset.includesAtom(atoms[i])) {\r\n return this.opts.baseColor;\r\n }\r\n }\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nConditionalColorer.prototype.id = 'CO';\r\nConditionalColorer.prototype.name = 'Conditional';\r\nConditionalColorer.prototype.shortName = 'Conditional';\r\n\r\nexport default ConditionalColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass ConformationColorer extends Colorer {\r\n static id = 'CF';\r\n\r\n getAtomColor(atom, _complex) {\r\n return this.palette.getChainColor(String.fromCharCode(atom.location));\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.palette.defaultResidueColor;\r\n }\r\n}\r\n\r\nConformationColorer.prototype.id = 'CF';\r\nConformationColorer.prototype.name = 'Conformation';\r\nConformationColorer.prototype.shortName = 'Conformation';\r\n\r\nexport default ConformationColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Temperature\r\n *\r\n * @exports TemperatureColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Coloring algorithm based on temperature of chemical element.\r\n */\r\nclass TemperatureColorer extends Colorer {\r\n static id = 'TM';\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n let factor = 1;\r\n if (atom.temperature && opts) {\r\n if (opts.min === opts.max) {\r\n factor = atom.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (atom.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n if (!opts) {\r\n return this.palette.defaultGradientColor;\r\n }\r\n if (residue.temperature) {\r\n let factor = 0;\r\n if (opts.min === opts.max) {\r\n factor = residue.temperature > opts.max ? 1 : 0;\r\n } else {\r\n factor = (residue.temperature - opts.min) / (opts.max - opts.min);\r\n }\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n}\r\n\r\nTemperatureColorer.prototype.id = 'TM'; // [T]e[M]perature\r\nTemperatureColorer.prototype.name = 'Temperature';\r\nTemperatureColorer.prototype.shortName = 'Temperature';\r\n\r\nexport default TemperatureColorer;\r\n","import Colorer from './Colorer';\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @see Occupancy\r\n *\r\n * @exports OccupancyColorer\r\n * @augments Occupancy\r\n * @constructor\r\n * @classdesc Coloring algorithm based on occupancy of chemical element.\r\n */\r\nclass OccupancyColorer extends Colorer {\r\n static id = 'OC';\r\n\r\n _getColorByOccupancy(occupancy, opts) {\r\n if (occupancy !== undefined) {\r\n const factor = 1 - occupancy;\r\n return this.palette.getGradientColor(factor, opts.gradient);\r\n }\r\n return this.palette.defaultGradientColor;\r\n }\r\n\r\n getAtomColor(atom, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(atom.occupancy, opts);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const { opts } = this;\r\n return this._getColorByOccupancy(residue.occupancy, opts);\r\n }\r\n}\r\n\r\nOccupancyColorer.prototype.id = 'OC'; // [OC]cupancy\r\nOccupancyColorer.prototype.name = 'Occupancy';\r\nOccupancyColorer.prototype.shortName = 'Occupancy';\r\n\r\nexport default OccupancyColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass HydrophobicityColorer extends Colorer {\r\n static id = 'HY';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n let color = this.palette.defaultResidueColor;\r\n if (residue._type.hydrophobicity !== undefined) {\r\n // Kyte Doolitle hydro [-4.5,4.5]->[0.1]\r\n const min = -4.5;\r\n const max = 4.5;\r\n color = this.palette.getGradientColor((residue._type.hydrophobicity - min) / (max - min), this.opts.gradient);\r\n }\r\n return color;\r\n }\r\n}\r\n\r\nHydrophobicityColorer.prototype.id = 'HY';\r\nHydrophobicityColorer.prototype.name = 'Hydrophobicity';\r\nHydrophobicityColorer.prototype.shortName = 'Hydrophobicity';\r\n\r\nexport default HydrophobicityColorer;\r\n","import Colorer from './Colorer';\r\n\r\nclass MoleculeColorer extends Colorer {\r\n static id = 'MO';\r\n\r\n getAtomColor(atom, complex) {\r\n return this.getResidueColor(atom.residue, complex);\r\n }\r\n\r\n getResidueColor(residue, _complex) {\r\n const molecule = residue._molecule;\r\n const count = _complex.getMoleculeCount();\r\n if (count > 1) {\r\n return this.palette.getGradientColor((molecule.index - 1) / (count - 1), this.opts.gradient);\r\n }\r\n return this.palette.getGradientColor(0, this.opts.gradient);\r\n }\r\n}\r\n\r\nMoleculeColorer.prototype.id = 'MO';\r\nMoleculeColorer.prototype.name = 'Molecule';\r\nMoleculeColorer.prototype.shortName = 'Molecule';\r\n\r\nexport default MoleculeColorer;\r\n","import Colorer from './Colorer';\r\nimport Atom from '../../chem/Atom';\r\n\r\nfunction scaleColor(c, factor) {\r\n const r1 = (c >> 16) & 0xff;\r\n const g1 = (c >> 8) & 0xff;\r\n const b1 = c & 0xff;\r\n const r = factor * r1;\r\n const g = factor * g1;\r\n const b = factor * b1;\r\n return (r << 16) | (g << 8) | b;\r\n}\r\n\r\n/**\r\n * Create new colorer.\r\n *\r\n * @param {object=} opts - Options to override defaults with. See {@link Colorer}.\r\n *\r\n * @exports CarbonColorer\r\n * @augments Colorer\r\n * @constructor\r\n * @classdesc Bicolor coloring algorithm based on selection carbon atoms.\r\n */\r\nclass CarbonColorer extends Colorer {\r\n static id = 'CB';\r\n\r\n getAtomColor(atom, _complex) {\r\n const colorCarbon = this.opts.color;\r\n const colorNotCarbon = scaleColor(colorCarbon, this.opts.factor);\r\n return (atom.flags & Atom.Flags.CARBON) ? colorCarbon : colorNotCarbon;\r\n }\r\n\r\n getResidueColor(_residue, _complex) {\r\n return this.opts.color;\r\n }\r\n}\r\n\r\nCarbonColorer.prototype.id = 'CB';\r\nCarbonColorer.prototype.name = 'Carbon';\r\nCarbonColorer.prototype.shortName = 'Carbon';\r\n\r\nexport default CarbonColorer;\r\n","import EntityList from '../utils/EntityList';\r\n\r\nimport ElementColorer from './colorers/ElementColorer';\r\nimport ResidueTypeColorer from './colorers/ResidueTypeColorer';\r\nimport SequenceColorer from './colorers/SequenceColorer';\r\nimport ChainColorer from './colorers/ChainColorer';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\nimport UniformColorer from './colorers/UniformColorer';\r\nimport ConditionalColorer from './colorers/ConditionalColorer';\r\nimport ConformationColorer from './colorers/ConformationColorer';\r\nimport TemperatureColorer from './colorers/TemperatureColorer';\r\nimport OccupancyColorer from './colorers/OccupancyColorer';\r\nimport HydrophobicityColorer from './colorers/HydrophobicityColorer';\r\nimport MoleculeColorer from './colorers/MoleculeColorer';\r\nimport CarbonColorer from './colorers/CarbonColorer';\r\n\r\nconst colorers = new EntityList([\r\n ElementColorer,\r\n ResidueTypeColorer,\r\n SequenceColorer,\r\n ChainColorer,\r\n SecondaryStructureColorer,\r\n UniformColorer,\r\n ConditionalColorer,\r\n ConformationColorer,\r\n TemperatureColorer,\r\n OccupancyColorer,\r\n HydrophobicityColorer,\r\n MoleculeColorer,\r\n CarbonColorer,\r\n]);\r\n\r\nexport default colorers;\r\n","import * as THREE from 'three';\r\nimport EntityList from '../utils/EntityList';\r\n\r\nfunction neutralColor(intensity) {\r\n return new THREE.Color(intensity, intensity, intensity);\r\n}\r\n\r\nconst materialList = [\r\n {\r\n id: 'DF',\r\n name: 'Diffuse',\r\n shortName: 'Diffuse',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'SF',\r\n name: 'Soft Plastic',\r\n shortName: 'Soft',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.1),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'PL',\r\n name: 'Glossy Plastic',\r\n shortName: 'Glossy',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.28),\r\n shininess: 100,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'ME',\r\n name: 'Metal',\r\n shortName: 'Metal',\r\n uberOptions: {\r\n diffuse: neutralColor(0.56),\r\n specular: neutralColor(0.55),\r\n shininess: 30,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TR',\r\n name: 'Transparent',\r\n shortName: 'Transparent',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'GL',\r\n name: 'Glass',\r\n shortName: 'Glass',\r\n uberOptions: {\r\n diffuse: neutralColor(0.50),\r\n specular: neutralColor(0.65),\r\n shininess: 100,\r\n opacity: 0.5,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: true,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'BA',\r\n name: 'Backdrop',\r\n shortName: 'Backdrop',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: false,\r\n depthWrite: false,\r\n transparent: false,\r\n toonShading: false,\r\n },\r\n }, {\r\n id: 'TN',\r\n name: 'Toon',\r\n shortName: 'Toon',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 1,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: true,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n toonShading: true,\r\n },\r\n }, {\r\n id: 'FL',\r\n name: 'Flat',\r\n shortName: 'Flat',\r\n uberOptions: {\r\n diffuse: neutralColor(1.0),\r\n specular: neutralColor(0.0),\r\n shininess: 0,\r\n opacity: 1.0,\r\n },\r\n values: {\r\n lights: false,\r\n fog: true,\r\n depthWrite: true,\r\n transparent: false,\r\n },\r\n },\r\n];\r\n\r\nconst materials = new EntityList(materialList);\r\n\r\nexport default materials;\r\n","/**\r\n * Utils functions which is worked with meshes\r\n *\r\n * functions for doing something with all/specified meshes\r\n * functions for traversihg tree and create auxiliary meshes for transparency/shadowmaps...\r\n * functions for calculating data connected with meshes\r\n */\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _gatherObjects(root, meshTypes) {\r\n const meshes = [];\r\n root.traverse((object) => {\r\n for (let i = 0; i < meshTypes.length; i++) {\r\n if (object instanceof meshTypes[i]) {\r\n meshes[meshes.length] = object;\r\n break;\r\n }\r\n }\r\n });\r\n return meshes;\r\n}\r\n\r\n// new mesh with the same geometry and specified material values and layer\r\nfunction createDerivativeMesh(mesh, values, layer) {\r\n const material = mesh.material.createInstance();\r\n material.setValues(values);\r\n\r\n const newMesh = new mesh.constructor(mesh.geometry, material);\r\n newMesh.material.needsUpdate = true;\r\n newMesh.applyMatrix4(mesh.matrix);\r\n newMesh.layers.set(layer);\r\n return newMesh;\r\n}\r\n\r\nfunction traverseMeshes(root, meshTypes, func) {\r\n const meshes = _gatherObjects(root, meshTypes);\r\n\r\n for (let i = 0, n = meshes.length; i < n; ++i) {\r\n const mesh = meshes[i];\r\n if (!mesh.parent) {\r\n continue;\r\n }\r\n func(mesh);\r\n }\r\n}\r\n\r\nfunction applyTransformsToMeshes(root, mtc) {\r\n const mtcCount = mtc.length;\r\n if (mtcCount < 1) {\r\n return;\r\n }\r\n\r\n const meshTypes = [THREE.Mesh, THREE.LineSegments, THREE.Line];\r\n traverseMeshes(root, meshTypes, (mesh) => {\r\n mesh.applyMatrix4(mtc[0]);\r\n for (let j = 1; j < mtcCount; ++j) {\r\n const newMesh = new mesh.constructor(mesh.geometry, mesh.material);\r\n mesh.parent.add(newMesh);\r\n newMesh.applyMatrix4(mtc[j]);\r\n }\r\n });\r\n}\r\n\r\nconst processTransparentMaterial = (function () {\r\n const matValues = {\r\n prepassTransparancy: true,\r\n fakeOpacity: false,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n mesh.material.setValues({ prepassTransparancy: false, fakeOpacity: false });\r\n mesh.material.needsUpdate = true;\r\n mesh.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n\r\n const prepassTranspMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n mesh.parent.add(prepassTranspMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst processColFromPosMaterial = (function () {\r\n const matValues = {\r\n colorFromPos: true,\r\n transparent: false,\r\n colorFromDepth: false,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n overrideColor: false,\r\n fogTransparent: false,\r\n attrColor: false,\r\n attrColor2: false,\r\n attrAlphaColor: false,\r\n fakeOpacity: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n const colFromPosMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n mesh.parent.add(colFromPosMesh);\r\n });\r\n };\r\n}());\r\n\r\nconst createShadowmapMaterial = (function () {\r\n const matValues = {\r\n colorFromDepth: true,\r\n orthoCam: true,\r\n lights: false,\r\n shadowmap: false,\r\n fog: false,\r\n };\r\n\r\n return function (root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (!mesh.receiveShadow && mesh.material.shadowmap) { // remove shadow from non-receivers\r\n mesh.material.setValues({ shadowmap: false });\r\n }\r\n if (!mesh.material.lights) { // skip creating shadowmap meshes for materials without lighting\r\n return;\r\n }\r\n if (!mesh.castShadow) { // skip creating shadowmap meshes for non-casters\r\n return;\r\n }\r\n if (!gfxutils.belongToSelectLayers(mesh)) { // skip creating shadowmap meshes for selection layer\r\n return;\r\n }\r\n\r\n const shadowmapMesh = createDerivativeMesh(mesh, matValues, gfxutils.LAYERS.SHADOWMAP);\r\n shadowmapMesh.isShadowmapMesh = true;\r\n mesh.parent.add(shadowmapMesh);\r\n });\r\n };\r\n}());\r\n\r\nfunction removeShadowmapMaterial(root, material) {\r\n if (!(material instanceof UberMaterial)) {\r\n return;\r\n }\r\n\r\n traverseMeshes(root, [THREE.Mesh, THREE.LineSegments], (mesh) => {\r\n if (mesh.isShadowmapMesh) {\r\n mesh.parent.remove(mesh);\r\n }\r\n });\r\n}\r\n\r\nfunction forEachMeshInGroup(group, process) {\r\n function processObj(object) {\r\n if (object instanceof THREE.Mesh) {\r\n process(object);\r\n }\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n processObj(object.children[i]);\r\n }\r\n }\r\n processObj(group);\r\n}\r\n\r\nfunction _countMeshTriangles(mesh) {\r\n const geom = mesh.geometry;\r\n if (geom instanceof THREE.InstancedBufferGeometry) {\r\n const attribs = geom.attributes;\r\n for (const property in attribs) {\r\n if (attribs.hasOwnProperty(property) && attribs[property] instanceof THREE.InstancedBufferAttribute) {\r\n const currAttr = attribs[property];\r\n const indexSize = geom.index ? geom.index.array.length / 3 : 0;\r\n return indexSize * currAttr.array.length / currAttr.itemSize;\r\n }\r\n }\r\n return 0;\r\n }\r\n if (geom instanceof THREE.BufferGeometry) {\r\n return geom.index ? geom.index.array.length / 3 : 0;\r\n }\r\n return geom.faces ? geom.faces.length : 0;\r\n}\r\n\r\nfunction countTriangles(group) {\r\n let totalCount = 0;\r\n forEachMeshInGroup(group, (mesh) => {\r\n totalCount += _countMeshTriangles(mesh);\r\n });\r\n return totalCount;\r\n}\r\n\r\nexport default {\r\n applyTransformsToMeshes,\r\n processTransparentMaterial,\r\n processColFromPosMaterial,\r\n createShadowmapMaterial,\r\n removeShadowmapMaterial,\r\n forEachMeshInGroup,\r\n countTriangles,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport UberMaterial from './shaders/UberMaterial';\r\nimport gfxutils from './gfxutils';\r\nimport meshutils from './meshutils';\r\nimport settings from '../settings';\r\nimport materials from './materials';\r\nimport chem from '../chem';\r\n\r\nconst { selectors } = chem;\r\n\r\nclass Representation {\r\n constructor(index, mode, colorer, selector) {\r\n const startMaterialValues = {\r\n clipPlane: settings.now.draft.clipPlane,\r\n fogTransparent: settings.now.bg.transparent,\r\n shadowmap: settings.now.shadow.on,\r\n shadowmapType: settings.now.shadow.type,\r\n };\r\n this.index = index;\r\n this.mode = mode;\r\n this.colorer = colorer;\r\n this.selector = selector;\r\n this.selectorString = '';\r\n this.count = 0;\r\n this.material = new UberMaterial();\r\n this.material.setValues(startMaterialValues);\r\n this.material.setUberOptions({ fogAlpha: settings.now.fogAlpha });\r\n this.materialPreset = materials.first;\r\n this.needsRebuild = true;\r\n this.visible = true;\r\n\r\n // apply mode params & preset\r\n this.setMode(mode);\r\n }\r\n\r\n markAtoms(complex) {\r\n this.count = complex.markAtoms(this.selector, 1 << this.index);\r\n this.needsRebuild = true;\r\n return this.count;\r\n }\r\n\r\n unmarkAtoms(complex) {\r\n complex.clearAtomBits(1 << this.index);\r\n this.count = 0;\r\n }\r\n\r\n setMode(mode) {\r\n this.mode = mode;\r\n }\r\n\r\n setMaterialPreset(preset) {\r\n this.materialPreset = preset;\r\n this.material.setUberOptions(preset.uberOptions);\r\n this.material.setValues(preset.values);\r\n }\r\n\r\n reset() {\r\n this.geo = null;\r\n this.selectionGeo = null;\r\n }\r\n\r\n buildGeometry(complex) {\r\n this.reset();\r\n this.needsRebuild = false;\r\n\r\n if (settings.now.ao) {\r\n this.material.setValues({ normalsToGBuffer: settings.now.ao });\r\n }\r\n\r\n this.geo = this.mode.buildGeometry(complex, this.colorer, 1 << this.index, this.material);\r\n\r\n if (this.material.uberOptions.opacity < 0.99 && settings.now.transparency === 'prepass') {\r\n meshutils.processTransparentMaterial(this.geo, this.material);\r\n }\r\n this.geo.visible = this.visible;\r\n\r\n gfxutils.processObjRenderOrder(this.geo, this.materialPreset.id);\r\n meshutils.processColFromPosMaterial(this.geo, this.material);\r\n\r\n if (settings.now.shadow.on) {\r\n meshutils.createShadowmapMaterial(this.geo, this.material);\r\n }\r\n\r\n return this.geo;\r\n }\r\n\r\n buildSelectionGeometry(mask) {\r\n let sg = null;\r\n\r\n if (this.geo && ('getSubset' in this.geo)) {\r\n const meshes = this.geo.getSubset(mask);\r\n if (meshes && meshes.length > 0) {\r\n sg = new THREE.Group();\r\n sg.matrixAutoUpdate = false;\r\n sg.matrix = this.geo.matrix;\r\n\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n sg.add(m);\r\n }\r\n }\r\n }\r\n\r\n if (sg) {\r\n sg.visible = this.visible;\r\n }\r\n\r\n this.selectionGeo = sg;\r\n return this.selectionGeo;\r\n }\r\n\r\n /**\r\n * Create object that represents difference between current and another rep\r\n * anotherRep could be undefined. In this case everything is reported.\r\n */\r\n compare(repSettings) {\r\n const diff = {};\r\n\r\n const selStr = String(this.selector);\r\n if (!repSettings || selStr.valueOf() !== String(repSettings.selector).valueOf()) {\r\n diff.selector = selStr;\r\n }\r\n\r\n const modeDiff = this.mode.identify();\r\n if (!repSettings || Array.isArray(modeDiff) || modeDiff !== repSettings.mode) {\r\n diff.mode = modeDiff;\r\n }\r\n\r\n const colorerDiff = this.colorer.identify();\r\n if (!repSettings || Array.isArray(colorerDiff) || colorerDiff !== repSettings.colorer) {\r\n diff.colorer = colorerDiff;\r\n }\r\n\r\n if (!repSettings || this.materialPreset.id !== repSettings.material) {\r\n diff.material = this.materialPreset.id;\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n /**\r\n * Change representation. Write fields what was changed into new object, return it.\r\n */\r\n change(repSettings, complex, mode, color) {\r\n const diff = {};\r\n\r\n // modify selector\r\n if (repSettings.selector) {\r\n const newSelectorObject = selectors.parse(repSettings.selector).selector;\r\n const newSelector = String(newSelectorObject);\r\n if (this.selectorString !== newSelector) {\r\n diff.selector = newSelector;\r\n this.selectorString = newSelector;\r\n this.selector = newSelectorObject;\r\n this.markAtoms(complex);\r\n }\r\n }\r\n\r\n // modify mode\r\n if (repSettings.mode) {\r\n const newMode = repSettings.mode;\r\n if (!_.isEqual(this.mode.identify(), newMode)) {\r\n diff.mode = newMode;\r\n this.setMode(mode);\r\n }\r\n }\r\n\r\n // modify colorer\r\n if (repSettings.colorer) {\r\n const newColorer = repSettings.colorer;\r\n if (!_.isEqual(this.colorer.identify(), newColorer)) {\r\n diff.colorer = newColorer;\r\n this.colorer = color;\r\n }\r\n }\r\n\r\n // modify material\r\n if (repSettings.material) {\r\n const newMaterial = repSettings.material;\r\n if (!_.isEqual(this.materialPreset.id, newMaterial)) {\r\n diff.material = newMaterial;\r\n this.setMaterialPreset(materials.get(repSettings.material));\r\n }\r\n }\r\n\r\n return diff;\r\n }\r\n\r\n show(visible) {\r\n this.visible = visible;\r\n if (this.geo) {\r\n this.geo.visible = visible;\r\n }\r\n if (this.selectionGeo) {\r\n this.selectionGeo.visible = visible;\r\n }\r\n }\r\n}\r\n\r\nexport default Representation;\r\n","import * as THREE from 'three';\r\nimport logger from './utils/logger';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport './gfx/modes';\r\n\r\nfunction _traverseComponentGroups(root, component, callback) {\r\n const { children } = root;\r\n if (!children) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = children.length; i < n; ++i) {\r\n const child = children[i];\r\n if (child._component === component) {\r\n callback(child);\r\n }\r\n if (child instanceof gfxutils.RCGroup) {\r\n _traverseComponentGroups(child, component, callback);\r\n }\r\n }\r\n}\r\n\r\nfunction ComplexEditor() {\r\n}\r\n\r\nclass ComplexComponentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n // init component matrices\r\n this._componentTransforms = [];\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n const component = complex._components[i];\r\n this._componentTransforms[component._index] = new THREE.Object3D();\r\n }\r\n\r\n this._inProgress = true;\r\n\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const complex = this._complexVisual.getComplex();\r\n\r\n for (let i = 0; i < complex._components.length; ++i) {\r\n this._bakeComponentTransform(complex._components[i]);\r\n }\r\n\r\n complex.onAtomPositionChanged();\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n this._resetComponentTransform();\r\n\r\n this._complexVisual.finalizeEdit();\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n const visual = this._complexVisual;\r\n const component = visual.getSelectedComponent();\r\n\r\n if (component === null) {\r\n return res;\r\n }\r\n\r\n const selection = this._complexVisual.getSelectionGeo();\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n // find all geo nodes for this component\r\n _traverseComponentGroups(visual, component, (child) => {\r\n res.objects.push(child);\r\n });\r\n\r\n // find all selection nodes for this component\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component') && geo._component === component) {\r\n res.objects.push(geo);\r\n }\r\n }\r\n }\r\n\r\n // add dummy object that stores component transformation\r\n res.objects.push(this._componentTransforms[component._index]);\r\n\r\n const bbmin = new THREE.Vector3(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE);\r\n const bbmax = new THREE.Vector3(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE);\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (j = 0; j < atoms.length; ++j) {\r\n if (atoms[j].mask & selectionMask) {\r\n bbmin.min(atoms[j].position);\r\n bbmax.max(atoms[j].position);\r\n }\r\n }\r\n });\r\n\r\n res.pivot.lerpVectors(bbmin, bbmax, 0.5);\r\n return res;\r\n }\r\n\r\n _bakeComponentTransform(component) {\r\n const t = this._componentTransforms[component._index];\r\n if (t && (!(t.position.x === 0 && t.position.y === 0 && t.position.z === 0)\r\n || !(t.quaternion.x === 0 && t.quaternion.y === 0 && t.quaternion.z === 0 && t.quaternion.w === 1))) {\r\n t.updateMatrix();\r\n\r\n component.forEachResidue((residue) => {\r\n const atoms = residue._atoms;\r\n for (let j = 0; j < atoms.length; ++j) {\r\n atoms[j].position.applyMatrix4(t.matrix);\r\n }\r\n });\r\n }\r\n }\r\n\r\n _resetComponentTransform() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n let i;\r\n let j;\r\n let reprNode;\r\n let geo;\r\n\r\n for (i = 0; i < this._componentTransforms.length; ++i) {\r\n geo = this._componentTransforms[i];\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n\r\n // reset all geo nodes\r\n for (i = 0; i < visual.children.length; ++i) {\r\n reprNode = visual.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n // reset all selection nodes\r\n for (i = 0; i < selection.children.length; ++i) {\r\n reprNode = selection.children[i];\r\n for (j = 0; j < reprNode.children.length; ++j) {\r\n geo = reprNode.children[j];\r\n if (geo.hasOwnProperty('_component')) {\r\n geo.position.set(0, 0, 0);\r\n geo.quaternion.set(0, 0, 0, 1);\r\n }\r\n }\r\n }\r\n }\r\n}\r\n\r\nclass ComplexFragmentEditor extends ComplexEditor {\r\n constructor(complexVisual) {\r\n super();\r\n this._complexVisual = complexVisual;\r\n this._inProgress = false;\r\n }\r\n\r\n begin() {\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n const atoms = this._getSelectionBorderAtoms();\r\n if (atoms.length < 1 || atoms.length > 2) {\r\n logger.error('Can only edit fragments with one or two bound atoms.');\r\n return false;\r\n }\r\n\r\n this._fragmentBoundAtoms = atoms;\r\n\r\n const selectionMask = 1 << visual.getSelectionBit();\r\n\r\n // hide selected fragment in main model\r\n visual.disableSubset(selectionMask, true);\r\n\r\n // hide selection geo in main model\r\n for (let k = 0; k < selection.children.length; ++k) {\r\n selection.children[k].visible = false;\r\n }\r\n\r\n // create visible fragment representation to rotate\r\n const pivotPos = atoms[0].position.clone();\r\n\r\n if (atoms.length === 2) {\r\n pivotPos.lerp(atoms[1].position, 0.5);\r\n }\r\n\r\n this._fragmentGeo = new THREE.Group();\r\n visual.add(this._fragmentGeo);\r\n this._fragmentGeo.position.copy(pivotPos);\r\n\r\n this._fragmentSelectionGeo = new THREE.Group();\r\n selection.add(this._fragmentSelectionGeo);\r\n this._fragmentSelectionGeo.position.copy(pivotPos);\r\n\r\n const offset = pivotPos.clone();\r\n offset.negate();\r\n\r\n for (let i = 0; i < visual.children.length; ++i) {\r\n const g = visual.children[i];\r\n if (!('getSubset' in g)) {\r\n continue;\r\n }\r\n\r\n const vg = new THREE.Group();\r\n this._fragmentGeo.add(vg);\r\n\r\n const sg = new THREE.Group();\r\n this._fragmentSelectionGeo.add(sg);\r\n\r\n const meshes = g.getSubset(selectionMask, true);\r\n for (let j = 0; j < meshes.length; j++) {\r\n const m = meshes[j];\r\n vg.add(m);\r\n m.position.copy(offset);\r\n }\r\n\r\n const smeshes = g.getSubset(selectionMask, true);\r\n for (let h = 0; h < smeshes.length; h++) {\r\n const sm = smeshes[h];\r\n sg.add(sm);\r\n sm.position.copy(offset);\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(this._fragmentSelectionGeo);\r\n\r\n this._inProgress = true;\r\n return true;\r\n }\r\n\r\n apply() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selectionBit = visual.getSelectionBit();\r\n\r\n const p = this._fragmentGeo.position;\r\n const m = this._fragmentGeo.matrix.clone();\r\n m.multiply(new THREE.Matrix4().makeTranslation(-p.x, -p.y, -p.z));\r\n\r\n this._bakeAtomTransform(m, 1 << selectionBit);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << selectionBit, true);\r\n\r\n visual.getComplex().onAtomPositionChanged();\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n discard() {\r\n if (!this._inProgress) {\r\n return;\r\n }\r\n\r\n const visual = this._complexVisual;\r\n const selection = this._complexVisual.getSelectionGeo();\r\n\r\n this._fragmentGeo.parent.remove(this._fragmentGeo);\r\n\r\n // show selected fragment in main model\r\n visual.enableSubset(1 << visual.getSelectionBit(), true);\r\n\r\n // show selection geo in main model (+ remove fragment selection geo)\r\n for (let i = 0; i < selection.children.length; ++i) {\r\n const node = selection.children[i];\r\n if (node.visible) {\r\n selection.remove(node);\r\n } else {\r\n node.visible = true;\r\n }\r\n }\r\n\r\n visual.finalizeEdit();\r\n }\r\n\r\n isFreeRotationAllowed() {\r\n return (this._fragmentBoundAtoms.length < 2);\r\n }\r\n\r\n getAltObj() {\r\n const res = {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n\r\n res.objects.push(this._fragmentGeo, this._fragmentSelectionGeo);\r\n\r\n const boundAtoms = this._fragmentBoundAtoms;\r\n if (boundAtoms.length === 1) {\r\n if (boundAtoms[0].bonds.length === 1) {\r\n // single external bond allows rotation about bond axis\r\n const bond = boundAtoms[0].bonds[0];\r\n res.axis = new THREE.Vector3().subVectors(bond._right.position, bond._left.position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n } else if (boundAtoms.length === 2) {\r\n // two bound atoms allow rotation only about axis running through their centers\r\n res.axis = new THREE.Vector3().subVectors(boundAtoms[1].position, boundAtoms[0].position);\r\n res.axis.normalize();\r\n res.axis.transformDirection(this._complexVisual.matrixWorld);\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _getSelectionBorderAtoms() {\r\n const complex = this._complexVisual.getComplex();\r\n\r\n const selectionMask = 1 << this._complexVisual.getSelectionBit();\r\n const atomHash = {};\r\n\r\n complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n atomHash[bond._left.index] = 1;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n atomHash[bond._right.index] = 1;\r\n }\r\n });\r\n\r\n const atoms = [];\r\n const keys = Object.keys(atomHash);\r\n for (let i = 0, n = keys.length; i < n; ++i) {\r\n const idx = keys[i];\r\n atoms.push(complex._atoms[idx]);\r\n }\r\n\r\n return atoms;\r\n }\r\n\r\n _bakeAtomTransform(matrix, mask) {\r\n this._complexVisual.getComplex().forEachAtom((atom) => {\r\n if (atom.mask & mask) {\r\n atom.position.applyMatrix4(matrix);\r\n }\r\n });\r\n }\r\n}\r\n\r\nexport default {\r\n ComponentEditor: ComplexComponentEditor,\r\n FragmentEditor: ComplexFragmentEditor,\r\n};\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport utils from './utils';\r\nimport logger from './utils/logger';\r\nimport chem from './chem';\r\nimport settings from './settings';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport Visual from './Visual';\r\nimport ComplexVisualEdit from './ComplexVisualEdit';\r\nimport meshutils from './gfx/meshutils';\r\n\r\nconst { selectors } = chem;\r\n\r\nfunction lookupAndCreate(entityList, specs) {\r\n if (!Array.isArray(specs)) {\r\n specs = [specs];\r\n }\r\n const [id, opts] = specs;\r\n const Entity = entityList.get(id) || entityList.first;\r\n return new Entity(opts);\r\n}\r\n\r\nclass ComplexVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._complex = dataSource;\r\n\r\n /** @type {Representation[]} */\r\n this._reprList = [];\r\n /** @type {?Representation} */\r\n this._repr = null;\r\n this._reprListChanged = true;\r\n\r\n this._selectionBit = 0;\r\n this._reprUsedBits = 0;\r\n this._selectionCount = 0;\r\n\r\n this._selectionGeometry = new THREE.Group();\r\n }\r\n\r\n getBoundaries() {\r\n return this._complex.getBoundaries();\r\n }\r\n\r\n release() {\r\n if (this._selectionGeometry.parent) {\r\n this._selectionGeometry.remove(this._selectionGeometry);\r\n }\r\n Visual.prototype.release.call(this);\r\n }\r\n\r\n getComplex() {\r\n return this._complex;\r\n }\r\n\r\n getSelectionCount() {\r\n return this._selectionCount;\r\n }\r\n\r\n getSelectionGeo() {\r\n return this._selectionGeometry;\r\n }\r\n\r\n getSelectionBit() {\r\n return this._selectionBit;\r\n }\r\n\r\n getEditor() {\r\n return this._editor;\r\n }\r\n\r\n resetReps(reps) {\r\n // Create all necessary representations\r\n if (this._complex) {\r\n this._complex.clearAtomBits(~0);\r\n }\r\n this._reprListChanged = true;\r\n this._reprUsedBits = 0;\r\n this._reprList.length = reps.length;\r\n for (let i = 0, n = reps.length; i < n; ++i) {\r\n const rep = reps[i];\r\n\r\n let selector;\r\n let selectorString;\r\n if (typeof rep.selector === 'string') {\r\n selectorString = rep.selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else if (typeof rep.selector === 'undefined') {\r\n selectorString = settings.now.presets.default[0].selector;\r\n ({ selector } = selectors.parse(selectorString));\r\n } else {\r\n ({ selector } = rep);\r\n selectorString = selector.toString();\r\n }\r\n const mode = lookupAndCreate(modes, rep.mode);\r\n const colorer = lookupAndCreate(colorers, rep.colorer);\r\n const material = materials.get(rep.material) || materials.first;\r\n\r\n this._reprList[i] = new Representation(i, mode, colorer, selector);\r\n this._reprList[i].setMaterialPreset(material);\r\n this._reprList[i].selectorString = selectorString;\r\n\r\n if (this._complex) {\r\n this._complex.markAtoms(selector, 1 << i);\r\n }\r\n\r\n this._reprUsedBits |= 1 << i;\r\n }\r\n this._repr = reps.length > 0 ? this._reprList[0] : null;\r\n\r\n this._selectionBit = reps.length;\r\n this._reprUsedBits |= 1 << this._selectionBit; // selection uses one bit\r\n this._selectionCount = 0;\r\n\r\n if (this._complex) {\r\n this._complex.update();\r\n }\r\n }\r\n\r\n /**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\n repCount() {\r\n return this._reprList.length;\r\n }\r\n\r\n /**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\n repCurrent(index) {\r\n if (index >= 0 && index < this._reprList.length) {\r\n this._repr = this._reprList[index];\r\n } else {\r\n index = this._reprList.indexOf(this._repr);\r\n }\r\n return index;\r\n }\r\n\r\n /**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {Object} {desc, index, status} field desc contains rep description, index - index of correspondent rep,\r\n * status - one of three strings: 'created', 'changed', ''. 'created' means new rep was created during this function,\r\n * 'changed' - rep was changed during this function. '' - something else.\r\n */\r\n rep(index, rep) {\r\n // if index is missing then it is the current\r\n if (!rep && (index === undefined || index instanceof Object)) {\r\n rep = index;\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index > this._reprList.length) {\r\n logger.error(`Rep ${index} does not exist!`);\r\n return null;\r\n }\r\n\r\n // a special case of adding just after the end\r\n if (index === this._reprList.length) {\r\n const res = this.repAdd(rep);\r\n logger.warn(`Rep ${index} does not exist! New representation was created.`);\r\n return { desc: res.desc, index, status: 'created' };\r\n }\r\n\r\n // gather description\r\n const target = this._reprList[index];\r\n const desc = {\r\n selector: target.selectorString,\r\n mode: target.mode.identify(),\r\n colorer: target.colorer.identify(),\r\n material: target.materialPreset.id,\r\n };\r\n\r\n // modification is requested\r\n if (rep) {\r\n // modify\r\n const diff = target.change(\r\n rep,\r\n this._complex,\r\n lookupAndCreate(modes, rep.mode),\r\n lookupAndCreate(colorers, rep.colorer),\r\n );\r\n\r\n // something was changed\r\n if (!_.isEmpty(diff)) {\r\n target.needsRebuild = true;\r\n for (const key in diff) {\r\n if (diff.hasOwnProperty(key)) {\r\n desc[key] = diff[key];\r\n logger.debug(`rep[${index}].${key} changed to ${diff[key]}`);\r\n }\r\n }\r\n\r\n // safety trick: lower resolution for surface modes\r\n if (diff.mode && target.mode.isSurface\r\n && (settings.now.resolution === 'ultra' || settings.now.resolution === 'high')) {\r\n logger.report('Surface resolution was changed to \"medium\" to avoid hang-ups.');\r\n settings.set('resolution', 'medium');\r\n }\r\n return { desc, index, status: 'changed' };\r\n }\r\n }\r\n return { desc, index, status: '' };\r\n }\r\n\r\n /**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\n repGet(index) {\r\n // if index is missing then it is the current\r\n if (index === undefined || index instanceof Object) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return null;\r\n }\r\n\r\n return this._reprList[index];\r\n }\r\n\r\n _getFreeReprIdx() {\r\n let bits = this._reprUsedBits;\r\n for (let i = 0; i <= ComplexVisual.NUM_REPRESENTATION_BITS; ++i, bits >>= 1) {\r\n if ((bits & 1) === 0) {\r\n return i;\r\n }\r\n }\r\n return -1;\r\n }\r\n\r\n /**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {Object} {desc, index} field desc contains added rep description, index - index of this rep.\r\n */\r\n repAdd(rep) {\r\n if (this._reprList.length >= ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n return null;\r\n }\r\n\r\n const newSelectionBit = this._getFreeReprIdx();\r\n if (newSelectionBit < 0) {\r\n return null; // no more slots for representations\r\n }\r\n\r\n const originalSelection = this.buildSelectorFromMask(1 << this._selectionBit);\r\n\r\n // Fill in default values\r\n const def = settings.now.presets.default[0];\r\n const desc = _.merge({\r\n selector: def.selector,\r\n mode: def.mode,\r\n colorer: def.colorer,\r\n material: def.material,\r\n }, rep);\r\n\r\n const selector = (typeof desc.selector === 'string') ? selectors.parse(desc.selector).selector : desc.selector;\r\n const target = new Representation(\r\n this._selectionBit,\r\n lookupAndCreate(modes, desc.mode),\r\n lookupAndCreate(colorers, desc.colorer),\r\n selector,\r\n );\r\n target.selectorString = selector.toString();\r\n target.setMaterialPreset(materials.get(desc.material));\r\n target.markAtoms(this._complex);\r\n this._reprList.push(target);\r\n\r\n // change selection bit\r\n this._selectionBit = newSelectionBit;\r\n this._reprUsedBits |= 1 << this._selectionBit;\r\n\r\n // restore selection using new selection bit\r\n this._complex.markAtoms(originalSelection, 1 << this._selectionBit);\r\n\r\n return { desc, index: this._reprList.length - 1 };\r\n }\r\n\r\n /**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\n repRemove(index) {\r\n if (index === undefined) {\r\n index = this.repCurrent();\r\n }\r\n\r\n // catch out of bounds case\r\n let count = this._reprList.length;\r\n if (index < 0 || index >= count || count <= 1) { // do not allow to remove the single rep\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.unmarkAtoms(this._complex);\r\n this._reprUsedBits &= ~(1 << target.index);\r\n\r\n this._reprList.splice(index, 1);\r\n\r\n // update current rep\r\n if (target === this._repr) {\r\n --count;\r\n index = index < count ? index : count - 1;\r\n this._repr = this._reprList[index];\r\n }\r\n this._reprListChanged = true;\r\n }\r\n\r\n /**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\n repHide(index, hide) {\r\n if (hide === undefined) {\r\n hide = true;\r\n }\r\n\r\n // fail if out of bounds\r\n if (index < 0 || index >= this._reprList.length) {\r\n return;\r\n }\r\n\r\n const target = this._reprList[index];\r\n target.show(!hide);\r\n }\r\n\r\n /**\r\n * Select atoms with selector\r\n * @param {Selector} selector - selector\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\n select(selector, append) {\r\n if (append) {\r\n this._selectionCount += this._complex.markAtomsAdditionally(selector, 1 << this._selectionBit);\r\n } else {\r\n this._selectionCount = this._complex.markAtoms(selector, 1 << this._selectionBit);\r\n }\r\n this._complex.updateStructuresMask();\r\n this.rebuildSelectionGeometry();\r\n }\r\n\r\n resetSelectionMask() {\r\n if (this._selectionCount !== 0) {\r\n this._selectionCount = 0;\r\n if (this._complex) {\r\n this._complex.clearAtomBits(1 << this._selectionBit);\r\n }\r\n }\r\n }\r\n\r\n updateSelectionMask(pickedObj) {\r\n const self = this;\r\n const { atom } = pickedObj;\r\n let { residue, chain, molecule } = pickedObj;\r\n const setMask = 1 << this._selectionBit;\r\n const clearMask = ~setMask;\r\n\r\n if (atom) {\r\n residue = atom.residue;\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (atom.mask & setMask) {\r\n atom.mask &= clearMask;\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n if (molecule) {\r\n molecule.mask &= clearMask;\r\n }\r\n this._selectionCount--;\r\n } else {\r\n atom.mask |= setMask;\r\n this._selectionCount++;\r\n\r\n // select residue if all atoms in it are selected\r\n residue.collectMask();\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (residue) {\r\n chain = residue._chain;\r\n molecule = residue._molecule;\r\n\r\n if (residue._mask & setMask) {\r\n residue._mask &= clearMask;\r\n chain._mask &= clearMask;\r\n residue.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n } else {\r\n residue._mask |= setMask;\r\n residue.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n\r\n // select chain and molecule if all residues in it are selected\r\n chain.collectMask();\r\n if (molecule) {\r\n molecule.collectMask();\r\n }\r\n }\r\n } else if (chain || molecule) {\r\n const obj = chain || molecule;\r\n if (obj._mask & setMask) {\r\n obj._mask &= clearMask;\r\n obj.forEachResidue((r) => {\r\n if (r._mask & setMask) {\r\n r._mask &= clearMask;\r\n r.forEachAtom((a) => {\r\n if (a.mask & setMask) {\r\n a.mask &= clearMask;\r\n self._selectionCount--;\r\n }\r\n });\r\n r._mask &= clearMask;\r\n }\r\n });\r\n } else {\r\n obj._mask |= setMask;\r\n obj.forEachResidue((r) => {\r\n if (!(r._mask & setMask)) {\r\n r._mask |= setMask;\r\n r.forEachAtom((a) => {\r\n if (!(a.mask & setMask)) {\r\n a.mask |= setMask;\r\n self._selectionCount++;\r\n }\r\n });\r\n const otherObj = chain ? r.getMolecule() : r.getChain();\r\n if (otherObj) {\r\n otherObj.collectMask();\r\n }\r\n }\r\n });\r\n }\r\n } else {\r\n this.resetSelectionMask();\r\n }\r\n }\r\n\r\n expandSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms to add\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // select marked atoms\r\n const deselectionMask = ~tmpMask;\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask = (atom.mask & deselectionMask) | selectionMask;\r\n ++self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n shrinkSelection() {\r\n const self = this;\r\n const selectionMask = 1 << this._selectionBit;\r\n const tmpMask = 1 << 31;\r\n\r\n // mark atoms neighbouring to unselected ones\r\n this._complex.forEachBond((bond) => {\r\n if (bond._left.mask & selectionMask) {\r\n if ((bond._right.mask & selectionMask) === 0) {\r\n bond._left.mask |= tmpMask;\r\n }\r\n } else if (bond._right.mask & selectionMask) {\r\n bond._right.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // mark hanging atoms\r\n this._complex.forEachAtom((atom) => {\r\n if ((atom.mask & selectionMask) && (atom.bonds.length === 1)) {\r\n atom.mask |= tmpMask;\r\n }\r\n });\r\n\r\n // deselect marked atoms\r\n const deselectionMask = ~(selectionMask | tmpMask);\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & tmpMask) {\r\n atom.mask &= deselectionMask;\r\n --self._selectionCount;\r\n }\r\n });\r\n\r\n this._complex.updateStructuresMask();\r\n }\r\n\r\n getSelectedComponent() {\r\n const selectionMask = 1 << this._selectionBit;\r\n\r\n let component = null;\r\n let multiple = false;\r\n\r\n // find which component is selected (exclusively)\r\n this._complex.forEachAtom((atom) => {\r\n if (atom.mask & selectionMask) {\r\n if (component === null) {\r\n component = atom.residue._component;\r\n } else if (component !== atom.residue._component) {\r\n multiple = true;\r\n }\r\n }\r\n });\r\n\r\n return multiple ? null : component;\r\n }\r\n\r\n getSelectionCenter(center, includesAtom, selRule) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._complex.forEachAtom((atom) => {\r\n if (includesAtom(atom, selRule)) {\r\n center.add(atom.position);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.applyMatrix4(this.matrix);\r\n return true;\r\n }\r\n\r\n needsRebuild() {\r\n if (this._reprListChanged) {\r\n return true;\r\n }\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n if (repr.needsRebuild) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n }\r\n\r\n /**\r\n * Rebuild molecule geometry asynchronously.\r\n */\r\n rebuild() {\r\n const self = this;\r\n\r\n // Destroy current geometry\r\n gfxutils.clearTree(this);\r\n\r\n return new Promise(((resolve) => {\r\n // Nothing to do?\r\n const complex = self._complex;\r\n if (!complex) {\r\n resolve();\r\n return;\r\n }\r\n\r\n let errorOccured = false;\r\n setTimeout(() => {\r\n console.time('build');\r\n const reprList = self._reprList;\r\n const palette = palettes.get(settings.now.palette) || palettes.first;\r\n let hasGeometry = false;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n repr.colorer.palette = palette;\r\n\r\n if (repr.needsRebuild) {\r\n repr.reset();\r\n\r\n try {\r\n repr.buildGeometry(complex);\r\n } catch (e) {\r\n if (e instanceof utils.OutOfMemoryError) {\r\n repr.needsRebuild = false;\r\n repr.reset();\r\n logger.error(`Not enough memory to build geometry for representation ${repr.index + 1}`);\r\n errorOccured = true;\r\n } else {\r\n throw e;\r\n }\r\n }\r\n\r\n if (DEBUG && !errorOccured) {\r\n logger.debug(`Triangles count: ${meshutils.countTriangles(repr.geo)}`);\r\n }\r\n }\r\n\r\n hasGeometry = errorOccured || hasGeometry || gfxutils.groupHasGeometryToRender(repr.geo);\r\n\r\n if (repr.geo) {\r\n self.add(repr.geo);\r\n }\r\n }\r\n\r\n self._reprListChanged = false;\r\n\r\n console.timeEnd('build');\r\n resolve();\r\n }, 10);\r\n }));\r\n }\r\n\r\n setNeedsRebuild() {\r\n // invalidate all representations\r\n const reprList = this._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n reprList[i].needsRebuild = true;\r\n }\r\n }\r\n\r\n rebuildSelectionGeometry() {\r\n const mask = 1 << this._selectionBit;\r\n\r\n gfxutils.clearTree(this._selectionGeometry);\r\n\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const repr = this._reprList[i];\r\n const sg = repr.buildSelectionGeometry(mask);\r\n if (!sg) {\r\n continue;\r\n }\r\n\r\n this._selectionGeometry.add(sg);\r\n for (let j = 0; j < sg.children.length; j++) {\r\n const m = sg.children[j];\r\n\r\n // copy component transform (that's not applied yet)\r\n // TODO make this code obsolete, accessing editor is bad\r\n if (this._editor && this._editor._componentTransforms) {\r\n const t = this._editor._componentTransforms[m._component._index];\r\n if (t) {\r\n m.position.copy(t.position);\r\n m.quaternion.copy(t.quaternion);\r\n }\r\n }\r\n }\r\n\r\n gfxutils.applySelectionMaterial(sg);\r\n }\r\n }\r\n\r\n _buildSelectorFromSortedLists(atoms, residues, chains) {\r\n const complex = this._complex;\r\n\r\n function optimizeList(list) {\r\n const result = [];\r\n let k = 0;\r\n let first = NaN;\r\n let last = NaN;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n const value = list[i];\r\n if (value === last + 1) {\r\n last = value;\r\n } else {\r\n if (!Number.isNaN(first)) {\r\n result[k++] = new selectors.Range(first, last);\r\n }\r\n first = last = value;\r\n }\r\n }\r\n if (!Number.isNaN(first)) {\r\n result[k] = new selectors.Range(first, last);\r\n }\r\n return result;\r\n }\r\n\r\n let expression = null;\r\n if (chains.length === complex._chains.length) {\r\n expression = selectors.all();\r\n } else {\r\n let selector;\r\n if (chains.length > 0) {\r\n selector = selectors.chain(chains);\r\n expression = expression ? selectors.or(expression, selector) : selector;// NOSONAR\r\n }\r\n if (Object.keys(residues).length > 0) {\r\n for (const ch in residues) {\r\n if (residues.hasOwnProperty(ch)) {\r\n selector = selectors.and(\r\n selectors.chain(ch),\r\n selectors.residx(optimizeList(residues[ch])),\r\n );\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n }\r\n }\r\n if (atoms.length > 0) {\r\n selector = selectors.serial(optimizeList(atoms));\r\n expression = expression ? selectors.or(expression, selector) : selector;\r\n }\r\n\r\n if (!expression) {\r\n expression = selectors.none();\r\n }\r\n }\r\n\r\n return expression;\r\n }\r\n\r\n buildSelectorFromMask(mask) {\r\n const complex = this._complex;\r\n const chains = [];\r\n const residues = {};\r\n const atoms = [];\r\n\r\n complex.forEachChain((chain) => {\r\n if (chain._mask & mask) {\r\n chains.push(chain._name);\r\n }\r\n });\r\n\r\n complex.forEachResidue((residue) => {\r\n if (residue._mask & mask && !(residue._chain._mask & mask)) {\r\n const c = residue._chain._name;\r\n if (!(c in residues)) {\r\n residues[c] = [residue._index];\r\n } else {\r\n residues[c].push(residue._index);\r\n }\r\n }\r\n });\r\n\r\n complex.forEachAtom((atom) => {\r\n if (atom.mask & mask && !(atom.residue._mask & mask)) {\r\n atoms.push(atom.serial);\r\n }\r\n });\r\n\r\n return this._buildSelectorFromSortedLists(atoms, residues, chains);\r\n }\r\n\r\n forSelectedResidues(process) {\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.forEachResidue((residue) => {\r\n if (residue._mask & selectionMask) {\r\n process(residue);\r\n }\r\n });\r\n }\r\n\r\n beginComponentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.ComponentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n beginFragmentEdit() {\r\n if (this._editor) {\r\n return null;\r\n }\r\n\r\n const editor = new ComplexVisualEdit.FragmentEditor(this);\r\n if (!editor.begin()) {\r\n return null;\r\n }\r\n\r\n this._editor = editor;\r\n return editor;\r\n }\r\n\r\n // should only be called by editors\r\n finalizeEdit() {\r\n this._editor = null;\r\n }\r\n\r\n setMaterialValues(values, needTraverse = false, process = undefined) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setValues(values);\r\n if (needTraverse) {\r\n rep.geo.traverse((object) => {\r\n if (object instanceof THREE.Mesh) {\r\n object.material.setValues(values);\r\n\r\n if (process !== undefined) {\r\n process(object);\r\n }\r\n\r\n object.material.needsUpdate = true;\r\n }\r\n });\r\n }\r\n }\r\n }\r\n\r\n setUberOptions(values) {\r\n for (let i = 0, n = this._reprList.length; i < n; ++i) {\r\n const rep = this._reprList[i];\r\n rep.material.setUberOptions(values);\r\n }\r\n }\r\n\r\n /**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\n within(selector, radius) {\r\n const vw = this._complex.getVoxelWorld();\r\n if (vw === null) {\r\n return false;\r\n }\r\n\r\n // mark atoms of the group as selected\r\n const selectionMask = 1 << this._selectionBit;\r\n this._complex.markAtoms(selector, selectionMask);\r\n\r\n // mark all atoms within distance as selected\r\n if (vw) {\r\n vw.forEachAtomWithinDistFromMasked(this._complex, selectionMask, Number(radius), (atom) => {\r\n atom.mask |= selectionMask;\r\n });\r\n }\r\n\r\n // update selection count\r\n this._selectionCount = this._complex.countAtomsByMask(selectionMask);\r\n\r\n // update secondary structure mask\r\n this._complex.updateStructuresMask();\r\n\r\n return this.buildSelectorFromMask(selectionMask);\r\n }\r\n}\r\n// 32 bits = 30 bits for reps + 1 for selection + 1 for selection expansion\r\nComplexVisual.NUM_REPRESENTATION_BITS = 30;\r\n\r\nexport default ComplexVisual;\r\n","import * as THREE from 'three';\r\nimport vertexVolumeFaces from './VolumeFaces.vert';\r\nimport fragmentVolumeFaces from './VolumeFaces.frag';\r\nimport vertexVolume from './Volume.vert';\r\nimport fragmentVolume from './Volume.frag';\r\nimport vertexFarPlane from './VolumeFarPlane.vert';\r\nimport fragmentFarPlane from './VolumeFarPlane.frag';\r\nimport settings from '../../settings';\r\n\r\nconst volumeUniforms = THREE.UniformsUtils.merge([\r\n {\r\n volumeDim: { type: 'v3', value: new THREE.Vector3(512, 512, 512) },\r\n tileTex: { type: 't', value: null },\r\n tileTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n tileStride: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n\r\n boxAngles: { type: 'v3', value: new THREE.Vector3(1, 1, 1) },\r\n delta: { type: 'v3', value: new THREE.Vector3(0, 0, 0) },\r\n\r\n _isoLevel0: { type: 'v2', value: new THREE.Vector3(0.5, 0.75, 1.0) },\r\n _flipV: { type: 'f', value: 0.0 },\r\n _BFLeft: { type: 't', value: null },\r\n _BFRight: { type: 't', value: null },\r\n _FFLeft: { type: 't', value: null },\r\n _FFRight: { type: 't', value: null },\r\n _WFFLeft: { type: 't', value: null },\r\n _WFFRight: { type: 't', value: null },\r\n },\r\n]);\r\n\r\nfunction overrideUniforms(params, defUniforms) {\r\n const uniforms = THREE.UniformsUtils.clone(defUniforms);\r\n for (const p in params) {\r\n if (uniforms.hasOwnProperty(p)) {\r\n uniforms[p].value = params[p];\r\n }\r\n }\r\n return uniforms;\r\n}\r\n\r\nfunction facesPosMaterialParams(params, sideType) {\r\n return {\r\n uniforms: overrideUniforms(params, {}),\r\n vertexShader: vertexVolumeFaces,\r\n fragmentShader: fragmentVolumeFaces,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n side: sideType,\r\n };\r\n}\r\n\r\nclass BackFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const backFaceParams = facesPosMaterialParams(params, THREE.BackSide);\r\n super(backFaceParams);\r\n }\r\n}\r\n\r\nclass ShaderParams {\r\n constructor(params, uniforms, vertexShader, fragmentShader) {\r\n this.uniforms = overrideUniforms(params, uniforms);\r\n this.vertexShader = vertexShader;\r\n this.fragmentShader = fragmentShader;\r\n this.transparent = false;\r\n this.depthTest = false;\r\n this.depthWrite = false;\r\n this.side = THREE.FrontSide;\r\n }\r\n}\r\n\r\nclass BackFacePosMaterialFarPlane extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const matUniforms = THREE.UniformsUtils.merge([\r\n {\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n farZ: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n matWorld2Volume: { type: '4fv', value: new THREE.Matrix4() },\r\n },\r\n ]);\r\n\r\n const shaderParams = new ShaderParams(params, matUniforms, vertexFarPlane, fragmentFarPlane);\r\n super(shaderParams);\r\n }\r\n}\r\n\r\nclass FrontFacePosMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const frontFaceParams = facesPosMaterialParams(params, THREE.FrontSide);\r\n super(frontFaceParams);\r\n }\r\n}\r\n\r\nclass VolumeMaterial extends THREE.ShaderMaterial {\r\n constructor(params) {\r\n const shaderParams = new ShaderParams(params, volumeUniforms, vertexVolume, fragmentVolume);\r\n shaderParams.transparent = true;\r\n shaderParams.depthTest = true;\r\n\r\n super(shaderParams);\r\n this.updateDefines();\r\n }\r\n\r\n updateDefines() {\r\n this.defines = {\r\n ISO_MODE: settings.now.modes.VD.isoMode,\r\n STEPS_COUNT: settings.now.modes.VD.polyComplexity[settings.now.resolution] * 100,\r\n };\r\n this.needsUpdate = true;\r\n }\r\n}\r\n\r\nexport default {\r\n BackFacePosMaterial,\r\n BackFacePosMaterialFarPlane,\r\n FrontFacePosMaterial,\r\n VolumeMaterial,\r\n};\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport settings from '../settings';\r\n\r\nclass VolumeMesh extends THREE.Mesh {\r\n volumeInfo = {}; // data for noise filter\r\n\r\n constructor() {\r\n const geo = new THREE.BufferGeometry();\r\n super(geo);\r\n this.clipPlane = new THREE.Plane();\r\n const size = new THREE.Vector3(0.5, 0.5, 0.5);\r\n this.size = size;\r\n\r\n this.cullFlag = [\r\n true, true, true, true,\r\n true, true, true, true,\r\n false, false, false, false, false, false,\r\n ];\r\n\r\n this.faces = [\r\n { indices: [], norm: new THREE.Vector3(0, 0, -1) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 1) },\r\n { indices: [], norm: new THREE.Vector3(0, -1, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 1, 0) },\r\n { indices: [], norm: new THREE.Vector3(-1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(1, 0, 0) },\r\n { indices: [], norm: new THREE.Vector3(0, 0, 0) },\r\n ];\r\n\r\n this.vertices = [\r\n new THREE.Vector3(-size.x, -size.y, -size.z),\r\n new THREE.Vector3(-size.x, size.y, -size.z),\r\n new THREE.Vector3(size.x, -size.y, -size.z),\r\n new THREE.Vector3(size.x, size.y, -size.z),\r\n new THREE.Vector3(-size.x, -size.y, size.z),\r\n new THREE.Vector3(-size.x, size.y, size.z),\r\n new THREE.Vector3(size.x, -size.y, size.z),\r\n new THREE.Vector3(size.x, size.y, size.z),\r\n new THREE.Vector3(0.0, 0.0, 0.0), // Placeholder for section\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n new THREE.Vector3(0.0, 0.0, 0.0),\r\n ];\r\n\r\n geo.setAttribute('position', new THREE.BufferAttribute(new Float32Array(this.vertices.length * 3), 3));\r\n\r\n this.name = 'VolumeMesh';\r\n }\r\n\r\n static _corners = [\r\n // x, y, z, edge1, edge2, edge3\r\n [-1, -1, -1, 0, 4, 8],\r\n [1, -1, -1, 0, 5, 9],\r\n [1, 1, -1, 1, 5, 10],\r\n [-1, 1, -1, 1, 4, 11],\r\n [-1, -1, 1, 2, 6, 8],\r\n [1, -1, 1, 2, 7, 9],\r\n [1, 1, 1, 3, 7, 10],\r\n [-1, 1, 1, 3, 6, 11],\r\n ];\r\n\r\n static _edges = [\r\n // corner1, corner2, center_x, center_y, center_z\r\n [0, 1, 0, -1, -1],\r\n [2, 3, 0, 1, -1],\r\n [4, 5, 0, -1, 1],\r\n [6, 7, 0, 1, 1],\r\n [0, 3, -1, 0, -1],\r\n [1, 2, 1, 0, -1],\r\n [4, 7, -1, 0, 1],\r\n [5, 6, 1, 0, 1],\r\n [0, 4, -1, -1, 0],\r\n [1, 5, 1, -1, 0],\r\n [2, 6, -1, 1, 0],\r\n [3, 7, 1, 1, 0],\r\n ];\r\n\r\n static _edgeIntersections = (function () {\r\n const edgeIntersections = [];\r\n for (let j = 0; j < 12; ++j) {\r\n edgeIntersections.push(new THREE.Vector3());\r\n }\r\n return edgeIntersections;\r\n }());\r\n\r\n _updateVertices() {\r\n // Algorithm:\r\n // 1. Get plane parameters\r\n // 2. Compute culling flags for all vertices\r\n // 3. If intersection occurs => compute from 3 to 6 intersection points\r\n const corners = VolumeMesh._corners;\r\n const edges = VolumeMesh._edges;\r\n const edgeIntersections = VolumeMesh._edgeIntersections;\r\n\r\n let i;\r\n\r\n const norm = this.clipPlane.normal;\r\n const D = this.clipPlane.constant;\r\n\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n const cornerMark = [0, 0, 0, 0, 0, 0, 0, 0];\r\n const edgeMark = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1];\r\n\r\n const curEdge = new THREE.Vector3();\r\n let curEdgeInter = null;\r\n\r\n function CheckX() {\r\n if (norm.x === 0) return 0;\r\n const x = -(norm.dot(curEdge) + D) / norm.x;\r\n if (-size.x <= x && x <= size.x) {\r\n curEdgeInter.set(x, curEdge.y, curEdge.z);\r\n if (x === size.x) return 2;\r\n if (x === -size.x) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckY() {\r\n if (norm.y === 0) return 0;\r\n const y = -(norm.dot(curEdge) + D) / norm.y;\r\n if (-size.y <= y && y <= size.y) {\r\n curEdgeInter.set(curEdge.x, y, curEdge.z);\r\n if (y === size.y) return 2;\r\n if (y === -size.y) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n function CheckZ() {\r\n if (norm.z === 0) return 0;\r\n const z = -(norm.dot(curEdge) + D) / norm.z;\r\n if (-size.z <= z && z <= size.z) {\r\n curEdgeInter.set(curEdge.x, curEdge.y, z);\r\n if (z === size.z) return 2;\r\n if (z === -size.z) return -2;\r\n return 1;\r\n }\r\n return 0;\r\n }\r\n\r\n // for each edge\r\n for (let curEdgeIdx = 0; curEdgeIdx < 12; ++curEdgeIdx) {\r\n const curEdgeSource = edges[curEdgeIdx];\r\n curEdgeInter = edgeIntersections[curEdgeIdx];\r\n\r\n curEdge.set(curEdgeSource[2], curEdgeSource[3], curEdgeSource[4]);\r\n curEdge.multiply(size);\r\n\r\n // calculate intersection point\r\n let flag = 0;\r\n if (curEdgeSource[2] === 0) flag = CheckX();\r\n if (curEdgeSource[3] === 0) flag = CheckY();\r\n if (curEdgeSource[4] === 0) flag = CheckZ();\r\n\r\n // mark corresponding corner (if plane cuts through one)\r\n if (flag === -2) {\r\n cornerMark[curEdgeSource[0]] = 1;\r\n } else if (flag === 2) {\r\n cornerMark[curEdgeSource[1]] = 1;\r\n } else if (flag === 0) {\r\n // edge is not intersected by the plane (doesn't produce a vertex)\r\n edgeMark[curEdgeIdx] = 0;\r\n }\r\n }\r\n\r\n const face = {\r\n indices: [],\r\n norm: norm.clone().negate(),\r\n };\r\n\r\n let nextVertex = 8;\r\n\r\n // for each marked corner\r\n for (i = 0; i < 8; ++i) {\r\n if (cornerMark[i] === 1) {\r\n // add corner as vertex to the face\r\n vert[nextVertex].set(corners[i][0], corners[i][1], corners[i][2]).multiply(size);\r\n face.indices.push(nextVertex++);\r\n // skip adjacent edges\r\n edgeMark[corners[i][3]] = 0;\r\n edgeMark[corners[i][4]] = 0;\r\n edgeMark[corners[i][5]] = 0;\r\n }\r\n }\r\n\r\n // for each edge that has internal intersection\r\n for (i = 0; i < 12; ++i) {\r\n if (edgeMark[i] === 1) {\r\n // add intersection point as vertex to the face\r\n vert[nextVertex].copy(edgeIntersections[i]);\r\n face.indices.push(nextVertex++);\r\n }\r\n }\r\n\r\n this.faces[6] = face;\r\n\r\n const diff = new THREE.Vector3();\r\n const coplanarPoint = new THREE.Vector3();\r\n this.clipPlane.coplanarPoint(coplanarPoint);\r\n for (i = 0; i < vert.length; ++i) {\r\n this.cullFlag[i] = false;\r\n if (i < 8) {\r\n // corners should be culled by clipping plane\r\n diff.subVectors(vert[i], coplanarPoint);\r\n this.cullFlag[i] = (norm.dot(diff) >= 0.0);\r\n } else if (i < 8 + face.indices.length) {\r\n // cross section vertices don't get culled\r\n this.cullFlag[i] = true;\r\n }\r\n }\r\n\r\n // write data to vertex buffer\r\n const positions = this.geometry.getAttribute('position');\r\n let idx = 0;\r\n for (i = 0; i < vert.length; ++i) {\r\n positions.array[idx++] = vert[i].x;\r\n positions.array[idx++] = vert[i].y;\r\n positions.array[idx++] = vert[i].z;\r\n }\r\n positions.needsUpdate = true;\r\n }\r\n\r\n _collectVertices(face, filter) {\r\n let i;\r\n const vert = this.vertices;\r\n face.indices = [];\r\n for (i = 0; i < vert.length; ++i) {\r\n if (this.cullFlag[i] && filter(vert[i])) {\r\n face.indices.push(i);\r\n }\r\n }\r\n }\r\n\r\n _sortIndices(face, right) {\r\n let i;\r\n let j;\r\n const vert = this.vertices;\r\n const angle = [];\r\n\r\n const dir = new THREE.Vector3();\r\n for (i = 1; i < face.indices.length; ++i) {\r\n dir.subVectors(vert[face.indices[i]], vert[face.indices[0]]);\r\n dir.normalize();\r\n dir.cross(right);\r\n dir.negate();\r\n angle[i] = face.norm.dot(dir);\r\n }\r\n\r\n // Exchange sort\r\n for (i = 1; i < face.indices.length - 1; ++i) {\r\n for (j = i + 1; j < face.indices.length; ++j) {\r\n if (angle[j] < angle[i]) {\r\n // swap\r\n let t = angle[i];\r\n angle[i] = angle[j];\r\n angle[j] = t;\r\n\r\n t = face.indices[i];\r\n face.indices[i] = face.indices[j];\r\n face.indices[j] = t;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _updateIndices() {\r\n // Algorithm:\r\n // 1. Get plane vertices (from 3 to 6 vertices)\r\n // 2. Get \"right\" vector in plane\r\n // 3. Sort vertices using Graham-like method\r\n // 4. Create indices\r\n\r\n let i;\r\n let faceIdx;\r\n let face;\r\n const vert = this.vertices;\r\n const { size } = this;\r\n\r\n this._collectVertices(this.faces[0], (vertex) => vertex.z === -size.z);\r\n this._collectVertices(this.faces[1], (vertex) => vertex.z === size.z);\r\n this._collectVertices(this.faces[2], (vertex) => vertex.y === -size.y);\r\n this._collectVertices(this.faces[3], (vertex) => vertex.y === size.y);\r\n this._collectVertices(this.faces[4], (vertex) => vertex.x === -size.x);\r\n this._collectVertices(this.faces[5], (vertex) => vertex.x === size.x);\r\n\r\n const vCenter = new THREE.Vector3();\r\n const vRight = new THREE.Vector3();\r\n const vDir = new THREE.Vector3();\r\n\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n\r\n if (face.indices.length === 0) continue;\r\n\r\n vCenter.set(0, 0, 0);\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vCenter.add(vert[face.indices[i]]);\r\n }\r\n vCenter.multiplyScalar(1.0 / face.indices.length);\r\n vRight.subVectors(vert[face.indices[0]], vCenter);\r\n vRight.normalize();\r\n\r\n const rightProj = [];\r\n for (i = 0; i < face.indices.length; ++i) {\r\n vDir.subVectors(vert[face.indices[i]], vCenter);\r\n rightProj[i] = vDir.dot(vRight);\r\n }\r\n for (i = 1; i < face.indices.length; ++i) {\r\n if (rightProj[i] < rightProj[0]) {\r\n // swap\r\n let t = rightProj[0];\r\n rightProj[0] = rightProj[i];\r\n rightProj[i] = t;\r\n\r\n [t] = face.indices;\r\n face.indices[0] = face.indices[i];\r\n face.indices[i] = t;\r\n }\r\n }\r\n\r\n this._sortIndices(face, vRight);\r\n }\r\n\r\n let numIndices = 0;\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n if (face.indices.length >= 3) {\r\n numIndices += 3 * (face.indices.length - 2);\r\n }\r\n }\r\n let offset = 0;\r\n const indices = new Uint16Array(numIndices);\r\n for (faceIdx = 0; faceIdx < this.faces.length; ++faceIdx) {\r\n face = this.faces[faceIdx];\r\n for (i = 0; i < face.indices.length - 2; ++i) {\r\n indices[offset] = face.indices[0]; // eslint-disable-line prefer-destructuring\r\n indices[offset + 1] = face.indices[i + 1];\r\n indices[offset + 2] = face.indices[i + 2];\r\n offset += 3;\r\n }\r\n }\r\n\r\n this.geometry.setIndex(new THREE.BufferAttribute(indices, 1));\r\n }\r\n\r\n setDataSource(dataSource) {\r\n const vm = new VolumeMaterial.VolumeMaterial();\r\n const dim = dataSource.getDimensions();\r\n const stride = dataSource.getTiledTextureStride();\r\n const texture = dataSource.buildTiledTexture();\r\n const bbox = dataSource.getBox();\r\n vm.uniforms.volumeDim.value.set(dim[0], dim[1], dim[2]);\r\n vm.uniforms.tileTex.value = texture;\r\n vm.uniforms.tileTexSize.value.set(texture.image.width, texture.image.height);\r\n vm.uniforms.tileStride.value.set(stride[0], stride[1]);\r\n Object.assign(this.volumeInfo, dataSource.getVolumeInfo());\r\n\r\n const volInfo = this.volumeInfo;\r\n vm.uniforms.delta.value.copy(volInfo.delta);\r\n vm.uniforms.boxAngles.value.set(volInfo.obtuseAngle[0], volInfo.obtuseAngle[1], volInfo.obtuseAngle[2]);\r\n\r\n this.material = vm;\r\n\r\n bbox.getSize(this.scale);\r\n bbox.getCenter(this.position);\r\n }\r\n\r\n _updateIsoLevel() {\r\n const { kSigma, kSigmaMed, kSigmaMax } = settings.now.modes.VD;\r\n const volInfo = this.volumeInfo;\r\n const mean = volInfo.dmean - volInfo.dmin;\r\n const span = volInfo.dmax - volInfo.dmin;\r\n const level = (k) => (mean + k * volInfo.sd) / span;\r\n this.material.uniforms._isoLevel0.value.set(level(kSigma), level(kSigmaMed), level(kSigmaMax));\r\n }\r\n\r\n static _nearClipPlaneOffset = 0.2;\r\n\r\n static _pos = new THREE.Vector3();\r\n\r\n static _norm = new THREE.Vector3();\r\n\r\n static _norm4D = new THREE.Vector4();\r\n\r\n static _matrixWorldToLocal = new THREE.Matrix4();\r\n\r\n static _clipPlane = new THREE.Plane();\r\n\r\n rebuild(camera) {\r\n const nearClipPlaneOffset = VolumeMesh._nearClipPlaneOffset;\r\n const pos = VolumeMesh._pos;\r\n const norm = VolumeMesh._norm;\r\n const norm4D = VolumeMesh._norm4D;\r\n const matrixWorldToLocal = VolumeMesh._matrixWorldToLocal;\r\n const clipPlane = VolumeMesh._clipPlane;\r\n\r\n this._updateIsoLevel();\r\n\r\n // get clip plane in local space\r\n camera.getWorldDirection(norm);\r\n camera.getWorldPosition(pos);\r\n pos.addScaledVector(norm, camera.near + nearClipPlaneOffset);\r\n\r\n // transform pos to local CS\r\n matrixWorldToLocal.copy(this.matrixWorld).invert();\r\n pos.applyMatrix4(matrixWorldToLocal);\r\n\r\n // transform norm to local CS\r\n norm4D.set(norm.x, norm.y, norm.z, 0.0); // NOTE: use homogeneous norm for proper transformation\r\n norm4D.applyMatrix4(matrixWorldToLocal);\r\n norm.copy(norm4D);\r\n norm.normalize();\r\n\r\n clipPlane.setFromNormalAndCoplanarPoint(norm, pos);\r\n\r\n if (!this.clipPlane.equals(clipPlane)) {\r\n this.clipPlane = clipPlane.clone();\r\n this._updateVertices();\r\n this._updateIndices();\r\n }\r\n }\r\n}\r\n\r\nexport default VolumeMesh;\r\n","import * as THREE from 'three';\r\nimport gfxutils from './gfxutils';\r\n\r\nfunction _flattenArray(input) {\r\n const n = input.length;\r\n const output = new Float32Array(n * 3);\r\n for (let i = 0; i < n; ++i) {\r\n const j = 3 * i;\r\n const v = input[i];\r\n output[j] = v.x;\r\n output[j + 1] = v.y;\r\n output[j + 2] = v.z;\r\n }\r\n return output;\r\n}\r\n\r\nclass VolumeBounds {\r\n static _projectionTable = { // corresponds between (origin axes and angles between them) and between saving vector coordinates\r\n XY: ['x', 2],\r\n XZ: ['y', 1],\r\n YZ: ['z', 0],\r\n };\r\n\r\n constructor(bBox, volInfo) {\r\n const { delta } = volInfo; // {x: XY, y : XZ, z: YZ}\r\n const { obtuseAngle } = volInfo; // 1 - obtuse, 0 - acute\r\n\r\n const bSize = new THREE.Vector3();\r\n bBox.getSize(bSize);\r\n bSize.multiplyScalar(0.5);\r\n\r\n const offsetVert = this._getBaseVertices(delta, obtuseAngle);\r\n\r\n const geometry = new THREE.BufferGeometry();\r\n const vertices = [];\r\n\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(offsetVert[i].clone().multiply(bSize));\r\n vertices.push(offsetVert[(i + 1) % 4].clone().multiply(bSize));\r\n }\r\n const translation = new THREE.Vector3(2 * bSize.x * (1 - delta.x - delta.y), 0, 0);\r\n for (let i = 0; i < 8; i++) {\r\n vertices.push(vertices[i].clone().add(translation));\r\n }\r\n for (let i = 0; i < 4; i++) {\r\n vertices.push(vertices[i * 2].clone());\r\n vertices.push(vertices[i * 2 + 8].clone());\r\n }\r\n const center = new THREE.Vector3();\r\n bBox.getCenter(center);\r\n vertices.forEach((vertex) => vertex.add(center)); // pivot shift\r\n\r\n const flatVertices = _flattenArray(vertices);\r\n geometry.setAttribute('position', new THREE.BufferAttribute(flatVertices, 3));\r\n\r\n this._lines = new THREE.LineSegments(geometry, new THREE.LineBasicMaterial({ color: 0xFFFFFF }));\r\n this._lines.layers.set(gfxutils.LAYERS.VOLUME);\r\n }\r\n\r\n // Set one edge (4 points) of frame, from which with parallel transfer the rest of the frame points can be obtained\r\n _getBaseVertices(delta, obtuseAngle) {\r\n const projTable = VolumeBounds._projectionTable;\r\n\r\n const proj = ((index, inv) => { // tricky function to take account of projections: their position(related to box) and sign\r\n const currDelta = delta[projTable[index][0]];\r\n const angleValue = -0.5 * (inv - 1) + inv * obtuseAngle[projTable[index][1]];// inv = 1: alpha; inv = -1: 1 - alpha\r\n return angleValue * currDelta;\r\n });\r\n\r\n const offsetVert = [\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', 1)), -1 + 2 * proj('YZ', 1), -1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', 1)), -1 + 2 * proj('YZ', -1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', -1) + proj('XY', -1)), 1 - 2 * proj('YZ', 1), 1),\r\n new THREE.Vector3(-1 + 2 * (proj('XZ', 1) + proj('XY', -1)), 1 - 2 * proj('YZ', -1), -1),\r\n ];\r\n\r\n return offsetVert;\r\n }\r\n\r\n getMesh() {\r\n return this._lines;\r\n }\r\n}\r\n\r\nexport default VolumeBounds;\r\n","import * as THREE from 'three';\r\nimport VolumeMaterial from './shaders/VolumeMaterial';\r\nimport meshes from './meshes/meshes';\r\nimport gfxutils from './gfxutils';\r\n\r\n// Thes geometric far plane is required for correct filling in the BFTexture in case, when far plane cuts the volume\r\n// cube. In cut place of cube there is no correct data in BFTexture and volume rendering integral is calculated\r\n// with errors.\r\n// Far plane cuts the cube in case of large volume scale (zoom), because farplane doesn't change\r\nclass VolumeFarPlane {\r\n // create plane with unit corners coords (for future rescale in vshader according to camera properties)\r\n constructor(volume, width, height) {\r\n const planeGeo = this._initPlaneGeo(width, height);\r\n\r\n const mat = new VolumeMaterial.BackFacePosMaterialFarPlane();\r\n this._plane = new meshes.Mesh(planeGeo, mat);\r\n this._plane.frustumCulled = false;\r\n this._plane.doubleSided = true;\r\n const matWorldToVolume = new THREE.Matrix4();\r\n\r\n this._plane._onBeforeRender = function (_renderer, _scene, camera, _geometry, _material, _group) {\r\n const { material } = this;\r\n if (!volume || !material) {\r\n return;\r\n }\r\n\r\n // count point in world at farplane place\r\n const planeCamPos = new THREE.Vector4(0, 0, -(camera.far - 0.1), 1);\r\n planeCamPos.applyMatrix4(camera.matrixWorld);\r\n\r\n // recalc matrices to make plane be placed as farplane in the World relative to camera\r\n this.matrix.identity();\r\n this.matrix.makeTranslation(planeCamPos.x, planeCamPos.y, planeCamPos.z);\r\n this.matrixWorld.copy(this.matrix);\r\n this.modelViewMatrix.multiplyMatrices(camera.matrixWorldInverse, this.matrixWorld);\r\n this.normalMatrix.getNormalMatrix(this.modelViewMatrix);\r\n\r\n // build worldToVolume matrix to transform plane into volumeCS (volumeCS coords are written to BackFaceTexture)\r\n const volumeMatrix = volume.matrixWorld;\r\n matWorldToVolume.copy(volumeMatrix).invert();\r\n\r\n // update material props\r\n material.uniforms.aspectRatio.value = camera.aspect;\r\n material.uniforms.farZ.value = camera.far;\r\n material.uniforms.tanHalfFOV.value = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * camera.fov);\r\n material.uniforms.matWorld2Volume.value = matWorldToVolume;\r\n };\r\n\r\n // set it to special layer to draw only into BFTexture\r\n this._plane.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n }\r\n\r\n _initPlaneGeo(width, height) {\r\n const planeGeo = new THREE.BufferGeometry();\r\n\r\n width = width || 1;\r\n height = height || 1;\r\n\r\n const vertices = new Float32Array([\r\n -0.5 * width, 0.5 * height, 0,\r\n 0.5 * width, 0.5 * height, 0,\r\n -0.5 * width, -0.5 * height, 0,\r\n 0.5 * width, -0.5 * height, 0,\r\n ]);\r\n\r\n planeGeo.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n planeGeo.setIndex([0, 2, 1, 2, 3, 1]);\r\n\r\n return planeGeo;\r\n }\r\n\r\n getMesh() {\r\n return this._plane;\r\n }\r\n}\r\n\r\nexport default VolumeFarPlane;\r\n","import * as THREE from 'three';\r\nimport VolumeMesh from './gfx/VolumeMesh';\r\nimport VolumeBounds from './gfx/VolumeBounds';\r\nimport VolumeFarPlane from './gfx/VolumeFarPlane';\r\nimport Visual from './Visual';\r\nimport settings from './settings';\r\n\r\nclass VolumeVisual extends Visual {\r\n constructor(name, dataSource) {\r\n super(name, dataSource);\r\n this._mesh = new VolumeMesh();\r\n this._mesh.setDataSource(dataSource);\r\n this.add(this._mesh);\r\n\r\n this._frame = new VolumeBounds(this.getBoundaries().boundingBox, this._mesh.volumeInfo);\r\n this.add(this._frame.getMesh());\r\n this.showFrame(settings.now.modes.VD.frame);\r\n\r\n this._farPlane = new VolumeFarPlane(this._mesh, 2, 2);\r\n this.add(this._farPlane.getMesh());\r\n }\r\n\r\n getBoundaries() {\r\n const box = this._dataSource.getBox();\r\n const sphere = new THREE.Sphere();\r\n box.getBoundingSphere(sphere);\r\n\r\n return {\r\n boundingBox: box,\r\n boundingSphere: sphere,\r\n };\r\n }\r\n\r\n getMesh() {\r\n return this._mesh;\r\n }\r\n\r\n showFrame(needShow) {\r\n this._frame.getMesh().material.visible = needShow;\r\n }\r\n}\r\n\r\nexport default VolumeVisual;\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available loaders.\r\n * @extends EntityList\r\n */\r\nclass LoaderList extends EntityList {\r\n /**\r\n * Create a list of loaders.\r\n * The loaders are indexed by supported source types (`.types` property of a Loader\r\n * subclass).\r\n * The loaders can be retrieved later by matching against specs (see {@link LoaderList#find}).\r\n *\r\n * @param {!Array=} someLoaders A list of {@link Loader} subclasses to\r\n * automatically register at creation time.\r\n * @see LoaderList#register\r\n */\r\n constructor(someLoaders = []) {\r\n super(someLoaders, ['types']);\r\n }\r\n\r\n /**\r\n * Find a suitable loader for a source type.\r\n *\r\n * @param {Object} specs Loader specifications.\r\n * @param {string=} specs.type Supported source type.\r\n * @param {*=} specs.source Source to load from.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.type) {\r\n list = this._dict.types[specs.type.toLowerCase()] || [];\r\n } else if (specs.source) {\r\n return this._list.filter((SomeLoader) => SomeLoader.canProbablyLoad && SomeLoader.canProbablyLoad(specs.source));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default LoaderList;\r\n","import EventDispatcher from '../../utils/EventDispatcher';\r\nimport makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Loader extends EventDispatcher {\r\n constructor(source, options) {\r\n super();\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n this._agent = null;\r\n }\r\n\r\n load() {\r\n return Promise.reject(new Error('Loading from this source is not implemented'));\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n if (this._agent) {\r\n this._agent.abort();\r\n }\r\n }\r\n\r\n static extractName(_source) {\r\n return undefined;\r\n }\r\n}\r\n\r\nmakeContextDependent(Loader.prototype);\r\n","import Loader from './Loader';\r\n\r\nexport default class FileLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = options.binary === true;\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const blob = this._source;\r\n const reader = this._agent = new FileReader();\r\n\r\n reader.addEventListener('load', () => {\r\n resolve(reader.result);\r\n });\r\n reader.addEventListener('error', () => {\r\n reject(reader.error);\r\n });\r\n reader.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n reader.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n if (this._binary) {\r\n reader.readAsArrayBuffer(blob);\r\n } else {\r\n reader.readAsText(blob);\r\n }\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return (File && source instanceof File) || (Blob && source instanceof Blob);\r\n }\r\n\r\n static extractName(source) {\r\n return source && source.name;\r\n }\r\n}\r\n\r\nFileLoader.types = ['file', 'blob'];\r\n","import _ from 'lodash';\r\nimport Loader from './Loader';\r\n\r\n// we don't need to detect all kinds of URLs, just the evident ones\r\nconst urlStartRegexp = /^(https?|ftp):\\/\\//i;\r\n\r\nexport default class XHRLoader extends Loader {\r\n constructor(source, options) {\r\n super(source, options);\r\n\r\n options = this._options;\r\n this._binary = (options.binary === true);\r\n }\r\n\r\n load() {\r\n return new Promise((resolve, reject) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n\r\n const url = this._source;\r\n const request = this._agent = new XMLHttpRequest();\r\n\r\n request.addEventListener('load', () => {\r\n if (request.status === 200) {\r\n resolve(request.response);\r\n } else {\r\n reject(new Error(`HTTP ${request.status} while fetching ${url}`));\r\n }\r\n });\r\n request.addEventListener('error', () => {\r\n reject(new Error('HTTP request failed'));\r\n });\r\n request.addEventListener('abort', () => {\r\n reject(new Error('Loading aborted'));\r\n });\r\n request.addEventListener('progress', (event) => {\r\n this.dispatchEvent(event);\r\n });\r\n\r\n request.open('GET', url);\r\n if (this._binary) {\r\n request.responseType = 'arraybuffer';\r\n } else {\r\n request.responseType = 'text';\r\n }\r\n request.send();\r\n });\r\n }\r\n\r\n static canProbablyLoad(source) {\r\n return _.isString(source) && urlStartRegexp.test(source);\r\n }\r\n\r\n static extractName(source) {\r\n if (source) {\r\n const last = (source.indexOf('?') + 1 || source.lastIndexOf('#') + 1 || source.length + 1) - 1;\r\n return source.slice(source.lastIndexOf('/', last) + 1, last);\r\n }\r\n return undefined;\r\n }\r\n}\r\n\r\nXHRLoader.types = ['url'];\r\n","import Loader from './Loader';\r\n\r\nexport default class ImmediateLoader extends Loader {\r\n load() {\r\n return new Promise((resolve) => {\r\n if (this._abort) {\r\n throw new Error('Loading aborted');\r\n }\r\n resolve(this._source);\r\n });\r\n }\r\n\r\n static canProbablyLoad(_source) {\r\n return false;\r\n }\r\n}\r\n\r\nImmediateLoader.types = ['immediate'];\r\n","import LoaderList from './loaders/LoaderList';\r\n\r\nimport FileLoader from './loaders/FileLoader';\r\nimport XHRLoader from './loaders/XHRLoader';\r\nimport ImmediateLoader from './loaders/ImmediateLoader';\r\n\r\nexport default new LoaderList([\r\n // note: order might be important\r\n FileLoader,\r\n XHRLoader,\r\n ImmediateLoader,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available parsers.\r\n * @extends EntityList\r\n */\r\nclass ParserList extends EntityList {\r\n /**\r\n * Create a list of parsers.\r\n * The parsers are indexed by supported data formats and file extensions (`.formats` and\r\n * `.extensions` properties of a Parser subclass).\r\n * The parsers can be retrieved later by matching against specs (see {@link ParsrerList#find}).\r\n *\r\n * @param {!Array=} someParsers A list of {@link Parser} subclasses to\r\n * automatically register at creation time.\r\n * @see ParserList#register\r\n */\r\n constructor(someParsers = []) {\r\n super(someParsers, ['formats', 'extensions']);\r\n }\r\n\r\n /**\r\n * Find a suitable parser for data.\r\n *\r\n * @param {Object} specs Parser specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {string=} specs.ext Supported filename extension.\r\n * @param {*=} specs.data Data to parse.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n } else if (specs.ext) {\r\n list = this._dict.extensions[specs.ext.toLowerCase()] || [];\r\n }\r\n // autodetect only if no format is forced\r\n if (list.length === 0 && !specs.format && specs.data) {\r\n return this._list.filter((SomeParser) => SomeParser.canProbablyParse && SomeParser.canProbablyParse(specs.data));\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ParserList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Parser {\r\n constructor(data, options) {\r\n this._data = data;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n parseSync() {\r\n throw new Error('Parsing this type of data is not implemented');\r\n }\r\n\r\n parse() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Parsing aborted'));\r\n }\r\n return resolve(this.parseSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n // only for volume Parsers\r\n getModel() {\r\n this.model._parseHeader(this._data);\r\n return this.model;\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Parser.prototype);\r\n","import * as THREE from 'three';\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 290\".\r\n *\r\n * @exports Remark290\r\n * @constructor\r\n */\r\nclass Remark290 {\r\n constructor() {\r\n /** @type {THREE.Matrix4[]} */\r\n this.matrices = [];\r\n\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (stream.readString(12, 18) === ' SMTRY') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === this.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n this.matrices[this.matrices.length] = matrix;\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n }\r\n }\r\n}\r\n\r\nRemark290.prototype.id = 290;\r\n\r\nexport default Remark290;\r\n","import * as THREE from 'three';\r\nimport chem from '../../../chem';\r\n\r\nconst { Assembly } = chem;\r\n\r\n/**\r\n * Parser helper for PDB tag \"REMARK 350\".\r\n *\r\n * @exports Remark350\r\n * @constructor\r\n */\r\nclass Remark350 {\r\n constructor(complex) {\r\n /** @type {Complex} */\r\n this._complex = complex;\r\n /** @type {Assembly[]} */\r\n this.assemblies = [];\r\n\r\n /** @type {?Assembly} */\r\n this._assembly = null;\r\n /** @type {?THREE.Matrix4} */\r\n this._matrix = null;\r\n /** @type {number} */\r\n this._matrixIndex = -1;\r\n }\r\n\r\n /**\r\n * Parse a single line of a stream.\r\n * @param {PDBStream} stream - stream to parse\r\n */\r\n\r\n parse(stream) {\r\n /** @type {?Assembly} */\r\n let assembly = this._assembly;\r\n /** @type {?THREE.Matrix4} */\r\n let matrix = this._matrix;\r\n\r\n if (assembly && stream.readString(12, 18) === ' BIOMT') {\r\n const matrixRow = stream.readCharCode(19) - 49; // convert '1', '2', or '3' -> 0, 1, or 2\r\n const matrixData = stream.readString(20, 80).trim().split(/\\s+/);\r\n const matrixIndex = parseInt(matrixData[0], 10);\r\n if (this._matrix === null || matrixIndex !== this._matrixIndex) {\r\n // TODO: assert(matrixIndex === assembly.matrices.length + 1);\r\n this._matrixIndex = matrixIndex;\r\n this._matrix = matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n }\r\n\r\n const { elements } = matrix;\r\n elements[matrixRow] = parseFloat(matrixData[1]);\r\n elements[matrixRow + 4] = parseFloat(matrixData[2]);\r\n elements[matrixRow + 8] = parseFloat(matrixData[3]);\r\n elements[matrixRow + 12] = parseFloat(matrixData[4]);\r\n } else if (assembly && stream.readString(35, 41) === 'CHAINS:') {\r\n const entries = stream.readString(42, 80).split(',');\r\n for (let i = 0, n = entries.length; i < n; ++i) {\r\n const chain = entries[i].trim();\r\n if (chain.length > 0) {\r\n assembly.addChain(chain);\r\n }\r\n }\r\n } else if (stream.readString(12, 23) === 'BIOMOLECULE:') {\r\n // assert molIndex === this.assemblies.length + 1\r\n this._matrix = null;\r\n this._matrixIndex = -1;\r\n this._assembly = assembly = new Assembly(this._complex);\r\n this.assemblies.push(assembly);\r\n }\r\n }\r\n}\r\n\r\nRemark350.prototype.id = 350;\r\n\r\nexport default Remark350;\r\n","/** Helper class for stream-like reading input files. */\r\nclass PDBStream {\r\n /**\r\n * Create a stream\r\n * @param {String} data Input data\r\n */\r\n constructor(data) {\r\n /** @type String */\r\n this._data = data; // Input file\r\n /** @type Number */\r\n this._start = 0; // Starting position of line\r\n /** @type Number */\r\n this._nextCR = -1; // Position of next CR (0x0D)\r\n /** @type Number */\r\n this._nextLF = -1; // Position of next LF (0x0A)\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n /** @type Number */\r\n this._end = data.length; // End of data\r\n\r\n this.next();\r\n }\r\n\r\n /**\r\n * Reading next line.\r\n * @returns {String} Next line in data (ending with LF or CR)\r\n */\r\n readLine() {\r\n return this._data.slice(this._start, this._next);\r\n }\r\n\r\n /**\r\n * Reading character from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {String} Character from position\r\n */\r\n readChar(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data[pos] : ' ';\r\n }\r\n\r\n /**\r\n * Reading character code from position.\r\n * @param {Number} pos - Position in current line.\r\n * @returns {Number} Character code from position\r\n */\r\n readCharCode(pos) {\r\n pos = this._start + pos - 1;\r\n return pos < this._next ? this._data.charCodeAt(pos) : 32;\r\n }\r\n\r\n /**\r\n * Reading string from begin to end points.\r\n * For a reason unknown, numbering assumed not to start from 0, but from 1.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {String} String from begin to end\r\n */\r\n readString(begin, end) {\r\n const from = this._start + begin - 1;\r\n const to = this._start + end;\r\n return this._data.slice(from, to < this._next ? to : this._next);\r\n }\r\n\r\n /**\r\n * Reading integer from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Integer from begin to end\r\n */\r\n readInt(begin, end) {\r\n return parseInt(this.readString(begin, end), 10);\r\n }\r\n\r\n /**\r\n * Reading float from begin to end points.\r\n * @param {Number} begin - Begin point in current line.\r\n * @param {Number} end - End point in current line.\r\n * @returns {Number} Float from begin to end\r\n */\r\n readFloat(begin, end) {\r\n return parseFloat(this.readString(begin, end));\r\n }\r\n\r\n /**\r\n * Checking for end of data.\r\n * @returns {boolean} True if data is ended, false otherwise\r\n */\r\n end() {\r\n return this._start >= this._end;\r\n }\r\n\r\n /**\r\n * Procedure to re-arrange current pointers in data.\r\n */\r\n next() {\r\n const start = this._next + 1;\r\n this._start = start < this._end ? start : this._end;\r\n\r\n // support CR, LF, CR+LF line endings\r\n // do not support LF+CR, CR+CR+LF, and other strange combinations\r\n\r\n if (this._start > this._nextCR) {\r\n this._nextCR = (this._data.indexOf('\\r', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n if (this._start > this._nextLF) {\r\n this._nextLF = (this._data.indexOf('\\n', this._start) + 1 || this._end + 1) - 1;\r\n }\r\n this._next = this._nextCR + 1 < this._nextLF ? this._nextCR : this._nextLF;\r\n }\r\n}\r\n\r\nexport default PDBStream;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport Remark290 from './pdb/Remark290';\r\nimport Remark350 from './pdb/Remark350';\r\nimport PDBStream from './PDBStream';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst TAG_LENGTH = 6;\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\n// the most frequently used beginnings; although HEADER is mandatory, it is often missing in handmade files\r\nconst pdbStartRegexp = /^(HEADER\\s|COMPND\\s|REMARK\\s|ATOM {2}|HETATM|MODEL )/i;\r\n\r\nconst remarkParsers = {\r\n // NOTE: please forget the idea to build the method name in runtime, it can be obfuscated.\r\n 290: Remark290,\r\n 350: Remark350,\r\n};\r\n\r\nclass PDBParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._sheet = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._compaundFound = false;\r\n this._biomoleculeFound = false;\r\n this._allowedChainsIDs = null;\r\n this._lastMolId = -1;\r\n\r\n this._remarks = {};\r\n this._remark = null;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n this._compndCurrToken = '';\r\n\r\n this._options.fileType = 'pdb';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && pdbStartRegexp.test(data);\r\n }\r\n\r\n _finalize() {\r\n this._fixBondsArray();\r\n this._fixChains();\r\n\r\n // keep crystallographic symmetry transformations\r\n const remark290 = this._remarks[290];\r\n this._complex.symmetry = _.isUndefined(remark290) ? [] : remark290.matrices;\r\n\r\n // add loaded biological assemblies\r\n const remark350 = this._remarks[350];\r\n this._complex.units = this._complex.units.concat(_.isUndefined(remark350) ? [] : remark350.assemblies);\r\n\r\n // add loaded macromolecules\r\n this._finalizeMolecules();\r\n\r\n // create secondary structure etc.\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _finalizeMolecules() {\r\n // get chains from complex\r\n const chainDict = {};\r\n let i;\r\n const chains = this._complex._chains;\r\n for (i = 0; i < chains.length; ++i) {\r\n const chainObj = chains[i];\r\n const chainName = chainObj._name;\r\n chainDict[chainName] = chainObj;\r\n }\r\n\r\n // aggregate residues from chains\r\n for (i = 0; i < this._molecules.length; i++) {\r\n const m = this._molecules[i];\r\n let residues = [];\r\n for (let j = 0; j < m._chains.length; j++) {\r\n const name = m._chains[j];\r\n const chain = chainDict[name];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, m._name, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _fixChains() {\r\n const idChainMap = {};\r\n const complex = this._complex;\r\n\r\n // prepare\r\n for (let i = 0; i < complex._chains.length; i++) {\r\n const chain = complex._chains[i];\r\n idChainMap[chain._name.charCodeAt(0)] = chain;\r\n }\r\n }\r\n\r\n // FIXME: This function is redundant, CONECT records always follow ATOM and HETATM. Build the map online.\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseATOM(stream) {\r\n if (this._modelId !== 1) {\r\n return;\r\n }\r\n\r\n const het = stream.readCharCode(1) === 0x48;\r\n\r\n // field names according to wwPDB Format\r\n // NOTE: Chimera allows (nonstandard) use of columns 6-11 for the integer atom serial number in ATOM records.\r\n const serial = het ? stream.readInt(7, 11) : stream.readInt(6, 11);\r\n let name = stream.readString(13, 16);\r\n const altLoc = stream.readChar(17);\r\n const resName = stream.readString(18, 20).trim();\r\n const chainID = stream.readChar(22);\r\n const resSeq = stream.readInt(23, 26);\r\n const iCode = stream.readChar(27);\r\n const x = stream.readFloat(31, 38);\r\n const y = stream.readFloat(39, 46);\r\n const z = stream.readFloat(47, 54);\r\n const occupancy = stream.readFloat(55, 60);\r\n const tempFactor = stream.readFloat(61, 66);\r\n const element = stream.readString(77, 78).trim() || nameToElement(name);\r\n const charge = stream.readInt(79, 80) || 0;\r\n\r\n // skip waters (there may be lots of them)\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n // PDB uses positional system for atom names. It helps derive element type from the name\r\n // but names may include extra spaces. From this point on we don't need those spaces anymore.\r\n name = name.trim();\r\n\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name]; // FIXME: Maybe should use type as additional index (\" CA \" vs. \"CA \")\r\n\r\n // NOTE: Residues of a particular chain are not required to be listed next to each other.\r\n // https://github.com/biasmv/pv/commit/7319b898b7473ba380c26699e3b028b2b1a7e1a1\r\n let chain = this._chain;\r\n if (!chain || chain.getName() !== chainID) {\r\n this._chain = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n _parseENDMDL() {\r\n this._modelId += 1;\r\n }\r\n\r\n _parseCONECT(stream) {\r\n const serial0 = stream.readInt(7, 11);\r\n const serial1 = stream.readInt(12, 16);\r\n const serial2 = stream.readInt(17, 21);\r\n const serial3 = stream.readInt(22, 26);\r\n const serial4 = stream.readInt(27, 31);\r\n\r\n const complex = this._complex;\r\n\r\n // Keep bonds ordered by atom serial\r\n if (serial1 && serial1 > serial0) {\r\n complex.addBond(serial0, serial1, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial2 && serial2 > serial0) {\r\n complex.addBond(serial0, serial2, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial3 && serial3 > serial0) {\r\n complex.addBond(serial0, serial3, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n if (serial4 && serial4 > serial0) {\r\n complex.addBond(serial0, serial4, 0, Bond.BondType.UNKNOWN, true);\r\n }\r\n }\r\n\r\n _parseCOMPND(stream) {\r\n const str = stream.readString(11, 80);\r\n const tokenIdx = str.indexOf(':');\r\n this._compndCurrToken = tokenIdx > 0 ? str.substring(0, tokenIdx).trim() : this._compndCurrToken;\r\n\r\n // start reading new molecule\r\n if (this._compndCurrToken === 'MOL_ID') {\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = parseInt(str.substring(tokenIdx + 1, str.indexOf(';')), 10);\r\n this._molecules.push(this._molecule);\r\n // parse molecule name\r\n } else if (this._compndCurrToken === 'MOLECULE' && this._molecule != null) {\r\n this._molecule._name = str.substring(tokenIdx + 1, str.indexOf(';')).trim();\r\n // parse molecule chains\r\n } else if (this._compndCurrToken === 'CHAIN' && this._molecule != null) {\r\n let chainStr = str.substring(tokenIdx + 1, 80).trim();\r\n const lastChar = chainStr[chainStr.length - 1];\r\n if (lastChar === ';' || lastChar === ',') {\r\n chainStr = chainStr.slice(0, -1);\r\n }\r\n chainStr = chainStr.replace(/\\s+/g, '');\r\n const chains = chainStr.split(',');\r\n this._molecule._chains = this._molecule._chains.concat(chains);\r\n }\r\n }\r\n\r\n _parseREMARK(stream) {\r\n const remarkNum = stream.readInt(8, 10);\r\n\r\n // create remark parser if needed\r\n let remark = this._remarks[remarkNum];\r\n if (_.isUndefined(remark)) {\r\n const RemarkParser = remarkParsers[remarkNum];\r\n if (_.isFunction(RemarkParser)) {\r\n this._remarks[remarkNum] = remark = new RemarkParser(this._complex);\r\n }\r\n }\r\n\r\n // delegate parsing\r\n if (!_.isUndefined(remark)) {\r\n remark.parse(stream);\r\n }\r\n }\r\n\r\n _parseHELIX(stream) {\r\n const fields = [20, 22, 32, 34];\r\n\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addHelix(obj);\r\n this._complex.structures.push(obj);\r\n });\r\n }\r\n\r\n _parseSHEET(stream) {\r\n const fields = [22, 23, 33, 34];\r\n\r\n this._parseSTRUCTURE(stream, fields, (obj) => {\r\n this._complex.addSheet(obj);\r\n });\r\n }\r\n\r\n _parseSTRUCTURE(stream, pars, adder) {\r\n const startId = 0;\r\n const startIndex = 1;\r\n const endId = 2;\r\n const endIndex = 3;\r\n\r\n // identify fields: debugging and stuff\r\n\r\n const codeOfS = 0x53;\r\n const serialNumber = stream.readInt(8, 10);\r\n const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim()\r\n const comment = stream.readString(41, 70).trim();\r\n const helLength = stream.readInt(72, 76);\r\n const helixClass = stream.readInt(39, 40);\r\n const shWidth = stream.readInt(15, 16);\r\n const shCur = stream.readInt(42, 45);\r\n const shPrev = stream.readInt(57, 60);\r\n\r\n // file fields\r\n const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0);\r\n const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0);\r\n const startSequenceNumber = stream.readInt(pars[startIndex], pars[startIndex] + 3);\r\n let iCodeStr = stream.readString(pars[startIndex] + 4, pars[startIndex] + 4);\r\n let startICode = 0;\r\n\r\n if (iCodeStr.length > 0) {\r\n startICode = iCodeStr.charCodeAt(0);\r\n }\r\n const endSequenceNumber = stream.readInt(pars[endIndex], pars[endIndex] + 3);\r\n iCodeStr = stream.readString(pars[endIndex] + 4, pars[endIndex] + 4);\r\n let endICode = 0;\r\n if (iCodeStr.length > 0) {\r\n endICode = iCodeStr.charCodeAt(0);\r\n }\r\n\r\n let obj;\r\n let cs = this._sheet;\r\n if (stream.readCharCode(1) === codeOfS) {\r\n if (cs !== null && cs.getName() !== structureName) {\r\n cs = null;\r\n this._sheet = null;\r\n }\r\n if (cs === null) {\r\n this._sheet = obj = new Sheet(structureName, shWidth);\r\n adder(obj);\r\n } else {\r\n obj = cs;\r\n }\r\n const strand = new Strand(\r\n obj,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n helixClass,\r\n shCur,\r\n shPrev,\r\n );\r\n obj.addStrand(strand);\r\n this._complex.structures.push(strand);\r\n } else {\r\n obj = new Helix(\r\n helixClass,\r\n this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),\r\n this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),\r\n serialNumber,\r\n structureName,\r\n comment,\r\n helLength,\r\n );\r\n adder(obj);\r\n }\r\n }\r\n\r\n _parseHEADER(stream) {\r\n const { metadata } = this._complex;\r\n metadata.classification = stream.readString(11, 50).trim();\r\n metadata.date = stream.readString(51, 59).trim();\r\n\r\n const id = stream.readString(63, 66).trim();\r\n metadata.id = id;\r\n if (id) {\r\n this._complex.name = id;\r\n }\r\n metadata.format = 'pdb';\r\n }\r\n\r\n _parseTITLE(stream) {\r\n const { metadata } = this._complex;\r\n metadata.title = metadata.title || [];\r\n\r\n const line = stream.readInt(9, 10) || 1;\r\n metadata.title[line - 1] = stream.readString(11, 80).trim();\r\n }\r\n\r\n static tagParsers = {\r\n HEADER: PDBParser.prototype._parseHEADER,\r\n 'TITLE ': PDBParser.prototype._parseTITLE,\r\n 'ATOM ': PDBParser.prototype._parseATOM,\r\n HETATM: PDBParser.prototype._parseATOM,\r\n ENDMDL: PDBParser.prototype._parseENDMDL,\r\n CONECT: PDBParser.prototype._parseCONECT,\r\n COMPND: PDBParser.prototype._parseCOMPND,\r\n REMARK: PDBParser.prototype._parseREMARK,\r\n // 'SOURCE': PDBParser.prototype._parseSOURCE,\r\n 'HELIX ': PDBParser.prototype._parseHELIX,\r\n 'SHEET ': PDBParser.prototype._parseSHEET,\r\n\r\n // nonstandard extension to allow range 100,000 - 999,999\r\n 'ATOM 1': PDBParser.prototype._parseATOM,\r\n 'ATOM 2': PDBParser.prototype._parseATOM,\r\n 'ATOM 3': PDBParser.prototype._parseATOM,\r\n 'ATOM 4': PDBParser.prototype._parseATOM,\r\n 'ATOM 5': PDBParser.prototype._parseATOM,\r\n 'ATOM 6': PDBParser.prototype._parseATOM,\r\n 'ATOM 7': PDBParser.prototype._parseATOM,\r\n 'ATOM 8': PDBParser.prototype._parseATOM,\r\n 'ATOM 9': PDBParser.prototype._parseATOM,\r\n };\r\n\r\n parseSync() {\r\n const stream = new PDBStream(this._data);\r\n const result = this._complex = new Complex();\r\n\r\n // parse PDB line by line\r\n while (!stream.end()) {\r\n const tag = stream.readString(1, TAG_LENGTH);\r\n const func = PDBParser.tagParsers[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, stream);\r\n }\r\n stream.next();\r\n }\r\n\r\n // Resolve indices and serials to objects\r\n this._finalize();\r\n\r\n // cleanup\r\n this._serialAtomMap = null;\r\n this._sheet = null;\r\n this._residue = null;\r\n this._chain = null;\r\n this._complex = null;\r\n\r\n if (result.getAtomCount() === 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n return result;\r\n }\r\n}\r\n\r\nPDBParser.formats = ['pdb'];\r\nPDBParser.extensions = ['.pdb', '.ent'];\r\n\r\nexport default PDBParser;\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n SGroup,\r\n Bond,\r\n} = chem;\r\n\r\nconst cOrderCharCodes = {\r\n A: 0,\r\n S: 1,\r\n D: 2,\r\n T: 3,\r\n};\r\n\r\nconst cmlStartRegexp = /\\s*<\\?xml\\b[^?>]*\\?>\\s*<(?:cml|molecule)\\b/i;\r\n\r\nclass CMLParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._complex = null;\r\n this._residue = null;\r\n this._serialAtomMap = null;\r\n this._modelId = 1;\r\n this._lastMolId = -1;\r\n this._readOnlyOneMolecule = false;\r\n this._options.fileType = 'cml';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && cmlStartRegexp.test(data);\r\n }\r\n\r\n _rebuidBondIndexes(atoms, bonds) {\r\n const count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n\r\n const countBonds = bonds.length;\r\n for (let j = 0; j < countBonds; j++) {\r\n const idxs = bonds[j].atomRefs2.split(' ');\r\n if (idxs[0] === atomId) {\r\n bonds[j].start = i;\r\n }\r\n\r\n if (idxs[1] === atomId) {\r\n bonds[j].end = i;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _createSGroup(molecule, moleculeArr) {\r\n const newGroup = new SGroup(\r\n molecule.id,\r\n molecule.fieldData,\r\n new THREE.Vector3(parseFloat(molecule.x), parseFloat(molecule.y), 0),\r\n molecule.atomRefs,\r\n molecule,\r\n );\r\n if (molecule.placement === 'Relative') {\r\n newGroup._center = new THREE.Vector3(0, 0, 0);\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_CHARGE') {\r\n newGroup._charge = parseInt(molecule.fieldData, 10) || 0;\r\n }\r\n if (molecule.fieldName === 'MDLBG_FRAGMENT_COEFFICIENT') {\r\n newGroup._repeat = parseInt(molecule.fieldData, 10) || 1;\r\n }\r\n moleculeArr.push(newGroup);\r\n }\r\n\r\n _extractSGroup(molecule, moleculeArr) {\r\n if (!Array.isArray(moleculeArr)) {\r\n moleculeArr = [];\r\n }\r\n\r\n if (molecule) {\r\n if (Array.isArray(molecule)) {\r\n const count = molecule.length;\r\n for (let i = 0; i < count; i++) {\r\n if (molecule[i].molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule[i].molecule));\r\n }\r\n this._createSGroup(molecule[i], moleculeArr);\r\n }\r\n } else {\r\n if (molecule.molecule) {\r\n if (molecule.molecule) {\r\n moleculeArr = moleculeArr.concat(this._extractSGroup(molecule.molecule));\r\n }\r\n }\r\n this._createSGroup(molecule, moleculeArr);\r\n }\r\n }\r\n\r\n return moleculeArr;\r\n }\r\n\r\n _extractSGroups(molecule, atoms) {\r\n const moleculeArr = this._extractSGroup(molecule);\r\n\r\n const count = atoms.length;\r\n let i;\r\n let j;\r\n\r\n for (i = 0; i < count; i++) {\r\n const atomId = atoms[i].id;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n const firstAtomRef = moleculeArr[j]._atoms.split(' ')[0];\r\n if (firstAtomRef === atomId) {\r\n if (!atoms[i].sgroupRef) {\r\n atoms[i].sgroupRef = [];\r\n }\r\n atoms[i].sgroupRef.push(moleculeArr[j]);\r\n }\r\n }\r\n }\r\n // build sGroups centers\r\n let atomMap = {}; // sgrpmap cache\r\n let mapEntry = null;\r\n const nLimon = 100000000;\r\n const bLow = new THREE.Vector3(nLimon, nLimon, nLimon);\r\n const bHight = new THREE.Vector3(-nLimon, -nLimon, -nLimon);\r\n\r\n function cycleFuncInner(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n moleculeArr[j]._atoms.push(mapEntry.a);\r\n }\r\n }\r\n\r\n function cycleFunc(e) {\r\n mapEntry = atomMap[e];\r\n if (mapEntry) {\r\n bLow.set(Math.min(bLow.x, mapEntry.x), Math.min(bLow.y, mapEntry.y), Math.min(bLow.z, mapEntry.z));\r\n bHight.set(Math.max(bHight.x, mapEntry.x), Math.max(bHight.y, mapEntry.y), Math.max(bHight.z, mapEntry.z));\r\n cycleFuncInner(e);\r\n }\r\n }\r\n\r\n for (i = 0; i < atoms.length; i++) {\r\n atomMap[atoms[i].id] = {};\r\n atomMap[atoms[i].id].x = atoms[i].x2;\r\n if (atoms[i].x3) {\r\n atomMap[atoms[i].id].x = atoms[i].x3;\r\n }\r\n atomMap[atoms[i].id].x = parseFloat(atomMap[atoms[i].id].x);\r\n atomMap[atoms[i].id].y = atoms[i].y2;\r\n if (atoms[i].y3) {\r\n atomMap[atoms[i].id].y = atoms[i].y3;\r\n }\r\n atomMap[atoms[i].id].y = parseFloat(atomMap[atoms[i].id].y);\r\n atomMap[atoms[i].id].z = '0.0';\r\n if (atoms[i].z3) {\r\n atomMap[atoms[i].id].z = atoms[i].z3;\r\n }\r\n atomMap[atoms[i].id].z = parseFloat(atomMap[atoms[i].id].z);\r\n atomMap[atoms[i].id].a = atoms[i];\r\n }\r\n\r\n let atomsRef;\r\n for (j = 0; j < moleculeArr.length; j++) {\r\n if (moleculeArr[j]._center !== null) {\r\n bLow.set(nLimon, nLimon, nLimon);\r\n bHight.set(-nLimon, -nLimon, -nLimon);\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFunc);\r\n\r\n moleculeArr[j]._center.addVectors(bLow, bHight);\r\n moleculeArr[j]._center.multiplyScalar(0.5);\r\n } else {\r\n atomsRef = moleculeArr[j]._atoms.split(' ');\r\n moleculeArr[j]._atoms = [];\r\n atomsRef.forEach(cycleFuncInner);\r\n }\r\n }\r\n atomMap = null;\r\n }\r\n\r\n _traverseData(dom) {\r\n function isArray(o) {\r\n return Object.prototype.toString.apply(o) === '[object Array]';\r\n }\r\n\r\n function parseNode(xmlNode, result) {\r\n if (xmlNode.nodeName === '#text' && xmlNode.nodeValue.trim() === '') {\r\n return;\r\n }\r\n\r\n const jsonNode = {};\r\n jsonNode.xmlNode = xmlNode;\r\n const existing = result[xmlNode.nodeName];\r\n if (existing) {\r\n if (!isArray(existing)) {\r\n result[xmlNode.nodeName] = [existing, jsonNode];\r\n } else {\r\n result[xmlNode.nodeName].push(jsonNode);\r\n }\r\n } else {\r\n result[xmlNode.nodeName] = jsonNode;\r\n }\r\n\r\n let length;\r\n let i;\r\n if (xmlNode.attributes) {\r\n ({ length } = xmlNode.attributes);\r\n for (i = 0; i < length; i++) {\r\n const attribute = xmlNode.attributes[i];\r\n jsonNode[attribute.nodeName] = attribute.nodeValue;\r\n }\r\n }\r\n\r\n ({ length } = xmlNode.childNodes);\r\n for (i = 0; i < length; i++) {\r\n parseNode(xmlNode.childNodes[i], jsonNode);\r\n }\r\n }\r\n\r\n const result = {};\r\n if (dom.childNodes.length) {\r\n parseNode(dom.childNodes[0], result);\r\n }\r\n\r\n return result;\r\n }\r\n\r\n _findSuitableMolecule(data, molSet) {\r\n for (const key in data) {\r\n if (key === 'xmlNode') {\r\n continue;\r\n } else if (key === 'molecule') {\r\n if (data.molecule) {\r\n if (data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n molSet.push(data);\r\n }\r\n if (Array.isArray(data.molecule)) {\r\n for (let i = 0; i < data.molecule.length; i++) {\r\n if (data.molecule[i].atomArray && data.molecule[i].atomArray.atom) {\r\n molSet.push({ molecule: data.molecule[i] });\r\n }\r\n }\r\n }\r\n }\r\n } else if (data[key] && data[key] !== null && typeof (data[key]) === 'object') {\r\n this._findSuitableMolecule(data[key], molSet);\r\n }\r\n }\r\n }\r\n\r\n _selectComponents(text) {\r\n const parser = new DOMParser();\r\n const doc = parser.parseFromString(text, 'application/xml');\r\n const traversedData = this._traverseData(doc);\r\n let rawData;\r\n const self = this;\r\n\r\n function prepareComponentCompound(data) {\r\n let atoms = [];\r\n if (data.molecule && data.molecule.atomArray && data.molecule.atomArray.atom) {\r\n if (!Array.isArray(data.molecule.atomArray.atom)) {\r\n atoms.push(data.molecule.atomArray.atom);\r\n } else {\r\n atoms = data.molecule.atomArray.atom;\r\n }\r\n } else if (!data.molecule) {\r\n const ret = {};\r\n ret.atomLabels = null;\r\n ret.labelsCount = 1;\r\n return ret;\r\n }\r\n\r\n if (data.molecule.molecule) {\r\n self._extractSGroups(data.molecule.molecule, atoms);\r\n }\r\n\r\n let atom;\r\n let count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges = [];\r\n }\r\n\r\n let localBond = [];\r\n if (data.molecule.bondArray && data.molecule.bondArray.bond) {\r\n if (!Array.isArray(data.molecule.bondArray.bond)) {\r\n localBond.push(data.molecule.bondArray.bond);\r\n } else {\r\n localBond = data.molecule.bondArray.bond;\r\n }\r\n }\r\n let bond;\r\n count = localBond.length;\r\n self._rebuidBondIndexes(atoms, localBond);\r\n\r\n function addCurrBond(index) {\r\n bond = localBond[index];\r\n atom = atoms[bond.start];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.end);\r\n atom = atoms[bond.end];\r\n if (!atom) {\r\n return false;\r\n }\r\n atom.edges.push(bond.start);\r\n return true;\r\n }\r\n\r\n for (let i = 0; i < count; i++) {\r\n if (!addCurrBond(i)) {\r\n // ignore invalid bond\r\n continue;\r\n }\r\n const orderAttr = bond.xmlNode.getAttribute('order');\r\n const tc = parseInt(orderAttr, 10);\r\n // the default bond order is unknown\r\n localBond[i].order = 0;\r\n localBond[i].type = Bond.BondType.UNKNOWN;\r\n if (tc > 1) {\r\n localBond[i].order = tc;\r\n } else {\r\n // another option - bond order is a string\r\n const order = cOrderCharCodes[orderAttr];\r\n if (order !== undefined) {\r\n localBond[i].order = order;\r\n if (orderAttr === 'A') {\r\n localBond[i].type = Bond.BondType.AROMATIC;\r\n }\r\n }\r\n }\r\n }\r\n\r\n count = atoms.length;\r\n for (let i = 0; i < count; i++) {\r\n atom = atoms[i];\r\n atom.edges.sort();\r\n }\r\n\r\n const labels = self._breadWidthSearch(atoms, 0); // for now\r\n\r\n const retStruct = {};\r\n retStruct.atoms = atoms;\r\n retStruct.bonds = localBond;\r\n retStruct.labels = labels.atomLabels;\r\n retStruct.count = Math.min(1, labels.labelsCount); // for now\r\n retStruct.curr = -1;\r\n retStruct.originalCML = doc;\r\n\r\n return retStruct;\r\n }\r\n\r\n if (traversedData.cml) {\r\n rawData = traversedData.cml;\r\n } else {\r\n rawData = traversedData;\r\n }\r\n const retData = [];\r\n const filteredData = [];\r\n this._findSuitableMolecule(rawData, filteredData);\r\n if (this._readOnlyOneMolecule && filteredData.length > 1) {\r\n filteredData.splice(1, filteredData.length - 1);\r\n }\r\n filteredData.forEach((d) => {\r\n const rd = prepareComponentCompound(d);\r\n if (rd.atoms.length > 0) {\r\n retData.push(rd);\r\n }\r\n });\r\n return retData;\r\n }\r\n\r\n _packLabel(compId, molId) {\r\n const shift = 16;\r\n return (molId << shift) + compId;\r\n }\r\n\r\n _unpackLabel(l) {\r\n const shift = 16;\r\n const mask = (1 << shift) - 1;\r\n return { molId: l >>> shift, compId: l & mask };\r\n }\r\n\r\n _breadWidthSearch(atoms, molID) {\r\n const atomLabels = new Array(atoms.length);\r\n\r\n let id;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n atomLabels[id] = this._packLabel(0, molID);\r\n }\r\n\r\n const breadthQueue = [];\r\n let componentID = 0;\r\n let labeledAtoms = atoms.length;\r\n\r\n while (labeledAtoms > 0) {\r\n componentID++;\r\n\r\n let startID = -1;\r\n for (id = 0; id < atomLabels.length; id++) {\r\n if (this._unpackLabel(atomLabels[id]).compId === 0) {\r\n startID = id;\r\n break;\r\n }\r\n }\r\n\r\n if (startID < 0) {\r\n break;\r\n }\r\n\r\n // Bread first search\r\n breadthQueue.push(atoms[startID]);\r\n atomLabels[startID] = this._packLabel(componentID, molID);\r\n labeledAtoms--;\r\n\r\n while (breadthQueue.length > 0) {\r\n const curr = breadthQueue.shift();\r\n if (!curr) {\r\n continue;\r\n }\r\n\r\n for (let i = 0; i < curr.edges.length; i++) {\r\n if (atomLabels[curr.edges[i]] !== componentID) {\r\n breadthQueue.push(atoms[curr.edges[i]]);\r\n atomLabels[curr.edges[i]] = componentID;\r\n labeledAtoms--;\r\n }\r\n }\r\n }\r\n }\r\n const ret = {};\r\n ret.atomLabels = atomLabels;\r\n ret.labelsCount = componentID;\r\n return ret;\r\n }\r\n\r\n _parseBond(eAtom, mainAtom, order, type) {\r\n if (eAtom >= 0) {\r\n const h = [Math.min(eAtom, mainAtom), Math.max(eAtom, mainAtom)];\r\n this._complex.addBond(h[0], h[1], order, type, true);\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const complex = this._complex;\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, ni = atoms.length; i < ni; ++i) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n const bonds = complex._bonds;\r\n const { logger } = this;\r\n for (let j = 0, nj = bonds.length; j < nj; ++j) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n logger.debug('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _parseSet(varData) {\r\n const complex = this._complex = new Complex();\r\n const data = varData;\r\n const currentLabel = data.curr;\r\n const { atoms, labels } = data;\r\n let atom = null;\r\n let i;\r\n let j;\r\n const count = atoms.length;\r\n\r\n function addFunc(a) {\r\n a.xmlNodeRef = atom;\r\n if (atom.x2) {\r\n atom.x3 = atom.x2;\r\n delete atom.x2;\r\n }\r\n if (atom.y2) {\r\n atom.y3 = atom.y2;\r\n delete atom.y2;\r\n }\r\n if (!(atom.z3)) {\r\n atom.z3 = '0.0';\r\n }\r\n atom.complexAtom = a;\r\n }\r\n\r\n let chains = {};\r\n // parse atoms in label order\r\n const reorder = [];\r\n for (i = 0; i < count; i++) {\r\n reorder.push(i);\r\n }\r\n reorder.sort((a, b) => labels[a] - labels[b]);\r\n for (i = 0; i < count; i++) {\r\n const atomCharge = 0;\r\n const lLabel = labels[reorder[i]];\r\n if (this._unpackLabel(lLabel).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[reorder[i]];\r\n const atomFullNameStruct = atom.elementType;\r\n\r\n if (atom.sgroupRef) {\r\n const countRef = atom.sgroupRef.length;\r\n for (let k = 0; k < countRef; ++k) {\r\n complex._sgroups.push(atom.sgroupRef[k]);\r\n }\r\n }\r\n\r\n if (atom.x3 || atom.x2) {\r\n const currAtomComp = this._unpackLabel(lLabel).compId;\r\n // use ' ' by default instead of synthetic creation of chain names\r\n const chainID = ' '; //= String.fromCharCode('A'.charCodeAt(0) + currAtomComp);\r\n const resSeq = currAtomComp;\r\n const iCode = ' ';\r\n let strLabel = currAtomComp.toString();\r\n if (strLabel.length === 1) {\r\n strLabel = `0${strLabel}`;\r\n }\r\n const resName = `N${strLabel}`;\r\n let chain = chains[chainID];\r\n if (!chain || chain.getName() !== chainID) {\r\n chains[chainID] = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = null;\r\n }\r\n\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n this._residue = residue = chain.addResidue(resName, resSeq, iCode);\r\n }\r\n\r\n // _x, _y, _z, mname, mindex, atomNameFull, atomName, chainID, serial, isHet, atlLocInd, atomNameToTypeF\r\n let xyz = null;\r\n if (atom.x3) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x3), parseFloat(atom.y3), parseFloat(atom.z3));\r\n } else if (atom.x2) {\r\n xyz = new THREE.Vector3(parseFloat(atom.x2), parseFloat(atom.y2), 0);\r\n }\r\n let element = Element.ByName[atom.elementType.toUpperCase()];\r\n if (!element) {\r\n element = (JSON.parse(JSON.stringify(Element.ByName[\r\n Object.keys(Element.ByName)[Object.keys(Element.ByName).length - 1]])));\r\n element.number += 1;\r\n element.name = atom.elementType.toUpperCase();\r\n element.fullName = 'Unknown';\r\n Element.ByName[atom.elementType.toUpperCase()] = element;\r\n }\r\n const atomSerial = parseInt(atom.id.replace(/[^0-9]/, ''), 10);\r\n const added = residue.addAtom(\r\n atomFullNameStruct,\r\n element,\r\n xyz,\r\n Element.Role.SG,\r\n true,\r\n atomSerial,\r\n ' ',\r\n 1.0,\r\n 0.0,\r\n atomCharge,\r\n );\r\n if (atom.hydrogenCount) {\r\n added.hydrogenCount = parseInt(atom.hydrogenCount, 10);\r\n }\r\n if (atom.mrvValence) {\r\n added.valence = parseInt(atom.mrvValence, 10);\r\n }\r\n addFunc(added);\r\n }\r\n }\r\n }\r\n chains = null;// NOSONAR\r\n for (i = 0; i < data.bonds.length; i++) {\r\n const cb = data.bonds[i];\r\n if (this._unpackLabel(labels[cb.start]).molId === this._unpackLabel(currentLabel).molId\r\n && this._unpackLabel(labels[cb.end]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[cb.start];\r\n if (!atom || !(atoms[cb.end])) {\r\n continue; // skip invalid\r\n }\r\n this._parseBond(\r\n parseInt(atom.id.replace(/[^0-9]/, ''), 10),\r\n parseInt(atoms[cb.end].id.replace(/[^0-9]/, ''), 10),\r\n cb.order,\r\n cb.type,\r\n );\r\n }\r\n }\r\n\r\n for (i = 0; i < this._complex.getSGroupCount(); i++) {\r\n const sGrp = this._complex.getSGroups()[i];\r\n for (j = 0; j < sGrp._atoms.length; j++) {\r\n sGrp._atoms[j] = sGrp._atoms[j].complexAtom;\r\n }\r\n }\r\n for (i = 0; i < count; i++) {\r\n if (this._unpackLabel(labels[i]).molId === this._unpackLabel(currentLabel).molId) {\r\n atom = atoms[i];\r\n atom.complexAtom = null;\r\n delete atom.complexAtom;\r\n }\r\n }\r\n this._complex.originalCML = data.originalCML;\r\n this._fixBondsArray();\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n this._serialAtomMap = null;\r\n this._complex = null;\r\n return complex;\r\n }\r\n\r\n parseSync() {\r\n const complexes = [];\r\n const self = this;\r\n const moleculaSet = this._selectComponents(this._data);\r\n moleculaSet.forEach((molSet) => {\r\n molSet.curr = 2;\r\n if (molSet.count === 0) {\r\n molSet.count = 1;\r\n }\r\n for (let i = 0; i < molSet.count; i++) {\r\n molSet.curr = (i + 1);\r\n complexes.push(self._parseSet(molSet, false));\r\n }\r\n });\r\n\r\n let totalAtomsParsed = 0;\r\n complexes.forEach((c) => {\r\n totalAtomsParsed += c.getAtomCount();\r\n });\r\n if (totalAtomsParsed <= 0) {\r\n throw new Error('The data does not contain valid atoms');\r\n }\r\n\r\n if (complexes.length > 1) {\r\n const joinedComplex = new Complex();\r\n joinedComplex.joinComplexes(complexes);\r\n joinedComplex.originalCML = complexes[0].originalCML;\r\n return joinedComplex;\r\n }\r\n if (complexes.length === 1) {\r\n return complexes[0];\r\n }\r\n return new Complex();\r\n }\r\n}\r\n\r\nCMLParser.formats = ['cml'];\r\nCMLParser.extensions = ['.cml'];\r\n\r\nexport default CMLParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport MMTF from '../../../vendor/js/mmtf';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\n\r\nconst {\r\n Complex,\r\n Chain,\r\n Atom,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Bond,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nclass ArrayComparator {\r\n constructor(original) {\r\n this._original = Array.from(original);\r\n this._original.sort();\r\n\r\n this._sum = 0;\r\n for (let i = 0; i < this._original.length; ++i) {\r\n this._sum += this._original[i];\r\n }\r\n }\r\n\r\n compare(candidate) {\r\n const len = candidate.length;\r\n if (len !== this._original.length) {\r\n return false;\r\n }\r\n\r\n let sum = 0;\r\n let i;\r\n for (i = 0; i < len; ++i) {\r\n sum += candidate[i];\r\n }\r\n\r\n if (sum !== this._sum) {\r\n return false;\r\n }\r\n\r\n const sorted = Array.from(candidate);\r\n sorted.sort();\r\n\r\n for (i = 0; i < len; ++i) {\r\n if (sorted[i] !== this._original[i]) {\r\n return false;\r\n }\r\n }\r\n\r\n return true;\r\n }\r\n}\r\n\r\nArrayComparator.prototype.constructor = ArrayComparator;\r\n\r\nconst StructuralElementType = StructuralElement.Type;\r\n\r\n// see https://github.com/rcsb/mmtf-javascript/blob/master/src/mmtf-traverse.js\r\nconst secStructToType = [\r\n StructuralElementType.HELIX_PI, // 0\r\n StructuralElementType.BEND, // 1\r\n StructuralElementType.HELIX_ALPHA, // 2\r\n StructuralElementType.STRAND, // 3\r\n StructuralElementType.HELIX_310, // 4\r\n StructuralElementType.BRIDGE, // 5\r\n StructuralElementType.TURN, // 6\r\n StructuralElementType.COIL, // 7\r\n];\r\n\r\nfunction getFirstByte(buf) {\r\n const bytes = new Uint8Array(buf, 0, 1);\r\n return bytes[0];\r\n}\r\n\r\nclass MMTFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'mmtf';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n // check if it's binary MessagePack format containing a map (dictionary)\r\n // see https://github.com/msgpack/msgpack/blob/master/spec.md\r\n return _.isArrayBuffer(data) && ((getFirstByte(data) | 1) === 0xDF);\r\n }\r\n\r\n _onModel(_modelData) {\r\n }\r\n\r\n _onChain(chainData) {\r\n if (chainData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const chain = new Chain(this._complex, chainData.chainName);\r\n this._complex._chains[chainData.chainIndex] = chain;\r\n chain._index = chainData.chainIndex;\r\n }\r\n\r\n _onGroup(groupData) {\r\n if (groupData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n if (this.settings.now.nowater) {\r\n // skip water\r\n if (groupData.groupName === 'HOH' || groupData.groupName === 'WAT') {\r\n return;\r\n }\r\n }\r\n\r\n const chain = this._complex._chains[groupData.chainIndex];\r\n const icode = !groupData.insCode.charCodeAt(0) ? '' : groupData.insCode;\r\n const residue = chain.addResidue(groupData.groupName, groupData.groupId, icode);\r\n residue._index = groupData.groupIndex;\r\n\r\n this._updateSecStructure(this._complex, residue, groupData);\r\n }\r\n\r\n _onAtom(atomData) {\r\n if (atomData.modelIndex !== 0) {\r\n return;\r\n }\r\n\r\n const altLoc = !atomData.altLoc.charCodeAt(0) ? '' : atomData.altLoc;\r\n const atom = new Atom(\r\n atomData.groupIndex, // we store residue index here to replace it later with actual reference\r\n atomData.atomName,\r\n Element.getByName(atomData.element.toUpperCase()),\r\n new THREE.Vector3(atomData.xCoord, atomData.yCoord, atomData.zCoord),\r\n Element.Role[atomData.atomName],\r\n false, // hetero atoms will be marked later\r\n atomData.atomId,\r\n altLoc,\r\n atomData.occupancy,\r\n atomData.bFactor,\r\n atomData.formalCharge,\r\n );\r\n\r\n this._complex._atoms[atomData.atomIndex] = atom;\r\n atom.index = atomData.atomIndex;\r\n\r\n this._serialAtomMap[atomData.atomId] = atom;\r\n }\r\n\r\n _onBond(bondData) {\r\n const right = Math.max(bondData.atomIndex1, bondData.atomIndex2);\r\n if (right >= this._complex._atoms.length) {\r\n return;\r\n }\r\n const left = Math.min(bondData.atomIndex1, bondData.atomIndex2);\r\n this._complex.addBond(\r\n this._complex._atoms[left],\r\n this._complex._atoms[right],\r\n bondData.bondOrder,\r\n Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n\r\n _updateSecStructure(complex, residue, groupData) {\r\n const helixClasses = [3, -1, 1, -1, 5];\r\n\r\n if (!_.isUndefined(groupData) && groupData.secStruct === this._ssType) {\r\n residue._secondary = this._ssStruct;\r\n if (this._ssStruct) {\r\n this._ssStruct.term = residue;\r\n }\r\n return;\r\n }\r\n\r\n if (!_.isUndefined(groupData)) {\r\n // start new secondary structure\r\n const type = secStructToType[groupData.secStruct];\r\n this._ssType = groupData.secStruct;\r\n this._ssStart = residue;\r\n\r\n let struct = null;\r\n switch (this._ssType) {\r\n case -1: // undefined\r\n case 7: // coil\r\n break;\r\n case 0: // pi helix\r\n case 2: // alpha helix\r\n case 4: // 3-10 helix\r\n struct = new Helix(helixClasses[this._ssType], residue, residue, 0, '', '', 0);\r\n complex._helices.push(struct);\r\n break;\r\n case 3: { // extended\r\n const sheet = new Sheet('', 0);\r\n complex._sheets.push(sheet);\r\n struct = new Strand(sheet, residue, residue, 0, null, null);\r\n break;\r\n }\r\n default:\r\n if (type !== undefined) {\r\n struct = new StructuralElement(type, residue, residue);\r\n }\r\n break;\r\n }\r\n\r\n this._ssStruct = struct;\r\n residue._secondary = struct;\r\n if (struct) {\r\n complex.structures.push(struct);\r\n }\r\n }\r\n }\r\n\r\n _updateMolecules(mmtfData) {\r\n const entities = mmtfData.entityList;\r\n if (!entities) {\r\n return;\r\n }\r\n\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < entities.length; i++) {\r\n const entity = entities[i];\r\n const chains = entity.chainIndexList;\r\n let residues = [];\r\n for (let j = 0; j < chains.length; j++) {\r\n const chainIndex = chains[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n residues = residues.concat(chain._residues.slice());\r\n }\r\n const molecule = new Molecule(this._complex, entity.description, i + 1);\r\n molecule.residues = residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n // populate complex with chains, residues and atoms\r\n _traverse(mmtfData) {\r\n const self = this;\r\n\r\n // get metadata\r\n const { metadata } = this._complex;\r\n metadata.id = mmtfData.structureId;\r\n metadata.title = [];\r\n metadata.title[0] = mmtfData.title;\r\n metadata.date = mmtfData.releaseDate;\r\n metadata.format = 'mmtf';\r\n\r\n // create event callback functions\r\n const eventCallbacks = {\r\n onModel(modelData) {\r\n self._onModel(modelData);\r\n },\r\n onChain(chainData) {\r\n self._onChain(chainData);\r\n },\r\n onGroup(groupData) {\r\n self._onGroup(groupData);\r\n },\r\n onAtom(atomData) {\r\n self._onAtom(atomData);\r\n },\r\n onBond(bondData) {\r\n self._onBond(bondData);\r\n },\r\n };\r\n\r\n // temporary variables used during traversal to track secondary structures\r\n this._ssType = -1;\r\n this._ssStruct = null;\r\n this._ssStart = null;\r\n\r\n // traverse the structure and listen to the events\r\n MMTF.traverse(mmtfData, eventCallbacks);\r\n\r\n this._updateSecStructure(this._complex);\r\n this._updateMolecules(mmtfData);\r\n }\r\n\r\n // During traversal atoms and residues don't come sequentially\r\n // so a residue for certain atom can be unavailable. Thus we\r\n // store residue index in atom.\r\n // This function being called after traversal replaces the index\r\n // with actual reference, and also populates atom lists in residues.\r\n _linkAtomsToResidues() {\r\n for (let i = 0; i < this._complex._atoms.length; ++i) {\r\n const atom = this._complex._atoms[i];\r\n const residue = this._complex._residues[atom.residue];\r\n atom.residue = residue;\r\n residue._atoms.push(atom);\r\n }\r\n }\r\n\r\n _findSynonymousChains() {\r\n const named = {};\r\n for (let i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!named.hasOwnProperty(name)) {\r\n named[name] = [];\r\n }\r\n\r\n named[name].push(chain._index);\r\n }\r\n\r\n return named;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _parseAssemblyInfo(mmtfData) {\r\n let i;\r\n let j;\r\n let k;\r\n const assemblies = [];\r\n const { logger } = this;\r\n\r\n for (i = 0; i < mmtfData.bioAssemblyList.length; ++i) {\r\n const baInfo = mmtfData.bioAssemblyList[i];\r\n if (baInfo.transformList.length === 0) {\r\n continue;\r\n }\r\n\r\n const chains = baInfo.transformList[0].chainIndexList;\r\n const chainListCheck = new ArrayComparator(chains);\r\n\r\n // build list of chain names\r\n const chainNames = {};\r\n for (j = 0; j < chains.length; ++j) {\r\n chainNames[this._complex._chains[chains[j]].getName()] = 1;\r\n }\r\n\r\n // all chains with the same name should belong to assembly if one of them belongs\r\n const allChains = [];\r\n let name;\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n // just concat arrays -- there should be no duplicates\r\n Array.prototype.push.apply(allChains, this._chainsByName[name]);\r\n }\r\n }\r\n if (!chainListCheck.compare(allChains)) {\r\n // assembly is missing some of the chains\r\n logger.debug('MMTF: Assembly is missing some of the synonymous chains. Skipping...');\r\n }\r\n\r\n const a = new Assembly(this._complex);\r\n\r\n // add chains to assembly\r\n for (name in chainNames) {\r\n if (chainNames.hasOwnProperty(name)) {\r\n a.addChain(name);\r\n }\r\n }\r\n\r\n // add unique matrices to assembly\r\n a.addMatrix(new THREE.Matrix4().fromArray(baInfo.transformList[0].matrix).transpose());\r\n for (j = 1; j < baInfo.transformList.length; ++j) {\r\n const transform = baInfo.transformList[j];\r\n\r\n if (!chainListCheck.compare(transform.chainIndexList)) {\r\n // list of chains for this transform doesn't match that for other transforms\r\n // this is illegal in our structure\r\n logger.debug('MMTF: Chain lists differ for different transforms in one assembly. Skipping...');\r\n continue;\r\n }\r\n\r\n const m = new THREE.Matrix4().fromArray(transform.matrix).transpose();\r\n\r\n // check if matrix is already in the list\r\n for (k = 0; k < a.matrices.length; ++k) {\r\n if (a.matrices[k].equals(m)) {\r\n break;\r\n }\r\n }\r\n\r\n if (k === a.matrices.length) {\r\n a.addMatrix(m);\r\n }\r\n }\r\n\r\n a.finalize();\r\n assemblies.push(a);\r\n }\r\n\r\n return assemblies;\r\n }\r\n\r\n // NOTE: This function relies on original chain indices, so it must be called before any magic happens to chains.\r\n _markHeteroAtoms(mmtfData) {\r\n const chainsInModel0 = mmtfData.chainsPerModel[0];\r\n for (let i = 0; i < mmtfData.entityList.length; ++i) {\r\n const entity = mmtfData.entityList[i];\r\n if (entity.type !== 'polymer') {\r\n for (let j = 0; j < entity.chainIndexList.length; ++j) {\r\n const chainIndex = entity.chainIndexList[j];\r\n // skip chains in models other than the first one\r\n if (chainIndex >= chainsInModel0) {\r\n continue;\r\n }\r\n const chain = this._complex._chains[chainIndex];\r\n for (let k = 0; k < chain._residues.length; ++k) {\r\n const res = chain._residues[k];\r\n for (let m = 0; m < res._atoms.length; ++m) {\r\n res._atoms[m].het = true;\r\n }\r\n }\r\n }\r\n }\r\n }\r\n }\r\n\r\n // joins chains with the same name into single chain\r\n _joinSynonymousChains() {\r\n let i;\r\n let j;\r\n\r\n const primaryChainsArray = [];\r\n const primaryChainsHash = {};\r\n\r\n // join chains\r\n for (i = 0; i < this._complex._chains.length; ++i) {\r\n const chain = this._complex._chains[i];\r\n const name = chain.getName();\r\n if (!primaryChainsHash.hasOwnProperty(name)) {\r\n // new name -- this is a primary chain\r\n primaryChainsHash[name] = chain;\r\n chain._index = primaryChainsArray.length; // update index as this array will later replace original chain list\r\n primaryChainsArray.push(chain);\r\n continue;\r\n }\r\n\r\n // this chain should be joined with the primary chain of the same name\r\n const primary = primaryChainsHash[name];\r\n for (j = 0; j < chain._residues.length; ++j) {\r\n const residue = chain._residues[j];\r\n primary._residues.push(residue);\r\n residue._chain = primary;\r\n }\r\n }\r\n\r\n // replace chains list with one containing only primary chains\r\n // dropping references to all chains but primary\r\n this._complex._chains = primaryChainsArray;\r\n }\r\n\r\n parseSync() {\r\n const mmtfData = MMTF.decode(this._data);\r\n\r\n this._complex = new Complex();\r\n this._serialAtomMap = {}; // filled during traversal\r\n\r\n this._traverse(mmtfData);\r\n this._linkAtomsToResidues();\r\n this._markHeteroAtoms(mmtfData);\r\n this._chainsByName = this._findSynonymousChains();\r\n Array.prototype.push.apply(this._complex.units, this._parseAssemblyInfo(mmtfData));\r\n this._joinSynonymousChains();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n return this._complex;\r\n }\r\n}\r\n\r\nMMTFParser.formats = ['mmtf'];\r\nMMTFParser.extensions = ['.mmtf'];\r\nMMTFParser.binary = true;\r\n\r\nexport default MMTFParser;\r\n","class ParsingError extends Error {\r\n constructor(message, line, column) {\r\n super(`data:${line}:${column}: ${message}`);\r\n\r\n if (Error.captureStackTrace) {\r\n Error.captureStackTrace(this, ParsingError);\r\n }\r\n\r\n this.name = 'ParsingError';\r\n this.parseLine = line;\r\n this.parseColumn = column;\r\n }\r\n}\r\n\r\nexport default ParsingError;\r\n","import _ from 'lodash';\r\nimport ParsingError from './ParsingError';\r\n\r\n// Implemented and being tested against: https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax\r\n\r\nfunction _isWhitespace(ch) {\r\n return ch === 32 || ch === 10 || ch === 13 || ch === 9;\r\n}\r\n\r\nfunction _inlineIndexOf(ch0, str, idx) {\r\n const len = str.length;\r\n let ch = -1;\r\n while (idx < len) {\r\n ch = str.charCodeAt(idx);\r\n if (ch === ch0 || ch === 10) {\r\n break;\r\n }\r\n ++idx;\r\n }\r\n return ch === ch0 ? idx : -1;\r\n}\r\n\r\nexport default function readCIF(source) {\r\n let i = 0;\r\n let j = 0;\r\n const n = source.length;\r\n let code = NaN;\r\n let newline = true;\r\n let line = 1;\r\n let column = 1;\r\n let begin;\r\n let state = 0; // 0 - start, 1 - block, 2 - item, 3 - loop, 4 - values, 5 - value\r\n const result = {};\r\n let block = {};\r\n let keys = [];\r\n let keysCount = 0;\r\n let key = '';\r\n let values = [];\r\n let valuesCount = 0;\r\n let value;\r\n\r\n function _parseValue() {\r\n let val;\r\n if ((code === 46 || code === 63) && (i + 1 >= n || _isWhitespace(source.charCodeAt(i + 1)))) { // '.' or '?' .....\r\n // it's a missing value\r\n ++column;\r\n ++i;\r\n return undefined;\r\n }\r\n if (newline && code === 59) { // ';' ......................................................................\r\n // parse multi-line string\r\n j = i;\r\n let lines = 0;\r\n do {\r\n j = _inlineIndexOf(10, source, j + 1); // '\\n'\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated text block found', line, column);\r\n }\r\n ++lines;\r\n } while ((j + 1 < n && source.charCodeAt(j + 1) !== code) || j + 1 >= n);\r\n val = source.substring(i + 1, j).replace(/\\r/g, '');\r\n i = j + 2;\r\n line += lines;\r\n column = 1;\r\n newline = false;\r\n return val;\r\n }\r\n if (code === 39 || code === 34) { // ''' or '\"' ...........................................................\r\n // parse quoted string\r\n j = i;\r\n do {\r\n j = _inlineIndexOf(code, source, j + 1);\r\n if (j === -1) {\r\n throw new ParsingError('Unterminated quoted string found', line, column);\r\n }\r\n } while (j + 1 < n && !_isWhitespace(source.charCodeAt(j + 1)));\r\n val = source.substring(i + 1, j);\r\n column += j - i + 1;\r\n i = j + 1;\r\n return val;\r\n } // ......................................................................................................\r\n // parse until the first whitespace\r\n j = i;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n val = source.substring(i, j);\r\n column += j - i;\r\n i = j;\r\n // try to convert to a number\r\n const num = Number(val);\r\n if (!Number.isNaN(num)) {\r\n return num;\r\n }\r\n // or leave as an unquoted string\r\n return val;\r\n }\r\n\r\n function _storeKey(tag) {\r\n keys[keysCount++] = tag;\r\n }\r\n\r\n function _storeValue(val) {\r\n const keyIndex = valuesCount % keysCount;\r\n values[keyIndex].push(val);\r\n ++valuesCount;\r\n return val;\r\n }\r\n\r\n while (i <= n) {\r\n code = source.charCodeAt(i); // 'NaN' in place of ''\r\n if (code === 13) { // '\\r' .......................................................................................\r\n // just ignore\r\n } else if (code === 10) { // '\\n' ................................................................................\r\n // take note of new lines\r\n newline = true;\r\n ++line;\r\n column = 1;\r\n } else {\r\n // process inline characters\r\n if (code === 32 || code === 9) { // ' ' or '\\t' ................................................................\r\n // just ignore\r\n } else if (code === 35) { // '#' ...............................................................................\r\n // skip the comment until before the end of the line\r\n i = _inlineIndexOf(10, source, i + 1); // '\\n'\r\n if (i === -1) {\r\n break;\r\n } else {\r\n continue; // don't forget to process the new line\r\n }\r\n } else if (state === 0) { // start =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n j = i + 5;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new data block\r\n result[source.substring(begin, i)] = block = {};\r\n state = 1; // block\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Data block name missing', line, column);\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 1) { // block =============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n continue; // parse again in a different state\r\n } else if (code === 95) { // '_' .............................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // start new item\r\n key = source.substring(begin, i);\r\n state = 2; // item\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n i += 5;\r\n column += 5;\r\n if (i < n && !_isWhitespace(source.charCodeAt(i))) {\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n } else {\r\n // start new loop\r\n keys = [];\r\n keysCount = 0;\r\n values = [];\r\n valuesCount = 0;\r\n state = 3; // loop\r\n continue; // don't forget to process the whitespace\r\n }\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n break;\r\n } else { // ..................................................................................................\r\n throw new ParsingError(`Unexpected character in state ${state}`, line, column);\r\n }\r\n } else if (state === 2) { // item ==============================================================================\r\n if (Number.isNaN(code)) {\r\n break;\r\n }\r\n value = _parseValue();\r\n _.set(block, key, value);\r\n state = 1; // block\r\n continue;\r\n } else if (state === 3) { // loop ==============================================================================\r\n if (code === 95) { // '_' ....................................................................................\r\n j = i + 1;\r\n begin = j;\r\n while (j < n && !_isWhitespace(source.charCodeAt(j))) {\r\n ++j;\r\n }\r\n column += j - i;\r\n i = j;\r\n if (begin < i) {\r\n // add new key\r\n _storeKey(source.substring(begin, i));\r\n continue; // don't forget to process the whitespace\r\n } else {\r\n throw new ParsingError('Tag name missing', line, column);\r\n }\r\n } else { // ..................................................................................................\r\n if (keysCount > 0) {\r\n for (let keyIndex = 0; keyIndex < keysCount; ++keyIndex) {\r\n value = [];\r\n values[keyIndex] = value;\r\n _.set(block, keys[keyIndex], value);\r\n }\r\n state = 4;\r\n continue; // parse again in a different state\r\n }\r\n throw new ParsingError('Data tags are missing inside a loop', line, column);\r\n }\r\n } else if (state === 4) { // values ============================================================================\r\n if ((code === 68 || code === 100) && source.substr(i + 1, 4).toLowerCase() === 'ata_') { // 'data_' ..........\r\n state = 0; // start\r\n } else if (code === 95) { // '_' .............................................................................\r\n state = 1; // block\r\n } else if ((code === 76 || code === 108) && source.substr(i + 1, 4).toLowerCase() === 'oop_') { // 'loop_' ...\r\n state = 1; // block\r\n } else if (Number.isNaN(code)) { // ....................................................................\r\n state = 0;\r\n } else { // ..................................................................................................\r\n _storeValue(_parseValue());\r\n }\r\n continue; // parse again in a different state\r\n } else { // ====================================================================================================\r\n throw new ParsingError(`Unexpected internal state ${state}`, line, column);\r\n }\r\n\r\n newline = false;\r\n ++column;\r\n }\r\n ++i;\r\n }\r\n\r\n if (state === 2) { // item\r\n throw new ParsingError(`Unexpected end of file in state ${state}`, line, column);\r\n }\r\n\r\n return result;\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport StructuralElement from '../../chem/StructuralElement';\r\nimport readCIF from './readCIF';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Helix,\r\n Sheet,\r\n Strand,\r\n Assembly,\r\n Molecule,\r\n} = chem;\r\n\r\nconst cRequiredAtomFields = [\r\n 'auth_seq_id',\r\n 'Cartn_x',\r\n 'Cartn_y',\r\n 'Cartn_z',\r\n 'label_atom_id',\r\n];\r\n\r\nconst cSecondaryCoding = {\r\n helx: 'helix',\r\n turn: 'turn',\r\n strn: 'strand',\r\n};\r\n\r\nfunction getTypeFromId(string) {\r\n const typeId = /[A-Za-z]+/.exec(string);\r\n if (!typeId) {\r\n return null;\r\n }\r\n\r\n return cSecondaryCoding[typeId[0].toLowerCase()];\r\n}\r\n\r\n/**\r\n * Make valid object an array\r\n * @param arrayLikeObject\r\n * @return {array, object} array or object\r\n */\r\nfunction arrize(arrayLikeObject) {\r\n if (arrayLikeObject === null || arrayLikeObject === undefined || _.isArray(arrayLikeObject)) {\r\n return arrayLikeObject;\r\n }\r\n return [arrayLikeObject];\r\n}\r\n\r\nfunction nameToElement(name) {\r\n // http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\n //\r\n // http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note1\r\n //\r\n // Atom names start with element symbols right-justified in columns 13-14\r\n // as permitted by the length of the name. For example, the symbol FE for\r\n // iron appears in columns 13-14, whereas the symbol C for carbon appears\r\n // in column 14 (see Misaligned Atom Names). If an atom name has four\r\n // characters, however, it must start in column 13 even if the element\r\n // symbol is a single character (for example, see Hydrogen Atoms).\r\n\r\n const veryLong = name.trim().length === 4;\r\n return name.slice(0, veryLong ? 1 : 2).trim();\r\n}\r\n\r\nclass AtomDataError extends Error {\r\n constructor(message) {\r\n super();\r\n this.name = 'AtomDataError';\r\n this.message = message;\r\n }\r\n}\r\n\r\nfunction _getOperations(operList) {\r\n if (!operList) {\r\n return null;\r\n }\r\n const idc = arrize(operList.id);\r\n const { matrix, vector } = operList;\r\n if (!idc || !matrix || !vector) {\r\n return null;\r\n }\r\n\r\n const ops = [];\r\n for (let i = 0, n = idc.length; i < n; ++i) {\r\n const mtx = new THREE.Matrix4();\r\n const { elements } = mtx;\r\n\r\n for (let row = 0; row < 3; ++row) {\r\n const matrixData = matrix[row + 1];\r\n elements[row] = arrize(matrixData[1])[i];\r\n elements[row + 4] = arrize(matrixData[2])[i];\r\n elements[row + 8] = arrize(matrixData[3])[i];\r\n elements[row + 12] = arrize(vector[row + 1])[i];\r\n }\r\n ops[idc[i]] = mtx;\r\n }\r\n return ops;\r\n}\r\n\r\nfunction _extractOperations(assemblyGen, opsDict) {\r\n assemblyGen = _.isString(assemblyGen) ? assemblyGen : `${assemblyGen}`;\r\n const l = assemblyGen.replace(/\\)\\s*\\(/g, '!').replace(/[()']/g, '');\r\n const groupStr = l.split('!');\r\n const gps = [];\r\n\r\n for (let grIdx = 0, grCount = groupStr.length; grIdx < grCount; ++grIdx) {\r\n const gr = groupStr[grIdx].split(',');\r\n const gp = [];\r\n let idx = 0;\r\n for (let i = 0, n = gr.length; i < n; ++i) {\r\n const s = gr[i];\r\n if (s.includes('-')) {\r\n const es = s.split('-');\r\n let j = parseInt(es[0], 10);\r\n const m = parseInt(es[1], 10);\r\n for (; j <= m; ++j) {\r\n gp[idx++] = opsDict[j];\r\n }\r\n } else {\r\n gp[idx++] = opsDict[s];\r\n }\r\n }\r\n gps.push(gp);\r\n }\r\n\r\n // traverse all groups from the end of array and make all mults\r\n const matrices = [];\r\n let cnt = 0;\r\n function traverse(level, mtx) {\r\n for (let ii = 0, nn = gps[level].length; ii < nn; ++ii) {\r\n const newMtx = mtx ? mtx.clone() : new THREE.Matrix4();\r\n newMtx.multiplyMatrices(gps[level][ii], newMtx);\r\n if (level === 0) {\r\n matrices[cnt++] = newMtx;\r\n } else {\r\n traverse(level - 1, newMtx);\r\n }\r\n }\r\n }\r\n traverse(gps.length - 1);\r\n return matrices;\r\n}\r\n\r\nclass CIFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this.asymDict = {};\r\n this.molecules = [];\r\n this._options.fileType = 'cif';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*data_/i.test(data);\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing CIF file..');\r\n const data = readCIF(this._data);\r\n return this._toComplex(data);\r\n }\r\n\r\n /**\r\n * Convert intermediate structure into our valid Complex object\r\n * @param cifData intermediate CIF object\r\n * @returns {Complex} complex\r\n * @private\r\n */\r\n _toComplex(cifData) {\r\n const complex = new Complex();\r\n const complexData = cifData[Object.keys(cifData)[0]];\r\n this._extractAtoms(complex, complexData);\r\n this._extractSecondary(complex, complexData);\r\n this._extractAssemblies(complex, complexData);\r\n this._extractMolecules(complex, complexData);\r\n this._extractMetadata(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n\r\n return complex;\r\n }\r\n\r\n /**\r\n * Extract metadata\r\n * @param complex structure to fill\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n\r\n _extractMetadata(complex, complexData) {\r\n const { metadata } = complex;\r\n metadata.id = complexData.entry.id;\r\n metadata.classification = complexData.struct_keywords.pdbx_keywords;\r\n const databaserev = complexData.database_PDB_rev;\r\n metadata.date = (databaserev && databaserev.date_original) ? databaserev.date_original : '';\r\n metadata.format = 'cif';\r\n metadata.title = [];\r\n metadata.title[0] = complexData.struct.title;\r\n }\r\n\r\n /**\r\n * Extract molecules information from CIF structure (should be called strictly after _extractAtoms)\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractMolecules(complex, complexData) {\r\n const molData = complexData.entity;\r\n const names = arrize(molData.pdbx_description);\r\n const count = names.length;\r\n let i;\r\n\r\n // molecules names from cif\r\n for (i = 0; i < count; i++) {\r\n if (this.molecules[i]) { // molecule was created during atoms processing\r\n this.molecules[i].name = names[i];\r\n } else { // molecule wasn't created, because there is no atom which is contained\r\n this.molecules[i] = { name: names[i], residues: [] };\r\n }\r\n }\r\n\r\n // reorganize molecules for complex and check chains\r\n const molecules = complex.getMolecules();\r\n for (i = 0; i < count; i++) {\r\n const molecule = this.molecules[i];\r\n molecules[i] = new Molecule(complex, molecule.name, i + 1);\r\n molecules[i].residues = molecule.residues;\r\n }\r\n }\r\n\r\n /**\r\n * Extract atom information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAtoms(complex, complexData) {\r\n const atomData = complexData.atom_site;\r\n if (!atomData) {\r\n throw new AtomDataError('CIF parsing error: atom_site is not specified!');\r\n }\r\n\r\n for (let f = 0, n = cRequiredAtomFields.length; f < n; ++f) {\r\n if (!atomData[cRequiredAtomFields[f]]) {\r\n throw new AtomDataError(`CIF parsing error: requires field ${cRequiredAtomFields[f]} not found!`);\r\n }\r\n }\r\n\r\n const { asymDict } = this;\r\n // required fields\r\n const resIdc = arrize(atomData.auth_seq_id);\r\n const x = arrize(atomData.Cartn_x);\r\n const y = arrize(atomData.Cartn_y);\r\n const z = arrize(atomData.Cartn_z);\r\n const names = arrize(atomData.label_atom_id);\r\n const count = names.length;\r\n // optional fields\r\n const group = arrize(atomData.group_PDB) || [];\r\n const chainIdc = arrize(atomData.auth_asym_id) || [];\r\n const chainLabelIdc = arrize(atomData.label_asym_id) || [];\r\n const serials = arrize(atomData.id) || [];\r\n const iCodes = arrize(atomData.pdbx_PDB_ins_code) || [];\r\n const resNames = arrize(atomData.label_comp_id) || [];\r\n const elements = arrize(atomData.type_symbol) || [];\r\n const tempFactors = arrize(atomData.B_iso_or_equiv) || [];\r\n const occupancies = arrize(atomData.occupancy) || [];\r\n const charges = arrize(atomData.pdbx_formal_charge) || [];\r\n const altLocs = arrize(atomData.label_alt_id) || [];\r\n const models = arrize(atomData.pdbx_PDB_model_num) || [];\r\n const molecules = arrize(atomData.label_entity_id) || [];\r\n\r\n let chain = null;\r\n let residue = null;\r\n for (let i = 0; i < count; ++i) {\r\n const model = models[i] || 1;\r\n if (model !== 1) {\r\n continue;\r\n }\r\n const chainID = String(chainIdc[i] || ' ');\r\n\r\n if (!chain || chain.getName() !== chainID) {\r\n chain = complex.getChain(chainID) || complex.addChain(chainID);\r\n }\r\n asymDict[String(chainLabelIdc[i] || ' ')] = chainID;\r\n const resSeq = resIdc[i];\r\n const iCode = String(iCodes[i] || ' ');\r\n const resName = String(resNames[i] || '');\r\n if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {\r\n residue = chain.addResidue(resName, resSeq, iCode);\r\n\r\n // store residue in appropriate molecule\r\n const moleculeIdx = molecules[i] - 1;\r\n let entity = this.molecules[moleculeIdx];\r\n if (!entity) { // create new molecule if it hasn't been created\r\n this.molecules[moleculeIdx] = { name: '', residues: [] };\r\n entity = this.molecules[moleculeIdx];\r\n }\r\n entity.residues.push(residue);\r\n }\r\n\r\n const name = names[i];\r\n const element = elements[i] || nameToElement(name);\r\n const type = Element.getByName(element);\r\n const role = Element.Role[name.trim()];\r\n const xyz = new THREE.Vector3(x[i], y[i], z[i]);\r\n const het = group[i] === 'HETATM' || false;\r\n const serial = serials[i] || i;\r\n const tempFactor = tempFactors[i] || 0.0;\r\n const occupancy = occupancies[i] || 0.0;\r\n const altLoc = String(altLocs[i] || '');\r\n const charge = charges[i] || 0;\r\n\r\n residue.addAtom(\r\n name,\r\n type,\r\n xyz,\r\n role,\r\n het,\r\n serial,\r\n altLoc,\r\n occupancy,\r\n tempFactor,\r\n charge,\r\n );\r\n }\r\n }\r\n\r\n /**\r\n * Extracts secondary structure information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex - complex to fill\r\n * @param complexData - CIF complex data\r\n * @private\r\n */\r\n _extractSecondary(complex, complexData) {\r\n if (complexData.struct_conf) {\r\n this._extractConfs(complex, complexData.struct_conf);\r\n }\r\n if (complexData.struct_sheet_range) {\r\n this._extractSheets(complex, complexData.struct_sheet_range);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts sheets information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param sheetData\r\n * @private\r\n */\r\n _extractSheets(complex, sheetData) {\r\n const { asymDict } = this;\r\n if (!sheetData.sheet_id || !sheetData.id || !sheetData.beg_label_seq_id || !sheetData.end_label_seq_id\r\n || !sheetData.beg_label_asym_id) {\r\n return;\r\n }\r\n // Strand(sheet, start, end, sense, cur, prev)\r\n const sheets = complex._sheets;\r\n\r\n function getSheet(name) {\r\n const n = sheets.length;\r\n for (let i = 0; i < n; ++i) {\r\n if (sheets[i]._name === name) {\r\n return sheets[i];\r\n }\r\n }\r\n sheets[n] = new Sheet(name, 0);\r\n return sheets[n];\r\n }\r\n\r\n const sheetNames = arrize(sheetData.sheet_id);\r\n const strandNames = arrize(sheetData.id);\r\n const starts = arrize(sheetData.beg_auth_seq_id);\r\n const ends = arrize(sheetData.end_auth_seq_id);\r\n const chains = arrize(sheetData.beg_label_asym_id);\r\n const stICodes = arrize(sheetData.pdbx_beg_PDB_ins_code) || [];\r\n const endICodes = arrize(sheetData.pdbx_end_PDB_ins_code) || [];\r\n\r\n for (let i = 0, n = strandNames.length; i < n; ++i) {\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n const sheet = getSheet(sheetNames[i]);\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n\r\n const strand = new Strand(sheet, start[0], end[0], 0, null, null);\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = strand;\r\n }\r\n sheet.addStrand(strand);\r\n complex.structures.push(strand);\r\n }\r\n }\r\n\r\n /**\r\n * Extracts helix/turn/strand(?) information from CIF intermediate data\r\n * and adds it into complex\r\n * @param {Complex} complex\r\n * @param helicesData\r\n * @private\r\n */\r\n _extractConfs(complex, helicesData) {\r\n const { asymDict } = this;\r\n if (!helicesData.conf_type_id || !helicesData.beg_label_seq_id || !helicesData.end_label_seq_id\r\n || !helicesData.beg_label_asym_id) {\r\n return;\r\n }\r\n\r\n const types = arrize(helicesData.conf_type_id);\r\n const starts = arrize(helicesData.beg_auth_seq_id);\r\n const stICodes = arrize(helicesData.pdbx_beg_PDB_ins_code) || [];\r\n const ends = arrize(helicesData.end_auth_seq_id);\r\n const endICodes = arrize(helicesData.pdbx_end_PDB_ins_code) || [];\r\n const comments = arrize(helicesData.details) || [];\r\n const lengths = arrize(helicesData.pdbx_PDB_helix_length) || [];\r\n const helixClasses = arrize(helicesData.pdbx_PDB_helix_class) || [];\r\n const names = arrize(helicesData.id) || [];\r\n const chains = arrize(helicesData.beg_label_asym_id);\r\n\r\n for (let i = 0, n = types.length; i < n; ++i) {\r\n const type = getTypeFromId(types[i]);\r\n if (!type) {\r\n continue;\r\n }\r\n const name = names[i] || types[i];\r\n const chain = complex.getChain(asymDict[chains[i]]);\r\n\r\n const startIdx = starts[i];\r\n const endIdx = ends[i];\r\n const startICode = stICodes[i] || ' ';\r\n const endICode = endICodes[i] || ' ';\r\n\r\n const start = chain.findResidue(startIdx, startICode);\r\n const end = chain.findResidue(endIdx, endICode);\r\n\r\n // TODO think about last condition\r\n if (!start || !end) {\r\n continue;\r\n }\r\n const comment = comments[i] || '';\r\n const length = lengths[i] || 0;\r\n const helixClass = helixClasses[i] || ' ';\r\n let struct;\r\n if (type === 'helix') {\r\n const idx = complex._helices.length;\r\n struct = new Helix(helixClass, start[0], end[0], idx, name, comment, length);\r\n complex.addHelix(struct);\r\n complex.structures.push(struct);\r\n } else if (type === 'turn') {\r\n struct = new StructuralElement(StructuralElement.Type.TURN, start[0], end[0]);\r\n complex.structures.push(struct);\r\n } else {\r\n struct = null;\r\n }\r\n if (!struct) {\r\n continue;\r\n }\r\n const residues = chain.getResidues();\r\n for (let r = start[1]; r <= end[1]; ++r) {\r\n residues[r]._secondary = struct;\r\n }\r\n }\r\n }\r\n\r\n /**\r\n * Extract biological assemblies information from CIF structure and fill complex\r\n * @param {Complex} complex\r\n * @param complexData complex data from CIF file\r\n * @private\r\n */\r\n _extractAssemblies(complex, complexData) {\r\n const { asymDict } = this;\r\n const asmGen = complexData.pdbx_struct_assembly_gen;\r\n if (!asmGen) {\r\n return;\r\n }\r\n\r\n const asmIdx = arrize(asmGen.assembly_id);\r\n const asmOper = arrize(asmGen.oper_expression);\r\n const asmList = arrize(asmGen.asym_id_list);\r\n if (!asmIdx || !asmOper || !asmList) {\r\n return;\r\n }\r\n\r\n const operList = _getOperations(complexData.pdbx_struct_oper_list);\r\n if (!operList) {\r\n return;\r\n }\r\n\r\n for (let i = 0, n = asmIdx.length; i < n; ++i) {\r\n const asm = new Assembly(complex);\r\n const assemblyOps = _extractOperations(asmOper[i], operList);\r\n const entries = asmList[i].split(',');\r\n for (let ii = 0, nn = entries.length; ii < nn; ++ii) {\r\n const chain = entries[ii].trim();\r\n if (chain.length > 0) {\r\n asm.addChain(asymDict[chain]);\r\n }\r\n }\r\n asm.matrices = assemblyOps;\r\n complex.units.push(asm);\r\n }\r\n }\r\n}\r\n\r\nCIFParser.formats = ['cif', 'mmcif'];\r\nCIFParser.extensions = ['.cif', '.mmcif'];\r\n\r\nexport default CIFParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Volume from '../../chem/Volume';\r\n\r\nexport const valueType = {\r\n singular: 0,\r\n vector: 1,\r\n array: 2,\r\n buffer: 3,\r\n};\r\n\r\nclass VolumeModel {\r\n _xyz2crs = [];\r\n\r\n _origin = new THREE.Vector3(0, 0, 0);\r\n\r\n constructor() {\r\n this._header = {};\r\n this._boxSize = new THREE.Vector3();\r\n this._boxStart = new THREE.Vector3();\r\n this._header.delta = {};\r\n this._header.extent = [];\r\n this._header.nstart = [];\r\n this._header.grid = [];\r\n this._header.crs2xyz = [];\r\n this._header.cellDims = new THREE.Vector3();\r\n this._header.angles = [];\r\n this._header.origin = new THREE.Vector3(0, 0, 0);\r\n this._header.dmin = 0;\r\n this._header.dmean = 0;\r\n this._header.dmax = 0;\r\n }\r\n\r\n _typedCheck() {\r\n if (_.isTypedArray(this._buff)) {\r\n this._buff = this._buff.buffer;\r\n } else if (!_.isArrayBuffer(this._buff)) {\r\n throw new TypeError('Expected ArrayBuffer or TypedArray');\r\n }\r\n }\r\n\r\n _fillHeader(headerFormat, arrays) {\r\n for (const key in headerFormat) {\r\n if (headerFormat.hasOwnProperty(key)) {\r\n switch (headerFormat[key][0]) {\r\n case valueType.singular:\r\n this._header[key] = arrays[headerFormat[key][1]][headerFormat[key][2]];\r\n break;\r\n\r\n case valueType.array:\r\n this._parseArray(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.vector:\r\n this._parseVector(this._header[key], arrays[headerFormat[key][1]], headerFormat[key][2]);\r\n break;\r\n\r\n case valueType.buffer:\r\n this._header[key] = new Uint8Array(\r\n arrays[headerFormat[key][1]],\r\n [headerFormat[key][2]] * 4,\r\n [headerFormat[key][3]] * 4,\r\n );\r\n break;\r\n\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _parseVector(vector, arr, pos) {\r\n [vector.x, vector.y, vector.z] = [arr[pos], arr[pos + 1], arr[pos + 2]];\r\n }\r\n\r\n _parseArray(vector, arr, pos) {\r\n vector[0] = arr[pos];\r\n vector[1] = arr[pos + 1];\r\n vector[2] = arr[pos + 2];\r\n }\r\n\r\n _parseHeader(_buffer) {}\r\n\r\n _setAxisIndices() {}\r\n\r\n _setOrigins() {}\r\n\r\n _getAxis() {\r\n const header = this._header;\r\n\r\n const xScale = header.cellDims.x / header.grid[0];\r\n const yScale = header.cellDims.y / header.grid[1];\r\n const zScale = header.cellDims.z / header.grid[2];\r\n\r\n const [alpha, beta, gamma] = header.angles;\r\n\r\n const z1 = Math.cos(beta);\r\n const z2 = (Math.cos(alpha) - Math.cos(beta)\r\n * Math.cos(gamma)) / Math.sin(gamma);\r\n const z3 = Math.sqrt(1.0 - z1 * z1 - z2 * z2);\r\n\r\n const xaxis = new THREE.Vector3(xScale, 0, 0);\r\n const yaxis = new THREE.Vector3(Math.cos(gamma) * yScale, Math.sin(gamma) * yScale, 0);\r\n const zaxis = new THREE.Vector3(z1 * zScale, z2 * zScale, z3 * zScale);\r\n\r\n return [xaxis, yaxis, zaxis];\r\n }\r\n\r\n _getXYZdim() {\r\n return [this._header.extent[this._xyz2crs[0]],\r\n this._header.extent[this._xyz2crs[1]],\r\n this._header.extent[this._xyz2crs[2]]];\r\n }\r\n\r\n _getVolumeInfo() {\r\n const volInfo = _.pick(this._header, ['dmean', 'dmin', 'dmax', 'sd', 'delta']);\r\n volInfo.obtuseAngle = this._header.angles.map((angle) => Number(angle >= (Math.PI / 2)));\r\n return volInfo;\r\n }\r\n\r\n _setBoxParams(xaxis, yaxis, zaxis) {\r\n // if axes are not orthogonal, the origins might not match with box coordinates - need to make shift\r\n let shiftX = 0;\r\n let shiftY = 0;\r\n const [alpha, beta, gamma] = this._header.angles;\r\n\r\n if (gamma >= Math.PI / 2) {\r\n shiftX += Math.abs(yaxis.x);\r\n }\r\n if (beta >= Math.PI / 2) {\r\n shiftX += Math.abs(zaxis.x);\r\n }\r\n if (alpha >= Math.PI / 2) {\r\n shiftY += Math.abs(zaxis.y);\r\n }\r\n\r\n this._boxStart = new THREE.Vector3(this._origin.x - shiftX, this._origin.y - shiftY, this._origin.z);\r\n this._boxSize = new THREE.Vector3(\r\n Math.abs(xaxis.x) + Math.abs(yaxis.x) + Math.abs(zaxis.x),\r\n Math.abs(yaxis.y) + Math.abs(zaxis.y),\r\n Math.abs(zaxis.z),\r\n );\r\n\r\n const delta = (axe, proj) => (Math.abs(axe[proj]) / this._boxSize[proj]);\r\n this._header.delta.x = delta(yaxis, 'x');\r\n this._header.delta.y = delta(zaxis, 'x');\r\n this._header.delta.z = delta(zaxis, 'y');\r\n }\r\n\r\n _getXYZbox() {\r\n return new THREE.Box3(this._boxStart.clone(), this._boxStart.clone().add(this._boxSize));\r\n }\r\n\r\n _toXYZData() {}\r\n\r\n parse(data) {\r\n this._parseHeader(data);\r\n this._setOrigins();\r\n return new Volume(Float32Array, this._getXYZdim(), this._getXYZbox(), 1, this._toXYZData(), this._getVolumeInfo());\r\n }\r\n}\r\n\r\nexport default VolumeModel;\r\n","import Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\nconst CCP4Header = {\r\n extent: [valueType.array, 'u32', 0],\r\n type: [valueType.singular, 'u32', 3],\r\n nstart: [valueType.array, 'i32', 4],\r\n grid: [valueType.array, 'u32', 7],\r\n cellDims: [valueType.vector, 'f32', 10],\r\n angles: [valueType.array, 'f32', 13],\r\n crs2xyz: [valueType.array, 'i32', 16],\r\n dmin: [valueType.singular, 'f32', 19],\r\n dmax: [valueType.singular, 'f32', 20],\r\n dmean: [valueType.singular, 'f32', 21],\r\n ispg: [valueType.singular, 'u32', 22],\r\n nsymbt: [valueType.singular, 'u32', 23],\r\n lksflg: [valueType.singular, 'u32', 24],\r\n customData: [valueType.buffer, 'buffer', 25, 9],\r\n origin: [valueType.vector, 'f32', 34],\r\n map: [valueType.buffer, 'buffer', 52, 1],\r\n machine: [valueType.singular, 'u32', 53],\r\n sd: [valueType.singular, 'f32', 54],\r\n nlabel: [valueType.singular, 'f32', 55],\r\n label: [valueType.buffer, 'buffer', 56, 200],\r\n};\r\n\r\nclass Ccp4Model extends VolumeModel {\r\n // read header (http://www.ccp4.ac.uk/html/maplib.html)\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n const arrays = {};\r\n arrays.u32 = new Uint32Array(this._buff, 0, 56);\r\n arrays.i32 = new Int32Array(this._buff, 0, 56);\r\n arrays.f32 = new Float32Array(this._buff, 0, 56);\r\n arrays.buffer = this._buff;\r\n const header = this._header;\r\n\r\n this._fillHeader(CCP4Header, arrays);\r\n\r\n // calculate non-orthogonal unit cell coordinates\r\n header.angles.forEach((angle, i, a) => { a[i] *= Math.PI / 180.0; });\r\n }\r\n\r\n _setAxisIndices() {\r\n const header = this._header;\r\n\r\n if (header.cellDims.x === 0.0 && header.cellDims.y === 0.0 && header.cellDims.z === 0.0) {\r\n header.cellDims.set(1.0, 1.0, 1.0);\r\n }\r\n // Apply header conversion\r\n // Mapping between CCP4 column, row, section and VMD x, y, z.\r\n const { crs2xyz } = this._header;\r\n if (crs2xyz[0] === 0 && crs2xyz[1] === 0 && crs2xyz[2] === 0) {\r\n crs2xyz[0] = 1;\r\n crs2xyz[1] = 2;\r\n crs2xyz[2] = 3;\r\n }\r\n\r\n const xyz2crs = this._xyz2crs;\r\n xyz2crs[crs2xyz[0] - 1] = 0; // column\r\n xyz2crs[crs2xyz[1] - 1] = 1; // row\r\n xyz2crs[crs2xyz[2] - 1] = 2; // section\r\n }\r\n\r\n _setOrigins() {\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n const header = this._header;\r\n const xyz2crs = this._xyz2crs;\r\n // Handle both MRC-2000 and older format maps\r\n if (header.origin.x === 0.0 && header.origin.y === 0.0 && header.origin.z === 0.0) {\r\n this._origin.addScaledVector(xaxis, header.nstart[xyz2crs[0]]);\r\n this._origin.addScaledVector(yaxis, header.nstart[xyz2crs[1]]);\r\n this._origin.addScaledVector(zaxis, header.nstart[xyz2crs[2]]);\r\n } else {\r\n this._origin = header.origin;\r\n // Use ORIGIN records rather than old n[xyz]start records\r\n // http://www2.mrc-lmb.cam.ac.uk/image2000.html\r\n // XXX the ORIGIN field is only used by the EM community, and\r\n // has undefined meaning for non-orthogonal maps and/or non-cubic voxels, etc.\r\n }\r\n xaxis.multiplyScalar(header.extent[xyz2crs[0]] - 1);\r\n yaxis.multiplyScalar(header.extent[xyz2crs[1]] - 1);\r\n zaxis.multiplyScalar(header.extent[xyz2crs[2]] - 1);\r\n\r\n if (header.type === 2) {\r\n this._data = new Float32Array(\r\n this._buff,\r\n 1024 + header.nsymbt,\r\n header.extent[0] * header.extent[1] * header.extent[2],\r\n );\r\n } else {\r\n throw new Error(`CCP4: Unsupported format ${header.type}`);\r\n }\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const data = this._data;\r\n const xyz2crs = this._xyz2crs;\r\n const xyzData = new Float32Array(data.length);\r\n\r\n const dim = this._getXYZdim();\r\n const xSize = dim[0];\r\n const ySize = dim[1];\r\n\r\n let crsIdx = 0;\r\n const coord = [];\r\n let x;\r\n let y;\r\n let z;\r\n for (coord[2] = 0; coord[2] < header.extent[2]; coord[2]++) { // Site\r\n for (coord[1] = 0; coord[1] < header.extent[1]; coord[1]++) { // Row\r\n for (coord[0] = 0; coord[0] < header.extent[0]; coord[0]++, crsIdx++) { // Column\r\n x = coord[xyz2crs[0]];\r\n y = coord[xyz2crs[1]];\r\n z = coord[xyz2crs[2]];\r\n xyzData[x + xSize * (y + ySize * z)] = data[crsIdx];\r\n }\r\n }\r\n }\r\n\r\n return xyzData;\r\n }\r\n}\r\n\r\nclass CCP4Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'ccp4';\r\n this.model = new Ccp4Model();\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false; // Autodetection is not implemented yet\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nCCP4Parser.formats = ['ccp4'];\r\nCCP4Parser.extensions = ['.ccp4', '.map', '.mrc'];\r\nCCP4Parser.binary = true;\r\n\r\nexport default CCP4Parser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element, Molecule } = chem;\r\n\r\nclass XYZParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n this._options.fileType = 'xyz';\r\n this._fileName = options.name;\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && /^\\s*\\d+ *\\n[^\\n]*\\n\\s*\\w{1,3}\\s+-?\\d/.test(data);\r\n }\r\n\r\n _parseToAtomsInf(source) {\r\n const endnAtoms = source.indexOf('\\n');\r\n const nAtoms = parseInt(source.substring(0, endnAtoms), 10);\r\n const endComment = source.indexOf('\\n', endnAtoms + 1);\r\n let comment = source.slice(endnAtoms + 1, endComment).trim();\r\n if (comment.length === 0) {\r\n comment = this._fileName;\r\n }\r\n\r\n const startAtomsInf = endComment + source.substring(endComment).search(/\\S/);\r\n this._atomsInf = source.substring(startAtomsInf).split(/[\\s,]*\\n[\\s,]*/);\r\n if (!Number.isNaN(nAtoms) && (this._atomsInf.length - 1 !== nAtoms)) {\r\n this._complex.error = {\r\n message: 'wrong number of atoms',\r\n };\r\n return;\r\n }\r\n\r\n this._complex.metadata.format = 'xyz';\r\n this._complex.name = comment;\r\n }\r\n\r\n _parseAtomsInf() {\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n\r\n const chain = this._complex.addChain('A');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0; i < this._atomsInf.length - 1; i++) {\r\n const words = this._atomsInf[i].split(/[\\s,]+/);\r\n\r\n if (words.length !== 4) {\r\n this._complex.error = {\r\n message: 'missed parameters',\r\n };\r\n break;\r\n }\r\n\r\n const serial = i + 1;\r\n const name = words[0];\r\n const xyz = new THREE.Vector3(parseFloat(words[1]), parseFloat(words[2]), parseFloat(words[3]));\r\n const type = Element.getByName(name);\r\n const role = undefined;\r\n\r\n residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n const molecule = new Molecule(this._complex, this._complex.name, 1);\r\n molecule.residues = residue;\r\n this._complex._molecules[0] = molecule;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n\r\n this._parseToAtomsInf(this._data);\r\n this._parseAtomsInf();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n\r\n this._complex = null;\r\n this._atomsInf = null;\r\n\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n return result;\r\n }\r\n\r\n static formats = ['xyz'];\r\n\r\n static extensions = ['.xyz'];\r\n}\r\n\r\nexport default XYZParser;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst { Complex, Element } = chem;\r\n\r\nclass PubChemParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'pubchem+json';\r\n }\r\n\r\n static canProbablyParse(data) {\r\n return _.isString(data) && data[0] === '{';\r\n }\r\n\r\n parseSync() {\r\n this.logger.info('Parsing PubChem JSON file...');\r\n return this._toComplex(JSON.parse(this._data));\r\n }\r\n\r\n _toComplex(jsonData) {\r\n const complex = new Complex();\r\n const complexData = jsonData.PC_Compounds && jsonData.PC_Compounds[0];\r\n if (complexData) {\r\n this._extractAtoms(complex, complexData);\r\n complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n });\r\n }\r\n return complex;\r\n }\r\n\r\n _extractAtoms(complex, complexData) {\r\n let aids = complexData.atoms && complexData.atoms.aid;\r\n let elements = aids && complexData.atoms.element;\r\n if (!elements || aids.length !== elements.length) {\r\n throw new Error('Unable to parse atom elements');\r\n }\r\n elements = _.fromPairs(_.zip(aids, elements));\r\n const atoms = {};\r\n\r\n const coords = complexData.coords && complexData.coords[0];\r\n const model = coords && coords.conformers && coords.conformers[0];\r\n const xs = model && model.x;\r\n const ys = model && model.y;\r\n const zs = (model && model.z) || [];\r\n aids = coords && coords.aid;\r\n if (!aids || !xs || !ys) {\r\n throw new Error('Coordinates are not found in the file');\r\n }\r\n\r\n const chain = complex.addChain(' ');\r\n const residue = chain.addResidue('UNK', 1, ' ');\r\n\r\n for (let i = 0, n = aids.length; i < n; ++i) {\r\n const aid = aids[i];\r\n const element = Element.ByAtomicNumber[elements[aid]];\r\n const xyz = new THREE.Vector3(xs[i], ys[i], zs[i] || 0.0);\r\n atoms[aid] = residue.addAtom(element.name, element, xyz, undefined, true, aid, ' ', 1.0, 0.0, 0);\r\n }\r\n\r\n const aids1 = complexData.bonds && complexData.bonds.aid1;\r\n const aids2 = complexData.bonds && complexData.bonds.aid2;\r\n const orders = (complexData.bonds && complexData.bonds.order) || [];\r\n if (!aids1 || !aids2 || aids1.length !== aids2.length) {\r\n return;\r\n }\r\n\r\n for (let j = 0, m = aids1.length; j < m; ++j) {\r\n complex.addBond(atoms[aids1[j]], atoms[aids2[j]], orders[j] || 1, 0, true);\r\n }\r\n }\r\n}\r\n\r\nPubChemParser.formats = ['pubchem', 'pubchem+json', 'pc'];\r\nPubChemParser.extensions = ['.json'];\r\n\r\nexport default PubChemParser;\r\n","import _ from 'lodash';\r\n\r\nexport default class SDFStream {\r\n constructor(data) {\r\n this._strings = data.split(/\\r?\\n|\\r/);\r\n this._currentStart = 0;\r\n this._currentStringIndx = 0;\r\n }\r\n\r\n setStart(start) {\r\n if (start >= this._strings.length) {\r\n this._currentStart = this._strings.length - 1;\r\n this._currentStringIndx = this._strings.length - 1;\r\n } else {\r\n this._currentStart = start;\r\n this._currentStringIndx = start;\r\n }\r\n }\r\n\r\n getNextString() {\r\n return this._strings[++this._currentStringIndx];\r\n }\r\n\r\n getCurrentString() {\r\n return this._strings[this._currentStringIndx];\r\n }\r\n\r\n getStringFromStart(numb) {\r\n this._currentStringIndx = this._currentStart + numb;\r\n return this._strings[this._currentStart + numb];\r\n }\r\n\r\n findNextDataItem() {\r\n let curStr = this.getNextString();\r\n let res = false;\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n if (curStr.match(/>\\s+<(.*)>/)) {\r\n res = true;\r\n break;\r\n }\r\n curStr = this.getNextString();\r\n }\r\n\r\n return res;\r\n }\r\n\r\n findNextCompoundStart() {\r\n let curStr = this.getCurrentString();\r\n while (!_.isUndefined(curStr) && curStr.trim() !== '$$$$') {\r\n curStr = this.getNextString();\r\n }\r\n this.setStart(++this._currentStringIndx);\r\n return this.probablyHaveDataToParse();\r\n }\r\n\r\n probablyHaveDataToParse() {\r\n return this._currentStringIndx < this._strings.length - 2;\r\n }\r\n}\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport SDFStream from './SDFStream';\r\nimport Assembly from '../../chem/Assembly';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst chargeMap = [0, 3, 2, 1, 0, -1, -2, -3];\r\nconst orderMap = [0, 1, 2, 3, 1, 1, 1, 2];\r\nconst typeMap = [\r\n Bond.BondType.UNKNOWN, // 0 - error\r\n Bond.BondType.COVALENT, // 1 - single\r\n Bond.BondType.COVALENT, // 2 - double\r\n Bond.BondType.COVALENT, // 3 - triple\r\n Bond.BondType.AROMATIC, // 4 - aromatic\r\n Bond.BondType.UNKNOWN, // 5 - single or double\r\n Bond.BondType.AROMATIC, // 6 - single or aromatic\r\n Bond.BondType.AROMATIC, // 7 - double or aromatic\r\n // 8 - any\r\n // 9 - coordination\r\n // 10 - hydrogen\r\n];\r\n\r\nconst sdfAndMolRegexp = /.*(M\\s\\sEND).*|.*(^$$$$).*|.*>\\s+<(.+)>.*/;\r\nconst sdfRegExp = /.*($$$$).*|.*>\\s+<(.+)>.*/;\r\n\r\nconst fileFormat = { SDF: 'sdf', MOL: 'mol' };\r\n\r\nconst possibleNameTags = ['PUBCHEM_IUPAC_TRADITIONAL_NAME', /PUBCHEM_(.+)_NAME/, /(.+)name/, /(.+)NAME/];\r\nconst possibleIDTags = ['PUBCHEM_COMPOUND_CID', 'id', 'ID', /.*CID/, /.*ID/, /.*id/];\r\nconst possibleTitleTags = ['msg', 'MSG', 'message', 'title', 'description', 'desc'];\r\nconst tagsNames = ['name', 'id', 'title'];\r\nconst tags = { name: possibleNameTags, id: possibleIDTags, title: possibleTitleTags };\r\n\r\nfunction buildChainID(index) {\r\n if (!index) {\r\n return 'A';\r\n }\r\n\r\n const codes = [];\r\n while (index) {\r\n codes.push(65 + (index % 26));\r\n index = Math.trunc(index / 26);\r\n }\r\n if (codes.length > 1) {\r\n codes.reverse();\r\n codes[0] -= 1;\r\n }\r\n\r\n return String.fromCharCode(...codes);\r\n}\r\n\r\nexport default class SDFParser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._format = 'sdf';\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._molecules = null;\r\n this._metadata = {};\r\n this._metadata.molecules = [];\r\n this._currentMolProps = {};\r\n this._compoundIndx = -1;\r\n this._assemblies = [];\r\n this._atomsParsed = 0;\r\n this._atomsIndexes = [];\r\n }\r\n\r\n canProbablyParse(data) {\r\n return _.isString(data) && sdfAndMolRegexp.test(data);\r\n }\r\n\r\n _parseHeader(stream) {\r\n const molecule = {};\r\n molecule.name = stream.getStringFromStart(0);\r\n const date = parseInt(stream.getStringFromStart(1).substr(10, 6).trim(), 10);\r\n molecule.date = date.toString() || '';\r\n molecule.title = stream.getStringFromStart(2);\r\n this._metadata.molecules.push(molecule);\r\n }\r\n\r\n _parseAtoms(stream, atomsNum) {\r\n let curStr;\r\n let serial = this._atomsParsed;\r\n\r\n // each molecule = chain\\residue\r\n const chainID = buildChainID(this._compoundIndx);\r\n const resName = 'UNK';\r\n const resSeq = 1;\r\n\r\n this._chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);\r\n this._residue = this._chain.addResidue(resName, resSeq, ' ');\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n curStr = stream.getNextString();\r\n serial++;\r\n const x = parseFloat(curStr.substr(0, 10));\r\n const y = parseFloat(curStr.substr(10, 10));\r\n const z = parseFloat(curStr.substr(20, 10));\r\n const charge = chargeMap[parseInt(curStr.substr(36, 3), 10)];\r\n const xyz = new THREE.Vector3(x, y, z);\r\n let name = curStr.substr(31, 3).trim().toUpperCase();\r\n const type = Element.getByName(name);\r\n if (!this._atomsIndexes[name]) {\r\n this._atomsIndexes[name] = 0;\r\n }\r\n this._atomsIndexes[name] += 1;\r\n name += this._atomsIndexes[name]; // every atom need to have unique name.\r\n\r\n this._residue.addAtom(name, type, xyz, undefined, true, serial, ' ', 1.0, 0.0, charge);\r\n }\r\n }\r\n\r\n _parseBonds(stream, bondsNum) {\r\n let curStr;\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n curStr = stream.getNextString();\r\n let atom1 = parseInt(curStr.substr(0, 3), 10) + this._atomsParsed;\r\n let atom2 = parseInt(curStr.substr(3, 3), 10) + this._atomsParsed;\r\n const bondType = parseInt(curStr.substr(6, 3), 10);\r\n\r\n if (atom1 > atom2) {\r\n [atom1, atom2] = [atom2, atom1];\r\n }\r\n this._complex.addBond(\r\n atom1,\r\n atom2,\r\n orderMap[bondType] || 1,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _parseMOL(stream) {\r\n this._compoundIndx++;\r\n\r\n this._parseHeader(stream);\r\n const countsLine = stream.getStringFromStart(3);\r\n const atomsNum = parseInt(countsLine.substr(0, 3), 10);\r\n const bondsNum = parseInt(countsLine.substr(3, 3), 10);\r\n this._parseAtoms(stream, atomsNum);\r\n this._parseBonds(stream, bondsNum);\r\n\r\n this._atomsParsed += atomsNum;\r\n\r\n this._metadata.molecules[this._compoundIndx]._residues = [];\r\n this._metadata.molecules[this._compoundIndx]._residues.push(this._residue);\r\n }\r\n\r\n _parseDataItem(stream) {\r\n const tag = stream.getCurrentString();\r\n\r\n let data = [];\r\n let curStr = stream.getNextString();\r\n\r\n // read data\r\n while (curStr.trim() !== '') {\r\n data.push(curStr);\r\n curStr = stream.getNextString();\r\n }\r\n if (data.length === 1) {\r\n [data] = data;\r\n }\r\n this._currentMolProps[tag.replace(/[<>]/g, '').trim()] = data;\r\n }\r\n\r\n _parseCompound(stream) {\r\n this._parseMOL(stream);\r\n\r\n // parse data items block\r\n if (this._format === fileFormat.SDF) {\r\n this._currentMolProps = {};\r\n while (stream.findNextDataItem()) {\r\n this._parseDataItem(stream);\r\n }\r\n if (Object.keys(this._currentMolProps).length !== 0) {\r\n const molecule = this._metadata.molecules[this._compoundIndx];\r\n molecule.props = this._currentMolProps;\r\n this._tryToUpdateMoleculeData(molecule);\r\n }\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n if (bond._right < bond._left) {\r\n console.log('_fixBondsArray: Logic error.');\r\n }\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _buildAssemblies() {\r\n const chains = this._complex._chains;\r\n\r\n if (chains.length === 1) {\r\n return this._assemblies;\r\n }\r\n\r\n for (let i = 0; i < chains.length; i++) {\r\n const assembly = new Assembly(this._complex);\r\n const matrix = new THREE.Matrix4();\r\n assembly.addMatrix(matrix);\r\n assembly.addChain(chains[i]._name);\r\n this._assemblies.push(assembly);\r\n }\r\n\r\n return this._assemblies;\r\n }\r\n\r\n _buildMolecules() {\r\n this._complex._molecules = [];\r\n const { molecules } = this._metadata;\r\n for (let i = 0; i < molecules.length; i++) {\r\n const molecule = new Molecule(this._complex, molecules[i].name, i + 1);\r\n molecule.residues = molecules[i]._residues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n\r\n return this._complex._molecules;\r\n }\r\n\r\n _searchTag(tag, props) {\r\n for (let i = 0; i < props.length; i++) {\r\n if ((tag instanceof RegExp && tag.test(props[i].tag)) || tag === props[i].tag) {\r\n return props[i].data;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToFind(tagsList, props) {\r\n for (let j = 0; j < tagsList.length; j++) {\r\n const res = this._searchTag(tagsList[j], props);\r\n if (res) {\r\n return res;\r\n }\r\n }\r\n return undefined;\r\n }\r\n\r\n _tryToUpdateMoleculeData(molecule) {\r\n let res = false;\r\n for (let i = 0; i < tagsNames.length; i++) {\r\n const tagPossibleNames = tags[tagsNames[i]];\r\n const data = this._tryToFind(tagPossibleNames, molecule.props);\r\n if (data) {\r\n molecule[tagsNames[i]] = data;\r\n res = true;\r\n }\r\n }\r\n\r\n molecule.name = molecule.name || molecule.id;\r\n if (molecule.name.match(/^\\d+$/)) {\r\n molecule.name = `CID: ${molecule.name}`;\r\n }\r\n\r\n return res;\r\n }\r\n\r\n _finalizeMetadata() {\r\n const { molecules } = this._metadata;\r\n const { metadata } = this._complex;\r\n const complex = this._complex;\r\n\r\n if (molecules.length === 1) {\r\n complex.name = molecules[0].name;\r\n metadata.title = molecules[0].title;\r\n metadata.date = molecules[0].date;\r\n metadata.properties = molecules[0].props;\r\n } else if (molecules.length > 1) {\r\n metadata.molecules = [];\r\n for (let i = 0; i < molecules.length; i++) {\r\n metadata.molecules.push({\r\n name: molecules[i].name, date: molecules[i].date, title: molecules[i].title, properties: molecules[i].props,\r\n });\r\n }\r\n }\r\n }\r\n\r\n _finalize() {\r\n const serialAtomMap = this._serialAtomMap = {};\r\n const atoms = this._complex._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n serialAtomMap[atom.serial] = atom;\r\n }\r\n\r\n this._complex._finalizeBonds();\r\n this._fixBondsArray();\r\n this._finalizeMetadata();\r\n this._buildAssemblies();\r\n this._complex.units = this._complex.units.concat(this._assemblies);\r\n this._buildMolecules();\r\n this._complex.finalize({\r\n needAutoBonding: false, detectAromaticLoops: false, enableEditing: false, serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n defineFormat(data) {\r\n let format;\r\n if (sdfRegExp.test(data)) {\r\n format = fileFormat.SDF;\r\n } else {\r\n format = fileFormat.MOL;\r\n }\r\n\r\n return format;\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const stream = new SDFStream(this._data);\r\n\r\n this._format = this.defineFormat(this._data);\r\n result.metadata.format = this._format;\r\n\r\n do {\r\n this._parseCompound(stream);\r\n } while (stream.findNextCompoundStart());\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nSDFParser.formats = ['mol', 'sdf'];\r\nSDFParser.extensions = ['.mol', '.sdf'];\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport VolumeModel, { valueType } from './VolumeModel';\r\n\r\n// http://www.uoxray.uoregon.edu/tnt/manual/node104.html\r\nconst DSN6Header = {\r\n nstart: [valueType.array, 'i16', 0],\r\n extent: [valueType.array, 'i16', 3],\r\n grid: [valueType.array, 'i16', 6],\r\n cellDims: [valueType.vector, 'i16', 9],\r\n angles: [valueType.array, 'i16', 12],\r\n div: [valueType.singular, 'i16', 15],\r\n adder: [valueType.singular, 'i16', 16],\r\n scaleFactor: [valueType.singular, 'i16', 17],\r\n};\r\n\r\nclass DSN6Model extends VolumeModel {\r\n _parseHeader(_buffer) {\r\n this._buff = _buffer;\r\n this._typedCheck();\r\n\r\n const arrays = {};\r\n arrays.i16 = new Int16Array(this._buff);\r\n\r\n // check and reverse if big endian\r\n if (arrays.i16[18] !== 100) {\r\n for (let i = 0, n = arrays.i16.length; i < n; ++i) {\r\n const val = arrays.i16[i];\r\n arrays.i16[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff);\r\n }\r\n }\r\n if (arrays.i16[18] !== 100) {\r\n throw new Error('DSN6: Incorrect format ');\r\n }\r\n\r\n const header = this._header;\r\n\r\n this._fillHeader(DSN6Header, arrays);\r\n header.cellDims.multiplyScalar(1.0 / header.scaleFactor);\r\n header.angles.forEach((angle, i, a) => { a[i] *= (Math.PI / 180.0) / header.scaleFactor; });\r\n header.div /= 100;\r\n }\r\n\r\n _setAxisIndices() {\r\n this._xyz2crs[0] = 0;\r\n this._xyz2crs[1] = 1;\r\n this._xyz2crs[2] = 2;\r\n }\r\n\r\n _setOrigins() {\r\n const header = this._header;\r\n const [xaxis, yaxis, zaxis] = this._getAxis();\r\n this._setAxisIndices();\r\n\r\n this._origin.addScaledVector(xaxis, header.nstart[0]);\r\n this._origin.addScaledVector(yaxis, header.nstart[1]);\r\n this._origin.addScaledVector(zaxis, header.nstart[2]);\r\n\r\n xaxis.multiplyScalar(header.extent[0]);\r\n yaxis.multiplyScalar(header.extent[1]);\r\n zaxis.multiplyScalar(header.extent[2]);\r\n\r\n this._setBoxParams(xaxis, yaxis, zaxis);\r\n }\r\n\r\n _pointCalculate(xyzData, byteBuffer, z, y, x, pos, i) {\r\n const header = this._header;\r\n\r\n if (x < header.extent[0] && y < header.extent[1] && z < header.extent[2]) {\r\n const idx = x + header.extent[0] * (y + header.extent[1] * z);\r\n xyzData[idx] = (byteBuffer[pos.counter] - header.adder) / header.div;\r\n ++pos.counter;\r\n } else {\r\n pos.counter += 8 - i;\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n _blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos) {\r\n for (let k = 0; k < 8; ++k) {\r\n const z = 8 * zBlock + k;\r\n for (let j = 0; j < 8; ++j) {\r\n const y = 8 * yBlock + j;\r\n let inRange = true;\r\n let i = 0;\r\n while (inRange && i < 8) {\r\n const x = 8 * xBlock + i;\r\n inRange = this._pointCalculate(xyzData, byteBuffer, z, y, x, pos, i);\r\n i++;\r\n }\r\n }\r\n }\r\n }\r\n\r\n _toXYZData() {\r\n const header = this._header;\r\n const byteBuffer = new Uint8Array(this._buff);\r\n const xyzData = new Float32Array(header.extent[0] * header.extent[1] * header.extent[2]);\r\n\r\n const blocks = new THREE.Vector3(header.extent[0] / 8, header.extent[1] / 8, header.extent[2] / 8);\r\n\r\n const pos = {};\r\n pos.counter = 512;\r\n\r\n for (let zBlock = 0; zBlock < blocks.z; ++zBlock) {\r\n for (let yBlock = 0; yBlock < blocks.y; ++yBlock) {\r\n for (let xBlock = 0; xBlock < blocks.x; ++xBlock) {\r\n this._blockCalculate(xyzData, byteBuffer, zBlock, yBlock, xBlock, pos);\r\n }\r\n }\r\n }\r\n this._calculateInfoParams(xyzData);\r\n return xyzData;\r\n }\r\n\r\n _calculateInfoParams(xyzData) {\r\n this._header.dmean /= xyzData.length;\r\n let dispersion = 0;\r\n let minDensity = xyzData[0];\r\n let maxDensity = xyzData[0];\r\n for (let j = 0; j < xyzData.length; j++) {\r\n dispersion += (this._header.dmean - xyzData[j]) ** 2;\r\n\r\n if (xyzData[j] < minDensity) {\r\n minDensity = xyzData[j];\r\n }\r\n if (xyzData[j] > maxDensity) {\r\n maxDensity = xyzData[j];\r\n }\r\n }\r\n this._header.sd = Math.sqrt(dispersion / xyzData.length);\r\n this._header.dmax = maxDensity;\r\n this._header.dmin = minDensity;\r\n }\r\n}\r\n\r\nclass DSN6Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n this._options.fileType = 'dsn6';\r\n this.model = new DSN6Model();\r\n }\r\n\r\n static canParse(data, options) {\r\n if (!data) {\r\n return false;\r\n }\r\n return data instanceof ArrayBuffer && Parser.checkDataTypeOptions(options, 'dsn6');\r\n }\r\n\r\n static canProbablyParse(_data) {\r\n return false;\r\n }\r\n\r\n parseSync() {\r\n return this.model.parse(this._data);\r\n }\r\n}\r\n\r\nDSN6Parser.formats = ['dsn6'];\r\nDSN6Parser.extensions = ['.dsn6', '.omap'];\r\nDSN6Parser.binary = true;\r\n\r\nexport default DSN6Parser;\r\n","import PDBStream from './PDBStream';\r\n\r\n/**\r\n * Little helper class for GRO Parser usage.\r\n * @extends PDBStream\r\n */\r\nclass GROReader extends PDBStream {\r\n constructor(data) {\r\n super(data);\r\n /** @type Number */\r\n this._next = -1; // End position of line\r\n this.next();\r\n }\r\n\r\n /**\r\n * Getting end of string.\r\n * @returns {Number} Pointer to end of string\r\n */\r\n getNext() {\r\n return this._next;\r\n }\r\n}\r\n\r\nexport default GROReader;\r\n","import * as THREE from 'three';\r\nimport _ from 'lodash';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\nimport GROReader from './GROReader';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Molecule,\r\n} = chem;\r\n\r\n/**\r\n * Gromos87 file format parser.\r\n * @extends Parser\r\n */\r\nclass GROParser extends Parser {\r\n /**\r\n * Create parser for .gro file format\r\n *\r\n * @param {String} data Input file\r\n * @param {String} options Input options (optional field)\r\n */\r\n constructor(data, options) {\r\n super(data, options);\r\n /** @type Date */\r\n this._time = null; // Time in ps, optional field for animations\r\n /** @type Number */\r\n this._numAtoms = null; // Number of atoms in complex\r\n /** @type Number */\r\n this._residueNumber = null; // Number of exact residue\r\n /** @type String */\r\n this._residueName = ''; // Scientific name of exact residue\r\n /** @type String */\r\n this._atomName = ''; // Scientific name of exact atom\r\n /** @type Number */\r\n this._atomNumber = null; // Sorted number of exact atom\r\n /** @type Array */\r\n this._atomPosition = []; // Array which contains x, y, z position of exact atom\r\n /** @type Array */\r\n this._atomVelocity = []; // Array which contains x, y, z velocity of exact atom (optional)\r\n /** @type Complex */\r\n this._complex = null; // Complex structure for unified molecule representation\r\n /** @type Vector3 */\r\n this._molecules = []; // Molecules array\r\n /** @type Molecule */\r\n this._molecule = null; // Single molecule\r\n /** @type String */\r\n this._options.filetype = 'gro'; // Extension of data file.\r\n }\r\n\r\n /**\r\n * General check for possibility of parsing.\r\n * @param {String} data - Input file\r\n * @returns {boolean} true if this file is in ascii, false otherwise\r\n */\r\n canProbablyParse(data) {\r\n return _.isString(this._data) && /^\\s*[^\\n]*\\n\\s*\\d+ *\\n\\s*\\d+[^\\n\\d]{3}\\s*\\w+\\s*\\d+\\s*-?\\d/.test(data);\r\n }\r\n\r\n /**\r\n * Parsing title of molecule complex.\r\n * NOTE: that names are ESTIMATES, there is no strict rules in Gromos87 standard for first line in input file.\r\n * @param {GROReader} line - Line containing title and time.\r\n */\r\n _parseTitle(line) {\r\n const { metadata } = this._complex;\r\n metadata.id = line.readLine().trim();\r\n metadata.name = metadata.id.slice(metadata.id.lastIndexOf('\\\\') + 1, metadata.id.lastIndexOf('.'));\r\n metadata.format = 'gro';\r\n }\r\n\r\n /**\r\n * Parsing line containing number of atoms information.\r\n * @param {GROReader} line - Line containing number of atoms.\r\n */\r\n _parseNumberOfAtoms(line) {\r\n this._numAtoms = line.readInt(0, line.getNext());\r\n if (Number.isNaN(this._numAtoms)) {\r\n throw new Error('Line 2 is not representing atom number. Consider checking input file');\r\n }\r\n }\r\n\r\n /**\r\n * Parsing line containing information about residues, atoms etc. Also information about box vectors.\r\n * Format of atoms MUST (by Gromos87 standard) be this: (note that numbering starts not from 0, but from 1!)\r\n * ResidueNumber[1 - 5] ResidueName[6 - 10] AtomName[11 - 15] AtomNumber[16 - 20] Position[21 - 45] Velocity[46 - 69]\r\n * @param {GROReader} line - Line containing information about atom.\r\n */\r\n _parseAtom(line) {\r\n this._residueNumber = line.readInt(1, 5);\r\n this._residueName = line.readString(6, 10).trim();\r\n this._atomName = line.readString(11, 15).trim();\r\n this._atomNumber = line.readInt(16, 20);\r\n const positionX = line.readFloat(21, 28) * 10;\r\n const positionY = line.readFloat(29, 36) * 10;\r\n const positionZ = line.readFloat(37, 45) * 10;\r\n if (Number.isNaN(positionX) || Number.isNaN(positionY) || Number.isNaN(positionZ)) {\r\n this._complex.error = {\r\n message: `Atom position is invalid in \"${line.readLine()}\"`,\r\n };\r\n return;\r\n }\r\n /* const velocityX = line.readFloat(46, 53);\r\n const velocityY = line.readFloat(54, 61);\r\n const velocityZ = line.readFloat(62, 69); */\r\n /* Adding residue and atom to complex structure */\r\n const type = Element.getByName(this._atomName[0]); /* MAGIC 0. REASONS: This name is something like \"CA\", where\r\n C - is an element an A is something else. But what about Calcium? */\r\n if (type.fullName === 'Unknown') {\r\n this._complex.error = {\r\n message: `${this._atomName[0]} hasn't been recognised as an atom name.`,\r\n };\r\n return;\r\n }\r\n const role = Element.Role[this._atomName];\r\n /* Firstly, create a dummy chain */\r\n let chain = this._chain;\r\n if (!chain) {\r\n this._chain = chain = this._complex.addChain('A');\r\n }\r\n /* Secondly, add residue to that chain */\r\n let residue = this._residue;\r\n if (!residue || residue.getSequence() !== this._residueNumber) {\r\n this._residue = residue = chain.addResidue(this._residueName, this._residueNumber, ' ');\r\n }\r\n /* Lastly, add atom to that residue */\r\n this._atomPosition = new THREE.Vector3(positionX, positionY, positionZ);\r\n /* Adding default constants to correct atom addition process */\r\n const het = true;\r\n const altLoc = ' ';\r\n const occupancy = 1;\r\n const tempFactor = 1;\r\n const charge = 0;\r\n residue.addAtom(this._atomName, type, this._atomPosition, role, het, this._atomNumber, altLoc, occupancy, tempFactor, charge);\r\n }\r\n\r\n /**\r\n * Some finalizing procedures. In '.gro' file format there is only 1 chain and 1 molecule.\r\n */\r\n _finalize() {\r\n const molecule = new Molecule(this._complex, this._complex.metadata.name, 1);\r\n // aggregate residues from chain\r\n molecule.residues = this._chain._residues;\r\n molecule._chains = this._chain;\r\n this._complex._molecules[0] = molecule;\r\n this._molecules.push(molecule);\r\n this._complex.finalize({\r\n needAutoBonding: true,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n /**\r\n * Main parsing procedure.\r\n * @returns {Complex} Complex structure for visualizing.\r\n */\r\n parseSync() {\r\n /* Create \"Complex\" variable */\r\n const result = this._complex = new Complex();\r\n /* Parse input file line-by-line */\r\n const reader = new GROReader(this._data);\r\n let counter = 0; /* Simple counter regarding to format of .gro file */\r\n /* First two lines - technical information, other lines - Atoms */\r\n this._parseTitle(reader);\r\n reader.next();\r\n this._parseNumberOfAtoms(reader);\r\n reader.next();\r\n for (counter = 0; counter < this._numAtoms; ++counter) {\r\n if (!reader.end()) {\r\n this._parseAtom(reader);\r\n reader.next();\r\n } else break;\r\n }\r\n /* If number of atoms in second line is less then actual atoms in file */\r\n if (counter < this._numAtoms) {\r\n this._complex.error = {\r\n message: 'File ended unexpectedly.',\r\n };\r\n }\r\n /* Catch errors occurred in parsing process */\r\n if (result.error) {\r\n throw new Error(result.error.message);\r\n }\r\n\r\n /* Finalizing data */\r\n this._finalize();\r\n\r\n /* Cleaning up */\r\n this._atomPosition = null;\r\n this._complex = null;\r\n this._molecules = null;\r\n this._molecule = null;\r\n\r\n /* Return resulting Complex variable */\r\n return result;\r\n }\r\n}\r\n\r\nGROParser.formats = ['gro'];\r\nGROParser.extensions = ['.gro'];\r\n\r\nexport default GROParser;\r\n","import * as THREE from 'three';\r\nimport Parser from './Parser';\r\nimport chem from '../../chem';\r\n\r\nconst {\r\n Complex,\r\n Element,\r\n Bond,\r\n Molecule,\r\n} = chem;\r\n\r\nconst orderMap = {\r\n un: 0,\r\n 1: 1,\r\n 2: 2,\r\n 3: 3,\r\n ar: 1,\r\n am: 1,\r\n nc: 0,\r\n du: 1,\r\n};\r\nconst typeMap = {\r\n un: Bond.BondType.UNKNOWN, // unknown (cannot be determined from the parameter tables)\r\n 1: Bond.BondType.COVALENT, // single\r\n 2: Bond.BondType.COVALENT, // double\r\n 3: Bond.BondType.COVALENT, // triple\r\n ar: Bond.BondType.AROMATIC, // aromatic\r\n am: Bond.BondType.COVALENT, // amide\r\n nc: Bond.BondType.UNKNOWN, // not connected\r\n du: Bond.BondType.COVALENT, // dummy\r\n};\r\n\r\nconst resNumberRegex = /\\d+$/;\r\nconst spacesRegex = /\\s+/;\r\n\r\nfunction splitToFields(str) {\r\n return str.trim().split(spacesRegex);\r\n}\r\n/* There is no jsdoc documentation because of eslint corrections:\r\n * not all Parser methods are implemented\r\n */\r\n\r\nclass MOL2Parser extends Parser {\r\n constructor(data, options) {\r\n super(data, options);\r\n\r\n this._complex = null;\r\n this._chain = null;\r\n this._residue = null;\r\n this._compoundIndx = -1;\r\n\r\n this._molecules = [];\r\n this._molecule = null;\r\n\r\n this._currPosIdx = 0;\r\n this._currStartIdx = 0;\r\n\r\n this._serialAtomMap = {};\r\n\r\n this._options.fileType = 'mol2';\r\n }\r\n\r\n _parseRawStrings(data) {\r\n return data.split(/\\r?\\n|\\r/);\r\n }\r\n\r\n _toStringFromStart(numb, MOL2Data) {\r\n const newPosIdx = this._currStartIdx + numb;\r\n this._currPosIdx = (newPosIdx < MOL2Data.length) ? newPosIdx : this._currStartIdx;\r\n }\r\n\r\n _toHeaderString(header, MOL2Data) {\r\n this._toStringFromStart(0, MOL2Data);\r\n while (this._currPosIdx < MOL2Data.length) {\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`)) {\r\n return;\r\n }\r\n this._currPosIdx++;\r\n }\r\n this._toStringFromStart(0, MOL2Data);\r\n }\r\n\r\n _toStringFromHeader(header, numb, MOL2Data) {\r\n this._toHeaderString(header, MOL2Data);\r\n const newPosIdx = this._currPosIdx + numb;\r\n\r\n if (MOL2Data[this._currPosIdx].match(`@${header}`) && newPosIdx < MOL2Data.length) {\r\n this._currPosIdx = newPosIdx;\r\n }\r\n }\r\n\r\n _setStart(startPos, MOL2Data) {\r\n if (startPos >= MOL2Data.length) {\r\n this._currStartIdx = this._currPosIdx = MOL2Data.length - 1;\r\n } else {\r\n this._currStartIdx = this._currPosIdx = startPos;\r\n }\r\n }\r\n\r\n _probablyHaveDataToParse(MOL2Data) {\r\n return this._currPosIdx < MOL2Data.length - 2;\r\n }\r\n\r\n _findNextCompoundStart(MOL2Data) {\r\n while (this._currPosIdx < MOL2Data.length && MOL2Data[this._currPosIdx].trim() !== '@MOLECULE>') {\r\n this._currPosIdx++;\r\n }\r\n this._setStart(++this._currPosIdx, MOL2Data);\r\n return this._probablyHaveDataToParse(MOL2Data);\r\n }\r\n\r\n _parseMolecule(MOL2Data) {\r\n this._toHeaderString('MOLECULE', MOL2Data);\r\n\r\n const { metadata } = this._complex;\r\n metadata.name = MOL2Data[++this._currPosIdx];\r\n metadata.format = 'mol2';\r\n\r\n this._molecule = { _index: '', _chains: [] };\r\n this._molecule._index = this._compoundIndx + 1;\r\n this._molecules.push(this._molecule);\r\n }\r\n\r\n /* Atom format description:\r\n * atomId atomName x y z element [resSeq [resName [charge [statusBit]]]]\r\n * statusBits is the internal SYBYL status bits associated with the atom.\r\n * These should never be set by the user.\r\n * Source: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf\r\n */\r\n _parseAtoms(atomsNum, MOL2Data) {\r\n this._toHeaderString('ATOM', MOL2Data);\r\n\r\n for (let i = 0; i < atomsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 6) {\r\n throw new Error('MOL2 parsing error: Not enough information to create atom!');\r\n }\r\n const atomId = parseInt(parsedStr[0], 10);\r\n const atomName = parsedStr[1];\r\n\r\n const x = parseFloat(parsedStr[2]);\r\n const y = parseFloat(parsedStr[3]);\r\n const z = parseFloat(parsedStr[4]);\r\n\r\n const element = parsedStr[5].split('.')[0].toUpperCase();\r\n\r\n let charge = 0;\r\n if (parsedStr.length >= 9) {\r\n charge = parseFloat(parsedStr[8]) || 0.0;\r\n }\r\n\r\n let chain = this._chain;\r\n if (!chain) {\r\n // .mol2 may contain information about multiple molecules, but they can't be visualized\r\n // at the same time now. There is no need to create different chain IDs then.\r\n this._chain = chain = this._complex.getChain('A') || this._complex.addChain('A');\r\n this._residue = null;\r\n }\r\n if (!this._setResidue(parsedStr)) {\r\n continue;\r\n }\r\n\r\n // These fields are not listed in mol2 format. Set them default.\r\n // Atoms and het atoms doesn't differ in .mol2,\r\n // but het atoms have special residues. It can be used in next updates\r\n const het = false;\r\n const altLoc = ' ';\r\n const occupancy = 1.0;\r\n const tempFactor = 0.0;\r\n const type = Element.getByName(element);\r\n const role = Element.Role[atomName];\r\n\r\n const xyz = new THREE.Vector3(x, y, z);\r\n this._residue.addAtom(atomName, type, xyz, role, het, atomId, altLoc, occupancy, tempFactor, charge);\r\n }\r\n }\r\n\r\n _setResidue(parsedStr) {\r\n let resSeq = 1;\r\n let resName = 'UNK'; // The same meaning has '<0>' in some mol2 files\r\n\r\n if (parsedStr.length >= 7) {\r\n resSeq = parseInt(parsedStr[6], 10);\r\n }\r\n if (parsedStr.length >= 8 && parsedStr[7] !== '<0>') {\r\n resName = parsedStr[7].replace(resNumberRegex, '');\r\n }\r\n if (this.settings.now.nowater) {\r\n if (resName === 'HOH' || resName === 'WAT') {\r\n return false;\r\n }\r\n }\r\n const residue = this._residue;\r\n const chain = this._chain;\r\n if (!residue || residue.getSequence() !== resSeq) {\r\n this._residue = chain.addResidue(resName, resSeq, 'A');\r\n }\r\n return true;\r\n }\r\n\r\n /* Bond format description\r\n * bondId originAtomId targetAtomId bondType [statusBits]\r\n */\r\n _parseBonds(bondsNum, MOL2Data) {\r\n this._toHeaderString('BOND', MOL2Data);\r\n\r\n for (let i = 0; i < bondsNum; i++) {\r\n const parsedStr = splitToFields(MOL2Data[++this._currPosIdx]);\r\n\r\n if (parsedStr.length < 3) {\r\n throw new Error('MOL2 parsing error: Missing information about bonds!');\r\n }\r\n\r\n let originAtomId = parseInt(parsedStr[1], 10);\r\n let targetAtomId = parseInt(parsedStr[2], 10);\r\n const bondType = parsedStr[3];\r\n\r\n if (originAtomId > targetAtomId) {\r\n [originAtomId, targetAtomId] = [targetAtomId, originAtomId];\r\n }\r\n this._complex.addBond(\r\n originAtomId,\r\n targetAtomId,\r\n orderMap[bondType] || 0,\r\n typeMap[bondType] || Bond.BondType.UNKNOWN,\r\n true,\r\n );\r\n }\r\n }\r\n\r\n _fixSerialAtoms() {\r\n const atoms = this._complex._atoms;\r\n for (let i = 0; i < atoms.length; i++) {\r\n const atom = atoms[i];\r\n this._serialAtomMap[atom.serial] = atom;\r\n }\r\n }\r\n\r\n _fixBondsArray() {\r\n const serialAtomMap = this._serialAtomMap;\r\n const complex = this._complex;\r\n\r\n if (Object.keys(serialAtomMap).length === 0) {\r\n throw new Error('MOL2 parsing error: Missing atom information!');\r\n }\r\n\r\n const bonds = complex._bonds;\r\n for (let j = 0; j < bonds.length; j++) {\r\n const bond = bonds[j];\r\n bond._left = serialAtomMap[bond._left] || null;\r\n bond._right = serialAtomMap[bond._right] || null;\r\n }\r\n }\r\n\r\n _finalizeMolecules() {\r\n // Get chain from complex\r\n const chain = this._complex._chains[0];\r\n this._complex._molecules = [];\r\n\r\n // Aggregate residues from chains\r\n // (to be precise from the chain 'A')\r\n for (let i = 0; i < this._molecules.length; i++) {\r\n const currMolecule = this._molecules[i];\r\n const molResidues = chain._residues;\r\n const molecule = new Molecule(this._complex, currMolecule._name, i + 1);\r\n molecule.residues = molResidues;\r\n this._complex._molecules[i] = molecule;\r\n }\r\n }\r\n\r\n _finalize() {\r\n this._complex._finalizeBonds();\r\n this._fixSerialAtoms();\r\n this._fixBondsArray();\r\n this._finalizeMolecules();\r\n\r\n this._complex.finalize({\r\n needAutoBonding: false,\r\n detectAromaticLoops: this.settings.now.aromatic,\r\n enableEditing: this.settings.now.editing,\r\n serialAtomMap: this._serialAtomMap,\r\n });\r\n }\r\n\r\n _parseCompound(MOL2Data) {\r\n this._compoundIndx++;\r\n this._parseMolecule(MOL2Data);\r\n\r\n // Ignoring comments and everything before @MOLECULE block\r\n this._toStringFromHeader('MOLECULE', 2, MOL2Data);\r\n\r\n const parsedStr = MOL2Data[this._currPosIdx].trim().split(spacesRegex);\r\n const atomsNum = parsedStr[0];\r\n const bondsNum = parsedStr[1];\r\n\r\n this._parseAtoms(atomsNum, MOL2Data);\r\n this._parseBonds(bondsNum, MOL2Data);\r\n }\r\n\r\n parseSync() {\r\n const result = this._complex = new Complex();\r\n const MOL2Data = this._parseRawStrings(this._data);\r\n do {\r\n this._parseCompound(MOL2Data);\r\n } while (this._findNextCompoundStart(MOL2Data));\r\n\r\n this._finalize();\r\n\r\n return result;\r\n }\r\n}\r\n\r\nMOL2Parser.formats = ['mol2'];\r\nMOL2Parser.extensions = ['.mol2', '.ml2', '.sy2'];\r\n\r\nexport default MOL2Parser;\r\n","import ParserList from './parsers/ParserList';\r\n\r\nimport PDBParser from './parsers/PDBParser';\r\nimport CMLParser from './parsers/CMLParser';\r\nimport MMTFParser from './parsers/MMTFParser';\r\nimport CIFParser from './parsers/CIFParser';\r\nimport CCP4Parser from './parsers/CCP4Parser';\r\nimport XYZParser from './parsers/XYZParser';\r\nimport PubChemParser from './parsers/PubChemParser';\r\nimport SDFParser from './parsers/SDFParser';\r\nimport DSN6Parser from './parsers/DSN6Parser';\r\nimport GROParser from './parsers/GROParser';\r\nimport MOL2Parser from './parsers/MOL2Parser';\r\n\r\nexport default new ParserList([\r\n // note: order might be important\r\n PDBParser,\r\n CIFParser,\r\n MMTFParser,\r\n XYZParser,\r\n CMLParser,\r\n PubChemParser,\r\n SDFParser,\r\n CCP4Parser,\r\n DSN6Parser,\r\n GROParser,\r\n MOL2Parser,\r\n]);\r\n","import EntityList from '../../utils/EntityList';\r\n\r\n/**\r\n * A list of available exporters.\r\n * @extends EntityList\r\n */\r\nclass ExporterList extends EntityList {\r\n /**\r\n * Create a list of exporters.\r\n * The exporters are indexed by supported data formats (`.formats` and\r\n * `.extensions` properties of a Exporter subclass).\r\n * The Exporters can be retrieved later by matching against specs (see {@link ExporterList#find}).\r\n *\r\n * @param {!Array=} someExporters A list of {@link Exporter} subclasses to\r\n * automatically register at creation time.\r\n * @see ExporterList#register\r\n */\r\n constructor(someExporters = []) {\r\n super(someExporters, ['formats']);\r\n }\r\n\r\n /**\r\n * Find a suitable exporter for data.\r\n *\r\n * @param {Object} specs Exporter specifications.\r\n * @param {string=} specs.format Supported data format.\r\n * @param {*=} specs.data Data to export.\r\n */\r\n find(specs) {\r\n let list = [];\r\n if (specs.format) {\r\n list = this._dict.formats[specs.format.toLowerCase()] || [];\r\n }\r\n return [...list];\r\n }\r\n}\r\n\r\nexport default ExporterList;\r\n","import makeContextDependent from '../../utils/makeContextDependent';\r\n\r\nexport default class Exporter {\r\n constructor(source, options) {\r\n this._source = source;\r\n this._options = options || {};\r\n this._abort = false;\r\n }\r\n\r\n exportSync() {\r\n throw new Error('Exporting to this source is not implemented');\r\n }\r\n\r\n export() {\r\n return new Promise((resolve, reject) => {\r\n setTimeout(() => {\r\n try {\r\n if (this._abort) {\r\n return reject(new Error('Export aborted'));\r\n }\r\n return resolve(this.exportSync());\r\n } catch (error) {\r\n return reject(error);\r\n }\r\n });\r\n });\r\n }\r\n\r\n abort() {\r\n this._abort = true;\r\n }\r\n}\r\n\r\nmakeContextDependent(Exporter.prototype);\r\n","import _ from 'lodash';\r\nimport { Matrix4 } from 'three';\r\n\r\nexport default class PDBResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._currentStr = -1;\r\n this._tag = null;\r\n this._fixedNumeration = false;\r\n this._numeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n\r\n getResult() {\r\n this.writeString('\\n', 81, 81);\r\n return this._resultArray.join('');\r\n }\r\n\r\n _currentStrLength() {\r\n const curStr = this._resultArray[this._currentStr];\r\n return curStr ? curStr.length : 0;\r\n }\r\n\r\n // numeration can be number or boolean\r\n // if numeration is number then just put this number to 8-10 pos in string\r\n // if numeration is boolean then increase number for all new strings\r\n newTag(tag, numeration) {\r\n if (!tag) {\r\n this._tag = null;\r\n } else {\r\n this._tag = tag;\r\n }\r\n if (!_.isUndefined(numeration)) {\r\n if (_.isNumber(numeration)) {\r\n this._tagStrNum = numeration;\r\n this._numeration = true;\r\n this._fixedNumeration = true;\r\n } else if (_.isBoolean(numeration)) {\r\n this._tagStrNum = 0;\r\n this._numeration = numeration;\r\n this._fixedNumeration = false;\r\n }\r\n } else {\r\n this._numeration = false;\r\n this._fixedNumeration = false;\r\n this._tagStrNum = 0;\r\n }\r\n }\r\n\r\n newString(tag) {\r\n this.writeString('\\n', 81, 81);\r\n this._currentStr++;\r\n this._resultArray.push('');\r\n\r\n if (tag) {\r\n this.writeString(tag, 1, 6);\r\n } else if (this._tag) {\r\n this.writeString(this._tag, 1, 6);\r\n }\r\n\r\n if (this._numeration) {\r\n if (!this._fixedNumeration) {\r\n this._tagStrNum++;\r\n }\r\n if (this._tagStrNum !== 1) {\r\n this.writeString(this._tagStrNum.toString(), 10, 8);\r\n }\r\n }\r\n }\r\n\r\n writeEntireString(string, maxStrPos, concat) {\r\n if (!maxStrPos) {\r\n maxStrPos = 81;\r\n }\r\n for (let j = 0; j < string.length; j++) {\r\n if (this._currentStrLength() === maxStrPos && j !== string.length - 1) {\r\n this.newString();\r\n if (concat) { // pretty hardcoddy\r\n this.writeString(concat.tag, concat.begin, concat.end);\r\n }\r\n }\r\n if (string[j] === '\\n') {\r\n this.newString();\r\n } else {\r\n this.writeString(string[j]);\r\n }\r\n }\r\n }\r\n\r\n writeString(string, begin, end) {\r\n let curStr = this._resultArray[this._currentStr];\r\n let str;\r\n\r\n const curStrLength = curStr ? curStr.length : 0;\r\n\r\n if (_.isUndefined(string)) {\r\n return;\r\n }\r\n\r\n if (!_.isNumber(begin)) {\r\n begin = curStrLength + 1;\r\n }\r\n\r\n if (!_.isNumber(end)) {\r\n end = curStrLength + string.length;\r\n }\r\n\r\n if (!_.isString(string)) {\r\n str = string.toString();\r\n } else {\r\n str = string;\r\n }\r\n\r\n const finish = begin < end ? end : begin;\r\n const start = begin < end ? begin : end;\r\n\r\n if (str.length > Math.abs(begin - end) + 1) {\r\n str = str.substr(0, Math.abs(begin - end + 1));\r\n }\r\n\r\n // spaces before start of new data\r\n if (start > curStrLength + 1) {\r\n this._resultArray[this._currentStr] += ' '.repeat(start - curStrLength - 1);\r\n } else if (start <= curStrLength) {\r\n const cStr = this._resultArray[this._currentStr];\r\n this._resultArray[this._currentStr] = cStr.slice(0, start - 1);\r\n }\r\n\r\n // if reverse order\r\n // reverse order of end and begin means that user wants to align text right\r\n if (end < begin) {\r\n const len = begin - end + 1;\r\n str = ' '.repeat(len - str.length) + str;\r\n }\r\n\r\n // some hardcode fix for space between string numeration and data\r\n // (see pdb file format description)\r\n if (start === 11 && this._numeration && this._tagStrNum !== 1) {\r\n str = ` ${str}`;\r\n }\r\n\r\n // append new data to string\r\n this._resultArray[this._currentStr] += str;\r\n curStr = this._resultArray[this._currentStr];\r\n\r\n if (finish > curStr.length) {\r\n this._resultArray[this._currentStr] += ' '.repeat(finish - curStr.length);\r\n }\r\n }\r\n\r\n writeBondsArray(bonds, atom) {\r\n const bondsArrays = this._getSubArrays(bonds, 4);\r\n\r\n for (let k = 0; k < bondsArrays.length; k++) {\r\n this.newString();\r\n this.writeString(atom.serial, 11, 7);\r\n\r\n for (let j = 0; j < bondsArrays[k].length; j++) {\r\n const serial = (bondsArrays[k][j]._left.serial === atom.serial)\r\n ? bondsArrays[k][j]._right.serial : bondsArrays[k][j]._left.serial;\r\n\r\n this.writeString(serial, 16 + 5 * j, 12 + 5 * j);\r\n }\r\n }\r\n }\r\n\r\n _getSubArrays(arr, subArraySize) {\r\n const subArrays = [];\r\n for (let i = 0; i < arr.length; i += subArraySize) {\r\n subArrays.push(arr.slice(i, i + subArraySize));\r\n }\r\n return subArrays;\r\n }\r\n\r\n // function for writing matrix in Remark290 and Remark350 tags\r\n // (see pdb file description)\r\n writeMatrix(matrix, matrixIndx, tag) {\r\n for (let j = 0; j < 3; j++) {\r\n this.newString();\r\n this.writeString(tag, 14, 18);\r\n this.writeString((j + 1).toString(), 19, 19);\r\n this.writeString(matrixIndx.toString(), 23, 20);\r\n for (let k = 0; k < 3; k++) {\r\n const numb = parseFloat(matrix.elements[j * 4 + k]).toFixed(6);\r\n this.writeString(numb.toString(), 33 + k * 10, 24 + k * 10);\r\n }\r\n\r\n const numb = parseFloat(matrix.elements[j * 4 + 3]).toFixed(5);\r\n this.writeString(numb.toString(), 68, 55);\r\n }\r\n }\r\n\r\n writeMatrices(matrices, string) {\r\n if (!matrices) {\r\n return;\r\n }\r\n const matrix = new Matrix4();\r\n for (let j = 0; j < matrices.length; j++) {\r\n matrix.copy(matrices[j]).transpose();\r\n this.writeMatrix(matrix, j + 1, string);\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport Complex from '../../chem/Complex';\r\nimport Exporter from './Exporter';\r\nimport PDBResult from './PDBResult';\r\nimport Assembly from '../../chem/Assembly';\r\nimport { typeByPDBHelixClass } from '../../chem/Helix';\r\n\r\nexport default class PDBExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n this._tags = ['HEADER', 'TITLE', 'COMPND', 'REMARK', 'HELIX', 'SHEET', 'ATOM and HETATM', 'CONECT'];\r\n this._result = null;\r\n this._tagExtractors = {\r\n HEADER: this._extractHEADER,\r\n TITLE: this._extractTITLE,\r\n 'ATOM and HETATM': this._extractATOM,\r\n CONECT: this._extractCONECT,\r\n COMPND: this._extractCOMPND,\r\n REMARK: this._extractREMARK,\r\n HELIX: this._extractHELIX,\r\n SHEET: this._extractSHEET,\r\n };\r\n this._stringForRemark350 = 'COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN\\n'\r\n + 'BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE\\n'\r\n + 'MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS\\n'\r\n + 'GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND\\n'\r\n + 'CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.';\r\n\r\n this._stringForRemark290 = 'CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS\\n'\r\n + 'THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM\\n'\r\n + 'RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY\\n'\r\n + 'RELATED MOLECULES.';\r\n }\r\n\r\n exportSync() {\r\n const result = new PDBResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n for (let i = 0; i < this._tags.length; i++) {\r\n const tag = this._tags[i];\r\n const func = this._tagExtractors[tag];\r\n if (_.isFunction(func)) {\r\n func.call(this, result);\r\n }\r\n }\r\n\r\n this._result = result.getResult();\r\n\r\n return this._result;\r\n }\r\n\r\n _extractHEADER(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n result.newTag('HEADER');\r\n result.newString();\r\n if (metadata.classification) {\r\n result.writeString(metadata.classification, 11, 50);\r\n }\r\n if (metadata.date) {\r\n result.writeString(metadata.date, 51, 59);\r\n }\r\n if (metadata.id) {\r\n result.writeString(metadata.id, 63, 66);\r\n }\r\n }\r\n\r\n _extractTITLE(result) {\r\n if (!this._source.metadata) {\r\n return;\r\n }\r\n const { metadata } = this._source;\r\n if (!metadata.title) {\r\n return;\r\n }\r\n result.newTag('TITLE', true);\r\n for (let i = 0; i < metadata.title.length; i++) {\r\n result.newString();\r\n result.writeString(metadata.title[i], 11, 80);\r\n }\r\n }\r\n\r\n _extractCONECT(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n\r\n const atoms = this._source._atoms;\r\n result.newTag('CONECT');\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const fixedBonds = atoms[i].bonds.filter((bond) => bond._fixed);\r\n if (fixedBonds.length !== 0) {\r\n result.writeBondsArray(fixedBonds.reverse(), atoms[i]);\r\n }\r\n }\r\n }\r\n\r\n _extractSHEET(result) {\r\n if (!this._source._sheets) {\r\n return;\r\n }\r\n\r\n result.newTag('SHEET');\r\n\r\n const sheets = this._source._sheets;\r\n for (let i = 0; i < sheets.length; i++) {\r\n if (sheets[i]._strands) {\r\n const strands = sheets[i]._strands;\r\n for (let j = 0; j < strands.length; j++) {\r\n result.newString();\r\n result.writeString(j + 1, 10, 8);\r\n result.writeString(sheets[i]._name, 14, 12);\r\n result.writeString(strands.length, 16, 15);\r\n result.writeString(strands[j].init._type._name, 18, 20);\r\n result.writeString(strands[j].init._chain._name, 22, 22);\r\n result.writeString(strands[j].init._sequence, 26, 23);\r\n result.writeString(strands[j].init._icode, 27, 27);\r\n result.writeString(strands[j].term._type._name, 29, 31);\r\n result.writeString(strands[j].init._chain._name, 33, 33);\r\n result.writeString(strands[j].term._sequence, 37, 34);\r\n result.writeString(strands[j].term._icode, 38, 38);\r\n result.writeString(strands[j].sense, 40, 39);\r\n }\r\n }\r\n }\r\n }\r\n\r\n _extractHELIX(result) {\r\n if (!this._source._helices) {\r\n return;\r\n }\r\n\r\n result.newTag('HELIX');\r\n const helices = this._source._helices;\r\n for (let i = 0; i < helices.length; i++) {\r\n const helix = helices[i];\r\n const helixClass = _.invert(typeByPDBHelixClass);\r\n result.newString();\r\n result.writeString(helix.serial, 10, 8);\r\n result.writeString(helix.name, 14, 12);\r\n result.writeString(helix.init._type._name, 16, 18);\r\n result.writeString(helix.init._chain._name, 20, 20);\r\n result.writeString(helix.init._sequence, 25, 22);\r\n result.writeString(helix.init._icode, 26, 26);\r\n result.writeString(helix.term._type._name, 28, 30);\r\n result.writeString(helix.term._chain._name, 32, 32);\r\n result.writeString(helix.term._sequence, 37, 34);\r\n result.writeString(helix.term._icode, 38, 38);\r\n result.writeString(helixClass[helix.type], 40, 39);\r\n result.writeString(helix.comment, 41, 70);\r\n result.writeString(helix.length, 76, 72);\r\n }\r\n }\r\n\r\n _extractATOM(result) {\r\n if (!this._source._atoms) {\r\n return;\r\n }\r\n const atoms = this._source._atoms;\r\n\r\n for (let i = 0; i < atoms.length; i++) {\r\n const tag = atoms[i].het ? 'HETATM' : 'ATOM';\r\n result.newString(tag);\r\n const startIndx = (atoms[i].element.name.length > 1 || atoms[i].name.length > 3) ? 13 : 14;\r\n result.writeString(atoms[i].serial, 11, 7);\r\n result.writeString(atoms[i].name, startIndx, 16);\r\n result.writeString(String.fromCharCode(atoms[i].location), 17, 17);\r\n result.writeString(atoms[i].residue._type._name, 20, 18);\r\n result.writeString(atoms[i].residue._chain._name, 22, 22);\r\n result.writeString(atoms[i].residue._sequence, 26, 23);\r\n result.writeString(atoms[i].residue._icode, 27, 27);\r\n result.writeString(atoms[i].position.x.toFixed(3), 38, 31);\r\n result.writeString(atoms[i].position.y.toFixed(3), 46, 39);\r\n result.writeString(atoms[i].position.z.toFixed(3), 54, 47);\r\n result.writeString(atoms[i].occupancy.toFixed(2), 60, 55);\r\n result.writeString(atoms[i].temperature.toFixed(2), 66, 61);\r\n result.writeString(atoms[i].element.name, 78, 77);\r\n if (atoms[i].charge) {\r\n result.writeString(atoms[i].charge, 79, 80);\r\n }\r\n }\r\n }\r\n\r\n _extractCOMPND(result) {\r\n if (!this._source._molecules) {\r\n return;\r\n }\r\n const molecules = this._source._molecules;\r\n result.newTag('COMPND', true);\r\n\r\n for (let i = 0; i < molecules.length; i++) {\r\n const chains = this._getMoleculeChains(molecules[i]);\r\n result.newString();\r\n result.writeString(`MOL_ID: ${molecules[i].index};`, 11, 80);\r\n result.newString();\r\n result.writeString(`MOLECULE: ${molecules[i].name};`, 11, 80);\r\n result.newString();\r\n result.writeString('CHAIN: ', 11, 18);\r\n const chainsString = `${chains.join(', ')};`;\r\n result.writeEntireString(chainsString, 81);\r\n }\r\n }\r\n\r\n _extractREMARK(result) {\r\n this._Remark290(result);\r\n this._Remark350(result);\r\n }\r\n\r\n _Remark290(result) {\r\n if (!this._source.symmetry) {\r\n return;\r\n }\r\n\r\n if (this._source.symmetry.length !== 0) {\r\n const matrices = this._source.symmetry;\r\n result.newTag('REMARK', 290);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark290);\r\n result.writeMatrices(matrices, 'SMTRY');\r\n result.newString();\r\n result.newString();\r\n result.writeString('REMARK: NULL', 11, 80);\r\n }\r\n }\r\n\r\n _Remark350(result) {\r\n if (!this._source.units) {\r\n return;\r\n }\r\n const { units } = this._source;\r\n let biomolIndx = 0;\r\n\r\n result.newTag('REMARK', 350);\r\n result.newString();\r\n result.newString();\r\n result.writeEntireString(this._stringForRemark350);\r\n\r\n const assemblies = units.filter((unit) => unit instanceof Assembly);\r\n\r\n for (let i = 0; i < assemblies.length; i++) {\r\n result.newString();\r\n result.newString();\r\n biomolIndx++;\r\n result.writeString(`BIOMOLECULE: ${biomolIndx}`, 11, 80);\r\n const chains = assemblies[i].chains.join(', ');\r\n result.newString();\r\n result.writeString('APPLY THE FOLLOWING TO CHAINS: ');\r\n result.writeEntireString(chains, 69, { tag: 'AND CHAINS: ', begin: 31, end: 42 });\r\n\r\n const { matrices } = assemblies[i];\r\n result.writeMatrices(matrices, 'BIOMT');\r\n }\r\n }\r\n\r\n _getMoleculeChains(molecule) {\r\n function getChainName(residue) {\r\n return residue._chain._name;\r\n }\r\n const chainNames = molecule.residues.map(getChainName);\r\n return chainNames.filter((item, pos) => chainNames.indexOf(item) === pos);\r\n }\r\n}\r\n\r\nPDBExporter.formats = ['pdb'];\r\nPDBExporter.SourceClass = Complex;\r\n","import * as THREE from 'three';\r\n\r\nconst FBX_POS_SIZE = 3;\r\nconst FBX_NORM_SIZE = 3;\r\nconst FBX_COL_SIZE = 4;\r\n\r\nfunction copyFbxPoint3(src, srcIdx, dst, dstIdx) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n}\r\n\r\nfunction copyFbxPoint4(src, srcIdx, dst, dstIdx, value) {\r\n dst[dstIdx] = src[srcIdx];\r\n dst[dstIdx + 1] = src[srcIdx + 1];\r\n dst[dstIdx + 2] = src[srcIdx + 2];\r\n dst[dstIdx + 3] = value;\r\n}\r\n\r\nconst vector4 = new THREE.Vector4();\r\nfunction copyTransformedPoint3(src, srcIdx, dst, dstIdx, opts) {\r\n vector4.set(src[srcIdx], src[srcIdx + 1], src[srcIdx + 2], opts.w);\r\n vector4.applyMatrix4(opts.matrix);\r\n dst[dstIdx] = vector4.x;\r\n dst[dstIdx + 1] = vector4.y;\r\n dst[dstIdx + 2] = vector4.z;\r\n}\r\n\r\nfunction setSubArray(src, dst, count, copyFunctor, functorOpts) {\r\n if ((dst.array.length - dst.start) / dst.stride < count\r\n || (src.array.length - src.start) / src.stride < count) {\r\n return; // we've got no space\r\n }\r\n if (src.stride === dst.stride) { // stride is the same\r\n dst.array.set(src.array, dst.start);\r\n } else {\r\n let idx = dst.start;\r\n let arridx = src.start;\r\n for (let i = 0; i < count; ++i, idx += dst.stride, arridx += src.stride) {\r\n copyFunctor(src.array, arridx, dst.array, idx, functorOpts);\r\n }\r\n }\r\n}\r\n\r\nexport default class FBXModel {\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.lastPos = 0;\r\n this.lastNorm = 0;\r\n this.lastCol = 0;\r\n this.lastIdx = 0;\r\n }\r\n\r\n init(vertsCount, indsCount) {\r\n this.positions = new Float32Array(vertsCount * FBX_POS_SIZE);\r\n this.normals = new Float32Array(vertsCount * FBX_NORM_SIZE);\r\n this.colors = new Float32Array(vertsCount * FBX_COL_SIZE);\r\n this.indices = new Int32Array(indsCount);\r\n }\r\n\r\n setPositions(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.positions,\r\n start: this.lastPos,\r\n stride: FBX_POS_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setTransformedPositions(array, start, count, stride, matrix) {\r\n let idx = this.lastPos;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 1 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_POS_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.positions, idx, opts);\r\n }\r\n this.lastPos += count * FBX_POS_SIZE;\r\n }\r\n\r\n setNormals(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.normals,\r\n start: this.lastNorm,\r\n stride: FBX_NORM_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint3);\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setTransformedNormals(array, start, count, stride, matrix) {\r\n let idx = this.lastNorm;\r\n let arrIdx = start;\r\n const opts = { matrix, w: 0 };\r\n for (let i = 0; i < count; ++i, arrIdx += stride, idx += FBX_NORM_SIZE) {\r\n copyTransformedPoint3(array, arrIdx, this.normals, idx, opts);\r\n }\r\n this.lastNorm += count * FBX_NORM_SIZE;\r\n }\r\n\r\n setColors(array, start, count, stride) {\r\n const src = {\r\n array,\r\n start,\r\n stride,\r\n };\r\n const dst = {\r\n array: this.colors,\r\n start: this.lastCol,\r\n stride: FBX_COL_SIZE,\r\n };\r\n setSubArray(src, dst, count, copyFbxPoint4, 1);\r\n this.lastCol += count * FBX_COL_SIZE;\r\n }\r\n\r\n setIndices(array, start, count) {\r\n this.indices.set(array, this.lastIdx);\r\n this.lastIdx += count;\r\n }\r\n\r\n setShiftedIndices(array, count, shift) {\r\n const shifted = array.map((x) => x + shift);\r\n this.setIndices(shifted, 0, count);\r\n }\r\n\r\n getVerticesNumber() {\r\n return this.lastPos / FBX_POS_SIZE;\r\n }\r\n\r\n addInstance(matrix, geo) {\r\n // add indices at first to take old number of vertices for shift\r\n const currentCount = this.getVerticesNumber();\r\n this.setShiftedIndices(geo.indices, geo.indices.length, currentCount);\r\n // simply write vertices at empty space\r\n const size = geo.itemSize;\r\n this.setTransformedPositions(geo.positions, 0, geo.vertsCount, size.position, matrix);\r\n this.setTransformedNormals(geo.normals, 0, geo.vertsCount, size.normal, matrix);\r\n this.setColors(geo.colors, 0, geo.vertsCount, size.color);\r\n }\r\n}\r\n","/** Base class for fbx geometry contains simply organized attributes: positions+normals+colors, indices. */\r\nexport default class FBXGeometry {\r\n /**\r\n * Create a base geo with necessary members.\r\n */\r\n constructor() {\r\n this.positions = null;\r\n this.normals = null;\r\n this.colors = null;\r\n this.indices = null;\r\n this.vertsCount = 0;\r\n this.itemSize = null;\r\n }\r\n\r\n /**\r\n * Initialize base geo storing items info from attributes.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n const { attributes } = geo;\r\n // save item size\r\n this.itemSize = {\r\n position: attributes.position.itemSize,\r\n normal: attributes.normal.itemSize,\r\n color: attributes.color.itemSize,\r\n };\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes and creates colors filled with defined value.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX1CGeometry extends FBXGeometry {\r\n /**\r\n * Initialize geo storing positions, normals, indices and create colors.\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n */\r\n init(geo, _info) {\r\n super.init(geo, _info);\r\n const {\r\n attributes: {\r\n position,\r\n normal,\r\n },\r\n index,\r\n } = geo;\r\n // copy vertices attributes\r\n this.vertsCount = position.count;\r\n this.positions = position.array;\r\n this.normals = normal.array;\r\n // create color array\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n // indices\r\n this.indices = index.array;\r\n }\r\n\r\n /**\r\n * Set defined color for all items in color attribute\r\n * @param {Object} color - THREE.Color.\r\n */\r\n setColors(color) {\r\n let offset = 0;\r\n for (let i = 0, l = this.colors.length, cl = this.itemSize.color; i < l; i += cl) {\r\n this.colors[offset++] = color.r;\r\n this.colors[offset++] = color.g;\r\n this.colors[offset++] = color.b;\r\n }\r\n }\r\n}\r\n","import FBXGeometry from './FBXGeometry';\r\n\r\n/**\r\n * Fbx geometry, that copies positions+normals, indexes from cylinder geometry and creates colors filled with two\r\n * defined values.\r\n * @extends FBXGeometry\r\n */\r\nexport default class FBX2CCylinder extends FBXGeometry {\r\n constructor() {\r\n super();\r\n this._cutRawStart = 0;\r\n this._cutRawEnd = 0;\r\n this._facesPerSlice = 0;\r\n }\r\n\r\n /**\r\n * Initialize geo by creating new attributes, because we extend number of vertices to make cylinder two-colored.\r\n * Indices remain the same. We process open- end close-ended cylinders and consider cylinders od 2 segments\r\n * in height ONLY.\r\n * NOTE: cylinder consists of 2 height segments and stores parts in the order: tube, topCap, bottomCap\r\n * @param {Object} geo - THREE.BufferGeometry.\r\n * @param {Object} info - information needed for geo extend\r\n */\r\n init(geo, info) {\r\n super.init(geo, info);\r\n const {\r\n attributes: {\r\n position,\r\n },\r\n index,\r\n } = geo;\r\n // extend vertices arrays\r\n this.vertsCount = position.count + info.addPerCylinder;\r\n this._facesPerSlice = info.addPerCylinder;\r\n this.positions = new Float32Array(this.vertsCount * position.itemSize);\r\n this.normals = new Float32Array(this.vertsCount * this.itemSize.normal);\r\n this.colors = new Float32Array(this.vertsCount * this.itemSize.color);\r\n this._extendVertices(geo, info);\r\n // number of indices stays the same\r\n this.indices = new Uint32Array(index.count);\r\n this._extendIndices(geo, info);\r\n }\r\n\r\n /** Extend vertex attributes to have one more slice to make sharp middle startColor-endColor line. */\r\n _extendVertices(geo, info) {\r\n const { position } = geo.attributes;\r\n const { normal } = geo.attributes;\r\n const geoParams = geo.getGeoParams();\r\n const cutRaw = 1; // we expect cylinders of 2 segments in height => so half segment = 1\r\n this._cutRawStart = cutRaw * geoParams.radialSegments;\r\n this._cutRawEnd = this._cutRawStart + info.addPerCylinder;\r\n { // write first half of cylinder\r\n let temp = position.array.slice(0, this._cutRawEnd * position.itemSize);\r\n this.positions.set(temp, 0);\r\n temp = normal.array.slice(0, this._cutRawEnd * normal.itemSize);\r\n this.normals.set(temp, 0);\r\n }\r\n { // write second part of cylinder\r\n let temp = position.array.slice(this._cutRawStart * position.itemSize, position.array.length);\r\n this.positions.set(temp, this._cutRawEnd * position.itemSize);\r\n temp = normal.array.slice(this._cutRawStart * normal.itemSize, normal.array.length);\r\n this.normals.set(temp, this._cutRawEnd * normal.itemSize);\r\n }\r\n }\r\n\r\n /** Shift values of second part (+caps) indices by newly added vertices count. Number of faces remains the same. */\r\n _extendIndices(geo, info) {\r\n const { index } = geo;\r\n const indicesPerQuad = 6; // quad = 2 triangles => 6 indices\r\n const startToShift = info.addPerCylinder * indicesPerQuad;\r\n const shift = info.addPerCylinder;\r\n let shifted = index.array.slice(startToShift, index.count);\r\n shifted = shifted.map((x) => x + shift); // shift only the endings\r\n this.indices.set(index.array, 0);\r\n this.indices.set(shifted, startToShift);\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {number} start - start color index\r\n * @param {number} end - start color index\r\n * @param {array} array - array of colors\r\n * @param {array} color - color value components\r\n */\r\n _setColorRange(start, end, array, color) {\r\n const colorSize = color.length;\r\n for (let i = start; i < end; i += colorSize) {\r\n array.set(color, i);\r\n }\r\n }\r\n\r\n /**\r\n * Set defined colors: (first part + bottom cap), (second part + top cap)\r\n * @param {Object} color1 - THREE.Color.\r\n * @param {Object} color2 - THREE.Color.\r\n */\r\n setColors(color1, color2) {\r\n const colorSize = this.itemSize.color;\r\n const part1End = this._cutRawEnd * colorSize;\r\n const part2End = part1End * 2;\r\n this._setColorRange(0, part1End, this.colors, color1.toArray());\r\n this._setColorRange(part1End, part2End, this.colors, color2.toArray());\r\n if (part2End < this.colors.length) { // cylinder has caps, lets paint them\r\n const capSize = (this._facesPerSlice + 1) * colorSize;\r\n const cap1End = part2End + capSize;\r\n this._setColorRange(part2End, cap1End, this.colors, color2.toArray());\r\n const cap2End = cap1End + capSize; // should be equal to this.colors.length;\r\n this._setColorRange(cap1End, cap2End, this.colors, color1.toArray());\r\n }\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport * as THREE from 'three';\r\n\r\nimport utils from '../../../utils';\r\nimport gfxutils from '../../../gfx/gfxutils';\r\nimport logger from '../../../utils/logger';\r\n\r\nimport FBXModel from './FBXModel';\r\nimport ThickLineMesh from '../../../gfx/meshes/ThickLineMesh';\r\nimport ZSpriteMesh from '../../../gfx/meshes/ZSpriteMesh';\r\nimport InstancedSpheresGeometry from '../../../gfx/geometries/InstancedSpheresGeometry';\r\nimport Instanced2CCylindersGeometry from '../../../gfx/geometries/Instanced2CCylindersGeometry';\r\nimport FBX1CGeometry from './FBX1CGeometry';\r\nimport FBX2CCylinder from './FBX2CCylinder';\r\n\r\nexport default class FBXInfoExtractor {\r\n constructor() {\r\n this._materials = [];\r\n this._models = [];\r\n }\r\n\r\n process(data) {\r\n this._extractModelsAndMaterials(data);\r\n const models = this._flattenModels();\r\n\r\n return {\r\n name: data.name,\r\n models,\r\n materials: this._materials,\r\n };\r\n }\r\n\r\n /**\r\n * Extract fbx object information from ComplexVisual\r\n * @param {object} data - complexVisual to get geometry info from\r\n */\r\n _extractModelsAndMaterials(data) {\r\n const layersOfInterest = new THREE.Layers();\r\n layersOfInterest.set(gfxutils.LAYERS.DEFAULT);\r\n layersOfInterest.enable(gfxutils.LAYERS.TRANSPARENT);\r\n data.traverse((object) => {\r\n if (object instanceof THREE.Mesh && object.layers.test(layersOfInterest) && this.checkExportAbility(object)) {\r\n if (object.geometry.type === 'InstancedBufferGeometry') {\r\n this._collectInstancedGeoInfo(object);\r\n } else {\r\n this._collectGeoInfo(object);\r\n }\r\n }\r\n });\r\n }\r\n\r\n /**\r\n * Reworking indices buffer, see https://banexdevblog.wordpress.com/2014/06/23/a-quick-tutorial-about-the-fbx-ascii-format/\r\n * basically, every triangle in Miew has been represented hat way (e.g.) : 0,1,7, but we must (for FBX) rework that\r\n * into: 0,1,-8.\r\n * @param {array} indices - belongs to [0, maxVertIndex]\r\n */\r\n _reworkIndices(indices) {\r\n const faceSize = 3;\r\n for (let i = faceSize - 1; i < indices.length; i += faceSize) {\r\n indices[i] *= -1;\r\n indices[i]--;\r\n }\r\n }\r\n\r\n /**\r\n * Combine geometry from several models having the same material into one Model and finally prepare indices\r\n * @returns {array} models, combined by material id\r\n */\r\n _flattenModels() {\r\n let overallVertsCount = 0;\r\n function shift(x) {\r\n return x + overallVertsCount;\r\n }\r\n const combined = [];\r\n // flatten models geometry\r\n for (let i = 0, n = this._models.length; i < n; i++) {\r\n const models = this._models[i];\r\n let indices = [];\r\n let positions = [];\r\n let normals = [];\r\n let colors = [];\r\n // reorganize every attributes as array of arrays\r\n overallVertsCount = 0;\r\n for (let j = 0; j < models.length; j++) {\r\n const m = models[j];\r\n indices.push(m.indices.map(shift));\r\n overallVertsCount += m.getVerticesNumber();\r\n positions.push(m.positions);\r\n normals.push(m.normals);\r\n colors.push(m.colors);\r\n }\r\n // join all subarrays into one\r\n indices = utils.mergeTypedArraysUnsafe(indices);\r\n this._reworkIndices(indices);\r\n positions = utils.mergeTypedArraysUnsafe(positions);\r\n normals = utils.mergeTypedArraysUnsafe(normals);\r\n colors = utils.mergeTypedArraysUnsafe(colors);\r\n combined.push({\r\n indices,\r\n positions,\r\n normals,\r\n colors,\r\n verticesCount: overallVertsCount,\r\n });\r\n }\r\n return combined;\r\n }\r\n\r\n /**\r\n * Check ability to export the kind of mesh.\r\n * @param {object} mesh - given mesh to check\r\n * @returns {boolean} result of check\r\n */\r\n checkExportAbility(mesh) {\r\n // check mesh on not being empty\r\n if (mesh.geometry.attributes.position.count === 0) {\r\n return false;\r\n }\r\n // check type of mesh\r\n // if (mesh.geometry.isInstancedBufferGeometry && settings.now.zSprites) {\r\n if (mesh instanceof ZSpriteMesh) {\r\n logger.warn('Currently we cannot export \\'sprites\\' modes, like BS, WV, LC. Please turn of settings \\'zSprites\\' and try again');\r\n return false;\r\n }\r\n if (mesh instanceof ThickLineMesh) {\r\n logger.warn('Currently we cannot export Lines mode');\r\n return false;\r\n }\r\n return true;\r\n }\r\n\r\n /**\r\n * Save geometry info from common mesh, like Surface or Cartoon\r\n */\r\n _collectGeoInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n normal,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const vertCount = position.count;\r\n model.init(vertCount, index.count);\r\n if (matrix.isIdentity()) {\r\n model.setPositions(position.array, 0, vertCount, position.itemSize);\r\n model.setNormals(normal.array, 0, vertCount, normal.itemSize);\r\n } else {\r\n model.setTransformedPositions(position.array, 0, vertCount, position.itemSize, matrix);\r\n model.setTransformedNormals(normal.array, 0, vertCount, normal.itemSize, matrix);\r\n }\r\n model.setColors(color.array, 0, vertCount, color.itemSize);\r\n model.setIndices(index.array, 0, index.count);\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Collect instanced spheres geometry and materials.\r\n * @param {object} mesh - mesh with instanced spheres info\r\n */\r\n _collectSpheresInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount, instCount * indsCount);\r\n const geo = new FBX1CGeometry();\r\n geo.init(mesh.geometry);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const sphereColor = new THREE.Color();\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n sphereColor.fromArray(color.array, colorIdx);\r\n geo.setColors(sphereColor);\r\n // add instance to the model\r\n this._getSphereInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Getting all instanced cylinders from given mesh.\r\n * Divide cylinder (add additional vertexes) for prettiness therefore algorithm is a bit complicated\r\n * @param {object} mesh - given mesh with instanced cylinders\r\n */\r\n _collectCylindersInfo(mesh) {\r\n const {\r\n geometry: {\r\n attributes: {\r\n position,\r\n color,\r\n color2,\r\n },\r\n index,\r\n },\r\n matrix,\r\n } = mesh;\r\n\r\n const model = new FBXModel();\r\n const instCount = mesh.geometry.instanceCount;\r\n const oneCCylinder = new FBX1CGeometry();\r\n oneCCylinder.init(mesh.geometry);\r\n const splittingInfo = this._gatherCylindersColoringInfo(mesh.geometry);\r\n let twoCCylinder = null;\r\n if (splittingInfo.needToSplit > 0) {\r\n twoCCylinder = new FBX2CCylinder();\r\n twoCCylinder.init(mesh.geometry, splittingInfo);\r\n }\r\n const additionalVertsCount = splittingInfo.addPerCylinder * splittingInfo.needToSplit;\r\n const vertCount = position.count;\r\n const indsCount = index.count;\r\n model.init(instCount * vertCount + additionalVertsCount, instCount * indsCount);\r\n const instMatrix = new THREE.Matrix4();\r\n const objMatrix = new THREE.Matrix4();\r\n const colorStart = new THREE.Color();\r\n const colorEnd = new THREE.Color();\r\n let geo = {};\r\n for (let instanceIndex = 0; instanceIndex < instCount; ++instanceIndex) {\r\n // update colors in geometry\r\n const colorIdx = instanceIndex * color.itemSize;\r\n if (splittingInfo.is2Colored[instanceIndex]) {\r\n // .color2 contains starting color, and .color contains starting color (see uber.frag ATTR_COLOR2)\r\n colorStart.fromArray(color2.array, colorIdx);\r\n colorEnd.fromArray(color.array, colorIdx);\r\n if (twoCCylinder) {\r\n twoCCylinder.setColors(colorStart, colorEnd);\r\n geo = twoCCylinder;\r\n }\r\n } else {\r\n // has one color per cylinder\r\n colorStart.fromArray(color.array, colorIdx);\r\n oneCCylinder.setColors(colorStart);\r\n geo = oneCCylinder;\r\n }\r\n // add instance to the model\r\n this._getCylinderInstanceMatrix(mesh.geometry, instanceIndex, instMatrix);\r\n objMatrix.multiplyMatrices(matrix, instMatrix);\r\n model.addInstance(objMatrix, geo);\r\n }\r\n const material = this._collectMaterialInfo(mesh);\r\n this._addToPool(model, material);\r\n }\r\n\r\n /**\r\n * Adding model to pool of models or extend existing ones\r\n * @param {object} model - model to add\r\n * @param {object} material - material to add\r\n */\r\n _addToPool(model, material) {\r\n const materialIdx = this._checkExistingMaterial(material);\r\n if (materialIdx < 0) { // new model-material pair\r\n this._models.push([model]);\r\n this._materials.push(material);\r\n } else { // add model to existing model-material pair\r\n const models = this._models[materialIdx];\r\n models.push(model);\r\n }\r\n }\r\n\r\n /**\r\n * Checking if given material already was registered in materials pool (no need to create new one)\r\n * @param {object} material - given material\r\n * @returns {number} number of model-material pair\r\n */\r\n _checkExistingMaterial(material) {\r\n return _.findIndex(this._materials, (m) => _.isEqual(m, material));\r\n }\r\n\r\n _gatherCylindersColoringInfo(geo) {\r\n const instCount = geo.instanceCount;\r\n const color1 = geo.attributes.color.array;\r\n const color2 = geo.attributes.color2.array;\r\n const stride = geo.attributes.color.itemSize;\r\n const is2Colored = new Array(instCount);\r\n // analyze color instance attributes\r\n let needToSplit = 0;\r\n let colIdx = 0;\r\n for (let i = 0; i < instCount; i++, colIdx += stride) {\r\n const differs = (Math.abs(color1[colIdx] - color2[colIdx]) > 0.0000001) // compare ending colors\r\n || (Math.abs(color1[colIdx + 1] - color2[colIdx + 1]) > 0.0000001)\r\n || (Math.abs(color1[colIdx + 2] - color2[colIdx + 2]) > 0.0000001);\r\n is2Colored[i] = differs;\r\n needToSplit += differs; // count number of 2-colored cylinders\r\n }\r\n // calc number of vertices to add into 2-colored\r\n const geoParams = geo.getGeoParams();\r\n const addPerCylinder = geoParams.radialSegments;\r\n return { is2Colored, needToSplit, addPerCylinder };\r\n }\r\n\r\n /**\r\n * Collect instanced models and materials.\r\n * @param {object} mesh - given mesh with instanced something (spheres or cylinders)\r\n */\r\n _collectInstancedGeoInfo(mesh) {\r\n if (mesh.geometry instanceof InstancedSpheresGeometry) {\r\n this._collectSpheresInfo(mesh);\r\n } else if (mesh.geometry instanceof Instanced2CCylindersGeometry) {\r\n this._collectCylindersInfo(mesh);\r\n }\r\n }\r\n\r\n /**\r\n * Collect Material info from given mesh.\r\n * @param {object} mesh - given mesh with material info\r\n * @returns {object} material\r\n */\r\n _collectMaterialInfo(mesh) {\r\n const { uberOptions } = mesh.material;\r\n return ({\r\n diffuse: uberOptions.diffuse.toArray(),\r\n opacity: uberOptions.opacity,\r\n shininess: uberOptions.shininess,\r\n specular: uberOptions.specular.toArray(),\r\n });\r\n }\r\n\r\n _getCylinderInstanceMatrix(geo, instIdx, matrix) {\r\n const matVector1 = geo.attributes.matVector1.array;\r\n const matVector2 = geo.attributes.matVector2.array;\r\n const matVector3 = geo.attributes.matVector3.array;\r\n const idxOffset = instIdx * 4; // used 4 because offset arrays are stored in quads\r\n matrix.set(\r\n matVector1[idxOffset],\r\n matVector1[idxOffset + 1],\r\n matVector1[idxOffset + 2],\r\n matVector1[idxOffset + 3],\r\n matVector2[idxOffset],\r\n matVector2[idxOffset + 1],\r\n matVector2[idxOffset + 2],\r\n matVector2[idxOffset + 3],\r\n matVector3[idxOffset],\r\n matVector3[idxOffset + 1],\r\n matVector3[idxOffset + 2],\r\n matVector3[idxOffset + 3],\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n\r\n _getSphereInstanceMatrix(geo, instIdx, matrix) {\r\n const { offset } = geo.attributes;\r\n const idx = instIdx * offset.itemSize;\r\n const x = offset.array[idx];\r\n const y = offset.array[idx + 1];\r\n const z = offset.array[idx + 2];\r\n const scale = offset.array[idx + 3];\r\n matrix.set(\r\n scale,\r\n 0,\r\n 0,\r\n x,\r\n 0,\r\n scale,\r\n 0,\r\n y,\r\n 0,\r\n 0,\r\n scale,\r\n z,\r\n 0,\r\n 0,\r\n 0,\r\n 1,\r\n );\r\n }\r\n}\r\n","// Forming default definitions block\r\nconst defaultDefinitions = `\r\nDefinitions: {\r\n Version: 100\r\n Count: 3\r\n ObjectType: \"Model\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Geometry\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Material\" {\r\n Count: 1\r\n }\r\n ObjectType: \"Pose\" {\r\n Count: 1\r\n }\r\n ObjectType: \"GlobalSettings\" {\r\n Count: 1\r\n }\r\n} `;\r\n\r\n// Default model properties\r\nconst defaultProperties = `Properties60: {\r\n Property: \"QuaternionInterpolate\", \"bool\", \"\",0\r\n Property: \"Visibility\", \"Visibility\", \"A\",1\r\n Property: \"Lcl Translation\", \"Lcl Translation\", \"A\",0.000000000000000,0.000000000000000,-1789.238037109375000\r\n Property: \"Lcl Rotation\", \"Lcl Rotation\", \"A\",0.000009334667643,-0.000000000000000,0.000000000000000\r\n Property: \"Lcl Scaling\", \"Lcl Scaling\", \"A\",1.000000000000000,1.000000000000000,1.000000000000000\r\n Property: \"RotationOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingOffset\", \"Vector3D\", \"\",0,0,0\r\n Property: \"ScalingPivot\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationActive\", \"bool\", \"\",0\r\n Property: \"TranslationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TranslationMinX\", \"bool\", \"\",0\r\n Property: \"TranslationMinY\", \"bool\", \"\",0\r\n Property: \"TranslationMinZ\", \"bool\", \"\",0\r\n Property: \"TranslationMaxX\", \"bool\", \"\",0\r\n Property: \"TranslationMaxY\", \"bool\", \"\",0\r\n Property: \"TranslationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationOrder\", \"enum\", \"\",0\r\n Property: \"RotationSpaceForLimitOnly\", \"bool\", \"\",0\r\n Property: \"AxisLen\", \"double\", \"\",10\r\n Property: \"PreRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"PostRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationActive\", \"bool\", \"\",0\r\n Property: \"RotationMin\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMax\", \"Vector3D\", \"\",0,0,0\r\n Property: \"RotationMinX\", \"bool\", \"\",0\r\n Property: \"RotationMinY\", \"bool\", \"\",0\r\n Property: \"RotationMinZ\", \"bool\", \"\",0\r\n Property: \"RotationMaxX\", \"bool\", \"\",0\r\n Property: \"RotationMaxY\", \"bool\", \"\",0\r\n Property: \"RotationMaxZ\", \"bool\", \"\",0\r\n Property: \"RotationStiffnessX\", \"double\", \"\",0\r\n Property: \"RotationStiffnessY\", \"double\", \"\",0\r\n Property: \"RotationStiffnessZ\", \"double\", \"\",0\r\n Property: \"MinDampRangeX\", \"double\", \"\",0\r\n Property: \"MinDampRangeY\", \"double\", \"\",0\r\n Property: \"MinDampRangeZ\", \"double\", \"\",0\r\n Property: \"MaxDampRangeX\", \"double\", \"\",0\r\n Property: \"MaxDampRangeY\", \"double\", \"\",0\r\n Property: \"MaxDampRangeZ\", \"double\", \"\",0\r\n Property: \"MinDampStrengthX\", \"double\", \"\",0\r\n Property: \"MinDampStrengthY\", \"double\", \"\",0\r\n Property: \"MinDampStrengthZ\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthX\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthY\", \"double\", \"\",0\r\n Property: \"MaxDampStrengthZ\", \"double\", \"\",0\r\n Property: \"PreferedAngleX\", \"double\", \"\",0\r\n Property: \"PreferedAngleY\", \"double\", \"\",0\r\n Property: \"PreferedAngleZ\", \"double\", \"\",0\r\n Property: \"InheritType\", \"enum\", \"\",0\r\n Property: \"ScalingActive\", \"bool\", \"\",0\r\n Property: \"ScalingMin\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMax\", \"Vector3D\", \"\",1,1,1\r\n Property: \"ScalingMinX\", \"bool\", \"\",0\r\n Property: \"ScalingMinY\", \"bool\", \"\",0\r\n Property: \"ScalingMinZ\", \"bool\", \"\",0\r\n Property: \"ScalingMaxX\", \"bool\", \"\",0\r\n Property: \"ScalingMaxY\", \"bool\", \"\",0\r\n Property: \"ScalingMaxZ\", \"bool\", \"\",0\r\n Property: \"GeometricTranslation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricRotation\", \"Vector3D\", \"\",0,0,0\r\n Property: \"GeometricScaling\", \"Vector3D\", \"\",1,1,1\r\n Property: \"LookAtProperty\", \"object\", \"\"\r\n Property: \"UpVectorProperty\", \"object\", \"\"\r\n Property: \"Show\", \"bool\", \"\",1\r\n Property: \"NegativePercentShapeSupport\", \"bool\", \"\",1\r\n Property: \"DefaultAttributeIndex\", \"int\", \"\",0\r\n Property: \"Color\", \"Color\", \"A+\",0,0,0\r\n Property: \"Size\", \"double\", \"\",100\r\n Property: \"Look\", \"enum\", \"\",1\r\n }`;\r\n\r\n// Default materials layer\r\nconst defaultMaterialLayer = `\r\n LayerElementMaterial: 0 {\r\n Version: 101\r\n Name: \"\"\r\n MappingInformationType: \"AllSame\"\r\n ReferenceInformationType: \"Direct\"\r\n Materials: 0\r\n }`;\r\n\r\n// Default layers block\r\nconst defaultLayerBlock = `\r\n Layer: 0 {\r\n Version: 100\r\n LayerElement: {\r\n Type: \"LayerElementNormal\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementColor\"\r\n TypedIndex: 0\r\n }\r\n LayerElement: {\r\n Type: \"LayerElementMaterial\"\r\n TypedIndex: 0\r\n }\r\n }`;\r\n\r\n/**\r\n * globalSettings info in output file.\r\n */\r\nconst globalSettings = `GlobalSettings: {\r\n Version: 1000\r\n Properties60: {\r\n Property: \"UpAxis\", \"int\", \"\",1\r\n Property: \"UpAxisSign\", \"int\", \"\",1\r\n Property: \"FrontAxis\", \"int\", \"\",2\r\n Property: \"FrontAxisSign\", \"int\", \"\",1\r\n Property: \"CoordAxis\", \"int\", \"\",0\r\n Property: \"CoordAxisSign\", \"int\", \"\",1\r\n Property: \"UnitScaleFactor\", \"double\", \"\",1\r\n }\r\n }`;\r\n\r\nexport default class FBXResult {\r\n constructor() {\r\n this._resultArray = [];\r\n this._info = null;\r\n }\r\n\r\n getResult(info) {\r\n this._info = info;\r\n this._resultArray.push(this._writeHeader());\r\n this._resultArray.push(this._writeDefinitions());\r\n this._resultArray.push(this._writeObjects(info.models, info.materials));\r\n this._resultArray.push(this._writeRelations());\r\n this._resultArray.push(this._writeConnections()); // connections between models and materials)\r\n this._info = null;\r\n return this._resultArray.join('');\r\n }\r\n\r\n /**\r\n * Add FBXHeader info to output file.\r\n * Some fields are really confusing, but it seems that all listed fields are very informative\r\n */\r\n _writeHeader() {\r\n const FBXHeaderVersion = 1003; // 1003 is some number which appears to present in many 6.1 ASCII files\r\n const FBXVersion = 6100; // Mandatory and only supported version\r\n const date = new Date();\r\n const timeStampVersion = 1000;\r\n const creator = `Miew FBX Exporter v${this._info.version}`; // Supposed to be an engine\r\n\r\n return `; FBX 6.1.0 project file\r\n; Created by ${creator} Copyright (c) 2015-2026 EPAM Systems, Inc.\r\n; For support please contact miew@epam.com\r\n; ----------------------------------------------------\r\n\r\nFBXHeaderExtension: {\r\n FBXHeaderVersion: ${FBXHeaderVersion}\r\n FBXVersion: ${FBXVersion}\r\n CreationTimeStamp: {\r\n Version: ${timeStampVersion}\r\n Year: ${date.getFullYear()}\r\n Month: ${date.getMonth() + 1}\r\n Day: ${date.getDate()}\r\n Hour: ${date.getHours()}\r\n Minute: ${date.getMinutes()}\r\n Second: ${date.getSeconds()}\r\n Millisecond: ${date.getMilliseconds()}\r\n }\r\n Creator: \"${creator}\"\r\n OtherFlags: {\r\n FlagPLE: 0\r\n }\r\n}\r\nCreationTime: \"${date}\"\r\nCreator: \"${creator}\"\r\n`;\r\n }\r\n\r\n /**\r\n * Add Definitions info to output file.\r\n * Not exactly sure if this section is template section (as it is in 7.4+) or it should every time be like this\r\n */\r\n _writeDefinitions() {\r\n return `\r\n; Object definitions\r\n;------------------------------------------------------------------\r\n\r\n${defaultDefinitions}\r\n`;\r\n }\r\n\r\n /**\r\n * Adding gathered information about Models to resulting string.\r\n * Reminder - there may be more then 1 model in scene, but we must place materials after ALL models.\r\n * @returns {string} string containing all models (vertices, indices, colors, normals etc)\r\n */\r\n _models() {\r\n const modelVersion = 232;\r\n let allModels = '';\r\n const { models } = this._info;\r\n for (let i = 0; i < models.length; ++i) {\r\n const model = models[i];\r\n const vertCount = model.verticesCount;\r\n allModels += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n Version: ${modelVersion}\r\n ${defaultProperties}\r\n ${this._verticesIndices(model.positions, model.indices)}\r\n ${this._normalLayer(model.normals)}\r\n ${this._colorLayer(model.colors, vertCount)}\r\n ${defaultMaterialLayer}\r\n ${defaultLayerBlock}\r\n }`;\r\n }\r\n return allModels;\r\n }\r\n\r\n /**\r\n * Add Material info to result\r\n */\r\n _materials() {\r\n const materialVersion = 102;\r\n let allMaterials = '';\r\n const { materials } = this._info;\r\n for (let i = 0; i < materials.length; ++i) {\r\n const material = materials[i];\r\n allMaterials += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n Version: ${materialVersion}\r\n ShadingModel: \"lambert\"\r\n MultiLayer: 0\r\n ${this._materialProperties(material)}\r\n }`;\r\n }\r\n return allMaterials;\r\n }\r\n\r\n /**\r\n * Add Objects info to output file.\r\n */\r\n _writeObjects() {\r\n return `\r\n; Object properties\r\n;------------------------------------------------------------------\r\n\r\nObjects: {\r\n ${this._models()}\r\n ${this._materials()}\r\n ${globalSettings}\r\n}\r\n`;\r\n }\r\n\r\n /**\r\n * Add Relations info to output file.\r\n */\r\n _writeRelations() {\r\n let modelsList = '';\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Model: \"Model::${this._info.name}_${i}\", \"Mesh\" {\r\n }`;\r\n }\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Material: \"Material::${this._info.name}_${i}_default\", \"\" {\r\n }`;\r\n }\r\n\r\n return `\r\n; Object relations\r\n;------------------------------------------------------------------\r\n\r\nRelations: {\r\n ${modelsList}\r\n Model: \"Model::Producer Perspective\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Top\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Bottom\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Front\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Back\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Right\", \"Camera\" {\r\n }\r\n Model: \"Model::Producer Left\", \"Camera\" {\r\n }\r\n Model: \"Model::Camera Switcher\", \"CameraSwitcher\" {\r\n }\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Add Connections info to output file.\r\n */\r\n _writeConnections() {\r\n let modelsList = '';\r\n const { name } = this._info;\r\n for (let i = 0; i < this._info.models.length; ++i) {\r\n modelsList += `\r\n Connect: \"OO\", \"Model::${name}_${i}\", \"Model::Scene\"`;\r\n }\r\n\r\n let materialList = '';\r\n for (let i = 0; i < this._info.materials.length; ++i) {\r\n materialList += `\r\n Connect: \"OO\", \"Material::${name}_${i}_default\", \"Model::${name}_${i}\"`;\r\n }\r\n\r\n return `\r\n; Object connections\r\n;------------------------------------------------------------------\r\n\r\nConnections: {\r\n ${modelsList}\r\n ${materialList}\r\n}`;\r\n }\r\n\r\n /**\r\n * Write float array to string with limited precision\r\n * @param {Float32Array} array - array to be fixed\r\n * @returns {String} String with fixed floats\r\n */\r\n _floatArrayToString(array) {\r\n const str = [];\r\n for (let i = 0; i < array.length; ++i) {\r\n str[i] = array[i].toFixed(6);\r\n }\r\n return str.join(',');\r\n }\r\n\r\n /**\r\n * Adding color layer to resulting file\r\n * @param {Float32Array} colorArray attribute\r\n * @param {number} vertCount - number of vertices in the model\r\n * @returns {string} color layer info\r\n */\r\n _colorLayer(colorArray, vertCount) {\r\n const layerElementColorNumber = 0;\r\n const layerElementColorVersion = 101;\r\n const layerElementColorName = '';\r\n const colorsStr = this._floatArrayToString(colorArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n // As said [..Array(...)] - fastest and easiest way to produce [0, 1, .....] array\r\n const colorIndices = [...Array(vertCount).keys()];\r\n return `\r\n LayerElementColor: ${layerElementColorNumber} {\r\n Version: ${layerElementColorVersion}\r\n Name: \"${layerElementColorName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Colors: ${colorsStr}\r\n ColorIndex: ${colorIndices}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding normal layer to resulting file\r\n * @param {Float32Array} normalArray attribute\r\n * @returns {string} normal layer info\r\n */\r\n _normalLayer(normalArray) {\r\n const layerElementNormalNumber = 0;\r\n const layerElementNormalVersion = 101;\r\n const layerElementNormalName = '';\r\n const normalsStr = this._floatArrayToString(normalArray);\r\n // Mapping Information type and Reference Information type are mandatory for our Miew! Must not be changed\r\n return `\r\n LayerElementNormal: ${layerElementNormalNumber} {\r\n Version: ${layerElementNormalVersion}\r\n Name: \"${layerElementNormalName}\"\r\n MappingInformationType: \"ByVertice\"\r\n ReferenceInformationType: \"Direct\"\r\n Normals: ${normalsStr}\r\n }`;\r\n }\r\n\r\n /**\r\n * Adding vertices and indices to resulting string\r\n * @return {string} resulting string in FBX notation\r\n */\r\n _verticesIndices(positions, indices) {\r\n const multiLayer = 0;\r\n const multiTake = 1;\r\n const shading = 'Y';\r\n const culling = 'CullingOff';\r\n const geometryVersion = 124;\r\n const vertStr = this._floatArrayToString(positions);\r\n /* About _correctArrayNotation: Float32Arrays will contains only Float32 numbers, which implies that it will be floating points with 17 numbers after point.\r\n * We cannot (and it's logically incorrect) save all this information, so we convert this Float32Array into Array-like object with numbers with only 6 numbers after point\r\n * Reminder - this is big memory loss (as we must save at one moment two arrays with similar information) */\r\n return `MultiLayer: ${multiLayer}\r\n MultiTake: ${multiTake}\r\n Shading: ${shading}\r\n Culling: \"${culling}\"\r\n Vertices: ${vertStr}\r\n PolygonVertexIndex: ${indices}\r\n GeometryVersion: ${geometryVersion}`;\r\n }\r\n\r\n /**\r\n * Forming material properties block.\r\n * @param {Object} material - given material of model\r\n * @returns {String} material properties string\r\n */\r\n _materialProperties(material) {\r\n return `Properties60: {\r\n Property: \"ShadingModel\", \"KString\", \"\", \"Lambert\"\r\n Property: \"MultiLayer\", \"bool\", \"\",0\r\n Property: \"EmissiveColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"EmissiveFactor\", \"double\", \"\",0.0000\r\n Property: \"AmbientColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"AmbientFactor\", \"double\", \"\",0.0000\r\n Property: \"DiffuseColor\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"DiffuseFactor\", \"double\", \"\",1.0000\r\n Property: \"Bump\", \"Vector3D\", \"\",0,0,0\r\n Property: \"TransparentColor\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"TransparencyFactor\", \"double\", \"\",0.0000\r\n Property: \"SpecularColor\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"SpecularFactor\", \"double\", \"\",1.0000\r\n Property: \"ShininessExponent\", \"double\", \"\",${material.shininess}\r\n Property: \"ReflectionColor\", \"ColorRGB\", \"\",0,0,0\r\n Property: \"ReflectionFactor\", \"double\", \"\",1\r\n Property: \"Ambient\", \"ColorRGB\", \"\",1,1,1\r\n Property: \"Diffuse\", \"ColorRGB\", \"\",${material.diffuse}\r\n Property: \"Specular\", \"ColorRGB\", \"\",${material.specular}\r\n Property: \"Shininess\", \"double\", \"\",${material.shininess}\r\n Property: \"Opacity\", \"double\", \"\",${material.opacity}\r\n Property: \"Reflectivity\", \"double\", \"\",0\r\n }`;\r\n }\r\n}\r\n","import Exporter from './Exporter';\r\nimport FBXInfoExtractor from './fbx/FBXInfoExtractor';\r\nimport FBXResult from './fbx/FBXResult';\r\nimport ComplexVisual from '../../ComplexVisual';\r\n\r\nexport default class FBXExporter extends Exporter {\r\n constructor(source, options) {\r\n super(source, options);\r\n // Data\r\n this._data = source;\r\n this._version = options.miewVersion || '0.0-UNSPECIFIED';\r\n this._extractor = new FBXInfoExtractor();\r\n }\r\n\r\n /**\r\n * Entry point to exporter.\r\n */\r\n exportSync() {\r\n // Creating mandatory blocks\r\n const result = new FBXResult();\r\n if (!this._source) {\r\n return this._result;\r\n }\r\n\r\n const info = this._extractor.process(this._data);\r\n info.version = this._version;\r\n this._result = result.getResult(info);\r\n return this._result;\r\n }\r\n}\r\n\r\nFBXExporter.formats = ['fbx'];\r\nFBXExporter.SourceClass = ComplexVisual;\r\n","import ExporterList from './exporters/ExporterList';\r\n\r\nimport PDBExporter from './exporters/PDBExporter';\r\nimport FBXExporter from './exporters/FBXExporter';\r\n\r\nexport default new ExporterList([\r\n PDBExporter,\r\n FBXExporter,\r\n]);\r\n","import loaders from './loaders';\r\nimport parsers from './parsers';\r\nimport exporters from './exporters';\r\n\r\nexport default {\r\n loaders,\r\n parsers,\r\n exporters,\r\n};\r\n","/**\r\n * @author mrdoob / http://mrdoob.com/\r\n */\r\n\r\nimport * as THREE from 'three';\r\nimport CSS2DObject from './CSS2DObject';\r\n\r\nconst tempColor = new THREE.Color();\r\n\r\nclass CSS2DRenderer {\r\n constructor() {\r\n this._width = 0;\r\n this._height = 0;\r\n this._widthHalf = 0;\r\n this._heightHalf = 0;\r\n\r\n this._vector = new THREE.Vector3();\r\n this._viewMatrix = new THREE.Matrix4();\r\n this._projectionMatrix = new THREE.Matrix4();\r\n\r\n this._domElement = document.createElement('div');\r\n this._domElement.style.overflow = 'hidden';\r\n this._domElement.style.position = 'absolute';\r\n this._domElement.style.top = '0';\r\n this._domElement.style.zIndex = '0'; // start a new Stacking Context to enclose all z-ordered children\r\n this._domElement.style.pointerEvents = 'none';\r\n }\r\n\r\n getElement() {\r\n return this._domElement;\r\n }\r\n\r\n reset() {\r\n const myNode = this.getElement();\r\n while (myNode.firstChild) {\r\n myNode.removeChild(myNode.firstChild);\r\n }\r\n }\r\n\r\n setSize(width, height) {\r\n this._width = width;\r\n this._height = height;\r\n\r\n this._widthHalf = this._width / 2;\r\n this._heightHalf = this._height / 2;\r\n\r\n this._domElement.style.width = `${width}px`;\r\n this._domElement.style.height = `${height}px`;\r\n }\r\n\r\n _renderObject(object, camera, scene) {\r\n function lerpColorAsHex(a, b, t) {\r\n tempColor.setHex(a);\r\n tempColor.lerp(b, t);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n function colorAsHex(a) {\r\n tempColor.setHex(a);\r\n return `#${tempColor.getHexString()}`;\r\n }\r\n\r\n if (object instanceof CSS2DObject) {\r\n this._vector.setFromMatrixPosition(object.matrixWorld);\r\n\r\n if (object.userData !== undefined && object.userData.offset !== undefined) {\r\n const localOffset = new THREE.Vector3(object.userData.offset.x, object.userData.offset.y, 0);\r\n this._vector.add(localOffset.multiplyScalar(object.matrixWorld.getMaxScaleOnAxis()));\r\n }\r\n\r\n this._vector.applyMatrix4(this._viewMatrix);\r\n\r\n const visibility = this._vector.z > -camera.near ? 'hidden' : 'visible';\r\n const zIndex = 10000 * (camera.far - (-this._vector.z)) / (camera.far - camera.near);\r\n\r\n const element = object.getElement();\r\n if (typeof scene.fog === 'undefined') {\r\n element.style.color = colorAsHex(object.userData.color);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = colorAsHex(object.userData.background);\r\n }\r\n } else {\r\n const fogFactor = THREE.MathUtils.smoothstep(-this._vector.z, scene.fog.near, scene.fog.far);\r\n element.style.color = lerpColorAsHex(object.userData.color, scene.fog.color, fogFactor);\r\n if (object.userData.background !== 'transparent') {\r\n element.style.background = lerpColorAsHex(object.userData.background, scene.fog.color, fogFactor);\r\n }\r\n }\r\n\r\n this._vector.applyMatrix4(this._projectionMatrix);\r\n\r\n const style = `${object.userData !== {} ? object.userData.translation : 'translate(-50%, -50%) '\r\n }translate(${this._vector.x * this._widthHalf + this._widthHalf}px,${\r\n -this._vector.y * this._heightHalf + this._heightHalf}px)`;\r\n element.style.visibility = visibility;\r\n element.style.WebkitTransform = style;\r\n element.style.MozTransform = style;\r\n element.style.oTransform = style;\r\n element.style.transform = style;\r\n element.style.zIndex = Number(zIndex).toFixed(0);\r\n\r\n if (element.parentNode !== this._domElement) {\r\n this._domElement.appendChild(element);\r\n }\r\n }\r\n\r\n for (let i = 0, l = object.children.length; i < l; i++) {\r\n this._renderObject(object.children[i], camera, scene);\r\n }\r\n }\r\n\r\n render(scene, camera) {\r\n scene.updateMatrixWorld();\r\n\r\n if (camera.parent === null) {\r\n camera.updateMatrixWorld();\r\n }\r\n\r\n camera.matrixWorldInverse.copy(camera.matrixWorld).invert();\r\n\r\n this._viewMatrix.copy(camera.matrixWorldInverse);\r\n this._projectionMatrix.copy(camera.projectionMatrix);\r\n\r\n this._renderObject(scene, camera, scene);\r\n }\r\n}\r\nexport default CSS2DRenderer;\r\n","export default function getTopWindow() {\r\n // intercept the exception if we have cross-origin iframe\r\n try {\r\n if (window.top.location.href !== undefined) {\r\n return window.top;\r\n }\r\n } catch {\r\n // provide fallback\r\n }\r\n return window;\r\n}\r\n","import * as THREE from 'three';\r\nimport Timer from '../Timer';\r\nimport settings from '../settings';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\nimport getTopWindow from '../utils/getTopWindow';\r\n\r\nconst VK_LEFT = 37;\r\nconst VK_UP = 38;\r\nconst VK_RIGHT = 39;\r\nconst VK_DOWN = 40;\r\n\r\nconst STATE = {\r\n NONE: -1, ROTATE: 0, TRANSLATE: 1, SCALE: 2, TRANSLATE_PIVOT: 3,\r\n};\r\n\r\n// pausing for this amount of time before releasing mouse button prevents inertial rotation (seconds)\r\nconst FULL_STOP_THRESHOLD = 0.1;\r\n\r\nconst quaternion = new THREE.Quaternion();\r\nconst matrix4 = new THREE.Matrix4();\r\n\r\n// pivot -- local offset of the rotation pivot point\r\nfunction ObjectHandler(objects, camera, pivot, options) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n this.camera = camera;\r\n this.pivot = pivot;\r\n this.axis = new THREE.Vector3(0, 0, 1);\r\n this.options = options;\r\n\r\n this.lastRotation = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n}\r\n\r\nObjectHandler.prototype._rotate = (function () {\r\n const p = new THREE.Vector3();\r\n const q = new THREE.Quaternion();\r\n const s = new THREE.Vector3();\r\n\r\n const m = new THREE.Matrix4();\r\n\r\n return function (quat) {\r\n const zeroPivot = (this.pivot.x === 0.0 && this.pivot.y === 0.0 && this.pivot.z === 0.0);\r\n\r\n m.copy(this.object.matrix);\r\n\r\n if (zeroPivot) {\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n } else {\r\n m.multiply(matrix4.makeTranslation(this.pivot.x, this.pivot.y, this.pivot.z));\r\n m.multiply(matrix4.makeRotationFromQuaternion(quat));\r\n m.multiply(matrix4.makeTranslation(-this.pivot.x, -this.pivot.y, -this.pivot.z));\r\n }\r\n\r\n m.decompose(p, q, s);\r\n\r\n // update objects\r\n if (!zeroPivot) {\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].position.copy(p);\r\n }\r\n }\r\n\r\n for (let j = 0; j < this.objects.length; ++j) {\r\n this.objects[j].quaternion.copy(q);\r\n this.objects[j].updateMatrix();\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.setObjects = function (objects) {\r\n this.objects = objects;\r\n [this.object] = objects;\r\n};\r\n\r\nObjectHandler.prototype.rotate = (function () {\r\n const rot = {\r\n axis: new THREE.Vector3(),\r\n angle: 0.0,\r\n };\r\n\r\n return function (quat, mousePrevPos, mouseCurPos, aboutAxis) {\r\n this.mouse2rotation(rot, mousePrevPos, mouseCurPos, aboutAxis);\r\n quat.setFromAxisAngle(rot.axis, rot.angle);\r\n\r\n if (rot.angle) {\r\n this._rotate(quat);\r\n }\r\n\r\n this.lastRotation = rot;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.translate = (function () {\r\n const dir = new THREE.Vector3();\r\n const pivot = new THREE.Vector3();\r\n\r\n return function (delta) {\r\n // reverse-project viewport movement to view coords (compensate for screen aspect ratio)\r\n dir.set(\r\n delta.x / this.camera.projectionMatrix.elements[0],\r\n delta.y / this.camera.projectionMatrix.elements[5],\r\n 0,\r\n );\r\n let dist = dir.length();\r\n dir.normalize();\r\n\r\n // transform movement direction to object local coords\r\n dir.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // visible translate distance shouldn't depend on camera-to-object distance\r\n pivot.copy(this.pivot);\r\n this.object.localToWorld(pivot);\r\n dist *= Math.abs(pivot.z - this.camera.position.z);\r\n\r\n // visible translate distance shouldn't depend on object scale\r\n dist /= this.object.matrixWorld.getMaxScaleOnAxis();\r\n\r\n // all objects are translated similar to principal object\r\n // (we assume they all have identical pivot and scale)\r\n for (let i = 0; i < this.objects.length; ++i) {\r\n this.objects[i].translateOnAxis(dir, dist);\r\n }\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.update = (function () {\r\n const axis = new THREE.Vector3();\r\n\r\n return function (timeSinceLastUpdate, timeSinceMove) {\r\n if (settings.now.autoRotation !== 0.0) {\r\n // auto-rotation with constant speed\r\n\r\n // if rotation axis is fixed or hasn't been defined yet\r\n if (settings.now.autoRotationAxisFixed || this.lastRotation.axis.length() === 0.0) {\r\n // use Y-axis (transformed to local object coords)\r\n axis.set(0, 1, 0).transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n } else {\r\n // use axis defined by last user rotation\r\n axis.copy(this.lastRotation.axis);\r\n }\r\n\r\n this._rotate(quaternion.setFromAxisAngle(axis, settings.now.autoRotation * timeSinceLastUpdate));\r\n return true;\r\n }\r\n\r\n if (this.options.intertia && this.lastRotation.angle) {\r\n // inertial object rotation\r\n const angle = this.lastRotation.angle * ((1.0 - this.options.dynamicDampingFactor) ** (40.0 * timeSinceMove));\r\n\r\n if (Math.abs(angle) <= this.options.intertiaThreshold) {\r\n this.lastRotation.angle = 0.0;\r\n } else {\r\n this._rotate(quaternion.setFromAxisAngle(this.lastRotation.axis, angle));\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n };\r\n}());\r\n\r\nObjectHandler.prototype.stop = function () {\r\n this.lastRotation.angle = 0.0;\r\n};\r\n\r\n// calculate (axis, angle) pair from mouse/touch movement\r\nObjectHandler.prototype.mouse2rotation = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n const eye = new THREE.Vector3();\r\n const eyeDirection = new THREE.Vector3();\r\n\r\n const cameraUpDirection = new THREE.Vector3();\r\n const cameraSidewaysDirection = new THREE.Vector3();\r\n\r\n const moveDirection = new THREE.Vector3();\r\n\r\n const mouseDelta = new THREE.Vector2();\r\n\r\n return function (rot, mousePrev, mouseCur, aboutAxis) {\r\n if (aboutAxis) {\r\n rot.axis.copy(this.axis);\r\n rot.angle = this.options.axisRotateFactor * (mouseCur.y - mousePrev.y);\r\n\r\n /* cool method that allows rotation around Z axis to be \"tied\" to mouse cursor\r\n\r\n res.axis.copy(this.axis);\r\n\r\n var pivot = this.pivot.clone();\r\n this.object.localToWorld(pivot);\r\n pivot.project(this.camera);\r\n\r\n var v1 = new THREE.Vector3(mousePrev.x, mousePrev.y, this.camera.position.z);\r\n v1.sub(pivot);\r\n var v2 = new THREE.Vector3(mouseCur.x, mouseCur.y, this.camera.position.z);\r\n v2.sub(pivot);\r\n\r\n v1.sub(res.axis.clone().multiplyScalar(v1.dot(res.axis)));\r\n v2.sub(res.axis.clone().multiplyScalar(v2.dot(res.axis)));\r\n\r\n var abs = v1.length() * v2.length();\r\n if (abs > 0) {\r\n res.angle = res.axis.dot(v1.cross(v2)) / abs;\r\n }\r\n */\r\n } else {\r\n mouseDelta.subVectors(mouseCur, mousePrev);\r\n const angle = mouseDelta.length();\r\n if (angle === 0.0) {\r\n return;\r\n }\r\n\r\n center.copy(this.pivot);\r\n this.object.localToWorld(center);\r\n eye.subVectors(this.camera.position, center);\r\n eyeDirection.copy(eye).normalize();\r\n\r\n cameraUpDirection.copy(this.camera.up).normalize();\r\n cameraSidewaysDirection.crossVectors(cameraUpDirection, eyeDirection).normalize();\r\n\r\n cameraUpDirection.setLength(mouseDelta.y);\r\n cameraSidewaysDirection.setLength(mouseDelta.x);\r\n\r\n moveDirection.copy(cameraUpDirection.add(cameraSidewaysDirection));\r\n\r\n rot.axis.crossVectors(moveDirection, eye);\r\n\r\n rot.angle = -angle * this.options.rotateFactor;\r\n }\r\n\r\n rot.axis.transformDirection(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n // make sure angle is always positive (thus 'axis' defines both axis and direction of rotation)\r\n if (rot.angle < 0.0) {\r\n rot.axis.negate();\r\n rot.angle = -rot.angle;\r\n }\r\n };\r\n}());\r\n\r\nfunction ObjectControls(object, objectPivot, camera, domElement, getAltObj) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.object = object;\r\n this.objectPivot = objectPivot;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.getAltObj = getAltObj;\r\n\r\n // API\r\n\r\n this.enabled = true;\r\n this.hotkeysEnabled = true;\r\n\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n\r\n this.options = {\r\n rotateFactor: Math.PI, // full screen slide (along short side) would roughly mean 180 deg. rotation\r\n axisRotateFactor: 4 * Math.PI, // full screen slide (along short side) would roughly mean 720 deg. rotation\r\n intertia: true,\r\n dynamicDampingFactor: 0.1,\r\n intertiaThreshold: 1e-3,\r\n };\r\n\r\n // internals\r\n\r\n this._state = STATE.NONE;\r\n\r\n this._mousePrevPos = new THREE.Vector2();\r\n this._mouseCurPos = new THREE.Vector2();\r\n\r\n this._mainObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._altObj = new ObjectHandler([this.object], this.camera, new THREE.Vector3(0, 0, 0), this.options);\r\n this._affectedObj = this._mainObj;\r\n this._isAltObjFreeRotationAllowed = true;\r\n this._isTranslationAllowed = true;\r\n this._isKeysTranslatingObj = false;\r\n\r\n this._pressedKeys = [];\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n this._lastUpdateTime = this._clock.getElapsedTime();\r\n\r\n // events\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousewheel',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'DOMMouseScroll',\r\n handler(e) {\r\n self.mousewheel(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseout',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchstartend(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchmove',\r\n handler(e) {\r\n self.touchmove(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keydown',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: self.getKeyBindObject(),\r\n type: 'keyup',\r\n handler(e) {\r\n self.keydownup(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'blur',\r\n handler() {\r\n self.resetKeys();\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'contextmenu',\r\n handler(e) {\r\n self.contextmenu(e);\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n\r\n this.resetKeys();\r\n\r\n // force an update at start\r\n this.update();\r\n}\r\n\r\n// methods\r\n\r\nObjectControls.prototype = Object.create(EventDispatcher.prototype);\r\nObjectControls.prototype.constructor = ObjectControls;\r\n\r\nObjectControls.prototype.resetKeys = function () {\r\n this._pressedKeys[VK_LEFT] = false;\r\n this._pressedKeys[VK_UP] = false;\r\n this._pressedKeys[VK_RIGHT] = false;\r\n this._pressedKeys[VK_DOWN] = false;\r\n};\r\n\r\nObjectControls.prototype.contextmenu = function (e) {\r\n e.stopPropagation();\r\n e.preventDefault();\r\n};\r\n\r\nObjectControls.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nObjectControls.prototype.enable = function (enable) {\r\n this.enabled = enable;\r\n};\r\n\r\nObjectControls.prototype.enableHotkeys = function (enable) {\r\n this.hotkeysEnabled = enable;\r\n};\r\n\r\nObjectControls.prototype.allowTranslation = function (allow) {\r\n this._isTranslationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.allowAltObjFreeRotation = function (allow) {\r\n this._isAltObjFreeRotationAllowed = allow;\r\n};\r\n\r\nObjectControls.prototype.keysTranslateObj = function (on) {\r\n this._isKeysTranslatingObj = on;\r\n};\r\n\r\nObjectControls.prototype.isEditingAltObj = function () {\r\n return ((this._state === STATE.ROTATE) || (this._state === STATE.TRANSLATE))\r\n && (this._affectedObj === this._altObj);\r\n};\r\n\r\n// convert page coords of mouse/touch to uniform coords with smaller side being [-0.5, 0.5]\r\n// (uniform coords keep direct proportion with screen distance travelled by mouse regardless of screen aspect ratio)\r\nObjectControls.prototype.convertMouseToOnCircle = function (coords, pageX, pageY) {\r\n const screenSize = Math.min(this.screen.width, this.screen.height);\r\n\r\n if (screenSize === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n ((pageX - this.screen.width * 0.5 - this.screen.left) / screenSize),\r\n ((0.5 * this.screen.height + this.screen.top - pageY) / screenSize),\r\n );\r\n};\r\n\r\n// convert page coords of mouse/touch to viewport coords with both sides being [-1, 1]\r\n// (those are non-uniform coords affected by screen aspect ratio)\r\nObjectControls.prototype.convertMouseToViewport = function (coords, pageX, pageY) {\r\n if (this.screen.width === 0 || this.screen.height === 0) {\r\n coords.set(0, 0);\r\n return;\r\n }\r\n\r\n coords.set(\r\n (2.0 * (pageX - this.screen.width * 0.5 - this.screen.left) / this.screen.width),\r\n (2.0 * (0.5 * this.screen.height + this.screen.top - pageY) / this.screen.height),\r\n );\r\n};\r\n\r\nObjectControls.prototype.stop = function () {\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n};\r\n\r\n// rotate object based on latest mouse/touch movement\r\nObjectControls.prototype.rotateByMouse = (function () {\r\n const quat = new THREE.Quaternion();\r\n\r\n return function (aboutZAxis) {\r\n this._affectedObj.rotate(quat, this._mousePrevPos, this._mouseCurPos, aboutZAxis);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n };\r\n}());\r\n\r\n// rotate object by specified quaternion\r\nObjectControls.prototype.rotate = function (quat) {\r\n this.object.quaternion.multiply(quat);\r\n this.dispatchEvent({ type: 'change', action: 'rotate', quaternion: quat });\r\n};\r\n\r\n// get object's orientation\r\nObjectControls.prototype.getOrientation = function () {\r\n return this.object.quaternion;\r\n};\r\n\r\n// set object's orientation\r\nObjectControls.prototype.setOrientation = function (quat) {\r\n this.object.quaternion.copy(quat);\r\n};\r\n\r\n// translate object based on latest mouse/touch movement\r\nObjectControls.prototype.translate = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this._affectedObj.translate(delta);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n };\r\n}());\r\n\r\n// get object scale\r\nObjectControls.prototype.getScale = function () {\r\n return this.object.scale.x;\r\n};\r\n\r\n// set uniform object scale\r\nObjectControls.prototype.setScale = function (scale) {\r\n this.object.scale.set(scale, scale, scale);\r\n};\r\n\r\n// scale object by factor (factor should be greater than zero)\r\nObjectControls.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n return;\r\n }\r\n this.setScale(this.object.scale.x * factor);\r\n this.dispatchEvent({ type: 'change', action: 'zoom', factor });\r\n};\r\n\r\nObjectControls.prototype.update = (function () {\r\n const shift = new THREE.Vector2();\r\n\r\n return function () {\r\n const curTime = this._clock.getElapsedTime();\r\n const timeSinceLastUpdate = curTime - this._lastUpdateTime;\r\n\r\n // update object handler\r\n if (this._state === STATE.NONE) {\r\n const timeSinceMove = curTime - this._lastMouseMoveTime;\r\n if (this._mainObj.update(timeSinceLastUpdate, timeSinceMove)\r\n || this._altObj.update(timeSinceLastUpdate, timeSinceMove)) {\r\n this.dispatchEvent({ type: 'change', action: 'auto' });\r\n }\r\n }\r\n\r\n // apply arrow keys\r\n if (this._isKeysTranslatingObj) {\r\n const speedX = Number(this._pressedKeys[VK_RIGHT]) - Number(this._pressedKeys[VK_LEFT]);\r\n const speedY = Number(this._pressedKeys[VK_UP]) - Number(this._pressedKeys[VK_DOWN]);\r\n if (speedX !== 0.0 || speedY !== 0.0) {\r\n const delta = timeSinceLastUpdate;\r\n\r\n // update object translation\r\n const altObj = this.getAltObj();\r\n if (altObj.objects.length > 0) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n\r\n shift.set(delta * speedX, delta * speedY);\r\n this._altObj.translate(shift);\r\n this.dispatchEvent({ type: 'change', action: 'translate' });\r\n }\r\n }\r\n }\r\n\r\n this._lastUpdateTime = curTime;\r\n };\r\n}());\r\n\r\nObjectControls.prototype.reset = function () {\r\n this._state = STATE.NONE;\r\n\r\n this.object.quaternion.copy(quaternion.set(0, 0, 0, 1));\r\n};\r\n\r\n// listeners\r\n\r\nObjectControls.prototype.mousedown = function (event) {\r\n if (this.enabled === false || this._state !== STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (this._state === STATE.NONE) {\r\n if (event.button === 0) {\r\n this._affectedObj.stop(); // can edit only one object at a time\r\n\r\n let workWithAltObj = false;\r\n\r\n if (event.altKey) {\r\n const altObj = this.getAltObj();\r\n workWithAltObj = (altObj.objects.length > 0);\r\n if (workWithAltObj) {\r\n this._altObj.setObjects(altObj.objects);\r\n this._altObj.pivot = altObj.pivot;\r\n\r\n if ('axis' in altObj) {\r\n this._altObj.axis = altObj.axis.clone();\r\n } else {\r\n this._altObj.axis.set(0, 0, 1);\r\n }\r\n }\r\n }\r\n\r\n this._affectedObj = workWithAltObj ? this._altObj : this._mainObj;\r\n\r\n this._state = (workWithAltObj && event.ctrlKey && this._isTranslationAllowed) ? STATE.TRANSLATE : STATE.ROTATE;\r\n } else if (event.button === 2) {\r\n this._state = STATE.TRANSLATE_PIVOT;\r\n }\r\n }\r\n\r\n if (this._state === STATE.ROTATE) {\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n\r\n if (this._state === STATE.TRANSLATE || this._state === STATE.TRANSLATE_PIVOT) {\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousemove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.pageX, event.pageY);\r\n this.rotateByMouse((event.altKey && !this._isAltObjFreeRotationAllowed) || event.shiftKey);\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.TRANSLATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translate();\r\n break;\r\n\r\n case STATE.TRANSLATE_PIVOT:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToViewport(this._mouseCurPos, event.pageX, event.pageY);\r\n this.translatePivotByMouse();\r\n break;\r\n\r\n default: break;\r\n }\r\n};\r\n\r\nObjectControls.prototype.mousewheel = function (event) {\r\n if (this.enabled === false || !settings.now.zooming || this._state !== STATE.NONE || event.shiftKey) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n\r\n let delta = 0;\r\n\r\n if (event.wheelDelta) {\r\n // WebKit / Opera / Explorer 9\r\n delta = event.wheelDelta / 40;\r\n } else if (event.detail) {\r\n // Firefox\r\n delta = -event.detail / 3;\r\n }\r\n\r\n let factor = 1.0 + delta * 0.05;\r\n factor = Math.max(factor, 0.01);\r\n this.scale(factor);\r\n};\r\n\r\nObjectControls.prototype.mouseup = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n this._state = STATE.NONE;\r\n\r\n if (this._clock.getElapsedTime() - this._lastMouseMoveTime > FULL_STOP_THRESHOLD) {\r\n this._affectedObj.stop();\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchstartend = function (event) {\r\n if (this.enabled === false) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (event.touches.length) {\r\n case 1:\r\n this._state = STATE.ROTATE;\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n break;\r\n\r\n case 2: {\r\n // prevent inertial rotation\r\n this._mainObj.stop();\r\n this._altObj.stop();\r\n\r\n this._state = STATE.SCALE;\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = this._touchDistanceStart = Math.sqrt(dx * dx + dy * dy);\r\n this._scaleStart = this.object.scale.x;\r\n break;\r\n }\r\n\r\n default:\r\n this._state = STATE.NONE;\r\n }\r\n};\r\n\r\nObjectControls.prototype.touchmove = function (event) {\r\n if (this.enabled === false || this._state === STATE.NONE) {\r\n return;\r\n }\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n switch (this._state) {\r\n case STATE.ROTATE:\r\n this._mousePrevPos.copy(this._mouseCurPos);\r\n this.convertMouseToOnCircle(this._mouseCurPos, event.touches[0].pageX, event.touches[0].pageY);\r\n this.rotateByMouse(false);\r\n\r\n this._lastMouseMoveTime = this._clock.getElapsedTime();\r\n break;\r\n\r\n case STATE.SCALE:\r\n if (settings.now.zooming) {\r\n // update scale\r\n const dx = event.touches[0].pageX - event.touches[1].pageX;\r\n const dy = event.touches[0].pageY - event.touches[1].pageY;\r\n this._touchDistanceCur = Math.sqrt(dx * dx + dy * dy);\r\n const newScale = this._scaleStart * this._touchDistanceCur / this._touchDistanceStart;\r\n const factor = newScale / this.object.scale.x;\r\n this.scale(factor);\r\n }\r\n break;\r\n\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.keydownup = function (event) {\r\n if (this.enabled === false || this.hotkeysEnabled === false) {\r\n return;\r\n }\r\n\r\n switch (event.keyCode) {\r\n case VK_LEFT:\r\n case VK_UP:\r\n case VK_RIGHT:\r\n case VK_DOWN:\r\n this._pressedKeys[event.keyCode] = (event.type === 'keydown');\r\n event.preventDefault();\r\n event.stopPropagation();\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nObjectControls.prototype.getKeyBindObject = function () {\r\n return getTopWindow();\r\n};\r\n\r\nObjectControls.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nObjectControls.prototype.translatePivotByMouse = (function () {\r\n const delta = new THREE.Vector2();\r\n return function () {\r\n delta.subVectors(this._mouseCurPos, this._mousePrevPos);\r\n this.translatePivotInWorld(settings.now.translationSpeed * delta.x, settings.now.translationSpeed * delta.y, 0);\r\n };\r\n}());\r\n\r\n// Translate in WorldCS, translation is scaled with root scale matrix\r\nObjectControls.prototype.translatePivotInWorld = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.applyMatrix4(this.object.matrixWorld);\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n pos.applyMatrix4(matrix4.copy(this.object.matrixWorld).invert());\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Translate in ModelCS, x, y, z are Ang\r\nObjectControls.prototype.translatePivot = function (x, y, z) {\r\n const pos = this.objectPivot.position;\r\n pos.setX(pos.x + x);\r\n pos.setY(pos.y + y);\r\n pos.setZ(pos.z + z);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\n// Set pivot\r\nObjectControls.prototype.setPivot = function (newPivot) {\r\n this.objectPivot.position.copy(newPivot);\r\n\r\n this.dispatchEvent({ type: 'change', action: 'translatePivot' });\r\n};\r\n\r\nexport default ObjectControls;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\nimport Timer from '../Timer';\r\nimport EventDispatcher from '../utils/EventDispatcher';\r\n\r\nfunction Picker(gfxObj, camera, domElement) {\r\n EventDispatcher.call(this);\r\n const self = this;\r\n\r\n this.gfxObj = gfxObj;\r\n this.camera = camera;\r\n this.domElement = (typeof domElement !== 'undefined') ? domElement : document;\r\n this.screen = {\r\n left: 0, top: 0, width: 0, height: 0,\r\n };\r\n this._lastMousePos = new THREE.Vector2(0, 0);\r\n this._mouseTotalDist = 0.0;\r\n this._lastClickBeginTime = -1000.0;\r\n this._lastClickPos = new THREE.Vector2(0, 0);\r\n this._clickBeginTime = 0.0;\r\n\r\n this._clock = new Timer();\r\n this._clock.start();\r\n\r\n this._listeners = [\r\n {\r\n obj: self.domElement,\r\n type: 'mousedown',\r\n handler(e) {\r\n self.mousedown(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mouseup',\r\n handler(e) {\r\n self.mouseup(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'mousemove',\r\n handler(e) {\r\n self.mousemove(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchstart',\r\n handler(e) {\r\n self.touchstart(e);\r\n },\r\n },\r\n {\r\n obj: self.domElement,\r\n type: 'touchend',\r\n handler(e) {\r\n self.touchend(e);\r\n },\r\n },\r\n {\r\n obj: window,\r\n type: 'resize',\r\n handler() {\r\n self.handleResize();\r\n },\r\n }];\r\n\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.addEventListener(l.type, l.handler);\r\n }\r\n\r\n this.handleResize();\r\n}\r\n\r\nPicker.prototype = Object.create(EventDispatcher.prototype);\r\nPicker.prototype.constructor = Picker;\r\n\r\nPicker.prototype.reset = function () {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n};\r\n\r\nPicker.prototype.handleResize = function () {\r\n if (this.domElement === document) {\r\n this.screen.left = 0;\r\n this.screen.top = 0;\r\n this.screen.width = window.innerWidth;\r\n this.screen.height = window.innerHeight;\r\n } else {\r\n const box = this.domElement.getBoundingClientRect();\r\n // adjustments come from similar code in the jquery offset() function\r\n const d = this.domElement.ownerDocument.documentElement;\r\n this.screen.left = box.left + window.pageXOffset - d.clientLeft;\r\n this.screen.top = box.top + window.pageYOffset - d.clientTop;\r\n this.screen.width = box.width;\r\n this.screen.height = box.height;\r\n }\r\n};\r\n\r\nPicker.prototype.pickObject = function (screenPos) {\r\n if (!this.gfxObj) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n const { gfxObj } = this;\r\n const rayCaster = new THREE.Raycaster();\r\n rayCaster.ray.origin.setFromMatrixPosition(this.camera.matrixWorld);\r\n rayCaster.ray.direction.set(screenPos.x, screenPos.y, 0.5).unproject(this.camera).sub(rayCaster.ray.origin).normalize();\r\n\r\n const clipPlane = (settings.now.draft.clipPlane && this.clipPlaneValue) ? this.clipPlaneValue : Infinity;\r\n const fogFarPlane = (settings.now.fog && this.fogFarValue) ? this.fogFarValue : Infinity;\r\n const point = rayCaster.intersectVisibleObject(gfxObj, this.camera, clipPlane, fogFarPlane);\r\n if (!point) {\r\n this.picked = {};\r\n this.dispatchEvent({ type: 'newpick', obj: {} });\r\n return;\r\n }\r\n\r\n let picked = {};\r\n if (point.residue || point.atom) {\r\n const residue = point.residue || point.atom.residue;\r\n if (settings.now.pick === 'chain') {\r\n picked = { chain: residue.getChain() };\r\n } else if (settings.now.pick === 'molecule') {\r\n picked = { molecule: residue.getMolecule() };\r\n } else if (point.residue || settings.now.pick === 'residue') {\r\n picked = { residue };\r\n } else if (point.atom) {\r\n picked = { atom: point.atom };\r\n }\r\n }\r\n this.picked = picked;\r\n this.dispatchEvent({ type: 'newpick', obj: picked });\r\n};\r\n\r\nPicker.prototype.getMouseInViewport = function (pageX, pageY) {\r\n return new THREE.Vector2(\r\n (pageX - this.screen.left) / this.screen.width * 2 - 1,\r\n -(pageY - this.screen.top) / this.screen.height * 2 + 1,\r\n );\r\n};\r\n\r\nPicker.prototype.mousedown = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n this._lastMousePos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist = 0.0;\r\n this._clickBeginTime = this._clock.getElapsedTime();\r\n }\r\n};\r\n\r\nPicker.prototype.mousemove = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n const pos = this.getMouseInViewport(event.pageX, event.pageY);\r\n this._mouseTotalDist += pos.sub(this._lastMousePos).length();\r\n};\r\n\r\nPicker.prototype.mouseup = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.button === 0) {\r\n if (this._mouseTotalDist < 0.01) {\r\n const curTime = this._clock.getElapsedTime();\r\n const curPos = this.getMouseInViewport(event.pageX, event.pageY);\r\n\r\n const timeSinceLastClickBegin = curTime - this._lastClickBeginTime;\r\n if (timeSinceLastClickBegin < 0.7) {\r\n const clickDist = new THREE.Vector2().subVectors(curPos, this._lastClickPos);\r\n if (clickDist.length() < 0.01) {\r\n // it's a double click\r\n this.dispatchEvent({ type: 'dblclick', obj: this.picked });\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = -1000; // this click cannot serve as first click in double-click\r\n return;\r\n }\r\n }\r\n\r\n setTimeout(() => {\r\n self.pickObject(curPos);\r\n }, 0);\r\n\r\n this._lastClickPos = curPos;\r\n this._lastClickBeginTime = this._clickBeginTime;\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.touchstart = function (event) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 1) {\r\n this._lastTouchdownPos = this.getMouseInViewport(event.touches[0].pageX, event.touches[0].pageY);\r\n }\r\n};\r\n\r\nPicker.prototype.touchend = function (event) {\r\n const self = this;\r\n\r\n event.preventDefault();\r\n event.stopPropagation();\r\n\r\n if (event.touches.length === 0\r\n && event.changedTouches.length === 1) {\r\n const pos = this.getMouseInViewport(event.changedTouches[0].pageX, event.changedTouches[0].pageY);\r\n const dist = pos.sub(this._lastTouchdownPos).length();\r\n if (dist < 0.01) {\r\n setTimeout(() => {\r\n self.pickObject(self._lastTouchdownPos);\r\n }, 0);\r\n }\r\n }\r\n};\r\n\r\nPicker.prototype.dispose = function () {\r\n for (let i = 0; i < this._listeners.length; i++) {\r\n const l = this._listeners[i];\r\n l.obj.removeEventListener(l.type, l.handler);\r\n }\r\n};\r\n\r\nexport default Picker;\r\n","import * as THREE from 'three';\r\n\r\nclass Axes {\r\n constructor(target, targetCamera) {\r\n this._target = target;\r\n this._targetCamera = targetCamera;\r\n this._camera = new THREE.PerspectiveCamera(targetCamera.fov, targetCamera.aspect, 1, 100);\r\n this._object = new THREE.AxesHelper(1);\r\n this._scene = new THREE.Scene();\r\n this._scene.add(this._object);\r\n this._full = new THREE.Vector2();\r\n\r\n this._update();\r\n }\r\n\r\n _update() {\r\n const { fov } = this._targetCamera;\r\n const camera = this._camera;\r\n camera.aspect = this._targetCamera.aspect;\r\n camera.setMinimalFov(fov);\r\n camera.setDistanceToFit(1.0, fov);\r\n camera.updateProjectionMatrix();\r\n\r\n this._object.quaternion.copy(this._target.quaternion);\r\n }\r\n\r\n render(renderer) {\r\n this._update();\r\n\r\n renderer.getSize(this._full);\r\n const width = this._full.width * 0.25;\r\n const height = this._full.height * 0.25;\r\n\r\n const { autoClear } = renderer;\r\n renderer.autoClear = false;\r\n renderer.setViewport(0.0, 0.0, width, height);\r\n renderer.clear(false, true, false);\r\n renderer.render(this._scene, this._camera);\r\n renderer.setViewport(0, 0, this._full.width, this._full.height);\r\n renderer.autoClear = autoClear;\r\n }\r\n}\r\nexport default Axes;\r\n","import * as THREE from 'three';\r\nimport SecondaryStructureColorer from './colorers/SecondaryStructureColorer';\r\n\r\nconst cDataOffset = 12;\r\nconst cFirstMask = 0x0FFFFF00;\r\nconst cFirstShift = 8;\r\nconst cSecMask1 = 0x000000FF;\r\nconst cSecShift1 = 12;\r\nconst cSecMask2 = 0xFFF00000;\r\nconst cSecShift2 = 20;\r\nconst cThirdMask = 0x000FFFFF;\r\nconst cStrMask = 0xF0000000;\r\nconst cStrShift = 28;\r\nconst c219 = 1 << 19;\r\nconst c220 = 1 << 20;\r\n\r\nconst cHelixIdx = 1;\r\nconst cSheetIdx = 2;\r\nconst secTypes = ['helix', 'strand'];\r\nconst cSecNames = ['fs', 'ps', 'ns', 'us'];\r\n\r\nfunction _createSecondary(strArray, complex) {\r\n const residues = complex._residues;\r\n const nRes = residues.length;\r\n const resid = new Uint8Array(nRes);\r\n\r\n const atoms = complex._atoms;\r\n for (let i = 0, n = strArray.length; i < n; ++i) {\r\n const atom = atoms[i];\r\n resid[atom.residue._index] = strArray[i];\r\n }\r\n\r\n const secondary = [];\r\n let rIdx = 0;\r\n while (rIdx < nRes) {\r\n if (resid[rIdx] !== 0) {\r\n const start = rIdx;\r\n const val = resid[rIdx];\r\n while (rIdx < nRes - 1 && resid[rIdx + 1] === val\r\n && residues[rIdx].isConnected(residues[rIdx + 1])) {\r\n ++rIdx;\r\n }\r\n secondary.push({ start, end: rIdx, type: secTypes[val - 1] });\r\n }\r\n ++rIdx;\r\n }\r\n return secondary;\r\n}\r\n\r\nfunction fromUInt20ToInt20(uint20) {\r\n return uint20 >= c219 ? uint20 - c220 : uint20;\r\n}\r\n\r\nclass FrameInfo {\r\n constructor(complex, payload, callbacks) {\r\n this._complex = complex;\r\n this._secondary = null;\r\n this.isLoading = false;\r\n this._framesRange = {\r\n start: 0,\r\n end: -1,\r\n };\r\n this.frameIsReady = false;\r\n this._buffer = null;\r\n this._frameRequest = null;\r\n this._callbacks = callbacks;\r\n if (typeof payload === 'function') {\r\n this._framesRequestLength = 1;\r\n this._downloadDataFn = payload;\r\n } else {\r\n this.parseBinaryData(payload, true);\r\n }\r\n this.reset();\r\n this.setFrame(0);\r\n }\r\n\r\n _prepareBuffer(framesStart, framesEnd) {\r\n if (framesStart === undefined || framesStart === null) {\r\n framesStart = 0;\r\n }\r\n if (framesEnd === undefined || framesEnd === null) {\r\n framesEnd = framesStart + this._framesRequestLength;\r\n }\r\n if (this._framesCount !== undefined) {\r\n framesEnd = Math.min(this._framesCount - 1, framesEnd);\r\n }\r\n if (this._downloadDataFn) {\r\n const self = this;\r\n const onDone = function (data) {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n self._buffer = {\r\n data,\r\n state: 'ready',\r\n start: framesStart,\r\n end: framesEnd,\r\n };\r\n if (self._frameRequest !== null) {\r\n const idx = self._frameRequest;\r\n self._frameRequest = null;\r\n self.setFrame(idx);\r\n }\r\n };\r\n const onFail = function () {\r\n self.isLoading = false;\r\n if (self._callbacks && typeof self._callbacks.onError === 'function') {\r\n self._callbacks.onError('Streaming failed');\r\n }\r\n };\r\n if (!this._buffer) {\r\n this._buffer = {};\r\n }\r\n this._buffer.state = 'downloading';\r\n this.isLoading = true;\r\n if (self._callbacks && typeof self._callbacks.onLoadStatusChanged === 'function') {\r\n self._callbacks.onLoadStatusChanged();\r\n }\r\n this._downloadDataFn({ start: framesStart, end: framesEnd + 1 }, onDone, onFail);\r\n }\r\n }\r\n\r\n _parseBuffer() {\r\n if (this._buffer && this._buffer.state === 'ready') {\r\n this._framesRange = {\r\n start: this._buffer.start,\r\n end: this._buffer.end,\r\n };\r\n this.parseBinaryData(this._buffer.data, false);\r\n let _bufferRequestStart = (this._buffer.end + 1) % this._framesCount;\r\n if (_bufferRequestStart >= this._framesCount) {\r\n _bufferRequestStart = 0;\r\n }\r\n this._buffer = {\r\n state: 'none',\r\n };\r\n this._prepareBuffer(_bufferRequestStart, _bufferRequestStart + this._framesRequestLength);\r\n if (this._frameRequest !== null) {\r\n const idx = this._frameRequest;\r\n this._frameRequest = null;\r\n this.setFrame(idx);\r\n }\r\n }\r\n }\r\n\r\n parseBinaryData(arrayBuffer) {\r\n const dataView = new DataView(arrayBuffer);\r\n let offset = 0;\r\n const atomsCount = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const framesCount = dataView.getUint32(offset, true);\r\n this._framesCount = framesCount;\r\n this._framesRange.end = this._framesRange.end > 0\r\n ? Math.min(this._framesRange.end, framesCount - 1) : framesCount - 1;\r\n offset += 4;\r\n this._atomsCount = atomsCount;\r\n const maxSize = 1024 * 1024; // 1 MB\r\n this._framesRequestLength = Math.ceil(maxSize / (atomsCount * 8));\r\n const chunkedFramesCount = this._framesRange.end - this._framesRange.start + 1;\r\n if (atomsCount !== this._complex._atoms.length\r\n || arrayBuffer.byteLength !== cDataOffset + chunkedFramesCount * atomsCount * 8) {\r\n throw new Error();\r\n }\r\n const complex = this._complex;\r\n let timeStep = dataView.getUint32(offset, true);\r\n let iName = 0;\r\n while (timeStep > 1000 && iName < cSecNames.length - 1) {\r\n timeStep /= 1000;\r\n ++iName;\r\n }\r\n\r\n this._timeStep = `${timeStep.toString()} ${cSecNames[iName]}`;\r\n offset += 4;\r\n const secondary = [];\r\n const posData = new Float32Array(chunkedFramesCount * atomsCount * 3);\r\n let coordIdx = 0;\r\n const secondaryArr = new Int8Array(atomsCount);\r\n for (let j = 0; j < chunkedFramesCount; ++j) {\r\n for (let i = 0; i < atomsCount; ++i) {\r\n const hiWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const loWord = dataView.getUint32(offset, true);\r\n offset += 4;\r\n const str = (loWord & cStrMask) >>> cStrShift;\r\n const x = fromUInt20ToInt20(((loWord & cFirstMask) >>> cFirstShift) >> 0);\r\n const y = fromUInt20ToInt20((((loWord & cSecMask1) << cSecShift1)\r\n | ((hiWord & cSecMask2) >>> cSecShift2)) >> 0);\r\n const z = fromUInt20ToInt20((hiWord & cThirdMask) >> 0);\r\n secondaryArr[i] = 0;\r\n if (str > 0 && str < 4) {\r\n secondaryArr[i] = cHelixIdx;\r\n } else if (str === 4) {\r\n secondaryArr[i] = cSheetIdx;\r\n }\r\n posData[coordIdx++] = x / 100;\r\n posData[coordIdx++] = y / 100;\r\n posData[coordIdx++] = z / 100;\r\n }\r\n secondary.push(_createSecondary(secondaryArr, complex));\r\n }\r\n this._secondaryData = secondary;\r\n this._data = posData;\r\n }\r\n\r\n nextFrame() {\r\n this.setFrame((this._currFrame + 1) % this._framesCount);\r\n }\r\n\r\n needsColorUpdate(colorer) {\r\n return colorer instanceof SecondaryStructureColorer;\r\n }\r\n\r\n getAtomColor(colorer, atom) {\r\n return colorer.getResidueColor(this._residues[atom.residue._index], this._complex);\r\n }\r\n\r\n getResidueColor(colorer, residue) {\r\n return colorer.getResidueColor(this._residues[residue._index], this._complex);\r\n }\r\n\r\n _updateSecondary() {\r\n let i;\r\n const myResidues = this._residues;\r\n let n = myResidues.length;\r\n for (i = 0; i < n; ++i) {\r\n myResidues[i]._secondary = null;\r\n }\r\n const sec = this._secondaryData[this._currFrame - this._framesRange.start];\r\n for (i = 0, n = sec.length; i < n; ++i) {\r\n const oldSec = sec[i];\r\n const { start, end } = oldSec;\r\n const nSec = {\r\n _start: myResidues[start],\r\n _end: myResidues[end],\r\n type: oldSec.type,\r\n generic: oldSec.generic,\r\n };\r\n for (let j = start; j <= end; ++j) {\r\n myResidues[j]._secondary = nSec;\r\n }\r\n }\r\n }\r\n\r\n reset() {\r\n const compRes = this._complex._residues;\r\n const n = compRes.length;\r\n this._residues = new Array(n);\r\n const myResidues = this._residues;\r\n const getSec = function () {\r\n return this._secondary;\r\n };\r\n for (let i = 0; i < n; ++i) {\r\n myResidues[i] = {\r\n _type: compRes[i]._type,\r\n _isValid: compRes[i]._isValid,\r\n _controlPoint: null,\r\n _wingVector: null,\r\n _secondary: null,\r\n getSecondary: getSec,\r\n };\r\n }\r\n }\r\n\r\n setFrame(frameIdx) {\r\n this.frameIsReady = false;\r\n if (frameIdx >= this._framesRange.start && frameIdx <= this._framesRange.end) {\r\n this._currFrame = frameIdx;\r\n this._cachedResidues = false;\r\n this._updateSecondary();\r\n this.frameIsReady = true;\r\n } else {\r\n this._frameRequest = frameIdx;\r\n if (!this._buffer) {\r\n this._prepareBuffer(frameIdx);\r\n } else {\r\n const self = this;\r\n switch (this._buffer.state) {\r\n case 'none':\r\n this._prepareBuffer(frameIdx);\r\n break;\r\n case 'ready':\r\n self._parseBuffer();\r\n break;\r\n default:\r\n break;\r\n }\r\n }\r\n }\r\n }\r\n\r\n disableEvents() {\r\n this._callbacks = null;\r\n }\r\n\r\n /**\r\n * Returns link to atom pos vector, clone it if needed\r\n */\r\n\r\n static _vec = new THREE.Vector3();\r\n\r\n getAtomPos(atomIdx) {\r\n const vec = FrameInfo._vec;\r\n const self = this;\r\n const data = self._data;\r\n const idx = (self._atomsCount * (self._currFrame - self._framesRange.start) + atomIdx) * 3;\r\n vec.set(data[idx], data[idx + 1], data[idx + 2]);\r\n return vec;\r\n }\r\n\r\n getResidues() {\r\n if (this._cachedResidues) {\r\n return this._residues;\r\n }\r\n this._complex.updateToFrame(this);\r\n return this._residues;\r\n }\r\n}\r\nexport default FrameInfo;\r\n","import _ from 'lodash';\r\nimport settings from '../../settings';\r\nimport utils from '../../utils';\r\nimport gfxutils from '../gfxutils';\r\n\r\n/**\r\n * Create new scene object.\r\n *\r\n * @param {array=} params - Object required params.\r\n * @param {object=} opts - Options to override defaults with.\r\n *\r\n * These options are copied locally and not kept by reference, so the created instance will not reflect further\r\n * changes to the `opts` object. However, changes in defaults **will** affect the colorer after its creation.\r\n *\r\n * @exports SceneObject\r\n * @this SceneObject\r\n * @abstract\r\n * @constructor\r\n * @classdesc Basic class for all scene objects that are not reps.\r\n */\r\nclass SceneObject {\r\n constructor(params, opts) {\r\n if (this.constructor === SceneObject) {\r\n throw new Error('Can not instantiate abstract class!');\r\n }\r\n /**\r\n * Object's options inherited (prototyped) from defaults.\r\n * @type {object}\r\n */\r\n this.params = params;\r\n this.opts = _.merge(utils.deriveDeep(settings.now.objects[this.type], true), opts);\r\n this.needsRebuild = false;\r\n this._mesh = null;\r\n this.id = null;\r\n }\r\n\r\n /**\r\n * Get object identification, probably with options.\r\n * @returns {Object} field type contains type information, params - object's formal parameters,\r\n * opts - changed options\r\n * Options are returned if they were changed during or after object creation.\r\n */\r\n identify() {\r\n const result = {\r\n type: this.type,\r\n params: this.params,\r\n };\r\n const diff = utils.objectsDiff(this.opts, settings.now.modes[this.id]);\r\n if (!_.isEmpty(diff)) {\r\n result.opts = diff;\r\n }\r\n return result;\r\n }\r\n\r\n toString() {\r\n const paramsStr = `o=${this.type},${this.params.join(',')}`;\r\n const optsStr = utils.compareOptionsWithDefaults(this.opts, settings.defaults.objects[this.type]);\r\n return paramsStr + optsStr;\r\n }\r\n\r\n getGeometry() {\r\n return this._mesh;\r\n }\r\n\r\n destroy() {\r\n if (this._mesh) {\r\n gfxutils.destroyObject(this._mesh);\r\n }\r\n }\r\n}\r\n\r\n/**\r\n * Scene object identifier.\r\n * @type {string}\r\n */\r\nSceneObject.prototype.type = '__';\r\n\r\nexport default SceneObject;\r\n","import * as THREE from 'three';\r\nimport SceneObject from './SceneObject';\r\nimport meshutils from '../meshutils';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\nimport meshes from '../meshes/meshes';\r\nimport settings from '../../settings';\r\n\r\nclass LinesObj extends SceneObject {\r\n constructor(params, opts) {\r\n super(params, opts);\r\n if (params.length < 2) {\r\n throw new Error('Wrong number of argumets on line object creation!');\r\n }\r\n [this._id1, this._id2] = params;\r\n }\r\n\r\n _getAtomFromName(complex, atomId) {\r\n const err = ' - Wrong atom format it must be \\'#CHAIN_NAME.#RESIDUE_NUMBER.#ATOM_NAME\\' (e.g. \\'A.38.CO1\\')';\r\n const atom1 = complex.getAtomByFullname(atomId);\r\n if (!atom1) {\r\n throw new Error(atomId + err);\r\n }\r\n return atom1;\r\n }\r\n\r\n build(complex) {\r\n const geom = new THREE.BufferGeometry();\r\n this._atom1 = this._getAtomFromName(complex, this._id1);\r\n this._atom2 = this._getAtomFromName(complex, this._id2);\r\n\r\n const p1 = this._atom1.position;\r\n const p2 = this._atom2.position;\r\n const vertices = new Float32Array([\r\n p1.x, p1.y, p1.z,\r\n p2.x, p2.y, p2.z,\r\n ]);\r\n\r\n geom.setAttribute('position', new THREE.BufferAttribute(vertices, 3));\r\n geom.computeBoundingBox();\r\n\r\n this._line = new meshes.Line(geom, new UberMaterial({\r\n lights: false,\r\n overrideColor: true,\r\n dashedLine: true,\r\n fogTransparent: settings.now.bg.transparent,\r\n }));\r\n this._line.computeLineDistances();\r\n this._line.material.setUberOptions({\r\n fixedColor: new THREE.Color(this.opts.color),\r\n dashedLineSize: this.opts.dashSize,\r\n dashedLinePeriod: this.opts.dashSize + this.opts.gapSize,\r\n });\r\n this._line.material.updateUniforms();\r\n\r\n this._line.raycast = function (_raycaster, _intersects) {};\r\n this._mesh = this._line;\r\n const transforms = complex.getTransforms();\r\n if (transforms.length > 0) {\r\n this._mesh = new THREE.Group();\r\n this._mesh.add(this._line);\r\n meshutils.applyTransformsToMeshes(this._mesh, transforms);\r\n }\r\n }\r\n\r\n updateToFrame(frameData) {\r\n if (!this._atom1 || !this._atom2 || !this._line) {\r\n return;\r\n }\r\n\r\n const geo = this._line.geometry;\r\n geo.vertices[0].copy(frameData.getAtomPos(this._atom1.index));\r\n geo.vertices[1].copy(frameData.getAtomPos(this._atom2.index));\r\n this._line.computeLineDistances();\r\n geo.computeBoundingSphere();\r\n\r\n geo.verticesNeedUpdate = true;\r\n }\r\n}\r\n\r\nLinesObj.prototype.constructor = LinesObj;\r\nLinesObj.prototype.type = 'line';\r\n\r\nexport default LinesObj;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Outline.frag';\r\n\r\nclass OutlineMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n // add depth outline\r\n super(params);\r\n\r\n const settings = {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcDepthTex: { type: 't', value: null },\r\n srcTexSize: { type: 'v2', value: new THREE.Vector2(512, 512) },\r\n color: { type: 'v3', value: null },\r\n threshold: { type: 'f', value: null },\r\n opacity: { type: 'f', value: 1.0 },\r\n thickness: { type: 'v2', value: new THREE.Vector2(1, 1) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: true,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n\r\n this.setValues(settings);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n const defines = {};\r\n\r\n if (this.depth) {\r\n defines.DEPTH_OUTLINE = 1;\r\n }\r\n\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nOutlineMaterial.prototype.depth = false;\r\n\r\nexport default OutlineMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './FXAA.frag';\r\n\r\nclass FXAAMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n bgColor: { type: 'c', value: new THREE.Color(0xffffff) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n copy(source) {\r\n super.copy(source);\r\n this.depth = source.depth;\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.bgTransparent) {\r\n defines.BG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nFXAAMaterial.prototype.bgTransparent = false;\r\n\r\nexport default FXAAMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AO.frag';\r\nimport noise from '../noiseTexture';\r\n\r\nconst _samplesKernel = [\r\n // hemisphere samples adopted to sphere\r\n new THREE.Vector3(0.295184, 0.077723, 0.068429),\r\n new THREE.Vector3(-0.271976, -0.365221, 0.838363),\r\n new THREE.Vector3(0.547713, 0.467576, 0.488515),\r\n new THREE.Vector3(0.662808, -0.031733, 0.584758),\r\n new THREE.Vector3(-0.025717, 0.218955, 0.657094),\r\n new THREE.Vector3(-0.310153, -0.365223, 0.370701),\r\n new THREE.Vector3(-0.101407, -0.006313, 0.747665),\r\n new THREE.Vector3(-0.769138, 0.360399, 0.086847),\r\n new THREE.Vector3(-0.271988, -0.275140, 0.905353),\r\n new THREE.Vector3(0.096740, -0.566901, 0.700151),\r\n new THREE.Vector3(0.562872, -0.735136, 0.094647),\r\n new THREE.Vector3(0.379877, 0.359278, 0.190061),\r\n new THREE.Vector3(0.519064, -0.023055, 0.405068),\r\n new THREE.Vector3(-0.301036, 0.114696, 0.088885),\r\n new THREE.Vector3(-0.282922, 0.598305, 0.487214),\r\n new THREE.Vector3(-0.181859, 0.251670, 0.679702),\r\n new THREE.Vector3(-0.191463, -0.635818, 0.512919),\r\n new THREE.Vector3(-0.293655, 0.427423, 0.078921),\r\n new THREE.Vector3(-0.267983, 0.680534, 0.132880),\r\n new THREE.Vector3(0.139611, 0.319637, 0.477439),\r\n new THREE.Vector3(-0.352086, 0.311040, 0.653913),\r\n new THREE.Vector3(0.321032, 0.805279, 0.487345),\r\n new THREE.Vector3(0.073516, 0.820734, 0.414183),\r\n new THREE.Vector3(-0.155324, 0.589983, 0.411460),\r\n new THREE.Vector3(0.335976, 0.170782, 0.527627),\r\n new THREE.Vector3(0.463460, -0.355658, 0.167689),\r\n new THREE.Vector3(0.222654, 0.596550, 0.769406),\r\n new THREE.Vector3(0.922138, -0.042070, 0.147555),\r\n new THREE.Vector3(-0.727050, -0.329192, 0.369826),\r\n new THREE.Vector3(-0.090731, 0.533820, 0.463767),\r\n new THREE.Vector3(-0.323457, -0.876559, 0.238524),\r\n new THREE.Vector3(-0.663277, -0.372384, 0.342856),\r\n];\r\n\r\nclass AOMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n noiseTexture: { type: 't', value: noise.noiseTexture },\r\n noiseTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / noise.noiseWidth, 1.0 / noise.noiseHeight) },\r\n diffuseTexture: { type: 't', value: null },\r\n normalTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n camNearFar: { type: 'v2', value: new THREE.Vector2(1.0, 10.0) },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n samplesKernel: { type: 'v3v', value: _samplesKernel },\r\n kernelRadius: { type: 'f', value: 1.0 },\r\n depthThreshold: { type: 'f', value: 1.0 },\r\n factor: { type: 'f', value: 1.0 },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOHorBlur.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOHorBlurMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n }\r\n}\r\n\r\nexport default AOHorBlurMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './AOVertBlurWithBlend.frag';\r\n\r\nconst _kernelOffsets = [-2.0, -1.0, 0.0, 1.0, 2.0];\r\n\r\nclass AOVertBlurWithBlendMaterial extends THREE.RawShaderMaterial {\r\n constructor(params) {\r\n super(params);\r\n\r\n // set default values\r\n this.setValues.call(this, {\r\n uniforms: {\r\n diffuseTexture: { type: 't', value: null },\r\n depthTexture: { type: 't', value: null },\r\n srcTexelSize: { type: 'v2', value: new THREE.Vector2(1.0 / 512.0, 1.0 / 512.0) },\r\n aoMap: { type: 't', value: null },\r\n samplesOffsets: { type: 'fv1', value: _kernelOffsets },\r\n projMatrix: { type: 'mat4', value: new THREE.Matrix4() },\r\n aspectRatio: { type: 'f', value: 0.0 },\r\n tanHalfFOV: { type: 'f', value: 0.0 },\r\n fogNearFar: { type: 'v2', value: new THREE.Vector2(100.0, 100.0) },\r\n fogColor: { type: 'v4', value: new THREE.Vector4(0.0, 0.5, 0.0, 1.0) },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n this.setValues(params);\r\n }\r\n\r\n setValues(values) {\r\n if (typeof values === 'undefined') {\r\n return;\r\n }\r\n\r\n // set direct values\r\n super.setValues(values);\r\n\r\n const defines = {};\r\n\r\n if (this.useFog) {\r\n defines.USE_FOG = 1;\r\n }\r\n if (this.fogTransparent) {\r\n defines.FOG_TRANSPARENT = 1;\r\n }\r\n // set dependent values\r\n this.defines = defines;\r\n }\r\n}\r\n\r\nAOVertBlurWithBlendMaterial.prototype.useFog = true;\r\nAOVertBlurWithBlendMaterial.prototype.fogTransparent = false;\r\n\r\nexport default AOVertBlurWithBlendMaterial;\r\n","import * as THREE from 'three';\r\nimport vertexShader from './ScreenQuad.vert';\r\nimport fragmentShader from './Anaglyph.frag';\r\n\r\nclass AnaglyphMaterial extends THREE.RawShaderMaterial {\r\n constructor() {\r\n super();\r\n const settings = {\r\n uniforms: {\r\n srcL: { type: 't', value: null },\r\n srcR: { type: 't', value: null },\r\n },\r\n vertexShader,\r\n fragmentShader,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n };\r\n this.setValues(settings);\r\n }\r\n}\r\n\r\nexport default AnaglyphMaterial;\r\n","import * as THREE from 'three';\r\nimport settings from '../settings';\r\n\r\nclass View {\r\n constructor() {\r\n this.position = new THREE.Vector3(0, 0, 0);\r\n this.scale = 1;\r\n this.orientation = new THREE.Quaternion(0, 0, 0, 1);\r\n }\r\n\r\n set(position, scale, orientation) {\r\n this.position = position;\r\n this.scale = scale;\r\n this.orientation = orientation;\r\n }\r\n}\r\n\r\nconst _transitionTime = 1.5; // in seconds\r\n\r\nexport default class ViewInterpolator {\r\n setup(startView, endView) {\r\n this._startTime = undefined;\r\n this._endTime = undefined;\r\n this._isPaused = false;\r\n\r\n this._srcView = startView;\r\n this._dstView = endView;\r\n this._isMoving = false;\r\n }\r\n\r\n isMoving() {\r\n return this._isMoving;\r\n }\r\n\r\n wasStarted() {\r\n return typeof this._startTime !== 'undefined' && typeof this._endTime !== 'undefined';\r\n }\r\n\r\n start() {\r\n this._startTime = Date.now();\r\n const transTime = settings.now.interpolateViews ? _transitionTime * 1000 : 0;\r\n this._endTime = this._startTime + transTime;\r\n this._isMoving = true;\r\n }\r\n\r\n getCurrentView() {\r\n if (typeof this._srcView === 'undefined' || typeof this._dstView === 'undefined'\r\n || !this._isMoving || !this.wasStarted()) {\r\n return { success: false };\r\n }\r\n\r\n let view = this.createView();\r\n const time = Date.now();\r\n if (time > this._endTime) {\r\n view = this._dstView;\r\n this.reset();\r\n return { success: true, view };\r\n }\r\n\r\n const factor = (time - this._startTime) / (this._endTime - this._startTime);\r\n view.position.copy(this._srcView.position);\r\n view.position.lerp(this._dstView.position, factor);\r\n view.scale = (1 - factor) * this._srcView.scale + factor * this._dstView.scale;\r\n view.orientation.copy(this._srcView.orientation);\r\n view.orientation.slerp(this._dstView.orientation, factor);\r\n return { success: true, view };\r\n }\r\n\r\n reset() {\r\n this._startTime = this._endTime = 0;\r\n this._isMoving = false;\r\n }\r\n\r\n pause() {\r\n if (!this._isPaused) {\r\n this.setup(this.getCurrentView().view, this._dstView);\r\n this._isPaused = true;\r\n }\r\n }\r\n\r\n resume() {\r\n this._isPaused = false;\r\n }\r\n\r\n createView() {\r\n return new View();\r\n }\r\n}\r\n","import _ from 'lodash';\r\nimport makeContextDependent from './makeContextDependent';\r\n\r\nconst MAX_COOKIE_LEN = 4000;\r\nconst COUNT_SUFFIX = 'Cnt';\r\n\r\nfunction _chunkString(string, chunkLen) {\r\n const l = string.length;\r\n const chunks = [];\r\n for (let c = 0, lc = 0; lc < l; c++, lc += chunkLen) {\r\n chunks[c] = string.slice(lc, lc + chunkLen);\r\n }\r\n return chunks;\r\n}\r\n\r\n/**\r\n * Create new context dependent Cookie holder object.\r\n * @param context\r\n * @param {Object} opts - options\r\n * @param {string} opts.path - cookie path\r\n * @constructor\r\n */\r\nfunction Cookies(context, opts) {\r\n this.context = context;\r\n this._opts = _.merge({\r\n path: '/',\r\n }, opts);\r\n}\r\n\r\nmakeContextDependent(Cookies.prototype);\r\n\r\n/**\r\n * Remove cookie by the name.\r\n * @param key\r\n */\r\nCookies.prototype.removeCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n this._removeSimpleCookie(key);\r\n return;\r\n }\r\n this._removeSimpleCookie(cntKey);\r\n cntVal = parseInt(cntVal, 10);\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._removeSimpleCookie(key + i);\r\n }\r\n};\r\n\r\n/**\r\n * Set new cookie value. Automatically splits\r\n * values that are too large into multiple cookies.\r\n * @param key\r\n * @param value\r\n */\r\nCookies.prototype.setCookie = function (key, value) {\r\n this.removeCookie(key);\r\n value = encodeURIComponent(value);\r\n const values = _chunkString(value, MAX_COOKIE_LEN - key.length - 1);\r\n const cntVal = values.length;\r\n if (cntVal === 1) {\r\n this._setSimpleCookie(key, value);\r\n return;\r\n }\r\n const cntKey = this._toCount(key);\r\n this._setSimpleCookie(cntKey, cntVal.toString());\r\n for (let i = 0; i < cntVal; ++i) {\r\n this._setSimpleCookie(key + i, values[i]);\r\n }\r\n};\r\n\r\n/**\r\n * Obtain the value of a compound cookie.\r\n * @param key\r\n */\r\nCookies.prototype.getCookie = function (key) {\r\n const cntKey = this._toCount(key);\r\n let cntVal = this._getSimpleCookie(cntKey);\r\n if (!cntVal) {\r\n return this._getSimpleCookie(key);\r\n }\r\n cntVal = parseInt(cntVal, 10);\r\n const value = [];\r\n for (let i = 0; i < cntVal; ++i) {\r\n value[i] = this._getSimpleCookie(key + i);\r\n }\r\n return value.join('');\r\n};\r\n\r\nCookies.prototype._toCount = function (key) {\r\n return key + COUNT_SUFFIX;\r\n};\r\n\r\nCookies.prototype._removeSimpleCookie = function (key) {\r\n document.cookie = `${key}=; expires=Thu, 01 Jan 1970 00:00:01 GMT;`;\r\n};\r\n\r\nCookies.prototype._getExpirationDate = function () {\r\n const today = new Date();\r\n const EXP_PERIOD_YEARS = 10;\r\n today.setFullYear(today.getFullYear() + EXP_PERIOD_YEARS);\r\n return today;\r\n};\r\n\r\nCookies.prototype._setSimpleCookie = function (key, value) {\r\n document.cookie = `${key}=${value\r\n };expires=${this._getExpirationDate().toUTCString()\r\n };path=${this._opts.path}`;\r\n};\r\n\r\nCookies.prototype._getSimpleCookie = function (key) {\r\n const matches = document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n return matches ? decodeURIComponent(matches[1]) : '';\r\n};\r\n\r\nCookies.prototype._exists = function (key) {\r\n return document.cookie.match(new RegExp(`(?:^|; )${key}=([^;]*)`));\r\n};\r\n\r\nexport default Cookies;\r\n","/*\r\n * Toggling WebVR is done through button.click because of limitations on calling requestPresent in webVR:\r\n * VRDisplay::requestPresent should be called from user gesture:\r\n * https://developer.mozilla.org/en-US/docs/Web/API/VRDisplay/requestPresent\r\n */\r\nexport default function (webVRPoC) {\r\n function showEnterVR(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'pointer';\r\n button.style.left = 'calc(50% - 50px)';\r\n button.style.width = '100px';\r\n\r\n button.textContent = 'ENTER VR';\r\n\r\n let currentSession = null;\r\n\r\n function onSessionEnded(/* event */) {\r\n currentSession.removeEventListener('end', onSessionEnded);\r\n button.textContent = 'ENTER VR';\r\n currentSession = null;\r\n }\r\n\r\n function onSessionStarted(session) {\r\n session.addEventListener('end', onSessionEnded);\r\n webVRPoC._gfx.renderer.xr.setReferenceSpaceType('local');\r\n webVRPoC._gfx.renderer.xr.setSession(session);\r\n button.textContent = 'EXIT VR';\r\n currentSession = session;\r\n }\r\n\r\n button.onmouseenter = function () { button.style.opacity = '1.0'; };\r\n button.onmouseleave = function () { button.style.opacity = '0.5'; };\r\n\r\n button.onclick = function () {\r\n if (currentSession === null) {\r\n // WebXR's requestReferenceSpace only works if the corresponding feature\r\n // was requested at session creation time. For simplicity, just ask for\r\n // the interesting ones as optional features, but be aware that the\r\n // requestReferenceSpace call will fail if it turns out to be unavailable.\r\n // ('local' is always available for immersive sessions and doesn't need to\r\n // be requested separately.)\r\n\r\n const sessionInit = { optionalFeatures: ['local-floor', 'bounded-floor'] };\r\n navigator.xr.requestSession('immersive-vr', sessionInit).then(onSessionStarted);\r\n webVRPoC.moveSceneBehindHeadset();\r\n } else {\r\n currentSession.end();\r\n }\r\n };\r\n }\r\n\r\n function showWebXRNotFound(button) {\r\n button.style.display = '';\r\n button.style.cursor = 'auto';\r\n button.style.left = 'calc(50% - 75px)';\r\n button.style.width = '150px';\r\n button.textContent = 'VR NOT FOUND';\r\n button.onmouseenter = null;\r\n button.onmouseleave = null;\r\n button.onclick = null;\r\n }\r\n\r\n function stylizeElement(element) {\r\n element.style.position = 'absolute';\r\n element.style.bottom = '20px';\r\n element.style.padding = '12px 6px';\r\n element.style.border = '1px solid #fff';\r\n element.style.borderRadius = '4px';\r\n element.style.background = 'transparent';\r\n element.style.color = '#fff';\r\n element.style.font = 'normal 13px sans-serif';\r\n element.style.textAlign = 'center';\r\n element.style.opacity = '0.5';\r\n element.style.outline = 'none';\r\n element.style.zIndex = '999';\r\n }\r\n\r\n if ('xr' in navigator) {\r\n const button = document.createElement('button');\r\n button.style.display = 'none';\r\n stylizeElement(button);\r\n navigator.xr.isSessionSupported('immersive-vr').then((supported) => (\r\n supported ? showEnterVR(button) : showWebXRNotFound(button)\r\n ));\r\n return button;\r\n }\r\n const message = document.createElement('a');\r\n message.href = 'https://webvr.info';\r\n message.innerHTML = 'WEBXR NOT SUPPORTED';\r\n message.style.left = 'calc(50% - 90px)';\r\n message.style.width = '180px';\r\n message.style.textDecoration = 'none';\r\n stylizeElement(message);\r\n return message;\r\n}\r\n","import * as THREE from 'three';\r\nimport createWebVRButton from './createWebVRButton';\r\nimport gfxutils from '../gfxutils';\r\nimport logger from '../../utils/logger';\r\nimport settings from '../../settings';\r\nimport UberMaterial from '../shaders/UberMaterial';\r\n\r\nexport default class WebVRPoC {\r\n constructor(onToggle) {\r\n this._mainCamera = new THREE.PerspectiveCamera();\r\n this._button = null;\r\n this._onToggle = onToggle;\r\n\r\n this._molContainer = new gfxutils.RCGroup();\r\n this._user = new gfxutils.RCGroup();\r\n this._scalingPivot = new THREE.Object3D();\r\n this._user.add(this._scalingPivot);\r\n\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n this._pressedGripsCounter = 0;\r\n this._distance = 0;\r\n\r\n this._gfx = null;\r\n }\r\n\r\n startScalingByControllers() {\r\n // reset scale\r\n this._distance = this._controller1.position.distanceTo(this._controller2.position);\r\n gfxutils.getMiddlePoint(this._controller1.position, this._controller2.position, this._scalingPivot.position);\r\n this._scalingPivot.scale.set(1, 1, 1);\r\n this._scalingPivot.updateMatrix();\r\n this._scalingPivot.updateMatrixWorld();\r\n // link molecule to pivot\r\n this._scalingPivot.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n stopScalingByControllers() {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n\r\n handleGripsDown(event) {\r\n this._pressedGripsCounter++;\r\n if (this._pressedGripsCounter === 2) {\r\n this.startScalingByControllers();\r\n } else if (this._pressedGripsCounter === 1) {\r\n event.target.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n handleGripsUp(event) {\r\n this._pressedGripsCounter--;\r\n if (this._pressedGripsCounter === 1) {\r\n this.stopScalingByControllers();\r\n // reattach molecule to other controller\r\n const anotherController = event.target === this._controller1 ? this._controller2 : this._controller1;\r\n anotherController.addSavingWorldTransform(this._molContainer);\r\n } else if (this._pressedGripsCounter === 0) {\r\n this._gfx.scene.addSavingWorldTransform(this._molContainer);\r\n }\r\n }\r\n\r\n enable(gfx) {\r\n if (!gfx) {\r\n logger.warn('WebVR couldn\\'t be enabled, because gfx is not defined');\r\n return;\r\n }\r\n this._gfx = gfx;\r\n const { renderer, camera } = gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n if (!camera) {\r\n throw new Error('No camera is available to toggle WebVR');\r\n }\r\n\r\n // enable xr in renderer\r\n renderer.xr.enabled = true;\r\n // add button for turning vr mode\r\n if (!this._button) {\r\n this._button = createWebVRButton(this);\r\n document.body.appendChild(this._button);\r\n } else {\r\n this._button.style.display = 'block';\r\n }\r\n // store fog setting\r\n this._mainFog = settings.now.fog;\r\n settings.set('fog', false);\r\n\r\n this._plugVRNodesIntoScene(gfx, renderer);\r\n this._setControllersListeners();\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n _plugVRNodesIntoScene(gfx, renderer) {\r\n // store common scene camera\r\n this._mainCamera.copy(gfx.camera);\r\n // add hierarchical structure for webVR into scene\r\n gfx.scene.add(this._user);\r\n // turn on webvr transformation\r\n gfx.scene.add(this._molContainer);\r\n this._molContainer.add(gfx.root);\r\n\r\n this._controller1 = renderer.xr.getController(0);\r\n this._controller2 = renderer.xr.getController(1);\r\n const mesh = this._createControllerMesh();\r\n this._controller1.add(mesh);\r\n this._controller2.add(mesh.clone());\r\n this._user.add(this._controller1);\r\n this._user.add(this._controller2);\r\n }\r\n\r\n _setControllersListeners() {\r\n this._controller1.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('selectstart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('selectend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n\r\n this._controller1.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller1.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n this._controller2.addEventListener('squeezestart', (event) => {\r\n this.handleGripsDown(event);\r\n });\r\n this._controller2.addEventListener('squeezeend', (event) => {\r\n this.handleGripsUp(event);\r\n });\r\n }\r\n\r\n disable() {\r\n if (!this._gfx) {\r\n return;\r\n }\r\n const { renderer, camera } = this._gfx;\r\n if (!renderer) {\r\n throw new Error('No renderer is available to toggle WebVR');\r\n }\r\n\r\n // nullify webxr callback for animation frame\r\n renderer.setAnimationLoop(null);\r\n const session = renderer.xr.getSession();\r\n if (session) {\r\n session.end();\r\n }\r\n renderer.xr.enabled = false;\r\n // remove button of VR entering\r\n if (this._button) {\r\n this._button.style.display = 'none';\r\n }\r\n // restore fog param\r\n settings.set('fog', this._mainFog);\r\n\r\n this._unplugVRNodesFromScene(camera);\r\n\r\n // make some Miew job\r\n if (this._onToggle) {\r\n this._onToggle(false);\r\n }\r\n }\r\n\r\n _unplugVRNodesFromScene(camera) {\r\n // restore common camera\r\n if (this._mainCamera && camera) {\r\n camera.copy(this._mainCamera);\r\n }\r\n // turn off webvr transformation\r\n const root = this._molContainer.children[0];\r\n if (root) {\r\n this._gfx.scene.add(root);\r\n }\r\n this._molContainer.parent.remove(this._molContainer);\r\n if (this._user) {\r\n this._gfx.scene.remove(this._user);\r\n }\r\n // free scene nodes\r\n this._molContainer = null;\r\n this._user = null;\r\n this._scalingPivot = null;\r\n this._user = null;\r\n this._controller1 = null;\r\n this._controller2 = null;\r\n }\r\n\r\n _createControllerMesh() {\r\n // visualize controllers with cylinders\r\n const geometry = new THREE.CylinderGeometry(0.04, 0.04, 0.3);\r\n const material = new UberMaterial({ lights: false, overrideColor: true });\r\n material.setUberOptions({ fixedColor: new THREE.Color(0x4444ff) });\r\n material.updateUniforms();\r\n const cylinder = new THREE.Mesh(geometry, material);\r\n cylinder.rotateX(-Math.PI / 2);\r\n return cylinder;\r\n }\r\n\r\n updateMoleculeScale() {\r\n if (!this._controller1 || !this._controller2) {\r\n return;\r\n }\r\n\r\n const self = this;\r\n // update molecule scaling by controllers\r\n if (self._pressedGripsCounter === 2) {\r\n // recalc scaling pivot\r\n gfxutils.getMiddlePoint(self._controller1.position, self._controller2.position, self._scalingPivot.position);\r\n // recalc scaler\r\n const dist = self._controller1.position.distanceTo(self._controller2.position);\r\n const scaler = dist / self._distance;\r\n self._scalingPivot.scale.multiplyScalar(scaler);\r\n // save cur distance for next frame\r\n self._distance = dist;\r\n }\r\n }\r\n\r\n /**\r\n * Reposition molecule right before the camera.\r\n * @note The proper way is to initiate headset in the place of common Miew's camera.\r\n * But threejs limitations on setting new XRReferenceSpace enforce the molecule repositioning\r\n * Hope, something will change.\r\n */\r\n moveSceneBehindHeadset() {\r\n const gfx = this._gfx;\r\n const { camera } = gfx;\r\n\r\n // set container position in camera space\r\n const container = this._molContainer;\r\n container.matrix.identity();\r\n container.position.set(0, 0, -4.0);\r\n container.updateMatrix();\r\n\r\n // update container world matrix\r\n container.matrixWorld.multiplyMatrices(camera.matrixWorld, container.matrix);\r\n // readd to scene\r\n gfx.scene.addSavingWorldTransform(container);\r\n if (this._onToggle) {\r\n this._onToggle(true);\r\n }\r\n }\r\n\r\n getCanvas() {\r\n const gfx = this._gfx;\r\n return (gfx && gfx.renderer) ? gfx.renderer.domElement : null;\r\n }\r\n}\r\n","/* global PACKAGE_VERSION:false */\r\nimport _ from 'lodash';\r\nimport * as THREE from 'three';\r\nimport { Spinner } from 'spin.js';\r\nimport Stats from './gfx/Stats';\r\nimport utils from './utils';\r\nimport JobHandle from './utils/JobHandle';\r\nimport options from './options';\r\nimport settings from './settings';\r\nimport chem from './chem';\r\nimport Visual from './Visual';\r\nimport ComplexVisual from './ComplexVisual';\r\nimport Complex from './chem/Complex';\r\nimport VolumeVisual from './VolumeVisual';\r\nimport io from './io/io';\r\nimport modes from './gfx/modes';\r\nimport colorers from './gfx/colorers';\r\nimport palettes from './gfx/palettes';\r\nimport materials from './gfx/materials';\r\nimport Representation from './gfx/Representation';\r\nimport CSS2DRenderer from './gfx/CSS2DRenderer';\r\nimport ObjectControls from './ui/ObjectControls';\r\nimport Picker from './ui/Picker';\r\nimport Axes from './gfx/Axes';\r\nimport gfxutils from './gfx/gfxutils';\r\nimport meshutils from './gfx/meshutils';\r\nimport FrameInfo from './gfx/FrameInfo';\r\nimport meshes from './gfx/meshes/meshes';\r\nimport LinesObject from './gfx/objects/LinesObj';\r\nimport UberMaterial from './gfx/shaders/UberMaterial';\r\nimport OutlineMaterial from './gfx/shaders/OutlineMaterial';\r\nimport FXAAMaterial from './gfx/shaders/FXAAMaterial';\r\nimport AOMaterial from './gfx/shaders/AOMaterial';\r\nimport AOHorBlurMaterial from './gfx/shaders/AOHorBlurMaterial';\r\nimport AOVertBlurWithBlendMaterial from './gfx/shaders/AOVertBlurWithBlendMaterial';\r\nimport AnaglyphMaterial from './gfx/shaders/AnaglyphMaterial';\r\nimport VolumeMaterial from './gfx/shaders/VolumeMaterial';\r\nimport ViewInterpolator from './gfx/ViewInterpolator';\r\nimport EventDispatcher from './utils/EventDispatcher';\r\nimport logger from './utils/logger';\r\nimport Cookies from './utils/Cookies';\r\nimport capabilities from './gfx/capabilities';\r\nimport WebVRPoC from './gfx/vr/WebVRPoC';\r\nimport vertexScreenQuadShader from './gfx/shaders/ScreenQuad.vert';\r\nimport fragmentScreenQuadFromDistTex from './gfx/shaders/ScreenQuadFromDistortionTex.frag';\r\nimport getTopWindow from './utils/getTopWindow';\r\n\r\nconst {\r\n selectors,\r\n Atom,\r\n Residue,\r\n Chain,\r\n Molecule,\r\n} = chem;\r\n\r\nconst EDIT_MODE = { COMPLEX: 0, COMPONENT: 1, FRAGMENT: 2 };\r\n\r\nconst LOADER_NOT_FOUND = 'Could not find suitable loader for this source';\r\nconst PARSER_NOT_FOUND = 'Could not find suitable parser for this source';\r\n\r\n// Color management changed a lot in threejs 152+ version.\r\n// To keep miew colors we disable the new color management system\r\nTHREE.ColorManagement.enabled = false;\r\n\r\nconst { createElement } = utils;\r\n\r\nfunction updateFogRange(fog, center, radius) {\r\n fog.near = center - radius * settings.now.fogNearFactor;\r\n fog.far = center + radius * settings.now.fogFarFactor;\r\n}\r\n\r\nfunction removeExtension(fileName) {\r\n const dot = fileName.lastIndexOf('.');\r\n if (dot >= 0) {\r\n fileName = fileName.substr(0, dot);\r\n }\r\n return fileName;\r\n}\r\n\r\nfunction hasValidResidues(complex) {\r\n let hasValidRes = false;\r\n complex.forEachComponent((component) => {\r\n component.forEachResidue((residue) => {\r\n if (residue._isValid) {\r\n hasValidRes = true;\r\n }\r\n });\r\n });\r\n return hasValidRes;\r\n}\r\n\r\nfunction reportProgress(log, action, percent) {\r\n const TOTAL_PERCENT = 100;\r\n if (percent !== undefined) {\r\n log.debug(`${action}... ${Math.floor(percent * TOTAL_PERCENT)}%`);\r\n } else {\r\n log.debug(`${action}...`);\r\n }\r\n}\r\n\r\nfunction chooseFogColor() {\r\n return settings.now.fogColorEnable ? settings.now.fogColor : settings.now.bg.color;\r\n}\r\n\r\n// ////////////////////////////////////////////////////////////////////////////\r\n\r\n/**\r\n * Main 3D Molecular Viewer class.\r\n *\r\n * @param {object} opts - Viewer options.\r\n * @param {HTMLElement=} opts.container - DOM element that serves as a viewer container.\r\n * @param {object=} opts.settings - An object with properties to override default settings.\r\n * @param {string=} opts.settingsCookie='settings' - The name of the cookie to save current settings to.\r\n * @param {string=} opts.cookiePath='/' - The path option for cookies. Defaults to root.\r\n *\r\n * @exports Miew\r\n * @constructor\r\n */\r\nfunction Miew(opts) {\r\n EventDispatcher.call(this);\r\n this._opts = _.merge({\r\n settingsCookie: 'settings',\r\n cookiePath: '/',\r\n }, opts);\r\n /** @type {?object} */\r\n this._gfx = null;\r\n /** @type {ViewInterpolator} */\r\n this._interpolator = new ViewInterpolator();\r\n /** @type {HTMLElement} */\r\n this._container = (opts && opts.container)\r\n || document.getElementById('miew-container')\r\n || _.head(document.getElementsByClassName('miew-container'))\r\n || document.body;\r\n /** @type {HTMLElement} */\r\n this._containerRoot = this._container;\r\n\r\n /** @type {boolean} */\r\n this._running = false;\r\n /** @type {boolean} */\r\n this._halting = false;\r\n /** @type {boolean} */\r\n this._building = false;\r\n /** @type {boolean} */\r\n this._needRender = true;\r\n /** @type {boolean} */\r\n this._hotKeysEnabled = true;\r\n\r\n /** @type {Settings} */\r\n this.settings = settings;\r\n const log = logger;\r\n log.console = DEBUG;\r\n log.level = DEBUG ? 'debug' : 'info';\r\n /**\r\n * @type {Logger}\r\n * @example\r\n * miew.logger.addEventListener('message', function _onLogMessage(evt) {\r\n * console.log(evt.message);\r\n * });\r\n */\r\n this.logger = log;\r\n\r\n this._cookies = new Cookies(this);\r\n this.restoreSettings();\r\n if (opts && opts.settings) {\r\n this.settings.set(opts.settings);\r\n }\r\n\r\n /** @type {?Spinner} */\r\n this._spinner = null;\r\n /** @type {JobHandle[]} */\r\n this._loading = [];\r\n /** @type {?number}\r\n * @deprecated until Animation system refactoring\r\n */\r\n this._animInterval = null;\r\n\r\n /** @type {object} */\r\n this._visuals = {};\r\n /** @type {?string} */\r\n this._curVisualName = null;\r\n\r\n /** @type {array} */\r\n this._objects = [];\r\n\r\n /** @type {object} */\r\n this._sourceWindow = null;\r\n\r\n this.reset();\r\n\r\n if (this._repr) {\r\n log.debug(`Selected ${this._repr.mode.name} mode with ${this._repr.colorer.name} colorer.`);\r\n }\r\n\r\n const self = this;\r\n Miew.registeredPlugins.forEach((plugin) => {\r\n plugin.call(self);\r\n });\r\n\r\n this._initOnSettingsChanged();\r\n}\r\n\r\nMiew.prototype = Object.create(EventDispatcher.prototype);\r\nMiew.prototype.constructor = Miew;\r\n\r\nMiew.prototype.getMaxRepresentationCount = function () {\r\n return ComplexVisual.NUM_REPRESENTATION_BITS;\r\n};\r\n\r\n/**\r\n * Replace viewer container contents with a DOM element.\r\n * @param {HTMLElement} container - parent container.\r\n * @param {HTMLElement} element - DOM element to show.\r\n * @private\r\n */\r\nfunction _setContainerContents(container, element) {\r\n const parent = container;\r\n while (parent.firstChild) {\r\n parent.removeChild(parent.firstChild);\r\n }\r\n parent.appendChild(element);\r\n}\r\n\r\n/**\r\n * Update Shadow Camera target position and frustum.\r\n * @private\r\n */\r\nMiew.prototype._updateShadowCamera = (function () {\r\n const shadowMatrix = new THREE.Matrix4();\r\n const direction = new THREE.Vector3();\r\n const OBB = { center: new THREE.Vector3(), halfSize: new THREE.Vector3() };\r\n\r\n return function () {\r\n this._gfx.scene.updateMatrixWorld();\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = this._gfx.scene.children[i];\r\n shadowMatrix.copy(light.shadow.camera.matrixWorldInverse);\r\n this.getOBB(shadowMatrix, OBB);\r\n\r\n direction.subVectors(light.target.position, light.position);\r\n light.position.subVectors(OBB.center, direction);\r\n light.target.position.copy(OBB.center);\r\n\r\n light.shadow.bias = 0.09;\r\n light.shadow.camera.bottom = -OBB.halfSize.y;\r\n light.shadow.camera.top = OBB.halfSize.y;\r\n light.shadow.camera.right = OBB.halfSize.x;\r\n light.shadow.camera.left = -OBB.halfSize.x;\r\n light.shadow.camera.near = direction.length() - OBB.halfSize.z;\r\n light.shadow.camera.far = direction.length() + OBB.halfSize.z;\r\n\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Initialize the viewer.\r\n * @returns {boolean} true on success.\r\n * @throws Forwards exception raised during initialization.\r\n * @see Miew#term\r\n */\r\nMiew.prototype.init = function () {\r\n const container = this._container;\r\n const elem = utils.createElement('div', { class: 'miew-canvas' });\r\n _setContainerContents(container, elem);\r\n this._container = elem;\r\n\r\n const frag = document.createDocumentFragment();\r\n frag.appendChild(this._msgMode = createElement(\r\n 'div',\r\n { class: 'mode-message overlay' },\r\n createElement('p', {}, 'COMPONENT EDIT MODE'),\r\n ));\r\n frag.appendChild(this._msgAtomInfo = createElement(\r\n 'div',\r\n { class: 'atom-info overlay' },\r\n createElement('p', {}, ''),\r\n ));\r\n container.appendChild(frag);\r\n\r\n if (this._gfx !== null) { // block double init\r\n return true;\r\n }\r\n\r\n const self = this;\r\n this._showMessage('Viewer is being initialized...');\r\n try {\r\n this._initGfx();\r\n\r\n this._initListeners();\r\n this._spinner = new Spinner({\r\n lines: 13,\r\n length: 28,\r\n width: 14,\r\n radius: 42,\r\n color: '#fff',\r\n zIndex: 700,\r\n });\r\n\r\n const target = getTopWindow();\r\n target.addEventListener('keydown', (event) => {\r\n self._onKeyDown(event);\r\n });\r\n\r\n target.addEventListener('keyup', (event) => {\r\n self._onKeyUp(event);\r\n });\r\n\r\n this._objectControls = new ObjectControls(\r\n this._gfx.root,\r\n this._gfx.pivot,\r\n this._gfx.camera,\r\n this._gfx.renderer.domElement,\r\n () => self._getAltObj(),\r\n );\r\n this._objectControls.addEventListener('change', (e) => {\r\n if (settings.now.shadow.on) {\r\n self._updateShadowCamera();\r\n }\r\n // route rotate, zoom, translate and translatePivot events to the external API\r\n switch (e.action) {\r\n case 'rotate':\r\n self.dispatchEvent({ type: 'rotate', quaternion: e.quaternion });\r\n break;\r\n case 'zoom':\r\n self.dispatchEvent({ type: 'zoom', factor: e.factor });\r\n break;\r\n default:\r\n self.dispatchEvent({ type: e.action });\r\n }\r\n self.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n });\r\n\r\n const gfx = this._gfx;\r\n this._picker = new Picker(gfx.root, gfx.camera, gfx.renderer.domElement);\r\n this._picker.addEventListener('newpick', (event) => {\r\n self._onPick(event);\r\n });\r\n this._picker.addEventListener('dblclick', (event) => {\r\n self.center(event);\r\n });\r\n } catch (error) {\r\n if (error.name === 'TypeError' && error.message === 'Cannot read property \\'getExtension\\' of null') {\r\n this._showMessage('Could not create WebGL context.');\r\n } else if (error.message.search(/webgl/i) > 1) {\r\n this._showMessage(error.message);\r\n } else {\r\n this._showMessage('Viewer initialization failed.');\r\n throw error;\r\n }\r\n return false;\r\n }\r\n\r\n // automatically load default file\r\n const file = this._opts && this._opts.load;\r\n if (file) {\r\n const type = this._opts && this._opts.type;\r\n this.load(file, { fileType: type, keepRepsInfo: true });\r\n }\r\n\r\n return true;\r\n};\r\n\r\n/**\r\n * Terminate the viewer completely.\r\n * @see Miew#init\r\n */\r\nMiew.prototype.term = function () {\r\n this._showMessage('Viewer has been terminated.');\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n this.halt();\r\n this._gfx = null;\r\n};\r\n\r\n/**\r\n * Display message inside the viewer container, hiding WebGL canvas.\r\n * @param {string} msg - Message to show.\r\n * @private\r\n */\r\nMiew.prototype._showMessage = function (msg) {\r\n const element = document.createElement('div');\r\n element.setAttribute('class', 'miew-message');\r\n element.appendChild(document.createElement('p')).appendChild(document.createTextNode(msg));\r\n _setContainerContents(this._container, element);\r\n};\r\n\r\n/**\r\n * Display WebGL canvas inside the viewer container, hiding any message shown.\r\n * @private\r\n */\r\nMiew.prototype._showCanvas = function () {\r\n _setContainerContents(this._container, this._gfx.renderer.domElement);\r\n};\r\n\r\nMiew.prototype._requestAnimationFrame = function (callback) {\r\n const { xr } = this._gfx.renderer;\r\n if (xr && xr.enabled) {\r\n this._gfx.renderer.setAnimationLoop(callback);\r\n return;\r\n }\r\n requestAnimationFrame(callback);\r\n};\r\n\r\n/**\r\n * Initialize WebGL and set 3D scene up.\r\n * @private\r\n */\r\nMiew.prototype._initGfx = function () {\r\n const gfx = {\r\n width: this._container.clientWidth,\r\n height: this._container.clientHeight,\r\n };\r\n\r\n const webGLOptions = { preserveDrawingBuffer: true, alpha: true, premultipliedAlpha: false };\r\n if (settings.now.antialias) {\r\n webGLOptions.antialias = true;\r\n }\r\n\r\n gfx.renderer2d = new CSS2DRenderer();\r\n\r\n gfx.renderer = new THREE.WebGLRenderer(webGLOptions);\r\n gfx.renderer.shadowMap.enabled = settings.now.shadow.on;\r\n gfx.renderer.shadowMap.autoUpdate = false;\r\n gfx.renderer.shadowMap.type = THREE.PCFShadowMap;\r\n capabilities.init(gfx.renderer);\r\n\r\n gfx.renderer.autoClear = false;\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n gfx.camera = new THREE.PerspectiveCamera(\r\n settings.now.camFov,\r\n gfx.width / gfx.height,\r\n settings.now.camNear,\r\n settings.now.camFar,\r\n );\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.position.z = settings.now.camDistance;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME);\r\n gfx.camera.layers.enable(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n\r\n gfx.stereoCam = new THREE.StereoCamera();\r\n\r\n gfx.scene = new THREE.Scene();\r\n\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color, settings.now.camNear, settings.now.camFar);\r\n\r\n gfx.root = new gfxutils.RCGroup();\r\n gfx.scene.add(gfx.root);\r\n\r\n gfx.pivot = new gfxutils.RCGroup();\r\n gfx.root.add(gfx.pivot);\r\n\r\n gfx.selectionScene = new THREE.Scene();\r\n gfx.selectionRoot = new THREE.Group();\r\n gfx.selectionRoot.matrixAutoUpdate = false;\r\n gfx.selectionScene.add(gfx.selectionRoot);\r\n\r\n gfx.selectionPivot = new THREE.Group();\r\n gfx.selectionPivot.matrixAutoUpdate = false;\r\n gfx.selectionRoot.add(gfx.selectionPivot);\r\n\r\n const light12 = new THREE.DirectionalLight(0xffffff, 0.45);\r\n light12.position.set(0, 0.414, 1);\r\n light12.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n light12.castShadow = true;\r\n light12.shadow.bias = 0.09;\r\n light12.shadow.radius = settings.now.shadow.radius;\r\n light12.shadow.camera.layers.set(gfxutils.LAYERS.SHADOWMAP);\r\n\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n const shadowMapSize = Math.max(gfx.width, gfx.height) * pixelRatio;\r\n light12.shadow.mapSize.width = shadowMapSize;\r\n light12.shadow.mapSize.height = shadowMapSize;\r\n light12.target.position.set(0.0, 0.0, 0.0);\r\n gfx.scene.add(light12);\r\n gfx.scene.add(light12.target);\r\n\r\n const light3 = new THREE.AmbientLight(0x666666);\r\n light3.layers.enable(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.scene.add(light3);\r\n\r\n // add axes\r\n gfx.axes = new Axes(gfx.root, gfx.camera);\r\n const deviceWidth = gfx.width * pixelRatio;\r\n const deviceHeight = gfx.height * pixelRatio;\r\n\r\n gfx.offscreenBuf = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat, depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf.depthTexture = new THREE.DepthTexture();\r\n gfx.offscreenBuf.depthTexture.type = THREE.UnsignedShortType;\r\n\r\n gfx.offscreenBuf2 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf3 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf4 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf3;\r\n gfx.volFFTex = gfx.offscreenBuf4;\r\n gfx.volWFFTex = gfx.offscreenBuf;\r\n\r\n // use float textures for volume rendering (WebGL2 core feature)\r\n gfx.offscreenBuf5 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf6 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.offscreenBuf7 = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter,\r\n magFilter: THREE.LinearFilter,\r\n format: THREE.RGBAFormat,\r\n type: THREE.FloatType,\r\n depthBuffer: true,\r\n },\r\n );\r\n\r\n gfx.volBFTex = gfx.offscreenBuf5;\r\n gfx.volFFTex = gfx.offscreenBuf6;\r\n gfx.volWFFTex = gfx.offscreenBuf7;\r\n\r\n gfx.stereoBufL = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n gfx.stereoBufR = new THREE.WebGLRenderTarget(\r\n deviceWidth,\r\n deviceHeight,\r\n {\r\n minFilter: THREE.LinearFilter, magFilter: THREE.LinearFilter, format: THREE.RGBAFormat, depthBuffer: false,\r\n },\r\n );\r\n\r\n this._gfx = gfx;\r\n this._showCanvas();\r\n\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n\r\n this._container.appendChild(gfx.renderer2d.getElement());\r\n\r\n // add FPS counter\r\n const stats = new Stats();\r\n stats.domElement.style.position = 'absolute';\r\n stats.domElement.style.right = '0';\r\n stats.domElement.style.bottom = '0';\r\n this._container.appendChild(stats.domElement);\r\n this._fps = stats;\r\n this._fps.show(settings.now.fps);\r\n};\r\n\r\n/**\r\n * Setup event listeners.\r\n * @private\r\n */\r\nMiew.prototype._initListeners = function () {\r\n const self = this;\r\n window.addEventListener('resize', () => {\r\n self._onResize();\r\n });\r\n};\r\n\r\n/**\r\n * Try to add numbers to the base name to make it unique among visuals\r\n * @private\r\n */\r\nMiew.prototype._makeUniqueVisualName = function (baseName) {\r\n if (!baseName) {\r\n return Math.random().toString();\r\n }\r\n\r\n let name = baseName;\r\n let suffix = 1;\r\n while (this._visuals.hasOwnProperty(name)) {\r\n name = `${baseName} (${suffix.toString()})`;\r\n suffix++;\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Add visual to the viewer\r\n * @private\r\n */\r\nMiew.prototype._addVisual = function (visual) {\r\n if (!visual) {\r\n return null;\r\n }\r\n\r\n // change visual name in order to make it unique\r\n const name = this._makeUniqueVisualName(visual.name);\r\n visual.name = name;\r\n\r\n this._visuals[name] = visual;\r\n this._gfx.pivot.add(visual);\r\n if (visual.getSelectionGeo) {\r\n this._gfx.selectionPivot.add(visual.getSelectionGeo());\r\n }\r\n\r\n return name;\r\n};\r\n\r\n/**\r\n * Remove visual from the viewer\r\n * @private\r\n */\r\nMiew.prototype._removeVisual = function (visual) {\r\n let name = '';\r\n let obj = null;\r\n if (visual instanceof Visual) {\r\n ({ name } = visual);\r\n obj = visual;\r\n } else if (typeof visual === 'string') {\r\n name = visual;\r\n obj = this._visuals[name];\r\n }\r\n\r\n if (!obj || !this._visuals.hasOwnProperty(name) || this._visuals[name] !== obj) {\r\n return;\r\n }\r\n\r\n if (name === this._curVisualName) {\r\n this._curVisualName = undefined;\r\n }\r\n\r\n delete this._visuals[name];\r\n obj.release(); // removes nodes from scene\r\n\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Call specified function for each Visual\r\n * @private\r\n */\r\nMiew.prototype._forEachVisual = function (callback) {\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Release (destroy) all visuals in the scene\r\n * @private\r\n */\r\nMiew.prototype._releaseAllVisuals = function () {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)) {\r\n this._visuals[name].release();\r\n }\r\n }\r\n\r\n this._visuals = {};\r\n};\r\n\r\n/**\r\n * Call specified function for each ComplexVisual\r\n * @private\r\n */\r\nMiew.prototype._forEachComplexVisual = function (callback) {\r\n if (!this._gfx || !this._gfx.pivot) {\r\n return;\r\n }\r\n\r\n for (const name in this._visuals) {\r\n if (this._visuals.hasOwnProperty(name)\r\n && this._visuals[name] instanceof ComplexVisual) {\r\n callback(this._visuals[name]);\r\n }\r\n }\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual with specified name, or current (if not found), or any, or null\r\n * @private\r\n */\r\nMiew.prototype._getComplexVisual = function (name) {\r\n name = name || this._curVisualName;\r\n let any = null;\r\n let named = null;\r\n this._forEachComplexVisual((visual) => {\r\n any = visual;\r\n if (visual.name === name) {\r\n named = visual;\r\n }\r\n });\r\n return named || any;\r\n};\r\n\r\n/**\r\n * Returns first found VolumeVisual (no more than one should be present actually)\r\n * @private\r\n */\r\nMiew.prototype._getVolumeVisual = function () {\r\n let any = null;\r\n this._forEachVisual((visual) => {\r\n if (visual instanceof VolumeVisual) {\r\n any = visual;\r\n }\r\n });\r\n return any;\r\n};\r\n\r\n/**\r\n * Returns ComplexVisual corresponding to specified complex\r\n * @private\r\n */\r\nMiew.prototype._getVisualForComplex = function (complex) {\r\n if (!complex) {\r\n return null;\r\n }\r\n\r\n let found = null;\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getComplex() === complex) {\r\n found = visual;\r\n }\r\n });\r\n return found;\r\n};\r\n\r\n/*\r\n * Get a list of names of visuals currently shown by the viewer\r\n */\r\nMiew.prototype.getVisuals = function () {\r\n return Object.keys(this._visuals);\r\n};\r\n\r\n/*\r\n * Get complex visuals count\r\n */\r\nMiew.prototype.getComplexVisualsCount = function () {\r\n let count = 0;\r\n this._forEachComplexVisual(() => count++);\r\n return count;\r\n};\r\n\r\n/*\r\n * Get current visual\r\n */\r\nMiew.prototype.getCurrentVisual = function () {\r\n return this._curVisualName;\r\n};\r\n\r\n/*\r\n * Set current visual.\r\n * All further operations will be performed on this visual (complex) if not stated otherwise.\r\n */\r\nMiew.prototype.setCurrentVisual = function (name) {\r\n if (!this._visuals[name]) {\r\n return;\r\n }\r\n\r\n this._curVisualName = name;\r\n};\r\n\r\n/**\r\n * Run the viewer, start processing update/render frames periodically.\r\n * Has no effect if already running.\r\n * @see Miew#halt\r\n */\r\nMiew.prototype.run = function () {\r\n if (!this._running) {\r\n this._running = true;\r\n if (this._halting) {\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._objectControls.enable(true);\r\n this._interpolator.resume();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to stop.\r\n * Will be processed during the next frame.\r\n * @see Miew#run\r\n */\r\nMiew.prototype.halt = function () {\r\n if (this._running) {\r\n this._discardComponentEdit();\r\n this._discardFragmentEdit();\r\n this._objectControls.enable(false);\r\n this._interpolator.pause();\r\n this._halting = true;\r\n }\r\n};\r\n\r\n/**\r\n * Request the viewer to start / stop responsing\r\n * on hot keys.\r\n * @param enabled - start (true) or stop (false) response on hot keys.\r\n */\r\nMiew.prototype.enableHotKeys = function (enabled) {\r\n this._hotKeysEnabled = enabled;\r\n this._objectControls.enableHotkeys(enabled);\r\n};\r\n\r\n/**\r\n * Callback which processes window resize.\r\n * @private\r\n */\r\nMiew.prototype._onResize = function () {\r\n const gfx = this._gfx;\r\n if (!gfx) {\r\n return;\r\n }\r\n\r\n this._needRender = true;\r\n\r\n gfx.width = this._container.clientWidth;\r\n gfx.height = this._container.clientHeight;\r\n\r\n gfx.camera.aspect = gfx.width / gfx.height;\r\n gfx.camera.setMinimalFov(settings.now.camFov);\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n gfx.renderer.setSize(gfx.width, gfx.height);\r\n gfx.renderer2d.setSize(gfx.width, gfx.height);\r\n\r\n this.dispatchEvent({ type: 'resize' });\r\n};\r\n\r\nMiew.prototype._resizeOffscreenBuffers = function (width, height, stereo) {\r\n const gfx = this._gfx;\r\n stereo = stereo || 'NONE';\r\n const isAnaglyph = (stereo === 'NONE' || stereo === 'ANAGLYPH');\r\n const multi = isAnaglyph ? 1 : 0.5;\r\n gfx.offscreenBuf.setSize(multi * width, height);\r\n gfx.offscreenBuf2.setSize(multi * width, height);\r\n gfx.offscreenBuf3.setSize(multi * width, height);\r\n gfx.offscreenBuf4.setSize(multi * width, height);\r\n if (gfx.offscreenBuf5) {\r\n gfx.offscreenBuf5.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf6) {\r\n gfx.offscreenBuf6.setSize(multi * width, height);\r\n }\r\n if (gfx.offscreenBuf7) {\r\n gfx.offscreenBuf7.setSize(multi * width, height);\r\n }\r\n if (isAnaglyph) {\r\n gfx.stereoBufL.setSize(width, height);\r\n gfx.stereoBufR.setSize(width, height);\r\n }\r\n};\r\n\r\n/**\r\n * Callback which processes update/render frames.\r\n * @private\r\n */\r\nMiew.prototype._onTick = function () {\r\n if (this._halting) {\r\n this._running = false;\r\n this._halting = false;\r\n return;\r\n }\r\n\r\n this._fps.update();\r\n\r\n this._requestAnimationFrame(() => this._onTick());\r\n\r\n this._onUpdate();\r\n if (this._needRender) {\r\n this._onRender();\r\n this._needRender = !settings.now.suspendRender || settings.now.stereo === 'WEBVR';\r\n }\r\n};\r\n\r\nMiew.prototype._getBSphereRadius = function () {\r\n // calculate radius that would include all visuals\r\n let radius = 0;\r\n this._forEachVisual((visual) => {\r\n radius = Math.max(radius, visual.getBoundaries().boundingSphere.radius);\r\n });\r\n return radius * this._objectControls.getScale();\r\n};\r\n\r\n/**\r\n * Calculate bounding box that would include all visuals and being axis aligned in world defined by\r\n * transformation matrix: matrix\r\n * @param {Matrix4} matrix - transformation matrix.\r\n * @param {object} OBB - calculating bounding box.\r\n * @param {Vector3} OBB.center - OBB center.\r\n * @param {Vector3} OBB.halfSize - half magnitude of OBB sizes.\r\n */\r\nMiew.prototype.getOBB = (function () {\r\n const _bSphereForOneVisual = new THREE.Sphere();\r\n const _bBoxForOneVisual = new THREE.Box3();\r\n const _bBox = new THREE.Box3();\r\n\r\n const _invMatrix = new THREE.Matrix4();\r\n\r\n const _points = [\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n new THREE.Vector3(),\r\n ];\r\n\r\n return function (matrix, OBB) {\r\n _bBox.makeEmpty();\r\n\r\n this._forEachVisual((visual) => {\r\n _bSphereForOneVisual.copy(visual.getBoundaries().boundingSphere);\r\n _bSphereForOneVisual.applyMatrix4(visual.matrixWorld).applyMatrix4(matrix);\r\n _bSphereForOneVisual.getBoundingBox(_bBoxForOneVisual);\r\n _bBox.union(_bBoxForOneVisual);\r\n });\r\n _bBox.getCenter(OBB.center);\r\n\r\n _invMatrix.copy(matrix).invert();\r\n OBB.center.applyMatrix4(_invMatrix);\r\n\r\n const { min } = _bBox;\r\n const { max } = _bBox;\r\n _points[0].set(min.x, min.y, min.z); // 000\r\n _points[1].set(max.x, min.y, min.z); // 100\r\n _points[2].set(min.x, max.y, min.z); // 010\r\n _points[3].set(min.x, min.y, max.z); // 001\r\n for (let i = 0, l = _points.length; i < l; i++) {\r\n _points[i].applyMatrix4(_invMatrix);\r\n }\r\n\r\n OBB.halfSize.set(\r\n Math.abs(_points[0].x - _points[1].x),\r\n Math.abs(_points[0].y - _points[2].y),\r\n Math.abs(_points[0].z - _points[3].z),\r\n ).multiplyScalar(0.5);\r\n };\r\n}());\r\n\r\nMiew.prototype._updateFog = function () {\r\n const gfx = this._gfx;\r\n\r\n if (settings.now.fog) {\r\n if (typeof gfx.scene.fog === 'undefined' || gfx.scene.fog === null) {\r\n const color = chooseFogColor();\r\n gfx.scene.fog = new THREE.Fog(color);\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n updateFogRange(gfx.scene.fog, gfx.camera.position.z, this._getBSphereRadius());\r\n } else if (gfx.scene.fog) {\r\n gfx.scene.fog = undefined;\r\n this._setUberMaterialValues({ fog: settings.now.fog });\r\n }\r\n};\r\n\r\nMiew.prototype._onUpdate = function () {\r\n if (this.isScriptingCommandAvailable !== undefined && this.isScriptingCommandAvailable() && !this._building) {\r\n this.callNextCmd();\r\n }\r\n\r\n this._objectControls.update();\r\n\r\n this._forEachComplexVisual((visual) => {\r\n visual.getComplex().update();\r\n });\r\n\r\n if (settings.now.autobuild && !this._loading.length && !this._building && this._needRebuild()) {\r\n this.rebuild();\r\n }\r\n\r\n if (!this._loading.length && !this._building && !this._needRebuild()) {\r\n this._updateView();\r\n }\r\n\r\n this._updateFog();\r\n\r\n if (this._gfx.renderer.xr.enabled) {\r\n this.webVR.updateMoleculeScale();\r\n }\r\n};\r\n\r\nMiew.prototype._onRender = function () {\r\n const gfx = this._gfx;\r\n\r\n // update all matrices\r\n gfx.scene.updateMatrixWorld();\r\n gfx.camera.updateMatrixWorld();\r\n\r\n this._clipPlaneUpdateValue(this._getBSphereRadius());\r\n this._fogFarUpdateValue();\r\n\r\n gfx.renderer.setRenderTarget(null);\r\n gfx.renderer.clear();\r\n\r\n this._renderFrame(settings.now.stereo);\r\n};\r\n\r\nMiew.prototype._renderFrame = (function () {\r\n const _anaglyphMat = new AnaglyphMaterial();\r\n const _size = new THREE.Vector2();\r\n\r\n return function (stereo) {\r\n const gfx = this._gfx;\r\n const { renderer } = gfx;\r\n\r\n renderer.getSize(_size);\r\n\r\n if (stereo !== 'NONE') {\r\n gfx.camera.focus = gfx.camera.position.z; // set focus to the center of the object\r\n gfx.stereoCam.aspect = 1.0;\r\n\r\n // in anaglyph mode we render full-size image for each eye\r\n // while in other stereo modes only half-size (two images on the screen)\r\n if (stereo === 'ANAGLYPH') {\r\n gfx.stereoCam.update(gfx.camera);\r\n } else {\r\n gfx.stereoCam.updateHalfSized(gfx.camera, settings.now.camFov);\r\n }\r\n }\r\n\r\n // resize offscreen buffers to match the target\r\n const pixelRatio = gfx.renderer.getPixelRatio();\r\n this._resizeOffscreenBuffers(_size.width * pixelRatio, _size.height * pixelRatio, stereo);\r\n\r\n this._renderShadowMap();\r\n\r\n switch (stereo) {\r\n case 'WEBVR':\r\n case 'NONE':\r\n this._renderScene(gfx.camera, false);\r\n break;\r\n case 'SIMPLE':\r\n case 'DISTORTED':\r\n renderer.setScissorTest(true);\r\n\r\n renderer.setScissor(0, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(0, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraL, stereo === 'DISTORTED');\r\n\r\n renderer.setScissor(_size.width / 2, 0, _size.width / 2, _size.height);\r\n renderer.setViewport(_size.width / 2, 0, _size.width / 2, _size.height);\r\n this._renderScene(this._gfx.stereoCam.cameraR, stereo === 'DISTORTED');\r\n\r\n renderer.setScissorTest(false);\r\n break;\r\n case 'ANAGLYPH':\r\n this._renderScene(this._gfx.stereoCam.cameraL, false, gfx.stereoBufL);\r\n this._renderScene(this._gfx.stereoCam.cameraR, false, gfx.stereoBufR);\r\n renderer.setRenderTarget(null);\r\n _anaglyphMat.uniforms.srcL.value = gfx.stereoBufL.texture;\r\n _anaglyphMat.uniforms.srcR.value = gfx.stereoBufR.texture;\r\n gfx.renderer.renderScreenQuad(_anaglyphMat);\r\n break;\r\n default:\r\n }\r\n\r\n gfx.renderer2d.render(gfx.scene, gfx.camera);\r\n\r\n if (settings.now.axes && gfx.axes && !gfx.renderer.xr.enabled) {\r\n gfx.axes.render(renderer);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._onBgColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx) {\r\n if (gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onFogColorChanged = function () {\r\n const gfx = this._gfx;\r\n const color = chooseFogColor();\r\n if (gfx && gfx.scene.fog) {\r\n gfx.scene.fog.color.set(color);\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._setUberMaterialValues = function (values) {\r\n this._gfx.root.traverse((obj) => {\r\n if ((obj instanceof THREE.Mesh || obj instanceof THREE.LineSegments || obj instanceof THREE.Line)\r\n && obj.material instanceof UberMaterial) {\r\n obj.material.setValues(values);\r\n obj.material.needsUpdate = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._enableMRT = function (on, renderBuffer, textureBuffer) {\r\n const gfx = this._gfx;\r\n const gl = gfx.renderer.getContext();\r\n const { properties } = gfx.renderer;\r\n\r\n if (!on) {\r\n gl.drawBuffers([gl.COLOR_ATTACHMENT0, null]);\r\n return;\r\n }\r\n\r\n // take extra texture from Texture Buffer\r\n gfx.renderer.setRenderTarget(textureBuffer);\r\n const tx8 = properties.get(textureBuffer.texture).__webglTexture;\r\n gl.bindTexture(gl.TEXTURE_2D, tx8);\r\n\r\n // take texture and framebuffer from renderbuffer\r\n gfx.renderer.setRenderTarget(renderBuffer);\r\n const fb = properties.get(renderBuffer).__webglFramebuffer;\r\n const tx = properties.get(renderBuffer.texture).__webglTexture;\r\n\r\n // set framebuffer\r\n gl.bindFramebuffer(gl.FRAMEBUFFER, fb);\r\n fb.width = renderBuffer.width;\r\n fb.height = renderBuffer.height;\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT0, gl.TEXTURE_2D, tx, 0);\r\n gl.framebufferTexture2D(gl.FRAMEBUFFER, gl.COLOR_ATTACHMENT1, gl.TEXTURE_2D, tx8, 0);\r\n\r\n // mapping textures (MRT is core feature in WebGL2)\r\n gl.drawBuffers([gl.COLOR_ATTACHMENT0, gl.COLOR_ATTACHMENT1]);\r\n};\r\n\r\nMiew.prototype._renderScene = (function () {\r\n return function (camera, distortion, target) {\r\n distortion = distortion || false;\r\n target = target || null;\r\n\r\n const gfx = this._gfx;\r\n\r\n // render to offscreen buffer\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.clear();\r\n if (gfx.renderer.xr.enabled) {\r\n gfx.renderer.render(gfx.scene, camera);\r\n return;\r\n }\r\n\r\n // clean buffer for normals texture\r\n gfx.renderer.setClearColor(0x000000, 0.0);\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf4);\r\n gfx.renderer.clearColor();\r\n\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.clear();\r\n\r\n const bHaveComplexes = (this._getComplexVisual() !== null);\r\n const volumeVisual = this._getVolumeVisual();\r\n const ssao = bHaveComplexes && settings.now.ao;\r\n\r\n if (ssao) {\r\n this._enableMRT(true, gfx.offscreenBuf, gfx.offscreenBuf4);\r\n }\r\n\r\n if (settings.now.transparency === 'prepass') {\r\n this._renderWithPrepassTransparency(camera, gfx.offscreenBuf);\r\n } else if (settings.now.transparency === 'standard') {\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n }\r\n\r\n if (ssao) {\r\n this._enableMRT(false, null, null);\r\n }\r\n\r\n // when fxaa we should get resulting image in temp off-screen buff2 for further postprocessing with fxaa filter\r\n // otherwise we render to canvas\r\n const outline = bHaveComplexes && settings.now.outline.on;\r\n const fxaa = bHaveComplexes && settings.now.fxaa;\r\n const volume = (volumeVisual !== null) && (volumeVisual.getMesh().material != null);\r\n let dstBuffer = (ssao || outline || volume || fxaa || distortion) ? gfx.offscreenBuf2 : target;\r\n let srcBuffer = gfx.offscreenBuf;\r\n\r\n if (ssao) {\r\n this._performAO(\r\n srcBuffer,\r\n gfx.offscreenBuf4,\r\n gfx.offscreenBuf.depthTexture,\r\n dstBuffer,\r\n gfx.offscreenBuf3,\r\n gfx.offscreenBuf2,\r\n );\r\n if (!fxaa && !distortion && !volume && !outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = target;\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n } else {\r\n // just copy color buffer to dst buffer\r\n gfx.renderer.setRenderTarget(dstBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 1.0);\r\n }\r\n\r\n // outline\r\n if (outline) {\r\n srcBuffer = dstBuffer;\r\n dstBuffer = (volume || fxaa || distortion) ? gfx.offscreenBuf3 : target;\r\n if (srcBuffer != null) {\r\n this._renderOutline(camera, gfx.offscreenBuf, srcBuffer, dstBuffer);\r\n }\r\n }\r\n\r\n // render selected part with outline material\r\n this._renderSelection(camera, gfx.offscreenBuf, dstBuffer);\r\n\r\n if (volume) {\r\n // copy current picture to the buffer that retains depth-data of the original molecule render\r\n // so that volume renderer could use depth-test\r\n gfx.renderer.setRenderTarget(gfx.offscreenBuf);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n dstBuffer = gfx.offscreenBuf;\r\n this._renderVolume(volumeVisual, camera, dstBuffer, gfx.volBFTex, gfx.volFFTex, gfx.volWFFTex);\r\n\r\n // if this is the last stage -- copy image to target\r\n if (!fxaa && !distortion) {\r\n gfx.renderer.setRenderTarget(target);\r\n gfx.renderer.renderScreenQuadFromTex(dstBuffer.texture, 1.0);\r\n }\r\n }\r\n\r\n srcBuffer = dstBuffer;\r\n\r\n if (fxaa) {\r\n dstBuffer = distortion ? gfx.offscreenBuf4 : target;\r\n this._performFXAA(srcBuffer, dstBuffer);\r\n srcBuffer = dstBuffer;\r\n }\r\n\r\n if (distortion) {\r\n dstBuffer = target;\r\n this._performDistortion(srcBuffer, dstBuffer, true);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._performDistortion = (function () {\r\n const _scene = new THREE.Scene();\r\n const _camera = new THREE.OrthographicCamera(-1.0, 1.0, 1.0, -1.0, -500, 1000);\r\n\r\n const _material = new THREE.RawShaderMaterial({\r\n uniforms: {\r\n srcTex: { type: 't', value: null },\r\n aberration: { type: 'fv3', value: new THREE.Vector3(1.0) },\r\n },\r\n vertexShader: vertexScreenQuadShader,\r\n fragmentShader: fragmentScreenQuadFromDistTex,\r\n transparent: false,\r\n depthTest: false,\r\n depthWrite: false,\r\n });\r\n\r\n const _geo = gfxutils.buildDistorionMesh(10, 10, settings.now.debug.stereoBarrel);\r\n _scene.add(new meshes.Mesh(_geo, _material));\r\n\r\n return function (srcBuffer, targetBuffer, mesh) {\r\n this._gfx.renderer.setRenderTarget(targetBuffer);\r\n this._gfx.renderer.clear();\r\n\r\n if (mesh) {\r\n _material.uniforms.srcTex.value = srcBuffer.texture;\r\n _material.uniforms.aberration.value.set(0.995, 1.0, 1.01);\r\n this._gfx.renderer.render(_scene, _camera);\r\n } else {\r\n this._gfx.renderer.renderScreenQuadFromTexWithDistortion(srcBuffer, settings.now.debug.stereoBarrel);\r\n }\r\n };\r\n}());\r\n\r\nMiew.prototype._renderOutline = (function () {\r\n const _outlineMaterial = new OutlineMaterial({ depth: true });\r\n\r\n return function (camera, srcDepthBuffer, srcColorBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcColorBuffer.texture;\r\n _outlineMaterial.uniforms.srcDepthTex.value = srcDepthBuffer.depthTexture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcDepthBuffer.width, srcDepthBuffer.height);\r\n _outlineMaterial.uniforms.color.value = new THREE.Color(settings.now.outline.color);\r\n _outlineMaterial.uniforms.threshold.value = settings.now.outline.threshold;\r\n _outlineMaterial.uniforms.thickness.value = new THREE.Vector2(\r\n settings.now.outline.thickness,\r\n settings.now.outline.thickness,\r\n );\r\n\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._renderShadowMap = (function () {\r\n const pars = { minFilter: THREE.NearestFilter, magFilter: THREE.NearestFilter, format: THREE.RGBAFormat };\r\n\r\n return function () {\r\n if (!settings.now.shadow.on) {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n const currentRenderTarget = gfx.renderer.getRenderTarget();\r\n const activeCubeFace = gfx.renderer.getActiveCubeFace();\r\n const activeMipmapLevel = gfx.renderer.getActiveMipmapLevel();\r\n\r\n const _state = gfx.renderer.state;\r\n\r\n // Set GL state for depth map.\r\n _state.setBlending(THREE.NoBlending);\r\n _state.buffers.color.setClear(1, 1, 1, 1);\r\n _state.buffers.depth.setTest(true);\r\n _state.setScissorTest(false);\r\n\r\n for (let i = 0; i < gfx.scene.children.length; i++) {\r\n if (gfx.scene.children[i].type === 'DirectionalLight') {\r\n const light = gfx.scene.children[i];\r\n\r\n if (light.shadow.map == null) {\r\n light.shadow.map = new THREE.WebGLRenderTarget(light.shadow.mapSize.width, light.shadow.mapSize.height, pars);\r\n light.shadow.camera.updateProjectionMatrix();\r\n }\r\n light.shadow.updateMatrices(light);\r\n\r\n gfx.renderer.setRenderTarget(light.shadow.map);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.render(gfx.scene, light.shadow.camera);\r\n }\r\n }\r\n gfx.renderer.setRenderTarget(currentRenderTarget, activeCubeFace, activeMipmapLevel);\r\n };\r\n}());\r\n\r\n/**\r\n * Check if there is selection which must be rendered or not.\r\n * @private\r\n * @returns {boolean} true on existing selection to render\r\n */\r\nMiew.prototype._hasSelectionToRender = function () {\r\n const selPivot = this._gfx.selectionPivot;\r\n\r\n for (let i = 0; i < selPivot.children.length; i++) {\r\n const selPivotChild = selPivot.children[i];\r\n if (selPivotChild.children.length > 0) {\r\n return true;\r\n }\r\n }\r\n return false;\r\n};\r\n\r\nMiew.prototype._renderSelection = (function () {\r\n const _outlineMaterial = new OutlineMaterial();\r\n\r\n return function (camera, srcBuffer, targetBuffer) {\r\n const self = this;\r\n const gfx = self._gfx;\r\n\r\n // clear offscreen buffer (leave z-buffer intact)\r\n gfx.renderer.setClearColor('black', 0);\r\n\r\n // render selection to offscreen buffer\r\n gfx.renderer.setRenderTarget(srcBuffer);\r\n gfx.renderer.clear(true, false, false);\r\n if (self._hasSelectionToRender()) {\r\n gfx.selectionRoot.matrix = gfx.root.matrix;\r\n gfx.selectionPivot.matrix = gfx.pivot.matrix;\r\n gfx.renderer.render(gfx.selectionScene, camera);\r\n } else {\r\n // just render something to force \"target clear\" operation to finish\r\n gfx.renderer.renderDummyQuad();\r\n }\r\n\r\n // overlay to screen\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuadFromTex(srcBuffer.texture, 0.6);\r\n\r\n // apply Sobel filter -- draw outline\r\n _outlineMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _outlineMaterial.uniforms.srcTexSize.value.set(srcBuffer.width, srcBuffer.height);\r\n gfx.renderer.renderScreenQuad(_outlineMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._checkVolumeRenderingSupport = function (renderTarget) {\r\n if (!renderTarget) {\r\n return false;\r\n }\r\n const gfx = this._gfx;\r\n const oldRT = gfx.renderer.getRenderTarget();\r\n\r\n gfx.renderer.setRenderTarget(renderTarget);\r\n const context = gfx.renderer.getContext();\r\n const result = context.checkFramebufferStatus(context.FRAMEBUFFER);\r\n gfx.renderer.setRenderTarget(oldRT);\r\n if (result !== context.FRAMEBUFFER_COMPLETE) {\r\n // floatFrameBufferWarning = ;\r\n this.logger.warn('Device doesn\\'t support electron density rendering');\r\n return false;\r\n }\r\n return true;\r\n};\r\n\r\nMiew.prototype._renderVolume = (function () {\r\n const volumeBFMat = new VolumeMaterial.BackFacePosMaterial();\r\n const volumeFFMat = new VolumeMaterial.FrontFacePosMaterial();\r\n const cubeOffsetMat = new THREE.Matrix4().makeTranslation(0.5, 0.5, 0.5);\r\n const world2colorMat = new THREE.Matrix4();\r\n\r\n let volumeRenderingSupported;\r\n\r\n return function (volumeVisual, camera, dstBuf, tmpBuf1, tmpBuf2, tmpBuf3) {\r\n const gfx = this._gfx;\r\n\r\n if (typeof volumeRenderingSupported === 'undefined') {\r\n volumeRenderingSupported = this._checkVolumeRenderingSupport(tmpBuf1);\r\n }\r\n\r\n if (!volumeRenderingSupported) {\r\n return;\r\n }\r\n\r\n const mesh = volumeVisual.getMesh();\r\n\r\n mesh.rebuild(gfx.camera);\r\n\r\n // use main camera to prepare special textures to be used by volumetric rendering\r\n // these textures have the size of the window and are stored in offscreen buffers\r\n gfx.renderer.setClearColor('black', 0);\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n gfx.renderer.clear();\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.clear();\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf1);\r\n // draw plane with its own material, because it differs slightly from volumeBFMat\r\n camera.layers.set(gfxutils.LAYERS.VOLUME_BFPLANE);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeBFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.renderer.setRenderTarget(tmpBuf2);\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.scene.overrideMaterial = volumeFFMat;\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n gfx.scene.overrideMaterial = null;\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n\r\n // prepare texture that contains molecule positions\r\n world2colorMat.copy(mesh.matrixWorld).invert();\r\n UberMaterial.prototype.uberOptions.world2colorMatrix.multiplyMatrices(cubeOffsetMat, world2colorMat);\r\n camera.layers.set(gfxutils.LAYERS.COLOR_FROM_POSITION);\r\n gfx.renderer.setRenderTarget(tmpBuf3);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // render volume\r\n const vm = mesh.material;\r\n vm.uniforms._BFRight.value = tmpBuf1.texture;\r\n vm.uniforms._FFRight.value = tmpBuf2.texture;\r\n vm.uniforms._WFFRight.value = tmpBuf3.texture;\r\n camera.layers.set(gfxutils.LAYERS.VOLUME);\r\n gfx.renderer.setRenderTarget(dstBuf);\r\n gfx.renderer.render(gfx.scene, camera);\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\n/* Render scene with 'ZPrepass transparency Effect'\r\n * Idea: transparent objects are rendered in two passes. The first one writes result only into depth buffer.\r\n * The second pass reads depth buffer and writes only to color buffer. The method results in\r\n * correct image of front part of the semi-transparent objects, but we can see only front transparent objects\r\n * and opaque objects inside, there is no transparent objects inside.\r\n * Notes: 1. Opaque objects should be rendered strictly before semi-transparent ones.\r\n * 2. Realization doesn't use camera layers because scene traversing is used for material changes and\r\n * we can use it to select needed meshes and don't complicate meshes builders with layers\r\n */\r\nMiew.prototype._renderWithPrepassTransparency = (function () {\r\n return function (camera, targetBuffer) {\r\n const gfx = this._gfx;\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n\r\n // opaque objects\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // transparent objects z prepass\r\n camera.layers.set(gfxutils.LAYERS.PREPASS_TRANSPARENT);\r\n gfx.renderer.getContext().colorMask(false, false, false, false); // don't update color buffer\r\n gfx.renderer.render(gfx.scene, camera);\r\n gfx.renderer.getContext().colorMask(true, true, true, true); // update color buffer\r\n\r\n // transparent objects color pass\r\n camera.layers.set(gfxutils.LAYERS.TRANSPARENT);\r\n gfx.renderer.render(gfx.scene, camera);\r\n\r\n // restore default layer\r\n camera.layers.set(gfxutils.LAYERS.DEFAULT);\r\n };\r\n}());\r\n\r\nMiew.prototype._performFXAA = (function () {\r\n const _fxaaMaterial = new FXAAMaterial();\r\n\r\n return function (srcBuffer, targetBuffer) {\r\n if (typeof srcBuffer === 'undefined' || typeof targetBuffer === 'undefined') {\r\n return;\r\n }\r\n\r\n const gfx = this._gfx;\r\n\r\n // clear canvas\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.clear();\r\n\r\n // do fxaa processing of offscreen buff2\r\n _fxaaMaterial.uniforms.srcTex.value = srcBuffer.texture;\r\n _fxaaMaterial.uniforms.srcTexelSize.value.set(1.0 / srcBuffer.width, 1.0 / srcBuffer.height);\r\n _fxaaMaterial.uniforms.bgColor.value.set(settings.now.bg.color);\r\n\r\n if (_fxaaMaterial.bgTransparent !== settings.now.bg.transparent) {\r\n _fxaaMaterial.setValues({ bgTransparent: settings.now.bg.transparent });\r\n _fxaaMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.renderScreenQuad(_fxaaMaterial);\r\n };\r\n}());\r\n\r\nMiew.prototype._performAO = (function () {\r\n const _aoMaterial = new AOMaterial();\r\n const _horBlurMaterial = new AOHorBlurMaterial();\r\n const _vertBlurMaterial = new AOVertBlurWithBlendMaterial();\r\n\r\n const _scale = new THREE.Vector3();\r\n return function (srcColorBuffer, normalBuffer, srcDepthTexture, targetBuffer, tempBuffer, tempBuffer1) {\r\n if (!srcColorBuffer || !normalBuffer || !srcDepthTexture || !targetBuffer || !tempBuffer || !tempBuffer1) {\r\n return;\r\n }\r\n const gfx = this._gfx;\r\n const tanHalfFOV = Math.tan(THREE.MathUtils.DEG2RAD * 0.5 * gfx.camera.fov);\r\n\r\n _aoMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _aoMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _aoMaterial.uniforms.normalTexture.value = normalBuffer.texture;\r\n _aoMaterial.uniforms.srcTexelSize.value.set(1.0 / srcColorBuffer.width, 1.0 / srcColorBuffer.height);\r\n _aoMaterial.uniforms.camNearFar.value.set(gfx.camera.near, gfx.camera.far);\r\n _aoMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _aoMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _aoMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n gfx.root.matrix.extractScale(_scale);\r\n _aoMaterial.uniforms.kernelRadius.value = settings.now.debug.ssaoKernelRadius * _scale.x;\r\n _aoMaterial.uniforms.depthThreshold.value = 2.0 * this._getBSphereRadius(); // diameter\r\n _aoMaterial.uniforms.factor.value = settings.now.debug.ssaoFactor;\r\n // N: should be tempBuffer1 for proper use of buffers (see buffers using outside the function)\r\n gfx.renderer.setRenderTarget(tempBuffer1);\r\n gfx.renderer.renderScreenQuad(_aoMaterial);\r\n\r\n _horBlurMaterial.uniforms.aoMap.value = tempBuffer1.texture;\r\n _horBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer1.width, 1.0 / tempBuffer1.height);\r\n _horBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n gfx.renderer.setRenderTarget(tempBuffer);\r\n gfx.renderer.renderScreenQuad(_horBlurMaterial);\r\n\r\n _vertBlurMaterial.uniforms.aoMap.value = tempBuffer.texture;\r\n _vertBlurMaterial.uniforms.diffuseTexture.value = srcColorBuffer.texture;\r\n _vertBlurMaterial.uniforms.srcTexelSize.value.set(1.0 / tempBuffer.width, 1.0 / tempBuffer.height);\r\n _vertBlurMaterial.uniforms.depthTexture.value = srcDepthTexture;\r\n _vertBlurMaterial.uniforms.projMatrix.value = gfx.camera.projectionMatrix;\r\n _vertBlurMaterial.uniforms.aspectRatio.value = gfx.camera.aspect;\r\n _vertBlurMaterial.uniforms.tanHalfFOV.value = tanHalfFOV;\r\n const { fog } = gfx.scene;\r\n if (fog) {\r\n _vertBlurMaterial.uniforms.fogNearFar.value.set(fog.near, fog.far);\r\n _vertBlurMaterial.uniforms.fogColor.value.set(fog.color.r, fog.color.g, fog.color.b, settings.now.fogAlpha);\r\n }\r\n if ((_vertBlurMaterial.useFog !== settings.now.fog)\r\n || (_vertBlurMaterial.fogTransparent !== settings.now.bg.transparent)) {\r\n _vertBlurMaterial.setValues({ useFog: settings.now.fog, fogTransparent: settings.now.bg.transparent });\r\n _vertBlurMaterial.needsUpdate = true;\r\n }\r\n gfx.renderer.setRenderTarget(targetBuffer);\r\n gfx.renderer.renderScreenQuad(_vertBlurMaterial);\r\n };\r\n}());\r\n\r\n/**\r\n * Reset the viewer, unload molecules.\r\n * @param {boolean=} keepReps - Keep representations while resetting viewer state.\r\n */\r\nMiew.prototype.reset = function (/* keepReps */) {\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._lastPick = null;\r\n\r\n this._releaseAllVisuals();\r\n\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._resetObjects();\r\n\r\n if (this._gfx) {\r\n gfxutils.clearTree(this._gfx.pivot);\r\n this._gfx.renderer2d.reset();\r\n }\r\n\r\n this.setNeedRender();\r\n};\r\n\r\nMiew.prototype._resetScene = function () {\r\n this._objectControls.reset();\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n this.resetReps();\r\n this.resetPivot();\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype.resetView = function () {\r\n // reset controls\r\n if (this._picker) {\r\n this._picker.reset();\r\n }\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._resetScene();\r\n\r\n // reset selection\r\n this._forEachComplexVisual((visual) => {\r\n visual.updateSelectionMask({});\r\n visual.rebuildSelectionGeometry();\r\n });\r\n};\r\n\r\nMiew.prototype._export = function (format) {\r\n const TheExporter = _.head(io.exporters.find({ format }));\r\n if (!TheExporter) {\r\n this.logger.error('Could not find suitable exporter for this source');\r\n return Promise.reject(new Error('Could not find suitable exporter for this source'));\r\n }\r\n this.dispatchEvent({ type: 'exporting' });\r\n\r\n if (this._visuals[this._curVisualName] instanceof ComplexVisual) {\r\n let dataSource = null;\r\n if (TheExporter.SourceClass === ComplexVisual) {\r\n dataSource = this._visuals[this._curVisualName];\r\n } else if (TheExporter.SourceClass === Complex) {\r\n dataSource = this._visuals[this._curVisualName]._complex;\r\n }\r\n const exporter = new TheExporter(dataSource, { miewVersion: Miew.VERSION });\r\n return exporter.export().then((data) => data);\r\n }\r\n if (this._visuals[this._curVisualName] instanceof VolumeVisual) {\r\n return Promise.reject(new Error('Sorry, exporter for volume data not implemented yet'));\r\n }\r\n return Promise.reject(new Error('Unexpected format of data'));\r\n};\r\n\r\nconst rePdbId = /^(?:(pdb|cif|ccp4|dsn6):\\s*)?(\\d[a-z\\d]{3})$/i;\r\nconst rePubchem = /^(?:pc|pubchem):\\s*([a-z]+)$/i;\r\nconst reUrlScheme = /^([a-z][a-z\\d\\-+.]*):/i;\r\n\r\nfunction resolveSourceShortcut(source, opts) {\r\n if (!_.isString(source)) {\r\n return source;\r\n }\r\n\r\n // e.g. \"cif:1CRN\"\r\n const matchesPdbId = rePdbId.exec(source);\r\n if (matchesPdbId) {\r\n let [, format = 'pdb', id] = matchesPdbId;\r\n\r\n format = format.toLowerCase();\r\n id = id.toUpperCase();\r\n\r\n switch (format) {\r\n case 'pdb':\r\n source = `https://files.rcsb.org/download/${id}.pdb`;\r\n break;\r\n case 'cif':\r\n source = `https://files.rcsb.org/download/${id}.cif`;\r\n break;\r\n case 'ccp4':\r\n source = `https://www.ebi.ac.uk/pdbe/coordinates/files/${id.toLowerCase()}.ccp4`;\r\n break;\r\n case 'dsn6':\r\n source = `https://edmaps.rcsb.org/maps/${id.toLowerCase()}_2fofc.dsn6`;\r\n break;\r\n default:\r\n throw new Error('Unexpected data format shortcut');\r\n }\r\n\r\n opts.fileType = format;\r\n opts.fileName = `${id}.${format}`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // e.g. \"pc:aspirin\"\r\n const matchesPubchem = rePubchem.exec(source);\r\n if (matchesPubchem) {\r\n const compound = matchesPubchem[1].toLowerCase();\r\n source = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${compound}/JSON?record_type=3d`;\r\n opts.fileType = 'pubchem';\r\n opts.fileName = `${compound}.json`;\r\n opts.sourceType = 'url';\r\n return source;\r\n }\r\n\r\n // otherwise is should be an URL\r\n if (opts.sourceType === 'url' || opts.sourceType === undefined) {\r\n opts.sourceType = 'url';\r\n\r\n // e.g. \"./data/1CRN.pdb\"\r\n if (!reUrlScheme.test(source)) {\r\n source = utils.resolveURL(source);\r\n }\r\n }\r\n\r\n return source;\r\n}\r\n\r\nfunction updateBinaryMode(opts) {\r\n let { binary } = opts;\r\n\r\n // detect by format\r\n if (opts.fileType !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n } else {\r\n throw new Error('Could not find suitable parser for this format');\r\n }\r\n }\r\n\r\n // detect by file extension\r\n if (binary === undefined && opts.fileExt !== undefined) {\r\n const TheParser = _.head(io.parsers.find({ ext: opts.fileExt }));\r\n if (TheParser) {\r\n binary = TheParser.binary || false;\r\n }\r\n }\r\n\r\n // temporary workaround for animation\r\n if (opts.fileExt !== undefined && opts.fileExt.toLowerCase() === '.man') {\r\n opts.binary = true;\r\n opts.animation = true; // who cares?\r\n }\r\n\r\n // update if detected\r\n if (binary !== undefined) {\r\n if (opts.binary !== undefined && opts.binary !== binary) {\r\n opts.context.logger.warn('Overriding incorrect binary mode');\r\n }\r\n }\r\n\r\n opts.binary = binary || false;\r\n}\r\n\r\nfunction _fetchData(source, opts, job) {\r\n return new Promise(((resolve) => {\r\n if (job.shouldCancel()) {\r\n throw new Error('Operation cancelled');\r\n }\r\n job.notify({ type: 'fetching' });\r\n\r\n // allow for source shortcuts\r\n source = resolveSourceShortcut(source, opts);\r\n\r\n // detect a proper loader\r\n const TheLoader = _.head(io.loaders.find({ type: opts.sourceType, source }));\r\n if (!TheLoader) {\r\n throw new Error(LOADER_NOT_FOUND);\r\n }\r\n\r\n // split file name\r\n const fileName = opts.fileName || TheLoader.extractName(source);\r\n if (fileName) {\r\n const [name, fileExt] = utils.splitFileName(fileName);\r\n _.defaults(opts, { name, fileExt, fileName });\r\n }\r\n\r\n // should it be text or binary?\r\n updateBinaryMode(opts);\r\n\r\n // FIXME: All new settings retrieved from server are applied after the loading is complete. However, we need some\r\n // flags to alter the loading process itself. Here we apply them in advance. Dirty hack. Kill the server, remove\r\n // all hacks and everybody's happy.\r\n let newOptions = _.get(opts, 'preset.expression');\r\n if (!_.isUndefined(newOptions)) {\r\n newOptions = JSON.parse(newOptions);\r\n if (newOptions && newOptions.settings) {\r\n const keys = ['singleUnit'];\r\n for (let keyIndex = 0, keyCount = keys.length; keyIndex < keyCount; ++keyIndex) {\r\n const key = keys[keyIndex];\r\n const value = _.get(newOptions.settings, key);\r\n if (!_.isUndefined(value)) {\r\n settings.set(key, value);\r\n }\r\n }\r\n }\r\n }\r\n\r\n // create a loader\r\n const loader = new TheLoader(source, opts);\r\n loader.context = opts.context;\r\n job.addEventListener('cancel', () => loader.abort());\r\n\r\n loader.addEventListener('progress', (event) => {\r\n if (event.lengthComputable && event.total > 0) {\r\n reportProgress(loader.logger, 'Fetching', event.loaded / event.total);\r\n } else {\r\n reportProgress(loader.logger, 'Fetching');\r\n }\r\n });\r\n\r\n console.time('fetch');\r\n const promise = loader.load()\r\n .then((data) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.info('Fetching finished');\r\n job.notify({ type: 'fetchingDone', data });\r\n return data;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('fetch');\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Fetching failed');\r\n job.notify({ type: 'fetchingDone', error });\r\n throw error;\r\n });\r\n resolve(promise);\r\n }));\r\n}\r\n\r\nfunction _parseData(data, opts, job) {\r\n if (job.shouldCancel()) {\r\n return Promise.reject(new Error('Operation cancelled'));\r\n }\r\n\r\n job.notify({ type: 'parsing' });\r\n\r\n const TheParser = _.head(io.parsers.find({ format: opts.fileType, ext: opts.fileExt, data }));\r\n if (!TheParser) {\r\n return Promise.reject(new Error('Could not find suitable parser'));\r\n }\r\n\r\n const parser = new TheParser(data, opts);\r\n parser.context = opts.context;\r\n job.addEventListener('cancel', () => parser.abort());\r\n\r\n console.time('parse');\r\n return parser.parse()\r\n .then((dataSet) => {\r\n console.timeEnd('parse');\r\n job.notify({ type: 'parsingDone', data: dataSet });\r\n return dataSet;\r\n })\r\n .catch((error) => {\r\n console.timeEnd('parse');\r\n opts.error = error;\r\n opts.context.logger.debug(error.message);\r\n if (error.stack) {\r\n opts.context.logger.debug(error.stack);\r\n }\r\n opts.context.logger.error('Parsing failed');\r\n job.notify({ type: 'parsingDone', error });\r\n throw error;\r\n });\r\n}\r\n\r\n/**\r\n * Load molecule asynchronously.\r\n * @param {string|File} source - Molecule source to load (e.g. PDB ID, URL or File object).\r\n * @param {object=} opts - Options.\r\n * @param {string=} opts.sourceType - Data source type (e.g. 'url', 'file').\r\n * @param {string=} opts.fileType - Data contents type (e.g. 'pdb', 'cml').\r\n * @param {string=} opts.mdFile - .nc file path.\r\n * @param {boolean=} opts.keepRepsInfo - prevent reset of object and reps information.\r\n * @returns {Promise} name of the visual that was added to the viewer\r\n */\r\nMiew.prototype.load = function (source, opts) {\r\n opts = _.merge({}, opts, {\r\n context: this,\r\n });\r\n\r\n // for a single-file scenario\r\n if (!this.settings.now.use.multiFile) {\r\n // abort all loaders in progress\r\n if (this._loading.length) {\r\n this._loading.forEach((job) => {\r\n job.cancel();\r\n });\r\n this._loading.length = 0;\r\n }\r\n\r\n // reset\r\n if (!opts.animation) { // FIXME: sometimes it is set AFTERWARDS!\r\n this.reset(true);\r\n }\r\n }\r\n\r\n this._interpolator.reset();\r\n\r\n this.dispatchEvent({ type: 'loading', options: opts, source });\r\n\r\n const job = new JobHandle();\r\n this._loading.push(job);\r\n job.addEventListener('notification', (e) => {\r\n this.dispatchEvent(e.slaveEvent);\r\n });\r\n\r\n this._spinner.spin(this._container);\r\n\r\n const onLoadEnd = (anything) => {\r\n const jobIndex = this._loading.indexOf(job);\r\n if (jobIndex !== -1) {\r\n this._loading.splice(jobIndex, 1);\r\n }\r\n this._spinner.stop();\r\n this._refreshTitle();\r\n job.notify({ type: 'loadingDone', anything });\r\n return anything;\r\n };\r\n\r\n return _fetchData(source, opts, job)\r\n .then((data) => _parseData(data, opts, job))\r\n .then((object) => {\r\n const name = this._onLoad(object, opts);\r\n return onLoadEnd(name);\r\n })\r\n .catch((err) => {\r\n this.logger.error('Could not load data');\r\n this.logger.debug(err);\r\n throw onLoadEnd(err);\r\n });\r\n};\r\n\r\n/**\r\n * Unload molecule (delete corresponding visual).\r\n * @param {string=} name - name of the visual\r\n */\r\nMiew.prototype.unload = function (name) {\r\n this._removeVisual(name || this.getCurrentVisual());\r\n this.resetPivot();\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n};\r\n\r\n/**\r\n * Start new animation. Now is broken.\r\n * @param fileData - new data to animate\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._startAnimation = function (fileData) {\r\n this._stopAnimation();\r\n const self = this;\r\n const visual = this._getComplexVisual();\r\n if (visual === null) {\r\n this.logger.error('Unable to start animation - no molecule is loaded.');\r\n return;\r\n }\r\n try {\r\n this._frameInfo = new FrameInfo(\r\n visual.getComplex(),\r\n fileData,\r\n {\r\n onLoadStatusChanged() {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo ? self._frameInfo.isLoading : true,\r\n },\r\n });\r\n },\r\n onError(message) {\r\n self._stopAnimation();\r\n self.logger.error(message);\r\n },\r\n },\r\n );\r\n } catch {\r\n this.logger.error('Animation file does not fit to current complex!');\r\n return;\r\n }\r\n this._continueAnimation();\r\n};\r\n\r\n/**\r\n * Pause current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._pauseAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n this._isAnimating = false;\r\n clearInterval(this._animInterval);\r\n this._animInterval = null;\r\n if (this._frameInfo) {\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: this._isAnimating,\r\n isLoading: this._frameInfo.isLoading,\r\n },\r\n });\r\n }\r\n};\r\n\r\n/**\r\n * Continue current animation after pausing. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._continueAnimation = function () {\r\n this._isAnimating = true;\r\n let minFrameTime = 1000 / settings.now.maxfps;\r\n minFrameTime = Number.isNaN(minFrameTime) ? 0 : minFrameTime;\r\n const self = this;\r\n const { pivot } = self._gfx;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.resetSelectionMask();\r\n visual.rebuildSelectionGeometry();\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n }\r\n this._animInterval = setInterval(() => {\r\n self.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: {\r\n isPlaying: self._isAnimating,\r\n isLoading: self._frameInfo.isLoading,\r\n },\r\n });\r\n if (self._frameInfo.frameIsReady) {\r\n pivot.updateToFrame(self._frameInfo);\r\n self._updateObjsToFrame(self._frameInfo);\r\n self._refreshTitle(` Frame ${self._frameInfo._currFrame} of ${self._frameInfo._framesCount\r\n } time interval - ${self._frameInfo._timeStep}`);\r\n try {\r\n self._frameInfo.nextFrame();\r\n } catch {\r\n self.logger.error('Error during animation');\r\n self._stopAnimation();\r\n return;\r\n }\r\n self._needRender = true;\r\n }\r\n }, minFrameTime);\r\n};\r\n\r\n/**\r\n * Stop current animation. Now is broken.\r\n * @private\r\n * @deprecated until animation system refactoring.\r\n */\r\nMiew.prototype._stopAnimation = function () {\r\n if (this._animInterval === null) {\r\n return;\r\n }\r\n clearInterval(this._animInterval);\r\n this._frameInfo.disableEvents();\r\n this._frameInfo = null;\r\n this._animInterval = null;\r\n this.dispatchEvent({\r\n type: 'mdPlayerStateChanged',\r\n state: null,\r\n });\r\n};\r\n\r\n/**\r\n * Invoked upon successful loading of some data source\r\n * @param {DataSource} dataSource - Data source for visualization (molecular complex or other)\r\n * @param {object} opts - Options.\r\n * @private\r\n */\r\nMiew.prototype._onLoad = function (dataSource, opts) {\r\n const gfx = this._gfx;\r\n let visualName = null;\r\n\r\n if (opts.animation) {\r\n this._refreshTitle();\r\n this._startAnimation(dataSource);\r\n return null;\r\n }\r\n this._stopAnimation();\r\n if (!opts || !opts.keepRepsInfo) {\r\n this._opts.reps = null;\r\n this._opts._objects = null;\r\n }\r\n\r\n if (dataSource.id === 'Complex') {\r\n const complex = dataSource;\r\n\r\n // update title\r\n if (opts.fileName) {\r\n complex.name = complex.name || removeExtension(opts.fileName).toUpperCase();\r\n } else if (opts.amberFileName) {\r\n complex.name = complex.name || removeExtension(opts.amberFileName).toUpperCase();\r\n } else {\r\n complex.name = `Dynamic ${opts.fileType} molecule`;\r\n }\r\n\r\n visualName = this._addVisual(new ComplexVisual(complex.name, complex));\r\n this._curVisualName = visualName;\r\n\r\n const desc = this.info();\r\n this.logger.info(`Parsed ${opts.fileName} (${\r\n desc.atoms} atoms, ${\r\n desc.bonds} bonds, ${\r\n desc.residues} residues, ${\r\n desc.chains} chains).`);\r\n\r\n if (_.isNumber(this._opts.unit)) {\r\n complex.setCurrentUnit(this._opts.unit);\r\n }\r\n\r\n if (opts.preset) {\r\n // ...removed server access...\r\n } else if (settings.now.autoPreset) {\r\n switch (opts.fileType) {\r\n case 'cml':\r\n this.resetReps('small');\r\n break;\r\n case 'pdb':\r\n case 'mmtf':\r\n case 'cif':\r\n if (hasValidResidues(complex)) {\r\n this.resetReps('macro');\r\n } else {\r\n this.resetReps('small');\r\n }\r\n break;\r\n default:\r\n this.resetReps('default');\r\n break;\r\n }\r\n } else {\r\n this.resetReps('default');\r\n }\r\n } else if (dataSource.id === 'Volume') {\r\n this.resetEd();\r\n visualName = this._onLoadEd(dataSource);\r\n }\r\n\r\n gfx.camera.updateProjectionMatrix();\r\n this._updateFog();\r\n\r\n // reset global transform\r\n gfx.root.resetTransform();\r\n this.resetPivot();\r\n\r\n // set scale to fit everything on the screen\r\n this._objectControls.setScale(settings.now.radiusToFit / this._getBSphereRadius());\r\n\r\n this._resetObjects();\r\n\r\n if (settings.now.autoResolution) {\r\n this._tweakResolution();\r\n }\r\n\r\n if (settings.now.shadow.on) {\r\n this._updateShadowCamera();\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n this._refreshTitle();\r\n\r\n return visualName;\r\n};\r\n\r\nMiew.prototype.resetEd = function () {\r\n if (this._edLoader) {\r\n this._edLoader.abort();\r\n this._edLoader = null;\r\n }\r\n\r\n // free all resources\r\n this._removeVisual(this._getVolumeVisual());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype.loadEd = function (source) {\r\n this.resetEd();\r\n\r\n const TheLoader = _.head(io.loaders.find({ source }));\r\n if (!TheLoader) {\r\n this.logger.error(LOADER_NOT_FOUND);\r\n return Promise.reject(new Error(LOADER_NOT_FOUND));\r\n }\r\n\r\n const loader = this._edLoader = new TheLoader(source, { binary: true });\r\n loader.context = this;\r\n return loader.load().then((data) => {\r\n const TheParser = _.head(io.parsers.find({ format: 'ccp4' }));\r\n if (!TheParser) {\r\n throw new Error(PARSER_NOT_FOUND);\r\n }\r\n const parser = new TheParser(data);\r\n parser.context = this;\r\n return parser.parse().then((dataSource) => {\r\n this._onLoadEd(dataSource);\r\n });\r\n }).catch((error) => {\r\n this.logger.error('Could not load ED data');\r\n this.logger.debug(error);\r\n });\r\n};\r\n\r\nMiew.prototype._onLoadEd = function (dataSource) {\r\n dataSource.normalize();\r\n\r\n const volumeVisual = new VolumeVisual('volume', dataSource);\r\n volumeVisual.getMesh().layers.set(gfxutils.LAYERS.VOLUME); // volume mesh is not visible to common render\r\n const visualName = this._addVisual(volumeVisual);\r\n\r\n this._needRender = true;\r\n return visualName;\r\n};\r\n\r\nMiew.prototype._needRebuild = function () {\r\n let needsRebuild = false;\r\n this._forEachComplexVisual((visual) => {\r\n needsRebuild = needsRebuild || visual.needsRebuild();\r\n });\r\n return needsRebuild;\r\n};\r\n\r\nMiew.prototype._rebuildObjects = function () {\r\n const self = this;\r\n const gfx = this._gfx;\r\n let i;\r\n let n;\r\n\r\n // remove old object geometry\r\n const toRemove = [];\r\n for (i = 0; i < gfx.pivot.children.length; ++i) {\r\n const child = gfx.pivot.children[i];\r\n if (!(child instanceof Visual)) {\r\n toRemove.push(child);\r\n }\r\n }\r\n for (i = 0; i < toRemove.length; ++i) {\r\n toRemove[i].parent.remove(toRemove[i]);\r\n }\r\n\r\n setTimeout(() => {\r\n const objList = self._objects;\r\n for (i = 0, n = objList.length; i < n; ++i) {\r\n const obj = objList[i];\r\n if (obj.needsRebuild) {\r\n obj.build();\r\n }\r\n if (obj.getGeometry()) {\r\n gfx.pivot.add(obj.getGeometry());\r\n }\r\n }\r\n }, 10);\r\n};\r\n\r\nMiew.prototype.changeUnit = function (unitIdx, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n throw new Error('There is no complex to change!');\r\n }\r\n\r\n function currentUnitInfo() {\r\n const unit = visual ? visual.getComplex().getCurrentUnit() : 0;\r\n const type = unit > 0 ? (`Bio molecule ${unit}`) : 'Asymmetric unit';\r\n return `Current unit: ${unit} (${type})`;\r\n }\r\n\r\n if (unitIdx === undefined) {\r\n return currentUnitInfo();\r\n }\r\n if (_.isString(unitIdx)) {\r\n unitIdx = Math.max(parseInt(unitIdx, 10), 0);\r\n }\r\n if (visual.getComplex().setCurrentUnit(unitIdx)) {\r\n this._resetScene();\r\n this._updateInfoPanel();\r\n }\r\n return currentUnitInfo();\r\n};\r\n\r\n/**\r\n * Start to rebuild geometry asynchronously.\r\n */\r\nMiew.prototype.rebuild = function () {\r\n if (this._building) {\r\n this.logger.warn('Miew.rebuild(): already building!');\r\n return;\r\n }\r\n this._building = true;\r\n\r\n this.dispatchEvent({ type: 'rebuilding' });\r\n\r\n this._rebuildObjects();\r\n\r\n this._gfx.renderer2d.reset();\r\n\r\n const rebuildActions = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.needsRebuild()) {\r\n rebuildActions.push(visual.rebuild().then(() => new Promise(((resolve) => {\r\n visual.rebuildSelectionGeometry();\r\n resolve();\r\n }))));\r\n }\r\n });\r\n\r\n // Start asynchronous rebuild\r\n const self = this;\r\n this._spinner.spin(this._container);\r\n Promise.all(rebuildActions).then(() => {\r\n self._spinner.stop();\r\n\r\n self._needRender = true;\r\n\r\n self._refreshTitle();\r\n this.dispatchEvent({ type: 'buildingDone' });\r\n self._building = false;\r\n });\r\n};\r\n\r\n/** Mark all representations for rebuilding */\r\nMiew.prototype.rebuildAll = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setNeedsRebuild();\r\n });\r\n};\r\n\r\nMiew.prototype._refreshTitle = function (appendix) {\r\n let title;\r\n appendix = appendix === undefined ? '' : appendix;\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n title = visual.getComplex().name;\r\n const rep = visual.repGet(visual.repCurrent());\r\n title += (rep ? ` – ${rep.mode.name} Mode` : '');\r\n } else {\r\n title = Object.keys(this._visuals).length > 0 ? 'Unknown' : 'No Data';\r\n }\r\n title += appendix;\r\n\r\n this.dispatchEvent({ type: 'titleChanged', data: title });\r\n};\r\n\r\nMiew.prototype.setNeedRender = function () {\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._extractRepresentation = function () {\r\n const changed = [];\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCount() === 0) {\r\n return;\r\n }\r\n\r\n const selector = visual.buildSelectorFromMask(1 << visual.getSelectionBit());\r\n const defPreset = settings.now.presets.default;\r\n const res = visual.repAdd({\r\n selector,\r\n mode: defPreset[0].mode.id,\r\n colorer: defPreset[0].colorer.id,\r\n material: defPreset[0].material.id,\r\n });\r\n if (!res) {\r\n if (visual.repCount() === ComplexVisual.NUM_REPRESENTATION_BITS) {\r\n this.logger.warn(`Number of representations is limited to ${ComplexVisual.NUM_REPRESENTATION_BITS}`);\r\n }\r\n return;\r\n }\r\n\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n visual.repCurrent(res.index);\r\n\r\n changed.push(visual.name);\r\n });\r\n\r\n if (changed.length > 0) {\r\n this.logger.report(`New representation from selection for complexes: ${changed.join(', ')}`);\r\n }\r\n};\r\n\r\n/**\r\n * Change current representation list.\r\n * @param {array} reps - Representation list.\r\n */\r\nMiew.prototype._setReps = function (reps) {\r\n reps = reps || (this._opts && this._opts.reps) || [];\r\n this._forEachComplexVisual((visual) => visual.resetReps(reps));\r\n};\r\n\r\n/**\r\n * Apply existing preset to current scene.\r\n * @param preset\r\n */\r\nMiew.prototype.applyPreset = function (preset) {\r\n const { presets } = settings.now;\r\n const presList = [\r\n preset || settings.defaults.preset,\r\n settings.defaults.preset,\r\n Object.keys(presets)[0],\r\n ];\r\n let reps = null;\r\n for (let i = 0; !reps && i < presList.length; ++i) {\r\n settings.set('preset', presList[i]);\r\n reps = presets[settings.now.preset];\r\n if (!reps) {\r\n this.logger.warn(`Unknown preset \"${settings.now.preset}\"`);\r\n }\r\n }\r\n this._setReps(reps);\r\n};\r\n\r\n/**\r\n * Reset current representation list to initial values.\r\n * @param {string} [preset] - The source preset in case of uninitialized representation list.\r\n */\r\nMiew.prototype.resetReps = function (preset) {\r\n const reps = this._opts && this._opts.reps;\r\n if (reps) {\r\n this._setReps(reps);\r\n } else {\r\n this.applyPreset(preset);\r\n }\r\n};\r\n\r\n/**\r\n * Get number of representations created so far.\r\n * @returns {number} Number of reps.\r\n */\r\nMiew.prototype.repCount = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repCount() : 0;\r\n};\r\n\r\n/**\r\n * Get or set the current representation index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.\r\n * @param {string=} [name] - Complex name. Defaults to the current one.\r\n * @returns {number} The current index.\r\n */\r\nMiew.prototype.repCurrent = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n const newIdx = visual ? visual.repCurrent(index) : -1;\r\n if (index && newIdx !== index) {\r\n this.logger.warn(`Representation ${index} was not found. Current rep remains unchanged.`);\r\n }\r\n return newIdx;\r\n};\r\n\r\n/**\r\n * Get or set representation by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @param {object=} rep - Optional representation description.\r\n * @param {string=} rep.selector - Selector string.\r\n * @param {string=} rep.mode - Mode id.\r\n * @param {string=} rep.colorer - Colorer id.\r\n * @param {string=} rep.material - Material id.\r\n * @returns {?object} Representation description.\r\n */\r\nMiew.prototype.rep = function (index, rep) {\r\n const visual = this._getComplexVisual('');\r\n if (!visual) {\r\n return null;\r\n }\r\n const res = visual.rep(index, rep);\r\n if (res.status === 'created') {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name: visual.name });\r\n } else if (res.status === 'changed') {\r\n this.dispatchEvent({ type: 'repChanged', index: res.index, name: visual.name });\r\n }\r\n return res.desc;\r\n};\r\n\r\n/**\r\n * Get representation (not just description) by index.\r\n * @param {number=} index - Zero-based index, up to {@link Miew#repCount}(). Defaults to the current one.\r\n * @returns {?object} Representation.\r\n */\r\nMiew.prototype.repGet = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repGet(index) : null;\r\n};\r\n\r\n/**\r\n * Add new representation.\r\n * @param {object=} rep - Representation description.\r\n * @returns {number} Index of the new representation.\r\n */\r\nMiew.prototype.repAdd = function (rep, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return -1;\r\n }\r\n\r\n const res = visual.repAdd(rep);\r\n if (res) {\r\n this.dispatchEvent({ type: 'repAdded', index: res.index, name });\r\n return res.index;\r\n }\r\n return -1;\r\n};\r\n\r\n/**\r\n * Remove representation.\r\n * @param {number=} index - Zero-based representation index.\r\n */\r\nMiew.prototype.repRemove = function (index, name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n visual.repRemove(index);\r\n this.dispatchEvent({ type: 'repRemoved', index, name });\r\n};\r\n\r\n/**\r\n * Hide representation.\r\n * @param {number} index - Zero-based representation index.\r\n * @param {boolean=} hide - Specify false to make rep visible, true to hide (by default).\r\n */\r\nMiew.prototype.repHide = function (index, hide, name) {\r\n this._needRender = true;\r\n const visual = this._getComplexVisual(name);\r\n return visual ? visual.repHide(index, hide) : null;\r\n};\r\n\r\nMiew.prototype._setEditMode = function (mode) {\r\n this._editMode = mode;\r\n\r\n const elem = this._msgMode;\r\n if (elem) {\r\n elem.style.opacity = (mode === EDIT_MODE.COMPLEX) ? 0.0 : 1.0;\r\n\r\n if (mode !== EDIT_MODE.COMPLEX) {\r\n const t = elem.getElementsByTagName('p')[0];\r\n t.innerHTML = (mode === EDIT_MODE.COMPONENT) ? 'COMPONENT EDIT MODE' : 'FRAGMENT EDIT MODE';\r\n }\r\n }\r\n\r\n this.dispatchEvent({ type: 'editModeChanged', data: mode === EDIT_MODE.COMPLEX });\r\n};\r\n\r\nMiew.prototype._enterComponentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const editors = [];\r\n this._forEachComplexVisual((visual) => {\r\n const editor = visual.beginComponentEdit();\r\n if (editor) {\r\n editors.push(editor);\r\n }\r\n });\r\n\r\n if (editors.length === 0) {\r\n return;\r\n }\r\n\r\n this._editors = editors;\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- ON');\r\n this._setEditMode(EDIT_MODE.COMPONENT);\r\n this._objectControls.keysTranslateObj(true);\r\n};\r\n\r\nMiew.prototype._applyComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardComponentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.COMPONENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n this._objectControls.keysTranslateObj(false);\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('COMPONENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n\r\n this._needRender = true;\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._enterFragmentEditMode = function () {\r\n if (this._editMode !== EDIT_MODE.COMPLEX) {\r\n return;\r\n }\r\n\r\n const selectedVisuals = [];\r\n this._forEachComplexVisual((visual) => {\r\n if (visual instanceof ComplexVisual\r\n && visual.getSelectionCount() > 0) {\r\n selectedVisuals.push(visual);\r\n }\r\n });\r\n\r\n if (selectedVisuals.length !== 1) {\r\n // either we have no selection or\r\n // we have selected atoms in two or more visuals -- not supported\r\n return;\r\n }\r\n\r\n const editor = selectedVisuals[0].beginFragmentEdit();\r\n if (!editor) {\r\n return;\r\n }\r\n this._editors = [editor];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- ON (single bond)');\r\n this._setEditMode(EDIT_MODE.FRAGMENT);\r\n this._objectControls.allowTranslation(false);\r\n this._objectControls.allowAltObjFreeRotation(editor.isFreeRotationAllowed());\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._applyFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].apply();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (applied)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this.rebuildAll();\r\n};\r\n\r\nMiew.prototype._discardFragmentEdit = function () {\r\n if (this._editMode !== EDIT_MODE.FRAGMENT) {\r\n return;\r\n }\r\n\r\n this._objectControls.stop();\r\n\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n this._editors[i].discard();\r\n }\r\n this._editors = [];\r\n\r\n this.logger.info('FRAGMENT EDIT MODE -- OFF (discarded)');\r\n this._setEditMode(EDIT_MODE.COMPLEX);\r\n this._objectControls.allowTranslation(true);\r\n this._objectControls.allowAltObjFreeRotation(true);\r\n\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._onPick = function (event) {\r\n if (!settings.now.picking) {\r\n // picking is disabled\r\n return;\r\n }\r\n\r\n if (this._animInterval !== null) {\r\n // animation playback is on\r\n return;\r\n }\r\n\r\n if (this._editMode === EDIT_MODE.FRAGMENT) {\r\n // prevent picking in fragment edit mode\r\n return;\r\n }\r\n\r\n if (this._objectControls.isEditingAltObj()) {\r\n // prevent picking during component rotation\r\n return;\r\n }\r\n\r\n // update last pick & find complex\r\n let complex = null;\r\n if (event.obj.atom) {\r\n complex = event.obj.atom.residue.getChain().getComplex();\r\n this._lastPick = event.obj.atom;\r\n } else if (event.obj.residue) {\r\n complex = event.obj.residue.getChain().getComplex();\r\n this._lastPick = event.obj.residue;\r\n } else if (event.obj.chain) {\r\n complex = event.obj.chain.getComplex();\r\n this._lastPick = event.obj.chain;\r\n } else if (event.obj.molecule) {\r\n complex = event.obj.molecule.complex;\r\n this._lastPick = event.obj.molecule;\r\n } else {\r\n this._lastPick = null;\r\n }\r\n\r\n function _updateSelection(visual) {\r\n visual.updateSelectionMask(event.obj);\r\n visual.rebuildSelectionGeometry();\r\n }\r\n\r\n // update visual\r\n if (complex) {\r\n const visual = this._getVisualForComplex(complex);\r\n if (visual) {\r\n _updateSelection(visual);\r\n this._needRender = true;\r\n }\r\n } else {\r\n this._forEachComplexVisual(_updateSelection);\r\n this._needRender = true;\r\n }\r\n\r\n this._updateInfoPanel();\r\n this.dispatchEvent(event);\r\n};\r\n\r\nMiew.prototype._onKeyDown = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n // editing keys\r\n if (settings.now.editing) {\r\n switch (event.code) {\r\n case 'KeyC':\r\n this._enterComponentEditMode();\r\n break;\r\n case 'KeyF':\r\n this._enterFragmentEditMode();\r\n break;\r\n case 'KeyA':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._applyComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._applyFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n case 'KeyD':\r\n switch (this._editMode) {\r\n case EDIT_MODE.COMPONENT:\r\n this._discardComponentEdit();\r\n break;\r\n case EDIT_MODE.FRAGMENT:\r\n this._discardFragmentEdit();\r\n break;\r\n default:\r\n break;\r\n }\r\n break;\r\n default:\r\n }\r\n }\r\n\r\n // other keys\r\n switch (event.code) {\r\n case 'NumpadAdd':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.expandSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n case 'NumpadSubtract':\r\n if (event.altKey) {\r\n event.preventDefault();\r\n event.stopPropagation();\r\n this._forEachComplexVisual((visual) => {\r\n visual.shrinkSelection();\r\n visual.rebuildSelectionGeometry();\r\n });\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n }\r\n break;\r\n default:\r\n }\r\n};\r\n\r\nMiew.prototype._onKeyUp = function (event) {\r\n if (!this._running || !this._hotKeysEnabled) {\r\n return;\r\n }\r\n\r\n if (event.code === 'KeyX') {\r\n this._extractRepresentation();\r\n }\r\n};\r\n\r\nMiew.prototype._updateInfoPanel = function () {\r\n const info = this._msgAtomInfo.getElementsByTagName('p')[0];\r\n let atom;\r\n let residue;\r\n\r\n let count = 0;\r\n this._forEachComplexVisual((visual) => {\r\n count += visual.getSelectionCount();\r\n });\r\n\r\n while (info.firstChild) {\r\n info.removeChild(info.firstChild);\r\n }\r\n\r\n if (count === 0) {\r\n this._msgAtomInfo.style.opacity = 0.0;\r\n return;\r\n }\r\n\r\n let firstLine = `${String(count)} atom${count !== 1 ? 's' : ''} selected`;\r\n if (this._lastPick !== null) {\r\n firstLine += ', the last pick:';\r\n }\r\n let secondLine = '';\r\n let aName = '';\r\n let coordLine = '';\r\n\r\n if (this._lastPick instanceof Atom) {\r\n atom = this._lastPick;\r\n residue = atom.residue;\r\n\r\n aName = atom.name;\r\n const location = (atom.location !== 32) ? String.fromCharCode(atom.location) : ''; // 32 is code of white-space\r\n secondLine = `${atom.element.fullName} #${atom.serial}${location}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}.`;\r\n secondLine += aName;\r\n\r\n coordLine = `Coord: (${atom.position.x.toFixed(2).toString()},\\\r\n ${atom.position.y.toFixed(2).toString()},\\\r\n ${atom.position.z.toFixed(2).toString()})`;\r\n } else if (this._lastPick instanceof Residue) {\r\n residue = this._lastPick;\r\n\r\n secondLine = `${residue._type._fullName}: \\\r\n ${residue._chain._name}.${residue._type._name}${residue._sequence}${residue._icode.trim()}`;\r\n } else if (this._lastPick instanceof Chain) {\r\n secondLine = `chain ${this._lastPick._name}`;\r\n } else if (this._lastPick instanceof Molecule) {\r\n secondLine = `molecule ${this._lastPick._name}`;\r\n }\r\n\r\n info.appendChild(document.createTextNode(firstLine));\r\n\r\n if (secondLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(secondLine));\r\n }\r\n\r\n if (coordLine !== '') {\r\n info.appendChild(document.createElement('br'));\r\n info.appendChild(document.createTextNode(coordLine));\r\n }\r\n\r\n this._msgAtomInfo.style.opacity = 1.0;\r\n};\r\n\r\nMiew.prototype._getAltObj = function () {\r\n if (this._editors) {\r\n let altObj = null;\r\n for (let i = 0; i < this._editors.length; ++i) {\r\n const nextAltObj = this._editors[i].getAltObj();\r\n if (nextAltObj.objects.length > 0) {\r\n if (altObj) {\r\n // we have selected atoms in two or more visuals -- not supported\r\n altObj = null;\r\n break;\r\n }\r\n altObj = nextAltObj;\r\n }\r\n }\r\n if (altObj) {\r\n return altObj;\r\n }\r\n }\r\n\r\n return {\r\n objects: [],\r\n pivot: new THREE.Vector3(0, 0, 0),\r\n };\r\n};\r\n\r\nMiew.prototype.resetPivot = (function () {\r\n const boundingBox = new THREE.Box3();\r\n const center = new THREE.Vector3();\r\n\r\n return function () {\r\n boundingBox.makeEmpty();\r\n this._forEachVisual((visual) => {\r\n boundingBox.union(visual.getBoundaries().boundingBox);\r\n });\r\n\r\n boundingBox.getCenter(center);\r\n this._objectControls.setPivot(center.negate());\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotResidue = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (residue) {\r\n const visual = this._getVisualForComplex(residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n if (residue._controlPoint) {\r\n center.copy(residue._controlPoint);\r\n } else {\r\n let x = 0;\r\n let y = 0;\r\n let z = 0;\r\n const amount = residue._atoms.length;\r\n for (let i = 0; i < amount; ++i) {\r\n const p = residue._atoms[i].position;\r\n x += p.x / amount;\r\n y += p.y / amount;\r\n z += p.z / amount;\r\n }\r\n center.set(x, y, z);\r\n }\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotAtom = (function () {\r\n const center = new THREE.Vector3();\r\n\r\n return function (atom) {\r\n const visual = this._getVisualForComplex(atom.residue.getChain().getComplex());\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n center.copy(atom.position);\r\n center.applyMatrix4(visual.matrix).negate();\r\n this._objectControls.setPivot(center);\r\n this.dispatchEvent({ type: 'transform' });\r\n };\r\n}());\r\n\r\nMiew.prototype.getSelectionCenter = (function () {\r\n const _centerInVisual = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n return function (center, includesAtom, selector) {\r\n center.set(0.0, 0.0, 0.0);\r\n let count = 0;\r\n\r\n this._forEachComplexVisual((visual) => {\r\n if (visual.getSelectionCenter(_centerInVisual, includesAtom, selector || visual.getSelectionBit())) {\r\n center.add(_centerInVisual);\r\n count++;\r\n }\r\n });\r\n if (count === 0) {\r\n return false;\r\n }\r\n center.divideScalar(count);\r\n center.negate();\r\n return true;\r\n };\r\n}());\r\n\r\nMiew.prototype.setPivotSubset = (function () {\r\n const _center = new THREE.Vector3(0.0, 0.0, 0.0);\r\n\r\n function _includesInCurSelection(atom, selectionBit) {\r\n return atom.mask & (1 << selectionBit);\r\n }\r\n\r\n function _includesInSelector(atom, selector) {\r\n return selector.selector.includesAtom(atom);\r\n }\r\n\r\n return function (selector) {\r\n const includesAtom = (selector) ? _includesInSelector : _includesInCurSelection;\r\n\r\n if (this.getSelectionCenter(_center, includesAtom, selector)) {\r\n this._objectControls.setPivot(_center);\r\n this.dispatchEvent({ type: 'transform' });\r\n } else {\r\n this.logger.warn('selection is empty. Center operation not performed');\r\n }\r\n };\r\n}());\r\n\r\n/**\r\n * Makes a screenshot.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n * @returns {string} Data URL representing the image contents.\r\n */\r\nMiew.prototype.screenshot = function (width, height) {\r\n const gfx = this._gfx;\r\n const deviceWidth = gfx.renderer.domElement.width;\r\n const deviceHeight = gfx.renderer.domElement.height;\r\n\r\n function fov2Tan(fov) {\r\n return Math.tan(THREE.MathUtils.degToRad(0.5 * fov));\r\n }\r\n\r\n function tan2Fov(tan) {\r\n return THREE.MathUtils.radToDeg(Math.atan(tan)) * 2.0;\r\n }\r\n\r\n function getDataURL() {\r\n let dataURL;\r\n const currBrowser = utils.getBrowser();\r\n\r\n if (currBrowser === utils.browserType.SAFARI) {\r\n const canvas = document.createElement('canvas');\r\n const canvasContext = canvas.getContext('2d');\r\n\r\n canvas.width = width === undefined ? deviceWidth : width;\r\n canvas.height = height === undefined ? deviceHeight : height;\r\n\r\n canvasContext.drawImage(gfx.renderer.domElement, 0, 0, canvas.width, canvas.height);\r\n dataURL = canvas.toDataURL('image/png');\r\n } else {\r\n // Copy current canvas to screenshot\r\n dataURL = gfx.renderer.domElement.toDataURL('image/png');\r\n }\r\n return dataURL;\r\n }\r\n height = height || width;\r\n\r\n let screenshotURI;\r\n if ((width === undefined && height === undefined)\r\n || (width === deviceWidth && height === deviceHeight)) {\r\n // renderer.domElement.toDataURL('image/png') returns flipped image in Safari\r\n // It hasn't been resolved yet, but getScreenshotSafari()\r\n // fixes it using an extra canvas.\r\n screenshotURI = getDataURL();\r\n } else {\r\n const originalAspect = gfx.camera.aspect;\r\n const originalFov = gfx.camera.fov;\r\n const originalTanFov2 = fov2Tan(gfx.camera.fov);\r\n\r\n // screenshot should contain the principal area of interest (a centered square touching screen sides)\r\n const areaOfInterestSize = Math.min(gfx.width, gfx.height);\r\n const areaOfInterestTanFov2 = originalTanFov2 * areaOfInterestSize / gfx.height;\r\n\r\n // set appropriate camera aspect & FOV\r\n const shotAspect = width / height;\r\n gfx.renderer.setPixelRatio(1);\r\n gfx.camera.aspect = shotAspect;\r\n gfx.camera.fov = tan2Fov(areaOfInterestTanFov2 / Math.min(shotAspect, 1.0));\r\n gfx.camera.updateProjectionMatrix();\r\n\r\n // resize canvas to the required size of screenshot\r\n gfx.renderer.setDrawingBufferSize(width, height, 1);\r\n\r\n // make screenshot\r\n this._renderFrame(settings.now.stereo);\r\n screenshotURI = getDataURL();\r\n\r\n // restore original camera & canvas proportions\r\n gfx.renderer.setPixelRatio(window.devicePixelRatio);\r\n gfx.camera.aspect = originalAspect;\r\n gfx.camera.fov = originalFov;\r\n gfx.camera.updateProjectionMatrix();\r\n gfx.renderer.setDrawingBufferSize(gfx.width, gfx.height, window.devicePixelRatio);\r\n this._needRender = true;\r\n }\r\n\r\n return screenshotURI;\r\n};\r\n\r\n/**\r\n * Makes screenshot and initiates a download.\r\n * @param {string} [filename] - Name of a file. Default to a 'screenshot-XXXXX.png', where XXXXX is a current\r\n * date/time in seconds.\r\n * @param {number} [width] - Width of an image. Defaults to the canvas width.\r\n * @param {number} [height] - Height of an image. Defaults to the width (square) or canvas height,\r\n * if width is omitted too.\r\n */\r\nMiew.prototype.screenshotSave = function (filename, width, height) {\r\n const uri = this.screenshot(width, height);\r\n utils.shotDownload(uri, filename);\r\n};\r\n\r\nMiew.prototype.save = function (opts) {\r\n this._export(opts.fileType).then((dataString) => {\r\n const filename = this._visuals[this._curVisualName]._complex.name;\r\n utils.download(dataString, filename, opts.fileType);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone' });\r\n }).catch((error) => {\r\n this.logger.error('Could not export data');\r\n this.logger.debug(error);\r\n this._refreshTitle();\r\n this.dispatchEvent({ type: 'exportingDone', error });\r\n });\r\n};\r\n\r\nMiew.prototype._tweakResolution = function () {\r\n const maxPerf = [\r\n ['poor', 100],\r\n ['low', 500],\r\n ['medium', 1000],\r\n ['high', 5000],\r\n ['ultra', Number.MAX_VALUE],\r\n ];\r\n\r\n let atomCount = 0;\r\n this._forEachComplexVisual((visual) => {\r\n atomCount += visual.getComplex().getAtomCount();\r\n });\r\n\r\n if (atomCount > 0) {\r\n const performance = this._gfxScore * 10e5 / atomCount;\r\n // set resolution based on estimated performance\r\n for (let i = 0; i < maxPerf.length; ++i) {\r\n if (performance < maxPerf[i][1]) {\r\n this._autoChangeResolution(maxPerf[i][0]);\r\n break;\r\n }\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._autoChangeResolution = function (resolution) {\r\n if (resolution !== settings.now.resolution) {\r\n this.logger.report(`Your rendering resolution was changed to \"${resolution}\" for best performance.`);\r\n }\r\n settings.now.resolution = resolution;\r\n};\r\n\r\n/**\r\n * Save current settings to cookies.\r\n */\r\nMiew.prototype.saveSettings = function () {\r\n this._cookies.setCookie(this._opts.settingsCookie, JSON.stringify(this.settings.getDiffs(true)));\r\n};\r\n\r\n/**\r\n * Load settings from cookies.\r\n */\r\nMiew.prototype.restoreSettings = function () {\r\n try {\r\n const cookie = this._cookies.getCookie(this._opts.settingsCookie);\r\n const diffs = cookie ? JSON.parse(cookie) : {};\r\n this.settings.applyDiffs(diffs, true);\r\n } catch (e) {\r\n this.logger.error(`Cookies parse error: ${e.message}`);\r\n }\r\n};\r\n\r\n/**\r\n * Reset current settings to the defaults.\r\n */\r\nMiew.prototype.resetSettings = function () {\r\n this.settings.reset();\r\n};\r\n\r\n/*\r\n * DANGEROUS and TEMPORARY. The method should change or disappear in future versions.\r\n * @param {string|object} opts - See {@link Miew} constructor.\r\n * @see {@link Miew#set}, {@link Miew#repAdd}, {@link Miew#rep}.\r\n */\r\nMiew.prototype.setOptions = function (opts) {\r\n if (typeof opts === 'string') {\r\n opts = Miew.options.fromAttr(opts);\r\n }\r\n if (opts.reps) {\r\n this._opts.reps = null;\r\n }\r\n _.merge(this._opts, opts);\r\n if (opts.settings) {\r\n this.set(opts.settings);\r\n }\r\n\r\n this._opts._objects = opts._objects;\r\n this._resetObjects();\r\n\r\n if (opts.load) {\r\n this.load(opts.load, { fileType: opts.type });\r\n }\r\n\r\n if (opts.preset) {\r\n settings.now.preset = opts.preset;\r\n }\r\n\r\n if (opts.reps) {\r\n this.resetReps(opts.preset);\r\n }\r\n\r\n if (this._opts.view) {\r\n this.view(this._opts.view);\r\n delete this._opts.view;\r\n }\r\n\r\n const visual = this._getComplexVisual();\r\n if (visual) {\r\n visual.getComplex().resetCurrentUnit();\r\n if (_.isNumber(opts.unit)) {\r\n visual.getComplex().setCurrentUnit(opts.unit);\r\n }\r\n this.resetView();\r\n this.rebuildAll();\r\n }\r\n};\r\n\r\nMiew.prototype.info = function (name) {\r\n const visual = this._getComplexVisual(name);\r\n if (!visual) {\r\n return {};\r\n }\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n return {\r\n id: metadata.id || complex.name || 'UNKNOWN',\r\n title: (metadata.title && metadata.title.join(' ')) || 'UNKNOWN DATA',\r\n atoms: complex.getAtomCount(),\r\n bonds: complex.getBondCount(),\r\n residues: complex.getResidueCount(),\r\n chains: complex.getChainCount(),\r\n };\r\n};\r\n\r\n/*\r\n * OBJECTS SEGMENT\r\n */\r\n\r\nMiew.prototype.addObject = function (objData, bThrow) {\r\n let Ctor = null;\r\n\r\n if (objData.type === LinesObject.prototype.type) {\r\n Ctor = LinesObject;\r\n }\r\n\r\n if (Ctor === null) {\r\n throw new Error(`Unknown scene object type - ${objData.type}`);\r\n }\r\n\r\n try {\r\n const newObj = new Ctor(objData.params, objData.opts);\r\n this._addSceneObject(newObj);\r\n } catch (error) {\r\n if (!bThrow) {\r\n this.logger.debug(`Error during scene object creation: ${error.message}`);\r\n } else {\r\n throw error;\r\n }\r\n }\r\n this._needRender = true;\r\n};\r\n\r\nMiew.prototype._addSceneObject = function (sceneObject) {\r\n const visual = this._getComplexVisual();\r\n if (sceneObject.build && visual) {\r\n sceneObject.build(visual.getComplex());\r\n this._gfx.pivot.add(sceneObject.getGeometry());\r\n }\r\n const objects = this._objects;\r\n objects[objects.length] = sceneObject;\r\n};\r\n\r\nMiew.prototype._updateObjsToFrame = function (frameData) {\r\n const objs = this._objects;\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n if (objs[i].updateToFrame) {\r\n objs[i].updateToFrame(frameData);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._resetObjects = function () {\r\n const objs = this._opts._objects;\r\n\r\n this._objects = [];\r\n if (objs) {\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n this.addObject(objs[i], false);\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype.removeObject = function (index) {\r\n const obj = this._objects[index];\r\n if (!obj) {\r\n throw new Error(`Scene object with index ${index} does not exist`);\r\n }\r\n obj.destroy();\r\n this._objects.splice(index, 1);\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Get a string with a URL to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {string} URL\r\n */\r\nMiew.prototype.getURL = function (opts) {\r\n return options.toURL(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n })));\r\n};\r\n\r\n/**\r\n * Get a string with a script to reproduce the current scene.\r\n *\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=true] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=true] - when this flag is true, a view information is included\r\n * @returns {string} script\r\n */\r\nMiew.prototype.getScript = function (opts) {\r\n return options.toScript(this.getState(_.defaults(opts, {\r\n compact: true,\r\n settings: true,\r\n view: true,\r\n })));\r\n};\r\n\r\n/*\r\n * Generates object that represents the current state of representations list\r\n * @param {boolean} compareWithDefaults - when this flag is true, reps list is compared (if possible)\r\n * to preset's defaults and only diffs are generated\r\n */\r\nMiew.prototype._compareReps = function (complexVisual, compareWithDefaults) {\r\n const ans = {};\r\n let repCount = 0;\r\n\r\n if (complexVisual) {\r\n repCount = complexVisual.repCount();\r\n }\r\n\r\n const currPreset = settings.defaults.presets[settings.now.preset];\r\n let compare = compareWithDefaults;\r\n if (currPreset === undefined || currPreset.length > repCount) {\r\n compare = false;\r\n ans.preset = 'empty';\r\n } else if (settings.now.preset !== settings.defaults.preset) {\r\n ans.preset = settings.now.preset;\r\n }\r\n\r\n const repsDiff = [];\r\n let emptyReps = true;\r\n for (let i = 0, n = repCount; i < n; ++i) {\r\n repsDiff[i] = complexVisual.repGet(i).compare(compare ? currPreset[i] : null);\r\n if (!_.isEmpty(repsDiff[i])) {\r\n emptyReps = false;\r\n }\r\n }\r\n if (!emptyReps) {\r\n ans.reps = repsDiff;\r\n }\r\n return ans;\r\n};\r\n\r\n/*\r\n * Obtain object that represents current state of miew (might be used as options in constructor).\r\n * @param {boolean} [opts.compact=true] - set this flag to false if you want to include full\r\n * preset information regardless of the differences with settings\r\n * @param {boolean} [opts.settings=false] - when this flag is true, changes in settings are included\r\n * @param {boolean} [opts.view=false] - when this flag is true, a view information is included\r\n * @returns {Object} State object.\r\n */\r\nMiew.prototype.getState = function (opts) {\r\n const state = {};\r\n\r\n opts = _.defaults(opts, {\r\n compact: true,\r\n settings: false,\r\n view: false,\r\n });\r\n\r\n // load\r\n const visual = this._getComplexVisual();\r\n if (visual !== null) {\r\n const complex = visual.getComplex();\r\n const { metadata } = complex;\r\n if (metadata.id) {\r\n const format = metadata.format ? `${metadata.format}:` : '';\r\n state.load = format + metadata.id;\r\n }\r\n const unit = complex.getCurrentUnit();\r\n if (unit !== 1) {\r\n state.unit = unit;\r\n }\r\n }\r\n\r\n // representations\r\n const repsInfo = this._compareReps(visual, opts.compact);\r\n if (repsInfo.preset) {\r\n state.preset = repsInfo.preset;\r\n }\r\n\r\n if (repsInfo.reps) {\r\n state.reps = repsInfo.reps;\r\n }\r\n\r\n // objects\r\n const objects = this._objects;\r\n const objectsState = [];\r\n for (let i = 0, n = objects.length; i < n; ++i) {\r\n objectsState[i] = objects[i].identify();\r\n }\r\n if (objects.length > 0) {\r\n state._objects = objectsState;\r\n }\r\n\r\n // view\r\n if (opts.view) {\r\n state.view = this.view();\r\n }\r\n\r\n // settings\r\n if (opts.settings) {\r\n const diff = this.settings.getDiffs(false);\r\n if (!_.isEmpty(diff)) {\r\n state.settings = diff;\r\n }\r\n }\r\n\r\n return state;\r\n};\r\n\r\n/**\r\n * Get parameter value.\r\n * @param {string} param - Parameter name or path (e.g. 'modes.BS.atom').\r\n * @param {*=} value - Default value.\r\n * @returns {*} Parameter value.\r\n */\r\nMiew.prototype.get = function (param, value) {\r\n return settings.get(param, value);\r\n};\r\n\r\nMiew.prototype._clipPlaneUpdateValue = function (radius) {\r\n const clipPlaneValue = Math.max(\r\n this._gfx.camera.position.z - radius * settings.now.draft.clipPlaneFactor,\r\n settings.now.camNear,\r\n );\r\n\r\n const opts = { clipPlaneValue };\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions(opts);\r\n });\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setUberOptions(opts);\r\n }\r\n }\r\n if (this._picker !== null) {\r\n this._picker.clipPlaneValue = clipPlaneValue;\r\n }\r\n};\r\n\r\nMiew.prototype._fogFarUpdateValue = function () {\r\n if (this._picker !== null) {\r\n if (this._gfx.scene.fog) {\r\n this._picker.fogFarValue = this._gfx.scene.fog.far;\r\n } else {\r\n this._picker.fogFarValue = undefined;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._updateShadowmapMeshes = function (process) {\r\n this._forEachComplexVisual((visual) => {\r\n const reprList = visual._reprList;\r\n for (let i = 0, n = reprList.length; i < n; ++i) {\r\n const repr = reprList[i];\r\n process(repr.geo, repr.material);\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype._updateMaterials = function (values, needTraverse = false, process = undefined) {\r\n this._forEachComplexVisual((visual) => visual.setMaterialValues(values, needTraverse, process));\r\n for (let i = 0, n = this._objects.length; i < n; ++i) {\r\n const obj = this._objects[i];\r\n if (obj._line) {\r\n obj._line.material.setValues(values);\r\n obj._line.material.needsUpdate = true;\r\n }\r\n }\r\n};\r\n\r\nMiew.prototype._fogAlphaChanged = function () {\r\n this._forEachComplexVisual((visual) => {\r\n visual.setUberOptions({\r\n fogAlpha: settings.now.fogAlpha,\r\n });\r\n });\r\n};\r\n\r\nMiew.prototype._embedWebXR = function () {\r\n // switch off\r\n if (settings.now.stereo !== 'WEBVR') {\r\n if (this.webVR) {\r\n this.webVR.disable();\r\n }\r\n this.webVR = null;\r\n return;\r\n }\r\n // switch on\r\n if (!this.webVR) {\r\n this.webVR = new WebVRPoC(() => {\r\n this._requestAnimationFrame(() => this._onTick());\r\n this._needRender = true;\r\n this._onResize();\r\n });\r\n }\r\n this.webVR.enable(this._gfx);\r\n};\r\n\r\nMiew.prototype._initOnSettingsChanged = function () {\r\n const on = (props, func) => {\r\n props = _.isArray(props) ? props : [props];\r\n props.forEach((prop) => {\r\n this.settings.addEventListener(`change:${prop}`, func);\r\n });\r\n };\r\n\r\n on('modes.VD.frame', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.showFrame(settings.now.modes.VD.frame);\r\n this._needRender = true;\r\n });\r\n\r\n on('modes.VD.isoMode', () => {\r\n const volume = this._getVolumeVisual();\r\n if (volume === null) return;\r\n\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n });\r\n\r\n on('bg.color', () => {\r\n this._onBgColorChanged();\r\n });\r\n\r\n on('ao', () => {\r\n const values = { normalsToGBuffer: settings.now.ao };\r\n this._setUberMaterialValues(values);\r\n });\r\n\r\n on('zSprites', () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('fogColor', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('fogColorEnable', () => {\r\n this._onFogColorChanged();\r\n });\r\n\r\n on('bg.transparent', (evt) => {\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.setClearColor(settings.now.bg.color, Number(!settings.now.bg.transparent));\r\n }\r\n // update materials\r\n this._updateMaterials({ fogTransparent: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('draft.clipPlane', (evt) => {\r\n // update materials\r\n this._updateMaterials({ clipPlane: evt.value });\r\n this.rebuildAll();\r\n });\r\n\r\n on('shadow.on', (evt) => {\r\n // update materials\r\n const values = { shadowmap: evt.value, shadowmapType: settings.now.shadow.type };\r\n const gfx = this._gfx;\r\n if (gfx) {\r\n gfx.renderer.shadowMap.enabled = Boolean(values.shadowmap);\r\n }\r\n this._updateMaterials(values, true);\r\n if (values.shadowmap) {\r\n this._updateShadowCamera();\r\n this._updateShadowmapMeshes(meshutils.createShadowmapMaterial);\r\n } else {\r\n this._updateShadowmapMeshes(meshutils.removeShadowmapMaterial);\r\n }\r\n this._needRender = true;\r\n });\r\n\r\n on('shadow.type', (evt) => {\r\n // update materials if shadowmap is enable\r\n if (settings.now.shadow.on) {\r\n this._updateMaterials({ shadowmapType: evt.value }, true);\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on('shadow.radius', (evt) => {\r\n for (let i = 0; i < this._gfx.scene.children.length; i++) {\r\n if (this._gfx.scene.children[i].shadow !== undefined) {\r\n const light = this._gfx.scene.children[i];\r\n light.shadow.radius = evt.value;\r\n this._needRender = true;\r\n }\r\n }\r\n });\r\n\r\n on('fps', () => {\r\n this._fps.show(settings.now.fps);\r\n });\r\n\r\n on(['fog', 'fogNearFactor', 'fogFarFactor'], () => {\r\n this._updateFog();\r\n this._needRender = true;\r\n });\r\n\r\n on('fogAlpha', () => {\r\n const { fogAlpha } = settings.now;\r\n if (fogAlpha < 0 || fogAlpha > 1) {\r\n this.logger.warn('fogAlpha must belong range [0,1]');\r\n }\r\n this._fogAlphaChanged();\r\n this._needRender = true;\r\n });\r\n\r\n on('autoResolution', (evt) => {\r\n if (evt.value && !this._gfxScore) {\r\n this.logger.warn('Benchmarks are missed, autoresolution will not work! '\r\n + 'Autoresolution should be set during miew startup.');\r\n }\r\n });\r\n\r\n on('stereo', () => {\r\n this._embedWebXR(settings.now.stereo === 'WEBVR');\r\n this._needRender = true;\r\n });\r\n\r\n on(['transparency', 'palette'], () => {\r\n this.rebuildAll();\r\n });\r\n\r\n on('resolution', () => {\r\n // update complex visuals\r\n this.rebuildAll();\r\n\r\n // update volume visual\r\n const volume = this._getVolumeVisual();\r\n if (volume) {\r\n volume.getMesh().material.updateDefines();\r\n this._needRender = true;\r\n }\r\n });\r\n\r\n on(['axes', 'fxaa', 'ao',\r\n 'outline.on', 'outline.color', 'outline.threshold', 'outline.thickness'], () => {\r\n this._needRender = true;\r\n });\r\n};\r\n\r\n/**\r\n * Set parameter value.\r\n * @param {string|object} params - Parameter name or path (e.g. 'modes.BS.atom') or even settings object.\r\n * @param {*=} value - Value.\r\n */\r\nMiew.prototype.set = function (params, value) {\r\n settings.set(params, value);\r\n};\r\n\r\n/**\r\n * Select atoms with selection string.\r\n * @param {string} expression - string expression of selection\r\n * @param {boolean=} append - true to append selection atoms to current selection, false to rewrite selection\r\n */\r\nMiew.prototype.select = function (expression, append) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return;\r\n }\r\n\r\n let sel = expression;\r\n if (_.isString(expression)) {\r\n sel = selectors.parse(expression).selector;\r\n }\r\n\r\n visual.select(sel, append);\r\n this._lastPick = null;\r\n\r\n this._updateInfoPanel();\r\n this._needRender = true;\r\n};\r\n\r\nconst VIEW_VERSION = '1';\r\n\r\n/**\r\n * Get or set view info packed into string.\r\n *\r\n * **Note:** view is stored for *left-handed* cs, euler angles are stored in radians and *ZXY-order*,\r\n *\r\n * @param {string=} expression - Optional string encoded the view\r\n */\r\nMiew.prototype.view = function (expression) {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n let transform = [];\r\n const eulerOrder = 'ZXY';\r\n\r\n function encode() {\r\n const pos = pivot.position;\r\n const scale = self._objectControls.getScale() / settings.now.radiusToFit;\r\n const euler = new THREE.Euler();\r\n euler.setFromQuaternion(self._objectControls.getOrientation(), eulerOrder);\r\n transform = [\r\n pos.x, pos.y, pos.z,\r\n scale,\r\n euler.x, euler.y, euler.z,\r\n ];\r\n return VIEW_VERSION + utils.arrayToBase64(transform, Float32Array);\r\n }\r\n\r\n function decode() {\r\n // backwards compatible: old non-versioned view is the 0th version\r\n if (expression.length === 40) {\r\n expression = `0${expression}`;\r\n }\r\n\r\n const version = expression[0];\r\n transform = utils.arrayFromBase64(expression.substr(1), Float32Array);\r\n\r\n // apply adapter for old versions\r\n if (version !== VIEW_VERSION) {\r\n if (version === '0') {\r\n // cancel radiusToFit included in old views\r\n transform[3] /= 8.0;\r\n } else {\r\n // do nothing\r\n self.logger.warn(`Encoded view version mismatch, stored as ${version} vs ${VIEW_VERSION} expected`);\r\n return;\r\n }\r\n }\r\n\r\n const interpolator = self._interpolator;\r\n const srcView = interpolator.createView();\r\n srcView.position.copy(pivot.position);\r\n srcView.scale = self._objectControls.getScale();\r\n srcView.orientation.copy(self._objectControls.getOrientation());\r\n\r\n const dstView = interpolator.createView();\r\n dstView.position.set(transform[0], transform[1], transform[2]);\r\n\r\n // hack to make preset views work after we moved centering offset to visual nodes\r\n // FIXME should only store main pivot offset in preset\r\n if (self._getComplexVisual()) {\r\n dstView.position.sub(self._getComplexVisual().position);\r\n }\r\n\r\n dstView.scale = transform[3]; // eslint-disable-line prefer-destructuring\r\n dstView.orientation.setFromEuler(new THREE.Euler(transform[4], transform[5], transform[6], eulerOrder));\r\n\r\n interpolator.setup(srcView, dstView);\r\n }\r\n\r\n if (typeof expression === 'undefined') {\r\n return encode();\r\n }\r\n decode();\r\n\r\n return expression;\r\n};\r\n\r\n/*\r\n * Update current view due to viewinterpolator state\r\n */\r\nMiew.prototype._updateView = function () {\r\n const self = this;\r\n const { pivot } = this._gfx;\r\n\r\n const interpolator = this._interpolator;\r\n if (!interpolator.wasStarted()) {\r\n interpolator.start();\r\n }\r\n\r\n if (!interpolator.isMoving()) {\r\n return;\r\n }\r\n\r\n const res = interpolator.getCurrentView();\r\n if (res.success) {\r\n const curr = res.view;\r\n pivot.position.copy(curr.position);\r\n self._objectControls.setScale(curr.scale * settings.now.radiusToFit);\r\n self._objectControls.setOrientation(curr.orientation);\r\n this.dispatchEvent({ type: 'transform' });\r\n self._needRender = true;\r\n }\r\n};\r\n\r\n/**\r\n * Translate object by vector\r\n * @param {number} x - translation value (Ang) along model's X axis\r\n * @param {number} y - translation value (Ang) along model's Y axis\r\n * @param {number} z - translation value (Ang) along model's Z axis\r\n */\r\nMiew.prototype.translate = function (x, y, z) {\r\n this._objectControls.translatePivot(x, y, z);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Rotate object by Euler angles\r\n * @param {number} x - rotation angle around X axis in radians\r\n * @param {number} y - rotation angle around Y axis in radians\r\n * @param {number} z - rotation angle around Z axis in radians\r\n */\r\nMiew.prototype.rotate = function (x, y, z) {\r\n this._objectControls.rotate(new THREE.Quaternion().setFromEuler(new THREE.Euler(x, y, z, 'XYZ')));\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Scale object by factor\r\n * @param {number} factor - scale multiplier, should greater than zero\r\n */\r\nMiew.prototype.scale = function (factor) {\r\n if (factor <= 0) {\r\n throw new RangeError('Scale should be greater than zero');\r\n }\r\n this._objectControls.scale(factor);\r\n this.dispatchEvent({ type: 'transform' });\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Center view on selection\r\n * @param {empty | subset | string} selector - defines part of molecule which must be centered (\r\n * empty - center on current selection;\r\n * subset - center on picked atom/residue/molecule;\r\n * string - center on atoms correspond to selection string)\r\n */\r\nMiew.prototype.center = function (selector) {\r\n // no arguments - center on current selection;\r\n if (selector === undefined) {\r\n this.setPivotSubset();\r\n this._needRender = true;\r\n return;\r\n }\r\n // subset with atom or residue - center on picked atom/residue;\r\n if (selector.obj !== undefined && ('atom' in selector.obj || 'residue' in selector.obj)) { // from event with selection\r\n if ('atom' in selector.obj) {\r\n this.setPivotAtom(selector.obj.atom);\r\n } else {\r\n this.setPivotResidue(selector.obj.residue);\r\n }\r\n this._needRender = true;\r\n return;\r\n }\r\n // string - center on atoms correspond to selection string\r\n if (selector.obj === undefined && selector !== '') {\r\n const sel = selectors.parse(selector);\r\n if (sel.error === undefined) {\r\n this.setPivotSubset(sel);\r\n this._needRender = true;\r\n return;\r\n }\r\n }\r\n // empty subset or incorrect/empty string - center on all molecule;\r\n this.resetPivot();\r\n this._needRender = true;\r\n};\r\n\r\n/**\r\n * Build selector that contains all atoms within given distance from group of atoms\r\n * @param {Selector} selector - selector describing source group of atoms\r\n * @param {number} radius - distance\r\n * @returns {Selector} selector describing result group of atoms\r\n */\r\nMiew.prototype.within = function (selector, radius) {\r\n const visual = this._getComplexVisual();\r\n if (!visual) {\r\n return selectors.None();\r\n }\r\n\r\n if (selector instanceof String) {\r\n selector = selectors.parse(selector);\r\n }\r\n\r\n const res = visual.within(selector, radius);\r\n if (res) {\r\n visual.rebuildSelectionGeometry();\r\n this._needRender = true;\r\n }\r\n return res;\r\n};\r\n\r\n/**\r\n * Get atom position in 2D canvas coords\r\n * @param {string} fullAtomName - full atom name, like A.38.CG\r\n * @returns {Object} {x, y} or false if atom not found\r\n */\r\nMiew.prototype.projected = function (fullAtomName, complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return false;\r\n }\r\n\r\n const atom = visual.getComplex().getAtomByFullname(fullAtomName);\r\n if (atom === null) {\r\n return false;\r\n }\r\n\r\n const pos = atom.position.clone();\r\n // we consider atom position to be affected only by common complex transform\r\n // ignoring any transformations that may add during editing\r\n this._gfx.pivot.updateMatrixWorldRecursive();\r\n this._gfx.camera.updateMatrixWorldRecursive();\r\n this._gfx.pivot.localToWorld(pos);\r\n pos.project(this._gfx.camera);\r\n\r\n return {\r\n x: (pos.x + 1.0) * 0.5 * this._gfx.width,\r\n y: (1.0 - pos.y) * 0.5 * this._gfx.height,\r\n };\r\n};\r\n\r\n/**\r\n * Replace secondary structure with calculated one.\r\n *\r\n * DSSP algorithm implementation is used.\r\n *\r\n * Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and\r\n * geometrical features. Biopolymers. 22(12):2577-2637. doi:10.1002/bip.360221211.\r\n *\r\n * @param {string=} complexName - complex name\r\n */\r\nMiew.prototype.dssp = function (complexName) {\r\n const visual = this._getComplexVisual(complexName);\r\n if (!visual) {\r\n return;\r\n }\r\n visual.getComplex().dssp();\r\n\r\n // rebuild dependent representations (cartoon or ss-colored)\r\n visual._reprList.forEach((rep) => {\r\n if (rep.mode.id === 'CA' || rep.colorer.id === 'SS') {\r\n rep.needsRebuild = true;\r\n }\r\n });\r\n};\r\n\r\nMiew.prototype.exportCML = function () {\r\n const self = this;\r\n\r\n function extractRotation(m) {\r\n const xAxis = new THREE.Vector3();\r\n const yAxis = new THREE.Vector3();\r\n const zAxis = new THREE.Vector3();\r\n m.extractBasis(xAxis, yAxis, zAxis);\r\n xAxis.normalize();\r\n yAxis.normalize();\r\n zAxis.normalize();\r\n const retMat = new THREE.Matrix4();\r\n retMat.identity();\r\n retMat.makeBasis(xAxis, yAxis, zAxis);\r\n return retMat;\r\n }\r\n\r\n function updateCMLData(complex) {\r\n const { root } = self._gfx;\r\n const mat = extractRotation(root.matrixWorld);\r\n const v4 = new THREE.Vector4(0, 0, 0, 0);\r\n const vCenter = new THREE.Vector4(0, 0, 0, 0);\r\n let xml = null;\r\n let ap = null;\r\n\r\n // update atoms in cml\r\n complex.forEachAtom((atom) => {\r\n if (atom.xmlNodeRef && atom.xmlNodeRef.xmlNode) {\r\n xml = atom.xmlNodeRef.xmlNode;\r\n ap = atom.position;\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n v4.applyMatrix4(mat);\r\n xml.setAttribute('x3', v4.x.toString());\r\n xml.setAttribute('y3', v4.y.toString());\r\n xml.setAttribute('z3', v4.z.toString());\r\n xml.removeAttribute('x2');\r\n xml.removeAttribute('y2');\r\n }\r\n });\r\n // update stereo groups in cml\r\n complex.forEachSGroup((sGroup) => {\r\n if (sGroup.xmlNodeRef && sGroup.xmlNodeRef.xmlNode) {\r\n xml = sGroup.xmlNodeRef.xmlNode;\r\n ap = sGroup.getPosition();\r\n v4.set(ap.x, ap.y, ap.z, 1.0);\r\n const cp = sGroup.getCentralPoint();\r\n if (cp === null) {\r\n v4.applyMatrix4(mat);\r\n } else {\r\n vCenter.set(cp.x, cp.y, cp.z, 0.0);\r\n v4.add(vCenter);\r\n v4.applyMatrix4(mat); // pos in global space\r\n vCenter.set(cp.x, cp.y, cp.z, 1.0);\r\n vCenter.applyMatrix4(mat);\r\n v4.sub(vCenter);\r\n }\r\n xml.setAttribute('x', v4.x.toString());\r\n xml.setAttribute('y', v4.y.toString());\r\n xml.setAttribute('z', v4.z.toString());\r\n }\r\n });\r\n }\r\n\r\n const visual = self._getComplexVisual();\r\n const complex = visual ? visual.getComplex() : null;\r\n if (complex && complex.originalCML) {\r\n updateCMLData(complex);\r\n\r\n // serialize xml structure to string\r\n const oSerializer = new XMLSerializer();\r\n return oSerializer.serializeToString(complex.originalCML);\r\n }\r\n\r\n return null;\r\n};\r\n\r\n/**\r\n * Reproduce the RCSB PDB Molecule of the Month style by David S. Goodsell\r\n *\r\n * @see http://pdb101.rcsb.org/motm/motm-about\r\n */\r\nMiew.prototype.motm = function () {\r\n settings.set({\r\n fogColorEnable: true,\r\n fogColor: 0x000000,\r\n outline: { on: true, threshold: 0.01 },\r\n bg: { color: 0xffffff },\r\n });\r\n\r\n this._forEachComplexVisual((visual) => {\r\n const rep = [];\r\n const complex = visual.getComplex();\r\n const palette = palettes.get(settings.now.palette);\r\n for (let i = 0; i < complex.getChainCount(); i++) {\r\n const curChainName = complex._chains[i]._name;\r\n const curChainColor = palette.getChainColor(curChainName);\r\n rep[i] = {\r\n selector: `chain ${curChainName}`,\r\n mode: 'VW',\r\n colorer: ['CB', { color: curChainColor, factor: 0.9 }],\r\n material: 'FL',\r\n };\r\n }\r\n visual.resetReps(rep);\r\n });\r\n};\r\n\r\nMiew.prototype.VERSION = (typeof PACKAGE_VERSION !== 'undefined' && PACKAGE_VERSION) || '0.0.0-dev';\r\n\r\n// Uncomment this to get debug trace:\r\n// Miew.prototype.debugTracer = new utils.DebugTracer(Miew.prototype);\r\n\r\n_.assign(Miew, /** @lends Miew */ {\r\n VERSION: Miew.prototype.VERSION,\r\n\r\n registeredPlugins: [],\r\n\r\n // export namespaces // TODO: WIP: refactoring external interface\r\n chem,\r\n io,\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n utils,\r\n gfx: {\r\n Representation,\r\n },\r\n\r\n /**\r\n * Third-party libraries packaged together with Miew.\r\n *\r\n * @property {object} lodash - [Lodash](https://lodash.com/), a modern JavaScript utility library delivering\r\n * modularity, performance & extras.\r\n * @property {object} three - [three.js](https://threejs.org/), JavaScript 3D library.\r\n *\r\n * @example\r\n * var _ = Miew.thirdParty.lodash;\r\n * var opts = _.merge({ ... }, Miew.options.fromURL(window.location.search));\r\n * var miew = new Miew(opts);\r\n */\r\n thirdParty: {\r\n lodash: _,\r\n three: THREE,\r\n },\r\n});\r\n\r\nexport default Miew;\r\n","import palettes from '../gfx/palettes';\r\nimport settings from '../settings';\r\n\r\nconst modeIdDesc = {\r\n $help: [\r\n 'Rendering mode shortcut',\r\n ' BS - balls and sticks mode',\r\n ' LN - lines mode',\r\n ' LC - licorice mode',\r\n ' VW - van der waals mode',\r\n ' TR - trace mode',\r\n ' TU - tube mode',\r\n ' CA - cartoon mode',\r\n ' SA - isosurface mode',\r\n ' QS - quick surface mode',\r\n ' SE - solvent excluded mode',\r\n ' TX - text mode',\r\n ],\r\n BS: {\r\n $help: [\r\n ' Balls and sticks',\r\n ' aromrad = #aromatic radius',\r\n ' atom = #atom radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n CA: {\r\n $help: [\r\n ' Cartoon',\r\n ' arrow = #arrow size',\r\n ' depth = #depth of surface',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = #',\r\n ' width = #secondary width\\n',\r\n ],\r\n },\r\n LN: {\r\n $help: [\r\n ' Lines',\r\n ' atom = #atom radius',\r\n ' chunkarom = ',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' offsarom = \\n',\r\n ],\r\n },\r\n LC: {\r\n $help: [\r\n ' Licorice',\r\n ' aromrad = #aromatic radius',\r\n ' bond = #bond radius',\r\n ' multibond = #use multibond',\r\n ' showarom = #show aromatic',\r\n ' space = #space value\\n',\r\n ],\r\n },\r\n VW: {\r\n $help: [\r\n ' Van der Waals',\r\n ' nothing\\n',\r\n ],\r\n },\r\n TR: {\r\n $help: [\r\n ' Trace',\r\n ' radius = #tube radius\\n',\r\n ],\r\n },\r\n TU: {\r\n $help: [\r\n ' Tube',\r\n ' heightSegmentsRatio = ',\r\n ' radius = #tube radius',\r\n ' tension = \\n',\r\n ],\r\n },\r\n SA: {\r\n $help: [\r\n ' Surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n QS: {\r\n $help: [\r\n ' Quick surface',\r\n ' isoValue = ',\r\n ' scale = ',\r\n ' wireframe = ',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n SE: {\r\n $help: [\r\n ' Solvent excluded surface',\r\n ' zClip = #clip z plane\\n',\r\n ],\r\n },\r\n TX: {\r\n $help: [\r\n ' Text mode',\r\n ' template = string that can include \"{{ id }}\"',\r\n ' it will be replaced by value, id can be one of next:',\r\n ' serial, name, type, sequence, residue, chain, hetatm, water\\n',\r\n ' horizontalAlign = {\"left\", \"right\", \"center\"}',\r\n ' verticalAlign = {\"top\", \"bottom\", \"middle\"}',\r\n ' dx = #offset along x',\r\n ' dy = #offset along y',\r\n ' dz = #offset along z',\r\n ' fg = #text color modificator',\r\n ' could be keyword, named color or hex',\r\n ' fg = #back color modificator',\r\n ' could be keyword, named color or hex',\r\n ' showBg = #if set show background',\r\n ' plate under text',\r\n ],\r\n },\r\n};\r\n\r\nconst colorDesc = {\r\n $help: [\r\n 'Coloring mode shortcut',\r\n ' EL - color by element',\r\n ' CH - color by chain',\r\n ' SQ - color by sequence',\r\n ' RT - color by residue type',\r\n ' SS - color by secondary structure',\r\n ' UN - uniform',\r\n ],\r\n UN: {\r\n $help: [\r\n 'Parameters of coloring modes customization',\r\n ' Uniform',\r\n ' color = #RGB->HEX->dec\\n',\r\n ],\r\n color: {\r\n $help: Object.keys(palettes.get(settings.now.palette).namedColors).sort().join('\\n'),\r\n },\r\n },\r\n};\r\n\r\nconst materialDesc = {\r\n $help: [\r\n 'Material shortcut',\r\n ' DF - diffuse',\r\n ' TR - transparent',\r\n ' SF - soft plastic',\r\n ' PL - glossy plastic',\r\n ' ME - metal',\r\n ' GL - glass',\r\n ],\r\n};\r\n\r\nconst addRepDesc = {\r\n $help: [\r\n 'Short (packed) representation description as a set of variables',\r\n ' s=',\r\n ' selector property',\r\n ' m=[!:[,...]]',\r\n ' render mode property',\r\n ' c=[!:[,...]]',\r\n ' color mode property',\r\n ' mt=',\r\n ' material property',\r\n ],\r\n s: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n m: modeIdDesc,\r\n c: colorDesc,\r\n mt: materialDesc,\r\n};\r\n\r\nconst setGetParameterDesc = {\r\n $help: [\r\n 'Parameters of rendering modes customization: modes',\r\n 'Parameters of colorer customization: colorers',\r\n 'Autobuild: autobuild = (|)',\r\n ],\r\n modes: modeIdDesc,\r\n colorers: colorDesc,\r\n};\r\n\r\nconst help = {\r\n $help: [\r\n 'help (| )',\r\n 'You can get detailed information about command options',\r\n ' using \"help cmd.opt.opt.[...]\"\\n',\r\n ' you can use one line comments',\r\n ' everything started from (#|//) will be skipped',\r\n ' Example: >build //some comment\\n',\r\n 'List of available commands:',\r\n ],\r\n reset: {\r\n $help: [\r\n 'Reload current object, delete all representations',\r\n ' Nothing will work until load new object',\r\n ],\r\n },\r\n load: {\r\n $help: [\r\n 'load (||-f [<*.NC FILE URL STRING>])',\r\n ' Load new pdb object from selected source',\r\n ],\r\n PDBID: {\r\n $help: 'pdb id in remote molecule database',\r\n },\r\n URL: {\r\n $help: 'url to source file',\r\n },\r\n f: {\r\n $help: [\r\n 'open file system dialog to fetch local file',\r\n 'optionally you can determine trajectory file',\r\n 'via URL for *.top model',\r\n ],\r\n },\r\n },\r\n clear: {\r\n $help: 'No args. Clear terminal',\r\n },\r\n add: {\r\n $help: [\r\n 'add [] []',\r\n ' Add new item to representation set with',\r\n ' default or params',\r\n ],\r\n REP_NAME: {\r\n $help: 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n rep: {\r\n $help: [\r\n 'rep [|] []',\r\n ' set current representation by name or index',\r\n ' edit current representation by ',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n DESCRIPTION: addRepDesc,\r\n },\r\n remove: {\r\n $help: [\r\n 'remove (|)',\r\n 'Remove representation by name or index',\r\n ],\r\n REP_NAME: {\r\n $help: [\r\n 'Identifier string [_,a-z,A-Z,0-9] can not start from digit',\r\n 'Must be declared before',\r\n ],\r\n },\r\n REP_INDEX: {\r\n $help: 'Index of available representation',\r\n },\r\n },\r\n selector: {\r\n $help: [\r\n 'selector ',\r\n ' set selector from EXPRESSION to current representation',\r\n ],\r\n EXPRESSION: {\r\n $help: 'Selection expression string as it is in menu->representations->selection',\r\n },\r\n },\r\n mode: {\r\n $help: [\r\n 'mode [=...]',\r\n ' set rendering mode and apply parameters to current representation',\r\n ],\r\n MODE_ID: modeIdDesc,\r\n },\r\n color: {\r\n $help: [\r\n 'color [=...]',\r\n ' set colorer and apply parameters to current representation',\r\n ],\r\n COLORER_ID: colorDesc,\r\n },\r\n material: {\r\n $help: [\r\n 'material ',\r\n ' set material to current representation',\r\n ],\r\n MATERIAL_ID: materialDesc,\r\n },\r\n build: {\r\n $help: 'build help str',\r\n add: {\r\n $help: 'build.add',\r\n new: {\r\n $help: [\r\n 'add.new',\r\n 'add.new new line 1',\r\n 'add.new new line 2',\r\n 'add.new new line 3',\r\n ],\r\n },\r\n },\r\n del: {\r\n $help: 'build.del',\r\n },\r\n },\r\n list: {\r\n $help: [\r\n 'list [-e|-s||]',\r\n 'Print representations if no args print list of representations',\r\n ' -e expand list and show all representations',\r\n ' -s show all user-registered selectors',\r\n ' | show only current representation',\r\n ],\r\n },\r\n hide: {\r\n $help: [\r\n 'hide (|)',\r\n 'Hide representation referenced in args',\r\n ],\r\n },\r\n show: {\r\n $help: [\r\n 'show (|)',\r\n 'Show representation referenced in args',\r\n ],\r\n },\r\n get: {\r\n $help: [\r\n 'get ',\r\n 'Print value',\r\n ' - path to option use get.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set: {\r\n $help: [\r\n 'set ',\r\n 'Set with ',\r\n ' - path to option use set.PARAMETER to get more info',\r\n ],\r\n PARAMETER: setGetParameterDesc,\r\n },\r\n set_save: {\r\n $help: [\r\n 'set_save',\r\n 'Save current settings to cookie',\r\n ],\r\n },\r\n set_restore: {\r\n $help: [\r\n 'set_restore',\r\n 'Load and apply settings from cookie',\r\n ],\r\n },\r\n set_reset: {\r\n $help: [\r\n 'set_reset',\r\n 'Reset current settings to the defaults',\r\n ],\r\n },\r\n preset: {\r\n $help: [\r\n 'preset []',\r\n 'Reset current representation or set preset to ',\r\n ],\r\n PRESET: {\r\n $help: [\r\n 'default',\r\n 'wire',\r\n 'small',\r\n 'macro',\r\n ],\r\n },\r\n },\r\n unit: {\r\n $help: [\r\n 'unit []',\r\n 'Change current biological structure view. Zero value means asymmetric unit,',\r\n 'positive values set an assembly with corresponding number.',\r\n 'Being called with no parameters command prints current unit information.',\r\n ],\r\n },\r\n view: {\r\n $help: [\r\n 'view []',\r\n 'Get current encoded view or set if ENCODED_VIEW placed as argument',\r\n ],\r\n ENCODED_VIEW: {\r\n $help: [\r\n 'encoded view matrix string (binary code)',\r\n ],\r\n },\r\n },\r\n rotate: {\r\n $help: [\r\n 'rotate (x|y|z) [] [(x|y|z) []]...',\r\n 'Rotate scene',\r\n ],\r\n },\r\n scale: {\r\n $help: [\r\n 'scale ',\r\n 'Scale scene',\r\n ],\r\n },\r\n select: {\r\n $help: [\r\n 'select [as ]',\r\n 'Select atoms using selector defined in SELECTOR_STRING',\r\n ' and if SELECTOR_NAME is defined register it in viewer',\r\n ' you can use it later as a complex selector',\r\n ],\r\n },\r\n within: {\r\n $help: [\r\n 'within of as ',\r\n 'Build within named selector',\r\n ' DISTANCE ',\r\n ' SELECTOR_STRING ',\r\n ' SELECTOR_NAME ',\r\n ],\r\n },\r\n url: {\r\n $help: [\r\n 'url [-s] [-v]',\r\n 'Report URL encoded scene',\r\n ' if -s set that include settings in the URL',\r\n ' if -v set that include view in the URL',\r\n ],\r\n },\r\n screenshot: {\r\n $help: [\r\n 'screenshot [ []]',\r\n 'Make a screenshot of the scene',\r\n ' WIDTH in pixels',\r\n ' HEIGHT in pixels, equal to WIDTH by default',\r\n ],\r\n },\r\n line: {\r\n $help: [\r\n 'line [=]',\r\n 'Draw dashed line between two specified atoms',\r\n ],\r\n },\r\n removeobj: {\r\n $help: [\r\n 'removeobj ',\r\n 'Remove scene object by its index. Indices could be obtained by command',\r\n ],\r\n },\r\n listobj: {\r\n $help: [\r\n 'listobj',\r\n 'Display the list of all existing scene objects',\r\n ],\r\n },\r\n};\r\n\r\nexport default help;\r\n","import _ from 'lodash';\r\nimport Miew from './Miew';\r\nimport { parser as parsercli } from './utils/MiewCLIParser';\r\nimport clihelp from './utils/MiewCLIHelp';\r\nimport logger from './utils/logger';\r\nimport utils from './utils';\r\n\r\nconst {\r\n chem: { selectors },\r\n modes,\r\n colorers,\r\n materials,\r\n palettes,\r\n options,\r\n settings,\r\n} = Miew;\r\n\r\nfunction None() {\r\n}\r\n\r\nconst NULL = (function () {\r\n const obj = new None();\r\n return function () {\r\n return obj;\r\n };\r\n}());\r\n\r\nclass RepresentationMap {\r\n constructor() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n\r\n get(strId) {\r\n return this.representationMap[strId] || this.representationID[strId] || '';\r\n }\r\n\r\n add(strId, index) {\r\n if (strId === -1) {\r\n return 'Can not create representation: there is no data';\r\n }\r\n\r\n if (index !== undefined) {\r\n if (!this.representationMap.hasOwnProperty(strId)) {\r\n this.representationMap[strId.toString()] = index;\r\n this.representationID[index] = strId.toString();\r\n } else {\r\n return 'This name has already existed, registered without name';\r\n }\r\n }\r\n return `Representation ${strId} successfully added`;\r\n }\r\n\r\n remove(index) {\r\n if (index && this.representationID.hasOwnProperty(index)) {\r\n delete this.representationMap[this.representationID[index]];\r\n delete this.representationID[index];\r\n }\r\n\r\n const sortedKeys = Object.keys(this.representationID).sort();\r\n for (const i in sortedKeys) {\r\n if (sortedKeys.hasOwnProperty(i)) {\r\n const id = sortedKeys[i];\r\n if (id > index) {\r\n this.representationID[id - 1] = this.representationID[id];\r\n this.representationMap[this.representationID[id]] -= 1;\r\n delete this.representationID[id];\r\n }\r\n }\r\n }\r\n }\r\n\r\n clear() {\r\n this.representationMap = {};\r\n this.representationID = {};\r\n }\r\n}\r\n\r\nconst representationsStorage = new RepresentationMap();\r\n\r\nfunction keyRemap(key) {\r\n const keys = {\r\n s: 'selector',\r\n m: 'mode',\r\n c: 'colorer',\r\n mt: 'material',\r\n mode: 'modes',\r\n color: 'colorers',\r\n colorer: 'colorers',\r\n select: 'selector',\r\n material: 'materials',\r\n selector: 'selector',\r\n };\r\n const ans = keys[key];\r\n return ans === undefined ? key : ans;\r\n}\r\n\r\nclass CLIUtils {\r\n list(miew, repMap, key) {\r\n let ret = '';\r\n if (miew && repMap !== undefined) {\r\n if (key === undefined || key === '-e') {\r\n const count = miew.repCount();\r\n\r\n for (let i = 0; i < count; i++) {\r\n ret += this.listRep(miew, repMap, i, key);\r\n }\r\n }\r\n }\r\n return ret;\r\n }\r\n\r\n listRep(miew, repMap, repIndex, key) {\r\n let ret = '';\r\n const rep = miew.repGet(repIndex);\r\n if (!rep) {\r\n logger.warn(`Rep ${repIndex} does not exist!`);\r\n return ret;\r\n }\r\n const index = repIndex;\r\n const repName = repMap.get(index);\r\n\r\n const { mode, colorer } = rep;\r\n const selectionStr = rep.selectorString;\r\n const material = rep.materialPreset;\r\n\r\n ret += `#${index} : ${mode.name}${repName === '' ? '' : `, ${repName}`}\\n`;\r\n\r\n if (key !== undefined) {\r\n ret += ` selection : \"${selectionStr}\"\\n`;\r\n ret += ` mode : (${mode.id}), ${mode.name}\\n`;\r\n ret += ` colorer : (${colorer.id}), ${colorer.name}\\n`;\r\n ret += ` material : (${material.id}), ${material.name}\\n`;\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listSelector(miew, context) {\r\n let ret = '';\r\n\r\n for (const k in context) {\r\n if (context.hasOwnProperty(k)) {\r\n ret += `${k} : \"${context[k]}\"\\n`;\r\n }\r\n }\r\n\r\n return ret;\r\n }\r\n\r\n listObjs(miew) {\r\n const objs = miew._objects;\r\n\r\n if (!objs || !Array.isArray(objs) || objs.length === 0) {\r\n return 'There are no objects on the scene';\r\n }\r\n\r\n const strList = [];\r\n for (let i = 0, n = objs.length; i < n; ++i) {\r\n strList[i] = `${i}: ${objs[i].toString()}`;\r\n }\r\n\r\n return strList.join('\\n');\r\n }\r\n\r\n joinHelpStr(helpData) {\r\n if (helpData instanceof Array) {\r\n return helpData.join('\\n');\r\n }\r\n return helpData;\r\n }\r\n\r\n help(path) {\r\n if (_.isUndefined(path)) {\r\n return `${this.joinHelpStr(clihelp.$help)}\\n${_.slice(_.sortBy(_.keys(clihelp)), 1).join(', ')}\\n`;\r\n }\r\n\r\n const helpItem = _.get(clihelp, path);\r\n return _.isUndefined(helpItem) ? this.help() : `${this.joinHelpStr(helpItem.$help)}\\n`;\r\n }\r\n\r\n load(miew, arg) {\r\n if (miew === undefined || arg === undefined || arg === '-f') {\r\n return;\r\n }\r\n miew.awaitWhileCMDisInProcess();\r\n const finish = () => miew.finishAwaitingCMDInProcess();\r\n miew.load(arg).then(finish, finish);\r\n }\r\n\r\n checkArg(key, arg, modificate) {\r\n if (key !== undefined && arg !== undefined) {\r\n if (keyRemap(key) === 'selector') {\r\n const res = selectors.parse(arg);\r\n\r\n if (res.error !== undefined) {\r\n const selExc = { message: res.error };\r\n throw selExc;\r\n }\r\n\r\n if (modificate !== undefined && modificate) {\r\n return res.selector;\r\n }\r\n return arg;\r\n }\r\n\r\n const modificators = {\r\n colorers,\r\n modes,\r\n materials,\r\n };\r\n\r\n let modificator = key;\r\n let temp;\r\n while (modificator !== temp) {\r\n temp = modificator;\r\n modificator = keyRemap(temp);\r\n }\r\n\r\n if (modificators[modificator].get(arg) === undefined) {\r\n const exc = { message: `${arg} is not existed in ${modificator}` };\r\n throw exc;\r\n }\r\n return arg;\r\n }\r\n return NULL;\r\n }\r\n\r\n propagateProp(path, arg) {\r\n if (path !== undefined) {\r\n let argExc = {};\r\n const adapter = options.adapters[typeof _.get(settings.defaults, path)];\r\n if (adapter === undefined) {\r\n const pathExc = { message: `${path} is not existed` };\r\n throw pathExc;\r\n }\r\n\r\n if ((path.endsWith('.color') || path.endsWith('.baseColor')\r\n || path.endsWith('.EL.carbon')) && typeof arg !== 'number') {\r\n arg = palettes.get(settings.now.palette).getNamedColor(arg);\r\n }\r\n\r\n if (path.endsWith('.fg') || path.endsWith('.bg')) {\r\n if (typeof arg !== 'number') {\r\n const val = palettes.get(settings.now.palette).getNamedColor(arg, true);\r\n if (val !== undefined) {\r\n arg = `0x${val.toString(16)}`;\r\n }\r\n } else {\r\n arg = `0x${arg.toString(16)}`;\r\n }\r\n }\r\n\r\n if (path.endsWith('.template')) {\r\n arg = arg.replace(/\\\\n/g, '\\n');// NOSONAR\r\n }\r\n\r\n if (arg !== undefined && adapter(arg) !== arg && adapter(arg) !== (arg > 0)) {\r\n argExc = { message: `${path} must be a \"${typeof _.get(settings.defaults, path)}\"` };\r\n throw argExc;\r\n }\r\n }\r\n return arg;\r\n }\r\n\r\n unquoteString(value) {\r\n return utils.unquoteString(value);\r\n }\r\n}\r\n// repIndexOrRepMap could be RepresentationMap or index\r\n\r\nconst utilFunctions = new CLIUtils();\r\n\r\nfunction CreateObjectPair(a, b) {\r\n const obj = {};\r\n obj[a] = b;\r\n return obj;\r\n}\r\n\r\nfunction ArgList(arg) {\r\n if (arg instanceof this.constructor) {\r\n return arg;\r\n }\r\n if (arg instanceof Array) {\r\n this._values = arg.slice(0);\r\n } else if (arg) {\r\n this._values = [arg];\r\n } else {\r\n this._values = [];\r\n }\r\n}\r\n\r\nArgList.prototype.append = function (value) {\r\n const values = this._values;\r\n values[values.length] = value;\r\n return this;\r\n};\r\n\r\nArgList.prototype.remove = function (value) {\r\n const values = this._values;\r\n const index = values.indexOf(value);\r\n if (index >= 0) {\r\n values.splice(index, 1);\r\n }\r\n return this;\r\n};\r\n\r\nArgList.prototype.toJSO = function (cliUtils, cmd, arg) {\r\n const res = {};\r\n\r\n const list = this._values;\r\n for (let i = 0, n = list.length; i < n; ++i) {\r\n _.set(res, list[i].id, cliUtils.propagateProp(`${keyRemap(cmd)}.${arg}.${list[i].id}`, list[i].val));\r\n }\r\n\r\n return res;\r\n};\r\n\r\nfunction Arg(_id, _val) {\r\n this.id = _id;\r\n this.val = _val;\r\n}\r\n\r\nconst cliutils = Object.create({});\r\n\r\ncliutils.Arg = Arg;\r\ncliutils.ArgList = ArgList;\r\n\r\ncliutils.miew = null;\r\ncliutils.echo = null;\r\ncliutils.representations = representationsStorage;\r\ncliutils.utils = utilFunctions;\r\n\r\ncliutils._ = _;\r\ncliutils.CreateObjectPair = CreateObjectPair;\r\ncliutils.keyRemap = keyRemap;\r\ncliutils.Context = selectors.Context;\r\ncliutils.ClearContext = selectors.ClearContext;\r\n\r\ncliutils.NULL = NULL;\r\n\r\ncliutils.notimplemented = function () {\r\n return this.NULL;\r\n};\r\n\r\nMiew.prototype.script = function (script, _printCallback, _errorCallback) {\r\n parsercli.yy.miew = this;\r\n parsercli.yy.echo = _printCallback;\r\n parsercli.yy.error = _errorCallback;\r\n if (this.cmdQueue === undefined) {\r\n this.cmdQueue = [];\r\n }\r\n\r\n if (this.commandInAction === undefined) {\r\n this.commandInAction = false;\r\n }\r\n\r\n this.cmdQueue = this.cmdQueue.concat(script.split('\\n'));\r\n};\r\n\r\nMiew.prototype.awaitWhileCMDisInProcess = function () {\r\n this.commandInAction = true;\r\n};\r\n\r\nMiew.prototype.finishAwaitingCMDInProcess = function () {\r\n this.commandInAction = false;\r\n};\r\n\r\nMiew.prototype.isScriptingCommandAvailable = function () {\r\n return this.commandInAction !== undefined\r\n && !this.commandInAction\r\n && this.cmdQueue !== undefined\r\n && this.cmdQueue.length > 0;\r\n};\r\n\r\nMiew.prototype.callNextCmd = function () {\r\n if (this.isScriptingCommandAvailable()) {\r\n const cmd = this.cmdQueue.shift();\r\n\r\n const res = {};\r\n res.success = false;\r\n try {\r\n parsercli.parse(cmd);\r\n res.success = true;\r\n } catch (e) {\r\n res.error = e.message;\r\n parsercli.yy.error(res.error);\r\n this.finishAwaitingCMDInProcess();\r\n }\r\n return res;\r\n }\r\n return '';\r\n};\r\n\r\nparsercli.yy = cliutils;\r\n// workaround for incorrect JISON parser generator for AMD module\r\nparsercli.yy.parseError = parsercli.parseError;\r\n","import Miew from './Miew';\r\nimport './Miew-cli';\r\n\r\nexport default 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\ No newline at end of file diff --git a/packages/miew/docs/getting-started-for-dummies.md b/packages/miew/docs/getting-started-for-dummies.md index bd997c4c..81e52edd 100644 --- a/packages/miew/docs/getting-started-for-dummies.md +++ b/packages/miew/docs/getting-started-for-dummies.md @@ -1,6 +1,6 @@ # Getting Started with Miew Development: The Beginner's Guide -Copyright (c) 2015–2025 [EPAM Systems, Inc.](https://www.epam.com/) +Copyright (c) 2015–2026 [EPAM Systems, Inc.](https://www.epam.com/) ![Miew screenshot](https://github.com/epam/miew/raw/master/README.png) diff --git a/packages/miew/docs/tutorials/embed.md b/packages/miew/docs/tutorials/embed.md index 5bb3f833..7a6546aa 100644 --- a/packages/miew/docs/tutorials/embed.md +++ b/packages/miew/docs/tutorials/embed.md @@ -31,11 +31,11 @@ _index.html_ Miew via Global - + - + - +

Use Miew via browser globals

@@ -64,7 +64,7 @@ _index.html_ Miew via Require.js - + @@ -75,11 +75,11 @@ _index.html_ @@ -149,7 +149,7 @@ _package.json_ ```json { "dependencies": { - "miew": "0.9.0" + "miew": "0.12.0" } } ``` @@ -215,7 +215,7 @@ _package.json_ { "dependencies": { "css-loader": "6.8.1", - "miew": "0.9.0", + "miew": "0.12.0", "style-loader": "3.3.3", "webpack": "5.88.2", "webpack-cli": "5.1.4" diff --git a/packages/miew/examples/api.html b/packages/miew/examples/api.html index 074afa5a..eca78ec6 100644 --- a/packages/miew/examples/api.html +++ b/packages/miew/examples/api.html @@ -5,7 +5,7 @@ Miew API - + diff --git a/packages/miew/examples/empty.html b/packages/miew/examples/empty.html index aa6ac3b1..1b06b342 100644 --- a/packages/miew/examples/empty.html +++ b/packages/miew/examples/empty.html @@ -5,7 +5,7 @@ Miew via Global - + diff --git a/packages/miew/examples/events.html b/packages/miew/examples/events.html index 72e33802..e6b855e6 100644 --- a/packages/miew/examples/events.html +++ b/packages/miew/examples/events.html @@ -5,7 +5,7 @@ Miew events - + diff --git a/packages/miew/examples/fullscreen.html b/packages/miew/examples/fullscreen.html index 34543073..811bc0be 100644 --- a/packages/miew/examples/fullscreen.html +++ b/packages/miew/examples/fullscreen.html @@ -37,7 +37,7 @@ } - + diff --git a/packages/miew/examples/grid.html b/packages/miew/examples/grid.html index f58f40d3..a7b71c7a 100644 --- a/packages/miew/examples/grid.html +++ b/packages/miew/examples/grid.html @@ -86,12 +86,12 @@

Adverse effects

- Miew – 3D Molecular Viewer. Copyright (c) 2015–2025 EPAM Systems, Inc. + Miew – 3D Molecular Viewer. Copyright (c) 2015–2026 EPAM Systems, Inc.
- + + diff --git a/packages/miew/examples/load_from_string.html b/packages/miew/examples/load_from_string.html index d39a40d7..f7a345b3 100644 --- a/packages/miew/examples/load_from_string.html +++ b/packages/miew/examples/load_from_string.html @@ -5,7 +5,7 @@ Load serotonin from string - + diff --git a/packages/miew/examples/miew_via_global.html b/packages/miew/examples/miew_via_global.html index 7a8a288c..e9bdb811 100644 --- a/packages/miew/examples/miew_via_global.html +++ b/packages/miew/examples/miew_via_global.html @@ -5,7 +5,7 @@ Miew via Global - + diff --git a/packages/miew/examples/miew_via_require.html b/packages/miew/examples/miew_via_require.html index 8f5ff268..b497bc32 100644 --- a/packages/miew/examples/miew_via_require.html +++ b/packages/miew/examples/miew_via_require.html @@ -14,7 +14,7 @@

Use Miew via Require.js

+ diff --git a/packages/miew/examples/options.html b/packages/miew/examples/options.html index 2d302273..765d9282 100644 --- a/packages/miew/examples/options.html +++ b/packages/miew/examples/options.html @@ -5,7 +5,7 @@ Miew options - + diff --git a/packages/miew/examples/options_fromAttr.html b/packages/miew/examples/options_fromAttr.html index 4a9c3b35..c0fce344 100644 --- a/packages/miew/examples/options_fromAttr.html +++ b/packages/miew/examples/options_fromAttr.html @@ -5,7 +5,7 @@ .options.fromAttr() - Miew API - + diff --git a/packages/miew/examples/options_fromURL.html b/packages/miew/examples/options_fromURL.html index 590ff7df..b0a1c46a 100644 --- a/packages/miew/examples/options_fromURL.html +++ b/packages/miew/examples/options_fromURL.html @@ -5,7 +5,7 @@ .options.fromURL() - Miew API - + diff --git a/packages/miew/examples/projected.html b/packages/miew/examples/projected.html index 37fb9e94..84c8d8f8 100644 --- a/packages/miew/examples/projected.html +++ b/packages/miew/examples/projected.html @@ -25,7 +25,7 @@ } - + diff --git a/packages/miew/examples/sequence.html b/packages/miew/examples/sequence.html index 6a0cb4b6..aa8a0c94 100644 --- a/packages/miew/examples/sequence.html +++ b/packages/miew/examples/sequence.html @@ -5,7 +5,7 @@ Select residues from sequence - +